# IVA on MiSeq data run from AC
bsub -q long -P team146 -n 8 -R "span[hosts=1] select[mem>1500] rusage[mem=1500]" -M1500 -o 1036902_S9_L001.out -e 1036902_S9_L001.err iva --trimmomatic /software/pathogen/external/apps/usr/local/Trimmomatic-0.32/trimmomatic-0.32.jar --threads 8 -f 1036902_S9_L001_R1_001.fastq.gz -r 1036902_S9_L001_R2_001.fastq.gz ./1036902_S9_L001_R1_001;

bsub -q long -P team146 -n 8 -R "span[hosts=1] select[mem>1500] rusage[mem=1500]" -M1500 -o 1038154_S1_L001.out -e 1038154_S1_L001.err iva --trimmomatic /software/pathogen/external/apps/usr/local/Trimmomatic-0.32/trimmomatic-0.32.jar --threads 8 -f 1038154_S1_L001_R1_001.fastq.gz -r 1038154_S1_L001_R2_001.fastq.gz ./1038154_S1_L001_R1_001;

# IVA_QC on MiSeq data run from Sanger
bsub -q long -P team146 -n 8 -R "span[hosts=1] select[mem>1500] rusage[mem=1500]" -M1500 -e 13554_1#12.e -o 13554_1#12.o iva_qc --ref_db ~ag8/iva_qc_ref_db/HIV_only_db.2/ --threads 8 -f ../pathfind_13554_1/13554_1#12_1.fastq.gz -r ../pathfind_13554_1/13554_1#12_2.fastq.gz ../assemblyfind_13554_1/13554_1#12.contigs_iva.fa 13554_1#12