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GATK 2.8 Realigner Target Creator reference genome issue

grabbitmediagrabbitmedia lahore,PakistanMember

Hello everyone,

I want to use Realigner Target Creator provided in the toolshed with the GATK version2.8. Unfortunately, I have a strange error :

"Failed runtime validation of Using reference genome (A built-in reference genome is not available for the build associated with the selected input file)"

The strange thing is that I am using hg19 as reference and when I fill the form I can actually choose hg19. So I guess it means that it exists.

When I look into the details I have this first line in the table :

Input parameter : Choose the source for the reference list
Value : Choose the source for the reference list 
Note for rerun : None

And lastly, if I try to rerun the job (on the failed job) I have a different error :

Picked up _JAVA_OPTIONS:

ERROR ------------------------------------------------------------------------------------------
ERROR A USER ERROR has occurred (version 2.8-1-g932cd3a):
ERROR This means that one or more arguments or inputs in your command are incorrect.
ERROR The error message below tells you what is the problem.
ERROR If the problem is an invalid argument, please check the online documentation guide
ERROR (or rerun your command with --help) to view allowable command-line arguments for this tool.
ERROR Visit our website and forum for extensive documentation and answers to
ERROR commonly asked questions
ERROR Please do NOT post this error to the GATK forum unless you have really tried to fix it yourself.
ERROR MESSAGE: Input files reads and reference have incompatible contigs: Relative ordering of overlapping contigs differs, which is unsafe.
ERROR reads contigs = [chr1, chr2, etc...]
ERROR ------------------------------------------------------------------------------------------

Does that mean that the picked up option is wrong?

Thank you for your help.


  • SheilaSheila Broad InstituteMember, Broadie, Moderator admin


    You should really upgrade to the latest version of GATK. 2.8 is very old.

    As for your error, it looks like your BAM file is not using the same reference as your input reference. Can you post the exact command you ran? Are you using the exact same reference you aligned your reads to?


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