Can someone please provide some more details on how to prepare the input data for VFLP? Below are the steps I followed to run the pipeline.
- I’ve got a bunch of smile files that I curated by hand. I kept them in the following structure:
input-files |___ ligand1.smi |___ ligand2.smi . . .
- After running
./vf_prepare_folders.sh, I start the jobs with the following command
./vf_start_jobline.sh 1 2 templates/template1.slurm.sh submit 1
- The job does start with the following output
Syncing the jobfile of jobline 1 with the controlfile file ../../workflow/control/all.ctrl. Syncing the jobfile of jobline 2 with the controlfile file ../../workflow/control/all.ctrl. Submitted batch job 2 The job for jobline 1 has been submitted at Mon Sep 7 09:57:12 UTC 2020. Submitted batch job 3 The job for jobline 2 has been submitted at Mon Sep 7 09:57:13 UTC 2020.
- But once the jobs are finished, I don’t see any output in the
output-filesfolder. Is it because of the wrong input file structure?
- Can I just add smiles files as
input-files/*.smior do I need
- Or do I need a deeper level hierarchy like tranche names? If yes, then how do I decide, which letters to use for defining the meta-tranche?
- Do I also need to make any changes in
todo.allor anywhere else? If yes, what changes?