Starting /dee2/code/volunteer_pipeline.sh SRR1772236 current disk space = 1552298889216 free memory = 1605419832 SRR1772236 SRAfilesize 18351fed0eda358e294d3b1dbe2976ac SRR1772236.sra SRR1772236.sra file validated SRR1772236 is single end SRR1772236 is conventional basespace SRR1772236 read1 length is 50 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR1772236_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 44 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 32.7415 34.0 31.0 34.0 31.0 34.0 2 33.07 34.0 33.0 34.0 31.0 34.0 3 33.05425 34.0 33.0 34.0 31.0 34.0 4 36.4565 37.0 37.0 37.0 35.0 37.0 5 36.4045 37.0 37.0 37.0 35.0 37.0 6 36.265 37.0 37.0 37.0 35.0 37.0 7 36.36325 37.0 37.0 37.0 35.0 37.0 8 36.36175 37.0 37.0 37.0 35.0 37.0 9 38.1725 39.0 39.0 39.0 37.0 39.0 10 38.1485 39.0 39.0 39.0 37.0 39.0 11 38.13775 39.0 39.0 39.0 37.0 39.0 12 38.09925 39.0 39.0 39.0 35.0 39.0 13 38.0665 39.0 38.0 39.0 35.0 39.0 14 39.57075 41.0 40.0 41.0 37.0 41.0 15 39.5455 41.0 40.0 41.0 37.0 41.0 16 39.50025 41.0 40.0 41.0 37.0 41.0 17 39.52425 41.0 40.0 41.0 37.0 41.0 18 39.53425 41.0 40.0 41.0 37.0 41.0 19 39.414 41.0 39.0 41.0 36.0 41.0 20 39.39475 41.0 39.0 41.0 36.0 41.0 21 39.35175 41.0 39.0 41.0 36.0 41.0 22 39.35325 41.0 39.0 41.0 36.0 41.0 23 39.34825 41.0 39.0 41.0 36.0 41.0 24 39.257 41.0 39.0 41.0 36.0 41.0 25 39.12425 41.0 39.0 41.0 36.0 41.0 26 38.94675 41.0 39.0 41.0 36.0 41.0 27 38.96925 41.0 39.0 41.0 35.0 41.0 28 38.79075 40.0 38.0 41.0 35.0 41.0 29 38.8255 40.0 39.0 41.0 35.0 41.0 30 38.6805 40.0 38.0 41.0 35.0 41.0 31 38.55375 40.0 38.0 41.0 35.0 41.0 32 38.43525 40.0 38.0 41.0 34.0 41.0 33 38.247 40.0 38.0 41.0 34.0 41.0 34 38.22925 40.0 38.0 41.0 34.0 41.0 35 38.53125 40.0 38.0 41.0 35.0 41.0 36 38.50575 40.0 38.0 41.0 35.0 41.0 37 38.312 40.0 38.0 41.0 35.0 41.0 38 38.27075 40.0 38.0 41.0 34.0 41.0 39 37.95275 40.0 38.0 41.0 33.0 41.0 40 37.93425 40.0 38.0 41.0 33.0 41.0 41 37.97175 40.0 38.0 41.0 33.0 41.0 42 38.03625 40.0 38.0 41.0 34.0 41.0 43 37.8325 40.0 38.0 41.0 33.0 41.0 44 37.5885 40.0 38.0 41.0 33.0 41.0 45 37.29175 40.0 38.0 41.0 32.0 41.0 46 37.393 40.0 38.0 41.0 33.0 41.0 47 37.159 40.0 38.0 41.0 32.0 41.0 48 36.973 40.0 38.0 41.0 32.0 41.0 49 36.88875 40.0 37.0 41.0 32.0 41.0 50 36.58275 40.0 37.0 41.0 31.0 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 12 3.0 13 0.0 14 3.0 15 3.0 16 2.0 17 6.0 18 2.0 19 4.0 20 3.0 21 10.0 22 5.0 23 8.0 24 15.0 25 8.0 26 10.0 27 20.0 28 25.0 29 31.0 30 37.0 31 44.0 32 64.0 33 77.0 34 105.0 35 144.0 36 193.0 37 274.0 38 568.0 39 2336.0 >>END_MODULE >>Per base sequence content warn #Base G A T C 1 39.825 12.9 11.924999999999999 35.35 2 26.924999999999997 12.0 29.75 31.324999999999996 3 37.2093023255814 15.55388847211803 19.229807451862964 28.00700175043761 4 34.300000000000004 22.475 15.024999999999999 28.199999999999996 5 34.25 27.474999999999998 20.875 17.4 6 24.025 32.625 18.775 24.575 7 11.275 38.5 33.0 17.224999999999998 8 21.125 27.725 28.999999999999996 22.15 9 21.775 19.5 35.65 23.075000000000003 10 15.825 41.949999999999996 25.900000000000002 16.325 11 25.974999999999998 32.475 19.15 22.400000000000002 12 26.5 28.425 22.625 22.45 13 19.8 37.925 22.85 19.425 14 24.075 31.574999999999996 26.625 17.724999999999998 15 19.400000000000002 38.074999999999996 21.475 21.05 16 23.35 32.5 22.3 21.85 17 22.650000000000002 34.0 21.875 21.475 18 18.5 34.849999999999994 23.5 23.150000000000002 19 21.349999999999998 32.95 23.775 21.925 20 16.7 32.25 26.8 24.25 21 19.525000000000002 27.500000000000004 28.299999999999997 24.675 22 14.549999999999999 41.875 22.675 20.9 23 21.025 35.3 24.8 18.875 24 18.224999999999998 34.35 22.1 25.324999999999996 25 19.55 32.324999999999996 26.674999999999997 21.45 26 18.475 35.825 22.025 23.674999999999997 27 24.05 29.799999999999997 26.525 19.625 28 23.875 39.675 20.7 15.75 29 27.925 33.074999999999996 21.9 17.1 30 24.525 33.475 24.05 17.95 31 29.225 27.224999999999998 23.125 20.424999999999997 32 25.124999999999996 30.65 24.85 19.375 33 28.475 30.75 20.4 20.375 34 21.55 37.175000000000004 19.85 21.425 35 22.175 34.175 21.575 22.075 36 22.475 28.000000000000004 26.525 23.0 37 22.094188376753507 28.43186372745491 30.961923847695388 18.512024048096194 38 22.675 26.924999999999997 30.049999999999997 20.349999999999998 39 24.425 29.75 26.85 18.975 40 20.775 32.475 26.325 20.424999999999997 41 22.3 26.424999999999997 27.375 23.9 42 19.68976732549412 33.37503127345509 24.39329497122842 22.54190642982237 43 21.224999999999998 32.300000000000004 24.0 22.475 44 19.5 28.725 26.375 25.4 45 20.551378446115287 29.87468671679198 31.102756892230577 18.471177944862156 46 17.4468085106383 27.083854818523157 35.99499374217772 19.474342928660825 47 19.804707060590886 33.14972458688032 27.466199298948425 19.57936905358037 48 21.410705352676338 34.44222111055527 24.787393696848426 19.35967983991996 49 21.955488872218055 32.83320830207552 24.60615153788447 20.605151287821954 50 28.08904452226113 26.413206603301653 25.18759379689845 20.31015507753877 >>END_MODULE >>Per sequence GC content fail #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 5.0 20 10.0 21 6.5 22 3.0 23 3.5 24 4.0 25 17.5 26 31.0 27 37.0 28 43.0 29 42.5 30 42.0 31 50.0 32 58.0 33 100.5 34 143.0 35 257.5 36 372.0 37 458.0 38 544.0 39 433.0 40 322.0 41 323.5 42 325.0 43 377.0 44 429.0 45 421.0 46 413.0 47 311.0 48 209.0 49 262.0 50 315.0 51 261.0 52 207.0 53 164.0 54 121.0 55 96.5 56 72.0 57 59.5 58 47.0 59 43.0 60 39.0 61 42.5 62 46.0 63 35.0 64 24.0 65 24.5 66 25.0 67 31.0 68 37.0 69 37.0 70 37.0 71 38.5 72 40.0 73 26.5 74 13.0 75 11.0 76 9.0 77 7.0 78 5.0 79 6.0 80 7.0 81 4.0 82 1.0 83 2.5 84 4.0 85 2.0 86 0.0 87 0.0 88 0.0 89 1.0 90 2.0 91 1.0 92 0.0 93 0.5 94 1.0 95 0.5 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 0.025 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 0.075 43 0.0 44 0.0 45 0.25 46 0.125 47 0.15 48 0.05 49 0.025 50 0.05 >>END_MODULE >>Sequence Length Distribution pass #Length Count 50 4000.0 >>END_MODULE >>Sequence Duplication Levels fail #Total Deduplicated Percentage 49.625 #Duplication Level Percentage of deduplicated Percentage of total 1 84.43324937027708 41.9 2 6.448362720403022 6.4 3 2.6700251889168762 3.975 4 1.2090680100755666 2.4 5 0.8060453400503778 2.0 6 0.5541561712846348 1.6500000000000001 7 0.7556675062972292 2.625 8 0.3526448362720403 1.4000000000000001 9 0.2518891687657431 1.125 >10 2.1662468513853903 20.724999999999998 >50 0.2518891687657431 9.0 >100 0.10075566750629722 6.800000000000001 >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 170 4.25 No Hit CTGCGATGAAGGCGATAATAAATACAGAAGTTGCGGTCAATAAGGTAGGG 102 2.55 No Hit GATCGGAAGAGCACACGTCTGAACTCCAGTCACTCCTGAGCATCTCGTAT 88 2.1999999999999997 TruSeq Adapter, Index 6 (97% over 36bp) GTGCTCTGCCTGGAATACAATCATAAAGTTGAAAGTACCAGATATTCCTA 84 2.1 No Hit GCGGTCAATAAGGTAGGGATCATCAAAACACCGAACCATCCGATGTAAAG 68 1.7000000000000002 No Hit GGGAACTTCAAGAGCAGCTAGATCTAGAGGGAAGTTGTGAGCATTACGTT 65 1.625 No Hit TCTGCCTGGAATACAATCATAAAGTTGAAAGTACCAGATATTCCTAAAGG 55 1.375 No Hit ACGCGACCTTGACTATCAACTACAGATTGGTTGAAATTGAATCCATTTAG 45 1.125 No Hit CTCTGCCTGGAATACAATCATAAAGTTGAAAGTACCAGATATTCCTAAAG 44 1.0999999999999999 No Hit GTTGTGCTCTGCCTGGAATACAATCATAAAGTTGAAAGTACCAGATATTC 37 0.9249999999999999 No Hit CGGGAACTTCAAGAGCAGCTAGATCTAGAGGGAAGTTGTGAGCATTACGT 34 0.8500000000000001 No Hit CGCGACCTTGACTATCAACTACAGATTGGTTGAAATTGAATCCATTTAGG 34 0.8500000000000001 No Hit ATAAGGATGTTGTGCTCTGCCTGGAATACAATCATAAAGTTGAAAGTACC 30 0.75 No Hit GCGATGAAGGCGATAATAAATACAGAAGTTGCGGTCAATAAGGTAGGGAT 29 0.7250000000000001 No Hit GCGGAAAAACCTTATCCATTAATAGCGGGAACTTCAAGAGCAGCTAGATC 29 0.7250000000000001 No Hit CGGTCAATAAGGTAGGGATCATCAAAACACCGAACCATCCGATGTAAAGA 25 0.625 No Hit CGCAGAAGTAGGAATAATAGCACCAGAGATAATATTGTTTCCATAAAGTA 24 0.6 No Hit GCGACCTTGACTATCAACTACAGATTGGTTGAAATTGAATCCATTTAGGT 24 0.6 No Hit GCCTGGAATACAATCATAAAGTTGAAAGTACCAGATATTCCTAAAGGCAT 24 0.6 No Hit CGGAAAAACCTTATCCATTAATAGCGGGAACTTCAAGAGCAGCTAGATCT 22 0.5499999999999999 No Hit GTTCGCTGGAGTAGGCTGCGAGGCCCAAGCGGCCAAGGAGTGCAGCGGCC 20 0.5 No Hit GCTCTGCCTGGAATACAATCATAAAGTTGAAAGTACCAGATATTCCTAAA 20 0.5 No Hit GGCGATAATAAATACAGAAGTTGCGGTCAATAAGGTAGGGATCATCAAAA 19 0.475 No Hit GCTGCGATGAAGGCGATAATAAATACAGAAGTTGCGGTCAATAAGGTAGG 19 0.475 No Hit CTTTCTTTTCTTCAAAAATTCTTATATGTTAGCGGAAAAACCTTATCCAT 19 0.475 No Hit AGGGGCTGCGATGAAGGCGATAATAAATACAGAAGTTGCGGTCAATAAGG 19 0.475 No Hit CCCAAGTATTAATAACGCGACCTTGACTATCAACTACAGATTGGTTGAAA 18 0.44999999999999996 No Hit CTCGCGAATACCATCAATATCTACTGGAGGGGCTGCGATGAAGGCGATAA 18 0.44999999999999996 No Hit GGCCAAAATAACCATGAGCAGCCACAATATTATAAGTCTCTTCCTCTTGA 16 0.4 No Hit GCCAAAATAACCATGAGCAGCCACAATATTATAAGTCTCTTCCTCTTGAC 16 0.4 No Hit CTGGAATACAATCATAAAGTTGAAAGTACCAGATATTCCTAAAGGCATAC 16 0.4 No Hit CCAAGTATTAATAACGCGACCTTGACTATCAACTACAGATTGGTTGAAAT 15 0.375 No Hit CAATAAGGTAGGGATCATCAAAACACCGAACCATCCGATGTAAAGACGAT 14 0.35000000000000003 No Hit ATGCATAAGGATGTTGTGCTCTGCCTGGAATACAATCATAAAGTTGAAAG 14 0.35000000000000003 No Hit TTGTGCTCTGCCTGGAATACAATCATAAAGTTGAAAGTACCAGATATTCC 14 0.35000000000000003 No Hit GCTTTCTTTTCTTCAAAAATTCTTATATGTTAGCGGAAAAACCTTATCCA 13 0.325 No Hit GTCAATAAGGTAGGGATCATCAAAACACCGAACCATCCGATGTAAAGACG 13 0.325 No Hit GGAGGGGCTGCGATGAAGGCGATAATAAATACAGAAGTTGCGGTCAATAA 12 0.3 No Hit CCACCATTGTATAACCATTCATCAACGGATGCAGCTTCCCAAATTGGGTA 12 0.3 No Hit GCGCGACCTTGACTATCAACTACAGATTGGTTGAAATTGAATCCATTTAG 12 0.3 No Hit GGTCAATAAGGTAGGGATCATCAAAACACCGAACCATCCGATGTAAAGAC 12 0.3 No Hit AGCGGGAACTTCAAGAGCAGCTAGATCTAGAGGGAAGTTGTGAGCATTAC 12 0.3 No Hit CGCTGGAGTAGGCTGCGAGGCCCAAGCGGCCAAGGAGTGCAGCGGCCCGT 12 0.3 No Hit CGCGGGAACTTCAAGAGCAGCTAGATCTAGAGGGAAGTTGTGAGCATTAC 11 0.27499999999999997 No Hit CGCGTCTCTCTAAAATTGCAGTCATGGTAAGATCTTGGTTTATTCAAATT 11 0.27499999999999997 No Hit CTAGTTATCCAGTTGCAGAAGCGACCCCACAGGCTTGTACTTTCGCGTCT 11 0.27499999999999997 No Hit CGCGGTCAATAAGGTAGGGATCATCAAAACACCGAACCATCCGATGTAAA 10 0.25 No Hit GGATGCATAAGGATGTTGTGCTCTGCCTGGAATACAATCATAAAGTTGAA 10 0.25 No Hit CTCATTAGCAGATTCATTTTCAGTAGTTTCCCTGATCAAACTAGAGGTTA 10 0.25 No Hit CGATGAAGGCGATAATAAATACAGAAGTTGCGGTCAATAAGGTAGGGATC 10 0.25 No Hit CGCGAATACCATCAATATCTACTGGAGGGGCTGCGATGAAGGCGATAATA 9 0.22499999999999998 No Hit CCGCAGAAGTAGGAATAATAGCACCAGAGATAATATTGTTTCCATAAAGT 9 0.22499999999999998 No Hit TGCGGTCAATAAGGTAGGGATCATCAAAACACCGAACCATCCGATGTAAA 9 0.22499999999999998 No Hit CATAAGGATGTTGTGCTCTGCCTGGAATACAATCATAAAGTTGAAAGTAC 9 0.22499999999999998 No Hit AGCAGCCACAATATTATAAGTCTCTTCCTCTTGACCAAATTTGTAACCCT 9 0.22499999999999998 No Hit CTTTTCTTCAAAAATTCTTATATGTTAGCGGAAAAACCTTATCCATTAAT 8 0.2 No Hit GCCGAAAACACCAGCTACACCTAACATGTGAAATGGATGCATAAGGATGT 8 0.2 No Hit GCTAGTTATCCAGTTGCAGAAGCGACCCCACAGGCTTGTACTTTCGCGTC 8 0.2 No Hit CTCATAAGGACCACCATTGTATAACCATTCATCAACGGATGCAGCTTCCC 8 0.2 No Hit GTGCCTGCCAACATTATGGGCCGCGAAGCCTAGCTTTCGCTTAAGCTCCA 8 0.2 No Hit CTGCCTGGAATACAATCATAAAGTTGAAAGTACCAGATATTCCTAAAGGC 8 0.2 No Hit GGGGCTGCGATGAAGGCGATAATAAATACAGAAGTTGCGGTCAATAAGGT 8 0.2 No Hit GCGATAATAAATACAGAAGTTGCGGTCAATAAGGTAGGGATCATCAAAAC 7 0.17500000000000002 No Hit CTTCCTCTTGACCAAATTTGTAACCCTCATTAGCAGATTCATTTTCAGTA 7 0.17500000000000002 No Hit CTTGACTATCAACTACAGATTGGTTGAAATTGAATCCATTTAGGTTGAAC 7 0.17500000000000002 No Hit TTTCTTTTCTTCAAAAATTCTTATATGTTAGCGGAAAAACCTTATCCATT 7 0.17500000000000002 No Hit CAAGTATTAATAACGCGACCTTGACTATCAACTACAGATTGGTTGAAATT 7 0.17500000000000002 No Hit TGCGGGAACTTCAAGAGCAGCTAGATCTAGAGGGAAGTTGTGAGCATTAC 7 0.17500000000000002 No Hit CGTCTCTCTAAAATTGCAGTCATGGTAAGATCTTGGTTTATTCAAATTGC 7 0.17500000000000002 No Hit CCACAATATTATAAGTCTCTTCCTCTTGACCAAATTTGTAACCCTCATTA 7 0.17500000000000002 No Hit GCGAATACCATCAATATCTACTGGAGGGGCTGCGATGAAGGCGATAATAA 7 0.17500000000000002 No Hit TGTGCTCTGCCTGGAATACAATCATAAAGTTGAAAGTACCAGATATTCCT 7 0.17500000000000002 No Hit GCATAAGGATGTTGTGCTCTGCCTGGAATACAATCATAAAGTTGAAAGTA 7 0.17500000000000002 No Hit AATAAATACAGAAGTTGCGGTCAATAAGGTAGGGATCATCAAAACACCGA 7 0.17500000000000002 No Hit GTTGAAACTAGCATATTGGAAGATTAATCGGCCAAAATAACCATGAGCAG 7 0.17500000000000002 No Hit TAGTTATCCAGTTGCAGAAGCGACCCCACAGGCTTGTACTTTCGCGTCTC 7 0.17500000000000002 No Hit CGCTTTCTTTTCTTCAAAAATTCTTATATGTTAGCGGAAAAACCTTATCC 7 0.17500000000000002 No Hit TTCAAGAGCAGCTAGATCTAGAGGGAAGTTGTGAGCATTACGTTCGTGCA 6 0.15 No Hit CTGGAGTAGGCTGCGAGGCCCAAGCGGCCAAGGAGTGCAGCGGCCCGTTA 6 0.15 No Hit GACCACCATTGTATAACCATTCATCAACGGATGCAGCTTCCCAAATTGGG 6 0.15 No Hit ATAATTAACTGCATTGATCTCGGTAGCTACGCCACCCACGGAATTTAAAG 6 0.15 No Hit TGATGATATCAGCCCAAGTATTAATAACGCGACCTTGACTATCAACTACA 6 0.15 No Hit AACGCGACCTTGACTATCAACTACAGATTGGTTGAAATTGAATCCATTTA 6 0.15 No Hit GTTGATGATATCAGCCCAAGTATTAATAACGCGACCTTGACTATCAACTA 6 0.15 No Hit ACCAGAGATAATATTGTTTCCATAAAGTAAAGAACCAGAAACAGGCTCGC 6 0.15 No Hit CACGGTTGATGATATCAGCCCAAGTATTAATAACGCGACCTTGACTATCA 6 0.15 No Hit GTGAAATGGATGCATAAGGATGTTGTGCTCTGCCTGGAATACAATCATAA 6 0.15 No Hit CACCATTGTATAACCATTCATCAACGGATGCAGCTTCCCAAATTGGGTAA 6 0.15 No Hit CGCCATAGTACTAATACCTAAAGCAGTGAACCAGATTCCTACTACAGGCC 5 0.125 No Hit GGAAAAACCTTATCCATTAATAGCGGGAACTTCAAGAGCAGCTAGATCTA 5 0.125 No Hit CGACCTTGACTATCAACTACAGATTGGTTGAAATTGAATCCATTTAGGTT 5 0.125 No Hit CTGTGCCTGCCAACATTATGGGCCGCGAAGCCTAGCTTTCGCTTAAGCTC 5 0.125 No Hit GTGAGCATTACGTTCGTGCATTACTTCCATACCAAGATTAGCACGGTTGA 5 0.125 No Hit GGGCTGCGATGAAGGCGATAATAAATACAGAAGTTGCGGTCAATAAGGTA 5 0.125 No Hit AAGAGCAGCTAGATCTAGAGGGAAGTTGTGAGCATTACGTTCGTGCATTA 5 0.125 No Hit GTAGGGATCATCAAAACACCGAACCATCCGATGTAAAGACGATTTTCAGT 5 0.125 No Hit CGCAGCTGCAACAGGAGCTGAATATGCAACAGCAATCCAAGGGCGCATAC 5 0.125 No Hit CGGTTGATGATATCAGCCCAAGTATTAATAACGCGACCTTGACTATCAAC 5 0.125 No Hit ATAATAAATACAGAAGTTGCGGTCAATAAGGTAGGGATCATCAAAACACC 5 0.125 No Hit GTGCTAGTTATCCAGTTGCAGAAGCGACCCCACAGGCTTGTACTTTCGCG 5 0.125 No Hit TGCGATGAAGGCGATAATAAATACAGAAGTTGCGGTCAATAAGGTAGGGA 5 0.125 No Hit CTCTTGACCAAATTTGTAACCCTCATTAGCAGATTCATTTTCAGTAGTTT 5 0.125 No Hit TGCCGCAGAAGTAGGAATAATAGCACCAGAGATAATATTGTTTCCATAAA 5 0.125 No Hit CGGCCAAAATAACCATGAGCAGCCACAATATTATAAGTCTCTTCCTCTTG 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 ACACGTC 20 6.952051E-4 44.000004 13 GTCACTC 20 6.952051E-4 44.000004 29 ATCTCGT 20 6.952051E-4 44.000004 42 CTGAGCA 20 6.952051E-4 44.000004 36 CAGTCAC 20 6.952051E-4 44.000004 27 CACACGT 20 6.952051E-4 44.000004 12 ACGTCTG 20 6.952051E-4 44.000004 15 CTCCTGA 20 6.952051E-4 44.000004 33 CCAGTCA 20 6.952051E-4 44.000004 26 CACGTCT 20 6.952051E-4 44.000004 14 CATCTCG 20 6.952051E-4 44.000004 41 CTCCAGT 20 6.952051E-4 44.000004 24 ACTCCTG 20 6.952051E-4 44.000004 32 GATCGGA 20 6.952051E-4 44.000004 1 CCTGAGC 20 6.952051E-4 44.000004 35 ACTCCAG 20 6.952051E-4 44.000004 23 GTCTGAA 20 6.952051E-4 44.000004 17 TCCAGTC 20 6.952051E-4 44.000004 25 GAAGAGC 20 6.952051E-4 44.000004 6 TCGGAAG 20 6.952051E-4 44.000004 3 >>END_MODULE Read 770360 spots for SRR1772236.sra Written 770360 spots for SRR1772236.sra Read 770360 spots for SRR1772236.sra Written 770360 spots for SRR1772236.sra Read 770360 spots for SRR1772236.sra Written 770360 spots for SRR1772236.sra Read 770360 spots for SRR1772236.sra Written 770360 spots for SRR1772236.sra Read 770360 spots for SRR1772236.sra Written 770360 spots for SRR1772236.sra Read 770360 spots for SRR1772236.sra Written 770360 spots for SRR1772236.sra Read 770360 spots for SRR1772236.sra Written 770360 spots for SRR1772236.sra Read 770360 spots for SRR1772236.sra Written 770360 spots for SRR1772236.sra Read 770360 spots for SRR1772236.sra Written 770360 spots for SRR1772236.sra Read 770360 spots for SRR1772236.sra Written 770360 spots for SRR1772236.sra Read 770360 spots for SRR1772236.sra Written 770360 spots for SRR1772236.sra Read 770360 spots for SRR1772236.sra Written 770360 spots for SRR1772236.sra Read 770360 spots for SRR1772236.sra Written 770360 spots for SRR1772236.sra Read 770360 spots for SRR1772236.sra Written 770360 spots for SRR1772236.sra Read 770360 spots for SRR1772236.sra Written 770360 spots for SRR1772236.sra Read 770363 spots for SRR1772236.sra Written 770363 spots for SRR1772236.sra Read 770360 spots for SRR1772236.sra Written 770360 spots for SRR1772236.sra Read 770360 spots for SRR1772236.sra Written 770360 spots for SRR1772236.sra Read 770360 spots for SRR1772236.sra Written 770360 spots for SRR1772236.sra Read 770360 spots for SRR1772236.sra Written 770360 spots for SRR1772236.sra SRR ids: ['SRR1772236.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_urog3lcw SRR1772236.sra spots: 15407203 blocks: [[1, 770360], [770361, 1540720], [1540721, 2311080], [2311081, 3081440], [3081441, 3851800], [3851801, 4622160], [4622161, 5392520], [5392521, 6162880], [6162881, 6933240], [6933241, 7703600], [7703601, 8473960], [8473961, 9244320], [9244321, 10014680], [10014681, 10785040], [10785041, 11555400], [11555401, 12325760], [12325761, 13096120], [13096121, 13866480], [13866481, 14636840], [14636841, 15407203]] SRR1772236 file size 2659492 SRR1772236 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 SRR1772236 SRR1772236_1.fastq Input file: SRR1772236_1.fastq trimmed: SRR1772236-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 09:49:21 2024 >> started Fri Dec 6 09:49:31 2024 >> done (10.602s) 15407203 reads processed; of these: 2191 ( 0.01%) short reads filtered out after trimming by size control 332987 ( 2.16%) empty reads filtered out after trimming by size control 15072025 (97.82%) reads available; of these: 704179 ( 4.67%) trimmed reads available after processing 14367846 (95.33%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 1125 0.01% 19 1776 0.01% 20 4075 0.03% 21 4017 0.03% 22 4522 0.03% 23 4961 0.03% 24 6324 0.04% 25 6901 0.05% 26 6833 0.05% 27 7872 0.05% 28 7224 0.05% 29 13633 0.09% 30 12903 0.09% 31 10015 0.07% 32 17136 0.11% 33 11224 0.07% 34 11976 0.08% 35 13035 0.09% 36 12998 0.09% 37 20052 0.13% 38 14877 0.10% 39 16301 0.11% 40 22386 0.15% 41 20614 0.14% 42 30787 0.20% 43 34364 0.23% 44 54567 0.36% 45 49030 0.33% 46 61257 0.41% 47 71900 0.48% 48 81331 0.54% 49 68163 0.45% 50 14367846 95.33% 15072025 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=0.01 sequence-density-rank=39 fanout-score=49.50 fanout-score-rank=1 prefix-density=0.07 prefix-fanout=3.8 sequence=TTTTTATTTAGACCTTCTTCATATTTAGTTTTATCTATTAATCGATAGTATCTACCGGCGCGAACTCGAATTTGATCGCCTTCCATACTTCACAAGCTGCGGCTAGTTCAGGACTCCATTTGCAAGCTGCTCGGATAATTTCATTACCTTCACGAGCAAGATC Started job on | Dec 06 09:50:40 Started mapping on | Dec 06 09:50:40 Finished on | Dec 06 09:50:52 Mapping speed, Million of reads per hour | 4521.61 Number of input reads | 15072025 Average input read length | 49 UNIQUE READS: Uniquely mapped reads number | 3884327 Uniquely mapped reads % | 25.77% Average mapped length | 49.41 Number of splices: Total | 227629 Number of splices: Annotated (sjdb) | 215183 Number of splices: GT/AG | 223082 Number of splices: GC/AG | 2937 Number of splices: AT/AC | 97 Number of splices: Non-canonical | 1513 Mismatch rate per base, % | 0.26% Deletion rate per base | 0.01% Deletion average length | 1.52 Insertion rate per base | 0.01% Insertion average length | 1.33 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 10867258 % of reads mapped to multiple loci | 72.10% Number of reads mapped to too many loci | 98122 % of reads mapped to too many loci | 0.65% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 1.45% % of reads unmapped: other | 0.02% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 320440 320440 320440 N_multimapping 10867258 10867258 10867258 N_noFeature 829506 3749232 910369 N_ambiguous 86113 576 31766 UnstrandedReadsAssigned:2968708 PositiveStrandReadsAssigned:134519 NegativeStrandReadsAssigned:2942192 Dataset is classified negative stranded MeadianReadLen=50 20thPercentileLength=50 echo kmer=45 SRR1772236 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: SRR1772236-trimmed.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 15,072,025 reads, 12,413,827 reads pseudoaligned [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 979 rounds 52973 SRR1772236.ke.tsv 35125 SRR1772236.se.tsv 88098 total ==> SRR1772236.ke.tsv <== target_id length eff_length est_counts tpm PNS24245 936 837 11.8125 1.2572 PNS24247 1044 945 0 0 PNS24249 1928 1829 33.1875 1.6164 PNS24246 1044 945 0 0 PNS24248 1044 945 0 0 PNS24244 1471 1372 0 0 PNS24243 293 194 0 0 KQK14069 1603 1504 289.296 17.1349 KQK14071 474 375 112.45 26.7125 ==> SRR1772236.se.tsv <== BRADI_1g14170v3 569 BRADI_1g53295v3 1 BRADI_1g59795v3 17 BRADI_1g07683v3 0 BRADI_1g00485v3 0 BRADI_1g20270v3 19 BRADI_1g74790v3 6 BRADI_1g09890v3 0 BRADI_1g77505v3 41 BRADI_1g48960v3 0 SRR1772236 completed mapping pipeline successfully