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GATK: Difference between revisions
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(Created page with "{{DRAFT}} The '''Genome Analysis Toolkit (GATK)''' is a set of bioinformatic tools for analyzing high-throughput sequencing (HTS) and variant call format (VCF) data. The toolk...") |
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===Increasing the heap memory does not fix the java.lang.OutOfMemoryError: Java heap space === | ===Increasing the heap memory does not fix the java.lang.OutOfMemoryError: Java heap space === | ||
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. '''This approach does not work in all pipelines''' 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. '''This approach does not work in all pipelines''' 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 === | |||
Sometimes GATK/JAVA applications will use more memory or cpus/threads than the ones requested. This is often generated by the JAVA garbage collection. To add control for this, you can add '''-XX:ConcGCThreads=1''' to the '''--java-options''' argument. | |||
=References = | =References = | ||