When running GLM, Error– 0

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nag...@oregonstate.edu

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Jul 12, 2018, 5:46:05 PM7/12/18

to TASSEL - Trait Analysis by Association, Evolution and Linkage

I'm new to TASSEL5 and this usergroup so apologies if this is a very basic question and/or I missed something in the manual. I'm trying to run GLM, after loading PLINK .ped and .map files, finding top 3 covariates, building the kinship matrix, merging genotype with kinship and covariates, then selecting both the combined file and the phenotype filing and selecting GLM from the Analysis menu.

I'm getting an error box that just says "0" and am getting no output. Please find the log below.

This is different from the Size:0, Index:0 error I mentioned earlier, and which I am now unable to replicate.

[main] INFO net.maizegenetics.tassel.TasselLogging - Tassel Version: 5.2.44 Date: May 17, 2018

[main] INFO net.maizegenetics.tassel.TasselLogging - Max Available Memory Reported by JVM: 5333 MB

[main] INFO net.maizegenetics.tassel.TasselLogging - Java Version: 1.8.0_121

[main] INFO net.maizegenetics.tassel.TasselLogging - OS: Mac OS X

[main] INFO net.maizegenetics.tassel.TasselLogging - Number of Processors: 4

[Thread-6] INFO net.maizegenetics.plugindef.AbstractPlugin - Starting net.maizegenetics.analysis.data.FileLoadPlugin: time: Jul 12, 2018 14:38:12

[Thread-6] INFO net.maizegenetics.plugindef.AbstractPlugin -

FileLoadPlugin Parameters

format: Plink

sortPositions: false

keepDepth: true

[Thread-6] INFO net.maizegenetics.plugindef.AbstractPlugin - Starting net.maizegenetics.analysis.data.PlinkLoadPlugin: time: Jul 12, 2018 14:38:17

[Thread-6] INFO net.maizegenetics.plugindef.AbstractPlugin - net.maizegenetics.analysis.data.PlinkLoadPlugin Citation: Bradbury PJ, Zhang Z, Kroon DE, Casstevens TM, Ramdoss Y, Buckler ES. (2007) TASSEL: Software for association mapping of complex traits in diverse samples. Bioinformatics 23:2633-2635.

[Thread-6] INFO net.maizegenetics.plugindef.AbstractPlugin - Finished net.maizegenetics.analysis.data.FileLoadPlugin: time: Jul 12, 2018 14:38:18

[Thread-7] INFO net.maizegenetics.plugindef.AbstractPlugin - Starting net.maizegenetics.analysis.data.FileLoadPlugin: time: Jul 12, 2018 14:38:20

[Thread-7] INFO net.maizegenetics.plugindef.AbstractPlugin -

FileLoadPlugin Parameters

format: Plink

sortPositions: true

keepDepth: true

[Thread-7] INFO net.maizegenetics.plugindef.AbstractPlugin - Starting net.maizegenetics.analysis.data.PlinkLoadPlugin: time: Jul 12, 2018 14:38:54

[Thread-7] INFO net.maizegenetics.plugindef.AbstractPlugin -

PlinkLoadPlugin Parameters

pedFile: /Users/user/_Data/gatk_882_WG_genotypes_biallelic_snps_VQSR_0.49_filtered_from_tped_to_ped.ped

mapFile: /Users/user/_Data/gatk_882_WG_genotypes_biallelic_snps_VQSR_0.49_filtered_from_tped_to_ped.map

sortPositions: true

[Thread-7] INFO net.maizegenetics.dna.snp.io.BuilderFromPLINK - Reading: /Users/user/_Data/gatk_882_WG_genotypes_biallelic_snps_VQSR_0.49_filtered_from_tped_to_ped.ped and /Users/user/_Data/gatk_882_WG_genotypes_biallelic_snps_VQSR_0.49_filtered_from_tped_to_ped.map

[Thread-7] INFO net.maizegenetics.dna.snp.io.BuilderFromPLINK - Number of sites: 92727

[Thread-7] INFO net.maizegenetics.dna.snp.io.BuilderFromPLINK - Number of taxa: 882

[Thread-7] ERROR net.maizegenetics.dna.map.PositionListBuilder - validateOrdering: Position Chr:SCAFFOLD_102 Pos:31018 InsertionPos:0 Name:scaffold_102_31018 MAF:NaN Ref:N and Position Chr:SCAFFOLD_99 Pos:125373 InsertionPos:0 Name:scaffold_99_125373 MAF:NaN Ref:N out of order.

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

[Thread-7] INFO net.maizegenetics.plugindef.AbstractPlugin - Finished net.maizegenetics.analysis.data.PlinkLoadPlugin: time: Jul 12, 2018 14:39:19

[Thread-7] INFO net.maizegenetics.plugindef.AbstractPlugin - Finished net.maizegenetics.analysis.data.FileLoadPlugin: time: Jul 12, 2018 14:39:19

[Thread-8] INFO net.maizegenetics.plugindef.AbstractPlugin - Starting net.maizegenetics.analysis.data.PrincipalComponentsPlugin: time: Jul 12, 2018 14:39:34

[Thread-8] INFO net.maizegenetics.plugindef.AbstractPlugin -

PrincipalComponentsPlugin Parameters

covariance: true

limitBy: number_of_components

ncomponents: 3

minEigenval: 0.0

totalVar: 0.5

reportEigenvalues: true

reportEigenvectors: true

[Thread-8] INFO net.maizegenetics.plugindef.AbstractPlugin - Starting net.maizegenetics.analysis.numericaltransform.ImputationPlugin: time: Jul 12, 2018 14:40:4

[Thread-8] INFO net.maizegenetics.plugindef.AbstractPlugin -

ImputationPlugin Parameters

ByMean: true

nearestNeighbors: 5

distance: Euclidean

[Thread-9] INFO net.maizegenetics.plugindef.AbstractPlugin - Starting net.maizegenetics.analysis.distance.KinshipPlugin: time: Jul 12, 2018 14:40:9

[Thread-9] INFO net.maizegenetics.plugindef.AbstractPlugin -

KinshipPlugin Parameters

method: Centered_IBS

maxAlleles: 6

algorithmVariation: Observed_Allele_Freq

[Thread-9] INFO net.maizegenetics.analysis.distance.EndelmanDistanceMatrix - EndelmanDistanceMatrix: estimated time: 0 minutes

[AWT-EventQueue-0] INFO net.maizegenetics.analysis.data.FileLoadPlugin - Start Loading File: /Users/user/_Data/14_traits_combined_forMVP_882genos.txt time: Jul 12, 2018 14:40:18

[AWT-EventQueue-0] INFO net.maizegenetics.analysis.data.FileLoadPlugin - guessAtUnknowns: type: Phenotype

[AWT-EventQueue-0] INFO net.maizegenetics.analysis.data.FileLoadPlugin - Finished Loading File: /Users/user/_Data/14_traits_combined_forMVP_882genos.txt time: Jul 12, 2018 14:40:18

[AWT-EventQueue-0] INFO net.maizegenetics.tassel.DataTreePanel - initSelectionListener: node type: class net.maizegenetics.phenotype.CorePhenotype

[AWT-EventQueue-0] INFO net.maizegenetics.tassel.DataTreePanel - initSelectionListener: Table Report Size: 13230

[Thread-9] INFO net.maizegenetics.analysis.distance.EndelmanDistanceMatrix - EndelmanDistanceMatrix: actual time: 0 minutes

[Thread-9] INFO net.maizegenetics.plugindef.AbstractPlugin - Finished net.maizegenetics.analysis.distance.KinshipPlugin: time: Jul 12, 2018 14:40:20

[Thread-9] INFO net.maizegenetics.tassel.DataTreePanel - initSelectionListener: node type: class net.maizegenetics.taxa.distance.DistanceMatrix

[Thread-9] INFO net.maizegenetics.tassel.DataTreePanel - initSelectionListener: Table Report Size: 778806

[Thread-8] INFO net.maizegenetics.plugindef.AbstractPlugin - Finished net.maizegenetics.analysis.numericaltransform.ImputationPlugin: time: Jul 12, 2018 14:40:22

[Thread-8] INFO net.maizegenetics.matrixalgebra.Matrix.DoubleMatrixFactory - Using BLAS/LAPACK for DoubleMatrix operations

[Thread-8] INFO net.maizegenetics.plugindef.AbstractPlugin - Finished net.maizegenetics.analysis.data.PrincipalComponentsPlugin: time: Jul 12, 2018 14:41:21

[Thread-8] INFO net.maizegenetics.tassel.DataTreePanel - initSelectionListener: node type: class net.maizegenetics.phenotype.CorePhenotype

[Thread-8] INFO net.maizegenetics.tassel.DataTreePanel - initSelectionListener: Table Report Size: 3528

[Thread-10] INFO net.maizegenetics.tassel.DataTreePanel - initSelectionListener: node type: class net.maizegenetics.phenotype.GenotypePhenotype

[Thread-10] INFO net.maizegenetics.tassel.DataTreePanel - initSelectionListener: Table Report Size: 16758

[Thread-11] INFO net.maizegenetics.plugindef.AbstractPlugin - Starting net.maizegenetics.analysis.association.FixedEffectLMPlugin: time: Jul 12, 2018 14:41:46

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

FixedEffectLMPlugin Parameters

phenoOnly: false

saveToFile: false

siteFile: null

alleleFile: null

maxP: 1.0

permute: false

nperm: 0

genotypeComponent: Genotype

minClassSize: 0

biallelicOnly: false

siteStatsOut: false

siteStatFile: null

appendAddDom: false

[Thread-11] DEBUG net.maizegenetics.plugindef.AbstractPlugin - 0

java.lang.ArrayIndexOutOfBoundsException: 0

at net.maizegenetics.stats.linearmodels.ModelEffectUtils.getNumericCodingForAdditiveModel(ModelEffectUtils.java:224)

at net.maizegenetics.analysis.association.DiscreteSitesFELM.analyzeSite(DiscreteSitesFELM.java:95)

at net.maizegenetics.analysis.association.AbstractFixedEffectLM.solve(AbstractFixedEffectLM.java:162)

at net.maizegenetics.analysis.association.FixedEffectLMPlugin.processData(FixedEffectLMPlugin.java:172)

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)

nag...@oregonstate.edu

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Jul 12, 2018, 6:11:55 PM7/12/18

to TASSEL - Trait Analysis by Association, Evolution and Linkage

correction to a typing error: I used intersect-join to join genotype, covariates and phenotype. The kinship matrix of course was not included in the join, or used at all for GLM.

Peter Bradbury

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Jul 13, 2018, 9:36:29 AM7/13/18

to TASSEL - Trait Analysis by Association, Evolution and Linkage

The error appears to be the result of trying to analyze a site for which all genotypes are missing. Before running GLM it is a good idea to filter sites using Filter/Filter Genotype Table Sites. In particular, filter on Site Min Count and Site Min Allele Freq. The first controls the minimum amount of missing data for a site. The second the frequency of the minor allele. Appropriate values depend on the number of samples you have. For 880 sample I would not set those any lower than 200 and 0.03, but you may want to use higher values.