[Thread-9] INFO net.maizegenetics.plugindef.AbstractPlugin - Starting net.maizegenetics.analysis.filter.FilterTaxaBuilderPlugin: time: Feb 16, 2024 15:09:50

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

FilterTaxaBuilderPlugin Parameters

filterName: Filter

minNotMissing: 0.0

minHeterozygous: 0.0

maxHeterozygous: 1.0

includeTaxa: true

taxaList: #此处省略

taxaNames: null

Genotype Table Name: Datum_Filter

Number of Taxa: 653

Number of Sites: 1936413

Sites x Taxa: 1264477689

Chromosomes...

1: start site: 0 (31071) last site: 136284 (43269699) total: 136285

2: start site: 136285 (9619) last site: 261212 (35935728) total: 124928

3: start site: 261213 (39409) last site: 345844 (36411438) total: 84632

4: start site: 345845 (3263) last site: 473253 (35502063) total: 127409

5: start site: 473254 (491) last site: 613889 (29957320) total: 140636

6: start site: 613890 (1477) last site: 826908 (31247295) total: 213019

7: start site: 826909 (3980) last site: 1022438 (29696969) total: 195530

8: start site: 1022439 (1886) last site: 1136494 (28438981) total: 114056

9: start site: 1136495 (38465) last site: 1235412 (22993092) total: 98918

10: start site: 1235413 (1538) last site: 1404361 (23205938) total: 168949

11: start site: 1404362 (1242) last site: 1723060 (29018426) total: 318699

12: start site: 1723061 (3904) last site: 1936412 (27527280) total: 213352

[Thread-9] INFO net.maizegenetics.plugindef.AbstractPlugin - Finished net.maizegenetics.analysis.filter.FilterTaxaBuilderPlugin: time: Feb 16, 2024 15:09:50

[Thread-9] INFO net.maizegenetics.pipeline.TasselPipeline - net.maizegenetics.analysis.data.IntersectionAlignmentPlugin: time: Feb 16, 2024 15:09:50: progress: 100%

[Thread-9] INFO net.maizegenetics.plugindef.AbstractPlugin - Starting net.maizegenetics.analysis.association.FixedEffectLMPlugin: time: Feb 16, 2024 15:09:50

[Thread-9] 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-9] INFO net.maizegenetics.matrixalgebra.Matrix.DoubleMatrixFactory - TasselBlas library for system-specific BLAS/LAPACK not found. Using system-independent EJML for DoubleMatrix operations.

[Thread-9] INFO net.maizegenetics.pipeline.TasselPipeline - net.maizegenetics.analysis.association.FixedEffectLMPlugin: time: Feb 16, 2024 15:09:52: progress: 0%

[Thread-9] INFO net.maizegenetics.pipeline.TasselPipeline - net.maizegenetics.analysis.association.FixedEffectLMPlugin: time: Feb 16, 2024 15:10:10: progress: 10%

[Thread-9] INFO net.maizegenetics.pipeline.TasselPipeline - net.maizegenetics.analysis.association.FixedEffectLMPlugin: time: Feb 16, 2024 15:10:25: progress: 20%

[Thread-9] INFO net.maizegenetics.pipeline.TasselPipeline - net.maizegenetics.analysis.association.FixedEffectLMPlugin: time: Feb 16, 2024 15:10:41: progress: 30%

[Thread-9] INFO net.maizegenetics.pipeline.TasselPipeline - net.maizegenetics.analysis.association.FixedEffectLMPlugin: time: Feb 16, 2024 15:10:57: progress: 40%

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

Usage:

FixedEffectLMPlugin <options>

-phenoOnly <true | false> : Should the phenotype be analyzed with no markers and BLUEs generated? (BLUE = best linear unbiased estimate) (Default: false)

-saveToFile <true | false> : Should the results be saved to a file rather than stored in memory? It true, the results will be written to a file as each SNP is analyzed in order to reduce memory requirementsand the results will NOT be saved to the data tree. Default = false. (Default: false)

-siteFile <Statistics File> : The name of the file to which these results will be saved.

-alleleFile <Genotype Effect File> : The name of the file to which these results will be saved.

-maxP <max P value> : Only results with p <= maxPvalue will be reported. Default = 1.0. [0.0..1.0] (Default: 1.0)

-permute <true | false> : Should a permutation analysis be run? The permutation analysis controls the experiment-wise error rate for individual phenotypes. (Default: false)

-nperm <Number of Permutations> : The number of permutations to be run for the permutation analysis. (Default: 0)

-genotypeComponent <Genotype Component> : If the genotype table contains more than one type of genotype data, choose the type to use for the analysis. [Genotype, ReferenceProbability, AlleleProbability] (Default: Genotype)

-minClassSize <Minimum Class Size> : The minimum acceptable genotype class size. Genotypes in a class with a smaller size will be set to missing. (Default: 0)

-biallelicOnly <true | false> : Only test sites that are bi-allelic. The alternative is to test sites with two or more alleles. (Default: false)

-siteStatsOut <true | false> : Generate an output dataset with only p-val, F statistic, and number of obs per site for all sites. (Default: false)

-siteStatFile <Site Stat File> : Site Stat File

-appendAddDom <true | false> : If true, additive and dominance effect estimates will be added to the stats report for bi-allelic sites only. The effect will only be estimated when the data source is genotype (not a probability). The additive effect will always be non-negative. (Default: false)

[Thread-9] ERROR net.maizegenetics.plugindef.AbstractPlugin - 0