Starting /dee2/code/volunteer_pipeline.sh ERR6133311 current disk space = 1548140765184 free memory = 1601820896 ERR6133311 SRAfilesize 7012e02834c497f18389e0afb0c25c42 ERR6133311.sra ERR6133311.sra file validated ERR6133311 is single end ERR6133311 is conventional basespace ERR6133311 read1 length is 70-93 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename ERR6133311_1.fastq File type Conventional base calls Encoding Sanger / Illumina 1.9 Total Sequences 4000 Sequences flagged as poor quality 0 Sequence length 70-93 %GC 44 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 35.077 37.0 33.0 37.0 33.0 37.0 2 36.35875 37.0 37.0 37.0 33.0 37.0 3 35.89375 37.0 37.0 37.0 33.0 37.0 4 35.427 37.0 37.0 37.0 33.0 37.0 5 35.293 37.0 37.0 37.0 33.0 37.0 6 35.66525 37.0 37.0 37.0 33.0 37.0 7 37.462 40.0 37.0 40.0 33.0 40.0 8 37.42175 40.0 37.0 40.0 33.0 40.0 9 37.5315 40.0 37.0 40.0 33.0 40.0 10-11 37.425625 37.0 37.0 40.0 33.0 40.0 12-13 37.463625 38.5 37.0 40.0 33.0 40.0 14-15 37.320875 37.0 37.0 40.0 33.0 40.0 16-17 37.25175 37.0 37.0 40.0 33.0 40.0 18-19 37.141875 37.0 37.0 40.0 33.0 40.0 20-21 36.92 37.0 37.0 40.0 33.0 40.0 22-23 36.884125 37.0 37.0 40.0 33.0 40.0 24-25 37.028875 37.0 37.0 40.0 33.0 40.0 26-27 37.008875 37.0 37.0 40.0 33.0 40.0 28-29 36.85225 37.0 37.0 40.0 33.0 40.0 30-31 36.9195 37.0 37.0 40.0 33.0 40.0 32-33 36.689750000000004 37.0 37.0 40.0 33.0 40.0 34-35 36.589625 37.0 37.0 40.0 33.0 40.0 36-37 36.418375 37.0 37.0 40.0 33.0 40.0 38-39 36.235375 37.0 37.0 40.0 33.0 40.0 40-41 36.059875000000005 37.0 37.0 40.0 33.0 40.0 42-43 35.851375 37.0 35.0 40.0 33.0 40.0 44-45 35.420249999999996 37.0 33.0 40.0 30.0 40.0 46-47 35.071125 37.0 33.0 37.0 27.0 40.0 48-49 35.030375 37.0 33.0 37.0 27.0 40.0 50-51 34.92175 37.0 33.0 37.0 27.0 40.0 52-53 34.641375 37.0 33.0 37.0 27.0 40.0 54-55 34.608625 37.0 33.0 37.0 27.0 40.0 56-57 34.331999999999994 37.0 33.0 37.0 27.0 38.5 58-59 31.997374999999998 33.0 30.0 37.0 24.5 37.0 60-61 33.493875 35.0 33.0 37.0 27.0 37.0 62-63 33.712 37.0 33.0 37.0 27.0 37.0 64-65 33.662625000000006 37.0 33.0 37.0 27.0 37.0 66-67 33.41475 37.0 33.0 37.0 27.0 37.0 68-69 32.8545 35.0 33.0 37.0 27.0 37.0 70-71 32.888628865979385 33.0 33.0 37.0 27.0 37.0 72-73 33.08481617020824 37.0 33.0 37.0 27.0 37.0 74-75 33.236917012511654 37.0 33.0 37.0 27.0 37.0 76-77 33.193338096530404 37.0 33.0 37.0 27.0 37.0 78-79 33.24538391851648 37.0 33.0 37.0 27.0 37.0 80-81 33.20453978845683 37.0 33.0 37.0 27.0 37.0 82-83 33.00793014866581 33.0 33.0 37.0 27.0 37.0 84-85 32.801216861494865 33.0 33.0 37.0 27.0 37.0 86-87 32.6148 33.0 33.0 37.0 27.0 37.0 88-89 32.90346666666667 33.0 33.0 37.0 27.0 37.0 90-91 32.54813333333333 33.0 33.0 37.0 24.5 37.0 92-93 32.55493333333334 33.0 33.0 37.0 27.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 20 17.0 21 23.0 22 19.0 23 33.0 24 37.0 25 34.0 26 52.0 27 59.0 28 72.0 29 87.0 30 106.0 31 132.0 32 136.0 33 209.0 34 273.0 35 483.0 36 793.0 37 884.0 38 540.0 39 11.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 84.075 2.9000000000000004 4.45 8.575000000000001 2 65.5 20.349999999999998 9.4 4.75 3 32.550000000000004 39.525 16.650000000000002 11.275 4 32.775 26.35 20.075000000000003 20.8 5 20.549999999999997 32.375 31.175000000000004 15.9 6 18.7 39.675 24.575 17.05 7 34.875 28.499999999999996 21.025 15.6 8 27.775 28.425 26.325 17.474999999999998 9 24.55 27.05 28.449999999999996 19.950000000000003 10-11 23.1125 28.425 29.4375 19.025 12-13 25.1 26.200000000000003 29.65 19.05 14-15 20.7375 28.499999999999996 31.825 18.9375 16-17 22.8125 31.75 24.9125 20.525 18-19 23.3125 26.7125 28.799999999999997 21.175 20-21 24.33108277069267 26.51912978244561 29.119779944986245 20.030007501875467 22-23 27.0 23.674999999999997 27.5625 21.762500000000003 24-25 24.474999999999998 26.025 29.2 20.3 26-27 23.4625 26.974999999999998 32.4625 17.1 28-29 23.6875 28.237499999999997 28.199999999999996 19.875 30-31 25.6 26.387500000000003 28.225 19.787499999999998 32-33 23.375 26.575 29.8875 20.1625 34-35 25.2281535191899 26.59082385298162 27.628453556694588 20.55256907113389 36-37 25.112499999999997 26.075 28.325 20.4875 38-39 25.18759379689845 24.77488744372186 32.31615807903952 17.72136068034017 40-41 26.05 25.637500000000003 26.424999999999997 21.8875 42-43 23.865483185398176 29.61620202525316 27.54094261782723 18.977372171521438 44-45 22.202775346918365 26.89086135766971 30.066258282285286 20.840105013126642 46-47 23.69046130766346 25.640705088136016 28.92861607700963 21.7402175271909 48-49 23.35 25.5125 31.4625 19.675 50-51 23.540442555319416 28.26603325415677 29.1911488936117 19.002375296912113 52-53 24.0335293381709 29.638433629425748 26.41060928312273 19.91742774928062 54-55 23.3125 29.312500000000004 29.8875 17.4875 56-57 26.8 26.387500000000003 27.0625 19.75 58-59 23.0625 25.5 29.625 21.8125 60-61 24.3875 27.150000000000002 29.6625 18.8 62-63 20.2375 30.362499999999997 32.35 17.05 64-65 22.25 28.6625 30.55 18.5375 66-67 23.45 30.175 27.950000000000003 18.425 68-69 21.9 27.5625 28.825 21.712500000000002 70-71 25.222514729848317 25.69888429234048 28.694998119593834 20.383602858217376 72-73 26.259174892432295 25.664388762338646 27.841052898000505 20.23538344722855 74-75 22.95937858143385 27.86196358079715 29.415509996179807 19.763147841589202 76-77 22.34493386413253 27.23770386541672 28.6246307949146 21.79273147553615 78-79 22.48772926892276 26.052699560836995 31.63265306122449 19.82691810901576 80-81 22.748568453930247 30.101509630400834 29.971369078604894 17.17855283706403 82-83 22.551342812006318 26.224328593996844 30.344918378093734 20.879410215903107 84-85 21.746073995208942 24.141602342294384 34.322597817407505 19.78972584508917 86-87 22.133333333333333 26.68 32.04 19.14666666666667 88-89 20.906666666666666 30.0 30.62666666666667 18.46666666666667 90-91 25.466666666666665 26.479999999999997 29.599999999999998 18.453333333333333 92-93 21.213333333333335 32.10666666666667 27.386666666666663 19.293333333333333 >>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 0.0 16 0.0 17 10.5 18 11.0 19 1.0 20 1.5 21 1.5 22 0.5 23 1.5 24 5.5 25 9.5 26 12.5 27 14.0 28 31.5 29 50.5 30 54.5 31 58.0 32 63.5 33 88.0 34 94.5 35 100.5 36 141.0 37 203.0 38 230.0 39 211.5 40 197.5 41 179.0 42 197.0 43 223.0 44 202.5 45 175.0 46 172.5 47 159.5 48 146.0 49 175.0 50 184.5 51 164.5 52 137.5 53 143.5 54 131.0 55 70.0 56 46.0 57 43.5 58 36.5 59 27.0 60 22.5 61 18.0 62 14.0 63 14.5 64 14.5 65 17.5 66 17.0 67 10.5 68 9.5 69 7.0 70 5.5 71 6.0 72 6.0 73 5.0 74 3.5 75 2.5 76 1.0 77 0.5 78 0.5 79 0.0 80 0.0 81 0.0 82 0.0 83 0.0 84 0.0 85 0.0 86 0.0 87 0.0 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 0.0 2 0.0 3 0.0 4 0.0 5 0.0 6 0.0 7 0.0 8 0.0 9 0.0 10-11 0.0 12-13 0.0 14-15 0.0 16-17 0.0 18-19 0.0 20-21 0.025 22-23 0.0 24-25 0.0 26-27 0.0 28-29 0.0 30-31 0.0 32-33 0.0 34-35 0.0125 36-37 0.0 38-39 0.05 40-41 0.0 42-43 0.0125 44-45 0.0125 46-47 0.0125 48-49 0.0 50-51 0.0125 52-53 0.08750000000000001 54-55 0.0 56-57 0.0 58-59 0.0 60-61 0.0 62-63 0.0 64-65 0.0 66-67 0.0 68-69 0.0 70-71 0.0 72-73 0.0 74-75 0.0 76-77 0.0 78-79 0.0 80-81 0.0 82-83 0.0 84-85 0.0 86-87 0.0 88-89 0.0 90-91 0.0 92-93 0.0 >>END_MODULE >>Sequence Length Distribution warn #Length Count 70 23.0 71 18.0 72 16.0 73 7.0 74 19.0 75 16.0 76 15.0 77 11.0 78 8.0 79 15.0 80 20.0 81 21.0 82 26.0 83 21.0 84 14.0 85 0.0 86 0.0 87 0.0 88 0.0 89 0.0 90 0.0 91 0.0 92 0.0 93 3750.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 71.8 #Duplication Level Percentage of deduplicated Percentage of total 1 90.35515320334262 64.875 2 4.805013927576602 6.9 3 1.6016713091922006 3.45 4 0.8008356545961003 2.3 5 0.5571030640668524 2.0 6 0.31337047353760444 1.35 7 0.1392757660167131 0.7000000000000001 8 0.17409470752089137 1.0 9 0.17409470752089137 1.125 >10 1.0445682451253482 14.95 >50 0.034818941504178275 1.35 >100 0.0 0.0 >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 GGGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGT 54 1.35 No Hit GGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAA 50 1.25 No Hit TACCTAGGCACCCAGAGACGAGGAAGGGCGTAGCAAGCGACGAAATGCTT 42 1.05 No Hit GGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGTG 38 0.95 No Hit GGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCTTGG 31 0.775 No Hit GGGCGCGATCTTGCTCGTGAAGGTAATGAAATTATCCGAGCAGCTTGCAA 30 0.75 No Hit GGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGTGTACAAGCTCGTAA 28 0.7000000000000001 No Hit GGGATGATTCTGTATTACAATTTGGTGGAGGAACTTTAGGACATCCTTGG 26 0.65 No Hit GGGAGAGCAATACAAGCGTTGTGCTGCTAGGCGAAGCGGTTGAGTGCCGC 26 0.65 No Hit GGTAATGAAATTATCCGAGCAGCTTGCAAATGGAGTCCTGAACTAGCCGC 23 0.575 No Hit GGATGATTCTGTATTACAATTTGGTGGAGGAACTTTAGGACATCCTTGGG 21 0.525 No Hit GGAGTATCCTTGATATATAAATATATAGATAAATAGATTTAAATGGAAAA 21 0.525 No Hit GGCGTTCAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTC 19 0.475 No Hit GGACATCCTTGGGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTT 19 0.475 No Hit GGAGGAACTTTAGGACATCCTTGGGGAAATGCACCTGGTGCAGCAGCTAA 19 0.475 No Hit GGAGTCCTGAACTAGCCGCAGCTTGTGAAGTATGGAAGGCGATCAAATTC 17 0.42500000000000004 No Hit CAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAGGTC 17 0.42500000000000004 No Hit GTACAAGCTCGTAACGAAGGGCGCGATCTTGCTCGTGAAGGTAATGAAAT 15 0.375 No Hit GTAGGAATCTGGTTCACTGCTTTAGGTATTAGTACTATGGCGTTCAACCT 15 0.375 No Hit GTAGTAGGAATCTGGTTCACTGCTTTAGGTATTAGTACTATGGCGTTCAA 14 0.35000000000000003 No Hit GGGTTGTTTGGGAATGCAGCCCAAATCGGGCGGTAGACTCCGTCCAAGGC 13 0.325 No Hit GGAATCCCGTGTGAATCAGCAAGGACCACCTTGCAAGGCTAAATACTCCT 13 0.325 No Hit GGAAAAGAGGGGTTACTTTTTTTCATTTTTCCCTTAAAAGATAGGCTTTG 13 0.325 No Hit GGGGATGGAGCGACAGAAGTATGGAAATAGGATAAGGTAGCGGCGAGACG 12 0.3 No Hit GGGCTGATATCATCAACCGTGCTAATCTTGGTATGGAAGTAATGCACGAA 12 0.3 No Hit GGAGTTGAAAATAAGCATAGATCCGGAGATTCCCAAATAGGTCAACCTTT 11 0.27499999999999997 No Hit GAAGTATGGAAGGCGATCAAATTCGAGTTCGCGCCGGTAGATACTATCGA 11 0.27499999999999997 No Hit GGAGTCCCATATATATATGTATAAGATGCCAGCCCGGTTTCGTCAACCAT 11 0.27499999999999997 No Hit GAAGGTAATGAAATTATCCGAGCAGCTTGCAAATGGAGTCCTGAACTAGC 11 0.27499999999999997 No Hit GGGAAAAGAGGGGTTACTTTTTTTCATTTTTCCCTTAAAAGATAGGCTTT 10 0.25 No Hit GGGGATGATTCTGTATTACAATTTGGTGGAGGAACTTTAGGACATCCTTG 10 0.25 No Hit GTAATGAAATTATCCGAGCAGCTTGCAAATGGAGTCCTGAACTAGCCGCA 9 0.22499999999999998 No Hit GCAGCTTGCAAATGGAGTCCTGAACTAGCCGCAGCTTGTGAAGTATGGAA 9 0.22499999999999998 No Hit GGAAGAGCCCGAGCTGCTGCAGCAGGTTTTGAAAAGGGAATCGATCGTGA 9 0.22499999999999998 No Hit GTTCAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAG 9 0.22499999999999998 No Hit GGTTTTGAAAAGGGAATCGATCGTGATTTAGAACCTGTTCTTTACATGAA 9 0.22499999999999998 No Hit GGGCATTCGTATTTCATAGTCAGAGGTGAAATTCTTGGATTTATGAAAGA 8 0.2 No Hit GGCGCGATCTTGCTCGTGAAGGTAATGAAATTATCCGAGCAGCTTGCAAA 8 0.2 No Hit CAAGGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCT 8 0.2 No Hit GAAGGGCGCGATCTTGCTCGTGAAGGTAATGAAATTATCCGAGCAGCTTG 8 0.2 No Hit CAGCTTGTGAAGTATGGAAGGCGATCAAATTCGAGTTCGCGCCGGTAGAT 8 0.2 No Hit GGCCTGTAGTAGGAATCTGGTTCACTGCTTTAGGTATTAGTACTATGGCG 7 0.17500000000000002 No Hit GAGGAACTTTAGGACATCCTTGGGGAAATGCACCTGGTGCAGCAGCTAAT 7 0.17500000000000002 No Hit GGGAATCGATCGTGATTTAGAACCTGTTCTTTACATGAACCCTCTTAACT 7 0.17500000000000002 No Hit GGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTTA 7 0.17500000000000002 No Hit GGAAGAGTCCTCTTAATATTTATCTAATCTTATATAGGTTTCAGTATATT 6 0.15 No Hit GGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGTGT 6 0.15 No Hit GGGCTGCGAGGAATCCGGCAAGGCATAAACAACCAAGGACAGCTCCGTAT 6 0.15 No Hit GGAGGGTGAGAGCCCCGTCCGGCCCGGACCCTGTCGCCCCACGAGGCGCC 6 0.15 No Hit GGACATTTCTTCGAAAAAATTCGAATAGTGAGACGCATTAAAACGCAATT 6 0.15 No Hit GGAGTGACGACGGCAGCTGCCTTTACACCTTTTAAGCATGCCACTTTAAT 6 0.15 No Hit GTATTTAGCCTTGCAAGGTGGTCCTTGCTGATTCACACGGGATTCCACGT 6 0.15 No Hit GGAATAAGAATAAATCGCAACTCCTTTCCACTACACATAAAAATTGATTT 6 0.15 No Hit GGGGCATTCGTATTTCATAGTCAGAGGTGAAATTCTTGGATTTATGAAAG 6 0.15 No Hit GGGGAAGAAGAATGCTGGCAAAATTAATTTGCTTTTTTTGGGGAGAATGG 5 0.125 No Hit GGGCACGTGGAATCCCGTGTGAATCAGCAAGGACCACCTTGCAAGGCTAA 5 0.125 No Hit GGCTTTAGAAGCCTGTGTACAAGCTCGTAACGAAGGGCGCGATCTTGCTC 5 0.125 No Hit GGGGACGGACTGTAAATTCGTTGACAAAATGTCTACGCTGGTTCAAATCC 5 0.125 No Hit GGAACTTTAGGACATCCTTGGGGAAATGCACCTGGTGCAGCAGCTAATCG 5 0.125 No Hit GGGATGGAGCGACAGAAGTATGGAAATAGGATAAGGTAGCGGCGAGACGA 5 0.125 No Hit GGAAGGCGATCAAATTCGAGTTCGCGCCGGTAGATACTATCGATTAATAG 5 0.125 No Hit GGATATCGTGTGTGTACATTTGAATGTACCGACATGGGCTCGAGGAGCAT 5 0.125 No Hit GGGCCGGGTATCTCTCTGCATGTACGTATGCCTGTAATGTACGTAGCTAC 5 0.125 No Hit GGTTCTTATTCGAAGAACCCTTGCCTTTTGTTTAGCTTGAGACTCAATCA 5 0.125 No Hit GGGAGTATTATGAAAGGAGATTAATCATAGATTATCAAAAACCCTAGAAA 5 0.125 No Hit GGAATCTGGTTCACTGCTTTAGGTATTAGTACTATGGCGTTCAACCTAAA 5 0.125 No Hit GGGTGTCAATATATGATGATGTGTTGTTATAATGTACGCGCCTGCAAACT 5 0.125 No Hit GGGTTACTTTTTTTCATTTTTCCCTTAAAAGATAGGCTTTGAAATCGGAG 5 0.125 No Hit GGGGAGTTGAAAATAAGCATAGATCCGGAGATTCCCAAATAGGTCAACCT 5 0.125 No Hit CAACCATGGCATTTTGCTTTGCGTTTTTCCTTTCCGGTTTGTTATTTCTC 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 10-11 0.0 0.0 0.0 0.0 0.0 12-13 0.0 0.0 0.0 0.0 0.0 14-15 0.0 0.0 0.0 0.0 0.0 16-17 0.0 0.0 0.0 0.0 0.0 18-19 0.0125 0.0 0.0 0.0 0.0 20-21 0.025 0.0 0.0 0.0 0.0 22-23 0.025 0.0 0.0 0.0 0.0 24-25 0.025 0.0 0.0 0.0 0.0 26-27 0.025 0.0 0.0 0.0 0.0 28-29 0.025 0.0 0.0 0.0 0.0 30-31 0.025 0.0 0.0 0.0 0.0 32-33 0.025 0.0 0.0 0.0 0.0 34-35 0.025 0.0 0.0 0.0 0.0 36-37 0.025 0.0 0.0 0.0 0.0 38-39 0.025 0.0 0.0 0.0 0.0 40-41 0.05 0.0 0.0 0.0 0.0 42-43 0.075 0.0 0.0 0.0 0.0 44-45 0.075 0.0 0.0 0.0 0.0 46-47 0.075 0.0 0.0 0.0 0.0 48-49 0.075 0.0 0.0 0.0 0.0 50-51 0.075 0.0 0.0 0.0 0.0 52-53 0.075 0.0 0.0 0.0 0.0 54-55 0.075 0.0 0.0 0.0 0.0 56-57 0.075 0.0 0.0 0.0 0.0 58-59 0.0875 0.0 0.0 0.0 0.0 60-61 0.1 0.0 0.0 0.0 0.0 62-63 0.1 0.0 0.0 0.0 0.0 64-65 0.1 0.0 0.0 0.0 0.0 66-67 0.1 0.0 0.0 0.0 0.0 68-69 0.1 0.0 0.0 0.0 0.0 70-71 0.1375 0.0 0.0 0.0 0.0 72-73 0.15 0.0 0.0 0.0 0.0 74-75 0.15 0.0 0.0 0.0 0.0 76-77 0.15 0.0 0.0 0.0 0.0 78-79 0.15 0.0 0.0 0.0 0.0 80-81 0.2 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position CAGCTAA 20 0.0029332691 64.078125 8 GTGCAGC 20 0.0029332691 64.078125 2 AGCTAAT 20 0.0029332691 64.078125 9 TGCAGCA 20 0.0029332691 64.078125 3 GGTGCAG 20 0.0029332691 64.078125 1 CAGCAGC 25 0.007097952 51.262497 5 GCAGCTA 25 0.007097952 51.262497 7 GCAGCAG 25 0.007097952 51.262497 4 >>END_MODULE Rejected 162385 READS because READLEN < 1 Read 162385 spots for ERR6133311.sra Written 162385 spots for ERR6133311.sra Rejected 162385 READS because READLEN < 1 Read 162385 spots for ERR6133311.sra Written 162385 spots for ERR6133311.sra Rejected 162385 READS because READLEN < 1 Read 162385 spots for ERR6133311.sra Written 162385 spots for ERR6133311.sra Rejected 162385 READS because READLEN < 1 Read 162385 spots for ERR6133311.sra Written 162385 spots for ERR6133311.sra Rejected 162385 READS because READLEN < 1 Read 162385 spots for ERR6133311.sra Written 162385 spots for ERR6133311.sra Rejected 162385 READS because READLEN < 1 Read 162385 spots for ERR6133311.sra Written 162385 spots for ERR6133311.sra Rejected 162385 READS because READLEN < 1 Read 162385 spots for ERR6133311.sra Written 162385 spots for ERR6133311.sra Rejected 162385 READS because READLEN < 1 Read 162385 spots for ERR6133311.sra Written 162385 spots for ERR6133311.sra Rejected 162385 READS because READLEN < 1 Read 162385 spots for ERR6133311.sra Written 162385 spots for ERR6133311.sra Rejected 162385 READS because READLEN < 1 Read 162385 spots for ERR6133311.sra Written 162385 spots for ERR6133311.sra Rejected 162385 READS because READLEN < 1 Read 162385 spots for ERR6133311.sra Written 162385 spots for ERR6133311.sra Rejected 162385 READS because READLEN < 1 Read 162385 spots for ERR6133311.sra Written 162385 spots for ERR6133311.sra Rejected 162385 READS because READLEN < 1 Read 162385 spots for ERR6133311.sra Written 162385 spots for ERR6133311.sra Rejected 162385 READS because READLEN < 1 Read 162385 spots for ERR6133311.sra Written 162385 spots for ERR6133311.sra Rejected 162385 READS because READLEN < 1 Read 162385 spots for ERR6133311.sra Written 162385 spots for ERR6133311.sra Rejected 162385 READS because READLEN < 1 Read 162385 spots for ERR6133311.sra Written 162385 spots for ERR6133311.sra Rejected 162385 READS because READLEN < 1 Read 162385 spots for ERR6133311.sra Written 162385 spots for ERR6133311.sra Rejected 162385 READS because READLEN < 1 Read 162385 spots for ERR6133311.sra Written 162385 spots for ERR6133311.sra Rejected 162385 READS because READLEN < 1 Read 162385 spots for ERR6133311.sra Written 162385 spots for ERR6133311.sra Rejected 162390 READS because READLEN < 1 Read 162390 spots for ERR6133311.sra Written 162390 spots for ERR6133311.sra SRR ids: ['ERR6133311.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_0r5dabl3 ERR6133311.sra spots: 3247705 blocks: [[1, 162385], [162386, 324770], [324771, 487155], [487156, 649540], [649541, 811925], [811926, 974310], [974311, 1136695], [1136696, 1299080], [1299081, 1461465], [1461466, 1623850], [1623851, 1786235], [1786236, 1948620], [1948621, 2111005], [2111006, 2273390], [2273391, 2435775], [2435776, 2598160], [2598161, 2760545], [2760546, 2922930], [2922931, 3085315], [3085316, 3247705]] ERR6133311 file size 714594 ERR6133311 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 ERR6133311 ERR6133311_1.fastq Input file: ERR6133311_1.fastq trimmed: ERR6133311-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 00:25:49 2024 >> started Sat Dec 7 00:25:50 2024 >> done (1.945s) 3247705 reads processed; of these: 398 ( 0.01%) short reads filtered out after trimming by size control 48 ( 0.00%) empty reads filtered out after trimming by size control 3247259 (99.99%) reads available; of these: 56238 ( 1.73%) trimmed reads available after processing 3191021 (98.27%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 63 0.00% 19 203 0.01% 20 68 0.00% 21 81 0.00% 22 103 0.00% 23 19 0.00% 24 18 0.00% 25 17 0.00% 26 22 0.00% 27 33 0.00% 28 58 0.00% 29 50 0.00% 30 40 0.00% 31 83 0.00% 32 63 0.00% 33 34 0.00% 34 26 0.00% 35 204 0.01% 36 354 0.01% 37 46 0.00% 38 72 0.00% 39 312 0.01% 40 197 0.01% 41 70 0.00% 42 12 0.00% 43 22 0.00% 44 37 0.00% 45 16 0.00% 46 7 0.00% 47 7 0.00% 48 8 0.00% 49 22 0.00% 50 21 0.00% 51 80 0.00% 52 27 0.00% 53 13 0.00% 54 12 0.00% 55 7 0.00% 56 20 0.00% 57 27 0.00% 58 34 0.00% 59 17 0.00% 60 28 0.00% 61 11 0.00% 62 3 0.00% 63 5 0.00% 64 5 0.00% 65 7 0.00% 66 8 0.00% 67 24 0.00% 68 28 0.00% 69 150 0.00% 70 14564 0.45% 71 12024 0.37% 72 15072 0.46% 73 11440 0.35% 74 12696 0.39% 75 13847 0.43% 76 10358 0.32% 77 10429 0.32% 78 13421 0.41% 79 15492 0.48% 80 12981 0.40% 81 14898 0.46% 82 18284 0.56% 83 17564 0.54% 84 14537 0.45% 85 150 0.00% 86 294 0.01% 87 440 0.01% 88 795 0.02% 89 1598 0.05% 90 3185 0.10% 91 9560 0.29% 92 34988 1.08% 93 2985748 91.95% 3247259 reads passed initial QC criterion=sequence-density sequence-density=0.68 sequence-density-rank=1 fanout-score=2.01 fanout-score-rank=30 prefix-density=0.69 prefix-fanout=2.0 sequence=AGTATTATGAAA criterion=fanout-score sequence-density=0.01 sequence-density-rank=44 fanout-score=42.35 fanout-score-rank=1 prefix-density=0.05 prefix-fanout=4.4 sequence=TTATTTTCTCTCCATTTTGTCGAGTCATTACACGGATTCCATAAATGATTATCAAGTGGTTCTTATTCGAAGAACCCTTGCCTTTTGTTTAGCTTGAGACTCAATCATCGTGGCTCTAGTATGAATCTAAGGTTTAAATTGAACTGATTCATAGGATCGCAACAAGATAATTTCTATCAGAAAACTACTAGAATTTTGGCTTTCTTTATTTACTAGTAAATAAAGAGTAAATCCGCATTACACACAAAAA Started job on | Dec 07 00:26:10 Started mapping on | Dec 07 00:26:10 Finished on | Dec 07 00:26:16 Mapping speed, Million of reads per hour | 1948.36 Number of input reads | 3247259 Average input read length | 91 UNIQUE READS: Uniquely mapped reads number | 1913671 Uniquely mapped reads % | 58.93% Average mapped length | 91.35 Number of splices: Total | 55347 Number of splices: Annotated (sjdb) | 43625 Number of splices: GT/AG | 52168 Number of splices: GC/AG | 1340 Number of splices: AT/AC | 92 Number of splices: Non-canonical | 1747 Mismatch rate per base, % | 0.43% Deletion rate per base | 0.04% Deletion average length | 1.79 Insertion rate per base | 0.02% Insertion average length | 1.93 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 1195282 % of reads mapped to multiple loci | 36.81% Number of reads mapped to too many loci | 88734 % of reads mapped to too many loci | 2.73% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 1.34% % of reads unmapped: other | 0.19% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 138306 138306 138306 N_multimapping 1195282 1195282 1195282 N_noFeature 179149 196152 1834993 N_ambiguous 72544 10601 526 UnstrandedReadsAssigned:1661978 PositiveStrandReadsAssigned:1706918 NegativeStrandReadsAssigned:78152 Dataset is classified positive stranded MeadianReadLen=93 20thPercentileLength=93 echo kmer=89 ERR6133311 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: ERR6133311-trimmed.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 3,247,259 reads, 2,576,924 reads pseudoaligned [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 969 rounds 52973 ERR6133311.ke.tsv 35125 ERR6133311.se.tsv 88098 total ==> ERR6133311.ke.tsv <== target_id length eff_length est_counts tpm PNS24245 936 837 0 0 PNS24247 1044 945 0 0 PNS24249 1928 1829 0 0 PNS24246 1044 945 0 0 PNS24248 1044 945 0 0 PNS24244 1471 1372 30 11.402 PNS24243 293 194 0 0 KQK14069 1603 1504 4 1.38684 KQK14071 474 375 0 0 ==> ERR6133311.se.tsv <== BRADI_1g14170v3 5 BRADI_1g53295v3 8 BRADI_1g59795v3 13 BRADI_1g07683v3 0 BRADI_1g00485v3 0 BRADI_1g20270v3 23 BRADI_1g74790v3 24 BRADI_1g09890v3 0 BRADI_1g77505v3 50 BRADI_1g48960v3 0 ERR6133311 completed mapping pipeline successfully