I am running PF2 on a fairly large nucleotide dataset (456 taxa, ~60kb) but it seems to get stuck during the first part of the analysis (with raxml). After more than a day it is still at (log file attached):
INFO | 2020-04-21 14:04:42,789 | raxml | Using a separate GTR+G model for each data block
When opening the analysis/start_tree/RAxML_info.fastTREE, it randomly ends like this (file attached):
This stopped at the same time (2020-04-21 14:04) as the log file shortly after the analysis was started and since then nothing has happened.
To me that looks like it got stuck somehow. At first I thought that this partition has a problem but when I ran it again it stopped at another Partition 589.
With a different partitioning scheme on the same dataset I had a similar problem that it did not get over this step ("Using a separate GTR+G model for each data block") for more than 4 days (but here the analysis/start_tree/RAxML_info.fastTREE file stopped at:
Partion 366 number of Cats: 1
Partion 367 number of Cats: 1)
Could it be a problem with raxml? I cannot find why it stops at these random steps.
I hope this is not too confusing and that someone else might be more experienced with PF than me and could point me to a solution.