Tassel can't sort/load vcf file
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Tamara Miller
Oct 8, 2018, 5:35:31 PM10/8/18
to TASSEL - Trait Analysis by Association, Evolution and Linkage
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
Oct 8, 2018, 5:42:14 PM10/8/18
to Tassel User Group
Did you check the "Debug" box in the logging dialog?
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Tamara Miller
Oct 8, 2018, 5:43:53 PM10/8/18
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Yes.
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Tamara Miller
Oct 8, 2018, 5:45:17 PM10/8/18
to tas...@googlegroups.com
The error when trying to "load as" a vcf file with sorting option checked:
Error: java.lang.ArrayIndexOutOfBoundsException
Terry Casstevens
Oct 8, 2018, 5:46:58 PM10/8/18
to Tassel User Group
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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debug message would have that.
Is the file small enough for you to send it to me privately?
Tamara Miller
Oct 8, 2018, 5:49:43 PM10/8/18
to tas...@googlegroups.com
Here's the vcf and the TASSEL log.
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Terry Casstevens
Oct 8, 2018, 6:17:38 PM10/8/18
to Tassel User Group
You have quotation marks around a lot of fields. Those quotation
marks shouldn't be there.
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marks shouldn't be there.
Tamara Miller
Oct 8, 2018, 6:30:49 PM10/8/18
to tas...@googlegroups.com
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
Oct 8, 2018, 6:37:00 PM10/8/18
to Tassel User Group
See screenshot attached showing file you sent
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