v2.1.13

• Fix #454 issue. Prokka GFF files have FASTA sequences after a ##FASTA header, causing the parsing of GFF fields to crash. As for now, all lines below the ##FASTA header are ignored.
• Update 3 error messages in emapper.py referencing"download_eggnog_database.py". It should be "download_eggnog_data.py" (tyvm @ejrsimr !)
• Changes to hmm_mapper.py: added --data_dir option and also the possibility to use an EGGNOG_DATA_DIR environmental variable, to specify a custom user defined path the eggNOG data.

Release v2.1.12

• Updated novel families DB version and added novel families .pkl DB for annotation, which can be downloaded from http://eggnog6.embl.de/download/novel_fams-1.0.1 or using download_eggnog_data.py -D -F
• Using the novel families search -m novel_fams now provides new annotation fields in .emapper.annotations output file.

Release v2.1.11

• Bug on issue #432
• Bug when running --decorate_gff yes along with --resume

Release v2.1.10

• Bug fixes (see Pull Requests), including compatibility with python 3.11.
• HMMER database downloaded using download_eggnog_data.py can be saved with a user specified name (see Pull Requests).
• Paths of input and output files should now accept white spaces.
• --genepred prodigal should accept now gzipped files as input, fixing issue #439.
• Added --timeout_load_server to control the number of attempts made to fire up a hmmpgmd server, also used with the --usemem option.

Release v2.1.9

Added the option to search queries against the novel families identified at https://doi.org/10.1101/2022.01.26.477801

1 - Download the novel families diamond database: download_eggnog_data.py -F
2 - Search your queries against the novel families: emapper.py -m novel_fams

Release v2.1.8

Bug fixes related with hmmer searches using hmmpgmd servers (--usemem option, etc). Fixes #390

Release v2.1.7

• Changes in GFF decoration to (hopefully) fix issue #367 , in which positions were relative to the ORF (1-end) instead of relative to the contig which contains the ORF. Now, 2 GFF files will be created when using gene prediction and gff decoration: one ".genepred.gff" from either Prodigal or blastx-like hits, one ".decorated.gff" with the annotations added as attributes.
• Update the --resume procedure. Now, most files are created from scratch, being resumed the search (if a ".emapper.hits" exists) and annotations (if a ".emapper.hits" exists, or ".emapper.seed_orthologs" if using --annotate_hits_table option; and if a partial ".emapper.annotations" file exists).
• Now it should be possible to use Biopython 1.78 (python 3.9) which removed the BioAlphabet module.
• emapper.py's --temp_dir option is now linked to Diamond's --tmpdir option.
• Update / Bug fix (issue #328) regarding report of orthologs, where the seed ortholog was listed in every orthology category. Now the seed ortholog should be tagged as "seed" in the "orth_type" column.
• Help description and default values of parameters of emapper.py are now provided more consistently (PR #346 addressing issue #344, thanks @nick-youngblut). Also done by @nick-youngblut for all the other main scripts (PR #347).
• --version now reports the Diamond/MMseqs2 version found (either from PATH or from eggNOG-mapper bundled bin).
• Fixed a bug when transferring PFAM annotations from denovo hmmpgmd search and number of queries was large (>15000).

Release v2.1.6

• Updated citation of eggNOG-mapper.
• Updated citation of Diamond.
• Diamond's --iterate mode is now used by default. To disabled it when running emapper.py, use --dmnd_iterate no.
• Added --dmnd_ignore_warnings option, to activate Diamond's --ignore-warnings option.
• Added --dmnd_algo option, to control Diamond's --algo option. It can be used to perform a much faster search with small input sets of sequences using --dmnd_algo ctg.
• Added --mp_start_method option, to control the Python's multprocessing start method. Only use it when the default is not working properly in your OS.
• Minor changes related with hmmpgmd searches.

Release v2.1.5

• New Diamond version 2.0.11 bundled.
• Added new options for diamond mode (require using Diamond version 2.0.11): --dmnd_iterate (Diamond's --iterate option), --sensmode fast, and --sensmode default.
• Bug fix (issues #313 and #319), when parsing GFF files with "." in the "score" field.
• --dmnd_frameshift INT option to control Diamond's --frameshift/-F option.
• Bug fix / try to address the main spec bug (issue #299). For a fix in version 2.1.4, check pre-release [[https://github.com/eggnogdb/eggnog-mapper/releases/tag/2.1.4-main_spec]]
• Minor progress report text fix.

documentation: https://github.com/eggnogdb/eggnog-mapper/wiki/eggNOG-mapper-v2.1.5

Release v2.1.4-main_spec

This is a test release to check whether annotation can be run with multiprocessing and without issues related with spec in main (see issue #299