2023-05-17.build6771

This release is based on PGAP-6.5. It includes the following features and bug fixes:

• Addition of attributes (Gene Ontology terms, EC numbers, gene symbols) to more protein-coding features, by propagation from curated conserved domain architectures (CDD architectures)
• Incremental improvements in structural algorithm
• Addition of simple option for passing fasta and organism to pgap.py via parameters instead of a yaml file. This option is not sufficient and should NOT be used if the annotated assembly is intended for submission to GenBank.
• Improved help text for pgap.py
• Bug fixes:
  • for small circular plasmids, elimination of crashes when alignment covers almost all of the sequence of the plasmid
  • consistency of partiality and pseudo-status of features between cdregions and genes
  • fixed CPU handling in SLURM environment
  • use of fasta file name instead of 'gc_assm_name' as assembly name in ani-tax-report files

Third Party Software and Data versions used (no changes since last release):

• GeneOntology 2023-01-01
• tRNAscan-SE 2.0.12
• hmmer v.3.1b2
• CRISPR v.1.02
• AntiFam v.3.0
• Rfam v.14.4
• GeneMarkS2 v.1.14_1.25
• infernal v.1.1.1