BuilderFromPLINK error

[Zoë]

I am trying to run MLM with whole genome plink data (ped/map) and I keep getting this error. Do you have any advice on troubleshooting this? I never had this issue previously when using GBS data. 

[pool-1-thread-1] ERROR net.maizegenetics.plugindef.AbstractPlugin - BuilderFromPLINK: build: problem processing: / by zero

Here is my input script

run_pipeline.pl -Xms512m -Xmx200g -fork1 -plink -ped file.ped -map file.map  FilterSiteBuilderPlugin -siteMinAlleleFreq 0.01 -endPlugin -fork2 -importGuess trait.txt -fork3 -importGuess pcs.txt -fork4 -importGuess kinship.txt -combine5 -input1 -input2 -input3 -intersect -combine6 -input5 -input4 -mlm -mlmVarCompEst P3D -mlmCompressionLevel Optimum -export gwas

Thanks in advance for any help! 

[Zoë]

Alternatively, when I convert it to a vcf and try to run, I get this error instead when running something like this:

run_pipeline.pl -Xms512m -Xmx200g -fork1 -vcf file.vcf -sortPositions -fork2 -r trait.txt -fork3 -importGuess pcs1.txt -combine4 -input1 -input2 -input3 -intersect -fork5 -importGuess kinship.txt -combine6 -input4 -input5 -mlm -mlmVarCompEs

t P3D -mlmCompressionLevel Optimum —mlmOutputFile gwas

Here's the error:

[pool-1-thread-1] INFO net.maizegenetics.plugindef.AbstractPlugin - Finished net.maizegenetics.analysis.data.FileLoadPlugin: time: May 17, 2024 18:12:30

[Thread-11] INFO net.maizegenetics.plugindef.AbstractPlugin - Starting net.maizegenetics.analysis.filter.FilterTaxaBuilderPlugin: time: May 17, 2024 18:12:39

[Thread-11] INFO net.maizegenetics.plugindef.AbstractPlugin - 

FilterTaxaBuilderPlugin Parameters

filterName: Filter

minNotMissing: 0.0

minHeterozygous: 0.0

maxHeterozygous: 1.0

includeTaxa: true

taxaList: []

[Thread-11] WARN net.maizegenetics.gui.DialogUtils - No genotype data remained after filtering: Datum

[Thread-11] INFO net.maizegenetics.plugindef.AbstractPlugin - Finished net.maizegenetics.analysis.filter.FilterTaxaBuilderPlugin: time: May 17, 2024 18:12:39

[Thread-11] INFO net.maizegenetics.pipeline.TasselPipeline - net.maizegenetics.analysis.data.IntersectionAlignmentPlugin: time: May 17, 2024 18:12:39: progress:

 100%

java.lang.IndexOutOfBoundsException: Index 0 out of bounds for length 0

at java.base/jdk.internal.util.Preconditions.outOfBounds(Preconditions.java:64)

at java.base/jdk.internal.util.Preconditions.outOfBoundsCheckIndex(Preconditions.java:70)

at java.base/jdk.internal.util.Preconditions.checkIndex(Preconditions.java:248)

at java.base/java.util.Objects.checkIndex(Objects.java:373)

at java.base/java.util.ArrayList.get(ArrayList.java:425)

at net.maizegenetics.analysis.filter.FilterTaxaBuilderPlugin.runPlugin(FilterTaxaBuilderPlugin.java:195)

at net.maizegenetics.phenotype.GenotypePhenotypeBuilder.build(GenotypePhenotypeBuilder.java:78)

at net.maizegenetics.analysis.data.UnionAlignmentPlugin.processData(UnionAlignmentPlugin.java:99)

at net.maizegenetics.analysis.data.IntersectionAlignmentPlugin.performFunction(IntersectionAlignmentPlugin.java:32)

at net.maizegenetics.plugindef.AbstractPlugin.dataSetReturned(AbstractPlugin.java:2017)

at net.maizegenetics.plugindef.AbstractPlugin.fireDataSetReturned(AbstractPlugin.java:1918)

at net.maizegenetics.plugindef.AbstractPlugin.fireDataSetReturned(AbstractPlugin.java:1934)

at net.maizegenetics.analysis.data.CombineDataSetsPlugin.performFunction(CombineDataSetsPlugin.java:65)

at net.maizegenetics.analysis.data.CombineDataSetsPlugin.dataSetReturned(CombineDataSetsPlugin.java:126)

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

So neither seems to be working for me. 

[Terry Casstevens]

Are the taxa in these files the same?

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[Zoë]

Yes they are. 

It does say taxaList: []

So is it not identifying them as the same and putting no taxa? I made sure my phenotype file (trait.txt in the above) used the same names as my sequencing data. 

[Terry Casstevens]

If you want to send me your files privately, I can try it

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