Re-post to galaxy-...@bx.psu.edu

Todd - this will give your questions better visibility. This is your own tool? And other tools packaged with the standard Galaxy distribution or installed from the Tool Shed run OK on the cluster?


If your own tool (and others work, ruling out cluster set-up as an issue), you are probably already working from this wiki, but if not, section #42 covers exit codes:
http://wiki.g2.bx.psu.edu/Admin/Tools/Tool%20Config%20Syntax

Let's see what other feedback/advice comes from the developers,

Best,
Jen
Galaxy team

On 10/25/12 1:34 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_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!






___________________________________________________________
The Galaxy User list should be used for the discussion of
Galaxy analysis and other features on the public server
at usegalaxy.org.  Please keep all replies on the list by
using "reply all" in your mail client.  For discussion of
local Galaxy instances and the Galaxy source code, please
use the Galaxy Development list:

   http://lists.bx.psu.edu/listinfo/galaxy-dev

To manage your subscriptions to this and other Galaxy lists,
please use the interface at:

   http://lists.bx.psu.edu/

--
Jennifer Jackson
http://galaxyproject.org

___________________________________________________________
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:

  http://lists.bx.psu.edu/

Reply via email to