Open matany58 opened 2 years ago
jpaggi
commented
2 years ago I suspect this is arising in the mcss feature computation? If so, it is complaining that the mcss computation failed in an unexpected way. This part of the code requires use of Schrodinger "canvasMCS" utility. The code assumes that executable is at "$SCHRODINGER/utilities/canvasMCS" works. You might need to set the SCHRODINGER environmental variable to make this work.
matany58
commented
2 years ago How do I set the SCHRODINGER environment to make this work? The error is initiated by Computing mcss similarities. ERROR: non-zero return code [1] from /hpcf/authorized_apps/rhel7_apps/schrodinger/install/2021-1/canvas-v4.7/bin/Linux-x86_64/canvasMCS
matany58
commented
2 years ago The executable is in schrodinger/install/2021-1/canvas-v4.7/bin/Linux-x86_64/canvasMCS Please how do I make this work?
Thanks for your assistance
jpaggi
commented
2 years ago Ah I see. Sorry, I did not realize that some schrodinger installations have different directory structures.
You can solve this issue by updating line 72 of features/mcss.py from
cmd = "$SCHRODINGER/utilities/canvasMCS -imae {} -ocsv {} -stop 10 -atomtype C {}"
to
cmd = "schrodinger/install/2021-1/canvas-v4.7/bin/Linux-x86_64/canvasMCS -imae {} -ocsv {} -stop 10 -atomtype C {}"
You should use the absolute path to canvasMCS, instead of this relative path, so that the code can execute from any directory.
matany58
commented
2 years ago I change it but still having the same error the full error is
subprocess complete
Computing mcss similarities.
Traceback (most recent call last):
File "/hpcf/authorized_apps/rhel7_apps/combind/combind/combind", line 355, in
matany58
commented
2 years ago Please any idea on how to resolve this issue?
jpaggi
commented
2 years ago Hello, could you add the following two print statements and share the output with me:
At line 83 of features/mcss.py:
print(cmd.format(os.path.basename(mae), os.path.basename(csv), os.path.abspath(mcss_types_file)))
At line 92 of features/mcss.py:
print(str(r.stderr))
Thank you!
matany58
commented
2 years ago Okay
matany58
commented
2 years ago Error generated is below;
Extracting glide scores.
Extracting names.
Computing RMSDs to native poses
Computing interaction fingerprints.
Computing interaction similarities.
Computing shape similarities.
$SCHRODINGER/shape_screen -shape poses1.maegz -screen poses2.maegz -pharm -norm 1 -distinct -inplace -NOJOBID
subprocess complete
Computing mcss similarities.
cmd:
/hpcf/authorized_apps/rhel7_apps/schrodinger/install/2021-1/canvas-v4.7/bin/Linux-x86_64/canvasMCS -imae temp.maegz -ocsv temp.csv -stop 10 -atomtype C /home/manyanwu/features/mcss16.typ
Stdout:
None
Stderr:
b'cannot open /home/manyanwu/features/mcss16.typ to load rules\n\n'
Traceback (most recent call last):
File "/hpcf/authorized_apps/rhel7_apps/combind/combind/combind", line 355, in
matany58
commented
2 years ago It appears that it is looking for mcss16.typ in my home directory /home/manyanwu/features/mcss16.typ but the file is in the directory /research/rgs01/applications/hpcf/authorized_apps/rhel7_apps/combind/combind/features
jpaggi
commented
2 years ago Before running combind, you need to run source setup.sh from the root of the combind repo (/research/rgs01/applications/hpcf/authorized_apps/rhel7_apps/combind). This will set the path correctly.
matany58
commented
2 years ago got it working I run export COMBINDHOME=/research/rgs01/applications/hpcf/authorized_apps/rhel7_apps/combind/combind
I noticed the error below while executing combind featurize features docking//_pv.maegz
assert os.path.exists(csv) AssertionError
Does anyone know which CSV file is missing and in which directory/folder