partitionfinder issues

[Yu Sun]

 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]

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]

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]

Thank you.

[Yu Sun]

Thank you. I will try it.