funcotator error

zwzhangzwzhang Member, Broadie

Hi, FireCloud team

Sorry for the duplicated question. I just want to update the format.

I ran into a problem recently coming from Funcotator. I initially run Mutect2 coupled with Funcotator on FireCloud, GATK 4.0.4.0 version, but it throw out some error. And I also tried run Funcotator locally and it produces the almost identical error, see below

[June 6, 2018 1:47:32 PM EDT] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 12.63 minutes.
Runtime.totalMemory()=12082741248
java.lang.StringIndexOutOfBoundsException: String index out of range: -61
    at java.lang.String.substring(String.java:1967)
    at org.broadinstitute.hellbender.tools.funcotator.dataSources.gencode.GencodeFuncotationFactory.createUtrFuncotation(GencodeFuncotationFactory.java:1088)
    at org.broadinstitute.hellbender.tools.funcotator.dataSources.gencode.GencodeFuncotationFactory.createGencodeFuncotationOnTranscript(GencodeFuncotationFactory.java:601)
    at org.broadinstitute.hellbender.tools.funcotator.dataSources.gencode.GencodeFuncotationFactory.createFuncotationsHelper(GencodeFuncotationFactory.java:529)
    at org.broadinstitute.hellbender.tools.funcotator.dataSources.gencode.GencodeFuncotationFactory.createFuncotationsOnVariant(GencodeFuncotationFactory.java:276

I know Funcotator is still in beta version, but want to ask you help me debug this problem and I am also wondering is there any more stable Funcotator.

Thanks,
Zhouwei

Comments

  • KateNKateN Cambridge, MAMember, Broadie, Moderator admin

    Thank you for updating your format-- It certainly helps to see error messages in code brackets.

    Unfortunately, I'm unable to help you with your error, but I think one of my colleagues @Sheila or @shlee may be able to. I'm moving your question to the GATK forum where they will be able to assist with Funcotator.

  • shleeshlee CambridgeMember, Broadie ✭✭✭✭✭

    Hi @zwzhang,

    The developer says that updating to GATK4.0.5.0 should solve the issue. Also, please be sure to use the latest data sources.

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