simroux

Hi Michael, You're correct about the decontamination mode. For the cp flag, there is currently no way to only compare contigs to your custom database, the "--cp" is always on...

Correct, that is the expected behavior (I would suggest doing a backup copy of the "Phage_gene_catalog_plus_viromes" just in case though).

Hi Megan, Yes, unfortunately, you won't be able to feed "r_0" directory as "data_dir", because it doesn't have all the databases. The way this should (hopefully) work is as follows:...

Per the readme file: "--data-dir /path/to/virsorter-data", i.e. data-dir is used to give VirSorter the path to the folder containing the databases.

Hi Eric, Thanks for the suggestion ! Since there is no support for the development of VirSorter, I can not commit on any timeline for when I will be able...

Hi, Thanks for the suggestion, and thanks a lot for sharing the R Code to import VirSorter results. Unfortunately, there is no support for VirSorter development anymore, so I can't...

Hi Silas, Are you trying to run VirSorter through the Docker container or via cloning from GitHub + custom Conda environment ? If the latter, there is an option called...

The error message is weird, and doesn't seem to be accurate (sorry). VirSorter expects Pfam to be in the same directory as the virsorter data v2, in its own subfolder...

Hi, Could you paste or enclose the out and err files here ? It looks to me as an error in the step where VirSorter tries to use the results...

Ok, so it looks like VirSorter indeed completed successfully, and you should be able to work with the results you got. Let me know if ever you see anything weird...