Error first time an index is built

[zachary-foster]

When a VCF index is not present (.tbi file), one is made automatically, but then this error happens:

(.venv) /media/fosterz/external_primary/files/projects/work/current/krisp/scratch/rileys_error main : krisp_vcf metadata.csv reference.fasta --vcf variants.vcf.gz --groups NA1 NA2
Traceback (most recent call last):
  File "/media/fosterz/external_primary/files/projects/work/current/krisp/.venv/bin/krisp_vcf", line 8, in <module>
    sys.exit(main())
  File "/media/fosterz/external_primary/files/projects/work/current/krisp/src/krisp_vcf/krisp_vcf.py", line 1394, in main
    run_all()
  File "/media/fosterz/external_primary/files/projects/work/current/krisp/src/krisp_vcf/krisp_vcf.py", line 1336, in run_all
    contigs = read_vcf_contigs(args.vcf, reference=reference, chunk_size=100000, flank_size=1000,
  File "/media/fosterz/external_primary/files/projects/work/current/krisp/src/krisp_vcf/krisp_vcf.py", line 1026, in read_vcf_contigs
    index_handle = pysam.TabixFile(filename=path, index=index)
  File "pysam/libctabix.pyx", line 349, in pysam.libctabix.TabixFile.__cinit__
  File "pysam/libctabix.pyx", line 378, in pysam.libctabix.TabixFile._open
OSError: file `variants.vcf.gz.gz` not found