Starting /dee2/code/volunteer_pipeline.sh SRR1772232 current disk space = 1540032512000 free memory = 1434252312 SRR1772232 SRAfilesize cdfa3950d060240da7e7ecfd03fc3563 SRR1772232.sra SRR1772232.sra file validated SRR1772232 is single end SRR1772232 is conventional basespace SRR1772232 read1 length is 50 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR1772232_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 32.89575 34.0 31.0 34.0 31.0 34.0 2 33.022 34.0 31.0 34.0 31.0 34.0 3 32.83375 34.0 31.0 34.0 31.0 34.0 4 36.277 37.0 37.0 37.0 35.0 37.0 5 36.31725 37.0 37.0 37.0 35.0 37.0 6 36.193 37.0 37.0 37.0 35.0 37.0 7 36.24925 37.0 37.0 37.0 35.0 37.0 8 36.23425 37.0 37.0 37.0 35.0 37.0 9 37.98325 39.0 38.0 39.0 35.0 39.0 10 37.87975 39.0 38.0 39.0 35.0 39.0 11 37.9885 39.0 38.0 39.0 35.0 39.0 12 38.0245 39.0 38.0 39.0 35.0 39.0 13 37.9165 39.0 38.0 39.0 35.0 39.0 14 39.329 41.0 39.0 41.0 36.0 41.0 15 39.367 41.0 39.0 41.0 36.0 41.0 16 39.164 41.0 39.0 41.0 36.0 41.0 17 39.29725 41.0 39.0 41.0 36.0 41.0 18 39.36475 41.0 39.0 41.0 36.0 41.0 19 39.2185 41.0 39.0 41.0 36.0 41.0 20 39.251 41.0 39.0 41.0 36.0 41.0 21 39.12175 41.0 39.0 41.0 36.0 41.0 22 39.18025 41.0 39.0 41.0 36.0 41.0 23 38.97875 40.0 39.0 41.0 36.0 41.0 24 38.983 41.0 39.0 41.0 36.0 41.0 25 38.9915 40.0 39.0 41.0 36.0 41.0 26 38.4475 40.0 38.0 41.0 34.0 41.0 27 38.6775 40.0 38.0 41.0 35.0 41.0 28 38.7095 40.0 38.0 41.0 35.0 41.0 29 38.55825 40.0 38.0 41.0 35.0 41.0 30 38.5365 40.0 38.0 41.0 35.0 41.0 31 38.346 40.0 38.0 41.0 34.0 41.0 32 38.12525 40.0 38.0 41.0 33.0 41.0 33 37.99925 40.0 38.0 41.0 33.0 41.0 34 38.4375 40.0 38.0 41.0 35.0 41.0 35 38.3855 40.0 38.0 41.0 34.0 41.0 36 38.2935 40.0 38.0 41.0 34.0 41.0 37 38.09875 40.0 38.0 41.0 34.0 41.0 38 37.7655 40.0 38.0 41.0 33.0 41.0 39 37.9495 40.0 38.0 41.0 33.0 41.0 40 37.90575 40.0 38.0 41.0 33.0 41.0 41 37.799 40.0 38.0 41.0 33.0 41.0 42 37.89975 40.0 38.0 41.0 33.0 41.0 43 37.6675 40.0 38.0 41.0 33.0 41.0 44 37.43625 40.0 38.0 41.0 33.0 41.0 45 37.316 40.0 38.0 41.0 33.0 41.0 46 37.3385 40.0 38.0 41.0 33.0 41.0 47 36.93275 40.0 38.0 41.0 31.0 41.0 48 37.013 40.0 38.0 41.0 31.0 41.0 49 36.97 40.0 38.0 41.0 31.0 41.0 50 36.6995 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 2.0 13 2.0 14 3.0 15 3.0 16 2.0 17 7.0 18 2.0 19 6.0 20 8.0 21 6.0 22 7.0 23 13.0 24 11.0 25 8.0 26 15.0 27 24.0 28 26.0 29 33.0 30 36.0 31 48.0 32 77.0 33 77.0 34 107.0 35 151.0 36 199.0 37 315.0 38 571.0 39 2240.0 >>END_MODULE >>Per base sequence content warn #Base G A T C 1 37.10282712034025 11.833875406554917 13.635226419814861 37.42807105328997 2 30.15 10.375 29.95 29.525000000000002 3 39.27583605732964 18.481267286899673 16.947447824993713 25.29544883077697 4 32.5 27.750000000000004 15.925 23.825 5 31.8 30.175 20.375 17.65 6 21.9 34.025 19.375 24.7 7 11.1 36.975 35.75 16.175 8 22.1 25.7 30.349999999999998 21.85 9 20.25 20.45 32.675 26.625 10 16.225 43.625 24.925 15.225 11 24.15 32.925 19.125 23.799999999999997 12 27.525 29.375 22.125 20.974999999999998 13 18.875 37.974999999999994 23.025000000000002 20.125 14 25.324999999999996 33.1 25.35 16.225 15 19.375 36.475 21.175 22.975 16 22.2 36.75 23.225 17.825 17 21.45 36.0 22.15 20.4 18 17.8 36.625 22.45 23.125 19 20.225 33.975 27.200000000000003 18.6 20 16.075 35.175 26.075 22.675 21 16.825000000000003 29.849999999999998 28.375 24.95 22 14.774999999999999 41.25 23.95 20.025000000000002 23 19.35 35.225 25.324999999999996 20.1 24 19.55 35.75 21.75 22.95 25 17.05 34.625 27.325 21.0 26 18.65 37.3 23.75 20.3 27 24.5 31.225 26.75 17.525 28 24.2 39.175 21.2 15.425 29 24.275 33.2 23.200000000000003 19.325 30 27.6 31.025000000000002 23.525 17.849999999999998 31 29.65 28.275 23.075000000000003 19.0 32 25.825 30.575000000000003 24.55 19.05 33 28.050000000000004 34.949999999999996 18.675 18.325 34 23.724999999999998 36.775000000000006 19.775000000000002 19.725 35 21.375 35.449999999999996 23.75 19.425 36 21.825 28.9 29.75 19.525000000000002 37 23.460190285428144 29.56935403104657 29.56935403104657 17.40110165247872 38 19.900000000000002 27.375 31.35 21.375 39 24.25 26.825 27.950000000000003 20.974999999999998 40 18.05 34.475 27.800000000000004 19.675 41 23.275000000000002 26.05 29.299999999999997 21.375 42 20.625 31.45 25.3 22.625 43 20.3 34.35 23.400000000000002 21.95 44 19.525000000000002 29.4 28.675 22.400000000000002 45 19.87981972959439 32.42363545317977 29.669504256384577 18.02704056084126 46 18.21821821821822 29.32932932932933 34.73473473473474 17.71771771771772 47 18.663997998498875 34.375781836377286 27.120340255191394 19.83987990993245 48 23.21160580290145 34.592296148074034 23.836918459229615 18.3591795897949 49 23.1615807903952 30.740370185092548 25.6128064032016 20.485242621310658 50 26.525 27.250000000000004 25.974999999999998 20.25 >>END_MODULE >>Per sequence GC content fail #GC Content Count 0 0.0 1 0.5 2 1.0 3 0.5 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 1.5 18 3.0 19 5.0 20 7.0 21 5.5 22 4.0 23 7.5 24 11.0 25 30.0 26 49.0 27 41.0 28 33.0 29 38.5 30 44.0 31 61.5 32 79.0 33 140.0 34 201.0 35 296.5 36 392.0 37 449.5 38 507.0 39 423.0 40 339.0 41 373.5 42 408.0 43 433.5 44 459.0 45 434.0 46 409.0 47 325.5 48 242.0 49 271.5 50 301.0 51 205.0 52 109.0 53 95.0 54 81.0 55 70.0 56 59.0 57 49.5 58 40.0 59 34.5 60 29.0 61 30.0 62 31.0 63 29.5 64 28.0 65 25.5 66 23.0 67 26.0 68 29.0 69 28.5 70 28.0 71 24.0 72 20.0 73 15.5 74 11.0 75 7.5 76 4.0 77 7.0 78 10.0 79 6.0 80 2.0 81 2.5 82 3.0 83 2.0 84 1.0 85 1.0 86 1.0 87 1.0 88 1.0 89 1.0 90 1.0 91 0.5 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 0.575 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 0.15 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 0.1 47 0.075 48 0.05 49 0.05 50 0.0 >>END_MODULE >>Sequence Length Distribution pass #Length Count 50 4000.0 >>END_MODULE >>Sequence Duplication Levels fail #Total Deduplicated Percentage 49.8 #Duplication Level Percentage of deduplicated Percentage of total 1 84.83935742971887 42.25 2 5.873493975903615 5.8500000000000005 3 3.1626506024096384 4.725 4 1.104417670682731 2.1999999999999997 5 0.8032128514056224 2.0 6 0.4016064257028112 1.2 7 0.6024096385542169 2.1 8 0.4016064257028112 1.6 9 0.30120481927710846 1.35 >10 2.208835341365462 22.8 >50 0.15060240963855423 4.55 >100 0.15060240963855423 9.375 >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 152 3.8 No Hit GGGAACTTCAAGAGCAGCTAGATCTAGAGGGAAGTTGTGAGCATTACGTT 117 2.9250000000000003 No Hit CTGCGATGAAGGCGATAATAAATACAGAAGTTGCGGTCAATAAGGTAGGG 106 2.65 No Hit GTGCTCTGCCTGGAATACAATCATAAAGTTGAAAGTACCAGATATTCCTA 67 1.675 No Hit TCTGCCTGGAATACAATCATAAAGTTGAAAGTACCAGATATTCCTAAAGG 58 1.4500000000000002 No Hit GCGGTCAATAAGGTAGGGATCATCAAAACACCGAACCATCCGATGTAAAG 57 1.425 No Hit GCGATGAAGGCGATAATAAATACAGAAGTTGCGGTCAATAAGGTAGGGAT 47 1.175 No Hit CGCGACCTTGACTATCAACTACAGATTGGTTGAAATTGAATCCATTTAGG 40 1.0 No Hit CGGGAACTTCAAGAGCAGCTAGATCTAGAGGGAAGTTGTGAGCATTACGT 39 0.975 No Hit GTTGTGCTCTGCCTGGAATACAATCATAAAGTTGAAAGTACCAGATATTC 37 0.9249999999999999 No Hit GCCTGGAATACAATCATAAAGTTGAAAGTACCAGATATTCCTAAAGGCAT 37 0.9249999999999999 No Hit CGCAGAAGTAGGAATAATAGCACCAGAGATAATATTGTTTCCATAAAGTA 35 0.8750000000000001 No Hit GCGACCTTGACTATCAACTACAGATTGGTTGAAATTGAATCCATTTAGGT 35 0.8750000000000001 No Hit CGGTCAATAAGGTAGGGATCATCAAAACACCGAACCATCCGATGTAAAGA 35 0.8750000000000001 No Hit CTGGAATACAATCATAAAGTTGAAAGTACCAGATATTCCTAAAGGCATAC 35 0.8750000000000001 No Hit ATAAGGATGTTGTGCTCTGCCTGGAATACAATCATAAAGTTGAAAGTACC 34 0.8500000000000001 No Hit CTCTGCCTGGAATACAATCATAAAGTTGAAAGTACCAGATATTCCTAAAG 32 0.8 No Hit ACGCGACCTTGACTATCAACTACAGATTGGTTGAAATTGAATCCATTTAG 30 0.75 No Hit CGATGAAGGCGATAATAAATACAGAAGTTGCGGTCAATAAGGTAGGGATC 28 0.7000000000000001 No Hit TTTCTTTTCTTCAAAAATTCTTATATGTTAGCGGAAAAACCTTATCCATT 25 0.625 No Hit GTCAATAAGGTAGGGATCATCAAAACACCGAACCATCCGATGTAAAGACG 25 0.625 No Hit CAATAAGGTAGGGATCATCAAAACACCGAACCATCCGATGTAAAGACGAT 22 0.5499999999999999 No Hit GGCGATAATAAATACAGAAGTTGCGGTCAATAAGGTAGGGATCATCAAAA 22 0.5499999999999999 No Hit CTCGCGAATACCATCAATATCTACTGGAGGGGCTGCGATGAAGGCGATAA 22 0.5499999999999999 No Hit GGCCAAAATAACCATGAGCAGCCACAATATTATAAGTCTCTTCCTCTTGA 17 0.42500000000000004 No Hit AGGGGCTGCGATGAAGGCGATAATAAATACAGAAGTTGCGGTCAATAAGG 17 0.42500000000000004 No Hit GCGATAATAAATACAGAAGTTGCGGTCAATAAGGTAGGGATCATCAAAAC 15 0.375 No Hit GGTCAATAAGGTAGGGATCATCAAAACACCGAACCATCCGATGTAAAGAC 15 0.375 No Hit CTGCCTGGAATACAATCATAAAGTTGAAAGTACCAGATATTCCTAAAGGC 15 0.375 No Hit GGAGGGGCTGCGATGAAGGCGATAATAAATACAGAAGTTGCGGTCAATAA 14 0.35000000000000003 No Hit GCTGCGATGAAGGCGATAATAAATACAGAAGTTGCGGTCAATAAGGTAGG 14 0.35000000000000003 No Hit GCCAAAATAACCATGAGCAGCCACAATATTATAAGTCTCTTCCTCTTGAC 14 0.35000000000000003 No Hit CGCGAATACCATCAATATCTACTGGAGGGGCTGCGATGAAGGCGATAATA 13 0.325 No Hit CTTTTCTTCAAAAATTCTTATATGTTAGCGGAAAAACCTTATCCATTAAT 13 0.325 No Hit CCCAAGTATTAATAACGCGACCTTGACTATCAACTACAGATTGGTTGAAA 13 0.325 No Hit CCAAGTATTAATAACGCGACCTTGACTATCAACTACAGATTGGTTGAAAT 13 0.325 No Hit CTCATTAGCAGATTCATTTTCAGTAGTTTCCCTGATCAAACTAGAGGTTA 13 0.325 No Hit GGAACTTCAAGAGCAGCTAGATCTAGAGGGAAGTTGTGAGCATTACGTTC 13 0.325 No Hit GCGGAAAAACCTTATCCATTAATAGCGGGAACTTCAAGAGCAGCTAGATC 13 0.325 No Hit GATCGGAAGAGCACACGTCTGAACTCCAGTCACCATGCCTAATCTCGTAT 12 0.3 TruSeq Adapter, Index 12 (97% over 37bp) TGCGGGAACTTCAAGAGCAGCTAGATCTAGAGGGAAGTTGTGAGCATTAC 12 0.3 No Hit GCTCTGCCTGGAATACAATCATAAAGTTGAAAGTACCAGATATTCCTAAA 12 0.3 No Hit GGGGCTGCGATGAAGGCGATAATAAATACAGAAGTTGCGGTCAATAAGGT 12 0.3 No Hit AATAAGGTAGGGATCATCAAAACACCGAACCATCCGATGTAAAGACGATT 11 0.27499999999999997 No Hit CGGAAAAACCTTATCCATTAATAGCGGGAACTTCAAGAGCAGCTAGATCT 11 0.27499999999999997 No Hit CCACCATTGTATAACCATTCATCAACGGATGCAGCTTCCCAAATTGGGTA 10 0.25 No Hit GGGCTGCGATGAAGGCGATAATAAATACAGAAGTTGCGGTCAATAAGGTA 10 0.25 No Hit CCACAATATTATAAGTCTCTTCCTCTTGACCAAATTTGTAACCCTCATTA 10 0.25 No Hit GCGAATACCATCAATATCTACTGGAGGGGCTGCGATGAAGGCGATAATAA 10 0.25 No Hit TGTGCTCTGCCTGGAATACAATCATAAAGTTGAAAGTACCAGATATTCCT 10 0.25 No Hit GCCGAAAACACCAGCTACACCTAACATGTGAAATGGATGCATAAGGATGT 9 0.22499999999999998 No Hit GTAGGGATCATCAAAACACCGAACCATCCGATGTAAAGACGATTTTCAGT 9 0.22499999999999998 No Hit AGCGGGAACTTCAAGAGCAGCTAGATCTAGAGGGAAGTTGTGAGCATTAC 9 0.22499999999999998 No Hit TTGTGCTCTGCCTGGAATACAATCATAAAGTTGAAAGTACCAGATATTCC 9 0.22499999999999998 No Hit CTTTCTTTTCTTCAAAAATTCTTATATGTTAGCGGAAAAACCTTATCCAT 9 0.22499999999999998 No Hit GCAGCCACAATATTATAAGTCTCTTCCTCTTGACCAAATTTGTAACCCTC 9 0.22499999999999998 No Hit GGAAAAACCTTATCCATTAATAGCGGGAACTTCAAGAGCAGCTAGATCTA 8 0.2 No Hit TGTTGTGCTCTGCCTGGAATACAATCATAAAGTTGAAAGTACCAGATATT 8 0.2 No Hit ATGAAGGCGATAATAAATACAGAAGTTGCGGTCAATAAGGTAGGGATCAT 8 0.2 No Hit GGATGCATAAGGATGTTGTGCTCTGCCTGGAATACAATCATAAAGTTGAA 8 0.2 No Hit GCCACAATATTATAAGTCTCTTCCTCTTGACCAAATTTGTAACCCTCATT 8 0.2 No Hit CGCTGGAGTAGGCTGCGAGGCCCAAGCGGCCAAGGAGTGCAGCGGCCCGT 8 0.2 No Hit CACCATTGTATAACCATTCATCAACGGATGCAGCTTCCCAAATTGGGTAA 8 0.2 No Hit ATAACAAGCTACACCAAGTAAGAAGTGTAGAACAATTAGCTCATAAGGAC 8 0.2 No Hit CGCGGGAACTTCAAGAGCAGCTAGATCTAGAGGGAAGTTGTGAGCATTAC 7 0.17500000000000002 No Hit CTTCCTCTTGACCAAATTTGTAACCCTCATTAGCAGATTCATTTTCAGTA 7 0.17500000000000002 No Hit CGACCTTGACTATCAACTACAGATTGGTTGAAATTGAATCCATTTAGGTT 7 0.17500000000000002 No Hit CGTGCTCTGCCTGGAATACAATCATAAAGTTGAAAGTACCAGATATTCCT 7 0.17500000000000002 No Hit CGATAATAAATACAGAAGTTGCGGTCAATAAGGTAGGGATCATCAAAACA 7 0.17500000000000002 No Hit GTGAGCATTACGTTCGTGCATTACTTCCATACCAAGATTAGCACGGTTGA 7 0.17500000000000002 No Hit GCGCGACCTTGACTATCAACTACAGATTGGTTGAAATTGAATCCATTTAG 7 0.17500000000000002 No Hit ATAATAAATACAGAAGTTGCGGTCAATAAGGTAGGGATCATCAAAACACC 7 0.17500000000000002 No Hit AATAAATACAGAAGTTGCGGTCAATAAGGTAGGGATCATCAAAACACCGA 7 0.17500000000000002 No Hit TGCGATGAAGGCGATAATAAATACAGAAGTTGCGGTCAATAAGGTAGGGA 7 0.17500000000000002 No Hit CTCTTGACCAAATTTGTAACCCTCATTAGCAGATTCATTTTCAGTAGTTT 7 0.17500000000000002 No Hit AGCAGCCACAATATTATAAGTCTCTTCCTCTTGACCAAATTTGTAACCCT 7 0.17500000000000002 No Hit CTGGAGGGGCTGCGATGAAGGCGATAATAAATACAGAAGTTGCGGTCAAT 6 0.15 No Hit TAAGGATGTTGTGCTCTGCCTGGAATACAATCATAAAGTTGAAAGTACCA 6 0.15 No Hit TTCAAGAGCAGCTAGATCTAGAGGGAAGTTGTGAGCATTACGTTCGTGCA 6 0.15 No Hit TGCTCTGCCTGGAATACAATCATAAAGTTGAAAGTACCAGATATTCCTAA 6 0.15 No Hit GGGATCATCAAAACACCGAACCATCCGATGTAAAGACGATTTTCAGTGCT 6 0.15 No Hit TCTTCCTCTTGACCAAATTTGTAACCCTCATTAGCAGATTCATTTTCAGT 6 0.15 No Hit CGCAGCTGCAACAGGAGCTGAATATGCAACAGCAATCCAAGGGCGCATAC 6 0.15 No Hit GTTGATGATATCAGCCCAAGTATTAATAACGCGACCTTGACTATCAACTA 6 0.15 No Hit CCGCAGAAGTAGGAATAATAGCACCAGAGATAATATTGTTTCCATAAAGT 5 0.125 No Hit CAAAAATTCTTATATGTTAGCGGAAAAACCTTATCCATTAATAGCGGGAA 5 0.125 No Hit ATTACGTTCGTGCATTACTTCCATACCAAGATTAGCACGGTTGATGATAT 5 0.125 No Hit ATAATTAACTGCATTGATCTCGGTAGCTACGCCACCCACGGAATTTAAAG 5 0.125 No Hit CAAGTATTAATAACGCGACCTTGACTATCAACTACAGATTGGTTGAAATT 5 0.125 No Hit CCCCAGTTAAGTAGTCATGCATTACAATAGGAACACCTAATTCTCTCGCA 5 0.125 No Hit TGATGATATCAGCCCAAGTATTAATAACGCGACCTTGACTATCAACTACA 5 0.125 No Hit GTGTGCTCTGCCTGGAATACAATCATAAAGTTGAAAGTACCAGATATTCC 5 0.125 No Hit TGCGGTCAATAAGGTAGGGATCATCAAAACACCGAACCATCCGATGTAAA 5 0.125 No Hit CCATTGTATAACCATTCATCAACGGATGCAGCTTCCCAAATTGGGTAAAA 5 0.125 No Hit CACAATATTATAAGTCTCTTCCTCTTGACCAAATTTGTAACCCTCATTAG 5 0.125 No Hit TTGATGATATCAGCCCAAGTATTAATAACGCGACCTTGACTATCAACTAC 5 0.125 No Hit CTCATAAGGACCACCATTGTATAACCATTCATCAACGGATGCAGCTTCCC 5 0.125 No Hit GCATAAGGATGTTGTGCTCTGCCTGGAATACAATCATAAAGTTGAAAGTA 5 0.125 No Hit ATGAGCAGCCACAATATTATAAGTCTCTTCCTCTTGACCAAATTTGTAAC 5 0.125 No Hit GTTGAAACTAGCATATTGGAAGATTAATCGGCCAAAATAACCATGAGCAG 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 GTTGAAA 75 0.001063462 17.470001 28 >>END_MODULE Read 966682 spots for SRR1772232.sra Written 966682 spots for SRR1772232.sra Read 966682 spots for SRR1772232.sra Written 966682 spots for SRR1772232.sra Read 966682 spots for SRR1772232.sra Written 966682 spots for SRR1772232.sra Read 966682 spots for SRR1772232.sra Written 966682 spots for SRR1772232.sra Read 966682 spots for SRR1772232.sra Written 966682 spots for SRR1772232.sra Read 966682 spots for SRR1772232.sra Written 966682 spots for SRR1772232.sra Read 966682 spots for SRR1772232.sra Written 966682 spots for SRR1772232.sra Read 966700 spots for SRR1772232.sra Written 966700 spots for SRR1772232.sra Read 966682 spots for SRR1772232.sra Written 966682 spots for SRR1772232.sra Read 966682 spots for SRR1772232.sra Written 966682 spots for SRR1772232.sra Read 966682 spots for SRR1772232.sra Written 966682 spots for SRR1772232.sra Read 966682 spots for SRR1772232.sra Written 966682 spots for SRR1772232.sra Read 966682 spots for SRR1772232.sra Written 966682 spots for SRR1772232.sra Read 966682 spots for SRR1772232.sra Written 966682 spots for SRR1772232.sra Read 966682 spots for SRR1772232.sra Written 966682 spots for SRR1772232.sra Read 966682 spots for SRR1772232.sra Written 966682 spots for SRR1772232.sra Read 966682 spots for SRR1772232.sra Written 966682 spots for SRR1772232.sra Read 966682 spots for SRR1772232.sra Written 966682 spots for SRR1772232.sra Read 966682 spots for SRR1772232.sra Written 966682 spots for SRR1772232.sra Read 966682 spots for SRR1772232.sra Written 966682 spots for SRR1772232.sra SRR ids: ['SRR1772232.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_3_q_5u0r SRR1772232.sra spots: 19333658 blocks: [[1, 966682], [966683, 1933364], [1933365, 2900046], [2900047, 3866728], [3866729, 4833410], [4833411, 5800092], [5800093, 6766774], [6766775, 7733456], [7733457, 8700138], [8700139, 9666820], [9666821, 10633502], [10633503, 11600184], [11600185, 12566866], [12566867, 13533548], [13533549, 14500230], [14500231, 15466912], [15466913, 16433594], [16433595, 17400276], [17400277, 18366958], [18366959, 19333658]] SRR1772232 file size 3340007 SRR1772232 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 SRR1772232 SRR1772232_1.fastq Input file: SRR1772232_1.fastq trimmed: SRR1772232-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 19:34:58 2024 >> started Sat Dec 7 19:35:13 2024 >> done (14.778s) 19333658 reads processed; of these: 2229 ( 0.01%) short reads filtered out after trimming by size control 78257 ( 0.40%) empty reads filtered out after trimming by size control 19253172 (99.58%) reads available; of these: 845388 ( 4.39%) trimmed reads available after processing 18407784 (95.61%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 1148 0.01% 19 1714 0.01% 20 3909 0.02% 21 3842 0.02% 22 4760 0.02% 23 4559 0.02% 24 6636 0.03% 25 7341 0.04% 26 6481 0.03% 27 8499 0.04% 28 9535 0.05% 29 14593 0.08% 30 12564 0.07% 31 14475 0.08% 32 16573 0.09% 33 11984 0.06% 34 12638 0.07% 35 15875 0.08% 36 15512 0.08% 37 21226 0.11% 38 16933 0.09% 39 19360 0.10% 40 31110 0.16% 41 27105 0.14% 42 49723 0.26% 43 46317 0.24% 44 59815 0.31% 45 58913 0.31% 46 70556 0.37% 47 88220 0.46% 48 96866 0.50% 49 86606 0.45% 50 18407784 95.61% 19253172 reads passed initial QC criterion=sequence-density sequence-density=0.27 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=0.01 sequence-density-rank=32 fanout-score=24.29 fanout-score-rank=1 prefix-density=0.04 prefix-fanout=3.9 sequence=AAAAAGAATAGAGGTATGACAGGCATAAAATCCACGATTGGGTTGAAAATAGCATAAGCTTCGGGTAGTTTAGCAAAGAAAAAACTAGTCGGATAAAGAACACAATTAAAACAGATACAGGTTAAACTAAGTATATTAGGCATAACAAGCATTT Started job on | Dec 07 19:35:23 Started mapping on | Dec 07 19:35:23 Finished on | Dec 07 19:35:40 Mapping speed, Million of reads per hour | 4077.14 Number of input reads | 19253172 Average input read length | 49 UNIQUE READS: Uniquely mapped reads number | 4439292 Uniquely mapped reads % | 23.06% Average mapped length | 49.41 Number of splices: Total | 287625 Number of splices: Annotated (sjdb) | 272786 Number of splices: GT/AG | 282117 Number of splices: GC/AG | 3605 Number of splices: AT/AC | 163 Number of splices: Non-canonical | 1740 Mismatch rate per base, % | 0.25% Deletion rate per base | 0.01% Deletion average length | 1.44 Insertion rate per base | 0.01% Insertion average length | 1.38 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 14525289 % of reads mapped to multiple loci | 75.44% Number of reads mapped to too many loci | 42216 % of reads mapped to too many loci | 0.22% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 1.27% % of reads unmapped: other | 0.01% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 288591 288591 288591 N_multimapping 14525289 14525289 14525289 N_noFeature 1024441 4319743 1082972 N_ambiguous 90358 843 29208 UnstrandedReadsAssigned:3324493 PositiveStrandReadsAssigned:118706 NegativeStrandReadsAssigned:3327112 Dataset is classified negative stranded MeadianReadLen=50 20thPercentileLength=50 echo kmer=45 SRR1772232 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: SRR1772232-trimmed.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 19,253,172 reads, 16,441,057 reads pseudoaligned [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,378 rounds 52973 SRR1772232.ke.tsv 35125 SRR1772232.se.tsv 88098 total ==> SRR1772232.ke.tsv <== target_id length eff_length est_counts tpm PNS24245 936 837 13.125 1.07289 PNS24247 1044 945 0 0 PNS24249 1928 1829 36.875 1.37943 PNS24246 1044 945 0 0 PNS24248 1044 945 0 0 PNS24244 1471 1372 0 0 PNS24243 293 194 0 0 KQK14069 1603 1504 113.721 5.17339 KQK14071 474 375 49.8186 9.08956 ==> SRR1772232.se.tsv <== BRADI_1g14170v3 255 BRADI_1g53295v3 8 BRADI_1g59795v3 47 BRADI_1g07683v3 0 BRADI_1g00485v3 0 BRADI_1g20270v3 6 BRADI_1g74790v3 14 BRADI_1g09890v3 0 BRADI_1g77505v3 28 BRADI_1g48960v3 0 SRR1772232 completed mapping pipeline successfully