broadinstitute/mutect

mutect problem -- Malformed walker argument: Could not find walker with name: MuTect

xiaxuyang opened this issue · 3 comments

xiaxuyang commented

Hi.When I do "./run_regression.pl", I get a problem --Malformed walker argument: Could not find walker with name: MuTect .
So I can't install it and I don't know how to solve it.Can you help me ?Thanks!

sooheelee commented

This page and this page give some links and instructions to compile the mutect jar. I'm not sure if this is what you're asking for so let us know if it's not.

elsamah commented

were you able to fix it? running into a similar problem

AvrahamKahan123 commented

If it's still relevant for anyone, I think this is caused by using an improper version of Java (usually too new). You must use JDK 7.
You can use the jdk from https://download.java.net/openjdk/jdk7u75/ri/jdk_ri-7u75-b13-linux-x64-18_dec_2014.tar.gz on linux x86 64 bit systems.
Using this, along with the version of mutect available from conda ( https://anaconda.org/compbiocore/mutect/1.1.6/download/linux-64/mutect-1.1.6-1.tar.bz2 ) allowed me to run mutect properly