muTect analysis, error

Question

[Chirag Nepal]

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.

Answer 1

[russhh]

use java6 and repeat

[Chirag Nepal]

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!

[russhh]

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).

[Ram]

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?

[Chirag Nepal]

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

[Ram]

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

[Chirag Nepal]

Thanks, I just did.