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GATK: Difference between revisions
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For more information about Apptainer, | For more information about Apptainer, watch the recorded [https://www.youtube.com/watch?v=bpmrfVqBowY Apptainer webinar]. | ||
==Frequently asked questions == <!--T:23--> | ==Frequently asked questions == <!--T:23--> | ||
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===How do I deal with <code>java.lang.OutOfMemoryError: Java heap space</code> === <!--T:24--> | ===How do I deal with <code>java.lang.OutOfMemoryError: Java heap space</code> === <!--T:24--> | ||
Subprograms of GATK often require more memory to process your files. If you were not using the <code>-Xms</code> command, add it to the <code>--java-options</code>. For example, let's imagine that you run the following command: | |||
<pre> | <pre> | ||
gatk MarkDuplicates \ | gatk MarkDuplicates \ | ||
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but it gives you the <code>java.lang.OutOfMemoryError: Java heap space</code> error. Try: | |||
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If it fails again, keep increasing the memory until you find the required memory for your particular dataset. If you are using any of our systems,<b>remember to request enough memory for this</b>. | If it fails again, keep increasing the memory until you find the required memory for your particular dataset. If you are using any of our systems, <b>remember to request enough memory for this</b>. | ||
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