Starting /dee2/code/volunteer_pipeline.sh ERR6133404 current disk space = 1547657453568 free memory = 1592588692 ERR6133404 SRAfilesize 693b4a920412ab6cfe54cd5372918217 ERR6133404.sra ERR6133404.sra file validated ERR6133404 is single end ERR6133404 is conventional basespace ERR6133404 read1 length is 70-93 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename ERR6133404_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 fail #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 29.22675 33.0 27.0 33.0 15.0 37.0 2 33.38975 33.0 33.0 37.0 27.0 37.0 3 33.558 37.0 33.0 37.0 27.0 37.0 4 33.99175 37.0 33.0 37.0 27.0 37.0 5 33.92025 37.0 33.0 37.0 27.0 37.0 6 34.277 37.0 33.0 37.0 27.0 37.0 7 35.09075 37.0 33.0 37.0 27.0 40.0 8 35.284 37.0 33.0 40.0 27.0 40.0 9 35.343 37.0 33.0 40.0 27.0 40.0 10-11 35.379374999999996 37.0 33.0 40.0 27.0 40.0 12-13 35.1965 37.0 33.0 38.5 30.0 40.0 14-15 34.99275 37.0 33.0 37.0 27.0 40.0 16-17 34.85 37.0 33.0 37.0 27.0 40.0 18-19 34.819125 37.0 33.0 37.0 27.0 40.0 20-21 33.922125 37.0 33.0 37.0 24.5 40.0 22-23 33.86775 37.0 33.0 37.0 24.5 40.0 24-25 33.49125 37.0 33.0 37.0 22.0 40.0 26-27 33.257125 37.0 33.0 37.0 22.0 40.0 28-29 32.798125 37.0 33.0 37.0 22.0 40.0 30-31 32.746624999999995 35.0 33.0 37.0 22.0 40.0 32-33 32.17 33.0 30.0 37.0 22.0 40.0 34-35 31.52675 33.0 27.0 37.0 15.0 40.0 36-37 31.064375 33.0 27.0 37.0 15.0 38.5 38-39 31.483375 33.0 27.0 37.0 22.0 38.5 40-41 31.537374999999997 33.0 27.0 37.0 22.0 40.0 42-43 31.283625 33.0 27.0 37.0 18.5 40.0 44-45 30.908749999999998 33.0 27.0 37.0 15.0 38.5 46-47 30.357374999999998 33.0 27.0 37.0 15.0 37.0 48-49 30.07625 33.0 27.0 37.0 15.0 37.0 50-51 29.678125 33.0 27.0 37.0 15.0 37.0 52-53 29.431375000000003 33.0 27.0 37.0 15.0 37.0 54-55 29.279875 33.0 27.0 37.0 15.0 37.0 56-57 28.740375 33.0 27.0 37.0 15.0 37.0 58-59 28.61875 33.0 27.0 33.0 15.0 37.0 60-61 28.1585 33.0 27.0 33.0 15.0 37.0 62-63 27.680625 33.0 22.0 33.0 15.0 37.0 64-65 27.251625 33.0 22.0 33.0 10.5 37.0 66-67 26.737000000000002 27.0 22.0 33.0 6.0 37.0 68-69 26.425125 27.0 22.0 33.0 10.5 35.0 70-71 28.211159456740443 33.0 27.0 33.0 15.0 37.0 72-73 28.99191930460352 33.0 27.0 33.0 15.0 37.0 74-75 28.887028210598327 33.0 27.0 33.0 15.0 37.0 76-77 28.27832214590233 33.0 27.0 33.0 15.0 37.0 78-79 27.723045387517963 33.0 27.0 33.0 10.5 37.0 80-81 27.095755188350175 33.0 24.5 33.0 6.0 37.0 82-83 26.389441658318542 33.0 22.0 33.0 4.0 37.0 84-85 25.4543632470281 33.0 22.0 33.0 2.0 37.0 86-87 24.41258644536653 30.0 15.0 33.0 2.0 37.0 88-89 23.75103734439834 30.0 15.0 33.0 2.0 37.0 90-91 22.500829875518672 27.0 2.0 33.0 2.0 37.0 92-93 21.356293222683263 27.0 2.0 33.0 2.0 35.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 20 63.0 21 115.0 22 151.0 23 153.0 24 169.0 25 197.0 26 235.0 27 226.0 28 235.0 29 300.0 30 249.0 31 268.0 32 309.0 33 272.0 34 296.0 35 287.0 36 253.0 37 186.0 38 35.0 39 1.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 69.75 8.0 6.75 15.5 2 51.6 24.3 15.049999999999999 9.049999999999999 3 32.45 36.85 16.725 13.975000000000001 4 28.925 27.05 21.9 22.125 5 24.025 26.625 30.325000000000003 19.025 6 18.45 35.55 26.450000000000003 19.55 7 31.6 28.449999999999996 22.375 17.575 8 25.45 28.325 29.075 17.150000000000002 9 23.225 28.275 29.95 18.55 10-11 22.8375 28.199999999999996 29.4125 19.55 12-13 22.275 29.512500000000003 29.4875 18.725 14-15 19.75 30.675 29.75 19.825 16-17 23.5875 28.4375 25.5625 22.412499999999998 18-19 23.674999999999997 25.324999999999996 30.9 20.1 20-21 25.474999999999998 24.1875 29.212500000000002 21.125 22-23 27.950000000000003 23.474999999999998 28.175 20.4 24-25 23.400000000000002 27.1 28.325 21.175 26-27 23.4375 24.6 30.775000000000002 21.1875 28-29 23.2625 27.1375 29.7875 19.8125 30-31 26.400000000000002 27.700000000000003 25.637500000000003 20.2625 32-33 24.5125 24.462500000000002 29.849999999999998 21.175 34-35 21.9625 30.337500000000002 27.6 20.1 36-37 24.275 27.250000000000004 25.874999999999996 22.6 38-39 26.3625 24.837500000000002 29.025000000000002 19.775000000000002 40-41 24.349999999999998 25.4 29.4125 20.837500000000002 42-43 25.25 28.199999999999996 27.975 18.575 44-45 23.0875 26.5625 30.125 20.225 46-47 24.2 28.075 26.8375 20.8875 48-49 24.5375 25.7625 28.3375 21.3625 50-51 21.4 28.725 28.8375 21.0375 52-53 23.175 28.6375 26.5875 21.6 54-55 22.8125 27.525 29.8375 19.825 56-57 24.837500000000002 28.9 26.387500000000003 19.875 58-59 23.7375 28.525 27.3 20.4375 60-61 26.174999999999997 28.15 26.7625 18.912499999999998 62-63 21.4 27.825 30.15 20.625 64-65 22.225 32.3625 27.275 18.1375 66-67 23.8625 28.487499999999997 27.675 19.975 68-69 20.3 28.537499999999998 28.299999999999997 22.8625 70-71 23.834002006018054 27.72066198595787 27.39468405215647 21.050651955867604 72-73 23.743016759776538 26.96800406297613 30.066023362112748 19.222955815134586 74-75 24.993568304605095 29.18703370208387 27.797787496784153 18.021610496526886 76-77 22.554630593132156 26.183662851196672 29.136316337148806 22.125390218522373 78-79 22.714717874523217 27.59437064316717 29.383138234907275 20.30777324740234 80-81 21.51240330754868 33.00880234729261 27.140570818885035 18.338223526273673 82-83 22.63870094722598 27.253044654939107 26.617050067658997 23.491204330175915 84-85 21.645796064400717 26.86115315811201 30.23255813953488 21.26049263795239 86-87 21.369294605809127 29.419087136929463 26.528354080221302 22.68326417704011 88-89 20.138312586445366 29.363762102351316 29.170124481327804 21.327800829875518 90-91 24.854771784232366 31.18948824343015 25.36652835408022 18.589211618257263 92-93 19.889349930843707 33.33333333333333 26.486860304287692 20.29045643153527 >>END_MODULE >>Per sequence GC content warn #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 0.5 17 1.0 18 2.5 19 2.0 20 3.5 21 5.5 22 4.0 23 6.5 24 9.0 25 8.0 26 11.0 27 17.5 28 25.5 29 29.0 30 33.5 31 42.0 32 59.0 33 79.0 34 92.5 35 109.0 36 135.0 37 185.5 38 222.0 39 216.0 40 218.0 41 220.5 42 236.0 43 264.0 44 237.5 45 209.5 46 185.5 47 152.0 48 126.5 49 111.5 50 116.0 51 106.0 52 103.0 53 122.0 54 146.5 55 135.5 56 100.5 57 92.0 58 70.0 59 33.5 60 22.0 61 19.5 62 15.0 63 14.0 64 9.5 65 10.0 66 9.0 67 7.0 68 11.0 69 20.0 70 20.0 71 12.0 72 7.0 73 4.0 74 3.5 75 0.5 76 0.0 77 0.0 78 0.0 79 0.0 80 0.5 81 0.5 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 0.0 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 0.0 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 24.0 71 26.0 72 24.0 73 28.0 74 22.0 75 23.0 76 18.0 77 25.0 78 17.0 79 30.0 80 28.0 81 24.0 82 32.0 83 27.0 84 37.0 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 3615.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 75.75 #Duplication Level Percentage of deduplicated Percentage of total 1 92.24422442244224 69.875 2 3.72937293729373 5.65 3 1.155115511551155 2.625 4 0.9240924092409241 2.8000000000000003 5 0.39603960396039606 1.5 6 0.23102310231023102 1.05 7 0.297029702970297 1.575 8 0.09900990099009901 0.6 9 0.297029702970297 2.025 >10 0.5610561056105611 8.674999999999999 >50 0.066006600660066 3.6249999999999996 >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 GGGAGAGCAATACAAGCGTTGTGCTGCTAGGCGAAGCGGTTGAGTGCCGC 92 2.3 No Hit GGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCTTGG 53 1.325 No Hit GGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAA 49 1.225 No Hit GGGCTGATATCATCAACCGTGCTAATCTTGGTATGGAAGTAATGCACGAA 36 0.8999999999999999 No Hit GGCGTTCAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTC 32 0.8 No Hit CAAGGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCT 29 0.7250000000000001 No Hit GGGTTGTTTGGGAATGCAGCCCAAATCGGGCGGTAGACTCCGTCCAAGGC 26 0.65 No Hit CAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAATACTTGGGCTGATAT 22 0.5499999999999999 No Hit CAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAGGTC 20 0.5 No Hit GGGCACGTGGAATCCCGTGTGAATCAGCAAGGACCACCTTGCAAGGCTAA 18 0.44999999999999996 No Hit CAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAATACTTGGGCTG 17 0.42500000000000004 No Hit GTTCAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAG 14 0.35000000000000003 No Hit GGAGGGTGAGAGCCCCGTCCGGCCCGGACCCTGTCGCCCCACGAGGCGCC 13 0.325 No Hit GCAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAATACTTGGGCT 13 0.325 No Hit GGAATCCCGTGTGAATCAGCAAGGACCACCTTGCAAGGCTAAATACTCCT 13 0.325 No Hit GTATTAGTACTATGGCGTTCAACCTAAATGGATTCAATTTCAACCAATCT 12 0.3 No Hit CACGAACGTAATGCTCACAACTTCCCTCTAGATCTAGCTGCTCTTGAAGT 12 0.3 No Hit CAATTTCAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAATACTT 11 0.27499999999999997 No Hit GGAATCTGGTTCACTGCTTTAGGTATTAGTACTATGGCGTTCAACCTAAA 10 0.25 No Hit GGTTCACTGCTTTAGGTATTAGTACTATGGCGTTCAACCTAAATGGATTC 9 0.22499999999999998 No Hit GTACTATGGCGTTCAACCTAAATGGATTCAATTTCAACCAATCTGTAGTT 9 0.22499999999999998 No Hit GTAGTAGGAATCTGGTTCACTGCTTTAGGTATTAGTACTATGGCGTTCAA 9 0.22499999999999998 No Hit GGGCGCGATCTTGCTCGTGAAGGTAATGAAATTATCCGAGCAGCTTGCAA 9 0.22499999999999998 No Hit GGAGTTGAAAATAAGCATAGATCCGGAGATTCCCAAATAGGTCAACCTTT 9 0.22499999999999998 No Hit TACCTAGGCACCCAGAGACGAGGAAGGGCGTAGCAAGCGACGAAATGCTT 9 0.22499999999999998 No Hit GTGGAATCCCGTGTGAATCAGCAAGGACCACCTTGCAAGGCTAAATACTC 9 0.22499999999999998 No Hit GGGGAGTTGAAAATAAGCATAGATCCGGAGATTCCCAAATAGGTCAACCT 9 0.22499999999999998 No Hit GGGTGAGAGCCCCGTCCGGCCCGGACCCTGTCGCCCCACGAGGCGCCGTC 9 0.22499999999999998 No Hit GCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCTTGGTATG 8 0.2 No Hit GATTCAATTTCAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAAT 8 0.2 No Hit AACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAGGTCG 8 0.2 No Hit GGGGCAGAGGGAATTTCCGGTGGAGCGGTGAAATGCATTGAGATCGGAAA 7 0.17500000000000002 No Hit GGGAGGGTGAGAGCCCCGTCCGGCCCGGACCCTGTCGCCCCACGAGGCGC 7 0.17500000000000002 No Hit TGGGCTGATATCATCAACCGTGCTAATCTTGGTATGGAAGTAATGCACGA 7 0.17500000000000002 No Hit GTAGTTGATAGTCAAGGTCGCGTTATTAATACTTGGGCTGATATCATCAA 7 0.17500000000000002 No Hit GTAGGAATCTGGTTCACTGCTTTAGGTATTAGTACTATGGCGTTCAACCT 7 0.17500000000000002 No Hit GGCCCGGACCCTGTCGCCCCACGAGGCGCCGTCAACGAGTCGGGTTGTTT 7 0.17500000000000002 No Hit GGAGAGCAATACAAGCGTTGTGCTGCTAGGCGAAGCGGTTGAGTGCCGCA 7 0.17500000000000002 No Hit GGGGCACGTGGAATCCCGTGTGAATCAGCAAGGACCACCTTGCAAGGCTA 7 0.17500000000000002 No Hit TCAAAAGAGGAAAGGCTTGCGGTGGATACCTAGGCACCCAGAGACGAGGA 7 0.17500000000000002 No Hit GGAGTTTGGCTGGGGCGGCACATCTGTTAAAAGATAACGCAGGTGTCCTA 6 0.15 No Hit GGGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCTTG 6 0.15 No Hit GGCCTGTAGTAGGAATCTGGTTCACTGCTTTAGGTATTAGTACTATGGCG 6 0.15 No Hit GGGCAGAGGGAATTTCCGGTGGAGCGGTGAAATGCATTGAGATCGGAAAG 6 0.15 No Hit GGAAAAGAGGGGTTACTTTTTTTCATTTTTCCCTTAAAAGATAGGCTTTG 6 0.15 No Hit GGCACGTGGAATCCCGTGTGAATCAGCAAGGACCACCTTGCAAGGCTAAA 6 0.15 No Hit TCAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAATACTTGGGCT 6 0.15 No Hit CGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCTTGGTAT 5 0.125 No Hit GGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGTG 5 0.125 No Hit GGGAATGCAGCCCAAATCGGGCGGTAGACTCCGTCCAAGGCTAAATACAG 5 0.125 No Hit GTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCTTGGT 5 0.125 No Hit GGGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTA 5 0.125 No Hit AGTCAAGGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAA 5 0.125 No Hit GTTGTTTGGGAATGCAGCCCAAATCGGGCGGTAGACTCCGTCCAAGGCTA 5 0.125 No Hit GGGTTGTGGGAGAGCAATACAAGCGTTGTGCTGCTAGGCGAAGCGGTTGA 5 0.125 No Hit GTCAAGGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAAT 5 0.125 No Hit GAATCCCGTGTGAATCAGCAAGGACCACCTTGCAAGGCTAAATACTCCTG 5 0.125 No Hit AACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAATACTTGGGCTGA 5 0.125 No Hit GGGTTACTTTTTTTCATTTTTCCCTTAAAAGATAGGCTTTGAAATCGGAG 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 0.0 0.0 0.0 0.0 0.0 20-21 0.0 0.0 0.0 0.0 0.0 22-23 0.0 0.0 0.0 0.0 0.0 24-25 0.0 0.0 0.0 0.0 0.0 26-27 0.0 0.0 0.0 0.0 0.0 28-29 0.0 0.0 0.0 0.0 0.0 30-31 0.0 0.0 0.0 0.0 0.0 32-33 0.0 0.0 0.0 0.0 0.0 34-35 0.0 0.0 0.0 0.0 0.0 36-37 0.0 0.0 0.0 0.0 0.0 38-39 0.0 0.0 0.0 0.0 0.0 40-41 0.0 0.0 0.0 0.0 0.0 42-43 0.0 0.0 0.0 0.0 0.0 44-45 0.0 0.0 0.0 0.0 0.0 46-47 0.0 0.0 0.0 0.0 0.0 48-49 0.0 0.0 0.0 0.0 0.0 50-51 0.0125 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 0.05 0.0 0.0 0.0 0.0 78-79 0.05 0.0 0.0 0.0 0.0 80-81 0.05 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content pass >>END_MODULE Rejected 49473 READS because READLEN < 1 Read 49473 spots for ERR6133404.sra Written 49473 spots for ERR6133404.sra Rejected 49473 READS because READLEN < 1 Read 49473 spots for ERR6133404.sra Written 49473 spots for ERR6133404.sra Rejected 49473 READS because READLEN < 1 Read 49473 spots for ERR6133404.sra Written 49473 spots for ERR6133404.sra Rejected 49473 READS because READLEN < 1 Read 49473 spots for ERR6133404.sra Written 49473 spots for ERR6133404.sra Rejected 49473 READS because READLEN < 1 Read 49473 spots for ERR6133404.sra Written 49473 spots for ERR6133404.sra Rejected 49473 READS because READLEN < 1 Read 49473 spots for ERR6133404.sra Written 49473 spots for ERR6133404.sra Rejected 49473 READS because READLEN < 1 Read 49473 spots for ERR6133404.sra Written 49473 spots for ERR6133404.sra Rejected 49473 READS because READLEN < 1 Read 49473 spots for ERR6133404.sra Written 49473 spots for ERR6133404.sra Rejected 49473 READS because READLEN < 1 Read 49473 spots for ERR6133404.sra Written 49473 spots for ERR6133404.sra Rejected 49473 READS because READLEN < 1 Read 49473 spots for ERR6133404.sra Written 49473 spots for ERR6133404.sra Rejected 49473 READS because READLEN < 1 Read 49473 spots for ERR6133404.sra Written 49473 spots for ERR6133404.sra Rejected 49491 READS because READLEN < 1 Read 49491 spots for ERR6133404.sra Written 49491 spots for ERR6133404.sra Rejected 49473 READS because READLEN < 1 Read 49473 spots for ERR6133404.sra Written 49473 spots for ERR6133404.sra Rejected 49473 READS because READLEN < 1 Read 49473 spots for ERR6133404.sra Written 49473 spots for ERR6133404.sra Rejected 49473 READS because READLEN < 1 Read 49473 spots for ERR6133404.sra Written 49473 spots for ERR6133404.sra Rejected 49473 READS because READLEN < 1 Read 49473 spots for ERR6133404.sra Written 49473 spots for ERR6133404.sra Rejected 49473 READS because READLEN < 1 Read 49473 spots for ERR6133404.sra Written 49473 spots for ERR6133404.sra Rejected 49473 READS because READLEN < 1 Read 49473 spots for ERR6133404.sra Written 49473 spots for ERR6133404.sra Rejected 49473 READS because READLEN < 1 Read 49473 spots for ERR6133404.sra Written 49473 spots for ERR6133404.sra Rejected 49473 READS because READLEN < 1 Read 49473 spots for ERR6133404.sra Written 49473 spots for ERR6133404.sra SRR ids: ['ERR6133404.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_xwjw37sd ERR6133404.sra spots: 989478 blocks: [[1, 49473], [49474, 98946], [98947, 148419], [148420, 197892], [197893, 247365], [247366, 296838], [296839, 346311], [346312, 395784], [395785, 445257], [445258, 494730], [494731, 544203], [544204, 593676], [593677, 643149], [643150, 692622], [692623, 742095], [742096, 791568], [791569, 841041], [841042, 890514], [890515, 939987], [939988, 989478]] ERR6133404 file size 215010 ERR6133404 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 ERR6133404 ERR6133404_1.fastq Input file: ERR6133404_1.fastq trimmed: ERR6133404-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 03:17:11 2024 >> started Sat Dec 7 03:17:12 2024 >> done (1.079s) 989478 reads processed; of these: 23 ( 0.00%) short reads filtered out after trimming by size control 3 ( 0.00%) empty reads filtered out after trimming by size control 989452 (100.00%) reads available; of these: 254690 (25.74%) trimmed reads available after processing 734762 (74.26%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 4 0.00% 19 10 0.00% 20 3 0.00% 21 4 0.00% 22 5 0.00% 23 2 0.00% 24 1 0.00% 25 1 0.00% 26 3 0.00% 27 6 0.00% 28 5 0.00% 29 11 0.00% 30 0 0.00% 31 3 0.00% 32 15 0.00% 33 4 0.00% 34 4 0.00% 35 1 0.00% 36 2 0.00% 37 6 0.00% 38 10 0.00% 39 27 0.00% 40 36 0.00% 41 14 0.00% 42 15 0.00% 43 31 0.00% 44 21 0.00% 45 32 0.00% 46 43 0.00% 47 68 0.01% 48 91 0.01% 49 121 0.01% 50 149 0.02% 51 203 0.02% 52 295 0.03% 53 363 0.04% 54 497 0.05% 55 594 0.06% 56 777 0.08% 57 1251 0.13% 58 889 0.09% 59 1012 0.10% 60 1137 0.11% 61 1426 0.14% 62 1524 0.15% 63 1525 0.15% 64 1761 0.18% 65 1728 0.17% 66 1840 0.19% 67 1819 0.18% 68 1687 0.17% 69 1954 0.20% 70 7923 0.80% 71 8409 0.85% 72 9815 0.99% 73 9801 0.99% 74 10021 1.01% 75 10473 1.06% 76 11070 1.12% 77 12008 1.21% 78 12470 1.26% 79 13082 1.32% 80 14115 1.43% 81 17043 1.72% 82 17517 1.77% 83 17208 1.74% 84 19945 2.02% 85 12833 1.30% 86 13574 1.37% 87 14521 1.47% 88 16389 1.66% 89 18033 1.82% 90 19299 1.95% 91 20917 2.11% 92 17353 1.75% 93 642603 64.95% 989452 reads passed initial QC criterion=sequence-density sequence-density=5.39 sequence-density-rank=1 fanout-score=2.09 fanout-score-rank=20 prefix-density=5.53 prefix-fanout=2.0 sequence=CAAGGCTAAATAC criterion=fanout-score sequence-density=0.12 sequence-density-rank=14 fanout-score=77.72 fanout-score-rank=1 prefix-density=8.89 prefix-fanout=1.0 sequence=GATAGTCAAGGGCGCGTTATTAA Potential 3prime adapter identified. Now checking if in reference sequence Warning: gzbuffer added in zlib v1.2.3.5. Unable to change buffer size from default of 8192. 1 reads; of these: 1 (100.00%) were unpaired; of these: 0 (0.00%) aligned 0 times 0 (0.00%) aligned exactly 1 time 1 (100.00%) aligned >1 times 100.00% overall alignment rate Potential adapter found in reference sequence. Continuing without clipping. Started job on | Dec 07 03:17:25 Started mapping on | Dec 07 03:17:25 Finished on | Dec 07 03:17:32 Mapping speed, Million of reads per hour | 508.86 Number of input reads | 989452 Average input read length | 88 UNIQUE READS: Uniquely mapped reads number | 439673 Uniquely mapped reads % | 44.44% Average mapped length | 87.90 Number of splices: Total | 14839 Number of splices: Annotated (sjdb) | 12094 Number of splices: GT/AG | 14188 Number of splices: GC/AG | 258 Number of splices: AT/AC | 14 Number of splices: Non-canonical | 379 Mismatch rate per base, % | 0.84% Deletion rate per base | 0.04% Deletion average length | 1.70 Insertion rate per base | 0.02% Insertion average length | 1.76 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 417279 % of reads mapped to multiple loci | 42.17% Number of reads mapped to too many loci | 63909 % of reads mapped to too many loci | 6.46% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 5.86% % of reads unmapped: other | 1.07% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 132500 132500 132500 N_multimapping 417279 417279 417279 N_noFeature 42135 46632 420298 N_ambiguous 17929 3020 96 UnstrandedReadsAssigned:379609 PositiveStrandReadsAssigned:390021 NegativeStrandReadsAssigned:19279 Dataset is classified positive stranded MeadianReadLen=93 20thPercentileLength=84 echo kmer=79 ERR6133404 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: ERR6133404-trimmed.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 989,452 reads, 634,398 reads pseudoaligned [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 839 rounds 52973 ERR6133404.ke.tsv 35125 ERR6133404.se.tsv 88098 total ==> ERR6133404.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 8 12.1229 PNS24243 293 194 0 0 KQK14069 1603 1504 9 12.4413 KQK14071 474 375 0 0 ==> ERR6133404.se.tsv <== BRADI_1g14170v3 9 BRADI_1g53295v3 3 BRADI_1g59795v3 4 BRADI_1g07683v3 0 BRADI_1g00485v3 0 BRADI_1g20270v3 8 BRADI_1g74790v3 4 BRADI_1g09890v3 0 BRADI_1g77505v3 7 BRADI_1g48960v3 0 ERR6133404 completed mapping pipeline successfully