command quantify while running the below command

[KrithikaSubramanian]

If I run this command hap.py-build/bin/hap.py Platinum_genome/split/chr1.recode.vcf 11_Haplotypecaller_indelrealigner/SRR622457_chr1.vcf -f 11_gatk_targetrealign/Chr1_SRR622457.bed -r /root/Work/ref-gen/GRCh38_full_analysis_set_plus_decoy_hla.fa --scratch-prefix Temp/ -o test

2019-02-11 14:08:50,974 WARNING No reference file found at default locations. You can set the environment variable 'HGREF' or 'HG19' to point to a suitable Fasta file. 2019-02-11 14:08:50,975 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: 316061 [I] Non-reference VCF records: 316061 [W] overlapping records at chr1:21916069 for sample 0 [W] Variants that overlap on the reference allele: 43 [I] Total VCF records: 293051 [I] Non-reference VCF records: 292995 2019-02-11 14:09:37,806 ERROR [stderr] regex_error 2019-02-11 14:09:37,819 ERROR Command 'quantify /root/Work/gatk4_work/NA12878_qc/Temp/hap.py.result._j_1zJ.vcf.gz -o test.roc.tsv -r /root/Work/ref-gen/GRCh38_full_analysis_set_plus_decoy_hla.fa --threads 48 --output-vtc 0 --output-rocs 1 --type xcmp --qq IQQ --qq-header QUAL --roc-delta 0.500000 --clean-info 1 --fix-chr-regions 0 -v test.vcf.gz -R 'CONF_VARS:/root/Work/gatk4_work/NA12878_qc/Temp/tmpnwtGCs.bed' -R 'CONF:11_gatk_targetrealign/Chr1_SRR622457.bed' --roc-regions ''' returned non-zero exit status 1 2019-02-11 14:09:37,819 ERROR Traceback (most recent call last): 2019-02-11 14:09:37,819 ERROR File "hap.py-build/bin/hap.py", line 511, in 2019-02-11 14:09:37,820 ERROR main() 2019-02-11 14:09:37,820 ERROR File "hap.py-build/bin/hap.py", line 496, in main 2019-02-11 14:09:37,820 ERROR qfy.quantify(args) 2019-02-11 14:09:37,820 ERROR File "/root/Work/gatk4_work/NA12878_qc/hap.py-build/bin/qfy.py", line 129, in quantify 2019-02-11 14:09:37,821 ERROR strat_fixchr=args.strat_fixchr) 2019-02-11 14:09:37,821 ERROR File "/root/Work/gatk4_work/NA12878_qc/hap.py-build/lib/python27/Haplo/quantify.py", line 177, in run_quantify 2019-02-11 14:09:37,821 ERROR subprocess.check_call(run_str, shell=True, stdout=tfo, stderr=tfe) 2019-02-11 14:09:37,821 ERROR File "/usr/lib64/python2.7/subprocess.py", line 542, in check_call 2019-02-11 14:09:37,822 ERROR raise CalledProcessError(retcode, cmd) 2019-02-11 14:09:37,822 ERROR CalledProcessError: Command 'quantify /root/Work/gatk4_work/NA12878_qc/Temp/hap.py.result._j_1zJ.vcf.gz -o test.roc.tsv -r /root/Work/ref-gen/GRCh38_full_analysis_set_plus_decoy_hla.fa --threads 48 --output-vtc 0 --output-rocs 1 --type xcmp --qq IQQ --qq-header QUAL --roc-delta 0.500000 --clean-info 1 --fix-chr-regions 0 -v test.vcf.gz -R 'CONF_VARS:/root/Work/gatk4_work/NA12878_qc/Temp/tmpnwtGCs.bed' -R 'CONF:11_gatk_targetrealign/Chr1_SRR622457.bed' --roc-regions ''' returned non-zero exit status 1

Please help me to fix this issues

Krithika S

[pkrusche]

This is probably caused by an outdated version of g++ being used (< 4.9.x), see also https://github.com/Illumina/hap.py/issues/13#issuecomment-286348476

[pkrusche]

(the key thing is the regex_error in the output -- this happens with older versions of g++)

[KrithikaSubramanian]

@pkrusche

I have installed 4.9.2 version of g++. The below is the version detail

g++ --version g++ (GCC) 4.9.2 20150212 (Red Hat 4.9.2-6) Copyright (C) 2014 Free Software Foundation, Inc. This is free software; see the source for copying conditions. There is NO warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.

[KrithikaSubramanian]

Thanks its working