Bug in VariantAnnotator
Posted in Ask the GATK team | Last updated on 2012-10-18 00:57:09


Comments (2)

Hi,

Could you tell me when we can use new version of SnpEff with GATK?

I have some bugs :

ERROR ------------------------------------------------------------------------------------------
ERROR A USER ERROR has occurred (version 2.0-35-g2d70733):
ERROR The invalid arguments or inputs must be corrected before the GATK can proceed
ERROR Please do not post this error to the GATK forum
ERROR
ERROR See the documentation (rerun with -h) for this tool to view allowable command-line arguments.
ERROR Visit our website and forum for extensive documentation and answers to
ERROR commonly asked questions http://www.broadinstitute.org/gatk
ERROR
ERROR MESSAGE: Could not create module ActiveRegionBasedAnnotation because BUG: Cannot find expected constructor for class caused by exception org.broadinstitute.sting.gatk.walkers

.annotator.interfaces.ActiveRegionBasedAnnotation.()

ERROR ------------------------------------------------------------------------------------------
ERROR ------------------------------------------------------------------------------------------
ERROR A USER ERROR has occurred (version 2.0-35-g2d70733):
ERROR The invalid arguments or inputs must be corrected before the GATK can proceed
ERROR Please do not post this error to the GATK forum
ERROR
ERROR See the documentation (rerun with -h) for this tool to view allowable command-line arguments.
ERROR Visit our website and forum for extensive documentation and answers to
ERROR commonly asked questions http://www.broadinstitute.org/gatk
ERROR
ERROR MESSAGE: Could not create module ExperimentalAnnotation because BUG: Cannot find expected constructor for class

caused by exception org.broadinstitute.sting.gatk.walkers.annotator.interfaces.ExperimentalAnnotation.()

ERROR ------------------------------------------------------------------------------------------
ERROR ------------------------------------------------------------------------------------------
ERROR A USER ERROR has occurred (version 2.0-35-g2d70733):
ERROR The invalid arguments or inputs must be corrected before the GATK can proceed
ERROR Please do not post this error to the GATK forum
ERROR
ERROR See the documentation (rerun with -h) for this tool to view allowable command-line arguments.
ERROR Visit our website and forum for extensive documentation and answers to
ERROR commonly asked questions http://www.broadinstitute.org/gatk
ERROR
ERROR MESSAGE: Could not create module RankSumTest because BUG: cannot instantiate class: must be concrete class caused by exception null
ERROR ------------------------------------------------------------------------------------------

I don't know if I forget some other options linked these annotations. These options are important for me. So I deleted them but if somebody want to use them ...

Regards,

Tiphaine


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