kennthshang / cherry_mags Goto Github PK
View Code? Open in Web Editor NEWMAG version of CHERRY
License: GNU General Public License v3.0
MAG version of CHERRY
License: GNU General Public License v3.0
Hi, I run this pipeline on my own phage genomes and bacterial genomes to predict interactions between them. Based on the output, it seems that only one bacterial host is predicted for each phage genome. I wonder that how to predict all potential bacterial hosts of phage based on ones own phage and bacterial genomes using this pipeline? Thank you in advance!
Hi, thank you for providing this usefull software! When I am using this software to explore the interaction between my phage contigs and my bacterial genomes, an issue regarding "KeyError" occurred (see a part of issue below). can you please help to address this issue?
The log file (nohup.out.txt) is attached for your information.
nohup.out.txt
The prokaryote.csv file has been edited according to the input bacterial genome, and a beginning part of this file is below:
Accession,Superkingdom,Phylum,Class,Order,Family,Genus,Species,Name
G1_1_2_bin_24,G1_1_2_bin_24,G1_1_2_bin_24,G1_1_2_bin_24,G1_1_2_bin_24,G1_1_2_bin_24,G1_1_2_bin_24,G1_1_2_bin_24,G1_1_2_bin_24
G1_1_2_bin_25,G1_1_2_bin_25,G1_1_2_bin_25,G1_1_2_bin_25,G1_1_2_bin_25,G1_1_2_bin_25,G1_1_2_bin_25,G1_1_2_bin_25,G1_1_2_bin_25
G1_1_2_bin_27,G1_1_2_bin_27,G1_1_2_bin_27,G1_1_2_bin_27,G1_1_2_bin_27,G1_1_2_bin_27,G1_1_2_bin_27,G1_1_2_bin_27,G1_1_2_bin_27
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