Tuning parameters for possibly missed prophage

Hi @linsalrob and team,

Thanks for the great tool! We were trying to use it on https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/033/802/525/GCF_033802525.1_ASM3380252v1/GCF_033802525.1_ASM3380252v1_genomic.gbff.gz

Interestingly, we got slightly different results with PhiSpy, PhiSpy (PHROGs - used sed -i 's/HHsearch/HMMER3\/f/g' vogs/phrog.hhm to get it to run), PhiSpy (pVOG), PhiSpy (using -t data/trainSet_Ecoli.txt) and Genomad: phage_masker_comparison.xlsx

It looks to us like PhiSpy (pVOG) and Genomad got the correct end coordinate of pp8:

We started investigating the prophage information file: prophage_information.xlsx

Our questions are:

Any idea why default missed this region?
How can we tune parameters to capture it? Ideally we do not want to run the HMM due to speed constraints or negatively impact accuracy
Any idea why pVOG captured it but not PHROGs? We had tried PHROGs based on recommendation in https://github.com/linsalrob/PhiSpy/issues/61

Thanks again!

linsalrob / PhiSpy

Tuning parameters for possibly missed prophage #69