KMA issue

[Lcornet]

Dear Confindr team,

I would like to test confindr on a genome : This is my script

!/bin/bash

Submission script for Vega

SBATCH --time=1-06:00:00 # days-hh:mm:ss

#

SBATCH --ntasks=1

SBATCH --cpus-per-task=20

SBATCH --mem-per-cpu=2625 # megabytes

SBATCH --partition=defq

Uncomment the following line if your work

is floating point intensive and CPU-bound.

SBATCH --threads-per-core=1

export OMP_NUM_THREADS=20 export MKL_NUM_THREADS=20

module load Python/3.6.4-intel-2018a confindr -i in -o test --fasta -t 20

I have the following error : ESC[92m ESC[1m 2019-09-01 13:19:20 ESC[0m Welcome to ConFindr 0.7.1! Beginning analysis of your samples... ESC[92m ESC[1m 2019-09-01 13:19:20 ESC[0m Beginning analysis of sample GCA_000344075... ESC[92m ESC[1m 2019-09-01 13:19:20 ESC[0m Checking for cross-species contamination... ESC[92m ESC[1m 2019-09-01 13:19:27 ESC[0m Extracting conserved core genes... ESC[92m ESC[1m 2019-09-01 13:20:24 ESC[0m Quality trimming... ESC[92m ESC[1m 2019-09-01 13:20:26 ESC[0m Detecting contamination... ESC[92m ESC[1m 2019-09-01 13:20:26 ESC[0m Encountered error when attempting to run ConFindr on sample GCA_000344075. Skipping... ESC[92m ESC[1m 2019-09-01 13:20:26 ESC[0m Error encounted was: Traceback (most recent call last): File "/home/ulg/medgen/lcornet/.local/lib/python3.6/site-packages/confindr_src/confindr.py", line 1014, in confindr cross_details=args.cross_details) File "/home/ulg/medgen/lcornet/.local/lib/python3.6/site-packages/confindr_src/confindr.py", line 706, in find_contamination out, err = run_cmd(cmd) File "/home/ulg/medgen/lcornet/.local/lib/python3.6/site-packages/confindr_src/confindr.py", line 33, in run_cmd raise subprocess.CalledProcessError(p.returncode, cmd=cmd) subprocess.CalledProcessError: Command 'kma -i test/GCA_000344075/trimmed.fastq.gz -t_db /home/ulg/medgen/lcornet/.confindr_db/rMLST_combined_kma -o test/GCA_000344075/kma_rmlst -t 20' returned non-zero exit status 1.

ESC[92m ESC[1m 2019-09-01 13:20:26 ESC[0m Contamination detection complete!

Why is is looking for fastq.gz ?

Thanks

[luciagrami]

I have the same issue.

[adamkoziol]

Hi!

Sorry for the extremely long delay in responding to your issue - I only recently realised that once I took over this project, I wasn't automatically subscribed to it.

Looking into the code, the reason it is looking for the fastq.gz files, is that the program uses generic names when creating and processing files. I've updated ConFindr to 0.7.3 on bioconda, and I think the new version addresses your issue.

Please let me know if it works.

[pcrxn]

Closed as the fix has been implemented.