Starting /dee2/code/volunteer_pipeline.sh ERR6133540 current disk space = 1544476733440 free memory = 1597276116 ERR6133540 SRAfilesize 9ce62c989999b198e38397e69018a7f0 ERR6133540.sra ERR6133540.sra file validated ERR6133540 is single end ERR6133540 is conventional basespace ERR6133540 read1 length is 70-93 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename ERR6133540_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 pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 33.81275 33.0 33.0 37.0 27.0 37.0 2 35.9825 37.0 37.0 37.0 33.0 37.0 3 35.174 37.0 33.0 37.0 33.0 37.0 4 35.28525 37.0 37.0 37.0 33.0 37.0 5 35.327 37.0 37.0 37.0 33.0 37.0 6 35.67125 37.0 37.0 37.0 33.0 37.0 7 37.41975 37.0 37.0 40.0 33.0 40.0 8 37.4755 37.0 37.0 40.0 33.0 40.0 9 37.4925 37.0 37.0 40.0 33.0 40.0 10-11 37.513875 37.0 37.0 40.0 33.0 40.0 12-13 37.530625 37.0 37.0 40.0 33.0 40.0 14-15 37.50175 37.0 37.0 40.0 33.0 40.0 16-17 37.3955 37.0 37.0 40.0 33.0 40.0 18-19 37.307874999999996 37.0 37.0 40.0 33.0 40.0 20-21 37.187375 37.0 37.0 40.0 33.0 40.0 22-23 37.134 37.0 37.0 40.0 33.0 40.0 24-25 37.251000000000005 37.0 37.0 40.0 33.0 40.0 26-27 37.289500000000004 37.0 37.0 40.0 33.0 40.0 28-29 37.253125 37.0 37.0 40.0 33.0 40.0 30-31 37.20025 37.0 37.0 40.0 33.0 40.0 32-33 37.086749999999995 37.0 37.0 40.0 33.0 40.0 34-35 36.943 37.0 37.0 40.0 33.0 40.0 36-37 36.81275 37.0 37.0 40.0 33.0 40.0 38-39 36.675375 37.0 37.0 40.0 33.0 40.0 40-41 36.379125 37.0 37.0 40.0 33.0 40.0 42-43 36.40712499999999 37.0 37.0 40.0 33.0 40.0 44-45 36.085875 37.0 37.0 40.0 33.0 40.0 46-47 35.768125 37.0 35.0 37.0 33.0 40.0 48-49 35.67375 37.0 35.0 37.0 33.0 40.0 50-51 35.627375 37.0 33.0 37.0 33.0 40.0 52-53 35.379374999999996 37.0 33.0 37.0 33.0 40.0 54-55 35.301 37.0 33.0 37.0 33.0 40.0 56-57 35.19775 37.0 33.0 37.0 33.0 37.0 58-59 34.51575 37.0 33.0 37.0 27.0 37.0 60-61 34.7475 37.0 33.0 37.0 33.0 37.0 62-63 34.706125 37.0 33.0 37.0 30.0 37.0 64-65 34.659875 37.0 33.0 37.0 33.0 37.0 66-67 34.682125 37.0 33.0 37.0 33.0 37.0 68-69 33.8905 35.0 33.0 37.0 30.0 37.0 70-71 34.01119212904845 35.0 33.0 37.0 27.0 37.0 72-73 34.38089869081902 37.0 33.0 37.0 30.0 37.0 74-75 34.3355547775077 37.0 33.0 37.0 30.0 37.0 76-77 34.22299101029316 37.0 33.0 37.0 27.0 37.0 78-79 34.293220659050135 37.0 33.0 37.0 27.0 37.0 80-81 34.229015564826696 37.0 33.0 37.0 27.0 37.0 82-83 34.1229100111466 37.0 33.0 37.0 27.0 37.0 84-85 33.97563145931632 37.0 33.0 37.0 27.0 37.0 86-87 34.10773840541949 37.0 33.0 37.0 27.0 37.0 88-89 34.05575820739969 37.0 33.0 37.0 27.0 37.0 90-91 33.79794163626889 37.0 33.0 37.0 27.0 37.0 92-93 33.68616466909849 37.0 33.0 37.0 27.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 20 7.0 21 12.0 22 12.0 23 17.0 24 9.0 25 30.0 26 44.0 27 45.0 28 51.0 29 62.0 30 89.0 31 103.0 32 117.0 33 168.0 34 223.0 35 413.0 36 900.0 37 1004.0 38 682.0 39 12.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 89.075 2.85 2.5749999999999997 5.5 2 73.925 16.150000000000002 6.5 3.4250000000000003 3 35.475 39.85 14.75 9.925 4 31.65 28.799999999999997 19.675 19.875 5 25.275 31.125000000000004 25.724999999999998 17.875 6 21.725 35.725 24.575 17.974999999999998 7 38.550000000000004 28.15 18.65 14.649999999999999 8 31.15 31.775 23.375 13.700000000000001 9 26.85 28.15 28.075 16.925 10-11 25.525 28.712500000000002 28.0875 17.675 12-13 28.225 26.3625 28.95 16.4625 14-15 20.275000000000002 29.75 32.0125 17.962500000000002 16-17 22.237499999999997 33.3125 25.4 19.05 18-19 23.0 27.6375 29.775000000000002 19.5875 20-21 25.55 26.775 29.212500000000002 18.462500000000002 22-23 26.5 24.15 27.650000000000002 21.7 24-25 24.95 26.387500000000003 28.599999999999998 20.0625 26-27 24.2375 25.05 32.6 18.1125 28-29 24.975 27.3125 28.962500000000002 18.75 30-31 24.9 26.200000000000003 29.45 19.45 32-33 24.3 26.075 29.037499999999998 20.5875 34-35 23.617713284963724 26.845133850387793 27.833375031273455 21.70377783337503 36-37 24.4375 25.887500000000003 27.725 21.95 38-39 25.6125 25.25 30.4375 18.7 40-41 26.7575681761321 24.956217162872154 26.157117838378785 22.12909682261696 42-43 23.307894407606653 28.024521456274236 29.776054047291378 18.891530088827725 44-45 22.17913435076307 26.70753064798599 30.910683012259195 20.202651988991743 46-47 23.7125 24.4125 29.5 22.375 48-49 23.252906613326665 26.253281660207527 32.15401925240655 18.33979247405926 50-51 23.6375 26.650000000000002 30.5 19.2125 52-53 23.567675756817614 28.04603452589442 29.09682261696272 19.289467100325243 54-55 24.725 27.450000000000003 29.562500000000004 18.2625 56-57 25.7 25.7375 29.4875 19.075 58-59 23.599999999999998 25.7 30.125 20.575 60-61 24.099999999999998 26.1125 30.4375 19.35 62-63 21.3125 29.462500000000002 32.225 17.0 64-65 22.95 27.8375 30.4375 18.775 66-67 22.9375 28.1875 29.2375 19.6375 68-69 20.925 27.212500000000002 29.349999999999998 22.5125 70-71 23.449830890642616 25.792308655893777 29.19954904171364 21.55831141174997 72-73 24.987392839132628 25.731215330307617 30.358043368633385 18.923348461926373 74-75 23.778171689035197 25.81666244618891 31.324385920486197 19.080779944289695 76-77 22.957692796340996 26.7437428535129 29.386354973955026 20.912209376191083 78-79 22.70814739257937 23.77916613540737 32.576820094351646 20.935866377661608 80-81 22.233619694832672 29.619181946403383 29.272983715861006 18.87421464290294 82-83 21.95972114639814 27.13658662535502 30.699715982442548 20.203976245804288 84-85 23.150916417522424 24.151826335629796 32.796048355648 19.901208891199794 86-87 21.18290776446066 26.055237102657635 32.72537780093799 20.03647733194372 88-89 20.310057321521626 28.72589890568004 32.15216258467952 18.81188118811881 90-91 24.43981240229286 25.41688379364252 31.474726420010423 18.668577384054196 92-93 21.70401250651381 28.465346534653463 30.51068264721209 19.319958311620635 >>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 4.5 18 5.5 19 2.0 20 1.5 21 3.5 22 3.0 23 3.5 24 6.0 25 5.0 26 8.0 27 12.5 28 17.5 29 21.0 30 26.5 31 38.0 32 66.5 33 109.5 34 113.0 35 104.0 36 128.5 37 154.0 38 189.0 39 190.0 40 197.0 41 214.5 42 240.0 43 281.5 44 243.0 45 211.5 46 210.5 47 186.5 48 175.5 49 177.5 50 155.5 51 138.0 52 124.5 53 117.0 54 100.0 55 60.0 56 50.0 57 56.0 58 42.0 59 24.5 60 24.0 61 24.0 62 20.0 63 17.0 64 16.0 65 15.5 66 15.5 67 12.5 68 8.5 69 9.0 70 8.5 71 7.0 72 4.5 73 2.5 74 2.0 75 1.0 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 0.0 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 0.075 36-37 0.0 38-39 0.0 40-41 0.075 42-43 0.08750000000000001 44-45 0.075 46-47 0.0 48-49 0.0125 50-51 0.0 52-53 0.075 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 17.0 71 14.0 72 6.0 73 10.0 74 8.0 75 8.0 76 3.0 77 7.0 78 11.0 79 12.0 80 9.0 81 15.0 82 14.0 83 11.0 84 17.0 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 3838.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 75.7 #Duplication Level Percentage of deduplicated Percentage of total 1 90.78599735799207 68.72500000000001 2 4.821664464993395 7.3 3 1.486129458388375 3.375 4 0.8916776750330251 2.7 5 0.5284015852047557 2.0 6 0.19815059445178335 0.8999999999999999 7 0.26420079260237783 1.4000000000000001 8 0.2311756935270806 1.4000000000000001 9 0.13210039630118892 0.8999999999999999 >10 0.59445178335535 8.575000000000001 >50 0.06605019815059446 2.725 >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 GGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCTTGG 58 1.4500000000000002 No Hit GGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAA 51 1.275 No Hit GGGCGCGATCTTGCTCGTGAAGGTAATGAAATTATCCGAGCAGCTTGCAA 33 0.8250000000000001 No Hit GGGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGT 29 0.7250000000000001 No Hit GGGATGATTCTGTATTACAATTTGGTGGAGGAACTTTAGGACATCCTTGG 25 0.625 No Hit GGAGTTGAAAATAAGCATAGATCCGGAGATTCCCAAATAGGTCAACCTTT 24 0.6 No Hit TACCTAGGCACCCAGAGACGAGGAAGGGCGTAGCAAGCGACGAAATGCTT 24 0.6 No Hit GGAAAAGAGGGGTTACTTTTTTTCATTTTTCCCTTAAAAGATAGGCTTTG 22 0.5499999999999999 No Hit GGTAATGAAATTATCCGAGCAGCTTGCAAATGGAGTCCTGAACTAGCCGC 21 0.525 No Hit GGTTTTGAAAAGGGAATCGATCGTGATTTAGAACCTGTTCTTTACATGAA 20 0.5 No Hit GGGCTGATATCATCAACCGTGCTAATCTTGGTATGGAAGTAATGCACGAA 18 0.44999999999999996 No Hit GGGAGAGCAATACAAGCGTTGTGCTGCTAGGCGAAGCGGTTGAGTGCCGC 18 0.44999999999999996 No Hit GGGAAAAGAGGGGTTACTTTTTTTCATTTTTCCCTTAAAAGATAGGCTTT 16 0.4 No Hit GGCGTTCAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTC 15 0.375 No Hit GGATGATTCTGTATTACAATTTGGTGGAGGAACTTTAGGACATCCTTGGG 15 0.375 No Hit GGGAATCGATCGTGATTTAGAACCTGTTCTTTACATGAACCCTCTTAACT 15 0.375 No Hit GGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGTGTACAAGCTCGTAA 14 0.35000000000000003 No Hit GGACATCCTTGGGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTT 13 0.325 No Hit GAAGGTAATGAAATTATCCGAGCAGCTTGCAAATGGAGTCCTGAACTAGC 11 0.27499999999999997 No Hit GGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGTG 10 0.25 No Hit GGCGCGATCTTGCTCGTGAAGGTAATGAAATTATCCGAGCAGCTTGCAAA 9 0.22499999999999998 No Hit CAAGGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCT 9 0.22499999999999998 No Hit GGGGATGATTCTGTATTACAATTTGGTGGAGGAACTTTAGGACATCCTTG 9 0.22499999999999998 No Hit GGAGTATCCTTGATATATAAATATATAGATAAATAGATTTAAATGGAAAA 9 0.22499999999999998 No Hit GGGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCTTG 8 0.2 No Hit GGAAACAACGAGGTCATCATCGACATGATATATTGCTGCTATTTTCCACC 8 0.2 No Hit GGAATCGATCGTGATTTAGAACCTGTTCTTTACATGAACCCTCTTAACTA 8 0.2 No Hit GGGGATGGAGCGACAGAAGTATGGAAATAGGATAAGGTAGCGGCGAGACG 8 0.2 No Hit GGAGTCCCATATATATATGTATAAGATGCCAGCCCGGTTTCGTCAACCAT 8 0.2 No Hit GGGCCGGGTATCTCTCTGCATGTACGTATGCCTGTAATGTACGTAGCTAC 8 0.2 No Hit GGAAGAGCCCGAGCTGCTGCAGCAGGTTTTGAAAAGGGAATCGATCGTGA 8 0.2 No Hit GGAGTCCTGAACTAGCCGCAGCTTGTGAAGTATGGAAGGCGATCAAATTC 7 0.17500000000000002 No Hit CAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAATACTTGGGCTGATAT 7 0.17500000000000002 No Hit GGGTTGTTTGGGAATGCAGCCCAAATCGGGCGGTAGACTCCGTCCAAGGC 7 0.17500000000000002 No Hit GGGAGGGGCTTGGCTACAATTCCGAATACGCTATTACATGTTTGCGCTAG 7 0.17500000000000002 No Hit GGATATCGTGTGTGTACATTTGAATGTACCGACATGGGCTCGAGGAGCAT 7 0.17500000000000002 No Hit GGAAATGGTGAAGATGATACGAATATGCCGGCCGGGTGCTGATATTGTGA 7 0.17500000000000002 No Hit GGGACGCATGCAACGACCATCTACATATAGCTACTCGATCTACCGCTACC 7 0.17500000000000002 No Hit GGACAGCTCCGTATTAAGATGGACCATATATAAAGTGTCAGCTCAGTTTT 7 0.17500000000000002 No Hit GGGGATGGATGTTTGTGTATATATACGTGTCGACTTCTCTTCATTAGAGA 6 0.15 No Hit GGCTTTAGAAGCCTGTGTACAAGCTCGTAACGAAGGGCGCGATCTTGCTC 6 0.15 No Hit GTAGCAAGCGACGAAATGCTTCGGGGAGTTGAAAATAAGCATAGATCCGG 6 0.15 No Hit GGGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTA 6 0.15 No Hit GGGAGGAAGACGAAGAGTAGGTGGAGAGCAGAGCGCTGGTCTCCTTTGGT 6 0.15 No Hit GGGCCATTTGTGGCATGCAGGAAGAGCCCGAGCTGCTGCAGCAGGTTTTG 6 0.15 No Hit GGAACAAACGAGGATAAGATAAAATTTCTTTAAATTTATTTTGCCCAAGT 5 0.125 No Hit GGGAGTGGGGGTGCCATACGCAAAAAGGAAGCGACTCATAGAATGGCAGA 5 0.125 No Hit GGAAGGGCGTAGCAAGCGACGAAATGCTTCGGGGAGTTGAAAATAAGCAT 5 0.125 No Hit GGAGAAGGGTCACATATATGCTGCAGGATTCGGTTGAGCACGTTGTAGTA 5 0.125 No Hit GGAGATTCCCAAATAGGTCAACCTTTTAAACTGCCTGCTGAATCCATGAG 5 0.125 No Hit GCAGCTTGCAAATGGAGTCCTGAACTAGCCGCAGCTTGTGAAGTATGGAA 5 0.125 No Hit GGGAAATTAACAGTTGGAAAGGGCGATCGGTCTTGATCCCTCTGTGTTTC 5 0.125 No Hit GATACCTAGGCACCCAGAGACGAGGAAGGGCGTAGCAAGCGACGAAATGC 5 0.125 No Hit GGGATGATGATGATCGATCGATGGACTACTTGTAATTTTAAAGTTTCAAC 5 0.125 No Hit GGAGTACGGTAGGGGCAGAGGGAATTTCCGGTGGAGCGGTGAAATGCATT 5 0.125 No Hit GTACAAGCTCGTAACGAAGGGCGCGATCTTGCTCGTGAAGGTAATGAAAT 5 0.125 No Hit GGATGATTGGGAGAAGGGTCACATATATGCTGCAGGATTCGGTTGAGCAC 5 0.125 No Hit GGGAAACAACGAGGTCATCATCGACATGATATATTGCTGCTATTTTCCAC 5 0.125 No Hit CAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAGGTC 5 0.125 No Hit GGGTTACTTTTTTTCATTTTTCCCTTAAAAGATAGGCTTTGAAATCGGAG 5 0.125 No Hit GGAGGAACTTTAGGACATCCTTGGGGAAATGCACCTGGTGCAGCAGCTAA 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 0.025 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 0.05 0.0 0.0 0.0 0.0 54-55 0.05 0.0 0.0 0.0 0.0 56-57 0.05 0.0 0.0 0.0 0.0 58-59 0.05 0.0 0.0 0.0 0.0 60-61 0.05 0.0 0.0 0.0 0.0 62-63 0.05 0.0 0.0 0.0 0.0 64-65 0.05 0.0 0.0 0.0 0.0 66-67 0.05 0.0 0.0 0.0 0.0 68-69 0.05 0.0 0.0 0.0 0.0 70-71 0.05 0.0 0.0 0.0 0.0 72-73 0.05 0.0 0.0 0.0 0.0 74-75 0.05 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 170589 READS because READLEN < 1 Read 170589 spots for ERR6133540.sra Written 170589 spots for ERR6133540.sra Rejected 170589 READS because READLEN < 1 Read 170589 spots for ERR6133540.sra Written 170589 spots for ERR6133540.sra Rejected 170589 READS because READLEN < 1 Read 170589 spots for ERR6133540.sra Written 170589 spots for ERR6133540.sra Rejected 170589 READS because READLEN < 1 Read 170589 spots for ERR6133540.sra Written 170589 spots for ERR6133540.sra Rejected 170589 READS because READLEN < 1 Read 170589 spots for ERR6133540.sra Written 170589 spots for ERR6133540.sra Rejected 170589 READS because READLEN < 1 Read 170589 spots for ERR6133540.sra Written 170589 spots for ERR6133540.sra Rejected 170589 READS because READLEN < 1 Read 170589 spots for ERR6133540.sra Written 170589 spots for ERR6133540.sra Rejected 170589 READS because READLEN < 1 Read 170589 spots for ERR6133540.sra Written 170589 spots for ERR6133540.sra Rejected 170589 READS because READLEN < 1 Read 170589 spots for ERR6133540.sra Written 170589 spots for ERR6133540.sra Rejected 170589 READS because READLEN < 1 Read 170589 spots for ERR6133540.sra Written 170589 spots for ERR6133540.sra Rejected 170589 READS because READLEN < 1 Read 170589 spots for ERR6133540.sra Written 170589 spots for ERR6133540.sra Rejected 170589 READS because READLEN < 1 Read 170589 spots for ERR6133540.sra Written 170589 spots for ERR6133540.sra Rejected 170589 READS because READLEN < 1 Read 170589 spots for ERR6133540.sra Written 170589 spots for ERR6133540.sra Rejected 170589 READS because READLEN < 1 Read 170589 spots for ERR6133540.sra Written 170589 spots for ERR6133540.sra Rejected 170589 READS because READLEN < 1 Read 170589 spots for ERR6133540.sra Written 170589 spots for ERR6133540.sra Rejected 170589 READS because READLEN < 1 Read 170589 spots for ERR6133540.sra Written 170589 spots for ERR6133540.sra Rejected 170589 READS because READLEN < 1 Read 170589 spots for ERR6133540.sra Written 170589 spots for ERR6133540.sra Rejected 170589 READS because READLEN < 1 Read 170589 spots for ERR6133540.sra Written 170589 spots for ERR6133540.sra Rejected 170608 READS because READLEN < 1 Read 170608 spots for ERR6133540.sra Written 170608 spots for ERR6133540.sra Rejected 170589 READS because READLEN < 1 Read 170589 spots for ERR6133540.sra Written 170589 spots for ERR6133540.sra SRR ids: ['ERR6133540.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_r4wr9wgy ERR6133540.sra spots: 3411799 blocks: [[1, 170589], [170590, 341178], [341179, 511767], [511768, 682356], [682357, 852945], [852946, 1023534], [1023535, 1194123], [1194124, 1364712], [1364713, 1535301], [1535302, 1705890], [1705891, 1876479], [1876480, 2047068], [2047069, 2217657], [2217658, 2388246], [2388247, 2558835], [2558836, 2729424], [2729425, 2900013], [2900014, 3070602], [3070603, 3241191], [3241192, 3411799]] ERR6133540 file size 752687 ERR6133540 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 ERR6133540 ERR6133540_1.fastq Input file: ERR6133540_1.fastq trimmed: ERR6133540-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 08:14:01 2024 >> started Sat Dec 7 08:14:03 2024 >> done (2.045s) 3411799 reads processed; of these: 50 ( 0.00%) short reads filtered out after trimming by size control 6 ( 0.00%) empty reads filtered out after trimming by size control 3411743 (100.00%) reads available; of these: 50648 ( 1.48%) trimmed reads available after processing 3361095 (98.52%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 12 0.00% 19 33 0.00% 20 10 0.00% 21 7 0.00% 22 10 0.00% 23 5 0.00% 24 6 0.00% 25 4 0.00% 26 1 0.00% 27 2 0.00% 28 9 0.00% 29 12 0.00% 30 5 0.00% 31 4 0.00% 32 9 0.00% 33 7 0.00% 34 6 0.00% 35 43 0.00% 36 344 0.01% 37 9 0.00% 38 16 0.00% 39 46 0.00% 40 76 0.00% 41 15 0.00% 42 4 0.00% 43 7 0.00% 44 11 0.00% 45 5 0.00% 46 6 0.00% 47 6 0.00% 48 2 0.00% 49 9 0.00% 50 6 0.00% 51 49 0.00% 52 11 0.00% 53 6 0.00% 54 2 0.00% 55 6 0.00% 56 4 0.00% 57 4 0.00% 58 3 0.00% 59 8 0.00% 60 9 0.00% 61 7 0.00% 62 2 0.00% 63 3 0.00% 64 4 0.00% 65 10 0.00% 66 11 0.00% 67 15 0.00% 68 37 0.00% 69 110 0.00% 70 11851 0.35% 71 9316 0.27% 72 9729 0.29% 73 9037 0.26% 74 9871 0.29% 75 9479 0.28% 76 8635 0.25% 77 8728 0.26% 78 9908 0.29% 79 11616 0.34% 80 9872 0.29% 81 11462 0.34% 82 13140 0.39% 83 13262 0.39% 84 10640 0.31% 85 111 0.00% 86 216 0.01% 87 320 0.01% 88 613 0.02% 89 1229 0.04% 90 2793 0.08% 91 8168 0.24% 92 34535 1.01% 93 3206164 93.97% 3411743 reads passed initial QC criterion=sequence-density sequence-density=0.58 sequence-density-rank=1 fanout-score=3.08 fanout-score-rank=27 prefix-density=0.64 prefix-fanout=2.8 sequence=GTGTTGTGTTGT criterion=fanout-score sequence-density=0.01 sequence-density-rank=34 fanout-score=62.59 fanout-score-rank=1 prefix-density=0.09 prefix-fanout=6.0 sequence=AAGGAAGAGCACTTGCCATTCGTTGGTTATTAGAAGCATCCCAAAAGCGTCCGGGTCGAAATATGGCTTTCAAATTAAGTTCCGAATTAGTAGATGCTGCCAAAGGGAGTGGGGGTGCCATACGCAAAAAGGAAGCGACTCATAGAATGGCAGAGGCAAATAGAGCTCTTGCACATTTTCGTTAATCCATGAACAGAATCTAGGTATGTAGACACATGGATCCATACATCTCGATCGGAAAAGAATCAATAGAAGGAGAATCGGACGATATCTTTCTCGAAACAAACA Started job on | Dec 07 08:14:17 Started mapping on | Dec 07 08:14:17 Finished on | Dec 07 08:14:23 Mapping speed, Million of reads per hour | 2047.05 Number of input reads | 3411743 Average input read length | 92 UNIQUE READS: Uniquely mapped reads number | 2384797 Uniquely mapped reads % | 69.90% Average mapped length | 91.75 Number of splices: Total | 59090 Number of splices: Annotated (sjdb) | 47070 Number of splices: GT/AG | 55625 Number of splices: GC/AG | 1611 Number of splices: AT/AC | 42 Number of splices: Non-canonical | 1812 Mismatch rate per base, % | 0.49% Deletion rate per base | 0.05% Deletion average length | 1.89 Insertion rate per base | 0.02% Insertion average length | 1.84 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 944292 % of reads mapped to multiple loci | 27.68% Number of reads mapped to too many loci | 30303 % of reads mapped to too many loci | 0.89% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 1.48% % of reads unmapped: other | 0.05% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 82654 82654 82654 N_multimapping 944292 944292 944292 N_noFeature 182967 211871 2270356 N_ambiguous 95711 10471 327 UnstrandedReadsAssigned:2106119 PositiveStrandReadsAssigned:2162455 NegativeStrandReadsAssigned:114114 Dataset is classified positive stranded MeadianReadLen=93 20thPercentileLength=93 echo kmer=89 ERR6133540 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: ERR6133540-trimmed.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 3,411,743 reads, 2,778,489 reads pseudoaligned [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,110 rounds 52973 ERR6133540.ke.tsv 35125 ERR6133540.se.tsv 88098 total ==> ERR6133540.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 83 30.4176 PNS24243 293 194 0 0 KQK14069 1603 1504 341 114.001 KQK14071 474 375 0 0 ==> ERR6133540.se.tsv <== BRADI_1g14170v3 341 BRADI_1g53295v3 12 BRADI_1g59795v3 20 BRADI_1g07683v3 0 BRADI_1g00485v3 0 BRADI_1g20270v3 34 BRADI_1g74790v3 43 BRADI_1g09890v3 0 BRADI_1g77505v3 47 BRADI_1g48960v3 0 ERR6133540 completed mapping pipeline successfully