extract_kraken_reads.py not working when read mates have unique names

[RHaagmans]

Just ran into an issue where reads weren't being extracted from the second read file, and I realised it was because I had inadvertently earlier appended unique tags (R1 and R2) to the read IDs.

This might not be a common issue, and I'm not sure if there's a straightforward fix for this, since it is probably difficult to account for all the ways you could create unique read IDs. Nonetheless, I thought it might be good to post this here so people are aware :)