find . -name \*.fna.gz -print ./Apis\ mellifera/ncbi-genomes-2020-03-03/GCF_003254395.2_Amel_HAv3.1_genomic.fna.gz zcat ./Helianthus\ annuus/GCF_002127325.1_HanXRQr1.0_genomic.fna.gz > foo; hisat2-build -p 9 -f foo Helianthus_annuus zcat ./Cajanus\ cajan/GCF_000340665.1_C.cajan_V1.0_genomic.fna.gz > foo; hisat2-build -p 9 -f foo Cajanus_cajan zcat ./Papaver\ somniferum/ncbi-genomes-2020-03-03/GCF_003573695.1_ASM357369v1_genomic.fna.gz > foo; hisat2-build -p 9 -f foo Papaver_somniferum zcat ./Asparagus\ officinalis/GCF_001876935.1_Aspof.V1_genomic.fna.gz > foo; hisat2-build -p 9 -f foo Asparagus_officinalis zcat ./Olea\ europaea/GCF_002742605.1_O_europaea_v1_genomic.fna.gz > foo; hisat2-build -p 9 -f foo Olea_europaea zcat ./Artemisia\ annua/GCA_003112345.1_ASM311234v1_genomic.fna.gz > foo; hisat2-build -p 9 -f foo Artemisia_annua zcat ./Nosema\ ceranae/GCF_000988165.1_ASM98816v1_genomic.fna.gz > foo; hisat2-build -p 9 -f foo Nosema_ceranae /home/reczko/Elixir/metagenomics/species/varroa destructor zcat BEIS01.1.fsa_nt.gz | grep contig | wc 1425 14250 125715 #@ honeybee genome -> ~/Elixir/metagenomics/species/Apis mellifera/ https://www.ncbi.nlm.nih.gov/Traces/wgs/?val=QIUM02 reczko@max:~/Elixir/metagenomics/species/hisat$ hisat2-build -p 9 -f ../Apis\ mellifera/QIUM02.1.fsa_nt apis_mellifera reczko@max:~/Elixir/metagenomics/species/Vitis vinifera$ hisat2-build -p 6 -f GCF_000003745.3_12X_genomic.fna ../hisat/vitis_vinifera hisat2 -k 1 -p 6 --dta -x ~/Elixir/metagenomics/species/hisat/apis_mellifera -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_apis_mellifera.bam 8160732 reads; of these: 8160732 (100.00%) were unpaired; of these: 8147681 (99.84%) aligned 0 times 13051 (0.16%) aligned exactly 1 time 0 (0.00%) aligned >1 times 0.16% overall alignment rate hisat2 -k 1 -p 6 --dta -x ~/Elixir/metagenomics/species/hisat/vitis_vinifera -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_vitis_vinifera.bam 8160732 reads; of these: 8160732 (100.00%) were unpaired; of these: 8151055 (99.88%) aligned 0 times 9677 (0.12%) aligned exactly 1 time 0 (0.00%) aligned >1 times 0.12% overall alignment rate hisat2 -k 1 -p2 --dta --no-spliced-alignment --mp 12,4 -x ~/Elixir/metagenomics/species/hisat/vitis_vinifera -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_vitis_vinifera_strict.bam 8160732 reads; of these: 8160732 (100.00%) were unpaired; of these: 8155029 (99.93%) aligned 0 times 5703 (0.07%) aligned exactly 1 time 0 (0.00%) aligned >1 times 0.07% overall alignment rate hisat2 -k 1 -p2 --dta --no-spliced-alignment --mp 24,8 -x ~/Elixir/metagenomics/species/hisat/vitis_vinifera -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_vitis_vinifera_strict_24_8.bam 8160732 reads; of these: 8160732 (100.00%) were unpaired; of these: 8156858 (99.95%) aligned 0 times 3874 (0.05%) aligned exactly 1 time 0 (0.00%) aligned >1 times 0.05% overall alignment rate QHOT2:10181:02533 0 NC_012009.3 1949520 0 66M3D23M1D53M * 0 0 CTTTGGTGTCAAGGTAATAGCTATGAATAGTCATCGACTCCCGGGAAAGGGTAGAAGAATGGGACCTATGGGACATACAATGCATTACAACGTATGATCATTACGCTTCAACCGGGTTATTCTATTCCACCTCTTAGAAAGA 999+96=;<<=9>9=@;>=889==>=9>>=========<>@6;;67=<<<5;<188=7==9;<<==8<=====>85558:3:780/9////5588849:;<=7==7=7;;6;7;<8<;;;6;9=>9><<6<;;;3;< AS:i:-22 ZS:i:-22 XN:i:0 XM:i:0 XO:i:2 XG:i:4 NM:i:4 MD:Z:66^TAT23^G53 YT:Z:UU NH:i:1 --mp , max and min penalties for mismatch; lower qual = lower penalty <6,2> --rdg , read gap open, extend penalties (5,3) --rfg , reference gap open, extend penalties (5,3) 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 /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_vitis_vinifera_strict_24_8_rdg_10_6_rfg10_6.bam 8160732 reads; of these: 8160732 (100.00%) were unpaired; of these: 8157213 (99.96%) aligned 0 times 3519 (0.04%) aligned exactly 1 time 0 (0.00%) aligned >1 times 0.04% overall alignment rate #now omitted: QHOT2:10181:02533 4 * 0 0 * * 0 0 CTTTGGTGTCAAGGTAATAGCTATGAATAGTCATCGACTCCCGGGAAAGGGTAGAAGAATGGGACCTATGGGACATACAATGCATTACAACGTATGATCATTACGCTTCAACCGGGTTATTCTATTCCACCTCTTAGAAAGA 999+96=;<<=9>9=@;>=889==>=9>>=========<>@6;;67=<<<5;<188=7==9;<<==8<=====>85558:3:780/9////5588849:;<=7==7=7;;6;7;<8<;;;6;9=>9><<6<;;;3;< YT:Z:UU #1D QHOT2:07478:14803 0 NC_012007.3 17140077 0 95M1D34M3S * 0 0 CGGCGACTCATAGGCAGTGGCTTGGTTAAGGGAACCCACCGGAGCCGTAGCGAAAGCGAGTCTTCATAGGGCAATTGTCACTGCTTATGGACCCGACCTGGGTGATCTATCCATGACCAGGATGAAGCTGGG 887<555:9;<=<9==<<<9<<8<9>9=9=@8?8<<6<<5<5<;=9<<<==999+8?;?<==<9;;;88808=6<287<>=>???8;;<5;;<48887<=7779<<<<;6;<7<<9828....) AS:i:-19 ZS:i:-19 XN:i:0 XM:i:0 XO:i:1 XG:i:1 NM:i:1 MD:Z:95^A34 YT:Z:UU NH:i:1 #1I QHOT2:07562:14694 16 NC_012007.3 17140165 0 53M1I54M * 0 0 GGACCCGAACCTGGGTGATCTATCCATGACCAGGATGAAGCTTGGGTGAAACTAAAGTGGAGGTCCGAACCGACTGATGTTGAAGAATCAGCGGATGAGTTGTGGTTA >9=9==8C=?=<=<<==9==>=<8<<9=<=<9<=;8=7<<;<4;;<7+888:6:;6882<<8=9=<<<=<=<=7<<8<<;@>B?=>9?==?<<6<<<78283 AS:i:-16 ZS:i:-16 XN:i:0 XM:i:0 XO:i:1 XG:i:1 NM:i:1 MD:Z:107 YT:Z:UU NH:i:1 hisat2 -k 1 -p2 --dta --no-spliced-alignment --rdg 20,12 --rfg 20,12 --mp 24,8 -x ~/Elixir/metagenomics/species/hisat/vitis_vinifera -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_vitis_vinifera_strict_24_8_rdg_20_12_rfg20_12.bam 8160732 reads; of these: 8160732 (100.00%) were unpaired; of these: 8157543 (99.96%) aligned 0 times 3189 (0.04%) aligned exactly 1 time 0 (0.00%) aligned >1 times 0.04% overall alignment rate QHOT2:07562:14694 4 * 0 0 * * 0 0 TAACCACAACTCATCCGCTGATTCTTCAACATCAGTCGGTTCGGACCTCCACTTTAGTTTCACCCAAGCTTCATCCTGGTCATGGATAGATCACCCAGGTTCGGGTCC 38287<<<6<=?B>@;<<8<<7=<=<=<<<=9=8<<2886;:6:888+7<;;4<;<<7=8;=<9<=<=9<<8<=>==9==<<=<=?=C8==9=9>>?==9<6<;81998<=?@>;A<=<<6:488::588557:9:;6<5@><<9<><==<<9=<=?;6;;<<9398//*==7<<7=>><;7:;: AS:i:-32 ZS:i:-32 XN:i:0 XM:i:0 XO:i:1 XG:i:1 NM:i:1 MD:Z:71^T102 YT:Z:UU NH:i:1 QHOT2:07875:03969 16 NC_012019.3 11912771 0 37M1I164M * 0 0 ACGACTTCACTCCAGTCACTAGCCCTGCCTTCGGCATCCCCCCTCCTTGCGGTTAAGGTAACGACTTCGGGCATGGCCAGCTCCCATAGTGTGACGGGCGGTGTGTACAAGGCCCGGGAACGAATTCACCGCCGTATGGCTGACCGGCGATTACTAGCGATTCCGGCTTCATGCAGGCGAGTTGCAGCCTGCAATCCGAACT ;<;<;8==>=8489=====;=60776949467.8855&66666-06067-*-*:684::7<>=<9497188:.-)4/98895+555=<:<<<<<:1:::3::=<<==>9=9=7>91881====?9>>;5;;5;:<<8089;:;6:7::<;6<;;;=<<:95949455199=9==<<<9<=>9@=9=== AS:i:-32 ZS:i:-32 XN:i:0 XM:i:0 XO:i:1 XG:i:1 NM:i:1 MD:Z:201 YT:Z:UU NH:i:1 hisat2 -k 1 -p2 --dta --no-spliced-alignment --rdg 40,24 --rfg 40,24 --mp 24,8 -x ~/Elixir/metagenomics/species/hisat/vitis_vinifera -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_vitis_vinifera_strict_24_8_rdg_40_24_rfg40_24.bam 8160732 reads; of these: 8160732 (100.00%) were unpaired; of these: 8157604 (99.96%) aligned 0 times 3128 (0.04%) aligned exactly 1 time 0 (0.00%) aligned >1 times 0.04% overall alignment rate QHOT2:08737:11690 4 * 0 0 * * 0 0 GTCCTCAGTTCGGATTGCAGGCTGCAACTCGCCTGCATGAAGCCGGAATCGCTAGTAATCGCCGGTCAGCCATACGGCGGTGAATTCGTTCCCGGGCCTTGTCACACCGCCCGTCACACTATGGGAGCTGGCCATGCCCGAAGTCGTTACCTTAACCGCAAGGAGGGGGATGC :;:7;<>>=7<<7==*//8939<<;;6;?=<=9<<==<><9<<>@5<6;:9:755885::884:6<<=@?=<89918;<6<9==>8<<6=8489=====;=60776949467.8855&66666-06067-*-*:684::7<>=<9497188:.-)4/98895+555=<:<<<<<:1:::3::=<<==>9=9=7>91881====?9>>;5;;5;:<<8089;:;6:7::<;6<;;;=<<:95949455199=9==<<<9<=>9@=9=== AS:i:-38 ZS:i:-38 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:164 YT:Z:UU NH:i:1 no M1D or M1I