I've just recently started using RAxML via Cipres portal for a phylogeny project. My dataset consists of 97 taxa, composed of 5 concatenated gene alignments for each. I have attempted to define this in a text file using the format "DNA, gene1=#-#" for all five genes.
However, I keep getting an error message saying "ERROR: you specified the unknown model GTRCAT for partition 0."
Also worth noting is that I have designated GTRGAMMA for my model.
Any and all help is appreciated, and if you need more info, I'll gladly supply it.
You probably have an error in the format of your partition file, would you copy and paste it here?
This is the format of one partition file that would work:
DNA, p1 = 1-1143
DNA, p2 = 1144-1802
DNA, p3 = 1803-1907, 2029-2196
DNA, p4 = 1908-2028, 2198-2585\3, 2199-2583\3, 2587-3052\3, 2588-3053\3
DNA, p5 = 2197-2584\3, 2586-3051\3
You can also check the google forum for raxml that is maintained by Stamatakis himself
https://groups.google.com/forum/#!forum/raxml
Would it be possible to paste the command line in here directly? Try not specifying a partitions file, see if it runs, if it does you know that the format is the issue, although I don't think it would give you a model error if this is the issue.
This is the command line according to CIPRES in the log files:
raxmlHPC-HYBRID -T 4 -f a -N autoMRE -n RAxML Run 11 -s infile.txt -q part.txt -p 12345 -m GTRGAMMA -x 12345
Below is the text of my partition file:
DNA, 12S = 1-324
DNA, 16S = 325-668
DNA, 28S = 669-1405
DNA, H3 = 1406-1744
DNA, 18S = 1745-2230
My sequence data (input) is in phylip format from Geneious.
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