hap.py annotated VCF file as output issues running with docker

[achimmiri]

I am not running multisample VCF file

anusha@Precision-7920-Tower:~/TESTBEN1$ sudo docker run -it -v pwd:/data pkrusche/hap.py /opt/hap.py/bin/hap.py /data/NA12878.vcf.gz /data/PRO001B.vcf.gz -r /data/genome.fa -f /data/ConfidentRegions.bed.gz -V -o PRO001B_happy --no-leftshift --no-decompose --gender=none --engine=vcfeval [sudo] password for anusha: 2019-04-24 08:48:01,232 WARNING No reference file found at default locations. You can set the environment variable 'HGREF' or 'HG19' to point to a suitable Fasta file. 2019-04-24 08:48:01,244 WARNING No reference file found at default locations. You can set the environment variable 'HGREF' or 'HG19' to point to a suitable Fasta file. [I] Total VCF records: 4167900 [I] Non-reference VCF records: 4167900 [W] variant at chr1:1035169 has more than one base of reference padding [W] overlapping records at chr1:55075667 for sample 1 [W] Variants that have >1 base of reference padding: 2990 [W] Variants that overlap on the reference allele: 24 [I] Total VCF records: 4208286 [I] Non-reference VCF records: 4207104 2019-04-24 08:50:36,855 WARNING Creating template for vcfeval. You can speed this up by supplying a SDF template that corresponds to /data/genome.fa 2019-04-24 08:51:59,372 ERROR Error running rtg tools / vcfeval. Return code was 1, output: / Error: No sample name provided but calls is a multi-sample VCF.

2019-04-24 08:51:59,373 ERROR Traceback (most recent call last): 2019-04-24 08:51:59,373 ERROR File "/opt/hap.py/bin/hap.py", line 508, in 2019-04-24 08:51:59,373 ERROR main() 2019-04-24 08:51:59,373 ERROR File "/opt/hap.py/bin/hap.py", line 452, in main 2019-04-24 08:51:59,373 ERROR tempfiles += Haplo.vcfeval.runVCFEval(args.vcf1, args.vcf2, output_name, args) 2019-04-24 08:51:59,373 ERROR File "/opt/hap.py/lib/python27/Haplo/vcfeval.py", line 129, in runVCFEval 2019-04-24 08:51:59,373 ERROR raise Exception("Error running rtg tools / vcfeval. Return code was %i, output: %s / %s \n" % (rc, o, e)) 2019-04-24 08:51:59,373 ERROR Exception: Error running rtg tools / vcfeval. Return code was 1, output: / Error: No sample name provided but calls is a multi-sample VCF.

[pkrusche]

Can you paste the column header line of that VCF file? Maybe there is a spurious tab / space at the end of th e #CHROM ... line?