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mouse Base Quality Recalibration

xing_tangxing_tang Ohio State UniversityMember

Hi,
I met the belowing error when I do Base Quality Recalibration. I'm working on mouse genome.
I downloaded mm10 dbsnp from broad institue. Is it related to this dbsnp file?

INFO 16:25:16,159 ProgressMeter - Location processed.sites runtime per.1M.sites completed total.runtime remaining
INFO 16:25:46,168 ProgressMeter - chr12:87273626 3.33e+07 30.0 s 0.0 s 14.5% 3.4 m 2.9 m
INFO 16:25:49,333 HttpMethodDirector - I/O exception (java.net.ConnectException) caught when processing request: Connection refused
INFO 16:25:49,333 HttpMethodDirector - Retrying request
INFO 16:25:49,336 HttpMethodDirector - I/O exception (java.net.ConnectException) caught when processing request: Connection refused
INFO 16:25:49,336 HttpMethodDirector - Retrying request
INFO 16:25:49,338 HttpMethodDirector - I/O exception (java.net.ConnectException) caught when processing request: Connection refused
INFO 16:25:49,338 HttpMethodDirector - Retrying request
INFO 16:25:49,339 HttpMethodDirector - I/O exception (java.net.ConnectException) caught when processing request: Connection refused
INFO 16:25:49,340 HttpMethodDirector - Retrying request
INFO 16:25:49,341 HttpMethodDirector - I/O exception (java.net.ConnectException) caught when processing request: Connection refused
INFO 16:25:49,341 HttpMethodDirector - Retrying request

ERROR ------------------------------------------------------------------------------------------
ERROR stack trace

java.lang.ArrayIndexOutOfBoundsException: 1
at org.broadinstitute.sting.gatk.contexts.ReferenceContext.getBase(ReferenceContext.java:179)
at org.broadinstitute.sting.gatk.walkers.indels.RealignerTargetCreator.map(RealignerTargetCreator.java:219)
at org.broadinstitute.sting.gatk.walkers.indels.RealignerTargetCreator.map(RealignerTargetCreator.java:124)
at org.broadinstitute.sting.gatk.traversals.TraverseLociNano$TraverseLociMap.apply(TraverseLociNano.java:267)
at org.broadinstitute.sting.gatk.traversals.TraverseLociNano$TraverseLociMap.apply(TraverseLociNano.java:255)
at org.broadinstitute.sting.utils.nanoScheduler.NanoScheduler.executeSingleThreaded(NanoScheduler.java:274)
at org.broadinstitute.sting.utils.nanoScheduler.NanoScheduler.execute(NanoScheduler.java:245)
at org.broadinstitute.sting.gatk.traversals.TraverseLociNano.traverse(TraverseLociNano.java:144)
at org.broadinstitute.sting.gatk.traversals.TraverseLociNano.traverse(TraverseLociNano.java:92)
at org.broadinstitute.sting.gatk.traversals.TraverseLociNano.traverse(TraverseLociNano.java:48)
at org.broadinstitute.sting.gatk.executive.LinearMicroScheduler.execute(LinearMicroScheduler.java:99)
at org.broadinstitute.sting.gatk.GenomeAnalysisEngine.execute(GenomeAnalysisEngine.java:313)
at org.broadinstitute.sting.gatk.CommandLineExecutable.execute(CommandLineExecutable.java:121)
at org.broadinstitute.sting.commandline.CommandLineProgram.start(CommandLineProgram.java:248)
at org.broadinstitute.sting.commandline.CommandLineProgram.start(CommandLineProgram.java:155)
at org.broadinstitute.sting.gatk.CommandLineGATK.main(CommandLineGATK.java:107)

Answers

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