Closed axeljen closed 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!
Yup that did the trick, thanks for the quick response!
Cheers
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