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0.6.x is getting a bit long in the tooth and does not have the "bwa mem" feature, please update to the latest: http://sourceforge.net/projects/bio-bwa/
I hope to look at updating it this weekend. Thanks for the notification.
bwa-0.7.5a-2.fc20 has been submitted as an update for Fedora 20. https://admin.fedoraproject.org/updates/bwa-0.7.5a-2.fc20
bwa-0.7.5a-2.fc19 has been submitted as an update for Fedora 19. https://admin.fedoraproject.org/updates/bwa-0.7.5a-2.fc19
As noted in the update, 0.7.x requires SSE2, so it won't be available for other architectures. Please test this new build. Also, this makes updating the EPEL branches rather problematic. Are you using those?
Package bwa-0.7.5a-2.fc20: * should fix your issue, * was pushed to the Fedora 20 testing repository, * should be available at your local mirror within two days. Update it with: # su -c 'yum update --enablerepo=updates-testing bwa-0.7.5a-2.fc20' as soon as you are able to. Please go to the following url: https://admin.fedoraproject.org/updates/FEDORA-2013-20142/bwa-0.7.5a-2.fc20 then log in and leave karma (feedback).
bwa-0.7.5a-2.fc19 has been pushed to the Fedora 19 stable repository. If problems still persist, please make note of it in this bug report.
bwa-0.7.5a-2.fc20 has been pushed to the Fedora 20 stable repository. If problems still persist, please make note of it in this bug report.