unknown character state error

[Leon Kim]

Hello PhyML users,

I am currently using Phyml 3.0 on linux using command line. I keep getting unknown character state error on my MSA. I individually took each sequence out to test which sequence is causing trouble, and I found the following sequence to be causing the error.

>MYCTU|gi|b
LLLLRHGETAWSTLGRHTGGTEVELTDTGRTQAELAGQLLGELELPIVICSPRRRTLDTAKLAGLTVNEVTGLLAEWDYGSYEGLTTPQIRESEPDWL-WTHGCPAGESVAQVNDRADSAVALALERDVLFVSHGHFSRAVITRWVQLPJAEGSRFAMPTASIGICGFEHGVR-LAVLGLT


The file was in phylip format, but I put it in FASTA for easy reading in this post. I do not see why this sequence causes unknown character error. I prefer not to go through my sequences individually to debug next time I run analysis. Does anybody know why this error occurs?

[Stephane Guindon]

Dear Leon,
I might be able to figure out what is going on if you send me the whole sequence alignment.
Regards,
-Stephane-

[Leon Kim]

The problem fixed itself, but it was strange! Now I have another problem where I can't open phyml-mpi at all. I have been able to do

"mpirun -n 8 phyml-mpi <myseq> -b 100"

without problems, but when I tried today I get the following error:

=====================================================================================
=   BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES
=   EXIT CODE: 139
=   CLEANING UP REMAINING PROCESSES
=   YOU CAN IGNORE THE BELOW CLEANUP MESSAGES
=====================================================================================
APPLICATION TERMINATED WITH THE EXIT STRING: Segmentation fault (signal 11)


This error occurs only when I run phyml after compiling. I have tried running the (pre-compiled) executable found on the website, and I have no problem running phyml on <myseq> . I want to fix this bug or be able to run in parallel through PHYLIP-like interface (I don't know if this is possible)

[Stephane Guindon]

Dear Leon,

Use the following command instead:

mpirun -n 8 phyml-mpi -i <myseq> -b 100

Alternatively, use:

mpirun -n 8 phyml-mpi

and follow the instructions in order to select the
appropriate options using the PHYLIP interface.

Regards,

-Stephane-

[Leon Kim]

Thank you very much for replies. When I posted previously, I forgot to put "-i" (but I do believe I included it when I ran the analysis). I think for some reason my OS was not working properly. Rebooting solved the issue... (as many computer problems do).