I am new leaner about phylogeny. currently i ran MrBayes on cluster with whole mtDNA from 101 species.
Phylogenetic analysis were carried out twice separately, once with the third codon position, once were not. InvGAMMA mode for both analysis.
The strange thing is i can get ".con.tre" file with the third codon position input file, but cannot with non-third codon position input file.
i v ran the analysis twice, but still could not get the .con.tre file.
does anyone know why?
Here is my input file:
#NEXUS begin taxa; dimensions ntax=101; taxlabels Ancistrotermes_pakistanicus_Thailand Blatella_germanica ...... end; begin characters; dimensions nchar=16305; format datatype=dna missing=? gap=-; matrix Ancistrotermes_pakistanicus_Thailand AAGGAGTTTTATTCTTGC-TT-T... ...... ; end; begin mrbayes; CHARSET rna12-16S = 1-3141; CHARSET tRNA = 3142-4875; CHARSET coding_first = 4876-12495\2; CHARSET coding_second = 4877-12495\2; partition favored = 4: rna12-16S, tRNA, coding_first, coding_second; set partition = favored; set autoclose=yes nowarn=yes; lset applyto=(1,2,3,4) nst=6 rates=invgamma; unlink statefreq=(all) revmat=(all) shape=(all) pinvar=(all); prset applyto=(all) ratepr=variable; mcmcp ngen= 10000000 relburnin=yes burninfrac=0.1 printfreq=5000 samplefreq=5000 nchains=4 savebrlens=yes; mcmc; sumt; end; My script on cluster. #!/bin/bash #SBATCH --job-name=MrBayes #SBATCH --partition=compute #SBATCH --time=6-23 #SBATCH --mem-per-cpu=15G #SBATCH --ntasks=4 #SBATCH --cpus-per-task=8 #SBATCH --mail-type=BEGIN,FAIL,END export OMP_NUM_THREADS=$SLURM_CPUS_PER_TASK module load MrBayes.mpi/3.2.3 srun --mpi=pmi2 mb -i test_mrbayes
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