Question: Getting error in running GATK (GenomeAnalysisTK-3.7)?
1
gravatar for Mask
3.9 years ago by
Mask170
India
Mask170 wrote:

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 mutation picard gatk • 5.9k views
ADD COMMENTlink modified 3.7 years ago by LLinging000 • written 3.9 years ago by Mask170
1

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.

ADD REPLYlink written 3.9 years ago by andrew.j.skelton736.1k
1

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??

ADD REPLYlink modified 3.9 years ago • written 3.9 years ago by Mask170

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.
ADD REPLYlink written 3.9 years ago by andrew.j.skelton736.1k
1

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

ADD REPLYlink written 3.9 years ago by Mask170

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

ADD REPLYlink written 3.4 years ago by _r_am32k

what is this about ???

ADD REPLYlink modified 7 days ago • written 3.4 years ago by Mask170
1

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

ADD REPLYlink written 3.4 years ago by WouterDeCoster45k

Hi I am having the same issue with GATK.

How do get read of it?

Cheers,

ADD REPLYlink written 2.3 years ago by agrepaterne0
1
gravatar for Nandini
3.9 years ago by
Nandini890
Nandini890 wrote:

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

ADD COMMENTlink written 3.9 years ago by Nandini890
1

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

ADD REPLYlink written 3.9 years ago by Mask170
1
gravatar for youcai
3.9 years ago by
youcai60
Shenzhen
youcai60 wrote:

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)
ADD COMMENTlink written 3.9 years ago by youcai60

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.

ADD REPLYlink written 28 days ago by greekkey0
1

this post saved me from a headache

ADD REPLYlink written 25 days ago by LBG10
0
gravatar for LLinging00
3.7 years ago by
LLinging000
LLinging000 wrote:

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

ADD COMMENTlink written 3.7 years ago by LLinging000
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