/public/cau/lintao_group/yangjunwei/software/tassel-5/lib/jcommon-1.0.23.jar:/public/cau/lintao_group/yangjunwei/software/tassel-5/lib/phg.jar:/public/cau/lintao_group/yangjunwei/software/tassel-5/lib/commons-math3-3.4.1.jar:/public/cau/lintao_group/yangjunwei/software/tassel-5/lib/biojava-alignment-4.0.0.jar:/public/cau/lintao_group/yangjunwei/software/tassel-5/lib/sqlite-jdbc-3.8.5-pre1.jar:/public/cau/lintao_group/yangjunwei/software/tassel-5/lib/forester-1.038.jar:/public/cau/lintao_group/yangjunwei/software/tassel-5/lib/mail-1.4.jar:/public/cau/lintao_group/yangjunwei/software/tassel-5/lib/slf4j-simple-1.7.10.jar:/public/cau/lintao_group/yangjunwei/software/tassel-5/lib/ahocorasick-0.2.4.jar:/public/cau/lintao_group/yangjunwei/software/tassel-5/lib/gs-core-1.3.jar:/public/cau/lintao_group/yangjunwei/software/tassel-5/lib/scala-library-2.10.1.jar:/public/cau/lintao_group/yangjunwei/software/tassel-5/lib/jfreechart-1.0.19.jar:/public/cau/lintao_group/yangjunwei/software/tassel-5/lib/gs-ui-1.3.jar:/public/cau/lintao_group/yangjunwei/software/tassel-5/lib/trove-3.0.3.jar:/public/cau/lintao_group/yangjunwei/software/tassel-5/lib/htsjdk-2.14.0.jar:/public/cau/lintao_group/yangjunwei/software/tassel-5/lib/log4j-1.2.13.jar:/public/cau/lintao_group/yangjunwei/software/tassel-5/lib/slf4j-api-1.7.10.jar:/public/cau/lintao_group/yangjunwei/software/tassel-5/lib/commons-codec-1.10.jar:/public/cau/lintao_group/yangjunwei/software/tassel-5/lib/json-simple-1.1.1.jar:/public/cau/lintao_group/yangjunwei/software/tassel-5/lib/itextpdf-5.1.0.jar:/public/cau/lintao_group/yangjunwei/software/tassel-5/lib/jfreesvg-3.2.jar:/public/cau/lintao_group/yangjunwei/software/tassel-5/lib/junit-4.10.jar:/public/cau/lintao_group/yangjunwei/software/tassel-5/lib/biojava-phylo-4.0.0.jar:/public/cau/lintao_group/yangjunwei/software/tassel-5/lib/ejml-0.23.jar:/public/cau/lintao_group/yangjunwei/software/tassel-5/lib/postgresql-9.4-1201.jdbc41.jar:/public/cau/lintao_group/yangjunwei/software/tassel-5/lib/colt-1.2.0.jar:/public/cau/lintao_group/yangjunwei/software/tassel-5/lib/snappy-java-1.1.1.6.jar:/public/cau/lintao_group/yangjunwei/software/tassel-5/lib/biojava-core-4.0.0.jar:/public/cau/lintao_group/yangjunwei/software/tassel-5/lib/guava-22.0.jar:/public/cau/lintao_group/yangjunwei/software/tassel-5/lib/javax.json-1.0.4.jar:/public/cau/lintao_group/yangjunwei/software/tassel-5/lib/jhdf5-14.12.5.jar:/public/cau/lintao_group/yangjunwei/software/tassel-5/sTASSEL.jar
Memory Settings: -Xms512m -Xmx10g
Tassel Pipeline Arguments: -fork1 -vcf dh151px.vcf -fork2 -r Trait-PPWV.txt -fork3 -q Q.txt -excludeLastTrait -combine4 -input1 -input2 -input3 -intersect -glm -export tassel_glm_ -runfork1 -runfork2 -runfork3
[main] INFO net.maizegenetics.tassel.TasselLogging - Tassel Version: 5.2.48 Date: August 2, 2018
[main] INFO net.maizegenetics.tassel.TasselLogging - Max Available Memory Reported by JVM: 9102 MB
[main] INFO net.maizegenetics.tassel.TasselLogging - Java Version: 1.8.0_382
[main] INFO net.maizegenetics.tassel.TasselLogging - OS: Linux
[main] INFO net.maizegenetics.tassel.TasselLogging - Number of Processors: 72
[main] INFO net.maizegenetics.pipeline.TasselPipeline - Tassel Pipeline Arguments: [-fork1, -vcf, dh151px.vcf, -fork2, -r, Trait-PPWV.txt, -fork3, -q, Q.txt, -excludeLastTrait, -combine4, -input1, -input2, -input3, -intersect, -glm, -export, tassel_glm_, -runfork1, -runfork2, -runfork3]
net.maizegenetics.analysis.data.FileLoadPlugin
net.maizegenetics.analysis.data.CombineDataSetsPlugin
net.maizegenetics.analysis.data.IntersectionAlignmentPlugin
net.maizegenetics.analysis.association.FixedEffectLMPlugin
net.maizegenetics.analysis.data.ExportMultiplePlugin
net.maizegenetics.analysis.data.FileLoadPlugin
net.maizegenetics.analysis.data.FileLoadPlugin
net.maizegenetics.analysis.filter.FilterTraitsPlugin
[pool-1-thread-1] INFO net.maizegenetics.plugindef.AbstractPlugin - Starting net.maizegenetics.analysis.data.FileLoadPlugin: time: Nov 30, 2023 17:13:39
[pool-1-thread-3] INFO net.maizegenetics.plugindef.AbstractPlugin - Starting net.maizegenetics.analysis.data.FileLoadPlugin: time: Nov 30, 2023 17:13:39
[pool-1-thread-2] INFO net.maizegenetics.plugindef.AbstractPlugin - Starting net.maizegenetics.analysis.data.FileLoadPlugin: time: Nov 30, 2023 17:13:39
[pool-1-thread-1] INFO net.maizegenetics.plugindef.AbstractPlugin -
FileLoadPlugin Parameters
format: VCF
sortPositions: false
keepDepth: true
[pool-1-thread-3] INFO net.maizegenetics.plugindef.AbstractPlugin -
FileLoadPlugin Parameters
format: Phenotype
sortPositions: false
keepDepth: true
[pool-1-thread-2] INFO net.maizegenetics.plugindef.AbstractPlugin -
FileLoadPlugin Parameters
format: Phenotype
sortPositions: false
keepDepth: true
[pool-1-thread-1] INFO net.maizegenetics.analysis.data.FileLoadPlugin - Start Loading File: dh151px.vcf time: Nov 30, 2023 17:13:39
[pool-1-thread-3] INFO net.maizegenetics.analysis.data.FileLoadPlugin - Start Loading File: Q.txt time: Nov 30, 2023 17:13:39
[pool-1-thread-2] INFO net.maizegenetics.analysis.data.FileLoadPlugin - Start Loading File: Trait-PPWV.txt time: Nov 30, 2023 17:13:39
[pool-1-thread-3] INFO net.maizegenetics.analysis.data.FileLoadPlugin - Finished Loading File: Q.txt time: Nov 30, 2023 17:13:39
[pool-1-thread-2] INFO net.maizegenetics.analysis.data.FileLoadPlugin - Finished Loading File: Trait-PPWV.txt time: Nov 30, 2023 17:13:39
[pool-1-thread-3] INFO net.maizegenetics.plugindef.AbstractPlugin - Finished net.maizegenetics.analysis.data.FileLoadPlugin: time: Nov 30, 2023 17:13:39
[pool-1-thread-2] INFO net.maizegenetics.plugindef.AbstractPlugin - Finished net.maizegenetics.analysis.data.FileLoadPlugin: time: Nov 30, 2023 17:13:39
[pool-1-thread-2] INFO net.maizegenetics.pipeline.TasselPipeline - net.maizegenetics.analysis.data.FileLoadPlugin: time: Nov 30, 2023 17:13:39: progress: 100%
[pool-1-thread-2] INFO net.maizegenetics.plugindef.AbstractPlugin - net.maizegenetics.analysis.data.FileLoadPlugin 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.
[pool-1-thread-3] INFO net.maizegenetics.pipeline.TasselPipeline - net.maizegenetics.analysis.data.FileLoadPlugin: time: Nov 30, 2023 17:13:39: progress: 100%
[pool-1-thread-1] INFO net.maizegenetics.pipeline.TasselPipeline - net.maizegenetics.analysis.data.FileLoadPlugin: time: Nov 30, 2023 17:13:58: progress: 0%
[pool-1-thread-1] INFO net.maizegenetics.pipeline.TasselPipeline - net.maizegenetics.analysis.data.FileLoadPlugin: time: Nov 30, 2023 17:14:2: progress: 10%
[pool-1-thread-1] INFO net.maizegenetics.pipeline.TasselPipeline - net.maizegenetics.analysis.data.FileLoadPlugin: time: Nov 30, 2023 17:14:2: progress: 20%
[pool-1-thread-1] INFO net.maizegenetics.pipeline.TasselPipeline - net.maizegenetics.analysis.data.FileLoadPlugin: time: Nov 30, 2023 17:14:18: progress: 30%
[pool-1-thread-1] INFO net.maizegenetics.pipeline.TasselPipeline - net.maizegenetics.analysis.data.FileLoadPlugin: time: Nov 30, 2023 17:14:24: progress: 40%
[pool-1-thread-1] INFO net.maizegenetics.pipeline.TasselPipeline - net.maizegenetics.analysis.data.FileLoadPlugin: time: Nov 30, 2023 17:14:29: progress: 50%
[pool-1-thread-1] INFO net.maizegenetics.pipeline.TasselPipeline - net.maizegenetics.analysis.data.FileLoadPlugin: time: Nov 30, 2023 17:14:31: progress: 60%
[pool-1-thread-1] INFO net.maizegenetics.pipeline.TasselPipeline - net.maizegenetics.analysis.data.FileLoadPlugin: time: Nov 30, 2023 17:14:36: progress: 70%
[pool-1-thread-1] INFO net.maizegenetics.pipeline.TasselPipeline - net.maizegenetics.analysis.data.FileLoadPlugin: time: Nov 30, 2023 17:14:39: progress: 80%
[pool-1-thread-1] INFO net.maizegenetics.pipeline.TasselPipeline - net.maizegenetics.analysis.data.FileLoadPlugin: time: Nov 30, 2023 17:14:41: progress: 90%
[pool-1-thread-1] INFO net.maizegenetics.pipeline.TasselPipeline - net.maizegenetics.analysis.data.FileLoadPlugin: time: Nov 30, 2023 17:14:41: progress: 100%
BuilderFromVCF data timing 63.2659s
[pool-1-thread-1] INFO net.maizegenetics.analysis.data.FileLoadPlugin - Finished Loading File: dh151px.vcf time: Nov 30, 2023 17:14:43
Genotype Table Name: dh151px
Number of Taxa: 151
Number of Sites: 1481399
Sites x Taxa: 223691249
Chromosomes...
PEPPER1.55CH01: start site: 0 (1178) last site: 173307 (272704397) total: 173308
PEPPER1.55CH02: start site: 173308 (131) last site: 269812 (171124841) total: 96505
PEPPER1.55CH03: start site: 269813 (132) last site: 412707 (257894273) total: 142895
PEPPER1.55CH04: start site: 412708 (61217) last site: 528123 (222583855) total: 115416
PEPPER1.55CH05: start site: 528124 (25116) last site: 650029 (233467675) total: 121906
PEPPER1.55CH06: start site: 650030 (1225) last site: 791084 (236912039) total: 141055
PEPPER1.55CH07: start site: 791085 (105) last site: 951620 (231911427) total: 160536
PEPPER1.55CH08: start site: 951621 (14994) last site: 1009781 (145103167) total: 58161
PEPPER1.55CH09: start site: 1009782 (361) last site: 1143379 (252779195) total: 133598
PEPPER1.55CH10: start site: 1143380 (476) last site: 1246342 (233593740) total: 102963
PEPPER1.55CH11: start site: 1246343 (168) last site: 1353880 (259725933) total: 107538
PEPPER1.55CH12: start site: 1353881 (1479) last site: 1481398 (235688172) total: 127518
[pool-1-thread-1] INFO net.maizegenetics.plugindef.AbstractPlugin - Finished net.maizegenetics.analysis.data.FileLoadPlugin: time: Nov 30, 2023 17:14:43
[main] WARN net.maizegenetics.pipeline.TasselPipeline - parseArgs: NOTE: The -glm flags are deprecated.
parseArgs: PLEASE RUN THIS COMMAND TO GET USAGE: ./run_pipeline.pl -FixedEffectLMPlugin
[Thread-9] INFO net.maizegenetics.pipeline.TasselPipeline - net.maizegenetics.analysis.data.IntersectionAlignmentPlugin: time: Nov 30, 2023 17:14:43: progress: 100%
[Thread-9] INFO net.maizegenetics.plugindef.AbstractPlugin - Starting net.maizegenetics.analysis.association.FixedEffectLMPlugin: time: Nov 30, 2023 17:14:43
[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.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