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Need help to run lastz.psl-100k_sim.sh #1

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farhan-lab opened this issue Apr 25, 2022 · 12 comments
Open

Need help to run lastz.psl-100k_sim.sh #1

farhan-lab opened this issue Apr 25, 2022 · 12 comments

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@farhan-lab
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Dear Luohao,

I am trying to investigate the ZW similarity and evolutionary strata using your script "lastz.psl-100k_sim.sh" and following similar analysis as reported in your paper Xu et al. 2019. I have assembled pseudo-scaffold for each Z and W chromosomes. I tried to run the script according to your protocol as following command:

sh ./BOPsexChr-master/lastz.psl-100k_sim.sh result_test Z_masked.fasta W-scaff.masked.fasta

But I get the following error messages.

FAILURE: in init_from_anchors(), structure size would exceed 2^32 (362128816 + 128*45266102)
consider raising scoring threshold (--hspthresh or --exact) or breaking your target sequence into smaller pieces
./BOPsexChr-master/lastz.psl-100k_sim.sh: 17: ./BOPsexChr-master/lastz.psl-100k_sim.sh: faSize: not found
./BOPsexChr-master/lastz.psl-100k_sim.sh: 18: ./BOPsexChr-master/lastz.psl-100k_sim.sh: faSize: not found
./BOPsexChr-master/lastz.psl-100k_sim.sh: 19: ./BOPsexChr-master/lastz.psl-100k_sim.sh: chainPreNet: not found
./BOPsexChr-master/lastz.psl-100k_sim.sh: 21: ./BOPsexChr-master/lastz.psl-100k_sim.sh: chainNet: not found
./BOPsexChr-master/lastz.psl-100k_sim.sh: 21: ./BOPsexChr-master/lastz.psl-100k_sim.sh: netSyntenic: not found
./BOPsexChr-master/lastz.psl-100k_sim.sh: 23: ./BOPsexChr-master/lastz.psl-100k_sim.sh: faToTwoBit: not found
./BOPsexChr-master/lastz.psl-100k_sim.sh: 24: ./BOPsexChr-master/lastz.psl-100k_sim.sh: faToTwoBit: not found
./BOPsexChr-master/lastz.psl-100k_sim.sh: 26: ./BOPsexChr-master/lastz.psl-100k_sim.sh: ./BOPsexChr-master/lastz.psl-100k_sim.sh: 26: ./BOPsexChr-master/lastz.psl-100k_sim.sh: netToAxt: not found
axtSort: not found
./BOPsexChr-master/lastz.psl-100k_sim.sh: 28: ./BOPsexChr-master/lastz.psl-100k_sim.sh: axtToMaf: not found
./BOPsexChr-master/lastz.psl-100k_sim.sh: 30: ./BOPsexChr-master/lastz.psl-100k_sim.sh: mafToPsl: not found
./BOPsexChr-master/lastz.psl-100k_sim.sh: 33: ./BOPsexChr-master/lastz.psl-100k_sim.sh: pslScore: not found

Could you please guide me, how can I fix these warnings and run the script with success?
Many thanks,
Regards,
Farhan
@lurebgi
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lurebgi commented Apr 25, 2022 via email

@farhan-lab
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Hi,
Many thanks for your quick response. I already installed LASTZ tool, for ucsc genomic utilities, should I install all of the listed utilities or any specific?

@lurebgi
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lurebgi commented Apr 26, 2022

For the purpose of this task, installing what is needed, e.g. faSize, will be fine, though it never harms to install all of them.

@lurebgi
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lurebgi commented Apr 26, 2022 via email

@farhan-lab
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farhan-lab commented Apr 26, 2022 •
edited
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Thanks, I already install all utilities and run the script again, this time I got some files, but the main output files are empty:

./BOPsexChr-master/lastz.psl-100k_sim.sh: 7: ./BOPsexChr-master/lastz.psl-100k_sim.sh: module: not found
FAILURE: in init_from_anchors(), structure size would exceed 2^32 (393351136 + 128*49168891)
consider raising scoring threshold (--hspthresh or --exact) or breaking your target sequence into smaller pieces
Got 1 chroms in result_test/result_test.z.fa.size, 1 in result_test/result_test.w.list.mask.fa.size
Finishing nets
writing stdout
writing /dev/null
memory usage 41680896, utime 0 s/100, stime 1
result_test/result_test.z-w.psl is empty
Can't open perl script "psl-100k_sim.pl": No such file or directory

ls -lah
total 35M
-rwxrwxrwx 1 cytolab cytolab 402 Apr 26 14:14 result_test.axt
-rwxrwxrwx 1 cytolab cytolab 528 Apr 26 14:14 result_test.axt.chain
-rwxrwxrwx 1 cytolab cytolab 528 Apr 26 14:14 result_test.axt.chain.filt
-rwxrwxrwx 1 cytolab cytolab 95 Apr 26 14:14 result_test.chain.log
-rwxrwxrwx 1 cytolab cytolab 528 Apr 26 14:14 result_test.noClass.net
-rwxrwxrwx 1 cytolab cytolab 11M Apr 26 14:14 result_test.w.list.mask.fa.2bit
-rwxrwxrwx 1 cytolab cytolab 23 Apr 26 14:14 result_test.w.list.mask.fa.size
-rwxrwxrwx 1 cytolab cytolab 24M Apr 26 14:14 result_test.z.fa.2bit
-rwxrwxrwx 1 cytolab cytolab 23 Apr 26 14:14 result_test.z.fa.size
-rwxrwxrwx 1 cytolab cytolab 528 Apr 26 14:14 result_test.z-w.axt
-rwxrwxrwx 1 cytolab cytolab 559 Apr 26 14:14 result_test.z-w.maf
-rwxrwxrwx 1 cytolab cytolab 0 Apr 26 14:14 result_test.z-w.psl
-rwxrwxrwx 1 cytolab cytolab 0 Apr 26 14:14 result_test.z-w.psl.score
-rwxrwxrwx 1 cytolab cytolab 0 Apr 26 14:14 result_test.z-w.psl.score.ide95.filt
-rwxrwxrwx 1 cytolab cytolab 0 Apr 26 14:14 result_test.z-w.psl.score.ide95.filt.100k
-rwxrwxrwx 1 cytolab cytolab 0 Apr 26 14:14 result_test.z-w.psl.score.ide95.filt.ide-100k

Do you think it may be possible that , Z and W chromosome alignments were somehow restricted from the lastz filtering criterion "--hspthresh=2200 --inner=2000 --ydrop=3400 --gappedthresh=10000" which ended up no similarity?

Many thanks for your support

@lurebgi
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lurebgi commented Apr 26, 2022

can you show me result_test/result_test.z.fa.size

@farhan-lab
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Sure, Here it is:
chromosome_8 100101675

@lurebgi
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lurebgi commented Apr 26, 2022

how about result_test/result_test.w.list.mask.fa.size?

Perhaps try lastz with default settings, i.e. without "--hspthresh=2200 --inner=2000 --ydrop=3400 --gappedthresh=10000", and try with smaller size data to figure out the problem.

@farhan-lab
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cat result_test.w.list.mask.fa.size
Super-Scaffol 43643165

OK.. I will try lastz with default setting. and update on it soon

@lurebgi
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lurebgi commented Apr 26, 2022

maybe also try splitting Super-Scaffol into smaller pieces. The issue seems to be memory limitation.

@farhan-lab
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Hi I just re run with last options and the output files are still empty.

cat result_test.axt

lastz.v1.04.15 --step=19 --format=axt

hsp_threshold = 3000

gapped_threshold = 3000

x_drop = 910

y_drop = 9400

gap_open_penalty = 400

gap_extend_penalty = 30

A C G T

A 91 -114 -31 -123

C -114 100 -125 -31

G -31 -125 100 -114

T -123 -31 -114 91

Is it possible that my Z and W scaffolds sequences do not show any similarity or homology at all?

@lurebgi
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lurebgi commented Apr 26, 2022

please try with nucmer or other tools then - sorry but I couldn't be more helpful.

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