<p>I am using Mrbayes v 3.2.7 MPI version to infer phylogeny, and I set the ngeneration to 10,000,000, but it often stop at certain generation (usually far smaller than given generations). Even if I restart the analysis by invoking the <code>append=yes</code> , but it stops again.</p>
<p>Anyone have this problem? I would appreciate you for sharing your useful experience.</p>
<p>Best regards,</p>
<p>Yanpeng</p>
<p><strong>Version info</strong></p>
<pre><code>
Version:   3.2.7
Features:  SSE AVX FMA Beagle readline
Host type: x86_64-conda-linux-gnu (CPU: x86_64)
Compiler:  gnu 7.5.0
</code></pre>
<p><strong>Command line:</strong></p>
<pre><code>nohup mpirun -np 8 mb-mpi concatenate_phylipID.nex &lt; /dev/null &gt; /dev/null &amp;
</code></pre>
<p>Mrbayes block in nexus file:</p>
<pre><code>begin mrbayes;

    outgroup t1;

    charset Subset1 = 1-373 1953-2032;
    charset Subset2 = 374-531;
    charset Subset3 = 532-677 1583-1618;
    charset Subset4 = 678-1442;
    charset Subset5 = 1443-1582 1619-1725;
    charset Subset6 = 1726-1802 1803-1952;
    charset Subset7 = 2033-2661;

    partition PartitionFinder = 7:Subset1, Subset2, Subset3, Subset4, Subset5, Subset6, Subset7;
    set partition=PartitionFinder;

    lset applyto=(1) nst=6 rates=invgamma;
    lset applyto=(2) nst=6 rates=invgamma;
    prset applyto=(2) statefreqpr=fixed(equal);
    lset applyto=(3) nst=6 rates=invgamma;
    lset applyto=(4) nst=6 rates=invgamma;
    lset applyto=(5) nst=6 rates=invgamma;
    lset applyto=(6) nst=6 rates=gamma;
    lset applyto=(7) nst=6 rates=invgamma;

    prset applyto=(all) ratepr=variable;
    unlink statefreq=(all) revmat=(all) shape=(all) pinvar=(all) tratio=(all);
    mcmc nchains = 4 ngen = 10000000 samplefreq = 10000 printfreq = 10000 diagnfreq = 10000;
    sump;
    sumt;
    quit;
end;
</code></pre>

CC BY-SA 4.0
2021-03-10T11:30:01.210Z
How are you deciding it has stopped prior to 10,000,000 generations? Is it by counting the number of samples?
NatWH
CC BY-SA 4.0
2021-03-10T13:36:20.693Z
Check the log file,  It tells you how many generations have been done.
YP CHEN
CC BY-SA 4.0
2021-03-10T14:06:09.343Z
Have you tried running it in a screen or similar to see if it is something weird with nohup?
NatWH
CC BY-SA 4.0
2021-03-12T01:52:56.137Z
I prefer running prpgroms background if the analysis will take a long time. I think you are right. Ever I run it in PC five days, it works. Thanks.
YP CHEN
<phylogenetics><phylogeny>
Mrbayes stop at certain generation without error
# Mrbayes stop at certain generation without error

(Asked by: username_0 on 2021-03-09)

I am using Mrbayes v 3.2.7 MPI version to infer phylogeny, and I set the ngeneration to 10,000,000, but it often stop at certain generation (usually far smaller than given generations). Even if I restart the analysis by invoking the append=yes , but it stops again.
Anyone have this problem? I would appreciate you for sharing your useful experience.
Best regards,
Yanpeng
Version info

Version:   3.2.7
Features:  SSE AVX FMA Beagle readline
Host type: x86_64-conda-linux-gnu (CPU: x86_64)
Compiler:  gnu 7.5.0

Command line:
nohup mpirun -np 8 mb-mpi concatenate_phylipID.nex < /dev/null > /dev/null &

Mrbayes block in nexus file:
begin mrbayes;

    outgroup t1;

    charset Subset1 = 1-373 1953-2032;
    charset Subset2 = 374-531;
    charset Subset3 = 532-677 1583-1618;
    charset Subset4 = 678-1442;
    charset Subset5 = 1443-1582 1619-1725;
    charset Subset6 = 1726-1802 1803-1952;
    charset Subset7 = 2033-2661;

    partition PartitionFinder = 7:Subset1, Subset2, Subset3, Subset4, Subset5, Subset6, Subset7;
    set partition=PartitionFinder;

    lset applyto=(1) nst=6 rates=invgamma;
    lset applyto=(2) nst=6 rates=invgamma;
    prset applyto=(2) statefreqpr=fixed(equal);
    lset applyto=(3) nst=6 rates=invgamma;
    lset applyto=(4) nst=6 rates=invgamma;
    lset applyto=(5) nst=6 rates=invgamma;
    lset applyto=(6) nst=6 rates=gamma;
    lset applyto=(7) nst=6 rates=invgamma;

    prset applyto=(all) ratepr=variable;
    unlink statefreq=(all) revmat=(all) shape=(all) pinvar=(all) tratio=(all);
    mcmc nchains = 4 ngen = 10000000 samplefreq = 10000 printfreq = 10000 diagnfreq = 10000;
    sump;
    sumt;
    quit;
end;

**Tags:** phylogenetics, phylogeny
> **Comments:**
> **username_1**: How are you deciding it has stopped prior to 10,000,000 generations? Is it by counting the number of samples?  
> **username_0**: Check the log file,  It tells you how many generations have been done.  
> **username_1**: Have you tried running it in a screen or similar to see if it is something weird with nohup?  
> **username_0**: I prefer running prpgroms background if the analysis will take a long time. I think you are right. Ever I run it in PC five days, it works. Thanks.  

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## 0 answers

