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@pchaumeil pchaumeil released this 24 Apr 01:21
· 5 commits to master since this release
2.4.0
59609e2
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Learn about vigilant mode.

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  • FastANI has been replaced by skani as the primary tool for computing Average Nucleotide Identity (ANI).Users may notice slight variations in the results compared to those obtained using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

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