Starting /dee2/code/volunteer_pipeline.sh ERR6133446 current disk space = 1545682575360 free memory = 1597950720 ERR6133446 SRAfilesize 8ac600213106c5320c05a247a40f59bd ERR6133446.sra ERR6133446.sra file validated ERR6133446 is single end ERR6133446 is conventional basespace ERR6133446 read1 length is 70-93 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename ERR6133446_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 47 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 35.1905 37.0 33.0 37.0 33.0 37.0 2 36.34625 37.0 37.0 37.0 33.0 37.0 3 35.65975 37.0 37.0 37.0 33.0 37.0 4 35.48425 37.0 37.0 37.0 33.0 37.0 5 35.39725 37.0 37.0 37.0 33.0 37.0 6 35.66275 37.0 37.0 37.0 33.0 37.0 7 37.318 37.0 37.0 40.0 33.0 40.0 8 37.33 37.0 37.0 40.0 33.0 40.0 9 37.4355 37.0 37.0 40.0 33.0 40.0 10-11 37.33825 37.0 37.0 40.0 33.0 40.0 12-13 37.2125 37.0 37.0 40.0 33.0 40.0 14-15 37.172375 37.0 37.0 40.0 33.0 40.0 16-17 37.095625 37.0 37.0 40.0 33.0 40.0 18-19 37.10875 37.0 37.0 40.0 33.0 40.0 20-21 37.395250000000004 37.0 37.0 40.0 33.0 40.0 22-23 37.251 37.0 37.0 40.0 33.0 40.0 24-25 37.230875 37.0 37.0 40.0 33.0 40.0 26-27 37.0405 37.0 37.0 40.0 33.0 40.0 28-29 37.047124999999994 37.0 37.0 40.0 33.0 40.0 30-31 37.089625 37.0 37.0 40.0 33.0 40.0 32-33 37.035 37.0 37.0 40.0 33.0 40.0 34-35 36.867000000000004 37.0 37.0 40.0 33.0 40.0 36-37 36.80475 37.0 37.0 40.0 33.0 40.0 38-39 36.58225 37.0 37.0 40.0 33.0 40.0 40-41 36.561625 37.0 37.0 40.0 33.0 40.0 42-43 36.45875 37.0 37.0 40.0 33.0 40.0 44-45 36.175375 37.0 37.0 40.0 33.0 40.0 46-47 36.136875 37.0 37.0 37.0 33.0 40.0 48-49 35.911249999999995 37.0 35.0 37.0 33.0 40.0 50-51 35.63475 37.0 33.0 37.0 33.0 40.0 52-53 35.569874999999996 37.0 33.0 37.0 33.0 40.0 54-55 35.42275 37.0 33.0 37.0 33.0 40.0 56-57 35.330875000000006 37.0 33.0 37.0 33.0 37.0 58-59 34.89875 37.0 33.0 37.0 33.0 37.0 60-61 34.72725 37.0 33.0 37.0 33.0 37.0 62-63 34.815 37.0 33.0 37.0 33.0 37.0 64-65 34.371375 37.0 33.0 37.0 27.0 37.0 66-67 34.294 37.0 33.0 37.0 33.0 37.0 68-69 32.97425 35.0 33.0 35.0 27.0 37.0 70-71 33.31593656156156 33.0 33.0 37.0 27.0 37.0 72-73 34.056709133596655 37.0 33.0 37.0 27.0 37.0 74-75 34.320612966501805 37.0 33.0 37.0 33.0 37.0 76-77 34.108411987622674 37.0 33.0 37.0 30.0 37.0 78-79 34.25429656815582 37.0 33.0 37.0 30.0 37.0 80-81 34.20375476839831 37.0 33.0 37.0 33.0 37.0 82-83 33.77512764946651 37.0 33.0 37.0 27.0 37.0 84-85 33.79688140155514 37.0 33.0 37.0 27.0 37.0 86-87 33.71860643185299 37.0 33.0 37.0 27.0 37.0 88-89 33.811000510464524 37.0 33.0 37.0 27.0 37.0 90-91 33.523864216436955 35.0 33.0 37.0 27.0 37.0 92-93 33.363067891781526 35.0 33.0 37.0 27.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 20 5.0 21 13.0 22 17.0 23 12.0 24 19.0 25 19.0 26 31.0 27 43.0 28 48.0 29 55.0 30 76.0 31 87.0 32 141.0 33 168.0 34 246.0 35 542.0 36 992.0 37 1078.0 38 404.0 39 4.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 88.275 2.725 2.4 6.6000000000000005 2 72.66133066533267 16.133066533266632 7.003501750875437 4.202101050525263 3 37.3 37.85 12.775 12.075 4 35.099999999999994 28.349999999999998 17.875 18.675 5 24.375 31.2 25.974999999999998 18.45 6 19.950000000000003 37.55 24.775 17.724999999999998 7 35.85 29.049999999999997 19.475 15.625 8 32.425 30.575000000000003 20.925 16.075 9 26.474999999999998 27.975 26.825 18.725 10-11 26.8375 26.1 27.487499999999997 19.575 12-13 29.099999999999998 25.4 26.4125 19.0875 14-15 22.5875 29.862499999999997 27.875 19.675 16-17 24.4875 30.725 24.95 19.8375 18-19 24.349999999999998 26.724999999999998 25.85 23.075000000000003 20-21 24.4875 26.075 27.8375 21.6 22-23 27.025 23.225 27.075 22.675 24-25 27.237499999999997 24.0625 25.8125 22.8875 26-27 25.3125 24.712500000000002 30.825000000000003 19.15 28-29 27.437499999999996 25.587500000000002 26.5125 20.4625 30-31 27.625 24.8625 26.4125 21.099999999999998 32-33 24.925 27.437499999999996 26.224999999999998 21.4125 34-35 26.325 25.7 25.95 22.025 36-37 25.0125 24.349999999999998 28.000000000000004 22.6375 38-39 26.6125 25.25 29.6375 18.5 40-41 27.55 25.775 25.3 21.375 42-43 25.324999999999996 28.199999999999996 24.5375 21.9375 44-45 24.3625 25.137500000000003 28.3125 22.1875 46-47 24.4125 23.775 28.599999999999998 23.2125 48-49 25.95 24.275 28.625 21.15 50-51 25.5375 26.5125 27.875 20.075000000000003 52-53 25.937500000000004 27.1125 24.9125 22.037499999999998 54-55 23.3 28.249999999999996 28.425 20.025000000000002 56-57 25.224999999999998 25.324999999999996 27.6875 21.762500000000003 58-59 24.762500000000003 24.887500000000003 27.750000000000004 22.6 60-61 25.662499999999998 24.087500000000002 28.3625 21.8875 62-63 23.3625 27.0875 30.575000000000003 18.975 64-65 23.6875 26.825 28.6375 20.849999999999998 66-67 25.6125 26.487500000000004 27.5125 20.3875 68-69 23.9875 26.2125 27.35 22.45 70-71 25.15007503751876 25.56278139069535 27.926463231615806 21.360680340170084 72-73 26.617352056168503 23.182046138415245 27.64543630892678 22.55516549648947 74-75 23.48503897410108 27.69675634900679 28.09906965049032 20.719135026401812 76-77 23.238815374921234 25.645872715816004 28.99810964083176 22.117202268431 78-79 24.324324324324326 24.753725688305128 29.211922202576407 21.71002778479414 80-81 24.19599898708534 27.703216004051654 29.792352494302353 18.30843251456065 82-83 24.86342269089061 24.101130733070768 29.538813365518994 21.49663321051963 84-85 24.598111763204898 23.054350599642767 31.372799183465172 20.974738453687163 86-87 23.41755997958142 26.02092904543134 30.946911689637567 19.61459928534967 88-89 22.28177641653905 27.679938744257278 31.189382337927512 18.84890250127616 90-91 26.480347115875446 25.94435936702399 28.36906584992343 19.20622766717713 92-93 23.2899438489025 27.998979070954565 29.032669729453804 19.678407350689127 >>END_MODULE >>Per sequence GC content pass #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 5.5 18 7.0 19 2.5 20 1.5 21 2.5 22 2.5 23 3.5 24 6.0 25 6.0 26 7.5 27 10.5 28 14.0 29 16.0 30 18.0 31 24.0 32 34.5 33 51.5 34 61.5 35 67.5 36 82.5 37 115.0 38 163.5 39 174.0 40 170.5 41 180.0 42 175.5 43 174.0 44 174.0 45 176.0 46 214.0 47 220.0 48 182.5 49 164.5 50 146.0 51 151.5 52 154.5 53 159.0 54 152.0 55 109.0 56 86.5 57 83.0 58 76.5 59 70.0 60 66.0 61 52.0 62 43.0 63 43.0 64 41.5 65 35.0 66 29.0 67 24.5 68 22.0 69 15.5 70 6.5 71 6.0 72 4.5 73 3.0 74 3.5 75 2.5 76 0.5 77 0.0 78 0.0 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 0.05 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 0.0 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 0.0 36-37 0.0 38-39 0.0 40-41 0.0 42-43 0.0 44-45 0.0 46-47 0.0 48-49 0.0 50-51 0.0 52-53 0.0 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 0.012756729174639624 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 4.0 71 6.0 72 4.0 73 7.0 74 4.0 75 3.0 76 9.0 77 1.0 78 6.0 79 5.0 80 4.0 81 5.0 82 13.0 83 8.0 84 3.0 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 3918.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 80.875 #Duplication Level Percentage of deduplicated Percentage of total 1 93.19938176197836 75.375 2 4.234930448222566 6.8500000000000005 3 0.9273570324574961 2.25 4 0.3091190108191654 1.0 5 0.2472952086553323 1.0 6 0.18547140649149924 0.8999999999999999 7 0.12364760432766615 0.7000000000000001 8 0.09273570324574962 0.6 9 0.09273570324574962 0.675 >10 0.5564142194744977 9.325 >50 0.030911901081916538 1.325 >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 GGGATGATTCTGTATTACAATTTGGTGGAGGAACTTTAGGACATCCTTGG 53 1.325 No Hit GGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAA 43 1.075 No Hit GGGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGT 39 0.975 No Hit GGGAGAGCAATACAAGCGTTGTGCTGCTAGGCGAAGCGGTTGAGTGCCGC 33 0.8250000000000001 No Hit GGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGTG 32 0.8 No Hit GGGGATGATTCTGTATTACAATTTGGTGGAGGAACTTTAGGACATCCTTG 26 0.65 No Hit GGCGTTCAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTC 25 0.625 No Hit GGCCTGTAGTAGGAATCTGGTTCACTGCTTTAGGTATTAGTACTATGGCG 21 0.525 No Hit GTAGTAGGAATCTGGTTCACTGCTTTAGGTATTAGTACTATGGCGTTCAA 20 0.5 No Hit GGATGATTCTGTATTACAATTTGGTGGAGGAACTTTAGGACATCCTTGGG 20 0.5 No Hit GGACATCCTTGGGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTT 16 0.4 No Hit TACCTAGGCACCCAGAGACGAGGAAGGGCGTAGCAAGCGACGAAATGCTT 15 0.375 No Hit GGAGGAACTTTAGGACATCCTTGGGGAAATGCACCTGGTGCAGCAGCTAA 15 0.375 No Hit GGAGTATCCTTGATATATAAATATATAGATAAATAGATTTAAATGGAAAA 12 0.3 No Hit CAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAGGTC 12 0.3 No Hit GGAAAAGAAAGCAAAAGCGATTCCCGTAGTAGCGGCGAGCGAAATGGGAG 12 0.3 No Hit GGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCTTGG 11 0.27499999999999997 No Hit GGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGTGTACAAGCTCGTAA 11 0.27499999999999997 No Hit GGGCTGATATCATCAACCGTGCTAATCTTGGTATGGAAGTAATGCACGAA 10 0.25 No Hit GGGATGGAGCGACAGAAGTATGGAAATAGGATAAGGTAGCGGCGAGACGA 9 0.22499999999999998 No Hit GGTTCACTGCTTTAGGTATTAGTACTATGGCGTTCAACCTAAATGGATTC 9 0.22499999999999998 No Hit GGATTCTTCTTTTTTGTGGGCCATTTGTGGCATGCAGGAAGAGCCCGAGC 9 0.22499999999999998 No Hit GTAGGAATCTGGTTCACTGCTTTAGGTATTAGTACTATGGCGTTCAACCT 8 0.2 No Hit GGGCGCGATCTTGCTCGTGAAGGTAATGAAATTATCCGAGCAGCTTGCAA 8 0.2 No Hit GGGGAAGTACACCAGCGACGGCGAGGCCGCCGCCGCCAAGGAAGGCATGT 8 0.2 No Hit GGAACTTTAGGACATCCTTGGGGAAATGCACCTGGTGCAGCAGCTAATCG 7 0.17500000000000002 No Hit CAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAATACTTGGGCTGATAT 7 0.17500000000000002 No Hit GGGAGTATTATGAAAGGAGATTAATCATAGATTATCAAAAACCCTAGAAA 7 0.17500000000000002 No Hit GGTATTAGTACTATGGCGTTCAACCTAAATGGATTCAATTTCAACCAATC 7 0.17500000000000002 No Hit GGTGGAGGAACTTTAGGACATCCTTGGGGAAATGCACCTGGTGCAGCAGC 6 0.15 No Hit GGCGCGATCTTGCTCGTGAAGGTAATGAAATTATCCGAGCAGCTTGCAAA 6 0.15 No Hit GGAGTCCCATATATATATGTATAAGATGCCAGCCCGGTTTCGTCAACCAT 6 0.15 No Hit CAAGGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCT 6 0.15 No Hit GGAATAAGAATAAATCGCAACTCCTTTCCACTACACATAAAAATTGATTT 6 0.15 No Hit GGAGACCGGGGAGGTCATCGGCGTCTTCGAGAGCGTGCAGCCGTCCGACA 6 0.15 No Hit GAGGAACTTTAGGACATCCTTGGGGAAATGCACCTGGTGCAGCAGCTAAT 5 0.125 No Hit GGAAGAGCCCGAGCTGCTGCAGCAGGTTTTGAAAAGGGAATCGATCGTGA 5 0.125 No Hit GGAATCTGGTTCACTGCTTTAGGTATTAGTACTATGGCGTTCAACCTAAA 5 0.125 No Hit GGAGTACGGTAGGGGCAGAGGGAATTTCCGGTGGAGCGGTGAAATGCATT 5 0.125 No Hit GGAGCAGCCTAAACCGTGAAAACGGGGTTGTGGGAGAGCAATACAAGCGT 5 0.125 No Hit GGGAATCGATCGTGATTTAGAACCTGTTCTTTACATGAACCCTCTTAACT 5 0.125 No Hit GGTAGTAGGAATCTGGTTCACTGCTTTAGGTATTAGTACTATGGCGTTCA 5 0.125 No Hit GGGCCATTTGTGGCATGCAGGAAGAGCCCGAGCTGCTGCAGCAGGTTTTG 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 0.0125 0.0 0.0 0.0 0.0 14-15 0.025 0.0 0.0 0.0 0.0 16-17 0.025 0.0 0.0 0.0 0.0 18-19 0.025 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 0.025 0.0 0.0 0.0 0.0 42-43 0.025 0.0 0.0 0.0 0.0 44-45 0.025 0.0 0.0 0.0 0.0 46-47 0.025 0.0 0.0 0.0 0.0 48-49 0.025 0.0 0.0 0.0 0.0 50-51 0.025 0.0 0.0 0.0 0.0 52-53 0.025 0.0 0.0 0.0 0.0 54-55 0.025 0.0 0.0 0.0 0.0 56-57 0.025 0.0 0.0 0.0 0.0 58-59 0.025 0.0 0.0 0.0 0.0 60-61 0.025 0.0 0.0 0.0 0.0 62-63 0.025 0.0 0.0 0.0 0.0 64-65 0.025 0.0 0.0 0.0 0.0 66-67 0.025 0.0 0.0 0.0 0.0 68-69 0.025 0.0 0.0 0.0 0.0 70-71 0.025 0.0 0.0 0.0 0.0 72-73 0.025 0.0 0.0 0.0 0.0 74-75 0.025 0.0 0.0 0.0 0.0 76-77 0.025 0.0 0.0 0.0 0.0 78-79 0.025 0.0 0.0 0.0 0.0 80-81 0.025 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position GATTCTG 15 8.8845E-4 86.575 5 ATTCTGT 15 8.8845E-4 86.575 6 CTGTATT 15 8.8845E-4 86.575 9 GGATGAT 20 0.00278342 64.93125 1 ATGATTC 20 0.00278342 64.93125 3 TGATTCT 20 0.00278342 64.93125 4 GATGATT 20 0.00278342 64.93125 2 TCTGTAT 20 0.00278342 64.93125 8 >>END_MODULE Rejected 174817 READS because READLEN < 1 Read 174817 spots for ERR6133446.sra Written 174817 spots for ERR6133446.sra Rejected 174817 READS because READLEN < 1 Read 174817 spots for ERR6133446.sra Written 174817 spots for ERR6133446.sra Rejected 174817 READS because READLEN < 1 Read 174817 spots for ERR6133446.sra Written 174817 spots for ERR6133446.sra Rejected 174817 READS because READLEN < 1 Read 174817 spots for ERR6133446.sra Written 174817 spots for ERR6133446.sra Rejected 174817 READS because READLEN < 1 Read 174817 spots for ERR6133446.sra Written 174817 spots for ERR6133446.sra Rejected 174817 READS because READLEN < 1 Read 174817 spots for ERR6133446.sra Written 174817 spots for ERR6133446.sra Rejected 174817 READS because READLEN < 1 Read 174817 spots for ERR6133446.sra Written 174817 spots for ERR6133446.sra Rejected 174817 READS because READLEN < 1 Read 174817 spots for ERR6133446.sra Written 174817 spots for ERR6133446.sra Rejected 174817 READS because READLEN < 1 Read 174817 spots for ERR6133446.sra Written 174817 spots for ERR6133446.sra Rejected 174817 READS because READLEN < 1 Read 174817 spots for ERR6133446.sra Written 174817 spots for ERR6133446.sra Rejected 174817 READS because READLEN < 1 Read 174817 spots for ERR6133446.sra Written 174817 spots for ERR6133446.sra Rejected 174817 READS because READLEN < 1 Read 174817 spots for ERR6133446.sra Written 174817 spots for ERR6133446.sra Rejected 174817 READS because READLEN < 1 Read 174817 spots for ERR6133446.sra Written 174817 spots for ERR6133446.sra Rejected 174817 READS because READLEN < 1 Read 174817 spots for ERR6133446.sra Written 174817 spots for ERR6133446.sra Rejected 174817 READS because READLEN < 1 Read 174817 spots for ERR6133446.sra Written 174817 spots for ERR6133446.sra Rejected 174817 READS because READLEN < 1 Read 174817 spots for ERR6133446.sra Written 174817 spots for ERR6133446.sra Rejected 174817 READS because READLEN < 1 Read 174817 spots for ERR6133446.sra Written 174817 spots for ERR6133446.sra Rejected 174817 READS because READLEN < 1 Read 174817 spots for ERR6133446.sra Written 174817 spots for ERR6133446.sra Rejected 174817 READS because READLEN < 1 Read 174817 spots for ERR6133446.sra Written 174817 spots for ERR6133446.sra Rejected 174817 READS because READLEN < 1 Read 174817 spots for ERR6133446.sra Written 174817 spots for ERR6133446.sra SRR ids: ['ERR6133446.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_j7j4lngt ERR6133446.sra spots: 3496340 blocks: [[1, 174817], [174818, 349634], [349635, 524451], [524452, 699268], [699269, 874085], [874086, 1048902], [1048903, 1223719], [1223720, 1398536], [1398537, 1573353], [1573354, 1748170], [1748171, 1922987], [1922988, 2097804], [2097805, 2272621], [2272622, 2447438], [2447439, 2622255], [2622256, 2797072], [2797073, 2971889], [2971890, 3146706], [3146707, 3321523], [3321524, 3496340]] ERR6133446 file size 773830 ERR6133446 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 ERR6133446 ERR6133446_1.fastq Input file: ERR6133446_1.fastq trimmed: ERR6133446-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 06:10:24 2024 >> started Sat Dec 7 06:10:26 2024 >> done (1.855s) 3496340 reads processed; of these: 1577 ( 0.05%) short reads filtered out after trimming by size control 15 ( 0.00%) empty reads filtered out after trimming by size control 3494748 (99.95%) reads available; of these: 49706 ( 1.42%) trimmed reads available after processing 3445042 (98.58%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 27 0.00% 19 38 0.00% 20 21 0.00% 21 15 0.00% 22 14 0.00% 23 8 0.00% 24 15 0.00% 25 7 0.00% 26 7 0.00% 27 9 0.00% 28 11 0.00% 29 14 0.00% 30 6 0.00% 31 13 0.00% 32 11 0.00% 33 7 0.00% 34 10 0.00% 35 6 0.00% 36 6 0.00% 37 7 0.00% 38 11 0.00% 39 20 0.00% 40 41 0.00% 41 19 0.00% 42 17 0.00% 43 21 0.00% 44 27 0.00% 45 25 0.00% 46 34 0.00% 47 24 0.00% 48 18 0.00% 49 21 0.00% 50 30 0.00% 51 47 0.00% 52 26 0.00% 53 22 0.00% 54 27 0.00% 55 20 0.00% 56 28 0.00% 57 29 0.00% 58 22 0.00% 59 24 0.00% 60 21 0.00% 61 22 0.00% 62 2 0.00% 63 0 0.00% 64 2 0.00% 65 3 0.00% 66 6 0.00% 67 8 0.00% 68 18 0.00% 69 72 0.00% 70 5423 0.16% 71 4811 0.14% 72 5297 0.15% 73 4697 0.13% 74 5088 0.15% 75 4930 0.14% 76 4536 0.13% 77 4409 0.13% 78 5167 0.15% 79 5938 0.17% 80 5165 0.15% 81 6039 0.17% 82 6551 0.19% 83 6355 0.18% 84 5611 0.16% 85 113 0.00% 86 196 0.01% 87 295 0.01% 88 565 0.02% 89 1245 0.04% 90 2794 0.08% 91 8357 0.24% 92 34094 0.98% 93 3366113 96.32% 3494748 reads passed initial QC criterion=sequence-density sequence-density=0.41 sequence-density-rank=1 fanout-score=5.89 fanout-score-rank=16 prefix-density=0.94 prefix-fanout=2.5 sequence=GCCGCCGCCGCCAAGGAAGGCATGTTCGTCAAGAACTACAGCTACTGATCCTAATCGCATCAAGCTTCAACGCCTGTGAGTGAAAACCAGTGATGAGAGTGCTGCTGCTAGCTAGCGCCGGCATTGATGAGCTTGAGAGGGCACTGTAGCCAGTGTGTCAGTCGTTGTTAAATTACAGGTTGAGATCATCAGCGTACTCCGATGGGAGGTGGACATCAGAAAGTATACTGTGTTTTACCACCCTAATTAAGTAAACAACTTTTGGAATGGTGATCATCTTACTGTTTTAAATAAATCTGTTTC criterion=fanout-score sequence-density=0.01 sequence-density-rank=22 fanout-score=137.81 fanout-score-rank=1 prefix-density=0.22 prefix-fanout=7.8 sequence=AGGAAGAGGAGGATGCAGTCAGGGCTCACAAACAACCTGCCACTGCCGCCATTGGCCTTCTAAAACAGGAGAGGAGGGGTTAGATAGTTTCGATCTGCAAGGGGGTGGGGCAATGGGCATTCCGTTGAGTTTGTATGGTGGGTGCTGTTTTGCAGAAGCTGTATGCTTATGAGCAGCTATGGTACTTATCGAGGACAGTAGCGTACTTGAGGTGTTGTATTTTTATTTATTT Started job on | Dec 07 06:10:39 Started mapping on | Dec 07 06:10:39 Finished on | Dec 07 06:10:44 Mapping speed, Million of reads per hour | 2516.22 Number of input reads | 3494748 Average input read length | 92 UNIQUE READS: Uniquely mapped reads number | 2512525 Uniquely mapped reads % | 71.89% Average mapped length | 92.27 Number of splices: Total | 179593 Number of splices: Annotated (sjdb) | 152305 Number of splices: GT/AG | 174685 Number of splices: GC/AG | 3253 Number of splices: AT/AC | 63 Number of splices: Non-canonical | 1592 Mismatch rate per base, % | 0.40% Deletion rate per base | 0.04% Deletion average length | 1.98 Insertion rate per base | 0.02% Insertion average length | 1.95 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 904686 % of reads mapped to multiple loci | 25.89% Number of reads mapped to too many loci | 21359 % of reads mapped to too many loci | 0.61% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 1.57% % of reads unmapped: other | 0.04% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 77537 77537 77537 N_multimapping 904686 904686 904686 N_noFeature 140015 161770 2406430 N_ambiguous 94993 10641 363 UnstrandedReadsAssigned:2277517 PositiveStrandReadsAssigned:2340114 NegativeStrandReadsAssigned:105732 Dataset is classified positive stranded MeadianReadLen=93 20thPercentileLength=93 echo kmer=89 ERR6133446 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: ERR6133446-trimmed.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 3,494,748 reads, 2,989,199 reads pseudoaligned [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,001 rounds 52973 ERR6133446.ke.tsv 35125 ERR6133446.se.tsv 88098 total ==> ERR6133446.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 69 21.9585 PNS24243 293 194 0 0 KQK14069 1603 1504 27 7.83833 KQK14071 474 375 0 0 ==> ERR6133446.se.tsv <== BRADI_1g14170v3 27 BRADI_1g53295v3 21 BRADI_1g59795v3 18 BRADI_1g07683v3 0 BRADI_1g00485v3 0 BRADI_1g20270v3 45 BRADI_1g74790v3 20 BRADI_1g09890v3 0 BRADI_1g77505v3 60 BRADI_1g48960v3 0 ERR6133446 completed mapping pipeline successfully