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EBI-Metagenomics / mobilome-annotation-pipeline

Apache License 2.0
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Can the annotation software add bakta? #21

Open Dx-wmc opened 6 months ago

Dx-wmc commented 6 months ago

Hi, the publication date of prokka is too long and the annotation efficiency is very poor. The author of prokka currently recommends using bakta, and the files generated by bakta are similar to those of prokka. Is it possible to replace the annotation pipeline with bakta?

Dx-wmc commented 6 months ago

In addition, I encountered many difficulties when installing the software, and the Readme seems to be written too simply. In fact, I have already installed these software locally. Can I use the local software? In addition, I tried to download the docker container in the module, but errors still occurred during the running process.

Ales-ibt commented 6 months ago

Hello and thank you for your interest in using the Mobilome Annotation Pipeline.

Unfortunately, at the moment we have no plans to change the annotation tool, but we will consider it for future releases. However, you can use any annotator that suits you and feed the pipeline with your GFF file. This way, the mobilome predictions will be added to your GFF file.

Regarding problems installing the software for the modules, I'd recommend you to use the singularity profile. This way, Nextflow will solve the containers pulling from public repositories and you don't have to install anything. Just be sure you build the container for ICEfinder following the instructions provided.

I hope this is useful. Please provide more information like error messages or log files if you continue having problems running the pipeline.

Dx-wmc commented 4 months ago

My other problem is that there seems to be a problem with the icefinder.def you provide here. When I ran apptainer build icefinder-v1.0-local.sif icefinder-v1.0-local.def, it couldn't be completed smoothly. I repeated this operation on multiple servers, and all failed without exception. Error message: /.post.script: 18: cpanm: not found FATAL: While performing build: while running engine: exit status 127

Ales-ibt commented 4 months ago

We are currently refactoring the ICEfinder module and the dockerfile. I'll update you as soon as I have something for you to test.