bakta

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circos legend

2

Why is there no legend in the genome circle diagram? How to add legend ?Thanks!

3between7

As requested in #274, we could reduce the default locus_tag offset from `5` to `1`. A differing offset could be provided via a new parameter `--locus-tag-increment `.

oschwengers

tRNAscan-SE slow with multiple threads

3

Hi, not sure where to go with this so I'll start here to ask if anyone experienced something similar since I use tRNAscan-SE with bakta. I noticed on tRNAscan-SE would...

ohickl

pyrodigal has no attribute 'OrfFinder'

2

I installed the latest version of Bakta using conda (conda install -c conda-forge -c bioconda bakta) and the full database on 2024-06-27. I used the following command: bakta --db /home/sebastian/db/...

sebibarLE

pyhmmer not found

6

Hello, Installed via conda, ERROR: Pyhmmer could not be executed! Please make sure Pyhmmer is installed and executable or skip requiring workflow steps via via '--skip-cds --skip-sorf'. mamba install pyhmmer...

samlipworth

Hi Oliver, I performed quite a few runs now on metagenomes of various sizes with the modified Bakta version from #289 and had barely any problems except for one sample...

ohickl

Is there a way to deactivate the overlap detection so bakta does not filter my input proteins?

1

- The issue is related to the user-provided proteins feature and its associated issues. - I am trying to use bakta to perform annotation on a phage predicted protein file...

Daniel-Tichy

Diamond Error -9

3

Hi my error code is as below: Traceback (most recent call last): File "/data/cephfs/punim1258/chloe/new_rnaseq2024/bakta/myenv/bin/bakta", line 10, in sys.exit(main()) File "/data/cephfs/punim1258/chloe/new_rnaseq2024/bakta/myenv/lib/python3.10/site-packages/bakta/main.py", line 259, in main cdss_psc, cdss_pscc, cdss_not_found = psc.search(cdss_not_found) File...

cloeme

eggnog annotation

2

Hi, is there still a plan to incorporate further annotation resources like eggnog, as outlined in #102 ?

jotech

Different expected and conceptual translations for some partial CDS

1

Hi, I'm trying to submit embl flatfiles generated by bakta to the EBI but I am confronted with multiple errors related to the translation of some partial CDS. It seems...

tpillone