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GATK: Difference between revisions
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If it fails again, keep increasing the memory until you find the required memory for your particular | 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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===Increasing the heap memory does not fix the <code>java.lang.OutOfMemoryError: Java heap space</code> === <!--T:29--> | ===Increasing the heap memory does not fix the <code>java.lang.OutOfMemoryError: Java heap space</code> === <!--T:29--> | ||
There are cases in which the memory issue cannot be fixed with increasing the heap memory. This often happens with non-model organisms, and you are using too many scaffolds in your reference. In this case it is recommended to remove small scaffolds and create subsets of your reference. This implies that you have to map multiple times and run the pipelines in each of the subsets. | There are cases in which the memory issue cannot be fixed with increasing the heap memory. This often happens with non-model organisms, and you are using too many scaffolds in your reference. In this case it is recommended to remove small scaffolds and create subsets of your reference. This implies that you have to map multiple times and run the pipelines in each of the subsets. <b>This approach does not work in all pipelines</b> so review your results carefully. GATK is designed with the human genome in mind, and therefore other organism will require adjustment in many parameters and pipelines. | ||
===Using more resources than asked for === <!--T:30--> | ===Using more resources than asked for === <!--T:30--> | ||
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[https://gatk.broadinstitute.org/hc/en-us/articles/360035889611-How-can-I-make-GATK-tools-run-faster- Make GATK run faster] | [https://gatk.broadinstitute.org/hc/en-us/articles/360035889611-How-can-I-make-GATK-tools-run-faster- Make GATK tools run faster] | ||
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