Hi qiime2 developers,
I am trying to detect antibiotic resistance genes from metagenomic assemblies using the plugin q2-amrfinderplus in pathogenome suite.
I installed version 2026.1 and 2026.4 following the conda installation instructions:
2026.1:
conda env create
--name q2-pathogenome-2026.1 --file https://raw.githubusercontent.com/qiime2/distributions/refs/heads/dev/2026.4/pathogenome/released/rachis-pathogenome-linux-64-conda.yml
2026.4:
conda env create
--name rachis-pathogenome-2026.4 --file https://raw.githubusercontent.com/qiime2/distributions/refs/heads/dev/2026.4/pathogenome/released/rachis-pathogenome-linux-64-conda.yml
However, when I ran the command
qiime amrfinderplus annotate
I found plugin named 'assembly' could not be found in 2026.4, and 'partition_contigs' was not found for plugin 'assembly' in 2026.1. Then I ran
qiime info
and found:
2026.4 version:
System versions
Python version: 3.12.13
QIIME 2 release: 2026.4
QIIME 2 version: 2026.4.0
q2cli version: 2026.4.0
Installed plugins
amrfinderplus: 2026.4.0
demux: 2026.4.0
feature-table: 2026.4.0
metadata: 2026.4.0
types: 2026.4.0
viromics: 2026.4.0
vizard: 2026.4.0
2026.1 verion:
System versions
Python version: 3.10.14
QIIME 2 release: 2026.1
QIIME 2 version: 2026.1.0
q2cli version: 2026.1.0
Installed plugins
alignment: 2026.1.0
amrfinderplus: 2026.1.0
assembly: 2026.1.0
demux: 2026.1.0
feature-classifier: 2026.1.0
feature-table: 2026.1.0
fondue: 2026.1.0
longitudinal: 2026.1.0
metadata: 2026.1.0
quality-control: 2026.1.0
rescript: 2026.1.0
sample-classifier: 2026.1.0
taxa: 2026.1.0
types: 2026.1.0
viromics: 2026.1.0
vizard: 2026.1.0
It seems both versions don't have a complete set of plugins. Can I install the missing plugins individually? Can you give me some advice? Thanks for the help!
