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When trying to run the Haplotype caller using GATK Queue all my jobs failed because they couldn't write to the tmp files in the ./.queue directory.
This seems to be related to the working directory from which the Queue command is started, and the ./.queue directory is created.
The head node of the SGE grid I want to use and from where I start the Queue is server8.
When I start the Queue command on that server the working directory is translated from a path that is accessible from everywhere on the SGE cluster to a path that is only accessible locally.
Example working directory: /home/sge_share_sever8/variantCalling is translated to the absolute path /data/variantCalling which is only accesible locally.
If I start the Queue from a working directory that is mounted from another server everything workes fine.
Example working directory: /home/sge_share_sever12/variantCalling stays /home/sge_share_sever12/variantCalling and everything works fine.
Is it a bug or feature that the ./.queue directory is translated from a normal path to an absolute path?
Or can I specify another location for the ./.queue directory that will not be translated to an absolute path.