hisat2 -k 1 -p2 --dta --no-spliced-alignment --rdg 10,6 --rfg 10,6 --mp 24,8 -x ~/Elixir/metagenomics/species/hisat/Apis\_mellifera -U  ~/elixir/metagenomics/SPlab/reads/R_2020_02_12_12_23_36_user_IONAS-440-PMN-SPlab-DrMylonis_200212_PMNcAmp2-6_SPD5-10_IM3R7-10.SPD7_shot-H7.IonXpress_007.fastq |  /data/results/tools/samtools/samtools-1.3/samtools view -b -F 4 | /data/results/tools/samtools/samtools-1.3/samtools  sort -@ 2 -o SPD7_Apis\_mellifera.bam; samtools view SPD7_Apis\_mellifera.bam > SPD7_Apis\_mellifera.bam.sam
hisat2 -k 1 -p2 --dta --no-spliced-alignment --rdg 10,6 --rfg 10,6 --mp 24,8 -x ~/Elixir/metagenomics/species/hisat/Helianthus\_annuus -U  ~/elixir/metagenomics/SPlab/reads/R_2020_02_12_12_23_36_user_IONAS-440-PMN-SPlab-DrMylonis_200212_PMNcAmp2-6_SPD5-10_IM3R7-10.SPD7_shot-H7.IonXpress_007.fastq |  /data/results/tools/samtools/samtools-1.3/samtools view -b -F 4 | /data/results/tools/samtools/samtools-1.3/samtools  sort -@ 2 -o SPD7_Helianthus\_annuus.bam; samtools view SPD7_Helianthus\_annuus.bam > SPD7_Helianthus\_annuus.bam.sam
hisat2 -k 1 -p2 --dta --no-spliced-alignment --rdg 10,6 --rfg 10,6 --mp 24,8 -x ~/Elixir/metagenomics/species/hisat/Cajanus\_cajan -U  ~/elixir/metagenomics/SPlab/reads/R_2020_02_12_12_23_36_user_IONAS-440-PMN-SPlab-DrMylonis_200212_PMNcAmp2-6_SPD5-10_IM3R7-10.SPD7_shot-H7.IonXpress_007.fastq |  /data/results/tools/samtools/samtools-1.3/samtools view -b -F 4 | /data/results/tools/samtools/samtools-1.3/samtools  sort -@ 2 -o SPD7_Cajanus\_cajan.bam; samtools view SPD7_Cajanus\_cajan.bam > SPD7_Cajanus\_cajan.bam.sam
hisat2 -k 1 -p2 --dta --no-spliced-alignment --rdg 10,6 --rfg 10,6 --mp 24,8 -x ~/Elixir/metagenomics/species/hisat/Papaver\_somniferum -U  ~/elixir/metagenomics/SPlab/reads/R_2020_02_12_12_23_36_user_IONAS-440-PMN-SPlab-DrMylonis_200212_PMNcAmp2-6_SPD5-10_IM3R7-10.SPD7_shot-H7.IonXpress_007.fastq |  /data/results/tools/samtools/samtools-1.3/samtools view -b -F 4 | /data/results/tools/samtools/samtools-1.3/samtools  sort -@ 2 -o SPD7_Papaver\_somniferum.bam; samtools view SPD7_Papaver\_somniferum.bam > SPD7_Papaver\_somniferum.bam.sam
hisat2 -k 1 -p2 --dta --no-spliced-alignment --rdg 10,6 --rfg 10,6 --mp 24,8 -x ~/Elixir/metagenomics/species/hisat/Asparagus\_officinalis -U  ~/elixir/metagenomics/SPlab/reads/R_2020_02_12_12_23_36_user_IONAS-440-PMN-SPlab-DrMylonis_200212_PMNcAmp2-6_SPD5-10_IM3R7-10.SPD7_shot-H7.IonXpress_007.fastq |  /data/results/tools/samtools/samtools-1.3/samtools view -b -F 4 | /data/results/tools/samtools/samtools-1.3/samtools  sort -@ 2 -o SPD7_Asparagus\_officinalis.bam; samtools view SPD7_Asparagus\_officinalis.bam > SPD7_Asparagus\_officinalis.bam.sam
hisat2 -k 1 -p2 --dta --no-spliced-alignment --rdg 10,6 --rfg 10,6 --mp 24,8 -x ~/Elixir/metagenomics/species/hisat/Olea\_europaea -U  ~/elixir/metagenomics/SPlab/reads/R_2020_02_12_12_23_36_user_IONAS-440-PMN-SPlab-DrMylonis_200212_PMNcAmp2-6_SPD5-10_IM3R7-10.SPD7_shot-H7.IonXpress_007.fastq |  /data/results/tools/samtools/samtools-1.3/samtools view -b -F 4 | /data/results/tools/samtools/samtools-1.3/samtools  sort -@ 2 -o SPD7_Olea\_europaea.bam; samtools view SPD7_Olea\_europaea.bam > SPD7_Olea\_europaea.bam.sam
hisat2 -k 1 -p2 --dta --no-spliced-alignment --rdg 10,6 --rfg 10,6 --mp 24,8 -x ~/Elixir/metagenomics/species/hisat/Artemisia\_annua -U  ~/elixir/metagenomics/SPlab/reads/R_2020_02_12_12_23_36_user_IONAS-440-PMN-SPlab-DrMylonis_200212_PMNcAmp2-6_SPD5-10_IM3R7-10.SPD7_shot-H7.IonXpress_007.fastq |  /data/results/tools/samtools/samtools-1.3/samtools view -b -F 4 | /data/results/tools/samtools/samtools-1.3/samtools  sort -@ 2 -o SPD7_Artemisia\_annua.bam; samtools view SPD7_Artemisia\_annua.bam > SPD7_Artemisia\_annua.bam.sam
hisat2 -k 1 -p2 --dta --no-spliced-alignment --rdg 10,6 --rfg 10,6 --mp 24,8 -x ~/Elixir/metagenomics/species/hisat/Nosema\_ceranae -U  ~/elixir/metagenomics/SPlab/reads/R_2020_02_12_12_23_36_user_IONAS-440-PMN-SPlab-DrMylonis_200212_PMNcAmp2-6_SPD5-10_IM3R7-10.SPD7_shot-H7.IonXpress_007.fastq |  /data/results/tools/samtools/samtools-1.3/samtools view -b -F 4 | /data/results/tools/samtools/samtools-1.3/samtools  sort -@ 2 -o SPD7_Nosema\_ceranae.bam; samtools view SPD7_Nosema\_ceranae.bam > SPD7_Nosema\_ceranae.bam.sam
hisat2 -k 1 -p2 --dta --no-spliced-alignment --rdg 10,6 --rfg 10,6 --mp 24,8 -x ~/Elixir/metagenomics/species/hisat/vitis\_vinifera -U  ~/elixir/metagenomics/SPlab/reads/R_2020_02_12_12_23_36_user_IONAS-440-PMN-SPlab-DrMylonis_200212_PMNcAmp2-6_SPD5-10_IM3R7-10.SPD7_shot-H7.IonXpress_007.fastq |  /data/results/tools/samtools/samtools-1.3/samtools view -b -F 4 | /data/results/tools/samtools/samtools-1.3/samtools  sort -@ 2 -o SPD7_vitis\_vinifera.bam; samtools view SPD7_vitis\_vinifera.bam > SPD7_vitis\_vinifera.bam.sam
hisat2 -k 1 -p2 --dta --no-spliced-alignment --rdg 10,6 --rfg 10,6 --mp 24,8 -x ~/Elixir/metagenomics/species/hisat/varroa\_destructor -U  ~/elixir/metagenomics/SPlab/reads/R_2020_02_12_12_23_36_user_IONAS-440-PMN-SPlab-DrMylonis_200212_PMNcAmp2-6_SPD5-10_IM3R7-10.SPD7_shot-H7.IonXpress_007.fastq |  /data/results/tools/samtools/samtools-1.3/samtools view -b -F 4 | /data/results/tools/samtools/samtools-1.3/samtools  sort -@ 2 -o SPD7_varroa\_destructor.bam; samtools view SPD7_varroa\_destructor.bam > SPD7_varroa\_destructor.bam.sam