How to process results from a large-scale docking: Difference between revisions
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In a large calculation such as this one with tens of thousands of separate processes, it is not unusual for some jobs to fail for some reason. Checking for successful completion, and re-starting failed processes, is a normal part of running such a large job. | In a large calculation such as this one with tens of thousands of separate processes, it is not unusual for some jobs to fail for some reason. Checking for successful completion, and re-starting failed processes, is a normal part of running such a large job. | ||
Only do this if dirlist is the origenal and dirlist_ori does not exist | |||
cp dirlist dirlist_ori | |||
Run the script below in your docking directory | Run the script below in your docking directory | ||
csh /nfs/home/tbalius/zzz.github/DOCK/docking/submit/get_not_finished.csh | csh /nfs/home/tbalius/zzz.github/DOCK/docking/submit/get_not_finished.csh /path/to/docking | ||
This script puts all the directories of failed jobs in a file called dirlist_new. | This script puts all the directories of failed jobs in a file called dirlist_new. | ||
mv dirlist | mv dirlist dirlist_old | ||
mv dirlist_new dirlist | mv dirlist_new dirlist_new1 | ||
cp dirlist_new1 dirlist | |||
foreach dir (`cat dirlist`) | |||
echo $dir | |||
rm $dir/OUTDOCK $dir/test.mol2.gz $dir/stderr | |||
end | |||
Then resubmit them | Then resubmit them |
Revision as of 19:59, 18 October 2017
Written by Jiankun Lyu, 20171018
This tutorial uses the DOCK3.7.1rc1.
Check for completion and resubmit failed jobs
In a large calculation such as this one with tens of thousands of separate processes, it is not unusual for some jobs to fail for some reason. Checking for successful completion, and re-starting failed processes, is a normal part of running such a large job.
Only do this if dirlist is the origenal and dirlist_ori does not exist
cp dirlist dirlist_ori
Run the script below in your docking directory
csh /nfs/home/tbalius/zzz.github/DOCK/docking/submit/get_not_finished.csh /path/to/docking
This script puts all the directories of failed jobs in a file called dirlist_new.
mv dirlist dirlist_old mv dirlist_new dirlist_new1 cp dirlist_new1 dirlist
foreach dir (`cat dirlist`) echo $dir rm $dir/OUTDOCK $dir/test.mol2.gz $dir/stderr end
Then resubmit them
$DOCKBASE/docking/submit/submit.csh
Combine results
When docking is complete, merge the results of each separate docking job into a single sorted file.
cd your/docking/directory python $DOCKBASE/analysis/extract_all_blazing_fast.py dirlist extract_all.txt energy_cutoff