Big Sur update potential issue

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James Dorey

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Jan 23, 2021, 6:55:39 PMJan 23
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Hi there,

I've been using PartitionFinder for a few years without issue but I recently updated to MacOS Big Sur. Stupid, I know!

Since then my runs have not been working as expected. For example, the below run which took seconds previously is now stuck at the "Using a separate GTR+G model for each data block" stage (see below).

Any insights would be welcome!

Many thanks,

James


(base) jamesdorey@192:~$ python /Users/<path>/Partition_Finder/partitionfinder-2.1\ 2.1/PartitionFinder.py /Users/<path>/Partition_Finder/partitionfinder-2.1\ 2.1/partition_finder.cfg 

INFO     | 2021-01-23 23:08:27,055 | Note: NumExpr detected 16 cores but "NUMEXPR_MAX_THREADS" not set, so enforcing safe limit of 8.

INFO     | 2021-01-23 23:08:27,055 | NumExpr defaulting to 8 threads.

INFO     | 2021-01-23 23:08:29,559 | ------------- PartitionFinder 2.1.1 -----------------

INFO     | 2021-01-23 23:08:29,559 | You have Python version 2.7

INFO     | 2021-01-23 23:08:29,559 | Command-line arguments used: /Users/<path>/Partition_Finder/partitionfinder-2.1 2.1/PartitionFinder.py /Users/<path>/Partition_Finder/partitionfinder-2.1 2.1/partition_finder.cfg

INFO     | 2021-01-23 23:08:29,560 | ------------- Configuring Parameters -------------

INFO     | 2021-01-23 23:08:29,560 | Setting datatype to 'DNA'

INFO     | 2021-01-23 23:08:29,561 | Setting phylogeny program to 'phyml'

INFO     | 2021-01-23 23:08:29,561 | Program path is here /Users/<path>/PArtition_Finder/partitionfinder-2.1 2.1/programs

INFO     | 2021-01-23 23:08:29,562 | Setting working folder to: '/Users/<path>/Partition_Finder/partitionfinder-2.1 2.1'

INFO     | 2021-01-23 23:08:29,563 | Loading configuration at './partition_finder.cfg'

INFO     | 2021-01-23 23:08:29,573 | Setting 'alignment' to 'allodapine_cut.phy'

INFO     | 2021-01-23 23:08:29,574 | Setting 'branchlengths' to 'linked'

INFO     | 2021-01-23 23:08:29,574 | You set 'models' to: mrbayes

INFO     | 2021-01-23 23:08:29,625 | This analysis will use the following 24 models of molecular evolution

INFO     | 2021-01-23 23:08:29,626 | JC, K80, SYM, F81, HKY, GTR, JC+G, K80+G, SYM+G, F81+G, HKY+G, GTR+G, JC+I, K80+I, SYM+I, F81+I, HKY+I, GTR+I, JC+I+G, K80+I+G, SYM+I+G, F81+I+G, HKY+I+G, GTR+I+G

INFO     | 2021-01-23 23:08:29,632 | Setting 'model_selection' to 'bic'

INFO     | 2021-01-23 23:08:29,648 | Setting 'search' to 'greedy'

INFO     | 2021-01-23 23:08:29,648 | ------------------------ BEGINNING NEW RUN -------------------------------

INFO     | 2021-01-23 23:08:29,649 | Looking for alignment file './allodapine_cut.phy'...

INFO     | 2021-01-23 23:08:29,662 | Using 16 cpus

INFO     | 2021-01-23 23:08:29,662 | Beginning Analysis

INFO     | 2021-01-23 23:08:29,692 | Reading alignment file './allodapine_cut.phy'

INFO     | 2021-01-23 23:08:29,700 | Starting tree will be estimated from the data.

INFO     | 2021-01-23 23:08:29,702 | Estimating Maximum Likelihood tree with RAxML fast experimental tree search for ./analysis/start_tree/filtered_source.phy

INFO     | 2021-01-23 23:08:29,703 | Using a separate GTR+G model for each data block

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