VFLP not opening collections

VFLP VFLP 1
#1

Hello Everyone,
I’ve been trying to get VFLP to run using lsf for some time now. I changed the template1.lsh.sh resource requirements section to match the VFVS one since I was getting a resource requirement syntax error. Now the jobs get submitted and appear to be running, but on closer inspection, they are failing to open any of the ligand collections.
Here are the warnings I’m getting:
Warning: There exists an old (locked) todo file. Trying to take care of it…
Warning: The old todo file is a symlink or an empty file. Removing it…

By using the debug option for log files I can also find the last line the job attempts to run before moving on to the creation of a new job:
bash …/workflow/job-files/sub/one-step.sh
cp: cannot stat `/dev/shm/so787/VFLP/t//-1/workflow/output-files/queues/1//queue–1.*’: No such file or directory

I don’t get a line number from the cp error, but when looking through the one-step.sh script I suspect that the problem is that the variable: VF_queue_NO_12 is not being assigned a value. That and VF_queue_NO is being assigned a value including “-” which appears to also be wrong.
I’ve checked my All.ctrl multiple times just to make sure it’s not a typo on my end and I haven’t been able to find anything there can fix the problem
Does anyone have any suggestions?

Also, I see there a lot of people here who have had trouble with the VFLP package, has anyone gotten it working yet?

#2

Hey Sam,

I’m having the same trouble - jobs aren’t opening or beginning to process collections.

One question is what the format of ligand collections should look like? It seems to get a little farther into processing when I input as ligand-library/0000/[individual SMILES files] as opposed to the AA/AAxxxx.tar containing gzipped 00000/__.smi . Is this the correct way to input smi-formatted files?

That being said, I’m getting an error that I can’t trace using either input method:
after running for a couple min, the error is within …/workflow/output-files/jobs/job-1.1___.out and looks like:

  • echo ‘The todo lists for the queues were (re)filled in 0 second(s) (waiting time not included).’
    The todo lists for the queues were (re)filled in 0 second(s) (waiting time not included).

  • echo ‘The waiting time was 0 second(s).’
    The waiting time was 0 second(s).

  • echo

  • clean_up

  • cp /dev/shm/thomc/VFLP/l/1/prepare-todolists/todo.all …/…/workflow/ligand-collections/todo/todo.all.locked

  • mv …/…/workflow/ligand-collections/todo/todo.all.locked …/…/workflow/ligand-collections/todo/todo.all

  • rm -r /dev/shm/thomc/VFLP/l/1/prepare-todolists/

  • kill ‘#!’

  • true

  • cd …
    ++ seq 1 1

  • for VF_STEP_NO in ‘$(seq 1 ${VF_NODES_PER_JOB} )’

  • export VF_STEP_NO
    ++ hostname

  • echo ‘Starting job step VF_STEP_NO on host vengeance.’
    Starting job step VF_STEP_NO on host vengeance.

  • sleep 1

  • bash …/workflow/job-files/sub/one-step.sh
    Error was trapped
    Error in bash script one-step.sh
    Error on line 214

But this doesn’t seem to have to do with one-step.sh
Might someone have a suggestion on how to fix this?

Thanks,
Chris