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Bug #9401

closed

f48sn "cannot allocate memory" error when running cwl

Added by Jiayong Li almost 8 years ago. Updated over 7 years ago.

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

Actions #1

Updated by Jiayong Li almost 8 years ago

  • Description updated (diff)
Actions #2

Updated by Tom Morris over 7 years ago

  • Status changed from New to Closed
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