Question: muTect analysis, error
0
gravatar for Chirag Nepal
3.0 years ago by
Chirag Nepal1.9k
Copenhagen
Chirag Nepal1.9k 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 • 2.0k views
ADD COMMENTlink modified 2.9 years ago by Ram12k • written 3.0 years ago by Chirag Nepal1.9k
3
gravatar for russhh
3.0 years ago by
russhh2.7k
UK, U. Glasgow
russhh2.7k wrote:

use java6 and repeat

ADD COMMENTlink written 3.0 years ago by russhh2.7k

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 REPLYlink written 3.0 years ago by Chirag Nepal1.9k

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 REPLYlink written 3.0 years ago by russhh2.7k

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 REPLYlink modified 2.9 years ago • written 2.9 years ago by Ram12k

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

ADD REPLYlink written 2.9 years ago by Chirag Nepal1.9k

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

ADD REPLYlink written 2.9 years ago by Ram12k

Thanks, i just did.

ADD REPLYlink written 2.9 years ago by Chirag Nepal1.9k
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