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GATK Queue ./.queue/ directory translated to an absolute path? All jobs fail on SGE.

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.


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