Problem exporting HDF5 file to VCF in 5.2.11

[ch...@cornell.edu]

Hi,

I get the following error when trying to convert an HDF5 file to a VCF file using the GUI:

[Thread-1489] INFO net.maizegenetics.tassel.TasselLogging - Tassel Version: 5.2.11  Date: June 4, 2015

[Thread-1489] INFO net.maizegenetics.tassel.TasselLogging - Max Available Memory Reported by JVM: 25486 MB

[Thread-1489] INFO net.maizegenetics.tassel.TasselLogging - Java Version: 1.8.0_45

[Thread-1489] INFO net.maizegenetics.tassel.TasselLogging - OS: Linux

[AWT-EventQueue-0] INFO net.maizegenetics.tassel.DataTreePanel - initSelectionListener: node type: class net.maizegenetics.dna.snp.FilterGenotypeTable

[AWT-EventQueue-0] INFO net.maizegenetics.tassel.DataTreePanel - initSelectionListener: node type: class net.maizegenetics.dna.snp.CoreGenotypeTable

java.lang.ArrayIndexOutOfBoundsException

java.lang.IllegalArgumentException: Error writing VCF file: /home/Spring_2015/Genomic_Selection/TASSEL_Bowtie2_GBS_GS1_GS_2/vcf/test.vcf: null

at net.maizegenetics.dna.snp.ExportUtils.writeToVCF(ExportUtils.java:370)

at net.maizegenetics.analysis.data.ExportPlugin.performFunctionForAlignment(ExportPlugin.java:339)

at net.maizegenetics.analysis.data.ExportPlugin.performFunction(ExportPlugin.java:87)

at net.maizegenetics.plugindef.AbstractPlugin.dataSetReturned(AbstractPlugin.java:1481)

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

I am able to export the same HDF5 file to a VCF in version 5.2.10.

Chris 

[idalia claudia rojas barrera]

Hi Cris,

I have troubles when I convert from HDF5 to VCF, and try again to open the VCF file in TASSEL. I get the error:

"Allele ID larger than number of alleles"

Do you solved your problem? I see that no one answered your question in spite, HDF5 has many bugs.

Thanks,

Idalia

[Todd Yoder]

Hey Guys-- any luck with the HDF5 -> VCF conversion? Thanks!!

-Todd

[Terry Casstevens]

That should work. Please follow these instructions if you are having problems.

https://bitbucket.org/tasseladmin/tassel-5-source/wiki/docs/ReportingTassel5Issues.pdf

Best,

Terry

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