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abacus-gene / paml

PAML is a program package for model fitting and phylogenetic tree reconstruction using DNA and protein sequence data. Please report only **technical issues** on this repository (e.g., compiling, programs abort or do not run at all, etc.). Problems with input data and general questions should be posted at https://groups.google.com/g/pamlsoftware?pli
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Error after update to 4.10.7 #36

Closed axeljen closed 11 months ago

axeljen commented 11 months ago

Hi,

I've encountered an error in codeml after updating to 4.10.7, where the program runs almost to completion but then errors out with "error: end of tree file". The below example works fine in 4.9j, but not work with 4.10.7:

controlfile: seqfile = test_codeml_alignment.phy outfile = test_codeml_null.out treefile = test_codeml_tree.nwk noisy = 3 verbose = 1 seqtype = 1 CodonFreq = 2 ndata = 1 clock = 0 model = 2 NSsites = 2 icode = 0 fix_omega = 1 omega = 1 cleandata = 0

alignment: 6 87 sequence_1 ATGCAATCATATGCTTCTGCCATGTTAAGCGTATTTAACACTGATGGTTACAGTCCAGCTGCGCAACAGAATATTCCTGCTCTCCGG sequence_2 ATGCAATCATATGCTTCTGCCATGTTAAGCGTATTTAACACTGATGGTTACAGTCCAGCTGCGCAACAGAATATTCCTGCTCTCCGG sequence_3 ATGCAATCATATGCTTCTGCCATGTTAAGCGTGTTTAACACTGATGGTTACAGTCCAGCTGCGCAACAGCATATTCCTGCTCTCCGG sequence_4 ATGCAATCATATGCTTCTGCCATGTTAAGCGTATTTAACACTGATGGTTACAGTCCAGCTGCGCAACAGAATATTCCTGCTCTCCGG sequence_5 ATGCAATCATATGCTTCTGCCATGTTAAGCGTATTTAACACTGATGGTTACAGTCCAGCTGCGCAACAGAATATTCCTGCTCTCCGG sequence_6 ATGCAATCATATGCTTCTGCCATGTTAAGCGTATTTAACACTGATGGTTACAGTCCAGCTGCGCAACAGAATATTCCTGCTCTCCGG

tree: (sequence_6,sequence_3,((sequence_2,sequence_5),(sequence_4,sequence_1 #1)));

I'll just keep running 4.9j for now, but would be great to know if there's something that I'm missing here!

Thanks!

Axel

sabifo4 commented 11 months ago

Hi Axel,

I believe you are missing the PHYLIP header in the tree file. In your case, you have 6 sequences and 1 tree file, and thus the PHYLIP header should be the following:

6 1

All the details with regards to the input data format can be found on the PAML Wiki. You will also find an example on how to work with CODEML in our latest protocol for beginners (Álvarez-Carretero et al. 2023) as well as in the corresponding GitHub repository for the examples described in the paper.

Please let me know if that was the problem so I can close this issue.

Cheers!

axeljen commented 11 months ago

Yup that did the trick, thanks for the quick response!

Cheers