Starting /dee2/code/volunteer_pipeline.sh SRR1772224 current disk space = 1539996946432 free memory = 1607451288 SRR1772224 SRAfilesize 27208966f22b50fac9e3e54011a24896 SRR1772224.sra SRR1772224.sra file validated SRR1772224 is single end SRR1772224 is conventional basespace SRR1772224 read1 length is 50 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR1772224_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 32.8925 34.0 31.0 34.0 31.0 34.0 2 33.017 34.0 31.0 34.0 31.0 34.0 3 32.862 34.0 31.0 34.0 31.0 34.0 4 36.2825 37.0 37.0 37.0 35.0 37.0 5 36.28025 37.0 37.0 37.0 35.0 37.0 6 36.21575 37.0 37.0 37.0 35.0 37.0 7 36.233 37.0 37.0 37.0 35.0 37.0 8 36.16875 37.0 37.0 37.0 35.0 37.0 9 37.97225 39.0 38.0 39.0 35.0 39.0 10 37.86525 39.0 38.0 39.0 35.0 39.0 11 37.8915 39.0 38.0 39.0 35.0 39.0 12 37.922 39.0 38.0 39.0 35.0 39.0 13 37.871 39.0 38.0 39.0 35.0 39.0 14 39.15125 41.0 39.0 41.0 36.0 41.0 15 39.34075 41.0 39.0 41.0 36.0 41.0 16 39.17125 41.0 39.0 41.0 36.0 41.0 17 39.34025 41.0 39.0 41.0 36.0 41.0 18 39.379 41.0 39.0 41.0 36.0 41.0 19 39.236 41.0 39.0 41.0 36.0 41.0 20 39.1885 41.0 39.0 41.0 36.0 41.0 21 39.0275 41.0 39.0 41.0 35.0 41.0 22 39.1445 41.0 39.0 41.0 36.0 41.0 23 38.9635 40.0 39.0 41.0 35.0 41.0 24 39.04225 41.0 39.0 41.0 36.0 41.0 25 39.0255 40.0 39.0 41.0 35.0 41.0 26 38.535 40.0 38.0 41.0 34.0 41.0 27 38.5955 40.0 38.0 41.0 34.0 41.0 28 38.60825 40.0 38.0 41.0 34.0 41.0 29 38.5425 40.0 38.0 41.0 34.0 41.0 30 38.37375 40.0 38.0 41.0 34.0 41.0 31 38.2815 40.0 38.0 41.0 34.0 41.0 32 38.093 40.0 38.0 41.0 33.0 41.0 33 38.11 40.0 38.0 41.0 34.0 41.0 34 38.4775 40.0 38.0 41.0 35.0 41.0 35 38.432 40.0 38.0 41.0 34.0 41.0 36 38.24975 40.0 38.0 41.0 34.0 41.0 37 37.9505 40.0 38.0 41.0 33.0 41.0 38 37.677 40.0 38.0 41.0 33.0 41.0 39 37.7325 40.0 38.0 41.0 33.0 41.0 40 37.7585 40.0 38.0 41.0 33.0 41.0 41 37.676 40.0 38.0 41.0 33.0 41.0 42 37.78875 40.0 38.0 41.0 33.0 41.0 43 37.64725 40.0 38.0 41.0 33.0 41.0 44 37.529 40.0 38.0 41.0 33.0 41.0 45 37.27125 40.0 37.0 41.0 32.0 41.0 46 37.3275 40.0 38.0 41.0 33.0 41.0 47 36.896 40.0 37.0 41.0 31.0 41.0 48 36.75 40.0 37.0 41.0 31.0 41.0 49 36.76775 40.0 37.0 41.0 31.0 41.0 50 36.4555 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 1.0 13 0.0 14 1.0 15 1.0 16 2.0 17 3.0 18 5.0 19 1.0 20 6.0 21 6.0 22 11.0 23 8.0 24 14.0 25 16.0 26 16.0 27 16.0 28 24.0 29 30.0 30 58.0 31 69.0 32 83.0 33 89.0 34 109.0 35 148.0 36 202.0 37 313.0 38 584.0 39 2184.0 >>END_MODULE >>Per base sequence content warn #Base G A T C 1 40.970485242621315 12.331165582791396 11.680840420210105 35.01750875437719 2 30.325000000000003 11.075 29.625 28.975 3 37.37449799196787 16.76706827309237 20.055220883534137 25.803212851405622 4 33.550000000000004 24.25 16.400000000000002 25.8 5 31.75 29.549999999999997 21.075 17.625 6 23.875 31.95 18.925 25.25 7 11.975 35.75 35.75 16.525000000000002 8 21.075 27.675 28.9 22.35 9 20.875 19.25 34.625 25.25 10 16.775000000000002 42.0 24.575 16.650000000000002 11 23.974999999999998 33.175 19.625 23.225 12 25.45 28.000000000000004 24.9 21.65 13 19.400000000000002 37.974999999999994 23.724999999999998 18.9 14 23.674999999999997 32.65 26.400000000000002 17.275 15 20.375 35.199999999999996 21.45 22.975 16 21.875 34.775 23.325000000000003 20.025000000000002 17 22.125 34.0 23.05 20.825 18 17.849999999999998 35.075 23.549999999999997 23.525 19 20.525 33.900000000000006 24.474999999999998 21.099999999999998 20 16.6 33.85 27.1 22.45 21 17.724999999999998 29.75 28.575 23.95 22 16.3 40.175 23.7 19.825 23 19.950000000000003 35.25 25.224999999999998 19.575 24 18.55 34.55 22.85 24.05 25 18.6 33.775 27.500000000000004 20.125 26 18.6 35.025 24.5 21.875 27 23.325000000000003 29.475 27.0 20.200000000000003 28 24.0 36.875 21.925 17.2 29 26.974999999999998 32.300000000000004 23.150000000000002 17.575 30 25.8 31.6 23.575 19.025 31 29.65 26.075 23.674999999999997 20.599999999999998 32 24.825 30.8 24.8 19.575 33 26.5 33.95 20.075000000000003 19.475 34 23.974999999999998 33.175 19.225 23.625 35 23.375 33.225 23.05 20.349999999999998 36 22.375 28.375 29.65 19.6 37 24.297893681043128 29.739217652958878 27.708124373119357 18.254764292878637 38 21.825 26.75 29.75 21.675 39 24.7 26.125 28.575 20.599999999999998 40 18.275 34.875 26.05 20.8 41 24.575 27.375 27.200000000000003 20.849999999999998 42 21.175 30.75 24.45 23.625 43 20.599999999999998 32.675 25.1 21.625 44 20.1 29.7 26.700000000000003 23.5 45 20.476190476190474 30.0 30.250626566416038 19.273182957393484 46 18.573216520650814 29.637046307884855 32.390488110137674 19.39924906132666 47 19.994994994994993 32.85785785785786 26.05105105105105 21.096096096096094 48 22.961480740370185 32.566283141570786 25.46273136568284 19.009504752376188 49 22.6976976976977 31.78178178178178 25.100100100100097 20.42042042042042 50 26.556639159789945 26.63165791447862 26.456614153538382 20.355088772193046 >>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 1.0 14 2.0 15 1.0 16 0.0 17 1.0 18 2.0 19 3.0 20 4.0 21 3.0 22 2.0 23 9.0 24 16.0 25 27.0 26 38.0 27 38.5 28 39.0 29 41.5 30 44.0 31 58.0 32 72.0 33 119.0 34 166.0 35 262.0 36 358.0 37 447.0 38 536.0 39 436.5 40 337.0 41 341.5 42 346.0 43 380.5 44 415.0 45 405.5 46 396.0 47 307.0 48 218.0 49 276.0 50 334.0 51 232.5 52 131.0 53 118.0 54 105.0 55 95.0 56 85.0 57 76.5 58 68.0 59 62.0 60 56.0 61 46.5 62 37.0 63 33.5 64 30.0 65 27.5 66 25.0 67 29.5 68 34.0 69 32.0 70 30.0 71 29.0 72 28.0 73 20.5 74 13.0 75 13.0 76 13.0 77 10.5 78 8.0 79 7.0 80 6.0 81 4.0 82 2.0 83 1.5 84 1.0 85 1.5 86 2.0 87 1.5 88 1.0 89 0.5 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 0.4 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 0.3 38 0.0 39 0.0 40 0.0 41 0.0 42 0.0 43 0.0 44 0.0 45 0.25 46 0.125 47 0.1 48 0.05 49 0.1 50 0.025 >>END_MODULE >>Sequence Length Distribution pass #Length Count 50 4000.0 >>END_MODULE >>Sequence Duplication Levels warn #Total Deduplicated Percentage 56.175 #Duplication Level Percentage of deduplicated Percentage of total 1 87.76145972407654 49.3 2 5.07343124165554 5.7 3 2.0026702269692924 3.375 4 1.2016021361815754 2.7 5 0.5785491766800178 1.625 6 0.3115264797507788 1.05 7 0.3115264797507788 1.225 8 0.48954161103693816 2.1999999999999997 9 0.26702269692923897 1.35 >10 1.7356475300400533 19.75 >50 0.22251891410769914 8.625 >100 0.04450378282153983 3.1 >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 124 3.1 No Hit GGGAACTTCAAGAGCAGCTAGATCTAGAGGGAAGTTGTGAGCATTACGTT 85 2.125 No Hit CTGCGATGAAGGCGATAATAAATACAGAAGTTGCGGTCAATAAGGTAGGG 80 2.0 No Hit GTGCTCTGCCTGGAATACAATCATAAAGTTGAAAGTACCAGATATTCCTA 76 1.9 No Hit GCGGTCAATAAGGTAGGGATCATCAAAACACCGAACCATCCGATGTAAAG 53 1.325 No Hit GATCGGAAGAGCACACGTCTGAACTCCAGTCACCGTACTAGATCTCGTAT 51 1.275 TruSeq Adapter, Index 22 (97% over 38bp) TCTGCCTGGAATACAATCATAAAGTTGAAAGTACCAGATATTCCTAAAGG 50 1.25 No Hit CTCTGCCTGGAATACAATCATAAAGTTGAAAGTACCAGATATTCCTAAAG 39 0.975 No Hit CGGGAACTTCAAGAGCAGCTAGATCTAGAGGGAAGTTGTGAGCATTACGT 38 0.95 No Hit GCGATGAAGGCGATAATAAATACAGAAGTTGCGGTCAATAAGGTAGGGAT 38 0.95 No Hit GTTGTGCTCTGCCTGGAATACAATCATAAAGTTGAAAGTACCAGATATTC 36 0.8999999999999999 No Hit GCGACCTTGACTATCAACTACAGATTGGTTGAAATTGAATCCATTTAGGT 33 0.8250000000000001 No Hit CGCGACCTTGACTATCAACTACAGATTGGTTGAAATTGAATCCATTTAGG 33 0.8250000000000001 No Hit GCCTGGAATACAATCATAAAGTTGAAAGTACCAGATATTCCTAAAGGCAT 32 0.8 No Hit ACGCGACCTTGACTATCAACTACAGATTGGTTGAAATTGAATCCATTTAG 31 0.775 No Hit CTGGAATACAATCATAAAGTTGAAAGTACCAGATATTCCTAAAGGCATAC 28 0.7000000000000001 No Hit GCTGCGATGAAGGCGATAATAAATACAGAAGTTGCGGTCAATAAGGTAGG 25 0.625 No Hit GGCGATAATAAATACAGAAGTTGCGGTCAATAAGGTAGGGATCATCAAAA 24 0.6 No Hit CGGAAAAACCTTATCCATTAATAGCGGGAACTTCAAGAGCAGCTAGATCT 21 0.525 No Hit CGGTCAATAAGGTAGGGATCATCAAAACACCGAACCATCCGATGTAAAGA 21 0.525 No Hit GGTCAATAAGGTAGGGATCATCAAAACACCGAACCATCCGATGTAAAGAC 20 0.5 No Hit GCTCTGCCTGGAATACAATCATAAAGTTGAAAGTACCAGATATTCCTAAA 20 0.5 No Hit GTCAATAAGGTAGGGATCATCAAAACACCGAACCATCCGATGTAAAGACG 18 0.44999999999999996 No Hit GGCCAAAATAACCATGAGCAGCCACAATATTATAAGTCTCTTCCTCTTGA 17 0.42500000000000004 No Hit ATAAGGATGTTGTGCTCTGCCTGGAATACAATCATAAAGTTGAAAGTACC 17 0.42500000000000004 No Hit CGATGAAGGCGATAATAAATACAGAAGTTGCGGTCAATAAGGTAGGGATC 17 0.42500000000000004 No Hit TTGTGCTCTGCCTGGAATACAATCATAAAGTTGAAAGTACCAGATATTCC 16 0.4 No Hit CTCGCGAATACCATCAATATCTACTGGAGGGGCTGCGATGAAGGCGATAA 16 0.4 No Hit CAATAAGGTAGGGATCATCAAAACACCGAACCATCCGATGTAAAGACGAT 15 0.375 No Hit CGCAGAAGTAGGAATAATAGCACCAGAGATAATATTGTTTCCATAAAGTA 15 0.375 No Hit CGCGGGAACTTCAAGAGCAGCTAGATCTAGAGGGAAGTTGTGAGCATTAC 15 0.375 No Hit GCGATAATAAATACAGAAGTTGCGGTCAATAAGGTAGGGATCATCAAAAC 14 0.35000000000000003 No Hit AGCGGGAACTTCAAGAGCAGCTAGATCTAGAGGGAAGTTGTGAGCATTAC 12 0.3 No Hit CGCTGGAGTAGGCTGCGAGGCCCAAGCGGCCAAGGAGTGCAGCGGCCCGT 12 0.3 No Hit TTTCTTTTCTTCAAAAATTCTTATATGTTAGCGGAAAAACCTTATCCATT 11 0.27499999999999997 No Hit CCCAAGTATTAATAACGCGACCTTGACTATCAACTACAGATTGGTTGAAA 11 0.27499999999999997 No Hit GTTCGCTGGAGTAGGCTGCGAGGCCCAAGCGGCCAAGGAGTGCAGCGGCC 11 0.27499999999999997 No Hit CTGCCTGGAATACAATCATAAAGTTGAAAGTACCAGATATTCCTAAAGGC 11 0.27499999999999997 No Hit CTCATTAGCAGATTCATTTTCAGTAGTTTCCCTGATCAAACTAGAGGTTA 11 0.27499999999999997 No Hit GCGGAAAAACCTTATCCATTAATAGCGGGAACTTCAAGAGCAGCTAGATC 11 0.27499999999999997 No Hit GGGGCTGCGATGAAGGCGATAATAAATACAGAAGTTGCGGTCAATAAGGT 11 0.27499999999999997 No Hit CGCGAATACCATCAATATCTACTGGAGGGGCTGCGATGAAGGCGATAATA 10 0.25 No Hit GGAGGGGCTGCGATGAAGGCGATAATAAATACAGAAGTTGCGGTCAATAA 10 0.25 No Hit CCAAGTATTAATAACGCGACCTTGACTATCAACTACAGATTGGTTGAAAT 10 0.25 No Hit CTTTCTTTTCTTCAAAAATTCTTATATGTTAGCGGAAAAACCTTATCCAT 10 0.25 No Hit ATGCATAAGGATGTTGTGCTCTGCCTGGAATACAATCATAAAGTTGAAAG 9 0.22499999999999998 No Hit CCACCATTGTATAACCATTCATCAACGGATGCAGCTTCCCAAATTGGGTA 9 0.22499999999999998 No Hit TGCGGGAACTTCAAGAGCAGCTAGATCTAGAGGGAAGTTGTGAGCATTAC 9 0.22499999999999998 No Hit GCGCGACCTTGACTATCAACTACAGATTGGTTGAAATTGAATCCATTTAG 9 0.22499999999999998 No Hit GCGAATACCATCAATATCTACTGGAGGGGCTGCGATGAAGGCGATAATAA 9 0.22499999999999998 No Hit AGCAGCCACAATATTATAAGTCTCTTCCTCTTGACCAAATTTGTAACCCT 9 0.22499999999999998 No Hit AATAAGGTAGGGATCATCAAAACACCGAACCATCCGATGTAAAGACGATT 8 0.2 No Hit TGCTCTGCCTGGAATACAATCATAAAGTTGAAAGTACCAGATATTCCTAA 8 0.2 No Hit GCCGAAAACACCAGCTACACCTAACATGTGAAATGGATGCATAAGGATGT 8 0.2 No Hit CCGGGGTGTAGTAAGTCAATCTATAATCTTTAACACCAGCTTTAAATCCA 8 0.2 No Hit GGATGCATAAGGATGTTGTGCTCTGCCTGGAATACAATCATAAAGTTGAA 8 0.2 No Hit GTGTGCTCTGCCTGGAATACAATCATAAAGTTGAAAGTACCAGATATTCC 8 0.2 No Hit CCACAATATTATAAGTCTCTTCCTCTTGACCAAATTTGTAACCCTCATTA 8 0.2 No Hit TGTGCTCTGCCTGGAATACAATCATAAAGTTGAAAGTACCAGATATTCCT 8 0.2 No Hit AATAAATACAGAAGTTGCGGTCAATAAGGTAGGGATCATCAAAACACCGA 8 0.2 No Hit GCCAAAATAACCATGAGCAGCCACAATATTATAAGTCTCTTCCTCTTGAC 8 0.2 No Hit AGGGGCTGCGATGAAGGCGATAATAAATACAGAAGTTGCGGTCAATAAGG 8 0.2 No Hit CTTTTCTTCAAAAATTCTTATATGTTAGCGGAAAAACCTTATCCATTAAT 7 0.17500000000000002 No Hit GGAAAAACCTTATCCATTAATAGCGGGAACTTCAAGAGCAGCTAGATCTA 7 0.17500000000000002 No Hit TGTTGTGCTCTGCCTGGAATACAATCATAAAGTTGAAAGTACCAGATATT 7 0.17500000000000002 No Hit CCCCAGTTAAGTAGTCATGCATTACAATAGGAACACCTAATTCTCTCGCA 7 0.17500000000000002 No Hit GTGAGCATTACGTTCGTGCATTACTTCCATACCAAGATTAGCACGGTTGA 7 0.17500000000000002 No Hit GCTAGTTATCCAGTTGCAGAAGCGACCCCACAGGCTTGTACTTTCGCGTC 7 0.17500000000000002 No Hit CACCATTGTATAACCATTCATCAACGGATGCAGCTTCCCAAATTGGGTAA 7 0.17500000000000002 No Hit TAAGGTAGGGATCATCAAAACACCGAACCATCCGATGTAAAGACGATTTT 6 0.15 No Hit ATGAAGGCGATAATAAATACAGAAGTTGCGGTCAATAAGGTAGGGATCAT 6 0.15 No Hit GGGCTGCGATGAAGGCGATAATAAATACAGAAGTTGCGGTCAATAAGGTA 6 0.15 No Hit ATAATAAATACAGAAGTTGCGGTCAATAAGGTAGGGATCATCAAAACACC 6 0.15 No Hit GCTTTCTTTTCTTCAAAAATTCTTATATGTTAGCGGAAAAACCTTATCCA 6 0.15 No Hit CTCTTGACCAAATTTGTAACCCTCATTAGCAGATTCATTTTCAGTAGTTT 6 0.15 No Hit GGAACTTCAAGAGCAGCTAGATCTAGAGGGAAGTTGTGAGCATTACGTTC 6 0.15 No Hit GACCACCATTGTATAACCATTCATCAACGGATGCAGCTTCCCAAATTGGG 5 0.125 No Hit CGTGCTCTGCCTGGAATACAATCATAAAGTTGAAAGTACCAGATATTCCT 5 0.125 No Hit GTTGCGGTCAATAAGGTAGGGATCATCAAAACACCGAACCATCCGATGTA 5 0.125 No Hit GCATTACGTTCGTGCATTACTTCCATACCAAGATTAGCACGGTTGATGAT 5 0.125 No Hit CGTCTCTCTAAAATTGCAGTCATGGTAAGATCTTGGTTTATTCAAATTGC 5 0.125 No Hit CCCTCATTAGCAGATTCATTTTCAGTAGTTTCCCTGATCAAACTAGAGGT 5 0.125 No Hit GGGATCATCAAAACACCGAACCATCCGATGTAAAGACGATTTTCAGTGCT 5 0.125 No Hit CTCATAAGGACCACCATTGTATAACCATTCATCAACGGATGCAGCTTCCC 5 0.125 No Hit CCTGCCAACATTATGGGCCGCGAAGCCTAGCTTTCGCTTAAGCTCCAACG 5 0.125 No Hit GTGAAATGGATGCATAAGGATGTTGTGCTCTGCCTGGAATACAATCATAA 5 0.125 No Hit GTTGAAACTAGCATATTGGAAGATTAATCGGCCAAAATAACCATGAGCAG 5 0.125 No Hit TGCCGCAGAAGTAGGAATAATAGCACCAGAGATAATATTGTTTCCATAAA 5 0.125 No Hit GGGGGCTGCGATGAAGGCGATAATAAATACAGAAGTTGCGGTCAATAAGG 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 815029 spots for SRR1772224.sra Written 815029 spots for SRR1772224.sra Read 815029 spots for SRR1772224.sra Written 815029 spots for SRR1772224.sra Read 815029 spots for SRR1772224.sra Written 815029 spots for SRR1772224.sra Read 815029 spots for SRR1772224.sra Written 815029 spots for SRR1772224.sra Read 815029 spots for SRR1772224.sra Written 815029 spots for SRR1772224.sra Read 815029 spots for SRR1772224.sra Written 815029 spots for SRR1772224.sra Read 815029 spots for SRR1772224.sra Written 815029 spots for SRR1772224.sra Read 815029 spots for SRR1772224.sra Written 815029 spots for SRR1772224.sra Read 815029 spots for SRR1772224.sra Written 815029 spots for SRR1772224.sra Read 815029 spots for SRR1772224.sra Written 815029 spots for SRR1772224.sra Read 815029 spots for SRR1772224.sra Written 815029 spots for SRR1772224.sra Read 815029 spots for SRR1772224.sra Written 815029 spots for SRR1772224.sra Read 815029 spots for SRR1772224.sra Written 815029 spots for SRR1772224.sra Read 815029 spots for SRR1772224.sra Written 815029 spots for SRR1772224.sra Read 815029 spots for SRR1772224.sra Written 815029 spots for SRR1772224.sra Read 815029 spots for SRR1772224.sra Written 815029 spots for SRR1772224.sra Read 815029 spots for SRR1772224.sra Written 815029 spots for SRR1772224.sra Read 815037 spots for SRR1772224.sra Written 815037 spots for SRR1772224.sra Read 815029 spots for SRR1772224.sra Written 815029 spots for SRR1772224.sra Read 815029 spots for SRR1772224.sra Written 815029 spots for SRR1772224.sra SRR ids: ['SRR1772224.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_xvmalwc6 SRR1772224.sra spots: 16300588 blocks: [[1, 815029], [815030, 1630058], [1630059, 2445087], [2445088, 3260116], [3260117, 4075145], [4075146, 4890174], [4890175, 5705203], [5705204, 6520232], [6520233, 7335261], [7335262, 8150290], [8150291, 8965319], [8965320, 9780348], [9780349, 10595377], [10595378, 11410406], [11410407, 12225435], [12225436, 13040464], [13040465, 13855493], [13855494, 14670522], [14670523, 15485551], [15485552, 16300588]] SRR1772224 file size 2814330 SRR1772224 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 SRR1772224 SRR1772224_1.fastq Input file: SRR1772224_1.fastq trimmed: SRR1772224-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 19:45:34 2024 >> started Sat Dec 7 19:45:55 2024 >> done (20.488s) 16300588 reads processed; of these: 2779 ( 0.02%) short reads filtered out after trimming by size control 182701 ( 1.12%) empty reads filtered out after trimming by size control 16115108 (98.86%) reads available; of these: 812102 ( 5.04%) trimmed reads available after processing 15303006 (94.96%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 1440 0.01% 19 2096 0.01% 20 4187 0.03% 21 4659 0.03% 22 5498 0.03% 23 5110 0.03% 24 7782 0.05% 25 7924 0.05% 26 7047 0.04% 27 8946 0.06% 28 9947 0.06% 29 16695 0.10% 30 13638 0.08% 31 14818 0.09% 32 18430 0.11% 33 12520 0.08% 34 13121 0.08% 35 15953 0.10% 36 15750 0.10% 37 21636 0.13% 38 17021 0.11% 39 18569 0.12% 40 29302 0.18% 41 25776 0.16% 42 45853 0.28% 43 42778 0.27% 44 58211 0.36% 45 53247 0.33% 46 65869 0.41% 47 81508 0.51% 48 88713 0.55% 49 78058 0.48% 50 15303006 94.96% 16115108 reads passed initial QC criterion=sequence-density sequence-density=0.22 sequence-density-rank=1 fanout-score=0.00 fanout-score-rank=16 prefix-density=0.00 prefix-fanout=1.0 sequence=TGCGGGAACTTC criterion=fanout-score sequence-density=0.08 sequence-density-rank=9 fanout-score=16.77 fanout-score-rank=1 prefix-density=1.27 prefix-fanout=1.0 sequence=TCTCTAAAATTTCAGTCATGGTA Started job on | Dec 07 19:48:02 Started mapping on | Dec 07 19:48:03 Finished on | Dec 07 19:48:32 Mapping speed, Million of reads per hour | 2000.50 Number of input reads | 16115108 Average input read length | 49 UNIQUE READS: Uniquely mapped reads number | 4507253 Uniquely mapped reads % | 27.97% Average mapped length | 49.33 Number of splices: Total | 295366 Number of splices: Annotated (sjdb) | 278727 Number of splices: GT/AG | 289638 Number of splices: GC/AG | 3465 Number of splices: AT/AC | 149 Number of splices: Non-canonical | 2114 Mismatch rate per base, % | 0.29% Deletion rate per base | 0.01% Deletion average length | 1.50 Insertion rate per base | 0.01% Insertion average length | 1.39 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 11251625 % of reads mapped to multiple loci | 69.82% Number of reads mapped to too many loci | 60363 % of reads mapped to too many loci | 0.37% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 1.81% % of reads unmapped: other | 0.03% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 356230 356230 356230 N_multimapping 11251625 11251625 11251625 N_noFeature 1018932 4314334 1145108 N_ambiguous 105482 1212 38909 UnstrandedReadsAssigned:3382839 PositiveStrandReadsAssigned:191707 NegativeStrandReadsAssigned:3323236 Dataset is classified negative stranded MeadianReadLen=50 20thPercentileLength=50 echo kmer=45 SRR1772224 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: SRR1772224-trimmed.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 16,115,108 reads, 13,161,609 reads pseudoaligned [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 986 rounds 52973 SRR1772224.ke.tsv 35125 SRR1772224.se.tsv 88098 total ==> SRR1772224.ke.tsv <== target_id length eff_length est_counts tpm PNS24245 936 837 0 0 PNS24247 1044 945 6.27797 0.569892 PNS24249 1928 1829 29.4816 1.38274 PNS24246 1044 945 6.27797 0.569892 PNS24248 1044 945 6.27797 0.569892 PNS24244 1471 1372 7.68454 0.480473 PNS24243 293 194 0 0 KQK14069 1603 1504 139.738 7.97023 KQK14071 474 375 65.011 14.8717 ==> SRR1772224.se.tsv <== BRADI_1g14170v3 415 BRADI_1g53295v3 12 BRADI_1g59795v3 27 BRADI_1g07683v3 0 BRADI_1g00485v3 2 BRADI_1g20270v3 54 BRADI_1g74790v3 16 BRADI_1g09890v3 0 BRADI_1g77505v3 45 BRADI_1g48960v3 1 SRR1772224 completed mapping pipeline successfully