Open m-lazarova opened 4 years ago
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
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
I don't understand why this is breaking and how to fix it, please help. I use this in a conda environment