rsync -avz --progress rsync://hgdownload.cse.ucsc.edu/goldenPath/hg19/multiz46way/maf ./ for i in *.md5;do md5sum -c $i;done cd maf mkdir used for i in `ls chr*.maf.gz|grep -v chrUn|grep -v random|grep -v hap`;do newname=`basename $i .gz`; gunzip -c $i > used/$newname;done #program is hardcore as hell, so only start 2 processes, that might even be to much ls maf/used/*.maf|xargs -P 2 -n1 -I infile sh -c './a.out infile |gzip -c >maf/info/`basename infile`.info.gz' rm -rf used