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OLC-Bioinformatics / ConFindr

Intra-species bacterial contamination detection
https://olc-bioinformatics.github.io/ConFindr/
MIT License
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ConFindr error with trash data #59

Open happykhan opened 4 months ago

happykhan commented 4 months ago

Hi

I am running into issues when I give data that cannot be assigned a genus via the mash screen step. This is some bacteriophage genome sequence data to represent a trash dataset. My installation is provided through conda. The test dataset runs fine.

T7_R2.fastq.gz T7_R1.fastq.gz

The kma index phase fails for me. 

  2024-02-16 13:37:34  Beginning analysis of sample T4... 
  2024-02-16 13:37:34  Checking for cross-species contamination... 
  2024-02-16 13:37:36  Extracting conserved core genes... 
  2024-02-16 13:38:19  Quality trimming... 
  2024-02-16 13:38:20  Detecting contamination... 
  2024-02-16 15:07:02  Encountered error when attempting to run ConFindr on sample T4. Skipping... 
  2024-02-16 15:07:02  Error encounted was:
Traceback (most recent call last):
  File "/opt/conda/lib/python3.7/site-packages/confindr_src/confindr.py", line 1045, in confindr
    min_matching_hashes=min_matching_hashes)
  File "/opt/conda/lib/python3.7/site-packages/confindr_src/confindr.py", line 690, in find_contamination
    out, err = run_cmd(cmd)
  File "/opt/conda/lib/python3.7/site-packages/confindr_src/confindr.py", line 33, in run_cmd
    raise subprocess.CalledProcessError(p.returncode, cmd=cmd)
subprocess.CalledProcessError: Command 'kma index -i /confindr_db/rMLST_combined.fasta -o /confindr_db/rMLST_combined_kma' returned non-zero exit status 137.

  2024-02-16 15:07:02  Beginning analysis of sample T7... 
  2024-02-16 15:07:02  Checking for cross-species contamination... 
  2024-02-16 15:07:03  Extracting conserved core genes... 
  2024-02-16 15:07:48  Quality trimming... 
  2024-02-16 15:07:49  Detecting contamination... 
  2024-02-16 15:07:50  Encountered error when attempting to run ConFindr on sample T7. Skipping... 
  2024-02-16 15:07:50  Error encounted was:
Traceback (most recent call last):
  File "/opt/conda/lib/python3.7/site-packages/confindr_src/confindr.py", line 1045, in confindr
    min_matching_hashes=min_matching_hashes)
  File "/opt/conda/lib/python3.7/site-packages/confindr_src/confindr.py", line 701, in find_contamination
    out, err = run_cmd(cmd)
  File "/opt/conda/lib/python3.7/site-packages/confindr_src/confindr.py", line 33, in run_cmd
    raise subprocess.CalledProcessError(p.returncode, cmd=cmd)
subprocess.CalledProcessError: Command 'kma -ipe /data/test_1_confindr_out/T7/trimmed_R1.fastq.gz /data/test_1_confindr_out/T7/trimmed_R2.fastq.gz -t_db /confindr_db/rMLST_combined_kma -o /data/test_1_confindr_out/T7/kma_rmlst -t 6' returned non-zero exit status 1.
yingeddi2008 commented 3 months ago

I have the same error message, and don't know what's wrong with the sample.