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Yet another bam2feat error: Return code -11 #37

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amizeranschi opened this issue Jan 19, 2025 · 0 comments
Open

Yet another bam2feat error: Return code -11 #37

amizeranschi opened this issue Jan 19, 2025 · 0 comments

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@amizeranschi
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This issue has come up here before, but I can't figure out what the problem might be. Any help would be much appreciated.

[2025-01-19 17:52:23.499] [svc] [info] Processing contig: k121_43
[2025-01-19 17:52:23.499] [svc] [info] Getting per-read characteristics

Traceback (most recent call last):
  File "/usr/local/bin/resmico", line 10, in <module>
    sys.exit(main())
  File "/usr/local/lib/python3.10/site-packages/resmico/__main__.py", line 52, in main
    args.func(args)
  File "/usr/local/lib/python3.10/site-packages/resmico/commands/bam2feat.py", line 80, in main
    bam2feat.main(args)
  File "/usr/local/lib/python3.10/site-packages/resmico/bam2feat.py", line 277, in main
    feat_files = run_bam2feat(bam_fasta, exe, args)
  File "/usr/local/lib/python3.10/site-packages/resmico/bam2feat.py", line 250, in run_bam2feat
    return [x for x in res]
  File "/usr/local/lib/python3.10/site-packages/resmico/bam2feat.py", line 250, in <listcomp>
    return [x for x in res]
  File "/usr/local/lib/python3.10/site-packages/resmico/bam2feat.py", line 222, in _run_bam2feat
    bam2feat(bam_sub, ref_tmp, outdir_feat, exe['bam2feat'], args)
  File "/usr/local/lib/python3.10/site-packages/resmico/bam2feat.py", line 186, in bam2feat
    run_cmd(cmd)
  File "/usr/local/lib/python3.10/site-packages/resmico/bam2feat.py", line 102, in run_cmd
    raise ValueError('Return code: {}'.format(rc))
ValueError: Return code: -11

I checked contig k121_43 and there are no weird characters in it (no Ns, nothing besides As, Gs, Cs and Ts).

What could be causing this error?

P.S. I'm using version 1.1.1 from Docker, because the image for version 1.2.2 is missing Samtools and won't run without it (as reported here). More specifically, I'm using the following Docker image tag: 1.1.1--py310hc8f18ef_0 from Quay.io: https://quay.io/repository/biocontainers/resmico?tab=tags.

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