Question: Galaxy slurm cluster empty files
0
djevo1 • 60 wrote:
I have connected galaxy to our slurm cluster, but am having an issue with running jobs. Galaxy shows the jobs completed successfully, however the files are empty. An error is produced under each dataset that states
Uploaded temporary file (/mnt/VDisk/FTP/galaxy_upload/abc@mail.com/SampleSheet.csv) does not exist.
I am not sure how to solve this issue and below is the output form the console
galaxy.jobs.runners DEBUG 2016-10-04 12:15:12,741 execution of external set_meta for job 22 finished
galaxy.jobs.runners.drmaa DEBUG 2016-10-04 12:15:12,794 (23/27) state change: job finished normally
galaxy.tools.deps DEBUG 2016-10-04 12:15:13,171 Find dependency samtools version None
galaxy.tools.deps DEBUG 2016-10-04 12:15:13,172 Dependency samtools not found.
galaxy.jobs.runners DEBUG 2016-10-04 12:15:13,172 executing external set_meta script for job 23: GALAXY_LIB="/mnt/VDisk/galaxy_production/galaxy/lib"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi; GALAXY_VIRTUAL_ENV="/mnt/VDisk/galaxy_production/galaxy/.venv"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi; python "/mnt/VDisk/galaxy_production/galaxy/database/jobs_directory/000/23/set_metadata_goZM4c.py" "/mnt/VDisk/galaxy_production/galaxy/database/tmp/tmp9ha6d8" "/mnt/VDisk/galaxy_production/galaxy/database/jobs_directory/000/23/working/galaxy.json" "/mnt/VDisk/galaxy_production/galaxy/database/jobs_directory/000/23/metadata_in_HistoryDatasetAssociation_23_RCDUO_,/mnt/VDisk/galaxy_production/galaxy/database/jobs_directory/000/23/metadata_kwds_HistoryDatasetAssociation_23_WcifDY,/mnt/VDisk/galaxy_production/galaxy/database/jobs_directory/000/23/metadata_out_HistoryDatasetAssociation_23_YhzpRr,/mnt/VDisk/galaxy_production/galaxy/database/jobs_directory/000/23/metadata_results_HistoryDatasetAssociation_23_frJq2g,/mnt/VDisk/galaxy_production/galaxy/database/files/000/dataset_23.dat,/mnt/VDisk/galaxy_production/galaxy/database/jobs_directory/000/23/metadata_override_HistoryDatasetAssociation_23_bzh2Xf" 5242880
galaxy.jobs INFO 2016-10-04 12:15:13,419 Collecting metrics for Job 22
galaxy.jobs DEBUG 2016-10-04 12:15:13,446 job 22 ended (finish() executed in (542.541 ms))
This was a simple fix I missed, it is working now/