Gtdbtk

* 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.

- Bugfix for 3rd party software versions.

* 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.

* 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.

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

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