Stuck process of PF2

[Jinren Yu]

Hi there,

I'm running PF2 on a large dataset. Everything goes well but the process got stuck when 82.52 percent of subset  pairs were done:

INFO     | 2023-03-16 16:19:15,194 | progress   |       Finished subset 1994/2420, 82.40 percent done
INFO     | 2023-03-16 16:19:15,294 | progress   |       Finished subset 1995/2420, 82.44 percent done
INFO     | 2023-03-16 16:19:16,343 | progress   |       Finished subset 1996/2420, 82.48 percent done
INFO     | 2023-03-16 16:19:16,762 | progress   |       Finished subset 1997/2420, 82.52 percent done

Please help me with this issue! 

Jinren

[Rob Lanfear]

Hi Jinren,

I'm afraid it's very difficult to help without more information. One thing you could try is quitting (ctrl-c) and restarting. It should catch up to where it left off very quickly, and the restart might help RAxML get over whichever subset is troubling it. I'm assuming it's raxml which is hanging here? You could examine that by looking at what process is taking a long time with top.

If it doesn't work for you, the other option is to move to IQ-TREE2. There is a very good implementation of the relaxed clustering algorithm there.

Cheers,

Rob