Starting /dee2/code/volunteer_pipeline.sh SRR1772229 current disk space = 1540133650432 free memory = 1475880392 SRR1772229 SRAfilesize 0138f0e1445e6300f10df682c1f6ea48 SRR1772229.sra SRR1772229.sra file validated SRR1772229 is single end SRR1772229 is conventional basespace SRR1772229 read1 length is 50 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR1772229_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 32.71275 34.0 31.0 34.0 31.0 34.0 2 33.04875 34.0 31.0 34.0 31.0 34.0 3 33.00825 34.0 31.0 34.0 31.0 34.0 4 36.439 37.0 37.0 37.0 35.0 37.0 5 36.41675 37.0 37.0 37.0 35.0 37.0 6 36.3055 37.0 37.0 37.0 35.0 37.0 7 36.32825 37.0 37.0 37.0 35.0 37.0 8 36.3335 37.0 37.0 37.0 35.0 37.0 9 38.119 39.0 39.0 39.0 37.0 39.0 10 38.11025 39.0 39.0 39.0 37.0 39.0 11 38.1425 39.0 39.0 39.0 37.0 39.0 12 38.0835 39.0 39.0 39.0 37.0 39.0 13 37.9915 39.0 38.0 39.0 35.0 39.0 14 39.558 41.0 40.0 41.0 37.0 41.0 15 39.44125 41.0 40.0 41.0 37.0 41.0 16 39.51075 41.0 40.0 41.0 37.0 41.0 17 39.48225 41.0 40.0 41.0 36.0 41.0 18 39.538 41.0 40.0 41.0 37.0 41.0 19 39.46375 41.0 39.0 41.0 36.0 41.0 20 39.4055 41.0 39.0 41.0 36.0 41.0 21 39.3395 41.0 39.0 41.0 36.0 41.0 22 39.41725 41.0 39.0 41.0 36.0 41.0 23 39.365 41.0 39.0 41.0 36.0 41.0 24 39.371 41.0 39.0 41.0 36.0 41.0 25 39.18425 41.0 39.0 41.0 36.0 41.0 26 39.153 41.0 39.0 41.0 36.0 41.0 27 39.1165 41.0 39.0 41.0 36.0 41.0 28 38.90925 40.0 39.0 41.0 36.0 41.0 29 38.9 40.0 39.0 41.0 36.0 41.0 30 38.69325 40.0 39.0 41.0 35.0 41.0 31 38.65 40.0 38.0 41.0 35.0 41.0 32 38.47975 40.0 38.0 41.0 35.0 41.0 33 38.411 40.0 38.0 41.0 34.0 41.0 34 38.28525 40.0 38.0 41.0 34.0 41.0 35 38.56625 40.0 38.0 41.0 35.0 41.0 36 38.5715 40.0 38.0 41.0 35.0 41.0 37 38.40125 40.0 38.0 41.0 35.0 41.0 38 38.406 40.0 38.0 41.0 35.0 41.0 39 38.265 40.0 38.0 41.0 34.0 41.0 40 38.2515 40.0 38.0 41.0 34.0 41.0 41 38.2675 40.0 38.0 41.0 34.0 41.0 42 38.17025 40.0 38.0 41.0 34.0 41.0 43 37.94775 40.0 38.0 41.0 33.0 41.0 44 37.88525 40.0 38.0 41.0 33.0 41.0 45 37.58775 40.0 38.0 41.0 33.0 41.0 46 37.71375 40.0 38.0 41.0 33.0 41.0 47 37.303 40.0 38.0 41.0 32.0 41.0 48 37.00975 40.0 38.0 41.0 31.0 41.0 49 36.9975 40.0 38.0 41.0 31.0 41.0 50 36.654 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 0.0 15 2.0 16 2.0 17 4.0 18 3.0 19 3.0 20 3.0 21 6.0 22 10.0 23 10.0 24 13.0 25 11.0 26 11.0 27 15.0 28 18.0 29 27.0 30 49.0 31 42.0 32 69.0 33 86.0 34 84.0 35 133.0 36 182.0 37 299.0 38 550.0 39 2367.0 >>END_MODULE >>Per base sequence content warn #Base G A T C 1 42.775 11.65 11.1 34.475 2 27.425 12.525 27.500000000000004 32.550000000000004 3 38.07259073842303 16.245306633291616 19.09887359198999 26.583229036295368 4 33.025 25.15 15.45 26.375 5 32.9 28.525 20.3 18.275 6 25.6 33.275 17.575 23.549999999999997 7 10.424999999999999 40.6 32.125 16.85 8 20.175 30.15 27.85 21.825 9 22.275 19.175 34.675 23.875 10 14.174999999999999 44.275 26.174999999999997 15.375 11 25.775 31.474999999999998 18.4 24.349999999999998 12 26.025 29.9 21.075 23.0 13 17.95 40.725 22.55 18.775 14 23.9 32.7 25.424999999999997 17.974999999999998 15 19.5 38.375 20.849999999999998 21.275 16 22.35 34.925 21.675 21.05 17 23.325000000000003 34.300000000000004 21.475 20.9 18 16.950000000000003 36.95 23.875 22.225 19 20.150000000000002 32.824999999999996 25.75 21.275 20 15.024999999999999 35.3 27.625 22.05 21 19.325 28.15 27.675 24.85 22 14.45 42.35 22.725 20.474999999999998 23 19.525000000000002 38.074999999999996 24.025 18.375 24 18.275 34.55 21.224999999999998 25.95 25 18.05 33.7 28.599999999999998 19.650000000000002 26 17.275 36.7 21.7 24.325 27 22.55 29.825000000000003 26.400000000000002 21.224999999999998 28 25.474999999999998 39.175 19.85 15.5 29 28.249999999999996 31.474999999999998 22.325 17.95 30 24.0 31.724999999999998 25.474999999999998 18.8 31 30.525000000000002 25.3 21.175 23.0 32 24.775 32.65 22.900000000000002 19.675 33 26.424999999999997 33.35 19.525000000000002 20.7 34 22.900000000000002 36.05 22.6 18.45 35 20.375 39.300000000000004 21.9 18.425 36 21.15 30.375000000000004 28.675 19.8 37 25.64487853744052 28.12421738041573 27.723516153268218 18.50738792887553 38 22.275 27.200000000000003 30.775000000000002 19.75 39 24.625 24.75 27.425 23.200000000000003 40 20.8 32.4 25.025 21.775 41 23.0 30.049999999999997 24.95 22.0 42 19.30965482741371 32.61630815407704 25.312656328164078 22.761380690345174 43 19.8 31.35 26.875 21.975 44 19.900000000000002 27.3 26.775 26.025 45 19.639278557114228 29.984969939879758 32.289579158316634 18.086172344689377 46 18.031555221637866 27.07237665915352 35.161532682193844 19.734535437014774 47 22.03856749311295 31.705484598046578 27.29777109942399 18.95817680941648 48 22.025 32.95 25.3 19.725 49 21.224999999999998 34.55 23.150000000000002 21.075 50 26.35 27.55 27.224999999999998 18.875 >>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 1.0 18 1.0 19 1.0 20 1.0 21 1.5 22 2.0 23 7.0 24 12.0 25 24.0 26 36.0 27 32.5 28 29.0 29 26.0 30 23.0 31 37.0 32 51.0 33 107.5 34 164.0 35 252.0 36 340.0 37 450.0 38 560.0 39 452.0 40 344.0 41 354.0 42 364.0 43 405.5 44 447.0 45 437.0 46 427.0 47 323.5 48 220.0 49 329.5 50 439.0 51 277.5 52 116.0 53 110.5 54 105.0 55 81.0 56 57.0 57 48.0 58 39.0 59 38.0 60 37.0 61 30.5 62 24.0 63 25.5 64 27.0 65 24.0 66 21.0 67 23.5 68 26.0 69 25.5 70 25.0 71 24.5 72 24.0 73 17.0 74 10.0 75 9.0 76 8.0 77 7.5 78 7.0 79 7.0 80 7.0 81 5.0 82 3.0 83 1.5 84 0.0 85 0.5 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 0.0 2 0.0 3 0.125 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 0.05 43 0.0 44 0.0 45 0.2 46 0.17500000000000002 47 0.17500000000000002 48 0.0 49 0.0 50 0.0 >>END_MODULE >>Sequence Length Distribution pass #Length Count 50 4000.0 >>END_MODULE >>Sequence Duplication Levels fail #Total Deduplicated Percentage 47.225 #Duplication Level Percentage of deduplicated Percentage of total 1 83.11275807305452 39.25 2 6.881948120698782 6.5 3 3.5468501852832186 5.025 4 1.641079936474325 3.1 5 0.8999470619375332 2.125 6 0.37056643726839594 1.05 7 0.37056643726839594 1.225 8 0.31762837480148226 1.2 9 0.10587612493382743 0.44999999999999996 >10 2.3822128110111174 23.575 >50 0.2646903123345686 9.325 >100 0.10587612493382743 7.175 >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 170 4.25 No Hit GATCGGAAGAGCACACGTCTGAACTCCAGTCACTAAGGCGAATCTCGTAT 117 2.9250000000000003 TruSeq Adapter, Index 3 (97% over 39bp) GGGAACTTCAAGAGCAGCTAGATCTAGAGGGAAGTTGTGAGCATTACGTT 89 2.225 No Hit CTGCGATGAAGGCGATAATAAATACAGAAGTTGCGGTCAATAAGGTAGGG 81 2.025 No Hit GCGGTCAATAAGGTAGGGATCATCAAAACACCGAACCATCCGATGTAAAG 76 1.9 No Hit GTGCTCTGCCTGGAATACAATCATAAAGTTGAAAGTACCAGATATTCCTA 75 1.875 No Hit ACGCGACCTTGACTATCAACTACAGATTGGTTGAAATTGAATCCATTTAG 52 1.3 No Hit TCTGCCTGGAATACAATCATAAAGTTGAAAGTACCAGATATTCCTAAAGG 48 1.2 No Hit GCCTGGAATACAATCATAAAGTTGAAAGTACCAGATATTCCTAAAGGCAT 46 1.15 No Hit GTTGTGCTCTGCCTGGAATACAATCATAAAGTTGAAAGTACCAGATATTC 45 1.125 No Hit GCGACCTTGACTATCAACTACAGATTGGTTGAAATTGAATCCATTTAGGT 42 1.05 No Hit CTCTGCCTGGAATACAATCATAAAGTTGAAAGTACCAGATATTCCTAAAG 37 0.9249999999999999 No Hit GCGATGAAGGCGATAATAAATACAGAAGTTGCGGTCAATAAGGTAGGGAT 36 0.8999999999999999 No Hit CGGTCAATAAGGTAGGGATCATCAAAACACCGAACCATCCGATGTAAAGA 36 0.8999999999999999 No Hit CGCGACCTTGACTATCAACTACAGATTGGTTGAAATTGAATCCATTTAGG 36 0.8999999999999999 No Hit CGGGAACTTCAAGAGCAGCTAGATCTAGAGGGAAGTTGTGAGCATTACGT 30 0.75 No Hit GCGGAAAAACCTTATCCATTAATAGCGGGAACTTCAAGAGCAGCTAGATC 27 0.675 No Hit CTGGAATACAATCATAAAGTTGAAAGTACCAGATATTCCTAAAGGCATAC 26 0.65 No Hit CTCGCGAATACCATCAATATCTACTGGAGGGGCTGCGATGAAGGCGATAA 26 0.65 No Hit CGCAGAAGTAGGAATAATAGCACCAGAGATAATATTGTTTCCATAAAGTA 25 0.625 No Hit CCCAAGTATTAATAACGCGACCTTGACTATCAACTACAGATTGGTTGAAA 25 0.625 No Hit GGCCAAAATAACCATGAGCAGCCACAATATTATAAGTCTCTTCCTCTTGA 24 0.6 No Hit GGCGATAATAAATACAGAAGTTGCGGTCAATAAGGTAGGGATCATCAAAA 23 0.575 No Hit CGGAAAAACCTTATCCATTAATAGCGGGAACTTCAAGAGCAGCTAGATCT 23 0.575 No Hit GTCAATAAGGTAGGGATCATCAAAACACCGAACCATCCGATGTAAAGACG 20 0.5 No Hit CGATGAAGGCGATAATAAATACAGAAGTTGCGGTCAATAAGGTAGGGATC 20 0.5 No Hit CAATAAGGTAGGGATCATCAAAACACCGAACCATCCGATGTAAAGACGAT 19 0.475 No Hit ATAAGGATGTTGTGCTCTGCCTGGAATACAATCATAAAGTTGAAAGTACC 19 0.475 No Hit GCCAAAATAACCATGAGCAGCCACAATATTATAAGTCTCTTCCTCTTGAC 18 0.44999999999999996 No Hit GGAAAAACCTTATCCATTAATAGCGGGAACTTCAAGAGCAGCTAGATCTA 17 0.42500000000000004 No Hit TGTGCTCTGCCTGGAATACAATCATAAAGTTGAAAGTACCAGATATTCCT 17 0.42500000000000004 No Hit GCTGCGATGAAGGCGATAATAAATACAGAAGTTGCGGTCAATAAGGTAGG 16 0.4 No Hit GCTAGTTATCCAGTTGCAGAAGCGACCCCACAGGCTTGTACTTTCGCGTC 15 0.375 No Hit GGTCAATAAGGTAGGGATCATCAAAACACCGAACCATCCGATGTAAAGAC 15 0.375 No Hit CTTTCTTTTCTTCAAAAATTCTTATATGTTAGCGGAAAAACCTTATCCAT 15 0.375 No Hit GGGGCTGCGATGAAGGCGATAATAAATACAGAAGTTGCGGTCAATAAGGT 15 0.375 No Hit GGAGGGGCTGCGATGAAGGCGATAATAAATACAGAAGTTGCGGTCAATAA 14 0.35000000000000003 No Hit GCCGAAAACACCAGCTACACCTAACATGTGAAATGGATGCATAAGGATGT 14 0.35000000000000003 No Hit GCTCTGCCTGGAATACAATCATAAAGTTGAAAGTACCAGATATTCCTAAA 14 0.35000000000000003 No Hit TTTCTTTTCTTCAAAAATTCTTATATGTTAGCGGAAAAACCTTATCCATT 13 0.325 No Hit CCACAATATTATAAGTCTCTTCCTCTTGACCAAATTTGTAACCCTCATTA 13 0.325 No Hit CGCGAATACCATCAATATCTACTGGAGGGGCTGCGATGAAGGCGATAATA 11 0.27499999999999997 No Hit TGCGGGAACTTCAAGAGCAGCTAGATCTAGAGGGAAGTTGTGAGCATTAC 11 0.27499999999999997 No Hit GTGAGCATTACGTTCGTGCATTACTTCCATACCAAGATTAGCACGGTTGA 11 0.27499999999999997 No Hit CGCTGGAGTAGGCTGCGAGGCCCAAGCGGCCAAGGAGTGCAGCGGCCCGT 11 0.27499999999999997 No Hit CCGCAGAAGTAGGAATAATAGCACCAGAGATAATATTGTTTCCATAAAGT 10 0.25 No Hit TTCAAGAGCAGCTAGATCTAGAGGGAAGTTGTGAGCATTACGTTCGTGCA 10 0.25 No Hit CCACCATTGTATAACCATTCATCAACGGATGCAGCTTCCCAAATTGGGTA 10 0.25 No Hit AGCGGGAACTTCAAGAGCAGCTAGATCTAGAGGGAAGTTGTGAGCATTAC 10 0.25 No Hit GCGAATACCATCAATATCTACTGGAGGGGCTGCGATGAAGGCGATAATAA 10 0.25 No Hit CTCATTAGCAGATTCATTTTCAGTAGTTTCCCTGATCAAACTAGAGGTTA 10 0.25 No Hit GTTGAAACTAGCATATTGGAAGATTAATCGGCCAAAATAACCATGAGCAG 10 0.25 No Hit TGATGATATCAGCCCAAGTATTAATAACGCGACCTTGACTATCAACTACA 9 0.22499999999999998 No Hit AGGGGCTGCGATGAAGGCGATAATAAATACAGAAGTTGCGGTCAATAAGG 9 0.22499999999999998 No Hit AATAAGGTAGGGATCATCAAAACACCGAACCATCCGATGTAAAGACGATT 8 0.2 No Hit CTTTTCTTCAAAAATTCTTATATGTTAGCGGAAAAACCTTATCCATTAAT 8 0.2 No Hit GCGATAATAAATACAGAAGTTGCGGTCAATAAGGTAGGGATCATCAAAAC 8 0.2 No Hit TGCGGTCAATAAGGTAGGGATCATCAAAACACCGAACCATCCGATGTAAA 8 0.2 No Hit AATAAATACAGAAGTTGCGGTCAATAAGGTAGGGATCATCAAAACACCGA 8 0.2 No Hit CACCATTGTATAACCATTCATCAACGGATGCAGCTTCCCAAATTGGGTAA 8 0.2 No Hit CGCGGTCAATAAGGTAGGGATCATCAAAACACCGAACCATCCGATGTAAA 7 0.17500000000000002 No Hit CGTGCTCTGCCTGGAATACAATCATAAAGTTGAAAGTACCAGATATTCCT 7 0.17500000000000002 No Hit ATGAAGGCGATAATAAATACAGAAGTTGCGGTCAATAAGGTAGGGATCAT 7 0.17500000000000002 No Hit GGGCTGCGATGAAGGCGATAATAAATACAGAAGTTGCGGTCAATAAGGTA 7 0.17500000000000002 No Hit CCAAGTATTAATAACGCGACCTTGACTATCAACTACAGATTGGTTGAAAT 7 0.17500000000000002 No Hit AGCAGCCACAATATTATAAGTCTCTTCCTCTTGACCAAATTTGTAACCCT 7 0.17500000000000002 No Hit TAGTTATCCAGTTGCAGAAGCGACCCCACAGGCTTGTACTTTCGCGTCTC 7 0.17500000000000002 No Hit CGCCATAGTACTAATACCTAAAGCAGTGAACCAGATTCCTACTACAGGCC 6 0.15 No Hit GGTTGATGATATCAGCCCAAGTATTAATAACGCGACCTTGACTATCAACT 6 0.15 No Hit TGTTGTGCTCTGCCTGGAATACAATCATAAAGTTGAAAGTACCAGATATT 6 0.15 No Hit CCCCAGTTAAGTAGTCATGCATTACAATAGGAACACCTAATTCTCTCGCA 6 0.15 No Hit CTGCCTGGAATACAATCATAAAGTTGAAAGTACCAGATATTCCTAAAGGC 6 0.15 No Hit CTAGTTATCCAGTTGCAGAAGCGACCCCACAGGCTTGTACTTTCGCGTCT 6 0.15 No Hit CGGCCAAAATAACCATGAGCAGCCACAATATTATAAGTCTCTTCCTCTTG 6 0.15 No Hit CTTCCTCTTGACCAAATTTGTAACCCTCATTAGCAGATTCATTTTCAGTA 5 0.125 No Hit ATGCATAAGGATGTTGTGCTCTGCCTGGAATACAATCATAAAGTTGAAAG 5 0.125 No Hit CCGGGGTGTAGTAAGTCAATCTATAATCTTTAACACCAGCTTTAAATCCA 5 0.125 No Hit CCGCGACCTTGACTATCAACTACAGATTGGTTGAAATTGAATCCATTTAG 5 0.125 No Hit GCATTACGTTCGTGCATTACTTCCATACCAAGATTAGCACGGTTGATGAT 5 0.125 No Hit GGATGCATAAGGATGTTGTGCTCTGCCTGGAATACAATCATAAAGTTGAA 5 0.125 No Hit CCATTGTATAACCATTCATCAACGGATGCAGCTTCCCAAATTGGGTAAAA 5 0.125 No Hit TTCCTCTTGACCAAATTTGTAACCCTCATTAGCAGATTCATTTTCAGTAG 5 0.125 No Hit CGCATACCCAAACGGAAACTAAGTTCCCACTCACGACCCATATAACAAGC 5 0.125 No Hit GTTCGCTGGAGTAGGCTGCGAGGCCCAAGCGGCCAAGGAGTGCAGCGGCC 5 0.125 No Hit CTCATAAGGACCACCATTGTATAACCATTCATCAACGGATGCAGCTTCCC 5 0.125 No Hit GCGGCCTTGACTATCAACTACAGATTGGTTGAAATTGAATCCATTTAGGT 5 0.125 No Hit TTGTGCTCTGCCTGGAATACAATCATAAAGTTGAAAGTACCAGATATTCC 5 0.125 No Hit CACGGTTGATGATATCAGCCCAAGTATTAATAACGCGACCTTGACTATCA 5 0.125 No Hit GGAACTTCAAGAGCAGCTAGATCTAGAGGGAAGTTGTGAGCATTACGTTC 5 0.125 No Hit TAGCGGAAAAACCTTATCCATTAATAGCGGGAACTTCAAGAGCAGCTAGA 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 ACCATCC 25 0.002084305 35.2 35 CATCCGA 25 0.002084305 35.2 37 CACCGAA 25 0.002084305 35.2 29 GATGTAA 25 0.002084305 35.2 42 ACACCGA 25 0.002084305 35.2 28 CATCAAA 25 0.002084305 35.2 21 ACCGAAC 25 0.002084305 35.2 30 AACCATC 25 0.002084305 35.2 34 GAACCAT 25 0.002084305 35.2 33 CCATCCG 25 0.002084305 35.2 36 CGAACCA 25 0.002084305 35.2 32 GATCATC 25 0.002084305 35.2 18 ATCATCA 25 0.002084305 35.2 19 CGATGTA 25 0.002084305 35.2 41 ATGTAAA 25 0.002084305 35.2 43 ATCAAAA 25 0.002084305 35.2 22 TCCGATG 25 0.002084305 35.2 39 ATCCGAT 25 0.002084305 35.2 38 CCGATGT 25 0.002084305 35.2 40 AACACCG 25 0.002084305 35.2 27 >>END_MODULE Read 843856 spots for SRR1772229.sra Written 843856 spots for SRR1772229.sra Read 843856 spots for SRR1772229.sra Written 843856 spots for SRR1772229.sra Read 843856 spots for SRR1772229.sra Written 843856 spots for SRR1772229.sra Read 843856 spots for SRR1772229.sra Written 843856 spots for SRR1772229.sra Read 843870 spots for SRR1772229.sra Written 843870 spots for SRR1772229.sra Read 843856 spots for SRR1772229.sra Written 843856 spots for SRR1772229.sra Read 843856 spots for SRR1772229.sra Written 843856 spots for SRR1772229.sra Read 843856 spots for SRR1772229.sra Written 843856 spots for SRR1772229.sra Read 843856 spots for SRR1772229.sra Written 843856 spots for SRR1772229.sra Read 843856 spots for SRR1772229.sra Written 843856 spots for SRR1772229.sra Read 843856 spots for SRR1772229.sra Written 843856 spots for SRR1772229.sra Read 843856 spots for SRR1772229.sra Written 843856 spots for SRR1772229.sra Read 843856 spots for SRR1772229.sra Written 843856 spots for SRR1772229.sra Read 843856 spots for SRR1772229.sra Written 843856 spots for SRR1772229.sra Read 843856 spots for SRR1772229.sra Written 843856 spots for SRR1772229.sra Read 843856 spots for SRR1772229.sra Written 843856 spots for SRR1772229.sra Read 843856 spots for SRR1772229.sra Written 843856 spots for SRR1772229.sra Read 843856 spots for SRR1772229.sra Written 843856 spots for SRR1772229.sra Read 843856 spots for SRR1772229.sra Written 843856 spots for SRR1772229.sra Read 843856 spots for SRR1772229.sra Written 843856 spots for SRR1772229.sra SRR ids: ['SRR1772229.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_da6tibi_ SRR1772229.sra spots: 16877134 blocks: [[1, 843856], [843857, 1687712], [1687713, 2531568], [2531569, 3375424], [3375425, 4219280], [4219281, 5063136], [5063137, 5906992], [5906993, 6750848], [6750849, 7594704], [7594705, 8438560], [8438561, 9282416], [9282417, 10126272], [10126273, 10970128], [10970129, 11813984], [11813985, 12657840], [12657841, 13501696], [13501697, 14345552], [14345553, 15189408], [15189409, 16033264], [16033265, 16877134]] SRR1772229 file size 2914258 SRR1772229 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 SRR1772229 SRR1772229_1.fastq Input file: SRR1772229_1.fastq trimmed: SRR1772229-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 19:26:31 2024 >> started Sat Dec 7 19:27:28 2024 >> done (57.168s) 16877134 reads processed; of these: 1752 ( 0.01%) short reads filtered out after trimming by size control 535558 ( 3.17%) empty reads filtered out after trimming by size control 16339824 (96.82%) reads available; of these: 693883 ( 4.25%) trimmed reads available after processing 15645941 (95.75%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 887 0.01% 19 1267 0.01% 20 2901 0.02% 21 3212 0.02% 22 3620 0.02% 23 3721 0.02% 24 5141 0.03% 25 5680 0.03% 26 6056 0.04% 27 7358 0.05% 28 6729 0.04% 29 13202 0.08% 30 10984 0.07% 31 9234 0.06% 32 16410 0.10% 33 10334 0.06% 34 10379 0.06% 35 12045 0.07% 36 12116 0.07% 37 19331 0.12% 38 13576 0.08% 39 15455 0.09% 40 21300 0.13% 41 20121 0.12% 42 33185 0.20% 43 35781 0.22% 44 56010 0.34% 45 50954 0.31% 46 63366 0.39% 47 72896 0.45% 48 81575 0.50% 49 69057 0.42% 50 15645941 95.75% 16339824 reads passed initial QC criterion=sequence-density sequence-density=0.24 sequence-density-rank=1 fanout-score=0.00 fanout-score-rank=12 prefix-density=0.00 prefix-fanout=1.0 sequence=CGTGCTCTGCCT criterion=fanout-score sequence-density=0.01 sequence-density-rank=30 fanout-score=8.67 fanout-score-rank=1 prefix-density=0.02 prefix-fanout=2.8 sequence=AAAAACAACGTCGATGAAGGCGTGTAGGTGCACTATTACGTGGTAGGGATTGCAATTTTTCTCGCATTTTCGTTTTTTCACTCAAACTCAAGGGGGAAACTTTGCTTCTTATCTTTTTTTTTAAAGATTGGCGAATCAAATGAT Started job on | Dec 07 19:28:56 Started mapping on | Dec 07 19:28:57 Finished on | Dec 07 19:30:35 Mapping speed, Million of reads per hour | 600.24 Number of input reads | 16339824 Average input read length | 49 UNIQUE READS: Uniquely mapped reads number | 3506853 Uniquely mapped reads % | 21.46% Average mapped length | 49.47 Number of splices: Total | 208745 Number of splices: Annotated (sjdb) | 197315 Number of splices: GT/AG | 204300 Number of splices: GC/AG | 2748 Number of splices: AT/AC | 86 Number of splices: Non-canonical | 1611 Mismatch rate per base, % | 0.24% Deletion rate per base | 0.01% Deletion average length | 1.55 Insertion rate per base | 0.00% Insertion average length | 1.39 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 12581490 % of reads mapped to multiple loci | 77.00% Number of reads mapped to too many loci | 62375 % of reads mapped to too many loci | 0.38% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 1.14% % of reads unmapped: other | 0.01% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 251481 251481 251481 N_multimapping 12581490 12581490 12581490 N_noFeature 753293 3399253 812772 N_ambiguous 69744 767 21501 UnstrandedReadsAssigned:2683816 PositiveStrandReadsAssigned:106833 NegativeStrandReadsAssigned:2672580 Dataset is classified negative stranded MeadianReadLen=50 20thPercentileLength=50 echo kmer=45 SRR1772229 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: SRR1772229-trimmed.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 16,339,824 reads, 13,964,278 reads pseudoaligned [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 949 rounds 52973 SRR1772229.ke.tsv 35125 SRR1772229.se.tsv 88098 total ==> SRR1772229.ke.tsv <== target_id length eff_length est_counts tpm PNS24245 936 837 0 0 PNS24247 1044 945 0 0 PNS24249 1928 1829 28 1.21647 PNS24246 1044 945 0 0 PNS24248 1044 945 0 0 PNS24244 1471 1372 0 0 PNS24243 293 194 0 0 KQK14069 1603 1504 4.46409 0.235853 KQK14071 474 375 13.1786 2.7925 ==> SRR1772229.se.tsv <== BRADI_1g14170v3 91 BRADI_1g53295v3 3 BRADI_1g59795v3 15 BRADI_1g07683v3 0 BRADI_1g00485v3 0 BRADI_1g20270v3 13 BRADI_1g74790v3 4 BRADI_1g09890v3 0 BRADI_1g77505v3 11 BRADI_1g48960v3 0 SRR1772229 completed mapping pipeline successfully