Truvari error "Unable to fetch chrx" and TypeError: object of type 'NoneType' has no len()

Question

[guntul]

I run Truvari for benchmarking of 2 vcf files truvari bench -b NA12878_S1.genome.vcf.gz -c b1.vcf.gz -o out. However, it gives the following error. First vcf file contains format, info, filter, contig and maxdepth headers, which is the vcf file I found on Internet. The second vcf file is output of a CNV calling software, which I converted from a bed file. It contains CHROM POS ID REF ALT QUAL FILTER INFO FORMAT SAMPLE columns and

##fileformat=VCFv4.2
##INFO=<ID=END,Number=1,Type=Integer>`

this above header. It gives the following error. I tried to find a solution but none works. Ant help can be appreciated.

2023-06-19 09:00:52,243 [INFO] Params:
{
    "base": "/mnt/compgen/homes/user1/output_files/NA12878_S1.genome.vcf.gz",
    "comp": "/mnt/compgen/homes/user1/output_files/b1.vcf.gz",
    "output": "out4",
    "includebed": null,
    "extend": 0,
    "debug": false,
    "reference": null,
    "refdist": 500,
    "pctseq": 0.7,
    "minhaplen": 50,
    "pctsize": 0.7,
    "pctovl": 0.0,
    "typeignore": false,
    "chunksize": 1000,
    "bSample": "NA12878",
    "cSample": "SAMPLE",
    "dup_to_ins": false,
    "sizemin": 50,
    "sizefilt": 30,
    "sizemax": 50000,
    "passonly": false,
    "no_ref": false,
    "pick": "single"
}
2023-06-19 09:00:52,314 [WARNING] Excluding 1 contigs present in comparison calls header but not baseline calls.
2023-06-19 09:00:52,317 [WARNING] Unable to fetch chr1 from b'/mnt/compgen/homes/user1/output_files/b1.vcf.gz'
2023-06-19 09:00:52,317 [WARNING] Unable to fetch chr10 from b'/mnt/compgen/homes/user1/output_files/b1.vcf.gz'
2023-06-19 09:00:52,318 [WARNING] Unable to fetch chr11 from b'/mnt/compgen/homes/user1/output_files/b1.vcf.gz'
2023-06-19 09:00:52,318 [WARNING] Unable to fetch chr12 from b'/mnt/compgen/homes/user1/output_files/b1.vcf.gz'
2023-06-19 09:00:52,318 [WARNING] Unable to fetch chr13 from b'/mnt/compgen/homes/user1/output_files/b1.vcf.gz'
2023-06-19 09:00:52,318 [WARNING] Unable to fetch chr14 from b'/mnt/compgen/homes/user1/output_files/b1.vcf.gz'
2023-06-19 09:00:52,318 [WARNING] Unable to fetch chr15 from b'/mnt/compgen/homes/user1/output_files/b1.vcf.gz'
2023-06-19 09:00:52,318 [WARNING] Unable to fetch chr16 from b'/mnt/compgen/homes/user1/output_files/b1.vcf.gz'
2023-06-19 09:00:52,318 [WARNING] Unable to fetch chr17 from b'/mnt/compgen/homes/user1/output_files/b1.vcf.gz'
2023-06-19 09:00:52,318 [WARNING] Unable to fetch chr18 from b'/mnt/compgen/homes/user1/output_files/b1.vcf.gz'
2023-06-19 09:00:52,318 [WARNING] Unable to fetch chr19 from b'/mnt/compgen/homes/user1/output_files/b1.vcf.gz'
2023-06-19 09:00:52,318 [WARNING] Unable to fetch chr2 from b'/mnt/compgen/homes/user1/output_files/b1.vcf.gz'
2023-06-19 09:00:52,318 [WARNING] Unable to fetch chr20 from b'/mnt/compgen/homes/user1/output_files/b1.vcf.gz'
2023-06-19 09:00:52,318 [WARNING] Unable to fetch chr21 from b'/mnt/compgen/homes/user1/output_files/b1.vcf.gz'
2023-06-19 09:00:52,318 [WARNING] Unable to fetch chr22 from b'/mnt/compgen/homes/user1/output_files/b1.vcf.gz'
2023-06-19 09:00:52,318 [WARNING] Unable to fetch chr3 from b'/mnt/compgen/homes/user1/output_files/b1.vcf.gz'
2023-06-19 09:00:52,318 [WARNING] Unable to fetch chr4 from b'/mnt/compgen/homes/user1/output_files/b1.vcf.gz'
2023-06-19 09:00:52,318 [WARNING] Unable to fetch chr5 from b'/mnt/compgen/homes/user1/output_files/b1.vcf.gz'
2023-06-19 09:00:52,318 [WARNING] Unable to fetch chr6 from b'/mnt/compgen/homes/user1/output_files/b1.vcf.gz'
2023-06-19 09:00:52,319 [WARNING] Unable to fetch chr7 from b'/mnt/compgen/homes/user1/output_files/b1.vcf.gz'
2023-06-19 09:00:52,319 [WARNING] Unable to fetch chr8 from b'/mnt/compgen/homes/user1/output_files/b1.vcf.gz'
2023-06-19 09:00:52,319 [WARNING] Unable to fetch chr9 from b'/mnt/compgen/homes/user1/output_files/b1.vcf.gz'
2023-06-19 09:00:52,319 [WARNING] Unable to fetch chrM from b'/mnt/compgen/homes/user1/output_files/b1.vcf.gz'
2023-06-19 09:00:52,319 [WARNING] Unable to fetch chrX from b'/mnt/compgen/homes/user1/output_files/b1.vcf.gz'
2023-06-19 09:00:52,319 [WARNING] Unable to fetch chrY from b'/mnt/compgen/homes/user1/output_files/b1.vcf.gz'
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 293, in chunker
    if len(entry.alts) > 1:
TypeError: object of type 'NoneType' has no len()

[Pierre Lindenbaum]

##fileformat=VCFv4.2
##INFO=<ID=END,Number=1,Type=Integer>`

how about FORMAT/GT, contigs, INFO/SVTYPE,INFO/SVLEN etc...

and are your vcf.gz indexed ?

and do they both use the same chromosome notation ('chrX' vs 'X' vs 'x' )