Tassel is failing to sort a vcf file generated from GATK HaplotypeCaller

[John Baison]

Good Day,

I have generated a vcf file that i want to use, however i am getting the following error message and its failing to write out the sorted file. I have attached a link to the vcf file that i am using.

https://drive.google.com/file/d/0B1-HqyGsHwqFTnVudlR5c2NZSWM/view?usp=sharing

Tassel Pipeline Arguments: -SortGenotypeFilePlugin -inputFile Z4006.biallelic.recode.vcf -outputFile Z4006.biallelic.recode.vcf.sorted
[main] INFO net.maizegenetics.tassel.TasselLogging - Tassel Version: 5.2.17  Date: November 12, 2015
[main] INFO net.maizegenetics.tassel.TasselLogging - Max Available Memory Reported by JVM: 910222 MB
[main] INFO net.maizegenetics.tassel.TasselLogging - Java Version: 1.8.0_40
[main] INFO net.maizegenetics.tassel.TasselLogging - OS: Linux
[main] INFO net.maizegenetics.tassel.TasselLogging - Number of Processors: 16
[main] INFO net.maizegenetics.pipeline.TasselPipeline - Tassel Pipeline Arguments: [-fork1, -SortGenotypeFilePlugin, -inputFile, Z4006.biallelic.recode.vcf, -outputFile, Z4006.biallelic.recode.vcf.sorted, -runfork1]
net.maizegenetics.analysis.data.SortGenotypeFilePlugin
[pool-1-thread-1] INFO net.maizegenetics.plugindef.AbstractPlugin - Starting net.maizegenetics.analysis.data.SortGenotypeFilePlugin: time: May 21, 2017 20:22:28
[pool-1-thread-1] INFO net.maizegenetics.plugindef.AbstractPlugin -
SortGenotypeFilePlugin Parameters
inputFile: Z4006.biallelic.recode.vcf
outputFile: Z4006.biallelic.recode.vcf.sorted
fileType: VCF

[pool-1-thread-1] ERROR net.maizegenetics.dna.map.PositionListBuilder - validateOrdering: Position    Chr:MA_10    Pos:649    Name:SMA_10_649    Variants:G/T    MAF:NaN    Ref:G and Position    Chr:MA_5    Pos:87120    Name:SMA_5_87120    Variants:A/G    MAF:NaN    Ref:A out of order.
BuilderFromVCF data timing 62.7490s
java.lang.ArrayIndexOutOfBoundsException: 0
    at net.maizegenetics.dna.snp.ExportUtils.writeToVCF(ExportUtils.java:274)
    at net.maizegenetics.analysis.data.SortGenotypeFilePlugin.processData(SortGenotypeFilePlugin.java:61)
    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] ERROR net.maizegenetics.plugindef.AbstractPlugin - Error writing VCF file: Z4006.biallelic.recode.vcf.sorted.vcf: 0

May you please try to help me out.

Regards,

John.

[Terry Casstevens]

Please update to the latest build of TASSEL

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