search

bcbio / bcbio-nextgen

Validated, scalable, community developed variant calling, RNA-seq and small RNA analysis
https://bcbio-nextgen.readthedocs.io
MIT License
994 stars 354 forks source link

Unrecognized option: -baf when using PURPLE #3250

Open rkendar opened 4 years ago

rkendar commented 4 years ago

Hi Bcbio Team,

Do you know why the PURPLE does not recognize the -baf? I've checked bcbio PURPLE script https://github.com/bcbio/bcbio-nextgen/blob/86edda9bedb3e90b814b0c54f3efb74fdf23aba8/bcbio/structural/purple.py and actually it has -baf. I am not sure what I've done wrong. Is it because I'm using the older version of bcbio?

Version info

To Reproduce Command generated by bcbio: Command 'set -o pipefail; unset DISPLAY && PURPLE -Xms750m -Xmx21840m -XX:+UseSerialGC -Djava.io.tmpdir=/work/bcbiotx/tmpzoo_w41b -amber /work/structural/WHT158/purple/amber -baf /work/structural/WHT158/purple/amber/WHT158.amber.baf -cobalt /work/structural/WHT158/purple/cobalt -gc_profile /bcbio/genomes/Hsapiens/hg38/coverage/gc/GC_profile.1000bp.cnp -output_dir /work/bcbiotx/tmpzoo_w41b -ref_genome hg38 -run_dir /work/structural/WHT158/purple -threads 16 -tumor_sample WHT158 -ref_sample WHT157 -somatic_vcf /work/strelka2/batch1-effects-annotated.vcf.gz

Observed behavior Error message:

[2020-05-29T14:43Z] 22:43:28 - Segmentation Complete [2020-05-29T14:43Z] 22:43:28 - Complete [2020-05-29T14:43Z] PURPLE: purity and ploidy estimation [2020-05-29T14:43Z] 22:43:29 - Generating windows on chromosome chr22 [2020-05-29T14:43Z] 22:43:29 - PURPLE version: 2.32 [2020-05-29T14:43Z] Exception in thread "main" org.apache.commons.cli.UnrecognizedOptionException: Unrecognized option: -baf [2020-05-29T14:43Z] at org.apache.commons.cli.DefaultParser.handleUnknownToken(DefaultParser.java:347) [2020-05-29T14:43Z] at org.apache.commons.cli.DefaultParser.handleConcatenatedOptions(DefaultParser.java:689) [2020-05-29T14:43Z] at org.apache.commons.cli.DefaultParser.handleShortAndLongOption(DefaultParser.java:520) [2020-05-29T14:43Z] at org.apache.commons.cli.DefaultParser.handleToken(DefaultParser.java:243) [2020-05-29T14:43Z] at org.apache.commons.cli.DefaultParser.parse(DefaultParser.java:120) [2020-05-29T14:43Z] at org.apache.commons.cli.DefaultParser.parse(DefaultParser.java:76) [2020-05-29T14:43Z] at org.apache.commons.cli.DefaultParser.parse(DefaultParser.java:60) [2020-05-29T14:43Z] at com.hartwig.hmftools.purple.PurityPloidyEstimateApplication.createCommandLine(PurityPloidyEstimateApplication.java:365) [2020-05-29T14:43Z] at com.hartwig.hmftools.purple.PurityPloidyEstimateApplication.(PurityPloidyEstimateApplication.java:105) [2020-05-29T14:43Z] at com.hartwig.hmftools.purple.PurityPloidyEstimateApplication.main(PurityPloidyEstimateApplication.java:96) [2020-05-29T14:43Z] Uncaught exception occurred Traceback (most recent call last): File "/bcbio/anaconda/lib/python3.6/site-packages/bcbio/provenance/do.py", line 26, in run _do_run(cmd, checks, log_stdout, env=env) File "/bcbio/anaconda/lib/python3.6/site-packages/bcbio/provenance/do.py", line 106, in _do_run raise subprocess.CalledProcessError(exitcode, error_msg) subprocess.CalledProcessError: Command 'set -o pipefail; unset DISPLAY && PURPLE -Xms750m -Xmx21840m -XX:+UseSerialGC -Djava.io.tmpdir=/work/bcbiotx/tmpzoo_w41b -amber /work/structural/WHT158/purple/amber -baf /work/structural/WHT158/purple/amber/WHT158.amber.baf -cobalt /work/structural/WHT158/purple/cobalt -gc_profile /bcbio/genomes/Hsapiens/hg38/coverage/gc/GC_profile.1000bp.cnp -output_dir /work/bcbiotx/tmpzoo_w41b -ref_genome hg38 -run_dir /work/structural/WHT158/purple -threads 16 -tumor_sample WHT158 -ref_sample WHT157 -somatic_vcf /work/strelka2/batch1-effects-annotated.vcf.gz 22:43:29 - PURPLE version: 2.32 Exception in thread "main" org.apache.commons.cli.UnrecognizedOptionException: Unrecognized option: -baf at org.apache.commons.cli.DefaultParser.handleUnknownToken(DefaultParser.java:347) at org.apache.commons.cli.DefaultParser.handleConcatenatedOptions(DefaultParser.java:689) at org.apache.commons.cli.DefaultParser.handleShortAndLongOption(DefaultParser.java:520) at org.apache.commons.cli.DefaultParser.handleToken(DefaultParser.java:243) at org.apache.commons.cli.DefaultParser.parse(DefaultParser.java:120) at org.apache.commons.cli.DefaultParser.parse(DefaultParser.java:76) at org.apache.commons.cli.DefaultParser.parse(DefaultParser.java:60) at com.hartwig.hmftools.purple.PurityPloidyEstimateApplication.createCommandLine(PurityPloidyEstimateApplication.java:365) at com.hartwig.hmftools.purple.PurityPloidyEstimateApplication.(PurityPloidyEstimateApplication.java:105) at com.hartwig.hmftools.purple.PurityPloidyEstimateApplication.main(PurityPloidyEstimateApplication.java:96) ' returned non-zero exit status 1. [2020-05-29T14:43Z] 22:43:30 - Generating windows on chromosome chrX multiprocessing.pool.RemoteTraceback: """ Traceback (most recent call last): File "/bcbio/anaconda/lib/python3.6/multiprocessing/pool.py", line 119, in worker result = (True, func(*args, kwds)) File "//bcbio/anaconda/lib/python3.6/site-packages/joblib/_parallel_backends.py", line 567, in call return self.func(*args, *kwargs) File "/bcbio/anaconda/lib/python3.6/site-packages/joblib/parallel.py", line 225, in call for func, args, kwargs in self.items] File "/bcbio/anaconda/lib/python3.6/site-packages/joblib/parallel.py", line 225, in for func, args, kwargs in self.items] File "/bcbio/anaconda/lib/python3.6/site-packages/bcbio/utils.py", line 55, in wrapper return f(args, kwargs) File "/bcbio/anaconda/lib/python3.6/site-packages/bcbio/distributed/multitasks.py", line 324, in detect_sv return structural.detect_sv(*args) File "/bcbio/anaconda/lib/python3.6/site-packages/bcbio/structural/init.py", line 205, in detect_sv for svdata in caller_fn(items): File "/bcbio/anaconda/lib/python3.6/site-packages/bcbio/structural/purple.py", line 33, in run purple_out = _run_purple(paired, het_file, depth_file, vrn_files, work_dir) File "/bcbio/anaconda/lib/python3.6/site-packages/bcbio/structural/purple.py", line 76, in _run_purple do.run(cmd, "PURPLE: purity and ploidy estimation") File "/bcbio/anaconda/lib/python3.6/site-packages/bcbio/provenance/do.py", line 26, in run _do_run(cmd, checks, log_stdout, env=env) File "/bcbio/anaconda/lib/python3.6/site-packages/bcbio/provenance/do.py", line 106, in _do_run raise subprocess.CalledProcessError(exitcode, error_msg)

Thank you.

rkendar commented 4 years ago

Hi Bcbio team,

Is there anyone can help me with this? Thank you.

naumenko-sa commented 4 years ago

Hi @rkendar !

Please see this discussion: #2532

Purple is not documented and not productionalized in bcbio for now. Still, if you want to contribute to debugging, please provide your YAML file and more details on how you are running it.

Sergey