This is a test version of Biostars. For the public version, visit https://www.biostars.org.
Getting error in running GATK (GenomeAnalysisTK-3.7)?

I have reference genome as hg19.fa and duplicate removed reads using picard as deduped_reads.bam. Next, I am trying to run the command 

 - java -jar /home/snijeshv/bin/GenomeAnalysisTK-3.7/GenomeAnalysisTK.jar -T RealignerTargetCreator -R hg19.fa -I deduped_reads.bam -o realignment_targets.list

  • but I am getting an error as follows:

  • ~/Desktop/Genome$ java -jar /home/snijeshv/bin/GenomeAnalysisTK-3.7/GenomeAnalysisTK.jar -T RealignerTargetCreator -R hg19.fa -I deduped_reads.bam -o realignment_targets.list

    • <h5>ERROR ------------------------------------------------------------------------------------------</h5>
    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

    <h5>ERROR</h5>

rna-seq gatk picard mutation
• 15,910 views • link
updated by LLinging00 • LLinging00 • written by Mask Mask

Just in case... can you type out the command by hand, if you've copy/pasted, sometimes hidden characters are interpreted, which won't translate well when passed through. As far as I can see, the RealignerTargetCreator is still present in GATK 3.7, so something seems odd.

• 0 views • link
written by andrew.j.skelton73 andrew.j.skelton73

Dear, I have typed the commands not copy pasted. The tools for the pipeline used are bwa, samtools, picard and gatk. Will it be the compatibility issue with the soffwares I am using??

• 0 views • link
written by Mask Mask

Unlikely to be a java issue as you're getting a GATK error. The root of the error is the last line ERROR MESSAGE, which says there's a problem with finding the RealignerTargetCreator walker.

Can you try running the following to make sure we're seeing the right things:

java -jar /home/snijeshv/bin/GenomeAnalysisTK-3.7/GenomeAnalysisTK.jar --help

Check that RealignerTargetCreator is listed under the Indels section. 

java -jar /home/snijeshv/bin/GenomeAnalysisTK-3.7/GenomeAnalysisTK.jar -T RealignerTargetCreator

You should get an error, but make sure it says the last line says something like: 

ERROR MESSAGE: Walker requires a reference but none was provided.
• 0 views • link
written by andrew.j.skelton73 andrew.j.skelton73

Thank you, The problem got solved. It is the compatibility issue with picard and bwa. I have run "AddOrReplaceReadGroups" to make it comptible

• 0 views • link
written by Mask Mask

It is suspicious how _all_ your comments, no matter how trivial, receive exactly 2 upvotes. I'd request an admin to take a look at this. Devon Ryan

• 0 views • link
written by Ram Ram

what is this about ???

• 0 views • link
written by Mask Mask

Well, then you can also tell "your colleagues" to remove those unnecessary upvotes. You are not helping yourself by gaming the system.

• 0 views • link
written by WouterDeCoster WouterDeCoster

Hi I am having the same issue with GATK.

How do get read of it?

Cheers,

• 1 views • link
written by agrepaterne • agrepaterne

3 answers

The current version(GenomeAnalysisTK-3.7) requires Java 1.8. so you'd first run java -version

If the output looks something like java version "1.8.x", you are good to go

then you can use --debug to see what happens；

--debug / -debug
If specified, print out very verbose debug information (if -l DEBUG is also specified)
• 0 views • link
written by youcai • youcai

Yes, you are quite correct. I encountered this issue with GATK 3.8 when I just updated my computer to Ubuntu 20.04 and installed java 11. Then I reinstalled java 8 and everything went on well.

• 0 views • link
written by greekkey • greekkey

this post saved me from a headache

• 0 views • link
written by LBG • LBG

Hi, Can you check if the command you are running is correct ? From the GATK documentation page, I see that you need to provide a known indel file as well.

java -jar GenomeAnalysisTK.jar \
-T RealignerTargetCreator \
-R reference.fasta \
-I input.bam \
--known indels.vcf \
-o forIndelRealigner.intervals

Please check RealignerTargetCreator

• 0 views • link
written by NB NB

known indels are optional, not necessary. Do you think is it the problem with java version?. I am using latest version of java should I downgrade

• 0 views • link
written by Mask Mask

The file you working GATK was wrong. Try to cd the files existed java-version and ref.fa and so on at first.

• 0 views • link
written by LLinging00 • LLinging00

Log in to answer this question.

More posts like this