gistfile1.txt

81.104.40.232 - - [15/Mar/2018:18:44:46 +0000] "GET /api/webhooks/tool HTTP/1.0" 200 - "http://52.54.147.188/?job_id=a9c35477134349b6&__identifer=rkaxrenk5l" "Mozilla/5.0 (Windows NT 6.1; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/65.0.3325.146 Safari/537.36"
81.104.40.232 - - [15/Mar/2018:18:44:46 +0000] "GET /api/histories/e8d3f6db536fde44/contents?details=586e4e674b1f864c&order=hid&v=dev&q=update_time-ge&q=deleted&q=purged&qv=2018-03-15T18%3A48%3A12.864Z&qv=False&qv=False HTTP/1.0" 200 - "http://52.54.147.188/?job_id=a9c35477134349b6&__identifer=rkaxrenk5l" "Mozilla/5.0 (Windows NT 6.1; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/65.0.3325.146 Safari/537.36"
81.104.40.232 - - [15/Mar/2018:18:44:46 +0000] "GET /api/histories/e8d3f6db536fde44?keys=size%2Cnon_ready_jobs%2Ccontents_active%2Chid_counter HTTP/1.0" 200 - "http://52.54.147.188/?job_id=a9c35477134349b6&__identifer=rkaxrenk5l" "Mozilla/5.0 (Windows NT 6.1; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/65.0.3325.146 Safari/537.36"
galaxy.jobs DEBUG 2018-03-15 18:44:46,642 (5110) Working directory for job is: /mnt/galaxy/tmp/job_working_directory/005/5110
galaxy.jobs.handler DEBUG 2018-03-15 18:44:46,646 (5110) Dispatching to slurm runner
galaxy.jobs DEBUG 2018-03-15 18:44:46,674 (5110) Persisting job destination (destination id: slurm_cluster)
galaxy.jobs.runners DEBUG 2018-03-15 18:44:46,683 Job [5110] queued (36.639 ms)
galaxy.jobs.handler INFO 2018-03-15 18:44:46,693 (5110) Job dispatched
galaxy.tools.deps DEBUG 2018-03-15 18:44:46,898 Using dependency prokka version 1.12 of type conda
galaxy.jobs.command_factory INFO 2018-03-15 18:44:46,932 Built script [/mnt/galaxy/tmp/job_working_directory/005/5110/tool_script.sh] for tool command [[ "$CONDA_DEFAULT_ENV" = "/mnt/galaxy/tool_dependencies/_conda/envs/__prokka@1.12" ] ||
MAX_TRIES=3
COUNT=0
while [ $COUNT -lt $MAX_TRIES ]; do
. /mnt/galaxy/tool_dependencies/_conda/bin/activate '/mnt/galaxy/tool_dependencies/_conda/envs/__prokka@1.12' > conda_activate.log 2>&1
if [ $? -eq 0 ];then
break
else
let COUNT=COUNT+1
if [ $COUNT -eq $MAX_TRIES ];then
echo "Failed to activate conda environment! Error was:"
cat conda_activate.log
exit 1
fi
sleep 10s
fi
done ; prokka --version > /mnt/galaxy/tmp/GALAXY_VERSION_STRING_5110 2>&1; prokka --cpus ${GALAXY_SLOTS:-8} --quiet --outdir outdir --prefix prokka --locustag 'PROKKA' --increment 1 --gffver 3 --mincontig 200 --kingdom Bacteria --gcode 11 --evalue 1e-06 /mnt/galaxy/files/006/dataset_6747.dat]
galaxy.tools.deps DEBUG 2018-03-15 18:44:47,725 Using dependency samtools version None of type conda
galaxy.tools.deps DEBUG 2018-03-15 18:44:47,725 Using dependency bcftools version 1.5 of type conda
galaxy.jobs.runners DEBUG 2018-03-15 18:44:47,730 (5110) command is: rm -rf working; mkdir -p working; cd working; /mnt/galaxy/tmp/job_working_directory/005/5110/tool_script.sh; return_code=$?; if [ -f /mnt/galaxy/tmp/job_working_directory/005/5110/working/outdir/prokka.log ] ; then cp /mnt/galaxy/tmp/job_working_directory/005/5110/working/outdir/prokka.log /mnt/galaxy/files/007/dataset_7790.dat ; fi; if [ -f /mnt/galaxy/tmp/job_working_directory/005/5110/working/outdir/prokka.txt ] ; then cp /mnt/galaxy/tmp/job_working_directory/005/5110/working/outdir/prokka.txt /mnt/galaxy/files/007/dataset_7789.dat ; fi; if [ -f /mnt/galaxy/tmp/job_working_directory/005/5110/working/outdir/prokka.err ] ; then cp /mnt/galaxy/tmp/job_working_directory/005/5110/working/outdir/prokka.err /mnt/galaxy/files/007/dataset_7788.dat ; fi; if [ -f /mnt/galaxy/tmp/job_working_directory/005/5110/working/outdir/prokka.tbl ] ; then cp /mnt/galaxy/tmp/job_working_directory/005/5110/working/outdir/prokka.tbl /mnt/galaxy/files/007/dataset_7787.dat ; fi; if [ -f /mnt/galaxy/tmp/job_working_directory/005/5110/working/outdir/prokka.fsa ] ; then cp /mnt/galaxy/tmp/job_working_directory/005/5110/working/outdir/prokka.fsa /mnt/galaxy/files/007/dataset_7786.dat ; fi; if [ -f /mnt/galaxy/tmp/job