Tassel can't sort/load vcf file

[Tamara Miller]

I have the newest version of TASSEL and have followed directions in the manual for loading a sorted vcf file. However, TASSEL gives an error. 

[main] INFO net.maizegenetics.tassel.TasselLogging - Tassel Version: 5.2.49  Date: October 4, 2018

[main] INFO net.maizegenetics.tassel.TasselLogging - Max Available Memory Reported by JVM: 3598 MB

[main] INFO net.maizegenetics.tassel.TasselLogging - Java Version: 1.8.0_121

[main] INFO net.maizegenetics.tassel.TasselLogging - OS: Windows 10

[main] INFO net.maizegenetics.tassel.TasselLogging - Number of Processors: 4

[Thread-5] INFO net.maizegenetics.plugindef.AbstractPlugin - Starting net.maizegenetics.analysis.data.SortGenotypeFilePlugin: time: Oct 8, 2018 14:12:58

[Thread-5] INFO net.maizegenetics.plugindef.AbstractPlugin - 

SortGenotypeFilePlugin Parameters

inputFile: C:\Users\Tamaram\Documents\Publications\PvTFL1y2018\Data\genotyping\Chr01_PvTFL1y.vcf

outputFile: C:\Users\Tamaram\Documents\Publications\PvTFL1y2018\Data\genotyping\Chr01

fileType: VCF

Err Site Number:0

Err Site Number:0

[Thread-5] INFO net.maizegenetics.plugindef.AbstractPlugin - net.maizegenetics.analysis.data.SortGenotypeFilePlugin  Citation: Bradbury PJ, Zhang Z, Kroon DE, Casstevens TM, Ramdoss Y, Buckler ES. (2007) TASSEL: Software for association mapping of complex traits in diverse samples. Bioinformatics 23:2633-2635.

[Thread-6] INFO net.maizegenetics.plugindef.AbstractPlugin - Starting net.maizegenetics.analysis.data.FileLoadPlugin: time: Oct 8, 2018 14:13:55

[Thread-6] INFO net.maizegenetics.plugindef.AbstractPlugin - 

FileLoadPlugin Parameters

format: VCF

sortPositions: true

keepDepth: true

[Thread-6] INFO net.maizegenetics.analysis.data.FileLoadPlugin - Start Loading File: C:\Users\Tamaram\Documents\Publications\PvTFL1y2018\Data\genotyping\Chr01_PvTFL1y.vcf time: Oct 8, 2018 14:14:6

Err Site Number:0

Err Site Number:0

[Thread-7] INFO net.maizegenetics.plugindef.AbstractPlugin - Starting net.maizegenetics.analysis.data.FileLoadPlugin: time: Oct 8, 2018 14:15:47

[Thread-7] INFO net.maizegenetics.plugindef.AbstractPlugin - 

FileLoadPlugin Parameters

format: VCF

sortPositions: true

keepDepth: true

[Thread-7] INFO net.maizegenetics.analysis.data.FileLoadPlugin - Start Loading File: C:\Users\Tamaram\Documents\Publications\PvTFL1y2018\Data\genotyping\Chr01_PvTFL1y.vcf time: Oct 8, 2018 14:15:54

Err Site Number:0

Err Site Number:0

[Thread-8] INFO net.maizegenetics.plugindef.AbstractPlugin - Starting net.maizegenetics.analysis.data.FileLoadPlugin: time: Oct 8, 2018 14:18:17

[Thread-8] INFO net.maizegenetics.plugindef.AbstractPlugin - 

FileLoadPlugin Parameters

format: VCF

sortPositions: true

keepDepth: true

[Thread-8] INFO net.maizegenetics.analysis.data.FileLoadPlugin - Start Loading File: C:\Users\Tamaram\Documents\Publications\PvTFL1y2018\Data\genotyping\Chr01_PvTFL1y.vcf time: Oct 8, 2018 14:18:39

Err Site Number:0

Err Site Number:0

[AWT-EventQueue-0] INFO net.maizegenetics.tassel.DataTreePanel - initSelectionListener: node type: class java.lang.String

[Thread-9] INFO net.maizegenetics.plugindef.AbstractPlugin - Starting net.maizegenetics.analysis.data.SortGenotypeFilePlugin: time: Oct 8, 2018 14:18:47

[Thread-9] INFO net.maizegenetics.plugindef.AbstractPlugin - 

SortGenotypeFilePlugin Parameters

inputFile: C:\Users\Tamaram\Documents\Publications\PvTFL1y2018\Data\genotyping\Chr01_PvTFL1y.vcf

outputFile: C:\Users\Tamaram\Documents\Publications\PvTFL1y2018\Data\genotyping\Chr01

fileType: VCF

Err Site Number:0

Err Site Number:0

[Thread-10] INFO net.maizegenetics.plugindef.AbstractPlugin - Starting net.maizegenetics.analysis.data.FileLoadPlugin: time: Oct 8, 2018 14:18:57

[Thread-10] INFO net.maizegenetics.plugindef.AbstractPlugin - 

FileLoadPlugin Parameters

format: Make Best Guess

sortPositions: true

keepDepth: true

[Thread-10] INFO net.maizegenetics.analysis.data.FileLoadPlugin - Start Loading File: C:\Users\Tamaram\Documents\Publications\PvTFL1y2018\Data\genotyping\Chr01_PvTFL1y.vcf time: Oct 8, 2018 14:19:14

[Thread-10] INFO net.maizegenetics.analysis.data.FileLoadPlugin - guessAtUnknowns: type: VCF

Err Site Number:0

Err Site Number:0

[Terry Casstevens]

Did you check the "Debug" box in the logging dialog?

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[Tamara Miller]

Yes.

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[Tamara Miller]

The error when trying to "load as" a vcf file with sorting option checked:

Error: java.lang.ArrayIndexOutOfBoundsException

[Terry Casstevens]

This doesn't have the stack trace I need to diagnose. Normally the
debug message would have that.

Is the file small enough for you to send it to me privately?

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[Tamara Miller]

Here's the vcf and the TASSEL log.

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[Terry Casstevens]

You have quotation marks around a lot of fields. Those quotation
marks shouldn't be there.

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[Tamara Miller]

That is definitely not the case when I open the file....

I'm honestly not sure what to do at this point. 

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[Terry Casstevens]

See screenshot attached showing file you sent

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