When running GLM, Error– Index:0, Size: 0

[nag...@oregonstate.edu]

I am new to using TASSEL 5 and would greatly appreciate some tips for getting past this error. Using the TASSEL 5 GUI, I loaded plink files (.ped and .map) and made a kinship matrix and found covariates for the genotypes, then used intersect-join for the covariates, phenotypes and genotype file. I selected both of these and then selected GLM from the analysis window. This produced a dialog box with the following error:

Index:0, Size: 0

The log shows:

[Thread-21] DEBUG net.maizegenetics.plugindef.AbstractPlugin - Index: 0, Size: 0

java.lang.IndexOutOfBoundsException: Index: 0, Size: 0

at java.util.ArrayList.rangeCheck(ArrayList.java:653)

at java.util.ArrayList.get(ArrayList.java:429)

at net.maizegenetics.analysis.association.FixedEffectLMPlugin.processData(FixedEffectLMPlugin.java:150)

at net.maizegenetics.plugindef.AbstractPlugin.performFunction(AbstractPlugin.java:109)

at net.maizegenetics.plugindef.AbstractPlugin.dataSetReturned(AbstractPlugin.java:1840)

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

Thanks,

Michael Nagle

[Peter Bradbury]

When running GLM, after you intersect-join covariates, phenotypes and genotype you should select only the resulting data set that represents that intersection. If that does not solve the problem then follow the instructions in "Reporting TASSEL 5 Issues" (https://bytebucket.org/tasseladmin/tassel-5-source/wiki/docs/ReportingTassel5Issues.pdf?rev=566febe627936329144254bac52efcefa5fe7489).

Peter

[nag...@oregonstate.edu]

I still get the "Index:0, Size: 0" error if I select only the instersect-join product of the genotype, phenotype and covariates, without selecting the kinship matrix.

I'm sorry but I thought I did follow the instructions in "Reporting TASSEL 5 issues". I thought I attached the correct part of the log in my previous message, but please let me know if I'm missing something.

Thanks,

Michael

[Peter Bradbury]

It would be helpful if you post the entire log since the problem that eventually generated the error may have happened earlier and some of the other log messages might indicate what that is. The log output you posted indicated that you had selected a phenotype data set that had not been joined to a genotype. Otherwise, the point in the code that threw the error would not have been reached.

Peter