This is a stand alone instance of Galaxy built Nov 28 a small research cluster using LSF and built on RHEL6.2. galaxy.tools.actions.upload_common INFO 2013-12-05 14:33:01,106 tool upload1 created job id 10 Working directory for job is: /depot/shared/app/Galaxy/galaxy-dist/database/job_working_directory/000/10 galaxy.jobs.handler DEBUG 2013-12-05 14:33:01,290 (10) Dispatching to drmaa runner galaxy.jobs DEBUG 2013-12-05 14:33:01,441 (10) Persisting job destination (destination id: drmaa) galaxy.jobs.handler INFO 2013-12-05 14:33:01,471 (10) Job dispatched galaxy.tools.deps DEBUG 2013-12-05 14:33:01,693 Building dependency shell command for dependency 'samtools' galaxy.tools.deps WARNING 2013-12-05 14:33:01,693 Failed to resolve dependency on 'samtools', ignoring galaxy.jobs.runners.drmaa DEBUG 2013-12-05 14:33:02,352 (10) submitting file /depot/shared/app/Galaxy/galaxy-dist/database/job_working_directory/000/10/ galaxy_10.sh galaxy.jobs.runners.drmaa DEBUG 2013-12-05 14:33:02,352 (10) command is: pythonŠ. galaxy.jobs DEBUG 2013-12-05 14:33:02,379 (10) Changing ownership of working directory with: /usr/bin/sudo -E scripts/external_chown_script.py /depot/shared/app/Galaxy/galaxy-dist/database/job_working_directory/000/10 galaxy 50982 galaxy.jobs.runners.drmaa DEBUG 2013-12-05 14:33:02,528 (10) submitting with credentials: galaxy [uid: 50981] galaxy.jobs.runners.drmaa DEBUG 2013-12-05 14:33:02,574 (10) Job script for external submission is: /depot/shared/app/Galaxy/galaxy-dist/database/lsf/10.jt_json galaxy.jobs.runners.drmaa INFO 2013-12-05 14:33:02,772 (10) queued as Job <28526> is submitted to default queue <medium_priority>. 28526 galaxy.jobs DEBUG 2013-12-05 14:33:02,837 (10) Persisting job destination (destination id: drmaa) galaxy.jobs.runners.drmaa INFO 2013-12-05 14:33:03,237 (10/Job <28526> is submitted to default queue <medium_priority>. 28526) job left DRM queue with following message: code 18: invalid LSF job id: Job <28526> is submitted to default queue <medium_priority>. 28526 galaxy.jobs DEBUG 2013-12-05 14:33:03,303 (10) Changing ownership of working directory with: /usr/bin/sudo -E scripts/external_chown_script.py /depot/shared/app/Galaxy/galaxy-dist/database/job_working_directory/000/10 galaxy 50982 128.23.163.166 - - [05/Dec/2013:14:33:05 -0400] "GET /api/histories/50a7a2e81473b416/contents HTTP/1.1" 200 - "http://hpcc3.musc.edu:8089/root" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10.9; rv:25.0) Gecko/20100101 Firefox/25.0" galaxy.jobs.runners ERROR 2013-12-05 14:33:08,661 (10/Job <28526> is submitted to default queue <medium_priority>. 28526) Job output not returned from cluster: [Errno 2] No such file or directory: '/depot/shared/app/Galaxy/galaxy-dist/database/job_working_directory/000/10 /galaxy_10.o' galaxy.jobs DEBUG 2013-12-05 14:33:08,701 (10) Changing ownership of working directory with: /usr/bin/sudo -E scripts/external_chown_script.py /depot/shared/app/Galaxy/galaxy-dist/database/job_working_directory/000/10 galaxy 50982 galaxy.jobs DEBUG 2013-12-05 14:33:09,049 finish(): Moved /depot/shared/app/Galaxy/galaxy-dist/database/job_working_directory/000/10/ galaxy_dataset_16.dat to /depot/shared/app/Galaxy/galaxy-dist/database/files/000/dataset_16.dat galaxy.jobs DEBUG 2013-12-05 14:33:09,049 finish(): Moved /depot/shared/app/Galaxy/galaxy-dist/database/job_working_directory/000/10/ galaxy_dataset_15.dat to /depot/shared/app/Galaxy/galaxy-dist/database/files/000/dataset_15.dat galaxy.jobs DEBUG 2013-12-05 14:33:09,105 setting dataset state to ERROR galaxy.jobs DEBUG 2013-12-05 14:33:09,126 setting dataset state to ERROR galaxy.jobs DEBUG 2013-12-05 14:33:09,214 job 10 ended "Job output not returned from cluster² appears in History, BUT in fact files are being written to directories indicated in my universe_wsgi.ini I am having no success getting a solution to this error "job left DRM queue with following message: code 18: invalid LSF job id" This file "No such file or directory: '/depot/shared/app/Galaxy/galaxy-dist/database/job_working_directory/000/10 /galaxy_10.o¹ ³ exists AFTER the job finishes. SO at 2013-12-05 14:33:03 the file had not been written but does appear later. This operation is completing before the file can be uploaded and so an empty file is moved Moved /depot/shared/app/Galaxy/galaxy-dist/database/job_working_directory/000/10/ galaxy_dataset_15.dat to /depot/shared/app/Galaxy/galaxy-dist/database/files/000/dataset_15.dat
From my universe_wsgi.ini:
file_path = database/files new_file_path = database/job_working_directory job_working_directory = database/job_working_directory cluster_files_directory = database/job_working_directory Any troubleshooting suggestions appreciated. Starr