any progress indicator available? about photon

[jdrudolph]

Dear Krzysztof,

currently there is no progress indicator, but jobs should not be running longer than a few hours, especially for small data sets. Is your computer still 'busy' and using the CPU? Please update the image using docker pull jdrudolph/photon and try again after restarting the container.

Best, Jan

[jdrudolph]

I added progress logging to the development version of PHOTON. You can try it by running

docker pull jdrudolph/photon:dev
docker run -d -p 5000:5000 jdrudolph/photon:dev

Please tell me at what stage PHOTON is stuck.

[krzysztofpawlowskiWULS]

Dear Jan,
Thanks for adding the progress indicator!

When I'm using the dev version, my PHOTON job gets stuck at stage 3:
"Progress message: 3/5 calculated scores, infering subnetwork using ANAT..."

It happens only when I submit my own dataset. I suspect that there may be too few known interactions between proteins from my dataset for ANAT to perform well.

When I submit your sample dataset, I get full results rather quickly.

For my "stuck" job, is there a way to get the intermediate data,
e.g. signaling functionality scores?

Best,
Krzysztof

[jdrudolph]

Using the browser interface there is no way to obtain intermediate results. You could consider using PHOTON from a linux machine (command line), where each step of the analysis could be run independently.