On Apr 2, 2012, at 11:03 AM, Ann Black-Ziegelbein wrote:
> 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?
Hi Ann,
I haven't seen this, but if you set `cleanup_job = onsuccess` in your Galaxy
config, it'll leave behind files in the case of job failure.
--nate
>
> Thanks,
>
> Ann
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