Starting /dee2/code/volunteer_pipeline.sh ERR6133339 current disk space = 1548079738880 free memory = 1601809476 ERR6133339 SRAfilesize 9c5c2515b7553685d41ec9fef591677c ERR6133339.sra ERR6133339.sra file validated ERR6133339 is single end ERR6133339 is conventional basespace ERR6133339 read1 length is 70-93 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename ERR6133339_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 46 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 36.13525 37.0 37.0 37.0 33.0 37.0 2 36.631 37.0 37.0 37.0 37.0 37.0 3 36.59975 37.0 37.0 37.0 37.0 37.0 4 36.291 37.0 37.0 37.0 37.0 37.0 5 36.401 37.0 37.0 37.0 37.0 37.0 6 36.5205 37.0 37.0 37.0 37.0 37.0 7 38.63475 40.0 37.0 40.0 37.0 40.0 8 38.66375 40.0 37.0 40.0 37.0 40.0 9 38.682 40.0 37.0 40.0 37.0 40.0 10-11 38.63775 40.0 37.0 40.0 37.0 40.0 12-13 38.667375 40.0 37.0 40.0 37.0 40.0 14-15 38.659125 40.0 37.0 40.0 37.0 40.0 16-17 38.60575 40.0 37.0 40.0 37.0 40.0 18-19 38.549 40.0 37.0 40.0 37.0 40.0 20-21 38.493875 40.0 37.0 40.0 37.0 40.0 22-23 38.451499999999996 40.0 37.0 40.0 37.0 40.0 24-25 38.370125 40.0 37.0 40.0 37.0 40.0 26-27 38.373000000000005 40.0 37.0 40.0 37.0 40.0 28-29 38.37575 40.0 37.0 40.0 37.0 40.0 30-31 38.355000000000004 40.0 37.0 40.0 37.0 40.0 32-33 38.232875 40.0 37.0 40.0 37.0 40.0 34-35 38.052 40.0 37.0 40.0 37.0 40.0 36-37 38.012249999999995 40.0 37.0 40.0 37.0 40.0 38-39 37.959 38.5 37.0 40.0 37.0 40.0 40-41 37.799499999999995 37.0 37.0 40.0 35.0 40.0 42-43 37.760875 37.0 37.0 40.0 37.0 40.0 44-45 37.543375 37.0 37.0 40.0 35.0 40.0 46-47 37.4845 37.0 37.0 40.0 35.0 40.0 48-49 37.32275 37.0 37.0 40.0 33.0 40.0 50-51 37.21675 37.0 37.0 40.0 35.0 40.0 52-53 37.034125 37.0 37.0 38.5 33.0 40.0 54-55 36.904375 37.0 37.0 37.0 33.0 40.0 56-57 36.7395 37.0 37.0 37.0 33.0 40.0 58-59 36.558125000000004 37.0 37.0 37.0 33.0 40.0 60-61 36.437625 37.0 37.0 37.0 33.0 38.5 62-63 36.319500000000005 37.0 37.0 37.0 33.0 37.0 64-65 36.148875 37.0 37.0 37.0 33.0 37.0 66-67 35.993625 37.0 37.0 37.0 33.0 37.0 68-69 35.120125 35.0 35.0 37.0 33.0 37.0 70-71 35.342252518891684 37.0 33.0 37.0 33.0 37.0 72-73 35.80750068842255 37.0 37.0 37.0 33.0 37.0 74-75 35.726206899053196 37.0 37.0 37.0 33.0 37.0 76-77 35.814462545408325 37.0 37.0 37.0 33.0 37.0 78-79 35.782536100873216 37.0 37.0 37.0 33.0 37.0 80-81 35.7970934958069 37.0 37.0 37.0 33.0 37.0 82-83 35.60378940527092 37.0 35.0 37.0 33.0 37.0 84-85 35.60960293736042 37.0 37.0 37.0 33.0 37.0 86-87 35.56776978417266 37.0 37.0 37.0 33.0 37.0 88-89 35.66 37.0 37.0 37.0 33.0 37.0 90-91 35.6063309352518 37.0 37.0 37.0 33.0 37.0 92-93 35.436402877697844 37.0 33.0 37.0 33.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 21 3.0 22 2.0 23 4.0 24 6.0 25 6.0 26 6.0 27 8.0 28 15.0 29 15.0 30 29.0 31 35.0 32 41.0 33 61.0 34 92.0 35 200.0 36 928.0 37 1136.0 38 1330.0 39 83.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 68.60000000000001 8.9 8.05 14.45 2 51.6 25.35 13.450000000000001 9.6 3 35.625 35.275 15.174999999999999 13.925 4 29.825000000000003 30.85 20.3 19.025 5 29.7 26.174999999999997 25.324999999999996 18.8 6 19.825 36.449999999999996 26.424999999999997 17.299999999999997 7 36.4 25.45 22.35 15.8 8 27.800000000000004 26.05 24.9 21.25 9 24.55 29.4 27.150000000000002 18.9 10-11 25.412499999999998 29.3375 26.775 18.475 12-13 23.925 30.2375 25.587500000000002 20.25 14-15 21.9375 32.625 26.7125 18.725 16-17 26.1 28.725 22.5 22.675 18-19 26.6125 24.349999999999998 29.0875 19.950000000000003 20-21 27.3125 24.0 28.1375 20.549999999999997 22-23 29.25 24.1875 26.187500000000004 20.375 24-25 24.4125 26.125 27.775 21.6875 26-27 27.700000000000003 23.275000000000002 26.737499999999997 22.287499999999998 28-29 24.6 28.262500000000003 26.924999999999997 20.2125 30-31 29.799999999999997 25.525 25.25 19.425 32-33 27.725 25.174999999999997 24.9875 22.112499999999997 34-35 23.7625 31.525 24.075 20.6375 36-37 27.175 26.55 22.35 23.925 38-39 30.7 24.6125 25.0625 19.625 40-41 24.6625 24.5375 30.349999999999998 20.45 42-43 28.012500000000003 30.837500000000002 23.8375 17.3125 44-45 24.7375 28.4 27.775 19.0875 46-47 26.924999999999997 25.8 24.425 22.85 48-49 26.487500000000004 24.7 26.5875 22.225 50-51 22.112499999999997 29.7125 25.474999999999998 22.7 52-53 24.349999999999998 27.150000000000002 24.349999999999998 24.15 54-55 23.3 27.6375 27.462500000000002 21.6 56-57 26.487500000000004 29.875 24.4125 19.225 58-59 23.1 29.762499999999996 27.212500000000002 19.925 60-61 31.2375 25.087500000000002 24.4 19.275000000000002 62-63 21.925 28.775000000000002 29.462500000000002 19.8375 64-65 23.075000000000003 34.5625 24.887500000000003 17.474999999999998 66-67 25.825 32.4375 23.7625 17.974999999999998 68-69 22.8625 26.9625 27.537499999999998 22.6375 70-71 24.692597239648684 29.91217063989962 24.466750313676286 20.92848180677541 72-73 27.66309887869521 27.127930682976555 26.975025484199794 18.23394495412844 74-75 26.085266295192433 28.819489438901126 26.059349488143063 19.035894777763378 76-77 23.034373765310153 25.839589095219278 24.94402739365205 26.18200974581852 78-79 28.202728002139608 29.12543460818401 24.164215030756885 18.507622358919498 80-81 23.182684454124693 35.35257282875034 24.571195208276613 16.893547508848354 82-83 25.153203342618387 28.81615598885794 23.356545961002787 22.674094707520894 84-85 21.783876500857634 28.05889079473985 30.031446540880502 20.125786163522015 86-87 21.251798561151077 32.18705035971223 23.35251798561151 23.20863309352518 88-89 20.618705035971225 31.151079136690647 27.223021582733814 21.007194244604317 90-91 25.02158273381295 33.33812949640288 22.892086330935253 18.748201438848923 92-93 20.388489208633093 33.007194244604314 26.28776978417266 20.31654676258993 >>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 1.0 14 1.5 15 1.0 16 0.5 17 0.5 18 1.0 19 1.0 20 1.5 21 2.0 22 2.0 23 3.5 24 6.0 25 10.0 26 11.5 27 14.0 28 22.0 29 23.0 30 24.0 31 30.0 32 37.0 33 50.5 34 69.5 35 90.5 36 118.0 37 149.0 38 174.5 39 180.5 40 189.5 41 182.0 42 190.0 43 217.5 44 180.0 45 160.0 46 163.0 47 142.5 48 131.5 49 136.0 50 153.5 51 174.5 52 170.5 53 190.0 54 288.5 55 258.0 56 128.5 57 93.0 58 68.0 59 36.0 60 26.5 61 27.0 62 20.0 63 11.5 64 10.5 65 11.5 66 11.0 67 6.0 68 15.5 69 21.0 70 8.0 71 1.0 72 0.5 73 0.5 74 0.5 75 0.0 76 0.0 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 0.0 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 30.0 71 30.0 72 32.0 73 34.0 74 31.0 75 29.0 76 35.0 77 26.0 78 28.0 79 34.0 80 36.0 81 43.0 82 44.0 83 47.0 84 46.0 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 3475.0 >>END_MODULE >>Sequence Duplication Levels warn #Total Deduplicated Percentage 69.65 #Duplication Level Percentage of deduplicated Percentage of total 1 89.73438621679828 62.5 2 5.025125628140704 7.000000000000001 3 1.6511127063890882 3.45 4 0.8255563531945441 2.3 5 0.5025125628140703 1.7500000000000002 6 0.46661880832735103 1.95 7 0.3948312993539124 1.925 8 0.21536252692031585 1.2 9 0.21536252692031585 1.35 >10 0.9332376166547021 10.95 >50 0.0 0.0 >100 0.03589375448671931 5.625 >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 225 5.625 No Hit TACCTAGGCACCCAGAGACGAGGAAGGGCGTAGCAAGCGACGAAATGCTT 38 0.95 No Hit GGGTTGTTTGGGAATGCAGCCCAAATCGGGCGGTAGACTCCGTCCAAGGC 35 0.8750000000000001 No Hit GGAATCCCGTGTGAATCAGCAAGGACCACCTTGCAAGGCTAAATACTCCT 25 0.625 No Hit CAAGGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCT 23 0.575 No Hit GGAAAAGAAAGCAAAAGCGATTCCCGTAGTAGCGGCGAGCGAAATGGGAG 23 0.575 No Hit TCAAAAGAGGAAAGGCTTGCGGTGGATACCTAGGCACCCAGAGACGAGGA 22 0.5499999999999999 No Hit GGGCACGTGGAATCCCGTGTGAATCAGCAAGGACCACCTTGCAAGGCTAA 20 0.5 No Hit GGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCTTGG 20 0.5 No Hit GGAGTTGAAAATAAGCATAGATCCGGAGATTCCCAAATAGGTCAACCTTT 19 0.475 No Hit GGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAA 18 0.44999999999999996 No Hit GGGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGT 16 0.4 No Hit GGGGCACGTGGAATCCCGTGTGAATCAGCAAGGACCACCTTGCAAGGCTA 16 0.4 No Hit GGGTGAGAGCCCCGTCCGGCCCGGACCCTGTCGCCCCACGAGGCGCCGTC 15 0.375 No Hit GGGGTTGTGGGAGAGCAATACAAGCGTTGTGCTGCTAGGCGAAGCGGTTG 14 0.35000000000000003 No Hit GGGCGCGATCTTGCTCGTGAAGGTAATGAAATTATCCGAGCAGCTTGCAA 13 0.325 No Hit GAAGGTAATGAAATTATCCGAGCAGCTTGCAAATGGAGTCCTGAACTAGC 13 0.325 No Hit GGTTGTGGGAGAGCAATACAAGCGTTGTGCTGCTAGGCGAAGCGGTTGAG 12 0.3 No Hit GGCGTTCAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTC 11 0.27499999999999997 No Hit GGAGTCCTGAACTAGCCGCAGCTTGTGAAGTATGGAAGGCGATCAAATTC 11 0.27499999999999997 No Hit CAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAATACTTGGGCTGATAT 11 0.27499999999999997 No Hit GGGTTGTGGGAGAGCAATACAAGCGTTGTGCTGCTAGGCGAAGCGGTTGA 11 0.27499999999999997 No Hit GTGGAATCCCGTGTGAATCAGCAAGGACCACCTTGCAAGGCTAAATACTC 11 0.27499999999999997 No Hit GGAGAGCAATACAAGCGTTGTGCTGCTAGGCGAAGCGGTTGAGTGCCGCA 11 0.27499999999999997 No Hit GGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGTG 10 0.25 No Hit GGGAATTTCCGGTGGAGCGGTGAAATGCATTGAGATCGGAAAGAACACCA 10 0.25 No Hit GTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCTTGGT 10 0.25 No Hit CGAGTCGGGTTGTTTGGGAATGCAGCCCAAATCGGGCGGTAGACTCCGTC 9 0.22499999999999998 No Hit GGGATGATTCTGTATTACAATTTGGTGGAGGAACTTTAGGACATCCTTGG 9 0.22499999999999998 No Hit CAACGAGTCGGGTTGTTTGGGAATGCAGCCCAAATCGGGCGGTAGACTCC 9 0.22499999999999998 No Hit GGTAATGAAATTATCCGAGCAGCTTGCAAATGGAGTCCTGAACTAGCCGC 9 0.22499999999999998 No Hit CAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAATACTTGGGCTG 9 0.22499999999999998 No Hit GAACGTAATGCTCACAACTTCCCTCTAGATCTAGCTGCTCTTGAAGTTCC 9 0.22499999999999998 No Hit GAGGAAGGGCGTAGCAAGCGACGAAATGCTTCGGGGAGTTGAAAATAAGC 8 0.2 No Hit AACGTAATGCTCACAACTTCCCTCTAGATCTAGCTGCTCTTGAAGTTCCC 8 0.2 No Hit GTAGTTGATAGTCAAGGTCGCGTTATTAATACTTGGGCTGATATCATCAA 8 0.2 No Hit CGGGTTGTTTGGGAATGCAGCCCAAATCGGGCGGTAGACTCCGTCCAAGG 8 0.2 No Hit CAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAGGTC 8 0.2 No Hit GTTCAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAG 8 0.2 No Hit GGAGTTTGGCTGGGGCGGCACATCTGTTAAAAGATAACGCAGGTGTCCTA 7 0.17500000000000002 No Hit GGAGGGTGAGAGCCCCGTCCGGCCCGGACCCTGTCGCCCCACGAGGCGCC 7 0.17500000000000002 No Hit GGGAATGCAGCCCAAATCGGGCGGTAGACTCCGTCCAAGGCTAAATACAG 7 0.17500000000000002 No Hit GGACATCCTTGGGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTT 7 0.17500000000000002 No Hit GCAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAATACTTGGGCT 7 0.17500000000000002 No Hit GTATGGAAGGCGATCAAATTCGAGTTCGCGCCGGTAGATACTATCGATTA 7 0.17500000000000002 No Hit GCAGCTTGCAAATGGAGTCCTGAACTAGCCGCAGCTTGTGAAGTATGGAA 7 0.17500000000000002 No Hit GAAATTATCCGAGCAGCTTGCAAATGGAGTCCTGAACTAGCCGCAGCTTG 7 0.17500000000000002 No Hit GTTGTTTGGGAATGCAGCCCAAATCGGGCGGTAGACTCCGTCCAAGGCTA 7 0.17500000000000002 No Hit ATAGGTCAACCTTTTAAACTGCCTGCTGAATCCATGAGCAGGCAAGAGAC 7 0.17500000000000002 No Hit GGGGAGTTGAAAATAAGCATAGATCCGGAGATTCCCAAATAGGTCAACCT 7 0.17500000000000002 No Hit ATCATCAACCGTGCTAATCTTGGTATGGAAGTAATGCACGAACGTAATGC 6 0.15 No Hit GGGGAGAGCAATACAAGCGTTGTGCTGCTAGGCGAAGCGGTTGAGTGCCG 6 0.15 No Hit GTACTATGGCGTTCAACCTAAATGGATTCAATTTCAACCAATCTGTAGTT 6 0.15 No Hit GGGCGTAGCAAGCGACGAAATGCTTCGGGGAGTTGAAAATAAGCATAGAT 6 0.15 No Hit GCTCGTGAAGGTAATGAAATTATCCGAGCAGCTTGCAAATGGAGTCCTGA 6 0.15 No Hit GGATACCTAGGCACCCAGAGACGAGGAAGGGCGTAGCAAGCGACGAAATG 6 0.15 No Hit GATTCAATTTCAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAAT 6 0.15 No Hit GGGCTGATATCATCAACCGTGCTAATCTTGGTATGGAAGTAATGCACGAA 6 0.15 No Hit GTACAAGCTCGTAACGAAGGGCGCGATCTTGCTCGTGAAGGTAATGAAAT 6 0.15 No Hit CAAAAGAGGAAAGGCTTGCGGTGGATACCTAGGCACCCAGAGACGAGGAA 6 0.15 No Hit AACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAATACTTGGGCTGA 6 0.15 No Hit GGTTGAGTGCCGCACCCTAGATGGCTAAAGTCCAGTAGCCGAAAGCATCA 6 0.15 No Hit GGTTGTTTGGGAATGCAGCCCAAATCGGGCGGTAGACTCCGTCCAAGGCT 6 0.15 No Hit GCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCTTGGTATG 5 0.125 No Hit GTCAACGAGTCGGGTTGTTTGGGAATGCAGCCCAAATCGGGCGGTAGACT 5 0.125 No Hit GGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGTGTACAAGCTCGTAA 5 0.125 No Hit GGGTGAGTAACGCGTAAGAACCTGCCCTTGGGAGGGGAACAACAACTGGA 5 0.125 No Hit GGAGATTCCCAAATAGGTCAACCTTTTAAACTGCCTGCTGAATCCATGAG 5 0.125 No Hit GTTGAAAATAAGCATAGATCCGGAGATTCCCAAATAGGTCAACCTTTTAA 5 0.125 No Hit GGCTAAAGTCCAGTAGCCGAAAGCATCACTAGCTTACGCTCTGACCCGAG 5 0.125 No Hit AGGAAAAGAAAGCAAAAGCGATTCCCGTAGTAGCGGCGAGCGAAATGGGA 5 0.125 No Hit CGAGCAGCTTGCAAATGGAGTCCTGAACTAGCCGCAGCTTGTGAAGTATG 5 0.125 No Hit GGTGAGAGCCCCGTCCGGCCCGGACCCTGTCGCCCCACGAGGCGCCGTCA 5 0.125 No Hit GGAGCAGCCTAAACCGTGAAAACGGGGTTGTGGGAGAGCAATACAAGCGT 5 0.125 No Hit CAAGCGTTGTGCTGCTAGGCGAAGCGGTTGAGTGCCGCACCCTAGATGGC 5 0.125 No Hit GAGTCGGGTTGTTTGGGAATGCAGCCCAAATCGGGCGGTAGACTCCGTCC 5 0.125 No Hit GGTGGATACCTAGGCACCCAGAGACGAGGAAGGGCGTAGCAAGCGACGAA 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 0.025 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 0.0 0.025 0.0 0.0 0.0 22-23 0.0 0.025 0.0 0.0 0.0 24-25 0.0 0.025 0.0 0.0 0.0 26-27 0.0 0.025 0.0 0.0 0.0 28-29 0.0 0.025 0.0 0.0 0.0 30-31 0.0 0.025 0.0 0.0 0.0 32-33 0.0 0.025 0.0 0.0 0.0 34-35 0.025 0.025 0.0 0.0 0.0 36-37 0.025 0.025 0.0 0.0 0.0 38-39 0.025 0.025 0.0 0.0 0.0 40-41 0.025 0.025 0.0 0.0 0.0 42-43 0.025 0.025 0.0 0.0 0.0 44-45 0.025 0.025 0.0 0.0 0.0 46-47 0.025 0.025 0.0 0.0 0.0 48-49 0.025 0.025 0.0 0.0 0.0 50-51 0.05 0.025 0.0 0.0 0.0 52-53 0.05 0.025 0.0 0.0 0.0 54-55 0.05 0.025 0.0 0.0 0.0 56-57 0.05 0.025 0.0 0.0 0.0 58-59 0.05 0.025 0.0 0.0 0.0 60-61 0.05 0.025 0.0 0.0 0.0 62-63 0.05 0.025 0.0 0.0 0.0 64-65 0.05 0.025 0.0 0.0 0.0 66-67 0.05 0.025 0.0 0.0 0.0 68-69 0.05 0.025 0.0 0.0 0.0 70-71 0.0625 0.025 0.0 0.0 0.0 72-73 0.075 0.025 0.0 0.0 0.0 74-75 0.075 0.025 0.0 0.0 0.0 76-77 0.075 0.025 0.0 0.0 0.0 78-79 0.075 0.025 0.0 0.0 0.0 80-81 0.075 0.025 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position GGGAGAG 45 2.5044772E-5 46.993057 1 GGAGAGC 50 4.6686782E-5 42.29375 2 GCAATAC 55 8.193741E-5 38.448864 7 CAATACA 55 8.193741E-5 38.448864 8 GAGCAAT 55 8.193741E-5 38.448864 5 AGAGCAA 55 8.193741E-5 38.448864 4 GAGAGCA 55 8.193741E-5 38.448864 3 AATACAA 55 8.193741E-5 38.448864 9 AGCAATA 55 8.193741E-5 38.448864 6 CATCACT 40 6.7537057E-6 37.318016 82-83 TCACTAG 40 6.7537057E-6 37.318016 84-85 ACTAGCT 40 6.7537057E-6 37.318016 86-87 AGCATCA 45 1.5148658E-5 33.17157 80-81 AAAGCAT 45 1.5945821E-5 32.929443 78-79 CGAAAGC 45 1.8554898E-5 32.223812 76-77 GCCGAAA 45 2.3710098E-5 31.112644 74-75 ATCACTA 40 3.0815118E-4 31.098347 84-85 CACTAGC 40 3.0815118E-4 31.098347 86-87 TAGCCGA 45 2.7352069E-5 30.481983 72-73 AAAAAAA 35 0.006239738 28.432774 86-87 >>END_MODULE Rejected 46864 READS because READLEN < 1 Read 46864 spots for ERR6133339.sra Written 46864 spots for ERR6133339.sra Rejected 46864 READS because READLEN < 1 Read 46864 spots for ERR6133339.sra Written 46864 spots for ERR6133339.sra Rejected 46864 READS because READLEN < 1 Read 46864 spots for ERR6133339.sra Written 46864 spots for ERR6133339.sra Rejected 46864 READS because READLEN < 1 Read 46864 spots for ERR6133339.sra Written 46864 spots for ERR6133339.sra Rejected 46864 READS because READLEN < 1 Read 46864 spots for ERR6133339.sra Written 46864 spots for ERR6133339.sra Rejected 46864 READS because READLEN < 1 Read 46864 spots for ERR6133339.sra Written 46864 spots for ERR6133339.sra Rejected 46864 READS because READLEN < 1 Read 46864 spots for ERR6133339.sra Written 46864 spots for ERR6133339.sra Rejected 46864 READS because READLEN < 1 Read 46864 spots for ERR6133339.sra Written 46864 spots for ERR6133339.sra Rejected 46864 READS because READLEN < 1 Read 46864 spots for ERR6133339.sra Written 46864 spots for ERR6133339.sra Rejected 46864 READS because READLEN < 1 Read 46864 spots for ERR6133339.sra Written 46864 spots for ERR6133339.sra Rejected 46864 READS because READLEN < 1 Read 46864 spots for ERR6133339.sra Written 46864 spots for ERR6133339.sra Rejected 46864 READS because READLEN < 1 Read 46864 spots for ERR6133339.sra Written 46864 spots for ERR6133339.sra Rejected 46864 READS because READLEN < 1 Read 46864 spots for ERR6133339.sra Written 46864 spots for ERR6133339.sra Rejected 46864 READS because READLEN < 1 Read 46864 spots for ERR6133339.sra Written 46864 spots for ERR6133339.sra Rejected 46864 READS because READLEN < 1 Read 46864 spots for ERR6133339.sra Written 46864 spots for ERR6133339.sra Rejected 46864 READS because READLEN < 1 Read 46864 spots for ERR6133339.sra Written 46864 spots for ERR6133339.sra Rejected 46864 READS because READLEN < 1 Read 46864 spots for ERR6133339.sra Written 46864 spots for ERR6133339.sra Rejected 46869 READS because READLEN < 1 Read 46869 spots for ERR6133339.sra Written 46869 spots for ERR6133339.sra Rejected 46864 READS because READLEN < 1 Read 46864 spots for ERR6133339.sra Written 46864 spots for ERR6133339.sra Rejected 46864 READS because READLEN < 1 Read 46864 spots for ERR6133339.sra Written 46864 spots for ERR6133339.sra SRR ids: ['ERR6133339.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_3h7bqok_ ERR6133339.sra spots: 937285 blocks: [[1, 46864], [46865, 93728], [93729, 140592], [140593, 187456], [187457, 234320], [234321, 281184], [281185, 328048], [328049, 374912], [374913, 421776], [421777, 468640], [468641, 515504], [515505, 562368], [562369, 609232], [609233, 656096], [656097, 702960], [702961, 749824], [749825, 796688], [796689, 843552], [843553, 890416], [890417, 937285]] ERR6133339 file size 203018 ERR6133339 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 ERR6133339 ERR6133339_1.fastq Input file: ERR6133339_1.fastq trimmed: ERR6133339-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 00:59:25 2024 >> started Sat Dec 7 00:59:26 2024 >> done (0.630s) 937285 reads processed; of these: 57 ( 0.01%) short reads filtered out after trimming by size control 3 ( 0.00%) empty reads filtered out after trimming by size control 937225 (99.99%) reads available; of these: 6029 ( 0.64%) trimmed reads available after processing 931196 (99.36%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 2 0.00% 19 13 0.00% 20 4 0.00% 21 5 0.00% 22 5 0.00% 23 6 0.00% 24 4 0.00% 25 5 0.00% 26 4 0.00% 27 7 0.00% 28 8 0.00% 29 196 0.02% 30 3 0.00% 31 2 0.00% 32 21 0.00% 33 491 0.05% 34 2 0.00% 35 17 0.00% 36 6 0.00% 37 7 0.00% 38 9 0.00% 39 20 0.00% 40 30 0.00% 41 7 0.00% 42 2 0.00% 43 10 0.00% 44 12 0.00% 45 8 0.00% 46 7 0.00% 47 3 0.00% 48 9 0.00% 49 6 0.00% 50 9 0.00% 51 36 0.00% 52 3 0.00% 53 4 0.00% 54 6 0.00% 55 7 0.00% 56 3 0.00% 57 7 0.00% 58 7 0.00% 59 5 0.00% 60 8 0.00% 61 7 0.00% 62 3 0.00% 63 4 0.00% 64 6 0.00% 65 9 0.00% 66 1 0.00% 67 16 0.00% 68 25 0.00% 69 56 0.01% 70 7720 0.82% 71 7066 0.75% 72 7980 0.85% 73 7498 0.80% 74 6987 0.75% 75 6630 0.71% 76 6361 0.68% 77 7169 0.76% 78 7334 0.78% 79 7446 0.79% 80 7565 0.81% 81 10094 1.08% 82 10328 1.10% 83 8941 0.95% 84 10461 1.12% 85 42 0.00% 86 50 0.01% 87 91 0.01% 88 115 0.01% 89 183 0.02% 90 306 0.03% 91 759 0.08% 92 2495 0.27% 93 812451 86.69% 937225 reads passed initial QC criterion=sequence-density sequence-density=6.80 sequence-density-rank=1 fanout-score=2.02 fanout-score-rank=22 prefix-density=6.87 prefix-fanout=2.0 sequence=CAAGGCTAAATAC criterion=fanout-score sequence-density=0.06 sequence-density-rank=20 fanout-score=21.52 fanout-score-rank=1 prefix-density=0.26 prefix-fanout=5.0 sequence=ATATATATGTATAAGATGCCAGCCCGGTTTCGTCAACCATGGCATTTTGCTTTGCGTTTTTCCTTTCCGGTTTGTTATTTCTCTTTGTCCCTATGGATATCGTGTGTGTACATTTGA 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 00:59:44 Started mapping on | Dec 07 00:59:44 Finished on | Dec 07 00:59:49 Mapping speed, Million of reads per hour | 674.80 Number of input reads | 937225 Average input read length | 90 UNIQUE READS: Uniquely mapped reads number | 420855 Uniquely mapped reads % | 44.90% Average mapped length | 89.58 Number of splices: Total | 15036 Number of splices: Annotated (sjdb) | 12304 Number of splices: GT/AG | 14103 Number of splices: GC/AG | 305 Number of splices: AT/AC | 32 Number of splices: Non-canonical | 596 Mismatch rate per base, % | 0.44% Deletion rate per base | 0.04% Deletion average length | 1.71 Insertion rate per base | 0.02% Insertion average length | 1.93 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 430355 % of reads mapped to multiple loci | 45.92% Number of reads mapped to too many loci | 59156 % of reads mapped to too many loci | 6.31% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 2.59% % of reads unmapped: other | 0.28% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 86015 86015 86015 N_multimapping 430355 430355 430355 N_noFeature 34128 38278 401735 N_ambiguous 17140 2191 54 UnstrandedReadsAssigned:369587 PositiveStrandReadsAssigned:380386 NegativeStrandReadsAssigned:19066 Dataset is classified positive stranded MeadianReadLen=93 20thPercentileLength=93 echo kmer=89 ERR6133339 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: ERR6133339-trimmed.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 937,225 reads, 555,511 reads pseudoaligned [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 942 rounds 52973 ERR6133339.ke.tsv 35125 ERR6133339.se.tsv 88098 total ==> ERR6133339.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 9 16.1318 PNS24243 293 194 0 0 KQK14069 1603 1504 5 8.17554 KQK14071 474 375 0 0 ==> ERR6133339.se.tsv <== BRADI_1g14170v3 5 BRADI_1g53295v3 6 BRADI_1g59795v3 5 BRADI_1g07683v3 0 BRADI_1g00485v3 0 BRADI_1g20270v3 7 BRADI_1g74790v3 4 BRADI_1g09890v3 0 BRADI_1g77505v3 7 BRADI_1g48960v3 0 ERR6133339 completed mapping pipeline successfully