Bug #9401
Updated by Jiayong Li almost 8 years ago
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
<pre>
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
</pre>
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