Illegal "N" character causing error?

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Will Liao

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Oct 13, 2015, 1:55:37 PM10/13/15

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I am trying to get methylation ratios using Bis-SNP but get this error

##### ERROR ------------------------------------------------------------------------------------------

##### ERROR stack trace

org.broadinstitute.sting.utils.exceptions.ReviewedStingException: An error occurred during the traversal.

at org.broadinstitute.sting.gatk.executive.HierarchicalMicroScheduler.getTraversalError(HierarchicalMicroScheduler.java:356)

at org.broadinstitute.sting.gatk.executive.HierarchicalMicroScheduler.execute(HierarchicalMicroScheduler.java:105)

at org.broadinstitute.sting.gatk.GenomeAnalysisEngine.execute(GenomeAnalysisEngine.java:246)

at edu.usc.epigenome.uecgatk.bissnp.BisSNP.execute(BisSNP.java:170)

at org.broadinstitute.sting.commandline.CommandLineProgram.start(CommandLineProgram.java:236)

at org.broadinstitute.sting.commandline.CommandLineProgram.start(CommandLineProgram.java:146)

at edu.usc.epigenome.uecgatk.bissnp.BisSNP.main(BisSNP.java:107)

Caused by: java.lang.IllegalArgumentException: 78 is not a valid base character

at org.broadinstitute.sting.gatk.walkers.genotyper.DiploidGenotype.createHomGenotype(DiploidGenotype.java:86)

at edu.usc.epigenome.uecgatk.bissnp.BisulfiteSNPGenotypeLikelihoodsCalculationModel.setBsLikelihoods(BisulfiteSNPGenotypeLikelihoodsCalculationModel.j

ava:706)

at edu.usc.epigenome.uecgatk.bissnp.BisulfiteGenotyperEngine.calculateLikelihoods(BisulfiteGenotyperEngine.java:99)

at edu.usc.epigenome.uecgatk.bissnp.BisulfiteGenotyperEngine.calculateLikelihoodsAndGenotypes(BisulfiteGenotyperEngine.java:126)

at edu.usc.epigenome.uecgatk.bissnp.BisulfiteGenotyperEngine.<init>(BisulfiteGenotyperEngine.java:77)

at edu.usc.epigenome.uecgatk.bissnp.BisulfiteGenotyper.map(BisulfiteGenotyper.java:213)

at edu.usc.epigenome.uecgatk.bissnp.BisulfiteGenotyper.map(BisulfiteGenotyper.java:1)

at org.broadinstitute.sting.gatk.traversals.TraverseLoci.traverse(TraverseLoci.java:78)

at org.broadinstitute.sting.gatk.traversals.TraverseLoci.traverse(TraverseLoci.java:18)

at org.broadinstitute.sting.gatk.executive.ShardTraverser.call(ShardTraverser.java:72)

at java.util.concurrent.FutureTask.run(FutureTask.java:262)

at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1145)

at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:615)

at java.lang.Thread.run(Thread.java:745)

##### ERROR ------------------------------------------------------------------------------------------

##### ERROR A GATK RUNTIME ERROR has occurred (version 1.5-3-gbb2c10b):

##### ERROR

##### ERROR Please visit the wiki to see if this is a known problem

##### ERROR If not, please post the error, with stack trace, to the GATK forum

##### ERROR Visit our wiki for extensive documentation http://www.broadinstitute.org/gsa/wiki

##### ERROR Visit our forum to view answers to commonly asked questions http://getsatisfaction.com/gsa

##### ERROR

##### ERROR MESSAGE: An error occurred during the traversal.

##### ERROR ------------------------------------------------------------------------------------------

It seems the "78 is not a valid base character" refers to an N somewhere. I'm wondering how to fix/circumvent this position. I'm using the rheMac3 genome and it reproducibly effects chr10, but also I've seen it affect other chromosomes more sporadically.

Will Liao

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Oct 15, 2015, 5:36:14 PM10/15/15

to bissnp-help

Just to add to this, the occurrence in chr3 is reproducible in my BAM in the rheMac3 genome at positoin chr3:60944552 at the end of a string N's. However, this string of N's is flanked distally by other strings of N's so I'm curious why this particular one cause problems. Is it something specific to my file?

I actually see a variable region on chr10 where there is an error and so nothing is calculated downstream (on Watson reference). This region is roughly around chr10:38000000-40000000. On this chromosome, the walker seems to be able to span N strings up to this area where it dies--but dies at different regions and not in a string of N's. I've seen this over 10 or 20 samples or so.