Hello, I am setting up a local galaxy installation and using our local SGE cluster to run the jobs as real users. One of the first few tools I tested was the ncbi makebkastdb tool. When I try to run it the history for that particular job is immediately shown as follows: 0: (unnamed dataset) Failed to retrieve dataset information. An error occurred with this dataset:/hasattr(): attribute name must be string/ In the stdout of the job I was getting the following error: Fatal error: Matched on Error: Error: NCBI C++ Exception: "/usr/local/src/ncbiblast+/2.2.27/c++/src/objtools/blast/seqdb_writer/build_db.cpp", line 979: Error: ncbi::s_CreateDirectories() - Failed to create directory 'dataset_38_files' I finally figured out that the makedb wrapper was using $outfile.extra_files_path instead of $outfile.files_path. I fixed the wrapper and restarted the instance. The job now runs ok and reports successful completion in the stdout. But, the history for this particular job is still shown as explained above. Can somebody help me figure out what is going wrong in my setup? Here are some of the relevant logs: ==> web1.log <== 128.192.203.31 - - [19/Mar/2013:15:14:35 -0400] "POST /tool_runner/index HTTP/1.1" 200 - "http://galaxy.qbcg.uga.edu/tool_runner?tool_id=toolshed.g2.bx.psu.edu/repos/..." "Mozilla/5.0 (Windows NT 6.1; WOW64) AppleWebKit/537.22 (KHTML, like Gecko) Chrome/25.0.1364.172 Safari/537.22" ==> web0.log <== 128.192.203.31 - - [19/Mar/2013:15:14:36 -0400] "GET /history HTTP/1.1" 200 - "http://galaxy.qbcg.uga.edu/tool_runner/index" "Mozilla/5.0 (Windows NT 6.1; WOW64) AppleWebKit/537.22 (KHTML, like Gecko) Chrome/25.0.1364.172 Safari/537.22" galaxy.webapps.galaxy.api.history_contents ERROR 2013-03-19 15:14:36,161 Error in history API at listing contents with history d413a19dec13d11e, hda e89067bb68bee7a0: hasattr(): attribute name must be string galaxy.webapps.galaxy.api.history_contents ERROR 2013-03-19 15:14:36,316 Error in history API at listing contents with history d413a19dec13d11e, hda ba03619785539f8c: hasattr(): attribute name must be string galaxy.webapps.galaxy.api.history_contents ERROR 2013-03-19 15:14:36,316 Error in history API at listing contents with history d413a19dec13d11e, hda cbbbf59e8f08c98c: hasattr(): attribute name must be string galaxy.webapps.galaxy.api.history_contents ERROR 2013-03-19 15:14:36,317 Error in history API at listing contents with history d413a19dec13d11e, hda 964b37715ec9bd22: hasattr(): attribute name must be string galaxy.webapps.galaxy.api.history_contents ERROR 2013-03-19 15:14:36,317 Error in history API at listing contents with history d413a19dec13d11e, hda 1fad1eaf5f4f1766: hasattr(): attribute name must be string galaxy.webapps.galaxy.api.history_contents ERROR 2013-03-19 15:14:36,318 Error in history API at listing contents with history d413a19dec13d11e, hda 2fdbd5c5858e78fb: hasattr(): attribute name must be string ==> manager.log <== galaxy.jobs.manager DEBUG 2013-03-19 15:14:40,856 (42) Job assigned to handler 'handler0' ==> handler0.log <== galaxy.jobs DEBUG 2013-03-19 15:14:41,790 (42) Working directory for job is: /panfs/pstor.storage/home/qbcglab/galaxy_run/galaxy-dist/database/job_working_directory/000/42 galaxy.jobs.rules.200_rules DEBUG 2013-03-19 15:14:41,791 toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_makeblastdb/0.0.1 galaxy.jobs.handler DEBUG 2013-03-19 15:14:41,792 dispatching job 42 to drmaa runner galaxy.jobs.handler INFO 2013-03-19 15:14:41,882 (42) Job dispatched galaxy.tools DEBUG 2013-03-19 15:14:42,068 Building dependency shell command for dependency 'makeblastdb' galaxy.tools WARNING 2013-03-19 15:14:42,068 Failed to resolve dependency on 'makeblastdb', ignoring galaxy.jobs.runners.drmaa DEBUG 2013-03-19 15:14:42,453 (42) submitting file /panfs/pstor.storage/home/qbcglab/galaxy_run/galaxy-dist/database/pbs/galaxy_42.sh galaxy.jobs.runners.drmaa DEBUG 2013-03-19 15:14:42,453 (42) command is: makeblastdb -version &> /panfs/pstor.storage/home/qbcglab/galaxy_run/galaxy-dist/database/tmp/GALAXY_VERSION_STRING_42; makeblastdb -out /panfs/pstor.storage/home/qbcglab/galaxy_run/galaxy-dist/database/job_working_directory/000/42/dataset_41_files/blastdb -hash_index -in " /panfs/pstor.storage/home/qbcglab/galaxy_run/galaxy-dist/database/files/000/dataset_30.dat " -title "wert" -dbtype nucl; cd /panfs/pstor.storage/home/qbcglab/galaxy_run/galaxy-dist; /panfs/pstor.storage/home/qbcglab/galaxy_run/galaxy-dist/set_metadata.sh ./database/files /panfs/pstor.storage/home/qbcglab/galaxy_run/galaxy-dist/database/job_working_directory/000/42 . /panfs/pstor.storage/home/qbcglab/galaxy_run/galaxy-dist/universe_wsgi.ini /panfs/pstor.storage/home/qbcglab/galaxy_run/galaxy-dist/database/tmp/tmpxi116L /panfs/pstor.storage/home/qbcglab/galaxy_run/galaxy-dist/database/job_working_directory/000/42/galaxy.json /panfs/pstor.storage/home/qbcglab/galaxy_run/galaxy-dist/database/job_working_directory/000/42/metadata_in_HistoryDatasetAssociation_40_4YjnIJ,/panfs/pstor.storage/home/qbcglab/galaxy_run/galaxy-dist/database/job_working_directory/000/42/metadata_kwds_HistoryDatasetAssociation_40_fWHejS,/panfs/pstor.storage/home/qbcglab/galaxy_run/galaxy-dist/database/job_working_directory/000/42/metadata_out_HistoryDatasetAssociation_40_BwBD1y,/panfs/pstor.storage/home/qbcglab/galaxy_run/galaxy-dist/database/job_working_directory/000/42/metadata_results_HistoryDatasetAssociation_40_0IjMAn,/panfs/pstor.storage/home/qbcglab/galaxy_run/galaxy-dist/database/job_working_directory/000/42/galaxy_dataset_41.dat,/panfs/pstor.storage/home/qbcglab/galaxy_run/galaxy-dist/database/job_working_directory/000/42/metadata_override_HistoryDatasetAssociation_40_pXhQCd galaxy.jobs DEBUG 2013-03-19 15:14:42,456 (42) Changing ownership of working directory with: /usr/bin/sudo -E scripts/external_chown_script.py /panfs/pstor.storage/home/qbcglab/galaxy_run/galaxy-dist/database/job_working_directory/000/42 raj76 1083 galaxy.jobs.runners.drmaa DEBUG 2013-03-19 15:14:42,766 (42) submitting with credentials: raj76 [uid: 740] galaxy.jobs.runners.drmaa DEBUG 2013-03-19 15:14:42,774 (42) Job script for external submission is: /panfs/pstor.storage/home/qbcglab/galaxy_run/galaxy-dist/database/pbs/42.jt_json galaxy.jobs.runners.drmaa INFO 2013-03-19 15:14:43,198 (42) queued as 2246095 galaxy.jobs.runners.drmaa DEBUG 2013-03-19 15:14:43,420 (42/2246095) state change: job is queued and active galaxy.jobs.runners.drmaa DEBUG 2013-03-19 15:14:54,444 (42/2246095) state change: job is running galaxy.jobs.runners.drmaa DEBUG 2013-03-19 15:15:04,614 (42/2246095) job left DRM queue with following message: code 18: The job specified by the 'jobid' does not exist. galaxy.jobs DEBUG 2013-03-19 15:15:04,648 (42) Changing ownership of working directory with: /usr/bin/sudo -E scripts/external_chown_script.py /panfs/pstor.storage/home/qbcglab/galaxy_run/galaxy-dist/database/job_working_directory/000/42 galaxy 1234 galaxy.jobs DEBUG 2013-03-19 15:15:06,988 (42) Changing ownership of working directory with: /usr/bin/sudo -E scripts/external_chown_script.py /panfs/pstor.storage/home/qbcglab/galaxy_run/galaxy-dist/database/job_working_directory/000/42 galaxy 1234 galaxy.jobs DEBUG 2013-03-19 15:15:07,833 finish(): Moved /panfs/pstor.storage/home/qbcglab/galaxy_run/galaxy-dist/database/job_working_directory/000/42/galaxy_dataset_41.dat to /panfs/pstor.storage/home/qbcglab/galaxy_run/galaxy-dist/database/files/000/dataset_41.dat galaxy.tools DEBUG 2013-03-19 15:15:09,546 Error opening galaxy.json file: [Errno 2] No such file or directory: '/panfs/pstor.storage/home/qbcglab/galaxy_run/galaxy-dist/database/job_working_directory/000/42/galaxy.json' galaxy.jobs DEBUG 2013-03-19 15:15:09,626 job 42 ended galaxy.datatypes.metadata DEBUG 2013-03-19 15:15:09,626 Cleaning up external metadata files galaxy.objectstore CRITICAL 2013-03-19 15:15:09,665 /panfs/pstor.storage/home/qbcglab/galaxy_run/galaxy-dist/database/job_working_directory/000/42 delete error [Errno 39] Directory not empty: '/panfs/pstor.storage/home/qbcglab/galaxy_run/galaxy-dist/database/job_working_directory/000/42' ==> web1.log <== sqlalchemy.pool.QueuePool.0x...4350 WARNING 2013-03-19 15:16:14,801 Error closing cursor: current transaction is aborted, commands ignored until end of transaction block Thanks, -Raj