Actually the failure turned out to be from a different change I made. The "default_cluster_job_runner" change seemed to be fine.
(For the curious, the change that caused these errors was that I split the job_environment_setup_file PATH changes into two files and had job_environment_setup_file simply source the two files. I guess Galaxy didn't like that.) -Greg On Fri, Dec 14, 2012 at 2:07 PM, greg <margeem...@gmail.com> wrote: > 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. 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