Tutorial ligand write error


I am trying to get the tutorials running on an LSF cluster. I can get jobs and queues prepared, but it seems to fail when obtaining ligand names (line 797 below is “Getting the name of the first ligand of the first collection” ). When I recreate these steps manually, they work fine. While running VFVS there’s a tar: write error, although the correct ligand is identified.

Do I need to slow things down to allow time for tar extraction? This seems to be built in, though not occurring. Happy to send other info and expt parameters that would be helpful too.

When I allow the tutorial to run for a while, the jobs and queues seem to run on repeat without actually analyzing any ligands.

Any help would be greatly appreciated!

++ cp …/input-files/ligand-library/CF/CFCDBD.tar /project/voight_ML/thomc/thomc_results/VirtualFlow/Tutorial2/VFVS_GK/tmp/thomc/VFVS/a/1-1/1-1-1/input-files/ligands/pdbqt/CF/CFCDBD.tar
++ tar -xf /project/voight_ML/thomc/thomc_results/VirtualFlow/Tutorial2/VFVS_GK/tmp/thomc/VFVS/a/1-1/1-1-1/input-files/ligands/pdbqt/CF/CFCDBD.tar -C /project/voight_ML/thomc/thomc_results/VirtualFlow/Tutorial2/VFVS_GK/tmp/thomc/VFVS/a/1-1/1-1-1/input-files/ligands/pdbqt/CF/ CFCDBD/00001.tar.gz
++ gunzip /project/voight_ML/thomc/thomc_results/VirtualFlow/Tutorial2/VFVS_GK/tmp/thomc/VFVS/a/1-1/1-1-1/input-files/ligands/pdbqt/CF/CFCDBD/00001.tar.gz
++ ‘[’ ‘!’ -f /project/voight_ML/thomc/thomc_results/VirtualFlow/Tutorial2/VFVS_GK/tmp/thomc/VFVS/a/1-1/1-1-1/input-files/ligands/pdbqt/CF/CFCDBD/00001.tar ‘]’
++ tar -xf /project/voight_ML/thomc/thomc_results/VirtualFlow/Tutorial2/VFVS_GK/tmp/thomc/VFVS/a/1-1/1-1-1/input-files/ligands/pdbqt/CF/CFCDBD/00001.tar -C /project/voight_ML/thomc/thomc_results/VirtualFlow/Tutorial2/VFVS_GK/tmp/thomc/VFVS/a/1-1/1-1-1/input-files/ligands/pdbqt/CF/CFCDBD
++ for docking_scenario_name in ‘${docking_scenario_names[@]}’
++ ‘[’ true = false ‘]’
++ for docking_scenario_name in ‘${docking_scenario_names[@]}’
++ ‘[’ true = false ‘]’
++ [[ -f …/workflow/ligand-collections/ligand-lists/CF/CFCDBD/00001.status ]]
+++ tar -tf /project/voight_ML/thomc/thomc_results/VirtualFlow/Tutorial2/VFVS_GK/tmp/thomc/VFVS/a/1-1/1-1-1/input-files/ligands/pdbqt/CF/CFCDBD/00001.tar
+++ head -n 2
+++ tail -n 1
+++ awk -F ‘[/.]’ ‘{print $2}’
tar: write error
++ next_ligand=Z1549349423_1_T1
+++ error_response_std 797
+++ 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 797’
Error on line 797

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/


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