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Hi, I cannot load a hapmap with -/T etc, which codes for a deletion. Is there a value I could use so I can replace "-" as a deletion. Error: " Error Parsing RS#### -/T chr 1.... BuildFromHapMap: SNP Named: RS #### has illegal Value 11 11 = "-"
thanks dlc
Terry Casstevens
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Mar 6, 2015, 9:51:56 AM3/6/15
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Hapmap doesn't have / between the values. -T should work. Look at
this document how to report the issue. And consider sending me the
file privately.
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Hi, This error does not occur in Tassel 4, but when I export files in Tassel4 I get an error. dlc
Terry Casstevens
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Mar 6, 2015, 9:56:44 AM3/6/15
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Please send me step by step how to reproduce.
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Hi Terry, Tassel 4 will read file and precisely save tree file, but cannot export hapmap or VCF file. Tassel 5 will NOT read (see debug log below). Both the writing of file in Tassel 4 and reading in Tassel 5 stops at the 782 line with a "-" for a deletion
rs25591 -/TT chr22 16597078 + ncbi_b36 ........
I have attached an abbreviate file where the 11-12 row has the same exact information and same error (except the line number)
BOTTOM line, we cannot read/write Hapmap with deletion in the "alleles" column (2nd column). Any suggestions would be welcomed.
cheers Doug
LOG FILE DEBUG file [Thread-7] INFO net.maizegenetics.tassel.TasselLogging - Tassel Version: 5.2.6 Date: March 12, 2015 [Thread-7] INFO net.maizegenetics.tassel.TasselLogging - Max Available Memory Reported by JVM: 7282 MB [Thread-7] INFO net.maizegenetics.tassel.TasselLogging - Java Version: 1.8.0_40 [Thread-7] INFO net.maizegenetics.tassel.TasselLogging - OS: Mac OS X [pool-2-thread-1] ERROR net.maizegenetics.dna.snp.io.BuilderFromHapMap - Error parsing this row rs25591 -/TT chr22 16597078 + ncbi_b36 sanger urn:LSID:illumina.hapmap.org:Protocol:Human_1M_BeadChip:3 urn:LSID:sanger.hapmap.org:Assay:H1Mrs25591:3 urn:lsid:dcc.hapmap.org:Panel:US_African-30-trios:4 QC+ DI II II II II II II II II II II II II II II II II II II II II II II II II II II II II II II II II II II II II II II II II II II II II II II II II II DI II II II II II II II II II II II II II II II II II II II II II II II II II II II II II II II II II II II II [pool-2-thread-1] DEBUG net.maizegenetics.dna.snp.io.BuilderFromHapMap - BuilderFromHapMap: SNP Named: rs25591 has illegal value: DI java.lang.IllegalStateException: BuilderFromHapMap: SNP Named: rs25591 has illegal value: DI at net.maizegenetics.dna.snp.io.BuilderFromHapMap$ProcessHapmapBlock.call(BuilderFromHapMap.java:281) at net.maizegenetics.dna.snp.io.BuilderFromHapMap$ProcessHapmapBlock.call(BuilderFromHapMap.java:198) at java.util.concurrent.FutureTask.run(FutureTask.java:266) at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142) at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617) at java.lang.Thread.run(Thread.java:745) [Thread-8] DEBUG net.maizegenetics.dna.snp.io.BuilderFromHapMap - java.lang.IllegalStateException: BuilderFromHapMap: Error Parsing Line: rs25591 -/TT chr22 165970... BuilderFromHapMap: SNP Named: rs25591 has illegal value: DI java.util.concurrent.ExecutionException: java.lang.IllegalStateException: BuilderFromHapMap: Error Parsing Line: rs25591 -/TT chr22 165970... BuilderFromHapMap: SNP Named: rs25591 has illegal value: DI at java.util.concurrent.FutureTask.report(FutureTask.java:122) at java.util.concurrent.FutureTask.get(FutureTask.java:192) at net.maizegenetics.dna.snp.io.BuilderFromHapMap.build(BuilderFromHapMap.java:158) at net.maizegenetics.dna.snp.ImportUtils.readFromHapmap(ImportUtils.java:84) at net.maizegenetics.analysis.data.FileLoadPlugin.processDatum(FileLoadPlugin.java:324) at net.maizegenetics.analysis.data.FileLoadPlugin.performFunction(FileLoadPlugin.java:173) at net.maizegenetics.plugindef.AbstractPlugin.dataSetReturned(AbstractPlugin.java:1444) at net.maizegenetics.plugindef.ThreadedPluginListener.run(ThreadedPluginListener.java:29) Caused by: java.lang.IllegalStateException: BuilderFromHapMap: Error Parsing Line: rs25591 -/TT chr22 165970... BuilderFromHapMap: SNP Named: rs25591 has illegal value: DI at net.maizegenetics.dna.snp.io.BuilderFromHapMap$ProcessHapmapBlock.call(BuilderFromHapMap.java:295) at net.maizegenetics.dna.snp.io.BuilderFromHapMap$ProcessHapmapBlock.call(BuilderFromHapMap.java:198) at java.util.concurrent.FutureTask.run(FutureTask.java:266) at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142) at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617) at java.lang.Thread.run(Thread.java:745) [Thread-8] ERROR net.maizegenetics.analysis.data.FileLoadPlugin - java.lang.IllegalStateException: BuilderFromHapMap: Error Parsing Line: rs25591 -/TT chr22 165970... BuilderFromHapMap: SNP Named: rs25591 has illegal value: DI java.lang.IllegalStateException: java.lang.IllegalStateException: BuilderFromHapMap: Error Parsing Line: rs25591 -/TT chr22 165970... BuilderFromHapMap: SNP Named: rs25591 has illegal value: DI at net.maizegenetics.dna.snp.io.BuilderFromHapMap.build(BuilderFromHapMap.java:193) at net.maizegenetics.dna.snp.ImportUtils.readFromHapmap(ImportUtils.java:84) at net.maizegenetics.analysis.data.FileLoadPlugin.processDatum(FileLoadPlugin.java:324) at net.maizegenetics.analysis.data.FileLoadPlugin.performFunction(FileLoadPlugin.java:173) at net.maizegenetics.plugindef.AbstractPlugin.dataSetReturned(AbstractPlugin.java:1444) at net.maizegenetics.plugindef.ThreadedPluginListener.run(ThreadedPluginListener.java:29)