OrthoFinder problem

Question

[HERMAN]

Hi biostars,

I'm trying to run the OrthoFinder software on several groups of phylogenetically close species ( Arabidopsis and its parents, C.Elegans and its parents etc etc ). Every group of species as its CDS in a subdirectory that I use as input for orthofinder.

My problem is that I cannot run OF inside a bash " for loop " that simply iterates over each subdir. The software stops running at the same point every time.

Maybe ma question could have a browder scope : is it possible to run softwares written in Python that use subProcesses inside bash for loops, or any other " calling " script ? Isn't it messing with the subprocess handling ?

I'm kinda lost and don't know what to do ...

Best regards

[shelkmike]

What error message does OrthoFinder produce?

[HERMAN]

Hi Mike,

It does not produce any error message, the software just freezes. I let it run for 1h without any improvement.

I have come with a workaround for now however, thank you for your help and reply !