Jobs failing - problem with ligand library?

VFVS VFVS 1
#1

I have been playing with Virtual Flow on the supercomputer system at Indiana University (where I have access). I am going through the example you have on the website (tutorial 2). When I try to submit jobs (IU use a slurm system) it failed to launch any runs. I went through a log file and found, what I think is relevant, but I am hoping you might be able to explain what this error is and why its happening. I’ll paste it below

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++ head -n 1 /dev/shm/scrobson/VFVS/t/10/prepare-todolists/todo.all

  • next_ligand_collection_and_length=BDAA_00004-001.pdbqt.gz.tar

  • next_ligand_collection=BDAA_00004-001.pdbqt.gz.tar

  • ‘[’ BDAA_00004-001.pdbqt.gz.tar = Binary ‘]’

  • echo BDAA_00004-001.pdbqt.gz.tar

  • no_to_add=BDAA_00004-001.pdbqt.gz.tar

  • ‘[’ BDAA_00004-001.pdbqt.gz.tar -eq BDAA_00004-001.pdbqt.gz.tar ‘]’

prepare-todolists.sh: line 481: [: BDAA_00004-001.pdbqt.gz.tar: integer expression expected

  • echo ’ * Warning: Could not get the length of collection BDAA_00004-001.pdbqt.gz.tar. Found value is: BDAA_00004-001.pdbqt.gz.tar. Exiting.’
  • Warning: Could not get the length of collection BDAA_00004-001.pdbqt.gz.tar. Found value is: BDAA_00004-001.pdbqt.gz.tar. Exiting.

  • exit 1

  • clean_up

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This is from a job output file: specifically: job-10.1_324215.out in my case in directory ~/virtual-flow/VFVS_GK/workflow/output-files/jobs

It seems to be failing to get one of the ligand libraries - or something - what might be going on?

Any advice would be great.

#2

Did you upload the collection lenght file to your system? It could also be that you forgot to use the prepare command

#3

Hi Scott,

Welcome to the forum, nice to see you around :slight_smile:

As @kaneki rightly indicated, it seems you did not prepare the todo.all file in the tools/templates folder before you prepared the workflow folders with the vf_prepare_folders.sh command. This file specifies which ligand collections you want to screen, and is one of the required preparation steps before you can run a virtual screen. The value “BDAA_00004-001.pdbqt.gz.tar” which see in your logs is part of the default content of this file (but does not work, it needs to be replaced by the user with the collections which should be screened).

I suggested doing the two tutorials first which you can find here:

https://docs.

Let me know if that helps, or if there are other problems.

Stay safe,
Christoph