[jmjensen]

To extract the comment lines (and thus the lines with 0 hits), you could use:

awk '/^\#/' file > newfile

If you want only the 'Query' line, then you could use the following instead:

awk '/^\# Query/{print $0}' file > new file

[rhinoceros]

Any good tips on how to directly extract the queries with no hits?

cut -f 1 your_outfmt6_output_file.txt | sort -u > hitlist.txt

and then use this script or something similar on your query file.