Hi guys,

I'm really stuck on this one.

In my galaxy config file I changed the setting it uses to launch jobs from:

default_cluster_job_runner = drmaa://-V/
(which worked fine)

To
default_cluster_job_runner = drmaa://-V -pe batch 8/

Now whenever I run a job I see a message like this:

"Job output not returned from cluster"

(Is there any other information I can use to debug this?)

I see the information below in the log file if any of that is useful:

galaxy.jobs.manager DEBUG 2012-12-14 13:27:36,961 (104) Job assigned
to handler 'main'
galaxy.jobs DEBUG 2012-12-14 13:27:37,584 (104) Working directory for
job is: /home/galaxy/job_working_directory/000/104
galaxy.jobs.handler DEBUG 2012-12-14 13:27:37,586 dispatching job 104
to drmaa runner
galaxy.jobs.handler INFO 2012-12-14 13:27:37,772 (104) Job dispatched
galaxy.jobs.runners DEBUG 2012-12-14 13:27:38,078 Copying
/home/galaxy/job_working_directory/000/104/global_model.txt to
/home/galaxy/000/dataset_155.dat as directed by from_work_dir
galaxy.jobs.runners DEBUG 2012-12-14 13:27:38,111 Copying
/home/galaxy/job_working_directory/000/104/genes.fpkm_tracking to
/home/galaxy/000/dataset_152.dat as directed by from_work_dir
galaxy.jobs.runners DEBUG 2012-12-14 13:27:38,135 Copying
/home/galaxy/job_working_directory/000/104/isoforms.fpkm_tracking to
/home/galaxy/000/dataset_153.dat as directed by from_work_dir
galaxy.jobs.runners.drmaa DEBUG 2012-12-14 13:27:38,819 (104)
submitting file /home/galaxy/pbs/galaxy_104.sh
galaxy.jobs.runners.drmaa DEBUG 2012-12-14 13:27:38,820 (104) command
is: python /misc/local/galaxy/galaxy-dist/tools/ngs_rna/cufflinks_wrapper.py
             --input=/home/galaxy/000/dataset_93.dat
--assembled-isoforms-output=/home/galaxy/000/dataset_154.dat
  --num-threads="4"             -I 300000             -F 0.1
  -j 0.15; cp /home/galaxy/job_working_directory/000/104/global_model.txt
/home/galaxy/000/dataset_155.dat; cp
/home/galaxy/job_working_directory/000/104/genes.fpkm_tracking
/home/galaxy/000/dataset_152.dat; cp
/home/galaxy/job_working_directory/000/104/isoforms.fpkm_tracking
/home/galaxy/000/dataset_153.dat; cd /misc/local/galaxy/galaxy-dist;
/misc/local/galaxy/galaxy-dist/set_metadata.sh /home/galaxy
/home/galaxy/job_working_directory/000/104 .
/misc/local/galaxy/galaxy-dist/universe_wsgi.ini
/home/galaxy/job_working_directory/tmppjMj2j
/home/galaxy/job_working_directory/000/104/galaxy.json
/home/galaxy/job_working_directory/000/104/metadata_in_HistoryDatasetAssociation_176_zK8nkf,/home/galaxy/job_working_directory/000/104/metadata_kwds_HistoryDatasetAssociation_176_Dkq7kA,/home/galaxy/job_working_directory/000/104/metadata_out_HistoryDatasetAssociation_176_jR0e_Z,/home/galaxy/job_working_directory/000/104/metadata_results_HistoryDatasetAssociation_176_jl8W2w,,/home/galaxy/job_working_directory/000/104/metadata_override_HistoryDatasetAssociation_176_M6ctS5
/home/galaxy/job_working_directory/000/104/metadata_in_HistoryDatasetAssociation_177_Q1vGSc,/home/galaxy/job_working_directory/000/104/metadata_kwds_HistoryDatasetAssociation_177_MG96_w,/home/galaxy/job_working_directory/000/104/metadata_out_HistoryDatasetAssociation_177_NWTSVQ,/home/galaxy/job_working_directory/000/104/metadata_results_HistoryDatasetAssociation_177_iTNC5T,,/home/galaxy/job_working_directory/000/104/metadata_override_HistoryDatasetAssociation_177_MO0SIc
/home/galaxy/job_working_directory/000/104/metadata_in_HistoryDatasetAssociation_174_HcoiD4,/home/galaxy/job_working_directory/000/104/metadata_kwds_HistoryDatasetAssociation_174_4j5SRC,/home/galaxy/job_working_directory/000/104/metadata_out_HistoryDatasetAssociation_174_irlquD,/home/galaxy/job_working_directory/000/104/metadata_results_HistoryDatasetAssociation_174_jfK1zk,,/home/galaxy/job_working_directory/000/104/metadata_override_HistoryDatasetAssociation_174_YQzY4e
/home/galaxy/job_working_directory/000/104/metadata_in_HistoryDatasetAssociation_175_rjQ2Gp,/home/galaxy/job_working_directory/000/104/metadata_kwds_HistoryDatasetAssociation_175_HMeDGS,/home/galaxy/job_working_directory/000/104/metadata_out_HistoryDatasetAssociation_175_7sjyvl,/home/galaxy/job_working_directory/000/104/metadata_results_HistoryDatasetAssociation_175_cJ_Sw6,,/home/galaxy/job_working_directory/000/104/metadata_override_HistoryDatasetAssociation_175_JY4ngx
galaxy.jobs.runners.drmaa INFO 2012-12-14 13:27:38,884 (104) queued as 4076946
galaxy.jobs.runners.drmaa DEBUG 2012-12-14 13:27:39,822 (104/4076946)
state change: job is queued and active
galaxy.jobs.runners.drmaa DEBUG 2012-12-14 13:27:42,830 (104/4076946)
state change: job is running
galaxy.jobs.runners.drmaa DEBUG 2012-12-14 13:27:44,065 (104/4076946)
state change: job finished normally
galaxy.jobs.runners.drmaa DEBUG 2012-12-14 13:27:44,111 Job output not
returned from cluster
galaxy.jobs DEBUG 2012-12-14 13:27:44,147 Tool did not define exit
code or stdio handling; checking stderr for success
galaxy.jobs DEBUG 2012-12-14 13:27:44,187 setting dataset state to ERROR
galaxy.jobs DEBUG 2012-12-14 13:27:44,206 setting dataset state to ERROR
galaxy.jobs DEBUG 2012-12-14 13:27:44,226 setting dataset state to ERROR
galaxy.jobs DEBUG 2012-12-14 13:27:44,250 setting dataset state to ERROR
galaxy.jobs DEBUG 2012-12-14 13:27:44,432 job 104 ended
galaxy.datatypes.metadata DEBUG 2012-12-14 13:27:44,432 Cleaning up
external metadata files
galaxy.datatypes.metadata DEBUG 2012-12-14 13:27:44,452 Failed to
cleanup MetadataTempFile temp files from
/home/galaxy/job_working_directory/000/104/metadata_out_HistoryDatasetAssociation_176_jR0e_Z:
No JSON object could be decoded: line 1 column 0 (char 0)
galaxy.datatypes.metadata DEBUG 2012-12-14 13:27:44,475 Failed to
cleanup MetadataTempFile temp files from
/home/galaxy/job_working_directory/000/104/metadata_out_HistoryDatasetAssociation_177_NWTSVQ:
No JSON object could be decoded: line 1 column 0 (char 0)
galaxy.datatypes.metadata DEBUG 2012-12-14 13:27:44,491 Failed to
cleanup MetadataTempFile temp files from
/home/galaxy/job_working_directory/000/104/metadata_out_HistoryDatasetAssociation_175_7sjyvl:
No JSON object could be decoded: line 1 column 0 (char 0)
galaxy.datatypes.metadata DEBUG 2012-12-14 13:27:44,510 Failed to
cleanup MetadataTempFile temp files from
/home/galaxy/job_working_directory/000/104/metadata_out_HistoryDatasetAssociation_174_irlquD:
No JSON object could be decoded: line 1 column 0 (char 0)
galaxy.objectstore CRITICAL 2012-12-14 13:27:44,544
/home/galaxy/job_working_directory/000/104 delete error [Errno 39]
Directory not empty: '/home/galaxy/job_working_directory/000/104'

Thanks,

-Greg

___________________________________________________________
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