Hello everyone,
I am trying to run Tassel 4 in pipeline to compute MLM analysis (to do GWAS) on a server with Linux OS but I have some troubles to carry out. I think the error is related with the format of some of the files I’m using, but I don’t know exactly, the error message is “java.lang.IndexOutOfBoundsException: Index: 0, Size: 0”
I am using the following files (I also show the header of each one):
1) 1) Chr10.txt – Genotyping
<Annotated>
<Transposed> Yes
<Taxa_Number> 279
<Locus_Number> 33664
<Poly_Type> Catagorical
<Delimited_Values> Yes
<Taxon_Name> 4226 4722 33-16 38-11 …
<Chromosome_Number> <Genetic_Position> <Locus_Name> <Value>
2) 2) Permt_data_Borer_kernel.txt – this file contains 1000 permutations of BLUEs of 279 maize inbred lines.
<Trait> Permt1 Permt2 … Permt1000
4226 7.163 9.017 … 8.935
A554 8.708 7.887 … 7.491
CML52 6.979 7.887 … 8.365
.
.
3) 3) Population_structure_5k_SNP.txt
279 3 1
Q1 Q2 Q3
4226 0.216 0.107 0.677 …
4722 0.004 0.024 0.971 …
33-16 0.137 0.088 0.775 …
.
.
4) 4) Kinship_matrix_5k_SNP.txt
The script I'm using is:
run_pipeline.pl -fork1 -a Chr10.txt -fork2 -r Permt_data_Borer_kernel.txt -fork3 -p Population_structure_5k_SNP.txt -excludeLastTrait -fork4 -k Kinship_matrix_5k_SNP.txt -combine5 -input1 -input2 -input3 -union -combine6 -input5 -input4 -mlm -mlmVarCompEst P3D -mlmCompressionLevel Optimum -mlmMaxP 1e-3 -export mlm_BK_Chr10_output -runfork1 -runfork2 -runfork3 -runfork4
And the following is the error message:
Tassel Pipeline Arguments: -fork1 -a Chr10.txt -fork2 -r Permt_data_Borer_kernel.txt -fork3 -p Population_structure_5k_SNP.txt -excludeLastTrait -fork4 -k Kinship_matrix_5k_SNP.txt -combine5 -input1 -input2 -input3 -union -combine6 -input5 -input4 -mlm -mlmVarCompEst P3D -mlmCompressionLevel Optimum -mlmMaxP 1e-3 -export mlm_BK_Chr10_output -runfork1 -runfork2 -runfork3 -runfork4
Picked up _JAVA_OPTIONS: -Xmx2097152K
[main] INFO net.maizegenetics.pipeline.TasselPipeline - Tassel Version: 4.1.27 Date: April 11, 2013
[main] INFO net.maizegenetics.pipeline.TasselPipeline - Max Available Memory Reported by JVM: 1820 MB
[main] INFO net.maizegenetics.pipeline.TasselPipeline - loadFile: Chr10.txt
[main] INFO net.maizegenetics.pipeline.TasselPipeline - loadFile: Permt_data_Borer_kernel.txt
[main] INFO net.maizegenetics.pipeline.TasselPipeline - loadFile: Population_structure_5k_SNP.txt
[main] INFO net.maizegenetics.pipeline.TasselPipeline - loadFile: Kinship_matrix_5k_SNP.txt
net.maizegenetics.baseplugins.FileLoadPlugin
net.maizegenetics.baseplugins.CombineDataSetsPlugin
net.maizegenetics.baseplugins.UnionAlignmentPlugin
net.maizegenetics.baseplugins.CombineDataSetsPlugin
net.maizegenetics.baseplugins.MLMPlugin
net.maizegenetics.baseplugins.ExportMultiplePlugin
net.maizegenetics.baseplugins.FileLoadPlugin
net.maizegenetics.baseplugins.FileLoadPlugin
net.maizegenetics.baseplugins.FilterTraitsPlugin
net.maizegenetics.baseplugins.FileLoadPlugin
java.lang.IndexOutOfBoundsException: Index: 0, Size: 0
at java.util.ArrayList.RangeCheck(ArrayList.java:547)
at java.util.ArrayList.get(ArrayList.java:322)
at net.maizegenetics.baseplugins.FilterTraitsPlugin.performFunction(FilterTraitsPlugin.java:74)
at net.maizegenetics.plugindef.AbstractPlugin.dataSetReturned(AbstractPlugin.java:201)
at net.maizegenetics.plugindef.AbstractPlugin.fireDataSetReturned(AbstractPlugin.java:137)
at net.maizegenetics.baseplugins.FileLoadPlugin.performFunction(FileLoadPlugin.java:195)
at net.maizegenetics.plugindef.AbstractPlugin.dataSetReturned(AbstractPlugin.java:201)
at net.maizegenetics.plugindef.ThreadedPluginListener.run(ThreadedPluginListener.java:29)
[Thread-2] INFO net.maizegenetics.pipeline.TasselPipeline - net.maizegenetics.baseplugins.FileLoadPlugin: progress: 100%
[Thread-3] INFO net.maizegenetics.pipeline.TasselPipeline - net.maizegenetics.baseplugins.FileLoadPlugin: progress: 100%
[Thread-1] INFO net.maizegenetics.pipeline.TasselPipeline - net.maizegenetics.baseplugins.FileLoadPlugin: progress: 100%
[Thread-0] INFO net.maizegenetics.pipeline.TasselPipeline - net.maizegenetics.baseplugins.FileLoadPlugin: progress: 100%
Could someone help me?
Thanks
Fernando
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