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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
GNU General Public License v3.0
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error for run: codeml codem.ctl #39

Closed panpanchen123 closed 10 months ago

panpanchen123 commented 1 year ago

Hello, when I run codeml codeml.ctl ,it shows ns = 7 ls = 1643893 Reading sequences, sequential format.. Reading seq # 1: Arur
Reading seq # 2: Daca
Reading seq # 3: Dape
Reading seq # 4: Lesa

Error: EOF?.

Please tell me how should I solve this problem，thank you very much.

sabifo4 commented 10 months ago

Hi there,

This error message is letting you know that CODEML has reached the end of the sequence file and there are no more sequences to be read (i.e., you specified that you have 7 sequences in the PHYLIP header, but it seems you only have four, according to your message). Without the input files and the control files, it is hard to troubleshoot what may have gone wrong, however.

Please note that this is just an error message letting you know that there is a problem with your input data, not a technical problem with the program itself. In addition, this question has been asked several times on the PAML Google Group, e.g., latest thread. Most of the times, these questions have been asked before in the PAML Google Group, so you may want to first check if that's the case to avoid having duplicates of the same question that has already been resolved :)

Hope this helps!