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_directory/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/database/job_working_directory/000/34/metadata_results_HistoryDatasetAssociation_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:

{
    "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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