oschwengers bakta issues

oschwengers / bakta

Rapid & standardized annotation of bacterial genomes, MAGs & plasmids

GNU General Public License v3.0

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issues

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Introduce feature inference TSV output file

#331 oschwengers opened 7 hours ago
0
Errors in submitting annotations to NCBI

#330 kevinmyers opened 7 hours ago
2
gene= missing for some copies of the gene but present in others

#329 ebraginngd opened 2 days ago
1
Incorrect locus tag incrementation

#328 NonAggressiveHail closed 2 days ago
1
Add support for trusted user hmms

#327 oschwengers opened 3 days ago
0
Presumed GFF3/Gbff user regions file format error when replicon table is provided

#326 oschwengers closed 3 days ago
0
eggnog annotation

#325 jotech opened 1 week ago
0
Error on GenBank file with CompoundLocation overlapping sequence origin

#324 aekazakov opened 1 week ago
1
translation-table code 25

#323 ndombrowski closed 3 days ago
3
Increase verboisity for invalid --proteins options

#322 NonAggressiveHail closed 3 days ago
3
Old tRNAscan-SE in containers and environments

#321 fischuu closed 2 weeks ago
0
No pseudogenes being detected

#320 flashton2003 closed 3 days ago
4
AttributeError: module 'pyrodigal' has no attribute 'OrfFinder'

#319 cuongngh opened 3 weeks ago
6
Issue/Error in tRNAscan-SE running

#318 hackerzone85 opened 3 weeks ago
0
Missing genes in both faa files

#317 EdderDaniel closed 2 days ago
5
APIs get jobStatus ERROR, although jobs started, initiated and run.

#316 cuongngh closed 4 weeks ago
2
cmmscan for rRNA identification is probably configured incorrectly and does NOT use CM-only mode

#315 richardstoeckl closed 1 month ago
2
option to include scores in bakta output

#314 jvera888 opened 1 month ago
3
conda install did not install bakta_db

#313 JCSzamosi opened 1 month ago
3
Question regarding summary stats generation

#312 fischer-hub opened 1 month ago
6
tRNAscan-SE issue on HPC

#311 Sylvia-li closed 3 weeks ago
4
.conda/envs/bakta/lib/python3.10/site-packages/bakta/main.py", line 150, in main genome['features'][bc.FEATURE_T_RNA] = t_rna.predict_t_rnas(genome, contigs_path)

#310 davidmadariaga opened 1 month ago
1
Option for trusted HMMs

#309 StefDiV opened 2 months ago
1
Addition of custom codon table/improve 'rare' start codons prediction

#308 DanielleMStevens opened 2 months ago
2
Issue with trnascan-SE and bakta v1.9.4

#307 rubmc97 closed 2 months ago
1
reproducibility - amrfinderplus-db

#306 Juke34 closed 1 month ago
4
Bakta web version ignores translation table change

#305 AggressiveHayBale closed 2 months ago
1
(Re-)Generating bakta outputs from the JSON only

#304 oschwengers opened 2 months ago
0
Skip certain genes in user-provided regions

#303 oschwengers closed 2 months ago
0
Fix CRISPR parser

#302 oschwengers closed 2 months ago
0
fix(create_cdss): Handle different translation tables in meta mode

#301 ohickl closed 2 months ago
1
CRISPR prediction assertion error

#299 ohickl closed 2 months ago
1
pyrodigal has no attribute 'OrfFinder'

#298 sebibarLE closed 2 months ago
11
pyhmmer not found

#297 samlipworth closed 2 months ago
14
Inquiry on CDS annotation

#296 songmj86 closed 3 months ago
2
Is there a way to deactivate the overlap detection so bakta does not filter my input proteins?

#295 Daniel-Tichy opened 3 months ago
3
pyrodigal, pyhmmer dependencies test using sys.executable

#294 EricDeveaud closed 3 months ago
1
use sys.executable instead of 'python'

#293 EricDeveaud closed 3 months ago
2
Diamond Error -9

#292 cloeme closed 1 month ago
3
Bakta Web Does Not Work

#291 Dabiguina94 closed 3 months ago
6
PSC failed! diamond-error-code=-11

#290 DariaGI closed 2 months ago
2
tRNAscan-SE slow with multiple threads

#289 ohickl opened 4 months ago
3
Make the --region parameter better match the output of PGAP

#288 Dx-wmc opened 4 months ago
8
Name and Product don't match Dbxref

#287 ktmeaton closed 1 month ago
3
Possible issues running bakta in Singularity

#286 andreaswallberg closed 4 months ago
1
KEGG annotations - the number is much lower number than expected

#285 tvtv195 closed 1 month ago
4
Roary is not working with bakta-generated gff3-files

#284 LindavdGvB closed 2 months ago
1
Downgrading dependencies is needed when installing bakta from conda

#283 LeonCharlesTranchevent closed 3 months ago
2
Bakta run times on cluster

#282 loulanomics closed 2 months ago
4
Inquiry about the coding density equation

#281 AhmedElsherbini closed 3 months ago
4