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Error with GenomeAnalysisTK.jar finding tools

I'm trying to run GATK on my machine as part of a pipeline using Phyluce. As per the instructions here (https://phyluce.readthedocs.io/en/v1.6.8/installation.html#why-conda), I downloaded GATK 3.7-0, activated a conda environment, and imported the GATK package into conda using the following code:

*conda activate phyluce-1.7.1

*gatk-register /PATH/TO/GATK-3.7/JAR/GenomeAnalysisTK.jar**

Terminal recognizes the command 'gatk -h' and provides the appropriate message. But, whenever I try to use one of the tools, eg:

gatk -T RealignerTargetCreator

...the following error crops up:

##### ERROR MESSAGE: Invalid command line: Malformed walker argument: Could not find walker with name: RealignerTargetCreator

I've tried messing with a couple of different versions of GATK, as well as different tool arguments to make sure this wasn't a one-off deprecated command, but I keep getting the same thing. I've also tried calling the jarfile directly (code below), but the result is the same.

java -jar /PATH/TO/GATK-3.7/JAR/GenomeAnalysisTK.jar \ -T RealignerTargetCreator

Has anyone else experienced this issue, or know another way to run GATK? Thanks in advance for your time.

conda gatk walker phyluce
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updated by josloc • josloc • written by kacollier • kacollier

what is the output of

java -jar /PATH/TO/GATK-3.7/JAR/GenomeAnalysisTK.jar  -h | grep RealignerTarget

?

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written by Pierre Lindenbaum Pierre Lindenbaum

Nothing, not even the help message.

If you remove the -h from that command though, you get error output requesting an argument for -T.

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written by kacollier • kacollier

That is odd because I see using the launcher script.

/path_to.apps/gatk/3.7/gatk -h | grep RealignerTarget
   RealignerTargetCreator        Define intervals to target for local realignment
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written by GenoMax GenoMax

That is weird. What did you do to install the jarfile, and what version of Java are you using?

Edit: Actually, where did you find that particular distribution of gatk? It doesn't look like the same jarfile I'm trying to run, or at least the directory structure seems different.

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written by kacollier • kacollier

I had the same error message. I fixed It by removing java and installing the correct java 8. 1.8_301 I believe is the lates java 8 version

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written by josloc • josloc

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