Closed nylander closed 5 years ago
kusalananda
commented
6 years ago This one is a bit difficult to debug without knowing exactly what the run looked like. I can not reproduce this on OpenBSD using mb -i primates.nex and mcmc in the interactive session.
nylander
commented
5 years ago More details regarding this behavior now received (below). This seems to affect (at least) the compiled windows version for 3.2.6 on Win 10. This is a "won't fix" until new windows binaries for 3.2.7 can be tested.
"I am using Windows 10, installed MrBayes 3.2.6. and followed the manual MrBayes 3.2.:
execute primates.nex
lset nst=6
lset rates=invgamma
mcmcp diagnfreq=1000
mcmcp samplefreq=100
mcmcp printfreq=100
mcmc
MrBayes v3.2.6 x86
(Bayesian Analysis of Phylogeny)
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 > exe primates.nex
Executing file "primates.nex"
DOS line termination
Longest line length = 920
Parsing file
Expecting NEXUS formatted file
Reading data block
Allocated taxon set
Allocated matrix
Defining new matrix with 12 taxa and 898 characters
Data is Dna
Data matrix is not interleaved
Gaps coded as -
Taxon 1 -> Tarsius_syrichta
Taxon 2 -> Lemur_catta
Taxon 3 -> Homo_sapiens
Taxon 4 -> Pan
Taxon 5 -> Gorilla
Taxon 6 -> Pongo
Taxon 7 -> Hylobates
Taxon 8 -> Macaca_fuscata
Taxon 9 -> M_mulatta
Taxon 10 -> M_fascicularis
Taxon 11 -> M_sylvanus
Taxon 12 -> Saimiri_sciureus
Successfully read matrix
Setting default partition (does not divide up characters)
Setting model defaults
Seed (for generating default start values) = 1552911463
Setting output file names to "primates.nex.run<i>.<p|t>"
Exiting data block
Reached end of file
MrBayes > lset nst=6
Setting Nst to 6
Successfully set likelihood model parameters
MrBayes > lset rates=invgamma
Setting Rates to Invgamma
Successfully set likelihood model parameters
MrBayes > mcmcp diagnfreq=1000
Setting diagnosing frequency to 1000
Successfully set chain parameters
MrBayes > mcmcp samplefreq=100
Setting sample frequency to 100
Successfully set chain parameters
MrBayes > mcmcp printfreq=100
Setting print frequency to 100
Successfully set chain parameters
MrBayes > mcmc
Running Markov chain
MCMC stamp = 6033037634
Seed = 125270998
Swapseed = 1552911463
Model settings:
Data not partitioned --
Datatype = DNA
Nucmodel = 4by4
Nst = 6
Substitution rates, expressed as proportions
of the rate sum, have a Dirichlet prior
(1.00,1.00,1.00,1.00,1.00,1.00)
Covarion = No
# States = 4
State frequencies have a Dirichlet prior
(1.00,1.00,1.00,1.00)
Rates = Invgamma
The distribution is approximated using 4 categories.
Likelihood summarized over all rate categories in each generation.
Shape parameter is exponentially
distributed with parameter (1.00).
Proportion of invariable sites is uniformly dist-
ributed on the interval (0.00,1.00).
Active parameters:
Parameters
---------------------
Revmat 1
Statefreq 2
Shape 3
Pinvar 4
Ratemultiplier 5
Topology 6
Brlens 7
---------------------
1 -- Parameter = Revmat
Type = Rates of reversible rate matrix
Prior = Dirichlet(1.00,1.00,1.00,1.00,1.00,1.00)
2 -- Parameter = Pi
Type = Stationary state frequencies
Prior = Dirichlet
3 -- Parameter = Alpha
Type = Shape of scaled gamma distribution of site rates
Prior = Exponential(1.00)
4 -- Parameter = Pinvar
Type = Proportion of invariable sites
Prior = Uniform(0.00,1.00)
5 -- Parameter = Ratemultiplier
Type = Partition-specific rate multiplier
Prior = Fixed(1.0)
6 -- Parameter = Tau
Type = Topology
Prior = All topologies equally probable a priori
Subparam. = V
7 -- Parameter = V
Type = Branch lengths
Prior = Unconstrained:GammaDir(1.0,0.1000,1.0,1.0)
The MCMC sampler will use the following moves:
With prob. Chain will use move
0.93 % Dirichlet(Revmat)
0.93 % Slider(Revmat)
0.93 % Dirichlet(Pi)
0.93 % Slider(Pi)
1.85 % Multiplier(Alpha)
1.85 % Slider(Pinvar)
9.26 % ExtSPR(Tau,V)
9.26 % ExtTBR(Tau,V)
9.26 % NNI(Tau,V)
9.26 % ParsSPR(Tau,V)
37.04 % Multiplier(V)
12.96 % Nodeslider(V)
5.56 % TLMultiplier(V)
Division 1 has 413 unique site patterns
Initializing conditional likelihoods
Using standard SSE likelihood calculator for division 1 (single-precision)
Initializing invariable-site conditional likelihoods
Initial log likelihoods and log prior probs for run 1:
Chain 1 -- -8643.988265 -- 42.620562
Chain 2 -- -8383.035247 -- 42.620562
Chain 3 -- -9054.857928 -- 42.620562
Chain 4 -- -8757.217052 -- 42.620562
Initial log likelihoods and log prior probs for run 2:
Chain 1 -- -8752.756505 -- 42.620562
Chain 2 -- -9161.226472 -- 42.620562
Chain 3 -- -9070.270902 -- 42.620562
Chain 4 -- -8759.113541 -- 42.620562
Could not open file "primates.nex.mcmc"
Error preparing print files
Error in command "Mcmc"I tried this now on a machine running 64-bit MS Windows 10 Enterprise but could not reproduce the error (downloaded and used binaries in https://github.com/NBISweden/MrBayes/releases/download/v3.2.6/MrBayes-3.2.6_WIN32_x64.zip).
I suspect that users may have an issue with write permissions in the directory where the output files are supposed to end up.
Closing this for now.
Transferred from https://sourceforge.net/p/mrbayes/bugs/1655/
Created: 2018-01-03 Creator: Milos Macholan
I have downloaded and installed MrBayes 3.2.6 in C (x64-based processor, Windows 10 OS) and tried to analyse the "primates.nex" using the default values. After entering the "mcmc" command the following error message appeared: Could not open file "primates.nex.mcmc" Error preparing print files Error in command "Mcmc" Can you tell me what´s wrong? The older 3.1 version works without problems. Thank you