search

BergmannLab / MONET

MONET : MOdularising NEtwork Toolbox - https://doi.org/10.1093/bioinformatics/btaa236
GNU General Public License v3.0
41 stars 15 forks source link

Error: file 'input.txt' not found #42

Closed abrantesas closed 3 years ago

abrantesas commented 3 years ago

Hello, I am trying to run your example analysis and get this output:

M1: Running Team Aleph's code from the DREAM challenge on disease module identification

Error: file 'input.txt' not found

Calling monet like this:

monet --input='/nas/depts/007/sullilab/shared/Rainbo/data/monet/zachary_karate_club.txt' --method=M1 --container=singularity --output='/nas/depts/007/sullilab/shared/Rainbo/analysis/monet/'

I tried with no quotes, single quotes, and double quotes and got the same result.

I checked head /nas/depts/007/sullilab/shared/Rainbo/data/monet/zachary_karate_club.txt and the file is ok.

What would cause this? The IT guy who installed the package said to ask here. It doesn't seem like any error I could be making. Did he possibly install it incorrectly?

Thanks, Anthony

sergio-gomez commented 3 years ago

Hi Anthony,

The most plausive explanation is the lack of "write" permissions of the folder where the optimization method runs. The file "input.txt" is an intermediate file that is automatically generated before calling the optimization scripts, thus being not found means it has not been created properly. Please check if you have write permissions in the Monet folder and subfolders, in particular folders "M1_code" and "M1_code/sub-challenge1/".

Best,

Sergio.

abrantesas commented 3 years ago

That was it. Thanks! I had to install my own copy in a folder where I could have all permissions.