comparison test-data/Log_file.txt @ 4:652aafd88060 draft

planemo upload commit 475f4d7d8442a0d75e103af326ae5881c4d2a4ac
author dereeper
date Mon, 16 Apr 2018 08:54:41 -0400
parents
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3:0eebff4180d9 4:652aafd88060
1 /work/GALAXY/galaxy/dependencies/tassel/5.0/dereeper/package_tassel_5_0/097d4c366e0d/bin/lib/LiuExt.jar:/work/GALAXY/galaxy/dependencies/tassel/5.0/dereeper/package_tassel_5_0/097d4c366e0d/bin/lib/sqlite-jdbc-3.8.4.3-SNAPSHOT.jar:/work/GALAXY/galaxy/dependencies/tassel/5.0/dereeper/package_tassel_5_0/097d4c366e0d/bin/lib/itextpdf-5.1.0.jar:/work/GALAXY/galaxy/dependencies/tassel/5.0/dereeper/package_tassel_5_0/097d4c366e0d/bin/lib/biojava3-alignment-4.0.0.jar:/work/GALAXY/galaxy/dependencies/tassel/5.0/dereeper/package_tassel_5_0/097d4c366e0d/bin/lib/batik-css.jar:/work/GALAXY/galaxy/dependencies/tassel/5.0/dereeper/package_tassel_5_0/097d4c366e0d/bin/lib/xmlParserAPIs.jar:/work/GALAXY/galaxy/dependencies/tassel/5.0/dereeper/package_tassel_5_0/097d4c366e0d/bin/lib/poi-3.0.1-FINAL-20070705.jar:/work/GALAXY/galaxy/dependencies/tassel/5.0/dereeper/package_tassel_5_0/097d4c366e0d/bin/lib/batik-awt-util.jar:/work/GALAXY/galaxy/dependencies/tassel/5.0/dereeper/package_tassel_5_0/097d4c366e0d/bin/lib/jcommon-1.0.6.jar:/work/GALAXY/galaxy/dependencies/tassel/5.0/dereeper/package_tassel_5_0/097d4c366e0d/bin/lib/snappy-java-1.1.1.6.jar:/work/GALAXY/galaxy/dependencies/tassel/5.0/dereeper/package_tassel_5_0/097d4c366e0d/bin/lib/batik-util.jar:/work/GALAXY/galaxy/dependencies/tassel/5.0/dereeper/package_tassel_5_0/097d4c366e0d/bin/lib/commons-codec-1.10.jar:/work/GALAXY/galaxy/dependencies/tassel/5.0/dereeper/package_tassel_5_0/097d4c366e0d/bin/lib/log4j-1.2.13.jar:/work/GALAXY/galaxy/dependencies/tassel/5.0/dereeper/package_tassel_5_0/097d4c366e0d/bin/lib/biojava3-phylo-4.0.0.jar:/work/GALAXY/galaxy/dependencies/tassel/5.0/dereeper/package_tassel_5_0/097d4c366e0d/bin/lib/xml.jar:/work/GALAXY/galaxy/dependencies/tassel/5.0/dereeper/package_tassel_5_0/097d4c366e0d/bin/lib/geronimo-spec-activation-1.0.2-rc4.jar:/work/GALAXY/galaxy/dependencies/tassel/5.0/dereeper/package_tassel_5_0/097d4c366e0d/bin/lib/json-simple-1.1.1.jar:/work/GALAXY/galaxy/dependencies/tassel/5.0/dereeper/package_tassel_5_0/097d4c366e0d/bin/lib/jfreechart-1.0.3.jar:/work/GALAXY/galaxy/dependencies/tassel/5.0/dereeper/package_tassel_5_0/097d4c366e0d/bin/lib/batik-xml.jar:/work/GALAXY/galaxy/dependencies/tassel/5.0/dereeper/package_tassel_5_0/097d4c366e0d/bin/lib/colt.jar:/work/GALAXY/galaxy/dependencies/tassel/5.0/dereeper/package_tassel_5_0/097d4c366e0d/bin/lib/batik-dom.jar:/work/GALAXY/galaxy/dependencies/tassel/5.0/dereeper/package_tassel_5_0/097d4c366e0d/bin/lib/biojava3-core-4.0.0.jar:/work/GALAXY/galaxy/dependencies/tassel/5.0/dereeper/package_tassel_5_0/097d4c366e0d/bin/lib/junit-4.10.jar:/work/GALAXY/galaxy/dependencies/tassel/5.0/dereeper/package_tassel_5_0/097d4c366e0d/bin/lib/batik-gui-util.jar:/work/GALAXY/galaxy/dependencies/tassel/5.0/dereeper/package_tassel_5_0/097d4c366e0d/bin/lib/batik-ext.jar:/work/GALAXY/galaxy/dependencies/tassel/5.0/dereeper/package_tassel_5_0/097d4c366e0d/bin/lib/trove-3.0.3.jar:/work/GALAXY/galaxy/dependencies/tassel/5.0/dereeper/package_tassel_5_0/097d4c366e0d/bin/lib/mail-1.4.jar:/work/GALAXY/galaxy/dependencies/tassel/5.0/dereeper/package_tassel_5_0/097d4c366e0d/bin/lib/ejml-0.23.jar:/work/GALAXY/galaxy/dependencies/tassel/5.0/dereeper/package_tassel_5_0/097d4c366e0d/bin/lib/batik-gvt.jar:/work/GALAXY/galaxy/dependencies/tassel/5.0/dereeper/package_tassel_5_0/097d4c366e0d/bin/lib/forester.jar:/work/GALAXY/galaxy/dependencies/tassel/5.0/dereeper/package_tassel_5_0/097d4c366e0d/bin/lib/commons-math3-3.4.1.jar:/work/GALAXY/galaxy/dependencies/tassel/5.0/dereeper/package_tassel_5_0/097d4c366e0d/bin/lib/guava-14.0.1.jar:/work/GALAXY/galaxy/dependencies/tassel/5.0/dereeper/package_tassel_5_0/097d4c366e0d/bin/lib/xercesImpl.jar:/work/GALAXY/galaxy/dependencies/tassel/5.0/dereeper/package_tassel_5_0/097d4c366e0d/bin/lib/cisd-jhdf5-batteries_included_lin_win_mac.jar:/work/GALAXY/galaxy/dependencies/tassel/5.0/dereeper/package_tassel_5_0/097d4c366e0d/bin/lib/batik-svg-dom.jar:/work/GALAXY/galaxy/dependencies/tassel/5.0/dereeper/package_tassel_5_0/097d4c366e0d/bin/lib/batik-svggen.jar:/work/GALAXY/galaxy/dependencies/tassel/5.0/dereeper/package_tassel_5_0/097d4c366e0d/bin/lib/batik-parser.jar:/work/GALAXY/galaxy/dependencies/tassel/5.0/dereeper/package_tassel_5_0/097d4c366e0d/bin/sTASSEL.jar
2 Memory Settings: -Xms512m -Xmx1536m
3 Tassel Pipeline Arguments: -fork1 -h /work/GALAXY/galaxy/database/files/047/dataset_47692.dat -filterAlign -filterAlignMinFreq 0.05 -fork2 -r /work/GALAXY/galaxy/database/files/022/dataset_22503.dat -fork3 -q /work/GALAXY/galaxy/database/files/047/dataset_47687.dat -excludeLastTrait -combineA -input1 -input2 -input3 -intersect -glm -export tmpdir103174/TASSELGLM -runfork1 -runfork2 -runfork3
4 [main] INFO net.maizegenetics.tassel.TasselLogging - Tassel Version: 5.2.4 Date: February 19, 2015
5 [main] INFO net.maizegenetics.tassel.TasselLogging - Max Available Memory Reported by JVM: 1365 MB
6 [main] INFO net.maizegenetics.tassel.TasselLogging - Java Version: 1.8.0_31
7 [main] INFO net.maizegenetics.tassel.TasselLogging - OS: Linux
8 [main] INFO net.maizegenetics.pipeline.TasselPipeline - Tassel Pipeline Arguments: [-fork1, -h, /work/GALAXY/galaxy/database/files/047/dataset_47692.dat, -filterAlign, -filterAlignMinFreq, 0.05, -fork2, -r, /work/GALAXY/galaxy/database/files/022/dataset_22503.dat, -fork3, -q, /work/GALAXY/galaxy/database/files/047/dataset_47687.dat, -excludeLastTrait, -combineA, -input1, -input2, -input3, -intersect, -glm, -export, tmpdir103174/TASSELGLM, -runfork1, -runfork2, -runfork3]
9 [main] INFO net.maizegenetics.pipeline.TasselPipeline - loadFile: /work/GALAXY/galaxy/database/files/047/dataset_47692.dat
10 [main] INFO net.maizegenetics.pipeline.TasselPipeline - loadFile: /work/GALAXY/galaxy/database/files/022/dataset_22503.dat
11 [main] INFO net.maizegenetics.pipeline.TasselPipeline - loadFile: /work/GALAXY/galaxy/database/files/047/dataset_47687.dat
12 net.maizegenetics.analysis.data.FileLoadPlugin
13 net.maizegenetics.analysis.filter.FilterAlignmentPlugin
14 net.maizegenetics.analysis.data.CombineDataSetsPlugin
15 net.maizegenetics.analysis.data.IntersectionAlignmentPlugin
16 net.maizegenetics.analysis.association.FixedEffectLMPlugin
17 net.maizegenetics.analysis.data.ExportMultiplePlugin
18 net.maizegenetics.analysis.data.FileLoadPlugin
19 net.maizegenetics.analysis.data.FileLoadPlugin
20 net.maizegenetics.analysis.filter.FilterTraitsPlugin
21 [pool-1-thread-2] INFO net.maizegenetics.pipeline.TasselPipeline - net.maizegenetics.analysis.data.FileLoadPlugin: progress: 100%
22 [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.
23 [Thread-4] INFO net.maizegenetics.plugindef.AbstractPlugin - net.maizegenetics.analysis.data.CombineDataSetsPlugin 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.
24 [pool-1-thread-3] INFO net.maizegenetics.pipeline.TasselPipeline - net.maizegenetics.analysis.data.FileLoadPlugin: progress: 100%
25 [pool-1-thread-1] INFO net.maizegenetics.pipeline.TasselPipeline - net.maizegenetics.analysis.data.FileLoadPlugin: progress: 100%
26 [pool-1-thread-1] INFO net.maizegenetics.analysis.filter.FilterAlignmentPlugin - Resulting Number Sites: 12363
27 [pool-1-thread-1] INFO net.maizegenetics.pipeline.TasselPipeline - net.maizegenetics.analysis.filter.FilterAlignmentPlugin: progress: 100%
28 [pool-1-thread-1] INFO net.maizegenetics.pipeline.TasselPipeline - net.maizegenetics.analysis.data.FileLoadPlugin: progress: 100%
29 [main] WARN net.maizegenetics.pipeline.TasselPipeline - parseArgs: NOTE: The -glm flags are deprecated.
30 parseArgs: PLEASE RUN THIS COMMAND TO GET USAGE: ./run_pipeline.pl -FixedEffectLMPlugin
31
32 [Thread-35] INFO net.maizegenetics.pipeline.TasselPipeline - net.maizegenetics.analysis.data.IntersectionAlignmentPlugin: progress: 100%
33 [Thread-35] INFO net.maizegenetics.plugindef.AbstractPlugin -
34 FixedEffectLMPlugin Parameters
35 phenoOnly: false
36 saveToFile: false
37 siteFile: null
38 alleleFile: null
39 maxP: 1.0
40 permute: false
41 nperm: 0
42 genotypeComponent: Genotype
43
44 [Thread-35] INFO net.maizegenetics.matrixalgebra.Matrix.DoubleMatrixFactory - TasselBlas library for system-specific BLAS/LAPACK not found. Using system-independent EJML for DoubleMatrix operations.
45 [Thread-35] INFO net.maizegenetics.pipeline.TasselPipeline - net.maizegenetics.analysis.association.FixedEffectLMPlugin: progress: 0%
46 [Thread-35] INFO net.maizegenetics.pipeline.TasselPipeline - net.maizegenetics.analysis.association.FixedEffectLMPlugin: progress: 10%
47 [Thread-35] INFO net.maizegenetics.pipeline.TasselPipeline - net.maizegenetics.analysis.association.FixedEffectLMPlugin: progress: 20%
48 [Thread-35] INFO net.maizegenetics.pipeline.TasselPipeline - net.maizegenetics.analysis.association.FixedEffectLMPlugin: progress: 30%
49 [Thread-35] INFO net.maizegenetics.pipeline.TasselPipeline - net.maizegenetics.analysis.association.FixedEffectLMPlugin: progress: 40%
50 [Thread-35] INFO net.maizegenetics.pipeline.TasselPipeline - net.maizegenetics.analysis.association.FixedEffectLMPlugin: progress: 50%
51 [Thread-35] INFO net.maizegenetics.pipeline.TasselPipeline - net.maizegenetics.analysis.association.FixedEffectLMPlugin: progress: 60%
52 [Thread-35] INFO net.maizegenetics.pipeline.TasselPipeline - net.maizegenetics.analysis.association.FixedEffectLMPlugin: progress: 70%
53 [Thread-35] INFO net.maizegenetics.pipeline.TasselPipeline - net.maizegenetics.analysis.association.FixedEffectLMPlugin: progress: 80%
54 [Thread-35] INFO net.maizegenetics.pipeline.TasselPipeline - net.maizegenetics.analysis.association.FixedEffectLMPlugin: progress: 90%
55 [Thread-35] INFO net.maizegenetics.analysis.data.ExportPlugin - performFunction: wrote dataset: GLM_Stats_dataset_47692_chrChr1_Chr10_Chr11_Chr12_Chr2_Chr3_Chr4_Chr5_Chr6_Chr7_Chr8_Chr9_4299-22650481 + dataset_22503 + Filtered_dataset_47687 to file: /work/GALAXY/galaxy/database/job_working_directory/025/25260/working/tmpdir103174/TASSELGLM1.txt
56 [Thread-35] INFO net.maizegenetics.analysis.data.ExportMultiplePlugin - Datum: GLM_Stats_dataset_47692_chrChr1_Chr10_Chr11_Chr12_Chr2_Chr3_Chr4_Chr5_Chr6_Chr7_Chr8_Chr9_4299-22650481 + dataset_22503 + Filtered_dataset_47687 Written to: /work/GALAXY/galaxy/database/job_working_directory/025/25260/working/tmpdir103174/TASSELGLM1.txt
57 [Thread-35] INFO net.maizegenetics.analysis.data.ExportPlugin - performFunction: wrote dataset: GLM_Genotypes_dataset_47692_chrChr1_Chr10_Chr11_Chr12_Chr2_Chr3_Chr4_Chr5_Chr6_Chr7_Chr8_Chr9_4299-22650481 + dataset_22503 + Filtered_dataset_47687 to file: /work/GALAXY/galaxy/database/job_working_directory/025/25260/working/tmpdir103174/TASSELGLM2.txt
58 [Thread-35] INFO net.maizegenetics.analysis.data.ExportMultiplePlugin - Datum: GLM_Genotypes_dataset_47692_chrChr1_Chr10_Chr11_Chr12_Chr2_Chr3_Chr4_Chr5_Chr6_Chr7_Chr8_Chr9_4299-22650481 + dataset_22503 + Filtered_dataset_47687 Written to: /work/GALAXY/galaxy/database/job_working_directory/025/25260/working/tmpdir103174/TASSELGLM2.txt
59 [Thread-35] INFO net.maizegenetics.pipeline.TasselPipeline - net.maizegenetics.analysis.association.FixedEffectLMPlugin: progress: 100%