I tried to run the latest VFVS-2 branch with slurm. After submitting jobs, I get a FileNotFoundError when using an older VF1 ligand library (from Enamine-REAL-2018q12_isomers.pdbqt).
Has anyone successfully run the VFVS-2 code with slurm and the REAL-2018q12 tranches? I don’t have access to the real-space-2022q12 libraries yet, that is why I am trying with slurm and the older libraries.
Any help is much appreciated. Thanks!
Oliv
Error in /VirtualFlow/VFVS-vfvs-2/workflow/workunits/1/803_0.err:
File “/VirtualFlow/VFVS-vfvs-2/tools/./templates/vfvs_run.py”, line 157, in downloader
shutil.copyfile(Path(item[‘collection’][‘sharedfs_path’]), item[‘local_path’])
File “/miniconda3/lib/python3.10/shutil.py”, line 254, in copyfile
with open(src, ‘rb’) as fsrc:
FileNotFoundError: [Errno 2] No such file or directory: ‘/VirtualFlow/VFVS-vfvs-2/input-files/ligand-library/GACAAF/00000.tar.gz’
Hi Haroon,
No, I was not able to resolve it. I spent about one day debugging and rewriting code, then I gave up.
I decided to wait until VFVS-2 is fully baked and released which will hopefully happen soon.
Best, Oliv
Hello @oeidam ,
I was having similar issues, VFVS2 is finicky with relative file paths, I was able to get it to work by pointing it to a specific meta-tranche in collection_folder parameter of the all.ctrl file. My setting was to …/input-files/ligand-library/AB. I used it with a different dataset but it ran at least. I ran into many isses with setting file paths, and was only able to figure it out by going through the code and printing certain paths created by vfvs_run.py along the way to figure out what it wanted.
Also be aware that tar files (the format in which the ligands are contained) have a relative file path within them that is retained from the working directory of whatever script packaged them. So if they were processed with a path VFVS/input-library/A/… they would be extraced in the shared memory file sysstem with that same path which is not necessarily what Virtualflow expects. It was one issue I had.