Error with TagstoSNPByAlignmentPlugin- String index out of range:113

[Bill Holdsworth]

Hi Jeff,

I'm experiencing an error in the TASSEL SNP Discovery Pipeline that I don't see documented on the online forum.

I'm at the step where the TagsToSNPByAlignmentPlugin should output hapmap files for each chromosome. At chr:405, I get the following error message:

 Exception in thread "Thread-0" java.lang.StringIndexOutOfBoundsException: String index out of range: 113

    at java.lang.AbstractStringBuilder.substring(AbstractStringBuilder.java:870)
    at java.lang.StringBuilder.substring(StringBuilder.java:72)
    at net.maizegenetics.gbs.pipeline.TagsToSNPByAlignmentPlugin.addRefTag(TagsToSNPByAlignmentPlugin.java:748)
    at net.maizegenetics.gbs.pipeline.TagsToSNPByAlignmentPlugin.addSitesToMutableAlignment(TagsToSNPByAlignmentPlugin.java:399)
    at net.maizegenetics.gbs.pipeline.TagsToSNPByAlignmentPlugin.runTagsToSNPByAlignment(TagsToSNPByAlignmentPlugin.java:348)
    at net.maizegenetics.gbs.pipeline.TagsToSNPByAlignmentPlugin.performFunction(TagsToSNPByAlignmentPlugin.java:96)
    at net.maizegenetics.plugindef.AbstractPlugin.dataSetReturned(AbstractPlugin.java:201)
    at net.maizegenetics.plugindef.ThreadedPluginListener.run(ThreadedPluginListener.java:29)

I've run it a few times now, and it always stops at the same point. I don't see any obvious errors with either of the input files (topm or MergedTagsbyTaxa). The reason that the chromosome number is so high is that the genome is in scaffolds right now rather than chromosomes. But that shouldn't make any difference, should it? Can you shed any light on this?

Thanks!
Bill

[Terry Casstevens]

Hi Bill,

Can you send me the command you are running? Which version of Tassel
are you using?

Terry

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[Bill Holdsworth]

Hi Terry,

The command is: /programs/tassel/run_pipeline.pl -fork1 -TagsToSNPByAlignmentPlugin -i mergedTBT/SquashBgene.tbt.byte -y -m topm/AllSquashMasterTags.topm -mUpd topm/AllSquashMasterTags_updated.topm -Xmx12g -o hapmap/Squash_scaffold+.hmp.txt -mnMAF 0.25 -mnMAC 800 -ref zucchini_genome-0.1_TASSEL_format.fasta -mnLCov .25 -sC 1 -eC 1000 -endPlugin -runfork1

I'm actually not sure which version I'm using. I'm using a cbsu workstation (cbsum1c2b002)-->/programs/tassel/ I don't see any documentation in the directory or in the scripts to indicate which version it is. I would assume v3?

Thanks for your help!
Bill

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Bill Holdsworth
PhD Candidate
Plant Breeding and Genetics
Cornell University
253 Emerson Hall
Ithaca, NY 14853

[Terry Casstevens]

We may need Jeff's help when he returns from vacation.

Just guessing... Do you know if that tag on chr. 405 is in the reference file?

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[Jeff Glaubitz]

Hi Bill,

My best guess is that the tag locus on chr405 that the function addRefTag() is trying to obtain the reference genome tag for falls off of the end of the contig. You could fix this by padding either end of the contig with 100 A's. Either that, or omit the -ref option.

Best,

Jeff

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Jeff Glaubitz
Project Manager
Genetic Architecture of Maize and Teosinte
National Science Foundation award 0820619
http://www.panzea.org
Institute for Genomic Diversity
Cornell University
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Ithaca, NY 14853
Phone: 607-255-1386
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[Bill Holdsworth]

That seemed to be the problem. No error anymore. Thanks, Jeff!

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