LoadError when running Mentalist in my custom cgMLST scheme

[davidmaimoun]

Hi
Thank you for the great tool!
However, I encountered issues when I ran it on my cgmlst neisserai schema (downloaded from pubmlst)
In my folder "scheme", I have fastas file, 'NEIS0001.fas', "NEIS0004.fas" etc...

Command line:
mentalist build_db -k 25 --db niesseria_25.db -p scheme/neisseria.txt -f scheme/*.fas

Error
warning: parsing line table prologue at 0x0001cd5c should have ended at 0x0001d0f0 but it ended at 0x0001ce26
warning: parsing line table prologue at 0x0000e1c8 should have ended at 0x0000e52f but it ended at 0x0000e285
warning: parsing line table prologue at 0x00022486 should have ended at 0x0002411a but it ended at 0x00022527
warning: parsing line table prologue at 0x00003c27 should have ended at 0x00003ffc but it ended at 0x00003ce4
warning: parsing line table prologue at 0x0001357a should have ended at 0x0001390c but it ended at 0x00013637
warning: parsing line table prologue at 0x00007565 should have ended at 0x00007914 but it ended at 0x00007622
warning: parsing line table prologue at 0x0000a9c0 should have ended at 0x0000ace8 but it ended at 0x0000aa7d
warning: parsing line table prologue at 0x000086e2 should have ended at 0x00008ae4 but it ended at 0x000087f0
warning: parsing line table prologue at 0x00000000 should have ended at 0x0000041a but it ended at 0x00000152
ERROR: LoadError: error compiling init: could not load library "/home/user1/miniconda3/envs/mentalist/share/julia/site/v0.5/Blosc/src/../deps/libblosc"
/home/user1/miniconda3/envs/mentalist/share/julia/site/v0.5/Blosc/src/../deps/libblosc.so: cannot open shared object file: No such file or directory
...
...

Can you help me plaese?

[TorHou]

Hi David,

I have encountered this error as well, when I installed MentaLiST via bioconda (version 0.2.4)
What I had to do, to get this to work, was compiling the Blosc library myself. You will need cmake as well as a C++ (and C, I think) compiler.
Then you have to navigate to where the source code of Blosc is located, in your case:

cd /home/user1/miniconda3/envs/mentalist/share/julia/site/v0.5/Blosc/deps/c-blosc-1.12.1/

then you can use cmake like this

mkdir build
cd build
cmake ..

which should take care of finding the necessary compilers and build a Makefile for you. And then you should be able to simply build the library

make

Now you should have a folder blosc with the library libblosc.so. You can probably install this library with the Makefile somehow, but what I did was simply create a softlink to where Julia expects to find this library.

cd /home/user1/miniconda3/envs/mentalist/share/julia/site/v0.5/Blosc/deps
ln -s /home/user1/miniconda3/envs/mentalist/share/julia/site/v0.5/Blosc/deps/c-blosc-1.12.1/build/blosc/libblosc.so libblosc.so

I hope this works for you
Best,
Torsten