As reported here:
http://gatkforums.broadinstitute.org/discussion/comment/4114#Comment_4114

If you encounter this bug too, please don't post a new question about it. Feel free to comment in this thread to let us know you have also had the same problem.

Thank you for your patience while we work to fix this issue.

Update: the "Bad likelihoods detected error" is fixed in the latest version.


giorgiopea


Geraldine, I've encountered this issue, but I've seen this announcement just a moment too late and made my post at [http://gatkforums.broadinstitute.org/discussion/comment/4114#Comment_4114](http://gatkforums.broadinstitute.org/discussion/comment/4114#Comment_4114) My apologies! Giorgio

Thu 7 Mar 2013

Geraldine_VdAuwera


Don't worry about it. FYI we are working on a solution to the problem; we'll post updates in this thread.

Thu 7 Mar 2013

Geraldine_VdAuwera


Update: we have a theoretical fix for the "Bad likelihoods detected error" and are now working on implementing it.

Thu 7 Mar 2013

andrewseverin


I also have this error for this version ##### ERROR A GATK RUNTIME ERROR has occurred (version 2.4-7-g5e89f01): ##### ERROR ##### ERROR Please visit the wiki to see if this is a known problem ##### ERROR If not, please post the error, with stack trace, to the GATK forum ##### ERROR Visit our website and forum for extensive documentation and answers to ##### ERROR commonly asked questions http://www.broadinstitute.org/gatk ##### ERROR ##### ERROR MESSAGE: Bad likelihoods detected: 0.24761105283431561

Thu 7 Mar 2013

andrewseverin


I don't know if you have fixed this yet but I have the error in this version too. version nightly-2013-03-18-g9bf9a4a

Thu 7 Mar 2013

Geraldine_VdAuwera


This should be fixed in the very latest version, 2.4-9, which came out this morning I believe.

Thu 7 Mar 2013




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