Add option to change base name of sortmerna's output files

Two changes,

1. Add option to change base name of sortmerna's output files (needed for parallel sortmerna as to avoid writing to the same file)
2. Append pid to the sortmerna's index if it's built using pick_otus.py. This will avoid any seg faults which may occur if two processes to sortmerna write to the same index file
Why did you remove this section?