Running vfvs_postprocess_atg-prescreen.sh on Slurm #59
Description
Hi,
Thanks a lot for putting together this repository, it's been incredibly useful!
Following the documentation here, I tried to run vfvs_postprocess_atg-prescreen.sh.
The documentation says that I should include the screening size for the primary screen as an argument to this script, but when I do, the script complains:
Wrong number of arguments.
Usage: vfvs_postprocess_atg-prescreen.sh
Description: Postprocessing the ATG Prescreen, and preparing the todo files for the ATG Primary Screens. The script can handle multiple docking scenarios in the ATG Prescreen.
Exiting...
Looking inside the script, it's true that it doesn't actually seem to require any arguments at all, so next I ran it without any arguments, and I ran into the following error:
Creating output-files folder (if it does not yet exist) ...
Generating the ranking of docking scenario qvina02_rigid_receptor1 and downloading it to ../output-files/qvina02_rigid_receptor1.ranking.complete.csv ...
In order to use this query script, AWS must be configured
Creating a subset of the ranking file with fewer columns and storing it in ../output-files/qvina02_rigid_receptor1.subset-1.csv.gz ...
awk: cmd. line:1: fatal: cannot open file `qvina02_rigid_receptor1.ranking.complete.csv' for reading (No such file or directory)
Compressing the file ../output-files/qvina02_rigid_receptor1.ranking.complete.csv into ../output-files/qvina02_rigid_receptor1.ranking.complete.csv.gz ...
cat: qvina02_rigid_receptor1.ranking.complete.csv: No such file or directory
rm: cannot remove 'qvina02_rigid_receptor1.ranking.complete.csv': No such file or directory
This seems to be an issue with vfvs_get_top_results.py. Indeed if I look inside this script, the batch system must be set to awsbatch instead of slurm.
My question is - how can I do all the postprocessing etc on Slurm instead of AWS?
Thanks a lot!