Hi all -
In running a samtools sort, we experienced the following exception from
Galaxy:
galaxy.jobs.runners.drmaa ERROR 2012-04-01 12:01:27,200 Job wrapper
finish method failed
Traceback (most recent call last):
File "/Groups/Galaxy/galaxy-dist/lib/galaxy/jobs/runners/drmaa.py",
line 286, in finish_job
drm_job_state.job_wrapper.finish( stdout, stderr )
File "/Groups/Galaxy/galaxy-dist/lib/galaxy/jobs/__init__.py", line
609, in finish
( not
self.external_output_metadata.external_metadata_set_successfully(
dataset, self.sa_session ) \
File "/Groups/Galaxy/galaxy-dist/lib/galaxy/datatypes/metadata.py",
line 602, in external_metadata_set_successfully
rval, rstring = simplejson.load( open(
metadata_files.filename_results_code ) )
File
"/Groups/Galaxy/galaxy-dist/eggs/simplejson-2.1.1-py2.7-linux-x86_64-ucs2.egg/simplejson/__init__.py",
line 328, in load
use_decimal=use_decimal, **kw)
File
"/Groups/Galaxy/galaxy-dist/eggs/simplejson-2.1.1-py2.7-linux-x86_64-ucs2.egg/simplejson/__init__.py",
line 384, in loads
return _default_decoder.decode(s)
File
"/Groups/Galaxy/galaxy-dist/eggs/simplejson-2.1.1-py2.7-linux-x86_64-ucs2.egg/simplejson/decoder.py",
line 405, in decode
raise JSONDecodeError("Extra data", s, end, len(s))
JSONDecodeError: Extra data: line 1 column 41 - line 1 column 44 (char
41 - 44)
galaxy.jobs DEBUG 2012-04-02 10:07:16,655 dispatching job 4738 to drmaa
runner
galaxy.jobs INFO 2012-04-02 10:07:16,736 job 4738 dispatched
This resulted in a "hung" job from galaxy's perspective. The job was
left with the status "running" so the workflow could not fail.
Unfortunately, the json file was not preserved - it was removed. We
have not hit this problem before. minimally, if this problem arrises,
it would be nice for galaxy to preserve the json file for PD and fail
the job.
Thoughts? Anyone else hit this?
Thanks,
Ann
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