Starting /dee2/code/volunteer_pipeline.sh ERR6133405 current disk space = 1547677663232 free memory = 1389339320 ERR6133405 SRAfilesize 1da878f10e75cb5e2e76674e1c738d7e ERR6133405.sra ERR6133405.sra file validated ERR6133405 is single end ERR6133405 is conventional basespace ERR6133405 read1 length is 70-93 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename ERR6133405_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 29.01025 33.0 27.0 33.0 15.0 37.0 2 33.54425 33.0 33.0 37.0 27.0 37.0 3 33.9665 37.0 33.0 37.0 27.0 37.0 4 34.05025 37.0 33.0 37.0 27.0 37.0 5 34.126 37.0 33.0 37.0 27.0 37.0 6 34.428 37.0 33.0 37.0 27.0 37.0 7 35.109 37.0 33.0 40.0 27.0 40.0 8 35.23925 37.0 33.0 40.0 27.0 40.0 9 35.4735 37.0 33.0 40.0 27.0 40.0 10-11 35.432249999999996 37.0 33.0 40.0 30.0 40.0 12-13 35.334375 37.0 33.0 40.0 27.0 40.0 14-15 35.18325 37.0 33.0 37.0 27.0 40.0 16-17 34.914249999999996 37.0 33.0 37.0 27.0 40.0 18-19 34.883875 37.0 33.0 37.0 27.0 40.0 20-21 34.1125 37.0 33.0 37.0 27.0 40.0 22-23 33.905625 37.0 33.0 37.0 24.5 40.0 24-25 33.409 37.0 33.0 37.0 22.0 40.0 26-27 33.171875 37.0 33.0 37.0 22.0 40.0 28-29 32.829625 37.0 33.0 37.0 22.0 40.0 30-31 32.626625000000004 35.0 33.0 37.0 22.0 40.0 32-33 32.13725 33.0 30.0 37.0 22.0 40.0 34-35 31.487625 33.0 27.0 37.0 18.5 40.0 36-37 31.34775 33.0 27.0 37.0 18.5 38.5 38-39 31.523625 33.0 27.0 37.0 22.0 40.0 40-41 31.6285 33.0 27.0 37.0 22.0 40.0 42-43 31.2075 33.0 27.0 37.0 18.5 40.0 44-45 31.207375 33.0 27.0 37.0 18.5 40.0 46-47 30.408125 33.0 27.0 37.0 15.0 37.0 48-49 30.175375 33.0 27.0 37.0 15.0 37.0 50-51 29.677124999999997 33.0 27.0 37.0 15.0 37.0 52-53 29.46725 33.0 27.0 37.0 15.0 37.0 54-55 29.354625 33.0 27.0 37.0 15.0 37.0 56-57 28.648875 33.0 27.0 37.0 15.0 37.0 58-59 28.529875 33.0 27.0 33.0 15.0 37.0 60-61 28.24975 33.0 27.0 33.0 15.0 37.0 62-63 27.836125000000003 33.0 22.0 33.0 15.0 37.0 64-65 27.292749999999998 33.0 22.0 33.0 15.0 37.0 66-67 26.77975 33.0 22.0 33.0 6.0 37.0 68-69 26.491500000000002 27.0 22.0 33.0 10.5 35.0 70-71 28.305129727685326 33.0 27.0 33.0 15.0 37.0 72-73 28.949081792528887 33.0 27.0 33.0 15.0 37.0 74-75 28.595670359800792 33.0 27.0 33.0 15.0 37.0 76-77 28.044196670212486 33.0 27.0 33.0 15.0 37.0 78-79 27.776047492903118 33.0 27.0 33.0 15.0 37.0 80-81 27.077349502279553 33.0 24.5 33.0 6.0 37.0 82-83 26.222705908195707 33.0 22.0 33.0 2.0 37.0 84-85 25.42661313083016 33.0 18.5 33.0 2.0 37.0 86-87 24.349311217317965 30.0 15.0 33.0 2.0 37.0 88-89 23.747540061849875 30.0 15.0 33.0 2.0 33.0 90-91 22.843547933651955 27.0 4.0 33.0 2.0 33.0 92-93 21.765673320213665 27.0 2.0 33.0 2.0 33.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 20 87.0 21 101.0 22 127.0 23 150.0 24 186.0 25 200.0 26 217.0 27 217.0 28 247.0 29 253.0 30 271.0 31 289.0 32 306.0 33 273.0 34 289.0 35 305.0 36 269.0 37 170.0 38 43.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 70.5 7.95 6.4 15.15 2 50.475 24.9 15.975 8.649999999999999 3 29.7 38.675 18.0 13.625000000000002 4 28.775000000000002 27.55 21.825 21.85 5 24.025 27.0 28.199999999999996 20.775 6 20.599999999999998 33.975 26.8 18.625 7 30.65 28.349999999999998 24.425 16.575 8 26.400000000000002 26.650000000000002 28.449999999999996 18.5 9 22.900000000000002 28.4 28.725 19.975 10-11 24.9875 26.950000000000003 28.825 19.2375 12-13 22.6875 28.299999999999997 29.65 19.3625 14-15 20.2625 29.262500000000003 30.0875 20.3875 16-17 24.0625 28.537499999999998 25.4625 21.9375 18-19 23.175 25.374999999999996 30.375000000000004 21.075 20-21 26.125 23.8375 29.362500000000004 20.674999999999997 22-23 26.950000000000003 23.9375 28.3625 20.75 24-25 23.625 26.337500000000002 28.5625 21.475 26-27 24.65 24.65 29.675 21.025 28-29 23.4125 27.8875 29.5 19.2 30-31 25.6 26.875 27.55 19.975 32-33 24.9375 25.137500000000003 29.4 20.525 34-35 22.575 29.975 27.3625 20.0875 36-37 23.7125 27.375 26.5 22.412499999999998 38-39 27.025 24.5375 28.787499999999998 19.650000000000002 40-41 23.724999999999998 25.2 29.375 21.7 42-43 24.4875 28.749999999999996 27.9125 18.85 44-45 22.2 26.9625 30.625000000000004 20.2125 46-47 24.1625 26.5 27.437499999999996 21.9 48-49 23.1625 25.85 29.45 21.5375 50-51 22.3625 28.3625 28.325 20.95 52-53 22.575 27.625 28.0875 21.712500000000002 54-55 22.9875 28.012500000000003 29.525000000000002 19.475 56-57 24.375 27.1 28.0875 20.4375 58-59 23.05 28.725 28.5875 19.6375 60-61 25.7375 27.237499999999997 28.6625 18.3625 62-63 22.3125 28.299999999999997 28.975 20.4125 64-65 21.5625 31.637500000000003 28.462500000000002 18.337500000000002 66-67 24.4375 28.8625 27.2625 19.4375 68-69 21.475 28.449999999999996 28.275 21.8 70-71 23.211147376349487 28.383128295254835 28.094401205121766 20.311323123273915 72-73 24.136172383016703 26.571465000637513 30.052275914828506 19.240086701517274 74-75 24.687056394373467 27.280939476061427 28.63595302619693 19.396051103368176 76-77 22.04497907949791 27.340481171548113 28.97489539748954 21.639644351464433 78-79 23.737574552683895 26.90523525513585 29.489728296885353 19.8674618952949 80-81 22.084400701092086 31.144667655386275 27.140353242550898 19.630578400970744 82-83 22.627537026878773 27.413603949533737 27.852441031267144 22.106417992320353 84-85 21.74399105645612 27.110117384013417 30.547792062604806 20.598099496925656 86-87 21.197638459375877 29.631712116952485 26.736013494517852 22.43463592915378 88-89 21.324149564239526 29.758223221816138 27.944897385437166 20.97272982850717 90-91 23.390497610345797 30.601630587573798 25.962890075906664 20.04498172617374 92-93 19.482710149001967 32.11976384593759 28.043294911442228 20.354231093618218 >>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 0.0 14 0.0 15 0.0 16 0.0 17 2.0 18 4.0 19 3.5 20 2.5 21 2.0 22 3.0 23 4.0 24 6.0 25 8.0 26 12.0 27 15.5 28 25.5 29 38.0 30 36.0 31 49.5 32 73.0 33 76.5 34 75.0 35 98.5 36 149.0 37 195.5 38 215.5 39 217.0 40 236.0 41 234.0 42 231.0 43 248.0 44 222.5 45 200.5 46 171.5 47 130.5 48 123.0 49 128.5 50 134.5 51 129.0 52 121.5 53 120.0 54 132.0 55 124.0 56 89.5 57 76.0 58 61.5 59 39.5 60 24.0 61 19.5 62 17.5 63 13.5 64 9.5 65 9.5 66 11.5 67 10.0 68 12.5 69 14.5 70 14.0 71 13.0 72 12.5 73 7.0 74 1.5 75 1.0 76 1.0 77 0.5 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 34.0 71 32.0 72 25.0 73 24.0 74 21.0 75 29.0 76 22.0 77 28.0 78 25.0 79 35.0 80 33.0 81 30.0 82 32.0 83 31.0 84 42.0 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 3557.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 80.85 #Duplication Level Percentage of deduplicated Percentage of total 1 93.29004329004329 75.425 2 3.5559678416821274 5.75 3 0.8967223252937538 2.175 4 0.6802721088435374 2.1999999999999997 5 0.3710575139146568 1.5 6 0.27829313543599254 1.35 7 0.1855287569573284 1.05 8 0.06184291898577613 0.4 9 0.0927643784786642 0.675 >10 0.5565862708719851 7.625 >50 0.030921459492888066 1.8499999999999999 >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 74 1.8499999999999999 No Hit GGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCTTGG 32 0.8 No Hit GGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAA 26 0.65 No Hit CAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAATACTTGGGCTG 24 0.6 No Hit CAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAATACTTGGGCTGATAT 22 0.5499999999999999 No Hit CAAGGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCT 21 0.525 No Hit GGGCACGTGGAATCCCGTGTGAATCAGCAAGGACCACCTTGCAAGGCTAA 20 0.5 No Hit GGGTTGTTTGGGAATGCAGCCCAAATCGGGCGGTAGACTCCGTCCAAGGC 20 0.5 No Hit GGGCTGATATCATCAACCGTGCTAATCTTGGTATGGAAGTAATGCACGAA 19 0.475 No Hit GGCGTTCAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTC 17 0.42500000000000004 No Hit CAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAGGTC 15 0.375 No Hit GGAGGGTGAGAGCCCCGTCCGGCCCGGACCCTGTCGCCCCACGAGGCGCC 13 0.325 No Hit GGGCGCGATCTTGCTCGTGAAGGTAATGAAATTATCCGAGCAGCTTGCAA 13 0.325 No Hit GGAATCCCGTGTGAATCAGCAAGGACCACCTTGCAAGGCTAAATACTCCT 12 0.3 No Hit GGAGTTGAAAATAAGCATAGATCCGGAGATTCCCAAATAGGTCAACCTTT 11 0.27499999999999997 No Hit GGGAATGCAGCCCAAATCGGGCGGTAGACTCCGTCCAAGGCTAAATACAG 10 0.25 No Hit GGTAATGAAATTATCCGAGCAGCTTGCAAATGGAGTCCTGAACTAGCCGC 10 0.25 No Hit GGGGAGAGCAATACAAGCGTTGTGCTGCTAGGCGAAGCGGTTGAGTGCCG 10 0.25 No Hit GGGTGAGAGCCCCGTCCGGCCCGGACCCTGTCGCCCCACGAGGCGCCGTC 10 0.25 No Hit GGAGTCCTGAACTAGCCGCAGCTTGTGAAGTATGGAAGGCGATCAAATTC 9 0.22499999999999998 No Hit GTAGGAATCTGGTTCACTGCTTTAGGTATTAGTACTATGGCGTTCAACCT 9 0.22499999999999998 No Hit GAAGGTAATGAAATTATCCGAGCAGCTTGCAAATGGAGTCCTGAACTAGC 9 0.22499999999999998 No Hit GTATTAGTACTATGGCGTTCAACCTAAATGGATTCAATTTCAACCAATCT 8 0.2 No Hit GGGGCACGTGGAATCCCGTGTGAATCAGCAAGGACCACCTTGCAAGGCTA 8 0.2 No Hit GCAGCTTGCAAATGGAGTCCTGAACTAGCCGCAGCTTGTGAAGTATGGAA 7 0.17500000000000002 No Hit TACCTAGGCACCCAGAGACGAGGAAGGGCGTAGCAAGCGACGAAATGCTT 7 0.17500000000000002 No Hit AACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAATACTTGGGCTGA 7 0.17500000000000002 No Hit GGGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGT 7 0.17500000000000002 No Hit GGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGTG 7 0.17500000000000002 No Hit GTACTATGGCGTTCAACCTAAATGGATTCAATTTCAACCAATCTGTAGTT 7 0.17500000000000002 No Hit GCAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAATACTTGGGCT 6 0.15 No Hit GGCGCGATCTTGCTCGTGAAGGTAATGAAATTATCCGAGCAGCTTGCAAA 6 0.15 No Hit GGAATCTGGTTCACTGCTTTAGGTATTAGTACTATGGCGTTCAACCTAAA 6 0.15 No Hit GGAGTATCCTTGATATATAAATATATAGATAAATAGATTTAAATGGAAAA 6 0.15 No Hit GAATCCCGTGTGAATCAGCAAGGACCACCTTGCAAGGCTAAATACTCCTG 6 0.15 No Hit GTAGCATGGGGCACGTGGAATCCCGTGTGAATCAGCAAGGACCACCTTGC 6 0.15 No Hit GCAAGGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATC 6 0.15 No Hit GGGGCAGAGGGAATTTCCGGTGGAGCGGTGAAATGCATTGAGATCGGAAA 6 0.15 No Hit GGGAATTTCCGGTGGAGCGGTGAAATGCATTGAGATCGGAAAGAACACCA 6 0.15 No Hit GGAACTTTAGGACATCCTTGGGGAAATGCACCTGGTGCAGCAGCTAATCG 5 0.125 No Hit GTCCTGAACTAGCCGCAGCTTGTGAAGTATGGAAGGCGATCAAATTCGAG 5 0.125 No Hit GTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCTTGGTATGGA 5 0.125 No Hit GTTGTTTGGGAATGCAGCCCAAATCGGGCGGTAGACTCCGTCCAAGGCTA 5 0.125 No Hit GGTGAGAGCCCCGTCCGGCCCGGACCCTGTCGCCCCACGAGGCGCCGTCA 5 0.125 No Hit GGGGAGTTGAAAATAAGCATAGATCCGGAGATTCCCAAATAGGTCAACCT 5 0.125 No Hit GTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCTTGGT 5 0.125 No Hit GGAAGGCGATCAAATTCGAGTTCGCGCCGGTAGATACTATCGATTAATAG 5 0.125 No Hit GGGAGGGTGAGAGCCCCGTCCGGCCCGGACCCTGTCGCCCCACGAGGCGC 5 0.125 No Hit GTAATGCACGAACGTAATGCTCACAACTTCCCTCTAGATCTAGCTGCTCT 5 0.125 No Hit GTTCAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAG 5 0.125 No Hit GGAAAAGAAAGCAAAAGCGATTCCCGTAGTAGCGGCGAGCGAAATGGGAG 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 0.025 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 0.05 0.0 0.0 0.0 0.0 38-39 0.05 0.0 0.0 0.0 0.0 40-41 0.0625 0.0 0.0 0.0 0.0 42-43 0.075 0.0 0.0 0.0 0.0 44-45 0.075 0.0 0.0 0.0 0.0 46-47 0.075 0.0 0.0 0.0 0.0 48-49 0.075 0.0 0.0 0.0 0.0 50-51 0.075 0.0 0.0 0.0 0.0 52-53 0.075 0.0 0.0 0.0 0.0 54-55 0.075 0.0 0.0 0.0 0.0 56-57 0.1 0.0 0.0 0.0 0.0 58-59 0.1 0.0 0.0 0.0 0.0 60-61 0.1 0.0 0.0 0.0 0.0 62-63 0.1 0.0 0.0 0.0 0.0 64-65 0.1 0.0 0.0 0.0 0.0 66-67 0.1 0.0 0.0 0.0 0.0 68-69 0.1 0.0 0.0 0.0 0.0 70-71 0.1 0.0 0.0 0.0 0.0 72-73 0.1 0.0 0.0 0.0 0.0 74-75 0.1 0.0 0.0 0.0 0.0 76-77 0.1 0.0 0.0 0.0 0.0 78-79 0.125 0.0 0.0 0.0 0.0 80-81 0.15 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position AAAAAAA 30 0.0037541362 31.569445 86-87 >>END_MODULE Rejected 56321 READS because READLEN < 1 Read 56321 spots for ERR6133405.sra Written 56321 spots for ERR6133405.sra Rejected 56321 READS because READLEN < 1 Read 56321 spots for ERR6133405.sra Written 56321 spots for ERR6133405.sra Rejected 56321 READS because READLEN < 1 Read 56321 spots for ERR6133405.sra Written 56321 spots for ERR6133405.sra Rejected 56321 READS because READLEN < 1 Read 56321 spots for ERR6133405.sra Written 56321 spots for ERR6133405.sra Rejected 56321 READS because READLEN < 1 Read 56321 spots for ERR6133405.sra Written 56321 spots for ERR6133405.sra Rejected 56321 READS because READLEN < 1 Read 56321 spots for ERR6133405.sra Written 56321 spots for ERR6133405.sra Rejected 56321 READS because READLEN < 1 Read 56321 spots for ERR6133405.sra Written 56321 spots for ERR6133405.sra Rejected 56321 READS because READLEN < 1 Read 56321 spots for ERR6133405.sra Written 56321 spots for ERR6133405.sra Rejected 56321 READS because READLEN < 1 Read 56321 spots for ERR6133405.sra Written 56321 spots for ERR6133405.sra Rejected 56321 READS because READLEN < 1 Read 56321 spots for ERR6133405.sra Written 56321 spots for ERR6133405.sra Rejected 56321 READS because READLEN < 1 Read 56321 spots for ERR6133405.sra Written 56321 spots for ERR6133405.sra Rejected 56321 READS because READLEN < 1 Read 56321 spots for ERR6133405.sra Written 56321 spots for ERR6133405.sra Rejected 56321 READS because READLEN < 1 Read 56321 spots for ERR6133405.sra Written 56321 spots for ERR6133405.sra Rejected 56321 READS because READLEN < 1 Read 56321 spots for ERR6133405.sra Written 56321 spots for ERR6133405.sra Rejected 56335 READS because READLEN < 1 Read 56335 spots for ERR6133405.sra Written 56335 spots for ERR6133405.sra Rejected 56321 READS because READLEN < 1 Read 56321 spots for ERR6133405.sra Written 56321 spots for ERR6133405.sra Rejected 56321 READS because READLEN < 1 Read 56321 spots for ERR6133405.sra Written 56321 spots for ERR6133405.sra Rejected 56321 READS because READLEN < 1 Read 56321 spots for ERR6133405.sra Written 56321 spots for ERR6133405.sra Rejected 56321 READS because READLEN < 1 Read 56321 spots for ERR6133405.sra Written 56321 spots for ERR6133405.sra Rejected 56321 READS because READLEN < 1 Read 56321 spots for ERR6133405.sra Written 56321 spots for ERR6133405.sra SRR ids: ['ERR6133405.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_ryxze2dl ERR6133405.sra spots: 1126434 blocks: [[1, 56321], [56322, 112642], [112643, 168963], [168964, 225284], [225285, 281605], [281606, 337926], [337927, 394247], [394248, 450568], [450569, 506889], [506890, 563210], [563211, 619531], [619532, 675852], [675853, 732173], [732174, 788494], [788495, 844815], [844816, 901136], [901137, 957457], [957458, 1013778], [1013779, 1070099], [1070100, 1126434]] ERR6133405 file size 244892 ERR6133405 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 ERR6133405 ERR6133405_1.fastq Input file: ERR6133405_1.fastq trimmed: ERR6133405-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 03:19:41 2024 >> started Sat Dec 7 03:19:43 2024 >> done (1.864s) 1126434 reads processed; of these: 47 ( 0.00%) short reads filtered out after trimming by size control 6 ( 0.00%) empty reads filtered out after trimming by size control 1126381 (100.00%) reads available; of these: 283158 (25.14%) trimmed reads available after processing 843223 (74.86%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 7 0.00% 19 36 0.00% 20 8 0.00% 21 2 0.00% 22 6 0.00% 23 4 0.00% 24 2 0.00% 25 6 0.00% 26 5 0.00% 27 1 0.00% 28 13 0.00% 29 18 0.00% 30 1 0.00% 31 8 0.00% 32 14 0.00% 33 6 0.00% 34 7 0.00% 35 7 0.00% 36 8 0.00% 37 12 0.00% 38 17 0.00% 39 43 0.00% 40 55 0.00% 41 12 0.00% 42 8 0.00% 43 29 0.00% 44 34 0.00% 45 42 0.00% 46 53 0.00% 47 80 0.01% 48 99 0.01% 49 122 0.01% 50 165 0.01% 51 230 0.02% 52 292 0.03% 53 344 0.03% 54 462 0.04% 55 678 0.06% 56 878 0.08% 57 1347 0.12% 58 893 0.08% 59 1113 0.10% 60 1319 0.12% 61 1479 0.13% 62 1562 0.14% 63 1695 0.15% 64 1914 0.17% 65 1943 0.17% 66 1974 0.18% 67 2045 0.18% 68 2026 0.18% 69 2143 0.19% 70 9558 0.85% 71 10042 0.89% 72 11095 0.99% 73 11632 1.03% 74 11816 1.05% 75 12680 1.13% 76 12609 1.12% 77 13858 1.23% 78 14171 1.26% 79 15395 1.37% 80 16080 1.43% 81 18375 1.63% 82 19319 1.72% 83 20083 1.78% 84 22160 1.97% 85 14180 1.26% 86 15045 1.34% 87 16377 1.45% 88 18682 1.66% 89 20577 1.83% 90 21729 1.93% 91 23124 2.05% 92 19637 1.74% 93 732890 65.07% 1126381 reads passed initial QC criterion=sequence-density sequence-density=4.85 sequence-density-rank=1 fanout-score=2.09 fanout-score-rank=21 prefix-density=4.99 prefix-fanout=2.0 sequence=CAAGGCTAAATAC criterion=fanout-score sequence-density=0.05 sequence-density-rank=17 fanout-score=14.00 fanout-score-rank=1 prefix-density=0.24 prefix-fanout=3.2 sequence=TTTTTTCTATTTATTTTTCCATCTAGGATTAGAACTGTATATTTGTGAATAATAGTAACAGGACATTATGGCAAAAAAAAGTTTGATTCAGAGGGAAAAGAAGCGGCAGAAATTAGAACAAAAATATCATTTGATTCGCCAATCTT 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 03:20:16 Started mapping on | Dec 07 03:20:16 Finished on | Dec 07 03:20:28 Mapping speed, Million of reads per hour | 337.91 Number of input reads | 1126381 Average input read length | 88 UNIQUE READS: Uniquely mapped reads number | 556068 Uniquely mapped reads % | 49.37% Average mapped length | 88.05 Number of splices: Total | 17718 Number of splices: Annotated (sjdb) | 14013 Number of splices: GT/AG | 16598 Number of splices: GC/AG | 355 Number of splices: AT/AC | 16 Number of splices: Non-canonical | 749 Mismatch rate per base, % | 0.83% Deletion rate per base | 0.04% Deletion average length | 1.65 Insertion rate per base | 0.02% Insertion average length | 1.57 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 409027 % of reads mapped to multiple loci | 36.31% Number of reads mapped to too many loci | 73996 % of reads mapped to too many loci | 6.57% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 6.59% % of reads unmapped: other | 1.16% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 161286 161286 161286 N_multimapping 409027 409027 409027 N_noFeature 48848 54456 530941 N_ambiguous 23416 3899 118 UnstrandedReadsAssigned:483804 PositiveStrandReadsAssigned:497713 NegativeStrandReadsAssigned:25009 Dataset is classified positive stranded MeadianReadLen=93 20thPercentileLength=84 echo kmer=79 ERR6133405 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: ERR6133405-trimmed.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 1,126,381 reads, 735,796 reads pseudoaligned [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 896 rounds 52973 ERR6133405.ke.tsv 35125 ERR6133405.se.tsv 88098 total ==> ERR6133405.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 6 7.92711 PNS24243 293 194 0 0 KQK14069 1603 1504 4 4.82092 KQK14071 474 375 0 0 ==> ERR6133405.se.tsv <== BRADI_1g14170v3 5 BRADI_1g53295v3 7 BRADI_1g59795v3 3 BRADI_1g07683v3 0 BRADI_1g00485v3 0 BRADI_1g20270v3 12 BRADI_1g74790v3 2 BRADI_1g09890v3 0 BRADI_1g77505v3 12 BRADI_1g48960v3 0 ERR6133405 completed mapping pipeline successfully