Getting error in running GATK (GenomeAnalysisTK-3.7)?

Question

[Mask]

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>

[andrew.j.skelton73]

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.

[Mask]

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??

[andrew.j.skelton73]

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.

[Mask]

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

[Ram]

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

[Mask]

what is this about ???

[WouterDeCoster]

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

[agrepaterne]

Hi I am having the same issue with GATK.

How do get read of it?

Cheers,

Answer 1

[youcai]

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)

[greekkey]

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.

[LBG]

this post saved me from a headache

Answer 2

[NB]

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

[Mask]

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

Answer 3

[LLinging00]

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