Starting /dee2/code/volunteer_pipeline.sh SRR1772227 current disk space = 1540230361088 free memory = 1448319396 SRR1772227 SRAfilesize 8378dbb96b6cee51a52ae1055c9bb436 SRR1772227.sra SRR1772227.sra file validated SRR1772227 is single end SRR1772227 is conventional basespace SRR1772227 read1 length is 50 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR1772227_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 32.9295 34.0 31.0 34.0 31.0 34.0 2 33.06525 34.0 31.0 34.0 31.0 34.0 3 32.8265 34.0 31.0 34.0 31.0 34.0 4 36.226 37.0 37.0 37.0 35.0 37.0 5 36.31075 37.0 37.0 37.0 35.0 37.0 6 36.225 37.0 37.0 37.0 35.0 37.0 7 36.2765 37.0 37.0 37.0 35.0 37.0 8 36.29325 37.0 37.0 37.0 35.0 37.0 9 38.044 39.0 38.0 39.0 35.0 39.0 10 37.9135 39.0 38.0 39.0 35.0 39.0 11 37.981 39.0 38.0 39.0 35.0 39.0 12 38.04175 39.0 38.0 39.0 35.0 39.0 13 38.01 39.0 38.0 39.0 35.0 39.0 14 39.24525 41.0 39.0 41.0 36.0 41.0 15 39.4465 41.0 39.0 41.0 36.0 41.0 16 39.15375 41.0 39.0 41.0 36.0 41.0 17 39.40675 41.0 39.0 41.0 36.0 41.0 18 39.445 41.0 39.0 41.0 36.0 41.0 19 39.33175 41.0 39.0 41.0 36.0 41.0 20 39.3055 41.0 39.0 41.0 36.0 41.0 21 39.1805 41.0 39.0 41.0 36.0 41.0 22 39.25 41.0 39.0 41.0 36.0 41.0 23 39.0385 41.0 39.0 41.0 36.0 41.0 24 39.101 40.0 39.0 41.0 36.0 41.0 25 39.14075 41.0 39.0 41.0 36.0 41.0 26 38.62625 40.0 38.0 41.0 34.0 41.0 27 38.76925 40.0 38.0 41.0 35.0 41.0 28 38.82 40.0 38.0 41.0 35.0 41.0 29 38.73825 40.0 38.0 41.0 35.0 41.0 30 38.61375 40.0 38.0 41.0 35.0 41.0 31 38.51125 40.0 38.0 41.0 35.0 41.0 32 38.48275 40.0 38.0 41.0 35.0 41.0 33 38.508 40.0 38.0 41.0 34.0 41.0 34 38.8725 40.0 38.0 41.0 36.0 41.0 35 38.78125 40.0 38.0 41.0 35.0 41.0 36 38.72375 40.0 38.0 41.0 35.0 41.0 37 38.36975 40.0 38.0 41.0 34.0 41.0 38 37.96975 40.0 38.0 41.0 33.0 41.0 39 38.08475 40.0 38.0 41.0 33.0 41.0 40 38.004 40.0 38.0 41.0 33.0 41.0 41 37.88425 40.0 38.0 41.0 33.0 41.0 42 38.113 40.0 38.0 41.0 34.0 41.0 43 37.96675 40.0 38.0 41.0 33.0 41.0 44 37.8295 40.0 38.0 41.0 33.0 41.0 45 37.65675 40.0 38.0 41.0 33.0 41.0 46 37.7335 40.0 38.0 41.0 33.0 41.0 47 37.24075 40.0 38.0 41.0 32.0 41.0 48 37.22 40.0 38.0 41.0 33.0 41.0 49 37.30525 40.0 38.0 41.0 33.0 41.0 50 37.0045 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 11 1.0 12 0.0 13 2.0 14 2.0 15 2.0 16 2.0 17 3.0 18 1.0 19 2.0 20 6.0 21 2.0 22 9.0 23 3.0 24 8.0 25 9.0 26 13.0 27 23.0 28 22.0 29 20.0 30 35.0 31 42.0 32 72.0 33 96.0 34 124.0 35 143.0 36 212.0 37 305.0 38 605.0 39 2236.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 43.38253690267701 11.933950462847136 10.683012259194395 34.00050037528146 2 28.175 13.05 29.049999999999997 29.725 3 39.612188365650965 16.444220599345254 20.29715436917653 23.64643666582725 4 33.375 25.424999999999997 16.125 25.074999999999996 5 33.95 29.9 20.125 16.025 6 24.4 34.55 16.975 24.075 7 10.75 39.65 33.675 15.925 8 19.55 30.25 29.375 20.825 9 22.7 20.65 33.725 22.925 10 15.625 43.4 25.05 15.925 11 26.825 31.15 19.05 22.975 12 26.275 30.0 21.4 22.325 13 19.075 41.4 22.900000000000002 16.625 14 24.775 31.225 26.825 17.175 15 20.5 38.625 20.200000000000003 20.674999999999997 16 23.075000000000003 33.575 21.349999999999998 22.0 17 23.625 34.575 21.425 20.375 18 18.3 35.75 24.85 21.099999999999998 19 19.525000000000002 32.95 24.85 22.675 20 15.15 35.55 27.800000000000004 21.5 21 19.425 28.575 28.050000000000004 23.95 22 13.900000000000002 45.375 22.15 18.575 23 19.15 37.574999999999996 25.224999999999998 18.05 24 17.0 36.625 22.075 24.3 25 18.7 32.35 28.7 20.25 26 16.925 36.275 21.525 25.275 27 22.5 31.175000000000004 27.1 19.225 28 24.925 40.949999999999996 19.0 15.125 29 27.775 33.050000000000004 22.15 17.025000000000002 30 23.9 33.975 25.85 16.275000000000002 31 30.25 26.625 21.075 22.05 32 25.074999999999996 33.425 22.975 18.525 33 26.724999999999998 32.75 20.349999999999998 20.175 34 22.675 40.699999999999996 18.2 18.425 35 23.825 35.825 21.525 18.825 36 21.025 27.500000000000004 28.7 22.775000000000002 37 24.9248496993988 29.183366733466933 28.557114228456914 17.334669338677354 38 20.125 26.424999999999997 34.0 19.45 39 24.425 28.499999999999996 27.675 19.400000000000002 40 22.125 33.2 25.724999999999998 18.95 41 22.975 25.074999999999996 26.375 25.575 42 19.725 34.4 23.9 21.975 43 20.75 33.025 26.5 19.725 44 18.6 28.299999999999997 27.6 25.5 45 17.580766341096922 33.057851239669425 31.755572251440018 17.60581016779364 46 17.733866933466732 28.714357178589296 33.991995997999 19.559779889944974 47 21.060530265132567 32.91645822911456 26.91345672836418 19.109554777388695 48 21.45 33.75 25.474999999999998 19.325 49 20.05501375343836 34.98374593648413 24.33108277069267 20.630157539384847 50 26.55 25.75 27.650000000000002 20.05 >>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 0.5 10 1.0 11 1.0 12 1.0 13 0.5 14 0.0 15 0.5 16 1.0 17 1.5 18 2.0 19 4.0 20 6.0 21 8.5 22 11.0 23 9.0 24 7.0 25 22.5 26 38.0 27 35.5 28 33.0 29 32.0 30 31.0 31 52.0 32 73.0 33 129.0 34 185.0 35 280.5 36 376.0 37 460.0 38 544.0 39 442.0 40 340.0 41 350.5 42 361.0 43 422.5 44 484.0 45 431.0 46 378.0 47 290.5 48 203.0 49 258.5 50 314.0 51 275.0 52 236.0 53 165.5 54 95.0 55 78.0 56 61.0 57 47.0 58 33.0 59 37.0 60 41.0 61 32.5 62 24.0 63 22.0 64 20.0 65 21.0 66 22.0 67 19.5 68 17.0 69 18.5 70 20.0 71 19.0 72 18.0 73 15.5 74 13.0 75 7.0 76 1.0 77 3.0 78 5.0 79 3.5 80 2.0 81 2.0 82 2.0 83 1.5 84 1.0 85 0.5 86 0.0 87 0.0 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 0.075 2 0.0 3 0.7250000000000001 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 0.05 47 0.05 48 0.0 49 0.025 50 0.0 >>END_MODULE >>Sequence Length Distribution pass #Length Count 50 4000.0 >>END_MODULE >>Sequence Duplication Levels fail #Total Deduplicated Percentage 47.125 #Duplication Level Percentage of deduplicated Percentage of total 1 83.92572944297082 39.550000000000004 2 7.2148541114058355 6.800000000000001 3 2.493368700265252 3.5249999999999995 4 1.5384615384615385 2.9000000000000004 5 1.1140583554376657 2.625 6 0.15915119363395225 0.44999999999999996 7 0.47745358090185674 1.575 8 0.2652519893899204 1.0 9 0.3183023872679045 1.35 >10 2.0159151193633953 19.475 >50 0.3183023872679045 9.925 >100 0.15915119363395225 10.825 >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 182 4.55 No Hit GATCGGAAGAGCACACGTCTGAACTCCAGTCACAGCGTAGCATCTCGTAT 146 3.65 TruSeq Adapter, Index 1 (97% over 36bp) GGGAACTTCAAGAGCAGCTAGATCTAGAGGGAAGTTGTGAGCATTACGTT 105 2.625 No Hit CTGCGATGAAGGCGATAATAAATACAGAAGTTGCGGTCAATAAGGTAGGG 87 2.175 No Hit GTGCTCTGCCTGGAATACAATCATAAAGTTGAAAGTACCAGATATTCCTA 76 1.9 No Hit GCGGTCAATAAGGTAGGGATCATCAAAACACCGAACCATCCGATGTAAAG 68 1.7000000000000002 No Hit GTTGTGCTCTGCCTGGAATACAATCATAAAGTTGAAAGTACCAGATATTC 57 1.425 No Hit CTCTGCCTGGAATACAATCATAAAGTTGAAAGTACCAGATATTCCTAAAG 55 1.375 No Hit CGGGAACTTCAAGAGCAGCTAGATCTAGAGGGAAGTTGTGAGCATTACGT 54 1.35 No Hit GCGATGAAGGCGATAATAAATACAGAAGTTGCGGTCAATAAGGTAGGGAT 50 1.25 No Hit TCTGCCTGGAATACAATCATAAAGTTGAAAGTACCAGATATTCCTAAAGG 46 1.15 No Hit CGGTCAATAAGGTAGGGATCATCAAAACACCGAACCATCCGATGTAAAGA 36 0.8999999999999999 No Hit GCCTGGAATACAATCATAAAGTTGAAAGTACCAGATATTCCTAAAGGCAT 34 0.8500000000000001 No Hit GTCAATAAGGTAGGGATCATCAAAACACCGAACCATCCGATGTAAAGACG 34 0.8500000000000001 No Hit GCGGAAAAACCTTATCCATTAATAGCGGGAACTTCAAGAGCAGCTAGATC 33 0.8250000000000001 No Hit CGCGACCTTGACTATCAACTACAGATTGGTTGAAATTGAATCCATTTAGG 32 0.8 No Hit ACGCGACCTTGACTATCAACTACAGATTGGTTGAAATTGAATCCATTTAG 29 0.7250000000000001 No Hit CAATAAGGTAGGGATCATCAAAACACCGAACCATCCGATGTAAAGACGAT 28 0.7000000000000001 No Hit GCGACCTTGACTATCAACTACAGATTGGTTGAAATTGAATCCATTTAGGT 28 0.7000000000000001 No Hit CGCAGAAGTAGGAATAATAGCACCAGAGATAATATTGTTTCCATAAAGTA 26 0.65 No Hit ATAAGGATGTTGTGCTCTGCCTGGAATACAATCATAAAGTTGAAAGTACC 24 0.6 No Hit CTGGAATACAATCATAAAGTTGAAAGTACCAGATATTCCTAAAGGCATAC 24 0.6 No Hit CGGAAAAACCTTATCCATTAATAGCGGGAACTTCAAGAGCAGCTAGATCT 22 0.5499999999999999 No Hit GGCCAAAATAACCATGAGCAGCCACAATATTATAAGTCTCTTCCTCTTGA 21 0.525 No Hit GGCGATAATAAATACAGAAGTTGCGGTCAATAAGGTAGGGATCATCAAAA 21 0.525 No Hit GGTCAATAAGGTAGGGATCATCAAAACACCGAACCATCCGATGTAAAGAC 19 0.475 No Hit GCCAAAATAACCATGAGCAGCCACAATATTATAAGTCTCTTCCTCTTGAC 19 0.475 No Hit GCTCTGCCTGGAATACAATCATAAAGTTGAAAGTACCAGATATTCCTAAA 18 0.44999999999999996 No Hit AATAAATACAGAAGTTGCGGTCAATAAGGTAGGGATCATCAAAACACCGA 16 0.4 No Hit GCTGCGATGAAGGCGATAATAAATACAGAAGTTGCGGTCAATAAGGTAGG 15 0.375 No Hit CGATGAAGGCGATAATAAATACAGAAGTTGCGGTCAATAAGGTAGGGATC 15 0.375 No Hit CTCGCGAATACCATCAATATCTACTGGAGGGGCTGCGATGAAGGCGATAA 15 0.375 No Hit GGAGGGGCTGCGATGAAGGCGATAATAAATACAGAAGTTGCGGTCAATAA 14 0.35000000000000003 No Hit CTCATTAGCAGATTCATTTTCAGTAGTTTCCCTGATCAAACTAGAGGTTA 14 0.35000000000000003 No Hit TGTGCTCTGCCTGGAATACAATCATAAAGTTGAAAGTACCAGATATTCCT 13 0.325 No Hit TTGTGCTCTGCCTGGAATACAATCATAAAGTTGAAAGTACCAGATATTCC 13 0.325 No Hit GCGATAATAAATACAGAAGTTGCGGTCAATAAGGTAGGGATCATCAAAAC 12 0.3 No Hit CCCAAGTATTAATAACGCGACCTTGACTATCAACTACAGATTGGTTGAAA 12 0.3 No Hit CTTTCTTTTCTTCAAAAATTCTTATATGTTAGCGGAAAAACCTTATCCAT 12 0.3 No Hit TGCTCTGCCTGGAATACAATCATAAAGTTGAAAGTACCAGATATTCCTAA 11 0.27499999999999997 No Hit TGCGGGAACTTCAAGAGCAGCTAGATCTAGAGGGAAGTTGTGAGCATTAC 11 0.27499999999999997 No Hit GGATGCATAAGGATGTTGTGCTCTGCCTGGAATACAATCATAAAGTTGAA 11 0.27499999999999997 No Hit GGGGCTGCGATGAAGGCGATAATAAATACAGAAGTTGCGGTCAATAAGGT 11 0.27499999999999997 No Hit AATAAGGTAGGGATCATCAAAACACCGAACCATCCGATGTAAAGACGATT 10 0.25 No Hit GGAAAAACCTTATCCATTAATAGCGGGAACTTCAAGAGCAGCTAGATCTA 10 0.25 No Hit TTTCTTTTCTTCAAAAATTCTTATATGTTAGCGGAAAAACCTTATCCATT 10 0.25 No Hit GCGCGACCTTGACTATCAACTACAGATTGGTTGAAATTGAATCCATTTAG 10 0.25 No Hit ATGCATAAGGATGTTGTGCTCTGCCTGGAATACAATCATAAAGTTGAAAG 9 0.22499999999999998 No Hit CCACCATTGTATAACCATTCATCAACGGATGCAGCTTCCCAAATTGGGTA 9 0.22499999999999998 No Hit GTTCGCTGGAGTAGGCTGCGAGGCCCAAGCGGCCAAGGAGTGCAGCGGCC 9 0.22499999999999998 No Hit CCAAGTATTAATAACGCGACCTTGACTATCAACTACAGATTGGTTGAAAT 9 0.22499999999999998 No Hit CTGCCTGGAATACAATCATAAAGTTGAAAGTACCAGATATTCCTAAAGGC 9 0.22499999999999998 No Hit AGGGGCTGCGATGAAGGCGATAATAAATACAGAAGTTGCGGTCAATAAGG 9 0.22499999999999998 No Hit CCGCAGAAGTAGGAATAATAGCACCAGAGATAATATTGTTTCCATAAAGT 8 0.2 No Hit CGCGGTCAATAAGGTAGGGATCATCAAAACACCGAACCATCCGATGTAAA 8 0.2 No Hit GCTAGTTATCCAGTTGCAGAAGCGACCCCACAGGCTTGTACTTTCGCGTC 8 0.2 No Hit CGCTGGAGTAGGCTGCGAGGCCCAAGCGGCCAAGGAGTGCAGCGGCCCGT 8 0.2 No Hit ATAACAAGCTACACCAAGTAAGAAGTGTAGAACAATTAGCTCATAAGGAC 8 0.2 No Hit TTCAAGAGCAGCTAGATCTAGAGGGAAGTTGTGAGCATTACGTTCGTGCA 7 0.17500000000000002 No Hit CTGTGCCTGCCAACATTATGGGCCGCGAAGCCTAGCTTTCGCTTAAGCTC 7 0.17500000000000002 No Hit ATGAAGGCGATAATAAATACAGAAGTTGCGGTCAATAAGGTAGGGATCAT 7 0.17500000000000002 No Hit CGTCTCTCTAAAATTGCAGTCATGGTAAGATCTTGGTTTATTCAAATTGC 7 0.17500000000000002 No Hit CCACAATATTATAAGTCTCTTCCTCTTGACCAAATTTGTAACCCTCATTA 7 0.17500000000000002 No Hit AGCAGCCACAATATTATAAGTCTCTTCCTCTTGACCAAATTTGTAACCCT 7 0.17500000000000002 No Hit GTTGAAACTAGCATATTGGAAGATTAATCGGCCAAAATAACCATGAGCAG 7 0.17500000000000002 No Hit GGAACTTCAAGAGCAGCTAGATCTAGAGGGAAGTTGTGAGCATTACGTTC 7 0.17500000000000002 No Hit GCAGCCACAATATTATAAGTCTCTTCCTCTTGACCAAATTTGTAACCCTC 7 0.17500000000000002 No Hit CTTTTCTTCAAAAATTCTTATATGTTAGCGGAAAAACCTTATCCATTAAT 6 0.15 No Hit GTTGATGATATCAGCCCAAGTATTAATAACGCGACCTTGACTATCAACTA 6 0.15 No Hit CACGGTTGATGATATCAGCCCAAGTATTAATAACGCGACCTTGACTATCA 6 0.15 No Hit GCACGGTTGATGATATCAGCCCAAGTATTAATAACGCGACCTTGACTATC 5 0.125 No Hit AGAGAAGCTTCCTTGACCAATAGGGTAAATCAAGAAAACAGCAGTCGCAG 5 0.125 No Hit CGCCGCAGAAGTAGGAATAATAGCACCAGAGATAATATTGTTTCCATAAA 5 0.125 No Hit GCCGAAAACACCAGCTACACCTAACATGTGAAATGGATGCATAAGGATGT 5 0.125 No Hit CTGGAGTAGGCTGCGAGGCCCAAGCGGCCAAGGAGTGCAGCGGCCCGTTA 5 0.125 No Hit GGGTAATGTTGCTCCAATACCTAACCAAAGAGCTACTGCAGTACCGATTA 5 0.125 No Hit CGTGCTCTGCCTGGAATACAATCATAAAGTTGAAAGTACCAGATATTCCT 5 0.125 No Hit CAAGTATTAATAACGCGACCTTGACTATCAACTACAGATTGGTTGAAATT 5 0.125 No Hit CCCCAGTTAAGTAGTCATGCATTACAATAGGAACACCTAATTCTCTCGCA 5 0.125 No Hit TGATGATATCAGCCCAAGTATTAATAACGCGACCTTGACTATCAACTACA 5 0.125 No Hit TGGAGGGGCTGCGATGAAGGCGATAATAAATACAGAAGTTGCGGTCAATA 5 0.125 No Hit CGCGTCTCTCTAAAATTGCAGTCATGGTAAGATCTTGGTTTATTCAAATT 5 0.125 No Hit GTGAGCATTACGTTCGTGCATTACTTCCATACCAAGATTAGCACGGTTGA 5 0.125 No Hit GGGCTGCGATGAAGGCGATAATAAATACAGAAGTTGCGGTCAATAAGGTA 5 0.125 No Hit CGCAGCTGCAACAGGAGCTGAATATGCAACAGCAATCCAAGGGCGCATAC 5 0.125 No Hit AGCGGGAACTTCAAGAGCAGCTAGATCTAGAGGGAAGTTGTGAGCATTAC 5 0.125 No Hit GCGAATACCATCAATATCTACTGGAGGGGCTGCGATGAAGGCGATAATAA 5 0.125 No Hit GTGCTAGTTATCCAGTTGCAGAAGCGACCCCACAGGCTTGTACTTTCGCG 5 0.125 No Hit CTAGTTATCCAGTTGCAGAAGCGACCCCACAGGCTTGTACTTTCGCGTCT 5 0.125 No Hit GCTAGATCTAGAGGGAAGTTGTGAGCATTACGTTCGTGCATTACTTCCAT 5 0.125 No Hit CTCTTGACCAAATTTGTAACCCTCATTAGCAGATTCATTTTCAGTAGTTT 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 ACAGCGT 25 3.6958358E-5 44.0 32 ACACGTC 25 3.6958358E-5 44.0 13 ATCTCGT 25 3.6958358E-5 44.0 42 CAGTCAC 25 3.6958358E-5 44.0 27 GTCACAG 25 3.6958358E-5 44.0 29 CACACGT 25 3.6958358E-5 44.0 12 ACGTCTG 25 3.6958358E-5 44.0 15 CCAGTCA 25 3.6958358E-5 44.0 26 CACGTCT 25 3.6958358E-5 44.0 14 CATCTCG 25 3.6958358E-5 44.0 41 CTCCAGT 25 3.6958358E-5 44.0 24 GATCGGA 25 3.6958358E-5 44.0 1 ACTCCAG 25 3.6958358E-5 44.0 23 GTCTGAA 25 3.6958358E-5 44.0 17 CGTAGCA 25 3.6958358E-5 44.0 36 TCCAGTC 25 3.6958358E-5 44.0 25 TCGGAAG 25 3.6958358E-5 44.0 3 TAGCATC 25 3.6958358E-5 44.0 38 AACTCCA 25 3.6958358E-5 44.0 22 GAGCACA 25 3.6958358E-5 44.0 9 >>END_MODULE Read 1142686 spots for SRR1772227.sra Written 1142686 spots for SRR1772227.sra Read 1142686 spots for SRR1772227.sra Written 1142686 spots for SRR1772227.sra Read 1142686 spots for SRR1772227.sra Written 1142686 spots for SRR1772227.sra Read 1142686 spots for SRR1772227.sra Written 1142686 spots for SRR1772227.sra Read 1142686 spots for SRR1772227.sra Written 1142686 spots for SRR1772227.sra Read 1142686 spots for SRR1772227.sra Written 1142686 spots for SRR1772227.sra Read 1142686 spots for SRR1772227.sra Written 1142686 spots for SRR1772227.sra Read 1142686 spots for SRR1772227.sra Written 1142686 spots for SRR1772227.sra Read 1142686 spots for SRR1772227.sra Written 1142686 spots for SRR1772227.sra Read 1142686 spots for SRR1772227.sra Written 1142686 spots for SRR1772227.sra Read 1142692 spots for SRR1772227.sra Written 1142692 spots for SRR1772227.sra Read 1142686 spots for SRR1772227.sra Written 1142686 spots for SRR1772227.sra Read 1142686 spots for SRR1772227.sra Written 1142686 spots for SRR1772227.sra Read 1142686 spots for SRR1772227.sra Written 1142686 spots for SRR1772227.sra Read 1142686 spots for SRR1772227.sra Written 1142686 spots for SRR1772227.sra Read 1142686 spots for SRR1772227.sra Written 1142686 spots for SRR1772227.sra Read 1142686 spots for SRR1772227.sra Written 1142686 spots for SRR1772227.sra Read 1142686 spots for SRR1772227.sra Written 1142686 spots for SRR1772227.sra Read 1142686 spots for SRR1772227.sra Written 1142686 spots for SRR1772227.sra Read 1142686 spots for SRR1772227.sra Written 1142686 spots for SRR1772227.sra SRR ids: ['SRR1772227.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_x9uo44pd SRR1772227.sra spots: 22853726 blocks: [[1, 1142686], [1142687, 2285372], [2285373, 3428058], [3428059, 4570744], [4570745, 5713430], [5713431, 6856116], [6856117, 7998802], [7998803, 9141488], [9141489, 10284174], [10284175, 11426860], [11426861, 12569546], [12569547, 13712232], [13712233, 14854918], [14854919, 15997604], [15997605, 17140290], [17140291, 18282976], [18282977, 19425662], [19425663, 20568348], [20568349, 21711034], [21711035, 22853726]] SRR1772227 file size 3950108 SRR1772227 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 SRR1772227 SRR1772227_1.fastq Input file: SRR1772227_1.fastq trimmed: SRR1772227-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 19:20:39 2024 >> started Sat Dec 7 19:20:56 2024 >> done (17.212s) 22853726 reads processed; of these: 2882 ( 0.01%) short reads filtered out after trimming by size control 765811 ( 3.35%) empty reads filtered out after trimming by size control 22085033 (96.64%) reads available; of these: 1030471 ( 4.67%) trimmed reads available after processing 21054562 (95.33%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 1626 0.01% 19 2234 0.01% 20 5691 0.03% 21 5346 0.02% 22 6623 0.03% 23 5772 0.03% 24 8966 0.04% 25 9237 0.04% 26 7565 0.03% 27 9971 0.05% 28 11416 0.05% 29 19841 0.09% 30 16237 0.07% 31 18131 0.08% 32 22510 0.10% 33 14987 0.07% 34 15967 0.07% 35 19906 0.09% 36 19004 0.09% 37 27322 0.12% 38 20745 0.09% 39 22631 0.10% 40 37834 0.17% 41 31572 0.14% 42 59270 0.27% 43 54822 0.25% 44 74103 0.34% 45 69960 0.32% 46 84256 0.38% 47 106801 0.48% 48 117044 0.53% 49 103081 0.47% 50 21054562 95.33% 22085033 reads passed initial QC criterion=sequence-density sequence-density=0.28 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=27 fanout-score=21.19 fanout-score-rank=1 prefix-density=0.07 prefix-fanout=3.7 sequence=AAAAAAGAATAGAGGTATGACAGGCATAAAATCCACGATTGGGTTGAAAATAGCATAAGCTTCGGGTAGTTTAGCAAAGAAAAAACTAGTCGGATAAAGAACACAATTAAAACAGATACAGGTTAAACTAAGTATATTAGGCATAACAAGCATTT Started job on | Dec 07 19:21:08 Started mapping on | Dec 07 19:21:08 Finished on | Dec 07 19:21:25 Mapping speed, Million of reads per hour | 4676.83 Number of input reads | 22085033 Average input read length | 49 UNIQUE READS: Uniquely mapped reads number | 4872570 Uniquely mapped reads % | 22.06% Average mapped length | 49.42 Number of splices: Total | 303353 Number of splices: Annotated (sjdb) | 286882 Number of splices: GT/AG | 297334 Number of splices: GC/AG | 3791 Number of splices: AT/AC | 155 Number of splices: Non-canonical | 2073 Mismatch rate per base, % | 0.26% Deletion rate per base | 0.01% Deletion average length | 1.40 Insertion rate per base | 0.01% Insertion average length | 1.36 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 16881515 % of reads mapped to multiple loci | 76.44% Number of reads mapped to too many loci | 44374 % of reads mapped to too many loci | 0.20% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 1.29% % of reads unmapped: other | 0.01% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 330948 330948 330948 N_multimapping 16881515 16881515 16881515 N_noFeature 1106575 4739299 1172377 N_ambiguous 104634 922 37016 UnstrandedReadsAssigned:3661361 PositiveStrandReadsAssigned:132349 NegativeStrandReadsAssigned:3663177 Dataset is classified negative stranded MeadianReadLen=50 20thPercentileLength=50 echo kmer=45 SRR1772227 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: SRR1772227-trimmed.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 22,085,033 reads, 18,849,626 reads pseudoaligned [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,001 rounds 52973 SRR1772227.ke.tsv 35125 SRR1772227.se.tsv 88098 total ==> SRR1772227.ke.tsv <== target_id length eff_length est_counts tpm PNS24245 936 837 0 0 PNS24247 1044 945 3.43137 0.215267 PNS24249 1928 1829 34.7059 1.12494 PNS24246 1044 945 3.43137 0.215267 PNS24248 1044 945 3.43137 0.215267 PNS24244 1471 1372 0 0 PNS24243 293 194 0 0 KQK14069 1603 1504 63.6176 2.50767 KQK14071 474 375 33.154 5.24137 ==> SRR1772227.se.tsv <== BRADI_1g14170v3 159 BRADI_1g53295v3 4 BRADI_1g59795v3 33 BRADI_1g07683v3 0 BRADI_1g00485v3 0 BRADI_1g20270v3 20 BRADI_1g74790v3 14 BRADI_1g09890v3 0 BRADI_1g77505v3 32 BRADI_1g48960v3 0 SRR1772227 completed mapping pipeline successfully