Hi, Some of you have run into memory error when tried to run BWA. To solve the problem, you need to download the latest version and install it. Run these command. wget -O bwa-0.7.5.tar.bz2 http://sourceforge.net/projects/bio-bwa/files/bwa-0.7.5a.tar.bz2/download tar xvfj bwa-0.7.5.tar.bz2 cd bwa-0.7.5 make cp bwa /usr/local/bin It should work.