- Replaced Ray with HydraMPP
- Reduced number of dependencies making install easier
- Removed a redundant hmm search when using KOFam
- Organized output files
- Fixed resume feature for hmm step
- Fixed counting conflict between parser and filter steps
- Fixed Ray dependency issue for MetaCerberus-lite, or when Ray is not available.
- created "lite" version.
- removed hard dependency requirements, failing more gracefully to make some dependencies optional
- added linear override for Ray when Ray is not found
- Implemented PyHMMER
- Implemented Pyrodigal
- Implemented Pyrodigal-gv
- Added ORF start and end to output summary files
- Improved speed in creating final GFF files
- Fixed dependency checking for lite version
- Made N removal optional
- Improved Genbank output
- Fixed prodigal-gv GFF
- Fixed some Phanotate bugs
- Fixed bug with --protein option
- Fixed crash when GFF is not present
- Other minor bug fixes
- Custom download location for databases
- Ability to download individual databases
- Update downloaded databases (currently re-downloads the database)
- List available databases
- Custom database support -HMM file with .hmm extension (also supports .hmm.gz) -A TSV file is also required with minimum columns: ID, Function -The ID field must match the NAME field of the HMM file, one row per HMM entry
- Output files -reworked output directories to separate graphs/stats from annotation files -Final folder with annotation summary and files in GTF, genbank, GFF, .FAA, .FNA, .FFN
- Other improvements -Performance improvements -Improved some error handling and reporting
- Multi-domain in summary files -Individual database summary files contain a line per match found -The combined summary file lists only the best match based on e-value
- Slurm on cluster with multiple nodes now working
- Filtering algorithm fix (on rare circumstances it would enter an infinite loop)