Production SNP caller: Error writing VCF file with Tassel Version 5 (Build: April 28, 2016 Requires: Java 1.8) Mac OS or Windows

[Stéphanie BOCS ep. SIDIBE]

Hello,

When I try to run Production SNP caller from the GBSv2 menu of TASSEL 5.2.25 on my Mac OS X or from PC Windows I have an error and obtain a truncated VCF file (see details in logging_debug.txt attached file).

ava.lang.ArrayIndexOutOfBoundsException: 1

at net.maizegenetics.dna.snp.ExportUtils.writeToVCF(ExportUtils.java:650)

at net.maizegenetics.dna.snp.ExportUtils.writeToVCF(ExportUtils.java:216)

at net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2.processData(ProductionSNPCallerPluginV2.java:280)

at net.maizegenetics.plugindef.AbstractPlugin.performFunction(AbstractPlugin.java:110)

at net.maizegenetics.plugindef.AbstractPlugin.dataSetReturned(AbstractPlugin.java:1631)

at net.maizegenetics.plugindef.ThreadedPluginListener.run(ThreadedPluginListener.java:29)

If the problem comes from the new version 5.2.25 how can I obtain TASSEL_5_windows-x64.exe, TASSEL_5_windows.exe and TASSEL_5_macos.dmg for the older version 5.2.24 ?

Thanks,

Stéphanie

[Zack Miller]

Hello,  

This is a VCF Export bug that we are aware of and have fixed.  It will be working in the next version of TASSEL. 

Here is the guide to use older versions of TASSEL:

https://bytebucket.org/tasseladmin/tassel-5-source/wiki/docs/UpdatingTasselStandaloneUsingGit.pdf

If you revert back to 5.2.24 it should work properly.  If not try 5.2.23.

Please let us know if there are any additional problems.

Thanks,

Zack