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CHANGELOG.md

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Change Log

v1.8.13 (18-Mar-2025)

Changed

  • changed gtt-gen-SCG-HMMs to only use Pfam 37.0 for now (as later versions don't have one of the required files currently; see #104)

v1.8.12 (11-Mar-2025)

Changed

v1.8.11 (10-Mar-2025)

Added

  • VeryFastTree is now an available treeing program (-T)

Changed

  • when using gtt-get-accessions-from-GTDB, if the requested taxon has spaces in it (e.g., gtt-get-accessions-from-GTDB -t "Bacillus_A anthracis"), the output files will have spaces replaced with dashes now
    • e.g., one of the outputs will now be "GTDB-Bacillus_A-anthracis-species-accs.txt" instead of "GTDB-Bacillus_A anthracis-species-accs.txt"

v1.8.10 (3-Feb-2025)

Added

  • saving ncbi downloaded files is possible when debug flag (-d) is set as requested in #95, implemented in #102
    • with the debug flag set while running, it will keep specific files in <output_dir>/<tmp_dir>/ncbi-downloads/:
      • if amino-acid seqs are used, it will keep the downloaded amino-acid seqs
      • if there were no amino-acid seqs, and the genome had to be downloaded, it will keep the downloaded genome and the prodigal-called amino-acid seqs
      • if using nucleotide mode (-z), it will keep the downloaded genome and the prodigal-called nt cds and amino-acid seqs

v1.8.9 (31-Jan-2025)

Fixed

  • added logic to catch, exit, and report when muscle doesn't successfully produce an alignment for a single-copy gene-set (thanks to #101)

v1.8.8 (7-Oct-2024)

Changed

  • updated the call to FastTree and FastTreeMP to be include -nt and -gtr when GToTree is run in nucleotide mode (-z)

Fixed

  • properly saving additional pfam target HMMs when that functionality is used

v1.8.7 (29-Sep-2024)

Added

  • gtt-gen-SCG-HMMs now reports which version of PFAM was used (prints it out to the terminal and writes it to a file)

Changed

  • improvements to the "Universal" Hug et al. gene set thanks so much to @molly-kholodova digging in and reaching out!
    • PF00181 ("Ribosomal_L2") was changed to PF03947 ("Ribosomal_L2_C")
      • the C-terminal (which PF03947 covers) is better conserved
    • PF00827 ("Ribosomal_L15") was changed to PF00828 ("Ribosomal_L27A")
      • PF00827 was archaea/euk only, PF00828 holds the bac/arc L15 also
    • PF17135 ("Ribosomal_L18") was changed to PF00861 ("Ribosomal_L18p")
      • the PF00861 model is better distributed

v1.8.6 (8-May-2024)

Fixed

  • fixed when taxonomy information wasn't being added to labels when running in nucleotide mode (-z; #91)

v1.8.5 (1-May-2024)

Changed

  • update to gtt-gen-SCG-HMMs to deal with ncbi assembly summary files having a column name of "#assembly_accession" instead of what was once "# assembly_accession"

v1.8.4 (28-Nov-2023)

Fixed

  • fixed an issue that prevented moving forward when there were more than 12,500 input genomes (#83)

v1.8.3 (14-Oct-2023)

Changed

  • updated links to GTDB files as they switched from .tar.gz extensions to .tsv.gz extensions in latest release, thanks to note from @jmtsuji (#81)

v1.8.2 (26-Jul-2023)

Added

Fixed

  • updated gtt-get-ncbi-tax-data to appropriately pull from http instead of ftp also thanks to #78
  • fix to check for ncbi assemblies "date-retrieved.txt" file, as also caught and fixed by @hyphaltip (#80) 🙏

Earlier version changes are tracked on the releases page.