Starting /dee2/code/volunteer_pipeline.sh ERR6133305 current disk space = 1548381683712 free memory = 1600620620 ERR6133305 SRAfilesize c650ca24c7be2ff5da715f7d8b5fa071 ERR6133305.sra ERR6133305.sra file validated ERR6133305 is single end ERR6133305 is conventional basespace ERR6133305 read1 length is 70-93 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename ERR6133305_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 35.1185 37.0 33.0 37.0 33.0 37.0 2 36.31375 37.0 37.0 37.0 33.0 37.0 3 35.93375 37.0 37.0 37.0 33.0 37.0 4 35.32825 37.0 37.0 37.0 33.0 37.0 5 35.325 37.0 37.0 37.0 33.0 37.0 6 35.741 37.0 37.0 37.0 33.0 37.0 7 37.39975 37.0 37.0 40.0 33.0 40.0 8 37.334 37.0 37.0 40.0 33.0 40.0 9 37.468 37.0 37.0 40.0 33.0 40.0 10-11 37.337625 37.0 37.0 40.0 33.0 40.0 12-13 37.29475 37.0 37.0 40.0 33.0 40.0 14-15 37.337875 37.0 37.0 40.0 33.0 40.0 16-17 37.250375 37.0 37.0 40.0 33.0 40.0 18-19 37.131875 37.0 37.0 40.0 33.0 40.0 20-21 36.975875 37.0 37.0 40.0 33.0 40.0 22-23 36.92225 37.0 37.0 40.0 33.0 40.0 24-25 37.033874999999995 37.0 37.0 40.0 33.0 40.0 26-27 36.95625 37.0 37.0 40.0 33.0 40.0 28-29 36.873374999999996 37.0 37.0 40.0 33.0 40.0 30-31 36.869625 37.0 37.0 40.0 33.0 40.0 32-33 36.7225 37.0 37.0 40.0 33.0 40.0 34-35 36.542249999999996 37.0 37.0 40.0 33.0 40.0 36-37 36.3755 37.0 37.0 40.0 33.0 40.0 38-39 36.196625 37.0 37.0 40.0 33.0 40.0 40-41 35.953125 37.0 37.0 40.0 33.0 40.0 42-43 35.649874999999994 37.0 33.0 40.0 33.0 40.0 44-45 35.359875 37.0 33.0 40.0 27.0 40.0 46-47 35.030874999999995 37.0 33.0 37.0 27.0 40.0 48-49 35.025375 37.0 33.0 37.0 27.0 40.0 50-51 34.783500000000004 37.0 33.0 37.0 27.0 40.0 52-53 34.517125 37.0 33.0 37.0 27.0 40.0 54-55 34.438125 37.0 33.0 37.0 27.0 40.0 56-57 34.071875000000006 37.0 33.0 37.0 27.0 38.5 58-59 31.803874999999998 33.0 30.0 37.0 22.0 37.0 60-61 33.366875 35.0 33.0 37.0 27.0 37.0 62-63 33.6235 37.0 33.0 37.0 27.0 37.0 64-65 33.66175 37.0 33.0 37.0 27.0 37.0 66-67 33.30525 37.0 33.0 37.0 27.0 37.0 68-69 32.700625 35.0 33.0 37.0 27.0 37.0 70-71 32.831318030834794 33.0 33.0 37.0 27.0 37.0 72-73 33.06288266836837 37.0 33.0 37.0 27.0 37.0 74-75 33.11654588908128 37.0 33.0 37.0 27.0 37.0 76-77 33.125764252070134 37.0 33.0 37.0 27.0 37.0 78-79 33.07117342030119 37.0 33.0 37.0 27.0 37.0 80-81 33.09505094077805 37.0 33.0 37.0 27.0 37.0 82-83 32.930978247055364 33.0 33.0 37.0 27.0 37.0 84-85 32.6847316262469 33.0 33.0 37.0 27.0 37.0 86-87 32.56640833778728 33.0 33.0 37.0 27.0 37.0 88-89 32.749599144842335 33.0 33.0 37.0 27.0 37.0 90-91 32.46753073222875 33.0 33.0 37.0 24.5 37.0 92-93 32.44815606627472 33.0 33.0 37.0 24.5 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 20 17.0 21 22.0 22 26.0 23 37.0 24 41.0 25 41.0 26 54.0 27 57.0 28 68.0 29 71.0 30 112.0 31 116.0 32 177.0 33 217.0 34 286.0 35 440.0 36 796.0 37 821.0 38 587.0 39 14.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 84.925 3.1 4.324999999999999 7.6499999999999995 2 67.15 19.75 8.825 4.275 3 32.925 39.525 15.75 11.799999999999999 4 30.925000000000004 27.775 21.175 20.125 5 22.025 32.75 28.999999999999996 16.225 6 20.275000000000002 38.324999999999996 25.6 15.8 7 34.949999999999996 28.95 21.625 14.475 8 26.525 30.925000000000004 25.85 16.7 9 25.275 26.650000000000002 29.675 18.4 10-11 24.5125 26.6 29.825000000000003 19.0625 12-13 24.95 26.275 29.5 19.275000000000002 14-15 21.0125 28.4125 31.0375 19.537499999999998 16-17 23.175 31.574999999999996 25.912499999999998 19.3375 18-19 23.599999999999998 26.525 29.975 19.900000000000002 20-21 24.79059882485311 25.328166020752597 29.091136392049005 20.790098762345295 22-23 26.575 23.6125 28.975 20.837500000000002 24-25 25.6125 26.5875 28.9 18.9 26-27 24.8125 25.412499999999998 31.387500000000003 18.387500000000003 28-29 25.2875 28.0875 28.325 18.3 30-31 25.2875 26.3625 28.5625 19.787499999999998 32-33 23.7375 26.224999999999998 29.862499999999997 20.175 34-35 23.365420677584698 27.440930116264532 28.391048881110137 20.80260032504063 36-37 25.63140785196299 25.618904726181547 27.906976744186046 20.84271067766942 38-39 25.728580362726706 24.490306441525952 31.682301438399 18.098811757348344 40-41 25.775 25.7625 27.625 20.837500000000002 42-43 24.20605151287822 28.782195548887223 28.33208302075519 18.67966991747937 44-45 22.018004501125283 26.469117279319832 30.820205051262818 20.69267316829207 46-47 23.868467116779193 25.331332833208304 28.844711177794448 21.955488872218055 48-49 24.0 25.912499999999998 31.35 18.7375 50-51 23.452157598499063 26.303939962476548 30.181363352095058 20.06253908692933 52-53 23.935370741482966 28.181362725450903 27.56763527054108 20.31563126252505 54-55 24.025 27.650000000000002 30.075000000000003 18.25 56-57 25.9875 27.5125 27.875 18.625 58-59 23.75 25.95 30.775000000000002 19.525000000000002 60-61 25.275 26.6 29.212500000000002 18.912499999999998 62-63 21.3875 30.662499999999998 30.525000000000002 17.424999999999997 64-65 23.150000000000002 28.475 29.65 18.725 66-67 24.125 28.1875 30.025000000000002 17.6625 68-69 21.775 27.187499999999996 29.825000000000003 21.212500000000002 70-71 23.720115158342722 26.937038427838278 29.903617474026788 19.439228939792212 72-73 25.639410356557896 26.39536348746378 29.494771324177897 18.470454831800428 74-75 24.034552845528456 27.007113821138212 29.14126016260163 19.817073170731707 76-77 22.837768679631527 26.906345957011258 28.36489252814739 21.890992835209826 78-79 22.992653692486144 26.008506250805517 31.138033251707693 19.860806805000646 80-81 22.337797425562343 30.1651280717722 29.35899102847484 18.138083474190612 82-83 22.08935611038108 26.596583442838373 31.077529566360052 20.2365308804205 84-85 22.34510326449034 23.877415056628916 33.48434377081945 20.293137908061293 86-87 21.833244254409408 27.124532335649388 31.493853554249064 19.548369855692144 88-89 20.64404061998931 29.529663281667556 31.133083912346336 18.693212185996792 90-91 24.98663816141101 28.567610903260288 28.474078033137364 17.97167290219134 92-93 21.833244254409408 31.694281133083912 29.14216996258685 17.330304649919828 >>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 0.5 14 1.0 15 1.5 16 1.0 17 13.0 18 15.0 19 2.0 20 0.0 21 0.5 22 2.0 23 3.5 24 5.5 25 9.5 26 17.5 27 21.0 28 26.0 29 34.5 30 38.5 31 45.5 32 60.0 33 97.5 34 110.0 35 120.5 36 152.0 37 183.5 38 228.5 39 219.5 40 187.0 41 190.5 42 215.0 43 228.5 44 192.5 45 174.5 46 188.0 47 166.5 48 146.0 49 148.0 50 150.5 51 142.0 52 128.5 53 124.0 54 117.5 55 79.0 56 51.5 57 56.5 58 50.0 59 32.5 60 19.5 61 15.5 62 18.0 63 21.0 64 18.0 65 13.0 66 8.0 67 5.5 68 7.5 69 11.5 70 9.5 71 6.0 72 9.0 73 12.0 74 7.5 75 3.0 76 3.5 77 2.5 78 1.5 79 1.0 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 0.0125 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 0.025 38-39 0.0625 40-41 0.0 42-43 0.025 44-45 0.025 46-47 0.025 48-49 0.0 50-51 0.0625 52-53 0.2 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 11.0 71 14.0 72 13.0 73 15.0 74 22.0 75 13.0 76 8.0 77 17.0 78 15.0 79 16.0 80 21.0 81 17.0 82 26.0 83 29.0 84 21.0 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 3742.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 77.525 #Duplication Level Percentage of deduplicated Percentage of total 1 92.13157046114156 71.42500000000001 2 4.417929700096742 6.8500000000000005 3 1.2576588197355691 2.9250000000000003 4 0.5482102547565302 1.7000000000000002 5 0.16123831022250887 0.625 6 0.32247662044501774 1.5 7 0.032247662044501774 0.17500000000000002 8 0.19348597226701064 1.2 9 0.09674298613350532 0.675 >10 0.8061915511125444 11.575000000000001 >50 0.032247662044501774 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 GGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAA 54 1.35 No Hit GGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCTTGG 40 1.0 No Hit GGGAGAGCAATACAAGCGTTGTGCTGCTAGGCGAAGCGGTTGAGTGCCGC 39 0.975 No Hit TACCTAGGCACCCAGAGACGAGGAAGGGCGTAGCAAGCGACGAAATGCTT 38 0.95 No Hit GGGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGT 36 0.8999999999999999 No Hit GGAGTATCCTTGATATATAAATATATAGATAAATAGATTTAAATGGAAAA 29 0.7250000000000001 No Hit GGGATGATTCTGTATTACAATTTGGTGGAGGAACTTTAGGACATCCTTGG 23 0.575 No Hit GGGCATTCGTATTTCATAGTCAGAGGTGAAATTCTTGGATTTATGAAAGA 20 0.5 No Hit GGGTTGTTTGGGAATGCAGCCCAAATCGGGCGGTAGACTCCGTCCAAGGC 19 0.475 No Hit GGCGTTCAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTC 18 0.44999999999999996 No Hit GGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGTG 18 0.44999999999999996 No Hit GGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGTGTACAAGCTCGTAA 14 0.35000000000000003 No Hit GGGCGCGATCTTGCTCGTGAAGGTAATGAAATTATCCGAGCAGCTTGCAA 14 0.35000000000000003 No Hit GTATGGAAGGCGATCAAATTCGAGTTCGCGCCGGTAGATACTATCGATTA 14 0.35000000000000003 No Hit GGAAAAGAGGGGTTACTTTTTTTCATTTTTCCCTTAAAAGATAGGCTTTG 14 0.35000000000000003 No Hit CAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAGGTC 13 0.325 No Hit GGTAATGAAATTATCCGAGCAGCTTGCAAATGGAGTCCTGAACTAGCCGC 13 0.325 No Hit GGATGATTCTGTATTACAATTTGGTGGAGGAACTTTAGGACATCCTTGGG 13 0.325 No Hit GGAGTCCTGAACTAGCCGCAGCTTGTGAAGTATGGAAGGCGATCAAATTC 12 0.3 No Hit GGAGGAACTTTAGGACATCCTTGGGGAAATGCACCTGGTGCAGCAGCTAA 12 0.3 No Hit GGGATGGAGCGACAGAAGTATGGAAATAGGATAAGGTAGCGGCGAGACGA 11 0.27499999999999997 No Hit GAAGGTAATGAAATTATCCGAGCAGCTTGCAAATGGAGTCCTGAACTAGC 11 0.27499999999999997 No Hit GGAGTTGAAAATAAGCATAGATCCGGAGATTCCCAAATAGGTCAACCTTT 11 0.27499999999999997 No Hit GGGCTGATATCATCAACCGTGCTAATCTTGGTATGGAAGTAATGCACGAA 11 0.27499999999999997 No Hit GGGAAAAGAGGGGTTACTTTTTTTCATTTTTCCCTTAAAAGATAGGCTTT 10 0.25 No Hit GGAATCCCGTGTGAATCAGCAAGGACCACCTTGCAAGGCTAAATACTCCT 10 0.25 No Hit GGAGGGTGAGAGCCCCGTCCGGCCCGGACCCTGTCGCCCCACGAGGCGCC 9 0.22499999999999998 No Hit GGCGCGATCTTGCTCGTGAAGGTAATGAAATTATCCGAGCAGCTTGCAAA 9 0.22499999999999998 No Hit GGCCTGTAGTAGGAATCTGGTTCACTGCTTTAGGTATTAGTACTATGGCG 9 0.22499999999999998 No Hit GGAACTTTAGGACATCCTTGGGGAAATGCACCTGGTGCAGCAGCTAATCG 8 0.2 No Hit GAAGTATGGAAGGCGATCAAATTCGAGTTCGCGCCGGTAGATACTATCGA 8 0.2 No Hit CAAGGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCT 8 0.2 No Hit GGGCCGGGTATCTCTCTGCATGTACGTATGCCTGTAATGTACGTAGCTAC 8 0.2 No Hit GGGGCATTCGTATTTCATAGTCAGAGGTGAAATTCTTGGATTTATGAAAG 8 0.2 No Hit GGGTGAGAGCCCCGTCCGGCCCGGACCCTGTCGCCCCACGAGGCGCCGTC 8 0.2 No Hit GTAGGAATCTGGTTCACTGCTTTAGGTATTAGTACTATGGCGTTCAACCT 7 0.17500000000000002 No Hit GGGAATGCAGCCCAAATCGGGCGGTAGACTCCGTCCAAGGCTAAATACAG 6 0.15 No Hit GTAGTAGGAATCTGGTTCACTGCTTTAGGTATTAGTACTATGGCGTTCAA 6 0.15 No Hit GGGGATGGAGCGACAGAAGTATGGAAATAGGATAAGGTAGCGGCGAGACG 6 0.15 No Hit GAAGCCTGTGTACAAGCTCGTAACGAAGGGCGCGATCTTGCTCGTGAAGG 6 0.15 No Hit GGGACAGTCGGGGGCATTCGTATTTCATAGTCAGAGGTGAAATTCTTGGA 6 0.15 No Hit GGGTTACTTTTTTTCATTTTTCCCTTAAAAGATAGGCTTTGAAATCGGAG 6 0.15 No Hit GTATTTAGCCTTGCAAGGTGGTCCTTGCTGATTCACACGGGATTCCACGT 6 0.15 No Hit GTACAAGCTCGTAACGAAGGGCGCGATCTTGCTCGTGAAGGTAATGAAAT 6 0.15 No Hit GGGGATGATTCTGTATTACAATTTGGTGGAGGAACTTTAGGACATCCTTG 6 0.15 No Hit GGTTTTGAAAAGGGAATCGATCGTGATTTAGAACCTGTTCTTTACATGAA 6 0.15 No Hit GGAAAGGCTTGCGGTGGATACCTAGGCACCCAGAGACGAGGAAGGGCGTA 5 0.125 No Hit GGACATCCTTGGGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTT 5 0.125 No Hit GGTCAACCTTTTAAACTGCCTGCTGAATCCATGAGCAGGCAAGAGACAAC 5 0.125 No Hit GGGAGGGTGAGAGCCCCGTCCGGCCCGGACCCTGTCGCCCCACGAGGCGC 5 0.125 No Hit GGCATATGCCAGCTCTGACCGAAATCTTTGGGGATGATTCTGTATTACAA 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 0.025 0.0 0.0 0.0 2 0.0 0.025 0.0 0.0 0.0 3 0.0 0.025 0.0 0.0 0.0 4 0.0 0.025 0.0 0.0 0.0 5 0.0 0.025 0.0 0.0 0.0 6 0.0 0.025 0.0 0.0 0.0 7 0.0 0.025 0.0 0.0 0.0 8 0.0 0.025 0.0 0.0 0.0 9 0.0 0.025 0.0 0.0 0.0 10-11 0.0 0.025 0.0 0.0 0.0 12-13 0.0 0.025 0.0 0.0 0.0 14-15 0.0 0.025 0.0 0.0 0.0 16-17 0.0 0.025 0.0 0.0 0.0 18-19 0.0 0.025 0.0 0.0 0.0 20-21 0.025 0.025 0.0 0.0 0.0 22-23 0.025 0.025 0.0 0.0 0.0 24-25 0.025 0.025 0.0 0.0 0.0 26-27 0.025 0.025 0.0 0.0 0.0 28-29 0.025 0.025 0.0 0.0 0.0 30-31 0.025 0.025 0.0 0.0 0.0 32-33 0.05 0.025 0.0 0.0 0.0 34-35 0.05 0.025 0.0 0.0 0.0 36-37 0.05 0.025 0.0 0.0 0.0 38-39 0.05 0.025 0.0 0.0 0.0 40-41 0.075 0.025 0.0 0.0 0.0 42-43 0.075 0.025 0.0 0.0 0.0 44-45 0.075 0.025 0.0 0.0 0.0 46-47 0.075 0.025 0.0 0.0 0.0 48-49 0.075 0.025 0.0 0.0 0.0 50-51 0.075 0.025 0.0 0.0 0.0 52-53 0.075 0.025 0.0 0.0 0.0 54-55 0.075 0.025 0.0 0.0 0.0 56-57 0.0875 0.025 0.0 0.0 0.0 58-59 0.125 0.025 0.0 0.0 0.0 60-61 0.125 0.025 0.0 0.0 0.0 62-63 0.125 0.025 0.0 0.0 0.0 64-65 0.125 0.025 0.0 0.0 0.0 66-67 0.125 0.025 0.0 0.0 0.0 68-69 0.125 0.025 0.0 0.0 0.0 70-71 0.125 0.025 0.0 0.0 0.0 72-73 0.15 0.025 0.0 0.0 0.0 74-75 0.15 0.025 0.0 0.0 0.0 76-77 0.15 0.025 0.0 0.0 0.0 78-79 0.15 0.025 0.0 0.0125 0.0 80-81 0.16249999999999998 0.025 0.0 0.025 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position TTCAATT 15 9.5289975E-4 85.0625 4 AATTTCA 15 9.5289975E-4 85.0625 7 ATTCAAT 15 9.5289975E-4 85.0625 3 CAATTTC 20 0.0029848693 63.796875 6 GGATTCA 20 0.0029848693 63.796875 1 TTTCAAC 20 0.0029848693 63.796875 9 TCAATTT 20 0.0029848693 63.796875 5 ATTTCAA 20 0.0029848693 63.796875 8 GATTCAA 25 0.0072225328 51.0375 2 >>END_MODULE Rejected 203479 READS because READLEN < 1 Read 203479 spots for ERR6133305.sra Written 203479 spots for ERR6133305.sra Rejected 203479 READS because READLEN < 1 Read 203479 spots for ERR6133305.sra Written 203479 spots for ERR6133305.sra Rejected 203479 READS because READLEN < 1 Read 203479 spots for ERR6133305.sra Written 203479 spots for ERR6133305.sra Rejected 203479 READS because READLEN < 1 Read 203479 spots for ERR6133305.sra Written 203479 spots for ERR6133305.sra Rejected 203479 READS because READLEN < 1 Read 203479 spots for ERR6133305.sra Written 203479 spots for ERR6133305.sra Rejected 203479 READS because READLEN < 1 Read 203479 spots for ERR6133305.sra Written 203479 spots for ERR6133305.sra Rejected 203479 READS because READLEN < 1 Read 203479 spots for ERR6133305.sra Written 203479 spots for ERR6133305.sra Rejected 203479 READS because READLEN < 1 Read 203479 spots for ERR6133305.sra Written 203479 spots for ERR6133305.sra Rejected 203479 READS because READLEN < 1 Read 203479 spots for ERR6133305.sra Written 203479 spots for ERR6133305.sra Rejected 203479 READS because READLEN < 1 Read 203479 spots for ERR6133305.sra Written 203479 spots for ERR6133305.sra Rejected 203479 READS because READLEN < 1 Read 203479 spots for ERR6133305.sra Written 203479 spots for ERR6133305.sra Rejected 203479 READS because READLEN < 1 Read 203479 spots for ERR6133305.sra Written 203479 spots for ERR6133305.sra Rejected 203479 READS because READLEN < 1 Read 203479 spots for ERR6133305.sra Written 203479 spots for ERR6133305.sra Rejected 203479 READS because READLEN < 1 Read 203479 spots for ERR6133305.sra Written 203479 spots for ERR6133305.sra Rejected 203479 READS because READLEN < 1 Read 203479 spots for ERR6133305.sra Written 203479 spots for ERR6133305.sra Rejected 203479 READS because READLEN < 1 Read 203479 spots for ERR6133305.sra Written 203479 spots for ERR6133305.sra Rejected 203479 READS because READLEN < 1 Read 203479 spots for ERR6133305.sra Written 203479 spots for ERR6133305.sra Rejected 203479 READS because READLEN < 1 Read 203479 spots for ERR6133305.sra Written 203479 spots for ERR6133305.sra Rejected 203490 READS because READLEN < 1 Read 203490 spots for ERR6133305.sra Written 203490 spots for ERR6133305.sra Rejected 203479 READS because READLEN < 1 Read 203479 spots for ERR6133305.sra Written 203479 spots for ERR6133305.sra SRR ids: ['ERR6133305.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_krheinhz ERR6133305.sra spots: 4069591 blocks: [[1, 203479], [203480, 406958], [406959, 610437], [610438, 813916], [813917, 1017395], [1017396, 1220874], [1220875, 1424353], [1424354, 1627832], [1627833, 1831311], [1831312, 2034790], [2034791, 2238269], [2238270, 2441748], [2441749, 2645227], [2645228, 2848706], [2848707, 3052185], [3052186, 3255664], [3255665, 3459143], [3459144, 3662622], [3662623, 3866101], [3866102, 4069591]] ERR6133305 file size 895012 ERR6133305 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 ERR6133305 ERR6133305_1.fastq Input file: ERR6133305_1.fastq trimmed: ERR6133305-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 00:17:12 2024 >> started Sat Dec 7 00:17:16 2024 >> done (3.203s) 4069591 reads processed; of these: 241 ( 0.01%) short reads filtered out after trimming by size control 32 ( 0.00%) empty reads filtered out after trimming by size control 4069318 (99.99%) reads available; of these: 68599 ( 1.69%) trimmed reads available after processing 4000719 (98.31%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 43 0.00% 19 89 0.00% 20 56 0.00% 21 73 0.00% 22 91 0.00% 23 20 0.00% 24 27 0.00% 25 15 0.00% 26 21 0.00% 27 28 0.00% 28 61 0.00% 29 55 0.00% 30 52 0.00% 31 89 0.00% 32 48 0.00% 33 25 0.00% 34 40 0.00% 35 248 0.01% 36 521 0.01% 37 75 0.00% 38 108 0.00% 39 389 0.01% 40 194 0.00% 41 126 0.00% 42 18 0.00% 43 15 0.00% 44 25 0.00% 45 17 0.00% 46 16 0.00% 47 14 0.00% 48 10 0.00% 49 12 0.00% 50 17 0.00% 51 51 0.00% 52 12 0.00% 53 14 0.00% 54 12 0.00% 55 8 0.00% 56 17 0.00% 57 16 0.00% 58 33 0.00% 59 13 0.00% 60 44 0.00% 61 15 0.00% 62 1 0.00% 63 8 0.00% 64 4 0.00% 65 7 0.00% 66 9 0.00% 67 17 0.00% 68 60 0.00% 69 203 0.00% 70 17602 0.43% 71 17344 0.43% 72 19593 0.48% 73 16813 0.41% 74 17671 0.43% 75 19043 0.47% 76 16087 0.40% 77 16407 0.40% 78 19022 0.47% 79 20722 0.51% 80 19497 0.48% 81 22782 0.56% 82 25172 0.62% 83 24522 0.60% 84 22515 0.55% 85 203 0.00% 86 356 0.01% 87 536 0.01% 88 1155 0.03% 89 1961 0.05% 90 3962 0.10% 91 12009 0.30% 92 42008 1.03% 93 3709154 91.15% 4069318 reads passed initial QC criterion=sequence-density sequence-density=0.49 sequence-density-rank=1 fanout-score=5.44 fanout-score-rank=23 prefix-density=1.49 prefix-fanout=1.8 sequence=AGGCTAAATACTCCTGGGTGACCGATAGCG criterion=fanout-score sequence-density=0.02 sequence-density-rank=23 fanout-score=173.87 fanout-score-rank=1 prefix-density=0.35 prefix-fanout=7.4 sequence=GAAGAAGAAAAGTTTTCTCAACATGGGGAGGAAGTCCCTCCGAAATTTGATTTGTTATTGTATTGTAAGGGGCTTTTTTAGTATTTATCTAAAGGAAGGAACAAACGAGGATAAGATAAAATTTCTTTAAATTTATTTTGCCCAAGTGGGATATATGGCATACTATTCTTTCCATTTTCATCTTTTTTTCTATTCCACTCCATCTAGATATAAGAAAGAACCCAATGCAATGAAATTCCACTAATATACAATACAAAAAAGAAGAATAGATACAGGGTCTCAAACCTTGCTATAGAGTTTTTGCTTTAAAG Started job on | Dec 07 00:17:33 Started mapping on | Dec 07 00:17:33 Finished on | Dec 07 00:17:40 Mapping speed, Million of reads per hour | 2092.79 Number of input reads | 4069318 Average input read length | 91 UNIQUE READS: Uniquely mapped reads number | 2626441 Uniquely mapped reads % | 64.54% Average mapped length | 91.18 Number of splices: Total | 84351 Number of splices: Annotated (sjdb) | 68324 Number of splices: GT/AG | 79221 Number of splices: GC/AG | 2482 Number of splices: AT/AC | 29 Number of splices: Non-canonical | 2619 Mismatch rate per base, % | 0.53% Deletion rate per base | 0.05% Deletion average length | 1.77 Insertion rate per base | 0.03% Insertion average length | 1.71 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 1229469 % of reads mapped to multiple loci | 30.21% Number of reads mapped to too many loci | 131897 % of reads mapped to too many loci | 3.24% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 1.78% % of reads unmapped: other | 0.22% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 213408 213408 213408 N_multimapping 1229469 1229469 1229469 N_noFeature 226705 251764 2504630 N_ambiguous 113957 16944 682 UnstrandedReadsAssigned:2285779 PositiveStrandReadsAssigned:2357733 NegativeStrandReadsAssigned:121129 Dataset is classified positive stranded MeadianReadLen=93 20thPercentileLength=93 echo kmer=89 ERR6133305 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: ERR6133305-trimmed.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 4,069,318 reads, 3,178,312 reads pseudoaligned [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,005 rounds 52973 ERR6133305.ke.tsv 35125 ERR6133305.se.tsv 88098 total ==> ERR6133305.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 57 17.832 PNS24243 293 194 0 0 KQK14069 1603 1504 9 2.56847 KQK14071 474 375 0 0 ==> ERR6133305.se.tsv <== BRADI_1g14170v3 9 BRADI_1g53295v3 82 BRADI_1g59795v3 32 BRADI_1g07683v3 0 BRADI_1g00485v3 1 BRADI_1g20270v3 45 BRADI_1g74790v3 45 BRADI_1g09890v3 0 BRADI_1g77505v3 67 BRADI_1g48960v3 0 ERR6133305 completed mapping pipeline successfully