Malformed walker argument

mac

Hello,
I installed GATK package as explained in the documentation, but I am not able to use the "walkers" with go with it. I always this error message:
java -jar GenomeAnalysisTK.jar -T IndelRealigner

ERROR ------------------------------------------------------------------------------------------

ERROR A USER ERROR has occurred (version 3.7-0-gcfedb67):

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 https://software.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: IndelRealigner

Any help is more than welcome, I cannot find the problem...
Thank you

Sheila

@ehscholl
Hi,

What do you get when you type java -version into your terminal? You need Java 1.8 for GATK to work.

-Sheila

shlee

Hi @mac,

Typing java -jar GenomeAnalysisTK.jar -h should list all the tools available and should also list IndelRealigner. This release of GATK (version 3.7-0-gcfedb67) definitely has IndelRealigner as I have used it recently.

If the problem persists, can you be sure to download the jar afresh and try again.

ehscholl

Mac - did you ever find a solution?

I'm having a similar issue - with ANY tool I try to run
java -jar /usr/local/bin/GenomeAnalysisTK.jar -T BaseRecalibrator
Also -T MuTect
-T IndelRealigner
-T PrintReads
-T SplitSamFIle
-T VariantRecalibrator

At this point I gave up.
This is with a downloaded-today version 3.7-0-gcfedb67

(Also with a version 3.6 and a version 3.5 I've had on my machine....)

The ONLY thing I can think of is if it's our version of Java, which is on a cluster I'm running on and so out of my control.
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)

Otherwise - why would NOTHING work?

shlee

Hi @ehscholl,

Are you running UNIX or LINUX?

Can you download the latest GATK4 jar from https://github.com/broadinstitute/gatk/releases, download the gatk-4.beta.1.zip, unzip and run gatk-launch --list? Do you see a list of tools?

Sheila

@ehscholl
Hi,

What do you get when you type java -version into your terminal? You need Java 1.8 for GATK to work.

-Sheila

mac

Problem was java version. Thanks for your help

ehscholl

Sheila - see above.
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)

I've downloaded 4.beta.4 and it appears to be running OK now.

(I wanted to update, for other people who may be having the same issue - version 4 seems to work with java 9)

Sheila

@ehscholl
Hi,

I am checking with the developers whether it is okay to use Java 9. Sometimes things run, but could cause silent errors/odd results. I will get back to you soon.

-Sheila

Sheila

@ehscholl
Hi again,

The developers say they honestly don't know if you can use Java 9 safely. They have not tested it. To be safe, you should stick with using Java 8 which has been tested and is known to be safe to use.

-Sheila