FILLIN chromosome break error

[amk...@truman.edu]

I'm trying to impute using a HapMap formatted genotype file. It has been sorted using the SortGenotypeFilePlugin. FILLIN quits with the following error

pool-1-thread-1] DEBUG net.maizegenetics.plugindef.AbstractPlugin - FilterGenotypeTable: init: start site: 1989 is larger than end site: 1988

java.lang.IllegalArgumentException: FilterGenotypeTable: init: start site: 1989 is larger than end site: 1988

at net.maizegenetics.dna.snp.FilterGenotypeTable.<init>(FilterGenotypeTable.java:214)

at net.maizegenetics.dna.snp.FilterGenotypeTable.getInstance(FilterGenotypeTable.java:455)

at net.maizegenetics.analysis.imputation.FILLINFindHaplotypesPlugin.createHaplotypeAlignment(FILLINFindHaplotypesPlugin.java:183)

at net.maizegenetics.analysis.imputation.FILLINFindHaplotypesPlugin.processData(FILLINFindHaplotypesPlugin.java:166)

at net.maizegenetics.plugindef.AbstractPlugin.performFunction(AbstractPlugin.java:110)

at net.maizegenetics.plugindef.AbstractPlugin.dataSetReturned(AbstractPlugin.java:1652)

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

at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:511)

at java.util.concurrent.FutureTask.run(FutureTask.java:266)

at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)

at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)

at java.lang.Thread.run(Thread.java:745)

Looking back up at the output, there is an issue with determining the break between chromosome 4 and 5 as follows:

Chromosome Divisions: 4 start:1924 end:1988 

Chromosome Divisions: 5 start:1989 end:1988 

Chromosome Divisions: 5 start:1989 end:1988 

Chromosome Divisions: 5 start:1989 end:1988 

Chromosome Divisions: 5 start:1989 end:1988 

Chromosome Divisions: 5 start:1989 end:1988 

Chromosome Divisions: 5 start:1989 end:2350 

Chromosome Divisions: 6 start:2351 end:2350 

Chromosome Divisions: 6 start:2351 end:2350 

Chromosome Divisions: 6 start:2351 end:2350 

Chromosome Divisions: 6 start:2351 end:2604 

The problem also extends to chromosome 6.

Everything is order in the input file as it should be after sorting, and there is no obvious reason why this should be a problem.

I'm using the latest version of TASSEL, updated today. I've also tried running FILLIN using a different genotype file that I've used extensively in the past and I have imputed with. It no longer works either.

[Terry Casstevens]

When you say "updated", did you build from source?

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[Terry Casstevens]

Please follow these instructions to get more information.

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

On Tue, Sep 6, 2016 at 2:59 PM, <amk...@truman.edu> wrote:

[Terry Casstevens]

My colleague suggests "set sites per
haplotype to 128. FILLIN was designed for much higher numbers of markers,
so I do not know if will work very well for this data."

On Tue, Sep 6, 2016 at 2:59 PM, <amk...@truman.edu> wrote:

[amk...@truman.edu]

It completed using sites per haplotype of 128 but didn't output any haplotypes. The smallest number of markers on a chromosome is 254. Trying multiples of 64 up to 256 sites per haplotype still doesn't output any haplotypes. It seems likely that there aren't enough markers and samples for FILLIN. Thanks for the help; we'll look for a different option.