Starting /dee2/code/volunteer_pipeline.sh SRR7472588 current disk space = 3087910014976 free memory = 1477220868 SRR7472588 SRAfilesize c8e50ff08e1d104cc78e879896bcc89f SRR7472588.sra SRR7472588.sra file validated SRR7472588 is single end SRR7472588 is conventional basespace SRR7472588 read1 length is 51 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR7472588_1.fastq File type Conventional base calls Encoding Sanger / Illumina 1.9 Total Sequences 4000 Sequences flagged as poor quality 0 Sequence length 51 %GC 51 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 30.867 32.0 32.0 32.0 27.0 32.0 2 31.4015 32.0 32.0 32.0 32.0 32.0 3 31.34075 32.0 32.0 32.0 32.0 32.0 4 31.43 32.0 32.0 32.0 32.0 32.0 5 31.2185 32.0 32.0 32.0 32.0 32.0 6 35.29375 37.0 37.0 37.0 32.0 37.0 7 35.51025 37.0 37.0 37.0 32.0 37.0 8 35.33975 37.0 37.0 37.0 32.0 37.0 9 35.2735 37.0 37.0 37.0 32.0 37.0 10 35.63625 37.0 37.0 37.0 32.0 37.0 11 35.354 37.0 37.0 37.0 32.0 37.0 12 35.5025 37.0 37.0 37.0 32.0 37.0 13 35.61225 37.0 37.0 37.0 32.0 37.0 14 35.32375 37.0 37.0 37.0 32.0 37.0 15 35.622 37.0 37.0 37.0 32.0 37.0 16 35.6605 37.0 37.0 37.0 32.0 37.0 17 35.6475 37.0 37.0 37.0 32.0 37.0 18 35.345 37.0 37.0 37.0 32.0 37.0 19 35.157 37.0 37.0 37.0 32.0 37.0 20 35.02375 37.0 37.0 37.0 32.0 37.0 21 35.1745 37.0 37.0 37.0 32.0 37.0 22 35.203 37.0 37.0 37.0 32.0 37.0 23 35.338 37.0 37.0 37.0 32.0 37.0 24 35.12075 37.0 37.0 37.0 32.0 37.0 25 35.382 37.0 37.0 37.0 32.0 37.0 26 35.60775 37.0 37.0 37.0 32.0 37.0 27 35.68325 37.0 37.0 37.0 32.0 37.0 28 35.51225 37.0 37.0 37.0 32.0 37.0 29 35.55675 37.0 37.0 37.0 32.0 37.0 30 35.41575 37.0 37.0 37.0 32.0 37.0 31 35.5705 37.0 37.0 37.0 32.0 37.0 32 35.6885 37.0 37.0 37.0 37.0 37.0 33 35.64675 37.0 37.0 37.0 32.0 37.0 34 35.816 37.0 37.0 37.0 37.0 37.0 35 35.75625 37.0 37.0 37.0 37.0 37.0 36 35.79775 37.0 37.0 37.0 37.0 37.0 37 35.79075 37.0 37.0 37.0 37.0 37.0 38 35.694 37.0 37.0 37.0 37.0 37.0 39 35.7025 37.0 37.0 37.0 32.0 37.0 40 35.3845 37.0 37.0 37.0 32.0 37.0 41 35.66725 37.0 37.0 37.0 32.0 37.0 42 35.639 37.0 37.0 37.0 32.0 37.0 43 35.60275 37.0 37.0 37.0 32.0 37.0 44 35.443 37.0 37.0 37.0 32.0 37.0 45 35.625 37.0 37.0 37.0 32.0 37.0 46 35.2625 37.0 37.0 37.0 32.0 37.0 47 35.10175 37.0 37.0 37.0 32.0 37.0 48 35.594 37.0 37.0 37.0 32.0 37.0 49 35.203 37.0 37.0 37.0 32.0 37.0 50 35.2655 37.0 37.0 37.0 32.0 37.0 51 34.90475 37.0 37.0 37.0 32.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 19 2.0 20 1.0 21 3.0 22 4.0 23 13.0 24 9.0 25 14.0 26 34.0 27 29.0 28 43.0 29 45.0 30 68.0 31 50.0 32 128.0 33 168.0 34 393.0 35 1236.0 36 1760.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 20.150000000000002 30.825000000000003 29.25 19.775000000000002 2 27.6 25.525 21.55 25.324999999999996 3 27.875 27.775 22.125 22.225 4 32.475 28.299999999999997 19.7 19.525000000000002 5 27.400000000000002 35.025 18.95 18.625 6 28.622087132725433 25.253292806484296 19.199594731509624 26.92502532928065 7 27.05 26.55 22.425 23.974999999999998 8 24.9 30.55 21.65 22.900000000000002 9 30.3 28.025 21.025 20.65 10 34.975 25.775 17.974999999999998 21.275 11 30.75 22.975 22.85 23.425 12 29.675 21.775 25.6 22.95 13 26.0 22.900000000000002 27.05 24.05 14 22.6 32.4 21.8 23.200000000000003 15 26.950000000000003 36.925000000000004 18.675 17.45 16 25.25 26.775 24.95 23.025000000000002 17 21.349999999999998 28.725 31.6 18.325 18 26.200000000000003 25.3 22.325 26.174999999999997 19 25.85 22.650000000000002 28.65 22.85 20 26.325 27.150000000000002 23.849999999999998 22.675 21 27.1 28.000000000000004 20.349999999999998 24.55 22 21.825 26.724999999999998 34.675 16.775000000000002 23 33.15 26.950000000000003 21.875 18.025 24 33.7 22.025 27.400000000000002 16.875 25 24.575 28.599999999999998 31.924999999999997 14.899999999999999 26 33.074999999999996 29.849999999999998 22.95 14.124999999999998 27 31.4 24.474999999999998 29.849999999999998 14.274999999999999 28 17.86339754816112 34.07555666750062 31.973980485364024 16.08706529897423 29 20.25 27.875 26.825 25.05 30 18.85 16.6 49.025 15.525 31 21.8 14.774999999999999 36.075 27.35 32 32.125 13.100000000000001 22.875 31.900000000000002 33 34.325 13.175 35.275 17.224999999999998 34 38.175 13.475000000000001 23.674999999999997 24.675 35 42.075 12.2 31.7 14.025000000000002 36 48.825 13.375 25.05 12.75 37 37.2 15.6 18.975 28.225 38 25.374999999999996 14.2 33.074999999999996 27.35 39 31.324999999999996 24.775 20.825 23.075000000000003 40 25.362681340670335 26.538269134567283 17.508754377188595 30.590295147573787 41 35.26763381690846 17.70885442721361 17.258629314657327 29.764882441220607 42 38.99449724862431 27.763881940970485 13.881940970485243 19.35967983991996 43 29.425 39.074999999999996 13.975000000000001 17.525 44 41.9 31.15 10.45 16.5 45 38.875 22.75 10.225 28.15 46 25.05 30.5 22.15 22.3 47 21.775 33.5 12.950000000000001 31.775 48 20.1 23.599999999999998 10.8 45.5 49 19.754938734683673 30.732683170792697 20.655163790947736 28.857214303575894 50 30.052592036063107 25.018782870022537 10.293012772351616 34.63561232156274 51 19.65982991495748 26.563281640820406 19.609804902451224 34.167083541770886 >>END_MODULE >>Per sequence GC content warn #GC Content Count 0 0.0 1 0.0 2 0.0 3 0.0 4 0.0 5 0.0 6 0.0 7 0.0 8 0.0 9 0.0 10 0.0 11 0.0 12 0.0 13 0.0 14 0.0 15 0.0 16 0.0 17 0.0 18 0.0 19 0.0 20 0.0 21 0.5 22 1.0 23 0.5 24 0.0 25 0.0 26 1.5 27 3.0 28 2.5 29 2.0 30 2.5 31 3.0 32 6.5 33 10.0 34 11.5 35 13.0 36 15.0 37 17.0 38 26.5 39 36.0 40 60.5 41 85.0 42 181.0 43 277.0 44 262.5 45 248.0 46 285.5 47 323.0 48 346.5 49 370.0 50 516.5 51 663.0 52 643.0 53 623.0 54 551.5 55 480.0 56 483.5 57 487.0 58 306.5 59 126.0 60 101.0 61 76.0 62 74.5 63 73.0 64 60.0 65 47.0 66 35.5 67 24.0 68 16.0 69 8.0 70 4.5 71 1.0 72 1.0 73 1.0 74 0.5 75 0.5 76 1.0 77 0.5 78 0.0 79 0.0 80 0.0 81 0.0 82 0.0 83 0.0 84 0.0 85 0.0 86 0.0 87 0.0 88 0.0 89 0.0 90 0.0 91 1.0 92 2.0 93 1.0 94 0.0 95 0.0 96 0.0 97 0.0 98 0.0 99 0.0 100 0.0 >>END_MODULE >>Per base N content pass #Base N-Count 1 0.0 2 0.0 3 0.0 4 0.0 5 0.0 6 1.3 7 0.0 8 0.0 9 0.0 10 0.0 11 0.0 12 0.0 13 0.0 14 0.0 15 0.0 16 0.0 17 0.0 18 0.0 19 0.0 20 0.0 21 0.0 22 0.0 23 0.0 24 0.0 25 0.0 26 0.0 27 0.0 28 0.075 29 0.0 30 0.0 31 0.0 32 0.0 33 0.0 34 0.0 35 0.0 36 0.0 37 0.0 38 0.0 39 0.0 40 0.05 41 0.05 42 0.05 43 0.0 44 0.0 45 0.0 46 0.0 47 0.0 48 0.0 49 0.025 50 0.17500000000000002 51 0.05 >>END_MODULE >>Sequence Length Distribution pass #Length Count 51 4000.0 >>END_MODULE >>Sequence Duplication Levels warn #Total Deduplicated Percentage 65.675 #Duplication Level Percentage of deduplicated Percentage of total 1 91.6634944803959 60.199999999999996 2 4.377617053673392 5.75 3 1.1419870574800153 2.25 4 0.34259611724400457 0.8999999999999999 5 0.41872858774267224 1.375 6 0.15226494099733537 0.6 7 0.22839741149600304 1.05 8 0.1903311762466692 1.0 9 0.11419870574800152 0.675 >10 1.2561857632280167 18.15 >50 0.07613247049866768 3.4000000000000004 >100 0.03806623524933384 4.65 >500 0.0 0.0 >1k 0.0 0.0 >5k 0.0 0.0 >10k+ 0.0 0.0 >>END_MODULE >>Overrepresented sequences fail #Sequence Count Percentage Possible Source TCGGACCAGGCTTCATTCCCCTGGAATTCTCGGGTGCCAAGGAACTCCAGT 186 4.65 RNA PCR Primer, Index 1 (100% over 30bp) TCTCGGACCAGGCTTCATTCCTGGAATTCTCGGGTGCCAAGGAACTCCAGT 74 1.8499999999999999 RNA PCR Primer, Index 1 (100% over 30bp) CGATTGGGGGAGTAAGAATAGTATTTAATTGCTGGAATTCTCGGGTGCCAA 62 1.55 No Hit AGTTACTAATTCATGATCTGGCTGGAATTCTCGGGTGCCAAGGAACTCCAG 45 1.125 RNA PCR Primer, Index 1 (100% over 29bp) TCCTAACAGACCGGTAGACTTGAACTGGAATTCTCGGGTGCCAAGGAACTC 42 1.05 RNA PCR Primer, Index 1 (100% over 26bp) CTAACAGACCGGTAGACTTGAACTGGAATTCTCGGGTGCCAAGGAACTCCA 42 1.05 RNA PCR Primer, Index 1 (100% over 28bp) GGCGGATGTAGCCAAGTGGATCAAGGCAGTGGAATTCTCGGGTGCCAAGGA 40 1.0 RNA PCR Primer, Index 1 (100% over 22bp) ATCCGGTTAGGATCGATCTAAACCAGCCCTGGAATTCTCGGGTGCCAAGGA 40 1.0 RNA PCR Primer, Index 1 (100% over 22bp) CCTAACAGACCGGTAGACTTGAACTGGAATTCTCGGGTGCCAAGGAACTCC 34 0.8500000000000001 RNA PCR Primer, Index 1 (100% over 27bp) TAAACGACTCTCGGCAACGGATATCTCGGCTCTCGCATCGATGAAGAACGT 33 0.8250000000000001 No Hit TAACAGACCGGTAGACTTGAACTGGAATTCTCGGGTGCCAAGGAACTCCAG 28 0.7000000000000001 RNA PCR Primer, Index 1 (100% over 29bp) TGAGGCATCCTAACAGACCGGTAGACTTGAACTGGAATTCTCGGGTGCCAA 28 0.7000000000000001 No Hit AACGACTCTCGGCAACGGATATCTCGGCTCTCGCATCGATGAAGAACGTAG 27 0.675 No Hit GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCTGGAATTCTCGGGTGCCA 26 0.65 No Hit TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGTGAAAATCTCGTATGCC 26 0.65 RNA PCR Primer, Index 19 (100% over 51bp) GCATCCTAACAGACCGGTAGACTTGAACTGGAATTCTCGGGTGCCAAGGAA 25 0.625 RNA PCR Primer, Index 1 (100% over 23bp) AACAGACCGGTAGACTTGAACTGGAATTCTCGGGTGCCAAGGAACTCCAGT 24 0.6 RNA PCR Primer, Index 1 (100% over 30bp) AGGCATCCTAACAGACCGGTAGACTTGAACTGGAATTCTCGGGTGCCAAGG 22 0.5499999999999999 Illumina Small RNA Adapter 2 (100% over 21bp) CATCCTAACAGACCGGTAGACTTGAACTGGAATTCTCGGGTGCCAAGGAAC 20 0.5 RNA PCR Primer, Index 1 (100% over 24bp) GAGGCATCCTAACAGACCGGTAGACTTGAACTGGAATTCTCGGGTGCCAAG 19 0.475 No Hit ATCCTAACAGACCGGTAGACTTGAACTGGAATTCTCGGGTGCCAAGGAACT 19 0.475 RNA PCR Primer, Index 1 (100% over 25bp) CGATTGGGGGAGTAAGAATAGTATTTAATTGTGGAATTCTCGGGTGCCAAG 16 0.4 No Hit CGATTGGGGGAGTAAGAATAGTATTTAATTGCTTGGAATTCTCGGGTGCCA 15 0.375 No Hit TGCAGCTGAGGCATCCTAACAGACCGGTAGACTTGAACTGGAATTCTCGGG 14 0.35000000000000003 No Hit GTCGGGATAGCTCAGCAGGTAGAGCAGAGGACTGATGGAATTCTCGGGTGC 14 0.35000000000000003 No Hit AACGACTCTCGGCAACGGATATCTCGGCTTGGAATTCTCGGGTGCCAAGGA 13 0.325 RNA PCR Primer, Index 1 (100% over 22bp) GGCATCCTAACAGACCGGTAGACTTGAACTGGAATTCTCGGGTGCCAAGGA 12 0.3 RNA PCR Primer, Index 1 (100% over 22bp) ACAGACCGGTAGACTTGAACTGGAATTCTCGGGTGCCAAGGAACTCCAGTC 12 0.3 RNA PCR Primer, Index 1 (100% over 31bp) GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCTTGGAATTCTCGGGTGCC 12 0.3 No Hit GAGATTCAGCCCCATGTCGCTCCGATTCGTTGGAATTCTCGGGTGCCAAGG 12 0.3 Illumina Small RNA Adapter 2 (100% over 21bp) GATTGGGGGAGTAAGAATAGTATTTAATTGCTGGAATTCTCGGGTGCCAAG 12 0.3 No Hit CTAAACGACTCTCGGCAACGGATATCTCGGCTCTCGCATCGATGAAGAACG 11 0.27499999999999997 No Hit TAAACGACTCTCGGCAACGGATATCTCGGCTTGGAATTCTCGGGTGCCAAG 11 0.27499999999999997 No Hit GGGATTGTAGTTCAATTGGTCAGAGCACCGCCTGGAATTCTCGGGTGCCAA 11 0.27499999999999997 No Hit CTGAGGCATCCTAACAGACCGGTAGACTTGAACTGGAATTCTCGGGTGCCA 11 0.27499999999999997 No Hit AGTTACTAATTCATGATCTGGCATGGAATTCTCGGGTGCCAAGGAACTCCA 10 0.25 RNA PCR Primer, Index 1 (100% over 28bp) TGTGTTCTCAGGTCGCCCCTGTGGAATTCTCGGGTGCCAAGGAACTCCAGT 9 0.22499999999999998 RNA PCR Primer, Index 1 (100% over 30bp) TTCAGCCCCATGTCGCTCCGATTCGTTGGAATTCTCGGGTGCCAAGGAACT 9 0.22499999999999998 RNA PCR Primer, Index 1 (100% over 25bp) TTTGGATTGAAGGGAGCTCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTC 9 0.22499999999999998 RNA PCR Primer, Index 1 (100% over 31bp) GCTGAGGCATCCTAACAGACCGGTAGACTTGAACTGGAATTCTCGGGTGCC 8 0.2 No Hit ATTCAGCCCCATGTCGCTCCGATTCGTTGGAATTCTCGGGTGCCAAGGAAC 8 0.2 RNA PCR Primer, Index 1 (100% over 24bp) TTGGTCGAGGGCACGTCTGCCTGGGTGTCACGCTGGAATTCTCGGGTGCCA 8 0.2 No Hit TCAGCCCCATGTCGCTCCGATTCGTTGGAATTCTCGGGTGCCAAGGAACTC 8 0.2 RNA PCR Primer, Index 1 (100% over 26bp) GCGGATATAGTCGAATGGTAAAATTTCTCTTTGCCTGGAATTCTCGGGTGC 8 0.2 No Hit TTTGGATTGAAGGGAGCTCTATGGAATTCTCGGGTGCCAAGGAACTCCAGT 7 0.17500000000000002 RNA PCR Primer, Index 1 (100% over 30bp) AGCTGAGGCATCCTAACAGACCGGTAGACTTGAACTGGAATTCTCGGGTGC 7 0.17500000000000002 No Hit ACTGAGATTCAGCCCCATGTCGCTCCGATTCGTTGGAATTCTCGGGTGCCA 7 0.17500000000000002 No Hit GGTGGCTGTAGTTTAGTGGTGAGAATTCCACGTTGTTGGAATTCTCGGGTG 7 0.17500000000000002 No Hit CACTGAGATTCAGCCCCATGTCGCTCCGATTCGTTGGAATTCTCGGGTGCC 7 0.17500000000000002 No Hit CGCGGGGTAGAGCAGCTTGGTAGCTCGCAAGGCTCTGGAATTCTCGGGTGC 7 0.17500000000000002 No Hit CGATTGGGGGAGTAAGAATAGTATTTAATTGCTACTGGAATTCTCGGGTGC 6 0.15 No Hit AAACGACTCTCGGCAACGGATATCTCGGCTCTCGCATCGATGAAGAACGTA 6 0.15 No Hit ATGCAGCTGAGGCATCCTAACAGACCGGTAGACTTGAACTGGAATTCTCGG 6 0.15 No Hit AGTTACTAATTCATGATCTGGCATATGGAATTCTCGGGTGCCAAGGAACTC 6 0.15 RNA PCR Primer, Index 1 (100% over 26bp) GCCCCATGTCGCTCCGATTCGTTGGAATTCTCGGGTGCCAAGGAACTCCAG 5 0.125 RNA PCR Primer, Index 1 (100% over 29bp) TATGCAGCTGAGGCATCCTAACAGACCGGTAGACTTGAACTGGAATTCTCG 5 0.125 No Hit TCTTTCCAACGCCTCCCATACCTGGAATTCTCGGGTGCCAAGGAACTCCAG 5 0.125 RNA PCR Primer, Index 1 (100% over 29bp) GCGGATGTAGCCAAGTGGATCAAGGCAGTGGAATTCTCGGGTGCCAAGGAA 5 0.125 RNA PCR Primer, Index 1 (100% over 23bp) CAGACCGGTAGACTTGAACTGGAATTCTCGGGTGCCAAGGAACTCCAGTCA 5 0.125 RNA PCR Primer, Index 1 (100% over 32bp) TCTTGCCTACTCCTCCCATTCCTGGAATTCTCGGGTGCCAAGGAACTCCAG 5 0.125 RNA PCR Primer, Index 1 (100% over 29bp) AGCCCCATGTCGCTCCGATTCGTTGGAATTCTCGGGTGCCAAGGAACTCCA 5 0.125 RNA PCR Primer, Index 1 (100% over 28bp) AGACCGGTAGACTTGAACTGGAATTCTCGGGTGCCAAGGAACTCCAGTCAC 5 0.125 RNA PCR Primer, Index 1 (100% over 33bp) GTCGTTGTAGTATAGTGGTGAGTATTCCCGCCTTGGAATTCTCGGGTGCCA 5 0.125 No Hit CTAAACGACTCTCGGCAACGGATATCTCGGCTTGGAATTCTCGGGTGCCAA 5 0.125 No Hit GCGACCCCAGGTCAGGCGGGACTTGGAATTCTCGGGTGCCAAGGAACTCCA 5 0.125 RNA PCR Primer, Index 1 (100% over 28bp) >>END_MODULE >>Adapter Content fail #Position Illumina Universal Adapter Illumina Small RNA 3' Adapter Illumina Small RNA 5' Adapter Nextera Transposase Sequence SOLID Small RNA Adapter 1 0.0 0.75 0.0 0.0 0.0 2 0.0 0.75 0.0 0.0 0.0 3 0.0 0.75 0.0 0.0 0.0 4 0.0 0.75 0.0 0.0 0.0 5 0.0 0.8 0.0 0.0 0.0 6 0.0 0.825 0.0 0.0 0.0 7 0.0 0.825 0.0 0.0 0.0 8 0.0 0.825 0.0 0.0 0.0 9 0.0 0.875 0.0 0.0 0.0 10 0.0 0.975 0.0 0.0 0.0 11 0.0 1.025 0.0 0.0 0.0 12 0.0 1.1 0.0 0.0 0.0 13 0.0 1.2 0.0 0.0 0.0 14 0.0 1.325 0.0 0.0 0.0 15 0.0 1.4 0.0 0.0 0.0 16 0.0 1.65 0.0 0.0 0.0 17 0.0 2.0 0.0 0.0 0.0 18 0.0 2.425 0.0 0.0 0.0 19 0.0 2.975 0.0 0.0 0.0 20 0.0 4.1 0.0 0.0 0.0 21 0.0 6.25 0.0 0.0 0.0 22 0.0 18.875 0.0 0.0 0.0 23 0.0 24.3 0.0 0.0 0.0 24 0.0 29.125 0.0 0.0 0.0 25 0.0 43.425 0.0 0.0 0.0 26 0.0 48.075 0.0 0.0 0.0 27 0.0 51.55 0.0 0.0 0.0 28 0.0 55.525 0.0 0.0 0.0 29 0.0 58.55 0.0 0.0 0.0 30 0.0 64.35 0.0 0.0 0.0 31 0.0 67.85 0.0 0.0 0.0 32 0.0 71.8 0.0 0.0 0.0 33 0.0 77.025 0.0 0.0 0.0 34 0.0 81.4 0.0 0.0 0.0 35 0.0 84.0 0.0 0.0 0.0 36 0.0 86.725 0.0 0.0 0.0 37 0.0 88.4 0.0 0.0 0.0 38 0.0 89.475 0.0 0.0 0.0 39 0.0 90.325 0.0 0.0 0.0 >>END_MODULE >>Kmer Content fail #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position TCTCGGA 30 1.5451515E-6 45.493675 1 CTCGGAC 30 1.5451515E-6 45.493675 2 CATTCCT 30 1.6908471E-6 44.925003 16 TTCCTGG 30 1.6908471E-6 44.925003 18 ATTCCTG 30 1.6908471E-6 44.925003 17 TCCTGGA 35 4.886695E-6 38.507145 19 TTGTAGT 25 0.0017662444 36.394936 5 CTCCAGT 85 0.0 34.354412 45 GGACCAG 50 5.1459967E-5 27.296202 5 CGGACCA 50 5.1459967E-5 27.296202 4 TCGGACC 50 5.1459967E-5 27.296202 3 GACCAGG 50 5.1459967E-5 27.296202 6 TCATTCC 50 5.6257573E-5 26.955 15 ACCAGGC 50 5.6257573E-5 26.955 7 CCTGGAA 80 6.2123945E-8 25.270313 20 CTTCATT 45 0.0010358806 24.958332 13 TTCATTC 45 0.0010358806 24.958332 14 AGGCTTC 45 0.0010358806 24.958332 10 GGCTTCA 45 0.0010358806 24.958332 11 CAGGCTT 45 0.0010358806 24.958332 9 >>END_MODULE Rejected 791621 READS because READLEN < 1 Read 791621 spots for SRR7472588.sra Written 791621 spots for SRR7472588.sra Rejected 791621 READS because READLEN < 1 Read 791621 spots for SRR7472588.sra Written 791621 spots for SRR7472588.sra Rejected 791621 READS because READLEN < 1 Read 791621 spots for SRR7472588.sra Written 791621 spots for SRR7472588.sra Rejected 791621 READS because READLEN < 1 Read 791621 spots for SRR7472588.sra Written 791621 spots for SRR7472588.sra Rejected 791621 READS because READLEN < 1 Read 791621 spots for SRR7472588.sra Written 791621 spots for SRR7472588.sra Rejected 791621 READS because READLEN < 1 Read 791621 spots for SRR7472588.sra Written 791621 spots for SRR7472588.sra Rejected 791621 READS because READLEN < 1 Read 791621 spots for SRR7472588.sra Written 791621 spots for SRR7472588.sra Rejected 791621 READS because READLEN < 1 Read 791621 spots for SRR7472588.sra Written 791621 spots for SRR7472588.sra Rejected 791621 READS because READLEN < 1 Read 791621 spots for SRR7472588.sra Written 791621 spots for SRR7472588.sra Rejected 791621 READS because READLEN < 1 Read 791621 spots for SRR7472588.sra Written 791621 spots for SRR7472588.sra Rejected 791621 READS because READLEN < 1 Read 791621 spots for SRR7472588.sra Written 791621 spots for SRR7472588.sra Rejected 791621 READS because READLEN < 1 Read 791621 spots for SRR7472588.sra Written 791621 spots for SRR7472588.sra Rejected 791621 READS because READLEN < 1 Read 791621 spots for SRR7472588.sra Written 791621 spots for SRR7472588.sra Rejected 791621 READS because READLEN < 1 Read 791621 spots for SRR7472588.sra Written 791621 spots for SRR7472588.sra Rejected 791621 READS because READLEN < 1 Read 791621 spots for SRR7472588.sra Written 791621 spots for SRR7472588.sra Rejected 791621 READS because READLEN < 1 Read 791621 spots for SRR7472588.sra Written 791621 spots for SRR7472588.sra Rejected 791621 READS because READLEN < 1 Read 791621 spots for SRR7472588.sra Written 791621 spots for SRR7472588.sra Rejected 791621 READS because READLEN < 1 Read 791621 spots for SRR7472588.sra Written 791621 spots for SRR7472588.sra Rejected 791621 READS because READLEN < 1 Read 791621 spots for SRR7472588.sra Written 791621 spots for SRR7472588.sra Rejected 791621 READS because READLEN < 1 Read 791621 spots for SRR7472588.sra Written 791621 spots for SRR7472588.sra SRR ids: ['SRR7472588.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_5imchv0b SRR7472588.sra spots: 15832420 blocks: [[1, 791621], [791622, 1583242], [1583243, 2374863], [2374864, 3166484], [3166485, 3958105], [3958106, 4749726], [4749727, 5541347], [5541348, 6332968], [6332969, 7124589], [7124590, 7916210], [7916211, 8707831], [8707832, 9499452], [9499453, 10291073], [10291074, 11082694], [11082695, 11874315], [11874316, 12665936], [12665937, 13457557], [13457558, 14249178], [14249179, 15040799], [15040800, 15832420]] SRR7472588 file size 2235656 SRR7472588 completed basic pipeline successfully skewer v0.2.2 [April 4, 2016] COMMAND LINE: skewer -f sanger -l 18 -q 10 -k inf -t 20 -o SRR7472588 SRR7472588_1.fastq Input file: SRR7472588_1.fastq trimmed: SRR7472588-trimmed.fastq Parameters used: -- 3' end adapter sequence (-x): AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC -- maximum error ratio allowed (-r): 0.100 -- maximum indel error ratio allowed (-d): 0.030 -- end quality threshold (-q): 10 -- minimum read length allowed after trimming (-l): 18 -- file format (-f): Sanger/Illumina 1.8+ FASTQ -- minimum overlap length for adapter detection (-k): inf -- number of concurrent threads (-t): 20 Thu Feb 13 18:29:37 2025 >> started Thu Feb 13 18:29:44 2025 >> done (6.194s) 15832420 reads processed; of these: 0 ( 0.00%) short reads filtered out after trimming by size control 0 ( 0.00%) empty reads filtered out after trimming by size control 15832420 (100.00%) reads available; of these: 230587 ( 1.46%) trimmed reads available after processing 15601833 (98.54%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 37 1 0.00% 38 0 0.00% 39 0 0.00% 40 1 0.00% 41 15 0.00% 42 23 0.00% 43 36 0.00% 44 129 0.00% 45 296 0.00% 46 1007 0.01% 47 2921 0.02% 48 8437 0.05% 49 31105 0.20% 50 186616 1.18% 51 15601833 98.54% 15832420 reads passed initial QC criterion=sequence-density sequence-density=90.95 sequence-density-rank=1 fanout-score=25.21 fanout-score-rank=2 prefix-density=91.30 prefix-fanout=25.1 sequence=TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGTGAAAATCTCGTATGCCG criterion=fanout-score sequence-density=1.29 sequence-density-rank=2 fanout-score=28.34 fanout-score-rank=1 prefix-density=1.27 prefix-fanout=28.3 sequence=GACTGGAATTCT Potential 3prime adapter identified. Now checking if in reference sequence Warning: gzbuffer added in zlib v1.2.3.5. Unable to change buffer size from default of 8192. 1 reads; of these: 1 (100.00%) were unpaired; of these: 1 (100.00%) aligned 0 times 0 (0.00%) aligned exactly 1 time 0 (0.00%) aligned >1 times 0.00% overall alignment rate Adapter seq not found in reference. Now shuffling file before clipping skewer v0.2.2 [April 4, 2016] COMMAND LINE: skewer -f sanger -l 18 -t 20 -x TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGTGAAAATCTCGTATGCCG -o SRR7472588 - Input file: STDIN trimmed: SRR7472588-trimmed.fastq Parameters used: -- 3' end adapter sequence (-x): TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGTGAAAATCTCGTATGCCG -- maximum error ratio allowed (-r): 0.100 -- maximum indel error ratio allowed (-d): 0.030 -- minimum read length allowed after trimming (-l): 18 -- file format (-f): Sanger/Illumina 1.8+ FASTQ -- minimum overlap length for adapter detection (-k): 3 -- number of concurrent threads (-t): 20 Thu Feb 13 18:30:12 2025 >> started Thu Feb 13 18:30:22 2025 >> done (10.589s) 15484455 reads processed; of these: 277136 ( 1.79%) short reads filtered out after trimming by size control 206075 ( 1.33%) empty reads filtered out after trimming by size control 15001244 (96.88%) reads available; of these: 14373397 (95.81%) trimmed reads available after processing 627847 ( 4.19%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 154503 1.03% 19 213542 1.42% 20 382284 2.55% 21 2145605 14.30% 22 938923 6.26% 23 915561 6.10% 24 2204568 14.70% 25 759801 5.06% 26 566317 3.78% 27 560397 3.74% 28 572627 3.82% 29 796044 5.31% 30 517364 3.45% 31 551464 3.68% 32 784733 5.23% 33 616367 4.11% 34 423742 2.82% 35 423595 2.82% 36 292148 1.95% 37 167787 1.12% 38 121213 0.81% 39 82039 0.55% 40 58213 0.39% 41 31320 0.21% 42 41929 0.28% 43 18348 0.12% 44 10360 0.07% 45 8195 0.05% 46 6354 0.04% 47 5508 0.04% 48 9039 0.06% 49 11140 0.07% 50 31593 0.21% 51 578621 3.86% criterion=sequence-density sequence-density=2.48 sequence-density-rank=1 fanout-score=0.00 fanout-score-rank=12 prefix-density=0.00 prefix-fanout=1.0 sequence=TCTCGGACCAGGCTTCATTCCCCTGGAATTCT criterion=fanout-score sequence-density=0.06 sequence-density-rank=24 fanout-score=68.66 fanout-score-rank=1 prefix-density=4.03 prefix-fanout=1.0 sequence=TCCTAACAGACAGGTAGACTTGA Started job on | Feb 13 18:30:37 Started mapping on | Feb 13 18:30:37 Finished on | Feb 13 18:31:12 Mapping speed, Million of reads per hour | 1578.78 Number of input reads | 15349209 Average input read length | 28 UNIQUE READS: Uniquely mapped reads number | 5459099 Uniquely mapped reads % | 35.57% Average mapped length | 27.34 Number of splices: Total | 58126 Number of splices: Annotated (sjdb) | 25498 Number of splices: GT/AG | 56504 Number of splices: GC/AG | 735 Number of splices: AT/AC | 98 Number of splices: Non-canonical | 789 Mismatch rate per base, % | 0.39% Deletion rate per base | 0.00% Deletion average length | 1.17 Insertion rate per base | 0.00% Insertion average length | 1.11 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 2820255 % of reads mapped to multiple loci | 18.37% Number of reads mapped to too many loci | 6219546 % of reads mapped to too many loci | 40.52% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 4.40% % of reads unmapped: other | 1.14% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 7069855 7069855 7069855 N_multimapping 2820255 2820255 2820255 N_noFeature 2498155 2589223 4313076 N_ambiguous 1058070 2464 670 UnstrandedReadsAssigned:1902874 PositiveStrandReadsAssigned:2867412 NegativeStrandReadsAssigned:1145353 Dataset is classified unstranded MeadianReadLen=25 20thPercentileLength=22 echo kmer=19 SRR7472588 Starting Kallisto single end mapping to ensembl reference transcriptome. kmer=19 [quant] fragment length distribution is truncated gaussian with mean = 100, sd = 20 [index] k-mer length: 19 [index] number of targets: 52,400 [index] number of k-mers: 59,590,899 [index] number of equivalence classes: 293,668 [quant] running in single-end mode [quant] will process file 1: SRR7472588-trimmed.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 15,349,209 reads, 8,118,732 reads pseudoaligned [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,030 rounds 52401 SRR7472588.ke.tsv 34699 SRR7472588.se.tsv 87100 total ==> SRR7472588.ke.tsv <== target_id length eff_length est_counts tpm Potri.005G200100.1.v4.1 2018 1919 17.87 0.848912 Potri.005G024800.1.v4.1 1035 936 4 0.38958 Potri.004G059700.1.v4.1 961 862 0 0 Potri.007G009000.2.v4.1 1416 1317 0 0 Potri.003G141000.2.v4.1 2943 2844 11.4681 0.3676 Potri.016G087400.1.v4.1 270 171 5.41201 2.8852 Potri.015G069301.1.v4.1 564 465 7 1.37233 Potri.010G195200.1.v4.1 1773 1674 1 0.0544574 Potri.012G127500.1.v4.1 977 878 47 4.87995 ==> SRR7472588.se.tsv <== Potri.001G166300.v4.1 1 Potri.001G448400.v4.1 2 Potri.001G233950.v4.1 1 Potri.001G122700.v4.1 5 Potri.001G212900.v4.1 0 Potri.001G182400.v4.1 1 Potri.001G256600.v4.1 2 Potri.001G040500.v4.1 6 Potri.001G416900.v4.1 1 Potri.001G452600.v4.1 3 SRR7472588 completed mapping pipeline successfully