ERROR MESSAGE: Invalid command line: Malformed walker argument: Could not find walker with name
介绍和分析
我是用的环境是 GATK v3.7-0-gcfedb67 的 GenomeAnalysisTK.jar
Java环境为：
> java -version
openjdk version "9-internal"
OpenJDK Runtime Environment (build 9-internal+0-2016-04-14-195246.buildd.src)
OpenJDK 64-Bit Server VM (build 9-internal+0-2016-04-14-195246.buildd.src, mixed mode)但发现无论使用哪个 GATK Tool Name (-T) 都显示 ** Could not find walker with name**
ERROR MESSAGE: Invalid command line: Malformed walker argument: Could not find walker with name找了好的论坛，都是有问题没有结果的这种，气死人。
分析
- gatk 3.7是用 java 1.8调试过的，而1.9是没有测试的，可能是 Java 版本的问题
- 居然有人说我大小写写错了，妈的，我再眼瞎也不会把所有命令都写错吧
解决
** 安装 Java 1.8 ** （确实是 java 版本的问题）
- 下载 jre 解压，把 bin 加到 PATH 路径中， source， 就可以用了
- 或者你不像覆盖另外一个版本的 java， 可以（比较方便）
alias gatk.jar="path/to/jre/bin/java -jar /path/to/GenomeAnalysisTk.jar"转载于:https://www.cnblogs.com/raybiolee/p/6664259.html
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