java.lang.NumberFormatException: For input string: "C" Error - SNAPP v2.0.1

[George Pacheco]

Dear all,

I have been trying to run SNAPP v2.0.1 using GBS data. I have created the .xlm (attached) file using Beauti v2 having as input a .nxs file. I just follow the manual when doing so, but when I try to run it I get the following error:

java.lang.NumberFormatException: For input string: "C"

at java.lang.NumberFormatException.forInputString(Unknown Source)

at java.lang.Integer.parseInt(Unknown Source)

at java.lang.Integer.parseInt(Unknown Source)

at beast.evolution.datatype.DataType$Base.string2state(Unknown Source)

at beast.evolution.alignment.Sequence.getSequence(Unknown Source)

at snap.SNPSequence.getSequence(Unknown Source)

at beast.evolution.alignment.Alignment.initAndValidate(Unknown Source)

at snap.Data.initAndValidate(Unknown Source)

at beast.util.XMLParser.initPlugins(Unknown Source)

at beast.util.XMLParser.parse(Unknown Source)

at beast.util.XMLParser.parseFile(Unknown Source)

at beast.app.BeastMCMC.parseArgs(Unknown Source)

at beast.app.beastapp.BeastMain.main(Unknown Source)

Error 110 parsing the xml input file

validate and intialize error: For input string: "C"

Error detected about here:

  <beast>

      <run id='mcmc' spec='snap.MCMC'>

          <stateDistribution id='prior' spec='util.CompoundDistribution'>

              <distribution id='snapprior.FCN' spec='snap.likelihood.SnAPPrior'>

                  <tree id='Tree.FCN' spec='beast.util.ClusterTree'>

                      <taxa id='snap.FCN' spec='snap.Data'>

Any help would be very appreciated.
Best, George.

[Remco Bouckaert]

Hi George,

SNAPP assumes that the input file is binary. It looks like your data is nucleotide data, so it is not binary.

There is a bit more information about the file format here:

https://groups.google.com/forum/#!searchin/beast-users/snapp$20binary

Hope this helps,

Remco