Xmx java12/15/2023 ![]() ![]() 32 bit JVM or 64 bit JVM and operating system. Solution 2: that maximum heap size varies based upon machine architecture e.g. for the Error: Could not create the Java Virtual Machine. ie it means you have install the entire s/w. Solution 1: You can re-install the all components. That update does sound very enticing! Since I need to do this for a lot more samples and the previous test I started ran for over a week before crashing due to memory (since someone else was also using it heavily), so increasing the speed while reducing memory requirements sounds fantastic.We have couple of solutions for the above Problem However in the config file I set it to numThreads=70, so could there be something going wrong or something I didn't set that prevents this parameter to be passed to minimap? NumThreads - 2 because 2 threads are reserved for other operations. The number of threads that will be used to impute individual paths is This is 2 less than my machine has, so that would fit well with the Documentation saying: With the thread number, as GenoMax pointed out minimap uses 126 threads. Then I think I definitely need to limit Singularity, since I can't take up all the memory on this machiene. ![]() I thought the xmx parameter would be passed to the downstream commands called by the plugin. Hopefully this will be included in the next version of the PHG. Initial testing is very promising as the RAM usage is far lower(10-20GB) and the speed is very good(1-2 minutes for a 2-3x WGS paired end fastq pair) and the results are close enough to what minimap2 provides that the Path finding is nearly identical. This new version completely bypasses minimap2 and uses Kmers to figure out the read mappings. Just a note, we are currently investigating and implementing a new version of the Fastq -> ReadMapping file step which is likely what you are running into here. However once it hits that cap, it will likely stop. This should force anything run within the container to be limited to your request.
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