#hisat2 -k 1 -p 6 --dta -x ~/Elixir/metagenomics/species/hisat/varroa_destructor  -U    | /data/results/tools/samtools/samtools-1.3/samtools  sort -@ 8 -o /home/reczko/Elixir/metagenomics/SPlab/run440/genomic/
#~/Elixir/metagenomics/species/hisat/varroa_destructor

echo "SPD3_varroa.bam"
/data/results/tools/rnaseq/hisat/hisat2-2.1.0/hisat2 -k 1 -p 12 --mp 30,30 --rdg 30,30 --rfg 30,30 --dta -x ~/Elixir/metagenomics/species/hisat/varroa_destructor  -U  /data/images/proton2/run431/R_2019_08_07_16_07_46_user_IONAS-431-GKlab-MS_SPlab_190807_GK3R288-302_SP3R1-4.SPD3_fragDNA1.IonXpress_031.fastq  | /data/results/tools/samtools/samtools-1.3/samtools  sort -@ 8 -o /home/reczko/Elixir/metagenomics/SPlab/run440/genomic/SPD3_varroa_strict.bam
echo "SPD4_fragDNA2.IonXpress_032.varroa_strict.bam"
/data/results/tools/rnaseq/hisat/hisat2-2.1.0/hisat2 -k 1 -p 12 --mp 30,30 --rdg 30,30 --rfg 30,30 --dta -x ~/Elixir/metagenomics/species/hisat/varroa_destructor  -U /data/images/proton2/run431/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  sort -@ 8 -o /home/reczko/Elixir/metagenomics/SPlab/run440/genomic/SPD4_fragDNA2.IonXpress_032.varroa_strict.bam
echo "SPD10_DSM-H7.IonXpress_010.varroa_strict.bam"
/data/results/tools/rnaseq/hisat/hisat2-2.1.0/hisat2 -k 1 -p 12 --mp 30,30 --rdg 30,30 --rfg 30,30 --dta -x ~/Elixir/metagenomics/species/hisat/varroa_destructor  -U /data/images/proton2/run440/R_2020_02_12_12_23_36_user_IONAS-440-PMN-SPlab-DrMylonis_200212_PMNcAmp2-6_SPD5-10_IM3R7-10.SPD10_DSM-H7.IonXpress_010.fastq    | /data/results/tools/samtools/samtools-1.3/samtools  sort -@ 8 -o /home/reczko/Elixir/metagenomics/SPlab/run440/genomic/SPD10_DSM-H7.IonXpress_010.varroa_strict.bam
echo "SPD5_shot-H4.IonXpress_005.varroa_strict.bam"
/data/results/tools/rnaseq/hisat/hisat2-2.1.0/hisat2 -k 1 -p 12 --mp 30,30 --rdg 30,30 --rfg 30,30 --dta -x ~/Elixir/metagenomics/species/hisat/varroa_destructor  -U /data/images/proton2/run440/R_2020_02_12_12_23_36_user_IONAS-440-PMN-SPlab-DrMylonis_200212_PMNcAmp2-6_SPD5-10_IM3R7-10.SPD5_shot-H4.IonXpress_005.fastq    | /data/results/tools/samtools/samtools-1.3/samtools  sort -@ 8 -o /home/reczko/Elixir/metagenomics/SPlab/run440/genomic/SPD5_shot-H4.IonXpress_005.varroa_strict.bam
echo "SPD6_shot-H6.IonXpress_006.varroa_strict.bam"
/data/results/tools/rnaseq/hisat/hisat2-2.1.0/hisat2 -k 1 -p 12 --mp 30,30 --rdg 30,30 --rfg 30,30 --dta -x ~/Elixir/metagenomics/species/hisat/varroa_destructor  -U /data/images/proton2/run440/R_2020_02_12_12_23_36_user_IONAS-440-PMN-SPlab-DrMylonis_200212_PMNcAmp2-6_SPD5-10_IM3R7-10.SPD6_shot-H6.IonXpress_006.fastq    | /data/results/tools/samtools/samtools-1.3/samtools  sort -@ 8 -o /home/reczko/Elixir/metagenomics/SPlab/run440/genomic/SPD6_shot-H6.IonXpress_006.varroa_strict.bam
echo "SPD7_shot-H7.IonXpress_007.varroa_strict.bam"
/data/results/tools/rnaseq/hisat/hisat2-2.1.0/hisat2 -k 1 -p 12 --mp 30,30 --rdg 30,30 --rfg 30,30 --dta -x ~/Elixir/metagenomics/species/hisat/varroa_destructor  -U /data/images/proton2/run440/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  sort -@ 8 -o /home/reczko/Elixir/metagenomics/SPlab/run440/genomic/SPD7_shot-H7.IonXpress_007.varroa_strict.bam
echo "SPD8_DSM-H4.IonXpress_008.varroa_strict.bam"
/data/results/tools/rnaseq/hisat/hisat2-2.1.0/hisat2 -k 1 -p 12 --mp 30,30 --rdg 30,30 --rfg 30,30 --dta -x ~/Elixir/metagenomics/species/hisat/varroa_destructor  -U /data/images/proton2/run440/R_2020_02_12_12_23_36_user_IONAS-440-PMN-SPlab-DrMylonis_200212_PMNcAmp2-6_SPD5-10_IM3R7-10.SPD8_DSM-H4.IonXpress_008.fastq    | /data/results/tools/samtools/samtools-1.3/samtools  sort -@ 8 -o /home/reczko/Elixir/metagenomics/SPlab/run440/genomic/SPD8_DSM-H4.IonXpress_008.varroa_strict.bam
echo "SPD9_DSM-H6.IonXpress_009.varroa_strict.bam"
/data/results/tools/rnaseq/hisat/hisat2-2.1.0/hisat2 -k 1 -p 12 --mp 30,30 --rdg 30,30 --rfg 30,30 --dta -x ~/Elixir/metagenomics/species/hisat/varroa_destructor  -U /data/images/proton2/run440/R_2020_02_12_12_23_36_user_IONAS-440-PMN-SPlab-DrMylonis_200212_PMNcAmp2-6_SPD5-10_IM3R7-10.SPD9_DSM-H6.IonXpress_009.fastq    | /data/results/tools/samtools/samtools-1.3/samtools  sort -@ 8 -o /home/reczko/Elixir/metagenomics/SPlab/run440/genomic/SPD9_DSM-H6.IonXpress_009.varroa_strict.bam