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oschwengers / bakta

Rapid & standardized annotation of bacterial genomes, MAGs & plasmids
GNU General Public License v3.0
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AttributeError: module 'pyrodigal' has no attribute 'OrfFinder' #319

Open cuongngh opened 1 week ago

cuongngh commented 1 week ago

Describe the bug To fix any bugs and issues and also to help other users who might face the same issues, a concise description is beneficial and often necessary.

Therefore, please provide us with at least the following information:

Hi, I run bakta locally and has this error: AttributeError: module 'pyrodigal' has no attribute 'OrfFinder'. I tried to run pyrodigal separately and it works fine. Could you please help me to fix this? I installed pyrodigal separately because I have Mac with Apple silicon. Thanks so much.

oschwengers commented 1 week ago

Hi @cuongngh, this seems to be caused by an unsupported Pyrodigal version. I'd like to kindly refer you to https://github.com/oschwengers/bakta/issues/298 which deals with exactly this problem and provides a description/solution.

cuongngh commented 1 week ago

Hi @cuongngh, this seems to be caused by an unsupported Pyrodigal version. I'd like to kindly refer you to #298 which deals with exactly this problem and provides a description/solution.

@oschwengers, thank you so very much for the information.

Sarani-NS commented 5 days ago

Hi @cuongngh , did you manage to fix it ? I checked the #298 issue but I guess it doesn't apply, as I downloaded Bakta using Conda today only, so everything should be up to date & all dependencies installed. I still get the same error. Any lead ? Thanks in advance,

cuongngh commented 4 days ago

Hi @cuongngh , did you manage to fix it ? I checked the #298 issue but I guess it doesn't apply, as I downloaded Bakta using Conda today only, so everything should be up to date & all dependencies installed. I still get the same error. Any lead ? Thanks in advance,

Hi @Sarani-NS, unfortunately I did not manage to fix this. The problem is all about the Apple Silicon. As @oschwengers mentioned clearly the new Bakta needs new Pyrodigal. But in my case, there is no Bakta 1.9.. available for Apple M3, therefore it is not possible to have compatible Pyrodigal although after installing I have newest version of Pyrodigal. However, I could run Bakta by skipping CDS, and some other features. If you have any idea to fix it, I appreciate for that.

Sarani-NS commented 4 days ago

Hi @cuongngh , I am getting a new error but finally got past the ORFinder one. I just reinstalled bakta using conda, but in a new environment as suggested. However, I am using Linux.

Maybe you can try using the web version or install the equivalent of WSL for mac ? I used the web version of Bakta yesterday and (gladly !!), the results seem to be the same so far.

cuongngh commented 4 days ago

Hi @cuongngh , I am getting a new error but finally got past the ORFinder one. I just reinstalled bakta using conda, but in a new environment as suggested. However, I am using Linux.

Maybe you can try using the web version or install the equivalent of WSL for mac ? I used the web version of Bakta yesterday and (gladly !!), the results seem to be the same so far.

Hi @Sarani-NS, yes I tried the web. Thanks.