codeml: Species Ref? then stopping

[Beth S]

I'm trying to run codeml on OSX (paml4.7b) on some of my own mitochondrial DNA sequences but Species Ref? keeps coming up just after it starts running, causing everything to stop.

Is there some reason why its doing this and how can I fix it?

[Ziheng]

I am not sure where you got version 4.7b. I think the version on the web is 4.7a. Does it behave in the same way?
Ziheng

[HZ]

I also downloaded paml4.7a from the web (linux). When I run codeml the screen print says 4.7b.

[HZ]

I had similar problem when I used my own tree file as input. The tree file was not digested properly by paml and paml also spitted "Species whatever" and quit. My opinion is that the error information is not very informative (too concise). But it basically says it does not recognize the species "Ref" in your case.

[sher...@uchicago.edu]

Hello, 

I know this post is a bit old but I'm having the exact same problem (and probably is better to continue the discussion here rather than create a new post). I am using the Mac OS X version 4.8a. This is the output:

ns = 188   ls = 152

Reading sequences, sequential format..

Reading seq #188: Chelonoidis_abindgonii_Contig1354_MB            

Sequences read..

Counting site patterns..  0:00

         152 patterns at      152 /      152 sites (100.0%),  0:00

Counting frequencies..

   140624 bytes for distance

   48640 bytes for conP

   3648 bytes for fhK

   5000000 bytes for space

Species 1.628606?

I really don't understand what might be happening, is the first time I get this error with codeml. 

I'm attaching the alignment, tree and control file. Any help would be much appreciated.

Best, 

Santiago

[sher...@uchicago.edu]

Hi, 

Thanks for writing back. I think I finally understood what happened. I was using a tree that has node supports, which confuses codeml because it treats the supports as additional species' names and since it cannot find those "names" in the alignment it throws an error. The key is to use a tree without node support.

Hope this helps.