Question: Tools Always Failing?
0
Todd Yilk • 50 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_His
toryDatasetAssociation_59_MLg1Aw,/opt/galaxy/dev/Galaxy-JGI_galaxy-dev
/database/job_working_directory/000/34/metadata_out_HistoryDatasetAsso
ciation_59_ZVYBIT,/opt/galaxy/dev/Galaxy-JGI_galaxy-dev/database/job_w
orking_directory/000/34/metadata_results_HistoryDatasetAssociation_59_
q4FpIq,,/opt/galaxy/dev/Galaxy-JGI_galaxy-dev/database/job_working_dir
ectory/000/34/metadata_override_HistoryDatasetAssociation_59_3HXPLq
/opt/galaxy/dev/Galaxy-JGI_galaxy-dev/database/job_working_directory/0
00/34/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_Hist
oryDatasetAssociation_60_eEItGr,/opt/galaxy/dev/Galaxy-JGI_galaxy-dev/
database/job_working_directory/000/34/metadata_results_HistoryDatasetA
ssociation_60_bMa6HN,,/opt/galaxy/dev/Galaxy-JGI_galaxy-dev/database/j
ob_working_directory/000/34/metadata_override_HistoryDatasetAssociatio
n_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!