ERROR [stderr] Added region file '/tmp/tmpBkykHu.bed' as 'CONF'

[24natasya]

Hi i am getting this error for this sample. The error only occurs with this sample NA24385 by using bwa alignment. I did run analysis for the same sample by using other aligner and it works just fine. The other analysis uses the same bed files and truth file except different vcf by using different aligner and this occur.

[I] Total VCF records: 3608925 [I] Non-reference VCF records: 3608925 [W] overlapping records at 11:63682314 for sample 0 [W] Symbolic / SV ALT alleles at 11:67924558 [W] Variants that overlap on the reference allele: 2 [W] Variants that have symbolic ALT alleles: 1 [I] Total VCF records: 1624823 [I] Non-reference VCF records: 1624809 2019-08-23 07:53:54,382 WARNING Creating template for vcfeval. You can speed this up by supplying a SDF template that corresponds to /export/Projects/2019_MLVarCaller/01_BAMs/hs37d5.fa 2019-08-23 08:01:33,735 ERROR [stderr] Added region file '/tmp/tmpBkykHu.bed' as 'CONF' (3511122 intervals) 2019-08-23 08:01:34,508 ERROR [stderr] Added region file '/export/Projects/2019_MLVarCaller/02_TruthSets/GIAB_NA24385/HG002_GRCh37_GIAB_highconf_CG-IllFB-IllGATKHC-Ion-10X-SOLID_CHROM1-22_v.3.3.2_highconf_noinconsistent.bed' as 'CONF' (480903 intervals) 2019-08-23 08:01:34,509 ERROR [stderr] [/tmp/hap.py.result.JO0w7x.vcf.gz] Warning: no BGZF EOF marker; file may be truncated. 2019-08-23 08:01:34,509 ERROR [stderr] Invalid allele at 67924558: <NON_REF> 2019-08-23 08:01:34,735 ERROR Command 'quantify /tmp/hap.py.result.JO0w7x.vcf.gz -o /export/Projects/2019-Natasya/hap.py/bwa/octopus/raw/NA24385.novoalign.octopus.raw.happy.output.roc.tsv -r /export/Projects/2019_MLVarCaller/01_BAMs/hs37d5.fa --threads 24 --output-vtc 0 --output-rocs 1 --type ga4gh --qq QUAL --roc-delta 0.500000 --clean-info 1 --fix-chr-regions 0 -v /export/Projects/2019-Natasya/hap.py/bwa/octopus/raw/NA24385.novoalign.octopus.raw.happy.output.vcf.gz -R 'CONF_VARS:/tmp/tmpBkykHu.bed' -R 'CONF:/export/Projects/2019_MLVarCaller/02_TruthSets/GIAB_NA24385/HG002_GRCh37_GIAB_highconf_CG-IllFB-IllGATKHC-Ion-10X-SOLID_CHROM1-22_v.3.3.2_highconf_noinconsistent.bed' --roc-regions ''' returned non-zero exit status 1 2019-08-23 08:01:34,735 ERROR Traceback (most recent call last): 2019-08-23 08:01:34,735 ERROR File "./hap.py", line 508, in 2019-08-23 08:01:34,748 ERROR main() 2019-08-23 08:01:34,748 ERROR File "./hap.py", line 493, in main 2019-08-23 08:01:34,748 ERROR qfy.quantify(args) 2019-08-23 08:01:34,748 ERROR File "/opt/hap.py/bin/qfy.py", line 129, in quantify 2019-08-23 08:01:34,767 ERROR strat_fixchr=args.strat_fixchr) 2019-08-23 08:01:34,768 ERROR File "/opt/hap.py/lib/python27/Haplo/quantify.py", line 178, in run_quantify 2019-08-23 08:01:34,786 ERROR subprocess.check_call(run_str, shell=True, stdout=tfo, stderr=tfe) 2019-08-23 08:01:34,786 ERROR File "/usr/lib/python2.7/subprocess.py", line 541, in check_call 2019-08-23 08:01:34,839 ERROR raise CalledProcessError(retcode, cmd) 2019-08-23 08:01:34,839 ERROR CalledProcessError: Command 'quantify /tmp/hap.py.result.JO0w7x.vcf.gz -o /export/Projects/2019-Natasya/hap.py/bwa/octopus/raw/NA24385.novoalign.octopus.raw.happy.output.roc.tsv -r /export/Projects/2019_MLVarCaller/01_BAMs/hs37d5.fa --threads 24 --output-vtc 0 --output-rocs 1 --type ga4gh --qq QUAL --roc-delta 0.500000 --clean-info 1 --fix-chr-regions 0 -v /export/Projects/2019-Natasya/hap.py/bwa/octopus/raw/NA24385.novoalign.octopus.raw.happy.output.vcf.gz -R 'CONF_VARS:/tmp/tmpBkykHu.bed' -R 'CONF:/export/Projects/2019_MLVarCaller/02_TruthSets/GIAB_NA24385/HG002_GRCh37_GIAB_highconf_CG-IllFB-IllGATKHC-Ion-10X-SOLID_CHROM1-22_v.3.3.2_highconf_noinconsistent.bed' --roc-regions ''' returned non-zero exit status 1