Workflow not stopping after all ligands docked

VFVS VFVS 1
#1

I’m attempting to run tutorial 2 on a custom set of ligands that I downloaded from the VFVS library. there should be ~22800 total ligands using the MW 450, HBA 3-10, SlogP -inf to inf, HBD 4-5, TPSA 0-140, and RotB 0-10. It appears to be running, but when I use the ./vf_report.sh -c workflow I get the extremely verbose report included below. From what I can tell it acknowledges that there are 22834 ligands, two docking programs (qvina02 and smina), and replicas are set to 1:1. However, it also appears to be reporting 58636 successful dockings and it is still running. My understanding is it should have stopped at 45668 total dockings, so I’m unclear what’s going on at this point. Any help would be appreciated.

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     ::::   ::  :::.    ::   ::  ::  ::::::  ::      :::::  ::    ::  ::  ::::::::
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  • category_flag=false
  • verbosity_flag=false
  • docking_scenario_name_flag=false
  • show_vs_statistics_flag=false
  • number_highest_scores_flag=false
  • getopts :hc:v:d:n:s: option
  • case “$option” in
  • category=workflow
  • [[ workflow == \w\o\r\k\f\l\o\w ]]
  • category_flag=true
  • getopts :hc:v:d:n:s: option
  • ‘[’ true == false ‘]’
  • ‘[’ true == true ‘]’
  • [[ workflow == \v\s ]]
  • ‘[’ false == false ‘]’
  • verbosity=1
  • ‘[’ ‘’ == false ‘]’
  • ‘[’ false == false ‘]’
  • show_vs_statistics=true
    ++ grep -m 1 ‘^docking_scenario_replicas=’ …/workflow/control/all.ctrl
    ++ tr -d ‘[[:space:]]’
    ++ awk -F ‘[=#]’ ‘{print $2}’
  • docking_scenario_replicas_total=1:1
  • IFS=:
  • read -a docking_scenario_replicas_total
  • docking_runs_perligand=0
  • for value in ‘${docking_scenario_replicas_total[@]}’
  • docking_runs_perligand=1
  • for value in ‘${docking_scenario_replicas_total[@]}’
  • docking_runs_perligand=2
  • echo

++ date

  • echo ’ Fri Apr 24 10:35:44 EDT 2020 ’
    Fri Apr 24 10:35:44 EDT 2020

  • [[ workflow = \w\o\r\k\f\l\o\w ]]

  • echo

  • echo

  • echo ’ Workflow Status ’
    Workflow Status

  • echo ::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
    ::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::

  • echo

  • echo

  • echo ’ Joblines ’
    Joblines

  • echo …
    …

  • echo

++ ls …/workflow/job-files/main
++ wc -l

  • echo ’ Number of jobfiles in the workflow/jobfiles/main folder: 2’
    Number of jobfiles in the workflow/jobfiles/main folder: 2

  • [[ SLURM == \S\L\U\R\M ]]
    ++ bin/sqs
    ++ grep ‘t-’
    ++ grep vogta
    ++ grep -c ‘’

  • echo ’ Number of joblines in the batch system: 1’
    Number of joblines in the batch system: 1

  • ‘[’ SLURM = SLURM ‘]’
    ++ squeue -l
    ++ grep ‘t-’
    ++ grep vogta
    ++ awk ‘{print $2}’
    ++ sort
    ++ uniq
    ++ tr ‘\n’ ’ ’

  • queues='namd ’
    ++ squeue -l
    ++ grep ‘t-’
    ++ grep vogta
    ++ grep -i RUNNING
    ++ grep -c ‘’

  • echo ’ Number of joblines in the batch system currently running: 1’
    Number of joblines in the batch system currently running: 1

  • for queue in ‘${queues}’
    ++ squeue -l
    ++ grep ‘namd.*RUN’
    ++ grep ‘t-’
    ++ grep vogta
    ++ wc -l

  • echo ’ * Number of joblines in queue “namd” currently running: 1’

    • Number of joblines in queue “namd” currently running: 1
      ++ squeue -l
      ++ grep ‘t-’
      ++ grep vogta
      ++ grep -i -v RUNNING
      ++ grep -c ‘’
      ++ true

  • echo ’ Number of joblines in the batch system currently not running: 0’
    Number of joblines in the batch system currently not running: 0

  • for queue in ‘${queues}’
    ++ squeue -l
    ++ grep vogta
    ++ grep ‘t-’
    ++ grep namd
    ++ grep -v RUN
    ++ grep -v COMPL
    ++ wc -l

  • echo ’ * Number of joblines in queue “namd” currently not running: 0’

    • Number of joblines in queue “namd” currently not running: 0

  • [[ 1 -gt 2 ]]

  • [[ SLURM == \L\S\F ]]

  • [[ SLURM == \S\L\U\R\M ]]

  • [[ SLURM == \S\L\U\R\M ]]

  • squeue -o ‘%.18i %.9P %.8j %.8u %.8T %.10M %.9l %.6D %R %C’

  • grep RUN

  • grep vogta

  • grep ‘t-’

  • awk ‘{print $10}’

  • sumCores=0

  • IFS=

  • read -r line

  • ‘[’ 9 -eq 9 ‘]’
    ++ echo 96
    ++ awk -F ‘*’ ‘{print $1}’

  • coreNumber=96

  • sumCores=96

  • IFS=

  • read -r line

  • [[ -n ‘’ ]]

  • echo ’ Number of cores/slots currently used by the workflow: 96’
    Number of cores/slots currently used by the workflow: 96

  • rm /tmp/vogta/VFVS//vf_report_Fri_Apr_24_10_35_44_EDT_2020/report.tmp

  • echo

  • echo

  • echo ’ Collections ’
    Collections

  • echo …
    …

  • echo

++ grep -c ‘’ …/workflow/ligand-collections/var/todo.original

  • echo ’ Total number of ligand collections: 163’
    Total number of ligand collections: 163

  • ligand_collections_completed=0
    ++ find …/workflow/ligand-collections/done/ -mindepth 1 -maxdepth 1 -type d -printf ‘%f\n’

  • for folder1 in ‘$(find …/workflow/ligand-collections/done/ -mindepth 1 -maxdepth 1 -type d -printf “%f\n”)’
    ++ find …/workflow/ligand-collections/done/1/ -mindepth 1 -maxdepth 1 -type d -printf ‘%f\n’

  • for folder2 in ‘$(find …/workflow/ligand-collections/done/$folder1/ -mindepth 1 -maxdepth 1 -type d -printf “%f\n”)’
    ++ paste -sd+
    ++ bc
    ++ grep -ch ‘’ ‘…/workflow/ligand-collections/done/1/2/*’

  • ligand_collections_completed_toadd=

  • [[ -z ‘’ ]]

  • ligand_collections_completed_toadd=0

  • ligand_collections_completed=0

  • for folder2 in ‘$(find …/workflow/ligand-collections/done/$folder1/ -mindepth 1 -maxdepth 1 -type d -printf “%f\n”)’
    ++ paste -sd+
    ++ bc
    ++ grep -ch ‘’ …/workflow/ligand-collections/done/1/1/1-1-1 …/workflow/ligand-collections/done/1/1/1-1-10 …/workflow/ligand-collections/done/1/1/1-1-11 …/workflow/ligand-collections/done/1/1/1-1-12 …/workflow/ligand-collections/done/1/1/1-1-13 …/workflow/ligand-collections/done/1/1/1-1-14 …/workflow/ligand-collections/done/1/1/1-1-15 …/workflow/ligand-collections/done/1/1/1-1-16 …/workflow/ligand-collections/done/1/1/1-1-17 …/workflow/ligand-collections/done/1/1/1-1-18 …/workflow/ligand-collections/done/1/1/1-1-19 …/workflow/ligand-collections/done/1/1/1-1-2 …/workflow/ligand-collections/done/1/1/1-1-20 …/workflow/ligand-collections/done/1/1/1-1-21 …/workflow/ligand-collections/done/1/1/1-1-22 …/workflow/ligand-collections/done/1/1/1-1-23 …/workflow/ligand-collections/done/1/1/1-1-25 …/workflow/ligand-collections/done/1/1/1-1-26 …/workflow/ligand-collections/done/1/1/1-1-27 …/workflow/ligand-collections/done/1/1/1-1-28 …/workflow/ligand-collections/done/1/1/1-1-29 …/workflow/ligand-collections/done/1/1/1-1-3 …/workflow/ligand-collections/done/1/1/1-1-30 …/workflow/ligand-collections/done/1/1/1-1-31 …/workflow/ligand-collections/done/1/1/1-1-32 …/workflow/ligand-collections/done/1/1/1-1-33 …/workflow/ligand-collections/done/1/1/1-1-34 …/workflow/ligand-collections/done/1/1/1-1-35 …/workflow/ligand-collections/done/1/1/1-1-36 …/workflow/ligand-collections/done/1/1/1-1-37 …/workflow/ligand-collections/done/1/1/1-1-4 …/workflow/ligand-collections/done/1/1/1-1-5 …/workflow/ligand-collections/done/1/1/1-1-7 …/workflow/ligand-collections/done/1/1/1-1-8 …/workflow/ligand-collections/done/1/1/1-1-9

  • ligand_collections_completed_toadd=309

  • [[ -z 309 ]]

  • ligand_collections_completed=309

  • echo ’ Number of ligand collections completed: 309’
    Number of ligand collections completed: 309

  • ligand_collections_processing=0
    ++ find …/workflow/ligand-collections/current/ -mindepth 1 -maxdepth 1 -type d -printf ‘%f\n’

  • for folder1 in ‘$(find …/workflow/ligand-collections/current/ -mindepth 1 -maxdepth 1 -type d -printf “%f\n”)’
    ++ find …/workflow/ligand-collections/current/1/ -mindepth 1 -maxdepth 1 -type d -printf ‘%f\n’

  • for folder2 in ‘$(find …/workflow/ligand-collections/current/$folder1/ -mindepth 1 -maxdepth 1 -type d -printf “%f\n”)’
    ++ paste -sd+
    ++ bc
    ++ grep -ch ‘’ ‘…/workflow/ligand-collections/current/1/2/*’

  • ligand_collections_processing_toadd=

  • [[ -z ‘’ ]]

  • ligand_collections_processing_toadd=0

  • ligand_collections_processing=0

  • for folder2 in ‘$(find …/workflow/ligand-collections/current/$folder1/ -mindepth 1 -maxdepth 1 -type d -printf “%f\n”)’
    ++ paste -sd+
    ++ bc
    ++ grep -ch ‘’ …/workflow/ligand-collections/current/1/1/1-1-1 …/workflow/ligand-collections/current/1/1/1-1-10 …/workflow/ligand-collections/current/1/1/1-1-11 …/workflow/ligand-collections/current/1/1/1-1-12 …/workflow/ligand-collections/current/1/1/1-1-13 …/workflow/ligand-collections/current/1/1/1-1-14 …/workflow/ligand-collections/current/1/1/1-1-15 …/workflow/ligand-collections/current/1/1/1-1-16 …/workflow/ligand-collections/current/1/1/1-1-17 …/workflow/ligand-collections/current/1/1/1-1-18 …/workflow/ligand-collections/current/1/1/1-1-19 …/workflow/ligand-collections/current/1/1/1-1-2 …/workflow/ligand-collections/current/1/1/1-1-20 …/workflow/ligand-collections/current/1/1/1-1-21 …/workflow/ligand-collections/current/1/1/1-1-22 …/workflow/ligand-collections/current/1/1/1-1-23 …/workflow/ligand-collections/current/1/1/1-1-24 …/workflow/ligand-collections/current/1/1/1-1-25 …/workflow/ligand-collections/current/1/1/1-1-26 …/workflow/ligand-collections/current/1/1/1-1-27 …/workflow/ligand-collections/current/1/1/1-1-28 …/workflow/ligand-collections/current/1/1/1-1-29 …/workflow/ligand-collections/current/1/1/1-1-3 …/workflow/ligand-collections/current/1/1/1-1-30 …/workflow/ligand-collections/current/1/1/1-1-31 …/workflow/ligand-collections/current/1/1/1-1-32 …/workflow/ligand-collections/current/1/1/1-1-33 …/workflow/ligand-collections/current/1/1/1-1-34 …/workflow/ligand-collections/current/1/1/1-1-35 …/workflow/ligand-collections/current/1/1/1-1-36 …/workflow/ligand-collections/current/1/1/1-1-37 …/workflow/ligand-collections/current/1/1/1-1-4 …/workflow/ligand-collections/current/1/1/1-1-5 …/workflow/ligand-collections/current/1/1/1-1-6 …/workflow/ligand-collections/current/1/1/1-1-7 …/workflow/ligand-collections/current/1/1/1-1-8 …/workflow/ligand-collections/current/1/1/1-1-9

  • ligand_collections_processing_toadd=17

  • [[ -z 17 ]]

  • ligand_collections_processing=17

  • echo ’ Number of ligand collections in state “processing”: 17’
    Number of ligand collections in state “processing”: 17

  • ligand_collections_todo=0
    ++ find …/workflow/ligand-collections/todo/ -mindepth 1 -maxdepth 1 -type d -printf ‘%f\n’

  • for folder1 in ‘$(find …/workflow/ligand-collections/todo/ -mindepth 1 -maxdepth 1 -type d -printf “%f\n”)’
    ++ find …/workflow/ligand-collections/todo/1/ -mindepth 1 -maxdepth 1 -type d -printf ‘%f\n’

  • for folder2 in ‘$(find …/workflow/ligand-collections/todo/$folder1/ -mindepth 1 -maxdepth 1 -type d -printf “%f\n”)’
    ++ paste -sd+
    ++ bc
    ++ grep -ch ‘’ ‘…/workflow/ligand-collections/todo/1/2/*’

  • ligand_collections_todo_toadd=

  • [[ -z ‘’ ]]

  • ligand_collections_todo_toadd=0

  • ligand_collections_todo=0

  • for folder2 in ‘$(find …/workflow/ligand-collections/todo/$folder1/ -mindepth 1 -maxdepth 1 -type d -printf “%f\n”)’
    ++ paste -sd+
    ++ bc
    ++ grep -ch ‘’ …/workflow/ligand-collections/todo/1/1/1-1-1 …/workflow/ligand-collections/todo/1/1/1-1-10 …/workflow/ligand-collections/todo/1/1/1-1-11 …/workflow/ligand-collections/todo/1/1/1-1-12 …/workflow/ligand-collections/todo/1/1/1-1-13 …/workflow/ligand-collections/todo/1/1/1-1-14 …/workflow/ligand-collections/todo/1/1/1-1-15 …/workflow/ligand-collections/todo/1/1/1-1-16 …/workflow/ligand-collections/todo/1/1/1-1-17 …/workflow/ligand-collections/todo/1/1/1-1-18 …/workflow/ligand-collections/todo/1/1/1-1-19 …/workflow/ligand-collections/todo/1/1/1-1-2 …/workflow/ligand-collections/todo/1/1/1-1-20 …/workflow/ligand-collections/todo/1/1/1-1-21 …/workflow/ligand-collections/todo/1/1/1-1-22 …/workflow/ligand-collections/todo/1/1/1-1-23 …/workflow/ligand-collections/todo/1/1/1-1-24 …/workflow/ligand-collections/todo/1/1/1-1-25 …/workflow/ligand-collections/todo/1/1/1-1-26 …/workflow/ligand-collections/todo/1/1/1-1-27 …/workflow/ligand-collections/todo/1/1/1-1-28 …/workflow/ligand-collections/todo/1/1/1-1-29 …/workflow/ligand-collections/todo/1/1/1-1-3 …/workflow/ligand-collections/todo/1/1/1-1-30 …/workflow/ligand-collections/todo/1/1/1-1-31 …/workflow/ligand-collections/todo/1/1/1-1-32 …/workflow/ligand-collections/todo/1/1/1-1-33 …/workflow/ligand-collections/todo/1/1/1-1-34 …/workflow/ligand-collections/todo/1/1/1-1-35 …/workflow/ligand-collections/todo/1/1/1-1-36 …/workflow/ligand-collections/todo/1/1/1-1-37 …/workflow/ligand-collections/todo/1/1/1-1-4 …/workflow/ligand-collections/todo/1/1/1-1-5 …/workflow/ligand-collections/todo/1/1/1-1-6 …/workflow/ligand-collections/todo/1/1/1-1-7 …/workflow/ligand-collections/todo/1/1/1-1-8 …/workflow/ligand-collections/todo/1/1/1-1-9

  • ligand_collections_todo_toadd=0

  • [[ -z 0 ]]

  • ligand_collections_todo=0
    ++ paste -sd+
    ++ bc
    ++ grep -ch ‘’ …/workflow/ligand-collections/todo/todo.all.0000

  • ligand_collections_todo_toadd=0

  • [[ -z 0 ]]

  • ligand_collections_todo=0

  • echo ’ Number of ligand collections not yet started: 0’
    Number of ligand collections not yet started: 0

  • echo

  • echo

  • echo ’ Ligands (in completed collections) ’
    Ligands (in completed collections)

  • echo …
    …

  • echo

  • ligands_total=0

  • ‘[’ -s …/workflow/ligand-collections/var/todo.original ‘]’
    ++ awk ‘{print $2}’ …/workflow/ligand-collections/var/todo.original
    ++ paste -sd+
    ++ bc -l

  • ligands_total=22834

  • [[ -z 22834 ]]

  • echo ’ Total number of ligands: 22834’
    Total number of ligands: 22834

  • ligands_started=0
    ++ find …/workflow/ligand-collections/done/ -mindepth 1 -maxdepth 1 -type d -printf ‘%f\n’

  • for folder1 in ‘$(find …/workflow/ligand-collections/done/ -mindepth 1 -maxdepth 1 -type d -printf “%f\n”)’
    ++ find …/workflow/ligand-collections/done/1/ -mindepth 1 -maxdepth 1 -type d -printf ‘%f\n’

  • for folder2 in ‘$(find …/workflow/ligand-collections/done/$folder1/ -mindepth 1 -maxdepth 1 -type d -printf “%f\n”)’
    ++ awk -F : ‘{print $2}’
    ++ sed ‘/^$/d’
    ++ grep -ho ‘Ligands-started:[0-9]+’ ‘…/workflow/ligand-collections/done/1/2/*’
    ++ paste -sd+
    ++ bc -l

  • ligands_started_to_add=

  • [[ -z ‘’ ]]

  • ligands_started_to_add=0

  • ligands_started=0

  • for folder2 in ‘$(find …/workflow/ligand-collections/done/$folder1/ -mindepth 1 -maxdepth 1 -type d -printf “%f\n”)’
    ++ awk -F : ‘{print $2}’
    ++ sed ‘/^$/d’
    ++ paste -sd+
    ++ grep -ho ‘Ligands-started:[0-9]+’ …/workflow/ligand-collections/done/1/1/1-1-1 …/workflow/ligand-collections/done/1/1/1-1-10 …/workflow/ligand-collections/done/1/1/1-1-11 …/workflow/ligand-collections/done/1/1/1-1-12 …/workflow/ligand-collections/done/1/1/1-1-13 …/workflow/ligand-collections/done/1/1/1-1-14 …/workflow/ligand-collections/done/1/1/1-1-15 …/workflow/ligand-collections/done/1/1/1-1-16 …/workflow/ligand-collections/done/1/1/1-1-17 …/workflow/ligand-collections/done/1/1/1-1-18 …/workflow/ligand-collections/done/1/1/1-1-19 …/workflow/ligand-collections/done/1/1/1-1-2 …/workflow/ligand-collections/done/1/1/1-1-20 …/workflow/ligand-collections/done/1/1/1-1-21 …/workflow/ligand-collections/done/1/1/1-1-22 …/workflow/ligand-collections/done/1/1/1-1-23 …/workflow/ligand-collections/done/1/1/1-1-25 …/workflow/ligand-collections/done/1/1/1-1-26 …/workflow/ligand-collections/done/1/1/1-1-27 …/workflow/ligand-collections/done/1/1/1-1-28 …/workflow/ligand-collections/done/1/1/1-1-29 …/workflow/ligand-collections/done/1/1/1-1-3 …/workflow/ligand-collections/done/1/1/1-1-30 …/workflow/ligand-collections/done/1/1/1-1-31 …/workflow/ligand-collections/done/1/1/1-1-32 …/workflow/ligand-collections/done/1/1/1-1-33 …/workflow/ligand-collections/done/1/1/1-1-34 …/workflow/ligand-collections/done/1/1/1-1-35 …/workflow/ligand-collections/done/1/1/1-1-36 …/workflow/ligand-collections/done/1/1/1-1-37 …/workflow/ligand-collections/done/1/1/1-1-4 …/workflow/ligand-collections/done/1/1/1-1-5 …/workflow/ligand-collections/done/1/1/1-1-7 …/workflow/ligand-collections/done/1/1/1-1-8 …/workflow/ligand-collections/done/1/1/1-1-9
    ++ bc -l

  • ligands_started_to_add=29356

  • [[ -z 29356 ]]

  • ligands_started=29356

  • echo ’ Number of ligands started: 29356’
    Number of ligands started: 29356

  • ligands_success=0
    ++ find …/workflow/ligand-collections/done/ -mindepth 1 -maxdepth 1 -type d -printf ‘%f\n’

  • for folder1 in ‘$(find …/workflow/ligand-collections/done/ -mindepth 1 -maxdepth 1 -type d -printf “%f\n”)’
    ++ find …/workflow/ligand-collections/done/1/ -mindepth 1 -maxdepth 1 -type d -printf ‘%f\n’

  • for folder2 in ‘$(find …/workflow/ligand-collections/done/$folder1/ -mindepth 1 -maxdepth 1 -type d -printf “%f\n”)’
    ++ awk -F : ‘{print $2}’
    ++ sed ‘/^$/d’
    ++ paste -sd+
    ++ grep -ho ‘Ligands-succeeded:[0-9]+’ ‘…/workflow/ligand-collections/done/1/2/*’
    ++ bc -l

  • ligands_success_to_add=

  • [[ -z ‘’ ]]

  • ligands_success_to_add=0

  • ligands_success=0

  • for folder2 in ‘$(find …/workflow/ligand-collections/done/$folder1/ -mindepth 1 -maxdepth 1 -type d -printf “%f\n”)’
    ++ awk -F : ‘{print $2}’
    ++ sed ‘/^$/d’
    ++ paste -sd+
    ++ grep -ho ‘Ligands-succeeded:[0-9]+’ …/workflow/ligand-collections/done/1/1/1-1-1 …/workflow/ligand-collections/done/1/1/1-1-10 …/workflow/ligand-collections/done/1/1/1-1-11 …/workflow/ligand-collections/done/1/1/1-1-12 …/workflow/ligand-collections/done/1/1/1-1-13 …/workflow/ligand-collections/done/1/1/1-1-14 …/workflow/ligand-collections/done/1/1/1-1-15 …/workflow/ligand-collections/done/1/1/1-1-16 …/workflow/ligand-collections/done/1/1/1-1-17 …/workflow/ligand-collections/done/1/1/1-1-18 …/workflow/ligand-collections/done/1/1/1-1-19 …/workflow/ligand-collections/done/1/1/1-1-2 …/workflow/ligand-collections/done/1/1/1-1-20 …/workflow/ligand-collections/done/1/1/1-1-21 …/workflow/ligand-collections/done/1/1/1-1-22 …/workflow/ligand-collections/done/1/1/1-1-23 …/workflow/ligand-collections/done/1/1/1-1-25 …/workflow/ligand-collections/done/1/1/1-1-26 …/workflow/ligand-collections/done/1/1/1-1-27 …/workflow/ligand-collections/done/1/1/1-1-28 …/workflow/ligand-collections/done/1/1/1-1-29 …/workflow/ligand-collections/done/1/1/1-1-3 …/workflow/ligand-collections/done/1/1/1-1-30 …/workflow/ligand-collections/done/1/1/1-1-31 …/workflow/ligand-collections/done/1/1/1-1-32 …/workflow/ligand-collections/done/1/1/1-1-33 …/workflow/ligand-collections/done/1/1/1-1-34 …/workflow/ligand-collections/done/1/1/1-1-35 …/workflow/ligand-collections/done/1/1/1-1-36 …/workflow/ligand-collections/done/1/1/1-1-37 …/workflow/ligand-collections/done/1/1/1-1-4 …/workflow/ligand-collections/done/1/1/1-1-5 …/workflow/ligand-collections/done/1/1/1-1-7 …/workflow/ligand-collections/done/1/1/1-1-8 …/workflow/ligand-collections/done/1/1/1-1-9
    ++ bc -l

  • ligands_success_to_add=29318

  • [[ -z 29318 ]]

  • ligands_success=29318

  • echo ’ Number of ligands successfully completed: 29318’
    Number of ligands successfully completed: 29318

  • ligands_failed=0
    ++ find …/workflow/ligand-collections/done/ -mindepth 1 -maxdepth 1 -type d -printf ‘%f\n’

  • for folder1 in ‘$(find …/workflow/ligand-collections/done/ -mindepth 1 -maxdepth 1 -type d -printf “%f\n”)’
    ++ find …/workflow/ligand-collections/done/1/ -mindepth 1 -maxdepth 1 -type d -printf ‘%f\n’

  • for folder2 in ‘$(find …/workflow/ligand-collections/done/$folder1/ -mindepth 1 -maxdepth 1 -type d -printf “%f\n”)’
    ++ awk -F : ‘{print $2}’
    ++ sed ‘/^$/d’
    ++ paste -sd+
    ++ grep -ho ‘Ligands-failed:[0-9]+’ ‘…/workflow/ligand-collections/done/1/2/*’
    ++ bc -l

  • ligands_failed_to_add=

  • [[ -z ‘’ ]]

  • ligands_failed_to_add=0

  • ligands_failed=0

  • for folder2 in ‘$(find …/workflow/ligand-collections/done/$folder1/ -mindepth 1 -maxdepth 1 -type d -printf “%f\n”)’
    ++ awk -F : ‘{print $2}’
    ++ sed ‘/^$/d’
    ++ paste -sd+
    ++ bc -l
    ++ grep -ho ‘Ligands-failed:[0-9]+’ …/workflow/ligand-collections/done/1/1/1-1-1 …/workflow/ligand-collections/done/1/1/1-1-10 …/workflow/ligand-collections/done/1/1/1-1-11 …/workflow/ligand-collections/done/1/1/1-1-12 …/workflow/ligand-collections/done/1/1/1-1-13 …/workflow/ligand-collections/done/1/1/1-1-14 …/workflow/ligand-collections/done/1/1/1-1-15 …/workflow/ligand-collections/done/1/1/1-1-16 …/workflow/ligand-collections/done/1/1/1-1-17 …/workflow/ligand-collections/done/1/1/1-1-18 …/workflow/ligand-collections/done/1/1/1-1-19 …/workflow/ligand-collections/done/1/1/1-1-2 …/workflow/ligand-collections/done/1/1/1-1-20 …/workflow/ligand-collections/done/1/1/1-1-21 …/workflow/ligand-collections/done/1/1/1-1-22 …/workflow/ligand-collections/done/1/1/1-1-23 …/workflow/ligand-collections/done/1/1/1-1-25 …/workflow/ligand-collections/done/1/1/1-1-26 …/workflow/ligand-collections/done/1/1/1-1-27 …/workflow/ligand-collections/done/1/1/1-1-28 …/workflow/ligand-collections/done/1/1/1-1-29 …/workflow/ligand-collections/done/1/1/1-1-3 …/workflow/ligand-collections/done/1/1/1-1-30 …/workflow/ligand-collections/done/1/1/1-1-31 …/workflow/ligand-collections/done/1/1/1-1-32 …/workflow/ligand-collections/done/1/1/1-1-33 …/workflow/ligand-collections/done/1/1/1-1-34 …/workflow/ligand-collections/done/1/1/1-1-35 …/workflow/ligand-collections/done/1/1/1-1-36 …/workflow/ligand-collections/done/1/1/1-1-37 …/workflow/ligand-collections/done/1/1/1-1-4 …/workflow/ligand-collections/done/1/1/1-1-5 …/workflow/ligand-collections/done/1/1/1-1-7 …/workflow/ligand-collections/done/1/1/1-1-8 …/workflow/ligand-collections/done/1/1/1-1-9

  • ligands_failed_to_add=38

  • [[ -z 38 ]]

  • ligands_failed=38

  • echo ’ Number of ligands failed: 38’
    Number of ligands failed: 38

  • echo

  • echo

  • echo ’ Dockings (in completed collections) ’
    Dockings (in completed collections)

  • echo …
    …

  • echo

  • echo ’ Docking runs per ligand: 2’
    Docking runs per ligand: 2

  • dockings_started=0
    ++ find …/workflow/ligand-collections/done/ -mindepth 1 -maxdepth 1 -type d -printf ‘%f\n’

  • for folder1 in ‘$(find …/workflow/ligand-collections/done/ -mindepth 1 -maxdepth 1 -type d -printf “%f\n”)’
    ++ find …/workflow/ligand-collections/done/1/ -mindepth 1 -maxdepth 1 -type d -printf ‘%f\n’

  • for folder2 in ‘$(find …/workflow/ligand-collections/done/$folder1/ -mindepth 1 -maxdepth 1 -type d -printf “%f\n”)’
    ++ awk -F : ‘{print $2}’
    ++ sed ‘/^$/d’
    ++ paste -sd+
    ++ grep -ho ‘Dockings-started:[0-9]+’ ‘…/workflow/ligand-collections/done/1/2/*’
    ++ bc -l

  • dockings_started_to_add=

  • [[ -z ‘’ ]]

  • dockings_started_to_add=0

  • dockings_started=0

  • for folder2 in ‘$(find …/workflow/ligand-collections/done/$folder1/ -mindepth 1 -maxdepth 1 -type d -printf “%f\n”)’
    ++ awk -F : ‘{print $2}’
    ++ sed ‘/^$/d’
    ++ paste -sd+
    ++ grep -ho ‘Dockings-started:[0-9]+’ …/workflow/ligand-collections/done/1/1/1-1-1 …/workflow/ligand-collections/done/1/1/1-1-10 …/workflow/ligand-collections/done/1/1/1-1-11 …/workflow/ligand-collections/done/1/1/1-1-12 …/workflow/ligand-collections/done/1/1/1-1-13 …/workflow/ligand-collections/done/1/1/1-1-14 …/workflow/ligand-collections/done/1/1/1-1-15 …/workflow/ligand-collections/done/1/1/1-1-16 …/workflow/ligand-collections/done/1/1/1-1-17 …/workflow/ligand-collections/done/1/1/1-1-18 …/workflow/ligand-collections/done/1/1/1-1-19 …/workflow/ligand-collections/done/1/1/1-1-2 …/workflow/ligand-collections/done/1/1/1-1-20 …/workflow/ligand-collections/done/1/1/1-1-21 …/workflow/ligand-collections/done/1/1/1-1-22 …/workflow/ligand-collections/done/1/1/1-1-23 …/workflow/ligand-collections/done/1/1/1-1-25 …/workflow/ligand-collections/done/1/1/1-1-26 …/workflow/ligand-collections/done/1/1/1-1-27 …/workflow/ligand-collections/done/1/1/1-1-28 …/workflow/ligand-collections/done/1/1/1-1-29 …/workflow/ligand-collections/done/1/1/1-1-3 …/workflow/ligand-collections/done/1/1/1-1-30 …/workflow/ligand-collections/done/1/1/1-1-31 …/workflow/ligand-collections/done/1/1/1-1-32 …/workflow/ligand-collections/done/1/1/1-1-33 …/workflow/ligand-collections/done/1/1/1-1-34 …/workflow/ligand-collections/done/1/1/1-1-35 …/workflow/ligand-collections/done/1/1/1-1-36 …/workflow/ligand-collections/done/1/1/1-1-37 …/workflow/ligand-collections/done/1/1/1-1-4 …/workflow/ligand-collections/done/1/1/1-1-5 …/workflow/ligand-collections/done/1/1/1-1-7 …/workflow/ligand-collections/done/1/1/1-1-8 …/workflow/ligand-collections/done/1/1/1-1-9
    ++ bc -l

  • dockings_started_to_add=58674

  • [[ -z 58674 ]]

  • dockings_started=58674

  • echo ’ Number of dockings started: 58674’
    Number of dockings started: 58674

  • dockings_success=0
    ++ find …/workflow/ligand-collections/done/ -mindepth 1 -maxdepth 1 -type d -printf ‘%f\n’

  • for folder1 in ‘$(find …/workflow/ligand-collections/done/ -mindepth 1 -maxdepth 1 -type d -printf “%f\n”)’
    ++ find …/workflow/ligand-collections/done/1/ -mindepth 1 -maxdepth 1 -type d -printf ‘%f\n’

  • for folder2 in ‘$(find …/workflow/ligand-collections/done/$folder1/ -mindepth 1 -maxdepth 1 -type d -printf “%f\n”)’
    ++ awk -F : ‘{print $2}’
    ++ sed ‘/^$/d’
    ++ grep -ho ‘Dockings-succeeded:[0-9]+’ ‘…/workflow/ligand-collections/done/1/2/*’
    ++ paste -sd+
    ++ bc -l

  • dockings_success_to_add=

  • [[ -z ‘’ ]]

  • dockings_success_to_add=0

  • dockings_success=0

  • for folder2 in ‘$(find …/workflow/ligand-collections/done/$folder1/ -mindepth 1 -maxdepth 1 -type d -printf “%f\n”)’
    ++ awk -F : ‘{print $2}’
    ++ sed ‘/^$/d’
    ++ grep -ho ‘Dockings-succeeded:[0-9]+’ …/workflow/ligand-collections/done/1/1/1-1-1 …/workflow/ligand-collections/done/1/1/1-1-10 …/workflow/ligand-collections/done/1/1/1-1-11 …/workflow/ligand-collections/done/1/1/1-1-12 …/workflow/ligand-collections/done/1/1/1-1-13 …/workflow/ligand-collections/done/1/1/1-1-14 …/workflow/ligand-collections/done/1/1/1-1-15 …/workflow/ligand-collections/done/1/1/1-1-16 …/workflow/ligand-collections/done/1/1/1-1-17 …/workflow/ligand-collections/done/1/1/1-1-18 …/workflow/ligand-collections/done/1/1/1-1-19 …/workflow/ligand-collections/done/1/1/1-1-2 …/workflow/ligand-collections/done/1/1/1-1-20 …/workflow/ligand-collections/done/1/1/1-1-21 …/workflow/ligand-collections/done/1/1/1-1-22 …/workflow/ligand-collections/done/1/1/1-1-23 …/workflow/ligand-collections/done/1/1/1-1-25 …/workflow/ligand-collections/done/1/1/1-1-26 …/workflow/ligand-collections/done/1/1/1-1-27 …/workflow/ligand-collections/done/1/1/1-1-28 …/workflow/ligand-collections/done/1/1/1-1-29 …/workflow/ligand-collections/done/1/1/1-1-3 …/workflow/ligand-collections/done/1/1/1-1-30 …/workflow/ligand-collections/done/1/1/1-1-31 …/workflow/ligand-collections/done/1/1/1-1-32 …/workflow/ligand-collections/done/1/1/1-1-33 …/workflow/ligand-collections/done/1/1/1-1-34 …/workflow/ligand-collections/done/1/1/1-1-35 …/workflow/ligand-collections/done/1/1/1-1-36 …/workflow/ligand-collections/done/1/1/1-1-37 …/workflow/ligand-collections/done/1/1/1-1-4 …/workflow/ligand-collections/done/1/1/1-1-5 …/workflow/ligand-collections/done/1/1/1-1-7 …/workflow/ligand-collections/done/1/1/1-1-8 …/workflow/ligand-collections/done/1/1/1-1-9
    ++ paste -sd+
    ++ bc -l

  • dockings_success_to_add=58636

  • [[ -z 58636 ]]

  • dockings_success=58636

  • echo ’ Number of dockings successfully completed: 58636’
    Number of dockings successfully completed: 58636

  • dockings_failed=0
    ++ find …/workflow/ligand-collections/done/ -mindepth 1 -maxdepth 1 -type d -printf ‘%f\n’

  • for folder1 in ‘$(find …/workflow/ligand-collections/done/ -mindepth 1 -maxdepth 1 -type d -printf “%f\n”)’
    ++ find …/workflow/ligand-collections/done/1/ -mindepth 1 -maxdepth 1 -type d -printf ‘%f\n’

  • for folder2 in ‘$(find …/workflow/ligand-collections/done/$folder1/ -mindepth 1 -maxdepth 1 -type d -printf “%f\n”)’
    ++ awk -F : ‘{print $2}’
    ++ grep -ho ‘Dockings-failed:[0-9]+’ ‘…/workflow/ligand-collections/done/1/2/*’
    ++ sed ‘/^$/d’
    ++ paste -sd+
    ++ bc -l

  • dockings_failed_to_add=

  • [[ -z ‘’ ]]

  • dockings_failed_to_add=0

  • dockings_failed=0

  • for folder2 in ‘$(find …/workflow/ligand-collections/done/$folder1/ -mindepth 1 -maxdepth 1 -type d -printf “%f\n”)’
    ++ awk -F : ‘{print $2}’
    ++ sed ‘/^$/d’
    ++ paste -sd+
    ++ bc -l
    ++ grep -ho ‘Dockings-failed:[0-9]+’ …/workflow/ligand-collections/done/1/1/1-1-1 …/workflow/ligand-collections/done/1/1/1-1-10 …/workflow/ligand-collections/done/1/1/1-1-11 …/workflow/ligand-collections/done/1/1/1-1-12 …/workflow/ligand-collections/done/1/1/1-1-13 …/workflow/ligand-collections/done/1/1/1-1-14 …/workflow/ligand-collections/done/1/1/1-1-15 …/workflow/ligand-collections/done/1/1/1-1-16 …/workflow/ligand-collections/done/1/1/1-1-17 …/workflow/ligand-collections/done/1/1/1-1-18 …/workflow/ligand-collections/done/1/1/1-1-19 …/workflow/ligand-collections/done/1/1/1-1-2 …/workflow/ligand-collections/done/1/1/1-1-20 …/workflow/ligand-collections/done/1/1/1-1-21 …/workflow/ligand-collections/done/1/1/1-1-22 …/workflow/ligand-collections/done/1/1/1-1-23 …/workflow/ligand-collections/done/1/1/1-1-25 …/workflow/ligand-collections/done/1/1/1-1-26 …/workflow/ligand-collections/done/1/1/1-1-27 …/workflow/ligand-collections/done/1/1/1-1-28 …/workflow/ligand-collections/done/1/1/1-1-29 …/workflow/ligand-collections/done/1/1/1-1-3 …/workflow/ligand-collections/done/1/1/1-1-30 …/workflow/ligand-collections/done/1/1/1-1-31 …/workflow/ligand-collections/done/1/1/1-1-32 …/workflow/ligand-collections/done/1/1/1-1-33 …/workflow/ligand-collections/done/1/1/1-1-34 …/workflow/ligand-collections/done/1/1/1-1-35 …/workflow/ligand-collections/done/1/1/1-1-36 …/workflow/ligand-collections/done/1/1/1-1-37 …/workflow/ligand-collections/done/1/1/1-1-4 …/workflow/ligand-collections/done/1/1/1-1-5 …/workflow/ligand-collections/done/1/1/1-1-7 …/workflow/ligand-collections/done/1/1/1-1-8 …/workflow/ligand-collections/done/1/1/1-1-9

  • dockings_failed_to_add=38

  • [[ -z 38 ]]

  • dockings_failed=38

  • echo ’ Number of dockings failed: 38’
    Number of dockings failed: 38

  • echo

  • echo

  • [[ workflow = \v\s ]]

  • echo -e ‘\n\n’

  • clean_up

  • rm -r /tmp/vogta/VFVS//vf_report_Fri_Apr_24_10_35_44_EDT_2020/

#2

I ran another run using the same ligand library (22834 ligands) against a new receptor using the version of VFVS that you get by the “wget -O VFVS.tar.gz https://github.com/VirtualFlow/VFVS/archive/develop.tar.gz” command. I set up five identical screens (same receptor, same ligand library, different workflow names). I’m having a really hard time understanding the numbers that are coming out of the reports. When I enter ./vf_reports -c workflow I get the following:

                                        Joblines

…

Number of jobfiles in the workflow/jobfiles/main folder: 1
Number of joblines in the batch system: 0
Number of joblines in the batch system currently running: 0
Number of joblines in the batch system currently not running: 0
Number of cores/slots currently used by the workflow: 0

                                        Collections

…

Total number of ligand collections: 163
Number of ligand collections completed: 263
Number of ligand collections in state “processing”: 17
Number of ligand collections not yet started: 46

                             Ligands (in completed collections)

…

Total number of ligands: 22834
Number of ligands started: 26939
Number of ligands successfully completed: 26902
Number of ligands failed: 40

                            Dockings (in completed collections)

…

Docking runs per ligand: 5
Number of dockings started: 134525
Number of dockings successfully completed: 134485
Number of dockings failed: 40

Which seems to be telling me that there were 22834 total ligands in the library, but 26939 ligands were started. This means that more ligands were docked than were actually present in the library. It also says 134525 dockings were started and 134485 dockings were successfully completed. This number roughly corresponds to 5 times the 26939 ligands (although I still have no idea where the extra ligands came from).

When I use the ./vf_report.sh -c vs -d workflow_name command and sum up the ligands in each bin, each workflow has either 19475 or 19474 ligands in it. This comes out to a total of 97373 dockings, which doesn’t match the number of successful docking reported or the number of ligands that should have been docked if my original library of 22834 ligands had been docked 5 times. Am I misunderstanding what these numbers are supposed to be reporting?

#3

Hello Austin (@advogt),

When I run ./vf_report.sh for Tutorial: 2, I don’t get this verbose output. What you’ve pasted appears to also include parts of the code. I’ve pasted below my exact output from running ./vf_report.sh -c workflow post-docking a custom set of ~29k ligands:

                                 Joblines

…

Number of jobfiles in the workflow/jobfiles/main folder: 10
Number of joblines in the batch system: 0
Number of joblines in the batch system currently running: 0
Number of joblines in the batch system currently not running: 0
Number of cores/slots currently used by the workflow: 0

                                Collections

…

Total number of ligand collections: 30
Number of ligand collections completed: 24
Number of ligand collections in state “processing”: 4
Number of ligand collections not yet started: 2

                     Ligands (in completed collections)

…

Total number of ligands: 28983
Number of ligands started: 27315
Number of ligands successfully completed: 27304
Number of ligands failed: 11

                    Dockings (in completed collections)

…

Docking runs per ligand: 2
Number of dockings started: 54619
Number of dockings successfully completed: 54608
Number of dockings failed: 11

Looking at the numbers in the bottom two “completed” sections, the numbers add up in my case.
27315 ligands started out of 28983. 27315 x 2 runs each = 54630 - 11 failed dockings = 54619. And 27304 ligands successfully completed x 2 = 54608.

Perhaps in your case there are additional ligand files that the program is reading from previous runs? Running ./vf_prepare_folders.sh (present in tools dir) will delete old files from previous runs if present, and prepare the workflow folder, which is used by VirtualFlow during runtime to organize and log the workflow.

Anita

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