GenomeSTRiP Runtime Error: Cannot handle multiple junction records

I am getting the error message below when genotyping a list of deletions (generated by another sv program) with GenomeSTRiP..
Are there any workarounds/solutions for this? I am getting this error messages at multiple sites.

The site in the vcf file starts with this....
1 28026606 rs764989478 CTTTT CT,C

INFO 21:07:28,727 SVGenotyper - Genotyping site: CNP rs763157369 NA 1 10450561 10450560 10450568 10450567
WARN 21:07:28,728 VariantJunctionGenerator - rs763157369_1: trimming 1/0 matching bases from junction
WARN 21:07:28,728 VariantJunctionGenerator - rs763157369_1: detected VNTR event of length 6: TTTTTT
WARN 21:07:28,728 VariantJunctionGenerator - rs763157369_2: detected VNTR event of length 7: TTTTTTT
INFO 21:07:28,728 SVGenotyper - GenotypingDepthModule processing site rs763157369 ...
Error: Exception processing cnp: Cannot handle multiple junction records: rs763157369
CNP: rs763157369 1:10450561-10450567
INFO 21:07:29,146 GATKRunReport - Uploaded run statistics report to AWS S3

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

java.lang.RuntimeException: Cannot handle multiple junction records: rs763157369
at org.broadinstitute.sv.genotyping.GenotypingDepthModule.getRefDepthInterval(GenotypingDepthModule.java:1179)
at org.broadinstitute.sv.genotyping.GenotypingDepthModule.getRefDepthIntervals(GenotypingDepthModule.java:1152)
at org.broadinstitute.sv.genotyping.GenotypingDepthModule.computeRefReadCounts(GenotypingDepthModule.java:227)
at org.broadinstitute.sv.genotyping.GenotypingDepthModule.getReadCounts(GenotypingDepthModule.java:220)
at org.broadinstitute.sv.genotyping.GenotypingDepthModule.getCnpReadCounts(GenotypingDepthModule.java:207)
at org.broadinstitute.sv.genotyping.GenotypingDepthModule.genotypeCnp(GenotypingDepthModule.java:135)
at org.broadinstitute.sv.genotyping.GenotypingDepthModule.genotypeCnp(GenotypingDepthModule.java:55)
at org.broadinstitute.sv.genotyping.GenotypingAlgorithm.genotypeCnpInternal(GenotypingAlgorithm.java:141)
at org.broadinstitute.sv.genotyping.GenotypingAlgorithm.genotypeCnp(GenotypingAlgorithm.java:106)
at org.broadinstitute.sv.genotyping.SVGenotyperWalker.processVCFFile(SVGenotyperWalker.java:268)
at org.broadinstitute.sv.genotyping.SVGenotyperWalker.map(SVGenotyperWalker.java:214)
at org.broadinstitute.sv.genotyping.SVGenotyperWalker.map(SVGenotyperWalker.java:56)
at org.broadinstitute.gatk.engine.traversals.TraverseLociNano.traverse(TraverseLociNano.java:106)
at org.broadinstitute.gatk.engine.traversals.TraverseLociNano.traverse(TraverseLociNano.java:48)
at org.broadinstitute.gatk.engine.executive.LinearMicroScheduler.execute(LinearMicroScheduler.java:99)
at org.broadinstitute.gatk.engine.GenomeAnalysisEngine.execute(GenomeAnalysisEngine.java:319)
at org.broadinstitute.gatk.engine.CommandLineExecutable.execute(CommandLineExecutable.java:121)
at org.broadinstitute.sv.main.SVCommandLine.execute(SVCommandLine.java:125)
at org.broadinstitute.gatk.utils.commandline.CommandLineProgram.start(CommandLineProgram.java:248)
at org.broadinstitute.gatk.utils.commandline.CommandLineProgram.start(CommandLineProgram.java:155)
at org.broadinstitute.sv.main.SVCommandLine.main(SVCommandLine.java:79)
at org.broadinstitute.sv.main.SVGenotyper.main(SVGenotyper.java:21)

ERROR ------------------------------------------------------------------------------------------
ERROR A GATK RUNTIME ERROR has occurred (version ):
ERROR
ERROR This might be a bug. Please check the documentation guide to see if this is a known problem.
ERROR If not, please post the error message, with stack trace, to the GATK forum.
ERROR Visit our website and forum for extensive documentation and answers to
ERROR commonly asked questions http://www.broadinstitute.org/gatk
ERROR
ERROR MESSAGE: Cannot handle multiple junction records: rs763157369
ERROR ------------------------------------------------------------------------------------------

Best Answer

Answers

Sign In or Register to comment.