2.2.0

2.2.0

Minor changes:

• (#433) Added additional checks to ensure that the --outgroup_taxon cannot be set to a domain (root, de_novo_wf).
• (#459/ #462 ) Fix deprecated np.bool in prodigal_biolib.py. Special thanks to @neoformit for his contribution.
• (#466 ) RED value has been rounded to 5 decimals after the comma.
• (#451 ) Extra checks have been added when Prodigal fails.
• (#448) Warning has been added when all the genomes are filtered out and not classified.

Bug Fixes:

• (#420 ) Fixed an issue where GTDB-Tk might hang when classifying TIGRFAM markers (identify, classify_wf, de_novo_wf). Special thanks to @lfenske-93 and @sjaenick for their contribution.
• (#428) Fixed an issue where the --gtdbtk_classification_file would raise an error trying to read the classify summary (root, de_novo_wf).
• (#439) Fix the pipeline when using protein files instead of nucleotide files. symlink uses absolute path instead.

2.1.1

• (#399) Fix --genes options
• (#400) Modify config.py file to resolve this issue
• Updated documentation ( including #410 , documentation for itol)

2.1.0

Major changes:

• GTDB-TK now uses a divide-and-conquer approach where the bacterial reference tree is split into multiple class-level subtrees. This reduces the memory requirements of GTDB-Tk from 320 GB of RAM when using the full GTDB R07-RS207 reference tree to approximately 55 GB. A manuscript describing this approach is in preparation. If you wish to continue using the full GTDB reference tree use the --full-tree flag. This is the main change from v2.0.0. The split tree approach has been modified from order-level trees to class-level trees to resolve specific classification issues (see #383).
• Genomes that cannot be assigned to a domain (e.g. genomes with no bacterial or archaeal markers or genomes with no genes called by Prodigal) are now reported in the gtdbtk.bac120.summary.tsv as 'Unclassified'
• Genomes filtered out during the alignment step are now reported in the gtdbtk.bac120.summary.tsv or gtdbtk.ar53.summary.tsv as 'Unclassified Bacteria/Archaea'
• --write_single_copy_genes flag in now available in the classify_wf and de_novo_wf workflows.

Features:

• (#392) --write_single_copy_genes flag available in workflows.
• (#387) specific memory requirements set in classify_wf depending on the classification approach.

Important

This version is not backwards compatible with GTDB package R207 v1.
This version requires a new reference package

2.0.0

Major changes:

• GTDB-TK now uses a divide-and-conquer approach where the bacterial reference tree is split into multiple order-level subtrees. This reduces the memory requirements of GTDB-Tk from 320 GB of RAM when using the full GTDB R07-RS207 reference tree to approximately 35 GB. A manuscript describing this approach is in preparation. If you wish to continue using the full GTDB reference tree use the --full-tree flag.
• Archaeal classification now uses a refined set of 53 archaeal-specific marker genes based on the recent publication by Dombrowski et al., 2020. This set of archaeal marker genes is now used by GTDB for curating the archaeal taxonomy.
• By default, all directories containing intermediate results are now removed by default at the end of the classify_wf and de_novo_wf pipelines. If you wish to retain these intermediates files use the --keep-intermediates flag.
• All MSA files produced by the align step are now compressed with gzip.
• The classification summary and failed genomes files are now the only files linked in the root directory of classify_wf.

Features:

• convert_to_itol to convert trees into iTOL format (#373)
• Output FASTA files are compressed by default (#369)
• Intermediate files will be removed by default when using classify/de-novo workflows unless specified by --keep_intermediates (#369)
• Add --genes flag for Error (#362)
• A warning will be displayed if pplacer fails to place a genome (#360 / #356)

Important

• This version is not backwards compatible with GTDB release 202.
• This version requires a new reference package

1.7.0

• (#336) Warn the user if they have provided an incorrectly formatted taxonomy file.
• (#348) Gracefully exit the program if no single copy hits could be identified.
• (#351) Fixed an issue where GTDB-Tk would crash if spaces were present in the reference data path.
• (#354) Added optional --tmpdir argument to set temporary directory (thanks @tr11-sanger ).

1.6.0

• (#337) Set minimum tqdm version to 4.35.0
• (#335) Fixed typo in output log messages (@fplaza)
• Removed the option to re-calculate RED values (–recalculate_red)

1.5.1

Changelog:

• #327 Disallow spaces in genome names/file paths due to downstream application issues.
• #326 Disallow genome names that are blank.

1.5.0

Changes:

• Updated to use PFAM 33.1 markers.
• Updated to use GTDB R202 taxonomy (note, this will require an update to the reference package https://ecogenomics.github.io/GTDBTk/installing/index.html#gtdb-tk-reference-data)

Fixes:

• Automatic drop of genome leads to error in downstream modules of classify_wf (#312)
• --scratch_dir not working in v 1.4.1 (#311)

1.4.1

• Updated GitHub CI/CD to trigger docker build / tag version on release.
• (#255) (#297) Fixed 'Namespace' object has no attribute errors by adding default arguments to argparse.

1.4.0

• Check if stdout is being piped to a file before adding colour.
• (#283) Significantly improved classify performance (noticeable when running trees > 1,000 taxa).
• Automatically cap pplacer CPUs to 64 unless specifying --pplacer_cpus to prevent pplacer from hanging.
• (#262) Added --write_single_copy_genes to the identify command. Writes unaligned single-copy AR122/BAC120 marker genes to disk.
• When running -version warn if GTDB-Tk is not running the most up-to-date version (disable via GTDBTK_VER_CHECK = False in config.py). If GTDB-Tk encounters an error it will silently continue (3 second timeout).
• (#276) Renamed the column aa_percent to msa_percent in summary.tsv (produced by classify).
• (#286) Fixed a file not found error when the reference data is a symbolic link (thanks davidealbanese!).
• (#277) Fixed an issue where if the user overrides the translation table using the optional 3rd column in the batchfile, the other coding density would appear as -100. Both translation table densities are now reported.
• The check_install command now also checks that all third party binaries can be found on the system path.
• The align step is now approximately 10x faster.
• (#289) Added --min_af to classify and classify_wf which allows the user to specify the minimum alignment fraction for FastANI.
• Added the --mash_db command to re-use the GTDB-Tk Mash reference database in ani_rep.