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# Error: Can't connect to window server - not enough permissions, when running "RealignerTargetCreator

DenverPosts: 66Member
edited July 2013

I started with BWA-MEM to do alignment, used Picard to process the .SAM files (converted to bam, reorder, addorreplacegroup, etc). The GATK version I'm using is version 2.5-2-gf57256b, I cannot run 2.6 because the server only has Java 6 and I cannot upgrade it to Java 7.

I got a huge stack of error message when I run this command line (RealignerTargetCrator):

##### ERROR A GATK RUNTIME ERROR has occurred (version 2.5-2-gf57256b):
Post edited by rcholic on
Tagged:

• DenverPosts: 66Member

I think I found the answer to my question. After I include the "-Djava.awt.headless=true" option before "-jar" in my above command, GATK runs perfectly fine on my remote Mac server. I post this in case other people may find it helpful in future. - cheers.

Thanks for posting the solution to your issue, @rcholic -- and sorry for not responding earlier. Glad your issue is resolved.

Geraldine Van der Auwera, PhD

• DenverPosts: 66Member

@Geraldine_VdAuwera said: Thanks for posting the solution to your issue, rcholic -- and sorry for not responding earlier. Glad your issue is resolved.

sure, you are welcome. Thank YOU GUYS for offering GATK. I think the code in GATK package may somehow triggers awt (accidentally?, might be a bug) during running, which is not possible to execute in SSH. I guess this is the main cause for my error messages posted in the original post. -cheers