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Note that all options passed to <code>--java-options</code> have to be within quotation marks. | Note that all options passed to <code>--java-options</code> have to be within quotation marks. | ||
=== Considerations in our systems === | === Considerations in our systems === <!--T:50--> | ||
To use GATK in our systems we recommend you use the <code>--tmp-dir</code> option and set it to <code>${SLURM_TMPDIR}</code> when in a sbatch job so that the temporary files are redirected to the local storage. | To use GATK in our systems we recommend you use the <code>--tmp-dir</code> option and set it to <code>${SLURM_TMPDIR}</code> when in a sbatch job so that the temporary files are redirected to the local storage. | ||
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Also, when using <code>GenomicsDBImport</code> make sure to have the option <code>--genomicsdb-shared-posixfs-optimizations</code> enabled as it "Allow[s] for optimizations to improve the usability and performance for shared Posix Filesystems(e.g. NFS, Lustre)". If not possible or if you are using GNU parallel to run multiple intervals at the same time, please copy your database to <code>${SLURM_TMPDIR}</code> and run it from there as your IO operations might disrupt the function of the Filesystem. <code>${SLURM_TMPDIR}</code> is a local storage and therefore is not only faster, but the IO operations would not affect other users. | Also, when using <code>GenomicsDBImport</code> make sure to have the option <code>--genomicsdb-shared-posixfs-optimizations</code> enabled as it "Allow[s] for optimizations to improve the usability and performance for shared Posix Filesystems(e.g. NFS, Lustre)". If not possible or if you are using GNU parallel to run multiple intervals at the same time, please copy your database to <code>${SLURM_TMPDIR}</code> and run it from there as your IO operations might disrupt the function of the Filesystem. <code>${SLURM_TMPDIR}</code> is a local storage and therefore is not only faster, but the IO operations would not affect other users. | ||