songweizhi / metachip2 Goto Github PK

Hey developer,

Thanks for your great efforts to release the new push of MetaCHIP

I've followed the guide:

conda create -n metachip2env -c conda-forge -c bioconda gtdbtk=2.3.2
source activate metachip2env
pip install MetaCHIP2
conda install -c bioconda blast
conda install -c bioconda diamond
conda install -c bioconda mmseqs2
conda install -c conda-forge r-base

and successfully install the software and database.

However, the tutorial is not very instructive on how to use the metachip part:

For example, what does the gbk refers to, is it the identified MAGs? and How can I get the rooted.tree file?

MetaCHIP2 detect -i gbk_dir -x gbk -c taxon.tsv -s rooted.tree -v -t 12 -f -p demo -r pcofg -m

I have tried to put the pipeline as below:

MetaCHIP2 detect -i ./ -x fa -c ./gnms_GTDB_r214/gnms_GTDB_r214.bac120.summary.tsv -s ./gnms_GTDB_r214/classify/gnms_GTDB_r214.backbone.bac120.classify.tree -t 12 -f -r pcofg -m -o mtchp2

the ./ directory contains my MAG bins (.fa); the taxa and tree files were generated by gtdb-tk
gnms_GTDB_r214.bac120.zip
. Could you please help me check my pipeline and teach me how to prepare the required gbk and tree files, if they are not right.

Thanks