Error in tree and phylip alignment file

[Sebastin Raveendar]

Hi Im using paml-tutorial/positive-selection/01_protocol_analyses/01_site_models

by running in linux codeml4.10.6 codeml-sites.ctl | tee logfile_codeml-sites.txt

Nice code, uuh?
ns = 10   ls = 76095
Reading sequences, sequential format..
Reading seq #10: NC_018552      
Sequences read..
Counting site patterns..  0:00
Compressing,    454 patterns at  25365 /  25365 sites (100.0%),  0:00
Collecting fpatt[] & pose[],    454 patterns at  25365 /  25365 sites (100.0%),  0:00
Counting codons..


      360 bytes for distance
   443104 bytes for conP
        0 bytes for fhK
  5000000 bytes for space

Error: species 'KR078314' in tree file not found in the sequence alignment file.

TIA

Sebastin

[Janet Young]

hi Sebastin,

Your tree file looks strange - I think it contains 20 trees (and therefore KR078314 is there 20 times).  I think if you fix that it should work.

Janet