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. Since Java SE 6 was needed as well, to maintain backword compatibility OpenJDK 6 was released by removing the OpenJDK 7 features inappropriate for a Java SE 6 specification.Previously I have been able to run the CNV-LOH pipeline with no problems whatsoever. OpenJDK 7 was released on 28th July 2011,Since decision to Open Source JDK came late in the life cycle of the development of JDK 6, JDK 7 was first released as open source. For more details you can refer the official Java SE 7 specification from Java Community Process here. OpenJDK 7 is the reference implementation of the Java SE 7 Specification. OpenJDK is the open source implementation of the Java Platform Standard Edition and is free to use with General Public License Version 2 GPLv2. Main difference between Oracle JDK and OpenJDK is that OpenJDK is free for all while Oracle Java Development Kit or Oracle JDK requires commercial license. OpenJDK is the short form of Open Java Development Kit similar to Oracle's Java Development Kit used to develop Java Applications. These features make it easier to develop applications that run on multiple platforms. In addition to the above benefits, the Oracle JDK offers additional features such as JMX monitoring, remote debugging, and application server integration. It also includes updates and bug fixes as soon as possible after they become available. The Oracle JDK comes with extensive documentation and training materials. Another reason to consider using the Oracle JDK is because of its support. For instance, the OpenJDK cannot be used in certain countries where Oracle has exclusive rights to the Java trademark. Both versions of the JDK are free to download and use, but there are some restrictions with the OpenJDK. There are several reasons why one might choose to use either the OpenJDK or Oracle JDK. Finally, you need to understand the differences between the two versions because they offer different levels of support. Third, you need to understand what features each version offers so you can choose the one that meets your needs. Second, you need to understand how the licensing works so you can make sure you're not violating any terms. First, there are some security concerns with open source software. There are several reasons why you might care about the differences between open source and proprietary software. Why You Should Care About The Differences Between OpenJDK AndOracleJDK ? OpenJDK vs OracleJDK - Which Java DevelopmentKit Is Better?
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