Previously, there was a check that looked for overlap between all ASVs in the input FASTA and the feature table, but there were downstream errors that could be caused by having duplicated sequence IDs in the input fasta. This fix adds a check that no sequence IDs in the input FASTA appear more than once.

- Zipped default file that was previously unzipped
- Added metacyc reaction mapping pathways (modified from HUMAnN3)
- Added line to castor_hsp.R that ensures no issues running maximum parsimony method even if edge lengths of tree have zeroes

Some new scripts have been added:
- default_split.py: locations of new default files for when we're running bacteria/archaea separately
- split_domains.py: functions for choosing the best domain for each sequence based on which has the lowest NSTI
- pick_best_domain.py: wrapper for picking the best domain to use for each sequence when we're running bacteria/archaea separately. Note that this would be run between hsp.py with the 16S/marker gene file and running hsp.py with any other trait files
- combine_domains.py: wrapper for combining functional predictions from hsp.py for when we're running multiple domains. This would be run before the metagenome_pipeline step
- Functions in util.py have been added for steps like reading in and pruning the tree files

Update to add scripts for running both bacterial and archaeal predictions

Added requirement for ete3 to yaml file

Added check for when no sequences match with one of the domains

Note that this file still needs testing

Archaea reference files now work with SEPP

Added new -db flag to pathway_pipeline.py

…ia and archaea