Diagnosing pipeline failure

[jsoghigian]

Hi there!

Thanks again for the great tool. I've been trying it on my personal data and I think it is finishing the OrthoFinder step now. I am not sure exactly where it fails, but I think it may be failing to complete aligning single copy genes. On the macse alignment step I noticed the error log had a number of messages like this:

Exception in thread "main" java.lang.OutOfMemoryError: Java heap space at align.ProfileAligner.<init>(ProfileAligner.java:120) at align.CodingMSA.<init>(CodingMSA.java:64) at align.CodingMSA.buildAlignmentReliable(CodingMSA.java:633) at align.CodingMSA.run(CodingMSA.java:659) at utils.MacseMain.main(MacseMain.java:426)

I have tried various configurations for memory and processors (last run was 3 processors + 120 gb of memory)...

This is a set of 5 insect genomes...