Body: <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>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2021-03-10T11:30:01.210Z
Comments.Text: How are you deciding it has stopped prior to 10,000,000 generations? Is it by counting the number of samples?
Comments.UserDisplayName: NatWH
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2021-03-10T13:36:20.693Z
Comments.Text: Check the log file,  It tells you how many generations have been done.
Comments.UserDisplayName: YP CHEN
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2021-03-10T14:06:09.343Z
Comments.Text: Have you tried running it in a screen or similar to see if it is something weird with nohup?
Comments.UserDisplayName: NatWH
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2021-03-12T01:52:56.137Z
Comments.Text: 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.
Comments.UserDisplayName: YP CHEN
Tags: <phylogenetics><phylogeny>
Title: Mrbayes stop at certain generation without error
ThreadText: # 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.  
  
  ---
  
  ## 0 answers
  
  