run rgi (Resistance Gene Identifier)

rgi.sh

pip install biopython==1.78
sudo apt install -y prodigal

# PATH need contain diamond, blast, kma, samtools, bamtools, bedtools2

git clone https://github.com/arpcard/rgi.git -b 6.0.1

cd rgi

# app/Diamond.py
# cmd = ('diamond prepdb -d {db} && diamond {program} --in {in_ref} --db {db} \

python setup.py install

wget -O card-data-v3.2.5.tar.bz2 https://card.mcmaster.ca/download/0/broadstreet-v3.2.5.tar.bz2
tar -a -x -v -f card-data-v3.2.5.tar.bz2 ./card.json

wget -O card-prevalence-v4.0.0.tar.bz2 https://card.mcmaster.ca/download/6/prevalence-v4.0.0.tar.bz2
mkdir -p wildcard
tar -a -x -v -f card-prevalence-v4.0.0.tar.bz2 -C wildcard
gunzip wildcard/*.gz

rgi card_annotation -i card.json > card_annotation.log 2>&1
rgi wildcard_annotation -i wildcard --card_json card.json -v 4.0.0 > wildcard_annotation.log 2>&1

rgi load \
  --card_json card.json \
  --debug \
  --card_annotation card_database_v3.2.5.fasta \
  --card_annotation_all_models card_database_v3.2.5_all.fasta \
  --wildcard_annotation wildcard_database_v4.0.0.fasta \
  --wildcard_annotation_all_models wildcard_database_v4.0.0_all.fasta \
  --wildcard_index wildcard/index-for-model-sequences.txt \
  --wildcard_version 4.0.0 \
  --amr_kmers wildcard/all_amr_61mers.txt \
  --kmer_database wildcard/61_kmer_db.json \
  --kmer_size 61

rgi main \
 --input_type contig \
 --alignment_tool DIAMOND \
 --num_threads $(nproc) \
 --include_loose \
 --split_prodigal_jobs \
 --input_sequence sample.contigs.fa \
 --output_file sample

rgi bwt \
 -n $(nproc) \
 --include_wildcard \
 --include_other_models \
 -1 sample.R1.fastq.gz \
 -2 sample.R1.fastq.gz \
 -o sample