GATK jar file not found

[kwinker]

Hi, Brant. Sorry to bother you, but it looks like there is a dependency issue with gatk in the new version of phyluce. When giving a gatk command, this error message appears:

GATK jar file not found. Have you run "gatk-register"?

First I looked for jar files in Miniconda2/jar, per the readthedocs Install page, but that directory doesn't exist. When I try to run gatk-register to see if that might straighten it out, that generates an error also:

Extracting gatk-3.7-py27_0.tar.bz2
tar: Error opening archive: Failed to open '/Users/.../gatk-3.7-py27_0.tar.bz2'
Error: Unable to access jarfile ./GenomeAnalysisTK.jar
The version of the jar specified, , does not match the version expected by conda: 3.7

There is no gatk.jar or GenomeAlaysisTK.jar on the drive. Suggestions?

[brantfaircloth]

Hi Kevin,

No worries - this is a result of the licensing policy changes made by the Broad for GATK. In order to "install" GATK, you need to download it from the Broad, directly. I believe they may you register to do this, and you must agree to their license terms.

Although GATK 4 is out, you probably want GATK 3 (v3.5), which you can find at this link.

Once you have downloaded GATK 3.5 somewhere on your system, you will need to unzip the archive, then run:

gatk-register /path/to/GenomeAnalysisTK-3.5-0-g36282e4/GenomeAnalysisTK.jar

To get that path, you can also generally drop the GenomeAnalysisTK.jar onto your terminal window. This should take care of everything.

[brantfaircloth]

I have added a version of the instructions above to the documentation, which should build in the next few minutes and be available online after that.

[kwinker]

Thanks, Brant. That almost works:
"The version of the jar specified, 3.5, does not match the version expected by conda: 3.7"

[brantfaircloth]

Looks like you got a later version of the conda gatk package. if you run conda list in the appropriate environment, you should see which one is installed. I've got gatk 3.5. You could either install an older gatk package from bioconda or you could download a newer version of gatk (e.g. v3.7 as suggested).

[kwinker]

Thanks. I downloaded and installed gatk 3.7 and all is running as planned. Thanks again!

[brantfaircloth]

Cool. I'm also updating the phyluce distribution to fix this/make it clearer.

[ghost]

Thanks. I downloaded and installed gatk 3.7 and all is running as planned. Thanks again!

Hi! Could you please share GATK 3.7 installation notes for ubuntu 16.04 ?

[brantfaircloth]

You can download archived GATK packages (3.7 and 3.8 are now archived) from here. Then run:

gatk-register /path/to/GenomeAnalysisTK-3.x-x-xxxxx/GenomeAnalysisTK.jar

[kwinker]

Thanks, Brant, but I have no idea how I came up in this thread. Weird.

…

On Wed, Mar 11, 2020 at 5:14 AM Brant Faircloth ***@***.***> wrote: You can download archived GATK packages (3.7 and 3.8 are now archived) from here <https://console.cloud.google.com/storage/browser/gatk-software/package-archive/gatk/?pli=1>. Then run: gatk-register /path/to/GenomeAnalysisTK-3.x-x-xxxxx/GenomeAnalysisTK.jar — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub <#112 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ACFD4BI2EUPFJDQV35NHHJLRG6FCVANCNFSM4FIANJMA> .

-- Kevin Winker Brina Kessel Curator of Birds University of Alaska Museum 907 Yukon Drive Fairbanks, AK 99775 Professor, Dept. Biology & Wildlife and Inst. of Arctic Biology <kevin.winker@alaska.edu> kevin.winker@alaska.edu

[brantfaircloth]

You are included because of your previous comments on this issue. You can click up at the top of the thread to turn off notifications.

[kwinker]

Got it. Thanks.

…

On Wed, Mar 11, 2020 at 9:45 AM Brant Faircloth ***@***.***> wrote: You are included because of your previous comments on this issue. You can click up at the top of the thread to turn off notifications. — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub <#112 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ACFD4BNJ2MA6R32LCIHFGQTRG7E2DANCNFSM4FIANJMA> .

-- Kevin Winker Brina Kessel Curator of Birds University of Alaska Museum 907 Yukon Drive Fairbanks, AK 99775 Professor, Dept. Biology & Wildlife and Inst. of Arctic Biology <kevin.winker@alaska.edu> kevin.winker@alaska.edu

[BirdmanRidesAgain]

I'm a little late to this thread, but I'm having some issues with the archived GATK 3.7/3.8 copies. I ran

'gatk-register /my/path/GenomeAnalysisTK-3.7-0-gcfedb67/GenomeAnalysisTK.jar'

to install the archived version, and 'conda list' confirms that I have gatk 3.7 activated. My system responds appropriately to 'gatk --help', but none of the .jar files that contain the tools themselves appear to be present.

Eg:

(phyluce-1.7.1) melospiza@Colliers-iMac pluvialis-df-mtDNA-bwa-alignments % gatk -T RealignerTargetCreator

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: RealignerTargetCreator

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

Is there something else that I need to do to get the toolkit functions online?

[brantfaircloth]

Something seems off here. I just tested:

gatk-register /Users/bcf/Anaconda/envs/phyluce/jar/GenomeAnalysisTK.jar

Which produced the following output:

ENV_PREFIX /Users/bcf/Anaconda/envs/phyluce
Processing GenomeAnalysisTK.jar as *.jar
jar file specified matches expected version
Copying GenomeAnalysisTK.jar to /Users/bcf/Anaconda/envs/phyluce/opt/gatk-3.8

Then I ran gatk -h, which behaved normally. I also ran gatk -T RealignerTargetCreator -h, which behaved normally. Regardless, you don't necessarily need the gatk shim/app that is installed as part of conda - with an appropriate java installation, you should also be able to run java -jar /Users/bcf/Anaconda/envs/phyluce/jar/GenomeAnalysisTK.jar (I.e. just using the path to the jar file you downloaded.

As an aside, GATK3 is not longer supported by the GATK folks.

[BirdmanRidesAgain]

Yes, something is weird here. Everything works just like in your code, right up until I try to call RealignerTargetCreator, at which point I get the malformed walker argument error.
Does the gatk distribution that you're using have files besides 'GenomeAnalysisTK.jar'? Aside from a couple of usage example files, that's the only file included in my archived distribution, and I remember each individual tool having a separate .jar (eg, RealignerTargetCreator.jar) the last time I ran gatk.

Either way, I guess I'll just download the latest version of gatk and install/run that separately.

[brantfaircloth]

Things have been integrated to a single *.jar file for a while, so there are no other files besides GenomeAnalysisTK.jar.

[BirdmanRidesAgain]

Then something is weird with my system here. Either way, calling the file manually is working for me, and I'm fine just circumventing the problem. Thanks for your help!