hap.py failing with errors

[m-lazarova]

I don't understand why this is breaking and how to fix it, please help. I use this in a conda environment

[W] overlapping records at chr1:37070742 for sample 0
[W] Variants that overlap on the reference allele: 93
[I] Total VCF records:         3619471
[I] Non-reference VCF records: 3619471
[W] variant at chr1:10140 has more than one base of reference padding 
[W] Variants that have >1 base of reference padding: 35930
[I] Total VCF records:         425203
[I] Non-reference VCF records: 332340
2020-04-13 16:58:41,370 ERROR    [stderr] regex_error
2020-04-13 16:58:41,410 ERROR    Command 'quantify /tmp/hap.py.result.onATn4.vcf.gz -o test.roc.tsv -r genome.fa --threads 12 --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:/tmp/tmpQLk_sE.bed' -R 'CONF:confident.bed' --roc-regions '*'' returned non-zero exit status 1
2020-04-13 16:58:41,411 ERROR    Traceback (most recent call last):
2020-04-13 16:58:41,411 ERROR      File "/home/user/miniconda3/envs/py27/bin/hap.py", line 511, in <module>
2020-04-13 16:58:41,412 ERROR        main()
2020-04-13 16:58:41,412 ERROR      File "/home/user/miniconda3/envs/py27/bin/hap.py", line 496, in main
2020-04-13 16:58:41,412 ERROR        qfy.quantify(args)
2020-04-13 16:58:41,412 ERROR      File "/home/user/miniconda3/envs/py27/bin/qfy.py", line 129, in quantify
2020-04-13 16:58:41,413 ERROR        strat_fixchr=args.strat_fixchr)
2020-04-13 16:58:41,413 ERROR      File "/home/mariya/miniconda3/envs/py27/lib/python27/Haplo/quantify.py", line 177, in run_quantify
2020-04-13 16:58:41,418 ERROR        subprocess.check_call(run_str, shell=True, stdout=tfo, stderr=tfe)
2020-04-13 16:58:41,418 ERROR      File "/home/user/miniconda3/envs/py27/lib/python2.7/subprocess.py", line 190, in check_call
2020-04-13 16:58:41,422 ERROR        raise CalledProcessError(retcode, cmd)
2020-04-13 16:58:41,422 ERROR    CalledProcessError: Command 'quantify /tmp/hap.py.result.onATn4.vcf.gz -o test.roc.tsv -r genome.fa --threads 12 --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:/tmp/tmpQLk_sE.bed' -R 'CONF:confident.bed' --roc-regions '*'' returned non-zero exit status 1

[joys8998]

Hi @m-lazarova,

I get the same error and I got no clue on how to fix it. Did you managed to solve it?

Thanks