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mskcc / tempo

CCS research pipeline to process WES and WGS TN pairs
https://cmotempo.netlify.com/
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`QcConpair` exits with error #924

Open anoronh4 opened 2 years ago

anoronh4 commented 2 years ago

A small minority of samples (so far 1 in wes_repo) repeatedly error out with the following:

Traceback (most recent call last):
  File "/usr/bin/conpair/scripts/verify_concordances.py", line 315, in <module>
    main()
  File "/usr/bin/conpair/scripts/verify_concordances.py", line 183, in main
    str_return = run_verify_concordance(N_pileup, T_pileup, MARKER_FILE, MMQ, MBQ, COVERAGE_THRESHOLD, AA_BB_only)
  File "/usr/bin/conpair/scripts/verify_concordances.py", line 220, in run_verify_concordance
    Tumor_genotype_likelihoods = genotype_likelihoods_for_markers(Markers, T_pileup, min_map_quality=MMQ, min_base_quality=MBQ)
  File "/usr/bin/conpair/modules/ContaminationMarker.py", line 106, in genotype_likelihoods_for_markers
    pileup = parse_mpileup_line(line, min_map_quality=min_map_quality, min_base_quality=min_base_quality)
  File "/usr/bin/conpair/modules/ContaminationMarker.py", line 76, in parse_mpileup_line
    mapqs_above_threshold = set([i for i in range(0, len(mapqs)) if int(mapqs[i]) >= min_map_quality])
ValueError: invalid literal for int() with base 10: 'A00227:20:H3CFFDMXX:1:1440:7500:17'

I will try to remove the cached directories for the previous step (QcPileup) to see if that gets rid of the error. If it does, then we should try to see if we can validate the Pileup file before proceeding to QcConpair.

anoronh4 commented 2 years ago

after forcing nextflow to repeat QcPileup for the normal sample, the QcConpair completed with success. So far this occurred in 1 sample, so this is definitely not high priority