deletions

Douglas Crawford

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Mar 6, 2015, 9:36:04 AM3/6/15

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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.

https://bitbucket.org/tasseladmin/tassel-5-source/wiki/docs/ReportingTassel5Issues.pdf

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Douglas Crawford

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Mar 6, 2015, 9:53:08 AM3/6/15

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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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Douglas Crawford

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Mar 16, 2015, 2:10:11 PM3/16/15

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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)

ASW_short22.txt

Terry Casstevens

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Mar 16, 2015, 4:17:27 PM3/16/15

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The error message is saying DI is an invalid genotype. Deletions are
"-" and insertions are "+"

https://bitbucket.org/tasseladmin/tassel-5-source/wiki/UserManual/NucleotideCodes/NucleotideCodes

> https://groups.google.com/d/msgid/tassel/5c9623e3-62f0-4a19-a873-ee32a3633e83%40googlegroups.com.

Douglas Crawford

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Mar 17, 2015, 7:46:54 AM3/17/15

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Terry,
Thank you. I should have notice that.
cheers
dlc

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