Starting /dee2/code/volunteer_pipeline.sh ERR6133462 current disk space = 1545233395712 free memory = 1427102664 ERR6133462 SRAfilesize fe0c81d00606f736e2f40377482b9a3e ERR6133462.sra ERR6133462.sra file validated ERR6133462 is single end ERR6133462 is conventional basespace ERR6133462 read1 length is 70-93 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename ERR6133462_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 34.83675 37.0 33.0 37.0 33.0 37.0 2 36.17075 37.0 37.0 37.0 33.0 37.0 3 35.40925 37.0 33.0 37.0 33.0 37.0 4 35.2545 37.0 37.0 37.0 33.0 37.0 5 35.0295 37.0 37.0 37.0 33.0 37.0 6 35.4145 37.0 37.0 37.0 33.0 37.0 7 36.9215 37.0 37.0 40.0 33.0 40.0 8 37.0005 37.0 37.0 40.0 33.0 40.0 9 37.198 37.0 37.0 40.0 33.0 40.0 10-11 37.124625 37.0 37.0 40.0 33.0 40.0 12-13 36.940749999999994 37.0 37.0 40.0 33.0 40.0 14-15 36.983999999999995 37.0 37.0 40.0 33.0 40.0 16-17 36.697500000000005 37.0 37.0 40.0 33.0 40.0 18-19 36.43625 37.0 37.0 40.0 33.0 40.0 20-21 36.23375 37.0 37.0 40.0 33.0 40.0 22-23 35.93625 37.0 35.0 40.0 33.0 40.0 24-25 36.072874999999996 37.0 37.0 40.0 33.0 40.0 26-27 36.367374999999996 37.0 37.0 40.0 33.0 40.0 28-29 36.24625 37.0 37.0 40.0 33.0 40.0 30-31 36.36925 37.0 37.0 40.0 33.0 40.0 32-33 36.142625 37.0 37.0 40.0 33.0 40.0 34-35 36.2025 37.0 37.0 40.0 33.0 40.0 36-37 36.16275 37.0 37.0 40.0 33.0 40.0 38-39 36.065375 37.0 35.0 40.0 33.0 40.0 40-41 35.94025 37.0 33.0 40.0 33.0 40.0 42-43 35.833124999999995 37.0 35.0 40.0 33.0 40.0 44-45 35.533249999999995 37.0 33.0 38.5 33.0 40.0 46-47 35.490375 37.0 33.0 37.0 33.0 40.0 48-49 35.529875000000004 37.0 33.0 37.0 33.0 40.0 50-51 35.357749999999996 37.0 33.0 37.0 33.0 40.0 52-53 35.0835 37.0 33.0 37.0 30.0 40.0 54-55 34.994249999999994 37.0 33.0 37.0 27.0 40.0 56-57 34.712 37.0 33.0 37.0 27.0 38.5 58-59 34.177375 37.0 33.0 37.0 27.0 37.0 60-61 34.476375 37.0 33.0 37.0 27.0 37.0 62-63 34.376374999999996 37.0 33.0 37.0 27.0 37.0 64-65 34.1825 37.0 33.0 37.0 27.0 37.0 66-67 34.06925 37.0 33.0 37.0 27.0 37.0 68-69 33.18275 35.0 33.0 37.0 27.0 37.0 70-71 33.45798090886329 35.0 33.0 37.0 27.0 37.0 72-73 33.73367027407525 37.0 33.0 37.0 27.0 37.0 74-75 33.728530528358974 37.0 33.0 37.0 27.0 37.0 76-77 33.88800499667424 37.0 33.0 37.0 27.0 37.0 78-79 33.943394329326935 37.0 33.0 37.0 27.0 37.0 80-81 33.867591013562844 37.0 33.0 37.0 27.0 37.0 82-83 33.64527483608046 37.0 33.0 37.0 27.0 37.0 84-85 33.38496854592406 35.0 33.0 37.0 27.0 37.0 86-87 33.24935600206079 35.0 33.0 37.0 27.0 37.0 88-89 33.40932509015971 33.0 33.0 37.0 27.0 37.0 90-91 33.049072642967545 33.0 33.0 37.0 27.0 37.0 92-93 32.98995363214838 33.0 33.0 37.0 27.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 20 9.0 21 19.0 22 15.0 23 25.0 24 21.0 25 35.0 26 42.0 27 55.0 28 64.0 29 96.0 30 97.0 31 128.0 32 174.0 33 213.0 34 290.0 35 486.0 36 843.0 37 891.0 38 488.0 39 9.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 83.775 3.2750000000000004 5.075 7.875 2 66.475 19.425 9.325 4.775 3 33.875 36.75 14.774999999999999 14.6 4 32.2 26.174999999999997 19.3 22.325 5 24.25 27.425 30.525000000000002 17.8 6 18.325 37.95 25.924999999999997 17.8 7 35.6 29.349999999999998 20.025000000000002 15.024999999999999 8 27.750000000000004 31.6 24.525 16.125 9 22.45 30.25 27.450000000000003 19.85 10-11 22.6 27.725 30.049999999999997 19.625 12-13 24.9875 27.487499999999997 26.85 20.674999999999997 14-15 21.8125 33.4375 26.187500000000004 18.5625 16-17 23.3125 31.5625 24.4 20.724999999999998 18-19 23.0125 27.425 28.475 21.087500000000002 20-21 25.09377344336084 24.99374843710928 29.782445611402853 20.130032508127034 22-23 28.475 22.775000000000002 26.9125 21.837500000000002 24-25 24.887500000000003 27.675 27.375 20.0625 26-27 23.9 25.55 31.9875 18.5625 28-29 24.8 28.1625 27.462500000000002 19.575 30-31 26.724999999999998 27.1125 26.5375 19.625 32-33 24.525 26.650000000000002 28.5875 20.2375 34-35 22.6875 30.6875 25.55 21.075 36-37 24.7 26.087500000000002 26.700000000000003 22.5125 38-39 28.585719644866824 24.02150806552457 29.561085407027637 17.831686882580968 40-41 27.397774165311993 26.822558459422286 25.334500437664126 20.4451669376016 42-43 25.842415132155832 28.9865965175999 25.93010146561443 19.240886884629838 44-45 24.552845528455283 26.59161976235147 28.905565978736707 19.949968730456536 46-47 24.337500000000002 25.525 27.925 22.2125 48-49 24.3625 24.975 30.2125 20.45 50-51 22.3625 28.475 28.4125 20.75 52-53 24.92793583155784 27.497180097756612 25.366587291640556 22.208296779044993 54-55 24.8906113264158 27.47843480435054 29.80372546568321 17.827228403550443 56-57 28.1375 26.8 25.5625 19.5 58-59 24.5375 24.337500000000002 29.062500000000004 22.0625 60-61 24.075 27.3875 29.65 18.8875 62-63 20.0875 30.875000000000004 31.412499999999998 17.625 64-65 20.875 31.974999999999998 28.6375 18.512500000000003 66-67 23.5625 29.25 28.0625 19.125 68-69 20.95 27.875 25.887500000000003 25.2875 70-71 23.167375531648737 27.958468851638727 27.08281210908181 21.79134350763072 72-73 26.333626208108445 24.199824275134933 29.283293586042426 20.183255930714196 74-75 23.98942198715527 28.49767031859967 27.96876967636318 19.544138017881878 76-77 23.134234120469756 25.39462053289557 26.922591236267206 24.54855411036747 78-79 24.315415821501013 25.456389452332655 29.86815415821501 20.36004056795132 80-81 21.40127388535032 32.35668789808917 29.01910828025478 17.222929936305732 82-83 21.738573806170784 27.000384073742158 28.075790551785946 23.185251568301112 84-85 23.553612753921314 21.599382874775007 33.09334019028028 21.7536641810234 86-87 21.496651210716124 27.79495105615662 29.340546110252447 21.367851622874806 88-89 19.023699124162803 29.63678516228748 29.89438433797012 21.4451313755796 90-91 26.107676455435342 26.97063369397218 28.271509531169496 18.650180319422976 92-93 21.612570839773312 31.336939721792888 27.627511591962907 19.42297784647089 >>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 1.0 17 14.0 18 14.0 19 3.0 20 4.0 21 5.0 22 6.0 23 6.5 24 5.5 25 5.5 26 11.0 27 12.5 28 18.5 29 27.0 30 30.0 31 35.5 32 39.5 33 54.5 34 62.5 35 67.5 36 106.5 37 159.5 38 232.5 39 229.5 40 213.5 41 210.5 42 205.0 43 238.0 44 197.0 45 178.5 46 187.5 47 152.5 48 140.5 49 143.0 50 163.5 51 172.5 52 143.5 53 150.5 54 155.5 55 104.0 56 64.0 57 64.0 58 56.5 59 41.5 60 30.0 61 34.0 62 32.0 63 19.5 64 18.5 65 22.5 66 21.0 67 14.5 68 14.0 69 8.5 70 2.0 71 2.0 72 2.5 73 3.0 74 1.5 75 1.0 76 1.0 77 0.0 78 0.0 79 0.0 80 0.0 81 0.0 82 0.0 83 0.0 84 0.0 85 0.0 86 0.0 87 0.0 88 0.0 89 0.0 90 0.0 91 0.0 92 0.0 93 0.0 94 0.0 95 0.0 96 0.0 97 0.0 98 0.0 99 0.0 100 0.0 >>END_MODULE >>Per base N content pass #Base N-Count 1 0.0 2 0.0 3 0.0 4 0.0 5 0.0 6 0.0 7 0.0 8 0.0 9 0.0 10-11 0.0 12-13 0.0 14-15 0.0 16-17 0.0 18-19 0.0 20-21 0.025 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 0.0375 40-41 0.0375 42-43 0.21250000000000002 44-45 0.0625 46-47 0.0 48-49 0.0 50-51 0.0 52-53 0.2625 54-55 0.0125 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 6.0 71 9.0 72 3.0 73 7.0 74 9.0 75 3.0 76 7.0 77 8.0 78 8.0 79 12.0 80 6.0 81 12.0 82 9.0 83 5.0 84 14.0 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 3882.0 >>END_MODULE >>Sequence Duplication Levels warn #Total Deduplicated Percentage 67.15 #Duplication Level Percentage of deduplicated Percentage of total 1 91.17647058823529 61.224999999999994 2 4.318689501116903 5.800000000000001 3 1.4892032762472078 3.0 4 0.6329113924050633 1.7000000000000002 5 0.37230081906180196 1.25 6 0.4095309009679821 1.6500000000000001 7 0.14892032762472077 0.7000000000000001 8 0.03723008190618019 0.2 9 0.2606105733432614 1.575 >10 0.967982129560685 12.675 >50 0.18615040953090098 10.225 >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 GGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAA 94 2.35 No Hit GGGAGAGCAATACAAGCGTTGTGCTGCTAGGCGAAGCGGTTGAGTGCCGC 86 2.15 No Hit GGCGTTCAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTC 82 2.0500000000000003 No Hit TACCTAGGCACCCAGAGACGAGGAAGGGCGTAGCAAGCGACGAAATGCTT 76 1.9 No Hit GGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCTTGG 71 1.775 No Hit GGGCTGATATCATCAACCGTGCTAATCTTGGTATGGAAGTAATGCACGAA 39 0.975 No Hit GGGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGT 38 0.95 No Hit GGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGTG 34 0.8500000000000001 No Hit GTAGTAGGAATCTGGTTCACTGCTTTAGGTATTAGTACTATGGCGTTCAA 34 0.8500000000000001 No Hit GGCCTGTAGTAGGAATCTGGTTCACTGCTTTAGGTATTAGTACTATGGCG 33 0.8250000000000001 No Hit CAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAGGTC 30 0.75 No Hit GGGATGATTCTGTATTACAATTTGGTGGAGGAACTTTAGGACATCCTTGG 26 0.65 No Hit GGAGTATCCTTGATATATAAATATATAGATAAATAGATTTAAATGGAAAA 24 0.6 No Hit GGACATCCTTGGGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTT 23 0.575 No Hit GGAGTTGAAAATAAGCATAGATCCGGAGATTCCCAAATAGGTCAACCTTT 20 0.5 No Hit GGGAGTATTATGAAAGGAGATTAATCATAGATTATCAAAAACCCTAGAAA 20 0.5 No Hit GGGGATGATTCTGTATTACAATTTGGTGGAGGAACTTTAGGACATCCTTG 20 0.5 No Hit GTAGGAATCTGGTTCACTGCTTTAGGTATTAGTACTATGGCGTTCAACCT 18 0.44999999999999996 No Hit GGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGTGTACAAGCTCGTAA 14 0.35000000000000003 No Hit GGGATGGAGCGACAGAAGTATGGAAATAGGATAAGGTAGCGGCGAGACGA 14 0.35000000000000003 No Hit CAAGGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCT 13 0.325 No Hit GGGGATGGAGCGACAGAAGTATGGAAATAGGATAAGGTAGCGGCGAGACG 12 0.3 No Hit TCAAAAGAGGAAAGGCTTGCGGTGGATACCTAGGCACCCAGAGACGAGGA 12 0.3 No Hit GGATGATTCTGTATTACAATTTGGTGGAGGAACTTTAGGACATCCTTGGG 11 0.27499999999999997 No Hit GGGTTGTTTGGGAATGCAGCCCAAATCGGGCGGTAGACTCCGTCCAAGGC 11 0.27499999999999997 No Hit GGGCGCGATCTTGCTCGTGAAGGTAATGAAATTATCCGAGCAGCTTGCAA 11 0.27499999999999997 No Hit CAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAATACTTGGGCTGATAT 10 0.25 No Hit GGGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTA 10 0.25 No Hit GGAATCTGGTTCACTGCTTTAGGTATTAGTACTATGGCGTTCAACCTAAA 10 0.25 No Hit GGAAAAGAGGGGTTACTTTTTTTCATTTTTCCCTTAAAAGATAGGCTTTG 10 0.25 No Hit GTTCAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAG 10 0.25 No Hit GTATTTAGCCTTGCAAGGTGGTCCTTGCTGATTCACACGGGATTCCACGT 9 0.22499999999999998 No Hit GAGGAAAGGCTTGCGGTGGATACCTAGGCACCCAGAGACGAGGAAGGGCG 9 0.22499999999999998 No Hit GGGGAGTTGAAAATAAGCATAGATCCGGAGATTCCCAAATAGGTCAACCT 9 0.22499999999999998 No Hit GGAGGAACTTTAGGACATCCTTGGGGAAATGCACCTGGTGCAGCAGCTAA 9 0.22499999999999998 No Hit GGTAATGAAATTATCCGAGCAGCTTGCAAATGGAGTCCTGAACTAGCCGC 9 0.22499999999999998 No Hit GGTGGATACCTAGGCACCCAGAGACGAGGAAGGGCGTAGCAAGCGACGAA 9 0.22499999999999998 No Hit CAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAATACTTGGGCTG 9 0.22499999999999998 No Hit GATACCTAGGCACCCAGAGACGAGGAAGGGCGTAGCAAGCGACGAAATGC 8 0.2 No Hit GGGCACGTGGAATCCCGTGTGAATCAGCAAGGACCACCTTGCAAGGCTAA 7 0.17500000000000002 No Hit GGTTCACTGCTTTAGGTATTAGTACTATGGCGTTCAACCTAAATGGATTC 7 0.17500000000000002 No Hit GATTCAATTTCAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAAT 7 0.17500000000000002 No Hit GGGCCATTCACAGACACACACAACTACACAAGAGCTCTCAGCTGCTGCCC 7 0.17500000000000002 No Hit GGGAAAAGAGGGGTTACTTTTTTTCATTTTTCCCTTAAAAGATAGGCTTT 6 0.15 No Hit GAAGGAACAAACGAGGATAAGATAAAATTTCTTTAAATTTATTTTGCCCA 6 0.15 No Hit GGGAGTGGGGGTGCCATACGCAAAAAGGAAGCGACTCATAGAATGGCAGA 6 0.15 No Hit GGAAGGGCGTAGCAAGCGACGAAATGCTTCGGGGAGTTGAAAATAAGCAT 6 0.15 No Hit GGATACCTAGGCACCCAGAGACGAGGAAGGGCGTAGCAAGCGACGAAATG 6 0.15 No Hit GGCTGCTTGGCCTGTAGTAGGAATCTGGTTCACTGCTTTAGGTATTAGTA 6 0.15 No Hit GTAGCAAGCGACGAAATGCTTCGGGGAGTTGAAAATAAGCATAGATCCGG 6 0.15 No Hit GGCGCGATCTTGCTCGTGAAGGTAATGAAATTATCCGAGCAGCTTGCAAA 6 0.15 No Hit GGAGCAGCCTAAACCGTGAAAACGGGGTTGTGGGAGAGCAATACAAGCGT 6 0.15 No Hit GAAGGTAATGAAATTATCCGAGCAGCTTGCAAATGGAGTCCTGAACTAGC 6 0.15 No Hit GCAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAGGT 6 0.15 No Hit GGCTGATATCATCAACCGTGCTAATCTTGGTATGGAAGTAATGCACGAAC 5 0.125 No Hit GGGGGTCGCAGTGACCAGGCCCGGGCGACTGTTTACCAAAAACACAGGTC 5 0.125 No Hit CACCCAGAGACGAGGAAGGGCGTAGCAAGCGACGAAATGCTTCGGGGAGT 5 0.125 No Hit AGGAAAGGCTTGCGGTGGATACCTAGGCACCCAGAGACGAGGAAGGGCGT 5 0.125 No Hit GGAAGAGCCCGAGCTGCTGCAGCAGGTTTTGAAAAGGGAATCGATCGTGA 5 0.125 No Hit GGAATAAGAATAAATCGCAACTCCTTTCCACTACACATAAAAATTGATTT 5 0.125 No Hit CGAGGAAGGGCGTAGCAAGCGACGAAATGCTTCGGGGAGTTGAAAATAAG 5 0.125 No Hit GGGGAAGTACACCAGCGACGGCGAGGCCGCCGCCGCCAAGGAAGGCATGT 5 0.125 No Hit CACGAACGTAATGCTCACAACTTCCCTCTAGATCTAGCTGCTCTTGAAGT 5 0.125 No Hit GGTTTTGAAAAGGGAATCGATCGTGATTTAGAACCTGTTCTTTACATGAA 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 0.025 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 0.025 0.0 0.0 0.0 0.0 54-55 0.025 0.0 0.0 0.0 0.0 56-57 0.025 0.0 0.0 0.0 0.0 58-59 0.025 0.0 0.0 0.0 0.0 60-61 0.025 0.0 0.0 0.0 0.0 62-63 0.025 0.0 0.0 0.0 0.0 64-65 0.025 0.0 0.0 0.0 0.0 66-67 0.025 0.0 0.0 0.0 0.0 68-69 0.025 0.0 0.0 0.0 0.0 70-71 0.025 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 warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position GGCACCC 20 0.002799412 64.8375 7 CCTGTAG 20 0.002799412 64.8375 3 CTAGGCA 20 0.002799412 64.8375 4 GGCCTGT 20 0.002799412 64.8375 1 CACCCAG 20 0.002799412 64.8375 9 TGTAGTA 20 0.002799412 64.8375 5 AGGCACC 20 0.002799412 64.8375 6 GCACCCA 20 0.002799412 64.8375 8 ACCTAGG 20 0.002799412 64.8375 2 GCCTGTA 20 0.002799412 64.8375 2 CCTAGGC 20 0.002799412 64.8375 3 TAGGCAC 20 0.002799412 64.8375 5 TACCTAG 25 0.006774748 51.87 1 >>END_MODULE Rejected 234772 READS because READLEN < 1 Read 234772 spots for ERR6133462.sra Written 234772 spots for ERR6133462.sra Rejected 234772 READS because READLEN < 1 Read 234772 spots for ERR6133462.sra Written 234772 spots for ERR6133462.sra Rejected 234772 READS because READLEN < 1 Read 234772 spots for ERR6133462.sra Written 234772 spots for ERR6133462.sra Rejected 234772 READS because READLEN < 1 Read 234772 spots for ERR6133462.sra Written 234772 spots for ERR6133462.sra Rejected 234772 READS because READLEN < 1 Read 234772 spots for ERR6133462.sra Written 234772 spots for ERR6133462.sra Rejected 234772 READS because READLEN < 1 Read 234772 spots for ERR6133462.sra Written 234772 spots for ERR6133462.sra Rejected 234772 READS because READLEN < 1 Read 234772 spots for ERR6133462.sra Written 234772 spots for ERR6133462.sra Rejected 234772 READS because READLEN < 1 Read 234772 spots for ERR6133462.sra Written 234772 spots for ERR6133462.sra Rejected 234772 READS because READLEN < 1 Read 234772 spots for ERR6133462.sra Written 234772 spots for ERR6133462.sra Rejected 234772 READS because READLEN < 1 Read 234772 spots for ERR6133462.sra Written 234772 spots for ERR6133462.sra Rejected 234772 READS because READLEN < 1 Read 234772 spots for ERR6133462.sra Written 234772 spots for ERR6133462.sra Rejected 234772 READS because READLEN < 1 Read 234772 spots for ERR6133462.sra Written 234772 spots for ERR6133462.sra Rejected 234772 READS because READLEN < 1 Read 234772 spots for ERR6133462.sra Written 234772 spots for ERR6133462.sra Rejected 234772 READS because READLEN < 1 Read 234772 spots for ERR6133462.sra Written 234772 spots for ERR6133462.sra Rejected 234778 READS because READLEN < 1 Read 234778 spots for ERR6133462.sra Written 234778 spots for ERR6133462.sra Rejected 234772 READS because READLEN < 1 Read 234772 spots for ERR6133462.sra Written 234772 spots for ERR6133462.sra Rejected 234772 READS because READLEN < 1 Read 234772 spots for ERR6133462.sra Written 234772 spots for ERR6133462.sra Rejected 234772 READS because READLEN < 1 Read 234772 spots for ERR6133462.sra Written 234772 spots for ERR6133462.sra Rejected 234772 READS because READLEN < 1 Read 234772 spots for ERR6133462.sra Written 234772 spots for ERR6133462.sra Rejected 234772 READS because READLEN < 1 Read 234772 spots for ERR6133462.sra Written 234772 spots for ERR6133462.sra SRR ids: ['ERR6133462.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_1c5ew3w5 ERR6133462.sra spots: 4695446 blocks: [[1, 234772], [234773, 469544], [469545, 704316], [704317, 939088], [939089, 1173860], [1173861, 1408632], [1408633, 1643404], [1643405, 1878176], [1878177, 2112948], [2112949, 2347720], [2347721, 2582492], [2582493, 2817264], [2817265, 3052036], [3052037, 3286808], [3286809, 3521580], [3521581, 3756352], [3756353, 3991124], [3991125, 4225896], [4225897, 4460668], [4460669, 4695446]] ERR6133462 file size 1038422 ERR6133462 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 ERR6133462 ERR6133462_1.fastq Input file: ERR6133462_1.fastq trimmed: ERR6133462-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 06:33:41 2024 >> started Sat Dec 7 06:33:44 2024 >> done (2.579s) 4695446 reads processed; of these: 128 ( 0.00%) short reads filtered out after trimming by size control 17 ( 0.00%) empty reads filtered out after trimming by size control 4695301 (100.00%) reads available; of these: 69483 ( 1.48%) trimmed reads available after processing 4625818 (98.52%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 11 0.00% 19 28 0.00% 20 12 0.00% 21 14 0.00% 22 20 0.00% 23 11 0.00% 24 4 0.00% 25 7 0.00% 26 4 0.00% 27 9 0.00% 28 7 0.00% 29 23 0.00% 30 6 0.00% 31 14 0.00% 32 15 0.00% 33 14 0.00% 34 18 0.00% 35 90 0.00% 36 724 0.02% 37 15 0.00% 38 22 0.00% 39 70 0.00% 40 43 0.00% 41 34 0.00% 42 14 0.00% 43 14 0.00% 44 16 0.00% 45 11 0.00% 46 12 0.00% 47 14 0.00% 48 5 0.00% 49 13 0.00% 50 10 0.00% 51 29 0.00% 52 5 0.00% 53 11 0.00% 54 8 0.00% 55 10 0.00% 56 10 0.00% 57 4 0.00% 58 12 0.00% 59 1 0.00% 60 6 0.00% 61 9 0.00% 62 3 0.00% 63 1 0.00% 64 10 0.00% 65 6 0.00% 66 7 0.00% 67 17 0.00% 68 32 0.00% 69 89 0.00% 70 10154 0.22% 71 8597 0.18% 72 9946 0.21% 73 8809 0.19% 74 9367 0.20% 75 9103 0.19% 76 8352 0.18% 77 8721 0.19% 78 10230 0.22% 79 11743 0.25% 80 11361 0.24% 81 13979 0.30% 82 16136 0.34% 83 14308 0.30% 84 12760 0.27% 85 157 0.00% 86 281 0.01% 87 492 0.01% 88 923 0.02% 89 1859 0.04% 90 3875 0.08% 91 12126 0.26% 92 46248 0.98% 93 4464180 95.08% 4695301 reads passed initial QC criterion=sequence-density sequence-density=0.77 sequence-density-rank=1 fanout-score=1.99 fanout-score-rank=31 prefix-density=0.77 prefix-fanout=2.0 sequence=CAAGGCTAAATAC criterion=fanout-score sequence-density=0.01 sequence-density-rank=23 fanout-score=66.27 fanout-score-rank=1 prefix-density=0.11 prefix-fanout=7.7 sequence=AAAAGAAGGGGTGTTCCATCTCCGGACGACGATCCTGCCTGCAGAGGAAGACATGCCGGCGATCATGTCGAGCTTCAAGAAGTTCAACGACTCATTCATGGAGCAATACCAAGACTACTCCAGGCTGTGATGTGAAGAGGGAAACAACGAGGTCATCATCGACATGATATATTGCTGCTATTTTCCACCAGCGATTAAAAGTTAAAAAATTTAGCTGTAAGCTGTAACTATCTTGAAGAAACTAAACTGGTTGCTGTGCTT Started job on | Dec 07 06:34:13 Started mapping on | Dec 07 06:34:13 Finished on | Dec 07 06:34:21 Mapping speed, Million of reads per hour | 2112.89 Number of input reads | 4695301 Average input read length | 92 UNIQUE READS: Uniquely mapped reads number | 2493289 Uniquely mapped reads % | 53.10% Average mapped length | 91.90 Number of splices: Total | 136699 Number of splices: Annotated (sjdb) | 112778 Number of splices: GT/AG | 131388 Number of splices: GC/AG | 2578 Number of splices: AT/AC | 122 Number of splices: Non-canonical | 2611 Mismatch rate per base, % | 0.46% Deletion rate per base | 0.04% Deletion average length | 1.83 Insertion rate per base | 0.02% Insertion average length | 1.98 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 2082240 % of reads mapped to multiple loci | 44.35% Number of reads mapped to too many loci | 49782 % of reads mapped to too many loci | 1.06% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 1.41% % of reads unmapped: other | 0.08% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 119772 119772 119772 N_multimapping 2082240 2082240 2082240 N_noFeature 232977 260182 2387101 N_ambiguous 94170 15016 513 UnstrandedReadsAssigned:2166142 PositiveStrandReadsAssigned:2218091 NegativeStrandReadsAssigned:105675 Dataset is classified positive stranded MeadianReadLen=93 20thPercentileLength=93 echo kmer=89 ERR6133462 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: ERR6133462-trimmed.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 4,695,301 reads, 3,602,214 reads pseudoaligned [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 982 rounds 52973 ERR6133462.ke.tsv 35125 ERR6133462.se.tsv 88098 total ==> ERR6133462.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 84 21.8937 PNS24243 293 194 0 0 KQK14069 1603 1504 89 21.161 KQK14071 474 375 0 0 ==> ERR6133462.se.tsv <== BRADI_1g14170v3 89 BRADI_1g53295v3 4 BRADI_1g59795v3 20 BRADI_1g07683v3 0 BRADI_1g00485v3 1 BRADI_1g20270v3 17 BRADI_1g74790v3 31 BRADI_1g09890v3 0 BRADI_1g77505v3 45 BRADI_1g48960v3 0 ERR6133462 completed mapping pipeline successfully