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。