Starting /dee2/code/volunteer_pipeline.sh SRR1772231 current disk space = 1539996946432 free memory = 1607445604 SRR1772231 SRAfilesize a38b8db0a5597d844a69891f818039b2 SRR1772231.sra SRR1772231.sra file validated SRR1772231 is single end SRR1772231 is conventional basespace SRR1772231 read1 length is 50 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR1772231_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 32.91275 34.0 31.0 34.0 31.0 34.0 2 33.0055 34.0 31.0 34.0 31.0 34.0 3 32.85025 34.0 31.0 34.0 31.0 34.0 4 36.26875 37.0 37.0 37.0 35.0 37.0 5 36.29 37.0 37.0 37.0 35.0 37.0 6 36.1265 37.0 37.0 37.0 35.0 37.0 7 36.23925 37.0 37.0 37.0 35.0 37.0 8 36.20475 37.0 37.0 37.0 35.0 37.0 9 37.9015 39.0 38.0 39.0 35.0 39.0 10 37.78525 39.0 38.0 39.0 35.0 39.0 11 37.913 39.0 38.0 39.0 35.0 39.0 12 37.97225 39.0 38.0 39.0 35.0 39.0 13 37.9025 39.0 38.0 39.0 35.0 39.0 14 39.17075 41.0 39.0 41.0 36.0 41.0 15 39.2495 41.0 39.0 41.0 36.0 41.0 16 39.058 40.0 39.0 41.0 36.0 41.0 17 39.3015 41.0 39.0 41.0 36.0 41.0 18 39.346 41.0 39.0 41.0 36.0 41.0 19 39.231 41.0 39.0 41.0 36.0 41.0 20 39.2095 41.0 39.0 41.0 36.0 41.0 21 39.17125 41.0 39.0 41.0 36.0 41.0 22 39.162 41.0 39.0 41.0 36.0 41.0 23 38.89475 40.0 39.0 41.0 35.0 41.0 24 38.82125 40.0 39.0 41.0 35.0 41.0 25 38.97525 40.0 39.0 41.0 35.0 41.0 26 38.495 40.0 38.0 41.0 34.0 41.0 27 38.69575 40.0 38.0 41.0 34.0 41.0 28 38.65675 40.0 38.0 41.0 35.0 41.0 29 38.52275 40.0 38.0 41.0 34.0 41.0 30 38.57625 40.0 38.0 41.0 35.0 41.0 31 38.25825 40.0 38.0 41.0 34.0 41.0 32 38.278 40.0 38.0 41.0 34.0 41.0 33 38.22 40.0 38.0 41.0 34.0 41.0 34 38.50925 40.0 38.0 41.0 35.0 41.0 35 38.5825 40.0 38.0 41.0 35.0 41.0 36 38.4665 40.0 38.0 41.0 34.0 41.0 37 38.15775 40.0 38.0 41.0 34.0 41.0 38 37.97525 40.0 38.0 41.0 33.0 41.0 39 38.015 40.0 38.0 41.0 33.0 41.0 40 37.934 40.0 38.0 41.0 33.0 41.0 41 37.876 40.0 38.0 41.0 33.0 41.0 42 37.90925 40.0 38.0 41.0 33.0 41.0 43 37.757 40.0 38.0 41.0 33.0 41.0 44 37.73075 40.0 38.0 41.0 33.0 41.0 45 37.45525 40.0 38.0 41.0 33.0 41.0 46 37.4685 40.0 38.0 41.0 33.0 41.0 47 37.1465 40.0 37.0 41.0 32.0 41.0 48 37.1655 40.0 37.0 41.0 32.0 41.0 49 37.13875 40.0 37.0 41.0 32.0 41.0 50 36.7585 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 13 3.0 14 2.0 15 0.0 16 2.0 17 2.0 18 4.0 19 1.0 20 5.0 21 4.0 22 8.0 23 11.0 24 11.0 25 12.0 26 16.0 27 15.0 28 26.0 29 33.0 30 51.0 31 53.0 32 71.0 33 87.0 34 124.0 35 141.0 36 211.0 37 346.0 38 588.0 39 2173.0 >>END_MODULE >>Per base sequence content warn #Base G A T C 1 37.75331498623968 12.109081811358518 14.010507880910684 36.12709532149112 2 29.675 11.200000000000001 29.275000000000002 29.849999999999998 3 38.90005022601707 17.57910597689603 17.57910597689603 25.94173782019086 4 33.6 25.775 15.875 24.75 5 31.85 28.475 21.975 17.7 6 22.8 34.225 18.75 24.224999999999998 7 12.7 34.925 35.525 16.85 8 21.65 25.0 31.25 22.1 9 20.375 19.775000000000002 34.775 25.074999999999996 10 16.175 41.275 25.7 16.85 11 24.0 32.300000000000004 19.175 24.525 12 26.125 28.65 23.549999999999997 21.675 13 19.15 37.075 24.474999999999998 19.3 14 24.525 31.7 27.200000000000003 16.575 15 20.9 35.325 21.675 22.1 16 22.3 34.599999999999994 22.875 20.225 17 22.0 33.825 22.275 21.9 18 18.35 35.55 22.725 23.375 19 20.200000000000003 32.7 26.700000000000003 20.4 20 17.375 33.900000000000006 26.674999999999997 22.05 21 17.45 31.15 26.875 24.525 22 15.675 40.025 24.775 19.525000000000002 23 19.8 33.300000000000004 27.875 19.025 24 20.125 33.45 23.025000000000002 23.400000000000002 25 18.05 33.525 26.6 21.825 26 17.974999999999998 37.225 23.625 21.175 27 22.7 31.225 27.075 19.0 28 23.974999999999998 38.0 21.3 16.725 29 25.275 32.1 23.200000000000003 19.425 30 25.05 31.65 23.45 19.85 31 28.9 27.625 23.175 20.3 32 24.85 30.95 22.6 21.6 33 26.424999999999997 33.15 21.8 18.625 34 23.5 35.8 20.8 19.900000000000002 35 23.65 34.949999999999996 22.1 19.3 36 21.825 28.175 28.15 21.85 37 22.70107742420446 29.616637434227012 28.238536707592083 19.443748433976445 38 21.925 27.975 29.975 20.125 39 23.45 26.924999999999997 29.075 20.549999999999997 40 18.975 31.724999999999998 27.55 21.75 41 22.2 26.674999999999997 27.575 23.549999999999997 42 20.974999999999998 30.8 24.925 23.3 43 21.275 32.65 24.425 21.65 44 21.15 28.525 27.275 23.05 45 19.434009516654143 31.63035311795642 29.07588279489106 19.85975457049837 46 18.72340425531915 30.48811013767209 33.29161451814768 17.496871088861077 47 18.873591989987485 33.61702127659574 26.958698372966204 20.550688360450565 48 22.441831373530146 32.82461846384789 23.71778834125594 21.015761821366024 49 23.30413016270338 30.58823529411765 24.58072590738423 21.526908635794744 50 24.88744372186093 26.863431715857928 26.863431715857928 21.38569284642321 >>END_MODULE >>Per sequence GC content fail #GC Content Count 0 1.0 1 1.0 2 1.0 3 0.5 4 0.0 5 0.0 6 0.0 7 0.0 8 0.0 9 0.5 10 1.0 11 0.5 12 0.0 13 0.5 14 1.0 15 1.0 16 1.0 17 1.0 18 1.0 19 3.5 20 6.0 21 5.5 22 5.0 23 9.5 24 14.0 25 23.5 26 33.0 27 42.5 28 52.0 29 53.5 30 55.0 31 65.5 32 76.0 33 125.5 34 175.0 35 271.5 36 368.0 37 432.5 38 497.0 39 414.5 40 332.0 41 348.0 42 364.0 43 393.5 44 423.0 45 419.5 46 416.0 47 341.0 48 266.0 49 270.5 50 275.0 51 196.0 52 117.0 53 99.5 54 82.0 55 72.5 56 63.0 57 58.5 58 54.0 59 53.5 60 53.0 61 52.0 62 51.0 63 41.0 64 31.0 65 36.5 66 42.0 67 39.0 68 36.0 69 34.0 70 32.0 71 27.5 72 23.0 73 22.0 74 21.0 75 16.0 76 11.0 77 8.0 78 5.0 79 5.5 80 6.0 81 5.0 82 4.0 83 4.0 84 4.0 85 3.0 86 2.0 87 1.0 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 0.44999999999999996 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 0.22499999999999998 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 0.125 47 0.125 48 0.075 49 0.125 50 0.05 >>END_MODULE >>Sequence Length Distribution pass #Length Count 50 4000.0 >>END_MODULE >>Sequence Duplication Levels warn #Total Deduplicated Percentage 57.725 #Duplication Level Percentage of deduplicated Percentage of total 1 86.35773061931572 49.85 2 6.27977479428324 7.249999999999999 3 2.425292334343872 4.2 4 0.996102208748376 2.3 5 0.86617583369424 2.5 6 0.34647033347769596 1.2 7 0.25985275010827197 1.05 8 0.25985275010827197 1.2 9 0.17323516673884798 0.8999999999999999 >10 1.7756604590731917 17.974999999999998 >50 0.21654395842356 8.450000000000001 >100 0.043308791684711995 3.125 >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 125 3.125 No Hit GGGAACTTCAAGAGCAGCTAGATCTAGAGGGAAGTTGTGAGCATTACGTT 85 2.125 No Hit CTGCGATGAAGGCGATAATAAATACAGAAGTTGCGGTCAATAAGGTAGGG 78 1.95 No Hit GCGGTCAATAAGGTAGGGATCATCAAAACACCGAACCATCCGATGTAAAG 63 1.575 No Hit GTGCTCTGCCTGGAATACAATCATAAAGTTGAAAGTACCAGATATTCCTA 57 1.425 No Hit CGGGAACTTCAAGAGCAGCTAGATCTAGAGGGAAGTTGTGAGCATTACGT 55 1.375 No Hit GTTGTGCTCTGCCTGGAATACAATCATAAAGTTGAAAGTACCAGATATTC 40 1.0 No Hit TCTGCCTGGAATACAATCATAAAGTTGAAAGTACCAGATATTCCTAAAGG 38 0.95 No Hit GCGATGAAGGCGATAATAAATACAGAAGTTGCGGTCAATAAGGTAGGGAT 35 0.8750000000000001 No Hit GCGACCTTGACTATCAACTACAGATTGGTTGAAATTGAATCCATTTAGGT 32 0.8 No Hit GCCTGGAATACAATCATAAAGTTGAAAGTACCAGATATTCCTAAAGGCAT 31 0.775 No Hit CTCTGCCTGGAATACAATCATAAAGTTGAAAGTACCAGATATTCCTAAAG 29 0.7250000000000001 No Hit CAATAAGGTAGGGATCATCAAAACACCGAACCATCCGATGTAAAGACGAT 24 0.6 No Hit ACGCGACCTTGACTATCAACTACAGATTGGTTGAAATTGAATCCATTTAG 24 0.6 No Hit CGGTCAATAAGGTAGGGATCATCAAAACACCGAACCATCCGATGTAAAGA 24 0.6 No Hit CGCGACCTTGACTATCAACTACAGATTGGTTGAAATTGAATCCATTTAGG 22 0.5499999999999999 No Hit CTCATTAGCAGATTCATTTTCAGTAGTTTCCCTGATCAAACTAGAGGTTA 20 0.5 No Hit GCCAAAATAACCATGAGCAGCCACAATATTATAAGTCTCTTCCTCTTGAC 19 0.475 No Hit ATAAGGATGTTGTGCTCTGCCTGGAATACAATCATAAAGTTGAAAGTACC 18 0.44999999999999996 No Hit CTGGAATACAATCATAAAGTTGAAAGTACCAGATATTCCTAAAGGCATAC 18 0.44999999999999996 No Hit GTCAATAAGGTAGGGATCATCAAAACACCGAACCATCCGATGTAAAGACG 17 0.42500000000000004 No Hit CTCGCGAATACCATCAATATCTACTGGAGGGGCTGCGATGAAGGCGATAA 17 0.42500000000000004 No Hit CGGAAAAACCTTATCCATTAATAGCGGGAACTTCAAGAGCAGCTAGATCT 16 0.4 No Hit CGATGAAGGCGATAATAAATACAGAAGTTGCGGTCAATAAGGTAGGGATC 16 0.4 No Hit GGCCAAAATAACCATGAGCAGCCACAATATTATAAGTCTCTTCCTCTTGA 15 0.375 No Hit CCAAGTATTAATAACGCGACCTTGACTATCAACTACAGATTGGTTGAAAT 15 0.375 No Hit TTGTGCTCTGCCTGGAATACAATCATAAAGTTGAAAGTACCAGATATTCC 15 0.375 No Hit GCGGAAAAACCTTATCCATTAATAGCGGGAACTTCAAGAGCAGCTAGATC 15 0.375 No Hit GCTCTGCCTGGAATACAATCATAAAGTTGAAAGTACCAGATATTCCTAAA 15 0.375 No Hit GGGGCTGCGATGAAGGCGATAATAAATACAGAAGTTGCGGTCAATAAGGT 15 0.375 No Hit CGCAGAAGTAGGAATAATAGCACCAGAGATAATATTGTTTCCATAAAGTA 13 0.325 No Hit GATCGGAAGAGCACACGTCTGAACTCCAGTCACAGGAGTCCATCTCGTAT 13 0.325 TruSeq Adapter, Index 15 (97% over 36bp) GGAGGGGCTGCGATGAAGGCGATAATAAATACAGAAGTTGCGGTCAATAA 12 0.3 No Hit AGCGGGAACTTCAAGAGCAGCTAGATCTAGAGGGAAGTTGTGAGCATTAC 12 0.3 No Hit CTGCCTGGAATACAATCATAAAGTTGAAAGTACCAGATATTCCTAAAGGC 12 0.3 No Hit CTTTTCTTCAAAAATTCTTATATGTTAGCGGAAAAACCTTATCCATTAAT 11 0.27499999999999997 No Hit GGAAAAACCTTATCCATTAATAGCGGGAACTTCAAGAGCAGCTAGATCTA 11 0.27499999999999997 No Hit TGCGGGAACTTCAAGAGCAGCTAGATCTAGAGGGAAGTTGTGAGCATTAC 11 0.27499999999999997 No Hit GGTCAATAAGGTAGGGATCATCAAAACACCGAACCATCCGATGTAAAGAC 11 0.27499999999999997 No Hit GCTGCGATGAAGGCGATAATAAATACAGAAGTTGCGGTCAATAAGGTAGG 11 0.27499999999999997 No Hit CGCTGGAGTAGGCTGCGAGGCCCAAGCGGCCAAGGAGTGCAGCGGCCCGT 11 0.27499999999999997 No Hit CTTTCTTTTCTTCAAAAATTCTTATATGTTAGCGGAAAAACCTTATCCAT 11 0.27499999999999997 No Hit GGCGATAATAAATACAGAAGTTGCGGTCAATAAGGTAGGGATCATCAAAA 10 0.25 No Hit CCCAAGTATTAATAACGCGACCTTGACTATCAACTACAGATTGGTTGAAA 10 0.25 No Hit GGGCTGCGATGAAGGCGATAATAAATACAGAAGTTGCGGTCAATAAGGTA 10 0.25 No Hit TGTGCTCTGCCTGGAATACAATCATAAAGTTGAAAGTACCAGATATTCCT 10 0.25 No Hit AGGGGCTGCGATGAAGGCGATAATAAATACAGAAGTTGCGGTCAATAAGG 10 0.25 No Hit CGCGAATACCATCAATATCTACTGGAGGGGCTGCGATGAAGGCGATAATA 9 0.22499999999999998 No Hit GCCGAAAACACCAGCTACACCTAACATGTGAAATGGATGCATAAGGATGT 9 0.22499999999999998 No Hit CGTCTCTCTAAAATTGCAGTCATGGTAAGATCTTGGTTTATTCAAATTGC 9 0.22499999999999998 No Hit AATAAATACAGAAGTTGCGGTCAATAAGGTAGGGATCATCAAAACACCGA 9 0.22499999999999998 No Hit AATAAGGTAGGGATCATCAAAACACCGAACCATCCGATGTAAAGACGATT 8 0.2 No Hit GCGATAATAAATACAGAAGTTGCGGTCAATAAGGTAGGGATCATCAAAAC 8 0.2 No Hit CTTCCTCTTGACCAAATTTGTAACCCTCATTAGCAGATTCATTTTCAGTA 8 0.2 No Hit GTTAAGTAGTCATGCATTACAATAGGAACACCTAATTCTCTCGCAAAAAC 8 0.2 No Hit CGTGCTCTGCCTGGAATACAATCATAAAGTTGAAAGTACCAGATATTCCT 8 0.2 No Hit GCGCGACCTTGACTATCAACTACAGATTGGTTGAAATTGAATCCATTTAG 8 0.2 No Hit TTTCTTTTCTTCAAAAATTCTTATATGTTAGCGGAAAAACCTTATCCATT 7 0.17500000000000002 No Hit CCACCATTGTATAACCATTCATCAACGGATGCAGCTTCCCAAATTGGGTA 7 0.17500000000000002 No Hit GGATGCATAAGGATGTTGTGCTCTGCCTGGAATACAATCATAAAGTTGAA 7 0.17500000000000002 No Hit CCACAATATTATAAGTCTCTTCCTCTTGACCAAATTTGTAACCCTCATTA 7 0.17500000000000002 No Hit GCTTTCTTTTCTTCAAAAATTCTTATATGTTAGCGGAAAAACCTTATCCA 7 0.17500000000000002 No Hit AGCAGCCACAATATTATAAGTCTCTTCCTCTTGACCAAATTTGTAACCCT 7 0.17500000000000002 No Hit CTGGAGTAGGCTGCGAGGCCCAAGCGGCCAAGGAGTGCAGCGGCCCGTTA 6 0.15 No Hit CCGGGGTGTAGTAAGTCAATCTATAATCTTTAACACCAGCTTTAAATCCA 6 0.15 No Hit CGCGGTCAATAAGGTAGGGATCATCAAAACACCGAACCATCCGATGTAAA 6 0.15 No Hit CCCCAGTTAAGTAGTCATGCATTACAATAGGAACACCTAATTCTCTCGCA 6 0.15 No Hit TGGAGGGGCTGCGATGAAGGCGATAATAAATACAGAAGTTGCGGTCAATA 6 0.15 No Hit GGGAAGTTGTGAGCATTACGTTCGTGCATTACTTCCATACCAAGATTAGC 6 0.15 No Hit CACGGTTGATGATATCAGCCCAAGTATTAATAACGCGACCTTGACTATCA 6 0.15 No Hit CTCTTGACCAAATTTGTAACCCTCATTAGCAGATTCATTTTCAGTAGTTT 6 0.15 No Hit GGGCGCATACCCAAACGGAAACTAAGTTCCCACTCACGACCCATATAACA 5 0.125 No Hit AGAGAAGCTTCCTTGACCAATAGGGTAAATCAAGAAAACAGCAGTCGCAG 5 0.125 No Hit CCGCAGAAGTAGGAATAATAGCACCAGAGATAATATTGTTTCCATAAAGT 5 0.125 No Hit TGCTCTGCCTGGAATACAATCATAAAGTTGAAAGTACCAGATATTCCTAA 5 0.125 No Hit CGCGGGAACTTCAAGAGCAGCTAGATCTAGAGGGAAGTTGTGAGCATTAC 5 0.125 No Hit TAAGGTAGGGATCATCAAAACACCGAACCATCCGATGTAAAGACGATTTT 5 0.125 No Hit GTTGCGGTCAATAAGGTAGGGATCATCAAAACACCGAACCATCCGATGTA 5 0.125 No Hit ATGAAGGCGATAATAAATACAGAAGTTGCGGTCAATAAGGTAGGGATCAT 5 0.125 No Hit CGCGTCTCTCTAAAATTGCAGTCATGGTAAGATCTTGGTTTATTCAAATT 5 0.125 No Hit CGCGGCAATAATGAGCCAAAGTAGTATTTGCGGTGAATCCCCCAGTTAAG 5 0.125 No Hit GGGATCATCAAAACACCGAACCATCCGATGTAAAGACGATTTTCAGTGCT 5 0.125 No Hit GCTAGTTATCCAGTTGCAGAAGCGACCCCACAGGCTTGTACTTTCGCGTC 5 0.125 No Hit TCTTCCTCTTGACCAAATTTGTAACCCTCATTAGCAGATTCATTTTCAGT 5 0.125 No Hit CGCATACCCAAACGGAAACTAAGTTCCCACTCACGACCCATATAACAAGC 5 0.125 No Hit GCGGCTAGTTCAGGACTCCATTTGCAAGCTGCTCGGATAATTTCATTACC 5 0.125 No Hit CAGCAGTCGCAGCTGCAACAGGAGCTGAATATGCAACAGCAATCCAAGGG 5 0.125 No Hit TCGGCCAAAATAACCATGAGCAGCCACAATATTATAAGTCTCTTCCTCTT 5 0.125 No Hit CACCATTGTATAACCATTCATCAACGGATGCAGCTTCCCAAATTGGGTAA 5 0.125 No Hit GGGGGCTGCGATGAAGGCGATAATAAATACAGAAGTTGCGGTCAATAAGG 5 0.125 No Hit CCCCCAGTTAAGTAGTCATGCATTACAATAGGAACACCTAATTCTCTCGC 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 938919 spots for SRR1772231.sra Written 938919 spots for SRR1772231.sra Read 938919 spots for SRR1772231.sra Written 938919 spots for SRR1772231.sra Read 938919 spots for SRR1772231.sra Written 938919 spots for SRR1772231.sra Read 938919 spots for SRR1772231.sra Written 938919 spots for SRR1772231.sra Read 938919 spots for SRR1772231.sra Written 938919 spots for SRR1772231.sra Read 938919 spots for SRR1772231.sra Written 938919 spots for SRR1772231.sra Read 938925 spots for SRR1772231.sra Written 938925 spots for SRR1772231.sra Read 938919 spots for SRR1772231.sra Written 938919 spots for SRR1772231.sra Read 938919 spots for SRR1772231.sra Written 938919 spots for SRR1772231.sra Read 938919 spots for SRR1772231.sra Written 938919 spots for SRR1772231.sra Read 938919 spots for SRR1772231.sra Written 938919 spots for SRR1772231.sra Read 938919 spots for SRR1772231.sra Written 938919 spots for SRR1772231.sra Read 938919 spots for SRR1772231.sra Written 938919 spots for SRR1772231.sra Read 938919 spots for SRR1772231.sra Written 938919 spots for SRR1772231.sra Read 938919 spots for SRR1772231.sra Written 938919 spots for SRR1772231.sra Read 938919 spots for SRR1772231.sra Written 938919 spots for SRR1772231.sra Read 938919 spots for SRR1772231.sra Written 938919 spots for SRR1772231.sra Read 938919 spots for SRR1772231.sra Written 938919 spots for SRR1772231.sra Read 938919 spots for SRR1772231.sra Written 938919 spots for SRR1772231.sra Read 938919 spots for SRR1772231.sra Written 938919 spots for SRR1772231.sra SRR ids: ['SRR1772231.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_bh81qv1f SRR1772231.sra spots: 18778386 blocks: [[1, 938919], [938920, 1877838], [1877839, 2816757], [2816758, 3755676], [3755677, 4694595], [4694596, 5633514], [5633515, 6572433], [6572434, 7511352], [7511353, 8450271], [8450272, 9389190], [9389191, 10328109], [10328110, 11267028], [11267029, 12205947], [12205948, 13144866], [13144867, 14083785], [14083786, 15022704], [15022705, 15961623], [15961624, 16900542], [16900543, 17839461], [17839462, 18778386]] SRR1772231 file size 3243763 SRR1772231 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 SRR1772231 SRR1772231_1.fastq Input file: SRR1772231_1.fastq trimmed: SRR1772231-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 19:45:57 2024 >> done (22.230s) 18778386 reads processed; of these: 2607 ( 0.01%) short reads filtered out after trimming by size control 95959 ( 0.51%) empty reads filtered out after trimming by size control 18679820 (99.48%) reads available; of these: 845505 ( 4.53%) trimmed reads available after processing 17834315 (95.47%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 1423 0.01% 19 1952 0.01% 20 3970 0.02% 21 4054 0.02% 22 5210 0.03% 23 5261 0.03% 24 7463 0.04% 25 8212 0.04% 26 7242 0.04% 27 8918 0.05% 28 10141 0.05% 29 15326 0.08% 30 13538 0.07% 31 14614 0.08% 32 17550 0.09% 33 12664 0.07% 34 13443 0.07% 35 16539 0.09% 36 16616 0.09% 37 21813 0.12% 38 17865 0.10% 39 19901 0.11% 40 29881 0.16% 41 26926 0.14% 42 45425 0.24% 43 43880 0.23% 44 59279 0.32% 45 56378 0.30% 46 69220 0.37% 47 85272 0.46% 48 96198 0.51% 49 89331 0.48% 50 17834315 95.47% 18679820 reads passed initial QC criterion=sequence-density sequence-density=0.25 sequence-density-rank=1 fanout-score=0.00 fanout-score-rank=20 prefix-density=0.00 prefix-fanout=1.0 sequence=TGCGGGAACTTC criterion=fanout-score sequence-density=0.01 sequence-density-rank=26 fanout-score=33.67 fanout-score-rank=1 prefix-density=0.06 prefix-fanout=5.2 sequence=AAAAAGAATAGAGGTATGACAGGCATAAAATCCACGATTGGGTTGAAAATAGCATAAGCTTCGGGTAGTTTAGCAAAGAAAAAACTAGTCGGATAAAGAACACAATTAAAACAGATACAGGTTAAACTAAGTATATTAGGCATAACAAGCATTTCG Started job on | Dec 07 19:48:02 Started mapping on | Dec 07 19:48:04 Finished on | Dec 07 19:48:35 Mapping speed, Million of reads per hour | 2169.27 Number of input reads | 18679820 Average input read length | 49 UNIQUE READS: Uniquely mapped reads number | 4914632 Uniquely mapped reads % | 26.31% Average mapped length | 49.33 Number of splices: Total | 322806 Number of splices: Annotated (sjdb) | 306522 Number of splices: GT/AG | 316590 Number of splices: GC/AG | 3905 Number of splices: AT/AC | 159 Number of splices: Non-canonical | 2152 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 | 1.36 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 13364910 % of reads mapped to multiple loci | 71.55% Number of reads mapped to too many loci | 59558 % of reads mapped to too many loci | 0.32% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 1.80% % of reads unmapped: other | 0.03% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 400278 400278 400278 N_multimapping 13364910 13364910 13364910 N_noFeature 1026722 4768336 1099974 N_ambiguous 106127 902 32945 UnstrandedReadsAssigned:3781783 PositiveStrandReadsAssigned:145394 NegativeStrandReadsAssigned:3781713 Dataset is classified negative stranded MeadianReadLen=50 20thPercentileLength=50 echo kmer=45 SRR1772231 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: SRR1772231-trimmed.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 18,679,820 reads, 15,632,608 reads pseudoaligned [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,241 rounds 52973 SRR1772231.ke.tsv 35125 SRR1772231.se.tsv 88098 total ==> SRR1772231.ke.tsv <== target_id length eff_length est_counts tpm PNS24245 936 837 0 0 PNS24247 1044 945 4.51426 0.346255 PNS24249 1928 1829 33.4572 1.32592 PNS24246 1044 945 4.51426 0.346255 PNS24248 1044 945 4.51426 0.346255 PNS24244 1471 1372 0 0 PNS24243 293 194 0 0 KQK14069 1603 1504 42.3753 2.04224 KQK14071 474 375 20.0236 3.87036 ==> SRR1772231.se.tsv <== BRADI_1g14170v3 142 BRADI_1g53295v3 1 BRADI_1g59795v3 38 BRADI_1g07683v3 0 BRADI_1g00485v3 0 BRADI_1g20270v3 21 BRADI_1g74790v3 17 BRADI_1g09890v3 0 BRADI_1g77505v3 31 BRADI_1g48960v3 0 SRR1772231 completed mapping pipeline successfully