v1.5.1

This is the first v1.5 patch release (v1.5.1) fixing a crucial bug causing Diamond runtime errors during the pseudogene detection step. A patch upgrade is highly recommended!

Improvements:

• Added a --debug option in order to keep temporary files for debugging purposes: #137 #141 (Thanks @EricDeveaud)
• Bakta now obeys the number of available CPUs instead of mere CPU counts on Linux: #135 #139 (Thanks @EricDeveaud)
• The Docker image now allows the direct execution of Bakta via Singularity's exec mode in Nextflow: #138 #144 (Thanks @rujinlong & @lukasjelonek)

Bug fixes:

• Fixed an IndexError during the pseudogene detection: #130 #133 (Thanks @samnooij & @jhahnfeld)
• Fixed an off-by-1 error: #131 (Thanks @jhahnfeld)

v1.5 - Pseudogenes, they're coming...

This is the fifth minor release (v1.5) introducing the detection of pseudogenes and KEGG Kofams, along with several improvements.

Compatible database scheme version: 4

New features:

• detection of CDS pseudogenes: #4 (Thanks @jhahnfeld)
• pre-annotation of PSCs with KEGG's Kofams also massively increasing the number of available E.C. numbers: #9

Improvements:

• pre-annotation of PSCs with NCBI's NCBIfams leading to many improved functional annotations: e268df2 #102 (Thanks @hkaspersen)
• add CI tests for species / strain parameters: a98670b
• revert oriCVT inference tags in compliant mode: 4f31ab4
• improve the functional pre-annotation: 46e645a de55d30 1893220 1835574

v1.4.2

This is the second v1.4 patch release (v1.4.2) fixing wrong EC annotations in compliant mode.

Improvements:

• added GFF3 inference tags in compliant mode for ncRNA region, CRISPR, oriC, oriV, oriT: 85c9c42 d81d9b7 a5b31af
• improved chromosome/plasmid auto detection: 9a83055
• refactored code: 606c237 21e6470 b36172c

Bug fixes:

• fixed EC_number annotation in compliant mode: 2960e6b

v1.4.1

This is the first v1.4 patch release (v1.4.1) fixing a tiny simple but critical bug causing all imported contigs being treated as complete sequences. A patch upgrade is highly recommended!

Improvements:

• removed trailing asterik chars on AA import #97: a447f32
• caught AA bulk annotation import errors #97: 58cedf1

Bug fixes:

• fixed fasta import contig attribute types #108
• fixed dnaA/repA revisions #108 (Thanks @conmeehan)

v1.4 - Some exceptional translations

This is the fourth minor release (v1.4) introducing the detection of translational exceptions and protein bulk annotations.

Compatible database scheme version: 3

New features:

• detection & annotation of selenocysteine translational exceptions: #100
• support for protein bulk annotations (direct annotation of proteins w/o genomes): #101 (Thanks @conmeehan)

Improvements:

• maintainability improvements like Python type hints code refactorings: #96 943485c
• added a large(r) genome test dataset and a corresponding Nextflow script: 32e0f9e
• add more CI tests: ce2c68f 4549f25

Bug fixes:

• fixed molecular weight in hypothetical tsv output d83c1b8

And of course all improvements and bug fixes from all v1.3.x patch releases.

v1.3.3

This is the third v1.3 patch release (v1.3.3).

This is a quick fix reverting an alive-progress version bump to v2.1.0 that is not available via Conda. Sorry for any inconvenience caused.

Bug fixes:

• fixed a file permission issue on bakta_db update: de42d3f
• pinned alive-progress version to v1.6.2 to fix potential API errors: dbc79ac 60ac3ed

v1.3.2

This is the second v1.3 patch release (v1.3.2).

Bug fixes:

• fixed a file permission issue on bakta_db update: de42d3f
• bumped alive-progress version to >=v2.1.0 to fix potential API errors: dbc79ac

v1.3.1

This is the first v1.3 patch release (v1.3.1).

Bug fixes:

• fixed the locus-tag checks: use a more relaxed format as default and INSDC restrictions on --compliant: e2651c3 (Thanks @taylorreiter)
• skip /pseudo annotated genes in --proteins-provided GenBank files: 0f0165d (Thanks Charlotte Reuschel)

v1.3 - Quo vadis, protein?

This is the third minor release (v1.3) introducing a new feature and many improvements and bug fixes.

Compatible database scheme version: 3

New features:

• prediction of signal peptides via DeepSig: #32 (Thanks @Anna-Rehm)

Improvements:

• provide summary with genome & annotation statistics as .txt file: #88 (Thanks @hkaspersen)
• accept user provided proteins in GenBank format: #89 (Thanks @Tonny-zhou)
• removed alignment gaps (-) in input sequences: #87 (Thanks @RotimiDada)
• improved sORF overlap filter runtime performance: cb204fb
• improved outputs: 76e07a4 90bfe99
• added more checks & tests: b779e1f 4e6c35d f4103f0 08ebb03 1672a87 26a8ed2
• added --gram to CWL file: 2246319

Bug fixes:

• fixed tmRNA predictions that cross sequence origins: #90 (Thanks @LuisFF)
• moved oriC/T/V product to Note in INSDC and compliant GFF3 outputs: 2f5cb1d 716302e 5e1a0d8
• fixed sequence description on Fasta import: bfdf67f
• fixed Fasta import log error: 5209672
• fixed EDAM out types in CWL file: a1a0ad1

And of course all improvements and bug fixes from all v1.2.x patch releases.

v1.2.4

This is the 4th v1.2 patch release (v1.2.4) fixing a database download issue.

Bug fixes:

• fixed the database download/update logic by restoring an accidentally removed URL: 247a047 (Thanks @andreaniml)