match criteria for iphop

Hi Simon,

Thank you for providing this useful tool!

Regarding the match criteria for iphop, I have come across some articles on host analysis using iphop that mention the following match criteria: d2* values ≤ 0.2 for VHM, p-values ≤ 0.05 for WIsH, the predicted 'maxScoreHost' for PHP, and FaFAH_scores > 0.14 for RaFAH.

I tried looking for this information on the website but couldn't seem to find what I was looking for. Could you please confirm if these are indeed the matching criteria for iphop, as described in these papers, or if there are any parameters that need to be set? I would greatly appreciate your guidance or assistance on this. Thank you!

(iphop_env) emma@emma-PowerEdge-R730xd:/media/HD1/LY$ iphop predict -h
Run full pipeline to predict host of input bacteriophage/archaeal virus genomes
usage: iphop predict --fa_file <input genomes> --out_dir <output directory> [options]

optional arguments:
-h, --help show this help message and exit
--fa_file INPUT_FILE, -f INPUT_FILE
input fasta file of virus sequences
--out_dir OUT_DIR, -o OUT_DIR
output directory (default = ./)
--db_dir DB_PATH, -d DB_PATH
database directory (default = /media/HD1/LY/db)
--num_threads THREADS, -t THREADS
number of threads (default = 1)
--step STEP, -s STEP To run only specific step(s) (default: all, options: compute / classify)
--min_score MIN_SCORE, -m MIN_SCORE
Minimum confidence score for final output file - between 75 and 100. Default is 90, i.e. ~10% FDR (roughly). For ~5% overall (roughly)
estimated FDR, use a minimum score of 95, etc.').
--no_qc Bypass the automated QC that filters out input sequences with > 10% Ns or with characters other than ATCGN. Warning: if set to true, low-
quality sequences (with Ns or unusual characters) may lead to unexpected failures at multiple steps. (default = False)
--debug Run in a more verbose mode for debugging / troubleshooting purposes (warning: iPHoP becomes quite chatty in this mode..)
--single_thread_wish Force the recoded version of wish to run on a single thread instead of all the threads given to iPHoP (with --num_threads)

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