for i in *_clean_R1.fq.gz;

do base=$(basename $i _clean_R1.fq.gz);

echo $base;

concatenate.py ../bin/$base/${base}_catalogue.fna ../3_assembly/${base}_contig.fa --nozip -m 1500;

/home/roo/biosoft/minimap2-2.17_x64-linux/minimap2 -d ../bin/$base/${base}_catalogue.mmi ../bin/$base/${base}_catalogue.fna;

/home/roo/biosoft/minimap2-2.17_x64-linux/minimap2 -t 32 -N 50 -ax sr ../bin/$base/${base}_catalogue.mmi ${base}_clean_R1.fq.gz ${base}_clean_R2.fq.gz | samtools view -F 3584 -b --threads 32 > ../bin/$base/${base}.bam;

samtools sort -@ 32 -l 9 ../bin/$base/${base}.bam -o ../bin/$base/${base}.sort.bam;

jgi_summarize_bam_contig_depths --outputDepth ../bin/$base/${base}.depth.txt ../bin/$base/${base}.sort.bam;

metabat2 -m 1500 -t 32 -i ../bin/$base/${base}_catalogue.fna -a ../bin/$base/${base}.depth.txt -o ../bin/$base/all -v;

done

for i in *_clean_R1.fq.gz;

do base=$(basename $i _clean_R1.fq.gz);

echo $base;

dRep dereplicate ../bin/$base/derep -g ../bin/$base/*.fa -sa 0.95 -nc 0.30 -p 12 -comp 50 -con 10;

checkm lineage_wf -x fa ../bin/$base/derep/dereplicated_genomes ../bin/$base/derep/checkm_out -t 12;

done

wget http://eddylab.org/software/hmmer3/3.1b2/hmmer-3.1b2-linux-intel-x86_64.tar.gz

tar -zxvf hmmer-3.1b2-linux-intel-x86_64.tar.gz

cd /home/roo/biosoft/hmmsearch/hmmer-3.1b2-linux-intel-x86_64/

sudo vim ./configure

PATH=$PATH:/home/roo/biosoft/hmmsearch/hmmer-3.1b2-linux-intel-x86_64/binaries

source .configure

for i in *_clean_R1.fq.gz;

do base=$(basename $i _clean_R1.fq.gz);

echo $base;

cut_up_fasta.py ../../bin/$base/${base}_catalogue.fna -c 10000 -o 0 --merge_last -b ../../bin/$base/contigs_10K.bed > ../../bin/$base/contigs_10K.fa;

concoct_coverage_table.py ../../bin/$base/contigs_10K.bed ../../bin/$base/${base}.sort.bam > ../../bin/$base/coverage_table.tsv;

concoct -t 32 --composition_file ../../bin/$base/contigs_10K.fa --coverage_file ../../bin/$base/coverage_table.tsv -b ../../bin/$base/concoct_output/;

merge_cutup_clustering.py ../../bin/$base/concoct_output/clustering_gt1000.csv > ../../bin/$base/concoct_output/clustering_merged.csv;

mkdir ../../bin/$base/concoct_output/fasta_bins;

extract_fasta_bins.py ../../bin/$base/${base}_catalogue.fna ../../bin/$base/concoct_output/clustering_merged.csv --output_path ../../bin/$base/concoct_output/fasta_bins;

done