1.3.0

This version of GTDB-Tk requires a new version of the GTDB-Tk reference package (gtdbtk_r95_data.tar.gz) available here.

Features:

• Updated reference package to use the GTDB Release 95 taxonomy.
• Report if the species-specific ANI circumscription criteria is satisfied in the ani_closest.tsv file output by ani_rep.
• Estimated time until completion has been dampened.

1.2.0

Bug fixes:

• (#241) Moved GTDB-Tk entry point to main.py instead of bin/gtdbtk to support execution in some HPC systems (gtdbtk will still be aliased on install).
• (#251) Allow parsing of FastANI v1.0 output files. However, a warning will be displayed to update FastANI.
• (#254) Fixed an issue where --scratch_dir would fail, and not clean-up the mmap file.

Features:

• (#242) Added the decorate command allowing the de novo workflow to be run
• (#244) Added the infer_rank method which established the taxonomic ranks of internal nodes of user trees based on RED
• (#248) If the identify command is run on the same directory, genomes which were already processed will be skipped.
• (#248) Improved pplacer output with running the classify command

1.1.1

• Fix a issue with Tree parsing

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 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 threads would timeout with FastANI returned a non-zero exit code.
  • Versions affected: 1.0.0, and 1.0.1.

1.0.1

• Bugfix for 3rd party software versions.

1.0.0

• Migrated to Python 3, you must be running at least Python 3.6 or later to use this version.
• 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

• A bug has been fixed which affected classify and classify_wf when using the --batchfile argument with genome IDs that differed from the FASTA filename. This issue resulted in the assigned taxonomy being derived only from tree placement without any ANI calculations being considered. Consequently, in some cases genomes may have been classified as a new species within a genus when they should have been assigned to an existing species. If you have genomes with species assignments this bug did not impact you.
• Progress is now displayed for: hmmalign, and pplacer.
• Fixed an issue where the root command could not be run independently.
• Improved MSA masking performance.

0.3.2

• FastANI calculations are more robust.
• Optimisation of RED calculations.
• Improved output messages when errors are encountered.

0.3.1

• Pplacer taxonomy is now available in the summary file.
• FastANI species assignment will be selected over phylogenetic placement (Topology case).