GATK3.5GATK4.0与java版本的关系

探序基因肿瘤研究院  整理

操作系统centos stream9

yum 安装java后，输入java -version

可看到：
openjdk version "11.0.20.1" 2023-08-24 LTS
OpenJDK Runtime Environment (Red_Hat-11.0.20.1.1-2) (build 11.0.20.1+1-LTS)
OpenJDK 64-Bit Server VM (Red_Hat-11.0.20.1.1-2) (build 11.0.20.1+1-LTS, mixed mode, sharing)

再运行GATK3.5，java -jar GenomeAnalysisTK3.5.jar -T RealignerTargetCreator

发现错误：

##### ERROR ------------------------------------------------------------------------------------------
##### ERROR A USER ERROR has occurred (version 3.5-0-g36282e4):
##### ERROR
##### ERROR This means that one or more arguments or inputs in your command are incorrect.
##### ERROR The error message below tells you what is the problem.
##### ERROR
##### ERROR If the problem is an invalid argument, please check the online documentation guide
##### ERROR (or rerun your command with --help) to view allowable command-line arguments for this tool.
##### ERROR
##### ERROR Visit our website and forum for extensive documentation and answers to
##### ERROR commonly asked questions http://www.broadinstitute.org/gatk
##### ERROR
##### ERROR Please do NOT post this error to the GATK forum unless you have really tried to fix it yourself.
##### ERROR
##### ERROR MESSAGE: Invalid command line: Malformed walker argument: Could not find walker with name: RealignerTargetCreator
##### ERROR ------------------------------------------------------------------------------------------

于是我们去下载java1.8的版本，进入：https://www.oracle.com/cn/java/technologies/downloads/

找到JAVA 8，下载jdk-8u421-linux-x64.tar.gz，有个登陆界面，输入账号密码就行，就可以下载。

解压缩后，为文件夹jdk1.8.0_421，里面有bin,lib等文件夹，也不用什么编译安装，直接使用：

/software/jdk1.8.0_421/bin/java -jar GenomeAnalysisTK3.5.jar -T RealignerTargetCreator

可以使用了。

运行gatk-4.4.0.0出错：

错误: 加载主类 org.broadinstitute.hellbender.Main 时出现 LinkageError
    java.lang.UnsupportedClassVersionError: org/broadinstitute/hellbender/Main has been compiled by a more recent version of the Java Runtime (class file version 61.0), this version of the Java Runtime only recognizes class file versions up to 55.0

运行：java -version
可以看到：

openjdk version "11.0.20.1" 2023-08-24 LTS
OpenJDK Runtime Environment (Red_Hat-11.0.20.1.1-2) (build 11.0.20.1+1-LTS)
OpenJDK 64-Bit Server VM (Red_Hat-11.0.20.1.1-2) (build 11.0.20.1+1-LTS, mixed mode, sharing)