Starting /dee2/code/volunteer_pipeline.sh SRR11389836 current disk space = 1544408612864 free memory = 1604096980 SRR11389836 SRAfilesize 3cff93f5f61ab80ddff83dde6f4c9068 SRR11389836.sra SRR11389836.sra file validated SRR11389836 is paired end SRR11389836 is conventional basespace SRR11389836 read1 length is 35-76 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR11389836_1.fastq File type Conventional base calls Encoding Sanger / Illumina 1.9 Total Sequences 4000 Sequences flagged as poor quality 0 Sequence length 35-76 %GC 47 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 31.04575 32.0 32.0 32.0 32.0 32.0 2 30.9725 32.0 32.0 32.0 32.0 32.0 3 31.02425 32.0 32.0 32.0 32.0 32.0 4 31.166 32.0 32.0 32.0 32.0 32.0 5 31.04725 32.0 32.0 32.0 32.0 32.0 6 34.01125 36.0 36.0 36.0 32.0 36.0 7 33.989 36.0 36.0 36.0 32.0 36.0 8 33.92125 36.0 36.0 36.0 32.0 36.0 9 34.11225 36.0 36.0 36.0 32.0 36.0 10-11 33.949124999999995 36.0 36.0 36.0 32.0 36.0 12-13 34.05875 36.0 36.0 36.0 32.0 36.0 14-15 34.07275 36.0 36.0 36.0 32.0 36.0 16-17 34.110875 36.0 36.0 36.0 32.0 36.0 18-19 33.96925 36.0 36.0 36.0 32.0 36.0 20-21 33.915375 36.0 36.0 36.0 32.0 36.0 22-23 33.713625 36.0 36.0 36.0 29.5 36.0 24-25 33.884 36.0 36.0 36.0 32.0 36.0 26-27 33.605500000000006 36.0 36.0 36.0 26.5 36.0 28-29 33.508125 36.0 36.0 36.0 27.0 36.0 30-31 33.346625 36.0 36.0 36.0 21.0 36.0 32-33 33.347750000000005 36.0 36.0 36.0 21.0 36.0 34-35 33.323499999999996 36.0 36.0 36.0 21.0 36.0 36-37 33.16725043782837 36.0 36.0 36.0 14.0 36.0 38-39 33.26564064064064 36.0 36.0 36.0 21.0 36.0 40-41 33.26589089089089 36.0 36.0 36.0 21.0 36.0 42-43 33.142767767767765 36.0 36.0 36.0 17.5 36.0 44-45 32.87083939383689 36.0 36.0 36.0 14.0 36.0 46-47 32.979349186483105 36.0 36.0 36.0 14.0 36.0 48-49 32.76758448060075 36.0 36.0 36.0 14.0 36.0 50-51 32.7153942428035 36.0 34.0 36.0 14.0 36.0 52-53 32.655170396466225 36.0 34.0 36.0 14.0 36.0 54-55 32.28934725016734 36.0 32.0 36.0 14.0 36.0 56-57 32.3481696849432 36.0 32.0 36.0 14.0 36.0 58-59 32.09784244856999 36.0 32.0 36.0 14.0 36.0 60-61 32.13725094165905 36.0 32.0 36.0 14.0 36.0 62-63 32.00216088420367 36.0 32.0 36.0 14.0 36.0 64-65 32.111600402617015 36.0 32.0 36.0 14.0 36.0 66-67 31.980433908183116 36.0 32.0 36.0 14.0 36.0 68-69 31.935831566400047 36.0 32.0 36.0 14.0 36.0 70-71 31.883983929336907 36.0 32.0 36.0 14.0 36.0 72-73 31.581614409797744 36.0 32.0 36.0 14.0 36.0 74-75 31.684644565129986 36.0 32.0 36.0 14.0 36.0 76 30.294799850355407 36.0 27.0 36.0 14.0 36.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 2 3.0 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 0.0 18 0.0 19 0.0 20 1.0 21 2.0 22 8.0 23 14.0 24 34.0 25 48.0 26 68.0 27 116.0 28 128.0 29 176.0 30 245.0 31 316.0 32 430.0 33 560.0 34 853.0 35 998.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 32.89967475606705 10.382787090317738 14.961220915686765 41.75631723792845 2 23.842882161621215 13.535151363522644 31.64873655241431 30.97322992244183 3 23.167375531648737 18.01351013259945 25.41906429822367 33.400050037528146 4 27.795846885163872 24.74355766825119 21.4160620465349 26.044533400050035 5 26.745058794095574 28.49637227920941 23.01726294721041 21.74130597948461 6 20.540405303977984 34.22566925193895 26.294721040780583 18.939204403302476 7 16.03702777082812 25.719289467100324 38.704028021015766 19.53965474105579 8 19.11433575181386 24.64348261195897 32.849637227920944 23.39254440830623 9 18.914185639229423 22.61696272204153 35.47660745559169 22.992244183137352 10-11 21.878909181886414 30.823117338003502 25.39404553415061 21.90392794595947 12-13 22.454340755566676 25.30647985989492 28.19614711033275 24.043032274205654 14-15 22.12909682261696 26.407305479109333 28.04603452589442 23.417563172379285 16-17 22.041531148361273 26.732549412059043 26.857643232424316 24.36827620715537 18-19 21.928946710032523 26.21966474856142 27.45809357017763 24.39329497122842 20-21 21.99149362021516 27.132849637227917 27.445584188141105 23.430072554415812 22-23 22.15411558669002 26.832624468351263 27.24543407555667 23.767825869402053 24-25 21.491118338754063 26.619964973730298 26.845133850387793 25.04378283712785 26-27 21.37853390042532 26.157117838378785 27.683262446835126 24.78108581436077 28-29 22.37928446334751 26.09457092819615 26.870152614460846 24.655991993995496 30-31 22.34175631723793 27.145359019264447 26.257192894671004 24.25569176882662 32-33 21.290968226169625 26.444833625218916 27.795846885163872 24.468351263447584 34-35 21.353515136352264 26.82011508631474 27.695771828871653 24.130597948461347 36-37 22.629472104078058 26.670002501876404 25.894420815611706 24.806104578433825 38-39 22.097097097097095 26.764264264264266 27.677677677677675 23.46096096096096 40-41 21.75925925925926 26.413913913913913 27.515015015015017 24.31181181181181 42-43 22.51001001001001 25.0 27.765265265265267 24.724724724724727 44-45 21.962207483418847 26.091853335001876 27.130521837066702 24.81541734451258 46-47 22.65331664580726 26.082603254067582 26.670838548185234 24.593241551939926 48-49 22.090112640801003 26.18272841051314 27.496871088861074 24.23028785982478 50-51 22.35294117647059 24.668335419274094 28.010012515644554 24.96871088861076 52-53 22.561662701890572 25.165894578690374 26.230123951421056 26.042318767997997 54-55 21.94235588972431 26.829573934837093 26.516290726817044 24.711779448621556 56-57 21.5853505581337 25.611438605292864 27.379907186755297 25.423303649818134 58-59 22.980431510286 25.439036628198696 27.65930757651781 23.921224284997493 60-61 21.965608133550898 25.517760763147983 27.739425128655704 24.777205974645412 62-63 22.03219315895372 25.75452716297787 27.96780684104628 24.245472837022135 64-65 22.684952189229996 25.150981378963262 28.195772521389028 23.968293910417714 66-67 22.093462652727045 25.015745056052403 27.660914472855524 25.229877818365033 68-69 22.485804416403784 24.99684542586751 26.876971608832807 25.6403785488959 70-71 22.656052565074553 25.17058377558757 27.129138236037402 25.04422542330048 72-73 22.467912059982208 25.949930105477186 27.06824247045368 24.513915364086923 74-75 23.258306538049304 22.869774919614148 27.934083601286176 25.937834941050376 76 25.439580995136552 0.0 38.57089412644969 35.98952487841377 >>END_MODULE >>Per sequence GC content fail #GC Content Count 0 52.0 1 32.0 2 9.0 3 4.5 4 3.0 5 3.5 6 3.5 7 2.0 8 1.0 9 1.0 10 1.0 11 0.5 12 0.0 13 1.0 14 1.5 15 2.0 16 4.0 17 5.5 18 10.0 19 19.5 20 29.5 21 35.0 22 29.5 23 19.5 24 13.5 25 9.5 26 14.0 27 17.5 28 16.5 29 23.5 30 32.0 31 40.0 32 41.5 33 39.5 34 52.5 35 78.0 36 103.5 37 118.5 38 131.0 39 152.0 40 164.5 41 172.5 42 203.0 43 230.5 44 234.0 45 221.0 46 222.5 47 224.0 48 202.0 49 180.5 50 167.0 51 159.5 52 150.5 53 133.5 54 118.5 55 109.5 56 108.5 57 110.0 58 104.0 59 98.5 60 95.0 61 97.0 62 100.5 63 88.0 64 66.5 65 56.5 66 52.0 67 48.5 68 41.0 69 38.5 70 35.5 71 31.5 72 29.5 73 22.5 74 17.0 75 14.0 76 14.5 77 13.0 78 8.0 79 5.0 80 5.5 81 5.0 82 2.5 83 1.5 84 0.5 85 0.5 86 0.5 87 0.0 88 0.5 89 0.5 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 0.5 99 0.5 100 0.0 >>END_MODULE >>Per base N content pass #Base N-Count 1 0.075 2 0.075 3 0.075 4 0.075 5 0.075 6 0.075 7 0.075 8 0.075 9 0.075 10-11 0.075 12-13 0.075 14-15 0.075 16-17 0.075 18-19 0.075 20-21 0.075 22-23 0.075 24-25 0.075 26-27 0.075 28-29 0.075 30-31 0.075 32-33 0.075 34-35 0.075 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 0.0 >>END_MODULE >>Sequence Length Distribution warn #Length Count 35 3.0 36 0.0 37 1.0 38 0.0 39 0.0 40 0.0 41 0.0 42 0.0 43 0.0 44 1.0 45 0.0 46 0.0 47 0.0 48 0.0 49 0.0 50 0.0 51 1.0 52 1.0 53 1.0 54 4.0 55 1.0 56 1.0 57 0.0 58 0.0 59 1.0 60 3.0 61 5.0 62 2.0 63 1.0 64 0.0 65 3.0 66 3.0 67 4.0 68 3.0 69 3.0 70 2.0 71 9.0 72 25.0 73 79.0 74 222.0 75 948.0 76 2673.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 93.35 #Duplication Level Percentage of deduplicated Percentage of total 1 96.51847884306373 90.10000000000001 2 2.169255490091055 4.05 3 0.7766470273165506 2.175 4 0.18746652383502946 0.7000000000000001 5 0.21424745581146223 1.0 6 0.05356186395286556 0.3 7 0.02678093197643278 0.17500000000000002 8 0.0 0.0 9 0.0 0.0 >10 0.05356186395286556 1.5 >50 0.0 0.0 >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 warn #Sequence Count Percentage Possible Source TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 40 1.0 No Hit GTCAATTAGAAGAATAAAGAAGAATTACTGCATTTCGTAACTTATTTTTT 20 0.5 No Hit GATCGGAAGAGCACACGTCTGAACTCCAGTCACCTGAAGCTATCTCGTAT 7 0.17500000000000002 TruSeq Adapter, Index 19 (97% over 38bp) CCGGGTTGTTGGGAGAGATCACATGCATAAATACAACATGAAACAAACGT 6 0.15 No Hit GCATTTCGTAACTTATTTTTTCTCTTTTTATTTTGTTTCTTTTTATTTAGACCTTCTTCATATTTAGTTTTATCT 6 0.15 No Hit CGTAACTTATTTTTTCTCTTTTTATTTTGTTTCTTTTTATTTAGACCTTC 5 0.125 No Hit GCCCTTCGTTACGAGCTTGTACACAGGCTTCTAAAGCCACTCGATTAGCT 5 0.125 No Hit GCAGTCAATTAGAAGAATAAAGAAGAATTACTGCATTTCGTAACTTATTT 5 0.125 No Hit CAAAGATTTCGGTCAGAGCTGGCATATGCCAAACATGAATACCACCTGAAGCTACTGGTATAACACCTGGCATGG 5 0.125 No Hit TCGTTACGAGCTTGTACACAGGCTTCTAAAGCCACTCGATTAGCTGCTGC 5 0.125 No Hit CTCCATTTGCAAGCTGCTCGGATAATTTCATTACCTTCACGAGCAAGATC 5 0.125 No Hit CTTCGTTACGAGCTTGTACACAGGCTTCTAAAGCCACTCGATTAGCTGCT 5 0.125 No Hit CTGCATTTCGTAACTTATTTTTTCTCTTTTTATTTTGTTTCTTTTTATTT 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 0.0 0.0 0.0 0.0 0.0 11 0.0 0.0 0.0 0.0 0.0 12 0.0 0.0 0.0 0.0 0.0 13 0.0 0.0 0.0 0.0 0.0 14 0.0 0.0 0.0 0.0 0.0 15 0.0 0.0 0.0 0.0 0.0 16 0.0 0.0 0.0 0.0 0.0 17 0.0 0.0 0.0 0.0 0.0 18 0.0 0.0 0.0 0.0 0.0 19 0.0 0.0 0.0 0.0 0.0 20 0.0 0.0 0.0 0.0 0.0 21 0.0 0.0 0.0 0.0 0.0 22 0.0 0.0 0.0 0.0 0.0 23 0.0 0.0 0.0 0.0 0.0 24 0.0 0.0 0.0 0.0 0.0 25 0.0 0.0 0.0 0.0 0.0 26 0.0 0.0 0.0 0.0 0.0 27 0.0 0.0 0.0 0.0 0.0 28 0.0 0.0 0.0 0.0 0.0 29 0.0 0.0 0.0 0.0 0.0 30 0.0 0.0 0.0 0.0 0.0 31 0.0 0.0 0.0 0.0 0.0 32 0.0 0.0 0.0 0.0 0.0 33 0.0 0.0 0.0 0.0 0.0 34 0.0 0.0 0.0 0.0 0.0 35 0.0 0.0 0.0 0.0 0.0 36 0.0 0.0 0.0 0.0 0.0 37 0.0 0.0 0.0 0.0 0.0 38 0.0 0.0 0.0 0.0 0.0 39 0.0 0.0 0.0 0.0 0.0 40 0.0 0.0 0.0 0.0 0.0 41 0.0 0.0 0.0 0.0 0.0 42 0.0 0.0 0.0 0.0 0.0 43 0.0 0.0 0.0 0.0 0.0 44 0.0 0.0 0.0 0.0 0.0 45 0.0 0.0 0.0 0.0 0.0 46 0.0 0.0 0.0 0.0 0.0 47 0.0 0.0 0.0 0.0 0.0 48 0.0 0.0 0.0 0.0 0.0 49 0.0 0.0 0.0 0.0 0.0 50 0.0 0.0 0.0 0.0 0.0 51 0.0 0.0 0.0 0.0 0.0 52 0.0 0.0 0.0 0.0 0.0 53 0.0 0.0 0.0 0.0 0.0 54 0.0 0.0 0.0 0.0 0.0 55 0.0 0.0 0.0 0.0 0.0 56 0.0 0.0 0.0 0.0 0.0 57 0.0 0.0 0.0 0.0 0.0 58 0.0 0.0 0.0 0.0 0.0 59 0.0 0.0 0.0 0.0 0.0 60 0.0 0.0 0.0 0.0 0.0 61 0.0 0.0 0.0 0.0 0.0 62 0.0 0.0 0.0 0.0 0.0 63 0.0 0.0 0.0 0.0 0.0 64 0.0 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content pass >>END_MODULE SRR11389836 read2 length is 35-76 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR11389836_2.fastq File type Conventional base calls Encoding Sanger / Illumina 1.9 Total Sequences 4000 Sequences flagged as poor quality 0 Sequence length 35-76 %GC 49 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 29.94875 32.0 32.0 32.0 21.0 32.0 2 29.7405 32.0 32.0 32.0 14.0 32.0 3 29.53075 32.0 32.0 32.0 14.0 32.0 4 29.61475 32.0 32.0 32.0 14.0 32.0 5 29.63425 32.0 32.0 32.0 14.0 32.0 6 32.534 36.0 32.0 36.0 14.0 36.0 7 32.475 36.0 32.0 36.0 14.0 36.0 8 32.217 36.0 32.0 36.0 14.0 36.0 9 32.374 36.0 36.0 36.0 14.0 36.0 10-11 32.118 36.0 32.0 36.0 14.0 36.0 12-13 32.443875 36.0 32.0 36.0 14.0 36.0 14-15 32.297625 36.0 32.0 36.0 14.0 36.0 16-17 32.43075 36.0 32.0 36.0 14.0 36.0 18-19 32.167 36.0 32.0 36.0 14.0 36.0 20-21 32.008125 36.0 32.0 36.0 14.0 36.0 22-23 31.971625000000003 36.0 32.0 36.0 14.0 36.0 24-25 31.888875 36.0 32.0 36.0 14.0 36.0 26-27 31.896625 36.0 32.0 36.0 14.0 36.0 28-29 31.902875 36.0 32.0 36.0 14.0 36.0 30-31 31.865625 36.0 32.0 36.0 14.0 36.0 32-33 31.79225 36.0 32.0 36.0 14.0 36.0 34-35 31.60575 36.0 32.0 36.0 14.0 36.0 36-37 31.450350175087543 36.0 32.0 36.0 14.0 36.0 38-39 31.503377533149862 36.0 32.0 36.0 14.0 36.0 40-41 31.579559669752314 36.0 32.0 36.0 14.0 36.0 42-43 31.221791343507633 36.0 32.0 36.0 14.0 36.0 44-45 31.338421452475743 36.0 32.0 36.0 14.0 36.0 46-47 31.229354354354356 36.0 32.0 36.0 14.0 36.0 48-49 31.09622122122122 36.0 32.0 36.0 14.0 36.0 50-51 30.976976976976978 36.0 32.0 36.0 14.0 36.0 52-53 30.839674593241554 36.0 32.0 36.0 14.0 36.0 54-55 30.8088586513856 36.0 32.0 36.0 14.0 36.0 56-57 30.62805205538903 36.0 27.0 36.0 14.0 36.0 58-59 30.607572718154465 36.0 27.0 36.0 14.0 36.0 60-61 30.59048194282019 36.0 27.0 36.0 14.0 36.0 62-63 30.539725841373787 36.0 27.0 36.0 14.0 36.0 64-65 30.730450088006037 36.0 29.5 36.0 14.0 36.0 66-67 30.500405810774314 36.0 27.0 36.0 14.0 36.0 68-69 30.4570485262243 36.0 27.0 36.0 14.0 36.0 70-71 30.265788681547924 36.0 27.0 36.0 14.0 36.0 72-73 30.21833760164632 36.0 27.0 36.0 14.0 36.0 74-75 29.990137035965 36.0 27.0 36.0 14.0 36.0 76 29.04321223709369 32.0 21.0 36.0 14.0 36.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 2 2.0 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 9.0 15 18.0 16 23.0 17 14.0 18 17.0 19 17.0 20 19.0 21 21.0 22 28.0 23 36.0 24 60.0 25 85.0 26 144.0 27 164.0 28 192.0 29 249.0 30 356.0 31 405.0 32 502.0 33 619.0 34 680.0 35 340.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 32.79139569784893 16.633316658329164 15.08254127063532 35.4927463731866 2 31.315657828914457 24.462231115557778 25.237618809404704 18.98449224612306 3 27.188594297148573 29.189594797398698 20.535267633816908 23.08654327163582 4 30.240120060030012 32.61630815407704 17.283641820910457 19.85992996498249 5 29.48974487243622 33.39169584792396 18.98449224612306 18.13406703351676 6 24.087043521760883 35.41770885442722 21.11055527763882 19.384692346173086 7 22.71135567783892 19.259629814907452 34.492246123061534 23.536768384192097 8 25.012506253126567 22.936468234117058 26.638319159579787 25.41270635317659 9 23.411705852926463 23.111555777888945 28.83941970985493 24.637318659329665 10-11 27.226113056528263 28.4392196098049 20.96048024012006 23.374187093546773 12-13 26.425712856428213 22.786393196598297 25.325162581290645 25.46273136568284 14-15 25.86293146573287 25.80040020010005 25.175087543771884 23.1615807903952 16-17 28.414207103551774 23.649324662331164 23.774387193596798 24.16208104052026 18-19 26.163081540770385 24.537268634317158 25.53776888444222 23.761880940470235 20-21 26.40070035017509 25.437718859429715 25.437718859429715 22.723861930965484 22-23 26.850925462731368 25.63781890945473 24.662331165582792 22.848924462231114 24-25 25.87543771885943 27.201100550275136 24.12456228114057 22.798899449724864 26-27 26.050525262631314 26.28814407203602 25.287643821910955 22.373686843421712 28-29 27.163581790895446 25.887943971985994 23.59929964982491 23.349174587293646 30-31 26.388194097048522 25.3751875937969 24.949974987493746 23.28664332166083 32-33 25.82541270635318 26.263131565782892 25.0 22.911455727863935 34-35 26.900950475237618 25.52526263131566 24.287143571785894 23.28664332166083 36-37 26.500750375187593 25.65032516258129 23.84942471235618 23.999499749874936 38-39 25.806855141356017 25.55666750062547 25.04378283712785 23.592694520890667 40-41 26.695021265949464 25.03127345509132 24.0180135101326 24.25569176882662 42-43 26.494871153365025 26.307230422817113 24.218163622717036 22.979734801100825 44-45 24.834229951207305 26.448142124358814 25.760040035030652 22.95758788940323 46-47 25.900900900900904 26.476476476476474 23.76126126126126 23.86136136136136 48-49 26.2012012012012 26.45145145145145 24.024024024024023 23.323323323323322 50-51 26.33883883883884 25.563063063063062 24.44944944944945 23.64864864864865 52-53 26.33291614518148 26.307884856070086 24.831038798498124 22.528160200250312 54-55 27.55511022044088 26.553106212424847 24.010521042084168 21.8812625250501 56-57 25.485771593330824 26.601479252851952 24.533032468346498 23.37971668547073 58-59 26.216148445336007 25.58926780341023 24.77432296890672 23.42026078234704 60-61 26.408229833145153 26.39568435578974 24.313135114791116 22.882950696273994 62-63 26.275446091982914 26.84091480271425 24.579039959788894 22.304599145513947 64-65 26.98013578073925 25.86120191098818 23.673623334171488 23.48503897410108 66-67 25.726872246696036 26.117054751415985 24.25424795468848 23.901825047199495 68-69 26.200983482536884 26.314462236792334 24.29706216113983 23.187492119530955 70-71 27.082016934158982 25.312776443826614 24.56716795147226 23.038038670542146 72-73 24.532621136970622 25.740811395141804 25.48645555131629 24.240111916571284 74-75 26.59732540861813 24.571119816290693 25.20599756855329 23.625557206537888 76 28.068833652007648 0.0 36.09942638623327 35.831739961759084 >>END_MODULE >>Per sequence GC content fail #GC Content Count 0 37.0 1 18.5 2 1.0 3 2.0 4 2.0 5 2.0 6 2.0 7 2.0 8 2.0 9 1.5 10 1.0 11 1.0 12 1.0 13 1.5 14 2.5 15 3.5 16 3.5 17 4.0 18 6.0 19 10.5 20 11.5 21 8.0 22 8.5 23 9.5 24 12.5 25 14.5 26 17.0 27 20.0 28 19.5 29 18.0 30 20.0 31 31.0 32 37.5 33 37.5 34 49.5 35 67.5 36 84.0 37 101.5 38 117.0 39 135.5 40 161.5 41 180.5 42 186.5 43 194.5 44 195.0 45 185.5 46 189.0 47 192.5 48 180.5 49 181.0 50 187.0 51 161.5 52 132.5 53 129.5 54 128.5 55 111.0 56 110.0 57 114.0 58 112.5 59 124.5 60 126.5 61 113.0 62 96.5 63 90.0 64 82.0 65 73.0 66 67.5 67 68.0 68 72.5 69 65.5 70 48.0 71 36.5 72 42.5 73 43.0 74 28.5 75 20.0 76 19.5 77 16.0 78 12.0 79 11.5 80 9.0 81 6.0 82 4.5 83 4.0 84 4.5 85 5.0 86 4.0 87 3.0 88 3.0 89 2.0 90 1.5 91 2.0 92 2.0 93 2.0 94 2.5 95 2.0 96 1.0 97 2.0 98 2.5 99 3.5 100 5.0 >>END_MODULE >>Per base N content pass #Base N-Count 1 0.05 2 0.05 3 0.05 4 0.05 5 0.05 6 0.05 7 0.05 8 0.05 9 0.05 10-11 0.05 12-13 0.05 14-15 0.05 16-17 0.05 18-19 0.05 20-21 0.05 22-23 0.05 24-25 0.05 26-27 0.05 28-29 0.05 30-31 0.05 32-33 0.05 34-35 0.05 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 0.0 >>END_MODULE >>Sequence Length Distribution warn #Length Count 35 2.0 36 0.0 37 1.0 38 0.0 39 0.0 40 0.0 41 0.0 42 0.0 43 0.0 44 1.0 45 0.0 46 0.0 47 0.0 48 0.0 49 0.0 50 0.0 51 1.0 52 0.0 53 1.0 54 4.0 55 1.0 56 1.0 57 0.0 58 0.0 59 1.0 60 3.0 61 4.0 62 2.0 63 1.0 64 0.0 65 3.0 66 3.0 67 4.0 68 3.0 69 3.0 70 9.0 71 8.0 72 25.0 73 76.0 74 283.0 75 945.0 76 2615.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 95.575 #Duplication Level Percentage of deduplicated Percentage of total 1 97.41041067224693 93.10000000000001 2 1.831022756997123 3.5000000000000004 3 0.47083442322783153 1.35 4 0.0523149359142035 0.2 5 0.07847240387130526 0.375 6 0.0523149359142035 0.3 7 0.0 0.0 8 0.0 0.0 9 0.0 0.0 >10 0.104629871828407 1.175 >50 0.0 0.0 >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 warn #Sequence Count Percentage Possible Source GGAACTTTAGGACATCCTTGGGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGTGTACA 13 0.325 No Hit AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 13 0.325 No Hit TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 11 0.27499999999999997 No Hit CGCGAAATCACTTTAGGTTTTGTTGATTTATTGCGCGACGATTTTATTGA 10 0.25 No Hit CTGTATTACAATTTGGTGGAGGAACTTTAGGACATCCTTGGGGAAATGCA 6 0.15 No Hit CTTTAGGACATCCTTGGGGAAATGCACCTGGTGCAGCAGCTAATCGAGTG 6 0.15 No Hit TGCAAATGGAGTCCTGAACTAGCCGCAGCTTGTGAAGTATGGAAGGCGATCAAATTCGAGTTCGCGCCGGTAGAT 5 0.125 No Hit AAATTATCCGAGCAGCTTGCAAATGGAGTCCTGAACTAGCCGCAGCTTGTGAAGTATGGAAGGCGATCAAATTCG 5 0.125 No Hit GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG 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 0.0 0.0 0.0 0.0 0.0 11 0.0 0.0 0.0 0.0 0.0 12 0.0 0.0 0.0 0.0 0.0 13 0.0 0.0 0.0 0.0 0.0 14 0.0 0.0 0.0 0.0 0.0 15 0.0 0.0 0.0 0.0 0.0 16 0.0 0.0 0.0 0.0 0.0 17 0.0 0.0 0.0 0.0 0.0 18 0.0 0.0 0.0 0.0 0.0 19 0.0 0.0 0.0 0.0 0.0 20 0.0 0.0 0.0 0.0 0.0 21 0.0 0.0 0.0 0.0 0.0 22 0.0 0.0 0.0 0.0 0.0 23 0.0 0.0 0.0 0.0 0.0 24 0.0 0.0 0.0 0.0 0.0 25 0.0 0.0 0.0 0.0 0.0 26 0.025 0.0 0.0 0.0 0.0 27 0.025 0.0 0.0 0.0 0.0 28 0.025 0.0 0.0 0.0 0.0 29 0.025 0.0 0.0 0.0 0.0 30 0.025 0.0 0.0 0.0 0.0 31 0.025 0.0 0.0 0.0 0.0 32 0.025 0.0 0.0 0.0 0.0 33 0.025 0.0 0.0 0.0 0.0 34 0.025 0.0 0.0 0.0 0.0 35 0.025 0.0 0.0 0.0 0.0 36 0.025 0.0 0.0 0.0 0.0 37 0.025 0.0 0.0 0.0 0.0 38 0.025 0.0 0.0 0.0 0.0 39 0.025 0.0 0.0 0.0 0.0 40 0.025 0.0 0.0 0.0 0.0 41 0.025 0.0 0.0 0.0 0.0 42 0.025 0.0 0.0 0.0 0.0 43 0.025 0.0 0.0 0.0 0.0 44 0.025 0.0 0.0 0.0 0.0 45 0.025 0.0 0.0 0.0 0.0 46 0.025 0.0 0.0 0.0 0.0 47 0.025 0.0 0.0 0.0 0.0 48 0.025 0.0 0.0 0.0 0.0 49 0.025 0.0 0.0 0.0 0.0 50 0.025 0.0 0.0 0.0 0.0 51 0.025 0.0 0.0 0.0 0.0 52 0.025 0.0 0.0 0.0 0.0 53 0.025 0.0 0.0 0.0 0.0 54 0.025 0.0 0.0 0.0 0.0 55 0.025 0.0 0.0 0.0 0.0 56 0.025 0.0 0.0 0.0 0.0 57 0.025 0.0 0.0 0.0 0.0 58 0.025 0.0 0.0 0.0 0.0 59 0.025 0.0 0.0 0.0 0.0 60 0.025 0.0 0.0 0.0 0.0 61 0.025 0.0 0.0 0.0 0.0 62 0.025 0.0 0.0 0.0 0.0 63 0.025 0.0 0.0 0.0 0.0 64 0.025 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content pass >>END_MODULE Read 574998 spots for SRR11389836.sra Written 574998 spots for SRR11389836.sra Read 574998 spots for SRR11389836.sra Written 574998 spots for SRR11389836.sra Read 574998 spots for SRR11389836.sra Written 574998 spots for SRR11389836.sra Read 574998 spots for SRR11389836.sra Written 574998 spots for SRR11389836.sra Read 574998 spots for SRR11389836.sra Written 574998 spots for SRR11389836.sra Read 574998 spots for SRR11389836.sra Written 574998 spots for SRR11389836.sra Read 574998 spots for SRR11389836.sra Written 574998 spots for SRR11389836.sra Read 574998 spots for SRR11389836.sra Written 574998 spots for SRR11389836.sra Read 574998 spots for SRR11389836.sra Written 574998 spots for SRR11389836.sra Read 574998 spots for SRR11389836.sra Written 574998 spots for SRR11389836.sra Read 574998 spots for SRR11389836.sra Written 574998 spots for SRR11389836.sra Read 574998 spots for SRR11389836.sra Written 574998 spots for SRR11389836.sra Read 575017 spots for SRR11389836.sra Written 575017 spots for SRR11389836.sra Read 574998 spots for SRR11389836.sra Written 574998 spots for SRR11389836.sra Read 574998 spots for SRR11389836.sra Written 574998 spots for SRR11389836.sra Read 574998 spots for SRR11389836.sra Written 574998 spots for SRR11389836.sra Read 574998 spots for SRR11389836.sra Written 574998 spots for SRR11389836.sra Read 574998 spots for SRR11389836.sra Written 574998 spots for SRR11389836.sra Read 574998 spots for SRR11389836.sra Written 574998 spots for SRR11389836.sra Read 574998 spots for SRR11389836.sra Written 574998 spots for SRR11389836.sra SRR ids: ['SRR11389836.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_f11sl277 SRR11389836.sra spots: 11499979 blocks: [[1, 574998], [574999, 1149996], [1149997, 1724994], [1724995, 2299992], [2299993, 2874990], [2874991, 3449988], [3449989, 4024986], [4024987, 4599984], [4599985, 5174982], [5174983, 5749980], [5749981, 6324978], [6324979, 6899976], [6899977, 7474974], [7474975, 8049972], [8049973, 8624970], [8624971, 9199968], [9199969, 9774966], [9774967, 10349964], [10349965, 10924962], [10924963, 11499979]] SRR11389836 file size 2170016 SRR11389836 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 SRR11389836 SRR11389836_1.fastq SRR11389836_2.fastq Input file: SRR11389836_1.fastq Paired file: SRR11389836_2.fastq trimmed: SRR11389836-trimmed-pair1.fastq, SRR11389836-trimmed-pair2.fastq Parameters used: -- 3' end adapter sequence (-x): AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC -- paired 3' end adapter sequence (-y): AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTA -- 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 -- number of concurrent threads (-t): 20 Sat Dec 7 07:47:26 2024 >> started Sat Dec 7 07:47:36 2024 >> done (9.361s) 11499979 read pairs processed; of these: 212 ( 0.00%) short read pairs filtered out after trimming by size control 231337 ( 2.01%) empty read pairs filtered out after trimming by size control 11268430 (97.99%) read pairs available; of these: 92003 ( 0.82%) trimmed read pairs available after processing 11176427 (99.18%) untrimmed read pairs available after processing Length distribution of reads after trimming: length count percentage 18 116 0.00% 19 1 0.00% 20 110 0.00% 21 5 0.00% 22 122 0.00% 23 1 0.00% 24 120 0.00% 25 2 0.00% 26 125 0.00% 27 3 0.00% 28 122 0.00% 29 2 0.00% 30 60 0.00% 31 2 0.00% 32 50 0.00% 33 0 0.00% 34 29 0.00% 35 384 0.00% 36 540 0.00% 37 528 0.00% 38 694 0.01% 39 836 0.01% 40 1036 0.01% 41 1160 0.01% 42 1349 0.01% 43 1497 0.01% 44 1705 0.02% 45 1815 0.02% 46 1832 0.02% 47 2132 0.02% 48 2410 0.02% 49 2740 0.02% 50 3069 0.03% 51 3344 0.03% 52 3867 0.03% 53 4212 0.04% 54 4570 0.04% 55 5082 0.05% 56 5659 0.05% 57 6215 0.06% 58 6961 0.06% 59 7680 0.07% 60 7977 0.07% 61 8654 0.08% 62 9571 0.08% 63 10325 0.09% 64 11159 0.10% 65 12515 0.11% 66 13094 0.12% 67 14192 0.13% 68 14745 0.13% 69 16140 0.14% 70 17296 0.15% 71 19990 0.18% 72 29997 0.27% 73 111181 0.99% 74 853863 7.58% 75 4958203 44.00% 76 5087341 45.15% 11268430 reads passed initial QC criterion=sequence-density sequence-density=0.92 sequence-density-rank=1 fanout-score=1.99 fanout-score-rank=26 prefix-density=0.90 prefix-fanout=2.0 sequence=TTCAAATGTACA criterion=fanout-score sequence-density=0.01 sequence-density-rank=34 fanout-score=63.94 fanout-score-rank=1 prefix-density=0.06 prefix-fanout=6.5 sequence=AAAAAAAAGTATGTTTGCATCAATGATAATCCCAAAGTAGGAAGTGTGTACGTAGTAGCAAGTGTTATACATACATAAAATTAAGCGATGCGTTTCGATCAAGTACTTGGCATCATCGATCACATACGTACATTTCACAGCAGGTAGCTACGTACATTACAGGCATACGTACATGCAGAGAGATACCCGGCCCTGTGTTGTGTTTGCAATTGCATAGATGAGAATGAGATGACTTGATTCTTAATTAGCCGGCGAGAGCGCTGGTGTTGTAGACGAGGAGGGCGCCGCCGCCGAGGAGGCCGGCCAGGGTGACGGCCCAGATCAGGAGCCCCGTCGTCCCACCGGCGTAGCGGTCGCCAGATTCGGACCATACCTCCGGCGTGTAGATCGGGCTGTAGCCGTCGACGTTGGCGCCGTACTTGTCAACAAACTGGTACACACCCTTTCCCGTGCCCTTCCTGCCGTTGGCGTCGATGTCCACCGTCAAGCCACCTCCGATCCCGAGGGGCTT criterion=sequence-density sequence-density=0.65 sequence-density-rank=1 fanout-score=2.00 fanout-score-rank=26 prefix-density=0.64 prefix-fanout=2.0 sequence=GACGCCTATGTCCGCATCATCGGCTTCGACAACACCCGGCAGGTGCAGTGCATCAGCTTCATCGCCTTCAAGCC criterion=fanout-score sequence-density=0.02 sequence-density-rank=31 fanout-score=5.11 fanout-score-rank=1 prefix-density=0.05 prefix-fanout=2.1 sequence=CCTCAAGCCAAAGCCTCTTGCTAAGCGTACCACACTATACAGACGTGCGCGCGCAGCCATGGCACCCACCGTGATGGCTTCCTCCGCCACCTCCGTGGCTCCTTTCCA SRR11389836 testing PE reads STAR mapping to Ensembl genome Started job on | Dec 07 07:48:05 Started mapping on | Dec 07 07:48:05 Finished on | Dec 07 07:49:04 Mapping speed, Million of reads per hour | 687.57 Number of input reads | 11268430 Average input read length | 150 UNIQUE READS: Uniquely mapped reads number | 8767373 Uniquely mapped reads % | 77.80% Average mapped length | 149.72 Number of splices: Total | 3355073 Number of splices: Annotated (sjdb) | 3186481 Number of splices: GT/AG | 3311760 Number of splices: GC/AG | 39150 Number of splices: AT/AC | 925 Number of splices: Non-canonical | 3238 Mismatch rate per base, % | 0.77% Deletion rate per base | 0.01% Deletion average length | 1.34 Insertion rate per base | 0.00% Insertion average length | 1.36 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 1610809 % of reads mapped to multiple loci | 14.29% Number of reads mapped to too many loci | 20948 % of reads mapped to too many loci | 0.19% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 6.65% % of reads unmapped: other | 1.06% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 890248 890248 890248 N_multimapping 1610809 1610809 1610809 N_noFeature 299210 8459615 432573 N_ambiguous 251001 1589 86097 UnstrandedReadsAssigned:8217162 PositiveStrandReadsAssigned:306169 NegativeStrandReadsAssigned:8248703 Dataset is classified negative stranded MeadianReadLen=76 20thPercentileLength=75 echo kmer=71 SRR11389836 Starting Kallisto paired end mapping to ensembl reference transcriptome [quant] fragment length distribution will be estimated from the data [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 paired-end mode [quant] will process pair 1: SRR11389836-trimmed-pair1.fastq SRR11389836-trimmed-pair2.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 11,268,430 reads, 9,996,503 reads pseudoaligned [quant] estimated average fragment length: 188.908 [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,058 rounds 52973 SRR11389836.ke.tsv 35125 SRR11389836.se.tsv 88098 total ==> SRR11389836.ke.tsv <== target_id length eff_length est_counts tpm PNS24245 936 748.214 0 0 PNS24247 1044 856.092 18.9519 3.00376 PNS24249 1928 1740.09 25.1796 1.96341 PNS24246 1044 856.092 18.9519 3.00376 PNS24248 1044 856.092 18.9519 3.00376 PNS24244 1471 1283.09 47.9648 5.07224 PNS24243 293 127.88 1 1.06104 KQK14069 1603 1415.09 1681.79 161.259 KQK14071 474 289.542 95.1112 44.5712 ==> SRR11389836.se.tsv <== BRADI_1g14170v3 1901 BRADI_1g53295v3 14 BRADI_1g59795v3 171 BRADI_1g07683v3 0 BRADI_1g00485v3 0 BRADI_1g20270v3 100 BRADI_1g74790v3 254 BRADI_1g09890v3 0 BRADI_1g77505v3 84 BRADI_1g48960v3 0 SRR11389836 completed mapping pipeline successfully