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mutect runtime performance poor

messiemessie Skaneateles, nyMember

Hi, I'm trying to run MuTect against 10G input (tumor/normal) data files (10G each). The machine has 16G of memory and 4 CPUs :

NAG2:/big/mutect/data/large2/1234$ uname -a
Linux #24-Ubuntu SMP Fri Jan 7 18:30:50 UTC 2011 x86_64 GNU/Linux

However, MuTect is taking on average around 8 days to fully complete against these files. I'm relatively new to MuTect, so not sure if this is typical. From other posts on the forum, looks like others have experienced runtime in the hours (not days). Any suggestions on what I may be doing wrong or be able to change to improve this performance ?? I've also tried varying the -Xmx memory variable to different levels, but no real change in performance. Here is the specific run call I'm using :

/big/mutect/software/java/jre1.6.0_34/bin/java -Xmx12g -jar /big/mutect/software/muTect-1.1.4.jar -T MuTect -R /big/referenceGenome/b37/human_g1k_v37.
fasta -XL 2 --cosmic /big/referenceGenome/cosmic/b37_cosmic_v54_120711.vcf --dbsnp /big/referenceGenome/dbsnp/dbsnp_137.b37.vcf --input_file:normal /b
ig/mutect/data/large2/1234/control1234.bam --input_file:tumor /big/mutect/data/large2/1234/tumor1234.bam --out call_stats2014JAN13.out --coverage_file


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