ERROR [stderr] regex_error

Xingsl commented 6 years ago

Dear, when i run this hap.py Standard.wes.vcf Standard.wes.vcf -o NA12878 --threads 6 it produced

2018-11-03 14:53:14,187 ERROR [stderr] regex_error 2018-11-03 14:53:14,199 ERROR Command 'quantify /tmp/hap.py.result.P5wuqJ.vcf.gz -o NA12878.roc.tsv -r /data/Reference/fasta/hs.grch38.fa --threads 6 --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 NA12878.vcf.gz --roc-regions ''' returned non-zero exit status 1 2018-11-03 14:53:14,200 ERROR Traceback (most recent call last): 2018-11-03 14:53:14,200 ERROR File "/bin/hap.py", line 511, in 2018-11-03 14:53:14,201 ERROR main() 2018-11-03 14:53:14,201 ERROR File "/bin/hap.py", line 496, in main 2018-11-03 14:53:14,201 ERROR qfy.quantify(args) 2018-11-03 14:53:14,201 ERROR File "/bin/qfy.py", line 129, in quantify 2018-11-03 14:53:14,202 ERROR strat_fixchr=args.strat_fixchr) 2018-11-03 14:53:14,202 ERROR File "/bin/lib/python27/Haplo/quantify.py", line 178, in run_quantify 2018-11-03 14:53:14,202 ERROR subprocess.check_call(run_str, shell=True, stdout=tfo, stderr=tfe) 2018-11-03 14:53:14,202 ERROR File "/anaconda2/envs/python27/lib/python2.7/subprocess.py", line 190, in check_call 2018-11-03 14:53:14,204 ERROR raise CalledProcessError(retcode, cmd) 2018-11-03 14:53:14,204 ERROR CalledProcessError: Command 'quantify /tmp/hap.py.result.P5wuqJ.vcf.gz -o NA12878.roc.tsv -r /data/Reference/fasta/hs.grch38.fa --threads 6 --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 NA12878.vcf.gz --roc-regions ''' returned non-zero exit status 1

pkrusche commented 6 years ago

Which version of g++ are you using to compile hap.py? Older versions than 4.9.2 can cause issues with their implementation of std::regex.

nh13 commented 5 years ago

I hit this same error installed using bioconda. g++ is version 4.8.5. The hap.py README states:

GCC/G++ 4.8+ for compiling

afkoeppel commented 5 years ago

I'm getting this exact same error, but with gcc 7.2.0.

hap.py NA12878.chrfix.vcf.gz NA12878.filt.decomp.norm.annot.ready.vcf.gz -o test -r $HG19 --no-leftshift --no-decompose --gender=none [I] Total VCF records: 4049512 [I] Non-reference VCF records: 4049512 [W] overlapping records at 1:7164311 for sample 0 [W] Variants that overlap on the reference allele: 6 [I] Total VCF records: 4602744 [I] Non-reference VCF records: 4525967 2018-12-18 09:48:52,094 ERROR [stderr] regex_error 2018-12-18 09:48:52,393 ERROR Command 'quantify /tmp/hap.py.result.dGcyjP.vcf.gz -o fulltest.roc.tsv -r /home/afk2s/data/fastq2vcf/ASSETS/human_g1k_v37.fasta --threads 72 --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 fulltest.vcf.gz --roc-regions ''' returned non-zero exit status 1 2018-12-18 09:48:52,396 ERROR Traceback (most recent call last): 2018-12-18 09:48:52,397 ERROR File "/home/afk2s/Software/miniconda3/envs/happy/bin/hap.py", line 511, in 2018-12-18 09:48:52,398 ERROR main() 2018-12-18 09:48:52,398 ERROR File "/home/afk2s/Software/miniconda3/envs/happy/bin/hap.py", line 496, in main 2018-12-18 09:48:52,398 ERROR qfy.quantify(args) 2018-12-18 09:48:52,398 ERROR File "/home/afk2s/Software/miniconda3/envs/happy/bin/qfy.py", line 129, in quantify 2018-12-18 09:48:52,399 ERROR strat_fixchr=args.strat_fixchr) 2018-12-18 09:48:52,399 ERROR File "/home/afk2s/Software/miniconda3/envs/happy/lib/python27/Haplo/quantify.py", line 177, in run_quantify 2018-12-18 09:48:52,400 ERROR subprocess.check_call(run_str, shell=True, stdout=tfo, stderr=tfe) 2018-12-18 09:48:52,400 ERROR File "/home/afk2s/Software/miniconda3/envs/happy/lib/python2.7/subprocess.py", line 190, in check_call 2018-12-18 09:48:52,401 ERROR raise CalledProcessError(retcode, cmd) 2018-12-18 09:48:52,401 ERROR CalledProcessError: Command 'quantify /tmp/hap.py.result.dGcyjP.vcf.gz -o fulltest.roc.tsv -r /home/afk2s/data/fastq2vcf/ASSETS/human_g1k_v37.fasta --threads 72 --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 fulltest.vcf.gz --roc-regions ''' returned non-zero exit status 1

Any help or advice would be appreciated. Thanks.

nh13 commented 5 years ago

See https://github.com/bioconda/bioconda-recipes/pull/12581

It’s not working in bioconda either.

stephenturner commented 5 years ago

I'm running into the same problem. My gcc is 4.8.5. Not working via bioconda either.

wdecoster commented 5 years ago

I have the same problem, installed using bioconda, using gcc 7.3.0. If there is anything I can test to debug this, please let me know.

pkrusche commented 5 years ago

@nh13 @stephenturner @wdecoster hap.py has issues with gcc < 4.9.x (regex errors) and apparently also with 7.3 (unit test failure). From what I can tell, Bioconda has been in the process of switching from 4.8 to 7.3, so there will be issues with both.

Here is a branch that should fix these issues:

https://github.com/pkrusche/hap.py/tree/fix-with-gcc-7-3

stephenturner commented 5 years ago

Awesome. I will try this out soon. cc @punkrockscience, give it a try?

wdecoster commented 5 years ago

I tried, but if I'm not installing using conda it fails building, and I cannot figure out what's wrong. I've attached the output log to this message. The error refers to a /tmp/buildL4RUN_/CMakeFiles/CMakeOutput.log which doesn't seem to exist. I tried installing using python2.7 install.py ~/hap.py-install (my default python interpreter is python3).

building-log.txt

pkrusche commented 5 years ago

Seems you’re missing libbz2-dev for building boost.

You could supply your own Boost build (the readme has instructions) or install libbz2-dev.

HuTaoJiaZiAckerman commented 1 year ago

When I use gcc or g++ 11.2 from conda, but it not work.

Because I can't install right g++ version, I use hap.py from docker. It seemly get result.

Good luck!

Illumina / hap.py

ERROR [stderr] regex_error #66