Starting /dee2/code/volunteer_pipeline.sh SRR1772233 current disk space = 1552305922048 free memory = 1605461980 SRR1772233 SRAfilesize fa880302f21b320c441ac876a84a10bc SRR1772233.sra SRR1772233.sra file validated SRR1772233 is single end SRR1772233 is conventional basespace SRR1772233 read1 length is 50 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR1772233_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 32.93625 34.0 31.0 34.0 31.0 34.0 2 33.04175 34.0 31.0 34.0 31.0 34.0 3 32.8035 34.0 31.0 34.0 31.0 34.0 4 36.25875 37.0 37.0 37.0 35.0 37.0 5 36.3335 37.0 37.0 37.0 35.0 37.0 6 36.22 37.0 37.0 37.0 35.0 37.0 7 36.282 37.0 37.0 37.0 35.0 37.0 8 36.264 37.0 37.0 37.0 35.0 37.0 9 38.01325 39.0 39.0 39.0 35.0 39.0 10 37.83575 39.0 38.0 39.0 35.0 39.0 11 38.00975 39.0 38.0 39.0 35.0 39.0 12 38.02675 39.0 38.0 39.0 35.0 39.0 13 37.9965 39.0 38.0 39.0 35.0 39.0 14 39.37 41.0 39.0 41.0 36.0 41.0 15 39.45775 41.0 39.0 41.0 36.0 41.0 16 39.162 41.0 39.0 41.0 36.0 41.0 17 39.41725 41.0 39.0 41.0 36.0 41.0 18 39.51075 41.0 39.0 41.0 36.0 41.0 19 39.34975 41.0 39.0 41.0 36.0 41.0 20 39.3235 41.0 39.0 41.0 36.0 41.0 21 39.25225 41.0 39.0 41.0 36.0 41.0 22 39.27225 41.0 39.0 41.0 36.0 41.0 23 39.0055 41.0 39.0 41.0 35.0 41.0 24 39.0995 41.0 39.0 41.0 36.0 41.0 25 39.13925 41.0 39.0 41.0 36.0 41.0 26 38.6325 40.0 38.0 41.0 34.0 41.0 27 38.66775 40.0 38.0 41.0 35.0 41.0 28 38.6435 40.0 38.0 41.0 35.0 41.0 29 38.609 40.0 38.0 41.0 34.0 41.0 30 38.512 40.0 38.0 41.0 34.0 41.0 31 38.3835 40.0 38.0 41.0 34.0 41.0 32 38.331 40.0 38.0 41.0 34.0 41.0 33 38.29075 40.0 38.0 41.0 34.0 41.0 34 38.5955 40.0 38.0 41.0 35.0 41.0 35 38.64025 40.0 38.0 41.0 35.0 41.0 36 38.5545 40.0 38.0 41.0 34.0 41.0 37 38.213 40.0 38.0 41.0 34.0 41.0 38 37.90475 40.0 38.0 41.0 33.0 41.0 39 38.05575 40.0 38.0 41.0 33.0 41.0 40 38.04475 40.0 38.0 41.0 34.0 41.0 41 37.8715 40.0 38.0 41.0 33.0 41.0 42 37.919 40.0 38.0 41.0 33.0 41.0 43 37.84625 40.0 38.0 41.0 33.0 41.0 44 37.71275 40.0 38.0 41.0 33.0 41.0 45 37.52025 40.0 38.0 41.0 33.0 41.0 46 37.61125 40.0 38.0 41.0 33.0 41.0 47 37.20125 40.0 37.0 41.0 32.0 41.0 48 37.2615 40.0 37.0 41.0 32.0 41.0 49 37.283 40.0 38.0 41.0 33.0 41.0 50 36.941 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 1.0 13 0.0 14 1.0 15 0.0 16 3.0 17 1.0 18 2.0 19 8.0 20 2.0 21 12.0 22 7.0 23 9.0 24 7.0 25 7.0 26 9.0 27 17.0 28 20.0 29 25.0 30 45.0 31 65.0 32 83.0 33 77.0 34 112.0 35 138.0 36 210.0 37 328.0 38 578.0 39 2232.0 >>END_MODULE >>Per base sequence content warn #Base G A T C 1 39.04452226113057 11.880940470235117 12.831415707853926 36.24312156078039 2 28.425 11.600000000000001 30.325000000000003 29.65 3 37.12846347607053 17.178841309823678 18.66498740554156 27.027707808564234 4 32.324999999999996 25.5 16.525000000000002 25.650000000000002 5 31.2 30.349999999999998 21.625 16.825000000000003 6 23.849999999999998 34.1 17.675 24.375 7 11.15 36.3 36.95 15.6 8 21.8 25.45 30.025000000000002 22.725 9 21.099999999999998 19.875 33.925 25.1 10 16.35 41.825 26.375 15.45 11 25.4 32.275 19.5 22.825 12 26.424999999999997 28.875 22.15 22.55 13 18.275 37.974999999999994 24.125 19.625 14 24.15 31.874999999999996 26.55 17.424999999999997 15 21.3 35.225 21.85 21.625 16 22.575 34.150000000000006 22.425 20.849999999999998 17 21.275 35.275 22.275 21.175 18 17.925 34.725 23.95 23.400000000000002 19 20.45 31.775 26.474999999999998 21.3 20 15.75 34.475 26.450000000000003 23.325000000000003 21 18.55 28.449999999999996 27.375 25.624999999999996 22 14.899999999999999 40.425 22.85 21.825 23 19.75 35.65 25.525 19.075 24 19.35 33.45 22.875 24.325 25 17.424999999999997 35.099999999999994 26.900000000000002 20.575 26 18.65 36.8 22.325 22.225 27 23.9 29.275000000000002 27.800000000000004 19.025 28 23.35 38.224999999999994 20.974999999999998 17.45 29 25.174999999999997 31.874999999999996 24.05 18.9 30 23.799999999999997 31.6 25.45 19.15 31 29.25 26.075 23.799999999999997 20.875 32 23.925 30.3 24.925 20.849999999999998 33 25.45 34.675 20.674999999999997 19.2 34 22.425 35.625 20.849999999999998 21.099999999999998 35 21.6 35.225 23.724999999999998 19.45 36 22.25 28.799999999999997 28.725 20.225 37 24.47955856533735 28.041133684474538 27.715073990469026 19.764233759719087 38 19.775000000000002 29.075 30.025000000000002 21.125 39 23.7 27.675 28.1 20.525 40 17.95 34.050000000000004 26.174999999999997 21.825 41 24.474999999999998 26.1 27.375 22.05 42 20.175 32.525 24.525 22.775000000000002 43 20.875 33.6 24.375 21.15 44 19.400000000000002 31.025000000000002 26.450000000000003 23.125 45 19.45837512537613 30.566700100300903 30.26579739217653 19.709127382146438 46 18.83295767593288 29.676934635612323 33.20811419984974 18.281993488605057 47 19.754631947921883 31.97295943915874 27.766649974962444 20.505758637956937 48 22.127659574468083 32.21526908635794 25.15644555694618 20.500625782227786 49 23.184777165748624 30.64596895343015 25.28793189784677 20.881321982974463 50 26.163081540770385 28.38919459729865 24.96248124062031 20.485242621310658 >>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 0.5 6 1.0 7 1.0 8 1.0 9 0.5 10 0.0 11 0.0 12 0.0 13 0.0 14 0.0 15 0.5 16 1.0 17 2.5 18 4.0 19 6.5 20 9.0 21 7.0 22 5.0 23 8.0 24 11.0 25 24.5 26 38.0 27 35.5 28 33.0 29 40.0 30 47.0 31 67.5 32 88.0 33 124.0 34 160.0 35 253.5 36 347.0 37 439.0 38 531.0 39 444.0 40 357.0 41 361.0 42 365.0 43 405.5 44 446.0 45 430.0 46 414.0 47 313.5 48 213.0 49 268.0 50 323.0 51 219.0 52 115.0 53 109.0 54 103.0 55 85.0 56 67.0 57 57.5 58 48.0 59 47.5 60 47.0 61 42.0 62 37.0 63 31.5 64 26.0 65 30.5 66 35.0 67 31.5 68 28.0 69 27.0 70 26.0 71 27.0 72 28.0 73 18.5 74 9.0 75 13.5 76 18.0 77 13.5 78 9.0 79 6.5 80 4.0 81 3.5 82 3.0 83 2.0 84 1.0 85 1.0 86 1.0 87 1.0 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 0.75 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 0.325 38 0.0 39 0.0 40 0.0 41 0.0 42 0.0 43 0.0 44 0.0 45 0.3 46 0.17500000000000002 47 0.15 48 0.125 49 0.15 50 0.05 >>END_MODULE >>Sequence Length Distribution pass #Length Count 50 4000.0 >>END_MODULE >>Sequence Duplication Levels warn #Total Deduplicated Percentage 56.474999999999994 #Duplication Level Percentage of deduplicated Percentage of total 1 85.96724214254094 48.55 2 6.905710491367861 7.8 3 2.1248339973439574 3.5999999999999996 4 1.3280212483399734 3.0 5 0.796812749003984 2.25 6 0.619743249225321 2.1 7 0.17706949977866313 0.7000000000000001 8 0.08853474988933156 0.4 9 0.22133687472332889 1.125 >10 1.593625498007968 20.875 >50 0.13280212483399734 6.1 >100 0.04426737494466578 3.5000000000000004 >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 140 3.5000000000000004 No Hit GGGAACTTCAAGAGCAGCTAGATCTAGAGGGAAGTTGTGAGCATTACGTT 86 2.15 No Hit GTGCTCTGCCTGGAATACAATCATAAAGTTGAAAGTACCAGATATTCCTA 80 2.0 No Hit CTGCGATGAAGGCGATAATAAATACAGAAGTTGCGGTCAATAAGGTAGGG 78 1.95 No Hit GCGGTCAATAAGGTAGGGATCATCAAAACACCGAACCATCCGATGTAAAG 49 1.225 No Hit GTTGTGCTCTGCCTGGAATACAATCATAAAGTTGAAAGTACCAGATATTC 47 1.175 No Hit GATCGGAAGAGCACACGTCTGAACTCCAGTCACGTAGAGAGATCTCGTAT 44 1.0999999999999999 TruSeq Adapter, Index 3 (97% over 37bp) TCTGCCTGGAATACAATCATAAAGTTGAAAGTACCAGATATTCCTAAAGG 41 1.0250000000000001 No Hit CGGGAACTTCAAGAGCAGCTAGATCTAGAGGGAAGTTGTGAGCATTACGT 38 0.95 No Hit CGCGACCTTGACTATCAACTACAGATTGGTTGAAATTGAATCCATTTAGG 35 0.8750000000000001 No Hit GCCTGGAATACAATCATAAAGTTGAAAGTACCAGATATTCCTAAAGGCAT 33 0.8250000000000001 No Hit CGGTCAATAAGGTAGGGATCATCAAAACACCGAACCATCCGATGTAAAGA 30 0.75 No Hit GCGACCTTGACTATCAACTACAGATTGGTTGAAATTGAATCCATTTAGGT 28 0.7000000000000001 No Hit ACGCGACCTTGACTATCAACTACAGATTGGTTGAAATTGAATCCATTTAG 27 0.675 No Hit CTCTGCCTGGAATACAATCATAAAGTTGAAAGTACCAGATATTCCTAAAG 27 0.675 No Hit CTGGAATACAATCATAAAGTTGAAAGTACCAGATATTCCTAAAGGCATAC 27 0.675 No Hit GCGATGAAGGCGATAATAAATACAGAAGTTGCGGTCAATAAGGTAGGGAT 26 0.65 No Hit GCCAAAATAACCATGAGCAGCCACAATATTATAAGTCTCTTCCTCTTGAC 26 0.65 No Hit CAATAAGGTAGGGATCATCAAAACACCGAACCATCCGATGTAAAGACGAT 25 0.625 No Hit ATAAGGATGTTGTGCTCTGCCTGGAATACAATCATAAAGTTGAAAGTACC 24 0.6 No Hit GTCAATAAGGTAGGGATCATCAAAACACCGAACCATCCGATGTAAAGACG 23 0.575 No Hit CGCAGAAGTAGGAATAATAGCACCAGAGATAATATTGTTTCCATAAAGTA 21 0.525 No Hit CTCATTAGCAGATTCATTTTCAGTAGTTTCCCTGATCAAACTAGAGGTTA 21 0.525 No Hit TTGTGCTCTGCCTGGAATACAATCATAAAGTTGAAAGTACCAGATATTCC 20 0.5 No Hit CGATGAAGGCGATAATAAATACAGAAGTTGCGGTCAATAAGGTAGGGATC 20 0.5 No Hit GGCCAAAATAACCATGAGCAGCCACAATATTATAAGTCTCTTCCTCTTGA 19 0.475 No Hit GGTCAATAAGGTAGGGATCATCAAAACACCGAACCATCCGATGTAAAGAC 19 0.475 No Hit CCCAAGTATTAATAACGCGACCTTGACTATCAACTACAGATTGGTTGAAA 18 0.44999999999999996 No Hit GCTCTGCCTGGAATACAATCATAAAGTTGAAAGTACCAGATATTCCTAAA 16 0.4 No Hit CTCGCGAATACCATCAATATCTACTGGAGGGGCTGCGATGAAGGCGATAA 16 0.4 No Hit GCTGCGATGAAGGCGATAATAAATACAGAAGTTGCGGTCAATAAGGTAGG 15 0.375 No Hit CGGAAAAACCTTATCCATTAATAGCGGGAACTTCAAGAGCAGCTAGATCT 14 0.35000000000000003 No Hit GGCGATAATAAATACAGAAGTTGCGGTCAATAAGGTAGGGATCATCAAAA 12 0.3 No Hit TTTCTTTTCTTCAAAAATTCTTATATGTTAGCGGAAAAACCTTATCCATT 11 0.27499999999999997 No Hit CCACCATTGTATAACCATTCATCAACGGATGCAGCTTCCCAAATTGGGTA 11 0.27499999999999997 No Hit CTGCCTGGAATACAATCATAAAGTTGAAAGTACCAGATATTCCTAAAGGC 11 0.27499999999999997 No Hit AGGGGCTGCGATGAAGGCGATAATAAATACAGAAGTTGCGGTCAATAAGG 11 0.27499999999999997 No Hit GGAGGGGCTGCGATGAAGGCGATAATAAATACAGAAGTTGCGGTCAATAA 10 0.25 No Hit GCGAATACCATCAATATCTACTGGAGGGGCTGCGATGAAGGCGATAATAA 10 0.25 No Hit CACGGTTGATGATATCAGCCCAAGTATTAATAACGCGACCTTGACTATCA 10 0.25 No Hit GGAAAAACCTTATCCATTAATAGCGGGAACTTCAAGAGCAGCTAGATCTA 9 0.22499999999999998 No Hit GTGAGCATTACGTTCGTGCATTACTTCCATACCAAGATTAGCACGGTTGA 9 0.22499999999999998 No Hit CGCTGGAGTAGGCTGCGAGGCCCAAGCGGCCAAGGAGTGCAGCGGCCCGT 9 0.22499999999999998 No Hit GCGGAAAAACCTTATCCATTAATAGCGGGAACTTCAAGAGCAGCTAGATC 9 0.22499999999999998 No Hit GGGGCTGCGATGAAGGCGATAATAAATACAGAAGTTGCGGTCAATAAGGT 9 0.22499999999999998 No Hit GCCCTCATTAGCAGATTCATTTTCAGTAGTTTCCCTGATCAAACTAGAGG 8 0.2 No Hit CCAAGTATTAATAACGCGACCTTGACTATCAACTACAGATTGGTTGAAAT 8 0.2 No Hit CGCGAATACCATCAATATCTACTGGAGGGGCTGCGATGAAGGCGATAATA 7 0.17500000000000002 No Hit TTCAAGAGCAGCTAGATCTAGAGGGAAGTTGTGAGCATTACGTTCGTGCA 7 0.17500000000000002 No Hit CCGGGGTGTAGTAAGTCAATCTATAATCTTTAACACCAGCTTTAAATCCA 7 0.17500000000000002 No Hit GCAGCCACAATATTATAAGTCTCTTCCTCTTGACCAAATTTGTAACCCTC 7 0.17500000000000002 No Hit CCGCAGAAGTAGGAATAATAGCACCAGAGATAATATTGTTTCCATAAAGT 6 0.15 No Hit TGCTCTGCCTGGAATACAATCATAAAGTTGAAAGTACCAGATATTCCTAA 6 0.15 No Hit CGCGGGAACTTCAAGAGCAGCTAGATCTAGAGGGAAGTTGTGAGCATTAC 6 0.15 No Hit TGATGATATCAGCCCAAGTATTAATAACGCGACCTTGACTATCAACTACA 6 0.15 No Hit GATGATATCAGCCCAAGTATTAATAACGCGACCTTGACTATCAACTACAG 6 0.15 No Hit GGATGCATAAGGATGTTGTGCTCTGCCTGGAATACAATCATAAAGTTGAA 6 0.15 No Hit GCGCGACCTTGACTATCAACTACAGATTGGTTGAAATTGAATCCATTTAG 6 0.15 No Hit CGCAGCTGCAACAGGAGCTGAATATGCAACAGCAATCCAAGGGCGCATAC 6 0.15 No Hit ATGATATCAGCCCAAGTATTAATAACGCGACCTTGACTATCAACTACAGA 6 0.15 No Hit CTCTTGACCAAATTTGTAACCCTCATTAGCAGATTCATTTTCAGTAGTTT 6 0.15 No Hit AGCAGCCACAATATTATAAGTCTCTTCCTCTTGACCAAATTTGTAACCCT 6 0.15 No Hit GGAACTTCAAGAGCAGCTAGATCTAGAGGGAAGTTGTGAGCATTACGTTC 6 0.15 No Hit CACCATTGTATAACCATTCATCAACGGATGCAGCTTCCCAAATTGGGTAA 6 0.15 No Hit CGGCCAAAATAACCATGAGCAGCCACAATATTATAAGTCTCTTCCTCTTG 6 0.15 No Hit GCGATAATAAATACAGAAGTTGCGGTCAATAAGGTAGGGATCATCAAAAC 5 0.125 No Hit GCCGAAAACACCAGCTACACCTAACATGTGAAATGGATGCATAAGGATGT 5 0.125 No Hit ATGCATAAGGATGTTGTGCTCTGCCTGGAATACAATCATAAAGTTGAAAG 5 0.125 No Hit GGTTGATGATATCAGCCCAAGTATTAATAACGCGACCTTGACTATCAACT 5 0.125 No Hit GGCGCATACCCAAACGGAAACTAAGTTCCCACTCACGACCCATATAACAA 5 0.125 No Hit TGGAGGGGCTGCGATGAAGGCGATAATAAATACAGAAGTTGCGGTCAATA 5 0.125 No Hit TAGTAAGTCAATCTATAATCTTTAACACCAGCTTTAAATCCAACACTTGC 5 0.125 No Hit TCAATAAGGTAGGGATCATCAAAACACCGAACCATCCGATGTAAAGACGA 5 0.125 No Hit CGTCTCTCTAAAATTGCAGTCATGGTAAGATCTTGGTTTATTCAAATTGC 5 0.125 No Hit GCTAGTTATCCAGTTGCAGAAGCGACCCCACAGGCTTGTACTTTCGCGTC 5 0.125 No Hit TGCGGTCAATAAGGTAGGGATCATCAAAACACCGAACCATCCGATGTAAA 5 0.125 No Hit GTGGTTCGCTGGAGTAGGCTGCGAGGCCCAAGCGGCCAAGGAGTGCAGCG 5 0.125 No Hit GTTCGCTGGAGTAGGCTGCGAGGCCCAAGCGGCCAAGGAGTGCAGCGGCC 5 0.125 No Hit CCACAATATTATAAGTCTCTTCCTCTTGACCAAATTTGTAACCCTCATTA 5 0.125 No Hit TGTGCTCTGCCTGGAATACAATCATAAAGTTGAAAGTACCAGATATTCCT 5 0.125 No Hit GTTGAAACTAGCATATTGGAAGATTAATCGGCCAAAATAACCATGAGCAG 5 0.125 No Hit AGCAGATTCATTTTCAGTAGTTTCCCTGATCAAACTAGAGGTTACCAAGG 5 0.125 No Hit CCTCATTAGCAGATTCATTTTCAGTAGTTTCCCTGATCAAACTAGAGGTT 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 fail #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position GCGGGAA 35 5.1839525E-6 38.15913 1 CGGGAAC 45 2.90481E-5 29.679323 2 TGTGAGC 45 3.1762444E-5 29.308334 38 TCTAGAG 45 3.1762444E-5 29.308334 25 GCTAGAT 45 3.1762444E-5 29.308334 19 ATCTAGA 45 3.1762444E-5 29.308334 24 AGAGGGA 45 3.1762444E-5 29.308334 28 GAGCATT 45 3.1762444E-5 29.308334 41 GTGAGCA 45 3.1762444E-5 29.308334 39 AGGGAAG 45 3.1762444E-5 29.308334 30 CATTACG 45 3.1762444E-5 29.308334 44 GATCTAG 45 3.1762444E-5 29.308334 23 GGAAGTT 45 3.1762444E-5 29.308334 32 AGCATTA 45 3.1762444E-5 29.308334 42 TAGAGGG 45 3.1762444E-5 29.308334 27 CTAGATC 45 3.1762444E-5 29.308334 20 GGGAAGT 45 3.1762444E-5 29.308334 31 GAGGGAA 45 3.1762444E-5 29.308334 29 AGATCTA 45 3.1762444E-5 29.308334 22 TTGTGAG 45 3.1762444E-5 29.308334 37 >>END_MODULE Read 982412 spots for SRR1772233.sra Written 982412 spots for SRR1772233.sra Read 982412 spots for SRR1772233.sra Written 982412 spots for SRR1772233.sra Read 982412 spots for SRR1772233.sra Written 982412 spots for SRR1772233.sra Read 982412 spots for SRR1772233.sra Written 982412 spots for SRR1772233.sra Read 982412 spots for SRR1772233.sra Written 982412 spots for SRR1772233.sra Read 982412 spots for SRR1772233.sra Written 982412 spots for SRR1772233.sra Read 982412 spots for SRR1772233.sra Written 982412 spots for SRR1772233.sra Read 982426 spots for SRR1772233.sra Written 982426 spots for SRR1772233.sra Read 982412 spots for SRR1772233.sra Written 982412 spots for SRR1772233.sra Read 982412 spots for SRR1772233.sra Written 982412 spots for SRR1772233.sra Read 982412 spots for SRR1772233.sra Written 982412 spots for SRR1772233.sra Read 982412 spots for SRR1772233.sra Written 982412 spots for SRR1772233.sra Read 982412 spots for SRR1772233.sra Written 982412 spots for SRR1772233.sra Read 982412 spots for SRR1772233.sra Written 982412 spots for SRR1772233.sra Read 982412 spots for SRR1772233.sra Written 982412 spots for SRR1772233.sra Read 982412 spots for SRR1772233.sra Written 982412 spots for SRR1772233.sra Read 982412 spots for SRR1772233.sra Written 982412 spots for SRR1772233.sra Read 982412 spots for SRR1772233.sra Written 982412 spots for SRR1772233.sra Read 982412 spots for SRR1772233.sra Written 982412 spots for SRR1772233.sra Read 982412 spots for SRR1772233.sra Written 982412 spots for SRR1772233.sra SRR ids: ['SRR1772233.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_994o84x1 SRR1772233.sra spots: 19648254 blocks: [[1, 982412], [982413, 1964824], [1964825, 2947236], [2947237, 3929648], [3929649, 4912060], [4912061, 5894472], [5894473, 6876884], [6876885, 7859296], [7859297, 8841708], [8841709, 9824120], [9824121, 10806532], [10806533, 11788944], [11788945, 12771356], [12771357, 13753768], [13753769, 14736180], [14736181, 15718592], [15718593, 16701004], [16701005, 17683416], [17683417, 18665828], [18665829, 19648254]] SRR1772233 file size 3394534 SRR1772233 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 SRR1772233 SRR1772233_1.fastq Input file: SRR1772233_1.fastq trimmed: SRR1772233-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 09:49:04 2024 >> started Fri Dec 6 09:49:15 2024 >> done (10.812s) 19648254 reads processed; of these: 2598 ( 0.01%) short reads filtered out after trimming by size control 215979 ( 1.10%) empty reads filtered out after trimming by size control 19429677 (98.89%) reads available; of these: 843850 ( 4.34%) trimmed reads available after processing 18585827 (95.66%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 1218 0.01% 19 1757 0.01% 20 3696 0.02% 21 4400 0.02% 22 5170 0.03% 23 5029 0.03% 24 7658 0.04% 25 7784 0.04% 26 7136 0.04% 27 8660 0.04% 28 9681 0.05% 29 14569 0.07% 30 12675 0.07% 31 14266 0.07% 32 16604 0.09% 33 11728 0.06% 34 13119 0.07% 35 16312 0.08% 36 16349 0.08% 37 21488 0.11% 38 17459 0.09% 39 19607 0.10% 40 29877 0.15% 41 26333 0.14% 42 46164 0.24% 43 44237 0.23% 44 59848 0.31% 45 56781 0.29% 46 69954 0.36% 47 86818 0.45% 48 97451 0.50% 49 90022 0.46% 50 18585827 95.66% 19429677 reads passed initial QC criterion=sequence-density sequence-density=0.24 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=26 fanout-score=13.99 fanout-score-rank=1 prefix-density=0.10 prefix-fanout=1.2 sequence=AGGAGAGCCGCCGACTCCAACTATCGTCCATGTACGATCCATACTAGATCTGACCAACTGCCCATCCTACCTCCTCTACCTTTTTGACAGCCCATCTTTTTGTCTCAGTAGAGTCTTTCAGTGGCATGTTTCAGTCCTCTTCCCCATTACTTAGAAAAAGTGAGCCACCGGTTCAGGTACAAGATACTATCATTACCGCCTGGACAATTAGACAGCCAACC Started job on | Dec 06 09:51:23 Started mapping on | Dec 06 09:51:24 Finished on | Dec 06 09:51:38 Mapping speed, Million of reads per hour | 4996.20 Number of input reads | 19429677 Average input read length | 49 UNIQUE READS: Uniquely mapped reads number | 4775783 Uniquely mapped reads % | 24.58% Average mapped length | 49.35 Number of splices: Total | 319621 Number of splices: Annotated (sjdb) | 303163 Number of splices: GT/AG | 313228 Number of splices: GC/AG | 4031 Number of splices: AT/AC | 182 Number of splices: Non-canonical | 2180 Mismatch rate per base, % | 0.27% 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 | 14334661 % of reads mapped to multiple loci | 73.78% Number of reads mapped to too many loci | 72079 % of reads mapped to too many loci | 0.37% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 1.26% % of reads unmapped: other | 0.01% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 319233 319233 319233 N_multimapping 14334661 14334661 14334661 N_noFeature 1056842 4637096 1123906 N_ambiguous 105861 1000 34239 UnstrandedReadsAssigned:3613080 PositiveStrandReadsAssigned:137687 NegativeStrandReadsAssigned:3617638 Dataset is classified negative stranded MeadianReadLen=50 20thPercentileLength=50 echo kmer=45 SRR1772233 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: SRR1772233-trimmed.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 19,429,677 reads, 16,274,921 reads pseudoaligned [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,308 rounds 52973 SRR1772233.ke.tsv 35125 SRR1772233.se.tsv 88098 total ==> SRR1772233.ke.tsv <== target_id length eff_length est_counts tpm PNS24245 936 837 0 0 PNS24247 1044 945 7.3641 0.543973 PNS24249 1928 1829 28.9077 1.10329 PNS24246 1044 945 7.3641 0.543973 PNS24248 1044 945 7.3641 0.543973 PNS24244 1471 1372 0 0 PNS24243 293 194 0 0 KQK14069 1603 1504 83.8836 3.89331 KQK14071 474 375 79.0431 14.7137 ==> SRR1772233.se.tsv <== BRADI_1g14170v3 344 BRADI_1g53295v3 1 BRADI_1g59795v3 48 BRADI_1g07683v3 0 BRADI_1g00485v3 1 BRADI_1g20270v3 22 BRADI_1g74790v3 8 BRADI_1g09890v3 0 BRADI_1g77505v3 23 BRADI_1g48960v3 0 SRR1772233 completed mapping pipeline successfully