example_data.ipynb

{
 "cells": [
  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {},
   "outputs": [],
   "source": [
    "import os\n",
    "import glob\n",
    "import itertools"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### download the bams"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "--2019-05-21 15:52:09--  http://popgen.dk/software/download/angsd/bams.tar.gz\n",
      "Resolving popgen.dk (popgen.dk)... 130.225.98.44\n",
      "Connecting to popgen.dk (popgen.dk)|130.225.98.44|:80... connected.\n",
      "HTTP request sent, awaiting response... 200 OK\n",
      "Length: 102283097 (98M) [application/x-gzip]\n",
      "Saving to: ‘bams.tar.gz’\n",
      "\n",
      "bams.tar.gz         100%[===================>]  97.54M   109MB/s    in 0.9s    \n",
      "\n",
      "2019-05-21 15:52:10 (109 MB/s) - ‘bams.tar.gz’ saved [102283097/102283097]\n",
      "\n"
     ]
    }
   ],
   "source": [
    "!wget http://popgen.dk/software/download/angsd/bams.tar.gz"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### untar and index the bams"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "metadata": {},
   "outputs": [],
   "source": [
    "!tar xf bams.tar.gz\n",
    "!for i in bams/*.bam;do samtools index $i;done"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### download and index the ancestral state fasta file"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "--2019-05-21 15:52:14--  http://popgen.dk/software/download/angsd/hg19ancNoChr.fa.gz\n",
      "Resolving popgen.dk (popgen.dk)... 130.225.98.44\n",
      "Connecting to popgen.dk (popgen.dk)|130.225.98.44|:80... connected.\n",
      "HTTP request sent, awaiting response... 200 OK\n",
      "Length: 850829230 (811M) [application/x-gzip]\n",
      "Saving to: ‘hg19ancNoChr.fa.gz’\n",
      "\n",
      "hg19ancNoChr.fa.gz  100%[===================>] 811.41M   112MB/s    in 7.3s    \n",
      "\n",
      "2019-05-21 15:52:22 (111 MB/s) - ‘hg19ancNoChr.fa.gz’ saved [850829230/850829230]\n",
      "\n"
     ]
    }
   ],
   "source": [
    "!wget http://popgen.dk/software/download/angsd/hg19ancNoChr.fa.gz\n",
    "!samtools faidx hg19ancNoChr.fa.gz"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### make the bam filelists for use by angsd"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "metadata": {},
   "outputs": [],
   "source": [
    "## make a single overall filelist\n",
    "!ls bams/*.bam > all.filelist"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "metadata": {},
   "outputs": [],
   "source": [
    "# one filelist for each sample\n",
    "samples = []\n",
    "for sample_bam in glob.glob('bams/*.bam'):\n",
    "    sampleID = sample_bam.split('/')[1].split('.')[0]\n",
    "    samples.append(sampleID)\n",
    "    !echo {sample_bam} > {sampleID}.filelist.ind"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### paths to the analysis programs"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 22,
   "metadata": {},
   "outputs": [],
   "source": [
    "# will need to be replaced your local installation\n",
    "ANGSD = '/home/ryan/programs/angsd/angsd'\n",
    "realSFS = '/home/ryan/programs/angsd/misc/realSFS'\n",
    "IBS = '/home/ryan/programs/angsd/misc/ibs'"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "#  realSFS method"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 8,
   "metadata": {},
   "outputs": [],
   "source": [
    "!mkdir results_realsfs"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 9,
   "metadata": {
    "scrolled": true
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "\t-> angsd version: 0.919-43-g0b5946e (htslib: 1.6-2-g8bbc018) build(Oct  6 2017 11:20:17)\n",
      "\t-> Reading fasta: hg19ancNoChr.fa.gz\n",
      "\t-> Parsing 1 number of samples \n",
      "\t-> Printing at chr: 20 pos:14048474 chunknumber 1800 contains 681 sites\n",
      "\t-> Done reading data waiting for calculations to finish\n",
      "\t-> Done waiting for threads\n",
      "\t-> Output filenames:\n",
      "\t\t->\"smallNA07000.arg\"\n",
      "\t\t->\"smallNA07000.saf.gz\"\n",
      "\t\t->\"smallNA07000.saf.pos.gz\"\n",
      "\t\t->\"smallNA07000.saf.idx\"\n",
      "\t\t->\"smallNA07000.depthSample\"\n",
      "\t\t->\"smallNA07000.depthGlobal\"\n",
      "\t-> Tue May 21 15:53:16 2019\n",
      "\t-> Arguments and parameters for all analysis are located in .arg file\n",
      "\t[ALL done] cpu-time used =  23.97 sec\n",
      "\t[ALL done] walltime used =  24.00 sec\n",
      "\t-> angsd version: 0.919-43-g0b5946e (htslib: 1.6-2-g8bbc018) build(Oct  6 2017 11:20:17)\n",
      "\t-> Reading fasta: hg19ancNoChr.fa.gz\n",
      "\t-> Parsing 1 number of samples \n",
      "\t-> Printing at chr: 20 pos:14044661 chunknumber 800 contains 1793 sites\n",
      "\t-> Done reading data waiting for calculations to finish\n",
      "\t-> Done waiting for threads\n",
      "\t-> Output filenames:\n",
      "\t\t->\"smallNA11840.arg\"\n",
      "\t\t->\"smallNA11840.saf.gz\"\n",
      "\t\t->\"smallNA11840.saf.pos.gz\"\n",
      "\t\t->\"smallNA11840.saf.idx\"\n",
      "\t\t->\"smallNA11840.depthSample\"\n",
      "\t\t->\"smallNA11840.depthGlobal\"\n",
      "\t-> Tue May 21 15:53:40 2019\n",
      "\t-> Arguments and parameters for all analysis are located in .arg file\n",
      "\t[ALL done] cpu-time used =  23.50 sec\n",
      "\t[ALL done] walltime used =  23.00 sec\n",
      "\t-> angsd version: 0.919-43-g0b5946e (htslib: 1.6-2-g8bbc018) build(Oct  6 2017 11:20:17)\n",
      "\t-> Reading fasta: hg19ancNoChr.fa.gz\n",
      "\t-> Parsing 1 number of samples \n",
      "\t-> Printing at chr: 20 pos:14084084 chunknumber 2900 contains 529 sites\n",
      "\t-> Done reading data waiting for calculations to finish\n",
      "\t-> Done waiting for threads\n",
      "\t-> Output filenames:\n",
      "\t\t->\"smallNA07357.arg\"\n",
      "\t\t->\"smallNA07357.saf.gz\"\n",
      "\t\t->\"smallNA07357.saf.pos.gz\"\n",
      "\t\t->\"smallNA07357.saf.idx\"\n",
      "\t\t->\"smallNA07357.depthSample\"\n",
      "\t\t->\"smallNA07357.depthGlobal\"\n",
      "\t-> Tue May 21 15:54:04 2019\n",
      "\t-> Arguments and parameters for all analysis are located in .arg file\n",
      "\t[ALL done] cpu-time used =  23.75 sec\n",
      "\t[ALL done] walltime used =  24.00 sec\n",
      "\t-> angsd version: 0.919-43-g0b5946e (htslib: 1.6-2-g8bbc018) build(Oct  6 2017 11:20:17)\n",
      "\t-> Reading fasta: hg19ancNoChr.fa.gz\n",
      "\t-> Parsing 1 number of samples \n",
      "\t-> Printing at chr: 20 pos:14055654 chunknumber 900 contains 1238 sites\n",
      "\t-> Done reading data waiting for calculations to finish\n",
      "\t-> Done waiting for threads\n",
      "\t-> Output filenames:\n",
      "\t\t->\"smallNA11832.arg\"\n",
      "\t\t->\"smallNA11832.saf.gz\"\n",
      "\t\t->\"smallNA11832.saf.pos.gz\"\n",
      "\t\t->\"smallNA11832.saf.idx\"\n",
      "\t\t->\"smallNA11832.depthSample\"\n",
      "\t\t->\"smallNA11832.depthGlobal\"\n",
      "\t-> Tue May 21 15:54:27 2019\n",
      "\t-> Arguments and parameters for all analysis are located in .arg file\n",
      "\t[ALL done] cpu-time used =  22.81 sec\n",
      "\t[ALL done] walltime used =  23.00 sec\n",
      "\t-> angsd version: 0.919-43-g0b5946e (htslib: 1.6-2-g8bbc018) build(Oct  6 2017 11:20:17)\n",
      "\t-> Reading fasta: hg19ancNoChr.fa.gz\n",
      "\t-> Parsing 1 number of samples \n",
      "\t-> Printing at chr: 20 pos:14066282 chunknumber 2500 contains 763 sites\n",
      "\t-> Done reading data waiting for calculations to finish\n",
      "\t-> Done waiting for threads\n",
      "\t-> Output filenames:\n",
      "\t\t->\"smallNA06994.arg\"\n",
      "\t\t->\"smallNA06994.saf.gz\"\n",
      "\t\t->\"smallNA06994.saf.pos.gz\"\n",
      "\t\t->\"smallNA06994.saf.idx\"\n",
      "\t\t->\"smallNA06994.depthSample\"\n",
      "\t\t->\"smallNA06994.depthGlobal\"\n",
      "\t-> Tue May 21 15:54:51 2019\n",
      "\t-> Arguments and parameters for all analysis are located in .arg file\n",
      "\t[ALL done] cpu-time used =  23.68 sec\n",
      "\t[ALL done] walltime used =  24.00 sec\n",
      "\t-> angsd version: 0.919-43-g0b5946e (htslib: 1.6-2-g8bbc018) build(Oct  6 2017 11:20:17)\n",
      "\t-> Reading fasta: hg19ancNoChr.fa.gz\n",
      "\t-> Parsing 1 number of samples \n",
      "\t-> Printing at chr: 18 pos:14090804 chunknumber 700 contains 2643 sites\n",
      "\t-> Done reading data waiting for calculations to finish\n",
      "\t-> Done waiting for threads\n",
      "\t-> Output filenames:\n",
      "\t\t->\"smallNA06985.arg\"\n",
      "\t\t->\"smallNA06985.saf.gz\"\n",
      "\t\t->\"smallNA06985.saf.pos.gz\"\n",
      "\t\t->\"smallNA06985.saf.idx\"\n",
      "\t\t->\"smallNA06985.depthSample\"\n",
      "\t\t->\"smallNA06985.depthGlobal\"\n",
      "\t-> Tue May 21 15:55:14 2019\n",
      "\t-> Arguments and parameters for all analysis are located in .arg file\n",
      "\t[ALL done] cpu-time used =  23.26 sec\n",
      "\t[ALL done] walltime used =  23.00 sec\n",
      "\t-> angsd version: 0.919-43-g0b5946e (htslib: 1.6-2-g8bbc018) build(Oct  6 2017 11:20:17)\n",
      "\t-> Reading fasta: hg19ancNoChr.fa.gz\n",
      "\t-> Parsing 1 number of samples \n",
      "\t-> Printing at chr: 20 pos:14067509 chunknumber 2700 contains 620 sitess\n",
      "\t-> Done reading data waiting for calculations to finish\n",
      "\t-> Done waiting for threads\n",
      "\t-> Output filenames:\n",
      "\t\t->\"smallNA11831.arg\"\n",
      "\t\t->\"smallNA11831.saf.gz\"\n",
      "\t\t->\"smallNA11831.saf.pos.gz\"\n",
      "\t\t->\"smallNA11831.saf.idx\"\n",
      "\t\t->\"smallNA11831.depthSample\"\n",
      "\t\t->\"smallNA11831.depthGlobal\"\n",
      "\t-> Tue May 21 15:55:38 2019\n",
      "\t-> Arguments and parameters for all analysis are located in .arg file\n",
      "\t[ALL done] cpu-time used =  24.05 sec\n",
      "\t[ALL done] walltime used =  24.00 sec\n",
      "\t-> angsd version: 0.919-43-g0b5946e (htslib: 1.6-2-g8bbc018) build(Oct  6 2017 11:20:17)\n",
      "\t-> Reading fasta: hg19ancNoChr.fa.gz\n",
      "\t-> Parsing 1 number of samples \n",
      "\t-> Printing at chr: 20 pos:14062084 chunknumber 2200 contains 1059 sites\n",
      "\t-> Done reading data waiting for calculations to finish\n",
      "\t-> Done waiting for threads\n",
      "\t-> Output filenames:\n",
      "\t\t->\"smallNA11829.arg\"\n",
      "\t\t->\"smallNA11829.saf.gz\"\n",
      "\t\t->\"smallNA11829.saf.pos.gz\"\n",
      "\t\t->\"smallNA11829.saf.idx\"\n",
      "\t\t->\"smallNA11829.depthSample\"\n",
      "\t\t->\"smallNA11829.depthGlobal\"\n",
      "\t-> Tue May 21 15:56:02 2019\n",
      "\t-> Arguments and parameters for all analysis are located in .arg file\n",
      "\t[ALL done] cpu-time used =  24.04 sec\n",
      "\t[ALL done] walltime used =  24.00 sec\n",
      "\t-> angsd version: 0.919-43-g0b5946e (htslib: 1.6-2-g8bbc018) build(Oct  6 2017 11:20:17)\n",
      "\t-> Reading fasta: hg19ancNoChr.fa.gz\n",
      "\t-> Parsing 1 number of samples \n",
      "\t-> Printing at chr: 20 pos:14080568 chunknumber 2000 contains 1089 sites\n",
      "\t-> Done reading data waiting for calculations to finish\n",
      "\t-> Done waiting for threads\n",
      "\t-> Output filenames:\n",
      "\t\t->\"smallNA07056.arg\"\n",
      "\t\t->\"smallNA07056.saf.gz\"\n",
      "\t\t->\"smallNA07056.saf.pos.gz\"\n",
      "\t\t->\"smallNA07056.saf.idx\"\n",
      "\t\t->\"smallNA07056.depthSample\"\n",
      "\t\t->\"smallNA07056.depthGlobal\"\n",
      "\t-> Tue May 21 15:56:27 2019\n",
      "\t-> Arguments and parameters for all analysis are located in .arg file\n",
      "\t[ALL done] cpu-time used =  23.89 sec\n",
      "\t[ALL done] walltime used =  24.00 sec\n",
      "\t-> angsd version: 0.919-43-g0b5946e (htslib: 1.6-2-g8bbc018) build(Oct  6 2017 11:20:17)\n",
      "\t-> Reading fasta: hg19ancNoChr.fa.gz\n",
      "\t-> Parsing 1 number of samples \n",
      "\t-> Printing at chr: 20 pos:14086888 chunknumber 2600 contains 444 sites\n",
      "\t-> Done reading data waiting for calculations to finish\n",
      "\t-> Done waiting for threads\n",
      "\t-> Output filenames:\n",
      "\t\t->\"smallNA11830.arg\"\n",
      "\t\t->\"smallNA11830.saf.gz\"\n",
      "\t\t->\"smallNA11830.saf.pos.gz\"\n",
      "\t\t->\"smallNA11830.saf.idx\"\n",
      "\t\t->\"smallNA11830.depthSample\"\n",
      "\t\t->\"smallNA11830.depthGlobal\"\n",
      "\t-> Tue May 21 15:56:51 2019\n",
      "\t-> Arguments and parameters for all analysis are located in .arg file\n",
      "\t[ALL done] cpu-time used =  24.21 sec\n",
      "\t[ALL done] walltime used =  24.00 sec\n"
     ]
    }
   ],
   "source": [
    "for sample in samples:\n",
    "    !{ANGSD} -b {sample}.filelist.ind \\\n",
    "    -anc hg19ancNoChr.fa.gz \\\n",
    "    -minMapQ 30 -minQ 20 -GL 2 \\\n",
    "    -doSaf 1 -doDepth 1 -doCounts 1 \\\n",
    "    -out {sample}"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 10,
   "metadata": {},
   "outputs": [],
   "source": [
    "# iterate over each pair of samples\n",
    "pairs = list(itertools.combinations(samples, 2))"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 11,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "\t-> Version of fname:smallNA07000.saf.idx is:2\n",
      "\t-> Assuming .saf.gz file: smallNA07000.saf.gz\n",
      "\t-> Assuming .saf.pos.gz: smallNA07000.saf.pos.gz\n",
      "\t-> Version of fname:smallNA11840.saf.idx is:2\n",
      "\t-> Assuming .saf.gz file: smallNA11840.saf.gz\n",
      "\t-> Assuming .saf.pos.gz: smallNA11840.saf.pos.gz\n",
      "\t-> args: tole:0.000001 nthreads:4 maxiter:100 nsites:0 start:(null) chr:(null) start:-1 stop:-1 fstout:(null) oldout:0 seed:1558447011 bootstrap:0 whichFst:0 fold:0 ref:(null) anc:(null)\n",
      "\t-> Multi SFS is 'still' under development. Please report strange behaviour\n",
      "\t-> nSites: 1451016\n",
      "\t-> The choice of -nSites will require atleast: 55.351868 megabyte memory, that is at least: 0.01% of total memory\n",
      "\t-> dim(smallNA07000.saf.idx):3\n",
      "\t-> dim(smallNA11840.saf.idx):3\n",
      "\t-> Dimension of parameter space: 9\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:1\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[1] from pop0:\t69166\n",
      "\t-> Sites to keep[1] from pop1:\t69166\n",
      "\t-> [readdata] lastread:69166 posi:14000296\n",
      "\t-> Comparing positions: 1 with 0 has:69166\n",
      "\t-> Only read nSites: 69166 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:10\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[10] from pop0:\t74338\n",
      "\t-> Sites to keep[10] from pop1:\t74338\n",
      "\t-> [readdata] lastread:74338 posi:14000296\n",
      "\t-> Comparing positions: 1 with 0 has:143504\n",
      "\t-> Only read nSites: 143504 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:11\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[11] from pop0:\t72548\n",
      "\t-> Sites to keep[11] from pop1:\t72548\n",
      "\t-> [readdata] lastread:72548 posi:14000296\n",
      "\t-> Comparing positions: 1 with 0 has:216052\n",
      "\t-> Only read nSites: 216052 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:12\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[12] from pop0:\t74841\n",
      "\t-> Sites to keep[12] from pop1:\t74841\n",
      "\t-> [readdata] lastread:74841 posi:14000296\n",
      "\t-> Comparing positions: 1 with 0 has:290893\n",
      "\t-> Only read nSites: 290893 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:16\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[16] from pop0:\t69510\n",
      "\t-> Sites to keep[16] from pop1:\t69510\n",
      "\t-> [readdata] lastread:69510 posi:14000296\n",
      "\t-> Comparing positions: 1 with 0 has:360403\n",
      "\t-> Only read nSites: 360403 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:17\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[17] from pop0:\t55424\n",
      "\t-> Sites to keep[17] from pop1:\t55424\n",
      "\t-> [readdata] lastread:55424 posi:14000296\n",
      "\t-> Comparing positions: 1 with 0 has:415827\n",
      "\t-> Only read nSites: 415827 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:18\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[18] from pop0:\t63016\n",
      "\t-> Sites to keep[18] from pop1:\t63016\n",
      "\t-> [readdata] lastread:63016 posi:14000296\n",
      "\t-> Comparing positions: 1 with 0 has:478843\n",
      "\t-> Only read nSites: 478843 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:19\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[19] from pop0:\t53675\n",
      "\t-> Sites to keep[19] from pop1:\t53675\n",
      "\t-> [readdata] lastread:53675 posi:14000296\n",
      "\t-> Comparing positions: 1 with 0 has:532518\n",
      "\t-> Only read nSites: 532518 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:2\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[2] from pop0:\t58633\n",
      "\t-> Sites to keep[2] from pop1:\t58633\n",
      "\t-> [readdata] lastread:58633 posi:14000296\n",
      "\t-> Comparing positions: 1 with 0 has:591151\n",
      "\t-> Only read nSites: 591151 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:20\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[20] from pop0:\t62256\n",
      "\t-> Sites to keep[20] from pop1:\t62256\n",
      "\t-> [readdata] lastread:62256 posi:14000296\n",
      "\t-> Comparing positions: 1 with 0 has:653407\n",
      "\t-> Only read nSites: 653407 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:3\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[3] from pop0:\t55750\n",
      "\t-> Sites to keep[3] from pop1:\t55750\n",
      "\t-> [readdata] lastread:55750 posi:14000296\n",
      "\t-> Comparing positions: 1 with 0 has:709157\n",
      "\t-> Only read nSites: 709157 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:4\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[4] from pop0:\t69568\n",
      "\t-> Sites to keep[4] from pop1:\t69568\n",
      "\t-> [readdata] lastread:69568 posi:14000296\n",
      "\t-> Comparing positions: 1 with 0 has:778725\n",
      "\t-> Only read nSites: 778725 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:5\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[5] from pop0:\t70002\n",
      "\t-> Sites to keep[5] from pop1:\t70002\n",
      "\t-> [readdata] lastread:70002 posi:14000296\n",
      "\t-> Comparing positions: 1 with 0 has:848727\n",
      "\t-> Only read nSites: 848727 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:6\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[6] from pop0:\t72579\n",
      "\t-> Sites to keep[6] from pop1:\t72579\n",
      "\t-> [readdata] lastread:72579 posi:14000296\n",
      "\t-> Comparing positions: 1 with 0 has:921306\n",
      "\t-> Only read nSites: 921306 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:7\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[7] from pop0:\t63710\n",
      "\t-> Sites to keep[7] from pop1:\t63710\n",
      "\t-> [readdata] lastread:63710 posi:14000296\n",
      "\t-> Comparing positions: 1 with 0 has:985016\n",
      "\t-> Only read nSites: 985016 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:8\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "\t-> Sites to keep[8] from pop0:\t61147\n",
      "\t-> Sites to keep[8] from pop1:\t61147\n",
      "\t-> [readdata] lastread:61147 posi:14000296\n",
      "\t-> Comparing positions: 1 with 0 has:1046163\n",
      "\t-> Only read nSites: 1046163 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:9\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[9] from pop0:\t73554\n",
      "\t-> Sites to keep[9] from pop1:\t73554\n",
      "\t-> [readdata] lastread:73554 posi:14000296\n",
      "\t-> Comparing positions: 1 with 0 has:1119717\n",
      "\t-> Only read nSites: 1119717 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Will run optimization on nSites: 1119717\n",
      "------------\n",
      "startlik=-2593701.166205\n",
      "lik[2]=-198864.341967 diff=2.394837e+06 alpha:1.000000 sr2:4.120179e-01\n",
      "lik[5]=-100104.713145 diff=9.875963e+04 alpha:1.351338 sr2:1.203756e-02\n",
      "lik[8]=-100020.577949 diff=8.413520e+01 alpha:2.559383 sr2:2.584763e-08\n",
      "lik[11]=-99988.041884 diff=3.253607e+01 alpha:2.956788 sr2:1.779950e-10\n",
      "lik[14]=-99977.038663 diff=1.100322e+01 alpha:4.000000 sr2:3.556392e-10\n",
      "lik[17]=-99976.837398 diff=2.012650e-01 alpha:3.368543 sr2:2.603086e-11\n",
      "\t-> Breaking EM(sq2) at iter:19, sqrt(sq2):6.949050e-07\n",
      "likelihood: -99976.837398\n",
      "------------\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Only read nSites: 0 will therefore prepare next chromosome (or exit)\n",
      "\n",
      "\t-> NB NB output is no longer log probs of the frequency spectrum!\n",
      "\t-> Output is now simply the expected values! \n",
      "\t-> You can convert to the old format simply with log(norm(x))\n",
      "\t-> Version of fname:smallNA07000.saf.idx is:2\n",
      "\t-> Assuming .saf.gz file: smallNA07000.saf.gz\n",
      "\t-> Assuming .saf.pos.gz: smallNA07000.saf.pos.gz\n",
      "\t-> Version of fname:smallNA07357.saf.idx is:2\n",
      "\t-> Assuming .saf.gz file: smallNA07357.saf.gz\n",
      "\t-> Assuming .saf.pos.gz: smallNA07357.saf.pos.gz\n",
      "\t-> args: tole:0.000001 nthreads:4 maxiter:100 nsites:0 start:(null) chr:(null) start:-1 stop:-1 fstout:(null) oldout:0 seed:1558447013 bootstrap:0 whichFst:0 fold:0 ref:(null) anc:(null)\n",
      "\t-> Multi SFS is 'still' under development. Please report strange behaviour\n",
      "\t-> nSites: 1450698\n",
      "\t-> The choice of -nSites will require atleast: 55.339737 megabyte memory, that is at least: 0.01% of total memory\n",
      "\t-> dim(smallNA07000.saf.idx):3\n",
      "\t-> dim(smallNA07357.saf.idx):3\n",
      "\t-> Dimension of parameter space: 9\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:1\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[1] from pop0:\t72998\n",
      "\t-> Sites to keep[1] from pop1:\t72998\n",
      "\t-> [readdata] lastread:72998 posi:14000253\n",
      "\t-> Comparing positions: 1 with 0 has:72998\n",
      "\t-> Only read nSites: 72998 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:10\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[10] from pop0:\t80472\n",
      "\t-> Sites to keep[10] from pop1:\t80472\n",
      "\t-> [readdata] lastread:80472 posi:14000253\n",
      "\t-> Comparing positions: 1 with 0 has:153470\n",
      "\t-> Only read nSites: 153470 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:11\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[11] from pop0:\t77499\n",
      "\t-> Sites to keep[11] from pop1:\t77499\n",
      "\t-> [readdata] lastread:77499 posi:14000253\n",
      "\t-> Comparing positions: 1 with 0 has:230969\n",
      "\t-> Only read nSites: 230969 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:12\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[12] from pop0:\t79830\n",
      "\t-> Sites to keep[12] from pop1:\t79830\n",
      "\t-> [readdata] lastread:79830 posi:14000253\n",
      "\t-> Comparing positions: 1 with 0 has:310799\n",
      "\t-> Only read nSites: 310799 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:16\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[16] from pop0:\t72768\n",
      "\t-> Sites to keep[16] from pop1:\t72768\n",
      "\t-> [readdata] lastread:72768 posi:14000253\n",
      "\t-> Comparing positions: 1 with 0 has:383567\n",
      "\t-> Only read nSites: 383567 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:17\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[17] from pop0:\t58417\n",
      "\t-> Sites to keep[17] from pop1:\t58417\n",
      "\t-> [readdata] lastread:58417 posi:14000253\n",
      "\t-> Comparing positions: 1 with 0 has:441984\n",
      "\t-> Only read nSites: 441984 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:18\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[18] from pop0:\t65098\n",
      "\t-> Sites to keep[18] from pop1:\t65098\n",
      "\t-> [readdata] lastread:65098 posi:14000253\n",
      "\t-> Comparing positions: 1 with 0 has:507082\n",
      "\t-> Only read nSites: 507082 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:19\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[19] from pop0:\t65927\n",
      "\t-> Sites to keep[19] from pop1:\t65927\n",
      "\t-> [readdata] lastread:65927 posi:14000253\n",
      "\t-> Comparing positions: 1 with 0 has:573009\n",
      "\t-> Only read nSites: 573009 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:2\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[2] from pop0:\t60813\n",
      "\t-> Sites to keep[2] from pop1:\t60813\n",
      "\t-> [readdata] lastread:60813 posi:14000253\n",
      "\t-> Comparing positions: 1 with 0 has:633822\n",
      "\t-> Only read nSites: 633822 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:20\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[20] from pop0:\t63185\n",
      "\t-> Sites to keep[20] from pop1:\t63185\n",
      "\t-> [readdata] lastread:63185 posi:14000253\n",
      "\t-> Comparing positions: 1 with 0 has:697007\n",
      "\t-> Only read nSites: 697007 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:3\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[3] from pop0:\t57388\n",
      "\t-> Sites to keep[3] from pop1:\t57388\n",
      "\t-> [readdata] lastread:57388 posi:14000253\n",
      "\t-> Comparing positions: 1 with 0 has:754395\n",
      "\t-> Only read nSites: 754395 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:4\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[4] from pop0:\t73769\n",
      "\t-> Sites to keep[4] from pop1:\t73769\n",
      "\t-> [readdata] lastread:73769 posi:14000253\n",
      "\t-> Comparing positions: 1 with 0 has:828164\n",
      "\t-> Only read nSites: 828164 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:5\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "\t-> Sites to keep[5] from pop0:\t75862\n",
      "\t-> Sites to keep[5] from pop1:\t75862\n",
      "\t-> [readdata] lastread:75862 posi:14000253\n",
      "\t-> Comparing positions: 1 with 0 has:904026\n",
      "\t-> Only read nSites: 904026 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:6\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[6] from pop0:\t77910\n",
      "\t-> Sites to keep[6] from pop1:\t77910\n",
      "\t-> [readdata] lastread:77910 posi:14000253\n",
      "\t-> Comparing positions: 1 with 0 has:981936\n",
      "\t-> Only read nSites: 981936 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:7\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[7] from pop0:\t67142\n",
      "\t-> Sites to keep[7] from pop1:\t67142\n",
      "\t-> [readdata] lastread:67142 posi:14000253\n",
      "\t-> Comparing positions: 1 with 0 has:1049078\n",
      "\t-> Only read nSites: 1049078 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:8\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[8] from pop0:\t63912\n",
      "\t-> Sites to keep[8] from pop1:\t63912\n",
      "\t-> [readdata] lastread:63912 posi:14000253\n",
      "\t-> Comparing positions: 1 with 0 has:1112990\n",
      "\t-> Only read nSites: 1112990 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:9\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[9] from pop0:\t76930\n",
      "\t-> Sites to keep[9] from pop1:\t76930\n",
      "\t-> [readdata] lastread:76930 posi:14000253\n",
      "\t-> Comparing positions: 1 with 0 has:1189920\n",
      "\t-> Only read nSites: 1189920 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Will run optimization on nSites: 1189920\n",
      "------------\n",
      "startlik=-3295499.379610\n",
      "lik[2]=-671936.971750 diff=2.623562e+06 alpha:1.000000 sr2:3.079325e-01\n",
      "lik[5]=-111757.000553 diff=5.601800e+05 alpha:1.705500 sr2:1.773156e-01\n",
      "lik[8]=-111118.729808 diff=6.382707e+02 alpha:1.502014 sr2:3.776958e-07\n",
      "lik[11]=-111104.701401 diff=1.402841e+01 alpha:2.753213 sr2:1.159374e-09\n",
      "lik[14]=-111021.389502 diff=8.331190e+01 alpha:1.443829 sr2:6.760094e-12\n",
      "lik[17]=-110840.982706 diff=1.804068e+02 alpha:2.558721 sr2:2.761461e-09\n",
      "lik[20]=-110839.909743 diff=1.072963e+00 alpha:1.672894 sr2:1.402133e-10\n",
      "lik[23]=-110839.871314 diff=3.842885e-02 alpha:4.000000 sr2:3.133923e-12\n",
      "\t-> Breaking EM(sr2) at iter:24, sqrt(sr2):7.629226e-08\n",
      "likelihood: -110839.871314\n",
      "------------\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Only read nSites: 0 will therefore prepare next chromosome (or exit)\n",
      "\n",
      "\t-> NB NB output is no longer log probs of the frequency spectrum!\n",
      "\t-> Output is now simply the expected values! \n",
      "\t-> You can convert to the old format simply with log(norm(x))\n",
      "\t-> Version of fname:smallNA07000.saf.idx is:2\n",
      "\t-> Assuming .saf.gz file: smallNA07000.saf.gz\n",
      "\t-> Assuming .saf.pos.gz: smallNA07000.saf.pos.gz\n",
      "\t-> Version of fname:smallNA11832.saf.idx is:2\n",
      "\t-> Assuming .saf.gz file: smallNA11832.saf.gz\n",
      "\t-> Assuming .saf.pos.gz: smallNA11832.saf.pos.gz\n",
      "\t-> args: tole:0.000001 nthreads:4 maxiter:100 nsites:0 start:(null) chr:(null) start:-1 stop:-1 fstout:(null) oldout:0 seed:1558447016 bootstrap:0 whichFst:0 fold:0 ref:(null) anc:(null)\n",
      "\t-> Multi SFS is 'still' under development. Please report strange behaviour\n",
      "\t-> nSites: 1265795\n",
      "\t-> The choice of -nSites will require atleast: 48.286247 megabyte memory, that is at least: 0.01% of total memory\n",
      "\t-> dim(smallNA07000.saf.idx):3\n",
      "\t-> dim(smallNA11832.saf.idx):3\n",
      "\t-> Dimension of parameter space: 9\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:1\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[1] from pop0:\t60083\n",
      "\t-> Sites to keep[1] from pop1:\t60083\n",
      "\t-> [readdata] lastread:60083 posi:14000319\n",
      "\t-> Comparing positions: 1 with 0 has:60083\n",
      "\t-> Only read nSites: 60083 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:10\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[10] from pop0:\t66691\n",
      "\t-> Sites to keep[10] from pop1:\t66691\n",
      "\t-> [readdata] lastread:66691 posi:14000319\n",
      "\t-> Comparing positions: 1 with 0 has:126774\n",
      "\t-> Only read nSites: 126774 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:11\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[11] from pop0:\t63721\n",
      "\t-> Sites to keep[11] from pop1:\t63721\n",
      "\t-> [readdata] lastread:63721 posi:14000319\n",
      "\t-> Comparing positions: 1 with 0 has:190495\n",
      "\t-> Only read nSites: 190495 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:12\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[12] from pop0:\t66430\n",
      "\t-> Sites to keep[12] from pop1:\t66430\n",
      "\t-> [readdata] lastread:66430 posi:14000319\n",
      "\t-> Comparing positions: 1 with 0 has:256925\n",
      "\t-> Only read nSites: 256925 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:16\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[16] from pop0:\t60907\n",
      "\t-> Sites to keep[16] from pop1:\t60907\n",
      "\t-> [readdata] lastread:60907 posi:14000319\n",
      "\t-> Comparing positions: 1 with 0 has:317832\n",
      "\t-> Only read nSites: 317832 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:17\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[17] from pop0:\t47428\n",
      "\t-> Sites to keep[17] from pop1:\t47428\n",
      "\t-> [readdata] lastread:47428 posi:14000319\n",
      "\t-> Comparing positions: 1 with 0 has:365260\n",
      "\t-> Only read nSites: 365260 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:18\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[18] from pop0:\t54225\n",
      "\t-> Sites to keep[18] from pop1:\t54225\n",
      "\t-> [readdata] lastread:54225 posi:14000319\n",
      "\t-> Comparing positions: 1 with 0 has:419485\n",
      "\t-> Only read nSites: 419485 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:19\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "\t-> Sites to keep[19] from pop0:\t50453\n",
      "\t-> Sites to keep[19] from pop1:\t50453\n",
      "\t-> [readdata] lastread:50453 posi:14000319\n",
      "\t-> Comparing positions: 1 with 0 has:469938\n",
      "\t-> Only read nSites: 469938 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:2\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[2] from pop0:\t49280\n",
      "\t-> Sites to keep[2] from pop1:\t49280\n",
      "\t-> [readdata] lastread:49280 posi:14000319\n",
      "\t-> Comparing positions: 1 with 0 has:519218\n",
      "\t-> Only read nSites: 519218 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:20\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[20] from pop0:\t50084\n",
      "\t-> Sites to keep[20] from pop1:\t50084\n",
      "\t-> [readdata] lastread:50084 posi:14000319\n",
      "\t-> Comparing positions: 1 with 0 has:569302\n",
      "\t-> Only read nSites: 569302 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:3\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[3] from pop0:\t46955\n",
      "\t-> Sites to keep[3] from pop1:\t46955\n",
      "\t-> [readdata] lastread:46955 posi:14000319\n",
      "\t-> Comparing positions: 1 with 0 has:616257\n",
      "\t-> Only read nSites: 616257 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:4\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[4] from pop0:\t61716\n",
      "\t-> Sites to keep[4] from pop1:\t61716\n",
      "\t-> [readdata] lastread:61716 posi:14000319\n",
      "\t-> Comparing positions: 1 with 0 has:677973\n",
      "\t-> Only read nSites: 677973 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:5\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[5] from pop0:\t62941\n",
      "\t-> Sites to keep[5] from pop1:\t62941\n",
      "\t-> [readdata] lastread:62941 posi:14000319\n",
      "\t-> Comparing positions: 1 with 0 has:740914\n",
      "\t-> Only read nSites: 740914 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:6\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[6] from pop0:\t63995\n",
      "\t-> Sites to keep[6] from pop1:\t63995\n",
      "\t-> [readdata] lastread:63995 posi:14000319\n",
      "\t-> Comparing positions: 1 with 0 has:804909\n",
      "\t-> Only read nSites: 804909 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:7\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[7] from pop0:\t53747\n",
      "\t-> Sites to keep[7] from pop1:\t53747\n",
      "\t-> [readdata] lastread:53747 posi:14000319\n",
      "\t-> Comparing positions: 1 with 0 has:858656\n",
      "\t-> Only read nSites: 858656 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:8\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[8] from pop0:\t51888\n",
      "\t-> Sites to keep[8] from pop1:\t51888\n",
      "\t-> [readdata] lastread:51888 posi:14000319\n",
      "\t-> Comparing positions: 1 with 0 has:910544\n",
      "\t-> Only read nSites: 910544 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:9\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[9] from pop0:\t64862\n",
      "\t-> Sites to keep[9] from pop1:\t64862\n",
      "\t-> [readdata] lastread:64862 posi:14000319\n",
      "\t-> Comparing positions: 1 with 0 has:975406\n",
      "\t-> Only read nSites: 975406 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Will run optimization on nSites: 975406\n",
      "------------\n",
      "startlik=-1695470.779729\n",
      "lik[2]=-135885.756887 diff=1.559585e+06 alpha:1.000000 sr2:4.720139e-01\n",
      "lik[5]=-88454.733074 diff=4.743102e+04 alpha:1.425159 sr2:3.419794e-03\n",
      "lik[8]=-88244.916470 diff=2.098166e+02 alpha:2.071332 sr2:1.958948e-07\n",
      "lik[11]=-88195.404468 diff=4.951200e+01 alpha:4.000000 sr2:4.299315e-09\n",
      "lik[14]=-88190.550578 diff=4.853891e+00 alpha:3.025225 sr2:2.676804e-10\n",
      "lik[17]=-88189.965506 diff=5.850715e-01 alpha:3.957403 sr2:3.296353e-11\n",
      "lik[20]=-88189.942356 diff=2.315016e-02 alpha:2.244944 sr2:4.461082e-12\n",
      "\t-> Breaking EM(sr2) at iter:21, sqrt(sr2):4.918831e-07\n",
      "likelihood: -88189.942356\n",
      "------------\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Only read nSites: 0 will therefore prepare next chromosome (or exit)\n",
      "\n",
      "\t-> NB NB output is no longer log probs of the frequency spectrum!\n",
      "\t-> Output is now simply the expected values! \n",
      "\t-> You can convert to the old format simply with log(norm(x))\n",
      "\t-> Version of fname:smallNA07000.saf.idx is:2\n",
      "\t-> Assuming .saf.gz file: smallNA07000.saf.gz\n",
      "\t-> Assuming .saf.pos.gz: smallNA07000.saf.pos.gz\n",
      "\t-> Version of fname:smallNA06994.saf.idx is:2\n",
      "\t-> Assuming .saf.gz file: smallNA06994.saf.gz\n",
      "\t-> Assuming .saf.pos.gz: smallNA06994.saf.pos.gz\n",
      "\t-> args: tole:0.000001 nthreads:4 maxiter:100 nsites:0 start:(null) chr:(null) start:-1 stop:-1 fstout:(null) oldout:0 seed:1558447017 bootstrap:0 whichFst:0 fold:0 ref:(null) anc:(null)\n",
      "\t-> Multi SFS is 'still' under development. Please report strange behaviour\n",
      "\t-> nSites: 1372028\n",
      "\t-> The choice of -nSites will require atleast: 52.338715 megabyte memory, that is at least: 0.01% of total memory\n",
      "\t-> dim(smallNA07000.saf.idx):3\n",
      "\t-> dim(smallNA06994.saf.idx):3\n",
      "\t-> Dimension of parameter space: 9\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:1\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[1] from pop0:\t69322\n",
      "\t-> Sites to keep[1] from pop1:\t69322\n",
      "\t-> [readdata] lastread:69322 posi:14000242\n",
      "\t-> Comparing positions: 1 with 0 has:69322\n",
      "\t-> Only read nSites: 69322 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:10\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[10] from pop0:\t75456\n",
      "\t-> Sites to keep[10] from pop1:\t75456\n",
      "\t-> [readdata] lastread:75456 posi:14000242\n",
      "\t-> Comparing positions: 1 with 0 has:144778\n",
      "\t-> Only read nSites: 144778 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:11\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[11] from pop0:\t74980\n",
      "\t-> Sites to keep[11] from pop1:\t74980\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "\t-> [readdata] lastread:74980 posi:14000242\n",
      "\t-> Comparing positions: 1 with 0 has:219758\n",
      "\t-> Only read nSites: 219758 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:12\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[12] from pop0:\t77814\n",
      "\t-> Sites to keep[12] from pop1:\t77814\n",
      "\t-> [readdata] lastread:77814 posi:14000242\n",
      "\t-> Comparing positions: 1 with 0 has:297572\n",
      "\t-> Only read nSites: 297572 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:16\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[16] from pop0:\t68263\n",
      "\t-> Sites to keep[16] from pop1:\t68263\n",
      "\t-> [readdata] lastread:68263 posi:14000242\n",
      "\t-> Comparing positions: 1 with 0 has:365835\n",
      "\t-> Only read nSites: 365835 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:17\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[17] from pop0:\t56460\n",
      "\t-> Sites to keep[17] from pop1:\t56460\n",
      "\t-> [readdata] lastread:56460 posi:14000242\n",
      "\t-> Comparing positions: 1 with 0 has:422295\n",
      "\t-> Only read nSites: 422295 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:18\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[18] from pop0:\t63123\n",
      "\t-> Sites to keep[18] from pop1:\t63123\n",
      "\t-> [readdata] lastread:63123 posi:14000242\n",
      "\t-> Comparing positions: 1 with 0 has:485418\n",
      "\t-> Only read nSites: 485418 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:19\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[19] from pop0:\t50572\n",
      "\t-> Sites to keep[19] from pop1:\t50572\n",
      "\t-> [readdata] lastread:50572 posi:14000242\n",
      "\t-> Comparing positions: 1 with 0 has:535990\n",
      "\t-> Only read nSites: 535990 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:2\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[2] from pop0:\t60299\n",
      "\t-> Sites to keep[2] from pop1:\t60299\n",
      "\t-> [readdata] lastread:60299 posi:14000242\n",
      "\t-> Comparing positions: 1 with 0 has:596289\n",
      "\t-> Only read nSites: 596289 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:20\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[20] from pop0:\t60692\n",
      "\t-> Sites to keep[20] from pop1:\t60692\n",
      "\t-> [readdata] lastread:60692 posi:14000242\n",
      "\t-> Comparing positions: 1 with 0 has:656981\n",
      "\t-> Only read nSites: 656981 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:3\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[3] from pop0:\t51822\n",
      "\t-> Sites to keep[3] from pop1:\t51822\n",
      "\t-> [readdata] lastread:51822 posi:14000242\n",
      "\t-> Comparing positions: 1 with 0 has:708803\n",
      "\t-> Only read nSites: 708803 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:4\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[4] from pop0:\t72895\n",
      "\t-> Sites to keep[4] from pop1:\t72895\n",
      "\t-> [readdata] lastread:72895 posi:14000242\n",
      "\t-> Comparing positions: 1 with 0 has:781698\n",
      "\t-> Only read nSites: 781698 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:5\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[5] from pop0:\t72204\n",
      "\t-> Sites to keep[5] from pop1:\t72204\n",
      "\t-> [readdata] lastread:72204 posi:14000242\n",
      "\t-> Comparing positions: 1 with 0 has:853902\n",
      "\t-> Only read nSites: 853902 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:6\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[6] from pop0:\t73161\n",
      "\t-> Sites to keep[6] from pop1:\t73161\n",
      "\t-> [readdata] lastread:73161 posi:14000242\n",
      "\t-> Comparing positions: 1 with 0 has:927063\n",
      "\t-> Only read nSites: 927063 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:7\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[7] from pop0:\t66802\n",
      "\t-> Sites to keep[7] from pop1:\t66802\n",
      "\t-> [readdata] lastread:66802 posi:14000242\n",
      "\t-> Comparing positions: 1 with 0 has:993865\n",
      "\t-> Only read nSites: 993865 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:8\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[8] from pop0:\t63395\n",
      "\t-> Sites to keep[8] from pop1:\t63395\n",
      "\t-> [readdata] lastread:63395 posi:14000242\n",
      "\t-> Comparing positions: 1 with 0 has:1057260\n",
      "\t-> Only read nSites: 1057260 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:9\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[9] from pop0:\t75430\n",
      "\t-> Sites to keep[9] from pop1:\t75430\n",
      "\t-> [readdata] lastread:75430 posi:14000242\n",
      "\t-> Comparing positions: 1 with 0 has:1132690\n",
      "\t-> Only read nSites: 1132690 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Will run optimization on nSites: 1132690\n",
      "------------\n",
      "startlik=-1917831.862715\n",
      "lik[2]=-212019.335570 diff=1.705813e+06 alpha:1.000000 sr2:2.751823e-01\n",
      "lik[5]=-107952.457098 diff=1.040669e+05 alpha:1.354203 sr2:1.222607e-02\n",
      "lik[8]=-107796.242748 diff=1.562143e+02 alpha:1.884069 sr2:1.793755e-07\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "lik[11]=-107792.648386 diff=3.594361e+00 alpha:2.586955 sr2:3.139571e-10\n",
      "lik[14]=-107785.007053 diff=7.641333e+00 alpha:4.000000 sr2:1.163626e-11\n",
      "lik[17]=-107782.897637 diff=2.109417e+00 alpha:5.261490 sr2:2.658007e-11\n",
      "lik[20]=-107781.987937 diff=9.096998e-01 alpha:3.094626 sr2:5.615945e-12\n",
      "lik[23]=-107781.765670 diff=2.222667e-01 alpha:4.578733 sr2:2.860646e-12\n",
      "\t-> Breaking EM(sr2) at iter:24, sqrt(sr2):7.730103e-07\n",
      "likelihood: -107781.765670\n",
      "------------\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Only read nSites: 0 will therefore prepare next chromosome (or exit)\n",
      "\n",
      "\t-> NB NB output is no longer log probs of the frequency spectrum!\n",
      "\t-> Output is now simply the expected values! \n",
      "\t-> You can convert to the old format simply with log(norm(x))\n",
      "\t-> Version of fname:smallNA07000.saf.idx is:2\n",
      "\t-> Assuming .saf.gz file: smallNA07000.saf.gz\n",
      "\t-> Assuming .saf.pos.gz: smallNA07000.saf.pos.gz\n",
      "\t-> Version of fname:smallNA06985.saf.idx is:2\n",
      "\t-> Assuming .saf.gz file: smallNA06985.saf.gz\n",
      "\t-> Assuming .saf.pos.gz: smallNA06985.saf.pos.gz\n",
      "\t-> args: tole:0.000001 nthreads:4 maxiter:100 nsites:0 start:(null) chr:(null) start:-1 stop:-1 fstout:(null) oldout:0 seed:1558447020 bootstrap:0 whichFst:0 fold:0 ref:(null) anc:(null)\n",
      "\t-> Multi SFS is 'still' under development. Please report strange behaviour\n",
      "\t-> nSites: 1430342\n",
      "\t-> The choice of -nSites will require atleast: 54.563217 megabyte memory, that is at least: 0.01% of total memory\n",
      "\t-> dim(smallNA07000.saf.idx):3\n",
      "\t-> dim(smallNA06985.saf.idx):3\n",
      "\t-> Dimension of parameter space: 9\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:1\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[1] from pop0:\t69774\n",
      "\t-> Sites to keep[1] from pop1:\t69774\n",
      "\t-> [readdata] lastread:69774 posi:14000242\n",
      "\t-> Comparing positions: 1 with 0 has:69774\n",
      "\t-> Only read nSites: 69774 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:10\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[10] from pop0:\t76796\n",
      "\t-> Sites to keep[10] from pop1:\t76796\n",
      "\t-> [readdata] lastread:76796 posi:14000242\n",
      "\t-> Comparing positions: 1 with 0 has:146570\n",
      "\t-> Only read nSites: 146570 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:11\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[11] from pop0:\t74325\n",
      "\t-> Sites to keep[11] from pop1:\t74325\n",
      "\t-> [readdata] lastread:74325 posi:14000242\n",
      "\t-> Comparing positions: 1 with 0 has:220895\n",
      "\t-> Only read nSites: 220895 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:12\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[12] from pop0:\t74117\n",
      "\t-> Sites to keep[12] from pop1:\t74117\n",
      "\t-> [readdata] lastread:74117 posi:14000242\n",
      "\t-> Comparing positions: 1 with 0 has:295012\n",
      "\t-> Only read nSites: 295012 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:16\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[16] from pop0:\t68851\n",
      "\t-> Sites to keep[16] from pop1:\t68851\n",
      "\t-> [readdata] lastread:68851 posi:14000242\n",
      "\t-> Comparing positions: 1 with 0 has:363863\n",
      "\t-> Only read nSites: 363863 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:17\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[17] from pop0:\t54545\n",
      "\t-> Sites to keep[17] from pop1:\t54545\n",
      "\t-> [readdata] lastread:54545 posi:14000242\n",
      "\t-> Comparing positions: 1 with 0 has:418408\n",
      "\t-> Only read nSites: 418408 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:18\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[18] from pop0:\t60856\n",
      "\t-> Sites to keep[18] from pop1:\t60856\n",
      "\t-> [readdata] lastread:60856 posi:14000242\n",
      "\t-> Comparing positions: 1 with 0 has:479264\n",
      "\t-> Only read nSites: 479264 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:19\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[19] from pop0:\t63845\n",
      "\t-> Sites to keep[19] from pop1:\t63845\n",
      "\t-> [readdata] lastread:63845 posi:14000242\n",
      "\t-> Comparing positions: 1 with 0 has:543109\n",
      "\t-> Only read nSites: 543109 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:2\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[2] from pop0:\t52778\n",
      "\t-> Sites to keep[2] from pop1:\t52778\n",
      "\t-> [readdata] lastread:52778 posi:14000242\n",
      "\t-> Comparing positions: 1 with 0 has:595887\n",
      "\t-> Only read nSites: 595887 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:20\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[20] from pop0:\t58258\n",
      "\t-> Sites to keep[20] from pop1:\t58258\n",
      "\t-> [readdata] lastread:58258 posi:14000242\n",
      "\t-> Comparing positions: 1 with 0 has:654145\n",
      "\t-> Only read nSites: 654145 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:3\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[3] from pop0:\t55585\n",
      "\t-> Sites to keep[3] from pop1:\t55585\n",
      "\t-> [readdata] lastread:55585 posi:14000242\n",
      "\t-> Comparing positions: 1 with 0 has:709730\n",
      "\t-> Only read nSites: 709730 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:4\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[4] from pop0:\t70234\n",
      "\t-> Sites to keep[4] from pop1:\t70234\n",
      "\t-> [readdata] lastread:70234 posi:14000242\n",
      "\t-> Comparing positions: 1 with 0 has:779964\n",
      "\t-> Only read nSites: 779964 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:5\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[5] from pop0:\t73629\n",
      "\t-> Sites to keep[5] from pop1:\t73629\n",
      "\t-> [readdata] lastread:73629 posi:14000242\n",
      "\t-> Comparing positions: 1 with 0 has:853593\n",
      "\t-> Only read nSites: 853593 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:6\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "\t-> Sites to keep[6] from pop0:\t75387\n",
      "\t-> Sites to keep[6] from pop1:\t75387\n",
      "\t-> [readdata] lastread:75387 posi:14000242\n",
      "\t-> Comparing positions: 1 with 0 has:928980\n",
      "\t-> Only read nSites: 928980 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:7\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[7] from pop0:\t58902\n",
      "\t-> Sites to keep[7] from pop1:\t58902\n",
      "\t-> [readdata] lastread:58902 posi:14000242\n",
      "\t-> Comparing positions: 1 with 0 has:987882\n",
      "\t-> Only read nSites: 987882 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:8\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[8] from pop0:\t54431\n",
      "\t-> Sites to keep[8] from pop1:\t54431\n",
      "\t-> [readdata] lastread:54431 posi:14000242\n",
      "\t-> Comparing positions: 1 with 0 has:1042313\n",
      "\t-> Only read nSites: 1042313 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:9\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[9] from pop0:\t71271\n",
      "\t-> Sites to keep[9] from pop1:\t71271\n",
      "\t-> [readdata] lastread:71271 posi:14000242\n",
      "\t-> Comparing positions: 1 with 0 has:1113584\n",
      "\t-> Only read nSites: 1113584 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Will run optimization on nSites: 1113584\n",
      "------------\n",
      "startlik=-3144465.367301\n",
      "lik[2]=-203809.412276 diff=2.940656e+06 alpha:1.000000 sr2:4.358977e-01\n",
      "lik[5]=-100455.267132 diff=1.033541e+05 alpha:1.363603 sr2:1.166902e-02\n",
      "lik[8]=-100308.160988 diff=1.471061e+02 alpha:2.056727 sr2:6.938636e-08\n",
      "lik[11]=-100274.419343 diff=3.374164e+01 alpha:3.069293 sr2:7.742072e-10\n",
      "lik[14]=-100270.906852 diff=3.512491e+00 alpha:4.000000 sr2:2.141709e-10\n",
      "lik[17]=-100270.892621 diff=1.423107e-02 alpha:1.567627 sr2:5.965016e-12\n",
      "\t-> Breaking EM(sr2) at iter:18, sqrt(sr2):3.069922e-07\n",
      "likelihood: -100270.892621\n",
      "------------\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Only read nSites: 0 will therefore prepare next chromosome (or exit)\n",
      "\n",
      "\t-> NB NB output is no longer log probs of the frequency spectrum!\n",
      "\t-> Output is now simply the expected values! \n",
      "\t-> You can convert to the old format simply with log(norm(x))\n",
      "\t-> Version of fname:smallNA07000.saf.idx is:2\n",
      "\t-> Assuming .saf.gz file: smallNA07000.saf.gz\n",
      "\t-> Assuming .saf.pos.gz: smallNA07000.saf.pos.gz\n",
      "\t-> Version of fname:smallNA11831.saf.idx is:2\n",
      "\t-> Assuming .saf.gz file: smallNA11831.saf.gz\n",
      "\t-> Assuming .saf.pos.gz: smallNA11831.saf.pos.gz\n",
      "\t-> args: tole:0.000001 nthreads:4 maxiter:100 nsites:0 start:(null) chr:(null) start:-1 stop:-1 fstout:(null) oldout:0 seed:1558447022 bootstrap:0 whichFst:0 fold:0 ref:(null) anc:(null)\n",
      "\t-> Multi SFS is 'still' under development. Please report strange behaviour\n",
      "\t-> nSites: 1556469\n",
      "\t-> The choice of -nSites will require atleast: 59.374580 megabyte memory, that is at least: 0.02% of total memory\n",
      "\t-> dim(smallNA07000.saf.idx):3\n",
      "\t-> dim(smallNA11831.saf.idx):3\n",
      "\t-> Dimension of parameter space: 9\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:1\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[1] from pop0:\t74281\n",
      "\t-> Sites to keep[1] from pop1:\t74281\n",
      "\t-> [readdata] lastread:74281 posi:14000284\n",
      "\t-> Comparing positions: 1 with 0 has:74281\n",
      "\t-> Only read nSites: 74281 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:10\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[10] from pop0:\t80883\n",
      "\t-> Sites to keep[10] from pop1:\t80883\n",
      "\t-> [readdata] lastread:80883 posi:14000284\n",
      "\t-> Comparing positions: 1 with 0 has:155164\n",
      "\t-> Only read nSites: 155164 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:11\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[11] from pop0:\t78959\n",
      "\t-> Sites to keep[11] from pop1:\t78959\n",
      "\t-> [readdata] lastread:78959 posi:14000284\n",
      "\t-> Comparing positions: 1 with 0 has:234123\n",
      "\t-> Only read nSites: 234123 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:12\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[12] from pop0:\t81390\n",
      "\t-> Sites to keep[12] from pop1:\t81390\n",
      "\t-> [readdata] lastread:81390 posi:14000284\n",
      "\t-> Comparing positions: 1 with 0 has:315513\n",
      "\t-> Only read nSites: 315513 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:16\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[16] from pop0:\t75359\n",
      "\t-> Sites to keep[16] from pop1:\t75359\n",
      "\t-> [readdata] lastread:75359 posi:14000284\n",
      "\t-> Comparing positions: 1 with 0 has:390872\n",
      "\t-> Only read nSites: 390872 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:17\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[17] from pop0:\t60991\n",
      "\t-> Sites to keep[17] from pop1:\t60991\n",
      "\t-> [readdata] lastread:60991 posi:14000284\n",
      "\t-> Comparing positions: 1 with 0 has:451863\n",
      "\t-> Only read nSites: 451863 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:18\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[18] from pop0:\t67633\n",
      "\t-> Sites to keep[18] from pop1:\t67633\n",
      "\t-> [readdata] lastread:67633 posi:14000284\n",
      "\t-> Comparing positions: 1 with 0 has:519496\n",
      "\t-> Only read nSites: 519496 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:19\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[19] from pop0:\t63775\n",
      "\t-> Sites to keep[19] from pop1:\t63775\n",
      "\t-> [readdata] lastread:63775 posi:14000284\n",
      "\t-> Comparing positions: 1 with 0 has:583271\n",
      "\t-> Only read nSites: 583271 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:2\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[2] from pop0:\t63598\n",
      "\t-> Sites to keep[2] from pop1:\t63598\n",
      "\t-> [readdata] lastread:63598 posi:14000284\n",
      "\t-> Comparing positions: 1 with 0 has:646869\n",
      "\t-> Only read nSites: 646869 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:20\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[20] from pop0:\t66596\n",
      "\t-> Sites to keep[20] from pop1:\t66596\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "\t-> [readdata] lastread:66596 posi:14000284\n",
      "\t-> Comparing positions: 1 with 0 has:713465\n",
      "\t-> Only read nSites: 713465 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:3\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[3] from pop0:\t60197\n",
      "\t-> Sites to keep[3] from pop1:\t60197\n",
      "\t-> [readdata] lastread:60197 posi:14000284\n",
      "\t-> Comparing positions: 1 with 0 has:773662\n",
      "\t-> Only read nSites: 773662 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:4\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[4] from pop0:\t75423\n",
      "\t-> Sites to keep[4] from pop1:\t75423\n",
      "\t-> [readdata] lastread:75423 posi:14000284\n",
      "\t-> Comparing positions: 1 with 0 has:849085\n",
      "\t-> Only read nSites: 849085 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:5\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[5] from pop0:\t77747\n",
      "\t-> Sites to keep[5] from pop1:\t77747\n",
      "\t-> [readdata] lastread:77747 posi:14000284\n",
      "\t-> Comparing positions: 1 with 0 has:926832\n",
      "\t-> Only read nSites: 926832 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:6\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[6] from pop0:\t79340\n",
      "\t-> Sites to keep[6] from pop1:\t79340\n",
      "\t-> [readdata] lastread:79340 posi:14000284\n",
      "\t-> Comparing positions: 1 with 0 has:1006172\n",
      "\t-> Only read nSites: 1006172 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:7\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[7] from pop0:\t69929\n",
      "\t-> Sites to keep[7] from pop1:\t69929\n",
      "\t-> [readdata] lastread:69929 posi:14000284\n",
      "\t-> Comparing positions: 1 with 0 has:1076101\n",
      "\t-> Only read nSites: 1076101 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:8\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[8] from pop0:\t68114\n",
      "\t-> Sites to keep[8] from pop1:\t68114\n",
      "\t-> [readdata] lastread:68114 posi:14000284\n",
      "\t-> Comparing positions: 1 with 0 has:1144215\n",
      "\t-> Only read nSites: 1144215 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:9\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[9] from pop0:\t79185\n",
      "\t-> Sites to keep[9] from pop1:\t79185\n",
      "\t-> [readdata] lastread:79185 posi:14000284\n",
      "\t-> Comparing positions: 1 with 0 has:1223400\n",
      "\t-> Only read nSites: 1223400 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Will run optimization on nSites: 1223400\n",
      "------------\n",
      "startlik=-1944250.671013\n",
      "lik[2]=-137095.817852 diff=1.807155e+06 alpha:1.000000 sr2:5.592137e-01\n",
      "lik[5]=-116235.474007 diff=2.086034e+04 alpha:1.318269 sr2:4.643012e-04\n",
      "lik[8]=-116091.983570 diff=1.434904e+02 alpha:2.028033 sr2:5.949876e-08\n",
      "lik[11]=-116051.717468 diff=4.026610e+01 alpha:4.000000 sr2:1.309146e-09\n",
      "lik[14]=-116049.998647 diff=1.718821e+00 alpha:1.749292 sr2:1.838807e-10\n",
      "lik[17]=-116049.948909 diff=4.973886e-02 alpha:4.158811 sr2:5.464500e-12\n",
      "\t-> Breaking EM(sr2) at iter:18, sqrt(sr2):2.107295e-07\n",
      "likelihood: -116049.948909\n",
      "------------\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Only read nSites: 0 will therefore prepare next chromosome (or exit)\n",
      "\n",
      "\t-> NB NB output is no longer log probs of the frequency spectrum!\n",
      "\t-> Output is now simply the expected values! \n",
      "\t-> You can convert to the old format simply with log(norm(x))\n",
      "\t-> Version of fname:smallNA07000.saf.idx is:2\n",
      "\t-> Assuming .saf.gz file: smallNA07000.saf.gz\n",
      "\t-> Assuming .saf.pos.gz: smallNA07000.saf.pos.gz\n",
      "\t-> Version of fname:smallNA11829.saf.idx is:2\n",
      "\t-> Assuming .saf.gz file: smallNA11829.saf.gz\n",
      "\t-> Assuming .saf.pos.gz: smallNA11829.saf.pos.gz\n",
      "\t-> args: tole:0.000001 nthreads:4 maxiter:100 nsites:0 start:(null) chr:(null) start:-1 stop:-1 fstout:(null) oldout:0 seed:1558447024 bootstrap:0 whichFst:0 fold:0 ref:(null) anc:(null)\n",
      "\t-> Multi SFS is 'still' under development. Please report strange behaviour\n",
      "\t-> nSites: 1542786\n",
      "\t-> The choice of -nSites will require atleast: 58.852615 megabyte memory, that is at least: 0.02% of total memory\n",
      "\t-> dim(smallNA07000.saf.idx):3\n",
      "\t-> dim(smallNA11829.saf.idx):3\n",
      "\t-> Dimension of parameter space: 9\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:1\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[1] from pop0:\t73598\n",
      "\t-> Sites to keep[1] from pop1:\t73598\n",
      "\t-> [readdata] lastread:73598 posi:14000242\n",
      "\t-> Comparing positions: 1 with 0 has:73598\n",
      "\t-> Only read nSites: 73598 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:10\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[10] from pop0:\t79615\n",
      "\t-> Sites to keep[10] from pop1:\t79615\n",
      "\t-> [readdata] lastread:79615 posi:14000242\n",
      "\t-> Comparing positions: 1 with 0 has:153213\n",
      "\t-> Only read nSites: 153213 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:11\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[11] from pop0:\t78965\n",
      "\t-> Sites to keep[11] from pop1:\t78965\n",
      "\t-> [readdata] lastread:78965 posi:14000242\n",
      "\t-> Comparing positions: 1 with 0 has:232178\n",
      "\t-> Only read nSites: 232178 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:12\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[12] from pop0:\t80430\n",
      "\t-> Sites to keep[12] from pop1:\t80430\n",
      "\t-> [readdata] lastread:80430 posi:14000242\n",
      "\t-> Comparing positions: 1 with 0 has:312608\n",
      "\t-> Only read nSites: 312608 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:16\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[16] from pop0:\t73964\n",
      "\t-> Sites to keep[16] from pop1:\t73964\n",
      "\t-> [readdata] lastread:73964 posi:14000242\n",
      "\t-> Comparing positions: 1 with 0 has:386572\n",
      "\t-> Only read nSites: 386572 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:17\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "\t-> Sites to keep[17] from pop0:\t61412\n",
      "\t-> Sites to keep[17] from pop1:\t61412\n",
      "\t-> [readdata] lastread:61412 posi:14000242\n",
      "\t-> Comparing positions: 1 with 0 has:447984\n",
      "\t-> Only read nSites: 447984 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:18\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[18] from pop0:\t67010\n",
      "\t-> Sites to keep[18] from pop1:\t67010\n",
      "\t-> [readdata] lastread:67010 posi:14000242\n",
      "\t-> Comparing positions: 1 with 0 has:514994\n",
      "\t-> Only read nSites: 514994 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:19\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[19] from pop0:\t60680\n",
      "\t-> Sites to keep[19] from pop1:\t60680\n",
      "\t-> [readdata] lastread:60680 posi:14000242\n",
      "\t-> Comparing positions: 1 with 0 has:575674\n",
      "\t-> Only read nSites: 575674 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:2\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[2] from pop0:\t63859\n",
      "\t-> Sites to keep[2] from pop1:\t63859\n",
      "\t-> [readdata] lastread:63859 posi:14000242\n",
      "\t-> Comparing positions: 1 with 0 has:639533\n",
      "\t-> Only read nSites: 639533 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:20\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[20] from pop0:\t66313\n",
      "\t-> Sites to keep[20] from pop1:\t66313\n",
      "\t-> [readdata] lastread:66313 posi:14000242\n",
      "\t-> Comparing positions: 1 with 0 has:705846\n",
      "\t-> Only read nSites: 705846 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:3\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[3] from pop0:\t59833\n",
      "\t-> Sites to keep[3] from pop1:\t59833\n",
      "\t-> [readdata] lastread:59833 posi:14000242\n",
      "\t-> Comparing positions: 1 with 0 has:765679\n",
      "\t-> Only read nSites: 765679 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:4\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[4] from pop0:\t75091\n",
      "\t-> Sites to keep[4] from pop1:\t75091\n",
      "\t-> [readdata] lastread:75091 posi:14000242\n",
      "\t-> Comparing positions: 1 with 0 has:840770\n",
      "\t-> Only read nSites: 840770 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:5\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[5] from pop0:\t76761\n",
      "\t-> Sites to keep[5] from pop1:\t76761\n",
      "\t-> [readdata] lastread:76761 posi:14000242\n",
      "\t-> Comparing positions: 1 with 0 has:917531\n",
      "\t-> Only read nSites: 917531 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:6\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[6] from pop0:\t78598\n",
      "\t-> Sites to keep[6] from pop1:\t78598\n",
      "\t-> [readdata] lastread:78598 posi:14000242\n",
      "\t-> Comparing positions: 1 with 0 has:996129\n",
      "\t-> Only read nSites: 996129 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:7\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[7] from pop0:\t69686\n",
      "\t-> Sites to keep[7] from pop1:\t69686\n",
      "\t-> [readdata] lastread:69686 posi:14000242\n",
      "\t-> Comparing positions: 1 with 0 has:1065815\n",
      "\t-> Only read nSites: 1065815 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:8\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[8] from pop0:\t67420\n",
      "\t-> Sites to keep[8] from pop1:\t67420\n",
      "\t-> [readdata] lastread:67420 posi:14000242\n",
      "\t-> Comparing positions: 1 with 0 has:1133235\n",
      "\t-> Only read nSites: 1133235 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:9\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[9] from pop0:\t78847\n",
      "\t-> Sites to keep[9] from pop1:\t78847\n",
      "\t-> [readdata] lastread:78847 posi:14000242\n",
      "\t-> Comparing positions: 1 with 0 has:1212082\n",
      "\t-> Only read nSites: 1212082 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Will run optimization on nSites: 1212082\n",
      "------------\n",
      "startlik=-2421411.166155\n",
      "lik[2]=-149470.790177 diff=2.271940e+06 alpha:1.000000 sr2:5.452539e-01\n",
      "lik[5]=-116430.011370 diff=3.304078e+04 alpha:1.256628 sr2:1.396633e-03\n",
      "lik[8]=-116310.598512 diff=1.194129e+02 alpha:1.928593 sr2:1.000882e-07\n",
      "lik[11]=-116253.434002 diff=5.716451e+01 alpha:4.000000 sr2:7.709330e-10\n",
      "lik[14]=-116252.121485 diff=1.312516e+00 alpha:1.690889 sr2:2.242777e-10\n",
      "\t-> Breaking EM(sq2) at iter:16, sqrt(sq2):9.260033e-07\n",
      "likelihood: -116252.121485\n",
      "------------\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Only read nSites: 0 will therefore prepare next chromosome (or exit)\n",
      "\n",
      "\t-> NB NB output is no longer log probs of the frequency spectrum!\n",
      "\t-> Output is now simply the expected values! \n",
      "\t-> You can convert to the old format simply with log(norm(x))\n",
      "\t-> Version of fname:smallNA07000.saf.idx is:2\n",
      "\t-> Assuming .saf.gz file: smallNA07000.saf.gz\n",
      "\t-> Assuming .saf.pos.gz: smallNA07000.saf.pos.gz\n",
      "\t-> Version of fname:smallNA07056.saf.idx is:2\n",
      "\t-> Assuming .saf.gz file: smallNA07056.saf.gz\n",
      "\t-> Assuming .saf.pos.gz: smallNA07056.saf.pos.gz\n",
      "\t-> args: tole:0.000001 nthreads:4 maxiter:100 nsites:0 start:(null) chr:(null) start:-1 stop:-1 fstout:(null) oldout:0 seed:1558447026 bootstrap:0 whichFst:0 fold:0 ref:(null) anc:(null)\n",
      "\t-> Multi SFS is 'still' under development. Please report strange behaviour\n",
      "\t-> nSites: 1537126\n",
      "\t-> The choice of -nSites will require atleast: 58.636703 megabyte memory, that is at least: 0.02% of total memory\n",
      "\t-> dim(smallNA07000.saf.idx):3\n",
      "\t-> dim(smallNA07056.saf.idx):3\n",
      "\t-> Dimension of parameter space: 9\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:1\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[1] from pop0:\t73533\n",
      "\t-> Sites to keep[1] from pop1:\t73533\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "\t-> [readdata] lastread:73533 posi:14000242\n",
      "\t-> Comparing positions: 1 with 0 has:73533\n",
      "\t-> Only read nSites: 73533 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:10\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[10] from pop0:\t81312\n",
      "\t-> Sites to keep[10] from pop1:\t81312\n",
      "\t-> [readdata] lastread:81312 posi:14000242\n",
      "\t-> Comparing positions: 1 with 0 has:154845\n",
      "\t-> Only read nSites: 154845 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:11\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[11] from pop0:\t79290\n",
      "\t-> Sites to keep[11] from pop1:\t79290\n",
      "\t-> [readdata] lastread:79290 posi:14000242\n",
      "\t-> Comparing positions: 1 with 0 has:234135\n",
      "\t-> Only read nSites: 234135 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:12\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[12] from pop0:\t80039\n",
      "\t-> Sites to keep[12] from pop1:\t80039\n",
      "\t-> [readdata] lastread:80039 posi:14000242\n",
      "\t-> Comparing positions: 1 with 0 has:314174\n",
      "\t-> Only read nSites: 314174 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:16\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[16] from pop0:\t74922\n",
      "\t-> Sites to keep[16] from pop1:\t74922\n",
      "\t-> [readdata] lastread:74922 posi:14000242\n",
      "\t-> Comparing positions: 1 with 0 has:389096\n",
      "\t-> Only read nSites: 389096 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:17\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[17] from pop0:\t58587\n",
      "\t-> Sites to keep[17] from pop1:\t58587\n",
      "\t-> [readdata] lastread:58587 posi:14000242\n",
      "\t-> Comparing positions: 1 with 0 has:447683\n",
      "\t-> Only read nSites: 447683 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:18\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[18] from pop0:\t65566\n",
      "\t-> Sites to keep[18] from pop1:\t65566\n",
      "\t-> [readdata] lastread:65566 posi:14000242\n",
      "\t-> Comparing positions: 1 with 0 has:513249\n",
      "\t-> Only read nSites: 513249 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:19\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[19] from pop0:\t68729\n",
      "\t-> Sites to keep[19] from pop1:\t68729\n",
      "\t-> [readdata] lastread:68729 posi:14000242\n",
      "\t-> Comparing positions: 1 with 0 has:581978\n",
      "\t-> Only read nSites: 581978 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:2\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[2] from pop0:\t60752\n",
      "\t-> Sites to keep[2] from pop1:\t60752\n",
      "\t-> [readdata] lastread:60752 posi:14000242\n",
      "\t-> Comparing positions: 1 with 0 has:642730\n",
      "\t-> Only read nSites: 642730 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:20\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[20] from pop0:\t64309\n",
      "\t-> Sites to keep[20] from pop1:\t64309\n",
      "\t-> [readdata] lastread:64309 posi:14000242\n",
      "\t-> Comparing positions: 1 with 0 has:707039\n",
      "\t-> Only read nSites: 707039 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:3\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[3] from pop0:\t59382\n",
      "\t-> Sites to keep[3] from pop1:\t59382\n",
      "\t-> [readdata] lastread:59382 posi:14000242\n",
      "\t-> Comparing positions: 1 with 0 has:766421\n",
      "\t-> Only read nSites: 766421 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:4\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[4] from pop0:\t74753\n",
      "\t-> Sites to keep[4] from pop1:\t74753\n",
      "\t-> [readdata] lastread:74753 posi:14000242\n",
      "\t-> Comparing positions: 1 with 0 has:841174\n",
      "\t-> Only read nSites: 841174 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:5\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[5] from pop0:\t77685\n",
      "\t-> Sites to keep[5] from pop1:\t77685\n",
      "\t-> [readdata] lastread:77685 posi:14000242\n",
      "\t-> Comparing positions: 1 with 0 has:918859\n",
      "\t-> Only read nSites: 918859 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:6\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[6] from pop0:\t79752\n",
      "\t-> Sites to keep[6] from pop1:\t79752\n",
      "\t-> [readdata] lastread:79752 posi:14000242\n",
      "\t-> Comparing positions: 1 with 0 has:998611\n",
      "\t-> Only read nSites: 998611 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:7\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[7] from pop0:\t66492\n",
      "\t-> Sites to keep[7] from pop1:\t66492\n",
      "\t-> [readdata] lastread:66492 posi:14000242\n",
      "\t-> Comparing positions: 1 with 0 has:1065103\n",
      "\t-> Only read nSites: 1065103 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:8\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[8] from pop0:\t64997\n",
      "\t-> Sites to keep[8] from pop1:\t64997\n",
      "\t-> [readdata] lastread:64997 posi:14000242\n",
      "\t-> Comparing positions: 1 with 0 has:1130100\n",
      "\t-> Only read nSites: 1130100 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:9\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[9] from pop0:\t76239\n",
      "\t-> Sites to keep[9] from pop1:\t76239\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "\t-> [readdata] lastread:76239 posi:14000242\n",
      "\t-> Comparing positions: 1 with 0 has:1206339\n",
      "\t-> Only read nSites: 1206339 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Will run optimization on nSites: 1206339\n",
      "------------\n",
      "startlik=-2617243.196814\n",
      "lik[2]=-134868.647270 diff=2.482375e+06 alpha:1.000000 sr2:6.784365e-01\n",
      "lik[5]=-113878.724593 diff=2.098992e+04 alpha:1.246168 sr2:5.705902e-04\n",
      "lik[8]=-113746.331007 diff=1.323936e+02 alpha:2.084066 sr2:5.282918e-08\n",
      "lik[11]=-113735.963921 diff=1.036709e+01 alpha:3.808674 sr2:2.720190e-10\n",
      "lik[14]=-113735.886056 diff=7.786481e-02 alpha:1.675212 sr2:2.997240e-11\n",
      "\t-> Breaking EM(sr2) at iter:15, sqrt(sr2):4.561609e-07\n",
      "likelihood: -113735.886056\n",
      "------------\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Only read nSites: 0 will therefore prepare next chromosome (or exit)\n",
      "\n",
      "\t-> NB NB output is no longer log probs of the frequency spectrum!\n",
      "\t-> Output is now simply the expected values! \n",
      "\t-> You can convert to the old format simply with log(norm(x))\n",
      "\t-> Version of fname:smallNA07000.saf.idx is:2\n",
      "\t-> Assuming .saf.gz file: smallNA07000.saf.gz\n",
      "\t-> Assuming .saf.pos.gz: smallNA07000.saf.pos.gz\n",
      "\t-> Version of fname:smallNA11830.saf.idx is:2\n",
      "\t-> Assuming .saf.gz file: smallNA11830.saf.gz\n",
      "\t-> Assuming .saf.pos.gz: smallNA11830.saf.pos.gz\n",
      "\t-> args: tole:0.000001 nthreads:4 maxiter:100 nsites:0 start:(null) chr:(null) start:-1 stop:-1 fstout:(null) oldout:0 seed:1558447027 bootstrap:0 whichFst:0 fold:0 ref:(null) anc:(null)\n",
      "\t-> Multi SFS is 'still' under development. Please report strange behaviour\n",
      "\t-> nSites: 1584541\n",
      "\t-> The choice of -nSites will require atleast: 60.445442 megabyte memory, that is at least: 0.02% of total memory\n",
      "\t-> dim(smallNA07000.saf.idx):3\n",
      "\t-> dim(smallNA11830.saf.idx):3\n",
      "\t-> Dimension of parameter space: 9\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:1\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[1] from pop0:\t75227\n",
      "\t-> Sites to keep[1] from pop1:\t75227\n",
      "\t-> [readdata] lastread:75227 posi:14000242\n",
      "\t-> Comparing positions: 1 with 0 has:75227\n",
      "\t-> Only read nSites: 75227 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:10\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[10] from pop0:\t82183\n",
      "\t-> Sites to keep[10] from pop1:\t82183\n",
      "\t-> [readdata] lastread:82183 posi:14000242\n",
      "\t-> Comparing positions: 1 with 0 has:157410\n",
      "\t-> Only read nSites: 157410 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:11\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[11] from pop0:\t80015\n",
      "\t-> Sites to keep[11] from pop1:\t80015\n",
      "\t-> [readdata] lastread:80015 posi:14000242\n",
      "\t-> Comparing positions: 1 with 0 has:237425\n",
      "\t-> Only read nSites: 237425 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:12\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[12] from pop0:\t81931\n",
      "\t-> Sites to keep[12] from pop1:\t81931\n",
      "\t-> [readdata] lastread:81931 posi:14000242\n",
      "\t-> Comparing positions: 1 with 0 has:319356\n",
      "\t-> Only read nSites: 319356 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:16\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[16] from pop0:\t76272\n",
      "\t-> Sites to keep[16] from pop1:\t76272\n",
      "\t-> [readdata] lastread:76272 posi:14000242\n",
      "\t-> Comparing positions: 1 with 0 has:395628\n",
      "\t-> Only read nSites: 395628 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:17\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[17] from pop0:\t61394\n",
      "\t-> Sites to keep[17] from pop1:\t61394\n",
      "\t-> [readdata] lastread:61394 posi:14000242\n",
      "\t-> Comparing positions: 1 with 0 has:457022\n",
      "\t-> Only read nSites: 457022 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:18\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[18] from pop0:\t67987\n",
      "\t-> Sites to keep[18] from pop1:\t67987\n",
      "\t-> [readdata] lastread:67987 posi:14000242\n",
      "\t-> Comparing positions: 1 with 0 has:525009\n",
      "\t-> Only read nSites: 525009 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:19\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[19] from pop0:\t67981\n",
      "\t-> Sites to keep[19] from pop1:\t67981\n",
      "\t-> [readdata] lastread:67981 posi:14000242\n",
      "\t-> Comparing positions: 1 with 0 has:592990\n",
      "\t-> Only read nSites: 592990 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:2\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[2] from pop0:\t63855\n",
      "\t-> Sites to keep[2] from pop1:\t63855\n",
      "\t-> [readdata] lastread:63855 posi:14000242\n",
      "\t-> Comparing positions: 1 with 0 has:656845\n",
      "\t-> Only read nSites: 656845 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:20\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[20] from pop0:\t67110\n",
      "\t-> Sites to keep[20] from pop1:\t67110\n",
      "\t-> [readdata] lastread:67110 posi:14000242\n",
      "\t-> Comparing positions: 1 with 0 has:723955\n",
      "\t-> Only read nSites: 723955 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:3\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[3] from pop0:\t60894\n",
      "\t-> Sites to keep[3] from pop1:\t60894\n",
      "\t-> [readdata] lastread:60894 posi:14000242\n",
      "\t-> Comparing positions: 1 with 0 has:784849\n",
      "\t-> Only read nSites: 784849 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:4\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "\t-> Sites to keep[4] from pop0:\t76250\n",
      "\t-> Sites to keep[4] from pop1:\t76250\n",
      "\t-> [readdata] lastread:76250 posi:14000242\n",
      "\t-> Comparing positions: 1 with 0 has:861099\n",
      "\t-> Only read nSites: 861099 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:5\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[5] from pop0:\t78695\n",
      "\t-> Sites to keep[5] from pop1:\t78695\n",
      "\t-> [readdata] lastread:78695 posi:14000242\n",
      "\t-> Comparing positions: 1 with 0 has:939794\n",
      "\t-> Only read nSites: 939794 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:6\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[6] from pop0:\t80653\n",
      "\t-> Sites to keep[6] from pop1:\t80653\n",
      "\t-> [readdata] lastread:80653 posi:14000242\n",
      "\t-> Comparing positions: 1 with 0 has:1020447\n",
      "\t-> Only read nSites: 1020447 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:7\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[7] from pop0:\t70060\n",
      "\t-> Sites to keep[7] from pop1:\t70060\n",
      "\t-> [readdata] lastread:70060 posi:14000242\n",
      "\t-> Comparing positions: 1 with 0 has:1090507\n",
      "\t-> Only read nSites: 1090507 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:8\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[8] from pop0:\t67896\n",
      "\t-> Sites to keep[8] from pop1:\t67896\n",
      "\t-> [readdata] lastread:67896 posi:14000242\n",
      "\t-> Comparing positions: 1 with 0 has:1158403\n",
      "\t-> Only read nSites: 1158403 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:9\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[9] from pop0:\t79989\n",
      "\t-> Sites to keep[9] from pop1:\t79989\n",
      "\t-> [readdata] lastread:79989 posi:14000242\n",
      "\t-> Comparing positions: 1 with 0 has:1238392\n",
      "\t-> Only read nSites: 1238392 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Will run optimization on nSites: 1238392\n",
      "------------\n",
      "startlik=-2903772.017001\n",
      "lik[2]=-212538.320171 diff=2.691234e+06 alpha:1.000000 sr2:4.746959e-01\n",
      "lik[5]=-117607.934367 diff=9.493039e+04 alpha:1.387204 sr2:1.096166e-02\n",
      "lik[8]=-117525.030184 diff=8.290418e+01 alpha:1.976138 sr2:5.219256e-08\n",
      "lik[11]=-117511.752401 diff=1.327778e+01 alpha:2.650410 sr2:9.888159e-11\n",
      "lik[14]=-117498.838357 diff=1.291404e+01 alpha:4.000000 sr2:1.445781e-10\n",
      "lik[17]=-117498.583392 diff=2.549644e-01 alpha:1.678769 sr2:1.932188e-11\n",
      "\t-> Breaking EM(sr2) at iter:18, sqrt(sr2):9.287171e-07\n",
      "likelihood: -117498.583392\n",
      "------------\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Only read nSites: 0 will therefore prepare next chromosome (or exit)\n",
      "\n",
      "\t-> NB NB output is no longer log probs of the frequency spectrum!\n",
      "\t-> Output is now simply the expected values! \n",
      "\t-> You can convert to the old format simply with log(norm(x))\n",
      "\t-> Version of fname:smallNA11840.saf.idx is:2\n",
      "\t-> Assuming .saf.gz file: smallNA11840.saf.gz\n",
      "\t-> Assuming .saf.pos.gz: smallNA11840.saf.pos.gz\n",
      "\t-> Version of fname:smallNA07357.saf.idx is:2\n",
      "\t-> Assuming .saf.gz file: smallNA07357.saf.gz\n",
      "\t-> Assuming .saf.pos.gz: smallNA07357.saf.pos.gz\n",
      "\t-> args: tole:0.000001 nthreads:4 maxiter:100 nsites:0 start:(null) chr:(null) start:-1 stop:-1 fstout:(null) oldout:0 seed:1558447029 bootstrap:0 whichFst:0 fold:0 ref:(null) anc:(null)\n",
      "\t-> Multi SFS is 'still' under development. Please report strange behaviour\n",
      "\t-> nSites: 1451016\n",
      "\t-> The choice of -nSites will require atleast: 55.351868 megabyte memory, that is at least: 0.01% of total memory\n",
      "\t-> dim(smallNA11840.saf.idx):3\n",
      "\t-> dim(smallNA07357.saf.idx):3\n",
      "\t-> Dimension of parameter space: 9\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:1\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[1] from pop0:\t79381\n",
      "\t-> Sites to keep[1] from pop1:\t79381\n",
      "\t-> [readdata] lastread:79381 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:79381\n",
      "\t-> Only read nSites: 79381 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:10\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[10] from pop0:\t80014\n",
      "\t-> Sites to keep[10] from pop1:\t80014\n",
      "\t-> [readdata] lastread:80014 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:159395\n",
      "\t-> Only read nSites: 159395 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:11\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[11] from pop0:\t80254\n",
      "\t-> Sites to keep[11] from pop1:\t80254\n",
      "\t-> [readdata] lastread:80254 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:239649\n",
      "\t-> Only read nSites: 239649 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:12\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[12] from pop0:\t84394\n",
      "\t-> Sites to keep[12] from pop1:\t84394\n",
      "\t-> [readdata] lastread:84394 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:324043\n",
      "\t-> Only read nSites: 324043 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:16\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[16] from pop0:\t77333\n",
      "\t-> Sites to keep[16] from pop1:\t77333\n",
      "\t-> [readdata] lastread:77333 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:401376\n",
      "\t-> Only read nSites: 401376 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:17\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[17] from pop0:\t68188\n",
      "\t-> Sites to keep[17] from pop1:\t68188\n",
      "\t-> [readdata] lastread:68188 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:469564\n",
      "\t-> Only read nSites: 469564 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:18\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[18] from pop0:\t71546\n",
      "\t-> Sites to keep[18] from pop1:\t71546\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "\t-> [readdata] lastread:71546 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:541110\n",
      "\t-> Only read nSites: 541110 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:19\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[19] from pop0:\t58855\n",
      "\t-> Sites to keep[19] from pop1:\t58855\n",
      "\t-> [readdata] lastread:58855 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:599965\n",
      "\t-> Only read nSites: 599965 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:2\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[2] from pop0:\t74834\n",
      "\t-> Sites to keep[2] from pop1:\t74834\n",
      "\t-> [readdata] lastread:74834 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:674799\n",
      "\t-> Only read nSites: 674799 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:20\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[20] from pop0:\t75501\n",
      "\t-> Sites to keep[20] from pop1:\t75501\n",
      "\t-> [readdata] lastread:75501 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:750300\n",
      "\t-> Only read nSites: 750300 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:3\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[3] from pop0:\t65990\n",
      "\t-> Sites to keep[3] from pop1:\t65990\n",
      "\t-> [readdata] lastread:65990 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:816290\n",
      "\t-> Only read nSites: 816290 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:4\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[4] from pop0:\t77750\n",
      "\t-> Sites to keep[4] from pop1:\t77750\n",
      "\t-> [readdata] lastread:77750 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:894040\n",
      "\t-> Only read nSites: 894040 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:5\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[5] from pop0:\t77101\n",
      "\t-> Sites to keep[5] from pop1:\t77101\n",
      "\t-> [readdata] lastread:77101 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:971141\n",
      "\t-> Only read nSites: 971141 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:6\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[6] from pop0:\t79170\n",
      "\t-> Sites to keep[6] from pop1:\t79170\n",
      "\t-> [readdata] lastread:79170 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:1050311\n",
      "\t-> Only read nSites: 1050311 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:7\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[7] from pop0:\t77761\n",
      "\t-> Sites to keep[7] from pop1:\t77761\n",
      "\t-> [readdata] lastread:77761 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:1128072\n",
      "\t-> Only read nSites: 1128072 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:8\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[8] from pop0:\t75097\n",
      "\t-> Sites to keep[8] from pop1:\t75097\n",
      "\t-> [readdata] lastread:75097 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:1203169\n",
      "\t-> Only read nSites: 1203169 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:9\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[9] from pop0:\t81903\n",
      "\t-> Sites to keep[9] from pop1:\t81903\n",
      "\t-> [readdata] lastread:81903 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:1285072\n",
      "\t-> Only read nSites: 1285072 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Will run optimization on nSites: 1285072\n",
      "------------\n",
      "startlik=-1794408.718876\n",
      "lik[2]=-147811.306576 diff=1.646597e+06 alpha:1.000000 sr2:4.686174e-01\n",
      "lik[5]=-114147.891244 diff=3.366342e+04 alpha:1.313253 sr2:1.093607e-03\n",
      "lik[8]=-114067.444674 diff=8.044657e+01 alpha:1.894542 sr2:3.015563e-08\n",
      "lik[11]=-113979.268163 diff=8.817651e+01 alpha:3.958229 sr2:6.341605e-10\n",
      "lik[14]=-113975.929781 diff=3.338382e+00 alpha:2.145503 sr2:4.833900e-10\n",
      "\t-> Breaking EM(sq2) at iter:16, sqrt(sq2):8.995972e-07\n",
      "likelihood: -113975.929781\n",
      "------------\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Only read nSites: 0 will therefore prepare next chromosome (or exit)\n",
      "\n",
      "\t-> NB NB output is no longer log probs of the frequency spectrum!\n",
      "\t-> Output is now simply the expected values! \n",
      "\t-> You can convert to the old format simply with log(norm(x))\n",
      "\t-> Version of fname:smallNA11840.saf.idx is:2\n",
      "\t-> Assuming .saf.gz file: smallNA11840.saf.gz\n",
      "\t-> Assuming .saf.pos.gz: smallNA11840.saf.pos.gz\n",
      "\t-> Version of fname:smallNA11832.saf.idx is:2\n",
      "\t-> Assuming .saf.gz file: smallNA11832.saf.gz\n",
      "\t-> Assuming .saf.pos.gz: smallNA11832.saf.pos.gz\n",
      "\t-> args: tole:0.000001 nthreads:4 maxiter:100 nsites:0 start:(null) chr:(null) start:-1 stop:-1 fstout:(null) oldout:0 seed:1558447031 bootstrap:0 whichFst:0 fold:0 ref:(null) anc:(null)\n",
      "\t-> Multi SFS is 'still' under development. Please report strange behaviour\n",
      "\t-> nSites: 1451016\n",
      "\t-> The choice of -nSites will require atleast: 55.351868 megabyte memory, that is at least: 0.01% of total memory\n",
      "\t-> dim(smallNA11840.saf.idx):3\n",
      "\t-> dim(smallNA11832.saf.idx):3\n",
      "\t-> Dimension of parameter space: 9\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:1\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[1] from pop0:\t65834\n",
      "\t-> Sites to keep[1] from pop1:\t65834\n",
      "\t-> [readdata] lastread:65834 posi:14000039\n",
      "\t-> Comparing positions: 1 with 0 has:65834\n",
      "\t-> Only read nSites: 65834 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:10\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "\t-> Sites to keep[10] from pop0:\t67839\n",
      "\t-> Sites to keep[10] from pop1:\t67839\n",
      "\t-> [readdata] lastread:67839 posi:14000039\n",
      "\t-> Comparing positions: 1 with 0 has:133673\n",
      "\t-> Only read nSites: 133673 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:11\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[11] from pop0:\t67467\n",
      "\t-> Sites to keep[11] from pop1:\t67467\n",
      "\t-> [readdata] lastread:67467 posi:14000039\n",
      "\t-> Comparing positions: 1 with 0 has:201140\n",
      "\t-> Only read nSites: 201140 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:12\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[12] from pop0:\t70181\n",
      "\t-> Sites to keep[12] from pop1:\t70181\n",
      "\t-> [readdata] lastread:70181 posi:14000039\n",
      "\t-> Comparing positions: 1 with 0 has:271321\n",
      "\t-> Only read nSites: 271321 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:16\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[16] from pop0:\t65392\n",
      "\t-> Sites to keep[16] from pop1:\t65392\n",
      "\t-> [readdata] lastread:65392 posi:14000039\n",
      "\t-> Comparing positions: 1 with 0 has:336713\n",
      "\t-> Only read nSites: 336713 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:17\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[17] from pop0:\t56025\n",
      "\t-> Sites to keep[17] from pop1:\t56025\n",
      "\t-> [readdata] lastread:56025 posi:14000039\n",
      "\t-> Comparing positions: 1 with 0 has:392738\n",
      "\t-> Only read nSites: 392738 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:18\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[18] from pop0:\t62408\n",
      "\t-> Sites to keep[18] from pop1:\t62408\n",
      "\t-> [readdata] lastread:62408 posi:14000039\n",
      "\t-> Comparing positions: 1 with 0 has:455146\n",
      "\t-> Only read nSites: 455146 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:19\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[19] from pop0:\t48380\n",
      "\t-> Sites to keep[19] from pop1:\t48380\n",
      "\t-> [readdata] lastread:48380 posi:14000039\n",
      "\t-> Comparing positions: 1 with 0 has:503526\n",
      "\t-> Only read nSites: 503526 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:2\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[2] from pop0:\t59771\n",
      "\t-> Sites to keep[2] from pop1:\t59771\n",
      "\t-> [readdata] lastread:59771 posi:14000039\n",
      "\t-> Comparing positions: 1 with 0 has:563297\n",
      "\t-> Only read nSites: 563297 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:20\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[20] from pop0:\t61741\n",
      "\t-> Sites to keep[20] from pop1:\t61741\n",
      "\t-> [readdata] lastread:61741 posi:14000039\n",
      "\t-> Comparing positions: 1 with 0 has:625038\n",
      "\t-> Only read nSites: 625038 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:3\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[3] from pop0:\t55909\n",
      "\t-> Sites to keep[3] from pop1:\t55909\n",
      "\t-> [readdata] lastread:55909 posi:14000039\n",
      "\t-> Comparing positions: 1 with 0 has:680947\n",
      "\t-> Only read nSites: 680947 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:4\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[4] from pop0:\t64971\n",
      "\t-> Sites to keep[4] from pop1:\t64971\n",
      "\t-> [readdata] lastread:64971 posi:14000039\n",
      "\t-> Comparing positions: 1 with 0 has:745918\n",
      "\t-> Only read nSites: 745918 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:5\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[5] from pop0:\t65152\n",
      "\t-> Sites to keep[5] from pop1:\t65152\n",
      "\t-> [readdata] lastread:65152 posi:14000039\n",
      "\t-> Comparing positions: 1 with 0 has:811070\n",
      "\t-> Only read nSites: 811070 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:6\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[6] from pop0:\t66888\n",
      "\t-> Sites to keep[6] from pop1:\t66888\n",
      "\t-> [readdata] lastread:66888 posi:14000039\n",
      "\t-> Comparing positions: 1 with 0 has:877958\n",
      "\t-> Only read nSites: 877958 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:7\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[7] from pop0:\t62147\n",
      "\t-> Sites to keep[7] from pop1:\t62147\n",
      "\t-> [readdata] lastread:62147 posi:14000039\n",
      "\t-> Comparing positions: 1 with 0 has:940105\n",
      "\t-> Only read nSites: 940105 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:8\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[8] from pop0:\t61136\n",
      "\t-> Sites to keep[8] from pop1:\t61136\n",
      "\t-> [readdata] lastread:61136 posi:14000039\n",
      "\t-> Comparing positions: 1 with 0 has:1001241\n",
      "\t-> Only read nSites: 1001241 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:9\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[9] from pop0:\t69267\n",
      "\t-> Sites to keep[9] from pop1:\t69267\n",
      "\t-> [readdata] lastread:69267 posi:14000039\n",
      "\t-> Comparing positions: 1 with 0 has:1070508\n",
      "\t-> Only read nSites: 1070508 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Will run optimization on nSites: 1070508\n",
      "------------\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "startlik=-1544698.378687\n",
      "lik[2]=-180960.926092 diff=1.363737e+06 alpha:1.000000 sr2:3.222457e-01\n",
      "lik[5]=-92787.225633 diff=8.817370e+04 alpha:1.513940 sr2:1.034810e-02\n",
      "lik[8]=-92668.930184 diff=1.182954e+02 alpha:1.948587 sr2:3.248938e-08\n",
      "lik[11]=-92612.573802 diff=5.635638e+01 alpha:4.000000 sr2:1.715035e-09\n",
      "lik[14]=-92609.563578 diff=3.010224e+00 alpha:3.066773 sr2:2.698807e-10\n",
      "lik[17]=-92609.240376 diff=3.232026e-01 alpha:2.809565 sr2:3.327699e-11\n",
      "lik[20]=-92609.188796 diff=5.157970e-02 alpha:3.415162 sr2:4.101864e-12\n",
      "\t-> Breaking EM(sr2) at iter:21, sqrt(sr2):7.646085e-07\n",
      "likelihood: -92609.188796\n",
      "------------\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Only read nSites: 0 will therefore prepare next chromosome (or exit)\n",
      "\n",
      "\t-> NB NB output is no longer log probs of the frequency spectrum!\n",
      "\t-> Output is now simply the expected values! \n",
      "\t-> You can convert to the old format simply with log(norm(x))\n",
      "\t-> Version of fname:smallNA11840.saf.idx is:2\n",
      "\t-> Assuming .saf.gz file: smallNA11840.saf.gz\n",
      "\t-> Assuming .saf.pos.gz: smallNA11840.saf.pos.gz\n",
      "\t-> Version of fname:smallNA06994.saf.idx is:2\n",
      "\t-> Assuming .saf.gz file: smallNA06994.saf.gz\n",
      "\t-> Assuming .saf.pos.gz: smallNA06994.saf.pos.gz\n",
      "\t-> args: tole:0.000001 nthreads:4 maxiter:100 nsites:0 start:(null) chr:(null) start:-1 stop:-1 fstout:(null) oldout:0 seed:1558447034 bootstrap:0 whichFst:0 fold:0 ref:(null) anc:(null)\n",
      "\t-> Multi SFS is 'still' under development. Please report strange behaviour\n",
      "\t-> nSites: 1451016\n",
      "\t-> The choice of -nSites will require atleast: 55.351868 megabyte memory, that is at least: 0.01% of total memory\n",
      "\t-> dim(smallNA11840.saf.idx):3\n",
      "\t-> dim(smallNA06994.saf.idx):3\n",
      "\t-> Dimension of parameter space: 9\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:1\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[1] from pop0:\t75596\n",
      "\t-> Sites to keep[1] from pop1:\t75596\n",
      "\t-> [readdata] lastread:75596 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:75596\n",
      "\t-> Only read nSites: 75596 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:10\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[10] from pop0:\t74626\n",
      "\t-> Sites to keep[10] from pop1:\t74626\n",
      "\t-> [readdata] lastread:74626 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:150222\n",
      "\t-> Only read nSites: 150222 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:11\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[11] from pop0:\t77200\n",
      "\t-> Sites to keep[11] from pop1:\t77200\n",
      "\t-> [readdata] lastread:77200 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:227422\n",
      "\t-> Only read nSites: 227422 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:12\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[12] from pop0:\t82626\n",
      "\t-> Sites to keep[12] from pop1:\t82626\n",
      "\t-> [readdata] lastread:82626 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:310048\n",
      "\t-> Only read nSites: 310048 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:16\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[16] from pop0:\t72139\n",
      "\t-> Sites to keep[16] from pop1:\t72139\n",
      "\t-> [readdata] lastread:72139 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:382187\n",
      "\t-> Only read nSites: 382187 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:17\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[17] from pop0:\t65110\n",
      "\t-> Sites to keep[17] from pop1:\t65110\n",
      "\t-> [readdata] lastread:65110 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:447297\n",
      "\t-> Only read nSites: 447297 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:18\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[18] from pop0:\t69166\n",
      "\t-> Sites to keep[18] from pop1:\t69166\n",
      "\t-> [readdata] lastread:69166 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:516463\n",
      "\t-> Only read nSites: 516463 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:19\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[19] from pop0:\t45083\n",
      "\t-> Sites to keep[19] from pop1:\t45083\n",
      "\t-> [readdata] lastread:45083 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:561546\n",
      "\t-> Only read nSites: 561546 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:2\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[2] from pop0:\t74993\n",
      "\t-> Sites to keep[2] from pop1:\t74993\n",
      "\t-> [readdata] lastread:74993 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:636539\n",
      "\t-> Only read nSites: 636539 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:20\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[20] from pop0:\t72748\n",
      "\t-> Sites to keep[20] from pop1:\t72748\n",
      "\t-> [readdata] lastread:72748 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:709287\n",
      "\t-> Only read nSites: 709287 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:3\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[3] from pop0:\t58761\n",
      "\t-> Sites to keep[3] from pop1:\t58761\n",
      "\t-> [readdata] lastread:58761 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:768048\n",
      "\t-> Only read nSites: 768048 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:4\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[4] from pop0:\t76694\n",
      "\t-> Sites to keep[4] from pop1:\t76694\n",
      "\t-> [readdata] lastread:76694 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:844742\n",
      "\t-> Only read nSites: 844742 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:5\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[5] from pop0:\t73174\n",
      "\t-> Sites to keep[5] from pop1:\t73174\n",
      "\t-> [readdata] lastread:73174 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:917916\n",
      "\t-> Only read nSites: 917916 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:6\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[6] from pop0:\t74017\n",
      "\t-> Sites to keep[6] from pop1:\t74017\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "\t-> [readdata] lastread:74017 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:991933\n",
      "\t-> Only read nSites: 991933 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:7\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[7] from pop0:\t77444\n",
      "\t-> Sites to keep[7] from pop1:\t77444\n",
      "\t-> [readdata] lastread:77444 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:1069377\n",
      "\t-> Only read nSites: 1069377 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:8\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[8] from pop0:\t75514\n",
      "\t-> Sites to keep[8] from pop1:\t75514\n",
      "\t-> [readdata] lastread:75514 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:1144891\n",
      "\t-> Only read nSites: 1144891 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:9\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[9] from pop0:\t80999\n",
      "\t-> Sites to keep[9] from pop1:\t80999\n",
      "\t-> [readdata] lastread:80999 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:1225890\n",
      "\t-> Only read nSites: 1225890 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Will run optimization on nSites: 1225890\n",
      "------------\n",
      "startlik=-2609878.940293\n",
      "lik[2]=-263908.550811 diff=2.345970e+06 alpha:1.000000 sr2:2.866151e-01\n",
      "lik[5]=-111817.357288 diff=1.520912e+05 alpha:1.338735 sr2:2.049943e-02\n",
      "lik[8]=-111631.707535 diff=1.856498e+02 alpha:1.928003 sr2:6.535747e-08\n",
      "lik[11]=-111602.284213 diff=2.942332e+01 alpha:3.685473 sr2:3.010232e-10\n",
      "lik[14]=-111590.556964 diff=1.172725e+01 alpha:4.000000 sr2:1.622050e-10\n",
      "lik[17]=-111590.305451 diff=2.515129e-01 alpha:2.035319 sr2:2.876033e-11\n",
      "\t-> Breaking EM(sr2) at iter:18, sqrt(sr2):3.687476e-07\n",
      "likelihood: -111590.305451\n",
      "------------\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Only read nSites: 0 will therefore prepare next chromosome (or exit)\n",
      "\n",
      "\t-> NB NB output is no longer log probs of the frequency spectrum!\n",
      "\t-> Output is now simply the expected values! \n",
      "\t-> You can convert to the old format simply with log(norm(x))\n",
      "\t-> Version of fname:smallNA11840.saf.idx is:2\n",
      "\t-> Assuming .saf.gz file: smallNA11840.saf.gz\n",
      "\t-> Assuming .saf.pos.gz: smallNA11840.saf.pos.gz\n",
      "\t-> Version of fname:smallNA06985.saf.idx is:2\n",
      "\t-> Assuming .saf.gz file: smallNA06985.saf.gz\n",
      "\t-> Assuming .saf.pos.gz: smallNA06985.saf.pos.gz\n",
      "\t-> args: tole:0.000001 nthreads:4 maxiter:100 nsites:0 start:(null) chr:(null) start:-1 stop:-1 fstout:(null) oldout:0 seed:1558447036 bootstrap:0 whichFst:0 fold:0 ref:(null) anc:(null)\n",
      "\t-> Multi SFS is 'still' under development. Please report strange behaviour\n",
      "\t-> nSites: 1451016\n",
      "\t-> The choice of -nSites will require atleast: 55.351868 megabyte memory, that is at least: 0.01% of total memory\n",
      "\t-> dim(smallNA11840.saf.idx):3\n",
      "\t-> dim(smallNA06985.saf.idx):3\n",
      "\t-> Dimension of parameter space: 9\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:1\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[1] from pop0:\t77542\n",
      "\t-> Sites to keep[1] from pop1:\t77542\n",
      "\t-> [readdata] lastread:77542 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:77542\n",
      "\t-> Only read nSites: 77542 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:10\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[10] from pop0:\t79507\n",
      "\t-> Sites to keep[10] from pop1:\t79507\n",
      "\t-> [readdata] lastread:79507 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:157049\n",
      "\t-> Only read nSites: 157049 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:11\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[11] from pop0:\t80213\n",
      "\t-> Sites to keep[11] from pop1:\t80213\n",
      "\t-> [readdata] lastread:80213 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:237262\n",
      "\t-> Only read nSites: 237262 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:12\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[12] from pop0:\t78852\n",
      "\t-> Sites to keep[12] from pop1:\t78852\n",
      "\t-> [readdata] lastread:78852 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:316114\n",
      "\t-> Only read nSites: 316114 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:16\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[16] from pop0:\t76163\n",
      "\t-> Sites to keep[16] from pop1:\t76163\n",
      "\t-> [readdata] lastread:76163 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:392277\n",
      "\t-> Only read nSites: 392277 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:17\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[17] from pop0:\t66774\n",
      "\t-> Sites to keep[17] from pop1:\t66774\n",
      "\t-> [readdata] lastread:66774 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:459051\n",
      "\t-> Only read nSites: 459051 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:18\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[18] from pop0:\t75510\n",
      "\t-> Sites to keep[18] from pop1:\t75510\n",
      "\t-> [readdata] lastread:75510 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:534561\n",
      "\t-> Only read nSites: 534561 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:19\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[19] from pop0:\t63812\n",
      "\t-> Sites to keep[19] from pop1:\t63812\n",
      "\t-> [readdata] lastread:63812 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:598373\n",
      "\t-> Only read nSites: 598373 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:2\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[2] from pop0:\t66252\n",
      "\t-> Sites to keep[2] from pop1:\t66252\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "\t-> [readdata] lastread:66252 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:664625\n",
      "\t-> Only read nSites: 664625 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:20\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[20] from pop0:\t74129\n",
      "\t-> Sites to keep[20] from pop1:\t74129\n",
      "\t-> [readdata] lastread:74129 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:738754\n",
      "\t-> Only read nSites: 738754 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:3\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[3] from pop0:\t70846\n",
      "\t-> Sites to keep[3] from pop1:\t70846\n",
      "\t-> [readdata] lastread:70846 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:809600\n",
      "\t-> Only read nSites: 809600 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:4\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[4] from pop0:\t74805\n",
      "\t-> Sites to keep[4] from pop1:\t74805\n",
      "\t-> [readdata] lastread:74805 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:884405\n",
      "\t-> Only read nSites: 884405 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:5\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[5] from pop0:\t79297\n",
      "\t-> Sites to keep[5] from pop1:\t79297\n",
      "\t-> [readdata] lastread:79297 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:963702\n",
      "\t-> Only read nSites: 963702 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:6\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[6] from pop0:\t79796\n",
      "\t-> Sites to keep[6] from pop1:\t79796\n",
      "\t-> [readdata] lastread:79796 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:1043498\n",
      "\t-> Only read nSites: 1043498 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:7\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[7] from pop0:\t68464\n",
      "\t-> Sites to keep[7] from pop1:\t68464\n",
      "\t-> [readdata] lastread:68464 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:1111962\n",
      "\t-> Only read nSites: 1111962 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:8\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[8] from pop0:\t64092\n",
      "\t-> Sites to keep[8] from pop1:\t64092\n",
      "\t-> [readdata] lastread:64092 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:1176054\n",
      "\t-> Only read nSites: 1176054 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:9\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[9] from pop0:\t76536\n",
      "\t-> Sites to keep[9] from pop1:\t76536\n",
      "\t-> [readdata] lastread:76536 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:1252590\n",
      "\t-> Only read nSites: 1252590 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Will run optimization on nSites: 1252590\n",
      "------------\n",
      "startlik=-3085719.939659\n",
      "lik[2]=-587610.418756 diff=2.498110e+06 alpha:1.000000 sr2:2.013279e-01\n",
      "lik[5]=-107977.200304 diff=4.796332e+05 alpha:1.612123 sr2:1.148542e-01\n",
      "lik[8]=-107741.704635 diff=2.354957e+02 alpha:2.310056 sr2:2.198900e-08\n",
      "lik[11]=-107737.188747 diff=4.515888e+00 alpha:1.845853 sr2:4.659782e-10\n",
      "lik[14]=-107736.942846 diff=2.459017e-01 alpha:4.000000 sr2:1.702622e-11\n",
      "\t-> Breaking EM(sr2) at iter:15, sqrt(sr2):3.839477e-07\n",
      "likelihood: -107736.942846\n",
      "------------\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Only read nSites: 0 will therefore prepare next chromosome (or exit)\n",
      "\n",
      "\t-> NB NB output is no longer log probs of the frequency spectrum!\n",
      "\t-> Output is now simply the expected values! \n",
      "\t-> You can convert to the old format simply with log(norm(x))\n",
      "\t-> Version of fname:smallNA11840.saf.idx is:2\n",
      "\t-> Assuming .saf.gz file: smallNA11840.saf.gz\n",
      "\t-> Assuming .saf.pos.gz: smallNA11840.saf.pos.gz\n",
      "\t-> Version of fname:smallNA11831.saf.idx is:2\n",
      "\t-> Assuming .saf.gz file: smallNA11831.saf.gz\n",
      "\t-> Assuming .saf.pos.gz: smallNA11831.saf.pos.gz\n",
      "\t-> args: tole:0.000001 nthreads:4 maxiter:100 nsites:0 start:(null) chr:(null) start:-1 stop:-1 fstout:(null) oldout:0 seed:1558447038 bootstrap:0 whichFst:0 fold:0 ref:(null) anc:(null)\n",
      "\t-> Multi SFS is 'still' under development. Please report strange behaviour\n",
      "\t-> nSites: 1556469\n",
      "\t-> The choice of -nSites will require atleast: 59.374580 megabyte memory, that is at least: 0.02% of total memory\n",
      "\t-> dim(smallNA11840.saf.idx):3\n",
      "\t-> dim(smallNA11831.saf.idx):3\n",
      "\t-> Dimension of parameter space: 9\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:1\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[1] from pop0:\t82942\n",
      "\t-> Sites to keep[1] from pop1:\t82942\n",
      "\t-> [readdata] lastread:82942 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:82942\n",
      "\t-> Only read nSites: 82942 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:10\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[10] from pop0:\t82641\n",
      "\t-> Sites to keep[10] from pop1:\t82641\n",
      "\t-> [readdata] lastread:82641 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:165583\n",
      "\t-> Only read nSites: 165583 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:11\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[11] from pop0:\t84871\n",
      "\t-> Sites to keep[11] from pop1:\t84871\n",
      "\t-> [readdata] lastread:84871 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:250454\n",
      "\t-> Only read nSites: 250454 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:12\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[12] from pop0:\t87843\n",
      "\t-> Sites to keep[12] from pop1:\t87843\n",
      "\t-> [readdata] lastread:87843 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:338297\n",
      "\t-> Only read nSites: 338297 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:16\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[16] from pop0:\t83467\n",
      "\t-> Sites to keep[16] from pop1:\t83467\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "\t-> [readdata] lastread:83467 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:421764\n",
      "\t-> Only read nSites: 421764 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:17\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[17] from pop0:\t75107\n",
      "\t-> Sites to keep[17] from pop1:\t75107\n",
      "\t-> [readdata] lastread:75107 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:496871\n",
      "\t-> Only read nSites: 496871 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:18\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[18] from pop0:\t79791\n",
      "\t-> Sites to keep[18] from pop1:\t79791\n",
      "\t-> [readdata] lastread:79791 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:576662\n",
      "\t-> Only read nSites: 576662 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:19\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[19] from pop0:\t63220\n",
      "\t-> Sites to keep[19] from pop1:\t63220\n",
      "\t-> [readdata] lastread:63220 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:639882\n",
      "\t-> Only read nSites: 639882 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:2\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[2] from pop0:\t80683\n",
      "\t-> Sites to keep[2] from pop1:\t80683\n",
      "\t-> [readdata] lastread:80683 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:720565\n",
      "\t-> Only read nSites: 720565 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:20\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[20] from pop0:\t84130\n",
      "\t-> Sites to keep[20] from pop1:\t84130\n",
      "\t-> [readdata] lastread:84130 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:804695\n",
      "\t-> Only read nSites: 804695 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:3\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[3] from pop0:\t74121\n",
      "\t-> Sites to keep[3] from pop1:\t74121\n",
      "\t-> [readdata] lastread:74121 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:878816\n",
      "\t-> Only read nSites: 878816 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:4\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[4] from pop0:\t80625\n",
      "\t-> Sites to keep[4] from pop1:\t80625\n",
      "\t-> [readdata] lastread:80625 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:959441\n",
      "\t-> Only read nSites: 959441 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:5\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[5] from pop0:\t82807\n",
      "\t-> Sites to keep[5] from pop1:\t82807\n",
      "\t-> [readdata] lastread:82807 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:1042248\n",
      "\t-> Only read nSites: 1042248 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:6\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[6] from pop0:\t83840\n",
      "\t-> Sites to keep[6] from pop1:\t83840\n",
      "\t-> [readdata] lastread:83840 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:1126088\n",
      "\t-> Only read nSites: 1126088 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:7\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[7] from pop0:\t83384\n",
      "\t-> Sites to keep[7] from pop1:\t83384\n",
      "\t-> [readdata] lastread:83384 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:1209472\n",
      "\t-> Only read nSites: 1209472 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:8\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[8] from pop0:\t82617\n",
      "\t-> Sites to keep[8] from pop1:\t82617\n",
      "\t-> [readdata] lastread:82617 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:1292089\n",
      "\t-> Only read nSites: 1292089 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:9\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[9] from pop0:\t85706\n",
      "\t-> Sites to keep[9] from pop1:\t85706\n",
      "\t-> [readdata] lastread:85706 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:1377795\n",
      "\t-> Only read nSites: 1377795 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Will run optimization on nSites: 1377795\n",
      "------------\n",
      "startlik=-2271202.460058\n",
      "lik[2]=-181954.077744 diff=2.089248e+06 alpha:1.000000 sr2:4.396956e-01\n",
      "lik[5]=-124876.199850 diff=5.707788e+04 alpha:1.306934 sr2:2.653606e-03\n",
      "lik[8]=-124819.556120 diff=5.664373e+01 alpha:1.811621 sr2:3.878599e-08\n",
      "lik[11]=-124806.061301 diff=1.349482e+01 alpha:2.870644 sr2:5.158721e-11\n",
      "lik[14]=-124787.187352 diff=1.887395e+01 alpha:4.000000 sr2:7.355566e-11\n",
      "lik[17]=-124787.072978 diff=1.143742e-01 alpha:2.389461 sr2:2.050937e-11\n",
      "\t-> Breaking EM(sr2) at iter:18, sqrt(sr2):3.890662e-07\n",
      "likelihood: -124787.072978\n",
      "------------\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Only read nSites: 0 will therefore prepare next chromosome (or exit)\n",
      "\n",
      "\t-> NB NB output is no longer log probs of the frequency spectrum!\n",
      "\t-> Output is now simply the expected values! \n",
      "\t-> You can convert to the old format simply with log(norm(x))\n",
      "\t-> Version of fname:smallNA11840.saf.idx is:2\n",
      "\t-> Assuming .saf.gz file: smallNA11840.saf.gz\n",
      "\t-> Assuming .saf.pos.gz: smallNA11840.saf.pos.gz\n",
      "\t-> Version of fname:smallNA11829.saf.idx is:2\n",
      "\t-> Assuming .saf.gz file: smallNA11829.saf.gz\n",
      "\t-> Assuming .saf.pos.gz: smallNA11829.saf.pos.gz\n",
      "\t-> args: tole:0.000001 nthreads:4 maxiter:100 nsites:0 start:(null) chr:(null) start:-1 stop:-1 fstout:(null) oldout:0 seed:1558447040 bootstrap:0 whichFst:0 fold:0 ref:(null) anc:(null)\n",
      "\t-> Multi SFS is 'still' under development. Please report strange behaviour\n",
      "\t-> nSites: 1542786\n",
      "\t-> The choice of -nSites will require atleast: 58.852615 megabyte memory, that is at least: 0.02% of total memory\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "\t-> dim(smallNA11840.saf.idx):3\n",
      "\t-> dim(smallNA11829.saf.idx):3\n",
      "\t-> Dimension of parameter space: 9\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:1\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[1] from pop0:\t82247\n",
      "\t-> Sites to keep[1] from pop1:\t82247\n",
      "\t-> [readdata] lastread:82247 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:82247\n",
      "\t-> Only read nSites: 82247 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:10\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[10] from pop0:\t81549\n",
      "\t-> Sites to keep[10] from pop1:\t81549\n",
      "\t-> [readdata] lastread:81549 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:163796\n",
      "\t-> Only read nSites: 163796 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:11\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[11] from pop0:\t85053\n",
      "\t-> Sites to keep[11] from pop1:\t85053\n",
      "\t-> [readdata] lastread:85053 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:248849\n",
      "\t-> Only read nSites: 248849 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:12\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[12] from pop0:\t86370\n",
      "\t-> Sites to keep[12] from pop1:\t86370\n",
      "\t-> [readdata] lastread:86370 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:335219\n",
      "\t-> Only read nSites: 335219 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:16\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[16] from pop0:\t81250\n",
      "\t-> Sites to keep[16] from pop1:\t81250\n",
      "\t-> [readdata] lastread:81250 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:416469\n",
      "\t-> Only read nSites: 416469 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:17\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[17] from pop0:\t75745\n",
      "\t-> Sites to keep[17] from pop1:\t75745\n",
      "\t-> [readdata] lastread:75745 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:492214\n",
      "\t-> Only read nSites: 492214 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:18\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[18] from pop0:\t79942\n",
      "\t-> Sites to keep[18] from pop1:\t79942\n",
      "\t-> [readdata] lastread:79942 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:572156\n",
      "\t-> Only read nSites: 572156 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:19\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[19] from pop0:\t60318\n",
      "\t-> Sites to keep[19] from pop1:\t60318\n",
      "\t-> [readdata] lastread:60318 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:632474\n",
      "\t-> Only read nSites: 632474 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:2\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[2] from pop0:\t81218\n",
      "\t-> Sites to keep[2] from pop1:\t81218\n",
      "\t-> [readdata] lastread:81218 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:713692\n",
      "\t-> Only read nSites: 713692 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:20\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[20] from pop0:\t83282\n",
      "\t-> Sites to keep[20] from pop1:\t83282\n",
      "\t-> [readdata] lastread:83282 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:796974\n",
      "\t-> Only read nSites: 796974 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:3\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[3] from pop0:\t74259\n",
      "\t-> Sites to keep[3] from pop1:\t74259\n",
      "\t-> [readdata] lastread:74259 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:871233\n",
      "\t-> Only read nSites: 871233 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:4\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[4] from pop0:\t80665\n",
      "\t-> Sites to keep[4] from pop1:\t80665\n",
      "\t-> [readdata] lastread:80665 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:951898\n",
      "\t-> Only read nSites: 951898 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:5\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[5] from pop0:\t81846\n",
      "\t-> Sites to keep[5] from pop1:\t81846\n",
      "\t-> [readdata] lastread:81846 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:1033744\n",
      "\t-> Only read nSites: 1033744 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:6\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[6] from pop0:\t83193\n",
      "\t-> Sites to keep[6] from pop1:\t83193\n",
      "\t-> [readdata] lastread:83193 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:1116937\n",
      "\t-> Only read nSites: 1116937 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:7\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[7] from pop0:\t82836\n",
      "\t-> Sites to keep[7] from pop1:\t82836\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "\t-> [readdata] lastread:82836 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:1199773\n",
      "\t-> Only read nSites: 1199773 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:8\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[8] from pop0:\t81919\n",
      "\t-> Sites to keep[8] from pop1:\t81919\n",
      "\t-> [readdata] lastread:81919 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:1281692\n",
      "\t-> Only read nSites: 1281692 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:9\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[9] from pop0:\t85249\n",
      "\t-> Sites to keep[9] from pop1:\t85249\n",
      "\t-> [readdata] lastread:85249 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:1366941\n",
      "\t-> Only read nSites: 1366941 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Will run optimization on nSites: 1366941\n",
      "------------\n",
      "startlik=-2488003.407495\n",
      "lik[2]=-179552.870898 diff=2.308451e+06 alpha:1.000000 sr2:5.110480e-01\n",
      "lik[5]=-125258.053723 diff=5.429482e+04 alpha:1.330379 sr2:2.990583e-03\n",
      "lik[8]=-125189.429417 diff=6.862431e+01 alpha:1.935059 sr2:2.703159e-08\n",
      "lik[11]=-125158.670303 diff=3.075911e+01 alpha:4.000000 sr2:2.416857e-10\n",
      "lik[14]=-125153.112392 diff=5.557911e+00 alpha:6.035875 sr2:2.493211e-10\n",
      "lik[17]=-125152.654731 diff=4.576606e-01 alpha:2.003660 sr2:3.364268e-11\n",
      "\t-> Breaking EM(sq2) at iter:19, sqrt(sq2):8.512737e-07\n",
      "likelihood: -125152.654731\n",
      "------------\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Only read nSites: 0 will therefore prepare next chromosome (or exit)\n",
      "\n",
      "\t-> NB NB output is no longer log probs of the frequency spectrum!\n",
      "\t-> Output is now simply the expected values! \n",
      "\t-> You can convert to the old format simply with log(norm(x))\n",
      "\t-> Version of fname:smallNA11840.saf.idx is:2\n",
      "\t-> Assuming .saf.gz file: smallNA11840.saf.gz\n",
      "\t-> Assuming .saf.pos.gz: smallNA11840.saf.pos.gz\n",
      "\t-> Version of fname:smallNA07056.saf.idx is:2\n",
      "\t-> Assuming .saf.gz file: smallNA07056.saf.gz\n",
      "\t-> Assuming .saf.pos.gz: smallNA07056.saf.pos.gz\n",
      "\t-> args: tole:0.000001 nthreads:4 maxiter:100 nsites:0 start:(null) chr:(null) start:-1 stop:-1 fstout:(null) oldout:0 seed:1558447042 bootstrap:0 whichFst:0 fold:0 ref:(null) anc:(null)\n",
      "\t-> Multi SFS is 'still' under development. Please report strange behaviour\n",
      "\t-> nSites: 1537126\n",
      "\t-> The choice of -nSites will require atleast: 58.636703 megabyte memory, that is at least: 0.02% of total memory\n",
      "\t-> dim(smallNA11840.saf.idx):3\n",
      "\t-> dim(smallNA07056.saf.idx):3\n",
      "\t-> Dimension of parameter space: 9\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:1\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[1] from pop0:\t81981\n",
      "\t-> Sites to keep[1] from pop1:\t81981\n",
      "\t-> [readdata] lastread:81981 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:81981\n",
      "\t-> Only read nSites: 81981 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:10\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[10] from pop0:\t83185\n",
      "\t-> Sites to keep[10] from pop1:\t83185\n",
      "\t-> [readdata] lastread:83185 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:165166\n",
      "\t-> Only read nSites: 165166 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:11\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[11] from pop0:\t85115\n",
      "\t-> Sites to keep[11] from pop1:\t85115\n",
      "\t-> [readdata] lastread:85115 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:250281\n",
      "\t-> Only read nSites: 250281 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:12\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[12] from pop0:\t85529\n",
      "\t-> Sites to keep[12] from pop1:\t85529\n",
      "\t-> [readdata] lastread:85529 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:335810\n",
      "\t-> Only read nSites: 335810 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:16\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[16] from pop0:\t82619\n",
      "\t-> Sites to keep[16] from pop1:\t82619\n",
      "\t-> [readdata] lastread:82619 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:418429\n",
      "\t-> Only read nSites: 418429 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:17\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[17] from pop0:\t71277\n",
      "\t-> Sites to keep[17] from pop1:\t71277\n",
      "\t-> [readdata] lastread:71277 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:489706\n",
      "\t-> Only read nSites: 489706 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:18\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[18] from pop0:\t79258\n",
      "\t-> Sites to keep[18] from pop1:\t79258\n",
      "\t-> [readdata] lastread:79258 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:568964\n",
      "\t-> Only read nSites: 568964 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:19\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[19] from pop0:\t68159\n",
      "\t-> Sites to keep[19] from pop1:\t68159\n",
      "\t-> [readdata] lastread:68159 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:637123\n",
      "\t-> Only read nSites: 637123 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:2\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[2] from pop0:\t76419\n",
      "\t-> Sites to keep[2] from pop1:\t76419\n",
      "\t-> [readdata] lastread:76419 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:713542\n",
      "\t-> Only read nSites: 713542 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:20\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[20] from pop0:\t80370\n",
      "\t-> Sites to keep[20] from pop1:\t80370\n",
      "\t-> [readdata] lastread:80370 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:793912\n",
      "\t-> Only read nSites: 793912 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:3\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[3] from pop0:\t74240\n",
      "\t-> Sites to keep[3] from pop1:\t74240\n",
      "\t-> [readdata] lastread:74240 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:868152\n",
      "\t-> Only read nSites: 868152 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:4\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "\t-> Sites to keep[4] from pop0:\t80132\n",
      "\t-> Sites to keep[4] from pop1:\t80132\n",
      "\t-> [readdata] lastread:80132 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:948284\n",
      "\t-> Only read nSites: 948284 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:5\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[5] from pop0:\t83077\n",
      "\t-> Sites to keep[5] from pop1:\t83077\n",
      "\t-> [readdata] lastread:83077 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:1031361\n",
      "\t-> Only read nSites: 1031361 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:6\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[6] from pop0:\t84363\n",
      "\t-> Sites to keep[6] from pop1:\t84363\n",
      "\t-> [readdata] lastread:84363 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:1115724\n",
      "\t-> Only read nSites: 1115724 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:7\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[7] from pop0:\t78505\n",
      "\t-> Sites to keep[7] from pop1:\t78505\n",
      "\t-> [readdata] lastread:78505 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:1194229\n",
      "\t-> Only read nSites: 1194229 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:8\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[8] from pop0:\t77929\n",
      "\t-> Sites to keep[8] from pop1:\t77929\n",
      "\t-> [readdata] lastread:77929 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:1272158\n",
      "\t-> Only read nSites: 1272158 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:9\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[9] from pop0:\t81796\n",
      "\t-> Sites to keep[9] from pop1:\t81796\n",
      "\t-> [readdata] lastread:81796 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:1353954\n",
      "\t-> Only read nSites: 1353954 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Will run optimization on nSites: 1353954\n",
      "------------\n",
      "startlik=-3231701.437761\n",
      "lik[2]=-239931.268528 diff=2.991770e+06 alpha:1.000000 sr2:4.026887e-01\n",
      "lik[5]=-122686.103044 diff=1.172452e+05 alpha:1.321706 sr2:1.099106e-02\n",
      "lik[8]=-122602.084474 diff=8.401857e+01 alpha:1.799117 sr2:4.163378e-08\n",
      "lik[11]=-122515.739594 diff=8.634488e+01 alpha:2.274726 sr2:2.885533e-10\n",
      "lik[14]=-122502.856971 diff=1.288262e+01 alpha:4.000000 sr2:8.538622e-10\n",
      "lik[17]=-122502.744676 diff=1.122952e-01 alpha:3.459023 sr2:1.312641e-11\n",
      "\t-> Breaking EM(sr2) at iter:18, sqrt(sr2):2.105827e-07\n",
      "likelihood: -122502.744676\n",
      "------------\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Only read nSites: 0 will therefore prepare next chromosome (or exit)\n",
      "\n",
      "\t-> NB NB output is no longer log probs of the frequency spectrum!\n",
      "\t-> Output is now simply the expected values! \n",
      "\t-> You can convert to the old format simply with log(norm(x))\n",
      "\t-> Version of fname:smallNA11840.saf.idx is:2\n",
      "\t-> Assuming .saf.gz file: smallNA11840.saf.gz\n",
      "\t-> Assuming .saf.pos.gz: smallNA11840.saf.pos.gz\n",
      "\t-> Version of fname:smallNA11830.saf.idx is:2\n",
      "\t-> Assuming .saf.gz file: smallNA11830.saf.gz\n",
      "\t-> Assuming .saf.pos.gz: smallNA11830.saf.pos.gz\n",
      "\t-> args: tole:0.000001 nthreads:4 maxiter:100 nsites:0 start:(null) chr:(null) start:-1 stop:-1 fstout:(null) oldout:0 seed:1558447044 bootstrap:0 whichFst:0 fold:0 ref:(null) anc:(null)\n",
      "\t-> Multi SFS is 'still' under development. Please report strange behaviour\n",
      "\t-> nSites: 1584541\n",
      "\t-> The choice of -nSites will require atleast: 60.445442 megabyte memory, that is at least: 0.02% of total memory\n",
      "\t-> dim(smallNA11840.saf.idx):3\n",
      "\t-> dim(smallNA11830.saf.idx):3\n",
      "\t-> Dimension of parameter space: 9\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:1\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[1] from pop0:\t84227\n",
      "\t-> Sites to keep[1] from pop1:\t84227\n",
      "\t-> [readdata] lastread:84227 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:84227\n",
      "\t-> Only read nSites: 84227 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:10\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[10] from pop0:\t84502\n",
      "\t-> Sites to keep[10] from pop1:\t84502\n",
      "\t-> [readdata] lastread:84502 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:168729\n",
      "\t-> Only read nSites: 168729 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:11\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[11] from pop0:\t86148\n",
      "\t-> Sites to keep[11] from pop1:\t86148\n",
      "\t-> [readdata] lastread:86148 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:254877\n",
      "\t-> Only read nSites: 254877 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:12\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[12] from pop0:\t88024\n",
      "\t-> Sites to keep[12] from pop1:\t88024\n",
      "\t-> [readdata] lastread:88024 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:342901\n",
      "\t-> Only read nSites: 342901 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:16\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[16] from pop0:\t84260\n",
      "\t-> Sites to keep[16] from pop1:\t84260\n",
      "\t-> [readdata] lastread:84260 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:427161\n",
      "\t-> Only read nSites: 427161 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:17\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[17] from pop0:\t75773\n",
      "\t-> Sites to keep[17] from pop1:\t75773\n",
      "\t-> [readdata] lastread:75773 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:502934\n",
      "\t-> Only read nSites: 502934 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:18\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[18] from pop0:\t82087\n",
      "\t-> Sites to keep[18] from pop1:\t82087\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "\t-> [readdata] lastread:82087 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:585021\n",
      "\t-> Only read nSites: 585021 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:19\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[19] from pop0:\t67488\n",
      "\t-> Sites to keep[19] from pop1:\t67488\n",
      "\t-> [readdata] lastread:67488 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:652509\n",
      "\t-> Only read nSites: 652509 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:2\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[2] from pop0:\t80648\n",
      "\t-> Sites to keep[2] from pop1:\t80648\n",
      "\t-> [readdata] lastread:80648 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:733157\n",
      "\t-> Only read nSites: 733157 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:20\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[20] from pop0:\t84730\n",
      "\t-> Sites to keep[20] from pop1:\t84730\n",
      "\t-> [readdata] lastread:84730 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:817887\n",
      "\t-> Only read nSites: 817887 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:3\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[3] from pop0:\t76155\n",
      "\t-> Sites to keep[3] from pop1:\t76155\n",
      "\t-> [readdata] lastread:76155 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:894042\n",
      "\t-> Only read nSites: 894042 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:4\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[4] from pop0:\t81795\n",
      "\t-> Sites to keep[4] from pop1:\t81795\n",
      "\t-> [readdata] lastread:81795 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:975837\n",
      "\t-> Only read nSites: 975837 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:5\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[5] from pop0:\t84459\n",
      "\t-> Sites to keep[5] from pop1:\t84459\n",
      "\t-> [readdata] lastread:84459 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:1060296\n",
      "\t-> Only read nSites: 1060296 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:6\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[6] from pop0:\t85614\n",
      "\t-> Sites to keep[6] from pop1:\t85614\n",
      "\t-> [readdata] lastread:85614 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:1145910\n",
      "\t-> Only read nSites: 1145910 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:7\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[7] from pop0:\t83307\n",
      "\t-> Sites to keep[7] from pop1:\t83307\n",
      "\t-> [readdata] lastread:83307 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:1229217\n",
      "\t-> Only read nSites: 1229217 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:8\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[8] from pop0:\t82320\n",
      "\t-> Sites to keep[8] from pop1:\t82320\n",
      "\t-> [readdata] lastread:82320 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:1311537\n",
      "\t-> Only read nSites: 1311537 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:9\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[9] from pop0:\t86731\n",
      "\t-> Sites to keep[9] from pop1:\t86731\n",
      "\t-> [readdata] lastread:86731 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:1398268\n",
      "\t-> Only read nSites: 1398268 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Will run optimization on nSites: 1398268\n",
      "------------\n",
      "startlik=-3942804.158771\n",
      "lik[2]=-793500.114799 diff=3.149304e+06 alpha:1.000000 sr2:1.874626e-01\n",
      "lik[5]=-128256.559951 diff=6.652436e+05 alpha:1.547820 sr2:1.652473e-01\n",
      "lik[8]=-127251.064781 diff=1.005495e+03 alpha:1.348422 sr2:1.872819e-06\n",
      "lik[11]=-127229.977098 diff=2.108768e+01 alpha:2.236674 sr2:7.426775e-10\n",
      "lik[13]=-127137.923845 diff=9.205325e+01 alpha:1.000000 sr2:1.114477e-10\n",
      "lik[16]=-126933.025487 diff=2.048984e+02 alpha:2.180740 sr2:2.186172e-09\n",
      "lik[19]=-126928.184010 diff=4.841478e+00 alpha:3.262552 sr2:5.222961e-10\n",
      "\t-> Breaking EM(sq2) at iter:21, sqrt(sq2):7.160827e-07\n",
      "likelihood: -126928.184010\n",
      "------------\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Only read nSites: 0 will therefore prepare next chromosome (or exit)\n",
      "\n",
      "\t-> NB NB output is no longer log probs of the frequency spectrum!\n",
      "\t-> Output is now simply the expected values! \n",
      "\t-> You can convert to the old format simply with log(norm(x))\n",
      "\t-> Version of fname:smallNA07357.saf.idx is:2\n",
      "\t-> Assuming .saf.gz file: smallNA07357.saf.gz\n",
      "\t-> Assuming .saf.pos.gz: smallNA07357.saf.pos.gz\n",
      "\t-> Version of fname:smallNA11832.saf.idx is:2\n",
      "\t-> Assuming .saf.gz file: smallNA11832.saf.gz\n",
      "\t-> Assuming .saf.pos.gz: smallNA11832.saf.pos.gz\n",
      "\t-> args: tole:0.000001 nthreads:4 maxiter:100 nsites:0 start:(null) chr:(null) start:-1 stop:-1 fstout:(null) oldout:0 seed:1558447047 bootstrap:0 whichFst:0 fold:0 ref:(null) anc:(null)\n",
      "\t-> Multi SFS is 'still' under development. Please report strange behaviour\n",
      "\t-> nSites: 1450698\n",
      "\t-> The choice of -nSites will require atleast: 55.339737 megabyte memory, that is at least: 0.01% of total memory\n",
      "\t-> dim(smallNA07357.saf.idx):3\n",
      "\t-> dim(smallNA11832.saf.idx):3\n",
      "\t-> Dimension of parameter space: 9\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:1\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[1] from pop0:\t68219\n",
      "\t-> Sites to keep[1] from pop1:\t68219\n",
      "\t-> [readdata] lastread:68219 posi:14000039\n",
      "\t-> Comparing positions: 1 with 0 has:68219\n",
      "\t-> Only read nSites: 68219 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:10\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "\t-> Sites to keep[10] from pop0:\t71860\n",
      "\t-> Sites to keep[10] from pop1:\t71860\n",
      "\t-> [readdata] lastread:71860 posi:14000039\n",
      "\t-> Comparing positions: 1 with 0 has:140079\n",
      "\t-> Only read nSites: 140079 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:11\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[11] from pop0:\t70363\n",
      "\t-> Sites to keep[11] from pop1:\t70363\n",
      "\t-> [readdata] lastread:70363 posi:14000039\n",
      "\t-> Comparing positions: 1 with 0 has:210442\n",
      "\t-> Only read nSites: 210442 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:12\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[12] from pop0:\t73621\n",
      "\t-> Sites to keep[12] from pop1:\t73621\n",
      "\t-> [readdata] lastread:73621 posi:14000039\n",
      "\t-> Comparing positions: 1 with 0 has:284063\n",
      "\t-> Only read nSites: 284063 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:16\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[16] from pop0:\t66831\n",
      "\t-> Sites to keep[16] from pop1:\t66831\n",
      "\t-> [readdata] lastread:66831 posi:14000039\n",
      "\t-> Comparing positions: 1 with 0 has:350894\n",
      "\t-> Only read nSites: 350894 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:17\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[17] from pop0:\t56795\n",
      "\t-> Sites to keep[17] from pop1:\t56795\n",
      "\t-> [readdata] lastread:56795 posi:14000039\n",
      "\t-> Comparing positions: 1 with 0 has:407689\n",
      "\t-> Only read nSites: 407689 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:18\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[18] from pop0:\t60276\n",
      "\t-> Sites to keep[18] from pop1:\t60276\n",
      "\t-> [readdata] lastread:60276 posi:14000039\n",
      "\t-> Comparing positions: 1 with 0 has:467965\n",
      "\t-> Only read nSites: 467965 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:19\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[19] from pop0:\t55200\n",
      "\t-> Sites to keep[19] from pop1:\t55200\n",
      "\t-> [readdata] lastread:55200 posi:14000039\n",
      "\t-> Comparing positions: 1 with 0 has:523165\n",
      "\t-> Only read nSites: 523165 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:2\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[2] from pop0:\t60463\n",
      "\t-> Sites to keep[2] from pop1:\t60463\n",
      "\t-> [readdata] lastread:60463 posi:14000039\n",
      "\t-> Comparing positions: 1 with 0 has:583628\n",
      "\t-> Only read nSites: 583628 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:20\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[20] from pop0:\t60160\n",
      "\t-> Sites to keep[20] from pop1:\t60160\n",
      "\t-> [readdata] lastread:60160 posi:14000039\n",
      "\t-> Comparing positions: 1 with 0 has:643788\n",
      "\t-> Only read nSites: 643788 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:3\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[3] from pop0:\t54846\n",
      "\t-> Sites to keep[3] from pop1:\t54846\n",
      "\t-> [readdata] lastread:54846 posi:14000039\n",
      "\t-> Comparing positions: 1 with 0 has:698634\n",
      "\t-> Only read nSites: 698634 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:4\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[4] from pop0:\t68439\n",
      "\t-> Sites to keep[4] from pop1:\t68439\n",
      "\t-> [readdata] lastread:68439 posi:14000039\n",
      "\t-> Comparing positions: 1 with 0 has:767073\n",
      "\t-> Only read nSites: 767073 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:5\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[5] from pop0:\t68538\n",
      "\t-> Sites to keep[5] from pop1:\t68538\n",
      "\t-> [readdata] lastread:68538 posi:14000039\n",
      "\t-> Comparing positions: 1 with 0 has:835611\n",
      "\t-> Only read nSites: 835611 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:6\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[6] from pop0:\t69359\n",
      "\t-> Sites to keep[6] from pop1:\t69359\n",
      "\t-> [readdata] lastread:69359 posi:14000039\n",
      "\t-> Comparing positions: 1 with 0 has:904970\n",
      "\t-> Only read nSites: 904970 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:7\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[7] from pop0:\t64730\n",
      "\t-> Sites to keep[7] from pop1:\t64730\n",
      "\t-> [readdata] lastread:64730 posi:14000039\n",
      "\t-> Comparing positions: 1 with 0 has:969700\n",
      "\t-> Only read nSites: 969700 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:8\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[8] from pop0:\t62481\n",
      "\t-> Sites to keep[8] from pop1:\t62481\n",
      "\t-> [readdata] lastread:62481 posi:14000039\n",
      "\t-> Comparing positions: 1 with 0 has:1032181\n",
      "\t-> Only read nSites: 1032181 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:9\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[9] from pop0:\t72074\n",
      "\t-> Sites to keep[9] from pop1:\t72074\n",
      "\t-> [readdata] lastread:72074 posi:14000039\n",
      "\t-> Comparing positions: 1 with 0 has:1104255\n",
      "\t-> Only read nSites: 1104255 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Will run optimization on nSites: 1104255\n",
      "------------\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "startlik=-1821854.189524\n",
      "lik[2]=-131781.657291 diff=1.690073e+06 alpha:1.000000 sr2:5.095267e-01\n",
      "lik[5]=-99184.638437 diff=3.259702e+04 alpha:1.292208 sr2:1.575344e-03\n",
      "lik[8]=-98989.342125 diff=1.952963e+02 alpha:2.052992 sr2:1.817951e-07\n",
      "lik[11]=-98947.891227 diff=4.145090e+01 alpha:3.764934 sr2:8.204168e-10\n",
      "lik[14]=-98935.090943 diff=1.280028e+01 alpha:4.000000 sr2:3.231456e-10\n",
      "lik[17]=-98934.921864 diff=1.690791e-01 alpha:1.627681 sr2:7.059639e-11\n",
      "\t-> Breaking EM(sr2) at iter:18, sqrt(sr2):6.606225e-07\n",
      "likelihood: -98934.921864\n",
      "------------\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Only read nSites: 0 will therefore prepare next chromosome (or exit)\n",
      "\n",
      "\t-> NB NB output is no longer log probs of the frequency spectrum!\n",
      "\t-> Output is now simply the expected values! \n",
      "\t-> You can convert to the old format simply with log(norm(x))\n",
      "\t-> Version of fname:smallNA07357.saf.idx is:2\n",
      "\t-> Assuming .saf.gz file: smallNA07357.saf.gz\n",
      "\t-> Assuming .saf.pos.gz: smallNA07357.saf.pos.gz\n",
      "\t-> Version of fname:smallNA06994.saf.idx is:2\n",
      "\t-> Assuming .saf.gz file: smallNA06994.saf.gz\n",
      "\t-> Assuming .saf.pos.gz: smallNA06994.saf.pos.gz\n",
      "\t-> args: tole:0.000001 nthreads:4 maxiter:100 nsites:0 start:(null) chr:(null) start:-1 stop:-1 fstout:(null) oldout:0 seed:1558447048 bootstrap:0 whichFst:0 fold:0 ref:(null) anc:(null)\n",
      "\t-> Multi SFS is 'still' under development. Please report strange behaviour\n",
      "\t-> nSites: 1450698\n",
      "\t-> The choice of -nSites will require atleast: 55.339737 megabyte memory, that is at least: 0.01% of total memory\n",
      "\t-> dim(smallNA07357.saf.idx):3\n",
      "\t-> dim(smallNA06994.saf.idx):3\n",
      "\t-> Dimension of parameter space: 9\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:1\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[1] from pop0:\t79661\n",
      "\t-> Sites to keep[1] from pop1:\t79661\n",
      "\t-> [readdata] lastread:79661 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:79661\n",
      "\t-> Only read nSites: 79661 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:10\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[10] from pop0:\t80696\n",
      "\t-> Sites to keep[10] from pop1:\t80696\n",
      "\t-> [readdata] lastread:80696 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:160357\n",
      "\t-> Only read nSites: 160357 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:11\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[11] from pop0:\t82817\n",
      "\t-> Sites to keep[11] from pop1:\t82817\n",
      "\t-> [readdata] lastread:82817 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:243174\n",
      "\t-> Only read nSites: 243174 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:12\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[12] from pop0:\t87375\n",
      "\t-> Sites to keep[12] from pop1:\t87375\n",
      "\t-> [readdata] lastread:87375 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:330549\n",
      "\t-> Only read nSites: 330549 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:16\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[16] from pop0:\t75683\n",
      "\t-> Sites to keep[16] from pop1:\t75683\n",
      "\t-> [readdata] lastread:75683 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:406232\n",
      "\t-> Only read nSites: 406232 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:17\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[17] from pop0:\t67739\n",
      "\t-> Sites to keep[17] from pop1:\t67739\n",
      "\t-> [readdata] lastread:67739 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:473971\n",
      "\t-> Only read nSites: 473971 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:18\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[18] from pop0:\t71399\n",
      "\t-> Sites to keep[18] from pop1:\t71399\n",
      "\t-> [readdata] lastread:71399 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:545370\n",
      "\t-> Only read nSites: 545370 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:19\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[19] from pop0:\t55591\n",
      "\t-> Sites to keep[19] from pop1:\t55591\n",
      "\t-> [readdata] lastread:55591 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:600961\n",
      "\t-> Only read nSites: 600961 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:2\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[2] from pop0:\t76518\n",
      "\t-> Sites to keep[2] from pop1:\t76518\n",
      "\t-> [readdata] lastread:76518 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:677479\n",
      "\t-> Only read nSites: 677479 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:20\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[20] from pop0:\t73458\n",
      "\t-> Sites to keep[20] from pop1:\t73458\n",
      "\t-> [readdata] lastread:73458 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:750937\n",
      "\t-> Only read nSites: 750937 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:3\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[3] from pop0:\t60770\n",
      "\t-> Sites to keep[3] from pop1:\t60770\n",
      "\t-> [readdata] lastread:60770 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:811707\n",
      "\t-> Only read nSites: 811707 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:4\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[4] from pop0:\t81018\n",
      "\t-> Sites to keep[4] from pop1:\t81018\n",
      "\t-> [readdata] lastread:81018 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:892725\n",
      "\t-> Only read nSites: 892725 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:5\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[5] from pop0:\t78936\n",
      "\t-> Sites to keep[5] from pop1:\t78936\n",
      "\t-> [readdata] lastread:78936 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:971661\n",
      "\t-> Only read nSites: 971661 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:6\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[6] from pop0:\t79384\n",
      "\t-> Sites to keep[6] from pop1:\t79384\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "\t-> [readdata] lastread:79384 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:1051045\n",
      "\t-> Only read nSites: 1051045 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:7\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[7] from pop0:\t80730\n",
      "\t-> Sites to keep[7] from pop1:\t80730\n",
      "\t-> [readdata] lastread:80730 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:1131775\n",
      "\t-> Only read nSites: 1131775 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:8\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[8] from pop0:\t77459\n",
      "\t-> Sites to keep[8] from pop1:\t77459\n",
      "\t-> [readdata] lastread:77459 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:1209234\n",
      "\t-> Only read nSites: 1209234 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:9\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[9] from pop0:\t84562\n",
      "\t-> Sites to keep[9] from pop1:\t84562\n",
      "\t-> [readdata] lastread:84562 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:1293796\n",
      "\t-> Only read nSites: 1293796 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Will run optimization on nSites: 1293796\n",
      "------------\n",
      "startlik=-2590286.072709\n",
      "lik[2]=-176648.469412 diff=2.413638e+06 alpha:1.000000 sr2:4.969013e-01\n",
      "lik[5]=-122261.740461 diff=5.438673e+04 alpha:1.274397 sr2:3.233830e-03\n",
      "lik[8]=-122082.699761 diff=1.790407e+02 alpha:1.807499 sr2:1.150161e-07\n",
      "lik[11]=-122010.993395 diff=7.170637e+01 alpha:2.562377 sr2:5.726600e-10\n",
      "lik[14]=-122007.269540 diff=3.723855e+00 alpha:3.388067 sr2:3.597011e-10\n",
      "\t-> Breaking EM(sr2) at iter:15, sqrt(sr2):4.700450e-07\n",
      "likelihood: -122007.269540\n",
      "------------\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Only read nSites: 0 will therefore prepare next chromosome (or exit)\n",
      "\n",
      "\t-> NB NB output is no longer log probs of the frequency spectrum!\n",
      "\t-> Output is now simply the expected values! \n",
      "\t-> You can convert to the old format simply with log(norm(x))\n",
      "\t-> Version of fname:smallNA07357.saf.idx is:2\n",
      "\t-> Assuming .saf.gz file: smallNA07357.saf.gz\n",
      "\t-> Assuming .saf.pos.gz: smallNA07357.saf.pos.gz\n",
      "\t-> Version of fname:smallNA06985.saf.idx is:2\n",
      "\t-> Assuming .saf.gz file: smallNA06985.saf.gz\n",
      "\t-> Assuming .saf.pos.gz: smallNA06985.saf.pos.gz\n",
      "\t-> args: tole:0.000001 nthreads:4 maxiter:100 nsites:0 start:(null) chr:(null) start:-1 stop:-1 fstout:(null) oldout:0 seed:1558447050 bootstrap:0 whichFst:0 fold:0 ref:(null) anc:(null)\n",
      "\t-> Multi SFS is 'still' under development. Please report strange behaviour\n",
      "\t-> nSites: 1450698\n",
      "\t-> The choice of -nSites will require atleast: 55.339737 megabyte memory, that is at least: 0.01% of total memory\n",
      "\t-> dim(smallNA07357.saf.idx):3\n",
      "\t-> dim(smallNA06985.saf.idx):3\n",
      "\t-> Dimension of parameter space: 9\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:1\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[1] from pop0:\t79157\n",
      "\t-> Sites to keep[1] from pop1:\t79157\n",
      "\t-> [readdata] lastread:79157 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:79157\n",
      "\t-> Only read nSites: 79157 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:10\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[10] from pop0:\t82709\n",
      "\t-> Sites to keep[10] from pop1:\t82709\n",
      "\t-> [readdata] lastread:82709 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:161866\n",
      "\t-> Only read nSites: 161866 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:11\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[11] from pop0:\t82354\n",
      "\t-> Sites to keep[11] from pop1:\t82354\n",
      "\t-> [readdata] lastread:82354 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:244220\n",
      "\t-> Only read nSites: 244220 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:12\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[12] from pop0:\t82389\n",
      "\t-> Sites to keep[12] from pop1:\t82389\n",
      "\t-> [readdata] lastread:82389 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:326609\n",
      "\t-> Only read nSites: 326609 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:16\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[16] from pop0:\t76194\n",
      "\t-> Sites to keep[16] from pop1:\t76194\n",
      "\t-> [readdata] lastread:76194 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:402803\n",
      "\t-> Only read nSites: 402803 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:17\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[17] from pop0:\t65045\n",
      "\t-> Sites to keep[17] from pop1:\t65045\n",
      "\t-> [readdata] lastread:65045 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:467848\n",
      "\t-> Only read nSites: 467848 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:18\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[18] from pop0:\t68449\n",
      "\t-> Sites to keep[18] from pop1:\t68449\n",
      "\t-> [readdata] lastread:68449 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:536297\n",
      "\t-> Only read nSites: 536297 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:19\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[19] from pop0:\t70447\n",
      "\t-> Sites to keep[19] from pop1:\t70447\n",
      "\t-> [readdata] lastread:70447 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:606744\n",
      "\t-> Only read nSites: 606744 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:2\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[2] from pop0:\t65694\n",
      "\t-> Sites to keep[2] from pop1:\t65694\n",
      "\t-> [readdata] lastread:65694 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:672438\n",
      "\t-> Only read nSites: 672438 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:20\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[20] from pop0:\t69991\n",
      "\t-> Sites to keep[20] from pop1:\t69991\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "\t-> [readdata] lastread:69991 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:742429\n",
      "\t-> Only read nSites: 742429 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:3\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[3] from pop0:\t64812\n",
      "\t-> Sites to keep[3] from pop1:\t64812\n",
      "\t-> [readdata] lastread:64812 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:807241\n",
      "\t-> Only read nSites: 807241 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:4\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[4] from pop0:\t77745\n",
      "\t-> Sites to keep[4] from pop1:\t77745\n",
      "\t-> [readdata] lastread:77745 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:884986\n",
      "\t-> Only read nSites: 884986 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:5\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[5] from pop0:\t80328\n",
      "\t-> Sites to keep[5] from pop1:\t80328\n",
      "\t-> [readdata] lastread:80328 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:965314\n",
      "\t-> Only read nSites: 965314 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:6\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[6] from pop0:\t81945\n",
      "\t-> Sites to keep[6] from pop1:\t81945\n",
      "\t-> [readdata] lastread:81945 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:1047259\n",
      "\t-> Only read nSites: 1047259 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:7\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[7] from pop0:\t70214\n",
      "\t-> Sites to keep[7] from pop1:\t70214\n",
      "\t-> [readdata] lastread:70214 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:1117473\n",
      "\t-> Only read nSites: 1117473 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:8\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[8] from pop0:\t65001\n",
      "\t-> Sites to keep[8] from pop1:\t65001\n",
      "\t-> [readdata] lastread:65001 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:1182474\n",
      "\t-> Only read nSites: 1182474 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:9\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[9] from pop0:\t78606\n",
      "\t-> Sites to keep[9] from pop1:\t78606\n",
      "\t-> [readdata] lastread:78606 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:1261080\n",
      "\t-> Only read nSites: 1261080 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Will run optimization on nSites: 1261080\n",
      "------------\n",
      "startlik=-3146092.518269\n",
      "lik[2]=-169265.187354 diff=2.976827e+06 alpha:1.000000 sr2:5.932190e-01\n",
      "lik[5]=-111984.696105 diff=5.728049e+04 alpha:1.314520 sr2:3.284890e-03\n",
      "lik[8]=-111886.906405 diff=9.778970e+01 alpha:1.814452 sr2:4.946672e-08\n",
      "lik[11]=-111856.838851 diff=3.006755e+01 alpha:4.000000 sr2:3.794339e-10\n",
      "lik[14]=-111852.857571 diff=3.981279e+00 alpha:3.109304 sr2:2.133417e-10\n",
      "lik[17]=-111852.822087 diff=3.548462e-02 alpha:1.860052 sr2:4.970159e-12\n",
      "\t-> Breaking EM(sr2) at iter:18, sqrt(sr2):2.221761e-07\n",
      "likelihood: -111852.822087\n",
      "------------\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Only read nSites: 0 will therefore prepare next chromosome (or exit)\n",
      "\n",
      "\t-> NB NB output is no longer log probs of the frequency spectrum!\n",
      "\t-> Output is now simply the expected values! \n",
      "\t-> You can convert to the old format simply with log(norm(x))\n",
      "\t-> Version of fname:smallNA07357.saf.idx is:2\n",
      "\t-> Assuming .saf.gz file: smallNA07357.saf.gz\n",
      "\t-> Assuming .saf.pos.gz: smallNA07357.saf.pos.gz\n",
      "\t-> Version of fname:smallNA11831.saf.idx is:2\n",
      "\t-> Assuming .saf.gz file: smallNA11831.saf.gz\n",
      "\t-> Assuming .saf.pos.gz: smallNA11831.saf.pos.gz\n",
      "\t-> args: tole:0.000001 nthreads:4 maxiter:100 nsites:0 start:(null) chr:(null) start:-1 stop:-1 fstout:(null) oldout:0 seed:1558447052 bootstrap:0 whichFst:0 fold:0 ref:(null) anc:(null)\n",
      "\t-> Multi SFS is 'still' under development. Please report strange behaviour\n",
      "\t-> nSites: 1556469\n",
      "\t-> The choice of -nSites will require atleast: 59.374580 megabyte memory, that is at least: 0.02% of total memory\n",
      "\t-> dim(smallNA07357.saf.idx):3\n",
      "\t-> dim(smallNA11831.saf.idx):3\n",
      "\t-> Dimension of parameter space: 9\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:1\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[1] from pop0:\t85033\n",
      "\t-> Sites to keep[1] from pop1:\t85033\n",
      "\t-> [readdata] lastread:85033 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:85033\n",
      "\t-> Only read nSites: 85033 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:10\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[10] from pop0:\t87052\n",
      "\t-> Sites to keep[10] from pop1:\t87052\n",
      "\t-> [readdata] lastread:87052 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:172085\n",
      "\t-> Only read nSites: 172085 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:11\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[11] from pop0:\t87684\n",
      "\t-> Sites to keep[11] from pop1:\t87684\n",
      "\t-> [readdata] lastread:87684 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:259769\n",
      "\t-> Only read nSites: 259769 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:12\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[12] from pop0:\t91528\n",
      "\t-> Sites to keep[12] from pop1:\t91528\n",
      "\t-> [readdata] lastread:91528 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:351297\n",
      "\t-> Only read nSites: 351297 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:16\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "\t-> Sites to keep[16] from pop0:\t83712\n",
      "\t-> Sites to keep[16] from pop1:\t83712\n",
      "\t-> [readdata] lastread:83712 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:435009\n",
      "\t-> Only read nSites: 435009 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:17\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[17] from pop0:\t74061\n",
      "\t-> Sites to keep[17] from pop1:\t74061\n",
      "\t-> [readdata] lastread:74061 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:509070\n",
      "\t-> Only read nSites: 509070 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:18\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[18] from pop0:\t76476\n",
      "\t-> Sites to keep[18] from pop1:\t76476\n",
      "\t-> [readdata] lastread:76476 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:585546\n",
      "\t-> Only read nSites: 585546 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:19\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[19] from pop0:\t70022\n",
      "\t-> Sites to keep[19] from pop1:\t70022\n",
      "\t-> [readdata] lastread:70022 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:655568\n",
      "\t-> Only read nSites: 655568 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:2\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[2] from pop0:\t80800\n",
      "\t-> Sites to keep[2] from pop1:\t80800\n",
      "\t-> [readdata] lastread:80800 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:736368\n",
      "\t-> Only read nSites: 736368 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:20\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[20] from pop0:\t80634\n",
      "\t-> Sites to keep[20] from pop1:\t80634\n",
      "\t-> [readdata] lastread:80634 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:817002\n",
      "\t-> Only read nSites: 817002 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:3\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[3] from pop0:\t70951\n",
      "\t-> Sites to keep[3] from pop1:\t70951\n",
      "\t-> [readdata] lastread:70951 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:887953\n",
      "\t-> Only read nSites: 887953 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:4\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[4] from pop0:\t84276\n",
      "\t-> Sites to keep[4] from pop1:\t84276\n",
      "\t-> [readdata] lastread:84276 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:972229\n",
      "\t-> Only read nSites: 972229 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:5\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[5] from pop0:\t85025\n",
      "\t-> Sites to keep[5] from pop1:\t85025\n",
      "\t-> [readdata] lastread:85025 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:1057254\n",
      "\t-> Only read nSites: 1057254 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:6\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[6] from pop0:\t86319\n",
      "\t-> Sites to keep[6] from pop1:\t86319\n",
      "\t-> [readdata] lastread:86319 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:1143573\n",
      "\t-> Only read nSites: 1143573 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:7\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[7] from pop0:\t84745\n",
      "\t-> Sites to keep[7] from pop1:\t84745\n",
      "\t-> [readdata] lastread:84745 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:1228318\n",
      "\t-> Only read nSites: 1228318 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:8\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[8] from pop0:\t83173\n",
      "\t-> Sites to keep[8] from pop1:\t83173\n",
      "\t-> [readdata] lastread:83173 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:1311491\n",
      "\t-> Only read nSites: 1311491 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:9\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[9] from pop0:\t88383\n",
      "\t-> Sites to keep[9] from pop1:\t88383\n",
      "\t-> [readdata] lastread:88383 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:1399874\n",
      "\t-> Only read nSites: 1399874 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Will run optimization on nSites: 1399874\n",
      "------------\n",
      "startlik=-1848187.957013\n",
      "lik[2]=-146206.999388 diff=1.701981e+06 alpha:1.000000 sr2:4.956902e-01\n",
      "lik[5]=-130940.586091 diff=1.526641e+04 alpha:1.246630 sr2:2.576683e-04\n",
      "lik[8]=-130856.396941 diff=8.418915e+01 alpha:1.858708 sr2:1.468915e-08\n",
      "lik[11]=-130843.028463 diff=1.336848e+01 alpha:4.000000 sr2:4.370370e-10\n",
      "lik[14]=-130842.057742 diff=9.707210e-01 alpha:2.423033 sr2:7.808696e-11\n",
      "\t-> Breaking EM(sr2) at iter:15, sqrt(sr2):3.268921e-07\n",
      "likelihood: -130842.057742\n",
      "------------\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Only read nSites: 0 will therefore prepare next chromosome (or exit)\n",
      "\n",
      "\t-> NB NB output is no longer log probs of the frequency spectrum!\n",
      "\t-> Output is now simply the expected values! \n",
      "\t-> You can convert to the old format simply with log(norm(x))\n",
      "\t-> Version of fname:smallNA07357.saf.idx is:2\n",
      "\t-> Assuming .saf.gz file: smallNA07357.saf.gz\n",
      "\t-> Assuming .saf.pos.gz: smallNA07357.saf.pos.gz\n",
      "\t-> Version of fname:smallNA11829.saf.idx is:2\n",
      "\t-> Assuming .saf.gz file: smallNA11829.saf.gz\n",
      "\t-> Assuming .saf.pos.gz: smallNA11829.saf.pos.gz\n",
      "\t-> args: tole:0.000001 nthreads:4 maxiter:100 nsites:0 start:(null) chr:(null) start:-1 stop:-1 fstout:(null) oldout:0 seed:1558447055 bootstrap:0 whichFst:0 fold:0 ref:(null) anc:(null)\n",
      "\t-> Multi SFS is 'still' under development. Please report strange behaviour\n",
      "\t-> nSites: 1542786\n",
      "\t-> The choice of -nSites will require atleast: 58.852615 megabyte memory, that is at least: 0.02% of total memory\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "\t-> dim(smallNA07357.saf.idx):3\n",
      "\t-> dim(smallNA11829.saf.idx):3\n",
      "\t-> Dimension of parameter space: 9\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:1\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[1] from pop0:\t84077\n",
      "\t-> Sites to keep[1] from pop1:\t84077\n",
      "\t-> [readdata] lastread:84077 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:84077\n",
      "\t-> Only read nSites: 84077 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:10\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[10] from pop0:\t85955\n",
      "\t-> Sites to keep[10] from pop1:\t85955\n",
      "\t-> [readdata] lastread:85955 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:170032\n",
      "\t-> Only read nSites: 170032 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:11\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[11] from pop0:\t87604\n",
      "\t-> Sites to keep[11] from pop1:\t87604\n",
      "\t-> [readdata] lastread:87604 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:257636\n",
      "\t-> Only read nSites: 257636 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:12\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[12] from pop0:\t90327\n",
      "\t-> Sites to keep[12] from pop1:\t90327\n",
      "\t-> [readdata] lastread:90327 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:347963\n",
      "\t-> Only read nSites: 347963 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:16\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[16] from pop0:\t81979\n",
      "\t-> Sites to keep[16] from pop1:\t81979\n",
      "\t-> [readdata] lastread:81979 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:429942\n",
      "\t-> Only read nSites: 429942 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:17\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[17] from pop0:\t74666\n",
      "\t-> Sites to keep[17] from pop1:\t74666\n",
      "\t-> [readdata] lastread:74666 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:504608\n",
      "\t-> Only read nSites: 504608 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:18\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[18] from pop0:\t75940\n",
      "\t-> Sites to keep[18] from pop1:\t75940\n",
      "\t-> [readdata] lastread:75940 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:580548\n",
      "\t-> Only read nSites: 580548 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:19\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[19] from pop0:\t66915\n",
      "\t-> Sites to keep[19] from pop1:\t66915\n",
      "\t-> [readdata] lastread:66915 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:647463\n",
      "\t-> Only read nSites: 647463 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:2\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[2] from pop0:\t81092\n",
      "\t-> Sites to keep[2] from pop1:\t81092\n",
      "\t-> [readdata] lastread:81092 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:728555\n",
      "\t-> Only read nSites: 728555 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:20\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[20] from pop0:\t80491\n",
      "\t-> Sites to keep[20] from pop1:\t80491\n",
      "\t-> [readdata] lastread:80491 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:809046\n",
      "\t-> Only read nSites: 809046 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:3\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[3] from pop0:\t70503\n",
      "\t-> Sites to keep[3] from pop1:\t70503\n",
      "\t-> [readdata] lastread:70503 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:879549\n",
      "\t-> Only read nSites: 879549 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:4\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[4] from pop0:\t83833\n",
      "\t-> Sites to keep[4] from pop1:\t83833\n",
      "\t-> [readdata] lastread:83833 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:963382\n",
      "\t-> Only read nSites: 963382 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:5\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[5] from pop0:\t84054\n",
      "\t-> Sites to keep[5] from pop1:\t84054\n",
      "\t-> [readdata] lastread:84054 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:1047436\n",
      "\t-> Only read nSites: 1047436 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:6\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[6] from pop0:\t85646\n",
      "\t-> Sites to keep[6] from pop1:\t85646\n",
      "\t-> [readdata] lastread:85646 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:1133082\n",
      "\t-> Only read nSites: 1133082 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:7\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[7] from pop0:\t84573\n",
      "\t-> Sites to keep[7] from pop1:\t84573\n",
      "\t-> [readdata] lastread:84573 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:1217655\n",
      "\t-> Only read nSites: 1217655 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:8\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[8] from pop0:\t82583\n",
      "\t-> Sites to keep[8] from pop1:\t82583\n",
      "\t-> [readdata] lastread:82583 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:1300238\n",
      "\t-> Only read nSites: 1300238 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:9\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "\t-> Sites to keep[9] from pop0:\t88147\n",
      "\t-> Sites to keep[9] from pop1:\t88147\n",
      "\t-> [readdata] lastread:88147 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:1388385\n",
      "\t-> Only read nSites: 1388385 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Will run optimization on nSites: 1388385\n",
      "------------\n",
      "startlik=-1886321.369441\n",
      "lik[2]=-186871.082741 diff=1.699450e+06 alpha:1.000000 sr2:3.676728e-01\n",
      "lik[5]=-132355.076861 diff=5.451601e+04 alpha:1.243059 sr2:1.985397e-03\n",
      "lik[8]=-132172.619482 diff=1.824574e+02 alpha:1.850889 sr2:4.793345e-08\n",
      "lik[11]=-132113.744048 diff=5.887543e+01 alpha:4.000000 sr2:2.056524e-09\n",
      "lik[14]=-132105.840042 diff=7.904006e+00 alpha:2.137857 sr2:9.999016e-10\n",
      "\t-> Breaking EM(sq2) at iter:16, sqrt(sq2):8.422924e-07\n",
      "likelihood: -132105.840042\n",
      "------------\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Only read nSites: 0 will therefore prepare next chromosome (or exit)\n",
      "\n",
      "\t-> NB NB output is no longer log probs of the frequency spectrum!\n",
      "\t-> Output is now simply the expected values! \n",
      "\t-> You can convert to the old format simply with log(norm(x))\n",
      "\t-> Version of fname:smallNA07357.saf.idx is:2\n",
      "\t-> Assuming .saf.gz file: smallNA07357.saf.gz\n",
      "\t-> Assuming .saf.pos.gz: smallNA07357.saf.pos.gz\n",
      "\t-> Version of fname:smallNA07056.saf.idx is:2\n",
      "\t-> Assuming .saf.gz file: smallNA07056.saf.gz\n",
      "\t-> Assuming .saf.pos.gz: smallNA07056.saf.pos.gz\n",
      "\t-> args: tole:0.000001 nthreads:4 maxiter:100 nsites:0 start:(null) chr:(null) start:-1 stop:-1 fstout:(null) oldout:0 seed:1558447057 bootstrap:0 whichFst:0 fold:0 ref:(null) anc:(null)\n",
      "\t-> Multi SFS is 'still' under development. Please report strange behaviour\n",
      "\t-> nSites: 1537126\n",
      "\t-> The choice of -nSites will require atleast: 58.636703 megabyte memory, that is at least: 0.02% of total memory\n",
      "\t-> dim(smallNA07357.saf.idx):3\n",
      "\t-> dim(smallNA07056.saf.idx):3\n",
      "\t-> Dimension of parameter space: 9\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:1\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[1] from pop0:\t83944\n",
      "\t-> Sites to keep[1] from pop1:\t83944\n",
      "\t-> [readdata] lastread:83944 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:83944\n",
      "\t-> Only read nSites: 83944 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:10\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[10] from pop0:\t87299\n",
      "\t-> Sites to keep[10] from pop1:\t87299\n",
      "\t-> [readdata] lastread:87299 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:171243\n",
      "\t-> Only read nSites: 171243 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:11\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[11] from pop0:\t87623\n",
      "\t-> Sites to keep[11] from pop1:\t87623\n",
      "\t-> [readdata] lastread:87623 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:258866\n",
      "\t-> Only read nSites: 258866 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:12\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[12] from pop0:\t89253\n",
      "\t-> Sites to keep[12] from pop1:\t89253\n",
      "\t-> [readdata] lastread:89253 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:348119\n",
      "\t-> Only read nSites: 348119 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:16\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[16] from pop0:\t82796\n",
      "\t-> Sites to keep[16] from pop1:\t82796\n",
      "\t-> [readdata] lastread:82796 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:430915\n",
      "\t-> Only read nSites: 430915 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:17\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[17] from pop0:\t70385\n",
      "\t-> Sites to keep[17] from pop1:\t70385\n",
      "\t-> [readdata] lastread:70385 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:501300\n",
      "\t-> Only read nSites: 501300 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:18\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[18] from pop0:\t73965\n",
      "\t-> Sites to keep[18] from pop1:\t73965\n",
      "\t-> [readdata] lastread:73965 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:575265\n",
      "\t-> Only read nSites: 575265 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:19\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[19] from pop0:\t76054\n",
      "\t-> Sites to keep[19] from pop1:\t76054\n",
      "\t-> [readdata] lastread:76054 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:651319\n",
      "\t-> Only read nSites: 651319 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:2\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[2] from pop0:\t76742\n",
      "\t-> Sites to keep[2] from pop1:\t76742\n",
      "\t-> [readdata] lastread:76742 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:728061\n",
      "\t-> Only read nSites: 728061 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:20\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[20] from pop0:\t77269\n",
      "\t-> Sites to keep[20] from pop1:\t77269\n",
      "\t-> [readdata] lastread:77269 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:805330\n",
      "\t-> Only read nSites: 805330 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:3\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[3] from pop0:\t69873\n",
      "\t-> Sites to keep[3] from pop1:\t69873\n",
      "\t-> [readdata] lastread:69873 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:875203\n",
      "\t-> Only read nSites: 875203 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:4\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[4] from pop0:\t83220\n",
      "\t-> Sites to keep[4] from pop1:\t83220\n",
      "\t-> [readdata] lastread:83220 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:958423\n",
      "\t-> Only read nSites: 958423 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:5\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[5] from pop0:\t84650\n",
      "\t-> Sites to keep[5] from pop1:\t84650\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "\t-> [readdata] lastread:84650 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:1043073\n",
      "\t-> Only read nSites: 1043073 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:6\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[6] from pop0:\t86704\n",
      "\t-> Sites to keep[6] from pop1:\t86704\n",
      "\t-> [readdata] lastread:86704 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:1129777\n",
      "\t-> Only read nSites: 1129777 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:7\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[7] from pop0:\t79966\n",
      "\t-> Sites to keep[7] from pop1:\t79966\n",
      "\t-> [readdata] lastread:79966 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:1209743\n",
      "\t-> Only read nSites: 1209743 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:8\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[8] from pop0:\t78578\n",
      "\t-> Sites to keep[8] from pop1:\t78578\n",
      "\t-> [readdata] lastread:78578 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:1288321\n",
      "\t-> Only read nSites: 1288321 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:9\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[9] from pop0:\t84950\n",
      "\t-> Sites to keep[9] from pop1:\t84950\n",
      "\t-> [readdata] lastread:84950 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:1373271\n",
      "\t-> Only read nSites: 1373271 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Will run optimization on nSites: 1373271\n",
      "------------\n",
      "startlik=-3008435.442488\n",
      "lik[2]=-168636.962605 diff=2.839798e+06 alpha:1.000000 sr2:6.151854e-01\n",
      "lik[5]=-128166.222531 diff=4.047074e+04 alpha:1.239474 sr2:1.659595e-03\n",
      "lik[8]=-127977.418876 diff=1.888037e+02 alpha:1.868274 sr2:4.435244e-08\n",
      "lik[11]=-127952.130261 diff=2.528862e+01 alpha:4.000000 sr2:1.218471e-09\n",
      "lik[14]=-127950.503781 diff=1.626479e+00 alpha:2.300134 sr2:1.551907e-10\n",
      "\t-> Breaking EM(sr2) at iter:15, sqrt(sr2):3.735084e-07\n",
      "likelihood: -127950.503781\n",
      "------------\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Only read nSites: 0 will therefore prepare next chromosome (or exit)\n",
      "\n",
      "\t-> NB NB output is no longer log probs of the frequency spectrum!\n",
      "\t-> Output is now simply the expected values! \n",
      "\t-> You can convert to the old format simply with log(norm(x))\n",
      "\t-> Version of fname:smallNA07357.saf.idx is:2\n",
      "\t-> Assuming .saf.gz file: smallNA07357.saf.gz\n",
      "\t-> Assuming .saf.pos.gz: smallNA07357.saf.pos.gz\n",
      "\t-> Version of fname:smallNA11830.saf.idx is:2\n",
      "\t-> Assuming .saf.gz file: smallNA11830.saf.gz\n",
      "\t-> Assuming .saf.pos.gz: smallNA11830.saf.pos.gz\n",
      "\t-> args: tole:0.000001 nthreads:4 maxiter:100 nsites:0 start:(null) chr:(null) start:-1 stop:-1 fstout:(null) oldout:0 seed:1558447058 bootstrap:0 whichFst:0 fold:0 ref:(null) anc:(null)\n",
      "\t-> Multi SFS is 'still' under development. Please report strange behaviour\n",
      "\t-> nSites: 1584541\n",
      "\t-> The choice of -nSites will require atleast: 60.445442 megabyte memory, that is at least: 0.02% of total memory\n",
      "\t-> dim(smallNA07357.saf.idx):3\n",
      "\t-> dim(smallNA11830.saf.idx):3\n",
      "\t-> Dimension of parameter space: 9\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:1\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[1] from pop0:\t85926\n",
      "\t-> Sites to keep[1] from pop1:\t85926\n",
      "\t-> [readdata] lastread:85926 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:85926\n",
      "\t-> Only read nSites: 85926 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:10\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[10] from pop0:\t88436\n",
      "\t-> Sites to keep[10] from pop1:\t88436\n",
      "\t-> [readdata] lastread:88436 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:174362\n",
      "\t-> Only read nSites: 174362 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:11\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[11] from pop0:\t88674\n",
      "\t-> Sites to keep[11] from pop1:\t88674\n",
      "\t-> [readdata] lastread:88674 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:263036\n",
      "\t-> Only read nSites: 263036 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:12\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[12] from pop0:\t91928\n",
      "\t-> Sites to keep[12] from pop1:\t91928\n",
      "\t-> [readdata] lastread:91928 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:354964\n",
      "\t-> Only read nSites: 354964 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:16\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[16] from pop0:\t84540\n",
      "\t-> Sites to keep[16] from pop1:\t84540\n",
      "\t-> [readdata] lastread:84540 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:439504\n",
      "\t-> Only read nSites: 439504 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:17\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[17] from pop0:\t74555\n",
      "\t-> Sites to keep[17] from pop1:\t74555\n",
      "\t-> [readdata] lastread:74555 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:514059\n",
      "\t-> Only read nSites: 514059 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:18\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[18] from pop0:\t76938\n",
      "\t-> Sites to keep[18] from pop1:\t76938\n",
      "\t-> [readdata] lastread:76938 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:590997\n",
      "\t-> Only read nSites: 590997 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:19\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[19] from pop0:\t74990\n",
      "\t-> Sites to keep[19] from pop1:\t74990\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "\t-> [readdata] lastread:74990 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:665987\n",
      "\t-> Only read nSites: 665987 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:2\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[2] from pop0:\t81004\n",
      "\t-> Sites to keep[2] from pop1:\t81004\n",
      "\t-> [readdata] lastread:81004 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:746991\n",
      "\t-> Only read nSites: 746991 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:20\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[20] from pop0:\t81098\n",
      "\t-> Sites to keep[20] from pop1:\t81098\n",
      "\t-> [readdata] lastread:81098 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:828089\n",
      "\t-> Only read nSites: 828089 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:3\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[3] from pop0:\t71841\n",
      "\t-> Sites to keep[3] from pop1:\t71841\n",
      "\t-> [readdata] lastread:71841 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:899930\n",
      "\t-> Only read nSites: 899930 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:4\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[4] from pop0:\t85086\n",
      "\t-> Sites to keep[4] from pop1:\t85086\n",
      "\t-> [readdata] lastread:85086 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:985016\n",
      "\t-> Only read nSites: 985016 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:5\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[5] from pop0:\t86159\n",
      "\t-> Sites to keep[5] from pop1:\t86159\n",
      "\t-> [readdata] lastread:86159 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:1071175\n",
      "\t-> Only read nSites: 1071175 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:6\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[6] from pop0:\t87609\n",
      "\t-> Sites to keep[6] from pop1:\t87609\n",
      "\t-> [readdata] lastread:87609 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:1158784\n",
      "\t-> Only read nSites: 1158784 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:7\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[7] from pop0:\t85044\n",
      "\t-> Sites to keep[7] from pop1:\t85044\n",
      "\t-> [readdata] lastread:85044 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:1243828\n",
      "\t-> Only read nSites: 1243828 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:8\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[8] from pop0:\t82740\n",
      "\t-> Sites to keep[8] from pop1:\t82740\n",
      "\t-> [readdata] lastread:82740 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:1326568\n",
      "\t-> Only read nSites: 1326568 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:9\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[9] from pop0:\t89202\n",
      "\t-> Sites to keep[9] from pop1:\t89202\n",
      "\t-> [readdata] lastread:89202 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:1415770\n",
      "\t-> Only read nSites: 1415770 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Will run optimization on nSites: 1415770\n",
      "------------\n",
      "startlik=-3459935.798266\n",
      "lik[2]=-251740.852871 diff=3.208195e+06 alpha:1.000000 sr2:3.258789e-01\n",
      "lik[5]=-132605.273308 diff=1.191356e+05 alpha:1.220661 sr2:1.109961e-02\n",
      "lik[8]=-132398.511222 diff=2.067621e+02 alpha:1.670374 sr2:7.059395e-08\n",
      "lik[11]=-132362.785570 diff=3.572565e+01 alpha:4.000000 sr2:1.464344e-09\n",
      "lik[14]=-132360.644364 diff=2.141206e+00 alpha:2.470656 sr2:2.199634e-10\n",
      "\t-> Breaking EM(sr2) at iter:15, sqrt(sr2):6.396233e-07\n",
      "likelihood: -132360.644364\n",
      "------------\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Only read nSites: 0 will therefore prepare next chromosome (or exit)\n",
      "\n",
      "\t-> NB NB output is no longer log probs of the frequency spectrum!\n",
      "\t-> Output is now simply the expected values! \n",
      "\t-> You can convert to the old format simply with log(norm(x))\n",
      "\t-> Version of fname:smallNA11832.saf.idx is:2\n",
      "\t-> Assuming .saf.gz file: smallNA11832.saf.gz\n",
      "\t-> Assuming .saf.pos.gz: smallNA11832.saf.pos.gz\n",
      "\t-> Version of fname:smallNA06994.saf.idx is:2\n",
      "\t-> Assuming .saf.gz file: smallNA06994.saf.gz\n",
      "\t-> Assuming .saf.pos.gz: smallNA06994.saf.pos.gz\n",
      "\t-> args: tole:0.000001 nthreads:4 maxiter:100 nsites:0 start:(null) chr:(null) start:-1 stop:-1 fstout:(null) oldout:0 seed:1558447061 bootstrap:0 whichFst:0 fold:0 ref:(null) anc:(null)\n",
      "\t-> Multi SFS is 'still' under development. Please report strange behaviour\n",
      "\t-> nSites: 1372028\n",
      "\t-> The choice of -nSites will require atleast: 52.338715 megabyte memory, that is at least: 0.01% of total memory\n",
      "\t-> dim(smallNA11832.saf.idx):3\n",
      "\t-> dim(smallNA06994.saf.idx):3\n",
      "\t-> Dimension of parameter space: 9\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:1\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[1] from pop0:\t65604\n",
      "\t-> Sites to keep[1] from pop1:\t65604\n",
      "\t-> [readdata] lastread:65604 posi:14000039\n",
      "\t-> Comparing positions: 1 with 0 has:65604\n",
      "\t-> Only read nSites: 65604 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:10\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[10] from pop0:\t67498\n",
      "\t-> Sites to keep[10] from pop1:\t67498\n",
      "\t-> [readdata] lastread:67498 posi:14000039\n",
      "\t-> Comparing positions: 1 with 0 has:133102\n",
      "\t-> Only read nSites: 133102 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:11\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[11] from pop0:\t67558\n",
      "\t-> Sites to keep[11] from pop1:\t67558\n",
      "\t-> [readdata] lastread:67558 posi:14000039\n",
      "\t-> Comparing positions: 1 with 0 has:200660\n",
      "\t-> Only read nSites: 200660 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:12\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[12] from pop0:\t72027\n",
      "\t-> Sites to keep[12] from pop1:\t72027\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "\t-> [readdata] lastread:72027 posi:14000039\n",
      "\t-> Comparing positions: 1 with 0 has:272687\n",
      "\t-> Only read nSites: 272687 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:16\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[16] from pop0:\t63660\n",
      "\t-> Sites to keep[16] from pop1:\t63660\n",
      "\t-> [readdata] lastread:63660 posi:14000039\n",
      "\t-> Comparing positions: 1 with 0 has:336347\n",
      "\t-> Only read nSites: 336347 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:17\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[17] from pop0:\t54625\n",
      "\t-> Sites to keep[17] from pop1:\t54625\n",
      "\t-> [readdata] lastread:54625 posi:14000039\n",
      "\t-> Comparing positions: 1 with 0 has:390972\n",
      "\t-> Only read nSites: 390972 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:18\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[18] from pop0:\t58722\n",
      "\t-> Sites to keep[18] from pop1:\t58722\n",
      "\t-> [readdata] lastread:58722 posi:14000039\n",
      "\t-> Comparing positions: 1 with 0 has:449694\n",
      "\t-> Only read nSites: 449694 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:19\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[19] from pop0:\t43017\n",
      "\t-> Sites to keep[19] from pop1:\t43017\n",
      "\t-> [readdata] lastread:43017 posi:14000039\n",
      "\t-> Comparing positions: 1 with 0 has:492711\n",
      "\t-> Only read nSites: 492711 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:2\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[2] from pop0:\t60557\n",
      "\t-> Sites to keep[2] from pop1:\t60557\n",
      "\t-> [readdata] lastread:60557 posi:14000039\n",
      "\t-> Comparing positions: 1 with 0 has:553268\n",
      "\t-> Only read nSites: 553268 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:20\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[20] from pop0:\t58749\n",
      "\t-> Sites to keep[20] from pop1:\t58749\n",
      "\t-> [readdata] lastread:58749 posi:14000039\n",
      "\t-> Comparing positions: 1 with 0 has:612017\n",
      "\t-> Only read nSites: 612017 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:3\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[3] from pop0:\t49600\n",
      "\t-> Sites to keep[3] from pop1:\t49600\n",
      "\t-> [readdata] lastread:49600 posi:14000039\n",
      "\t-> Comparing positions: 1 with 0 has:661617\n",
      "\t-> Only read nSites: 661617 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:4\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[4] from pop0:\t67723\n",
      "\t-> Sites to keep[4] from pop1:\t67723\n",
      "\t-> [readdata] lastread:67723 posi:14000039\n",
      "\t-> Comparing positions: 1 with 0 has:729340\n",
      "\t-> Only read nSites: 729340 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:5\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[5] from pop0:\t65560\n",
      "\t-> Sites to keep[5] from pop1:\t65560\n",
      "\t-> [readdata] lastread:65560 posi:14000039\n",
      "\t-> Comparing positions: 1 with 0 has:794900\n",
      "\t-> Only read nSites: 794900 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:6\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[6] from pop0:\t65609\n",
      "\t-> Sites to keep[6] from pop1:\t65609\n",
      "\t-> [readdata] lastread:65609 posi:14000039\n",
      "\t-> Comparing positions: 1 with 0 has:860509\n",
      "\t-> Only read nSites: 860509 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:7\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[7] from pop0:\t64331\n",
      "\t-> Sites to keep[7] from pop1:\t64331\n",
      "\t-> [readdata] lastread:64331 posi:14000039\n",
      "\t-> Comparing positions: 1 with 0 has:924840\n",
      "\t-> Only read nSites: 924840 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:8\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[8] from pop0:\t62626\n",
      "\t-> Sites to keep[8] from pop1:\t62626\n",
      "\t-> [readdata] lastread:62626 posi:14000039\n",
      "\t-> Comparing positions: 1 with 0 has:987466\n",
      "\t-> Only read nSites: 987466 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:9\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[9] from pop0:\t70869\n",
      "\t-> Sites to keep[9] from pop1:\t70869\n",
      "\t-> [readdata] lastread:70869 posi:14000039\n",
      "\t-> Comparing positions: 1 with 0 has:1058335\n",
      "\t-> Only read nSites: 1058335 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Will run optimization on nSites: 1058335\n",
      "------------\n",
      "startlik=-1579256.479162\n",
      "lik[2]=-148502.319822 diff=1.430754e+06 alpha:1.000000 sr2:4.125705e-01\n",
      "lik[5]=-97630.762370 diff=5.087156e+04 alpha:1.385374 sr2:3.541032e-03\n",
      "lik[8]=-97448.683648 diff=1.820787e+02 alpha:1.970237 sr2:2.615860e-07\n",
      "lik[11]=-97437.428149 diff=1.125550e+01 alpha:2.929593 sr2:6.757095e-10\n",
      "lik[14]=-97411.734761 diff=2.569339e+01 alpha:4.000000 sr2:8.577351e-11\n",
      "lik[17]=-97408.520565 diff=3.214195e+00 alpha:6.116832 sr2:1.754892e-10\n",
      "lik[20]=-97408.429193 diff=9.137257e-02 alpha:1.487251 sr2:2.278726e-11\n",
      "\t-> Breaking EM(sr2) at iter:21, sqrt(sr2):8.728496e-07\n",
      "likelihood: -97408.429193\n",
      "------------\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Only read nSites: 0 will therefore prepare next chromosome (or exit)\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "\n",
      "\t-> NB NB output is no longer log probs of the frequency spectrum!\n",
      "\t-> Output is now simply the expected values! \n",
      "\t-> You can convert to the old format simply with log(norm(x))\n",
      "\t-> Version of fname:smallNA11832.saf.idx is:2\n",
      "\t-> Assuming .saf.gz file: smallNA11832.saf.gz\n",
      "\t-> Assuming .saf.pos.gz: smallNA11832.saf.pos.gz\n",
      "\t-> Version of fname:smallNA06985.saf.idx is:2\n",
      "\t-> Assuming .saf.gz file: smallNA06985.saf.gz\n",
      "\t-> Assuming .saf.pos.gz: smallNA06985.saf.pos.gz\n",
      "\t-> args: tole:0.000001 nthreads:4 maxiter:100 nsites:0 start:(null) chr:(null) start:-1 stop:-1 fstout:(null) oldout:0 seed:1558447063 bootstrap:0 whichFst:0 fold:0 ref:(null) anc:(null)\n",
      "\t-> Multi SFS is 'still' under development. Please report strange behaviour\n",
      "\t-> nSites: 1430342\n",
      "\t-> The choice of -nSites will require atleast: 54.563217 megabyte memory, that is at least: 0.01% of total memory\n",
      "\t-> dim(smallNA11832.saf.idx):3\n",
      "\t-> dim(smallNA06985.saf.idx):3\n",
      "\t-> Dimension of parameter space: 9\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:1\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[1] from pop0:\t65592\n",
      "\t-> Sites to keep[1] from pop1:\t65592\n",
      "\t-> [readdata] lastread:65592 posi:14000039\n",
      "\t-> Comparing positions: 1 with 0 has:65592\n",
      "\t-> Only read nSites: 65592 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:10\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[10] from pop0:\t70404\n",
      "\t-> Sites to keep[10] from pop1:\t70404\n",
      "\t-> [readdata] lastread:70404 posi:14000039\n",
      "\t-> Comparing positions: 1 with 0 has:135996\n",
      "\t-> Only read nSites: 135996 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:11\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[11] from pop0:\t68973\n",
      "\t-> Sites to keep[11] from pop1:\t68973\n",
      "\t-> [readdata] lastread:68973 posi:14000039\n",
      "\t-> Comparing positions: 1 with 0 has:204969\n",
      "\t-> Only read nSites: 204969 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:12\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[12] from pop0:\t69394\n",
      "\t-> Sites to keep[12] from pop1:\t69394\n",
      "\t-> [readdata] lastread:69394 posi:14000039\n",
      "\t-> Comparing positions: 1 with 0 has:274363\n",
      "\t-> Only read nSites: 274363 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:16\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[16] from pop0:\t64550\n",
      "\t-> Sites to keep[16] from pop1:\t64550\n",
      "\t-> [readdata] lastread:64550 posi:14000039\n",
      "\t-> Comparing positions: 1 with 0 has:338913\n",
      "\t-> Only read nSites: 338913 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:17\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[17] from pop0:\t53157\n",
      "\t-> Sites to keep[17] from pop1:\t53157\n",
      "\t-> [readdata] lastread:53157 posi:14000039\n",
      "\t-> Comparing positions: 1 with 0 has:392070\n",
      "\t-> Only read nSites: 392070 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:18\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[18] from pop0:\t60705\n",
      "\t-> Sites to keep[18] from pop1:\t60705\n",
      "\t-> [readdata] lastread:60705 posi:14000039\n",
      "\t-> Comparing positions: 1 with 0 has:452775\n",
      "\t-> Only read nSites: 452775 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:19\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[19] from pop0:\t56395\n",
      "\t-> Sites to keep[19] from pop1:\t56395\n",
      "\t-> [readdata] lastread:56395 posi:14000039\n",
      "\t-> Comparing positions: 1 with 0 has:509170\n",
      "\t-> Only read nSites: 509170 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:2\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[2] from pop0:\t52139\n",
      "\t-> Sites to keep[2] from pop1:\t52139\n",
      "\t-> [readdata] lastread:52139 posi:14000039\n",
      "\t-> Comparing positions: 1 with 0 has:561309\n",
      "\t-> Only read nSites: 561309 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:20\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[20] from pop0:\t57128\n",
      "\t-> Sites to keep[20] from pop1:\t57128\n",
      "\t-> [readdata] lastread:57128 posi:14000039\n",
      "\t-> Comparing positions: 1 with 0 has:618437\n",
      "\t-> Only read nSites: 618437 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:3\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[3] from pop0:\t54833\n",
      "\t-> Sites to keep[3] from pop1:\t54833\n",
      "\t-> [readdata] lastread:54833 posi:14000039\n",
      "\t-> Comparing positions: 1 with 0 has:673270\n",
      "\t-> Only read nSites: 673270 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:4\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[4] from pop0:\t65053\n",
      "\t-> Sites to keep[4] from pop1:\t65053\n",
      "\t-> [readdata] lastread:65053 posi:14000039\n",
      "\t-> Comparing positions: 1 with 0 has:738323\n",
      "\t-> Only read nSites: 738323 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:5\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[5] from pop0:\t67686\n",
      "\t-> Sites to keep[5] from pop1:\t67686\n",
      "\t-> [readdata] lastread:67686 posi:14000039\n",
      "\t-> Comparing positions: 1 with 0 has:806009\n",
      "\t-> Only read nSites: 806009 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:6\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[6] from pop0:\t69313\n",
      "\t-> Sites to keep[6] from pop1:\t69313\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "\t-> [readdata] lastread:69313 posi:14000039\n",
      "\t-> Comparing positions: 1 with 0 has:875322\n",
      "\t-> Only read nSites: 875322 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:7\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[7] from pop0:\t56535\n",
      "\t-> Sites to keep[7] from pop1:\t56535\n",
      "\t-> [readdata] lastread:56535 posi:14000039\n",
      "\t-> Comparing positions: 1 with 0 has:931857\n",
      "\t-> Only read nSites: 931857 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:8\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[8] from pop0:\t53141\n",
      "\t-> Sites to keep[8] from pop1:\t53141\n",
      "\t-> [readdata] lastread:53141 posi:14000039\n",
      "\t-> Comparing positions: 1 with 0 has:984998\n",
      "\t-> Only read nSites: 984998 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:9\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[9] from pop0:\t66698\n",
      "\t-> Sites to keep[9] from pop1:\t66698\n",
      "\t-> [readdata] lastread:66698 posi:14000039\n",
      "\t-> Comparing positions: 1 with 0 has:1051696\n",
      "\t-> Only read nSites: 1051696 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Will run optimization on nSites: 1051696\n",
      "------------\n",
      "startlik=-959754.499711\n",
      "lik[2]=-147354.465796 diff=8.124000e+05 alpha:1.000000 sr2:2.335711e-01\n",
      "lik[5]=-91046.938826 diff=5.630753e+04 alpha:1.444515 sr2:3.771919e-03\n",
      "lik[8]=-90876.406838 diff=1.705320e+02 alpha:2.292567 sr2:1.067082e-07\n",
      "lik[11]=-90838.475224 diff=3.793161e+01 alpha:4.000000 sr2:1.597088e-09\n",
      "lik[14]=-90834.770263 diff=3.704961e+00 alpha:2.039586 sr2:4.375318e-10\n",
      "lik[17]=-90830.834375 diff=3.935888e+00 alpha:3.523575 sr2:7.165565e-12\n",
      "lik[20]=-90825.413355 diff=5.421020e+00 alpha:7.841349 sr2:2.328195e-11\n",
      "lik[23]=-90824.931740 diff=4.816151e-01 alpha:1.917205 sr2:5.284856e-11\n",
      "\t-> Breaking EM(sr2) at iter:24, sqrt(sr2):9.744032e-07\n",
      "likelihood: -90824.931740\n",
      "------------\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Only read nSites: 0 will therefore prepare next chromosome (or exit)\n",
      "\n",
      "\t-> NB NB output is no longer log probs of the frequency spectrum!\n",
      "\t-> Output is now simply the expected values! \n",
      "\t-> You can convert to the old format simply with log(norm(x))\n",
      "\t-> Version of fname:smallNA11832.saf.idx is:2\n",
      "\t-> Assuming .saf.gz file: smallNA11832.saf.gz\n",
      "\t-> Assuming .saf.pos.gz: smallNA11832.saf.pos.gz\n",
      "\t-> Version of fname:smallNA11831.saf.idx is:2\n",
      "\t-> Assuming .saf.gz file: smallNA11831.saf.gz\n",
      "\t-> Assuming .saf.pos.gz: smallNA11831.saf.pos.gz\n",
      "\t-> args: tole:0.000001 nthreads:4 maxiter:100 nsites:0 start:(null) chr:(null) start:-1 stop:-1 fstout:(null) oldout:0 seed:1558447065 bootstrap:0 whichFst:0 fold:0 ref:(null) anc:(null)\n",
      "\t-> Multi SFS is 'still' under development. Please report strange behaviour\n",
      "\t-> nSites: 1556469\n",
      "\t-> The choice of -nSites will require atleast: 59.374580 megabyte memory, that is at least: 0.02% of total memory\n",
      "\t-> dim(smallNA11832.saf.idx):3\n",
      "\t-> dim(smallNA11831.saf.idx):3\n",
      "\t-> Dimension of parameter space: 9\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:1\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[1] from pop0:\t70531\n",
      "\t-> Sites to keep[1] from pop1:\t70531\n",
      "\t-> [readdata] lastread:70531 posi:14000039\n",
      "\t-> Comparing positions: 1 with 0 has:70531\n",
      "\t-> Only read nSites: 70531 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:10\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[10] from pop0:\t73266\n",
      "\t-> Sites to keep[10] from pop1:\t73266\n",
      "\t-> [readdata] lastread:73266 posi:14000039\n",
      "\t-> Comparing positions: 1 with 0 has:143797\n",
      "\t-> Only read nSites: 143797 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:11\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[11] from pop0:\t72998\n",
      "\t-> Sites to keep[11] from pop1:\t72998\n",
      "\t-> [readdata] lastread:72998 posi:14000039\n",
      "\t-> Comparing positions: 1 with 0 has:216795\n",
      "\t-> Only read nSites: 216795 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:12\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[12] from pop0:\t76026\n",
      "\t-> Sites to keep[12] from pop1:\t76026\n",
      "\t-> [readdata] lastread:76026 posi:14000039\n",
      "\t-> Comparing positions: 1 with 0 has:292821\n",
      "\t-> Only read nSites: 292821 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:16\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[16] from pop0:\t70953\n",
      "\t-> Sites to keep[16] from pop1:\t70953\n",
      "\t-> [readdata] lastread:70953 posi:14000039\n",
      "\t-> Comparing positions: 1 with 0 has:363774\n",
      "\t-> Only read nSites: 363774 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:17\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[17] from pop0:\t60429\n",
      "\t-> Sites to keep[17] from pop1:\t60429\n",
      "\t-> [readdata] lastread:60429 posi:14000039\n",
      "\t-> Comparing positions: 1 with 0 has:424203\n",
      "\t-> Only read nSites: 424203 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:18\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[18] from pop0:\t65658\n",
      "\t-> Sites to keep[18] from pop1:\t65658\n",
      "\t-> [readdata] lastread:65658 posi:14000039\n",
      "\t-> Comparing positions: 1 with 0 has:489861\n",
      "\t-> Only read nSites: 489861 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:19\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[19] from pop0:\t56521\n",
      "\t-> Sites to keep[19] from pop1:\t56521\n",
      "\t-> [readdata] lastread:56521 posi:14000039\n",
      "\t-> Comparing positions: 1 with 0 has:546382\n",
      "\t-> Only read nSites: 546382 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:2\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[2] from pop0:\t64153\n",
      "\t-> Sites to keep[2] from pop1:\t64153\n",
      "\t-> [readdata] lastread:64153 posi:14000039\n",
      "\t-> Comparing positions: 1 with 0 has:610535\n",
      "\t-> Only read nSites: 610535 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:20\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[20] from pop0:\t65712\n",
      "\t-> Sites to keep[20] from pop1:\t65712\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "\t-> [readdata] lastread:65712 posi:14000039\n",
      "\t-> Comparing positions: 1 with 0 has:676247\n",
      "\t-> Only read nSites: 676247 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:3\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[3] from pop0:\t59336\n",
      "\t-> Sites to keep[3] from pop1:\t59336\n",
      "\t-> [readdata] lastread:59336 posi:14000039\n",
      "\t-> Comparing positions: 1 with 0 has:735583\n",
      "\t-> Only read nSites: 735583 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:4\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[4] from pop0:\t70487\n",
      "\t-> Sites to keep[4] from pop1:\t70487\n",
      "\t-> [readdata] lastread:70487 posi:14000039\n",
      "\t-> Comparing positions: 1 with 0 has:806070\n",
      "\t-> Only read nSites: 806070 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:5\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[5] from pop0:\t71634\n",
      "\t-> Sites to keep[5] from pop1:\t71634\n",
      "\t-> [readdata] lastread:71634 posi:14000039\n",
      "\t-> Comparing positions: 1 with 0 has:877704\n",
      "\t-> Only read nSites: 877704 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:6\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[6] from pop0:\t72519\n",
      "\t-> Sites to keep[6] from pop1:\t72519\n",
      "\t-> [readdata] lastread:72519 posi:14000039\n",
      "\t-> Comparing positions: 1 with 0 has:950223\n",
      "\t-> Only read nSites: 950223 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:7\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[7] from pop0:\t67913\n",
      "\t-> Sites to keep[7] from pop1:\t67913\n",
      "\t-> [readdata] lastread:67913 posi:14000039\n",
      "\t-> Comparing positions: 1 with 0 has:1018136\n",
      "\t-> Only read nSites: 1018136 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:8\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[8] from pop0:\t67647\n",
      "\t-> Sites to keep[8] from pop1:\t67647\n",
      "\t-> [readdata] lastread:67647 posi:14000039\n",
      "\t-> Comparing positions: 1 with 0 has:1085783\n",
      "\t-> Only read nSites: 1085783 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:9\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[9] from pop0:\t74736\n",
      "\t-> Sites to keep[9] from pop1:\t74736\n",
      "\t-> [readdata] lastread:74736 posi:14000039\n",
      "\t-> Comparing positions: 1 with 0 has:1160519\n",
      "\t-> Only read nSites: 1160519 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Will run optimization on nSites: 1160519\n",
      "------------\n",
      "startlik=-2422930.072517\n",
      "lik[2]=-176387.612733 diff=2.246542e+06 alpha:1.000000 sr2:4.628494e-01\n",
      "lik[5]=-106461.162235 diff=6.992645e+04 alpha:1.375322 sr2:5.694370e-03\n",
      "lik[8]=-106223.559224 diff=2.376030e+02 alpha:1.817451 sr2:3.427114e-07\n",
      "lik[11]=-106200.803639 diff=2.275559e+01 alpha:2.765950 sr2:9.153067e-10\n",
      "lik[14]=-106166.487820 diff=3.431582e+01 alpha:4.000000 sr2:2.296494e-10\n",
      "lik[17]=-106160.257759 diff=6.230061e+00 alpha:7.594570 sr2:3.148019e-10\n",
      "lik[20]=-106159.478772 diff=7.789871e-01 alpha:1.666032 sr2:6.643910e-11\n",
      "lik[23]=-106159.371722 diff=1.070497e-01 alpha:5.980628 sr2:5.628789e-12\n",
      "\t-> Breaking EM(sr2) at iter:24, sqrt(sr2):3.599332e-07\n",
      "likelihood: -106159.371722\n",
      "------------\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Only read nSites: 0 will therefore prepare next chromosome (or exit)\n",
      "\n",
      "\t-> NB NB output is no longer log probs of the frequency spectrum!\n",
      "\t-> Output is now simply the expected values! \n",
      "\t-> You can convert to the old format simply with log(norm(x))\n",
      "\t-> Version of fname:smallNA11832.saf.idx is:2\n",
      "\t-> Assuming .saf.gz file: smallNA11832.saf.gz\n",
      "\t-> Assuming .saf.pos.gz: smallNA11832.saf.pos.gz\n",
      "\t-> Version of fname:smallNA11829.saf.idx is:2\n",
      "\t-> Assuming .saf.gz file: smallNA11829.saf.gz\n",
      "\t-> Assuming .saf.pos.gz: smallNA11829.saf.pos.gz\n",
      "\t-> args: tole:0.000001 nthreads:4 maxiter:100 nsites:0 start:(null) chr:(null) start:-1 stop:-1 fstout:(null) oldout:0 seed:1558447068 bootstrap:0 whichFst:0 fold:0 ref:(null) anc:(null)\n",
      "\t-> Multi SFS is 'still' under development. Please report strange behaviour\n",
      "\t-> nSites: 1542786\n",
      "\t-> The choice of -nSites will require atleast: 58.852615 megabyte memory, that is at least: 0.02% of total memory\n",
      "\t-> dim(smallNA11832.saf.idx):3\n",
      "\t-> dim(smallNA11829.saf.idx):3\n",
      "\t-> Dimension of parameter space: 9\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:1\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[1] from pop0:\t70210\n",
      "\t-> Sites to keep[1] from pop1:\t70210\n",
      "\t-> [readdata] lastread:70210 posi:14000039\n",
      "\t-> Comparing positions: 1 with 0 has:70210\n",
      "\t-> Only read nSites: 70210 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:10\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[10] from pop0:\t72256\n",
      "\t-> Sites to keep[10] from pop1:\t72256\n",
      "\t-> [readdata] lastread:72256 posi:14000039\n",
      "\t-> Comparing positions: 1 with 0 has:142466\n",
      "\t-> Only read nSites: 142466 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:11\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[11] from pop0:\t73111\n",
      "\t-> Sites to keep[11] from pop1:\t73111\n",
      "\t-> [readdata] lastread:73111 posi:14000039\n",
      "\t-> Comparing positions: 1 with 0 has:215577\n",
      "\t-> Only read nSites: 215577 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:12\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[12] from pop0:\t75128\n",
      "\t-> Sites to keep[12] from pop1:\t75128\n",
      "\t-> [readdata] lastread:75128 posi:14000039\n",
      "\t-> Comparing positions: 1 with 0 has:290705\n",
      "\t-> Only read nSites: 290705 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:16\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[16] from pop0:\t69765\n",
      "\t-> Sites to keep[16] from pop1:\t69765\n",
      "\t-> [readdata] lastread:69765 posi:14000039\n",
      "\t-> Comparing positions: 1 with 0 has:360470\n",
      "\t-> Only read nSites: 360470 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:17\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "\t-> Sites to keep[17] from pop0:\t61023\n",
      "\t-> Sites to keep[17] from pop1:\t61023\n",
      "\t-> [readdata] lastread:61023 posi:14000039\n",
      "\t-> Comparing positions: 1 with 0 has:421493\n",
      "\t-> Only read nSites: 421493 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:18\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[18] from pop0:\t65364\n",
      "\t-> Sites to keep[18] from pop1:\t65364\n",
      "\t-> [readdata] lastread:65364 posi:14000039\n",
      "\t-> Comparing positions: 1 with 0 has:486857\n",
      "\t-> Only read nSites: 486857 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:19\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[19] from pop0:\t54353\n",
      "\t-> Sites to keep[19] from pop1:\t54353\n",
      "\t-> [readdata] lastread:54353 posi:14000039\n",
      "\t-> Comparing positions: 1 with 0 has:541210\n",
      "\t-> Only read nSites: 541210 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:2\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[2] from pop0:\t64526\n",
      "\t-> Sites to keep[2] from pop1:\t64526\n",
      "\t-> [readdata] lastread:64526 posi:14000039\n",
      "\t-> Comparing positions: 1 with 0 has:605736\n",
      "\t-> Only read nSites: 605736 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:20\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[20] from pop0:\t64861\n",
      "\t-> Sites to keep[20] from pop1:\t64861\n",
      "\t-> [readdata] lastread:64861 posi:14000039\n",
      "\t-> Comparing positions: 1 with 0 has:670597\n",
      "\t-> Only read nSites: 670597 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:3\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[3] from pop0:\t59228\n",
      "\t-> Sites to keep[3] from pop1:\t59228\n",
      "\t-> [readdata] lastread:59228 posi:14000039\n",
      "\t-> Comparing positions: 1 with 0 has:729825\n",
      "\t-> Only read nSites: 729825 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:4\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[4] from pop0:\t70099\n",
      "\t-> Sites to keep[4] from pop1:\t70099\n",
      "\t-> [readdata] lastread:70099 posi:14000039\n",
      "\t-> Comparing positions: 1 with 0 has:799924\n",
      "\t-> Only read nSites: 799924 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:5\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[5] from pop0:\t71070\n",
      "\t-> Sites to keep[5] from pop1:\t71070\n",
      "\t-> [readdata] lastread:71070 posi:14000039\n",
      "\t-> Comparing positions: 1 with 0 has:870994\n",
      "\t-> Only read nSites: 870994 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:6\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[6] from pop0:\t71895\n",
      "\t-> Sites to keep[6] from pop1:\t71895\n",
      "\t-> [readdata] lastread:71895 posi:14000039\n",
      "\t-> Comparing positions: 1 with 0 has:942889\n",
      "\t-> Only read nSites: 942889 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:7\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[7] from pop0:\t67871\n",
      "\t-> Sites to keep[7] from pop1:\t67871\n",
      "\t-> [readdata] lastread:67871 posi:14000039\n",
      "\t-> Comparing positions: 1 with 0 has:1010760\n",
      "\t-> Only read nSites: 1010760 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:8\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[8] from pop0:\t67025\n",
      "\t-> Sites to keep[8] from pop1:\t67025\n",
      "\t-> [readdata] lastread:67025 posi:14000039\n",
      "\t-> Comparing positions: 1 with 0 has:1077785\n",
      "\t-> Only read nSites: 1077785 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:9\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[9] from pop0:\t74243\n",
      "\t-> Sites to keep[9] from pop1:\t74243\n",
      "\t-> [readdata] lastread:74243 posi:14000039\n",
      "\t-> Comparing positions: 1 with 0 has:1152028\n",
      "\t-> Only read nSites: 1152028 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Will run optimization on nSites: 1152028\n",
      "------------\n",
      "startlik=-1555050.379221\n",
      "lik[2]=-164177.859285 diff=1.390873e+06 alpha:1.000000 sr2:3.677789e-01\n",
      "lik[5]=-107592.441171 diff=5.658542e+04 alpha:1.448923 sr2:4.182989e-03\n",
      "lik[8]=-107444.039592 diff=1.484016e+02 alpha:1.891677 sr2:2.049113e-07\n",
      "lik[11]=-107407.162397 diff=3.687719e+01 alpha:3.150597 sr2:6.781163e-10\n",
      "lik[14]=-107382.546291 diff=2.461611e+01 alpha:4.000000 sr2:5.091571e-10\n",
      "lik[17]=-107382.254439 diff=2.918523e-01 alpha:2.172321 sr2:7.281920e-11\n",
      "\t-> Breaking EM(sq2) at iter:19, sqrt(sq2):8.366895e-07\n",
      "likelihood: -107382.254439\n",
      "------------\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Only read nSites: 0 will therefore prepare next chromosome (or exit)\n",
      "\n",
      "\t-> NB NB output is no longer log probs of the frequency spectrum!\n",
      "\t-> Output is now simply the expected values! \n",
      "\t-> You can convert to the old format simply with log(norm(x))\n",
      "\t-> Version of fname:smallNA11832.saf.idx is:2\n",
      "\t-> Assuming .saf.gz file: smallNA11832.saf.gz\n",
      "\t-> Assuming .saf.pos.gz: smallNA11832.saf.pos.gz\n",
      "\t-> Version of fname:smallNA07056.saf.idx is:2\n",
      "\t-> Assuming .saf.gz file: smallNA07056.saf.gz\n",
      "\t-> Assuming .saf.pos.gz: smallNA07056.saf.pos.gz\n",
      "\t-> args: tole:0.000001 nthreads:4 maxiter:100 nsites:0 start:(null) chr:(null) start:-1 stop:-1 fstout:(null) oldout:0 seed:1558447070 bootstrap:0 whichFst:0 fold:0 ref:(null) anc:(null)\n",
      "\t-> Multi SFS is 'still' under development. Please report strange behaviour\n",
      "\t-> nSites: 1537126\n",
      "\t-> The choice of -nSites will require atleast: 58.636703 megabyte memory, that is at least: 0.02% of total memory\n",
      "\t-> dim(smallNA11832.saf.idx):3\n",
      "\t-> dim(smallNA07056.saf.idx):3\n",
      "\t-> Dimension of parameter space: 9\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:1\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[1] from pop0:\t69587\n",
      "\t-> Sites to keep[1] from pop1:\t69587\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "\t-> [readdata] lastread:69587 posi:14000039\n",
      "\t-> Comparing positions: 1 with 0 has:69587\n",
      "\t-> Only read nSites: 69587 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:10\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[10] from pop0:\t73686\n",
      "\t-> Sites to keep[10] from pop1:\t73686\n",
      "\t-> [readdata] lastread:73686 posi:14000039\n",
      "\t-> Comparing positions: 1 with 0 has:143273\n",
      "\t-> Only read nSites: 143273 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:11\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[11] from pop0:\t73237\n",
      "\t-> Sites to keep[11] from pop1:\t73237\n",
      "\t-> [readdata] lastread:73237 posi:14000039\n",
      "\t-> Comparing positions: 1 with 0 has:216510\n",
      "\t-> Only read nSites: 216510 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:12\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[12] from pop0:\t74250\n",
      "\t-> Sites to keep[12] from pop1:\t74250\n",
      "\t-> [readdata] lastread:74250 posi:14000039\n",
      "\t-> Comparing positions: 1 with 0 has:290760\n",
      "\t-> Only read nSites: 290760 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:16\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[16] from pop0:\t70161\n",
      "\t-> Sites to keep[16] from pop1:\t70161\n",
      "\t-> [readdata] lastread:70161 posi:14000039\n",
      "\t-> Comparing positions: 1 with 0 has:360921\n",
      "\t-> Only read nSites: 360921 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:17\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[17] from pop0:\t57350\n",
      "\t-> Sites to keep[17] from pop1:\t57350\n",
      "\t-> [readdata] lastread:57350 posi:14000039\n",
      "\t-> Comparing positions: 1 with 0 has:418271\n",
      "\t-> Only read nSites: 418271 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:18\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[18] from pop0:\t64237\n",
      "\t-> Sites to keep[18] from pop1:\t64237\n",
      "\t-> [readdata] lastread:64237 posi:14000039\n",
      "\t-> Comparing positions: 1 with 0 has:482508\n",
      "\t-> Only read nSites: 482508 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:19\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[19] from pop0:\t60424\n",
      "\t-> Sites to keep[19] from pop1:\t60424\n",
      "\t-> [readdata] lastread:60424 posi:14000039\n",
      "\t-> Comparing positions: 1 with 0 has:542932\n",
      "\t-> Only read nSites: 542932 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:2\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[2] from pop0:\t61272\n",
      "\t-> Sites to keep[2] from pop1:\t61272\n",
      "\t-> [readdata] lastread:61272 posi:14000039\n",
      "\t-> Comparing positions: 1 with 0 has:604204\n",
      "\t-> Only read nSites: 604204 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:20\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[20] from pop0:\t62410\n",
      "\t-> Sites to keep[20] from pop1:\t62410\n",
      "\t-> [readdata] lastread:62410 posi:14000039\n",
      "\t-> Comparing positions: 1 with 0 has:666614\n",
      "\t-> Only read nSites: 666614 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:3\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[3] from pop0:\t59022\n",
      "\t-> Sites to keep[3] from pop1:\t59022\n",
      "\t-> [readdata] lastread:59022 posi:14000039\n",
      "\t-> Comparing positions: 1 with 0 has:725636\n",
      "\t-> Only read nSites: 725636 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:4\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[4] from pop0:\t69479\n",
      "\t-> Sites to keep[4] from pop1:\t69479\n",
      "\t-> [readdata] lastread:69479 posi:14000039\n",
      "\t-> Comparing positions: 1 with 0 has:795115\n",
      "\t-> Only read nSites: 795115 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:5\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[5] from pop0:\t71656\n",
      "\t-> Sites to keep[5] from pop1:\t71656\n",
      "\t-> [readdata] lastread:71656 posi:14000039\n",
      "\t-> Comparing positions: 1 with 0 has:866771\n",
      "\t-> Only read nSites: 866771 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:6\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[6] from pop0:\t72825\n",
      "\t-> Sites to keep[6] from pop1:\t72825\n",
      "\t-> [readdata] lastread:72825 posi:14000039\n",
      "\t-> Comparing positions: 1 with 0 has:939596\n",
      "\t-> Only read nSites: 939596 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:7\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[7] from pop0:\t64297\n",
      "\t-> Sites to keep[7] from pop1:\t64297\n",
      "\t-> [readdata] lastread:64297 posi:14000039\n",
      "\t-> Comparing positions: 1 with 0 has:1003893\n",
      "\t-> Only read nSites: 1003893 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:8\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[8] from pop0:\t64074\n",
      "\t-> Sites to keep[8] from pop1:\t64074\n",
      "\t-> [readdata] lastread:64074 posi:14000039\n",
      "\t-> Comparing positions: 1 with 0 has:1067967\n",
      "\t-> Only read nSites: 1067967 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:9\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[9] from pop0:\t71999\n",
      "\t-> Sites to keep[9] from pop1:\t71999\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "\t-> [readdata] lastread:71999 posi:14000039\n",
      "\t-> Comparing positions: 1 with 0 has:1139966\n",
      "\t-> Only read nSites: 1139966 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Will run optimization on nSites: 1139966\n",
      "------------\n",
      "startlik=-1646319.755442\n",
      "lik[2]=-163793.345212 diff=1.482526e+06 alpha:1.000000 sr2:4.088392e-01\n",
      "lik[5]=-103789.272924 diff=6.000407e+04 alpha:1.493986 sr2:4.713342e-03\n",
      "lik[8]=-103687.558845 diff=1.017141e+02 alpha:2.030312 sr2:9.474722e-08\n",
      "lik[11]=-103658.400356 diff=2.915849e+01 alpha:3.326972 sr2:3.950915e-10\n",
      "lik[14]=-103639.611159 diff=1.878920e+01 alpha:4.000000 sr2:3.920558e-10\n",
      "lik[17]=-103639.379071 diff=2.320870e-01 alpha:2.189699 sr2:4.482582e-11\n",
      "\t-> Breaking EM(sq2) at iter:19, sqrt(sq2):7.806008e-07\n",
      "likelihood: -103639.379071\n",
      "------------\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Only read nSites: 0 will therefore prepare next chromosome (or exit)\n",
      "\n",
      "\t-> NB NB output is no longer log probs of the frequency spectrum!\n",
      "\t-> Output is now simply the expected values! \n",
      "\t-> You can convert to the old format simply with log(norm(x))\n",
      "\t-> Version of fname:smallNA11832.saf.idx is:2\n",
      "\t-> Assuming .saf.gz file: smallNA11832.saf.gz\n",
      "\t-> Assuming .saf.pos.gz: smallNA11832.saf.pos.gz\n",
      "\t-> Version of fname:smallNA11830.saf.idx is:2\n",
      "\t-> Assuming .saf.gz file: smallNA11830.saf.gz\n",
      "\t-> Assuming .saf.pos.gz: smallNA11830.saf.pos.gz\n",
      "\t-> args: tole:0.000001 nthreads:4 maxiter:100 nsites:0 start:(null) chr:(null) start:-1 stop:-1 fstout:(null) oldout:0 seed:1558447072 bootstrap:0 whichFst:0 fold:0 ref:(null) anc:(null)\n",
      "\t-> Multi SFS is 'still' under development. Please report strange behaviour\n",
      "\t-> nSites: 1584541\n",
      "\t-> The choice of -nSites will require atleast: 60.445442 megabyte memory, that is at least: 0.02% of total memory\n",
      "\t-> dim(smallNA11832.saf.idx):3\n",
      "\t-> dim(smallNA11830.saf.idx):3\n",
      "\t-> Dimension of parameter space: 9\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:1\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[1] from pop0:\t71294\n",
      "\t-> Sites to keep[1] from pop1:\t71294\n",
      "\t-> [readdata] lastread:71294 posi:14000039\n",
      "\t-> Comparing positions: 1 with 0 has:71294\n",
      "\t-> Only read nSites: 71294 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:10\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[10] from pop0:\t74673\n",
      "\t-> Sites to keep[10] from pop1:\t74673\n",
      "\t-> [readdata] lastread:74673 posi:14000039\n",
      "\t-> Comparing positions: 1 with 0 has:145967\n",
      "\t-> Only read nSites: 145967 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:11\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[11] from pop0:\t74067\n",
      "\t-> Sites to keep[11] from pop1:\t74067\n",
      "\t-> [readdata] lastread:74067 posi:14000039\n",
      "\t-> Comparing positions: 1 with 0 has:220034\n",
      "\t-> Only read nSites: 220034 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:12\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[12] from pop0:\t76536\n",
      "\t-> Sites to keep[12] from pop1:\t76536\n",
      "\t-> [readdata] lastread:76536 posi:14000039\n",
      "\t-> Comparing positions: 1 with 0 has:296570\n",
      "\t-> Only read nSites: 296570 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:16\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[16] from pop0:\t71622\n",
      "\t-> Sites to keep[16] from pop1:\t71622\n",
      "\t-> [readdata] lastread:71622 posi:14000039\n",
      "\t-> Comparing positions: 1 with 0 has:368192\n",
      "\t-> Only read nSites: 368192 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:17\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[17] from pop0:\t60871\n",
      "\t-> Sites to keep[17] from pop1:\t60871\n",
      "\t-> [readdata] lastread:60871 posi:14000039\n",
      "\t-> Comparing positions: 1 with 0 has:429063\n",
      "\t-> Only read nSites: 429063 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:18\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[18] from pop0:\t66924\n",
      "\t-> Sites to keep[18] from pop1:\t66924\n",
      "\t-> [readdata] lastread:66924 posi:14000039\n",
      "\t-> Comparing positions: 1 with 0 has:495987\n",
      "\t-> Only read nSites: 495987 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:19\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[19] from pop0:\t60156\n",
      "\t-> Sites to keep[19] from pop1:\t60156\n",
      "\t-> [readdata] lastread:60156 posi:14000039\n",
      "\t-> Comparing positions: 1 with 0 has:556143\n",
      "\t-> Only read nSites: 556143 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:2\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[2] from pop0:\t64452\n",
      "\t-> Sites to keep[2] from pop1:\t64452\n",
      "\t-> [readdata] lastread:64452 posi:14000039\n",
      "\t-> Comparing positions: 1 with 0 has:620595\n",
      "\t-> Only read nSites: 620595 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:20\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[20] from pop0:\t66083\n",
      "\t-> Sites to keep[20] from pop1:\t66083\n",
      "\t-> [readdata] lastread:66083 posi:14000039\n",
      "\t-> Comparing positions: 1 with 0 has:686678\n",
      "\t-> Only read nSites: 686678 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:3\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[3] from pop0:\t60211\n",
      "\t-> Sites to keep[3] from pop1:\t60211\n",
      "\t-> [readdata] lastread:60211 posi:14000039\n",
      "\t-> Comparing positions: 1 with 0 has:746889\n",
      "\t-> Only read nSites: 746889 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:4\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[4] from pop0:\t71115\n",
      "\t-> Sites to keep[4] from pop1:\t71115\n",
      "\t-> [readdata] lastread:71115 posi:14000039\n",
      "\t-> Comparing positions: 1 with 0 has:818004\n",
      "\t-> Only read nSites: 818004 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:5\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[5] from pop0:\t72756\n",
      "\t-> Sites to keep[5] from pop1:\t72756\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "\t-> [readdata] lastread:72756 posi:14000039\n",
      "\t-> Comparing positions: 1 with 0 has:890760\n",
      "\t-> Only read nSites: 890760 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:6\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[6] from pop0:\t73714\n",
      "\t-> Sites to keep[6] from pop1:\t73714\n",
      "\t-> [readdata] lastread:73714 posi:14000039\n",
      "\t-> Comparing positions: 1 with 0 has:964474\n",
      "\t-> Only read nSites: 964474 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:7\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[7] from pop0:\t68100\n",
      "\t-> Sites to keep[7] from pop1:\t68100\n",
      "\t-> [readdata] lastread:68100 posi:14000039\n",
      "\t-> Comparing positions: 1 with 0 has:1032574\n",
      "\t-> Only read nSites: 1032574 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:8\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[8] from pop0:\t67345\n",
      "\t-> Sites to keep[8] from pop1:\t67345\n",
      "\t-> [readdata] lastread:67345 posi:14000039\n",
      "\t-> Comparing positions: 1 with 0 has:1099919\n",
      "\t-> Only read nSites: 1099919 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:9\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[9] from pop0:\t75341\n",
      "\t-> Sites to keep[9] from pop1:\t75341\n",
      "\t-> [readdata] lastread:75341 posi:14000039\n",
      "\t-> Comparing positions: 1 with 0 has:1175260\n",
      "\t-> Only read nSites: 1175260 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Will run optimization on nSites: 1175260\n",
      "------------\n",
      "startlik=-2539802.144750\n",
      "lik[2]=-194786.810758 diff=2.345015e+06 alpha:1.000000 sr2:4.234736e-01\n",
      "lik[5]=-107563.040680 diff=8.722377e+04 alpha:1.478024 sr2:8.848660e-03\n",
      "lik[8]=-107358.487277 diff=2.045534e+02 alpha:1.584769 sr2:1.521311e-07\n",
      "lik[11]=-107331.279103 diff=2.720817e+01 alpha:3.283878 sr2:1.005785e-09\n",
      "lik[14]=-107320.219953 diff=1.105915e+01 alpha:4.000000 sr2:2.364638e-10\n",
      "lik[17]=-107320.154232 diff=6.572071e-02 alpha:2.080067 sr2:1.659644e-11\n",
      "\t-> Breaking EM(sr2) at iter:18, sqrt(sr2):3.623595e-07\n",
      "likelihood: -107320.154232\n",
      "------------\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Only read nSites: 0 will therefore prepare next chromosome (or exit)\n",
      "\n",
      "\t-> NB NB output is no longer log probs of the frequency spectrum!\n",
      "\t-> Output is now simply the expected values! \n",
      "\t-> You can convert to the old format simply with log(norm(x))\n",
      "\t-> Version of fname:smallNA06994.saf.idx is:2\n",
      "\t-> Assuming .saf.gz file: smallNA06994.saf.gz\n",
      "\t-> Assuming .saf.pos.gz: smallNA06994.saf.pos.gz\n",
      "\t-> Version of fname:smallNA06985.saf.idx is:2\n",
      "\t-> Assuming .saf.gz file: smallNA06985.saf.gz\n",
      "\t-> Assuming .saf.pos.gz: smallNA06985.saf.pos.gz\n",
      "\t-> args: tole:0.000001 nthreads:4 maxiter:100 nsites:0 start:(null) chr:(null) start:-1 stop:-1 fstout:(null) oldout:0 seed:1558447074 bootstrap:0 whichFst:0 fold:0 ref:(null) anc:(null)\n",
      "\t-> Multi SFS is 'still' under development. Please report strange behaviour\n",
      "\t-> nSites: 1430342\n",
      "\t-> The choice of -nSites will require atleast: 54.563217 megabyte memory, that is at least: 0.01% of total memory\n",
      "\t-> dim(smallNA06994.saf.idx):3\n",
      "\t-> dim(smallNA06985.saf.idx):3\n",
      "\t-> Dimension of parameter space: 9\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:1\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[1] from pop0:\t74424\n",
      "\t-> Sites to keep[1] from pop1:\t74424\n",
      "\t-> [readdata] lastread:74424 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:74424\n",
      "\t-> Only read nSites: 74424 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:10\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[10] from pop0:\t76419\n",
      "\t-> Sites to keep[10] from pop1:\t76419\n",
      "\t-> [readdata] lastread:76419 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:150843\n",
      "\t-> Only read nSites: 150843 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:11\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[11] from pop0:\t78580\n",
      "\t-> Sites to keep[11] from pop1:\t78580\n",
      "\t-> [readdata] lastread:78580 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:229423\n",
      "\t-> Only read nSites: 229423 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:12\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[12] from pop0:\t79896\n",
      "\t-> Sites to keep[12] from pop1:\t79896\n",
      "\t-> [readdata] lastread:79896 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:309319\n",
      "\t-> Only read nSites: 309319 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:16\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[16] from pop0:\t70251\n",
      "\t-> Sites to keep[16] from pop1:\t70251\n",
      "\t-> [readdata] lastread:70251 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:379570\n",
      "\t-> Only read nSites: 379570 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:17\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[17] from pop0:\t60545\n",
      "\t-> Sites to keep[17] from pop1:\t60545\n",
      "\t-> [readdata] lastread:60545 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:440115\n",
      "\t-> Only read nSites: 440115 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:18\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[18] from pop0:\t65819\n",
      "\t-> Sites to keep[18] from pop1:\t65819\n",
      "\t-> [readdata] lastread:65819 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:505934\n",
      "\t-> Only read nSites: 505934 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:19\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "\t-> Sites to keep[19] from pop0:\t52107\n",
      "\t-> Sites to keep[19] from pop1:\t52107\n",
      "\t-> [readdata] lastread:52107 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:558041\n",
      "\t-> Only read nSites: 558041 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:2\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[2] from pop0:\t65076\n",
      "\t-> Sites to keep[2] from pop1:\t65076\n",
      "\t-> [readdata] lastread:65076 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:623117\n",
      "\t-> Only read nSites: 623117 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:20\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[20] from pop0:\t66504\n",
      "\t-> Sites to keep[20] from pop1:\t66504\n",
      "\t-> [readdata] lastread:66504 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:689621\n",
      "\t-> Only read nSites: 689621 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:3\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[3] from pop0:\t57387\n",
      "\t-> Sites to keep[3] from pop1:\t57387\n",
      "\t-> [readdata] lastread:57387 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:747008\n",
      "\t-> Only read nSites: 747008 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:4\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[4] from pop0:\t76413\n",
      "\t-> Sites to keep[4] from pop1:\t76413\n",
      "\t-> [readdata] lastread:76413 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:823421\n",
      "\t-> Only read nSites: 823421 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:5\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[5] from pop0:\t75707\n",
      "\t-> Sites to keep[5] from pop1:\t75707\n",
      "\t-> [readdata] lastread:75707 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:899128\n",
      "\t-> Only read nSites: 899128 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:6\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[6] from pop0:\t76306\n",
      "\t-> Sites to keep[6] from pop1:\t76306\n",
      "\t-> [readdata] lastread:76306 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:975434\n",
      "\t-> Only read nSites: 975434 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:7\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[7] from pop0:\t69269\n",
      "\t-> Sites to keep[7] from pop1:\t69269\n",
      "\t-> [readdata] lastread:69269 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:1044703\n",
      "\t-> Only read nSites: 1044703 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:8\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[8] from pop0:\t63966\n",
      "\t-> Sites to keep[8] from pop1:\t63966\n",
      "\t-> [readdata] lastread:63966 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:1108669\n",
      "\t-> Only read nSites: 1108669 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:9\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[9] from pop0:\t77174\n",
      "\t-> Sites to keep[9] from pop1:\t77174\n",
      "\t-> [readdata] lastread:77174 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:1185843\n",
      "\t-> Only read nSites: 1185843 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Will run optimization on nSites: 1185843\n",
      "------------\n",
      "startlik=-3337134.849569\n",
      "lik[2]=-206814.398100 diff=3.130320e+06 alpha:1.000000 sr2:4.018323e-01\n",
      "lik[5]=-108462.936214 diff=9.835146e+04 alpha:1.294352 sr2:9.395940e-03\n",
      "lik[8]=-108284.874805 diff=1.780614e+02 alpha:1.812501 sr2:1.284130e-07\n",
      "lik[11]=-108246.987284 diff=3.788752e+01 alpha:2.939176 sr2:6.517346e-10\n",
      "lik[14]=-108232.997485 diff=1.398980e+01 alpha:4.000000 sr2:2.783383e-10\n",
      "lik[17]=-108232.732924 diff=2.645609e-01 alpha:2.163779 sr2:2.038712e-11\n",
      "\t-> Breaking EM(sr2) at iter:18, sqrt(sr2):2.980115e-07\n",
      "likelihood: -108232.732924\n",
      "------------\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Only read nSites: 0 will therefore prepare next chromosome (or exit)\n",
      "\n",
      "\t-> NB NB output is no longer log probs of the frequency spectrum!\n",
      "\t-> Output is now simply the expected values! \n",
      "\t-> You can convert to the old format simply with log(norm(x))\n",
      "\t-> Version of fname:smallNA06994.saf.idx is:2\n",
      "\t-> Assuming .saf.gz file: smallNA06994.saf.gz\n",
      "\t-> Assuming .saf.pos.gz: smallNA06994.saf.pos.gz\n",
      "\t-> Version of fname:smallNA11831.saf.idx is:2\n",
      "\t-> Assuming .saf.gz file: smallNA11831.saf.gz\n",
      "\t-> Assuming .saf.pos.gz: smallNA11831.saf.pos.gz\n",
      "\t-> args: tole:0.000001 nthreads:4 maxiter:100 nsites:0 start:(null) chr:(null) start:-1 stop:-1 fstout:(null) oldout:0 seed:1558447076 bootstrap:0 whichFst:0 fold:0 ref:(null) anc:(null)\n",
      "\t-> Multi SFS is 'still' under development. Please report strange behaviour\n",
      "\t-> nSites: 1556469\n",
      "\t-> The choice of -nSites will require atleast: 59.374580 megabyte memory, that is at least: 0.02% of total memory\n",
      "\t-> dim(smallNA06994.saf.idx):3\n",
      "\t-> dim(smallNA11831.saf.idx):3\n",
      "\t-> Dimension of parameter space: 9\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:1\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[1] from pop0:\t81179\n",
      "\t-> Sites to keep[1] from pop1:\t81179\n",
      "\t-> [readdata] lastread:81179 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:81179\n",
      "\t-> Only read nSites: 81179 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:10\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[10] from pop0:\t80756\n",
      "\t-> Sites to keep[10] from pop1:\t80756\n",
      "\t-> [readdata] lastread:80756 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:161935\n",
      "\t-> Only read nSites: 161935 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:11\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[11] from pop0:\t84131\n",
      "\t-> Sites to keep[11] from pop1:\t84131\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "\t-> [readdata] lastread:84131 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:246066\n",
      "\t-> Only read nSites: 246066 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:12\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[12] from pop0:\t89463\n",
      "\t-> Sites to keep[12] from pop1:\t89463\n",
      "\t-> [readdata] lastread:89463 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:335529\n",
      "\t-> Only read nSites: 335529 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:16\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[16] from pop0:\t77977\n",
      "\t-> Sites to keep[16] from pop1:\t77977\n",
      "\t-> [readdata] lastread:77977 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:413506\n",
      "\t-> Only read nSites: 413506 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:17\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[17] from pop0:\t70531\n",
      "\t-> Sites to keep[17] from pop1:\t70531\n",
      "\t-> [readdata] lastread:70531 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:484037\n",
      "\t-> Only read nSites: 484037 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:18\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[18] from pop0:\t74033\n",
      "\t-> Sites to keep[18] from pop1:\t74033\n",
      "\t-> [readdata] lastread:74033 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:558070\n",
      "\t-> Only read nSites: 558070 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:19\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[19] from pop0:\t52794\n",
      "\t-> Sites to keep[19] from pop1:\t52794\n",
      "\t-> [readdata] lastread:52794 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:610864\n",
      "\t-> Only read nSites: 610864 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:2\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[2] from pop0:\t80876\n",
      "\t-> Sites to keep[2] from pop1:\t80876\n",
      "\t-> [readdata] lastread:80876 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:691740\n",
      "\t-> Only read nSites: 691740 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:20\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[20] from pop0:\t77751\n",
      "\t-> Sites to keep[20] from pop1:\t77751\n",
      "\t-> [readdata] lastread:77751 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:769491\n",
      "\t-> Only read nSites: 769491 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:3\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[3] from pop0:\t63344\n",
      "\t-> Sites to keep[3] from pop1:\t63344\n",
      "\t-> [readdata] lastread:63344 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:832835\n",
      "\t-> Only read nSites: 832835 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:4\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[4] from pop0:\t83065\n",
      "\t-> Sites to keep[4] from pop1:\t83065\n",
      "\t-> [readdata] lastread:83065 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:915900\n",
      "\t-> Only read nSites: 915900 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:5\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[5] from pop0:\t80771\n",
      "\t-> Sites to keep[5] from pop1:\t80771\n",
      "\t-> [readdata] lastread:80771 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:996671\n",
      "\t-> Only read nSites: 996671 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:6\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[6] from pop0:\t80807\n",
      "\t-> Sites to keep[6] from pop1:\t80807\n",
      "\t-> [readdata] lastread:80807 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:1077478\n",
      "\t-> Only read nSites: 1077478 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:7\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[7] from pop0:\t84679\n",
      "\t-> Sites to keep[7] from pop1:\t84679\n",
      "\t-> [readdata] lastread:84679 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:1162157\n",
      "\t-> Only read nSites: 1162157 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:8\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[8] from pop0:\t83609\n",
      "\t-> Sites to keep[8] from pop1:\t83609\n",
      "\t-> [readdata] lastread:83609 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:1245766\n",
      "\t-> Only read nSites: 1245766 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:9\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[9] from pop0:\t87256\n",
      "\t-> Sites to keep[9] from pop1:\t87256\n",
      "\t-> [readdata] lastread:87256 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:1333022\n",
      "\t-> Only read nSites: 1333022 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Will run optimization on nSites: 1333022\n",
      "------------\n",
      "startlik=-2245936.332820\n",
      "lik[2]=-150555.138547 diff=2.095381e+06 alpha:1.000000 sr2:5.663306e-01\n",
      "lik[5]=-129144.902382 diff=2.141024e+04 alpha:1.276161 sr2:4.818114e-04\n",
      "lik[8]=-129002.682215 diff=1.422202e+02 alpha:1.919783 sr2:4.207822e-08\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "lik[11]=-128975.945483 diff=2.673673e+01 alpha:3.418160 sr2:4.316068e-10\n",
      "lik[14]=-128975.676943 diff=2.685400e-01 alpha:1.672378 sr2:2.834219e-11\n",
      "\t-> Breaking EM(sr2) at iter:15, sqrt(sr2):3.999003e-07\n",
      "likelihood: -128975.676943\n",
      "------------\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Only read nSites: 0 will therefore prepare next chromosome (or exit)\n",
      "\n",
      "\t-> NB NB output is no longer log probs of the frequency spectrum!\n",
      "\t-> Output is now simply the expected values! \n",
      "\t-> You can convert to the old format simply with log(norm(x))\n",
      "\t-> Version of fname:smallNA06994.saf.idx is:2\n",
      "\t-> Assuming .saf.gz file: smallNA06994.saf.gz\n",
      "\t-> Assuming .saf.pos.gz: smallNA06994.saf.pos.gz\n",
      "\t-> Version of fname:smallNA11829.saf.idx is:2\n",
      "\t-> Assuming .saf.gz file: smallNA11829.saf.gz\n",
      "\t-> Assuming .saf.pos.gz: smallNA11829.saf.pos.gz\n",
      "\t-> args: tole:0.000001 nthreads:4 maxiter:100 nsites:0 start:(null) chr:(null) start:-1 stop:-1 fstout:(null) oldout:0 seed:1558447078 bootstrap:0 whichFst:0 fold:0 ref:(null) anc:(null)\n",
      "\t-> Multi SFS is 'still' under development. Please report strange behaviour\n",
      "\t-> nSites: 1542786\n",
      "\t-> The choice of -nSites will require atleast: 58.852615 megabyte memory, that is at least: 0.02% of total memory\n",
      "\t-> dim(smallNA06994.saf.idx):3\n",
      "\t-> dim(smallNA11829.saf.idx):3\n",
      "\t-> Dimension of parameter space: 9\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:1\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[1] from pop0:\t80460\n",
      "\t-> Sites to keep[1] from pop1:\t80460\n",
      "\t-> [readdata] lastread:80460 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:80460\n",
      "\t-> Only read nSites: 80460 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:10\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[10] from pop0:\t79746\n",
      "\t-> Sites to keep[10] from pop1:\t79746\n",
      "\t-> [readdata] lastread:79746 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:160206\n",
      "\t-> Only read nSites: 160206 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:11\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[11] from pop0:\t84053\n",
      "\t-> Sites to keep[11] from pop1:\t84053\n",
      "\t-> [readdata] lastread:84053 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:244259\n",
      "\t-> Only read nSites: 244259 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:12\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[12] from pop0:\t88448\n",
      "\t-> Sites to keep[12] from pop1:\t88448\n",
      "\t-> [readdata] lastread:88448 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:332707\n",
      "\t-> Only read nSites: 332707 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:16\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[16] from pop0:\t76751\n",
      "\t-> Sites to keep[16] from pop1:\t76751\n",
      "\t-> [readdata] lastread:76751 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:409458\n",
      "\t-> Only read nSites: 409458 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:17\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[17] from pop0:\t70621\n",
      "\t-> Sites to keep[17] from pop1:\t70621\n",
      "\t-> [readdata] lastread:70621 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:480079\n",
      "\t-> Only read nSites: 480079 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:18\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[18] from pop0:\t73629\n",
      "\t-> Sites to keep[18] from pop1:\t73629\n",
      "\t-> [readdata] lastread:73629 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:553708\n",
      "\t-> Only read nSites: 553708 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:19\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[19] from pop0:\t51131\n",
      "\t-> Sites to keep[19] from pop1:\t51131\n",
      "\t-> [readdata] lastread:51131 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:604839\n",
      "\t-> Only read nSites: 604839 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:2\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[2] from pop0:\t80984\n",
      "\t-> Sites to keep[2] from pop1:\t80984\n",
      "\t-> [readdata] lastread:80984 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:685823\n",
      "\t-> Only read nSites: 685823 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:20\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[20] from pop0:\t77395\n",
      "\t-> Sites to keep[20] from pop1:\t77395\n",
      "\t-> [readdata] lastread:77395 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:763218\n",
      "\t-> Only read nSites: 763218 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:3\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[3] from pop0:\t62996\n",
      "\t-> Sites to keep[3] from pop1:\t62996\n",
      "\t-> [readdata] lastread:62996 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:826214\n",
      "\t-> Only read nSites: 826214 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:4\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[4] from pop0:\t82697\n",
      "\t-> Sites to keep[4] from pop1:\t82697\n",
      "\t-> [readdata] lastread:82697 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:908911\n",
      "\t-> Only read nSites: 908911 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:5\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[5] from pop0:\t79763\n",
      "\t-> Sites to keep[5] from pop1:\t79763\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "\t-> [readdata] lastread:79763 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:988674\n",
      "\t-> Only read nSites: 988674 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:6\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[6] from pop0:\t80218\n",
      "\t-> Sites to keep[6] from pop1:\t80218\n",
      "\t-> [readdata] lastread:80218 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:1068892\n",
      "\t-> Only read nSites: 1068892 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:7\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[7] from pop0:\t84366\n",
      "\t-> Sites to keep[7] from pop1:\t84366\n",
      "\t-> [readdata] lastread:84366 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:1153258\n",
      "\t-> Only read nSites: 1153258 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:8\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[8] from pop0:\t82592\n",
      "\t-> Sites to keep[8] from pop1:\t82592\n",
      "\t-> [readdata] lastread:82592 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:1235850\n",
      "\t-> Only read nSites: 1235850 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:9\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[9] from pop0:\t86996\n",
      "\t-> Sites to keep[9] from pop1:\t86996\n",
      "\t-> [readdata] lastread:86996 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:1322846\n",
      "\t-> Only read nSites: 1322846 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Will run optimization on nSites: 1322846\n",
      "------------\n",
      "startlik=-2260757.228555\n",
      "lik[2]=-167949.072329 diff=2.092808e+06 alpha:1.000000 sr2:4.641731e-01\n",
      "lik[5]=-129142.306780 diff=3.880677e+04 alpha:1.244824 sr2:1.516323e-03\n",
      "lik[8]=-129034.725342 diff=1.075814e+02 alpha:1.779596 sr2:6.871507e-08\n",
      "lik[11]=-128984.141955 diff=5.058339e+01 alpha:4.000000 sr2:7.575351e-10\n",
      "lik[14]=-128980.397269 diff=3.744686e+00 alpha:2.046281 sr2:4.053938e-10\n",
      "\t-> Breaking EM(sq2) at iter:16, sqrt(sq2):7.842853e-07\n",
      "likelihood: -128980.397269\n",
      "------------\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Only read nSites: 0 will therefore prepare next chromosome (or exit)\n",
      "\n",
      "\t-> NB NB output is no longer log probs of the frequency spectrum!\n",
      "\t-> Output is now simply the expected values! \n",
      "\t-> You can convert to the old format simply with log(norm(x))\n",
      "\t-> Version of fname:smallNA06994.saf.idx is:2\n",
      "\t-> Assuming .saf.gz file: smallNA06994.saf.gz\n",
      "\t-> Assuming .saf.pos.gz: smallNA06994.saf.pos.gz\n",
      "\t-> Version of fname:smallNA07056.saf.idx is:2\n",
      "\t-> Assuming .saf.gz file: smallNA07056.saf.gz\n",
      "\t-> Assuming .saf.pos.gz: smallNA07056.saf.pos.gz\n",
      "\t-> args: tole:0.000001 nthreads:4 maxiter:100 nsites:0 start:(null) chr:(null) start:-1 stop:-1 fstout:(null) oldout:0 seed:1558447080 bootstrap:0 whichFst:0 fold:0 ref:(null) anc:(null)\n",
      "\t-> Multi SFS is 'still' under development. Please report strange behaviour\n",
      "\t-> nSites: 1537126\n",
      "\t-> The choice of -nSites will require atleast: 58.636703 megabyte memory, that is at least: 0.02% of total memory\n",
      "\t-> dim(smallNA06994.saf.idx):3\n",
      "\t-> dim(smallNA07056.saf.idx):3\n",
      "\t-> Dimension of parameter space: 9\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:1\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[1] from pop0:\t79354\n",
      "\t-> Sites to keep[1] from pop1:\t79354\n",
      "\t-> [readdata] lastread:79354 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:79354\n",
      "\t-> Only read nSites: 79354 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:10\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[10] from pop0:\t80791\n",
      "\t-> Sites to keep[10] from pop1:\t80791\n",
      "\t-> [readdata] lastread:80791 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:160145\n",
      "\t-> Only read nSites: 160145 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:11\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[11] from pop0:\t83718\n",
      "\t-> Sites to keep[11] from pop1:\t83718\n",
      "\t-> [readdata] lastread:83718 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:243863\n",
      "\t-> Only read nSites: 243863 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:12\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[12] from pop0:\t86870\n",
      "\t-> Sites to keep[12] from pop1:\t86870\n",
      "\t-> [readdata] lastread:86870 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:330733\n",
      "\t-> Only read nSites: 330733 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:16\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[16] from pop0:\t76683\n",
      "\t-> Sites to keep[16] from pop1:\t76683\n",
      "\t-> [readdata] lastread:76683 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:407416\n",
      "\t-> Only read nSites: 407416 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:17\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[17] from pop0:\t66497\n",
      "\t-> Sites to keep[17] from pop1:\t66497\n",
      "\t-> [readdata] lastread:66497 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:473913\n",
      "\t-> Only read nSites: 473913 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:18\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[18] from pop0:\t71300\n",
      "\t-> Sites to keep[18] from pop1:\t71300\n",
      "\t-> [readdata] lastread:71300 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:545213\n",
      "\t-> Only read nSites: 545213 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:19\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[19] from pop0:\t56159\n",
      "\t-> Sites to keep[19] from pop1:\t56159\n",
      "\t-> [readdata] lastread:56159 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:601372\n",
      "\t-> Only read nSites: 601372 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:2\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[2] from pop0:\t76395\n",
      "\t-> Sites to keep[2] from pop1:\t76395\n",
      "\t-> [readdata] lastread:76395 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:677767\n",
      "\t-> Only read nSites: 677767 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:20\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "\t-> Sites to keep[20] from pop0:\t73705\n",
      "\t-> Sites to keep[20] from pop1:\t73705\n",
      "\t-> [readdata] lastread:73705 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:751472\n",
      "\t-> Only read nSites: 751472 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:3\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[3] from pop0:\t61886\n",
      "\t-> Sites to keep[3] from pop1:\t61886\n",
      "\t-> [readdata] lastread:61886 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:813358\n",
      "\t-> Only read nSites: 813358 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:4\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[4] from pop0:\t81864\n",
      "\t-> Sites to keep[4] from pop1:\t81864\n",
      "\t-> [readdata] lastread:81864 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:895222\n",
      "\t-> Only read nSites: 895222 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:5\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[5] from pop0:\t79878\n",
      "\t-> Sites to keep[5] from pop1:\t79878\n",
      "\t-> [readdata] lastread:79878 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:975100\n",
      "\t-> Only read nSites: 975100 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:6\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[6] from pop0:\t80579\n",
      "\t-> Sites to keep[6] from pop1:\t80579\n",
      "\t-> [readdata] lastread:80579 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:1055679\n",
      "\t-> Only read nSites: 1055679 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:7\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[7] from pop0:\t79656\n",
      "\t-> Sites to keep[7] from pop1:\t79656\n",
      "\t-> [readdata] lastread:79656 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:1135335\n",
      "\t-> Only read nSites: 1135335 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:8\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[8] from pop0:\t78417\n",
      "\t-> Sites to keep[8] from pop1:\t78417\n",
      "\t-> [readdata] lastread:78417 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:1213752\n",
      "\t-> Only read nSites: 1213752 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:9\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[9] from pop0:\t83272\n",
      "\t-> Sites to keep[9] from pop1:\t83272\n",
      "\t-> [readdata] lastread:83272 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:1297024\n",
      "\t-> Only read nSites: 1297024 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Will run optimization on nSites: 1297024\n",
      "------------\n",
      "startlik=-3147294.702026\n",
      "lik[2]=-158775.434570 diff=2.988519e+06 alpha:1.000000 sr2:6.146502e-01\n",
      "lik[5]=-124237.828842 diff=3.453761e+04 alpha:1.257473 sr2:1.212065e-03\n",
      "lik[8]=-124087.787923 diff=1.500409e+02 alpha:1.885581 sr2:6.293957e-08\n",
      "lik[11]=-124052.672604 diff=3.511532e+01 alpha:4.000000 sr2:8.159472e-10\n",
      "lik[14]=-124051.029895 diff=1.642709e+00 alpha:1.826935 sr2:1.419102e-10\n",
      "lik[17]=-124050.998351 diff=3.154420e-02 alpha:4.026161 sr2:2.609979e-12\n",
      "\t-> Breaking EM(sr2) at iter:18, sqrt(sr2):2.279282e-07\n",
      "likelihood: -124050.998351\n",
      "------------\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Only read nSites: 0 will therefore prepare next chromosome (or exit)\n",
      "\n",
      "\t-> NB NB output is no longer log probs of the frequency spectrum!\n",
      "\t-> Output is now simply the expected values! \n",
      "\t-> You can convert to the old format simply with log(norm(x))\n",
      "\t-> Version of fname:smallNA06994.saf.idx is:2\n",
      "\t-> Assuming .saf.gz file: smallNA06994.saf.gz\n",
      "\t-> Assuming .saf.pos.gz: smallNA06994.saf.pos.gz\n",
      "\t-> Version of fname:smallNA11830.saf.idx is:2\n",
      "\t-> Assuming .saf.gz file: smallNA11830.saf.gz\n",
      "\t-> Assuming .saf.pos.gz: smallNA11830.saf.pos.gz\n",
      "\t-> args: tole:0.000001 nthreads:4 maxiter:100 nsites:0 start:(null) chr:(null) start:-1 stop:-1 fstout:(null) oldout:0 seed:1558447083 bootstrap:0 whichFst:0 fold:0 ref:(null) anc:(null)\n",
      "\t-> Multi SFS is 'still' under development. Please report strange behaviour\n",
      "\t-> nSites: 1584541\n",
      "\t-> The choice of -nSites will require atleast: 60.445442 megabyte memory, that is at least: 0.02% of total memory\n",
      "\t-> dim(smallNA06994.saf.idx):3\n",
      "\t-> dim(smallNA11830.saf.idx):3\n",
      "\t-> Dimension of parameter space: 9\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:1\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[1] from pop0:\t81731\n",
      "\t-> Sites to keep[1] from pop1:\t81731\n",
      "\t-> [readdata] lastread:81731 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:81731\n",
      "\t-> Only read nSites: 81731 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:10\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[10] from pop0:\t82010\n",
      "\t-> Sites to keep[10] from pop1:\t82010\n",
      "\t-> [readdata] lastread:82010 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:163741\n",
      "\t-> Only read nSites: 163741 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:11\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[11] from pop0:\t85025\n",
      "\t-> Sites to keep[11] from pop1:\t85025\n",
      "\t-> [readdata] lastread:85025 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:248766\n",
      "\t-> Only read nSites: 248766 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:12\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[12] from pop0:\t89685\n",
      "\t-> Sites to keep[12] from pop1:\t89685\n",
      "\t-> [readdata] lastread:89685 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:338451\n",
      "\t-> Only read nSites: 338451 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:16\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[16] from pop0:\t78562\n",
      "\t-> Sites to keep[16] from pop1:\t78562\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "\t-> [readdata] lastread:78562 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:417013\n",
      "\t-> Only read nSites: 417013 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:17\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[17] from pop0:\t70676\n",
      "\t-> Sites to keep[17] from pop1:\t70676\n",
      "\t-> [readdata] lastread:70676 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:487689\n",
      "\t-> Only read nSites: 487689 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:18\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[18] from pop0:\t74431\n",
      "\t-> Sites to keep[18] from pop1:\t74431\n",
      "\t-> [readdata] lastread:74431 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:562120\n",
      "\t-> Only read nSites: 562120 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:19\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[19] from pop0:\t55907\n",
      "\t-> Sites to keep[19] from pop1:\t55907\n",
      "\t-> [readdata] lastread:55907 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:618027\n",
      "\t-> Only read nSites: 618027 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:2\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[2] from pop0:\t80786\n",
      "\t-> Sites to keep[2] from pop1:\t80786\n",
      "\t-> [readdata] lastread:80786 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:698813\n",
      "\t-> Only read nSites: 698813 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:20\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[20] from pop0:\t78005\n",
      "\t-> Sites to keep[20] from pop1:\t78005\n",
      "\t-> [readdata] lastread:78005 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:776818\n",
      "\t-> Only read nSites: 776818 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:3\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[3] from pop0:\t63794\n",
      "\t-> Sites to keep[3] from pop1:\t63794\n",
      "\t-> [readdata] lastread:63794 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:840612\n",
      "\t-> Only read nSites: 840612 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:4\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[4] from pop0:\t83738\n",
      "\t-> Sites to keep[4] from pop1:\t83738\n",
      "\t-> [readdata] lastread:83738 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:924350\n",
      "\t-> Only read nSites: 924350 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:5\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[5] from pop0:\t81469\n",
      "\t-> Sites to keep[5] from pop1:\t81469\n",
      "\t-> [readdata] lastread:81469 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:1005819\n",
      "\t-> Only read nSites: 1005819 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:6\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[6] from pop0:\t81459\n",
      "\t-> Sites to keep[6] from pop1:\t81459\n",
      "\t-> [readdata] lastread:81459 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:1087278\n",
      "\t-> Only read nSites: 1087278 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:7\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[7] from pop0:\t84578\n",
      "\t-> Sites to keep[7] from pop1:\t84578\n",
      "\t-> [readdata] lastread:84578 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:1171856\n",
      "\t-> Only read nSites: 1171856 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:8\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[8] from pop0:\t82764\n",
      "\t-> Sites to keep[8] from pop1:\t82764\n",
      "\t-> [readdata] lastread:82764 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:1254620\n",
      "\t-> Only read nSites: 1254620 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:9\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[9] from pop0:\t87908\n",
      "\t-> Sites to keep[9] from pop1:\t87908\n",
      "\t-> [readdata] lastread:87908 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:1342528\n",
      "\t-> Only read nSites: 1342528 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Will run optimization on nSites: 1342528\n",
      "------------\n",
      "startlik=-2303670.373896\n",
      "lik[2]=-154107.766459 diff=2.149563e+06 alpha:1.000000 sr2:5.555697e-01\n",
      "lik[5]=-130115.913079 diff=2.399185e+04 alpha:1.284821 sr2:6.620637e-04\n",
      "lik[8]=-129908.505184 diff=2.074079e+02 alpha:1.959218 sr2:4.941965e-08\n",
      "lik[11]=-129883.229122 diff=2.527606e+01 alpha:3.787946 sr2:2.190879e-09\n",
      "lik[14]=-129882.570332 diff=6.587905e-01 alpha:2.551175 sr2:9.331378e-11\n",
      "\t-> Breaking EM(sr2) at iter:15, sqrt(sr2):5.346436e-07\n",
      "likelihood: -129882.570332\n",
      "------------\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Only read nSites: 0 will therefore prepare next chromosome (or exit)\n",
      "\n",
      "\t-> NB NB output is no longer log probs of the frequency spectrum!\n",
      "\t-> Output is now simply the expected values! \n",
      "\t-> You can convert to the old format simply with log(norm(x))\n",
      "\t-> Version of fname:smallNA06985.saf.idx is:2\n",
      "\t-> Assuming .saf.gz file: smallNA06985.saf.gz\n",
      "\t-> Assuming .saf.pos.gz: smallNA06985.saf.pos.gz\n",
      "\t-> Version of fname:smallNA11831.saf.idx is:2\n",
      "\t-> Assuming .saf.gz file: smallNA11831.saf.gz\n",
      "\t-> Assuming .saf.pos.gz: smallNA11831.saf.pos.gz\n",
      "\t-> args: tole:0.000001 nthreads:4 maxiter:100 nsites:0 start:(null) chr:(null) start:-1 stop:-1 fstout:(null) oldout:0 seed:1558447085 bootstrap:0 whichFst:0 fold:0 ref:(null) anc:(null)\n",
      "\t-> Multi SFS is 'still' under development. Please report strange behaviour\n",
      "\t-> nSites: 1556469\n",
      "\t-> The choice of -nSites will require atleast: 59.374580 megabyte memory, that is at least: 0.02% of total memory\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "\t-> dim(smallNA06985.saf.idx):3\n",
      "\t-> dim(smallNA11831.saf.idx):3\n",
      "\t-> Dimension of parameter space: 9\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:1\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[1] from pop0:\t82607\n",
      "\t-> Sites to keep[1] from pop1:\t82607\n",
      "\t-> [readdata] lastread:82607 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:82607\n",
      "\t-> Only read nSites: 82607 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:10\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[10] from pop0:\t85506\n",
      "\t-> Sites to keep[10] from pop1:\t85506\n",
      "\t-> [readdata] lastread:85506 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:168113\n",
      "\t-> Only read nSites: 168113 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:11\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[11] from pop0:\t86784\n",
      "\t-> Sites to keep[11] from pop1:\t86784\n",
      "\t-> [readdata] lastread:86784 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:254897\n",
      "\t-> Only read nSites: 254897 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:12\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[12] from pop0:\t85135\n",
      "\t-> Sites to keep[12] from pop1:\t85135\n",
      "\t-> [readdata] lastread:85135 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:340032\n",
      "\t-> Only read nSites: 340032 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:16\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[16] from pop0:\t82353\n",
      "\t-> Sites to keep[16] from pop1:\t82353\n",
      "\t-> [readdata] lastread:82353 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:422385\n",
      "\t-> Only read nSites: 422385 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:17\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[17] from pop0:\t71667\n",
      "\t-> Sites to keep[17] from pop1:\t71667\n",
      "\t-> [readdata] lastread:71667 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:494052\n",
      "\t-> Only read nSites: 494052 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:18\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[18] from pop0:\t76797\n",
      "\t-> Sites to keep[18] from pop1:\t76797\n",
      "\t-> [readdata] lastread:76797 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:570849\n",
      "\t-> Only read nSites: 570849 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:19\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[19] from pop0:\t73273\n",
      "\t-> Sites to keep[19] from pop1:\t73273\n",
      "\t-> [readdata] lastread:73273 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:644122\n",
      "\t-> Only read nSites: 644122 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:2\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[2] from pop0:\t70211\n",
      "\t-> Sites to keep[2] from pop1:\t70211\n",
      "\t-> [readdata] lastread:70211 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:714333\n",
      "\t-> Only read nSites: 714333 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:20\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[20] from pop0:\t78457\n",
      "\t-> Sites to keep[20] from pop1:\t78457\n",
      "\t-> [readdata] lastread:78457 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:792790\n",
      "\t-> Only read nSites: 792790 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:3\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[3] from pop0:\t72294\n",
      "\t-> Sites to keep[3] from pop1:\t72294\n",
      "\t-> [readdata] lastread:72294 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:865084\n",
      "\t-> Only read nSites: 865084 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:4\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[4] from pop0:\t80455\n",
      "\t-> Sites to keep[4] from pop1:\t80455\n",
      "\t-> [readdata] lastread:80455 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:945539\n",
      "\t-> Only read nSites: 945539 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:5\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[5] from pop0:\t86171\n",
      "\t-> Sites to keep[5] from pop1:\t86171\n",
      "\t-> [readdata] lastread:86171 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:1031710\n",
      "\t-> Only read nSites: 1031710 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:6\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[6] from pop0:\t86617\n",
      "\t-> Sites to keep[6] from pop1:\t86617\n",
      "\t-> [readdata] lastread:86617 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:1118327\n",
      "\t-> Only read nSites: 1118327 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:7\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[7] from pop0:\t75293\n",
      "\t-> Sites to keep[7] from pop1:\t75293\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "\t-> [readdata] lastread:75293 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:1193620\n",
      "\t-> Only read nSites: 1193620 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:8\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[8] from pop0:\t71241\n",
      "\t-> Sites to keep[8] from pop1:\t71241\n",
      "\t-> [readdata] lastread:71241 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:1264861\n",
      "\t-> Only read nSites: 1264861 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:9\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[9] from pop0:\t81935\n",
      "\t-> Sites to keep[9] from pop1:\t81935\n",
      "\t-> [readdata] lastread:81935 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:1346796\n",
      "\t-> Only read nSites: 1346796 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Will run optimization on nSites: 1346796\n",
      "------------\n",
      "startlik=-2514096.535974\n",
      "lik[2]=-178971.317445 diff=2.335125e+06 alpha:1.000000 sr2:4.662374e-01\n",
      "lik[5]=-122255.290953 diff=5.671603e+04 alpha:1.297006 sr2:2.743430e-03\n",
      "lik[8]=-122141.624950 diff=1.136660e+02 alpha:1.810544 sr2:5.471750e-08\n",
      "lik[11]=-122098.811890 diff=4.281306e+01 alpha:4.000000 sr2:5.567604e-10\n",
      "lik[14]=-122089.609054 diff=9.202836e+00 alpha:2.592988 sr2:3.855811e-10\n",
      "lik[17]=-122089.505301 diff=1.037531e-01 alpha:2.359254 sr2:1.047160e-11\n",
      "\t-> Breaking EM(sr2) at iter:18, sqrt(sr2):4.127705e-07\n",
      "likelihood: -122089.505301\n",
      "------------\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Only read nSites: 0 will therefore prepare next chromosome (or exit)\n",
      "\n",
      "\t-> NB NB output is no longer log probs of the frequency spectrum!\n",
      "\t-> Output is now simply the expected values! \n",
      "\t-> You can convert to the old format simply with log(norm(x))\n",
      "\t-> Version of fname:smallNA06985.saf.idx is:2\n",
      "\t-> Assuming .saf.gz file: smallNA06985.saf.gz\n",
      "\t-> Assuming .saf.pos.gz: smallNA06985.saf.pos.gz\n",
      "\t-> Version of fname:smallNA11829.saf.idx is:2\n",
      "\t-> Assuming .saf.gz file: smallNA11829.saf.gz\n",
      "\t-> Assuming .saf.pos.gz: smallNA11829.saf.pos.gz\n",
      "\t-> args: tole:0.000001 nthreads:4 maxiter:100 nsites:0 start:(null) chr:(null) start:-1 stop:-1 fstout:(null) oldout:0 seed:1558447087 bootstrap:0 whichFst:0 fold:0 ref:(null) anc:(null)\n",
      "\t-> Multi SFS is 'still' under development. Please report strange behaviour\n",
      "\t-> nSites: 1542786\n",
      "\t-> The choice of -nSites will require atleast: 58.852615 megabyte memory, that is at least: 0.02% of total memory\n",
      "\t-> dim(smallNA06985.saf.idx):3\n",
      "\t-> dim(smallNA11829.saf.idx):3\n",
      "\t-> Dimension of parameter space: 9\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:1\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[1] from pop0:\t81928\n",
      "\t-> Sites to keep[1] from pop1:\t81928\n",
      "\t-> [readdata] lastread:81928 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:81928\n",
      "\t-> Only read nSites: 81928 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:10\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[10] from pop0:\t84173\n",
      "\t-> Sites to keep[10] from pop1:\t84173\n",
      "\t-> [readdata] lastread:84173 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:166101\n",
      "\t-> Only read nSites: 166101 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:11\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[11] from pop0:\t86972\n",
      "\t-> Sites to keep[11] from pop1:\t86972\n",
      "\t-> [readdata] lastread:86972 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:253073\n",
      "\t-> Only read nSites: 253073 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:12\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[12] from pop0:\t83994\n",
      "\t-> Sites to keep[12] from pop1:\t83994\n",
      "\t-> [readdata] lastread:83994 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:337067\n",
      "\t-> Only read nSites: 337067 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:16\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[16] from pop0:\t79967\n",
      "\t-> Sites to keep[16] from pop1:\t79967\n",
      "\t-> [readdata] lastread:79967 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:417034\n",
      "\t-> Only read nSites: 417034 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:17\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[17] from pop0:\t72371\n",
      "\t-> Sites to keep[17] from pop1:\t72371\n",
      "\t-> [readdata] lastread:72371 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:489405\n",
      "\t-> Only read nSites: 489405 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:18\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[18] from pop0:\t76711\n",
      "\t-> Sites to keep[18] from pop1:\t76711\n",
      "\t-> [readdata] lastread:76711 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:566116\n",
      "\t-> Only read nSites: 566116 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:19\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[19] from pop0:\t69437\n",
      "\t-> Sites to keep[19] from pop1:\t69437\n",
      "\t-> [readdata] lastread:69437 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:635553\n",
      "\t-> Only read nSites: 635553 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:2\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[2] from pop0:\t70957\n",
      "\t-> Sites to keep[2] from pop1:\t70957\n",
      "\t-> [readdata] lastread:70957 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:706510\n",
      "\t-> Only read nSites: 706510 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:20\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[20] from pop0:\t77632\n",
      "\t-> Sites to keep[20] from pop1:\t77632\n",
      "\t-> [readdata] lastread:77632 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:784142\n",
      "\t-> Only read nSites: 784142 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:3\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[3] from pop0:\t72398\n",
      "\t-> Sites to keep[3] from pop1:\t72398\n",
      "\t-> [readdata] lastread:72398 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:856540\n",
      "\t-> Only read nSites: 856540 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:4\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "\t-> Sites to keep[4] from pop0:\t80535\n",
      "\t-> Sites to keep[4] from pop1:\t80535\n",
      "\t-> [readdata] lastread:80535 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:937075\n",
      "\t-> Only read nSites: 937075 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:5\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[5] from pop0:\t85060\n",
      "\t-> Sites to keep[5] from pop1:\t85060\n",
      "\t-> [readdata] lastread:85060 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:1022135\n",
      "\t-> Only read nSites: 1022135 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:6\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[6] from pop0:\t86081\n",
      "\t-> Sites to keep[6] from pop1:\t86081\n",
      "\t-> [readdata] lastread:86081 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:1108216\n",
      "\t-> Only read nSites: 1108216 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:7\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[7] from pop0:\t74829\n",
      "\t-> Sites to keep[7] from pop1:\t74829\n",
      "\t-> [readdata] lastread:74829 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:1183045\n",
      "\t-> Only read nSites: 1183045 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:8\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[8] from pop0:\t70120\n",
      "\t-> Sites to keep[8] from pop1:\t70120\n",
      "\t-> [readdata] lastread:70120 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:1253165\n",
      "\t-> Only read nSites: 1253165 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:9\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[9] from pop0:\t81441\n",
      "\t-> Sites to keep[9] from pop1:\t81441\n",
      "\t-> [readdata] lastread:81441 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:1334606\n",
      "\t-> Only read nSites: 1334606 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Will run optimization on nSites: 1334606\n",
      "------------\n",
      "startlik=-2840247.303135\n",
      "lik[2]=-186188.661577 diff=2.654059e+06 alpha:1.000000 sr2:5.368027e-01\n",
      "lik[5]=-123469.414312 diff=6.271925e+04 alpha:1.325672 sr2:3.191128e-03\n",
      "lik[8]=-123391.409082 diff=7.800523e+01 alpha:1.888191 sr2:3.966793e-08\n",
      "lik[11]=-123338.315024 diff=5.309406e+01 alpha:4.000000 sr2:2.669970e-10\n",
      "lik[14]=-123336.131056 diff=2.183968e+00 alpha:2.910030 sr2:2.128215e-10\n",
      "\t-> Breaking EM(sq2) at iter:16, sqrt(sq2):6.307042e-07\n",
      "likelihood: -123336.131056\n",
      "------------\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Only read nSites: 0 will therefore prepare next chromosome (or exit)\n",
      "\n",
      "\t-> NB NB output is no longer log probs of the frequency spectrum!\n",
      "\t-> Output is now simply the expected values! \n",
      "\t-> You can convert to the old format simply with log(norm(x))\n",
      "\t-> Version of fname:smallNA06985.saf.idx is:2\n",
      "\t-> Assuming .saf.gz file: smallNA06985.saf.gz\n",
      "\t-> Assuming .saf.pos.gz: smallNA06985.saf.pos.gz\n",
      "\t-> Version of fname:smallNA07056.saf.idx is:2\n",
      "\t-> Assuming .saf.gz file: smallNA07056.saf.gz\n",
      "\t-> Assuming .saf.pos.gz: smallNA07056.saf.pos.gz\n",
      "\t-> args: tole:0.000001 nthreads:4 maxiter:100 nsites:0 start:(null) chr:(null) start:-1 stop:-1 fstout:(null) oldout:0 seed:1558447089 bootstrap:0 whichFst:0 fold:0 ref:(null) anc:(null)\n",
      "\t-> Multi SFS is 'still' under development. Please report strange behaviour\n",
      "\t-> nSites: 1537126\n",
      "\t-> The choice of -nSites will require atleast: 58.636703 megabyte memory, that is at least: 0.02% of total memory\n",
      "\t-> dim(smallNA06985.saf.idx):3\n",
      "\t-> dim(smallNA07056.saf.idx):3\n",
      "\t-> Dimension of parameter space: 9\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:1\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[1] from pop0:\t82885\n",
      "\t-> Sites to keep[1] from pop1:\t82885\n",
      "\t-> [readdata] lastread:82885 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:82885\n",
      "\t-> Only read nSites: 82885 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:10\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[10] from pop0:\t86469\n",
      "\t-> Sites to keep[10] from pop1:\t86469\n",
      "\t-> [readdata] lastread:86469 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:169354\n",
      "\t-> Only read nSites: 169354 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:11\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[11] from pop0:\t87492\n",
      "\t-> Sites to keep[11] from pop1:\t87492\n",
      "\t-> [readdata] lastread:87492 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:256846\n",
      "\t-> Only read nSites: 256846 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:12\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[12] from pop0:\t83532\n",
      "\t-> Sites to keep[12] from pop1:\t83532\n",
      "\t-> [readdata] lastread:83532 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:340378\n",
      "\t-> Only read nSites: 340378 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:16\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[16] from pop0:\t82003\n",
      "\t-> Sites to keep[16] from pop1:\t82003\n",
      "\t-> [readdata] lastread:82003 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:422381\n",
      "\t-> Only read nSites: 422381 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:17\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[17] from pop0:\t68428\n",
      "\t-> Sites to keep[17] from pop1:\t68428\n",
      "\t-> [readdata] lastread:68428 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:490809\n",
      "\t-> Only read nSites: 490809 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:18\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[18] from pop0:\t76645\n",
      "\t-> Sites to keep[18] from pop1:\t76645\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "\t-> [readdata] lastread:76645 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:567454\n",
      "\t-> Only read nSites: 567454 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:19\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[19] from pop0:\t80430\n",
      "\t-> Sites to keep[19] from pop1:\t80430\n",
      "\t-> [readdata] lastread:80430 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:647884\n",
      "\t-> Only read nSites: 647884 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:2\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[2] from pop0:\t67427\n",
      "\t-> Sites to keep[2] from pop1:\t67427\n",
      "\t-> [readdata] lastread:67427 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:715311\n",
      "\t-> Only read nSites: 715311 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:20\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[20] from pop0:\t75371\n",
      "\t-> Sites to keep[20] from pop1:\t75371\n",
      "\t-> [readdata] lastread:75371 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:790682\n",
      "\t-> Only read nSites: 790682 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:3\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[3] from pop0:\t72993\n",
      "\t-> Sites to keep[3] from pop1:\t72993\n",
      "\t-> [readdata] lastread:72993 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:863675\n",
      "\t-> Only read nSites: 863675 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:4\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[4] from pop0:\t80582\n",
      "\t-> Sites to keep[4] from pop1:\t80582\n",
      "\t-> [readdata] lastread:80582 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:944257\n",
      "\t-> Only read nSites: 944257 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:5\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[5] from pop0:\t86798\n",
      "\t-> Sites to keep[5] from pop1:\t86798\n",
      "\t-> [readdata] lastread:86798 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:1031055\n",
      "\t-> Only read nSites: 1031055 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:6\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[6] from pop0:\t87765\n",
      "\t-> Sites to keep[6] from pop1:\t87765\n",
      "\t-> [readdata] lastread:87765 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:1118820\n",
      "\t-> Only read nSites: 1118820 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:7\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[7] from pop0:\t72054\n",
      "\t-> Sites to keep[7] from pop1:\t72054\n",
      "\t-> [readdata] lastread:72054 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:1190874\n",
      "\t-> Only read nSites: 1190874 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:8\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[8] from pop0:\t67990\n",
      "\t-> Sites to keep[8] from pop1:\t67990\n",
      "\t-> [readdata] lastread:67990 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:1258864\n",
      "\t-> Only read nSites: 1258864 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:9\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[9] from pop0:\t78822\n",
      "\t-> Sites to keep[9] from pop1:\t78822\n",
      "\t-> [readdata] lastread:78822 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:1337686\n",
      "\t-> Only read nSites: 1337686 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Will run optimization on nSites: 1337686\n",
      "------------\n",
      "startlik=-3408901.995403\n",
      "lik[2]=-251790.013194 diff=3.157112e+06 alpha:1.000000 sr2:3.617810e-01\n",
      "lik[5]=-121554.938267 diff=1.302351e+05 alpha:1.304712 sr2:1.309130e-02\n",
      "lik[8]=-121415.189262 diff=1.397490e+02 alpha:1.752661 sr2:5.388610e-08\n",
      "lik[11]=-121340.620216 diff=7.456905e+01 alpha:3.531047 sr2:6.657132e-10\n",
      "lik[14]=-121339.499982 diff=1.120235e+00 alpha:1.813029 sr2:1.716519e-10\n",
      "\t-> Breaking EM(sr2) at iter:15, sqrt(sr2):6.796528e-07\n",
      "likelihood: -121339.499982\n",
      "------------\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Only read nSites: 0 will therefore prepare next chromosome (or exit)\n",
      "\n",
      "\t-> NB NB output is no longer log probs of the frequency spectrum!\n",
      "\t-> Output is now simply the expected values! \n",
      "\t-> You can convert to the old format simply with log(norm(x))\n",
      "\t-> Version of fname:smallNA06985.saf.idx is:2\n",
      "\t-> Assuming .saf.gz file: smallNA06985.saf.gz\n",
      "\t-> Assuming .saf.pos.gz: smallNA06985.saf.pos.gz\n",
      "\t-> Version of fname:smallNA11830.saf.idx is:2\n",
      "\t-> Assuming .saf.gz file: smallNA11830.saf.gz\n",
      "\t-> Assuming .saf.pos.gz: smallNA11830.saf.pos.gz\n",
      "\t-> args: tole:0.000001 nthreads:4 maxiter:100 nsites:0 start:(null) chr:(null) start:-1 stop:-1 fstout:(null) oldout:0 seed:1558447091 bootstrap:0 whichFst:0 fold:0 ref:(null) anc:(null)\n",
      "\t-> Multi SFS is 'still' under development. Please report strange behaviour\n",
      "\t-> nSites: 1584541\n",
      "\t-> The choice of -nSites will require atleast: 60.445442 megabyte memory, that is at least: 0.02% of total memory\n",
      "\t-> dim(smallNA06985.saf.idx):3\n",
      "\t-> dim(smallNA11830.saf.idx):3\n",
      "\t-> Dimension of parameter space: 9\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:1\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[1] from pop0:\t84197\n",
      "\t-> Sites to keep[1] from pop1:\t84197\n",
      "\t-> [readdata] lastread:84197 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:84197\n",
      "\t-> Only read nSites: 84197 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:10\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[10] from pop0:\t87278\n",
      "\t-> Sites to keep[10] from pop1:\t87278\n",
      "\t-> [readdata] lastread:87278 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:171475\n",
      "\t-> Only read nSites: 171475 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:11\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[11] from pop0:\t88240\n",
      "\t-> Sites to keep[11] from pop1:\t88240\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "\t-> [readdata] lastread:88240 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:259715\n",
      "\t-> Only read nSites: 259715 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:12\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[12] from pop0:\t85784\n",
      "\t-> Sites to keep[12] from pop1:\t85784\n",
      "\t-> [readdata] lastread:85784 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:345499\n",
      "\t-> Only read nSites: 345499 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:16\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[16] from pop0:\t83373\n",
      "\t-> Sites to keep[16] from pop1:\t83373\n",
      "\t-> [readdata] lastread:83373 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:428872\n",
      "\t-> Only read nSites: 428872 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:17\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[17] from pop0:\t72661\n",
      "\t-> Sites to keep[17] from pop1:\t72661\n",
      "\t-> [readdata] lastread:72661 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:501533\n",
      "\t-> Only read nSites: 501533 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:18\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[18] from pop0:\t79369\n",
      "\t-> Sites to keep[18] from pop1:\t79369\n",
      "\t-> [readdata] lastread:79369 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:580902\n",
      "\t-> Only read nSites: 580902 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:19\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[19] from pop0:\t79063\n",
      "\t-> Sites to keep[19] from pop1:\t79063\n",
      "\t-> [readdata] lastread:79063 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:659965\n",
      "\t-> Only read nSites: 659965 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:2\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[2] from pop0:\t70800\n",
      "\t-> Sites to keep[2] from pop1:\t70800\n",
      "\t-> [readdata] lastread:70800 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:730765\n",
      "\t-> Only read nSites: 730765 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:20\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[20] from pop0:\t79048\n",
      "\t-> Sites to keep[20] from pop1:\t79048\n",
      "\t-> [readdata] lastread:79048 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:809813\n",
      "\t-> Only read nSites: 809813 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:3\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[3] from pop0:\t74298\n",
      "\t-> Sites to keep[3] from pop1:\t74298\n",
      "\t-> [readdata] lastread:74298 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:884111\n",
      "\t-> Only read nSites: 884111 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:4\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[4] from pop0:\t81743\n",
      "\t-> Sites to keep[4] from pop1:\t81743\n",
      "\t-> [readdata] lastread:81743 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:965854\n",
      "\t-> Only read nSites: 965854 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:5\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[5] from pop0:\t87910\n",
      "\t-> Sites to keep[5] from pop1:\t87910\n",
      "\t-> [readdata] lastread:87910 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:1053764\n",
      "\t-> Only read nSites: 1053764 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:6\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[6] from pop0:\t88960\n",
      "\t-> Sites to keep[6] from pop1:\t88960\n",
      "\t-> [readdata] lastread:88960 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:1142724\n",
      "\t-> Only read nSites: 1142724 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:7\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[7] from pop0:\t75973\n",
      "\t-> Sites to keep[7] from pop1:\t75973\n",
      "\t-> [readdata] lastread:75973 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:1218697\n",
      "\t-> Only read nSites: 1218697 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:8\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[8] from pop0:\t71302\n",
      "\t-> Sites to keep[8] from pop1:\t71302\n",
      "\t-> [readdata] lastread:71302 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:1289999\n",
      "\t-> Only read nSites: 1289999 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:9\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[9] from pop0:\t82849\n",
      "\t-> Sites to keep[9] from pop1:\t82849\n",
      "\t-> [readdata] lastread:82849 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:1372848\n",
      "\t-> Only read nSites: 1372848 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Will run optimization on nSites: 1372848\n",
      "------------\n",
      "startlik=-2197168.603529\n",
      "lik[2]=-143514.446220 diff=2.053654e+06 alpha:1.000000 sr2:5.974274e-01\n",
      "lik[5]=-125724.416804 diff=1.779003e+04 alpha:1.332832 sr2:3.667813e-04\n",
      "lik[8]=-125673.461579 diff=5.095522e+01 alpha:1.892596 sr2:1.467437e-08\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "lik[11]=-125638.522000 diff=3.493958e+01 alpha:3.911870 sr2:2.802106e-10\n",
      "lik[14]=-125637.154132 diff=1.367868e+00 alpha:1.812501 sr2:1.170872e-10\n",
      "\t-> Breaking EM(sq2) at iter:16, sqrt(sq2):9.709660e-07\n",
      "likelihood: -125637.154132\n",
      "------------\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Only read nSites: 0 will therefore prepare next chromosome (or exit)\n",
      "\n",
      "\t-> NB NB output is no longer log probs of the frequency spectrum!\n",
      "\t-> Output is now simply the expected values! \n",
      "\t-> You can convert to the old format simply with log(norm(x))\n",
      "\t-> Version of fname:smallNA11831.saf.idx is:2\n",
      "\t-> Assuming .saf.gz file: smallNA11831.saf.gz\n",
      "\t-> Assuming .saf.pos.gz: smallNA11831.saf.pos.gz\n",
      "\t-> Version of fname:smallNA11829.saf.idx is:2\n",
      "\t-> Assuming .saf.gz file: smallNA11829.saf.gz\n",
      "\t-> Assuming .saf.pos.gz: smallNA11829.saf.pos.gz\n",
      "\t-> args: tole:0.000001 nthreads:4 maxiter:100 nsites:0 start:(null) chr:(null) start:-1 stop:-1 fstout:(null) oldout:0 seed:1558447093 bootstrap:0 whichFst:0 fold:0 ref:(null) anc:(null)\n",
      "\t-> Multi SFS is 'still' under development. Please report strange behaviour\n",
      "\t-> nSites: 1556469\n",
      "\t-> The choice of -nSites will require atleast: 59.374580 megabyte memory, that is at least: 0.02% of total memory\n",
      "\t-> dim(smallNA11831.saf.idx):3\n",
      "\t-> dim(smallNA11829.saf.idx):3\n",
      "\t-> Dimension of parameter space: 9\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:1\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[1] from pop0:\t87760\n",
      "\t-> Sites to keep[1] from pop1:\t87760\n",
      "\t-> [readdata] lastread:87760 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:87760\n",
      "\t-> Only read nSites: 87760 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:10\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[10] from pop0:\t88140\n",
      "\t-> Sites to keep[10] from pop1:\t88140\n",
      "\t-> [readdata] lastread:88140 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:175900\n",
      "\t-> Only read nSites: 175900 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:11\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[11] from pop0:\t92014\n",
      "\t-> Sites to keep[11] from pop1:\t92014\n",
      "\t-> [readdata] lastread:92014 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:267914\n",
      "\t-> Only read nSites: 267914 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:12\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[12] from pop0:\t93575\n",
      "\t-> Sites to keep[12] from pop1:\t93575\n",
      "\t-> [readdata] lastread:93575 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:361489\n",
      "\t-> Only read nSites: 361489 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:16\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[16] from pop0:\t87923\n",
      "\t-> Sites to keep[16] from pop1:\t87923\n",
      "\t-> [readdata] lastread:87923 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:449412\n",
      "\t-> Only read nSites: 449412 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:17\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[17] from pop0:\t81332\n",
      "\t-> Sites to keep[17] from pop1:\t81332\n",
      "\t-> [readdata] lastread:81332 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:530744\n",
      "\t-> Only read nSites: 530744 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:18\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[18] from pop0:\t83694\n",
      "\t-> Sites to keep[18] from pop1:\t83694\n",
      "\t-> [readdata] lastread:83694 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:614438\n",
      "\t-> Only read nSites: 614438 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:19\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[19] from pop0:\t69471\n",
      "\t-> Sites to keep[19] from pop1:\t69471\n",
      "\t-> [readdata] lastread:69471 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:683909\n",
      "\t-> Only read nSites: 683909 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:2\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[2] from pop0:\t87051\n",
      "\t-> Sites to keep[2] from pop1:\t87051\n",
      "\t-> [readdata] lastread:87051 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:770960\n",
      "\t-> Only read nSites: 770960 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:20\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[20] from pop0:\t88957\n",
      "\t-> Sites to keep[20] from pop1:\t88957\n",
      "\t-> [readdata] lastread:88957 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:859917\n",
      "\t-> Only read nSites: 859917 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:3\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[3] from pop0:\t78004\n",
      "\t-> Sites to keep[3] from pop1:\t78004\n",
      "\t-> [readdata] lastread:78004 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:937921\n",
      "\t-> Only read nSites: 937921 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:4\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[4] from pop0:\t86910\n",
      "\t-> Sites to keep[4] from pop1:\t86910\n",
      "\t-> [readdata] lastread:86910 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:1024831\n",
      "\t-> Only read nSites: 1024831 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:5\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[5] from pop0:\t89735\n",
      "\t-> Sites to keep[5] from pop1:\t89735\n",
      "\t-> [readdata] lastread:89735 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:1114566\n",
      "\t-> Only read nSites: 1114566 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:6\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "\t-> Sites to keep[6] from pop0:\t90378\n",
      "\t-> Sites to keep[6] from pop1:\t90378\n",
      "\t-> [readdata] lastread:90378 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:1204944\n",
      "\t-> Only read nSites: 1204944 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:7\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[7] from pop0:\t90285\n",
      "\t-> Sites to keep[7] from pop1:\t90285\n",
      "\t-> [readdata] lastread:90285 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:1295229\n",
      "\t-> Only read nSites: 1295229 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:8\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[8] from pop0:\t90409\n",
      "\t-> Sites to keep[8] from pop1:\t90409\n",
      "\t-> [readdata] lastread:90409 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:1385638\n",
      "\t-> Only read nSites: 1385638 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:9\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[9] from pop0:\t91714\n",
      "\t-> Sites to keep[9] from pop1:\t91714\n",
      "\t-> [readdata] lastread:91714 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:1477352\n",
      "\t-> Only read nSites: 1477352 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Will run optimization on nSites: 1477352\n",
      "------------\n",
      "startlik=-2734619.025697\n",
      "lik[2]=-168126.442971 diff=2.566493e+06 alpha:1.000000 sr2:5.929458e-01\n",
      "lik[5]=-143873.512401 diff=2.425293e+04 alpha:1.246287 sr2:5.429294e-04\n",
      "lik[8]=-143742.090681 diff=1.314217e+02 alpha:1.891768 sr2:2.596264e-08\n",
      "lik[11]=-143734.499447 diff=7.591235e+00 alpha:3.355352 sr2:4.971104e-10\n",
      "lik[14]=-143734.430854 diff=6.859282e-02 alpha:2.313781 sr2:8.056757e-12\n",
      "\t-> Breaking EM(sr2) at iter:15, sqrt(sr2):1.002503e-07\n",
      "likelihood: -143734.430854\n",
      "------------\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Only read nSites: 0 will therefore prepare next chromosome (or exit)\n",
      "\n",
      "\t-> NB NB output is no longer log probs of the frequency spectrum!\n",
      "\t-> Output is now simply the expected values! \n",
      "\t-> You can convert to the old format simply with log(norm(x))\n",
      "\t-> Version of fname:smallNA11831.saf.idx is:2\n",
      "\t-> Assuming .saf.gz file: smallNA11831.saf.gz\n",
      "\t-> Assuming .saf.pos.gz: smallNA11831.saf.pos.gz\n",
      "\t-> Version of fname:smallNA07056.saf.idx is:2\n",
      "\t-> Assuming .saf.gz file: smallNA07056.saf.gz\n",
      "\t-> Assuming .saf.pos.gz: smallNA07056.saf.pos.gz\n",
      "\t-> args: tole:0.000001 nthreads:4 maxiter:100 nsites:0 start:(null) chr:(null) start:-1 stop:-1 fstout:(null) oldout:0 seed:1558447095 bootstrap:0 whichFst:0 fold:0 ref:(null) anc:(null)\n",
      "\t-> Multi SFS is 'still' under development. Please report strange behaviour\n",
      "\t-> nSites: 1556469\n",
      "\t-> The choice of -nSites will require atleast: 59.374580 megabyte memory, that is at least: 0.02% of total memory\n",
      "\t-> dim(smallNA11831.saf.idx):3\n",
      "\t-> dim(smallNA07056.saf.idx):3\n",
      "\t-> Dimension of parameter space: 9\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:1\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[1] from pop0:\t87418\n",
      "\t-> Sites to keep[1] from pop1:\t87418\n",
      "\t-> [readdata] lastread:87418 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:87418\n",
      "\t-> Only read nSites: 87418 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:10\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[10] from pop0:\t89825\n",
      "\t-> Sites to keep[10] from pop1:\t89825\n",
      "\t-> [readdata] lastread:89825 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:177243\n",
      "\t-> Only read nSites: 177243 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:11\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[11] from pop0:\t92238\n",
      "\t-> Sites to keep[11] from pop1:\t92238\n",
      "\t-> [readdata] lastread:92238 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:269481\n",
      "\t-> Only read nSites: 269481 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:12\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[12] from pop0:\t92422\n",
      "\t-> Sites to keep[12] from pop1:\t92422\n",
      "\t-> [readdata] lastread:92422 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:361903\n",
      "\t-> Only read nSites: 361903 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:16\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[16] from pop0:\t89345\n",
      "\t-> Sites to keep[16] from pop1:\t89345\n",
      "\t-> [readdata] lastread:89345 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:451248\n",
      "\t-> Only read nSites: 451248 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:17\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[17] from pop0:\t76772\n",
      "\t-> Sites to keep[17] from pop1:\t76772\n",
      "\t-> [readdata] lastread:76772 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:528020\n",
      "\t-> Only read nSites: 528020 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:18\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[18] from pop0:\t81896\n",
      "\t-> Sites to keep[18] from pop1:\t81896\n",
      "\t-> [readdata] lastread:81896 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:609916\n",
      "\t-> Only read nSites: 609916 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:19\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[19] from pop0:\t78597\n",
      "\t-> Sites to keep[19] from pop1:\t78597\n",
      "\t-> [readdata] lastread:78597 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:688513\n",
      "\t-> Only read nSites: 688513 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:2\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[2] from pop0:\t81941\n",
      "\t-> Sites to keep[2] from pop1:\t81941\n",
      "\t-> [readdata] lastread:81941 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:770454\n",
      "\t-> Only read nSites: 770454 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:20\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[20] from pop0:\t85672\n",
      "\t-> Sites to keep[20] from pop1:\t85672\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "\t-> [readdata] lastread:85672 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:856126\n",
      "\t-> Only read nSites: 856126 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:3\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[3] from pop0:\t77237\n",
      "\t-> Sites to keep[3] from pop1:\t77237\n",
      "\t-> [readdata] lastread:77237 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:933363\n",
      "\t-> Only read nSites: 933363 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:4\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[4] from pop0:\t86266\n",
      "\t-> Sites to keep[4] from pop1:\t86266\n",
      "\t-> [readdata] lastread:86266 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:1019629\n",
      "\t-> Only read nSites: 1019629 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:5\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[5] from pop0:\t90693\n",
      "\t-> Sites to keep[5] from pop1:\t90693\n",
      "\t-> [readdata] lastread:90693 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:1110322\n",
      "\t-> Only read nSites: 1110322 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:6\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[6] from pop0:\t91624\n",
      "\t-> Sites to keep[6] from pop1:\t91624\n",
      "\t-> [readdata] lastread:91624 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:1201946\n",
      "\t-> Only read nSites: 1201946 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:7\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[7] from pop0:\t85747\n",
      "\t-> Sites to keep[7] from pop1:\t85747\n",
      "\t-> [readdata] lastread:85747 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:1287693\n",
      "\t-> Only read nSites: 1287693 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:8\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[8] from pop0:\t85832\n",
      "\t-> Sites to keep[8] from pop1:\t85832\n",
      "\t-> [readdata] lastread:85832 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:1373525\n",
      "\t-> Only read nSites: 1373525 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:9\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[9] from pop0:\t88011\n",
      "\t-> Sites to keep[9] from pop1:\t88011\n",
      "\t-> [readdata] lastread:88011 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:1461536\n",
      "\t-> Only read nSites: 1461536 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Will run optimization on nSites: 1461536\n",
      "------------\n",
      "startlik=-3152181.517627\n",
      "lik[2]=-194106.463861 diff=2.958075e+06 alpha:1.000000 sr2:5.288821e-01\n",
      "lik[5]=-140190.841371 diff=5.391562e+04 alpha:1.226473 sr2:2.511108e-03\n",
      "lik[8]=-140014.028145 diff=1.768132e+02 alpha:1.785354 sr2:3.928784e-08\n",
      "lik[11]=-139985.591445 diff=2.843670e+01 alpha:4.000000 sr2:7.491422e-10\n",
      "lik[14]=-139981.819412 diff=3.772034e+00 alpha:2.217838 sr2:3.742197e-10\n",
      "\t-> Breaking EM(sr2) at iter:15, sqrt(sr2):8.260068e-07\n",
      "likelihood: -139981.819412\n",
      "------------\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Only read nSites: 0 will therefore prepare next chromosome (or exit)\n",
      "\n",
      "\t-> NB NB output is no longer log probs of the frequency spectrum!\n",
      "\t-> Output is now simply the expected values! \n",
      "\t-> You can convert to the old format simply with log(norm(x))\n",
      "\t-> Version of fname:smallNA11831.saf.idx is:2\n",
      "\t-> Assuming .saf.gz file: smallNA11831.saf.gz\n",
      "\t-> Assuming .saf.pos.gz: smallNA11831.saf.pos.gz\n",
      "\t-> Version of fname:smallNA11830.saf.idx is:2\n",
      "\t-> Assuming .saf.gz file: smallNA11830.saf.gz\n",
      "\t-> Assuming .saf.pos.gz: smallNA11830.saf.pos.gz\n",
      "\t-> args: tole:0.000001 nthreads:4 maxiter:100 nsites:0 start:(null) chr:(null) start:-1 stop:-1 fstout:(null) oldout:0 seed:1558447098 bootstrap:0 whichFst:0 fold:0 ref:(null) anc:(null)\n",
      "\t-> Multi SFS is 'still' under development. Please report strange behaviour\n",
      "\t-> nSites: 1584541\n",
      "\t-> The choice of -nSites will require atleast: 60.445442 megabyte memory, that is at least: 0.02% of total memory\n",
      "\t-> dim(smallNA11831.saf.idx):3\n",
      "\t-> dim(smallNA11830.saf.idx):3\n",
      "\t-> Dimension of parameter space: 9\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:1\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[1] from pop0:\t89867\n",
      "\t-> Sites to keep[1] from pop1:\t89867\n",
      "\t-> [readdata] lastread:89867 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:89867\n",
      "\t-> Only read nSites: 89867 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:10\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[10] from pop0:\t91207\n",
      "\t-> Sites to keep[10] from pop1:\t91207\n",
      "\t-> [readdata] lastread:91207 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:181074\n",
      "\t-> Only read nSites: 181074 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:11\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[11] from pop0:\t93237\n",
      "\t-> Sites to keep[11] from pop1:\t93237\n",
      "\t-> [readdata] lastread:93237 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:274311\n",
      "\t-> Only read nSites: 274311 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:12\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[12] from pop0:\t95257\n",
      "\t-> Sites to keep[12] from pop1:\t95257\n",
      "\t-> [readdata] lastread:95257 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:369568\n",
      "\t-> Only read nSites: 369568 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:16\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[16] from pop0:\t90957\n",
      "\t-> Sites to keep[16] from pop1:\t90957\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "\t-> [readdata] lastread:90957 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:460525\n",
      "\t-> Only read nSites: 460525 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:17\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[17] from pop0:\t81594\n",
      "\t-> Sites to keep[17] from pop1:\t81594\n",
      "\t-> [readdata] lastread:81594 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:542119\n",
      "\t-> Only read nSites: 542119 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:18\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[18] from pop0:\t85406\n",
      "\t-> Sites to keep[18] from pop1:\t85406\n",
      "\t-> [readdata] lastread:85406 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:627525\n",
      "\t-> Only read nSites: 627525 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:19\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[19] from pop0:\t77873\n",
      "\t-> Sites to keep[19] from pop1:\t77873\n",
      "\t-> [readdata] lastread:77873 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:705398\n",
      "\t-> Only read nSites: 705398 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:2\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[2] from pop0:\t86713\n",
      "\t-> Sites to keep[2] from pop1:\t86713\n",
      "\t-> [readdata] lastread:86713 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:792111\n",
      "\t-> Only read nSites: 792111 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:20\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[20] from pop0:\t90275\n",
      "\t-> Sites to keep[20] from pop1:\t90275\n",
      "\t-> [readdata] lastread:90275 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:882386\n",
      "\t-> Only read nSites: 882386 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:3\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[3] from pop0:\t79636\n",
      "\t-> Sites to keep[3] from pop1:\t79636\n",
      "\t-> [readdata] lastread:79636 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:962022\n",
      "\t-> Only read nSites: 962022 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:4\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[4] from pop0:\t88041\n",
      "\t-> Sites to keep[4] from pop1:\t88041\n",
      "\t-> [readdata] lastread:88041 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:1050063\n",
      "\t-> Only read nSites: 1050063 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:5\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[5] from pop0:\t92475\n",
      "\t-> Sites to keep[5] from pop1:\t92475\n",
      "\t-> [readdata] lastread:92475 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:1142538\n",
      "\t-> Only read nSites: 1142538 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:6\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[6] from pop0:\t92695\n",
      "\t-> Sites to keep[6] from pop1:\t92695\n",
      "\t-> [readdata] lastread:92695 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:1235233\n",
      "\t-> Only read nSites: 1235233 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:7\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[7] from pop0:\t91249\n",
      "\t-> Sites to keep[7] from pop1:\t91249\n",
      "\t-> [readdata] lastread:91249 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:1326482\n",
      "\t-> Only read nSites: 1326482 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:8\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[8] from pop0:\t90970\n",
      "\t-> Sites to keep[8] from pop1:\t90970\n",
      "\t-> [readdata] lastread:90970 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:1417452\n",
      "\t-> Only read nSites: 1417452 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:9\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[9] from pop0:\t93146\n",
      "\t-> Sites to keep[9] from pop1:\t93146\n",
      "\t-> [readdata] lastread:93146 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:1510598\n",
      "\t-> Only read nSites: 1510598 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Will run optimization on nSites: 1510598\n",
      "------------\n",
      "startlik=-5402697.890442\n",
      "lik[2]=-288910.933437 diff=5.113787e+06 alpha:1.000000 sr2:4.150039e-01\n",
      "lik[5]=-145021.755650 diff=1.438892e+05 alpha:1.194627 sr2:1.609562e-02\n",
      "lik[8]=-144871.646675 diff=1.501090e+02 alpha:1.626725 sr2:5.928644e-08\n",
      "lik[11]=-144832.496077 diff=3.915060e+01 alpha:4.000000 sr2:6.468574e-10\n",
      "lik[14]=-144824.257552 diff=8.238525e+00 alpha:2.131251 sr2:8.812961e-10\n",
      "\t-> Breaking EM(sq2) at iter:16, sqrt(sq2):5.060953e-07\n",
      "likelihood: -144824.257552\n",
      "------------\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Only read nSites: 0 will therefore prepare next chromosome (or exit)\n",
      "\n",
      "\t-> NB NB output is no longer log probs of the frequency spectrum!\n",
      "\t-> Output is now simply the expected values! \n",
      "\t-> You can convert to the old format simply with log(norm(x))\n",
      "\t-> Version of fname:smallNA11829.saf.idx is:2\n",
      "\t-> Assuming .saf.gz file: smallNA11829.saf.gz\n",
      "\t-> Assuming .saf.pos.gz: smallNA11829.saf.pos.gz\n",
      "\t-> Version of fname:smallNA07056.saf.idx is:2\n",
      "\t-> Assuming .saf.gz file: smallNA07056.saf.gz\n",
      "\t-> Assuming .saf.pos.gz: smallNA07056.saf.pos.gz\n",
      "\t-> args: tole:0.000001 nthreads:4 maxiter:100 nsites:0 start:(null) chr:(null) start:-1 stop:-1 fstout:(null) oldout:0 seed:1558447100 bootstrap:0 whichFst:0 fold:0 ref:(null) anc:(null)\n",
      "\t-> Multi SFS is 'still' under development. Please report strange behaviour\n",
      "\t-> nSites: 1542786\n",
      "\t-> The choice of -nSites will require atleast: 58.852615 megabyte memory, that is at least: 0.02% of total memory\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "\t-> dim(smallNA11829.saf.idx):3\n",
      "\t-> dim(smallNA07056.saf.idx):3\n",
      "\t-> Dimension of parameter space: 9\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:1\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[1] from pop0:\t86585\n",
      "\t-> Sites to keep[1] from pop1:\t86585\n",
      "\t-> [readdata] lastread:86585 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:86585\n",
      "\t-> Only read nSites: 86585 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:10\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[10] from pop0:\t88530\n",
      "\t-> Sites to keep[10] from pop1:\t88530\n",
      "\t-> [readdata] lastread:88530 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:175115\n",
      "\t-> Only read nSites: 175115 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:11\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[11] from pop0:\t92338\n",
      "\t-> Sites to keep[11] from pop1:\t92338\n",
      "\t-> [readdata] lastread:92338 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:267453\n",
      "\t-> Only read nSites: 267453 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:12\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[12] from pop0:\t90943\n",
      "\t-> Sites to keep[12] from pop1:\t90943\n",
      "\t-> [readdata] lastread:90943 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:358396\n",
      "\t-> Only read nSites: 358396 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:16\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[16] from pop0:\t87020\n",
      "\t-> Sites to keep[16] from pop1:\t87020\n",
      "\t-> [readdata] lastread:87020 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:445416\n",
      "\t-> Only read nSites: 445416 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:17\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[17] from pop0:\t76792\n",
      "\t-> Sites to keep[17] from pop1:\t76792\n",
      "\t-> [readdata] lastread:76792 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:522208\n",
      "\t-> Only read nSites: 522208 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:18\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[18] from pop0:\t81946\n",
      "\t-> Sites to keep[18] from pop1:\t81946\n",
      "\t-> [readdata] lastread:81946 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:604154\n",
      "\t-> Only read nSites: 604154 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:19\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[19] from pop0:\t74482\n",
      "\t-> Sites to keep[19] from pop1:\t74482\n",
      "\t-> [readdata] lastread:74482 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:678636\n",
      "\t-> Only read nSites: 678636 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:2\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[2] from pop0:\t82393\n",
      "\t-> Sites to keep[2] from pop1:\t82393\n",
      "\t-> [readdata] lastread:82393 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:761029\n",
      "\t-> Only read nSites: 761029 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:20\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[20] from pop0:\t84827\n",
      "\t-> Sites to keep[20] from pop1:\t84827\n",
      "\t-> [readdata] lastread:84827 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:845856\n",
      "\t-> Only read nSites: 845856 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:3\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[3] from pop0:\t77183\n",
      "\t-> Sites to keep[3] from pop1:\t77183\n",
      "\t-> [readdata] lastread:77183 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:923039\n",
      "\t-> Only read nSites: 923039 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:4\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[4] from pop0:\t86240\n",
      "\t-> Sites to keep[4] from pop1:\t86240\n",
      "\t-> [readdata] lastread:86240 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:1009279\n",
      "\t-> Only read nSites: 1009279 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:5\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[5] from pop0:\t89646\n",
      "\t-> Sites to keep[5] from pop1:\t89646\n",
      "\t-> [readdata] lastread:89646 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:1098925\n",
      "\t-> Only read nSites: 1098925 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:6\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[6] from pop0:\t90810\n",
      "\t-> Sites to keep[6] from pop1:\t90810\n",
      "\t-> [readdata] lastread:90810 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:1189735\n",
      "\t-> Only read nSites: 1189735 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:7\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[7] from pop0:\t85182\n",
      "\t-> Sites to keep[7] from pop1:\t85182\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "\t-> [readdata] lastread:85182 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:1274917\n",
      "\t-> Only read nSites: 1274917 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:8\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[8] from pop0:\t84959\n",
      "\t-> Sites to keep[8] from pop1:\t84959\n",
      "\t-> [readdata] lastread:84959 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:1359876\n",
      "\t-> Only read nSites: 1359876 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:9\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[9] from pop0:\t87704\n",
      "\t-> Sites to keep[9] from pop1:\t87704\n",
      "\t-> [readdata] lastread:87704 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:1447580\n",
      "\t-> Only read nSites: 1447580 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Will run optimization on nSites: 1447580\n",
      "------------\n",
      "startlik=-2093511.434168\n",
      "lik[2]=-168207.705769 diff=1.925304e+06 alpha:1.000000 sr2:4.640896e-01\n",
      "lik[5]=-139953.241695 diff=2.825446e+04 alpha:1.251799 sr2:7.411659e-04\n",
      "lik[8]=-139797.816316 diff=1.554254e+02 alpha:1.913791 sr2:3.547014e-08\n",
      "lik[11]=-139790.936605 diff=6.879711e+00 alpha:3.087171 sr2:6.136259e-10\n",
      "\t-> Breaking EM(sq2) at iter:13, sqrt(sq2):7.303596e-07\n",
      "likelihood: -139790.936605\n",
      "------------\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Only read nSites: 0 will therefore prepare next chromosome (or exit)\n",
      "\n",
      "\t-> NB NB output is no longer log probs of the frequency spectrum!\n",
      "\t-> Output is now simply the expected values! \n",
      "\t-> You can convert to the old format simply with log(norm(x))\n",
      "\t-> Version of fname:smallNA11829.saf.idx is:2\n",
      "\t-> Assuming .saf.gz file: smallNA11829.saf.gz\n",
      "\t-> Assuming .saf.pos.gz: smallNA11829.saf.pos.gz\n",
      "\t-> Version of fname:smallNA11830.saf.idx is:2\n",
      "\t-> Assuming .saf.gz file: smallNA11830.saf.gz\n",
      "\t-> Assuming .saf.pos.gz: smallNA11830.saf.pos.gz\n",
      "\t-> args: tole:0.000001 nthreads:4 maxiter:100 nsites:0 start:(null) chr:(null) start:-1 stop:-1 fstout:(null) oldout:0 seed:1558447103 bootstrap:0 whichFst:0 fold:0 ref:(null) anc:(null)\n",
      "\t-> Multi SFS is 'still' under development. Please report strange behaviour\n",
      "\t-> nSites: 1584541\n",
      "\t-> The choice of -nSites will require atleast: 60.445442 megabyte memory, that is at least: 0.02% of total memory\n",
      "\t-> dim(smallNA11829.saf.idx):3\n",
      "\t-> dim(smallNA11830.saf.idx):3\n",
      "\t-> Dimension of parameter space: 9\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:1\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[1] from pop0:\t89033\n",
      "\t-> Sites to keep[1] from pop1:\t89033\n",
      "\t-> [readdata] lastread:89033 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:89033\n",
      "\t-> Only read nSites: 89033 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:10\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[10] from pop0:\t89820\n",
      "\t-> Sites to keep[10] from pop1:\t89820\n",
      "\t-> [readdata] lastread:89820 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:178853\n",
      "\t-> Only read nSites: 178853 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:11\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[11] from pop0:\t93406\n",
      "\t-> Sites to keep[11] from pop1:\t93406\n",
      "\t-> [readdata] lastread:93406 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:272259\n",
      "\t-> Only read nSites: 272259 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:12\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[12] from pop0:\t93847\n",
      "\t-> Sites to keep[12] from pop1:\t93847\n",
      "\t-> [readdata] lastread:93847 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:366106\n",
      "\t-> Only read nSites: 366106 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:16\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[16] from pop0:\t88713\n",
      "\t-> Sites to keep[16] from pop1:\t88713\n",
      "\t-> [readdata] lastread:88713 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:454819\n",
      "\t-> Only read nSites: 454819 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:17\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[17] from pop0:\t81915\n",
      "\t-> Sites to keep[17] from pop1:\t81915\n",
      "\t-> [readdata] lastread:81915 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:536734\n",
      "\t-> Only read nSites: 536734 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:18\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[18] from pop0:\t85416\n",
      "\t-> Sites to keep[18] from pop1:\t85416\n",
      "\t-> [readdata] lastread:85416 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:622150\n",
      "\t-> Only read nSites: 622150 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:19\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[19] from pop0:\t74194\n",
      "\t-> Sites to keep[19] from pop1:\t74194\n",
      "\t-> [readdata] lastread:74194 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:696344\n",
      "\t-> Only read nSites: 696344 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:2\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[2] from pop0:\t87081\n",
      "\t-> Sites to keep[2] from pop1:\t87081\n",
      "\t-> [readdata] lastread:87081 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:783425\n",
      "\t-> Only read nSites: 783425 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:20\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[20] from pop0:\t89410\n",
      "\t-> Sites to keep[20] from pop1:\t89410\n",
      "\t-> [readdata] lastread:89410 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:872835\n",
      "\t-> Only read nSites: 872835 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:3\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[3] from pop0:\t79408\n",
      "\t-> Sites to keep[3] from pop1:\t79408\n",
      "\t-> [readdata] lastread:79408 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:952243\n",
      "\t-> Only read nSites: 952243 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:4\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "\t-> Sites to keep[4] from pop0:\t87879\n",
      "\t-> Sites to keep[4] from pop1:\t87879\n",
      "\t-> [readdata] lastread:87879 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:1040122\n",
      "\t-> Only read nSites: 1040122 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:5\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[5] from pop0:\t91337\n",
      "\t-> Sites to keep[5] from pop1:\t91337\n",
      "\t-> [readdata] lastread:91337 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:1131459\n",
      "\t-> Only read nSites: 1131459 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:6\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[6] from pop0:\t92014\n",
      "\t-> Sites to keep[6] from pop1:\t92014\n",
      "\t-> [readdata] lastread:92014 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:1223473\n",
      "\t-> Only read nSites: 1223473 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:7\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[7] from pop0:\t90377\n",
      "\t-> Sites to keep[7] from pop1:\t90377\n",
      "\t-> [readdata] lastread:90377 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:1313850\n",
      "\t-> Only read nSites: 1313850 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:8\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[8] from pop0:\t90045\n",
      "\t-> Sites to keep[8] from pop1:\t90045\n",
      "\t-> [readdata] lastread:90045 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:1403895\n",
      "\t-> Only read nSites: 1403895 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:9\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[9] from pop0:\t92641\n",
      "\t-> Sites to keep[9] from pop1:\t92641\n",
      "\t-> [readdata] lastread:92641 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:1496536\n",
      "\t-> Only read nSites: 1496536 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Will run optimization on nSites: 1496536\n",
      "------------\n",
      "startlik=-3464322.520428\n",
      "lik[2]=-210817.496481 diff=3.253505e+06 alpha:1.000000 sr2:4.767664e-01\n",
      "lik[5]=-145816.421857 diff=6.500107e+04 alpha:1.217360 sr2:3.192777e-03\n",
      "lik[8]=-145663.687067 diff=1.527348e+02 alpha:1.642686 sr2:4.984111e-08\n",
      "lik[11]=-145620.779354 diff=4.290771e+01 alpha:4.000000 sr2:1.491300e-09\n",
      "lik[14]=-145616.236324 diff=4.543030e+00 alpha:2.246424 sr2:6.378143e-10\n",
      "\t-> Breaking EM(sr2) at iter:15, sqrt(sr2):8.277280e-07\n",
      "likelihood: -145616.236324\n",
      "------------\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Only read nSites: 0 will therefore prepare next chromosome (or exit)\n",
      "\n",
      "\t-> NB NB output is no longer log probs of the frequency spectrum!\n",
      "\t-> Output is now simply the expected values! \n",
      "\t-> You can convert to the old format simply with log(norm(x))\n",
      "\t-> Version of fname:smallNA07056.saf.idx is:2\n",
      "\t-> Assuming .saf.gz file: smallNA07056.saf.gz\n",
      "\t-> Assuming .saf.pos.gz: smallNA07056.saf.pos.gz\n",
      "\t-> Version of fname:smallNA11830.saf.idx is:2\n",
      "\t-> Assuming .saf.gz file: smallNA11830.saf.gz\n",
      "\t-> Assuming .saf.pos.gz: smallNA11830.saf.pos.gz\n",
      "\t-> args: tole:0.000001 nthreads:4 maxiter:100 nsites:0 start:(null) chr:(null) start:-1 stop:-1 fstout:(null) oldout:0 seed:1558447105 bootstrap:0 whichFst:0 fold:0 ref:(null) anc:(null)\n",
      "\t-> Multi SFS is 'still' under development. Please report strange behaviour\n",
      "\t-> nSites: 1584541\n",
      "\t-> The choice of -nSites will require atleast: 60.445442 megabyte memory, that is at least: 0.02% of total memory\n",
      "\t-> dim(smallNA07056.saf.idx):3\n",
      "\t-> dim(smallNA11830.saf.idx):3\n",
      "\t-> Dimension of parameter space: 9\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:1\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[1] from pop0:\t89012\n",
      "\t-> Sites to keep[1] from pop1:\t89012\n",
      "\t-> [readdata] lastread:89012 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:89012\n",
      "\t-> Only read nSites: 89012 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:10\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[10] from pop0:\t91721\n",
      "\t-> Sites to keep[10] from pop1:\t91721\n",
      "\t-> [readdata] lastread:91721 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:180733\n",
      "\t-> Only read nSites: 180733 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:11\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[11] from pop0:\t93581\n",
      "\t-> Sites to keep[11] from pop1:\t93581\n",
      "\t-> [readdata] lastread:93581 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:274314\n",
      "\t-> Only read nSites: 274314 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:12\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[12] from pop0:\t92955\n",
      "\t-> Sites to keep[12] from pop1:\t92955\n",
      "\t-> [readdata] lastread:92955 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:367269\n",
      "\t-> Only read nSites: 367269 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:16\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[16] from pop0:\t90613\n",
      "\t-> Sites to keep[16] from pop1:\t90613\n",
      "\t-> [readdata] lastread:90613 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:457882\n",
      "\t-> Only read nSites: 457882 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:17\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[17] from pop0:\t77498\n",
      "\t-> Sites to keep[17] from pop1:\t77498\n",
      "\t-> [readdata] lastread:77498 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:535380\n",
      "\t-> Only read nSites: 535380 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:18\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[18] from pop0:\t83971\n",
      "\t-> Sites to keep[18] from pop1:\t83971\n",
      "\t-> [readdata] lastread:83971 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:619351\n",
      "\t-> Only read nSites: 619351 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:19\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[19] from pop0:\t84759\n",
      "\t-> Sites to keep[19] from pop1:\t84759\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "\t-> [readdata] lastread:84759 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:704110\n",
      "\t-> Only read nSites: 704110 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:2\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[2] from pop0:\t81976\n",
      "\t-> Sites to keep[2] from pop1:\t81976\n",
      "\t-> [readdata] lastread:81976 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:786086\n",
      "\t-> Only read nSites: 786086 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:20\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[20] from pop0:\t86282\n",
      "\t-> Sites to keep[20] from pop1:\t86282\n",
      "\t-> [readdata] lastread:86282 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:872368\n",
      "\t-> Only read nSites: 872368 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:3\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[3] from pop0:\t79296\n",
      "\t-> Sites to keep[3] from pop1:\t79296\n",
      "\t-> [readdata] lastread:79296 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:951664\n",
      "\t-> Only read nSites: 951664 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:4\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[4] from pop0:\t87505\n",
      "\t-> Sites to keep[4] from pop1:\t87505\n",
      "\t-> [readdata] lastread:87505 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:1039169\n",
      "\t-> Only read nSites: 1039169 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:5\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[5] from pop0:\t92539\n",
      "\t-> Sites to keep[5] from pop1:\t92539\n",
      "\t-> [readdata] lastread:92539 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:1131708\n",
      "\t-> Only read nSites: 1131708 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:6\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[6] from pop0:\t93690\n",
      "\t-> Sites to keep[6] from pop1:\t93690\n",
      "\t-> [readdata] lastread:93690 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:1225398\n",
      "\t-> Only read nSites: 1225398 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:7\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[7] from pop0:\t86088\n",
      "\t-> Sites to keep[7] from pop1:\t86088\n",
      "\t-> [readdata] lastread:86088 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:1311486\n",
      "\t-> Only read nSites: 1311486 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:8\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[8] from pop0:\t85909\n",
      "\t-> Sites to keep[8] from pop1:\t85909\n",
      "\t-> [readdata] lastread:85909 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:1397395\n",
      "\t-> Only read nSites: 1397395 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Is in multi sfs, will now read data from chr:9\n",
      "\t-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect \n",
      "\t-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites\n",
      "\t-> Sites to keep[9] from pop0:\t89002\n",
      "\t-> Sites to keep[9] from pop1:\t89002\n",
      "\t-> [readdata] lastread:89002 posi:14000031\n",
      "\t-> Comparing positions: 1 with 0 has:1486397\n",
      "\t-> Only read nSites: 1486397 will therefore prepare next chromosome (or exit)\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Will run optimization on nSites: 1486397\n",
      "------------\n",
      "startlik=-3927644.873384\n",
      "lik[2]=-298081.140764 diff=3.629564e+06 alpha:1.000000 sr2:2.702135e-01\n",
      "lik[5]=-140843.137737 diff=1.572380e+05 alpha:1.209936 sr2:1.616967e-02\n",
      "lik[8]=-140718.641788 diff=1.244959e+02 alpha:1.600975 sr2:6.815642e-08\n",
      "lik[11]=-140673.834390 diff=4.480740e+01 alpha:3.784730 sr2:2.332272e-10\n",
      "lik[14]=-140670.849561 diff=2.984829e+00 alpha:2.040973 sr2:1.752269e-10\n",
      "\t-> Breaking EM(sr2) at iter:15, sqrt(sr2):4.947789e-07\n",
      "likelihood: -140670.849561\n",
      "------------\n",
      "\t-> Done reading data from chromosome will prepare next chromosome\n",
      "\t-> Only read nSites: 0 will therefore prepare next chromosome (or exit)\n",
      "\n",
      "\t-> NB NB output is no longer log probs of the frequency spectrum!\n",
      "\t-> Output is now simply the expected values! \n",
      "\t-> You can convert to the old format simply with log(norm(x))\n"
     ]
    }
   ],
   "source": [
    "# run realSFS for each pair of samples\n",
    "for sample1, sample2 in pairs:\n",
    "     !{realSFS} {sample1}.saf.idx {sample2}.saf.idx \\\n",
    "     > ./results_realsfs/{sample1}_{sample2}.2dsfs"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### get the R script to analyze the realSFS output"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 12,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "--2019-05-21 15:58:28--  https://raw.githubusercontent.com/rwaples/freqfree_suppl/master/read_realSFS.R\n",
      "Resolving raw.githubusercontent.com (raw.githubusercontent.com)... 151.101.0.133, 151.101.64.133, 151.101.128.133, ...\n",
      "Connecting to raw.githubusercontent.com (raw.githubusercontent.com)|151.101.0.133|:443... connected.\n",
      "HTTP request sent, awaiting response... 200 OK\n",
      "Length: 1212 (1.2K) [text/plain]\n",
      "Saving to: ‘read_realSFS.R’\n",
      "\n",
      "read_realSFS.R      100%[===================>]   1.18K  --.-KB/s    in 0s      \n",
      "\n",
      "2019-05-21 15:58:29 (81.7 MB/s) - ‘read_realSFS.R’ saved [1212/1212]\n",
      "\n"
     ]
    }
   ],
   "source": [
    "!wget https://raw.githubusercontent.com/rwaples/freqfree_suppl/master/read_realSFS.R"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### lets take a look at the results for a single pair of individuals"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 13,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "       sample1      sample2  nSites         Kin        R0        R1\r\n",
      "1 smallNA06985 smallNA11830 1372848 -0.04746918 0.6052391 0.3290302\r\n"
     ]
    }
   ],
   "source": [
    "!Rscript \\\n",
    "-e \"source('./read_realSFS.R')\" \\\n",
    "-e \"res = read_realSFS('results_realsfs/smallNA06985_smallNA11830.2dsfs')\" \\\n",
    "-e \"res['sample1'] = 'smallNA06985'; res['sample2'] = 'smallNA11830'\" \\\n",
    "-e \"print(res[,c('sample1', 'sample2', 'nSites', 'Kin', 'R0', 'R1') ])\""
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# IBS method"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 15,
   "metadata": {},
   "outputs": [],
   "source": []
  },
  {
   "cell_type": "code",
   "execution_count": 16,
   "metadata": {},
   "outputs": [],
   "source": [
    "!mkdir results_IBS"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### make a genotype likelihood file (glf) file, this file contains all individuals"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 17,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "\t-> angsd version: 0.919-43-g0b5946e (htslib: 1.6-2-g8bbc018) build(Oct  6 2017 11:20:17)\n",
      "\t-> Parsing 10 number of samples \n",
      "\t-> Printing at chr: 20 pos:14056689 chunknumber 2700 contains 663 sitess\n",
      "\t-> Done reading data waiting for calculations to finish\n",
      "\t-> Done waiting for threads\n",
      "\t-> Output filenames:\n",
      "\t\t->\"glf.arg\"\n",
      "\t\t->\"glf.glf.gz\"\n",
      "\t-> Tue May 21 15:58:56 2019\n",
      "\t-> Arguments and parameters for all analysis are located in .arg file\n",
      "\t[ALL done] cpu-time used =  25.55 sec\n",
      "\t[ALL done] walltime used =  27.00 sec\n"
     ]
    }
   ],
   "source": [
    "!{ANGSD} -b all.filelist \\\n",
    "-minMapQ 30 -minQ 20 -GL 2 \\\n",
    "-doGlf 1 \\\n",
    "-out glf"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### run the ibs inference "
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 18,
   "metadata": {
    "scrolled": true
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "using seed 0\n",
      "\t-> Dumping file: results_IBS/ibs.model0.results.log\n",
      "\t-> Dumping file: results_IBS/ibs.model0.results.ibspair\n",
      "reading data\n",
      "read 1689799 sites\n",
      "\tusing model 0 \n",
      "analysing pair 0 1\n",
      "\tusing nSites= 1199765 \n",
      "\ttol reached in 152 interations\tdiff=0.000000\tmodel=0\n",
      "analysing pair 0 2\n",
      "\tusing nSites= 1127797 \n",
      "\ttol reached in 130 interations\tdiff=0.000000\tmodel=0\n",
      "analysing pair 0 3\n",
      "\tusing nSites= 1359492 \n",
      "\ttol reached in 49 interations\tdiff=0.000000\tmodel=0\n",
      "analysing pair 0 4\n",
      "\tusing nSites= 1278230 \n",
      "\ttol reached in 73 interations\tdiff=0.000000\tmodel=0\n",
      "analysing pair 0 5\n",
      "\tusing nSites= 1355014 \n",
      "\ttol reached in 83 interations\tdiff=0.000000\tmodel=0\n",
      "analysing pair 0 6\n",
      "\tusing nSites= 1395178 \n",
      "\ttol reached in 59 interations\tdiff=0.000000\tmodel=0\n",
      "analysing pair 0 7\n",
      "\tusing nSites= 1367560 \n",
      "\ttol reached in 72 interations\tdiff=0.000000\tmodel=0\n",
      "analysing pair 0 8\n",
      "\tusing nSites= 1066307 \n",
      "\ttol reached in 204 interations\tdiff=0.000000\tmodel=0\n",
      "analysing pair 0 9\n",
      "\tusing nSites= 1272263 \n",
      "\ttol reached in 131 interations\tdiff=0.000000\tmodel=0\n",
      "analysing pair 1 2\n",
      "\tusing nSites= 1145072 \n",
      "\ttol reached in 108 interations\tdiff=0.000000\tmodel=0\n",
      "analysing pair 1 3\n",
      "\tusing nSites= 1311761 \n",
      "\ttol reached in 75 interations\tdiff=0.000000\tmodel=0\n",
      "analysing pair 1 4\n",
      "\tusing nSites= 1308251 \n",
      "\ttol reached in 54 interations\tdiff=0.000000\tmodel=0\n",
      "analysing pair 1 5\n",
      "\tusing nSites= 1337456 \n",
      "\ttol reached in 88 interations\tdiff=0.000000\tmodel=0\n",
      "analysing pair 1 6\n",
      "\tusing nSites= 1357989 \n",
      "\ttol reached in 83 interations\tdiff=0.000000\tmodel=0\n",
      "analysing pair 1 7\n",
      "\tusing nSites= 1347804 \n",
      "\ttol reached in 60 interations\tdiff=0.000000\tmodel=0\n",
      "analysing pair 1 8\n",
      "\tusing nSites= 1069941 \n",
      "\ttol reached in 131 interations\tdiff=0.000000\tmodel=0\n",
      "analysing pair 1 9\n",
      "\tusing nSites= 1239181 \n",
      "\ttol reached in 134 interations\tdiff=0.000000\tmodel=0\n",
      "analysing pair 2 3\n",
      "\tusing nSites= 1221714 \n",
      "\ttol reached in 127 interations\tdiff=0.000000\tmodel=0\n",
      "analysing pair 2 4\n",
      "\tusing nSites= 1204533 \n",
      "\ttol reached in 68 interations\tdiff=0.000000\tmodel=0\n",
      "analysing pair 2 5\n",
      "\tusing nSites= 1227003 \n",
      "\ttol reached in 103 interations\tdiff=0.000000\tmodel=0\n",
      "analysing pair 2 6\n",
      "\tusing nSites= 1254186 \n",
      "\ttol reached in 90 interations\tdiff=0.000000\tmodel=0\n",
      "analysing pair 2 7\n",
      "\tusing nSites= 1238576 \n",
      "\ttol reached in 93 interations\tdiff=0.000000\tmodel=0\n",
      "analysing pair 2 8\n",
      "\tusing nSites= 986915 \n",
      "\ttol reached in 289 interations\tdiff=0.000000\tmodel=0\n",
      "analysing pair 2 9\n",
      "\tusing nSites= 1133118 \n",
      "\ttol reached in 136 interations\tdiff=0.000000\tmodel=0\n",
      "analysing pair 3 4\n",
      "\tusing nSites= 1391489 \n",
      "\ttol reached in 49 interations\tdiff=0.000000\tmodel=0\n",
      "analysing pair 3 5\n",
      "\tusing nSites= 1468647 \n",
      "\ttol reached in 49 interations\tdiff=0.000000\tmodel=0\n",
      "analysing pair 3 6\n",
      "\tusing nSites= 1509452 \n",
      "\ttol reached in 52 interations\tdiff=0.000000\tmodel=0\n",
      "analysing pair 3 7\n",
      "\tusing nSites= 1482970 \n",
      "\ttol reached in 76 interations\tdiff=0.000000\tmodel=0\n",
      "analysing pair 3 8\n",
      "\tusing nSites= 1155639 \n",
      "\ttol reached in 138 interations\tdiff=0.000000\tmodel=0\n",
      "analysing pair 3 9\n",
      "\tusing nSites= 1374199 \n",
      "\ttol reached in 78 interations\tdiff=0.000000\tmodel=0\n",
      "analysing pair 4 5\n",
      "\tusing nSites= 1405968 \n",
      "\ttol reached in 56 interations\tdiff=0.000000\tmodel=0\n",
      "analysing pair 4 6\n",
      "\tusing nSites= 1434610 \n",
      "\ttol reached in 49 interations\tdiff=0.000000\tmodel=0\n",
      "analysing pair 4 7\n",
      "\tusing nSites= 1417672 \n",
      "\ttol reached in 66 interations\tdiff=0.000000\tmodel=0\n",
      "analysing pair 4 8\n",
      "\tusing nSites= 1117664 \n",
      "\ttol reached in 87 interations\tdiff=0.000000\tmodel=0\n",
      "analysing pair 4 9\n",
      "\tusing nSites= 1300943 \n",
      "\ttol reached in 62 interations\tdiff=0.000000\tmodel=0\n",
      "analysing pair 5 6\n",
      "\tusing nSites= 1518444 \n",
      "\ttol reached in 40 interations\tdiff=0.000000\tmodel=0\n",
      "analysing pair 5 7\n",
      "\tusing nSites= 1498111 \n",
      "\ttol reached in 38 interations\tdiff=0.000000\tmodel=0\n",
      "analysing pair 5 8\n",
      "\tusing nSites= 1167382 \n",
      "\ttol reached in 149 interations\tdiff=0.000000\tmodel=0\n",
      "analysing pair 5 9\n",
      "\tusing nSites= 1386348 \n",
      "\ttol reached in 67 interations\tdiff=0.000000\tmodel=0\n",
      "analysing pair 6 7\n",
      "\tusing nSites= 1532942 \n",
      "\ttol reached in 33 interations\tdiff=0.000000\tmodel=0\n",
      "analysing pair 6 8\n",
      "\tusing nSites= 1191341 \n",
      "\ttol reached in 90 interations\tdiff=0.000000\tmodel=0\n",
      "analysing pair 6 9\n",
      "\tusing nSites= 1419094 \n",
      "\ttol reached in 79 interations\tdiff=0.000000\tmodel=0\n",
      "analysing pair 7 8\n",
      "\tusing nSites= 1175799 \n",
      "\ttol reached in 109 interations\tdiff=0.000000\tmodel=0\n",
      "analysing pair 7 9\n",
      "\tusing nSites= 1397246 \n",
      "\ttol reached in 110 interations\tdiff=0.000000\tmodel=0\n",
      "analysing pair 8 9\n",
      "\tusing nSites= 1084868 \n",
      "\ttol reached in 172 interations\tdiff=0.000000\tmodel=0\n"
     ]
    }
   ],
   "source": [
    "!{IBS} -glf glf.glf.gz \\\n",
    "-model 0 \\\n",
    "-nInd 10 -allpairs 1 \\\n",
    "-outFileName results_IBS/ibs.model0.results"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 24,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "--2019-05-21 16:23:27--  https://raw.githubusercontent.com/rwaples/freqfree_suppl/master/read_IBS.R\n",
      "Resolving raw.githubusercontent.com (raw.githubusercontent.com)... 151.101.0.133, 151.101.64.133, 151.101.128.133, ...\n",
      "Connecting to raw.githubusercontent.com (raw.githubusercontent.com)|151.101.0.133|:443... connected.\n",
      "HTTP request sent, awaiting response... 200 OK\n",
      "Length: 4394 (4.3K) [text/plain]\n",
      "Saving to: ‘read_IBS.R’\n",
      "\n",
      "read_IBS.R          100%[===================>]   4.29K  --.-KB/s    in 0s      \n",
      "\n",
      "2019-05-21 16:23:27 (32.4 MB/s) - ‘read_IBS.R’ saved [4394/4394]\n",
      "\n"
     ]
    }
   ],
   "source": [
    "!wget https://raw.githubusercontent.com/rwaples/freqfree_suppl/master/read_IBS.R"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 25,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "  ind1 ind2  nSites         Kin        R0        R1\r\n",
      "6    0    6 1395178 -0.03655172 0.5791045 0.3439425\r\n"
     ]
    }
   ],
   "source": [
    "!Rscript \\\n",
    "-e \"source('./read_IBS.R')\" \\\n",
    "-e \"res = do_derived_stats(read_ibspair_model0('results_IBS/ibs.model0.results.ibspair'))\" \\\n",
    "-e \"print(res[6,c('ind1', 'ind2', 'nSites', 'Kin', 'R0', 'R1') ])\""
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 26,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "bams/smallNA06985.mapped.ILLUMINA.bwa.CEU.low_coverage.20111114.bam\r\n",
      "bams/smallNA06994.mapped.ILLUMINA.bwa.CEU.low_coverage.20111114.bam\r\n",
      "bams/smallNA07000.mapped.ILLUMINA.bwa.CEU.low_coverage.20111114.bam\r\n",
      "bams/smallNA07056.mapped.ILLUMINA.bwa.CEU.low_coverage.20111114.bam\r\n",
      "bams/smallNA07357.mapped.ILLUMINA.bwa.CEU.low_coverage.20111114.bam\r\n",
      "bams/smallNA11829.mapped.ILLUMINA.bwa.CEU.low_coverage.20111114.bam\r\n",
      "bams/smallNA11830.mapped.ILLUMINA.bwa.CEU.low_coverage.20111114.bam\r\n",
      "bams/smallNA11831.mapped.ILLUMINA.bwa.CEU.low_coverage.20111114.bam\r\n",
      "bams/smallNA11832.mapped.ILLUMINA.bwa.CEU.low_coverage.20111114.bam\r\n",
      "bams/smallNA11840.mapped.ILLUMINA.bwa.CEU.low_coverage.20111114.bam\r\n"
     ]
    }
   ],
   "source": [
    "# the ibs method in angsd reports the individuals as they appear in the filelist\n",
    "!cat all.filelist"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 28,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "       sample1      sample2  nSites         Kin        R0        R1\r\n",
      "1 smallNA06985 smallNA11830 1372848 -0.04746918 0.6052391 0.3290302\r\n"
     ]
    }
   ],
   "source": [
    "# and compare to the realSFS results\n",
    "!Rscript \\\n",
    "-e \"source('./read_realSFS.R')\" \\\n",
    "-e \"res = read_realSFS('results_realsfs/smallNA06985_smallNA11830.2dsfs')\" \\\n",
    "-e \"res['sample1'] = 'smallNA06985'; res['sample2'] = 'smallNA11830'\" \\\n",
    "-e \"print(res[,c('sample1', 'sample2', 'nSites', 'Kin', 'R0', 'R1') ])\""
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  }
 ],
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