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OLC-Bioinformatics / ConFindr

Intra-species bacterial contamination detection
https://olc-bioinformatics.github.io/ConFindr/
MIT License
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kma exit status issue #14

Closed pkmitchell closed 5 years ago

pkmitchell commented 5 years ago

Hello,

I get the following error when running Confindr. Same error has occurred across multiple input files (all Salmonella).

2019-05-22 15:06:55 Encountered error when attempting to run ConFindr on sample Sample5. Skipping... 2019-05-22 15:06:55 Error encounted was: Traceback (most recent call last): File "/workdir/miniconda3/envs/bacWGS/lib/python3.5/site-packages/confindr_src/confindr.py", line 975, in confindr use_rmlst=args.rmlst) File "/workdir/miniconda3/envs/bacWGS/lib/python3.5/site-packages/confindr_src/confindr.py", line 666, in find_contamination out, err = run_cmd(cmd) File "/workdir/miniconda3/envs/bacWGS/lib/python3.5/site-packages/confindr_src/confindr.py", line 33, in run_cmd raise subprocess.CalledProcessError(p.returncode, cmd=cmd) subprocess.CalledProcessError: Command 'kma -ipe confindr_output2/Sample5/trimmed_R1.fastq.gz confindr_output2/Sample5/trimmed_R2.fastq.gz -t_db /home/pkm57/.confindr_db/Salmonella_db_cgderived_kma -o confindr_output2/Sample5/kma_rmlst -t 16' returned non-zero exit status 1

I ran the kma command on its own and it seems to produce reasonable output with no obvious errors aside from returning an exit status of 1. Any idea why this might be occur? I am using ConFinder v 0.7.0 installed using conda. Same result has occurred with ConFindr installed in its own conda environment as well as in a general purpose environment with other tools.

lowandrew commented 5 years ago

That's odd, this is something I haven't seen before - can you let me know what version of kma you have installed in your environment? KMA got updated semi-recently, so it might be that the latest version doesn't play nicely.

It would also be helpful for me to be able to run ConFindr on your sequences; would you be able to send them to me so I can do some more in-depth debugging?

pkmitchell commented 5 years ago

I have kma version 1.2.3 installed. I got the same result using the example data as well as files on SRA (E. coli: SRR5928129 & SRR5928130; Salmonella: SRR5666354 & SRR5666356).

lowandrew commented 5 years ago

I've managed to reproduce your issue on my end - for me it was solved by downgrading the version of KMA that I had installed. Can you get KMA v1.2.0 installed in your conda env (conda install kma==1.2.0) and let me know if that fixes the issue for you too? If so I'll get the conda recipe updated so that the correct version of KMA is installed by default.

pkmitchell commented 5 years ago

Changing the kma version fixed the issue on my end as well. Thanks!

lowandrew commented 5 years ago

Should be fixed by https://github.com/bioconda/bioconda-recipes/pull/15626