Dear group,
uploading an mgf formatted file results in the error below and the file is not uploaded. The mgf is valid since upload to Galaxy-P works. The installation is linux, newest version of galaxy, no tools installed. What am I doing wrong ? Thanks a lot ! Thomas
galaxy.jobs.handler DEBUG 2018-01-24 15:18:00,030 (2) Dispatching to local runner galaxy.jobs DEBUG 2018-01-24 15:18:00,050 (2) Persisting job destination (destination id: local:///) galaxy.jobs.runners DEBUG 2018-01-24 15:18:00,135 Job [2] queued (105.209 ms) galaxy.jobs.handler INFO 2018-01-24 15:18:00,145 (2) Job dispatched galaxy.jobs.command_factory INFO 2018-01-24 15:18:00,283 Built script [/srv/opt/galaxy/database/jobs_directory/000/2/tool_script.sh] for tool command [python /srv/opt/galaxy/tools/data_source/upload.py /srv/opt/galaxy /srv/opt/galaxy/database/jobs_directory/000/2/registry.xml /srv/opt/galaxy/database/tmp/tmpdnGkds 2:/srv/opt/galaxy/database/jobs_directory/000/2/dataset_2_files:/srv/opt/galaxy/database/files/000/dataset_2.dat] galaxy.jobs.runners DEBUG 2018-01-24 15:18:00,408 (2) command is: rm -rf working; mkdir -p working; cd working; /srv/opt/galaxy/database/jobs_directory/000/2/tool_script.sh; return_code=$?; cd '/srv/opt/galaxy/database/jobs_directory/000/2'; [ "$GALAXY_VIRTUAL_ENV" = "None" ] && GALAXY_VIRTUAL_ENV="$_GALAXY_VIRTUAL_ENV"; _galaxy_setup_environment True python "/srv/opt/galaxy/database/jobs_directory/000/2/set_metadata_0UIi6Q.py" "/srv/opt/galaxy/database/jobs_directory/000/2/registry.xml" "/srv/opt/galaxy/database/jobs_directory/000/2/working/galaxy.json" "/srv/opt/galaxy/database/jobs_directory/000/2/metadata_in_HistoryDatasetAssociation_2_R5mxyR,/srv/opt/galaxy/database/jobs_directory/000/2/metadata_kwds_HistoryDatasetAssociation_2_Gm1ovZ,/srv/opt/galaxy/database/jobs_directory/000/2/metadata_out_HistoryDatasetAssociation_2_ZPd892,/srv/opt/galaxy/database/jobs_directory/000/2/metadata_results_HistoryDatasetAssociation_2_hcdHfJ,/srv/opt/galaxy/database/files/000/dataset_2.dat,/srv/opt/galaxy/database/jobs_directory/000/2/metadata_override_HistoryDatasetAssociation_2_erpNf2" 5242880; sh -c "exit $return_code" galaxy.jobs.runners.local DEBUG 2018-01-24 15:18:00,421 (2) executing job script: /srv/opt/galaxy/database/jobs_directory/000/2/galaxy_2.sh galaxy.jobs DEBUG 2018-01-24 15:18:00,432 (2) Persisting job destination (destination id: local:///) galaxy.jobs.runners.local DEBUG 2018-01-24 15:18:02,932 execution finished: /srv/opt/galaxy/database/jobs_directory/000/2/galaxy_2.sh galaxy.jobs.output_checker DEBUG 2018-01-24 15:18:02,936 Tool produced standard error failing job - [Traceback (most recent call last): File "/srv/opt/galaxy/tools/data_source/upload.py", line 431, in <module> __main__() File "/srv/opt/galaxy/tools/data_source/upload.py", line 419, in __main__ add_file(dataset, registry, json_file, outpu] galaxy.jobs DEBUG 2018-01-24 15:18:02,959 (2) setting dataset 2 state to ERROR galaxy.jobs INFO 2018-01-24 15:18:03,168 Collecting metrics for Job 2 galaxy.jobs DEBUG 2018-01-24 15:18:03,233 job 2 ended (finish() executed in (300.111 ms)) 77.119.242.227 - - [24/Jan/2018:15:18:03 +0200] "GET /galaxy/api/histories/f2db41e1fa331b3e/contents?details=f2db41e1fa331b3e&order=hid&v=dev&q=update_time-ge&q=deleted&q=purged&qv=2018-01-24T14%3A17%3A59.000Z&qv=False&qv=False HTTP/1.1" 200 - "https://server1.mohrkeg.co.at/galaxy/" "Mozilla/5.0 (X11; Linux x86_64; rv:58.0) Gecko/20100101 Firefox/58.0" galaxy.tools.error_reports DEBUG 2018-01-24 15:18:03,253 Bug report plugin <galaxy.tools.error_reports.plugins.sentry.sentryplugin object="" at="" 0x7f4fa59ca190=""> generated response None galaxy.model.metadata DEBUG 2018-01-24 15:18:03,253 Cleaning up external metadata files 77.119.242.227 - - [24/Jan/2018:15:18:03 +0200] "GET /galaxy/api/histories/f2db41e1fa331b3e?keys=size%2Cnon_ready_jobs%2Ccontents_active%2Chid_counter HTTP/1.1" 200 - "https://server1.mohrkeg.co.at/galaxy/" "Mozilla/5.0 (X11; Linux x86_64; rv:58.0) Gecko/20100101 Firefox/58.0" 77.119.242.227 - - [24/Jan/2018:15:18:09 +0200] "PUT /galaxy/api/histories/f2db41e1fa331b3e/contents/datasets/f597429621d6eb2b HTTP/1.1" 200 - "https://server1.mohrkeg.co.at/galaxy/" "Mozilla/5.0 (X11; Linux x86_64; rv:58.0) Gecko/20100101 Firefox/58.0"
