GTDBTk Versions Save

Bug Fixes:

• (#576) When all genomes fail the prodigal step in the classify_wf, The bac120 summary file is still produced with the all failed genomes listed as 'Unclassified'
• (#573) When running the 3 classify steps independently, a genome can be filtered out in the align step but still be classified in the identify step. To avoid duplication of row, the genome is classified with a warning.
• (#540 ) Empty files are skipped during the sketch step of Mash, they are then catched in the prodigal step and are returned as 'Unclassified'
• (#549) : --force has been modified to deal with #540. Prodigal wasn't returning the empty files as failed genomes, it was only skipping them. These genomes are now returned in the summary file and flagged as Unclassified.

Major Changes:

• FastANI has been replaced by skani as the primary tool for computing Average Nucleotide Identity (ANI).Users may notice slight variations in the results compared to those obtained using FastANI.

• In the generated summary.tsv files, several columns have been renamed for clarity and consistency. The following columns have been affected:

  • "fastani_reference" column has been renamed to "closest_genome_reference".
  • "fastani_reference_radius" column has been renamed to "closest_genome_reference_radius".
  • "fastani_taxonomy" column has been renamed to "closest_genome_taxonomy".
  • "fastani_ani" column has been renamed to "closest_genome_ani".
  • "fastani_af" column has been renamed to "closest_genome_af".

These changes have been implemented to improve the readability and understanding of the data within the summary.tsv files. Users should update their scripts or processes accordingly to reflect these renamed column headers.

Bug Fixes:

• (#528) (#529) setup.py has been modified to restrict pydantic version to >=1.9.2 and < 2.0a1

Minor Changes:

• (#526) change captures the Mash stderr in a separate buffer ( Thanks @wasade for your contribution)

-- Disregard this release

Bug Fixes:

• (#508) (#509) If ALL genomes for a specific domain are either filtered out or classified with ANI they are now reported in the summary file.

Minor changes:

• (#491) (#498) Allow GTDB-Tk to show --help and -v without GTDBTK_DATA_PATH being set.
  • WARNING: This is a breaking change if you are importing GTDB-Tk as a library and importing values from gtdbtk.config.config, instead you need to import as from gtdbtk.config.common import CONFIG then access values via CONFIG.<var>
• (#508) Mash distance is changed from 0.1 to 0.15 . This is will increase the number of FastANI comparisons but will cover cases wheere genomes have a larger Mash distance but a small ANI.
• (#497) Add a convert_to_species function is GTDB-Tk to replace GCA/GCF ids with their GTDB species name
• Add --db_version flag to check_install to check the version of previous GTDB-Tk packages.

2.2.6

Bug Fixes:

• (#493) Fix issue with --full-tree flag (related to skipping ANI steps)

Minor changes:

• Change URL for documentation to 'https://ecogenomics.github.io/GTDBTk/installing/index.html'
• Improve portability of the ANI_screen step by regenerating the paths of reference genomes in the current filesystem for mash_db.msh

2.2.5

Bug Fixes:

• gtdbtk.json is now reset when the pipeline is re run and the status of ani_screen is not 'complete'

Minor changes:

• When using --genes , ANI steps are skipped and warnings are raised to the user to inform them that classification is less accurate.
• (#486) Environment variables can be used in GTDBTK_DATA_PATH
• is_consistent function in mash.py compares only the filenames, not the full paths
• Add cutoff arguments to PfamScan ( Thanks @AroneyS for the contribution)

Bug Fixes:

• (#475) If all genomes are classified using ANI, Tk will skip the identify step and align steps

Minor changes:

• Add hidden '--skip_pplacer' flag to skip pplacer step ( useful for debugging)
• Improve documentation
• Convert stage_logger to a Singleton class
• Use existing ANI results if available

2.2.3

Bug Fixes:

• Fix prodigal_fail_counter issue

Bug Fix:

(#471): Fix pplacer issue

• (#470) Add missing Pydantic dependency.