Tutorial1 bug in workflow all.ctrl file?

Bugs
#1

Hi,

Tutorial 1 is failing with the following error message - I am not sure there is a targetformats= line in the workflow all.ctrl file. I’ve copied the message from …/workflow/output-files/queues/queue-1-1-1.out.all file. Does this need to be fixed?

Thanks,
Chris

++ [[ debug == \d\e\b\u\g ]]
++ set -x
++ [[ high == \h\i\g\h ]]
++ set -uo pipefail
++ trap ‘’ PIPE
++ trap ‘error_response_std $LINENO’ ERR
++ trap time_near_limit 1 2 3 9 10 12 15
++ trap clean_queue_files_tmp EXIT RETURN
++ ‘[’ debug = debug ‘]’
++ set -x
++ determine_controlfile
++ VF_CONTROLFILE=
+++ ls ‘…/workflow/control/-’
+++ true
++ ‘[’ -z ‘’ ‘]’
++ ‘[’ -f …/workflow/control/all.ctrl ‘]’
++ VF_CONTROLFILE=…/workflow/control/all.ctrl
+++ grep -m 1 ‘^targetformats=’ …/workflow/control/all.ctrl
+++ tr -d ‘[[:space:]]’
+++ awk -F ‘[=#]’ ‘{print $2}’
++ targetformats=
+++ error_response_std 597
+++ echo ‘Error was trapped’
Error was trapped
++++ basename …/workflow/job-files/sub/one-queue.sh
+++ echo ‘Error in bash script one-queue.sh’
Error in bash script one-queue.sh
+++ echo ‘Error on line 597’
Error on line 597

#2

This turned out to be an LSF environment issue -

By removing and adjusting the following lines, things ran fine:

  • deleted within templates/template1.lsf.sh *
    #BSUB -R “rusage[mem=400]”
    #BSUB -R “select[scratch]”
    #BSUB -R “span[ptile=4]”

  • changed within templates/template1.lsf.sh *
    #BSUB -q medium --> #BSUB -q /actualQueue/

Thanks,
Chris