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GATK: Difference between revisions
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→Running 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 | ==Running GATK via Singularity== | ||
If you encounter | 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 you to try another workflow by using the program via [[Singularity]]. | ||
A | A Docker image of GATK can be found [https://hub.docker.com/r/broadinstitute/gatk here] and other versions are available 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 a Singularity image from the Docker image]]. | ||
For example, to get the latest version | For example, to get the latest version, you can run the following commands on the cluster: | ||
<pre> | <pre> | ||