Bug in VariantAnnotator

Tiphaine

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

ebanks

Did you build from source? If so, you'll need to 'ant clean'. Otherwise, please update to the latest version of the code.

Tiphaine

I would like to do it but I read that in new version of GATK, BaseRecalibrator no longer uses multi-thread option and I would to finish analyse my data with same version of GATK.