SNAPPER Thread Java error

[littlelimia]

Hi all, I am running Speedemon-SNAPPER (-v 1.1.5). It starts running but after a few minutes the process comes to a halt and I get the following error

35 taxa
0 sites
2 patterns
RiviereCavaillon: 0 4
Exception in thread "Thread-4" java.lang.StackOverflowError
at java.base/java.lang.Exception.(Unknown Source)
at java.base/java.io.IOException.(Unknown Source)
at java.base/java.io.FileOutputStream.writeBytes(Native Method)
at java.base/java.io.FileOutputStream.write(Unknown Source)
at java.base/java.io.BufferedOutputStream.flushBuffer(Unknown Source)
at java.base/java.io.BufferedOutputStream.write(Unknown Source)
at java.base/java.io.PrintStream.write(Unknown Source)
at beastfx.app.util.Console$1.write(Unknown Source)
at java.base/java.io.PrintStream.write(Unknown Source)
at java.base/sun.nio.cs.StreamEncoder.writeBytes(Unknown Source)
at java.base/sun.nio.cs.StreamEncoder.implFlushBuffer(Unknown Source)
at java.base/sun.nio.cs.StreamEncoder.flushBuffer(Unknown Source)
at java.base/java.io.OutputStreamWriter.flushBuffer(Unknown Source)
at java.base/java.io.PrintStream.writeln(Unknown Source)
at java.base/java.io.PrintStream.println(Unknown Source)
at snapper.FilteredAlignment.calcPatterns(Unknown Source)
at snapper.FilteredAlignment.initAndValidate(Unknown Source)
at beast.base.core.BEASTInterface.initByName(Unknown Source)
at snapper.SnapperTreeLikelihood.initAndValidate(Unknown Source)
at beast.base.core.BEASTInterface.initByName(Unknown Source)
at snapper.SnapperTreeLikelihood.initAndValidate(Unknown Source)
at beast.base.core.BEASTInterface.initByName(Unknown Source)

Any ideas?

Thank you!

[rbouckaert]

This suggests more stack memory is required to run this particular dataset. Java needs to be told beforehand what the maximum allowable stack size is.

https://www.beast2.org/increasing-memory-usage/ describes how to increase stack size by setting a new upper limit.