conda activate metagenomics
cd Analyses/Initial_data/
fastqc  Sample1.R1.fastq.gz Sample1.R2.fastq.gz Sample2.R1.fastq.gz Sample2.R2.fastq.gz Sample3.R1.fastq.gz Sample3.R2.fastq.gz
multiqc ./
trimmomatic  PE Sample1.R1.fastq.gz Sample1.R2.fastq.gz Sample1_R1_trim.fastq.gz Sample1_R1_surv.fastq.gz  Sample1_R2_trim.fastq.gz Sample1_R2_surv.fastq.gz ILLUMINACLIP:/home/user/Support_files/illumina_adapters.fa:2:30:10  SLIDINGWINDOW:4:15 MINLEN:36 
nohup trimmomatic  PE Sample2.R1.fastq.gz Sample2.R2.fastq.gz Sample2_R1_trim.fastq.gz Sample2_R1_surv.fastq.gz  Sample2_R2_trim.fastq.gz Sample2_R2_surv.fastq.gz ILLUMINACLIP:/home/user/Support_files/illumina_adapters.fa:2:30:10  SLIDINGWINDOW:4:15 MINLEN:36 &
nohup trimmomatic  PE Sample3.R1.fastq.gz Sample3.R2.fastq.gz Sample3_R1_trim.fastq.gz Sample3_R1_surv.fastq.gz  Sample3_R2_trim.fastq.gz Sample3_R2_surv.fastq.gz ILLUMINACLIP:/home/user/Support_files/illumina_adapters.fa:2:30:10  SLIDINGWINDOW:4:15 MINLEN:36 &
mkdir Trimmed_data
mv Sample*_R*_trim.fastq.gz Trimmed_data/
cd Trimmed_data/
cat *R1* > All_R1.fastq.gz 
cat *R2* > All_R2.fastq.gz 
nohup megahit -1 All_R1.fastq.gz -2 All_R2.fastq.gz -o ./assembled_data &
cd ..
mkdir mapping
cd mapping/
mv ../Trimmed_data/assembled_data/final.contigs.fa ./co-assembled.fasta
bwa index co-assembled.fasta 
mkdir bwa_idx
mv co-assembled.fasta* bwa_idx/
bwa mem -t2 -o Sample1.sam bwa_idx/co-assembled.fasta ../Trimmed_data/Sample1_R1_trim.fastq.gz ../Trimmed_data/Sample1_R2_trim.fastq.gz 
nohup bwa mem -t2 -o Sample2.sam bwa_idx/co-assembled.fasta ../Trimmed_data/Sample2_R1_trim.fastq.gz ../Trimmed_data/Sample2_R2_trim.fastq.gz &
nohup bwa mem -t2 -o Sample3.sam bwa_idx/co-assembled.fasta ../Trimmed_data/Sample3_R1_trim.fastq.gz ../Trimmed_data/Sample3_R2_trim.fastq.gz &
samtools flagstats Sample1.sam 
samtools view -b -S Sample1.sam > Sample1.bam
nohup samtools view -b -S Sample2.sam > Sample2.bam &
nohup samtools view -b -S Sample3.sam > Sample3.bam &
samtools sort Sample1.bam > Sample1_sorted.bam
nohup samtools sort Sample2.bam > Sample2_sorted.bam &
nohup samtools sort Sample3.bam > Sample3_sorted.bam &
samtools index Sample1_sorted.bam 
samtools index Sample2_sorted.bam 
samtools index Sample3_sorted.bam 
runMetaBat.sh  -m 1500 -s 10000  bwa_idx/co-assembled.fasta Sample1_sorted.bam Sample2_sorted.bam Sample3_sorted.bam
less co-assembled.fasta.depth.txt
cd co-assembled.fasta.metabat-bins-20250916_104732/
conda deactivate
conda activate checkm2
checkm2 predict -x fa  --input bin.*.fa --output-directory ./checkm_out --database_path /home/user/databases/CheckM2_database/uniref100.KO.1.dmnd