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cpwardell / FiNGS

Filters for Next Generation Sequencing
Apache License 2.0
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list index out of range when writing filtered VCF #7

Open mheskett opened 2 years ago

mheskett commented 2 years ago

This happens for some of my samples but not all. It is able to write part of the VCF and then fails. With some debugging It seems like this only happens if you run multiple samples with the default output directory of ./results. 


  File "/home/users/heskett/miniconda3/envs/fings/bin/fings", line 10, in <module>
    sys.exit(main())
  File "/home/users/heskett/miniconda3/envs/fings/lib/python3.7/site-packages/fings/FiNGS.py", line 223, in main
    applyfilters(tdata,ndata,sdata,pdict,resultsdir,vcfpath,referencegenome,args.PASSonlyin,args.PASSonlyout)
  File "/home/users/heskett/miniconda3/envs/fings/lib/python3.7/site-packages/fings/filter_functions.py", line 121, in applyfilters
    record.FILTER=judgement(flist[passindex])
IndexError: list index out of range

call is:

fings -n .255J_N1.recal.bam -t .255J_T1.recal.bam -v snpEff.ann.vcf --PASSonlyin --PASSonlyout```