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oschwengers / bakta

Rapid & standardized annotation of bacterial genomes, MAGs & plasmids
GNU General Public License v3.0
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pyrodigal has no attribute 'OrfFinder' #298

Open sebibarLE opened 2 weeks ago

sebibarLE commented 2 weeks ago

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/ --output results/ --threads 32 Genome.fasta

The following happens:

parse genome sequences... imported: 172 filtered & revised: 172 contigs: 172

start annotation... predict tRNAs... found: 115 predict tmRNAs... found: 1 predict rRNAs... found: 18 predict ncRNAs... found: 10 predict ncRNA regions... found: 79 predict CRISPR arrays... found: 3 predict & annotate CDSs... Traceback (most recent call last): File "/home/sebastian/miniconda3/bin/bakta", line 10, in sys.exit(main()) ^^^^^^ File "/home/sebastian/miniconda3/lib/python3.12/site-packages/bakta/main.py", line 228, in main cdss = feat_cds.predict(genome, contigs_path) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/home/sebastian/miniconda3/lib/python3.12/site-packages/bakta/features/cds.py", line 40, in predict orffinder = pyrodigal.OrfFinder(meta=prodigal_metamode, closed=closed) ^^^^^^^^^^^^^^^^^^^ AttributeError: module 'pyrodigal' has no attribute 'OrfFinder'

What can I do?

oschwengers commented 1 week ago

Hi, in this case you seem to have an older version of Pyrodigal installed. You have to update Pyrodigal to >= 3.0

miaroig commented 1 week ago

I have the same issue 'pyrodigal' has no attribute 'OrfFinder'. My pyrodigal version is 3.4.1, bakta version 1.8.2, parse genome sequences... imported: 367 filtered & revised: 367 contigs: 367

start annotation... predict tRNAs... found: 54 predict tmRNAs... found: 1 predict rRNAs... found: 3 predict ncRNAs... found: 10 predict ncRNA regions... found: 18 predict CRISPR arrays... found: 0 predict & annotate CDSs... Traceback (most recent call last): File "/home/dwn-63/Apps/mamba/envs/ensamblaje/bin/bakta", line 10, in sys.exit(main()) File "/home/dwn-63/Apps/mamba/envs/ensamblaje/lib/python3.10/site-packages/bakta/main.py", line 228, in main cdss = feat_cds.predict(genome, contigs_path) File "/home/dwn-63/Apps/mamba/envs/ensamblaje/lib/python3.10/site-packages/bakta/features/cds.py", line 41, in predict orffinder = pyrodigal.OrfFinder(meta=prodigal_metamode, closed=closed) AttributeError: module 'pyrodigal' has no attribute 'OrfFinder' Bakta finished for CEL7_final_assembly.fasta

thh32 commented 5 days ago

Same issue here, updated pyrodigal to the latest version and still occurs.

oschwengers commented 3 days ago

@thh32 @miaroig the newer Pyrodigal version is only supported since Bakta version >= 1.9.0. Could you please update Bakta and check if the error remains?

rubmc97 commented 3 days ago

Same issue here, already tried to update bakta and the same error still pops up.

oschwengers commented 2 days ago

There is a mutual dependency limitation between Bakta and Pyrodigal.

Since version 1.9.0 Bakta's Conda package has a dependency specification, unfortunately, before it has not. I guess this is the source of this issue, since in older Bakta Conda package versions Pyrodigal can be updated beyond the supported version.