neherlab/pan-genome-analysis

Segmentation fault

Closed this issue · 5 comments

Hello,

I recently tried to run panX.py but I've been getting a Segmentation fault error. I installed all the dependencies via conda as suggested and then tried to run the test script. Instead, I got the error message below:

image

I'm not so sure what the problem is...maybe something with the python script? Really hope you can help.

Many thanks in advance

A little update. I realized that maybe it had to do with the threads being 64..since the remote server I use has 20, I just removed the threads option in general and I still got the same segmentation fault problem

I need more information here. What step did it fail at?

I don't think this is something in panX proper, but something involving external binaries that are called.

It failed when I tried to run-Testser.sh. I also tried to run the help command with panX.py ./panX.py -h but I still got the same "Segmentation fault" error

this suggests there is an issue with your python installation.

@rneher you're right. My normal "base" conda env runs on python version 2.7.15, so I just changed the python version in the yml script to that and renamed the env and it works now. Thank you.