Azul Platform PrimeĪzul Platform Prime, formerly Zing, is fully TCK compliant with the Java SE 11, 8, or 7 specifications. … We are now excited to continue building on this work by producing binaries based on OpenJDK 11 for 圆4 platforms covering the three major operating systems and to share this work with the Java community and our Microsoft Azure customers.” Regarding TCK compliance, Microsoft reports that “Our binaries for Java 11 have passed the Java Technology Compatibility Kit (TCK) for Java 11”. Per Microsoft: “Over the past 18 months, we contributed more than 50 patches covering areas such as macOS packaging, build and infrastructure, GC fixes, and enhancements for Windows. They’re also publishing an early-access binary for Java 16 for Windows on ARM, based on the latest OpenJDK 16+36 release, and providing a port to Windows ARM ( JEP-388 ) for Surface Pro X. It’S TCK compliant for Java 11 and includes binaries for Java 11, based on OpenJDK 11.0.10+9, on 圆4 server and desktop environments on macOS, Linux, and Windows. It’s an open-source, no-cost long-term support (LTS) distribution of OpenJDK that is free for anyone to deploy anywhere. They are essentially providing Windows-specific optimizations that haven’t made it back to the OpenJDK source code yet. Microsoft just announced its own OpenJDK build. Here’s a run-down of the most commonly used ones and their primary offerings. With all these choices, we felt like it was a good time to review the currently available OpenJDK builds. And others (e.g., Zulu and AdoptOpenJDK) appear to be trying to become a non-Oracle supplier of builds with their own (ostensibly cheaper) support contracts. Others (e.g., Zing and OpenJ9) are adding technology in some way. Some of them (e.g., Microsoft, Red Hat, and Amazon Corretto), seem to have a self-serving purpose-namely, to help Java run better (or at all) on their own technology. Now, well into 2021, we’re at the point where there are many alternatives to the original Oracle JDK build. Java e_async_io_read_samtools=false e_async_io_write_samtools=true e_async_io_write_tribble=false pression_level=2 -jar /igm/apps/gatk/gatk-4.1.3.0/gatk-package-4.1.3.0-local.jar CollectAllelicCountsĮxception in thread "main" : Java heap spaceĪt (Arrays.java:3210)Īt (Arrays.java:3181)Īt (ArrayList.java:265)Īt (ArrayList.java:239)Īt (ArrayList.java:231)Īt (ArrayList.java:583)Īt (BAMFileSpan.java:307)Īt (BAMFileReader.java:940)Īt (BAMFileReader.java:952)Īt (BAMFileReader.java:612)Īt $PrimitiveSamReaderToSamReaderAdapter.query(SamReader.java:533)Īt $PrimitiveSamReaderToSamReaderAdapter.queryOverlapping(SamReader.java:405)Īt .(SamReaderQueryingIterator.java:125)Īt .iterators.SamReaderQueryingIterator.(SamReaderQueryingIterator.java:66)Īt .ReadsDataSource.prepareIteratorsForTraversal(ReadsDataSource.java:404)Īt .erator(ReadsDataSource.java:330)Īt (Iterable.java:101)Īt .Utils.stream(Utils.java:1098)Īt .GATKTool.getTransformedReadStream(GATKTool.java:377)Īt .averse(LocusWalker.java:164)Īt .GATKTool.doWork(GATKTool.Ever since Oracle, in 2018, split its JDK build licensing into two tiers-commercial, which can be used for free in development and testing but you have to pay to use it in production, and open-source, which is free in any environment-quite a few open-source builds based on the OpenJDK source code have appeared. I did notice JAVA_TOOL_OPTIONS: -XX:ParallelGCThreads=1 -Djava.io.tmpdir=/igm/temp were no longer being included in the arguments, however upon adding them I still ran into the same error. I am hoping you could shed some light on how GATK previously tuned the amount of memory. However, such a hardcoded change is not ideal, as the demand changes depending on whether the input is WGS and number of samples (we are running CNV-LOH in parallel). I can manually go in and fix this by setting the jvm memory to -Xmx24G. We've switched to OpenJDK (OpenJ9) and we start to run into OOM errors. However recently Oracle JDK made a change to their license that has prevented our institution from using their software. Previously I have been able to run the CNV-LOH pipeline with no problems whatsoever.
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