On Oct 25, 2012, at 4:34 PM, Yilk, Todd A wrote:

> Hello all,
> 
> I'm using a local install of Galaxy connected to a UGE cluster and Python 
> 2.6.7. Most of my tools are reporting failures in the history with messages 
> like:
> 
>     An error occurred running this job: (34) Job output not returned from 
> cluster; exit status = "0"
> 
> With the relevant lines from Galaxy's log file looking like:
> 
> galaxy.jobs.runners.drmaa DEBUG 2012-10-25 10:31:26,586 job 34 working 
> directory is 
> /opt/galaxy/dev/Galaxy-JGI_galaxy-dev/database/job_working_directory/000/34
> galaxy.jobs.runners.drmaa DEBUG 2012-10-25 10:31:26,636 job 34 input = 
> [["/opt/galaxy/dev/Galaxy-JGI_galaxy-dev/database/files/000/dataset_48.dat", 
> "fastq", "5230830"]]
> galaxy.jobs.runners.drmaa DEBUG 2012-10-25 10:31:26,671 (34) submitting file 
> /opt/galaxy/dev/Galaxy-JGI_galaxy-dev/database/uge/galaxy_34.sh
> galaxy.jobs.runners.drmaa DEBUG 2012-10-25 10:31:26,672 (34) command is: 
> memtimepro -q -o 
> /opt/galaxy/dev/Galaxy-JGI_galaxy-dev/database/job_working_directory/000/34/34.drmmt
>  perl 
> /opt/galaxy/dev/Galaxy-JGI_galaxy-dev/tools/lanl/readMapping/fastqSplitter/separate_paired_end_reads.pl
>         -i 
> /opt/galaxy/dev/Galaxy-JGI_galaxy-dev/database/files/000/dataset_48.dat       
> -l /opt/galaxy/dev/Galaxy-JGI_galaxy-dev/database/files/000/dataset_53.dat    
>    -r /opt/galaxy/dev/Galaxy-JGI_galaxy-dev/database/files/000/dataset_54.dat 
> ; cd /opt/galaxy/dev/Galaxy-JGI_galaxy-dev; 
> /opt/galaxy/dev/Galaxy-JGI_galaxy-dev/set_metadata.sh ./database/files 
> /opt/galaxy/dev/Galaxy-JGI_galaxy-dev/database/job_working_directory/000/34 . 
> /opt/galaxy/dev/Galaxy-JGI_galaxy-dev/universe_wsgi.ini 
> /opt/galaxy/dev/Galaxy-JGI_galaxy-dev/database/tmp/tmp831aRx 
> /opt/galaxy/dev/Galaxy-JGI_galaxy-dev/database/job_working_directory/000/34/galaxy.json
>  /opt/galaxy/dev/Galaxy-JGI_galaxy-dev/database/job_working_di!
 
rectory/000/34/metadata_in_HistoryDatasetAssociation_59_fpBxRp,/opt/galaxy/dev/Galaxy-JGI_galaxy-dev/database/job_working_directory/000/34/metadata_kwds_HistoryDatasetAssociation_59_MLg1Aw,/opt/galaxy/dev/Galaxy-JGI_galaxy-dev/database/job_working_directory/000/34/metadata_out_HistoryDatasetAssociation_59_ZVYBIT,/opt/galaxy/dev/Galaxy-JGI_galaxy-dev/database/job_working_directory/000/34/metadata_results_HistoryDatasetAssociation_59_q4FpIq,,/opt/galaxy/dev/Galaxy-JGI_galaxy-dev/database/job_working_directory/000/34/metadata_override_HistoryDatasetAssociation_59_3HXPLq
 
/opt/galaxy/dev/Galaxy-JGI_galaxy-dev/database/job_working_directory/000/34/metadata_in_HistoryDatasetAssociation_60_Qw0GpA,/opt/galaxy/dev/Galaxy-JGI_galaxy-dev/database/job_working_directory/000/34/metadata_kwds_HistoryDatasetAssociation_60_ZF6Zk_,/opt/galaxy/dev/Galaxy-JGI_galaxy-dev/database/job_working_directory/000/34/metadata_out_HistoryDatasetAssociation_60_eEItGr,/opt/galaxy/dev/Galaxy-JGI_galaxy-dev/d!
 atabase/job_working_directory/000/34/metadata_results_HistoryD!
 atasetAs
sociation_60_bMa6HN,,/opt/galaxy/dev/Galaxy-JGI_galaxy-dev/database/job_working_directory/000/34/metadata_override_HistoryDatasetAssociation_60_X1El1z
> galaxy.jobs.runners.drmaa INFO 2012-10-25 10:31:26,720 (34) queued as 553774
> galaxy.jobs.runners.drmaa DEBUG 2012-10-25 10:31:28,947 (34/553774) state 
> change: job is running
> 
> -- snip --
> 
> galaxy.jobs.runners.drmaa DEBUG 2012-10-25 10:32:29,411 (34/553774) state 
> change: job finished normally
> 128.165.72.57 - - [25/Oct/2012:10:32:31 -0600] "POST 
> /root/history_item_updates HTTP/1.0" 200 - 
> "http://galaxy-dev.lanl.gov/history"; "Mozilla/5.0 (Macintosh; Intel Mac OS X 
> 10.6; rv:15.0) Gecko/20100101 Firefox/15.0.1"
> galaxy.jobs.runners.drmaa DEBUG 2012-10-25 10:32:31,241 (34) Job output not 
> returned from cluster; exit status = "0
> "
> galaxy.jobs DEBUG 2012-10-25 10:32:31,285 The tool did not define exit code 
> or stdio handling; checking stderr for success
> galaxy.jobs DEBUG 2012-10-25 10:32:31,427 setting dataset state to ERROR
> galaxy.jobs DEBUG 2012-10-25 10:32:31,471 setting dataset state to ERROR
> galaxy.jobs DEBUG 2012-10-25 10:32:31,728 job 34 ended
> galaxy.datatypes.metadata DEBUG 2012-10-25 10:32:31,729 Cleaning up external 
> metadata files
> 
> 
> And yet, for this example, the tool did actually run successfully with the 
> expected output files where they should be in the galaxy/database/files 
> directory.
> 
> Further, the 34.drmec file has just the exit code 0, the 34.drmout file is 
> empty and the 34.drmmt file is:

Hi Todd,

I've moved this over to galaxy-dev since it concerns a local installation.

There should be a 34.drmerr file in addition to 34.drmout and 34.drmec.  If any 
of the three are missing or unreadable when the job finishes, you'll encounter 
this error.  You might want to try increasing the value of 
"retry_job_output_collection".  Also, the changes in bfbd456ebbbe will show 
exactly which file is causing the problem, and the error message from the OS.

--nate

> 
> {
>     "program": "perl",
>     "arguments": [
>         
> "/opt/galaxy/dev/Galaxy-JGI_galaxy-dev/tools/lanl/readMapping/fastqSplitter/separate_paired_end_reads.pl",
>         "-i",
>         
> "/opt/galaxy/dev/Galaxy-JGI_galaxy-dev/database/files/000/dataset_48.dat",
>         "-l",
>         
> "/opt/galaxy/dev/Galaxy-JGI_galaxy-dev/database/files/000/dataset_53.dat",
>         "-r",
>         
> "/opt/galaxy/dev/Galaxy-JGI_galaxy-dev/database/files/000/dataset_54.dat"
>     ],
>     "exit_status": 0,
>     "start_time": 1351182686,
>     "wall_time": 0.223,
>     "usage": {
>         "utime": 0.04,
>         "stime": 0.08,
>         "max_vmem_kb": 11920,
>         "max_rss_kb": 156,
>         "start_time": 1351182686,
>         "wall_time": 0.223
>     }
> }
> 
> 
> So everything looks good to me but Galaxy is reporting a failed run. What 
> piece am I missing?
> 
> Thanks!
> 
> 
> 
> 
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