Can't Export Hapmap Union

[Crawford Drury]

Hi All,

I've got a bunch of hapmap files (produced by TASSEL 4 pipeline) that I need to join together before starting my analysis. I've successfully loaded them and completed the Union, but every time I try to export, it gives me a 'null' error:

"Error writing hapmap file: /Users/xxx/xxx/xx: 

null"

The export actually does begin to write the output file, but seems to abort after recording the position of the first loci (i.e. it writes all the headers and starts at the first loci before failing)

At first I thought this was a genotype sorting issue, so I tested a handfull of the hapmap files after sorting individually and doing the union and got the same error. It also appears to be specific to exporting hapmap, exporting a vcf works. Additionally, I've tried intersect and i can't export that hapmap product either.

Any help would be appreciated...

Thank you,

Ford

TASSEL 5 Version 20160204, Mac OS 10.10.3

[Terry Casstevens]

Please follow these instructions to get more information.

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

Best,

Terry

> --
> You received this message because you are subscribed to the Google Groups
> "TASSEL - Trait Analysis by Association, Evolution and Linkage" group.
> To unsubscribe from this group and stop receiving emails from it, send an
> email to tassel+un...@googlegroups.com.
> To post to this group, send email to tas...@googlegroups.com.
> To view this discussion on the web visit
> https://groups.google.com/d/msgid/tassel/a1d41d7c-30b7-4a6e-ae24-3524e5c62f6d%40googlegroups.com.
> For more options, visit https://groups.google.com/d/optout.

[Crawford Drury]

Terry, thanks for the quick response.

Below is the log after I've loaded all the individual hapmaps:

[Thread-7] INFO net.maizegenetics.tassel.DataTreePanel - initSelectionListener: node type: class net.maizegenetics.dna.snp.CoreGenotypeTable

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

[Thread-8] INFO net.maizegenetics.tassel.DataTreePanel - initSelectionListener: node type: class net.maizegenetics.dna.snp.CombineGenotypeTable

[Thread-9] DEBUG net.maizegenetics.dna.snp.ExportUtils - null

java.lang.ArrayIndexOutOfBoundsException

at java.lang.System.arraycopy(Native Method)

at net.maizegenetics.dna.snp.CombineGenotypeTable.genotypeAllTaxa(CombineGenotypeTable.java:408)

at net.maizegenetics.dna.snp.ExportUtils.writeToHapmap(ExportUtils.java:142)

at net.maizegenetics.analysis.data.ExportPlugin.performFunctionForAlignment(ExportPlugin.java:319)

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 Hapmap file: /Users/admin/CRD_GBS/CRD_Union.hmp.txt: null

at net.maizegenetics.dna.snp.ExportUtils.writeToHapmap(ExportUtils.java:198)

at net.maizegenetics.analysis.data.ExportPlugin.performFunctionForAlignment(ExportPlugin.java:319)

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)

[Terry Casstevens]

I have fixed this problem, and it will be in the next build of Tassel
5. If you want a development build containing the fix, I can send you
the jar privately.

Thank you for bringing this to my attention,

Terry

> https://groups.google.com/d/msgid/tassel/e02dad9f-9659-450a-adb2-92bbbf6c77ed%40googlegroups.com.

[Crawford Drury]

Terry,

That would be awesome, thank you so much.

My email is cdr...@rsmas.miami.edu, let me know if you'd like to share it a different way?

-Ford