[Thread-8] INFO net.maizegenetics.matrixalgebra.Matrix.DoubleMatrixFactory - TasselBlas library for system-specific BLAS/LAPACK not found. Using system-independent EJML for DoubleMatrix operations.

[Thread-8] INFO net.maizegenetics.pipeline.TasselPipeline - net.maizegenetics.analysis.association.FixedEffectLMPlugin: time: Aug 15, 2023 17:21:14: progress: 0%

[Thread-8] 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.

-bluesFile <BLUEs File> : Name of file to which BLUEs values will be saved

-anovaFile <ANOVA File> : Name of file to which ANOVA report 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-8] ERROR net.maizegenetics.plugindef.AbstractPlugin - Index 0 out of bounds for length 0

执行命令如下：run_pipeline.pl -Xms1g -Xmx100g \

  -fork1 -vcf  ./nip-snp-gwas.vcf  \

  -fork2  -t d3.trait.txt \

  -fork3 -q  structure_Q3.txt  -excludeLastTrait \

  -combine4 -input1 -input2 -input3 -intersect \

  -FixedEffectLMPlugin -endPlugin \

  -export glm_output