annotate module, perl5 librarie

bxlab / metaWRAP

MetaWRAP - a flexible pipeline for genome-resolved metagenomic data analysis

MIT License

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annotate module, perl5 librarie #193

Open ganiatgithub opened 5 years ago

ganiatgithub commented 5 years ago

Hi,

I tried both manual installation and conda installation for metawrap 1.2.1, both came across this issue when following the annotate module:

/user/tools/Miniconda3/envs/metawrap-1.2.1/lib/perl5/site_perl/5.22.0 does not           *****
*****                         exixt. Cannot set manual path to perl5 libraries. Exiting...

My code for running the conda environment:

source activate /user/tools/Miniconda3/envs/metawrap-1.2.1

metaWRAP annotate_bins \
-b /user/jiaoyang/metaWRAP/reassemble_out/reassembled_bins \
-o /user/jiaoyang/metaWRAP/annotate_out \
-t 24 

conda deactivate

Any tips on how to proceed?

Many thanks!

ursky commented 5 years ago

I never tested metawrap with miniconda3 - might be one of the issues. The problem is coming from prokka not being able to run. Can you see what error you get when you try to run prokka manually?

The manual path settings in metawrap tries to find the correct perl libraries in /user/tools/Miniconda3/envs/metawrap-1.2.1/lib/perl5/site_perl/5.22.0. Can you check if the folder is there (probably now), or what SHOULD be the correct folder with all your conda env perl libraries (might be a simmilar path).

ganiatgithub commented 5 years ago

I installed prokka 1.1.3 in a conda env, and it worked fine. In the dir /user/tools/Miniconda3/envs/metawrap-1.2.1/lib, there is no dir called perl5, will manually add the /perl5 dir work, where can I obtain this dir?

Thank you.

ursky commented 5 years ago

Thanks for the info! I found the problem. I updated the code on github, so try to replace your /user/tools/Miniconda3/envs/metawrap-1.2.1/bin/metawrap-modules/annotate_bins.sh with the one in this repository (clone it somewhere, or just download). The fix will come in the next version. Let me know if it works.

ganiatgithub commented 5 years ago

Hello,

I replaced the annotate_bins.sh from this repository, ran it again and got the follow message:

blastp: error while loading shared libraries: libssl.so.1.0.0: cannot open shared object file: No such file or directory
[09:54:43] Could not determine version of blastp - please install version 2.2 or higher

My code:

source activate /30days/uqgni1/tools/Miniconda3/envs/metawrap-1.2.1

metaWRAP annotate_bins \
-b /user/jiaoyang/metaWRAP/reassemble_out/reassembled_bins \
-o /user/jiaoyang/metaWRAP/annotate_out \
-t 24

conda deactivate

The miniconda3 should not be the problem, because I used this environment to run the classify module and that works. I used python=2.7 when I created the metawrap-1.2.1 environment.

Any tips?

ursky commented 5 years ago

Check out this discussion: https://github.com/bxlab/metaWRAP/issues/188. Its a pretty easy fix. The next metawrap version (1.2.2) should be fixed.

ganiatgithub commented 5 years ago

It worked, thanks a lot!