1.1.1
- Minor bug fixes.
1.1.0
- Bug fixes:
- In rare cases pplacer would assign an empty taxonomy string which would raise an error.
- (#229) Genomes using windows line carriage (\r\n) would raise an error.
- (#227) CentOS machines would fail when using `~` in paths.
- The bac120 symlink was pointing to the archaeal tree when using the `root` command.
- Features:
- Updated the `gtdb_to_ncbi_majority_vote.py` script for translating taxonomy.
- (#195) Added the `--pplacer_cpus` argument to specify the number of pplacer threads when running `classify` and `classify_wf` (#195).
- (#198) The `--debug` flag of `align` outputs aligned markers to disk before trimming.
- (#225) An optional third column in the `--batchfile` will specify an override to which translation table should be used. Leave blank to automatically determine the translation table (default).
- (#131) Users can now specify genomes which have NCBI accessions, as long as they are not GTDB-Tk representatives (a warning will be raised).
- (#191) Added a new command `ani_rep` which calculates the ANI of input genomes to all GTDB representative genomes. This command uses [Mash](https://github.com/marbl/Mash) in a pre-filtering step. If pre-filtering is enabled (default) then `mash` will need to be on the system path. To disable pre-filtering use the `--no_mash` flag.
- (#230) Improved how markers are used in determining the correct domain, and gene selection for the alignment.
1.0.2
- Fixed an issue where FastANI would timeout.
1.0.1
- Bugfix for 3rd party software versions.
1.0.0
- Migrated to Python3.
- check_install now does an exhaustive check of the reference data.
- Resolved an issue where gene calling would fail for low quality genomes (#192).
- Improved FastANI multiprocessing performance.
- Third party software versions are reported where possible.
0.3.3
- Bugfix for --batchfile users of classify and classify_wf.
- Display hmmalign, and pplacer progress.
- Fixed an issue where the root command could not be run independently.
- Improved MSA masking performance.
0.3.2
- Classify step is now taking the alignment fraction into account.
- Assigning pre-calculated RED value to the tree now takes seconds.
- FastANI now runs G1vsG2 and G2vsG1 and takes the best value.
- Logging has been improved.
0.3.1
- pplacer taxonomy added to the summary file.
- FastANI result is selected over pplacer topology.
0.3.0
- New options to export the untrimmed reference MSA files.
- Support for gzipped genomes (--extension .gz).
- By default, GTDB-Tk uses pre-calculated RED values.
- New option to recalculate RED value during classify step (--recalculate_red).
- Best translation table displayed in summary file.
- New option to skip_trimming during align step.
- New FAQ page available.
- New output structure.
- New option to use a custom taxonomy file when rooting a tree.
0.2.2
- Fix support for writing to a scratch file using pplacer (--mmap-file options).
0.2.1
- remove Perl dependencies
- remove Biolib,mpdl3,jinja dependencies
- add support for writing to a scratch file using pplacer (--mmap-file options)
- add random seed to trim MSA step to allow for reproducible results.
- use GTDBTK_DATA_PATH variable to set data directory.
- species classification based on ANI radii.
- new columns ( aa_percent,red_values,fastani_reference_radius,warnings )
- bug fixing
- gtdbtk test options
0.1.6
- align step in classify_wf and de_novo_wf function has been fixed.
- improve summary file output.
- "align" function now supports the same custom trimming GTDB will be performing.
- returns closest reference genome to summary file (even if the ANI is less than 95%)
0.1.5
- bug fixing
0.1.4
- "align" function now supports the same custom trimming GTDB will be performing.
- returns closest reference genome to summary file (even if the ANI is less than 95%)
0.1.3
- v0.1.3 resolves bug that would occur when a user genome has a FastANI >= 95% with reference genomes but not with the closest pplacer leaf node.
0.1.2
- resolve bug that would occasionally cause genomes to not be correctly associated with a reference genome in the pplacer tree. FastANI was still identifying correct species assignments.
0.1.1
- config_template.py updated
- rooting of the tree is now fixed.
0.1.0
- GTDB-Tk is now using archived (.gz) fna files
- summary.tsv file is now the main output file.
- fastani.tsv file is now combined with summary.tsv.
- red_value.tsv file has been removed.
- Each Pplacer placement on a species branch is now verify by FastANI and the ANI is compared with all other species in the same genus to check Pplacer accuracy.
- New functionality: "trim_msa" allows to trim an untrimmed MSA (41155AA for bac120 and 32675AA for ar122) based on GTDB-Tk masks
0.0.8b4
- bug fixing
0.0.8b3
- bug fixing
0.0.8b2
- bug fixing
0.0.8b1
- Using .fna.gz reference genome for FastANI
- Pplacer placement are verified by FastANI
0.0.7
0.0.6
- Migration to R83 and integration of UBA genomes
- add "debug" flag to classify options
- error handling improvement
0.0.5
- stable version for pip
0.0.4b3
- fastANI dependency fix
0.0.4b2
- fastANI dependency fix
0.0.4b1
- FastAni comparison bug fixing
0.0.4-beta
- Code cleaning
0.0.3
- FastAni multi-threaded.
0.0.2
- modified align command to automatically determine domain of each genome and process accordingly
0.0.1
- initial release
