Starting /dee2/code/volunteer_pipeline.sh SRR1772230 current disk space = 1540054417408 free memory = 1451766404 SRR1772230 SRAfilesize 06b251b21b41ac528bd4234347770bed SRR1772230.sra SRR1772230.sra file validated SRR1772230 is single end SRR1772230 is conventional basespace SRR1772230 read1 length is 50 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR1772230_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 45 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 32.777 34.0 31.0 34.0 31.0 34.0 2 33.071 34.0 33.0 34.0 31.0 34.0 3 33.03825 34.0 33.0 34.0 31.0 34.0 4 36.45325 37.0 37.0 37.0 35.0 37.0 5 36.44725 37.0 37.0 37.0 35.0 37.0 6 36.24075 37.0 37.0 37.0 35.0 37.0 7 36.35675 37.0 37.0 37.0 35.0 37.0 8 36.3315 37.0 37.0 37.0 35.0 37.0 9 38.1505 39.0 39.0 39.0 37.0 39.0 10 38.2075 39.0 39.0 39.0 37.0 39.0 11 38.13075 39.0 39.0 39.0 37.0 39.0 12 38.07025 39.0 39.0 39.0 35.0 39.0 13 38.082 39.0 39.0 39.0 35.0 39.0 14 39.6105 41.0 40.0 41.0 37.0 41.0 15 39.5185 41.0 40.0 41.0 37.0 41.0 16 39.5965 41.0 40.0 41.0 37.0 41.0 17 39.55025 41.0 40.0 41.0 37.0 41.0 18 39.51075 41.0 40.0 41.0 36.0 41.0 19 39.38575 41.0 39.0 41.0 36.0 41.0 20 39.35225 41.0 39.0 41.0 36.0 41.0 21 39.41 41.0 39.0 41.0 36.0 41.0 22 39.38275 41.0 39.0 41.0 37.0 41.0 23 39.31525 41.0 39.0 41.0 36.0 41.0 24 39.29375 41.0 39.0 41.0 36.0 41.0 25 39.197 41.0 39.0 41.0 36.0 41.0 26 39.06575 41.0 39.0 41.0 36.0 41.0 27 38.9545 40.0 39.0 41.0 35.0 41.0 28 38.80325 40.0 38.0 41.0 35.0 41.0 29 38.7645 40.0 39.0 41.0 35.0 41.0 30 38.57675 40.0 38.0 41.0 34.0 41.0 31 38.52125 40.0 38.0 41.0 34.0 41.0 32 38.3315 40.0 38.0 41.0 34.0 41.0 33 38.3245 40.0 38.0 41.0 34.0 41.0 34 38.12925 40.0 38.0 41.0 33.0 41.0 35 38.43575 40.0 38.0 41.0 35.0 41.0 36 38.4235 40.0 38.0 41.0 34.0 41.0 37 38.348 40.0 38.0 41.0 34.0 41.0 38 38.4145 40.0 38.0 41.0 35.0 41.0 39 38.0725 40.0 38.0 41.0 33.0 41.0 40 38.105 40.0 38.0 41.0 33.0 41.0 41 38.23825 40.0 38.0 41.0 34.0 41.0 42 38.19 40.0 38.0 41.0 34.0 41.0 43 38.01575 40.0 38.0 41.0 33.0 41.0 44 37.88975 40.0 38.0 41.0 33.0 41.0 45 37.66825 40.0 38.0 41.0 33.0 41.0 46 37.7595 40.0 38.0 41.0 33.0 41.0 47 37.638 40.0 38.0 41.0 33.0 41.0 48 37.45525 40.0 38.0 41.0 33.0 41.0 49 37.47775 40.0 38.0 41.0 33.0 41.0 50 37.05625 40.0 37.0 41.0 33.0 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 4.0 16 5.0 17 1.0 18 4.0 19 6.0 20 5.0 21 5.0 22 8.0 23 8.0 24 10.0 25 6.0 26 11.0 27 9.0 28 21.0 29 18.0 30 46.0 31 50.0 32 60.0 33 77.0 34 106.0 35 141.0 36 191.0 37 296.0 38 547.0 39 2363.0 >>END_MODULE >>Per base sequence content warn #Base G A T C 1 41.775 12.15 11.975 34.1 2 26.900000000000002 13.950000000000001 29.65 29.5 3 37.80945236309077 16.179044761190298 19.904976244061015 26.106526631657918 4 34.125 24.525 15.625 25.724999999999998 5 33.025 28.449999999999996 20.4 18.125 6 25.724999999999998 32.824999999999996 17.525 23.925 7 12.25 36.575 33.7 17.474999999999998 8 20.9 28.625 28.15 22.325 9 24.25 17.65 33.775 24.325 10 17.150000000000002 41.55 24.825 16.475 11 25.825 30.175 18.35 25.650000000000002 12 24.775 28.299999999999997 22.400000000000002 24.525 13 21.349999999999998 37.225 22.725 18.7 14 23.5 31.15 26.900000000000002 18.45 15 20.225 36.65 22.15 20.974999999999998 16 22.55 32.074999999999996 22.6 22.775000000000002 17 22.2 32.975 22.900000000000002 21.925 18 19.025 34.975 24.474999999999998 21.525 19 22.375 31.75 24.2 21.675 20 17.45 31.175000000000004 29.125 22.25 21 20.4 28.65 27.125 23.825 22 16.325 40.825 22.325 20.525 23 20.1 36.725 24.25 18.925 24 19.475 34.75 21.975 23.799999999999997 25 18.75 33.125 28.125 20.0 26 18.875 34.449999999999996 22.25 24.425 27 22.900000000000002 30.875000000000004 25.95 20.275000000000002 28 25.724999999999998 38.75 20.525 15.0 29 27.750000000000004 30.375000000000004 22.625 19.25 30 23.549999999999997 31.15 25.3 20.0 31 28.449999999999996 26.650000000000002 22.175 22.725 32 24.775 31.724999999999998 23.275000000000002 20.225 33 27.0 32.0 19.2 21.8 34 22.125 35.375 18.95 23.549999999999997 35 24.275 33.900000000000006 22.525000000000002 19.3 36 23.200000000000003 25.674999999999997 30.099999999999998 21.025 37 21.68584292146073 30.965482741370685 28.789394697348676 18.55927963981991 38 21.575 25.35 29.099999999999998 23.974999999999998 39 22.875 26.35 30.175 20.599999999999998 40 19.475 34.325 25.650000000000002 20.549999999999997 41 25.825 26.25 25.874999999999996 22.05 42 21.435717858929465 32.84142071035518 24.362181090545274 21.360680340170084 43 22.0 30.599999999999998 25.5 21.9 44 20.525 27.700000000000003 26.275 25.5 45 19.32415519399249 30.312891113892366 31.864831038798496 18.498122653316646 46 18.78439219609805 26.338169084542272 34.99249624812406 19.884942471235618 47 21.91095547773887 31.340670335167587 27.113556778389196 19.634817408704354 48 21.73043260815204 31.83295823955989 25.63140785196299 20.80520130032508 49 22.625 31.924999999999997 23.5 21.95 50 26.63165791447862 25.78144536134033 26.70667666916729 20.880220055013755 >>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 0.5 12 1.0 13 0.5 14 0.0 15 0.0 16 0.0 17 1.0 18 2.0 19 2.0 20 2.0 21 3.0 22 4.0 23 12.5 24 21.0 25 27.5 26 34.0 27 32.0 28 30.0 29 34.0 30 38.0 31 57.5 32 77.0 33 124.0 34 171.0 35 263.0 36 355.0 37 419.5 38 484.0 39 390.0 40 296.0 41 305.0 42 314.0 43 360.5 44 407.0 45 398.0 46 389.0 47 298.5 48 208.0 49 316.5 50 425.0 51 278.0 52 131.0 53 111.0 54 91.0 55 96.5 56 102.0 57 80.5 58 59.0 59 58.0 60 57.0 61 58.5 62 60.0 63 48.5 64 37.0 65 38.0 66 39.0 67 35.0 68 31.0 69 35.0 70 39.0 71 36.5 72 34.0 73 30.5 74 27.0 75 22.0 76 17.0 77 11.5 78 6.0 79 5.0 80 4.0 81 3.5 82 3.0 83 3.5 84 4.0 85 2.0 86 0.0 87 0.5 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 0.0 2 0.0 3 0.025 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 0.05 38 0.0 39 0.0 40 0.0 41 0.0 42 0.05 43 0.0 44 0.0 45 0.125 46 0.05 47 0.05 48 0.025 49 0.0 50 0.025 >>END_MODULE >>Sequence Length Distribution pass #Length Count 50 4000.0 >>END_MODULE >>Sequence Duplication Levels warn #Total Deduplicated Percentage 57.699999999999996 #Duplication Level Percentage of deduplicated Percentage of total 1 89.1681109185442 51.449999999999996 2 4.809358752166378 5.55 3 1.6897746967071057 2.9250000000000003 4 0.8232235701906412 1.9 5 0.5632582322357019 1.625 6 0.389948006932409 1.35 7 0.25996533795493937 1.05 8 0.34662045060658575 1.6 9 0.12998266897746968 0.675 >10 1.516464471403813 17.275 >50 0.21663778162911612 8.0 >100 0.08665511265164644 6.6000000000000005 >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 153 3.8249999999999997 No Hit GATCGGAAGAGCACACGTCTGAACTCCAGTCACCGTACTAGATCTCGTAT 111 2.775 TruSeq Adapter, Index 22 (97% over 38bp) GTGCTCTGCCTGGAATACAATCATAAAGTTGAAAGTACCAGATATTCCTA 75 1.875 No Hit GCGGTCAATAAGGTAGGGATCATCAAAACACCGAACCATCCGATGTAAAG 73 1.825 No Hit CTGCGATGAAGGCGATAATAAATACAGAAGTTGCGGTCAATAAGGTAGGG 65 1.625 No Hit GGGAACTTCAAGAGCAGCTAGATCTAGAGGGAAGTTGTGAGCATTACGTT 55 1.375 No Hit TCTGCCTGGAATACAATCATAAAGTTGAAAGTACCAGATATTCCTAAAGG 52 1.3 No Hit GCCTGGAATACAATCATAAAGTTGAAAGTACCAGATATTCCTAAAGGCAT 46 1.15 No Hit CTCTGCCTGGAATACAATCATAAAGTTGAAAGTACCAGATATTCCTAAAG 39 0.975 No Hit GTTGTGCTCTGCCTGGAATACAATCATAAAGTTGAAAGTACCAGATATTC 37 0.9249999999999999 No Hit CGCGACCTTGACTATCAACTACAGATTGGTTGAAATTGAATCCATTTAGG 37 0.9249999999999999 No Hit CGGGAACTTCAAGAGCAGCTAGATCTAGAGGGAAGTTGTGAGCATTACGT 35 0.8750000000000001 No Hit GCGATGAAGGCGATAATAAATACAGAAGTTGCGGTCAATAAGGTAGGGAT 33 0.8250000000000001 No Hit ACGCGACCTTGACTATCAACTACAGATTGGTTGAAATTGAATCCATTTAG 32 0.8 No Hit CTGGAATACAATCATAAAGTTGAAAGTACCAGATATTCCTAAAGGCATAC 32 0.8 No Hit CGGTCAATAAGGTAGGGATCATCAAAACACCGAACCATCCGATGTAAAGA 27 0.675 No Hit GCGGAAAAACCTTATCCATTAATAGCGGGAACTTCAAGAGCAGCTAGATC 26 0.65 No Hit GCGACCTTGACTATCAACTACAGATTGGTTGAAATTGAATCCATTTAGGT 25 0.625 No Hit GTCAATAAGGTAGGGATCATCAAAACACCGAACCATCCGATGTAAAGACG 20 0.5 No Hit CTGCCTGGAATACAATCATAAAGTTGAAAGTACCAGATATTCCTAAAGGC 19 0.475 No Hit GCTCTGCCTGGAATACAATCATAAAGTTGAAAGTACCAGATATTCCTAAA 19 0.475 No Hit GCTGCGATGAAGGCGATAATAAATACAGAAGTTGCGGTCAATAAGGTAGG 17 0.42500000000000004 No Hit CGCAGAAGTAGGAATAATAGCACCAGAGATAATATTGTTTCCATAAAGTA 16 0.4 No Hit CTCGCGAATACCATCAATATCTACTGGAGGGGCTGCGATGAAGGCGATAA 16 0.4 No Hit ATAAGGATGTTGTGCTCTGCCTGGAATACAATCATAAAGTTGAAAGTACC 15 0.375 No Hit GGTCAATAAGGTAGGGATCATCAAAACACCGAACCATCCGATGTAAAGAC 15 0.375 No Hit CGGAAAAACCTTATCCATTAATAGCGGGAACTTCAAGAGCAGCTAGATCT 14 0.35000000000000003 No Hit TTGTGCTCTGCCTGGAATACAATCATAAAGTTGAAAGTACCAGATATTCC 14 0.35000000000000003 No Hit TGTGCTCTGCCTGGAATACAATCATAAAGTTGAAAGTACCAGATATTCCT 13 0.325 No Hit CAATAAGGTAGGGATCATCAAAACACCGAACCATCCGATGTAAAGACGAT 12 0.3 No Hit GGCCAAAATAACCATGAGCAGCCACAATATTATAAGTCTCTTCCTCTTGA 12 0.3 No Hit GCCAAAATAACCATGAGCAGCCACAATATTATAAGTCTCTTCCTCTTGAC 12 0.3 No Hit CGATGAAGGCGATAATAAATACAGAAGTTGCGGTCAATAAGGTAGGGATC 12 0.3 No Hit GGAGGGGCTGCGATGAAGGCGATAATAAATACAGAAGTTGCGGTCAATAA 11 0.27499999999999997 No Hit CGCGGGAACTTCAAGAGCAGCTAGATCTAGAGGGAAGTTGTGAGCATTAC 11 0.27499999999999997 No Hit TTTCTTTTCTTCAAAAATTCTTATATGTTAGCGGAAAAACCTTATCCATT 11 0.27499999999999997 No Hit CCCAAGTATTAATAACGCGACCTTGACTATCAACTACAGATTGGTTGAAA 11 0.27499999999999997 No Hit CTCATAAGGACCACCATTGTATAACCATTCATCAACGGATGCAGCTTCCC 11 0.27499999999999997 No Hit AGGGGCTGCGATGAAGGCGATAATAAATACAGAAGTTGCGGTCAATAAGG 11 0.27499999999999997 No Hit CGCGGTCAATAAGGTAGGGATCATCAAAACACCGAACCATCCGATGTAAA 10 0.25 No Hit GGCGATAATAAATACAGAAGTTGCGGTCAATAAGGTAGGGATCATCAAAA 10 0.25 No Hit CCACCATTGTATAACCATTCATCAACGGATGCAGCTTCCCAAATTGGGTA 10 0.25 No Hit TGGAGGGGCTGCGATGAAGGCGATAATAAATACAGAAGTTGCGGTCAATA 9 0.22499999999999998 No Hit CGCTGGAGTAGGCTGCGAGGCCCAAGCGGCCAAGGAGTGCAGCGGCCCGT 9 0.22499999999999998 No Hit AGCAGCCACAATATTATAAGTCTCTTCCTCTTGACCAAATTTGTAACCCT 9 0.22499999999999998 No Hit GCACGGTTGATGATATCAGCCCAAGTATTAATAACGCGACCTTGACTATC 8 0.2 No Hit GCGATAATAAATACAGAAGTTGCGGTCAATAAGGTAGGGATCATCAAAAC 8 0.2 No Hit CTTGACTATCAACTACAGATTGGTTGAAATTGAATCCATTTAGGTTGAAC 8 0.2 No Hit CTGTGCCTGCCAACATTATGGGCCGCGAAGCCTAGCTTTCGCTTAAGCTC 8 0.2 No Hit GTGAGCATTACGTTCGTGCATTACTTCCATACCAAGATTAGCACGGTTGA 8 0.2 No Hit CTTTCTTTTCTTCAAAAATTCTTATATGTTAGCGGAAAAACCTTATCCAT 8 0.2 No Hit GGAACTTCAAGAGCAGCTAGATCTAGAGGGAAGTTGTGAGCATTACGTTC 8 0.2 No Hit GGGGCTGCGATGAAGGCGATAATAAATACAGAAGTTGCGGTCAATAAGGT 8 0.2 No Hit TTCAAGAGCAGCTAGATCTAGAGGGAAGTTGTGAGCATTACGTTCGTGCA 7 0.17500000000000002 No Hit CGTGCTCTGCCTGGAATACAATCATAAAGTTGAAAGTACCAGATATTCCT 7 0.17500000000000002 No Hit TGCGGGAACTTCAAGAGCAGCTAGATCTAGAGGGAAGTTGTGAGCATTAC 7 0.17500000000000002 No Hit GCGCGACCTTGACTATCAACTACAGATTGGTTGAAATTGAATCCATTTAG 7 0.17500000000000002 No Hit AGCGGGAACTTCAAGAGCAGCTAGATCTAGAGGGAAGTTGTGAGCATTAC 7 0.17500000000000002 No Hit GTGCCTGCCAACATTATGGGCCGCGAAGCCTAGCTTTCGCTTAAGCTCCA 7 0.17500000000000002 No Hit TGCTCTGCCTGGAATACAATCATAAAGTTGAAAGTACCAGATATTCCTAA 6 0.15 No Hit GCCGAAAACACCAGCTACACCTAACATGTGAAATGGATGCATAAGGATGT 6 0.15 No Hit GCTAGTTATCCAGTTGCAGAAGCGACCCCACAGGCTTGTACTTTCGCGTC 6 0.15 No Hit CCACAATATTATAAGTCTCTTCCTCTTGACCAAATTTGTAACCCTCATTA 6 0.15 No Hit CCAAGTATTAATAACGCGACCTTGACTATCAACTACAGATTGGTTGAAAT 6 0.15 No Hit CATAAGGATGTTGTGCTCTGCCTGGAATACAATCATAAAGTTGAAAGTAC 6 0.15 No Hit CACGGTTGATGATATCAGCCCAAGTATTAATAACGCGACCTTGACTATCA 6 0.15 No Hit CTCATTAGCAGATTCATTTTCAGTAGTTTCCCTGATCAAACTAGAGGTTA 6 0.15 No Hit CACCATTGTATAACCATTCATCAACGGATGCAGCTTCCCAAATTGGGTAA 6 0.15 No Hit CGCGAATACCATCAATATCTACTGGAGGGGCTGCGATGAAGGCGATAATA 5 0.125 No Hit CTTTTCTTCAAAAATTCTTATATGTTAGCGGAAAAACCTTATCCATTAAT 5 0.125 No Hit CCCCAGTTAAGTAGTCATGCATTACAATAGGAACACCTAATTCTCTCGCA 5 0.125 No Hit GATGATATCAGCCCAAGTATTAATAACGCGACCTTGACTATCAACTACAG 5 0.125 No Hit GGGATCATCAAAACACCGAACCATCCGATGTAAAGACGATTTTCAGTGCT 5 0.125 No Hit TGCGGTCAATAAGGTAGGGATCATCAAAACACCGAACCATCCGATGTAAA 5 0.125 No Hit ATAACCATTCATCAACGGATGCAGCTTCCCAAATTGGGTAAAAGTGCAAT 5 0.125 No Hit CCTGGAATACAATCATAAAGTTGAAAGTACCAGATATTCCTAAAGGCATA 5 0.125 No Hit TGCGATGAAGGCGATAATAAATACAGAAGTTGCGGTCAATAAGGTAGGGA 5 0.125 No Hit CTCTTGACCAAATTTGTAACCCTCATTAGCAGATTCATTTTCAGTAGTTT 5 0.125 No Hit CTGCCAACATTATGGGCCGCGAAGCCTAGCTTTCGCTTAAGCTCCAACGG 5 0.125 No Hit TAGTTATCCAGTTGCAGAAGCGACCCCACAGGCTTGTACTTTCGCGTCTC 5 0.125 No Hit ATAACAAGCTACACCAAGTAAGAAGTGTAGAACAATTAGCTCATAAGGAC 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 TGCTCTG 25 0.002084305 35.2 2 GCTCTGC 25 0.002084305 35.2 3 GTGCTCT 25 0.002084305 35.2 1 CTCTGCC 30 0.005095276 29.333332 4 TCTGCCT 30 0.005095276 29.333332 5 >>END_MODULE Read 857134 spots for SRR1772230.sra Written 857134 spots for SRR1772230.sra Read 857134 spots for SRR1772230.sra Written 857134 spots for SRR1772230.sra Read 857134 spots for SRR1772230.sra Written 857134 spots for SRR1772230.sra Read 857134 spots for SRR1772230.sra Written 857134 spots for SRR1772230.sra Read 857134 spots for SRR1772230.sra Written 857134 spots for SRR1772230.sra Read 857134 spots for SRR1772230.sra Written 857134 spots for SRR1772230.sra Read 857134 spots for SRR1772230.sra Written 857134 spots for SRR1772230.sra Read 857134 spots for SRR1772230.sra Written 857134 spots for SRR1772230.sra Read 857134 spots for SRR1772230.sra Written 857134 spots for SRR1772230.sra Read 857134 spots for SRR1772230.sra Written 857134 spots for SRR1772230.sra Read 857134 spots for SRR1772230.sra Written 857134 spots for SRR1772230.sra Read 857134 spots for SRR1772230.sra Written 857134 spots for SRR1772230.sra Read 857134 spots for SRR1772230.sra Written 857134 spots for SRR1772230.sra Read 857134 spots for SRR1772230.sra Written 857134 spots for SRR1772230.sra Read 857134 spots for SRR1772230.sra Written 857134 spots for SRR1772230.sra Read 857134 spots for SRR1772230.sra Written 857134 spots for SRR1772230.sra Read 857134 spots for SRR1772230.sra Written 857134 spots for SRR1772230.sra Read 857134 spots for SRR1772230.sra Written 857134 spots for SRR1772230.sra Read 857134 spots for SRR1772230.sra Written 857134 spots for SRR1772230.sra Read 857138 spots for SRR1772230.sra Written 857138 spots for SRR1772230.sra SRR ids: ['SRR1772230.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd__e87y_lh SRR1772230.sra spots: 17142684 blocks: [[1, 857134], [857135, 1714268], [1714269, 2571402], [2571403, 3428536], [3428537, 4285670], [4285671, 5142804], [5142805, 5999938], [5999939, 6857072], [6857073, 7714206], [7714207, 8571340], [8571341, 9428474], [9428475, 10285608], [10285609, 11142742], [11142743, 11999876], [11999877, 12857010], [12857011, 13714144], [13714145, 14571278], [14571279, 15428412], [15428413, 16285546], [16285547, 17142684]] SRR1772230 file size 2960284 SRR1772230 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 SRR1772230 SRR1772230_1.fastq Input file: SRR1772230_1.fastq trimmed: SRR1772230-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 19:33:19 2024 >> started Sat Dec 7 19:33:31 2024 >> done (11.654s) 17142684 reads processed; of these: 2702 ( 0.02%) short reads filtered out after trimming by size control 517259 ( 3.02%) empty reads filtered out after trimming by size control 16622723 (96.97%) reads available; of these: 695969 ( 4.19%) trimmed reads available after processing 15926754 (95.81%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 1055 0.01% 19 1575 0.01% 20 3159 0.02% 21 3395 0.02% 22 4046 0.02% 23 4656 0.03% 24 5543 0.03% 25 6643 0.04% 26 7249 0.04% 27 8381 0.05% 28 7950 0.05% 29 13093 0.08% 30 11909 0.07% 31 10037 0.06% 32 15406 0.09% 33 10931 0.07% 34 11534 0.07% 35 12363 0.07% 36 12968 0.08% 37 18404 0.11% 38 14535 0.09% 39 16547 0.10% 40 21363 0.13% 41 21552 0.13% 42 32683 0.20% 43 35625 0.21% 44 53925 0.32% 45 48082 0.29% 46 60872 0.37% 47 70337 0.42% 48 79992 0.48% 49 70159 0.42% 50 15926754 95.81% 16622723 reads passed initial QC criterion=sequence-density sequence-density=0.21 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=8.86 fanout-score-rank=1 prefix-density=0.02 prefix-fanout=3.0 sequence=CTTTTTATTTAGACCTTCTTCATATTTAGTTTTATCTATTAATCGATAGTATCTACCGGCGCGAACTCGAATTTGATCGCCTTCCATACTTCACAAGCTGCGGCTAGTTCAGGACTCCATTTGCAAGCTGCTCGGATAATTTCATTACCTTCACGAGCAAGATCGCGCCCTT Started job on | Dec 07 19:33:45 Started mapping on | Dec 07 19:33:45 Finished on | Dec 07 19:34:01 Mapping speed, Million of reads per hour | 3740.11 Number of input reads | 16622723 Average input read length | 49 UNIQUE READS: Uniquely mapped reads number | 5583555 Uniquely mapped reads % | 33.59% Average mapped length | 49.44 Number of splices: Total | 266113 Number of splices: Annotated (sjdb) | 250617 Number of splices: GT/AG | 260420 Number of splices: GC/AG | 3340 Number of splices: AT/AC | 120 Number of splices: Non-canonical | 2233 Mismatch rate per base, % | 0.31% Deletion rate per base | 0.01% Deletion average length | 1.55 Insertion rate per base | 0.01% Insertion average length | 1.35 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 10532184 % of reads mapped to multiple loci | 63.36% Number of reads mapped to too many loci | 168051 % of reads mapped to too many loci | 1.01% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 1.88% % of reads unmapped: other | 0.16% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 506984 506984 506984 N_multimapping 10532184 10532184 10532184 N_noFeature 1932468 5195377 2251408 N_ambiguous 100574 2715 29331 UnstrandedReadsAssigned:3550513 PositiveStrandReadsAssigned:385463 NegativeStrandReadsAssigned:3302816 Dataset is classified negative stranded MeadianReadLen=50 20thPercentileLength=50 echo kmer=45 SRR1772230 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: SRR1772230-trimmed.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 16,622,723 reads, 12,391,310 reads pseudoaligned [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,022 rounds 52973 SRR1772230.ke.tsv 35125 SRR1772230.se.tsv 88098 total ==> SRR1772230.ke.tsv <== target_id length eff_length est_counts tpm PNS24245 936 837 0.843751 0.0928609 PNS24247 1044 945 0 0 PNS24249 1928 1829 57.1562 2.87868 PNS24246 1044 945 0 0 PNS24248 1044 945 0 0 PNS24244 1471 1372 0 0 PNS24243 293 194 0 0 KQK14069 1603 1504 93.2657 5.71239 KQK14071 474 375 47.373 11.6371 ==> SRR1772230.se.tsv <== BRADI_1g14170v3 301 BRADI_1g53295v3 21 BRADI_1g59795v3 72 BRADI_1g07683v3 0 BRADI_1g00485v3 5 BRADI_1g20270v3 18 BRADI_1g74790v3 30 BRADI_1g09890v3 5 BRADI_1g77505v3 36 BRADI_1g48960v3 2 SRR1772230 completed mapping pipeline successfully