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GATK: Difference between revisions
GATK via singularity
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For the commands that do use spark, you can request multiple cpus. '''NOTE:''' please provide the exact number of cpus to the spark command, so if you requested 10 cpus, use <code>--spark-master local[10]</code> instead of <code>--spark-master local[*]</code>. If you want to scale the spark calls with multinode SPARK cluster, you have to first [https://docs.computecanada.ca/wiki/Apache_Spark/en deploy an SPARK cluster] and then set up the appropriate variables in the GATK4 spark command. | For the commands that do use spark, you can request multiple cpus. '''NOTE:''' please provide the exact number of cpus to the spark command, so if you requested 10 cpus, use <code>--spark-master local[10]</code> instead of <code>--spark-master local[*]</code>. If you want to scale the spark calls with multinode SPARK cluster, you have to first [https://docs.computecanada.ca/wiki/Apache_Spark/en deploy an SPARK cluster] and then set up the appropriate variables in the GATK4 spark command. | ||
==Running GATK via singularity== | |||
If you encounter some 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 you to try another workflow of using the program via [[singularity]]. | |||
A docker image can be found [https://hub.docker.com/r/broadinstitute/gatk here]. There are different versions to explore at this [https://hub.docker.com/r/broadinstitute/gatk/tags page]. You will need first to [[Singularity/en#Creating_an_image_using_Docker_Hub|build singularity image from docker]]. | |||
For example, you can run on the cluster: | |||
<code> | |||
module load singularity | |||
singularity build gatk.sif docker://broadinstitute/gatk | |||
</code> | |||
or | |||
<code> | |||
module load singularity | |||
singularity build gatk_VERSION.sif docker://broadinstitute/gatk:VERSION | |||
</code> | |||
for a particular version from the following [https://hub.docker.com/r/broadinstitute/gatk/tags%20page link]. | |||
==Frequently asked questions == <!--T:23--> | ==Frequently asked questions == <!--T:23--> | ||