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_2019_08_07_16_07_46_user_IONAS-431-GKlab-MS_SPlab_190807_GK3R288-302_SP3R1-4.SPD4_fragDNA2.IonXpress_032.fastq |  /data/results/tools/samtools/samtools-1.3/samtools view -b -F 4 | /data/results/tools/samtools/samtools-1.3/samtools  sort -@ 2 -o SPD4_Apis\_mellifera.bam; samtools view SPD4_Apis\_mellifera.bam > SPD4_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_2019_08_07_16_07_46_user_IONAS-431-GKlab-MS_SPlab_190807_GK3R288-302_SP3R1-4.SPD4_fragDNA2.IonXpress_032.fastq |  /data/results/tools/samtools/samtools-1.3/samtools view -b -F 4 | /data/results/tools/samtools/samtools-1.3/samtools  sort -@ 2 -o SPD4_Helianthus\_annuus.bam; samtools view SPD4_Helianthus\_annuus.bam > SPD4_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_2019_08_07_16_07_46_user_IONAS-431-GKlab-MS_SPlab_190807_GK3R288-302_SP3R1-4.SPD4_fragDNA2.IonXpress_032.fastq |  /data/results/tools/samtools/samtools-1.3/samtools view -b -F 4 | /data/results/tools/samtools/samtools-1.3/samtools  sort -@ 2 -o SPD4_Cajanus\_cajan.bam; samtools view SPD4_Cajanus\_cajan.bam > SPD4_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_2019_08_07_16_07_46_user_IONAS-431-GKlab-MS_SPlab_190807_GK3R288-302_SP3R1-4.SPD4_fragDNA2.IonXpress_032.fastq |  /data/results/tools/samtools/samtools-1.3/samtools view -b -F 4 | /data/results/tools/samtools/samtools-1.3/samtools  sort -@ 2 -o SPD4_Papaver\_somniferum.bam; samtools view SPD4_Papaver\_somniferum.bam > SPD4_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_2019_08_07_16_07_46_user_IONAS-431-GKlab-MS_SPlab_190807_GK3R288-302_SP3R1-4.SPD4_fragDNA2.IonXpress_032.fastq |  /data/results/tools/samtools/samtools-1.3/samtools view -b -F 4 | /data/results/tools/samtools/samtools-1.3/samtools  sort -@ 2 -o SPD4_Asparagus\_officinalis.bam; samtools view SPD4_Asparagus\_officinalis.bam > SPD4_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_2019_08_07_16_07_46_user_IONAS-431-GKlab-MS_SPlab_190807_GK3R288-302_SP3R1-4.SPD4_fragDNA2.IonXpress_032.fastq |  /data/results/tools/samtools/samtools-1.3/samtools view -b -F 4 | /data/results/tools/samtools/samtools-1.3/samtools  sort -@ 2 -o SPD4_Olea\_europaea.bam; samtools view SPD4_Olea\_europaea.bam > SPD4_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_2019_08_07_16_07_46_user_IONAS-431-GKlab-MS_SPlab_190807_GK3R288-302_SP3R1-4.SPD4_fragDNA2.IonXpress_032.fastq |  /data/results/tools/samtools/samtools-1.3/samtools view -b -F 4 | /data/results/tools/samtools/samtools-1.3/samtools  sort -@ 2 -o SPD4_Artemisia\_annua.bam; samtools view SPD4_Artemisia\_annua.bam > SPD4_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_2019_08_07_16_07_46_user_IONAS-431-GKlab-MS_SPlab_190807_GK3R288-302_SP3R1-4.SPD4_fragDNA2.IonXpress_032.fastq |  /data/results/tools/samtools/samtools-1.3/samtools view -b -F 4 | /data/results/tools/samtools/samtools-1.3/samtools  sort -@ 2 -o SPD4_Nosema\_ceranae.bam; samtools view SPD4_Nosema\_ceranae.bam > SPD4_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_2019_08_07_16_07_46_user_IONAS-431-GKlab-MS_SPlab_190807_GK3R288-302_SP3R1-4.SPD4_fragDNA2.IonXpress_032.fastq |  /data/results/tools/samtools/samtools-1.3/samtools view -b -F 4 | /data/results/tools/samtools/samtools-1.3/samtools  sort -@ 2 -o SPD4_vitis\_vinifera.bam; samtools view SPD4_vitis\_vinifera.bam > SPD4_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_2019_08_07_16_07_46_user_IONAS-431-GKlab-MS_SPlab_190807_GK3R288-302_SP3R1-4.SPD4_fragDNA2.IonXpress_032.fastq |  /data/results/tools/samtools/samtools-1.3/samtools view -b -F 4 | /data/results/tools/samtools/samtools-1.3/samtools  sort -@ 2 -o SPD4_varroa\_destructor.bam; samtools view SPD4_varroa\_destructor.bam > SPD4_varroa\_destructor.bam.sam