error in rule combine_linear_circular

slambrechts commented 2 years ago

Hi Alex,

I noticed one last error in my screen output. Not sure whether it actually affects anything important, because as you confirmed, the output I got from the test files is as expected, but thought I would post it here just in case/for completion:

an error in rule combine_linear_circular

Error in rule combine_linear_circular:
    jobid: 61
    output: iter-0/all.pdg.faa, iter-0/all.pdg.gff, iter-0/all.fna
    shell:

        # it's OK to cat gff directly
        cat  > iter-0/all.pdg.gff
        cat  > iter-0/all.pdg.faa
        cat  > iter-0/all.fna
        if [ ! -s iter-0/all.pdg.faa ]; then
            printf "
*** NOTE: No genes from the contigs are left in iter-0/all.pdg.faa after preprocess; virsorter replies on features from these genes for prediction; check quality of your contigs (too short or strange sequence composition), or just discard this sample

" | python /kyukon/scratch/gent/vo/000/gvo00043/vsc42339/virsearch/.snakemake/conda/67563fcffc73b3f93290e2e9f175e236/lib/python3.9/site-packages/virsorter/./scripts/echo.py
            touch EARLY-EXIT
            exit 234
        fi

        (one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode!)

Exiting because a job execution failed. Look above for error message

*** An error occurred. Detailed errors may not be printed for certain rules. Refer to the log file of the failed command for troubleshooting
Issues can be raised at: https://github.com/jiarong/VirSorter2/issues
/kyukon/scratch/gent/vo/000/gvo00043/vsc42339/virsearch/tools/rename_multifasta_prefix.py:7: DeprecationWarning: 'U' mode is deprecated
  for line in open(args.fasta_file, "rU"):

If I'm not mistaken, it only got printed once, in the beginning, pretty soon after running snakemake --use-conda -k -j 48

alexmsalmeida commented 2 years ago

Hi Sam,

Yup, that is the expected behaviour since none of the sequences in Sample 2 pass the length threshold. I added that as a test to make sure the pipeline would still successfully proceed in these situations.

Best, Alex

slambrechts commented 2 years ago

Ok great, thanks for the explanation

Best regards, Sam

alexmsalmeida / virsearch

error in rule combine_linear_circular #3