(If this is the wrong place to post this, please tell me where to go)
I am new to GATK, trying to build Picard because I apparently will need to build Picard sequence directories for my genomes of interest.
I have installed Java6, Java8, ant, and HTSJDK. I have downloaded Picard 2a49ee2.
Following instructions at broadinstitute.github.io/picard/building.html, I have defined JAVA6_HOME, cd'd into broadinstitute-picard-2a49ee2, and when I run ant -lib lib/ant package-commands I get this message (relevant part only) "BUILD FAILED ... Basedir .../broadinstitute-picard-2a49ee2/htsjdk does not exist"
So it seems I need to do something for the build to know where my HTSJDK lives. Or did my download fail? Am I supposed to make a symbolic link from .../broadinstitute-picard-2a49ee2/htsjdk over to someplace in my HTSJDK directory? If so, to where?
Thanks for any help, Bob H
When trying to run the UnifiedGenotyper, I keep getting the following
ERROR MESSAGE: There was a failure because temporary file /tmp/org.broadinstitute.sting.gatk.io.stubs.VariantContextWriterStub7040175770023361502.tmp could not be found while running the GATK with more than one thread. Possible causes for this problem include: your system's open file handle limit is too small, your output or temp directories do not have sufficient space, or just an isolated file system blip
About the suggested causes:
Or could there be still a different reason for the error?