Hi Nate, thank you for the help, I'm posting more details about the error, Did you ever see something like this?
Thank you so much,
WARNING:galaxy.datatypes.registry:Error loading datatype with extension 'ps': 'module' object has no attribute 'scripts' WARNING:galaxy.datatypes.registry:Error appending sniffer for datatype 'galaxy.datatypes.scripts:PostScript' to sniff_order: No module named scripts INFO:NetCDFwithTimeAxis:NetCDFwithTimeAxis set_meta INFO:NetCDFwithTimeAxis:NetCDF set_meta INFO:NetCDFwithTimeAxis:Climate set_meta [localhost] local: . /home/ramao/shed_tools/web.uniparthenope.it/repos/montella/galaxy_es_core/a8f8a904173c/galaxy_es_core/env.sh;cdo infon /home/ramao/galaxy/database/files/000/dataset_15.dat
Fatal error: local() encountered an error (return code 127) while executing '. /home/ramao/shed_tools/web.uniparthenope.it/repos/montella/galaxy_es_core/a8f8a904173c/galaxy_es_core/env.sh;cdo infon /home/ramao/galaxy/database/files/000/dataset_15.dat'
Aborting. [localhost] local: . /home/ramao/shed_tools/web.uniparthenope.it/repos/montella/galaxy_es_core/a8f8a904173c/galaxy_es_core/env.sh;cdo sinfo /home/ramao/galaxy/database/files/000/dataset_15.dat
Fatal error: local() encountered an error (return code 127) while executing '. /home/ramao/shed_tools/web.uniparthenope.it/repos/montella/galaxy_es_core/a8f8a904173c/galaxy_es_core/env.sh;cdo sinfo /home/ramao/galaxy/database/files/000/dataset_15.dat'
Aborting. [localhost] local: . /home/ramao/shed_tools/web.uniparthenope.it/repos/montella/galaxy_es_core/a8f8a904173c/galaxy_es_core/env.sh;ncdump -x /home/ramao/galaxy/database/files/000/dataset_15.dat
Fatal error: local() encountered an error (return code 127) while executing '. /home/ramao/shed_tools/web.uniparthenope.it/repos/montella/galaxy_es_core/a8f8a904173c/galaxy_es_core/env.sh;ncdump -x /home/ramao/galaxy/database/files/000/dataset_15.dat'
Aborting. galaxy.jobs.runners.local DEBUG 2013-04-17 09:51:59,955 execution of external set_meta for job 15 finished galaxy.jobs DEBUG 2013-04-17 09:51:59,979 Tool did not define exit code or stdio handling; checking stderr for success galaxy.datatypes.metadata DEBUG 2013-04-17 09:52:00,029 setting metadata externally failed for HistoryDatasetAssociation 15: External set_meta() not called NetCDFwithTimeAxis INFO 2013-04-17 09:52:00,029 NetCDFwithTimeAxis set_meta NetCDFwithTimeAxis INFO 2013-04-17 09:52:00,029 NetCDF set_meta NetCDFwithTimeAxis INFO 2013-04-17 09:52:00,029 Climate set_meta [localhost] local: . /home/ramao/shed_tools/web.uniparthenope.it/repos/montella/galaxy_es_core/a8f8a904173c/galaxy_es_core/env.sh;cdo infon /home/ramao/galaxy/database/files/000/dataset_15.dat
Fatal error: local() encountered an error (return code 127) while executing '. /home/ramao/shed_tools/web.uniparthenope.it/repos/montella/galaxy_es_core/a8f8a904173c/galaxy_es_core/env.sh;cdo infon /home/ramao/galaxy/database/files/000/dataset_15.dat'
Aborting. [localhost] local: . /home/ramao/shed_tools/web.uniparthenope.it/repos/montella/galaxy_es_core/a8f8a904173c/galaxy_es_core/env.sh;cdo sinfo /home/ramao/galaxy/database/files/000/dataset_15.dat
Fatal error: local() encountered an error (return code 127) while executing '. /home/ramao/shed_tools/web.uniparthenope.it/repos/montella/galaxy_es_core/a8f8a904173c/galaxy_es_core/env.sh;cdo sinfo /home/ramao/galaxy/database/files/000/dataset_15.dat'
Aborting. [localhost] local: . /home/ramao/shed_tools/web.uniparthenope.it/repos/montella/galaxy_es_core/a8f8a904173c/galaxy_es_core/env.sh;ncdump -x /home/ramao/galaxy/database/files/000/dataset_15.dat
Fatal error: local() encountered an error (return code 127) while executing '. /home/ramao/shed_tools/web.uniparthenope.it/repos/montella/galaxy_es_core/a8f8a904173c/galaxy_es_core/env.sh;ncdump -x /home/ramao/galaxy/database/files/000/dataset_15.dat'
Subject: Re: [galaxy-dev] Unable to finish job From: nate@bx.psu.edu Date: Tue, 16 Apr 2013 11:45:37 -0400 CC: galaxy-dev@lists.bx.psu.edu To: ramao_tiago_tiburski@hotmail.com
On Apr 16, 2013, at 9:37 AM, Ramon Tiburski wrote:
I,m getting this error when I try to convert some data, can someone help me?
Traceback (most recent call last): File "/home/ramao/galaxy/lib/galaxy/jobs/runners/local.py", line 156, in run_job job_wrapper.finish( stdout, stderr, exit_code ) File "/home/ramao/galaxy/lib/galaxy/jobs/__init__.py", line 412, in finish dataset.datatype.set_meta( dataset, overwrite = False ) #call datatype.set_meta directly for the initial set_meta call during dataset creation File "/home/ramao/shed_tools/web.uniparthenope.it/repos/montella/galaxy_es_core/a8f8a904173c/galaxy_es_core/earthsystem.py", line 318, in set_meta NetCDF.set_meta(self,dataset) File "/home/ramao/shed_tools/web.uniparthenope.it/repos/montella/galaxy_es_core/a8f8a904173c/galaxy_es_core/earthsystem.py", line 261, in set_meta ncml= execAndGetStdout("ncdump -x "+dataset.file_name) File "/home/ramao/shed_tools/web.uniparthenope.it/repos/montella/galaxy_es_core/a8f8a904173c/galaxy_es_core/earthsystem.py", line 48, in execAndGetStdout output=local(cmd, capture=True) File "/home/ramao/galaxy/eggs/Fabric-1.4.2-py2.7.egg/fabric/operations.py", line 1012, in local error(message=msg, stdout=out, stderr=err) File "/home/ramao/galaxy/eggs/Fabric-1.4.2-py2.7.egg/fabric/utils.py", line 305, in error return func(message) File "/home/ramao/galaxy/eggs/Fabric-1.4.2-py2.7.egg/fabric/utils.py", line 26, in abort sys.exit(1) SystemExit: 1
Hi Ramon,
For a definite answer, you'll want to contact the tool/datatype author. However, I would guess that the `ncdump` command is failing for some reason, and that would be the place to look.
--nate
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