Tuning parameters for possibly missed prophage

[schorlton-bugseq]

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!