Truvari error: Failed to parse TBX_VCF - "ead mapping qualities">"

Question

[guntul]

I am using truvari tools truvari bench -b basegenome.genome.vcf.gz -c genome1.vcf.gz -o out. But it gives the following error.

    2023-06-16 10:27:58,831 [WARNING] Excluding 1 contigs present in comparison calls header but not baseline calls.
[E::get_intv] Failed to parse TBX_VCF, was wrong -p [type] used?
The offending line was: "ead mapping qualities">"
Traceback (most recent call last):
  File "/home/user1/anaconda3/bin/truvari", line 8, in <module>
    sys.exit(main())
  File "/home/user1/anaconda3/lib/python3.9/site-packages/truvari/_main_.py", line 102, in main
    TOOLS[args.cmd](args.options)
  File "/home/user1/anaconda3/lib/python3.9/site-packages/truvari/bench.py", line 673, in bench_main
    output = m_bench.run()
  File "/home/user1/anaconda3/lib/python3.9/site-packages/truvari/bench.py", line 465, in run
    for match in itertools.chain.from_iterable(map(self.compare_chunk, chunks)):
  File "/home/user1/anaconda3/lib/python3.9/site-packages/truvari/matching.py", line 292, in chunker
    for key, entry in file_zipper(*files):
  File "/home/user1/anaconda3/lib/python3.9/site-packages/truvari/matching.py", line 257, in file_zipper
    markers.append([name, i, next(i)])
  File "/home/user1/anaconda3/lib/python3.9/site-packages/truvari/region_vcf_iter.py", line 80, in iterate
    for entry in vcf_file.fetch(chrom, intv.begin, intv.end):
  File "pysam/libcbcf.pyx", line 4006, in pysam.libcbcf.TabixIterator._next_
OSError: truncated file

What van be the possible reasons for this and how to solve this?

Answer 1

[WouterDeCoster]

Based on OSError: truncated file I suspect one of your VCFs is corrupted.