Starting /dee2/code/volunteer_pipeline.sh SRR1772228 current disk space = 1540195233792 free memory = 1601235000 SRR1772228 SRAfilesize 81773d923f64705b4a1630991307dca6 SRR1772228.sra SRR1772228.sra file validated SRR1772228 is single end SRR1772228 is conventional basespace SRR1772228 read1 length is 50 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR1772228_1.fastq File type Conventional base calls Encoding Sanger / Illumina 1.9 Total Sequences 4000 Sequences flagged as poor quality 0 Sequence length 50 %GC 43 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 32.85325 34.0 31.0 34.0 31.0 34.0 2 33.0065 34.0 31.0 34.0 31.0 34.0 3 32.77 34.0 31.0 34.0 31.0 34.0 4 36.19575 37.0 37.0 37.0 35.0 37.0 5 36.29925 37.0 37.0 37.0 35.0 37.0 6 36.21175 37.0 37.0 37.0 35.0 37.0 7 36.2055 37.0 37.0 37.0 35.0 37.0 8 36.17675 37.0 37.0 37.0 35.0 37.0 9 37.9385 39.0 38.0 39.0 35.0 39.0 10 37.84175 39.0 38.0 39.0 35.0 39.0 11 37.917 39.0 38.0 39.0 35.0 39.0 12 37.8715 39.0 38.0 39.0 35.0 39.0 13 37.9845 39.0 38.0 39.0 35.0 39.0 14 39.206 41.0 39.0 41.0 36.0 41.0 15 39.32875 41.0 39.0 41.0 36.0 41.0 16 39.1095 40.0 39.0 41.0 36.0 41.0 17 39.29975 41.0 39.0 41.0 36.0 41.0 18 39.3925 41.0 39.0 41.0 36.0 41.0 19 39.2245 41.0 39.0 41.0 36.0 41.0 20 39.2795 41.0 39.0 41.0 36.0 41.0 21 39.19225 41.0 39.0 41.0 36.0 41.0 22 39.217 41.0 39.0 41.0 36.0 41.0 23 38.90025 40.0 39.0 41.0 35.0 41.0 24 38.97325 41.0 39.0 41.0 35.0 41.0 25 39.058 41.0 39.0 41.0 36.0 41.0 26 38.46 40.0 38.0 41.0 34.0 41.0 27 38.59575 40.0 38.0 41.0 34.0 41.0 28 38.68375 40.0 38.0 41.0 35.0 41.0 29 38.47825 40.0 38.0 41.0 34.0 41.0 30 38.45825 40.0 38.0 41.0 35.0 41.0 31 38.351 40.0 38.0 41.0 34.0 41.0 32 38.192 40.0 38.0 41.0 34.0 41.0 33 38.15475 40.0 38.0 41.0 34.0 41.0 34 38.4295 40.0 38.0 41.0 35.0 41.0 35 38.4075 40.0 38.0 41.0 34.0 41.0 36 38.3165 40.0 38.0 41.0 34.0 41.0 37 37.9285 40.0 38.0 41.0 33.0 41.0 38 37.612 40.0 38.0 41.0 33.0 41.0 39 37.70925 40.0 38.0 41.0 33.0 41.0 40 37.707 40.0 38.0 41.0 33.0 41.0 41 37.61375 40.0 38.0 41.0 33.0 41.0 42 37.637 40.0 38.0 41.0 33.0 41.0 43 37.4315 40.0 38.0 41.0 33.0 41.0 44 37.2475 40.0 38.0 41.0 33.0 41.0 45 37.044 40.0 38.0 41.0 32.0 41.0 46 37.01325 40.0 38.0 41.0 32.0 41.0 47 36.6495 40.0 37.0 41.0 31.0 41.0 48 36.5605 40.0 37.0 41.0 30.0 41.0 49 36.58425 40.0 37.0 41.0 31.0 41.0 50 36.31425 40.0 37.0 41.0 30.0 41.0 >>END_MODULE >>Per tile sequence quality pass #Tile Base Mean 1101 1 0.0 1101 2 0.0 1101 3 0.0 1101 4 0.0 1101 5 0.0 1101 6 0.0 1101 7 0.0 1101 8 0.0 1101 9 0.0 1101 10 0.0 1101 11 0.0 1101 12 0.0 1101 13 0.0 1101 14 0.0 1101 15 0.0 1101 16 0.0 1101 17 0.0 1101 18 0.0 1101 19 0.0 1101 20 0.0 1101 21 0.0 1101 22 0.0 1101 23 0.0 1101 24 0.0 1101 25 0.0 1101 26 0.0 1101 27 0.0 1101 28 0.0 1101 29 0.0 1101 30 0.0 1101 31 0.0 1101 32 0.0 1101 33 0.0 1101 34 0.0 1101 35 0.0 1101 36 0.0 1101 37 0.0 1101 38 0.0 1101 39 0.0 1101 40 0.0 1101 41 0.0 1101 42 0.0 1101 43 0.0 1101 44 0.0 1101 45 0.0 1101 46 0.0 1101 47 0.0 1101 48 0.0 1101 49 0.0 1101 50 0.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 14 1.0 15 2.0 16 3.0 17 2.0 18 10.0 19 8.0 20 13.0 21 6.0 22 7.0 23 12.0 24 11.0 25 13.0 26 15.0 27 25.0 28 27.0 29 35.0 30 54.0 31 57.0 32 68.0 33 70.0 34 115.0 35 145.0 36 218.0 37 326.0 38 600.0 39 2157.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 39.77983487615712 11.233425068801601 13.159869902426822 35.82687015261446 2 30.25 11.475 30.45 27.825 3 40.52896725440806 17.682619647355164 16.90176322418136 24.886649874055415 4 31.825 28.4 16.475 23.3 5 32.525 31.724999999999998 20.8 14.95 6 23.125 35.4 16.35 25.124999999999996 7 10.549999999999999 38.025 36.525 14.899999999999999 8 21.575 27.900000000000002 29.349999999999998 21.175 9 20.8 19.775000000000002 34.275 25.15 10 16.175 45.074999999999996 23.9 14.85 11 26.25 32.725 17.849999999999998 23.175 12 29.099999999999998 28.499999999999996 21.275 21.125 13 17.7 40.65 22.85 18.8 14 25.674999999999997 32.074999999999996 26.400000000000002 15.85 15 20.05 37.5 19.950000000000003 22.5 16 21.825 37.4 21.75 19.025 17 22.8 36.775000000000006 20.7 19.725 18 17.025000000000002 37.25 22.875 22.85 19 19.55 34.75 25.3 20.4 20 14.774999999999999 36.449999999999996 26.325 22.45 21 18.4 29.7 28.050000000000004 23.849999999999998 22 14.725 44.275 21.05 19.950000000000003 23 18.075 37.8 25.825 18.3 24 18.2 36.375 20.8 24.625 25 17.175 35.675000000000004 27.05 20.1 26 17.95 38.05 23.275000000000002 20.724999999999998 27 23.775 30.75 27.975 17.5 28 25.2 41.199999999999996 17.825 15.775 29 26.424999999999997 32.7 21.625 19.25 30 27.500000000000004 31.275 22.650000000000002 18.575 31 31.6 25.924999999999997 21.875 20.599999999999998 32 24.375 31.65 24.175 19.8 33 27.525 35.55 18.95 17.974999999999998 34 23.275000000000002 37.025000000000006 19.375 20.325 35 20.75 38.125 23.375 17.75 36 22.675 27.275 31.3 18.75 37 23.897795591182362 27.90581162324649 29.308617234468937 18.887775551102205 38 19.025 26.0 32.675 22.3 39 25.25 25.7 29.5 19.55 40 18.25 34.9 26.35 20.5 41 24.65 26.05 27.875 21.425 42 19.650000000000002 33.25 24.15 22.95 43 19.925 34.825 23.674999999999997 21.575 44 20.575 29.45 28.349999999999998 21.625 45 21.763085399449036 31.179564237415473 29.501627848735286 17.555722514400202 46 17.838378784088064 30.5479109331999 34.475856892669505 17.137853390042533 47 18.584292146073036 35.942971485742866 25.962981490745374 19.50975487743872 48 24.20605151287822 32.98324581145287 24.50612653163291 18.30457614403601 49 22.0360180090045 33.06653326663332 25.012506253126567 19.884942471235618 50 26.356589147286826 26.556639159789945 27.00675168792198 20.080020005001252 >>END_MODULE >>Per sequence GC content fail #GC Content Count 0 1.0 1 0.5 2 0.0 3 0.0 4 0.0 5 0.0 6 0.0 7 0.0 8 0.0 9 0.5 10 1.0 11 1.0 12 1.0 13 0.5 14 0.0 15 1.0 16 2.0 17 1.5 18 1.0 19 3.5 20 6.0 21 8.0 22 10.0 23 13.5 24 17.0 25 29.0 26 41.0 27 32.5 28 24.0 29 30.5 30 37.0 31 48.0 32 59.0 33 147.5 34 236.0 35 307.0 36 378.0 37 457.5 38 537.0 39 441.0 40 345.0 41 350.0 42 355.0 43 403.5 44 452.0 45 456.5 46 461.0 47 333.5 48 206.0 49 260.0 50 314.0 51 204.0 52 94.0 53 110.5 54 127.0 55 95.0 56 63.0 57 52.5 58 42.0 59 34.5 60 27.0 61 23.0 62 19.0 63 22.0 64 25.0 65 22.0 66 19.0 67 22.5 68 26.0 69 25.0 70 24.0 71 22.5 72 21.0 73 13.5 74 6.0 75 5.5 76 5.0 77 5.0 78 5.0 79 6.5 80 8.0 81 5.0 82 2.0 83 2.0 84 2.0 85 1.5 86 1.0 87 0.5 88 0.0 89 0.0 90 0.0 91 0.0 92 0.0 93 0.0 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 0.075 2 0.0 3 0.75 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 0.0 22 0.0 23 0.0 24 0.0 25 0.0 26 0.0 27 0.0 28 0.0 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 0.2 38 0.0 39 0.0 40 0.0 41 0.0 42 0.0 43 0.0 44 0.0 45 0.17500000000000002 46 0.075 47 0.05 48 0.025 49 0.05 50 0.025 >>END_MODULE >>Sequence Length Distribution pass #Length Count 50 4000.0 >>END_MODULE >>Sequence Duplication Levels fail #Total Deduplicated Percentage 44.875 #Duplication Level Percentage of deduplicated Percentage of total 1 83.73259052924791 37.574999999999996 2 7.4094707520891365 6.65 3 1.9498607242339834 2.625 4 1.5041782729805013 2.7 5 0.8356545961002786 1.875 6 0.5013927576601671 1.35 7 0.5571030640668524 1.7500000000000002 8 0.22284122562674097 0.8 9 0.22284122562674097 0.8999999999999999 >10 2.6740947075208914 27.075 >50 0.22284122562674097 6.45 >100 0.1671309192200557 10.25 >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 GCGGGAACTTCAAGAGCAGCTAGATCTAGAGGGAAGTTGTGAGCATTACG 162 4.05 No Hit GGGAACTTCAAGAGCAGCTAGATCTAGAGGGAAGTTGTGAGCATTACGTT 135 3.375 No Hit CTGCGATGAAGGCGATAATAAATACAGAAGTTGCGGTCAATAAGGTAGGG 113 2.825 No Hit GCGGTCAATAAGGTAGGGATCATCAAAACACCGAACCATCCGATGTAAAG 79 1.975 No Hit GTGCTCTGCCTGGAATACAATCATAAAGTTGAAAGTACCAGATATTCCTA 67 1.675 No Hit CTGGAATACAATCATAAAGTTGAAAGTACCAGATATTCCTAAAGGCATAC 60 1.5 No Hit TCTGCCTGGAATACAATCATAAAGTTGAAAGTACCAGATATTCCTAAAGG 52 1.3 No Hit CGCGACCTTGACTATCAACTACAGATTGGTTGAAATTGAATCCATTTAGG 50 1.25 No Hit GTTGTGCTCTGCCTGGAATACAATCATAAAGTTGAAAGTACCAGATATTC 49 1.225 No Hit GCCTGGAATACAATCATAAAGTTGAAAGTACCAGATATTCCTAAAGGCAT 49 1.225 No Hit GCGATGAAGGCGATAATAAATACAGAAGTTGCGGTCAATAAGGTAGGGAT 45 1.125 No Hit CGGGAACTTCAAGAGCAGCTAGATCTAGAGGGAAGTTGTGAGCATTACGT 42 1.05 No Hit CGCAGAAGTAGGAATAATAGCACCAGAGATAATATTGTTTCCATAAAGTA 40 1.0 No Hit CGGTCAATAAGGTAGGGATCATCAAAACACCGAACCATCCGATGTAAAGA 39 0.975 No Hit ACGCGACCTTGACTATCAACTACAGATTGGTTGAAATTGAATCCATTTAG 37 0.9249999999999999 No Hit GATCGGAAGAGCACACGTCTGAACTCCAGTCACCAGCCTCGATCTCGTAT 36 0.8999999999999999 TruSeq Adapter, Index 10 (97% over 37bp) CAATAAGGTAGGGATCATCAAAACACCGAACCATCCGATGTAAAGACGAT 35 0.8750000000000001 No Hit GTCAATAAGGTAGGGATCATCAAAACACCGAACCATCCGATGTAAAGACG 35 0.8750000000000001 No Hit GCGACCTTGACTATCAACTACAGATTGGTTGAAATTGAATCCATTTAGGT 33 0.8250000000000001 No Hit GGTCAATAAGGTAGGGATCATCAAAACACCGAACCATCCGATGTAAAGAC 32 0.8 No Hit CTCTGCCTGGAATACAATCATAAAGTTGAAAGTACCAGATATTCCTAAAG 32 0.8 No Hit CGATGAAGGCGATAATAAATACAGAAGTTGCGGTCAATAAGGTAGGGATC 30 0.75 No Hit CTCGCGAATACCATCAATATCTACTGGAGGGGCTGCGATGAAGGCGATAA 28 0.7000000000000001 No Hit ATGAAGGCGATAATAAATACAGAAGTTGCGGTCAATAAGGTAGGGATCAT 26 0.65 No Hit ATAAGGATGTTGTGCTCTGCCTGGAATACAATCATAAAGTTGAAAGTACC 24 0.6 No Hit TTGTGCTCTGCCTGGAATACAATCATAAAGTTGAAAGTACCAGATATTCC 24 0.6 No Hit GGCGATAATAAATACAGAAGTTGCGGTCAATAAGGTAGGGATCATCAAAA 20 0.5 No Hit GCCGAAAACACCAGCTACACCTAACATGTGAAATGGATGCATAAGGATGT 19 0.475 No Hit CTCATTAGCAGATTCATTTTCAGTAGTTTCCCTGATCAAACTAGAGGTTA 18 0.44999999999999996 No Hit CGGAAAAACCTTATCCATTAATAGCGGGAACTTCAAGAGCAGCTAGATCT 17 0.42500000000000004 No Hit GGAGGGGCTGCGATGAAGGCGATAATAAATACAGAAGTTGCGGTCAATAA 16 0.4 No Hit CGTCTCTCTAAAATTGCAGTCATGGTAAGATCTTGGTTTATTCAAATTGC 16 0.4 No Hit GCCAAAATAACCATGAGCAGCCACAATATTATAAGTCTCTTCCTCTTGAC 16 0.4 No Hit GCGATAATAAATACAGAAGTTGCGGTCAATAAGGTAGGGATCATCAAAAC 15 0.375 No Hit TTCAAGAGCAGCTAGATCTAGAGGGAAGTTGTGAGCATTACGTTCGTGCA 15 0.375 No Hit TTTCTTTTCTTCAAAAATTCTTATATGTTAGCGGAAAAACCTTATCCATT 15 0.375 No Hit CGCTGGAGTAGGCTGCGAGGCCCAAGCGGCCAAGGAGTGCAGCGGCCCGT 15 0.375 No Hit GCTGCGATGAAGGCGATAATAAATACAGAAGTTGCGGTCAATAAGGTAGG 14 0.35000000000000003 No Hit CCACAATATTATAAGTCTCTTCCTCTTGACCAAATTTGTAACCCTCATTA 14 0.35000000000000003 No Hit CACCATTGTATAACCATTCATCAACGGATGCAGCTTCCCAAATTGGGTAA 14 0.35000000000000003 No Hit AGGGGCTGCGATGAAGGCGATAATAAATACAGAAGTTGCGGTCAATAAGG 14 0.35000000000000003 No Hit CTTTTCTTCAAAAATTCTTATATGTTAGCGGAAAAACCTTATCCATTAAT 13 0.325 No Hit GTAGGGATCATCAAAACACCGAACCATCCGATGTAAAGACGATTTTCAGT 13 0.325 No Hit GCTCTGCCTGGAATACAATCATAAAGTTGAAAGTACCAGATATTCCTAAA 13 0.325 No Hit GGGGCTGCGATGAAGGCGATAATAAATACAGAAGTTGCGGTCAATAAGGT 13 0.325 No Hit CGCGGGAACTTCAAGAGCAGCTAGATCTAGAGGGAAGTTGTGAGCATTAC 12 0.3 No Hit CTGCCTGGAATACAATCATAAAGTTGAAAGTACCAGATATTCCTAAAGGC 12 0.3 No Hit GCGGAAAAACCTTATCCATTAATAGCGGGAACTTCAAGAGCAGCTAGATC 12 0.3 No Hit CCCAAGTATTAATAACGCGACCTTGACTATCAACTACAGATTGGTTGAAA 11 0.27499999999999997 No Hit AATAAGGTAGGGATCATCAAAACACCGAACCATCCGATGTAAAGACGATT 10 0.25 No Hit CGCGTCTCTCTAAAATTGCAGTCATGGTAAGATCTTGGTTTATTCAAATT 10 0.25 No Hit GTGAGCATTACGTTCGTGCATTACTTCCATACCAAGATTAGCACGGTTGA 10 0.25 No Hit CCAAGTATTAATAACGCGACCTTGACTATCAACTACAGATTGGTTGAAAT 10 0.25 No Hit TGTGCTCTGCCTGGAATACAATCATAAAGTTGAAAGTACCAGATATTCCT 10 0.25 No Hit GGAACTTCAAGAGCAGCTAGATCTAGAGGGAAGTTGTGAGCATTACGTTC 10 0.25 No Hit TGCTCTGCCTGGAATACAATCATAAAGTTGAAAGTACCAGATATTCCTAA 9 0.22499999999999998 No Hit GGCCAAAATAACCATGAGCAGCCACAATATTATAAGTCTCTTCCTCTTGA 9 0.22499999999999998 No Hit GGAAAAACCTTATCCATTAATAGCGGGAACTTCAAGAGCAGCTAGATCTA 9 0.22499999999999998 No Hit GCGCGACCTTGACTATCAACTACAGATTGGTTGAAATTGAATCCATTTAG 9 0.22499999999999998 No Hit TGCGGGAACTTCAAGAGCAGCTAGATCTAGAGGGAAGTTGTGAGCATTAC 8 0.2 No Hit ATAAGGTAGGGATCATCAAAACACCGAACCATCCGATGTAAAGACGATTT 8 0.2 No Hit AGCGGGAACTTCAAGAGCAGCTAGATCTAGAGGGAAGTTGTGAGCATTAC 8 0.2 No Hit AATAAATACAGAAGTTGCGGTCAATAAGGTAGGGATCATCAAAACACCGA 8 0.2 No Hit CCGCAGAAGTAGGAATAATAGCACCAGAGATAATATTGTTTCCATAAAGT 7 0.17500000000000002 No Hit CTGGAGTAGGCTGCGAGGCCCAAGCGGCCAAGGAGTGCAGCGGCCCGTTA 7 0.17500000000000002 No Hit CGTGCTCTGCCTGGAATACAATCATAAAGTTGAAAGTACCAGATATTCCT 7 0.17500000000000002 No Hit TGATGATATCAGCCCAAGTATTAATAACGCGACCTTGACTATCAACTACA 7 0.17500000000000002 No Hit CCACCATTGTATAACCATTCATCAACGGATGCAGCTTCCCAAATTGGGTA 7 0.17500000000000002 No Hit GGGATCATCAAAACACCGAACCATCCGATGTAAAGACGATTTTCAGTGCT 7 0.17500000000000002 No Hit GCTAGTTATCCAGTTGCAGAAGCGACCCCACAGGCTTGTACTTTCGCGTC 7 0.17500000000000002 No Hit GGGCTGCGATGAAGGCGATAATAAATACAGAAGTTGCGGTCAATAAGGTA 7 0.17500000000000002 No Hit AAGAGCAGCTAGATCTAGAGGGAAGTTGTGAGCATTACGTTCGTGCATTA 7 0.17500000000000002 No Hit GTTGAAACTAGCATATTGGAAGATTAATCGGCCAAAATAACCATGAGCAG 7 0.17500000000000002 No Hit CGCGAATACCATCAATATCTACTGGAGGGGCTGCGATGAAGGCGATAATA 6 0.15 No Hit CGCCATAGTACTAATACCTAAAGCAGTGAACCAGATTCCTACTACAGGCC 6 0.15 No Hit GGCGCATACCCAAACGGAAACTAAGTTCCCACTCACGACCCATATAACAA 6 0.15 No Hit TGTTGTGCTCTGCCTGGAATACAATCATAAAGTTGAAAGTACCAGATATT 6 0.15 No Hit ATAAGGACCACCATTGTATAACCATTCATCAACGGATGCAGCTTCCCAAA 6 0.15 No Hit GGATGCATAAGGATGTTGTGCTCTGCCTGGAATACAATCATAAAGTTGAA 6 0.15 No Hit CGCAGCTGCAACAGGAGCTGAATATGCAACAGCAATCCAAGGGCGCATAC 6 0.15 No Hit GTTCGCTGGAGTAGGCTGCGAGGCCCAAGCGGCCAAGGAGTGCAGCGGCC 6 0.15 No Hit GGGGGCTGCGATGAAGGCGATAATAAATACAGAAGTTGCGGTCAATAAGG 6 0.15 No Hit CTTGACTATCAACTACAGATTGGTTGAAATTGAATCCATTTAGGTTGAAC 5 0.125 No Hit GCAGAAGTAGGAATAATAGCACCAGAGATAATATTGTTTCCATAAAGTAA 5 0.125 No Hit ATAATTAACTGCATTGATCTCGGTAGCTACGCCACCCACGGAATTTAAAG 5 0.125 No Hit CAAGTATTAATAACGCGACCTTGACTATCAACTACAGATTGGTTGAAATT 5 0.125 No Hit TTTTCTTCAAAAATTCTTATATGTTAGCGGAAAAACCTTATCCATTAATA 5 0.125 No Hit CACAATATTATAAGTCTCTTCCTCTTGACCAAATTTGTAACCCTCATTAG 5 0.125 No Hit CGCATACCCAAACGGAAACTAAGTTCCCACTCACGACCCATATAACAAGC 5 0.125 No Hit TAGTTATCCAGTTGCAGAAGCGACCCCACAGGCTTGTACTTTCGCGGCTC 5 0.125 No Hit CAGAAGTTGCGGTCAATAAGGTAGGGATCATCAAAACACCGAACCATCCG 5 0.125 No Hit GAAAAACCTTATCCATTAATAGCGGGAACTTCAAGAGCAGCTAGATCTAG 5 0.125 No Hit GTGCTAGTTATCCAGTTGCAGAAGCGACCCCACAGGCTTGTACTTTCGCG 5 0.125 No Hit GGACAAATAGCATAAAGAAATGTAACCAACGTTTGTTGGAAAAAGCAACA 5 0.125 No Hit CTTTCTTTTCTTCAAAAATTCTTATATGTTAGCGGAAAAACCTTATCCAT 5 0.125 No Hit GATGAAGGCGATAATAAATACAGAAGTTGCGGTCAATAAGGTAGGGATCA 5 0.125 No Hit CGCCGAAAACACCAGCTACACCTAACATGTGAAATGGATGCATAAGGATG 5 0.125 No Hit >>END_MODULE >>Adapter Content pass #Position Illumina Universal Adapter Illumina Small RNA 3' Adapter Illumina Small RNA 5' Adapter Nextera Transposase Sequence SOLID Small RNA Adapter 1 0.0 0.0 0.0 0.0 0.0 2 0.0 0.0 0.0 0.0 0.0 3 0.0 0.0 0.0 0.0 0.0 4 0.0 0.0 0.0 0.0 0.0 5 0.0 0.0 0.0 0.0 0.0 6 0.0 0.0 0.0 0.0 0.0 7 0.0 0.0 0.0 0.0 0.0 8 0.0 0.0 0.0 0.0 0.0 9 0.0 0.0 0.0 0.0 0.0 10 0.0 0.0 0.0 0.0 0.0 11 0.0 0.0 0.0 0.0 0.0 12 0.0 0.0 0.0 0.0 0.0 13 0.0 0.0 0.0 0.0 0.0 14 0.0 0.0 0.0 0.0 0.0 15 0.0 0.0 0.0 0.0 0.0 16 0.0 0.0 0.0 0.0 0.0 17 0.0 0.0 0.0 0.0 0.0 18 0.0 0.0 0.0 0.0 0.0 19 0.0 0.0 0.0 0.0 0.0 20 0.0 0.0 0.0 0.0 0.0 21 0.0 0.0 0.0 0.0 0.0 22 0.0 0.0 0.0 0.0 0.0 23 0.0 0.0 0.0 0.0 0.0 24 0.0 0.0 0.0 0.0 0.0 25 0.0 0.0 0.0 0.0 0.0 26 0.0 0.0 0.0 0.0 0.0 27 0.0 0.0 0.0 0.0 0.0 28 0.0 0.0 0.0 0.0 0.0 29 0.0 0.0 0.0 0.0 0.0 30 0.0 0.0 0.0 0.0 0.0 31 0.0 0.0 0.0 0.0 0.0 32 0.0 0.0 0.0 0.0 0.0 33 0.0 0.0 0.0 0.0 0.0 34 0.0 0.0 0.0 0.0 0.0 35 0.0 0.0 0.0 0.0 0.0 36 0.0 0.0 0.0 0.0 0.0 37 0.0 0.0 0.0 0.0 0.0 38 0.0 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position GCGGGAA 30 1.009108E-4 37.099155 1 CGGGAAC 35 2.499759E-4 31.799274 2 AAAGGCA 30 0.005116581 29.308332 43 AAGGCAT 30 0.005116581 29.308332 44 TTACGTT 30 0.005116581 29.308332 44 GGGAACT 55 0.0035058684 20.235903 3 TGTGAGC 55 0.0037800097 19.982954 38 CTTCAAG 55 0.0037800097 19.982954 8 CAAGAGC 55 0.0037800097 19.982954 11 TCAAGAG 55 0.0037800097 19.982954 10 TCTAGAG 55 0.0037800097 19.982954 25 TTCAAGA 55 0.0037800097 19.982954 9 ATCTAGA 55 0.0037800097 19.982954 24 AGAGGGA 55 0.0037800097 19.982954 28 GTGAGCA 55 0.0037800097 19.982954 39 AGGGAAG 55 0.0037800097 19.982954 30 AACTTCA 55 0.0037800097 19.982954 6 GAACTTC 55 0.0037800097 19.982954 5 GATCTAG 55 0.0037800097 19.982954 23 GGAAGTT 55 0.0037800097 19.982954 32 >>END_MODULE Read 1128101 spots for SRR1772228.sra Written 1128101 spots for SRR1772228.sra Read 1128101 spots for SRR1772228.sra Written 1128101 spots for SRR1772228.sra Read 1128101 spots for SRR1772228.sra Written 1128101 spots for SRR1772228.sra Read 1128101 spots for SRR1772228.sra Written 1128101 spots for SRR1772228.sra Read 1128101 spots for SRR1772228.sra Written 1128101 spots for SRR1772228.sra Read 1128101 spots for SRR1772228.sra Written 1128101 spots for SRR1772228.sra Read 1128101 spots for SRR1772228.sra Written 1128101 spots for SRR1772228.sra Read 1128101 spots for SRR1772228.sra Written 1128101 spots for SRR1772228.sra Read 1128101 spots for SRR1772228.sra Written 1128101 spots for SRR1772228.sra Read 1128101 spots for SRR1772228.sra Written 1128101 spots for SRR1772228.sra Read 1128120 spots for SRR1772228.sra Written 1128120 spots for SRR1772228.sra Read 1128101 spots for SRR1772228.sra Written 1128101 spots for SRR1772228.sra Read 1128101 spots for SRR1772228.sra Written 1128101 spots for SRR1772228.sra Read 1128101 spots for SRR1772228.sra Written 1128101 spots for SRR1772228.sra Read 1128101 spots for SRR1772228.sra Written 1128101 spots for SRR1772228.sra Read 1128101 spots for SRR1772228.sra Written 1128101 spots for SRR1772228.sra Read 1128101 spots for SRR1772228.sra Written 1128101 spots for SRR1772228.sra Read 1128101 spots for SRR1772228.sra Written 1128101 spots for SRR1772228.sra Read 1128101 spots for SRR1772228.sra Written 1128101 spots for SRR1772228.sra Read 1128101 spots for SRR1772228.sra Written 1128101 spots for SRR1772228.sra SRR ids: ['SRR1772228.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_kkt5qvfz SRR1772228.sra spots: 22562039 blocks: [[1, 1128101], [1128102, 2256202], [2256203, 3384303], [3384304, 4512404], [4512405, 5640505], [5640506, 6768606], [6768607, 7896707], [7896708, 9024808], [9024809, 10152909], [10152910, 11281010], [11281011, 12409111], [12409112, 13537212], [13537213, 14665313], [14665314, 15793414], [15793415, 16921515], [16921516, 18049616], [18049617, 19177717], [19177718, 20305818], [20305819, 21433919], [21433920, 22562039]] SRR1772228 file size 3899550 SRR1772228 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 SRR1772228 SRR1772228_1.fastq Input file: SRR1772228_1.fastq trimmed: SRR1772228-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 Sat Dec 7 19:24:11 2024 >> started Sat Dec 7 19:24:24 2024 >> done (13.274s) 22562039 reads processed; of these: 3205 ( 0.01%) short reads filtered out after trimming by size control 234212 ( 1.04%) empty reads filtered out after trimming by size control 22324622 (98.95%) reads available; of these: 1118765 ( 5.01%) trimmed reads available after processing 21205857 (94.99%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 2017 0.01% 19 2852 0.01% 20 6995 0.03% 21 6407 0.03% 22 7042 0.03% 23 6286 0.03% 24 8979 0.04% 25 10106 0.05% 26 8367 0.04% 27 12143 0.05% 28 14345 0.06% 29 22283 0.10% 30 19854 0.09% 31 21718 0.10% 32 25920 0.12% 33 16511 0.07% 34 17681 0.08% 35 20888 0.09% 36 20339 0.09% 37 29296 0.13% 38 21698 0.10% 39 25536 0.11% 40 44733 0.20% 41 35746 0.16% 42 73314 0.33% 43 61770 0.28% 44 77623 0.35% 45 77060 0.35% 46 90049 0.40% 47 108712 0.49% 48 119073 0.53% 49 103422 0.46% 50 21205857 94.99% 22324622 reads passed initial QC criterion=sequence-density sequence-density=0.30 sequence-density-rank=1 fanout-score=0.00 fanout-score-rank=20 prefix-density=0.00 prefix-fanout=1.0 sequence=TGCGGGAACTTC criterion=fanout-score sequence-density=0.01 sequence-density-rank=44 fanout-score=52.62 fanout-score-rank=1 prefix-density=0.07 prefix-fanout=3.6 sequence=TTTTTATTTAGACCTTCTTCATATTTAGTTTTATCTATTAATCGATAGTATCTACCGGCGCGAACTCGAATTTGATCGCCTTCCATACTTCACAAGCTGCGGCTAGTTCAGGACTCCATTTGCAAGCTGCTCGGATAATTTCATTACCTTCACGAGCAAGATCGC Started job on | Dec 07 19:24:33 Started mapping on | Dec 07 19:24:33 Finished on | Dec 07 19:24:49 Mapping speed, Million of reads per hour | 5023.04 Number of input reads | 22324622 Average input read length | 49 UNIQUE READS: Uniquely mapped reads number | 4689616 Uniquely mapped reads % | 21.01% Average mapped length | 49.41 Number of splices: Total | 294776 Number of splices: Annotated (sjdb) | 277977 Number of splices: GT/AG | 288992 Number of splices: GC/AG | 3565 Number of splices: AT/AC | 150 Number of splices: Non-canonical | 2069 Mismatch rate per base, % | 0.25% Deletion rate per base | 0.01% Deletion average length | 1.52 Insertion rate per base | 0.01% Insertion average length | 1.37 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 17325753 % of reads mapped to multiple loci | 77.61% Number of reads mapped to too many loci | 45197 % of reads mapped to too many loci | 0.20% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 1.17% % of reads unmapped: other | 0.01% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 309253 309253 309253 N_multimapping 17325753 17325753 17325753 N_noFeature 1070166 4551209 1140400 N_ambiguous 104647 923 36317 UnstrandedReadsAssigned:3514803 PositiveStrandReadsAssigned:137484 NegativeStrandReadsAssigned:3512899 Dataset is classified negative stranded MeadianReadLen=50 20thPercentileLength=50 echo kmer=45 SRR1772228 Starting Kallisto single end mapping to ensembl reference transcriptome. kmer=31 [quant] fragment length distribution is truncated gaussian with mean = 100, sd = 20 [index] k-mer length: 31 [index] number of targets: 52,972 [index] number of k-mers: 66,720,672 [index] number of equivalence classes: 111,837 [quant] running in single-end mode [quant] will process file 1: SRR1772228-trimmed.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 22,324,622 reads, 19,277,979 reads pseudoaligned [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 982 rounds 52973 SRR1772228.ke.tsv 35125 SRR1772228.se.tsv 88098 total ==> SRR1772228.ke.tsv <== target_id length eff_length est_counts tpm PNS24245 936 837 0 0 PNS24247 1044 945 2.74264 0.167895 PNS24249 1928 1829 37.7721 1.1947 PNS24246 1044 945 2.74264 0.167895 PNS24248 1044 945 2.74264 0.167895 PNS24244 1471 1372 0 0 PNS24243 293 194 0 0 KQK14069 1603 1504 105.765 4.06813 KQK14071 474 375 17.8898 2.75978 ==> SRR1772228.se.tsv <== BRADI_1g14170v3 199 BRADI_1g53295v3 6 BRADI_1g59795v3 29 BRADI_1g07683v3 0 BRADI_1g00485v3 0 BRADI_1g20270v3 19 BRADI_1g74790v3 6 BRADI_1g09890v3 0 BRADI_1g77505v3 31 BRADI_1g48960v3 0 SRR1772228 completed mapping pipeline successfully