partitionfinder issues

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Yu Sun

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Feb 22, 2021, 9:32:26 PMFeb 22
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 Hi guys,
     I was trying to run in on hopper( which a super computer from my university). the command line is "python /tools/partitionfinder-2.1.1/PartitionFinderProtein.py /home/yzs0104/infile"
 the error report is "Warning, you specified a working directory via "-w" Keep in mind that RAxML only accepts absolute path names, not relative ones! ERROR trying to assign model 10 to position 2931 while already model 9 has been assigned to this position"

 I am confused... if you know the problem solution...Thank you.

Best,
Yu

Rob Lanfear

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Feb 22, 2021, 9:33:45 PMFeb 22
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It looks to me like you might have overlapping data blocks (the bit in the error about assigning two models to one position). 

Can you post your .cfg file?

Rob

dongzh...@gmail.com

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Feb 22, 2021, 10:28:55 PMFeb 22
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Hi Yu,

You may also try PhyloSuite (http://phylosuite.jushengwu.com/, a graphic analysis platform), which integrated "Partitionfinder2" and make it easy for its configuration. By combining "Concatenation" function and "Partitionfinder2", PhyloSuite can auto-configure the data blocks, so it can avoid your question. It also supports converting the data blocks to codon mode. For how to use it, please see this demo: http://phylosuite.jushengwu.com/dongzhang0725.github.io/documentation/#5-10-1-Brief-example. You may also find a chinese video introduction here: https://www.bilibili.com/video/BV11h411X7LL/.

Best,
Dong

Yu Sun

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Feb 25, 2021, 6:06:22 PMFeb 25
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Thank you.
export_13.cfg

Yu Sun

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Feb 25, 2021, 6:07:39 PMFeb 25
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Thank you. I will try it.
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