use muscle path from config in /root/Anacapa_db/scripts/blca_from_bowtie.py

[max-mapper]

it seems like the muscle path isnt getting passed in, causing it to default to ./muscle

[limey-bean]

That is very interesting. That is why I had it in the Anacapa folder before. Funky things were happening. Are you using my hoffman@ anacapa db or something else?