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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>${SLURM_TMPDIR}</code> and run it from there as your IO operations might disrupt the function of the | Also, when using <code>GenomicsDBImport</code> make sure to have the option <code>--genomicsdb-shared-posixfs-optimizations</code> enabled as it "Allow[s] for optimizations to improve the usability and performance for shared Posix Filesystems(e.g. NFS, Lustre)". If not possible or if you are using GNU parallel to run multiple intervals at the same time, please copy your database to <code>${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. | ||
===Earlier versions than GATK 4 === <!--T:14--> | ===Earlier versions than GATK 4 === <!--T:14--> | ||
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For the commands that do use Spark, you can request multiple cpus. <b>NOTE:</b> Please provide the exact number of | For the commands that do use Spark, you can request multiple cpus. <b>NOTE:</b> Please provide the exact number of CPUs to the <code>spark</code> command. For example if you requested 10 CPUs, use <code>--spark-master local[10]</code> instead of <code>--spark-master local[*]</code>. If you want to use multiple nodes to scale the Spark cluster, you have to first [[Apache_Spark|deploy a SPARK cluster]] and then set the appropriate variables in the GATK command. | ||
==Running GATK via Apptainer== <!--T:36--> | ==Running GATK via Apptainer== <!--T:36--> | ||
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If you encounter errors like | If you encounter errors like [https://gatk.broadinstitute.org/hc/en-us/community/posts/360067054832-GATK-4-1-7-0-error-java-lang-IllegalArgumentException-malformed-input-off-17635906-length-1 IllegalArgumentException] while using the installed modules on our clusters, we recommend that you try another workflow by using the program via [[Apptainer]]. | ||
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===FAQ on GATK === <!--T:31--> | ===FAQ on GATK === <!--T:31--> | ||
You can find GATK's | You can find GATK's [https://gatk.broadinstitute.org/hc/en-us/sections/360007226791-Troubleshooting-GATK4-Issues FAQs on their website]. | ||
=References = <!--T:32--> | =References = <!--T:32--> | ||