I am using the conda installation of phylobayes-mpi v.1.9 on a dataset with 18 species and 1637925 positions with the command: mpirun -n 8 pb_mpi -s -cat -gtr -d $phy allseqs.CAT_GTR.chain0
It doesn't seem to be reading the phylip file correctly, as I am getting the following error. However, I think the file is formatted correctly as when I run it on a subset of the data (only the first 20000 amino acids for each species) it works. The supermatrix was created using catsequences (https://github.com/ChrisCreevey/catsequences).
model:
stick-breaking Dirichlet process mixture (cat)
exchangeabilities estimated from data (gtr)
discrete gamma distribution of rates across sites (4 categories)
read data from file : allseqslongnames.phy
error : found 0 taxa instead of 18 in datafile
error : found 0 taxa instead of 18 in datafile
error : found 0 taxa instead of 18 in datafile
error : found 0 taxa instead of 18 in datafile
--------------------------------------------------------------------------
Primary job terminated normally, but 1 process returned
a non-zero exit code. Per user-direction, the job has been aborted.
--------------------------------------------------------------------------
error : found 0 taxa instead of 18 in datafile
error : found 0 taxa instead of 18 in datafile
error : found 0 taxa instead of 18 in datafile
error : found 0 taxa instead of 18 in datafile
--------------------------------------------------------------------------
mpirun detected that one or more processes exited with non-zero status, thus causing
the job to be terminated. The first process to do so was:
Process name: [[45557,1],7]
Exit code: 1
Hello,
I am using the conda installation of phylobayes-mpi v.1.9 on a dataset with 18 species and 1637925 positions with the command:
mpirun -n 8 pb_mpi -s -cat -gtr -d $phy allseqs.CAT_GTR.chain0It doesn't seem to be reading the phylip file correctly, as I am getting the following error. However, I think the file is formatted correctly as when I run it on a subset of the data (only the first 20000 amino acids for each species) it works. The supermatrix was created using catsequences (https://github.com/ChrisCreevey/catsequences).
The first couple of lines of the phylip file are:
Could you please help me with this issue?
Many thanks in advance, Julia