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cpwardell / FiNGS

Filters for Next Generation Sequencing
Apache License 2.0
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IndexError: list index out of range #13

Open SAADAT-Abu opened 12 months ago

SAADAT-Abu commented 12 months ago

I install fings and the test run went well but with actual data it is giving this error 

File "/mnt/beegfs/asaadat/.local/bin/fings", line 8, in <module>
    sys.exit(main())
  File "/mnt/beegfs/asaadat/.local/lib/python3.9/site-packages/fings/FiNGS.py", line 223, in main
    applyfilters(tdata,ndata,sdata,pdict,resultsdir,vcfpath,referencegenome,args.PASSonlyin,args.PASSonlyout)
  File "/mnt/beegfs/asaadat/.local/lib/python3.9/site-packages/fings/filter_functions.py", line 83, in applyfilters
    ordered_fieldnames = flist[0].keys()
IndexError: list index out of range

Would be glad if someone can help

cpwardell commented 12 months ago

Can you upload the VCF file you're trying to filter and the log file from the failed run to some cloud storage for me to have a look at?

SAADAT-Abu commented 12 months ago

Here is a link to the data. https://drive.google.com/drive/folders/1jUhxJeNU6gXq9016M29auCTLYI2tCrs5?usp=sharing Thanks a lot. A. Saadat

cpwardell commented 11 months ago

Your log and input file look good. Let's try some more things.

1.) Minor issue, shouldn't case any problems: You've included a reference genome, but you're using the default filtering settings that don't need a reference genome. Out of interest, can you tell me how many lines are in your reference genome?

wc -l Homo_sapiens_assembly38.fasta

2.) Are your bam files ok? What sequencing technology was used to produce your data? Is it Illumina paired-end sequencing? It looks like your VCF was produced using CRAM files; are you sure converting them to BAM format went ok? Can you share your bam files in the same google drive as your VCF? If you upload your CRAM files I might add CRAM support. Alternatively, can you use samtools to give me some snippets from them? Please do this for both HK11.bam and WT11.bam.

How many reads are in the bam files?

samtools view HK11.bam | wc -l

What is the header like?

samtools view -H HK11.bam

I'm sure we can solve your problem. When that's done, I'm going to update FiNGS to clean it up, lots of the packages it depends on have changed and it's making installing/running it difficult for new users.