Starting /dee2/code/volunteer_pipeline.sh SRR1772238 current disk space = 1552302858240 free memory = 1604609364 SRR1772238 SRAfilesize 327f968b14a3bbe3c71d52a59b8072ad SRR1772238.sra SRR1772238.sra file validated SRR1772238 is single end SRR1772238 is conventional basespace SRR1772238 read1 length is 50 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR1772238_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 32.8215 34.0 31.0 34.0 31.0 34.0 2 33.12075 34.0 33.0 34.0 31.0 34.0 3 33.1065 34.0 33.0 34.0 31.0 34.0 4 36.51 37.0 37.0 37.0 35.0 37.0 5 36.45175 37.0 37.0 37.0 35.0 37.0 6 36.34175 37.0 37.0 37.0 35.0 37.0 7 36.4045 37.0 37.0 37.0 35.0 37.0 8 36.4405 37.0 37.0 37.0 35.0 37.0 9 38.2215 39.0 39.0 39.0 37.0 39.0 10 38.258 39.0 39.0 39.0 37.0 39.0 11 38.27875 39.0 39.0 39.0 37.0 39.0 12 38.1635 39.0 39.0 39.0 37.0 39.0 13 38.132 39.0 39.0 39.0 37.0 39.0 14 39.71925 41.0 40.0 41.0 37.0 41.0 15 39.64175 41.0 40.0 41.0 37.0 41.0 16 39.69725 41.0 40.0 41.0 37.0 41.0 17 39.635 41.0 40.0 41.0 37.0 41.0 18 39.70975 41.0 40.0 41.0 37.0 41.0 19 39.55125 41.0 40.0 41.0 37.0 41.0 20 39.50675 41.0 40.0 41.0 36.0 41.0 21 39.4575 41.0 39.0 41.0 37.0 41.0 22 39.5235 41.0 40.0 41.0 37.0 41.0 23 39.5145 41.0 40.0 41.0 37.0 41.0 24 39.4845 41.0 39.0 41.0 37.0 41.0 25 39.3515 41.0 39.0 41.0 36.0 41.0 26 39.23225 41.0 39.0 41.0 36.0 41.0 27 39.053 41.0 39.0 41.0 36.0 41.0 28 39.0025 40.0 39.0 41.0 36.0 41.0 29 39.0695 40.0 39.0 41.0 36.0 41.0 30 38.854 40.0 39.0 41.0 36.0 41.0 31 38.82225 40.0 39.0 41.0 35.0 41.0 32 38.6635 40.0 38.0 41.0 35.0 41.0 33 38.5595 40.0 38.0 41.0 35.0 41.0 34 38.46975 40.0 38.0 41.0 34.0 41.0 35 38.77675 40.0 39.0 41.0 35.0 41.0 36 38.7035 40.0 38.0 41.0 35.0 41.0 37 38.654 40.0 39.0 41.0 35.0 41.0 38 38.6705 40.0 38.0 41.0 35.0 41.0 39 38.49275 40.0 38.0 41.0 35.0 41.0 40 38.399 40.0 38.0 41.0 35.0 41.0 41 38.48725 40.0 38.0 41.0 35.0 41.0 42 38.479 40.0 38.0 41.0 35.0 41.0 43 38.269 40.0 38.0 41.0 34.0 41.0 44 38.09 40.0 38.0 41.0 34.0 41.0 45 37.88725 40.0 38.0 41.0 33.0 41.0 46 37.90425 40.0 38.0 41.0 34.0 41.0 47 37.719 40.0 38.0 41.0 33.0 41.0 48 37.64775 40.0 38.0 41.0 33.0 41.0 49 37.53 40.0 38.0 41.0 33.0 41.0 50 37.30475 40.0 38.0 41.0 33.0 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 13 1.0 14 0.0 15 1.0 16 2.0 17 3.0 18 2.0 19 6.0 20 4.0 21 7.0 22 7.0 23 4.0 24 7.0 25 10.0 26 8.0 27 3.0 28 19.0 29 25.0 30 34.0 31 44.0 32 53.0 33 62.0 34 109.0 35 135.0 36 184.0 37 265.0 38 575.0 39 2430.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 38.725 11.5 13.5 36.275 2 27.950000000000003 11.924999999999999 29.849999999999998 30.275000000000002 3 37.293646823411706 17.208604302151077 17.608804402201102 27.888944472236116 4 32.025 27.925 16.25 23.799999999999997 5 29.75 32.425 20.075000000000003 17.75 6 23.075000000000003 34.925 18.975 23.025000000000002 7 11.375 38.824999999999996 34.8 15.0 8 20.575 29.025000000000002 29.049999999999997 21.349999999999998 9 20.575 20.525 33.2 25.7 10 15.85 45.574999999999996 23.400000000000002 15.174999999999999 11 25.6 33.300000000000004 18.55 22.55 12 26.275 29.349999999999998 22.175 22.2 13 17.125 38.85 24.125 19.900000000000002 14 23.9 32.05 26.674999999999997 17.375 15 19.45 35.125 21.85 23.575 16 21.675 36.925000000000004 22.225 19.175 17 23.575 33.975 22.625 19.825 18 17.075000000000003 36.95 23.549999999999997 22.425 19 18.525 34.9 26.125 20.45 20 15.675 35.925000000000004 26.974999999999998 21.425 21 18.9 29.799999999999997 27.85 23.45 22 14.228557139284822 42.41060265066267 22.455613903475868 20.905226306576644 23 19.025 35.5 26.450000000000003 19.025 24 17.775 34.699999999999996 22.225 25.3 25 17.775 34.4 26.8 21.025 26 17.849999999999998 38.45 22.475 21.224999999999998 27 24.45 30.825000000000003 25.900000000000002 18.825 28 24.95 39.5 19.725 15.825 29 26.35 32.300000000000004 23.05 18.3 30 25.05 31.4 25.05 18.5 31 29.5 25.8 23.175 21.525 32 23.95598899724931 31.50787696924231 24.281070267566893 20.255063765941486 33 25.481370342585645 35.00875218804701 19.254813703425857 20.255063765941486 34 23.305826456614152 35.0587646911728 20.080020005001252 21.555388847211805 35 20.349999999999998 35.65 24.224999999999998 19.775000000000002 36 20.735367683841922 28.289144572286144 30.14007003501751 20.83541770885443 37 24.354798296166376 28.614382360310696 28.564269606614882 18.466549736908043 38 19.075 28.4 30.2 22.325 39 23.849999999999998 26.35 27.55 22.25 40 16.900000000000002 35.275 26.924999999999997 20.9 41 22.075 29.725 26.950000000000003 21.25 42 20.375469336670836 31.889862327909885 24.005006257822277 23.729662077597 43 20.025000000000002 34.4 23.625 21.95 44 19.759879939969984 30.240120060030012 27.763881940970485 22.236118059029515 45 20.511534603811434 29.739217652958878 31.94583751253761 17.803410230692077 46 19.333834209867266 29.601803155522166 32.70723766591535 18.357124968695217 47 21.348033074417437 33.47531946880481 26.634928589325984 18.541718867451767 48 23.58089522380595 32.6081520380095 23.48087021755439 20.330082520630157 49 21.925 32.675 25.474999999999998 19.925 50 25.4 28.525 26.85 19.225 >>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 0.0 10 0.0 11 1.0 12 2.0 13 1.0 14 0.0 15 1.0 16 2.0 17 1.5 18 1.0 19 3.5 20 6.0 21 6.5 22 7.0 23 9.5 24 12.0 25 33.0 26 54.0 27 44.0 28 34.0 29 37.0 30 40.0 31 55.5 32 71.0 33 138.0 34 205.0 35 285.5 36 366.0 37 462.5 38 559.0 39 444.5 40 330.0 41 332.0 42 334.0 43 405.5 44 477.0 45 458.5 46 440.0 47 315.0 48 190.0 49 267.5 50 345.0 51 226.5 52 108.0 53 100.0 54 92.0 55 76.0 56 60.0 57 49.5 58 39.0 59 46.0 60 53.0 61 42.5 62 32.0 63 28.5 64 25.0 65 26.5 66 28.0 67 22.5 68 17.0 69 18.0 70 19.0 71 20.5 72 22.0 73 14.0 74 6.0 75 7.5 76 9.0 77 7.5 78 6.0 79 5.0 80 4.0 81 3.0 82 2.0 83 1.0 84 0.0 85 1.0 86 2.0 87 1.0 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 0.0 2 0.0 3 0.05 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 0.025 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 0.025 33 0.025 34 0.025 35 0.0 36 0.05 37 0.22499999999999998 38 0.0 39 0.0 40 0.0 41 0.0 42 0.125 43 0.0 44 0.05 45 0.3 46 0.17500000000000002 47 0.22499999999999998 48 0.025 49 0.0 50 0.0 >>END_MODULE >>Sequence Length Distribution pass #Length Count 50 4000.0 >>END_MODULE >>Sequence Duplication Levels fail #Total Deduplicated Percentage 47.199999999999996 #Duplication Level Percentage of deduplicated Percentage of total 1 82.94491525423729 39.15 2 7.309322033898305 6.9 3 2.860169491525424 4.05 4 1.5360169491525424 2.9000000000000004 5 0.9533898305084746 2.25 6 0.6885593220338982 1.95 7 0.211864406779661 0.7000000000000001 8 0.31779661016949157 1.2 9 0.31779661016949157 1.35 >10 2.5423728813559325 26.0 >50 0.211864406779661 7.449999999999999 >100 0.1059322033898305 6.1 >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 130 3.25 No Hit GGGAACTTCAAGAGCAGCTAGATCTAGAGGGAAGTTGTGAGCATTACGTT 114 2.85 No Hit CTGCGATGAAGGCGATAATAAATACAGAAGTTGCGGTCAATAAGGTAGGG 98 2.45 No Hit GCGGTCAATAAGGTAGGGATCATCAAAACACCGAACCATCCGATGTAAAG 71 1.775 No Hit GTGCTCTGCCTGGAATACAATCATAAAGTTGAAAGTACCAGATATTCCTA 66 1.6500000000000001 No Hit GATCGGAAGAGCACACGTCTGAACTCCAGTCACCATGCCTAATCTCGTAT 63 1.575 TruSeq Adapter, Index 12 (97% over 37bp) TCTGCCTGGAATACAATCATAAAGTTGAAAGTACCAGATATTCCTAAAGG 49 1.225 No Hit GCCTGGAATACAATCATAAAGTTGAAAGTACCAGATATTCCTAAAGGCAT 48 1.2 No Hit GCGATGAAGGCGATAATAAATACAGAAGTTGCGGTCAATAAGGTAGGGAT 46 1.15 No Hit CGGTCAATAAGGTAGGGATCATCAAAACACCGAACCATCCGATGTAAAGA 44 1.0999999999999999 No Hit CGCGACCTTGACTATCAACTACAGATTGGTTGAAATTGAATCCATTTAGG 42 1.05 No Hit CGGGAACTTCAAGAGCAGCTAGATCTAGAGGGAAGTTGTGAGCATTACGT 41 1.0250000000000001 No Hit GTTGTGCTCTGCCTGGAATACAATCATAAAGTTGAAAGTACCAGATATTC 37 0.9249999999999999 No Hit GCGACCTTGACTATCAACTACAGATTGGTTGAAATTGAATCCATTTAGGT 36 0.8999999999999999 No Hit ACGCGACCTTGACTATCAACTACAGATTGGTTGAAATTGAATCCATTTAG 36 0.8999999999999999 No Hit GTCAATAAGGTAGGGATCATCAAAACACCGAACCATCCGATGTAAAGACG 33 0.8250000000000001 No Hit CTGGAATACAATCATAAAGTTGAAAGTACCAGATATTCCTAAAGGCATAC 31 0.775 No Hit CGCAGAAGTAGGAATAATAGCACCAGAGATAATATTGTTTCCATAAAGTA 28 0.7000000000000001 No Hit CCCAAGTATTAATAACGCGACCTTGACTATCAACTACAGATTGGTTGAAA 26 0.65 No Hit CTCTGCCTGGAATACAATCATAAAGTTGAAAGTACCAGATATTCCTAAAG 26 0.65 No Hit CTCGCGAATACCATCAATATCTACTGGAGGGGCTGCGATGAAGGCGATAA 26 0.65 No Hit GGCGATAATAAATACAGAAGTTGCGGTCAATAAGGTAGGGATCATCAAAA 25 0.625 No Hit ATAAGGATGTTGTGCTCTGCCTGGAATACAATCATAAAGTTGAAAGTACC 25 0.625 No Hit GGCCAAAATAACCATGAGCAGCCACAATATTATAAGTCTCTTCCTCTTGA 23 0.575 No Hit CAATAAGGTAGGGATCATCAAAACACCGAACCATCCGATGTAAAGACGAT 22 0.5499999999999999 No Hit CGATGAAGGCGATAATAAATACAGAAGTTGCGGTCAATAAGGTAGGGATC 22 0.5499999999999999 No Hit GGTCAATAAGGTAGGGATCATCAAAACACCGAACCATCCGATGTAAAGAC 19 0.475 No Hit CTGCCTGGAATACAATCATAAAGTTGAAAGTACCAGATATTCCTAAAGGC 19 0.475 No Hit TTTCTTTTCTTCAAAAATTCTTATATGTTAGCGGAAAAACCTTATCCATT 18 0.44999999999999996 No Hit CGGAAAAACCTTATCCATTAATAGCGGGAACTTCAAGAGCAGCTAGATCT 18 0.44999999999999996 No Hit GGAAAAACCTTATCCATTAATAGCGGGAACTTCAAGAGCAGCTAGATCTA 17 0.42500000000000004 No Hit GCGGAAAAACCTTATCCATTAATAGCGGGAACTTCAAGAGCAGCTAGATC 17 0.42500000000000004 No Hit TTCAAGAGCAGCTAGATCTAGAGGGAAGTTGTGAGCATTACGTTCGTGCA 15 0.375 No Hit GCCAAAATAACCATGAGCAGCCACAATATTATAAGTCTCTTCCTCTTGAC 15 0.375 No Hit GCTGCGATGAAGGCGATAATAAATACAGAAGTTGCGGTCAATAAGGTAGG 14 0.35000000000000003 No Hit TTGTGCTCTGCCTGGAATACAATCATAAAGTTGAAAGTACCAGATATTCC 14 0.35000000000000003 No Hit GGAGGGGCTGCGATGAAGGCGATAATAAATACAGAAGTTGCGGTCAATAA 13 0.325 No Hit CGCGGGAACTTCAAGAGCAGCTAGATCTAGAGGGAAGTTGTGAGCATTAC 13 0.325 No Hit TGCGGTCAATAAGGTAGGGATCATCAAAACACCGAACCATCCGATGTAAA 13 0.325 No Hit TGTGCTCTGCCTGGAATACAATCATAAAGTTGAAAGTACCAGATATTCCT 13 0.325 No Hit CTCATTAGCAGATTCATTTTCAGTAGTTTCCCTGATCAAACTAGAGGTTA 13 0.325 No Hit GCTCTGCCTGGAATACAATCATAAAGTTGAAAGTACCAGATATTCCTAAA 13 0.325 No Hit GCCGAAAACACCAGCTACACCTAACATGTGAAATGGATGCATAAGGATGT 12 0.3 No Hit GGGGCTGCGATGAAGGCGATAATAAATACAGAAGTTGCGGTCAATAAGGT 12 0.3 No Hit CTTTTCTTCAAAAATTCTTATATGTTAGCGGAAAAACCTTATCCATTAAT 11 0.27499999999999997 No Hit GCGATAATAAATACAGAAGTTGCGGTCAATAAGGTAGGGATCATCAAAAC 11 0.27499999999999997 No Hit CCACCATTGTATAACCATTCATCAACGGATGCAGCTTCCCAAATTGGGTA 11 0.27499999999999997 No Hit TAGTTATCCAGTTGCAGAAGCGACCCCACAGGCTTGTACTTTCGCGGCTC 11 0.27499999999999997 No Hit CCACAATATTATAAGTCTCTTCCTCTTGACCAAATTTGTAACCCTCATTA 11 0.27499999999999997 No Hit AATAAATACAGAAGTTGCGGTCAATAAGGTAGGGATCATCAAAACACCGA 11 0.27499999999999997 No Hit AATAAGGTAGGGATCATCAAAACACCGAACCATCCGATGTAAAGACGATT 10 0.25 No Hit CGCGAATACCATCAATATCTACTGGAGGGGCTGCGATGAAGGCGATAATA 10 0.25 No Hit CGCGGTCAATAAGGTAGGGATCATCAAAACACCGAACCATCCGATGTAAA 10 0.25 No Hit TAGTTATCCAGTTGCAGAAGCGACCCCACAGGCTTGTACTTTCGCGTCTC 10 0.25 No Hit CGCCATAGTACTAATACCTAAAGCAGTGAACCAGATTCCTACTACAGGCC 9 0.22499999999999998 No Hit TGATGATATCAGCCCAAGTATTAATAACGCGACCTTGACTATCAACTACA 9 0.22499999999999998 No Hit GGGATCATCAAAACACCGAACCATCCGATGTAAAGACGATTTTCAGTGCT 9 0.22499999999999998 No Hit GCGAATACCATCAATATCTACTGGAGGGGCTGCGATGAAGGCGATAATAA 9 0.22499999999999998 No Hit CTTTCTTTTCTTCAAAAATTCTTATATGTTAGCGGAAAAACCTTATCCAT 9 0.22499999999999998 No Hit GGAACTTCAAGAGCAGCTAGATCTAGAGGGAAGTTGTGAGCATTACGTTC 9 0.22499999999999998 No Hit GTTGCGGTCAATAAGGTAGGGATCATCAAAACACCGAACCATCCGATGTA 8 0.2 No Hit GCGCGACCTTGACTATCAACTACAGATTGGTTGAAATTGAATCCATTTAG 8 0.2 No Hit GTTGATGATATCAGCCCAAGTATTAATAACGCGACCTTGACTATCAACTA 8 0.2 No Hit CTCTTGACCAAATTTGTAACCCTCATTAGCAGATTCATTTTCAGTAGTTT 8 0.2 No Hit GTTGAAACTAGCATATTGGAAGATTAATCGGCCAAAATAACCATGAGCAG 8 0.2 No Hit CACCATTGTATAACCATTCATCAACGGATGCAGCTTCCCAAATTGGGTAA 8 0.2 No Hit CAAGTATTAATAACGCGACCTTGACTATCAACTACAGATTGGTTGAAATT 7 0.17500000000000002 No Hit GTGAGCATTACGTTCGTGCATTACTTCCATACCAAGATTAGCACGGTTGA 7 0.17500000000000002 No Hit CGCTGGAGTAGGCTGCGAGGCCCAAGCGGCCAAGGAGTGCAGCGGCCCGT 7 0.17500000000000002 No Hit AGCAGCCACAATATTATAAGTCTCTTCCTCTTGACCAAATTTGTAACCCT 7 0.17500000000000002 No Hit CTTCCTCTTGACCAAATTTGTAACCCTCATTAGCAGATTCATTTTCAGTA 6 0.15 No Hit CTTGACTATCAACTACAGATTGGTTGAAATTGAATCCATTTAGGTTGAAC 6 0.15 No Hit GCAGAAGTAGGAATAATAGCACCAGAGATAATATTGTTTCCATAAAGTAA 6 0.15 No Hit TGTTGTGCTCTGCCTGGAATACAATCATAAAGTTGAAAGTACCAGATATT 6 0.15 No Hit TGCGGGAACTTCAAGAGCAGCTAGATCTAGAGGGAAGTTGTGAGCATTAC 6 0.15 No Hit TTCTTTTCTTCAAAAATTCTTATATGTTAGCGGAAAAACCTTATCCATTA 6 0.15 No Hit CCATTGTATAACCATTCATCAACGGATGCAGCTTCCCAAATTGGGTAAAA 6 0.15 No Hit CGCAGCTGCAACAGGAGCTGAATATGCAACAGCAATCCAAGGGCGCATAC 6 0.15 No Hit CCAAGTATTAATAACGCGACCTTGACTATCAACTACAGATTGGTTGAAAT 6 0.15 No Hit GCTAGATCTAGAGGGAAGTTGTGAGCATTACGTTCGTGCATTACTTCCAT 6 0.15 No Hit CACGGTTGATGATATCAGCCCAAGTATTAATAACGCGACCTTGACTATCA 6 0.15 No Hit TGCGATGAAGGCGATAATAAATACAGAAGTTGCGGTCAATAAGGTAGGGA 6 0.15 No Hit ATAACAAGCTACACCAAGTAAGAAGTGTAGAACAATTAGCTCATAAGGAC 6 0.15 No Hit CCGCAGAAGTAGGAATAATAGCACCAGAGATAATATTGTTTCCATAAAGT 5 0.125 No Hit TGCTCTGCCTGGAATACAATCATAAAGTTGAAAGTACCAGATATTCCTAA 5 0.125 No Hit ATTACGTTCGTGCATTACTTCCATACCAAGATTAGCACGGTTGATGATAT 5 0.125 No Hit ATGAAGGCGATAATAAATACAGAAGTTGCGGTCAATAAGGTAGGGATCAT 5 0.125 No Hit GATGATATCAGCCCAAGTATTAATAACGCGACCTTGACTATCAACTACAG 5 0.125 No Hit CTACAGATTGGTTGAAATTGAATCCATTTAGGTTGAACGCCATAGTACTA 5 0.125 No Hit ATAAGGTAGGGATCATCAAAACACCGAACCATCCGATGTAAAGACGATTT 5 0.125 No Hit CACAATATTATAAGTCTCTTCCTCTTGACCAAATTTGTAACCCTCATTAG 5 0.125 No Hit CGCATACCCAAACGGAAACTAAGTTCCCACTCACGACCCATATAACAAGC 5 0.125 No Hit ATGATATCAGCCCAAGTATTAATAACGCGACCTTGACTATCAACTACAGA 5 0.125 No Hit CTCATAAGGACCACCATTGTATAACCATTCATCAACGGATGCAGCTTCCC 5 0.125 No Hit TGCCTGGAATACAATCATAAAGTTGAAAGTACCAGATATTCCTAAAGGCA 5 0.125 No Hit ATAATAAATACAGAAGTTGCGGTCAATAAGGTAGGGATCATCAAAACACC 5 0.125 No Hit ATCAATATCTACTGGAGGGGCTGCGATGAAGGCGATAATAAATACAGAAG 5 0.125 No Hit TAAAGAACGAGAGTTGTTGAAACTAGCATATTGGAAGATTAATCGGCCAA 5 0.125 No Hit TTGACTATCAACTACAGATTGGTTGAAATTGAATCCATTTAGGTTGAACG 5 0.125 No Hit GATGAAGGCGATAATAAATACAGAAGTTGCGGTCAATAAGGTAGGGATCA 5 0.125 No Hit GCCAAGAAGAAGTGTAAAGAACGAGAGTTGTTGAAACTAGCATATTGGAA 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 pass >>END_MODULE Read 953402 spots for SRR1772238.sra Written 953402 spots for SRR1772238.sra Read 953402 spots for SRR1772238.sra Written 953402 spots for SRR1772238.sra Read 953402 spots for SRR1772238.sra Written 953402 spots for SRR1772238.sra Read 953402 spots for SRR1772238.sra Written 953402 spots for SRR1772238.sra Read 953402 spots for SRR1772238.sra Written 953402 spots for SRR1772238.sra Read 953402 spots for SRR1772238.sra Written 953402 spots for SRR1772238.sra Read 953402 spots for SRR1772238.sra Written 953402 spots for SRR1772238.sra Read 953402 spots for SRR1772238.sra Written 953402 spots for SRR1772238.sra Read 953402 spots for SRR1772238.sra Written 953402 spots for SRR1772238.sra Read 953402 spots for SRR1772238.sra Written 953402 spots for SRR1772238.sra Read 953402 spots for SRR1772238.sra Written 953402 spots for SRR1772238.sra Read 953402 spots for SRR1772238.sra Written 953402 spots for SRR1772238.sra Read 953402 spots for SRR1772238.sra Written 953402 spots for SRR1772238.sra Read 953402 spots for SRR1772238.sra Written 953402 spots for SRR1772238.sra Read 953402 spots for SRR1772238.sra Written 953402 spots for SRR1772238.sra Read 953402 spots for SRR1772238.sra Written 953402 spots for SRR1772238.sra Read 953402 spots for SRR1772238.sra Written 953402 spots for SRR1772238.sra Read 953402 spots for SRR1772238.sra Written 953402 spots for SRR1772238.sra Read 953402 spots for SRR1772238.sra Written 953402 spots for SRR1772238.sra Read 953407 spots for SRR1772238.sra Written 953407 spots for SRR1772238.sra SRR ids: ['SRR1772238.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_jhz56hwt SRR1772238.sra spots: 19068045 blocks: [[1, 953402], [953403, 1906804], [1906805, 2860206], [2860207, 3813608], [3813609, 4767010], [4767011, 5720412], [5720413, 6673814], [6673815, 7627216], [7627217, 8580618], [8580619, 9534020], [9534021, 10487422], [10487423, 11440824], [11440825, 12394226], [12394227, 13347628], [13347629, 14301030], [14301031, 15254432], [15254433, 16207834], [16207835, 17161236], [17161237, 18114638], [18114639, 19068045]] SRR1772238 file size 3293976 SRR1772238 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 SRR1772238 SRR1772238_1.fastq Input file: SRR1772238_1.fastq trimmed: SRR1772238-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 Fri Dec 6 09:48:56 2024 >> started Fri Dec 6 09:49:07 2024 >> done (11.276s) 19068045 reads processed; of these: 1852 ( 0.01%) short reads filtered out after trimming by size control 277237 ( 1.45%) empty reads filtered out after trimming by size control 18788956 (98.54%) reads available; of these: 807679 ( 4.30%) trimmed reads available after processing 17981277 (95.70%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 1046 0.01% 19 1596 0.01% 20 4083 0.02% 21 3461 0.02% 22 4063 0.02% 23 4192 0.02% 24 5198 0.03% 25 6686 0.04% 26 6755 0.04% 27 8927 0.05% 28 8334 0.04% 29 14830 0.08% 30 14080 0.07% 31 11523 0.06% 32 19010 0.10% 33 12016 0.06% 34 12639 0.07% 35 14117 0.08% 36 13926 0.07% 37 21754 0.12% 38 15645 0.08% 39 18905 0.10% 40 26172 0.14% 41 24264 0.13% 42 41655 0.22% 43 43101 0.23% 44 62652 0.33% 45 62594 0.33% 46 73054 0.39% 47 82331 0.44% 48 92220 0.49% 49 76850 0.41% 50 17981277 95.70% 18788956 reads passed initial QC criterion=sequence-density sequence-density=0.28 sequence-density-rank=1 fanout-score=0.00 fanout-score-rank=19 prefix-density=0.00 prefix-fanout=1.0 sequence=TGCGGGAACTTC criterion=fanout-score sequence-density=0.08 sequence-density-rank=5 fanout-score=14.91 fanout-score-rank=1 prefix-density=1.16 prefix-fanout=1.0 sequence=TCTCTAAAATTTCAGTCATGGTA Started job on | Dec 06 09:50:23 Started mapping on | Dec 06 09:50:23 Finished on | Dec 06 09:50:37 Mapping speed, Million of reads per hour | 4831.45 Number of input reads | 18788956 Average input read length | 49 UNIQUE READS: Uniquely mapped reads number | 3911791 Uniquely mapped reads % | 20.82% Average mapped length | 49.48 Number of splices: Total | 212957 Number of splices: Annotated (sjdb) | 199742 Number of splices: GT/AG | 208203 Number of splices: GC/AG | 2839 Number of splices: AT/AC | 111 Number of splices: Non-canonical | 1804 Mismatch rate per base, % | 0.25% Deletion rate per base | 0.01% Deletion average length | 1.45 Insertion rate per base | 0.01% Insertion average length | 1.33 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 14505224 % of reads mapped to multiple loci | 77.20% Number of reads mapped to too many loci | 157830 % of reads mapped to too many loci | 0.84% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 1.12% % of reads unmapped: other | 0.02% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 371941 371941 371941 N_multimapping 14505224 14505224 14505224 N_noFeature 963853 3797677 1025243 N_ambiguous 77541 860 24639 UnstrandedReadsAssigned:2870397 PositiveStrandReadsAssigned:113254 NegativeStrandReadsAssigned:2861909 Dataset is classified negative stranded MeadianReadLen=50 20thPercentileLength=50 echo kmer=45 SRR1772238 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: SRR1772238-trimmed.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 18,788,956 reads, 15,805,414 reads pseudoaligned [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 981 rounds 52973 SRR1772238.ke.tsv 35125 SRR1772238.se.tsv 88098 total ==> SRR1772238.ke.tsv <== target_id length eff_length est_counts tpm PNS24245 936 837 0 0 PNS24247 1044 945 2.84342 0.20963 PNS24249 1928 1829 26.4697 1.00828 PNS24246 1044 945 2.84342 0.20963 PNS24248 1044 945 2.84342 0.20963 PNS24244 1471 1372 0 0 PNS24243 293 194 0 0 KQK14069 1603 1504 332.85 15.4186 KQK14071 474 375 52.1767 9.69369 ==> SRR1772238.se.tsv <== BRADI_1g14170v3 548 BRADI_1g53295v3 0 BRADI_1g59795v3 22 BRADI_1g07683v3 0 BRADI_1g00485v3 0 BRADI_1g20270v3 18 BRADI_1g74790v3 3 BRADI_1g09890v3 0 BRADI_1g77505v3 15 BRADI_1g48960v3 0 SRR1772238 completed mapping pipeline successfully