Screen terminated: ligand-collections/todo/todo.all did not meet the requirements for continuation

Hi there,

A while back I started a 62 million screen. It all went smooth until I reach around 40 million successful dockings. Then all my jobs stopped (and I did not changing anything). Resubmitting or creating new jobs doesn’t work either.

Looking the logfiles I see the following error:

The ligand-collections/todo/todo.all (if existent) did not meet the requirements for continuation (trial 1).
prepare-todolists.sh: line 479: [: DBCCC: integer expression expected
prepare-todolists.sh: line 483: [: DBCCC: integer expression expected

  • Warning: Could not get the length of collection DBCCC. Found value is: DBCCC. Exiting.
    Error was trapped
    Error in bash script /var/opt/sge/node-d00a-124/job_scripts/1230089
    Error on line 279

The todo.all located in:
…/workflow/ligand-collections/todo

has only one line:

$ more todo.all
1: DBCCC

The todo.all located in …/tools/templates is very different though and contains all the collections.

Any idea what the problem is and how I can fix it?

Help would be greatly appreciated! :slight_smile:

With kind regards
Morten

Hi Morten and welcome to the forum,

Can you please tell me how you generated the todo.all file? Are you using a subset of the REAL library in your screening?

Best,

Sorin

The problem was simply solved by deleting DBCCC from:

…/workflow/ligand-collections/todo/todo.all

Once the file was empty I was able to resubmit jobs and the screen continued.
I have no idea why this happened in the first place though.

NB! Let me emphasis that I removed one line only. The todo.all in this location only contained DBCCC. The todo.all located in …/tools/templates contains the entire collection.

This happened again and this time I was not able to fix the problem as I did above.
Job submission or re-submissions all fails with the following error:

prepare-todolists.sh: line 479: [: EBCDEE_00083: integer expression expected
prepare-todolists.sh: line 483: [: EBCDEE_00083: integer expression expected
 * Warning: Could not get the length of collection EBCDEE_00083. Found value is: EBCDEE_00083. Exiting.
Error was trapped
Error in bash script /var/opt/sge/node-h00a-044/job_scripts/1096037
Error on line 279

I have multiple todo.all files in …/workflow/ligand-collections/todo:

todo.all
todo.all.0000
todo.all.0001
todo.all.0002
todo.all.0003
todo.all.0004
todo.all.0005

todo.all contain EBCDEE_00083, as well as a long list of other collections. I was unable to resume my screen by emptying the todo.all.

This happened the same time as the computer cluster went down for a few days, so that may have causes an error with my todo.all files.

Any ideas on how to fix this?