MrBayes in CIPRES, program quited

[Debajyoti Kabiraj]

Hello Sir,

I have run MrBayes using CIPRES gateway using concatenated 335 genes about 192150 bp. But the it quited, here is the STDOUT file. 

Hoping for good suggestions.

Thanks,

CIPRES_THREADSPP=1
CIPRES_NP=8
paramfile=paramfile.txt
CIPRES_THREADSPP=1
CIPRES_NP=8
paramfile=paramfile.txt
CIPRES_THREADSPP=1
CIPRES_NP=8
paramfile=paramfile.txt
CIPRES_THREADSPP=1
CIPRES_NP=8
paramfile=paramfile.txt
CIPRES_THREADSPP=1
CIPRES_NP=8
paramfile=paramfile.txt
CIPRES_THREADSPP=1
CIPRES_NP=8
paramfile=paramfile.txt
running: /projects/ps-ngbt/opt/comet/mrbayes.centos7/3.2.7a.openmpi/mb < paramfile.txt
running: /projects/ps-ngbt/opt/comet/mrbayes.centos7/3.2.7a.openmpi/mb < paramfile.txt
running: /projects/ps-ngbt/opt/comet/mrbayes.centos7/3.2.7a.openmpi/mb < paramfile.txt
running: /projects/ps-ngbt/opt/comet/mrbayes.centos7/3.2.7a.openmpi/mb < paramfile.txt
running: /projects/ps-ngbt/opt/comet/mrbayes.centos7/3.2.7a.openmpi/mb < paramfile.txt
running: /projects/ps-ngbt/opt/comet/mrbayes.centos7/3.2.7a.openmpi/mb < paramfile.txt
CIPRES_THREADSPP=1
CIPRES_NP=8
paramfile=paramfile.txt
running: /projects/ps-ngbt/opt/comet/mrbayes.centos7/3.2.7a.openmpi/mb < paramfile.txt
CIPRES_THREADSPP=1
CIPRES_NP=8
paramfile=paramfile.txt
running: /projects/ps-ngbt/opt/comet/mrbayes.centos7/3.2.7a.openmpi/mb < paramfile.txt


                            MrBayes 3.2.7a x86_64

                      (Bayesian Analysis of Phylogeny)

                             (Parallel version)
                         (8 processors available)

              Distributed under the GNU General Public License


               Type "help" or "help <command>" for information
                     on the commands that are available.

                   Type "about" for authorship and general
                       information about the program.


MrBayes > 
   Setting autoclose to yes

MrBayes > 
   Setting nowarnings to yes

MrBayes > 
   Setting usebeagle to no

MrBayes > 
   Executing file "infile.nex"
   UNIX line termination
   Longest line length = 192160
   Parsing file
   Expecting NEXUS formatted file
   Reading data block
      Allocated taxon set
      Allocated matrix
      Defining new matrix with 54 taxa and 192150 characters
      Data is Dna
      Missing data coded as ?
      Gaps coded as -
      Taxon  1 -> taxon1
      Error while parsing a string. Token "GGTCTAATATGGACTATTAT...[followed by at least 99970  more charectors]" is too long.
      Maximum allowed length of a token is 99990
      There was an error on at least one processor
      The error occurred when reading char. 99980-99999 on line 6
         in the file 'infile.nex'

   Returning execution to command line ...

   Error in command "Execute"

MrBayes > 
   Deleting previously defined characters
   Deleting previously defined taxa
   Quitting program

[Mark Miller]

Hi there, and thanks for reporting the issue.

 

The key to the error message is here:

      Error while parsing a string. Token "GGTCTAATATGGACTATTAT...[followed by at least 99970  more charectors]" is too long.

      Maximum allowed length of a token is 99990

      There was an error on at least one processor

      The error occurred when reading char. 99980-99999 on line 6

         in the file 'infile.nex'

It means the application does not like your input file. It is probably just an issue with formatting. I do not think that MrBayes places a limit on the number of characters allowed in your matrix. However, you may have to put your data into an interleaved format.

See this issue:

https://www.biostars.org/p/389103/

Let me know if I can help further.

Best,

Mark