VirSorter predicts prophage larger than contig size about emg-viral-pipeline HOT 5 CLOSED

Thanks! I got it to work now using 1.0.6.

Closing this ticket 👍

from emg-viral-pipeline.

See VirSorter answer here:
simroux/VirSorter#68

So we can wait for a fix or simply adjust the length to the actual contig size in case the reported length is too long.

from emg-viral-pipeline.

the problem is fixed already in the recent github version of VirSorter:
simroux/VirSorter#68

from emg-viral-pipeline.

Pending update of container with latest release of virsorter (https://github.com/simroux/VirSorter/releases/tag/v1.0.6)

from emg-viral-pipeline.

Maybe helps to build a Docker from the 1.0.6 VirSorter branch: https://github.com/replikation/What_the_Phage/blob/master/phage-tool-Dockerfiles/virsorter/Dockerfile

Or this should also work:

FROM continuumio/miniconda3
ENV VERSION 1.0.6
ENV TOOL virsorter

RUN apt update && apt install -y procps wget gzip pigz bc && apt-get clean && rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*

RUN conda config --add channels conda-forge && \
		conda config --add channels bioconda && \
		conda config --add channels default

RUN conda install $TOOL=$VERSION && conda clean -a

based on the bioconda recipe.

Or that container also works for me in the dev branch :)

docker pull mhoelzer/virsorter:1.0.6

from emg-viral-pipeline.