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Question: muTect analysis, error
0
gravatar for Chirag Nepal
3.6 years ago by
Chirag Nepal • 2.0k
Copenhagen
Chirag Nepal • 2.0k wrote:

I am running muTect with the following parameter, and i have the following errors

java -Xmx8g -jar ~/unixTools/muTect-1.1.4-bin/muTect-1.1.4.jar  --analysis_type MuTect --reference_sequence ucsc.hg19.fasta --cosmic GATKDictionary/CosmicCodingMuts_v68_Modified.vcf --dbsnp GATKDictionary/dbsnp_138.hg19.vcf --input_file:normal bamRealigned/Sample_ST1_CC008T_IndelRealigned.bam --input_file:tumor bamRealigned/Sample_ST2_CC008N_IndelRealigned.bam --out Test.stats.out --coverage_file Test.wig.text

I did not provide --intervals option, so it would search on the whole genome.

I get this error:

Error processing chr1:1647928

java.lang.IllegalArgumentException: Comparison method violates its general contract!
    at java.util.TimSort.mergeLo(TimSort.java:747)
    at java.util.TimSort.mergeAt(TimSort.java:483)

I even tried running older version of muTect, and still get the error.

Any suggestions how to solve it.
mutect software error exome • 2.2k views
ADD COMMENT • link •
modified 3.4 years ago by Ram ♦ 15k • written 3.6 years ago by Chirag Nepal • 2.0k
3
gravatar for russhh
3.6 years ago by
russhh • 3.4k
UK, U. Glasgow
russhh • 3.4k wrote:

use java6 and repeat
ADD COMMENT • link written 3.6 years ago by russhh • 3.4k

As the server i am using have the latest version of Java, so do i need to install the older (which ?) version of Java. If you could write few lines about it, that would be helpful. thanks!

ADD REPLY • link written 3.6 years ago by Chirag Nepal • 2.0k

as I said, use JAVA6. Try it on your desktop/laptop if you can't install java 6 on the server (though I'd suspect you can find an earlier java already installed if you follow your nose).

ADD REPLY • link written 3.6 years ago by russhh • 3.4k

If you're on a HPC, try using module avail and module load, with specific Java versions.

Hi Chirag Nepal , please provide some feedback on members' comments. Did the suggestions help you?

ADD REPLY • link modified 3.4 years ago • written 3.4 years ago by Ram ♦ 15k

I installed Java6 on the server and it worked fine, without any errors.

ADD REPLY • link written 3.4 years ago by Chirag Nepal • 2.0k

That's wonderful. I just moved Russ's comment to an answer. Could you maybe accept it please? Thank you!

ADD REPLY • link written 3.4 years ago by Ram ♦ 15k

Thanks, i just did.

ADD REPLY • link written 3.4 years ago by Chirag Nepal • 2.0k
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