returned non-zero exit status 1

[a00101]

# hap.py NA12878.vcf.gz 01.Raw_variants.vcf.gz -f ConfidentRegions.bed.gz -o test -r hg38.fa

[I] Total VCF records:         4167900
[I] Non-reference VCF records: 4167900
[W] overlapping records at chr1:37070742 for sample 0
[W] Variants that overlap on the reference allele: 58
[I] Total VCF records:         1172477
[I] Non-reference VCF records: 1171661
2020-07-29 11:40:37,843 ERROR    [stderr] regex_error
2020-07-29 11:40:37,932 ERROR    Command 'quantify /tmp/hap.py.result.KDYrhc.vcf.gz -o test.roc.tsv -r hg38.fa --threads 80 --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/tmpDLVB93.bed' -R 'CONF:ConfidentRegions.bed.gz' --roc-regions '*'' returned non-zero exit status 1
2020-07-29 11:40:37,933 ERROR    Traceback (most recent call last):
2020-07-29 11:40:37,933 ERROR      File "/root/anaconda3/envs/happy/bin/hap.py", line 511, in <module>
2020-07-29 11:40:37,934 ERROR        main()
2020-07-29 11:40:37,934 ERROR      File "/root/anaconda3/envs/happy/bin/hap.py", line 496, in main
2020-07-29 11:40:37,934 ERROR        qfy.quantify(args)
2020-07-29 11:40:37,934 ERROR      File "/root/anaconda3/envs/happy/bin/qfy.py", line 129, in quantify
2020-07-29 11:40:37,935 ERROR        strat_fixchr=args.strat_fixchr)
2020-07-29 11:40:37,935 ERROR      File "/root/anaconda3/envs/happy/lib/python27/Haplo/quantify.py", line 177, in run_quantify
2020-07-29 11:40:37,935 ERROR        subprocess.check_call(run_str, shell=True, stdout=tfo, stderr=tfe)
2020-07-29 11:40:37,935 ERROR      File "/root/anaconda3/envs/happy/lib/python2.7/subprocess.py", line 190, in check_call
2020-07-29 11:40:37,936 ERROR        raise CalledProcessError(retcode, cmd)
2020-07-29 11:40:37,937 ERROR    CalledProcessError: Command 'quantify /tmp/hap.py.result.KDYrhc.vcf.gz -o test.roc.tsv -r hg38.fa --threads 80 --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/tmpDLVB93.bed' -R 'CONF:ConfidentRegions.bed.gz' --roc-regions '*'' returned non-zero exit status 1

[christinafliege]

Incidentally, I am getting an error at the same record in the VCF for pre.py. Here is the record and error message

chr1    37070742        rs66730050      ACG     A,ATGCG 857.73  PASS    AC=1,1;AF=0.5,0.5;AN=2;DB;DP=22;ExcessHet=3.0103;FS=0.000;MLEAC=1,1;MLEAF=0.5,0.5;MQ=60.00;QD=45.14;SOR=0.793;VQSLOD=3.8585;culprit=FS  GT:AD:DP:GQ:PL  1/2:0,9,10:19:99:895,417,379,387,0,348






[W] overlapping records at chr1:37070742 for sample 0
[W] Variants that overlap on the reference allele: 194
[I] Total VCF records:         4411364
[I] Non-reference VCF records: 4411364
2020-07-30 16:39:00,985 WARNING  stoll
2020-07-30 16:39:00,986 ERROR    Exception when running <function blocksplitWrapper at 0x2b6c681459b0>:
2020-07-30 16:39:00,986 ERROR    ------------------------------------------------------------
2020-07-30 16:39:00,986 ERROR    Traceback (most recent call last):
2020-07-30 16:39:00,986 ERROR      File "/usr/local/apps/bioapps/hap.py/hap.py-0.3.9/lib/python27/Tools/parallel.py", line 72, in parMapper
2020-07-30 16:39:00,986 ERROR        return arg[1]['fun'](arg[0], *arg[1]['args'], **arg[1]['kwargs'])
2020-07-30 16:39:00,986 ERROR      File "/usr/local/apps/bioapps/hap.py/hap.py-0.3.9/lib/python27/Haplo/partialcredit.py", line 121, in blocksplitWrapper
2020-07-30 16:39:00,998 ERROR        subprocess.check_call(to_run, shell=True, stdout=tfo, stderr=tfe)
2020-07-30 16:39:00,998 ERROR      File "/usr/local/apps/bioapps/anaconda/anaconda2.7/lib/python2.7/subprocess.py", line 186, in check_call
2020-07-30 16:39:01,011 ERROR        raise CalledProcessError(retcode, cmd)
2020-07-30 16:39:01,011 ERROR    CalledProcessError: Command 'blocksplit /tmp/tmpD6Q5Uh.vcf.gz -l 'HLA-DQA1*01:01:02' -o /tmp/result.HLA-DQA1*01:01:02XUqbCj.chunks.bed --window 10000 --nblocks 40 -f 0' returned non-zero exit status 1
2020-07-30 16:39:01,011 ERROR    ------------------------------------------------------------
2020-07-30 16:39:01,037 WARNING  stoll
2020-07-30 16:39:01,038 ERROR    Exception when running <function blocksplitWrapper at 0x2b6c681459b0>:
2020-07-30 16:39:01,038 ERROR    ------------------------------------------------------------
2020-07-30 16:39:01,038 ERROR    Traceback (most recent call last):
2020-07-30 16:39:01,038 ERROR      File "/usr/local/apps/bioapps/hap.py/hap.py-0.3.9/lib/python27/Tools/parallel.py", line 72, in parMapper
2020-07-30 16:39:01,038 ERROR        return arg[1]['fun'](arg[0], *arg[1]['args'], **arg[1]['kwargs'])
2020-07-30 16:39:01,038 ERROR      File "/usr/local/apps/bioapps/hap.py/hap.py-0.3.9/lib/python27/Haplo/partialcredit.py", line 121, in blocksplitWrapper
2020-07-30 16:39:01,038 ERROR        subprocess.check_call(to_run, shell=True, stdout=tfo, stderr=tfe)
2020-07-30 16:39:01,038 ERROR      File "/usr/local/apps/bioapps/anaconda/anaconda2.7/lib/python2.7/subprocess.py", line 186, in check_call
2020-07-30 16:39:01,038 ERROR        raise CalledProcessError(retcode, cmd)
2020-07-30 16:39:01,038 ERROR    CalledProcessError: Command 'blocksplit /tmp/tmpD6Q5Uh.vcf.gz -l 'HLA-DRB1*09:21' -o /tmp/result.HLA-DRB1*09:21Ov9LiJ.chunks.bed --window 10000 --nblocks 40 -f 0' returned non-zero exit status 1
2020-07-30 16:39:01,038 ERROR    ------------------------------------------------------------
Traceback (most recent call last):
  File "/usr/local/apps/bioapps/hap.py/hap.py-0.3.9/bin/pre.py", line 395, in <module>
    main()
  File "/usr/local/apps/bioapps/hap.py/hap.py-0.3.9/bin/pre.py", line 391, in main
    preprocessWrapper(args)
  File "/usr/local/apps/bioapps/hap.py/hap.py-0.3.9/bin/pre.py", line 241, in preprocessWrapper
    args.somatic_allele_conversion)
  File "/usr/local/apps/bioapps/hap.py/hap.py-0.3.9/bin/pre.py", line 203, in preprocess
    haploid_x=gender == "male")
  File "/usr/local/apps/bioapps/hap.py/hap.py-0.3.9/lib/python27/Haplo/partialcredit.py", line 192, in partialCredit
    raise Exception("One of the blocksplit processes failed.")
Exception: One of the blocksplit processes failed.

[joys8998]

@a00101 and @christinafliege Did you solve the issue? How did you do? Because I get the same error but I have noclue about how to fix it. Thanks!

[b-math]

Hi. Which version of hap.py did you use?

I first installed the default version using conda, and got the same error. Now I installed the newest version of hap.py in a new conda environment by using the following command: conda create -n happy conda activate happy conda install bcftools conda install "samtools>=1.10" conda install hap.py=0.3.14

For me, the error does not appear anymore when installing all of these packages in this order. However, I'm not sure if all of them are really required. I hope that this helps you.

[xmy1990]

hi @https://github.com/b-math Which version of python2 did you use? I have successed to install hap.py=0.3.14, bur failed to run hap.py with the same error: returned non-zero exit status 1

Thanks!