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Bug #9401
closedf48sn "cannot allocate memory" error when running cwl
Status:
Closed
Priority:
Normal
Assigned To:
-
Category:
-
Target version:
-
Story points:
-
Description
Running an exome pipeline bwa_gatk_hu34D5B9 on f48sn
https://workbench.f48sn.arvadosapi.com/pipeline_instances/f48sn-d1hrv-79c0ffzn15d1omj
and got the following traceback from arvados-cwl-runnder --debug
Unexpected exception Traceback (most recent call last): File "/home/jiayong/miniconda2/lib/python2.7/site-packages/cwltool/workflow.py", line 508, in job **kwargs): File "/home/jiayong/miniconda2/lib/python2.7/site-packages/cwltool/draft2tool.py", line 230, in job j.command_line = flatten(map(builder.generate_arg, builder.bindings)) File "/home/jiayong/miniconda2/lib/python2.7/site-packages/cwltool/builder.py", line 162, in generate_arg value = self.do_eval(binding["do_eval"], context=value) File "/home/jiayong/miniconda2/lib/python2.7/site-packages/cwltool/builder.py", line 204, in do_eval timeout=self.timeout) Traceback (most recent call last): File "build/bdist.linux-x86_64/egg/arvados_cwl/__init__.py", line 706, in arvExecutor for runnable in jobiter: File "/home/jiayong/miniconda2/lib/python2.7/site-packages/cwltool/workflow.py", line 397, in job for w in wj.job(builder.job, basedir, output_callback, **kwargs): File "/home/jiayong/miniconda2/lib/python2.7/site-packages/cwltool/workflow.py", line 312, in job for newjob in step.iterable: File "/home/jiayong/miniconda2/lib/python2.7/site-packages/cwltool/workflow.py", line 268, in try_make_job for j in jobs: File "/home/jiayong/miniconda2/lib/python2.7/site-packages/cwltool/workflow.py", line 151, in job for j in self.step.job(joborder, basedir, output_callback, **kwargs): File "/home/jiayong/miniconda2/lib/python2.7/site-packages/cwltool/workflow.py", line 515, in job raise WorkflowException(str(e)) WorkflowException: [Errno 12] Cannot allocate memory
Strange that the pipeline bwa_freebayes_hu34D5B9 with same run time constraint ran successfully two days ago
https://workbench.f48sn.arvadosapi.com/pipeline_instances/f48sn-d1hrv-fwwcofcmshktkui
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