Problem with -combine# in ./run_pipeline.p

[ningz...@gmail.com]

Hi, I'm new with TASSEL.

I'm having problem with the "-combine":

So I cd to TASSEL5 directory, and used command:

" ./run_pipeline.pl -fork1 -h TutorialData/mdp_genotype.hmp.txt -fork2 -r TutorialData/mdp_phenotype.txt -combine3 -input1 -input2 -intersect -FixedEffectLMPlugin -endPlugin -export glm_output"

But I cannot get glm results.

The output of the command is :

"./lib/jhdf5-14.12.5.jar:./lib/jfreesvg-3.2.jar:./lib/biojava-phylo-4.0.0.jar:./lib/slf4j-simple

-1.7.10.jar:./lib/biojava-core-4.0.0.jar:./lib/guava-22.0.jar:./lib/htsjdk-2.14.0.jar:./lib/sql

ite-jdbc-3.8.5-pre1.jar:./lib/commons-math3-3.4.1.jar:./lib/snappy-java-1.1.1.6.jar:./lib/itext

pdf-5.1.0.jar:./lib/ejml-0.23.jar:./lib/commons-codec-1.10.jar:./lib/log4j-1.2.13.jar:./lib/mai

l-1.4.jar:./lib/sTASSEL.jar:./lib/junit-4.10.jar:./lib/trove-3.0.3.jar:./lib/jfreechart-1.0.19.

jar:./lib/ahocorasick-0.2.4.jar:./lib/forester-1.038.jar:./lib/postgresql-9.4-1201.jdbc41.jar:.

/lib/biojava-alignment-4.0.0.jar:./lib/colt-1.2.0.jar:./lib/jcommon-1.0.23.jar:./lib/slf4j-api-

1.7.10.jar:./lib/json-simple-1.1.1.jar:./lib/javax.json-1.0.4.jar:./sTASSEL.jar

Memory Settings: -Xms512m -Xmx1536m

Tassel Pipeline Arguments: -fork1 -h TutorialData/mdp_genotype.hmp.txt -fork2 -r TutorialData/m

dp_phenotype.txt -combine3 -input1 -input2 -intersect -FixedEffectLMPlugin -endPlugin -export g

lm_output

[main] INFO net.maizegenetics.tassel.TasselLogging - Tassel Version: 5.2.42  Date: February 1, 

2018

[main] INFO net.maizegenetics.tassel.TasselLogging - Max Available Memory Reported by JVM: 1365

 MB

[main] INFO net.maizegenetics.tassel.TasselLogging - Java Version: 1.8.0_161

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

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

[main] INFO net.maizegenetics.pipeline.TasselPipeline - Tassel Pipeline Arguments: [-fork1, -h,

 TutorialData/mdp_genotype.hmp.txt, -fork2, -r, TutorialData/mdp_phenotype.txt, -combine3, -inp

ut1, -input2, -intersect, -FixedEffectLMPlugin, -endPlugin, -export, glm_output]

[ForkJoinPool.commonPool-worker-2] INFO net.maizegenetics.plugindef.AbstractPlugin - Starting n

et.maizegenetics.analysis.data.FileLoadPlugin: time: Feb 22, 2018 23:45:45

[ForkJoinPool.commonPool-worker-1] INFO net.maizegenetics.plugindef.AbstractPlugin - Starting n

et.maizegenetics.analysis.data.FileLoadPlugin: time: Feb 22, 2018 23:45:45

[ForkJoinPool.commonPool-worker-1] INFO net.maizegenetics.plugindef.AbstractPlugin - 

FileLoadPlugin Parameters

format: Hapmap

sortPositions: false

[ForkJoinPool.commonPool-worker-2] INFO net.maizegenetics.plugindef.AbstractPlugin - 

FileLoadPlugin Parameters

format: Phenotype

sortPositions: false

[ForkJoinPool.commonPool-worker-1] INFO net.maizegenetics.analysis.data.FileLoadPlugin - Start 

Loading File: TutorialData/mdp_genotype.hmp.txt time: Feb 22, 2018 23:45:45

[ForkJoinPool.commonPool-worker-2] INFO net.maizegenetics.analysis.data.FileLoadPlugin - Start 

Loading File: TutorialData/mdp_phenotype.txt time: Feb 22, 2018 23:45:45

[ForkJoinPool.commonPool-worker-2] INFO net.maizegenetics.analysis.data.FileLoadPlugin - Finish

ed Loading File: TutorialData/mdp_phenotype.txt time: Feb 22, 2018 23:45:46

[ForkJoinPool.commonPool-worker-2] INFO net.maizegenetics.plugindef.AbstractPlugin - Finished n

et.maizegenetics.analysis.data.FileLoadPlugin: time: Feb 22, 2018 23:45:46

[ForkJoinPool.commonPool-worker-2] INFO net.maizegenetics.pipeline.TasselPipeline - net.maizege

netics.analysis.data.FileLoadPlugin: time: Feb 22, 2018 23:45:46: progress: 100%

[ForkJoinPool.commonPool-worker-2] INFO net.maizegenetics.plugindef.AbstractPlugin - net.maizeg

enetics.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 div

erse samples. Bioinformatics 23:2633-2635.

[ForkJoinPool.commonPool-worker-1] INFO net.maizegenetics.pipeline.TasselPipeline - net.maizege

netics.analysis.data.FileLoadPlugin: time: Feb 22, 2018 23:45:46: progress: 100%

[ForkJoinPool.commonPool-worker-1] INFO net.maizegenetics.analysis.data.FileLoadPlugin - Finish

ed Loading File: TutorialData/mdp_genotype.hmp.txt time: Feb 22, 2018 23:45:46

Genotype Table Name: mdp_genotype

Number of Taxa: 281

Number of Sites: 3093

Sites x Taxa: 869133

Chromosomes...

1: start site: 0 (157104) last site: 539 (299170077) total: 540

2: start site: 540 (736367) last site: 932 (234574991) total: 393

3: start site: 933 (1240310) last site: 1287 (229544509) total: 355

4: start site: 1288 (139753) last site: 1606 (245131801) total: 319

5: start site: 1607 (656148) last site: 1963 (216431558) total: 357

6: start site: 1964 (2379148) last site: 2176 (167883450) total: 213

7: start site: 2177 (729478) last site: 2422 (170346253) total: 246

8: start site: 2423 (169137) last site: 2678 (172323795) total: 256

9: start site: 2679 (3873116) last site: 2891 (151289948) total: 213

10: start site: 2892 (838970) last site: 3092 (148907116) total: 201

[ForkJoinPool.commonPool-worker-1] INFO net.maizegenetics.plugindef.AbstractPlugin - Finished n

et.maizegenetics.analysis.data.FileLoadPlugin: time: Feb 22, 2018 23:45:46

[ForkJoinPool.commonPool-worker-1] INFO net.maizegenetics.pipeline.TasselPipeline - net.maizege

netics.analysis.data.FileLoadPlugin: time: Feb 22, 2018 23:45:46: progress: 100%

"

I also tried "./run_pipeline.pl -fork1 -h TutorialData/mdp_genotype.hmp.txt -fork2 -r TutorialData/mdp_phenotype.txt -combine3 -input1 -input2 -intersect -export combined.txt -exportType Table -runfork1 -runfork2 ", also without the output file.

Can you help resolve this problem?

Thanks!!

[Terry Casstevens]

The build that I posted today fixes this problem

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[ningz...@gmail.com]

Thanks Terry,

I downloaded the latest build from https://tassel.bitbucket.io/installer/TASSEL_5_unix.sh

command : "./run_pipeline.pl -fork1 -h TutorialData/mdp_genotype.hmp.txt -fork2 -r TutorialData/mdp_phenotype.txt -combine3 -input1 -input2 -intersect -FixedEffectLMPlugin -endPlugin -export glm_output"

now returns new error message:

[Thread-6] 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-6] ERROR net.maizegenetics.plugindef.AbstractPlugin - There are more phenotype observations than taxa with genotypes. Either some taxa have multiple phenotypes or some taxa do not have genotypes. Tassel version 5 will not run GLM when that is the case. Be sure to use an intersect join to merge genotypes and phenotypes.

Can you help look at this?

Thanks!!

[Peter Bradbury]

The problem is that mdp_phenotype.txt contains replicated taxa, which causes the error you saw. If you use mdp_traits.txt instead GLM will run. Alternatively, use GLM with mdp_phenotype.txt alone to generate BLUE's then combine that with the genotype.

Peter