JSONDecodeERROR thrown, job left in "running" state.
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
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 ___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at:
participants (2)
-
Ann Black-Ziegelbein -
Nate Coraor