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?


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