Running ~20 loci dataset

[aberaslop]

Dear Partitionfinder team,

I have run a small alignment of three genes through partitionfinder, and it has worked wonderfully. I have attached the .cfg file (in txt format). I then tried to do a larger analysis, 20 genes, and this somehow does not work. I have also attached the .cfg to this email for reference. In this latter case, I changed the scheme parameter from all to rcluster (~100 loci) just in case, but that didn’t solve the problem either.

Here is the error message I get (it always fails in the same place):

INFO | 2020-03-23 20:28:12,506 | NumExpr defaulting to 8 threads. INFO | 2020-03-23 20:28:13,556 | ------------- PartitionFinder 2.1.1 ----------------- INFO | 2020-03-23 20:28:13,557 | You have Python version 2.7 INFO | 2020-03-23 20:28:13,557 | Command-line arguments used: PartitionFinder.py ../../../Desktop/partitionfinder-results/ --raxml INFO | 2020-03-23 20:28:13,557 | ------------- Configuring Parameters ------------- INFO | 2020-03-23 20:28:13,557 | Setting datatype to 'DNA' INFO | 2020-03-23 20:28:13,557 | Setting phylogeny program to 'raxml' INFO | 2020-03-23 20:28:13,557 | Program path is here /Users/Documents/programs/partitionfinder-2.1.1/programs INFO | 2020-03-23 20:28:13,559 | Setting working folder to: '/Users/Desktop/partitionfinder-results' INFO | 2020-03-23 20:28:13,559 | Loading configuration at './partition_finder.cfg' INFO | 2020-03-23 20:28:13,566 | Setting 'alignment' to 'Big_alignment.phy' INFO | 2020-03-23 20:28:13,567 | Setting 'branchlengths' to 'linked' INFO | 2020-03-23 20:28:13,567 | You set 'models' to: GTR, GTR+G, GTR+I+G INFO | 2020-03-23 20:28:13,597 | This analysis will use the following 3 models of molecular evolution INFO | 2020-03-23 20:28:13,597 | GTR, GTR+G, GTR+I+G INFO | 2020-03-23 20:28:13,597 | Setting 'model_selection' to 'aicc' ERROR | 2020-03-23 20:28:13,602 | There was a problem loading your .cfg file, please check and try again ERROR | 2020-03-23 20:28:13,603 | Expected "[schemes]", found 'g' (at char 559), (line:24, col:1) INFO | 2020-03-23 20:28:13,603 | It looks like the '[schemes]' option might be missing or in the wrong place. Or perhaps something is wrong in the lines just before the '[schemes]' option is missing. Please double check the configuration file and try again ERROR | 2020-03-23 20:28:13,603 | Failed to run. See previous errors.

I would appreciate any insights you may have on where the error is.

Thank you so much!

L.

partition_finder_big.txt partition_finder_small.txt

[roblanf]

Hi there,

For general help, please use the google group.

Rob

On Tue, 24 Mar 2020 at 21:13, aberaslop [email protected] wrote:

Dear Partitionfinder team,

I have run a small alignment of three genes through partitionfinder, and it has worked wonderfully. I have attached the .cfg file (in txt format). I then tried to do a larger analysis, 20 genes, and this somehow does not work. I have also attached the .cfg to this email for reference. In this latter case, I changed the scheme parameter from all to rcluster (~100 loci) just in case, but that didn’t solve the problem either.

Here is the error message I get (it always fails in the same place):

INFO | 2020-03-23 20:28:12,506 | NumExpr defaulting to 8 threads. INFO | 2020-03-23 20:28:13,556 | ------------- PartitionFinder 2.1.1

INFO | 2020-03-23 20:28:13,557 | You have Python version 2.7 INFO | 2020-03-23 20:28:13,557 | Command-line arguments used: PartitionFinder.py ../../../Desktop/partitionfinder-results/ --raxml INFO | 2020-03-23 20:28:13,557 | ------------- Configuring Parameters

INFO | 2020-03-23 20:28:13,557 | Setting datatype to 'DNA' INFO | 2020-03-23 20:28:13,557 | Setting phylogeny program to 'raxml' INFO | 2020-03-23 20:28:13,557 | Program path is here /Users/Documents/programs/partitionfinder-2.1.1/programs INFO | 2020-03-23 20:28:13,559 | Setting working folder to: '/Users/Desktop/partitionfinder-results' INFO | 2020-03-23 20:28:13,559 | Loading configuration at './partition_finder.cfg' INFO | 2020-03-23 20:28:13,566 | Setting 'alignment' to 'Big_alignment.phy' INFO | 2020-03-23 20:28:13,567 | Setting 'branchlengths' to 'linked' INFO | 2020-03-23 20:28:13,567 | You set 'models' to: GTR, GTR+G, GTR+I+G INFO | 2020-03-23 20:28:13,597 | This analysis will use the following 3 models of molecular evolution INFO | 2020-03-23 20:28:13,597 | GTR, GTR+G, GTR+I+G INFO | 2020-03-23 20:28:13,597 | Setting 'model_selection' to 'aicc' ERROR | 2020-03-23 20:28:13,602 | There was a problem loading your .cfg file, please check and try again ERROR | 2020-03-23 20:28:13,603 | Expected "[schemes]", found 'g' (at char 559), (line:24, col:1) INFO | 2020-03-23 20:28:13,603 | It looks like the '[schemes]' option might be missing or in the wrong place. Or perhaps something is wrong in the lines just before the '[schemes]' option is missing. Please double check the configuration file and try again ERROR | 2020-03-23 20:28:13,603 | Failed to run. See previous errors.

I would appreciate any insights you may have on where the error is.

Thank you so much!

L.

partition_finder_big.txt https://github.com/brettc/partitionfinder/files/4374570/partition_finder_big.txt partition_finder_small.txt https://github.com/brettc/partitionfinder/files/4374574/partition_finder_small.txt

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-- Rob Lanfear Division of Ecology and Evolution, Research School of Biology, The Australian National University, Canberra

www.robertlanfear.com