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GATK: Difference between revisions
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If you are interested in knowing more about java heap space, you can start [https://plumbr.io/outofmemoryerror/java-heap-space here]. | If you are interested in knowing more about java heap space, you can start [https://plumbr.io/outofmemoryerror/java-heap-space here]. | ||
===Increasing the heap memory does not fix | ===Increasing the heap memory does not fix <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. <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. | 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. | ||