Starting /dee2/code/volunteer_pipeline.sh ERR6133476 current disk space = 1545010536448 free memory = 1600578736 ERR6133476 SRAfilesize 67be837674514c0798edc7b262a14c5b ERR6133476.sra ERR6133476.sra file validated ERR6133476 is single end ERR6133476 is conventional basespace ERR6133476 read1 length is 70-93 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename ERR6133476_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 45 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 35.42025 37.0 33.0 37.0 33.0 37.0 2 36.4305 37.0 37.0 37.0 37.0 37.0 3 35.72875 37.0 37.0 37.0 33.0 37.0 4 35.288 37.0 37.0 37.0 33.0 37.0 5 35.21775 37.0 37.0 37.0 33.0 37.0 6 35.501 37.0 37.0 37.0 33.0 37.0 7 37.20025 37.0 37.0 40.0 33.0 40.0 8 37.274 37.0 37.0 40.0 33.0 40.0 9 37.25025 37.0 37.0 40.0 33.0 40.0 10-11 37.22225 37.0 37.0 40.0 33.0 40.0 12-13 37.1505 37.0 37.0 40.0 33.0 40.0 14-15 37.15925 37.0 37.0 40.0 33.0 40.0 16-17 37.086625 37.0 37.0 40.0 33.0 40.0 18-19 36.958375000000004 37.0 37.0 40.0 33.0 40.0 20-21 36.692375 37.0 37.0 40.0 33.0 40.0 22-23 36.596999999999994 37.0 37.0 40.0 33.0 40.0 24-25 36.474625 37.0 37.0 40.0 33.0 40.0 26-27 36.695625 37.0 37.0 40.0 33.0 40.0 28-29 36.74525 37.0 37.0 40.0 33.0 40.0 30-31 36.675 37.0 37.0 40.0 33.0 40.0 32-33 36.574875 37.0 37.0 40.0 33.0 40.0 34-35 36.48575 37.0 37.0 40.0 33.0 40.0 36-37 36.31975 37.0 37.0 40.0 33.0 40.0 38-39 36.263999999999996 37.0 37.0 40.0 33.0 40.0 40-41 35.9815 37.0 37.0 40.0 33.0 40.0 42-43 36.0155 37.0 37.0 40.0 33.0 40.0 44-45 35.98125 37.0 35.0 40.0 33.0 40.0 46-47 35.83775 37.0 35.0 38.5 33.0 40.0 48-49 35.76075 37.0 33.0 37.0 33.0 40.0 50-51 35.597750000000005 37.0 33.0 37.0 33.0 40.0 52-53 35.393125 37.0 33.0 37.0 33.0 40.0 54-55 35.28375 37.0 33.0 37.0 33.0 40.0 56-57 35.12025 37.0 33.0 37.0 33.0 40.0 58-59 34.190625 37.0 33.0 37.0 27.0 37.0 60-61 34.621125 37.0 33.0 37.0 30.0 37.0 62-63 34.46825 37.0 33.0 37.0 27.0 37.0 64-65 34.467124999999996 37.0 33.0 37.0 30.0 37.0 66-67 34.4905 37.0 33.0 37.0 30.0 37.0 68-69 33.658 35.0 33.0 37.0 27.0 37.0 70-71 33.830684338031716 35.0 33.0 37.0 27.0 37.0 72-73 34.14093134475103 37.0 33.0 37.0 27.0 37.0 74-75 34.02587936974854 37.0 33.0 37.0 27.0 37.0 76-77 33.89397122612469 37.0 33.0 37.0 27.0 37.0 78-79 33.8253952066511 37.0 33.0 37.0 27.0 37.0 80-81 33.705999236102386 37.0 33.0 37.0 27.0 37.0 82-83 33.644715456871225 37.0 33.0 37.0 27.0 37.0 84-85 33.468186688752525 37.0 33.0 37.0 27.0 37.0 86-87 33.33678686759957 35.0 33.0 37.0 27.0 37.0 88-89 33.47510764262648 37.0 33.0 37.0 27.0 37.0 90-91 33.21232508073197 33.0 33.0 37.0 27.0 37.0 92-93 33.08100107642626 33.0 33.0 37.0 27.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 20 15.0 21 11.0 22 14.0 23 28.0 24 21.0 25 29.0 26 38.0 27 49.0 28 53.0 29 75.0 30 86.0 31 125.0 32 165.0 33 158.0 34 247.0 35 458.0 36 921.0 37 885.0 38 590.0 39 32.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 85.675 4.375 3.1 6.8500000000000005 2 70.0 17.525 7.675 4.8 3 38.15 36.125 14.899999999999999 10.825 4 32.4 29.15 18.875 19.575 5 25.974999999999998 30.049999999999997 25.3 18.675 6 18.95 39.550000000000004 24.45 17.05 7 36.4 28.349999999999998 19.75 15.5 8 29.849999999999998 29.625 22.775000000000002 17.75 9 25.624999999999996 30.349999999999998 27.55 16.475 10-11 25.387500000000003 28.875 28.249999999999996 17.4875 12-13 26.325 27.525 27.1375 19.0125 14-15 21.4125 31.424999999999997 29.1125 18.05 16-17 24.85 31.162499999999998 24.7875 19.2 18-19 24.587500000000002 27.1125 28.15 20.150000000000002 20-21 26.319079769942487 25.681420355088775 27.85696424106027 20.142535633908476 22-23 27.3875 23.2625 27.4125 21.9375 24-25 24.7375 24.5 28.3875 22.375 26-27 25.9625 25.3 29.375 19.3625 28-29 24.1875 27.212500000000002 27.9375 20.6625 30-31 27.5125 25.2 27.3375 19.950000000000003 32-33 24.9875 25.7875 27.962500000000002 21.2625 34-35 24.25 27.787499999999998 27.3125 20.65 36-37 25.525 24.3125 27.762500000000003 22.400000000000002 38-39 27.87787787787788 24.93743743743744 28.44094094094094 18.743743743743742 40-41 25.240775484677926 24.715447154471544 29.46841776110069 20.57535959974984 42-43 24.48112028007002 28.54463615903976 27.00675168792198 19.967491872968242 44-45 25.124999999999996 25.35 29.849999999999998 19.675 46-47 25.0625 23.75 27.275 23.9125 48-49 24.75 25.1 29.625 20.525 50-51 23.875 27.0875 28.237499999999997 20.8 52-53 24.207889793362554 27.351283656856605 27.03819661865999 21.40262993112085 54-55 23.3 26.974999999999998 29.225 20.5 56-57 25.218804701175294 27.419354838709676 27.769442360590148 19.592398099524882 58-59 23.175 26.0125 29.15 21.6625 60-61 25.775 24.8 29.1625 20.2625 62-63 21.6875 28.4375 30.662499999999998 19.2125 64-65 22.575 28.487499999999997 29.15 19.787499999999998 66-67 25.587500000000002 27.900000000000002 27.6875 18.825 68-69 22.037499999999998 27.150000000000002 29.0875 21.725 70-71 23.604665746895773 26.000250846607297 27.718550106609808 22.67653329988712 72-73 26.401721301101126 24.591823819769647 29.12289583597013 19.883559043159092 74-75 24.468629961587705 27.170294494238156 28.56594110115237 19.795134443021766 76-77 22.68267492899561 25.27756261296153 28.530854634650144 23.50890782339272 78-79 24.256590053239837 25.49019607843137 29.866251136216075 20.386962732112714 80-81 22.364971158888306 30.04719454640797 29.535920293654954 18.051914001048768 82-83 23.757125812011136 24.724910513058465 29.56383401829511 21.954129656635292 84-85 23.23489932885906 24.107382550335572 32.09395973154363 20.563758389261743 86-87 21.98600645855759 28.01399354144241 29.117330462863293 20.882669537136707 88-89 21.030678148546826 29.023143164693217 29.655543595263723 20.29063509149623 90-91 25.71313240043057 27.583423035522063 28.1216361679225 18.581808396124867 92-93 21.918729817007534 29.184607104413345 29.951560818083962 18.945102260495155 >>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 0.0 17 5.0 18 6.0 19 1.0 20 0.5 21 3.0 22 4.0 23 5.5 24 8.5 25 9.5 26 13.5 27 16.0 28 25.5 29 37.0 30 37.5 31 51.0 32 65.5 33 74.5 34 84.0 35 89.5 36 108.0 37 134.5 38 178.5 39 177.0 40 174.0 41 209.0 42 206.5 43 202.0 44 189.5 45 170.5 46 173.0 47 174.5 48 160.0 49 159.0 50 167.0 51 147.5 52 126.0 53 139.5 54 177.5 55 138.5 56 68.5 57 58.5 58 55.0 59 48.0 60 38.0 61 36.5 62 31.5 63 28.0 64 31.0 65 24.0 66 16.0 67 16.0 68 18.5 69 12.5 70 8.0 71 8.0 72 6.0 73 3.0 74 1.0 75 2.5 76 2.5 77 0.0 78 0.0 79 0.0 80 0.0 81 0.0 82 0.5 83 0.5 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 0.0 36-37 0.0 38-39 0.1 40-41 0.0625 42-43 0.025 44-45 0.0 46-47 0.0 48-49 0.0 50-51 0.0 52-53 0.1875 54-55 0.0 56-57 0.025 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 27.0 71 10.0 72 25.0 73 25.0 74 16.0 75 16.0 76 16.0 77 7.0 78 15.0 79 17.0 80 24.0 81 17.0 82 27.0 83 24.0 84 18.0 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 3716.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 80.475 #Duplication Level Percentage of deduplicated Percentage of total 1 92.60639950295123 74.52499999999999 2 4.659832246039143 7.5 3 0.8077042559801181 1.95 4 0.4970487729108419 1.6 5 0.40385212799005904 1.625 6 0.21745883814849334 1.05 7 0.15532774153463808 0.8750000000000001 8 0.062131096613855234 0.4 9 0.12426219322771047 0.8999999999999999 >10 0.4349176762969867 6.550000000000001 >50 0.0 0.0 >100 0.031065548306927617 3.025 >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 121 3.025 No Hit GGGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGT 40 1.0 No Hit GGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAA 28 0.7000000000000001 No Hit GGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGTG 27 0.675 No Hit GGGATGATTCTGTATTACAATTTGGTGGAGGAACTTTAGGACATCCTTGG 25 0.625 No Hit TACCTAGGCACCCAGAGACGAGGAAGGGCGTAGCAAGCGACGAAATGCTT 22 0.5499999999999999 No Hit GGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCTTGG 20 0.5 No Hit GGCGTTCAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTC 16 0.4 No Hit GGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGTGTACAAGCTCGTAA 15 0.375 No Hit GGGCGCGATCTTGCTCGTGAAGGTAATGAAATTATCCGAGCAGCTTGCAA 15 0.375 No Hit GGACATCCTTGGGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTT 12 0.3 No Hit GGCGCGATCTTGCTCGTGAAGGTAATGAAATTATCCGAGCAGCTTGCAAA 11 0.27499999999999997 No Hit GGTAATGAAATTATCCGAGCAGCTTGCAAATGGAGTCCTGAACTAGCCGC 11 0.27499999999999997 No Hit GGAGTCCTGAACTAGCCGCAGCTTGTGAAGTATGGAAGGCGATCAAATTC 10 0.25 No Hit GGAAAAGAAAGCAAAAGCGATTCCCGTAGTAGCGGCGAGCGAAATGGGAG 10 0.25 No Hit GGAAGAGCCCGAGCTGCTGCAGCAGGTTTTGAAAAGGGAATCGATCGTGA 9 0.22499999999999998 No Hit GGAGTATCCTTGATATATAAATATATAGATAAATAGATTTAAATGGAAAA 9 0.22499999999999998 No Hit GGGCTGATATCATCAACCGTGCTAATCTTGGTATGGAAGTAATGCACGAA 9 0.22499999999999998 No Hit GGAAAAGAGGGGTTACTTTTTTTCATTTTTCCCTTAAAAGATAGGCTTTG 9 0.22499999999999998 No Hit GGGAAAAGAGGGGTTACTTTTTTTCATTTTTCCCTTAAAAGATAGGCTTT 8 0.2 No Hit GGGGATGATTCTGTATTACAATTTGGTGGAGGAACTTTAGGACATCCTTG 8 0.2 No Hit GGAGTCCCATATATATATGTATAAGATGCCAGCCCGGTTTCGTCAACCAT 7 0.17500000000000002 No Hit GAAGGTAATGAAATTATCCGAGCAGCTTGCAAATGGAGTCCTGAACTAGC 7 0.17500000000000002 No Hit GGAGTTGAAAATAAGCATAGATCCGGAGATTCCCAAATAGGTCAACCTTT 7 0.17500000000000002 No Hit GGGCCATTTGTGGCATGCAGGAAGAGCCCGAGCTGCTGCAGCAGGTTTTG 7 0.17500000000000002 No Hit GGTTTTGAAAAGGGAATCGATCGTGATTTAGAACCTGTTCTTTACATGAA 7 0.17500000000000002 No Hit GGAACTTTAGGACATCCTTGGGGAAATGCACCTGGTGCAGCAGCTAATCG 6 0.15 No Hit GGGATGGAGCGACAGAAGTATGGAAATAGGATAAGGTAGCGGCGAGACGA 6 0.15 No Hit GGTGGAGGAACTTTAGGACATCCTTGGGGAAATGCACCTGGTGCAGCAGC 6 0.15 No Hit GGCCTGTAGTAGGAATCTGGTTCACTGCTTTAGGTATTAGTACTATGGCG 6 0.15 No Hit CAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAGGTC 6 0.15 No Hit GGGCTCGAGGAGCATATGTACATTTGAACCCTGACTACACATATACACAC 6 0.15 No Hit GGATTCCGGCGGAACAAACTAAAATCTAGTACTGCTCTTGGATTGGATCT 6 0.15 No Hit CAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAATACTTGGGCTGATAT 5 0.125 No Hit GGGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTA 5 0.125 No Hit GGGAGTATTATGAAAGGAGATTAATCATAGATTATCAAAAACCCTAGAAA 5 0.125 No Hit GGGCAAGGAGAAGTACAAGTGCGGATCCAACGTCTTCTGGAAATGGTGAA 5 0.125 No Hit GATATCTATCTGAACTGAGAACTGAGTCAGTATATACCAGTCTGTATCAC 5 0.125 No Hit GGATGATTCTGTATTACAATTTGGTGGAGGAACTTTAGGACATCCTTGGG 5 0.125 No Hit GGGAAATTAACAGTTGGAAAGGGCGATCGGTCTTGATCCCTCTGTGTTTC 5 0.125 No Hit GGGCAAGTTCATGTAAACATAGATCGATATATGGCGGAGCGCCATTTTAT 5 0.125 No Hit GGGAATCGATCGTGATTTAGAACCTGTTCTTTACATGAACCCTCTTAACT 5 0.125 No Hit GGGGAAGTACACCAGCGACGGCGAGGCCGCCGCCGCCAAGGAAGGCATGT 5 0.125 No Hit GGAGGAACTTTAGGACATCCTTGGGGAAATGCACCTGGTGCAGCAGCTAA 5 0.125 No Hit GGGCACTGTAGCCAGTGTGTCAGTCGTTGTTAAATTACAGGTTGAGATCA 5 0.125 No Hit CAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAATACTTGGGCTG 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 0.05 0.0 0.0 0.0 0.0 22-23 0.05 0.0 0.0 0.0 0.0 24-25 0.05 0.0 0.0 0.0 0.0 26-27 0.05 0.0 0.0 0.0 0.0 28-29 0.05 0.0 0.0 0.0 0.0 30-31 0.075 0.0 0.0 0.0 0.0 32-33 0.075 0.0 0.0 0.0 0.0 34-35 0.075 0.0 0.0 0.0 0.0 36-37 0.0875 0.0 0.0 0.0 0.0 38-39 0.1 0.0 0.0 0.0 0.0 40-41 0.1375 0.0 0.0 0.0 0.0 42-43 0.2 0.0 0.0 0.0 0.0 44-45 0.225 0.0 0.0 0.0 0.0 46-47 0.25 0.0 0.0 0.0 0.0 48-49 0.25 0.0 0.0 0.0 0.0 50-51 0.25 0.0 0.0 0.0 0.0 52-53 0.275 0.0 0.0 0.0 0.0 54-55 0.275 0.0 0.0 0.0 0.0 56-57 0.275 0.0 0.0 0.0 0.0 58-59 0.275 0.0 0.0 0.0 0.0 60-61 0.275 0.0 0.0 0.0 0.0 62-63 0.275 0.0 0.0 0.0 0.0 64-65 0.275 0.0 0.0 0.0 0.0 66-67 0.275 0.0 0.0 0.0 0.0 68-69 0.275 0.0 0.0 0.0 0.0 70-71 0.275 0.0 0.0 0.0 0.0 72-73 0.275 0.0 0.0 0.0 0.0 74-75 0.275 0.0 0.0 0.0 0.0 76-77 0.2875 0.0 0.0 0.0 0.0 78-79 0.3 0.0 0.0 0.0 0.0 80-81 0.3 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content fail #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position GGAGAGC 35 5.002221E-10 86.2125 2 GGGAGAG 35 5.002221E-10 86.2125 1 GAGCAAT 35 5.002221E-10 86.2125 5 AGAGCAA 35 5.002221E-10 86.2125 4 GAGAGCA 35 5.002221E-10 86.2125 3 GCAATAC 40 1.4442776E-9 75.43594 7 CAATACA 40 1.4442776E-9 75.43594 8 AATACAA 40 1.4442776E-9 75.43594 9 AGCAATA 40 1.4442776E-9 75.43594 6 CATCACT 35 9.492942E-8 45.375 82-83 ATCACTA 35 9.492942E-8 45.375 84-85 AGCATCA 35 9.492942E-8 45.375 80-81 CACTAGC 35 9.492942E-8 45.375 86-87 TCACTAG 35 9.492942E-8 45.375 84-85 ACTAGCT 35 9.492942E-8 45.375 86-87 AAAGCAT 35 9.492942E-8 45.375 78-79 GCATCAC 35 9.492942E-8 45.375 82-83 CGAAAGC 35 1.0007716E-7 45.07843 76-77 CCGAAAG 35 1.0007716E-7 45.07843 76-77 AGCCGAA 35 1.1110387E-7 44.496773 74-75 >>END_MODULE Rejected 93050 READS because READLEN < 1 Read 93050 spots for ERR6133476.sra Written 93050 spots for ERR6133476.sra Rejected 93050 READS because READLEN < 1 Read 93050 spots for ERR6133476.sra Written 93050 spots for ERR6133476.sra Rejected 93050 READS because READLEN < 1 Read 93050 spots for ERR6133476.sra Written 93050 spots for ERR6133476.sra Rejected 93050 READS because READLEN < 1 Read 93050 spots for ERR6133476.sra Written 93050 spots for ERR6133476.sra Rejected 93050 READS because READLEN < 1 Read 93050 spots for ERR6133476.sra Written 93050 spots for ERR6133476.sra Rejected 93050 READS because READLEN < 1 Read 93050 spots for ERR6133476.sra Written 93050 spots for ERR6133476.sra Rejected 93050 READS because READLEN < 1 Read 93050 spots for ERR6133476.sra Written 93050 spots for ERR6133476.sra Rejected 93050 READS because READLEN < 1 Read 93050 spots for ERR6133476.sra Written 93050 spots for ERR6133476.sra Rejected 93050 READS because READLEN < 1 Read 93050 spots for ERR6133476.sra Written 93050 spots for ERR6133476.sra Rejected 93050 READS because READLEN < 1 Read 93050 spots for ERR6133476.sra Written 93050 spots for ERR6133476.sra Rejected 93050 READS because READLEN < 1 Read 93050 spots for ERR6133476.sra Written 93050 spots for ERR6133476.sra Rejected 93062 READS because READLEN < 1 Read 93062 spots for ERR6133476.sra Written 93062 spots for ERR6133476.sra Rejected 93050 READS because READLEN < 1 Read 93050 spots for ERR6133476.sra Written 93050 spots for ERR6133476.sra Rejected 93050 READS because READLEN < 1 Read 93050 spots for ERR6133476.sra Written 93050 spots for ERR6133476.sra Rejected 93050 READS because READLEN < 1 Read 93050 spots for ERR6133476.sra Written 93050 spots for ERR6133476.sra Rejected 93050 READS because READLEN < 1 Read 93050 spots for ERR6133476.sra Written 93050 spots for ERR6133476.sra Rejected 93050 READS because READLEN < 1 Read 93050 spots for ERR6133476.sra Written 93050 spots for ERR6133476.sra Rejected 93050 READS because READLEN < 1 Read 93050 spots for ERR6133476.sra Written 93050 spots for ERR6133476.sra Rejected 93050 READS because READLEN < 1 Read 93050 spots for ERR6133476.sra Written 93050 spots for ERR6133476.sra Rejected 93050 READS because READLEN < 1 Read 93050 spots for ERR6133476.sra Written 93050 spots for ERR6133476.sra SRR ids: ['ERR6133476.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_13pg14_1 ERR6133476.sra spots: 1861012 blocks: [[1, 93050], [93051, 186100], [186101, 279150], [279151, 372200], [372201, 465250], [465251, 558300], [558301, 651350], [651351, 744400], [744401, 837450], [837451, 930500], [930501, 1023550], [1023551, 1116600], [1116601, 1209650], [1209651, 1302700], [1302701, 1395750], [1395751, 1488800], [1488801, 1581850], [1581851, 1674900], [1674901, 1767950], [1767951, 1861012]] ERR6133476 file size 407703 ERR6133476 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 ERR6133476 ERR6133476_1.fastq Input file: ERR6133476_1.fastq trimmed: ERR6133476-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 06:52:35 2024 >> started Sat Dec 7 06:52:37 2024 >> done (1.188s) 1861012 reads processed; of these: 513 ( 0.03%) short reads filtered out after trimming by size control 41 ( 0.00%) empty reads filtered out after trimming by size control 1860458 (99.97%) reads available; of these: 34017 ( 1.83%) trimmed reads available after processing 1826441 (98.17%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 67 0.00% 19 219 0.01% 20 61 0.00% 21 44 0.00% 22 46 0.00% 23 36 0.00% 24 21 0.00% 25 24 0.00% 26 18 0.00% 27 26 0.00% 28 41 0.00% 29 264 0.01% 30 26 0.00% 31 56 0.00% 32 42 0.00% 33 29 0.00% 34 25 0.00% 35 121 0.01% 36 503 0.03% 37 37 0.00% 38 56 0.00% 39 201 0.01% 40 121 0.01% 41 129 0.01% 42 39 0.00% 43 39 0.00% 44 152 0.01% 45 81 0.00% 46 85 0.00% 47 26 0.00% 48 34 0.00% 49 22 0.00% 50 60 0.00% 51 317 0.02% 52 61 0.00% 53 11 0.00% 54 17 0.00% 55 12 0.00% 56 39 0.00% 57 164 0.01% 58 27 0.00% 59 21 0.00% 60 47 0.00% 61 21 0.00% 62 0 0.00% 63 3 0.00% 64 3 0.00% 65 1 0.00% 66 4 0.00% 67 16 0.00% 68 23 0.00% 69 110 0.01% 70 11065 0.59% 71 9947 0.53% 72 9678 0.52% 73 9132 0.49% 74 9116 0.49% 75 9354 0.50% 76 8092 0.43% 77 8414 0.45% 78 9294 0.50% 79 9747 0.52% 80 8985 0.48% 81 9678 0.52% 82 10602 0.57% 83 11727 0.63% 84 8675 0.47% 85 58 0.00% 86 144 0.01% 87 214 0.01% 88 334 0.02% 89 603 0.03% 90 1404 0.08% 91 4246 0.23% 92 21168 1.14% 93 1685133 90.58% 1860458 reads passed initial QC criterion=sequence-density sequence-density=0.52 sequence-density-rank=1 fanout-score=2.04 fanout-score-rank=31 prefix-density=0.52 prefix-fanout=2.0 sequence=CAAGGCTAAATAC criterion=fanout-score sequence-density=0.01 sequence-density-rank=32 fanout-score=327.59 fanout-score-rank=1 prefix-density=0.71 prefix-fanout=6.5 sequence=GAAGAAGAAAAGTTTTCTCAACATGGGGAGGAAGTCCCTCCGAAATTTGATTTGTTATTGTATTGTAAGGGGCTTTTTTAGTATTTATCTAAAGGAAGGAACAAACGAGGATAAGATAAAATTTCTTTAAATTTATTTTGCCCAAGTGGGATATATGGCATACTATTCTTTCCATTTTCATCTTTTTTTCTATTCCACTCCATCTAGATATAAGAAAGAACCCAATGCAATGAAATTCCACTAATATACAATACAAAAAAGAAGAATAGATACAGGGTCTCAAACC Started job on | Dec 07 06:52:50 Started mapping on | Dec 07 06:52:50 Finished on | Dec 07 06:52:56 Mapping speed, Million of reads per hour | 1116.27 Number of input reads | 1860458 Average input read length | 91 UNIQUE READS: Uniquely mapped reads number | 1225894 Uniquely mapped reads % | 65.89% Average mapped length | 91.58 Number of splices: Total | 62684 Number of splices: Annotated (sjdb) | 53232 Number of splices: GT/AG | 60179 Number of splices: GC/AG | 1463 Number of splices: AT/AC | 49 Number of splices: Non-canonical | 993 Mismatch rate per base, % | 0.44% Deletion rate per base | 0.03% Deletion average length | 1.70 Insertion rate per base | 0.01% Insertion average length | 1.95 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 510771 % of reads mapped to multiple loci | 27.45% Number of reads mapped to too many loci | 15148 % of reads mapped to too many loci | 0.81% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 5.77% % of reads unmapped: other | 0.07% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 123793 123793 123793 N_multimapping 510771 510771 510771 N_noFeature 81375 93548 1173118 N_ambiguous 45424 4814 187 UnstrandedReadsAssigned:1099095 PositiveStrandReadsAssigned:1127532 NegativeStrandReadsAssigned:52589 Dataset is classified positive stranded MeadianReadLen=93 20thPercentileLength=93 echo kmer=89 ERR6133476 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: ERR6133476-trimmed.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 1,860,458 reads, 1,428,950 reads pseudoaligned [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 915 rounds 52973 ERR6133476.ke.tsv 35125 ERR6133476.se.tsv 88098 total ==> ERR6133476.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 44 30.1557 PNS24243 293 194 0 0 KQK14069 1603 1504 16 10.0033 KQK14071 474 375 0 0 ==> ERR6133476.se.tsv <== BRADI_1g14170v3 16 BRADI_1g53295v3 0 BRADI_1g59795v3 9 BRADI_1g07683v3 0 BRADI_1g00485v3 0 BRADI_1g20270v3 9 BRADI_1g74790v3 12 BRADI_1g09890v3 0 BRADI_1g77505v3 20 BRADI_1g48960v3 0 ERR6133476 completed mapping pipeline successfully