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ERROR Stack trace: java.lang.NumberFormatException: For input string: "2520503224"

bmlettbmlett Member

I am working with GenomeSTRiP v2.0 on some bovine samples. Java is version 1.8.0_201. I created my own reference ploidy map as discussed on the Reference Genome Metadata page using the locations from my reference index:

X 139009144 2520503224 F 2
X 139009144 2520503224 M 1
Y 43300181 2661249986 F 0
Y 43300181 2661249986 M 1
* * * * 2

However, I a running into this error:

##### ERROR stack trace
java.lang.NumberFormatException: For input string: "2520503224"
at java.lang.NumberFormatException.forInputString(NumberFormatException. java:65)
at java.lang.Integer.parseInt(Integer.java:583)
at java.lang.Integer.parseInt(Integer.java:615)
at org.broadinstitute.sv.metadata.ploidy.PloidyMap.parsePloidyMapFile(Pl oidyMap.java:252)
at org.broadinstitute.sv.metadata.ploidy.PloidyMap.open(PloidyMap.java:5 5)
at org.broadinstitute.sv.metadata.depth.ComputeReadDepthCoverageWalker.i nitialize(ComputeReadDepthCoverageWalker.java:131)
at org.broadinstitute.sv.metadata.ComputeMetadataWalker.initialize(Compu teMetadataWalker.java:202)
at org.broadinstitute.gatk.engine.executive.LinearMicroScheduler.execute (LinearMicroScheduler.java:83)
at org.broadinstitute.gatk.engine.GenomeAnalysisEngine.execute(GenomeAna lysisEngine.java:316)
at org.broadinstitute.gatk.engine.CommandLineExecutable.execute(CommandL ineExecutable.java:123)
at org.broadinstitute.sv.main.SVCommandLine.execute(SVCommandLine.java:1 41)
at org.broadinstitute.gatk.utils.commandline.CommandLineProgram.start(Co mmandLineProgram.java:256)
at org.broadinstitute.gatk.utils.commandline.CommandLineProgram.start(Co mmandLineProgram.java:158)
at org.broadinstitute.sv.main.SVCommandLine.main(SVCommandLine.java:91)
at org.broadinstitute.sv.main.SVCommandLine.main(SVCommandLine.java:65)
##### ERROR -------------------------------------------------------------------- ----------------------

I am not sure if this is an exception based on my ploidy map or a format issue with java and the size of the integer.
Any insight would be greatly appreciated!

(I apologize for any format issues)


  • bhandsakerbhandsaker Member, Broadie ✭✭✭✭

    I'm pretty sure it is the magnitude of the integer. Those are pretty big chromosomes!
    Is this correct? I see that the Bos taurus genome is about 2.6 gigabases in total.

    While it would be relatively easy to fix this particular case, I believe there are many places in Genome STRiP where correctly handling individual chromosomes larger than 2Gb would require code changes.

  • bmlettbmlett Member

    You are most likely correct that there was an error in my chromosome size! I am not 100% sure where I found the end sizes but I believe the issue was that the start should be 1 and the end value is what I listed as a start. Changing this seems to have allowed that step to start without errors.

    Thank you!
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