Hello, I found that in the genomad method of ViWrap, it using 'prodigal -p meta' in the 'run_annotate_by_VIBRANT_db.py' script to predict proteins. In contrast, genomad uses the 'pyrodigal-gv' software to achieve this step. I tested this two gene calling softwares and they produced different protein prediction results from the same contigs. However, ViWrap seems combine these two annotation results only based on the protein id... It have some problems because two proteins in the result of geNomad and run_annotate_by_VIBRANT_db.py may be different even they have the same protein id.
By the way, I also could not reproduce the same protein prediction result of genomad even using the 'pyrodigal-gv' in the genomad conda environment. I'm not sure the reason but I think that the combination of the annotation result of genomad and local annotations (whatever using prodigal -p meta or pyrodigal-gv) should be cautious.
Hello, I found that in the genomad method of ViWrap, it using 'prodigal -p meta' in the 'run_annotate_by_VIBRANT_db.py' script to predict proteins. In contrast, genomad uses the 'pyrodigal-gv' software to achieve this step. I tested this two gene calling softwares and they produced different protein prediction results from the same contigs. However, ViWrap seems combine these two annotation results only based on the protein id... It have some problems because two proteins in the result of geNomad and run_annotate_by_VIBRANT_db.py may be different even they have the same protein id.
By the way, I also could not reproduce the same protein prediction result of genomad even using the 'pyrodigal-gv' in the genomad conda environment. I'm not sure the reason but I think that the combination of the annotation result of genomad and local annotations (whatever using prodigal -p meta or pyrodigal-gv) should be cautious.