Transform traditional blast output to `--outfmt 6` I have run a blastx of metagenomic databases (raw illumina reads) using the nr database. Unfortunately, I forgot to add the --outfmt 6 argument to the code and got the traditional output.  

Could I parse this output into --outfmt 6?
The blast_formatter command allows you to produce output in any of the formats supported by BLAST. However, it requires that you run blastx with --outfmt 11 (ASN.1 format). I'm not sure there are any tools that will do the conversion from the full default BLAST report. This could potentially be scripted, but would be complex enough that you're probably better off re-running BLAST.