Support latest version of Bedtools

Merge pull request #264 from andrewjpage/fix_empty_accessory_binary

Fix empty accessory binary

Allow for massive bacteria & get rid of warning mesage from logger

v3.6.2

version 3.6.2

Prefix commands with roary

Merge pull request #244 from andrewjpage/prefix_commands_with_roary

prefix commands with roary