Error writing VCF file - ProductionSNPCallerPluginV2

[Elad Oren]

Hello,

I see this error was last reported a few months ago, would like to open a new thread as this is happening to me using the ProductionSNPCallerPluginV2.

I can use the plugin to create hdf5 file but when using the pipeline for vcf file i get the above error.

the command I'm using is:

run_pipeline.pl -Xms100G -Xmx200G -fork1 -ProductionSNPCallerPluginV2 -db /storage2/Projects/Amit_Gur/Mel180_GBS/Mel180_GBS.db -e ApeKI -i /storage2/Projects/Amit_Gur/Mel180_GBS/RAW -k /storage2/Projects/Amit_Gur/Mel180_GBS/RAW/C9AT7ANXX_3_fastq.gz.keys.txt -kmerLength 64 -o /storage2/Projects/Amit_Gur/Mel180_GBS/Mel180_GBS_1.vcf -ko true -endPlugin -runfork1

(note this happens with -ko false as well)

the error output is 

Finished processing batch 1

java.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)

        at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:511)

        at java.util.concurrent.FutureTask.run(FutureTask.java:266)

        at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)

        at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)

        at java.lang.Thread.run(Thread.java:745)

[pool-1-thread-1] INFO net.maizegenetics.plugindef.AbstractPlugin -

When trying to export the hdf5 to vcf from within the program i get the same error 

[AWT-EventQueue-0] INFO net.maizegenetics.tassel.TasselLogging - Tassel Version: 5.2.25  Date: April 28, 2016

[AWT-EventQueue-0] INFO net.maizegenetics.tassel.TasselLogging - Max Available Memory Reported by JVM: 14471 MB

[AWT-EventQueue-0] INFO net.maizegenetics.tassel.TasselLogging - Java Version: 1.8.0_31

[AWT-EventQueue-0] INFO net.maizegenetics.tassel.TasselLogging - OS: Windows 7

[AWT-EventQueue-0] INFO net.maizegenetics.tassel.TasselLogging - Number of Processors: 4

java.lang.ArrayIndexOutOfBoundsException: 1

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

at net.maizegenetics.analysis.data.ExportPlugin.performFunctionForAlignment(ExportPlugin.java:353)

at net.maizegenetics.analysis.data.ExportPlugin.performFunction(ExportPlugin.java:90)

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

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

java.lang.IllegalArgumentException: Error writing VCF file: C:\Users\aro\Desktop\Elad\Mel180_GBS\Mel180_GBS_3.vcf: 1

at net.maizegenetics.dna.snp.ExportUtils.writeToVCF(ExportUtils.java:677)

at net.maizegenetics.analysis.data.ExportPlugin.performFunctionForAlignment(ExportPlugin.java:353)

at net.maizegenetics.analysis.data.ExportPlugin.performFunction(ExportPlugin.java:90)

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

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

Thanks for your help

Elad