created by Geraldine_VdAuwera
on 2013-03-07
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.
haplotypecaller, 2.4, bug-fixed
Updated on 2013-03-19
From giorgiopea on 2013-03-08
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
From Geraldine_VdAuwera on 2013-03-08
Don’t worry about it.
FYI we are working on a solution to the problem; we’ll post updates in this thread.
From Geraldine_VdAuwera on 2013-03-12
Update: we have a theoretical fix for the “Bad likelihoods detected error” and are now working on implementing it.
From andrewseverin on 2013-03-15
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
From andrewseverin on 2013-03-19
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
From Geraldine_VdAuwera on 2013-03-19
This should be fixed in the very latest version, 2.4-9, which came out this morning I believe.