phosphopath create new network of pathway

[Leila Rato]

Hi, 

 

I am trying to create a new network from a few pathways I selected from the 'select a pathway' table and I keep getting this null error, caught exception executing task. 

I am at step 2.5 of the manual and everything had worked out so far.

Any idea how to fix this issue? 

Thanks!

Leila 

[Scooter Morris]

Hi Leila,

   I don't know much about the phosphopath app, but I might be able to help.  Can you tell me what OS your are on?  I need to see the actual backtrace from the null error you are getting, which should be in a log file.  Alternatively, you can run Cytoscape from a command prompt, and the backtrace should be visible.

-- scooter

[Leila Rato]

Hi, 

I am using windows 10 but could you tell me where I can find the log files? I am new to this and I really do not know what that means. 

Thank you so much for your help!

Leila 

[Leila Rato]

This is what I found, I hope this is it!

On Thursday, 1 April 2021 at 18:46:29 UTC+3 ssbsm...@gmail.com wrote:

[Scooter Morris]

That's exactly it.  So, the phosphopath App is getting an error in it's internal code that is trying to create a network.  Without access to the code it would be difficult for me to figure out exactly what's happening.  I would suggest sending e-mail to the phosphopath authors.

-- scooter

[Leila Rato]

Hi, 

I tried contacting the authors but it did not lead to anything so I was wondering if you have any other advice? I have not managed to go around it.

Best, 
Leila 

[Scooter Morris]

No, unfortunately, I don't have any other ideas.  Did you try it with the sample dataset provided at: https://github.com/linseyr/PhosphoPath?  If that works, maybe we can figure out how to work around the bug.

-- scooter