Problems with BEASTvntr

[OlivierD]

Hello,

I might need some help with BEASTvntr... I am trying to run BEASTvntr with microsatellite data from fish. So, following the example in the Readme on github and Arjun's indications in this post, I split the data in 2 allele-files. 

However, when I load each file as "Repeats, single partition" into BEAUTI, I need to load them twice before they show up in the Partition Tab. And, more troublesome, I then get the following error in BEAST :

Error 110 parsing the xml input file

validate and intialize error: initAndValidate() failed! 97

Error detected about here:

  <beast>
      <run id='mcmc' spec='MCMC'>
          <distribution id='posterior' spec='util.CompoundDistribution'>
              <distribution id='likelihood' spec='util.CompoundDistribution'>
                  <distribution id='treeLikelihood.ysat_tinn_1' spec='ThreadedTreeLikelihood'>

java.lang.ProcessImpl$ProcessPipeInputStream@6e6c3152

I don't really understand what is wrong or how to correct that problem here...

If I use "Repeats, multiple partitions" instead, for each file I get the following message when loading into BEAUTI :

Loading failed : two sequences of different length found 2 != 3

Yet, the files seem to load ok and show up in the partitions tab straight away. And after setting the model, BEAST starts sampling as expected... (although very very slowly and showing the following : WARNING: Frequencies has wrong size. Expected 74, but got 4. )

I am not really sure what I am doing wrong or what is going on... And I don't know how I should proceed here, so any help with this will be greatly appreciated! 

Olivier

[Carlo Pacioni]

Hi Olivier,

I'm not sure what's triggering the error, but if you want, you can send me (usign carlo....@gmail.com) your input file and I can have a look if I can replicate the error you are receiving and if so, whether I can understand what's happening.

cheers,

carlo

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[Remco Bouckaert]

> there are two problems. One is that when there are missing data ('?') currently vntr package doesn't correctly parse these. Remco had already a look at this and sent a pull request with a fix, but these changes are not yet implemented in the current release.

With the release of v0.1.3 of BEASTvntr, this should now be fixed. Let me know if there still is a problem loading alignments with missing data.

Cheers,

Remco

[ptes...@gmail.com]

Hi, I've just tested the following input using version 0.2.0, and missing data (?) is definitely still a problem. If the ? are replaced with numbers, it works. Is there some other strategy to deal with this?

Thanks

Peter

TZW150a,9,10,21,14,10,13,7,11,19,14,10,19,10,?,11,?,15,?,12,17,17,19,15
TZW150b,9,10,21,14,12,16,7,12,19,9,9,20,10,?,12,?,16,?,12,17,17,19,19
TZW151a,?,10,21,15,?,16,7,11,15,?,9,?,9,?,?,12,14,?,12,?,17,17,19
TZW151b,?,11,21,15,?,12,7,11,15,?,8,?,9,?,?,12,15,?,12,?,17,19,19
DUR11023a,10,9,21,12,11,?,7,11,16,14,9,?,9,20,12,11,12,15,12,15,15,16,19
DUR11023b,8,15,21,15,11,?,7,11,16,9,9,?,9,21,12,11,14,15,13,15,15,19,19
UMG10015a,8,?,?,?,9,18,14,11,19,9,9,23,?,16,?,?,12,18,13,?,15,16,?
UMG10015b,7,?,?,?,9,18,7,12,22,9,9,23,?,18,?,?,14,18,13,?,15,16,?
RB05144a,8,9,21,12,11,?,7,11,16,9,9,18,10,18,10,10,12,26,11,?,?,13,19
RB05144b,8,15,21,15,10,?,7,12,19,13,9,20,8,19,10,11,14,25,13,?,?,19,19
UMD16002a,8,9,21,11,11,15,14,11,18,7,9,20,9,17,12,12,14,17,?,?,?,16,15
UMD16002b,9,9,21,11,11,18,7,11,18,9,9,20,9,21,12,12,14,21,?,?,?,16,19
DUR08754a,8,9,21,12,11,14,7,11,?,9,9,20,9,?,?,?,12,21,12,16,17,17,19
DUR08754b,8,11,21,15,11,18,7,11,?,13,9,20,9,?,?,?,14,21,12,16,17,17,19
MG16001a,10,9,19,13,11,15,7,10,16,9,9,?,9,21,12,12,12,?,12,?,19,16,19
MG16001b,8,10,19,15,11,18,7,12,19,13,9,?,9,21,12,12,14,?,12,?,19,16,19
RB10012a,8,9,21,?,10,15,13,10,16,9,9,18,9,?,12,?,?,?,8,16,15,19,19
RB10012b,8,9,21,?,10,18,7,12,19,13,9,18,9,?,12,?,?,?,8,16,15,19,19
DUR06575a,8,9,12,14,11,?,14,12,19,9,9,22,9,?,12,12,13,21,12,?,?,16,19
DUR06575b,8,9,20,14,11,?,7,12,19,13,9,18,9,?,12,12,15,21,12,?,?,19,19
UMH04228a,9,9,?,14,11,15,14,11,19,13,10,?,10,?,12,11,12,21,8,?,14,16,19
UMH04228b,9,9,?,14,11,17,7,11,22,13,10,?,10,?,12,11,14,21,8,?,14,17,19
DUR04483a,10,9,21,12,11,?,7,11,19,9,9,?,9,19,12,?,12,18,12,17,15,16,19
DUR04483b,11,9,21,12,10,?,7,11,19,13,9,?,9,20,12,?,12,18,13,17,15,19,19
RB17003a,9,9,12,15,?,?,14,11,18,14,9,19,10,16,12,?,14,14,12,15,15,19,19
RB17003b,9,15,12,15,?,?,7,11,18,9,9,19,9,16,12,?,14,14,12,15,15,19,19
RB19010a,8,?,21,14,10,13,7,11,?,?,9,?,?,19,11,12,12,22,12,16,?,16,19
RB19010b,8,?,21,14,10,13,7,11,?,?,9,?,?,19,11,12,12,22,12,16,?,19,19
DUR19006a,8,9,?,12,11,13,14,11,18,9,9,19,10,16,12,12,14,15,12,17,15,16,19
DUR19006b,8,14,?,12,11,16,7,10,18,13,9,19,8,20,12,11,14,21,12,15,15,13,19
DUR08716a,10,9,21,12,11,?,14,11,?,9,9,?,10,20,?,11,14,26,11,16,?,16,19
DUR08716b,10,15,21,12,10,?,7,12,?,13,9,?,10,21,?,11,14,26,11,16,?,17,19
ZIN05067a,10,9,21,12,11,?,7,11,16,9,9,20,?,23,11,12,14,?,?,16,?,19,19
ZIN05067b,10,9,21,12,9,?,7,11,16,9,8,20,?,23,11,11,14,?,?,16,?,19,19
RB21004a,9,9,21,14,11,13,7,11,19,13,9,19,?,?,12,11,14,?,11,?,15,19,19
RB21004b,10,9,21,14,10,11,7,11,19,13,9,20,?,?,12,11,15,?,11,?,15,19,19
DUR06551a,8,9,19,12,11,?,14,11,19,9,9,?,10,18,12,12,14,20,12,15,15,16,19
DUR06551b,7,9,21,12,11,?,7,10,19,13,9,?,10,21,12,12,14,20,8,15,15,19,19
DUR08730a,?,9,12,?,11,13,14,11,16,9,9,14,?,20,12,?,14,?,8,?,15,19,19
DUR08730b,?,11,12,?,11,16,7,8,16,9,9,14,?,20,12,?,14,?,8,?,14,19,19
DUR15050a,10,9,21,12,11,16,14,11,16,14,9,?,9,16,12,?,12,?,12,17,17,16,19
DUR15050b,8,9,21,15,11,11,7,11,17,9,9,?,9,19,12,?,15,?,8,17,15,19,19
TRA20001a,10,9,21,11,11,?,7,11,19,9,9,19,9,17,?,12,12,22,12,16,?,16,19
TRA20001b,8,9,21,15,10,?,7,11,22,13,9,19,9,17,?,12,14,21,12,16,?,16,19
WAR15006a,6,9,21,?,11,18,7,12,16,9,9,19,10,16,?,12,14,19,12,15,15,16,?
WAR15006b,8,9,20,?,10,17,7,12,19,13,9,19,8,14,?,12,14,19,12,16,15,19,?