oschwengers / bakta

Rapid & standardized annotation of bacterial genomes, MAGs & plasmids

oschwengers/bakta Issues

tRNAscan-SE slow with multiple threads
Updated a day ago3
PSC failed! diamond-error-code=-11
Updated a day ago2
Bakta Web Does Not Work
Updated a day ago
Name and Product don't match Dbxref
Updated 8 days ago2
Make the --region parameter better match the output of PGAP
Updated 21 days ago1
Possible issues running bakta in Singularity
Closed a month ago1
Inquiry about the coding density equation
Updated a month ago4
KEGG annotations - the number is much lower number than expected
Updated a month ago1
Roary is not working with bakta-generated gff3-files
Updated a month ago1
Downgrading dependencies is needed when installing bakta from conda
Updated a month ago2
Bakta run times on cluster
Updated a month ago4
Color coding in bakta_plot --type cog
Closed a month ago2
circos legend
Updated 2 months ago1
'SQL error!', IndexError('tuple index out of range')
Updated 2 months ago7
DeepSig could not be executed! Please make sure DeepSig is installed and executable
Closed 2 months ago5
Bakta neither generated circular genome plots nor error messages for running circos command
Closed 2 months ago5
Reduce locus_tag offset from 5 to 1
Updated 2 months ago
Option to Skip the AMR detection step
Updated 3 months ago5
Bakta Diamond error
Closed 3 months ago4
Failed bakta run for some genomes
Closed 4 months ago8
CRISPR position doesn't include last spacer
Closed 3 months ago
Exception: diamond error! error code: -11
Closed 4 months ago6
Bakta fails using --regions if a sequence does not contain a valid start codon
Closed 4 months ago3
origin of replication detection not match Ori-Finder web server
Updated 5 months ago1
Add import feature for user-provided regions and/or features
Closed 6 months ago16
%2C instead of common in GFF3 files
Closed 6 months ago4
Something wrong with bakta_db download
Closed 6 months ago3
Increasing genome annotation: integrating StORF-Reporter functionality into bakta
Closed 6 months ago3
ERROR: Could not detect/read %s version!', command[0]
Closed 6 months ago2
MacOS M2 cannot install bakta using conda.
Closed 6 months ago1
Transfer annotations from similar genome
Updated 6 months ago5
Is it possible to import my own cds fasta file for annotation?
Closed 6 months ago3
bakta is renaming input contigs in its outputs
Closed 7 months ago4
pyrodigal issues with fresh 1.8.2 conda install
Closed 7 months ago5
produce the --replicons input content based on the flye assembly_info.txt
Updated 7 months ago3
Exception: amrfinder error! error code: 1
Closed 7 months ago4
CRISPR detection error or something else?
Closed 7 months ago6
Merge summary files into one excel sheet.
Closed 7 months ago3
[ERROR: Pyrodigal could not be executed! Please make sure Pyrodigal is installed and executable or skip requiring workflow steps via via '--skip-cds'.](https://confluence.ncbi.nlm.nih.gov/pages/viewpage.action?pageId=354897706)
Closed 7 months ago11
Cannot run bakta with biocontainer image
Closed 7 months ago1
Crispr and AMR errors
Closed 8 months ago6
Fix runtime duration report
Closed 8 months ago
Update to pyrodigal v3
Closed 9 months ago2
v1.8.2 error with cmscan error code: -6
Closed 9 months ago10
bakta installed via recommended conda installation has version 0.5 which is incompatible with latest db version 5.0
Closed 9 months ago6
different result comparing to prokka
Closed 9 months ago1
Installation of bakta on Google Colab
Closed 9 months ago5
Docker container: Open shell or run command other than "bakta", such as "bakta_db"
Closed 9 months ago1
get database version for custom db path
Closed 9 months ago2
gene missing from final output files
Closed 10 months ago2