On Apr 17, 2013, at 9:11 AM, Ramon Tiburski wrote:
Hi Nate, thank you for the help, I'm posting more details about the error, Did you ever see something like this?
Hi Ramon, Without being familiar with the tool, I am not sure what is happening here. Either the process of sourcing the env.sh file or calling cdo is failing, for unknown reasons. It could be that the command is not being executed through a shell, in which case the source (',') and the join (';') specials would not be recognized. --nate
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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