CalledProcessError

I am getting a CalledProcessError regarding the benchmark vcf, even though it has been indexed.

```
2021-05-05 18:27:33,391 WARNING No reference file found at default locations. You can set the environment variable 'HGREF' or 'HG19' to point to a suitable Fasta file.
Hap.py v0.3.14
[E::vcf_hdr_read] no sample line
**_**Failed to open or file not indexed: /u/home/n/neharajk/scratch/HG002_GRCh37_1_22_v4.2.1_benchmark_19.vcf**_**

2021-05-05 18:27:41,571 ERROR Command 'vcfcheck /u/home/n/neharajk/scratch/HG002_GRCh37_1_22_v4.2.1_benchmark_19.vcf --check-bcf-errors 1' returned non-zero exit status 1
2021-05-05 18:27:41,571 ERROR Traceback (most recent call last):
2021-05-05 18:27:41,571 ERROR File "./hap.py", line 540, in
2021-05-05 18:27:41,573 ERROR main()
2021-05-05 18:27:41,573 ERROR File "./hap.py", line 316, in main
2021-05-05 18:27:41,573 ERROR convert_gvcf_to_vcf=convert_gvcf_truth)
2021-05-05 18:27:41,573 ERROR File "/u/scratch/m/mdistler/hap.py-build/bin/pre.py", line 125, in preprocess
2021-05-05 18:27:41,576 ERROR mf = subprocess.check_output("vcfcheck %s --check-bcf-errors 1" % pipes.quote(vcf_input), shell=True)
2021-05-05 18:27:41,576 ERROR File "/u/local/apps/python/2.7.2/lib/python2.7/subprocess.py", line 544, in check_output
2021-05-05 18:27:41,599 ERROR raise CalledProcessError(retcode, cmd, output=output)
2021-05-05 18:27:41,600 ERROR CalledProcessError: Command 'vcfcheck /u/home/n/neharajk/scratch/HG002_GRCh37_1_22_v4.2.1_benchmark_19.vcf --check-bcf-errors 1' returned non-zero exit status 1
```

Any help?

Start with hap.py and the preprocess entry point in pre.py, especially the vcfcheck invocation shown in the traceback. Reproduce the command with the referenced benchmark VCF and determine whether the failure is caused by the file, its index, or missing VCF header content; done means identifying a reproducible cause and a documented resolution.

Written by the indexing model from the issue text.