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Illumina / hap.py

Haplotype VCF comparison tools
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Segmentation fault in qfy.quantify #103

Closed caspargross closed 1 year ago

caspargross commented 4 years ago

I get the following error message:

Log:

2019-11-19 17:31:03,363 ERROR    [stderr] Segmentation fault (core dumped)
2019-11-19 17:31:03,483 ERROR    Command 'quantify /tmp/hap.py.result.IJlnIM.vcf.gz -o /mnt/projects/external/promethion/vc_comparison_NA12878/out/promethion.roc.tsv -r /mnt/projects/external/promethion/reference_genomes/GCA_000001405.15_GRCh38_no_alt_analysis_set.fna --threads 5 --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 /mnt/projects/external/promethion/vc_comparison_NA12878/out/promethion.vcf.gz --roc-regions '*'' returned non-zero exit status 139
2019-11-19 17:31:03,483 ERROR    Traceback (most recent call last):
2019-11-19 17:31:03,483 ERROR      File "env/hap.py-install/bin/hap.py", line 529, in <module>
2019-11-19 17:31:03,506 ERROR        main()
2019-11-19 17:31:03,506 ERROR      File "env/hap.py-install/bin/hap.py", line 514, in main
2019-11-19 17:31:03,506 ERROR        qfy.quantify(args)
2019-11-19 17:31:03,506 ERROR      File "/mnt/SRV018/projects/external/promethion/vc_comparison_NA12878/env/hap.py-install/bin/qfy.py", line 129, in quantify
2019-11-19 17:31:03,507 ERROR        strat_fixchr=args.strat_fixchr)
2019-11-19 17:31:03,507 ERROR      File "/mnt/SRV018/projects/external/promethion/vc_comparison_NA12878/env/hap.py-install/lib/python27/Haplo/quantify.py", line 178, in run_quantify
2019-11-19 17:31:03,564 ERROR        subprocess.check_call(run_str, shell=True, stdout=tfo, stderr=tfe)
2019-11-19 17:31:03,564 ERROR      File "/usr/lib/python2.7/subprocess.py", line 190, in check_call
2019-11-19 17:31:03,575 ERROR        raise CalledProcessError(retcode, cmd)
2019-11-19 17:31:03,575 ERROR    CalledProcessError: Command 'quantify /tmp/hap.py.result.IJlnIM.vcf.gz -o /mnt/projects/external/promethion/vc_comparison_NA12878/out/promethion.roc.tsv -r /mnt/projects/external/promethion/reference_genomes/GCA_000001405.15_GRCh38_no_alt_analysis_set.fna --threads 5 --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 /mnt/projects/external/promethion/vc_comparison_NA12878/out/promethion.vcf.gz --roc-regions '*'' returned non-zero exit status 139

I was using g++ version 7.4.0 for the compilation. Is this a possible reason for the error?