Starting /dee2/code/volunteer_pipeline.sh SRR1772223 current disk space = 1540357869568 free memory = 1477523592 SRR1772223 SRAfilesize 877280aaf4d06c7e952e10abeef0ac12 SRR1772223.sra SRR1772223.sra file validated SRR1772223 is single end SRR1772223 is conventional basespace SRR1772223 read1 length is 50 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR1772223_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 32.84 34.0 31.0 34.0 31.0 34.0 2 32.9675 34.0 31.0 34.0 31.0 34.0 3 32.82075 34.0 31.0 34.0 31.0 34.0 4 36.244 37.0 37.0 37.0 35.0 37.0 5 36.2965 37.0 37.0 37.0 35.0 37.0 6 36.1605 37.0 37.0 37.0 35.0 37.0 7 36.1995 37.0 37.0 37.0 35.0 37.0 8 36.1585 37.0 37.0 37.0 35.0 37.0 9 37.92425 39.0 38.0 39.0 35.0 39.0 10 37.79275 39.0 38.0 39.0 35.0 39.0 11 37.87825 39.0 38.0 39.0 35.0 39.0 12 37.917 39.0 38.0 39.0 35.0 39.0 13 37.88225 39.0 38.0 39.0 35.0 39.0 14 39.2085 41.0 39.0 41.0 36.0 41.0 15 39.34225 41.0 39.0 41.0 36.0 41.0 16 39.149 41.0 39.0 41.0 36.0 41.0 17 39.21725 41.0 39.0 41.0 36.0 41.0 18 39.3225 41.0 39.0 41.0 36.0 41.0 19 39.22625 41.0 39.0 41.0 36.0 41.0 20 39.2685 41.0 39.0 41.0 36.0 41.0 21 39.05125 41.0 39.0 41.0 35.0 41.0 22 39.16225 40.0 39.0 41.0 36.0 41.0 23 38.8295 40.0 38.0 41.0 35.0 41.0 24 38.8815 40.0 39.0 41.0 35.0 41.0 25 38.967 40.0 39.0 41.0 36.0 41.0 26 38.42525 40.0 38.0 41.0 34.0 41.0 27 38.6335 40.0 38.0 41.0 34.0 41.0 28 38.6385 40.0 38.0 41.0 34.0 41.0 29 38.58875 40.0 38.0 41.0 35.0 41.0 30 38.4835 40.0 38.0 41.0 34.0 41.0 31 38.25125 40.0 38.0 41.0 34.0 41.0 32 38.17525 40.0 38.0 41.0 33.0 41.0 33 38.0615 40.0 38.0 41.0 33.0 41.0 34 38.39525 40.0 38.0 41.0 34.0 41.0 35 38.45925 40.0 38.0 41.0 35.0 41.0 36 38.39275 40.0 38.0 41.0 34.0 41.0 37 37.9985 40.0 38.0 41.0 33.0 41.0 38 37.74875 40.0 38.0 41.0 33.0 41.0 39 37.91075 40.0 38.0 41.0 33.0 41.0 40 37.82875 40.0 38.0 41.0 33.0 41.0 41 37.7225 40.0 38.0 41.0 33.0 41.0 42 37.70325 40.0 38.0 41.0 33.0 41.0 43 37.71325 40.0 38.0 41.0 33.0 41.0 44 37.5315 40.0 38.0 41.0 33.0 41.0 45 37.24575 40.0 37.0 41.0 32.0 41.0 46 37.3565 40.0 38.0 41.0 33.0 41.0 47 36.93425 40.0 37.0 41.0 31.0 41.0 48 36.7935 40.0 37.0 41.0 31.0 41.0 49 36.85125 40.0 37.0 41.0 31.0 41.0 50 36.4305 40.0 36.0 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 3.0 16 0.0 17 2.0 18 5.0 19 5.0 20 6.0 21 8.0 22 9.0 23 11.0 24 12.0 25 9.0 26 15.0 27 24.0 28 20.0 29 38.0 30 39.0 31 51.0 32 72.0 33 111.0 34 113.0 35 187.0 36 200.0 37 333.0 38 592.0 39 2134.0 >>END_MODULE >>Per base sequence content warn #Base G A T C 1 40.14507253626813 12.406203101550775 11.805902951475739 35.64282141070535 2 30.225 10.925 29.049999999999997 29.799999999999997 3 37.192365645404315 17.604218985434457 17.704671019588147 27.49874434957308 4 33.525 26.3 15.15 25.025 5 32.6 29.325000000000003 20.7 17.375 6 25.174999999999997 32.175 18.275 24.375 7 11.95 37.9 34.425 15.725 8 20.275000000000002 27.450000000000003 29.925 22.35 9 22.400000000000002 19.775000000000002 33.2 24.625 10 17.825 42.475 23.65 16.05 11 25.15 32.275 19.275000000000002 23.3 12 25.5 27.900000000000002 23.575 23.025000000000002 13 18.675 39.525 22.725 19.075 14 24.375 31.8 28.225 15.6 15 21.525 34.849999999999994 21.25 22.375 16 22.15 34.9 22.8 20.150000000000002 17 22.125 34.449999999999996 23.474999999999998 19.950000000000003 18 18.55 34.775 22.6 24.075 19 21.75 32.300000000000004 25.724999999999998 20.225 20 16.725 34.55 26.35 22.375 21 18.9 29.75 26.625 24.725 22 16.1 40.475 22.475 20.95 23 19.950000000000003 35.375 25.45 19.225 24 19.15 36.025 21.349999999999998 23.474999999999998 25 18.575 34.75 26.224999999999998 20.45 26 18.35 35.575 23.25 22.825 27 22.775000000000002 30.275000000000002 26.25 20.7 28 24.375 36.175000000000004 22.1 17.349999999999998 29 25.974999999999998 32.025 22.825 19.175 30 24.825 30.375000000000004 24.05 20.75 31 29.625 26.05 23.5 20.825 32 24.125 31.5 24.025 20.349999999999998 33 26.1 32.574999999999996 21.05 20.275000000000002 34 22.225 35.775 20.875 21.125 35 21.525 36.625 22.6 19.25 36 21.2 29.65 28.875 20.275000000000002 37 25.093914350112694 29.476584022038566 27.67342849987478 17.756073127973952 38 21.025 27.925 29.099999999999998 21.95 39 24.425 26.650000000000002 27.6 21.325 40 20.175 33.7 25.1 21.025 41 22.75 28.275 27.725 21.25 42 22.3 30.875000000000004 24.725 22.1 43 21.175 31.775 25.25 21.8 44 18.85 29.475 28.575 23.1 45 20.806209313970957 30.370555833750622 29.86980470706059 18.953430145217826 46 20.060030015007506 28.139069534767387 32.666333166583286 19.13456728364182 47 19.334667333666832 33.291645822911455 28.064032016008007 19.30965482741371 48 23.730932733183295 31.857964491122782 24.256064016004 20.155038759689923 49 23.43671835917959 32.3911955977989 22.36118059029515 21.810905452726363 50 25.481370342585645 28.532133033258315 25.581395348837212 20.40510127531883 >>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 0.5 16 1.0 17 2.0 18 3.0 19 3.0 20 3.0 21 3.5 22 4.0 23 7.5 24 11.0 25 22.0 26 33.0 27 31.5 28 30.0 29 35.0 30 40.0 31 56.5 32 73.0 33 104.5 34 136.0 35 236.5 36 337.0 37 414.0 38 491.0 39 424.0 40 357.0 41 378.0 42 399.0 43 437.5 44 476.0 45 440.5 46 405.0 47 309.0 48 213.0 49 272.5 50 332.0 51 223.5 52 115.0 53 120.5 54 126.0 55 112.0 56 98.0 57 70.5 58 43.0 59 46.5 60 50.0 61 42.5 62 35.0 63 33.0 64 31.0 65 35.5 66 40.0 67 34.0 68 28.0 69 29.5 70 31.0 71 30.0 72 29.0 73 18.0 74 7.0 75 7.5 76 8.0 77 8.5 78 9.0 79 6.0 80 3.0 81 1.5 82 0.0 83 1.0 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 0.05 2 0.0 3 0.44999999999999996 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 0.17500000000000002 38 0.0 39 0.0 40 0.0 41 0.0 42 0.0 43 0.0 44 0.0 45 0.15 46 0.05 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 warn #Total Deduplicated Percentage 53.025 #Duplication Level Percentage of deduplicated Percentage of total 1 85.1013672795851 45.125 2 6.742102781706742 7.1499999999999995 3 2.3573785950023574 3.75 4 1.3201320132013201 2.8000000000000003 5 0.7072135785007072 1.875 6 0.33003300330033003 1.05 7 0.7543611504007544 2.8000000000000003 8 0.2828854314002829 1.2 9 0.1885902876001886 0.8999999999999999 >10 1.933050447901933 21.7 >50 0.23573785950023576 8.4 >100 0.04714757190004715 3.25 >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 130 3.25 No Hit CTGCGATGAAGGCGATAATAAATACAGAAGTTGCGGTCAATAAGGTAGGG 86 2.15 No Hit GGGAACTTCAAGAGCAGCTAGATCTAGAGGGAAGTTGTGAGCATTACGTT 83 2.075 No Hit GTGCTCTGCCTGGAATACAATCATAAAGTTGAAAGTACCAGATATTCCTA 63 1.575 No Hit GCGGTCAATAAGGTAGGGATCATCAAAACACCGAACCATCCGATGTAAAG 53 1.325 No Hit GCGATGAAGGCGATAATAAATACAGAAGTTGCGGTCAATAAGGTAGGGAT 51 1.275 No Hit GTTGTGCTCTGCCTGGAATACAATCATAAAGTTGAAAGTACCAGATATTC 40 1.0 No Hit GATCGGAAGAGCACACGTCTGAACTCCAGTCACTAAGGCGAATCTCGTAT 40 1.0 TruSeq Adapter, Index 3 (97% over 39bp) CGGGAACTTCAAGAGCAGCTAGATCTAGAGGGAAGTTGTGAGCATTACGT 39 0.975 No Hit CGCGACCTTGACTATCAACTACAGATTGGTTGAAATTGAATCCATTTAGG 39 0.975 No Hit TCTGCCTGGAATACAATCATAAAGTTGAAAGTACCAGATATTCCTAAAGG 38 0.95 No Hit GCGACCTTGACTATCAACTACAGATTGGTTGAAATTGAATCCATTTAGGT 36 0.8999999999999999 No Hit GTCAATAAGGTAGGGATCATCAAAACACCGAACCATCCGATGTAAAGACG 33 0.8250000000000001 No Hit CGGTCAATAAGGTAGGGATCATCAAAACACCGAACCATCCGATGTAAAGA 29 0.7250000000000001 No Hit GCCTGGAATACAATCATAAAGTTGAAAGTACCAGATATTCCTAAAGGCAT 28 0.7000000000000001 No Hit CTCTGCCTGGAATACAATCATAAAGTTGAAAGTACCAGATATTCCTAAAG 28 0.7000000000000001 No Hit GGTCAATAAGGTAGGGATCATCAAAACACCGAACCATCCGATGTAAAGAC 27 0.675 No Hit CGGAAAAACCTTATCCATTAATAGCGGGAACTTCAAGAGCAGCTAGATCT 27 0.675 No Hit CTGGAATACAATCATAAAGTTGAAAGTACCAGATATTCCTAAAGGCATAC 27 0.675 No Hit ACGCGACCTTGACTATCAACTACAGATTGGTTGAAATTGAATCCATTTAG 26 0.65 No Hit ATAAGGATGTTGTGCTCTGCCTGGAATACAATCATAAAGTTGAAAGTACC 25 0.625 No Hit CTCGCGAATACCATCAATATCTACTGGAGGGGCTGCGATGAAGGCGATAA 24 0.6 No Hit GCTGCGATGAAGGCGATAATAAATACAGAAGTTGCGGTCAATAAGGTAGG 23 0.575 No Hit GCCAAAATAACCATGAGCAGCCACAATATTATAAGTCTCTTCCTCTTGAC 23 0.575 No Hit GGCCAAAATAACCATGAGCAGCCACAATATTATAAGTCTCTTCCTCTTGA 22 0.5499999999999999 No Hit CAATAAGGTAGGGATCATCAAAACACCGAACCATCCGATGTAAAGACGAT 19 0.475 No Hit GGAGGGGCTGCGATGAAGGCGATAATAAATACAGAAGTTGCGGTCAATAA 19 0.475 No Hit CGATGAAGGCGATAATAAATACAGAAGTTGCGGTCAATAAGGTAGGGATC 19 0.475 No Hit GCTCTGCCTGGAATACAATCATAAAGTTGAAAGTACCAGATATTCCTAAA 19 0.475 No Hit GGATGCATAAGGATGTTGTGCTCTGCCTGGAATACAATCATAAAGTTGAA 15 0.375 No Hit CCACCATTGTATAACCATTCATCAACGGATGCAGCTTCCCAAATTGGGTA 14 0.35000000000000003 No Hit AGCGGGAACTTCAAGAGCAGCTAGATCTAGAGGGAAGTTGTGAGCATTAC 14 0.35000000000000003 No Hit CTCATTAGCAGATTCATTTTCAGTAGTTTCCCTGATCAAACTAGAGGTTA 14 0.35000000000000003 No Hit GCGGAAAAACCTTATCCATTAATAGCGGGAACTTCAAGAGCAGCTAGATC 13 0.325 No Hit GGGGCTGCGATGAAGGCGATAATAAATACAGAAGTTGCGGTCAATAAGGT 13 0.325 No Hit AGGGGCTGCGATGAAGGCGATAATAAATACAGAAGTTGCGGTCAATAAGG 13 0.325 No Hit CGCGAATACCATCAATATCTACTGGAGGGGCTGCGATGAAGGCGATAATA 12 0.3 No Hit CGCAGAAGTAGGAATAATAGCACCAGAGATAATATTGTTTCCATAAAGTA 12 0.3 No Hit GGCGATAATAAATACAGAAGTTGCGGTCAATAAGGTAGGGATCATCAAAA 12 0.3 No Hit CCCAAGTATTAATAACGCGACCTTGACTATCAACTACAGATTGGTTGAAA 12 0.3 No Hit GGAAAAACCTTATCCATTAATAGCGGGAACTTCAAGAGCAGCTAGATCTA 11 0.27499999999999997 No Hit CGCTGGAGTAGGCTGCGAGGCCCAAGCGGCCAAGGAGTGCAGCGGCCCGT 11 0.27499999999999997 No Hit CTGCCTGGAATACAATCATAAAGTTGAAAGTACCAGATATTCCTAAAGGC 11 0.27499999999999997 No Hit AATAAATACAGAAGTTGCGGTCAATAAGGTAGGGATCATCAAAACACCGA 11 0.27499999999999997 No Hit CTGTGCCTGCCAACATTATGGGCCGCGAAGCCTAGCTTTCGCTTAAGCTC 10 0.25 No Hit GCTAGTTATCCAGTTGCAGAAGCGACCCCACAGGCTTGTACTTTCGCGTC 10 0.25 No Hit TGTGCTCTGCCTGGAATACAATCATAAAGTTGAAAGTACCAGATATTCCT 10 0.25 No Hit CCGGGGTGTAGTAAGTCAATCTATAATCTTTAACACCAGCTTTAAATCCA 9 0.22499999999999998 No Hit TTTCTTTTCTTCAAAAATTCTTATATGTTAGCGGAAAAACCTTATCCATT 9 0.22499999999999998 No Hit CCAAGTATTAATAACGCGACCTTGACTATCAACTACAGATTGGTTGAAAT 9 0.22499999999999998 No Hit TTGTGCTCTGCCTGGAATACAATCATAAAGTTGAAAGTACCAGATATTCC 9 0.22499999999999998 No Hit ATGCATAAGGATGTTGTGCTCTGCCTGGAATACAATCATAAAGTTGAAAG 8 0.2 No Hit CGCGGTCAATAAGGTAGGGATCATCAAAACACCGAACCATCCGATGTAAA 8 0.2 No Hit GGGCTGCGATGAAGGCGATAATAAATACAGAAGTTGCGGTCAATAAGGTA 8 0.2 No Hit CGCAGCTGCAACAGGAGCTGAATATGCAACAGCAATCCAAGGGCGCATAC 8 0.2 No Hit CTTTCTTTTCTTCAAAAATTCTTATATGTTAGCGGAAAAACCTTATCCAT 8 0.2 No Hit ATAACAAGCTACACCAAGTAAGAAGTGTAGAACAATTAGCTCATAAGGAC 8 0.2 No Hit AATAAGGTAGGGATCATCAAAACACCGAACCATCCGATGTAAAGACGATT 7 0.17500000000000002 No Hit CTTTTCTTCAAAAATTCTTATATGTTAGCGGAAAAACCTTATCCATTAAT 7 0.17500000000000002 No Hit CCGCAGAAGTAGGAATAATAGCACCAGAGATAATATTGTTTCCATAAAGT 7 0.17500000000000002 No Hit CGCGGGAACTTCAAGAGCAGCTAGATCTAGAGGGAAGTTGTGAGCATTAC 7 0.17500000000000002 No Hit GCCGAAAACACCAGCTACACCTAACATGTGAAATGGATGCATAAGGATGT 7 0.17500000000000002 No Hit CCCCAGTTAAGTAGTCATGCATTACAATAGGAACACCTAATTCTCTCGCA 7 0.17500000000000002 No Hit ATGAAGGCGATAATAAATACAGAAGTTGCGGTCAATAAGGTAGGGATCAT 7 0.17500000000000002 No Hit TGCGGTCAATAAGGTAGGGATCATCAAAACACCGAACCATCCGATGTAAA 7 0.17500000000000002 No Hit GTAGGGATCATCAAAACACCGAACCATCCGATGTAAAGACGATTTTCAGT 7 0.17500000000000002 No Hit GTTCGCTGGAGTAGGCTGCGAGGCCCAAGCGGCCAAGGAGTGCAGCGGCC 7 0.17500000000000002 No Hit CCACAATATTATAAGTCTCTTCCTCTTGACCAAATTTGTAACCCTCATTA 7 0.17500000000000002 No Hit GCGAATACCATCAATATCTACTGGAGGGGCTGCGATGAAGGCGATAATAA 7 0.17500000000000002 No Hit CTCATAAGGACCACCATTGTATAACCATTCATCAACGGATGCAGCTTCCC 7 0.17500000000000002 No Hit GTGCCTGCCAACATTATGGGCCGCGAAGCCTAGCTTTCGCTTAAGCTCCA 7 0.17500000000000002 No Hit CACGGTTGATGATATCAGCCCAAGTATTAATAACGCGACCTTGACTATCA 7 0.17500000000000002 No Hit AGCAGCCACAATATTATAAGTCTCTTCCTCTTGACCAAATTTGTAACCCT 7 0.17500000000000002 No Hit TTCAAGAGCAGCTAGATCTAGAGGGAAGTTGTGAGCATTACGTTCGTGCA 6 0.15 No Hit TGCGGGAACTTCAAGAGCAGCTAGATCTAGAGGGAAGTTGTGAGCATTAC 6 0.15 No Hit CCAAAATAACCATGAGCAGCCACAATATTATAAGTCTCTTCCTCTTGACC 6 0.15 No Hit CGCATACCCAAACGGAAACTAAGTTCCCACTCACGACCCATATAACAAGC 6 0.15 No Hit ATAACCATTCATCAACGGATGCAGCTTCCCAAATTGGGTAAAAGTGCAAT 6 0.15 No Hit GTTGAAATTGAATCCATTTAGGTTGAACGCCATAGTACTAATACCTAAAG 6 0.15 No Hit GTTGAAACTAGCATATTGGAAGATTAATCGGCCAAAATAACCATGAGCAG 6 0.15 No Hit CTTCCTCTTGACCAAATTTGTAACCCTCATTAGCAGATTCATTTTCAGTA 5 0.125 No Hit CTGGAGTAGGCTGCGAGGCCCAAGCGGCCAAGGAGTGCAGCGGCCCGTTA 5 0.125 No Hit ATAATTAACTGCATTGATCTCGGTAGCTACGCCACCCACGGAATTTAAAG 5 0.125 No Hit TGTTGTGCTCTGCCTGGAATACAATCATAAAGTTGAAAGTACCAGATATT 5 0.125 No Hit CCATTGTATAACCATTCATCAACGGATGCAGCTTCCCAAATTGGGTAAAA 5 0.125 No Hit AAGAGCAGCTAGATCTAGAGGGAAGTTGTGAGCATTACGTTCGTGCATTA 5 0.125 No Hit GTTGATGATATCAGCCCAAGTATTAATAACGCGACCTTGACTATCAACTA 5 0.125 No Hit ATAATAAATACAGAAGTTGCGGTCAATAAGGTAGGGATCATCAAAACACC 5 0.125 No Hit GCTTTCTTTTCTTCAAAAATTCTTATATGTTAGCGGAAAAACCTTATCCA 5 0.125 No Hit CTAGTTATCCAGTTGCAGAAGCGACCCCACAGGCTTGTACTTTCGCGTCT 5 0.125 No Hit CCTGCCAACATTATGGGCCGCGAAGCCTAGCTTTCGCTTAAGCTCCAACG 5 0.125 No Hit GGAACTTCAAGAGCAGCTAGATCTAGAGGGAAGTTGTGAGCATTACGTTC 5 0.125 No Hit CACCATTGTATAACCATTCATCAACGGATGCAGCTTCCCAAATTGGGTAA 5 0.125 No Hit GCAGCCACAATATTATAAGTCTCTTCCTCTTGACCAAATTTGTAACCCTC 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 warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position TGTGAGC 25 0.0020930516 35.17 38 GAGCATT 25 0.0020930516 35.17 41 GTGAGCA 25 0.0020930516 35.17 39 CATTACG 25 0.0020930516 35.17 44 GGAAGTT 25 0.0020930516 35.17 32 AGTTGTG 25 0.0020930516 35.17 35 AGCATTA 25 0.0020930516 35.17 42 GGGAAGT 25 0.0020930516 35.17 31 TTGTGAG 25 0.0020930516 35.17 37 TGAGCAT 25 0.0020930516 35.17 40 AAGTTGT 25 0.0020930516 35.17 34 GTTGTGA 25 0.0020930516 35.17 36 GCGGGAA 30 0.004803603 29.679325 1 TCTAGAG 30 0.005116581 29.308332 25 ATCTAGA 30 0.005116581 29.308332 24 AGAGGGA 30 0.005116581 29.308332 28 GATCTAG 30 0.005116581 29.308332 23 TAGAGGG 30 0.005116581 29.308332 27 CTAGAGG 30 0.005116581 29.308332 26 GAGGGAA 30 0.005116581 29.308332 29 >>END_MODULE Read 863259 spots for SRR1772223.sra Written 863259 spots for SRR1772223.sra Read 863259 spots for SRR1772223.sra Written 863259 spots for SRR1772223.sra Read 863259 spots for SRR1772223.sra Written 863259 spots for SRR1772223.sra Read 863259 spots for SRR1772223.sra Written 863259 spots for SRR1772223.sra Read 863259 spots for SRR1772223.sra Written 863259 spots for SRR1772223.sra Read 863259 spots for SRR1772223.sra Written 863259 spots for SRR1772223.sra Read 863259 spots for SRR1772223.sra Written 863259 spots for SRR1772223.sra Read 863259 spots for SRR1772223.sra Written 863259 spots for SRR1772223.sra Read 863259 spots for SRR1772223.sra Written 863259 spots for SRR1772223.sra Read 863259 spots for SRR1772223.sra Written 863259 spots for SRR1772223.sra Read 863259 spots for SRR1772223.sra Written 863259 spots for SRR1772223.sra Read 863259 spots for SRR1772223.sra Written 863259 spots for SRR1772223.sra Read 863259 spots for SRR1772223.sra Written 863259 spots for SRR1772223.sra Read 863259 spots for SRR1772223.sra Written 863259 spots for SRR1772223.sra Read 863259 spots for SRR1772223.sra Written 863259 spots for SRR1772223.sra Read 863274 spots for SRR1772223.sra Written 863274 spots for SRR1772223.sra Read 863259 spots for SRR1772223.sra Written 863259 spots for SRR1772223.sra Read 863259 spots for SRR1772223.sra Written 863259 spots for SRR1772223.sra Read 863259 spots for SRR1772223.sra Written 863259 spots for SRR1772223.sra Read 863259 spots for SRR1772223.sra Written 863259 spots for SRR1772223.sra SRR ids: ['SRR1772223.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_bbhqpahe SRR1772223.sra spots: 17265195 blocks: [[1, 863259], [863260, 1726518], [1726519, 2589777], [2589778, 3453036], [3453037, 4316295], [4316296, 5179554], [5179555, 6042813], [6042814, 6906072], [6906073, 7769331], [7769332, 8632590], [8632591, 9495849], [9495850, 10359108], [10359109, 11222367], [11222368, 12085626], [12085627, 12948885], [12948886, 13812144], [13812145, 14675403], [14675404, 15538662], [15538663, 16401921], [16401922, 17265195]] SRR1772223 file size 2981503 SRR1772223 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 SRR1772223 SRR1772223_1.fastq Input file: SRR1772223_1.fastq trimmed: SRR1772223-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 19:13:44 2024 >> started Sat Dec 7 19:13:57 2024 >> done (12.458s) 17265195 reads processed; of these: 2214 ( 0.01%) short reads filtered out after trimming by size control 172024 ( 1.00%) empty reads filtered out after trimming by size control 17090957 (98.99%) reads available; of these: 801213 ( 4.69%) trimmed reads available after processing 16289744 (95.31%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 1086 0.01% 19 1580 0.01% 20 3208 0.02% 21 3517 0.02% 22 4590 0.03% 23 4482 0.03% 24 6496 0.04% 25 7247 0.04% 26 6345 0.04% 27 8168 0.05% 28 8599 0.05% 29 15060 0.09% 30 12476 0.07% 31 13464 0.08% 32 16821 0.10% 33 11756 0.07% 34 12160 0.07% 35 15555 0.09% 36 14996 0.09% 37 21560 0.13% 38 16444 0.10% 39 18306 0.11% 40 29480 0.17% 41 25450 0.15% 42 45717 0.27% 43 42477 0.25% 44 58286 0.34% 45 54004 0.32% 46 66752 0.39% 47 83375 0.49% 48 90665 0.53% 49 81091 0.47% 50 16289744 95.31% 17090957 reads passed initial QC criterion=sequence-density sequence-density=0.22 sequence-density-rank=1 fanout-score=0.00 fanout-score-rank=18 prefix-density=0.00 prefix-fanout=1.0 sequence=TGCGGGAACTTC criterion=fanout-score sequence-density=0.01 sequence-density-rank=42 fanout-score=14.62 fanout-score-rank=1 prefix-density=0.07 prefix-fanout=1.2 sequence=AGGAGAGCCGCCGACTCCAACTATCGTCCATGTACGATCCATACTAGATCTGACCAACTGCCCATCCTACCTCCTCTACCTTTTTGACAGCCCATCTTTTTGTCTCAGTAGAGTCTTTCAGTGGCATGTTTCAGTCCTCTTCCCCATTACTTAGAAAAAGTGAGCCACCGGTTCAGGTACAAGATACTATCATTACCGCCTGGACAATTAGACAG Started job on | Dec 07 19:14:11 Started mapping on | Dec 07 19:14:11 Finished on | Dec 07 19:14:25 Mapping speed, Million of reads per hour | 4394.82 Number of input reads | 17090957 Average input read length | 49 UNIQUE READS: Uniquely mapped reads number | 4644321 Uniquely mapped reads % | 27.17% Average mapped length | 49.40 Number of splices: Total | 322957 Number of splices: Annotated (sjdb) | 306136 Number of splices: GT/AG | 316941 Number of splices: GC/AG | 3887 Number of splices: AT/AC | 166 Number of splices: Non-canonical | 1963 Mismatch rate per base, % | 0.26% Deletion rate per base | 0.01% Deletion average length | 1.54 Insertion rate per base | 0.01% Insertion average length | 1.40 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 12125079 % of reads mapped to multiple loci | 70.94% Number of reads mapped to too many loci | 34520 % of reads mapped to too many loci | 0.20% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 1.67% % of reads unmapped: other | 0.01% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 321557 321557 321557 N_multimapping 12125079 12125079 12125079 N_noFeature 888933 4505917 962176 N_ambiguous 96928 799 32084 UnstrandedReadsAssigned:3658460 PositiveStrandReadsAssigned:137605 NegativeStrandReadsAssigned:3650061 Dataset is classified negative stranded MeadianReadLen=50 20thPercentileLength=50 echo kmer=45 SRR1772223 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: SRR1772223-trimmed.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 17,090,957 reads, 14,426,771 reads pseudoaligned [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 976 rounds 52973 SRR1772223.ke.tsv 35125 SRR1772223.se.tsv 88098 total ==> SRR1772223.ke.tsv <== target_id length eff_length est_counts tpm PNS24245 936 837 0 0 PNS24247 1044 945 2.32774 0.19282 PNS24249 1928 1829 38.0168 1.62708 PNS24246 1044 945 2.32774 0.19282 PNS24248 1044 945 2.32774 0.19282 PNS24244 1471 1372 0 0 PNS24243 293 194 0 0 KQK14069 1603 1504 209.074 10.8818 KQK14071 474 375 106.546 22.241 ==> SRR1772223.se.tsv <== BRADI_1g14170v3 528 BRADI_1g53295v3 4 BRADI_1g59795v3 28 BRADI_1g07683v3 0 BRADI_1g00485v3 0 BRADI_1g20270v3 61 BRADI_1g74790v3 7 BRADI_1g09890v3 0 BRADI_1g77505v3 34 BRADI_1g48960v3 0 SRR1772223 completed mapping pipeline successfully