mutect writes logging info to STDOUT

[brentp]

I run mutect as:

java -Xmx8G -jar $M/muTect-1.1.5.jar \
    -T MuTect \
    --reference_sequence $FA \
    --cosmic $M/b37_cosmic_v54_120711.vcf.gz \
    --dbsnp $M/dbsnp_132_b37.leftAligned.vcf.gz \
    --input_file:normal $1 \
    --input_file:tumor $2 \
    --out $3.out \
    --coverage_file $3.wig.txt \
    | bgzip -c > $3.vcf.gz

and in the output vcf.gz, there are thousands of lines like:

INFO  14:00:07,692 MuTect - [MUTECT] Processed 9839608564 reads in 636 ms 

those should go to stderr (also the reads processed is off).