"Reconciling gene and species trees" step takes a very long time

[davidemms]

Sophos can cause the "Reconciling gene and species trees" step to take a very long time. This is because it performs checks every time OrthoFinder opens a file.

[davidemms]

I have submitted a fix for this issue which mostly resolves the problem: 87d3c77

It improves the situation considerably but not entirely. The fix is in OrthoFinder 2.3.7. To give an idea of the problem, for a dataset of 6 species on my computer the "Reconciling gene and species trees" step takes:

Time	Version
2 hours	OrthoFinder 2.3.3
2.5 mins	OrthoFinder 2.3.7
0.5 mins	Either version, Sophos deactivated

So the step is now about 50 times faster, but would be 240 times faster without Sophos.

The fix in OrthoFinder was to minimise the number of times files were opened and closed. If you are still having an issue with version 2.3.7 or later then

• Either deactivate Sophos:
  https://community.sophos.com/kb/en-us/133173
  systemctl stop sav-protect.service
systemctl stop sav-rms.service
• Or deactivate 'on-access scanning':
  https://www.sophos.com/en-us/medialibrary/PDFs/documentation/savl_9_cgeng.pdf
  /opt/sophos-av/bin/savdctl disable