Problem with loading file to TASSEL5
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yyo...@hotmail.com
Oct 12, 2016, 11:27:36 AM10/12/16
to TASSEL - Trait Analysis by Association, Evolution and Linkage
I am having problem with loading hapmap file into TASSEL. Error message attached & below. Please help.
Sue
[Thread-6] INFO net.maizegenetics.tassel.TasselLogging - Tassel Version: 5.2.30 Date: September 1, 2016
[Thread-6] INFO net.maizegenetics.tassel.TasselLogging - Max Available Memory Reported by JVM: 3506 MB
[Thread-6] INFO net.maizegenetics.tassel.TasselLogging - Java Version: 1.8.0_91
[Thread-6] INFO net.maizegenetics.tassel.TasselLogging - OS: Windows 7
[Thread-6] INFO net.maizegenetics.tassel.TasselLogging - Number of Processors: 4
[Thread-6] INFO net.maizegenetics.plugindef.AbstractPlugin - Finished net.maizegenetics.tassel.TasselLogging: time: Oct 12, 2016 11:10:18
[Thread-7] INFO net.maizegenetics.analysis.data.FileLoadPlugin - Start Loading File: U:\Flinders\project\Tassel\CIMMYT_hapmap_noambig_poschange.txt time: Oct 12, 2016 11:12:12
[Thread-7] DEBUG net.maizegenetics.dna.snp.io.BuilderFromHapMap - BuilderFromHapMap: Genotype coded wrong use 1 or 2 letters per genotype. Or first site has incorrect number of values.
java.lang.IllegalStateException: BuilderFromHapMap: Genotype coded wrong use 1 or 2 letters per genotype. Or first site has incorrect number of values.
at net.maizegenetics.dna.snp.io.BuilderFromHapMap.build(BuilderFromHapMap.java:122)
at net.maizegenetics.dna.snp.ImportUtils.readFromHapmap(ImportUtils.java:141)
at net.maizegenetics.analysis.data.FileLoadPlugin.processDatum(FileLoadPlugin.java:422)
at net.maizegenetics.analysis.data.FileLoadPlugin.performFunction(FileLoadPlugin.java:249)
at net.maizegenetics.plugindef.AbstractPlugin.dataSetReturned(AbstractPlugin.java:1652)
at net.maizegenetics.plugindef.ThreadedPluginListener.run(ThreadedPluginListener.java:29)
[Thread-7] ERROR net.maizegenetics.analysis.data.FileLoadPlugin - BuilderFromHapMap: Genotype coded wrong use 1 or 2 letters per genotype. Or first site has incorrect number of values.
java.lang.IllegalStateException: BuilderFromHapMap: Genotype coded wrong use 1 or 2 letters per genotype. Or first site has incorrect number of values.
at net.maizegenetics.dna.snp.io.BuilderFromHapMap.build(BuilderFromHapMap.java:193)
at net.maizegenetics.dna.snp.ImportUtils.readFromHapmap(ImportUtils.java:141)
at net.maizegenetics.analysis.data.FileLoadPlugin.processDatum(FileLoadPlugin.java:422)
at net.maizegenetics.analysis.data.FileLoadPlugin.performFunction(FileLoadPlugin.java:249)
at net.maizegenetics.plugindef.AbstractPlugin.dataSetReturned(AbstractPlugin.java:1652)
at net.maizegenetics.plugindef.ThreadedPluginListener.run(ThreadedPluginListener.java:29)
[Thread-7] DEBUG net.maizegenetics.analysis.data.FileLoadPlugin - BuilderFromHapMap: Genotype coded wrong use 1 or 2 letters per genotype. Or first site has incorrect number of values.
java.lang.IllegalStateException: BuilderFromHapMap: Genotype coded wrong use 1 or 2 letters per genotype. Or first site has incorrect number of values.
at net.maizegenetics.dna.snp.io.BuilderFromHapMap.build(BuilderFromHapMap.java:193)
at net.maizegenetics.dna.snp.ImportUtils.readFromHapmap(ImportUtils.java:141)
at net.maizegenetics.analysis.data.FileLoadPlugin.processDatum(FileLoadPlugin.java:422)
at net.maizegenetics.analysis.data.FileLoadPlugin.performFunction(FileLoadPlugin.java:249)
at net.maizegenetics.plugindef.AbstractPlugin.dataSetReturned(AbstractPlugin.java:1652)
at net.maizegenetics.plugindef.ThreadedPluginListener.run(ThreadedPluginListener.java:29)
[Thread-7] INFO net.maizegenetics.analysis.data.FileLoadPlugin - Nothing Loaded for File: U:\Flinders\project\Tassel\CIMMYT_hapmap_noambig_poschange.txt time: Oct 12, 2016 11:12:21
[Thread-8] INFO net.maizegenetics.plugindef.AbstractPlugin - Starting net.maizegenetics.tassel.TasselLogging: time: Oct 12, 2016 11:39:18
[Thread-8] INFO net.maizegenetics.plugindef.AbstractPlugin - Finished net.maizegenetics.tassel.TasselLogging: time: Oct 12, 2016 11:39:18
[Thread-6] INFO net.maizegenetics.tassel.TasselLogging - Max Available Memory Reported by JVM: 3506 MB
[Thread-6] INFO net.maizegenetics.tassel.TasselLogging - Java Version: 1.8.0_91
[Thread-6] INFO net.maizegenetics.tassel.TasselLogging - OS: Windows 7
[Thread-6] INFO net.maizegenetics.tassel.TasselLogging - Number of Processors: 4
[Thread-6] INFO net.maizegenetics.plugindef.AbstractPlugin - Finished net.maizegenetics.tassel.TasselLogging: time: Oct 12, 2016 11:10:18
[Thread-7] INFO net.maizegenetics.analysis.data.FileLoadPlugin - Start Loading File: U:\Flinders\project\Tassel\CIMMYT_hapmap_noambig_poschange.txt time: Oct 12, 2016 11:12:12
[Thread-7] DEBUG net.maizegenetics.dna.snp.io.BuilderFromHapMap - BuilderFromHapMap: Genotype coded wrong use 1 or 2 letters per genotype. Or first site has incorrect number of values.
java.lang.IllegalStateException: BuilderFromHapMap: Genotype coded wrong use 1 or 2 letters per genotype. Or first site has incorrect number of values.
at net.maizegenetics.dna.snp.io.BuilderFromHapMap.build(BuilderFromHapMap.java:122)
at net.maizegenetics.dna.snp.ImportUtils.readFromHapmap(ImportUtils.java:141)
at net.maizegenetics.analysis.data.FileLoadPlugin.processDatum(FileLoadPlugin.java:422)
at net.maizegenetics.analysis.data.FileLoadPlugin.performFunction(FileLoadPlugin.java:249)
at net.maizegenetics.plugindef.AbstractPlugin.dataSetReturned(AbstractPlugin.java:1652)
at net.maizegenetics.plugindef.ThreadedPluginListener.run(ThreadedPluginListener.java:29)
[Thread-7] ERROR net.maizegenetics.analysis.data.FileLoadPlugin - BuilderFromHapMap: Genotype coded wrong use 1 or 2 letters per genotype. Or first site has incorrect number of values.
java.lang.IllegalStateException: BuilderFromHapMap: Genotype coded wrong use 1 or 2 letters per genotype. Or first site has incorrect number of values.
at net.maizegenetics.dna.snp.io.BuilderFromHapMap.build(BuilderFromHapMap.java:193)
at net.maizegenetics.dna.snp.ImportUtils.readFromHapmap(ImportUtils.java:141)
at net.maizegenetics.analysis.data.FileLoadPlugin.processDatum(FileLoadPlugin.java:422)
at net.maizegenetics.analysis.data.FileLoadPlugin.performFunction(FileLoadPlugin.java:249)
at net.maizegenetics.plugindef.AbstractPlugin.dataSetReturned(AbstractPlugin.java:1652)
at net.maizegenetics.plugindef.ThreadedPluginListener.run(ThreadedPluginListener.java:29)
[Thread-7] DEBUG net.maizegenetics.analysis.data.FileLoadPlugin - BuilderFromHapMap: Genotype coded wrong use 1 or 2 letters per genotype. Or first site has incorrect number of values.
java.lang.IllegalStateException: BuilderFromHapMap: Genotype coded wrong use 1 or 2 letters per genotype. Or first site has incorrect number of values.
at net.maizegenetics.dna.snp.io.BuilderFromHapMap.build(BuilderFromHapMap.java:193)
at net.maizegenetics.dna.snp.ImportUtils.readFromHapmap(ImportUtils.java:141)
at net.maizegenetics.analysis.data.FileLoadPlugin.processDatum(FileLoadPlugin.java:422)
at net.maizegenetics.analysis.data.FileLoadPlugin.performFunction(FileLoadPlugin.java:249)
at net.maizegenetics.plugindef.AbstractPlugin.dataSetReturned(AbstractPlugin.java:1652)
at net.maizegenetics.plugindef.ThreadedPluginListener.run(ThreadedPluginListener.java:29)
[Thread-7] INFO net.maizegenetics.analysis.data.FileLoadPlugin - Nothing Loaded for File: U:\Flinders\project\Tassel\CIMMYT_hapmap_noambig_poschange.txt time: Oct 12, 2016 11:12:21
[Thread-8] INFO net.maizegenetics.plugindef.AbstractPlugin - Starting net.maizegenetics.tassel.TasselLogging: time: Oct 12, 2016 11:39:18
[Thread-8] INFO net.maizegenetics.plugindef.AbstractPlugin - Finished net.maizegenetics.tassel.TasselLogging: time: Oct 12, 2016 11:39:18
Terry Casstevens
Oct 12, 2016, 3:22:12 PM10/12/16
to Tassel User Group
"Genotype coded wrong use 1 or 2 letters per genotype. Or first site
has incorrect number of values"
https://bitbucket.org/tasseladmin/tassel-5-source/wiki/UserManual/Load/Load#markdown-header-hapmap
has incorrect number of values"
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