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dsilvestro / PyRate

PyRate is a program to estimate speciation, extinction, and preservation rates from fossil occurrence data using a Bayesian framework.
GNU Affero General Public License v3.0
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Error combining log files #42

Closed LauravanHolstein closed 1 year ago

LauravanHolstein commented 1 year ago

Hi again!

Here I am with another error... again, on a Mac M1, and with PyRate and numpy fully up-to-date. When combining log files across 10 replicates (with preservation prior TPP), I run into the following error:

Screenshot 2023-08-07 at 10 10 27

Any ideas would be appreciated!

Best wishes, Laura

thauffe commented 1 year ago

Hi Laura,

  1. Better use the -logCombRJ instead of -logComb when you aim to combine the output of RJMCMC analyses
  2. The root of the problem is that the number of columns in the mcmc.log files differ among your replicates. The "52" and "50" on your screenshot (9901, 52) indicate the number of rows and columns. In comparison to replicates 1 and 10, replicate 2 misses either one species or two shift points of sampling rate (-qtimes).

Hopefully this solves the error!

LauravanHolstein commented 1 year ago

You are truly my PyRate guardian angel - thank you once again for a flawless fix!