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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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tree file not found. #18

Closed lpipes closed 1 year ago

lpipes commented 2 years ago

Hello,

I tried to use the example alignment HIVenvSweden.txt with the following control file codeml.ctl:

   seqfile = HIVenvSweden.txt
   outfile = results.out
    noisy = 0  
   verbose = 0  
   runmode = -2  
   seqtype = 1  
  CodonFreq = 2  
    model = 0
   NSsites = 0

And I get the following error with codeml

CODONML in paml version 4.10.5, March 2022

tree file  not found.
ziheng-yang commented 2 years ago 
 treefile = HIVenvSweden.trees   * tree structure file name

the control file codeml.ctl on github has the above line. perhaps this was deleted by mistake? you can add it bck and try again. ziheng

lpipes commented 2 years ago

I am just testing these specific parameters on a control file. I thought for runmode = -2 no control file is needed? This control file works for paml 4.9.

ziheng-yang commented 1 year ago

yes, you are right. there should be no need for a species tree if runmode = -2, so that error check is wrong. i'll edit the code to get this fixed. ziheng