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```
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.