Corrected PR, minor fix and resolves #74

[cerebis]

In trying the latest master, I found two minor issues.

1. when getting the latest GTDB release files, the os package needed to be imported within download.py.
2. when running in contig mode, there was an referenced before assignment error regarding the variable log_file. This happens when certain arguments are supplied, as the logic did not encompass all possibilities.

The command line causing the error follows. I have left the shell variable substitutions in place, but these were initialised.

./CAT/CAT_pack/CAT contigs --tmpdir /scratch/$USER -n 50 -t cat_gtdb_db/tax -d cat_gtdb_db/db -c ${CTG} -o ${OUTBASE}