Starting /dee2/code/volunteer_pipeline.sh ERR6133507 current disk space = 1544451551232 free memory = 1438274896 ERR6133507 SRAfilesize 660ca12e44f937c5db7640514ab89ce0 ERR6133507.sra ERR6133507.sra file validated ERR6133507 is single end ERR6133507 is conventional basespace ERR6133507 read1 length is 70-93 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename ERR6133507_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 36.62975 37.0 37.0 37.0 37.0 37.0 2 36.851 37.0 37.0 37.0 37.0 37.0 3 36.526 37.0 37.0 37.0 37.0 37.0 4 35.94525 37.0 37.0 37.0 33.0 37.0 5 36.083 37.0 37.0 37.0 33.0 37.0 6 36.3175 37.0 37.0 37.0 33.0 37.0 7 38.3195 40.0 37.0 40.0 37.0 40.0 8 38.32 40.0 37.0 40.0 37.0 40.0 9 38.391 40.0 37.0 40.0 37.0 40.0 10-11 38.33475 40.0 37.0 40.0 37.0 40.0 12-13 38.2125 40.0 37.0 40.0 37.0 40.0 14-15 38.171375 40.0 37.0 40.0 37.0 40.0 16-17 38.1125 40.0 37.0 40.0 37.0 40.0 18-19 38.021625 40.0 37.0 40.0 37.0 40.0 20-21 38.021 40.0 37.0 40.0 37.0 40.0 22-23 38.1345 40.0 37.0 40.0 37.0 40.0 24-25 38.066125 40.0 37.0 40.0 37.0 40.0 26-27 38.010125 40.0 37.0 40.0 37.0 40.0 28-29 38.032125 40.0 37.0 40.0 37.0 40.0 30-31 38.041124999999994 40.0 37.0 40.0 37.0 40.0 32-33 38.058375 40.0 37.0 40.0 37.0 40.0 34-35 38.038250000000005 40.0 37.0 40.0 37.0 40.0 36-37 37.907375 37.0 37.0 40.0 37.0 40.0 38-39 37.78075 37.0 37.0 40.0 37.0 40.0 40-41 37.621375 37.0 37.0 40.0 37.0 40.0 42-43 37.562625 37.0 37.0 40.0 37.0 40.0 44-45 37.345875 37.0 37.0 40.0 35.0 40.0 46-47 37.251000000000005 37.0 37.0 40.0 33.0 40.0 48-49 37.116749999999996 37.0 37.0 38.5 33.0 40.0 50-51 36.938375 37.0 37.0 37.0 33.0 40.0 52-53 36.58625 37.0 37.0 37.0 33.0 40.0 54-55 36.558 37.0 37.0 37.0 33.0 40.0 56-57 36.414249999999996 37.0 37.0 37.0 33.0 38.5 58-59 36.06037499999999 37.0 37.0 37.0 33.0 37.0 60-61 36.19675 37.0 37.0 37.0 33.0 37.0 62-63 36.082875 37.0 37.0 37.0 33.0 37.0 64-65 35.985 37.0 37.0 37.0 33.0 37.0 66-67 35.911125 37.0 37.0 37.0 33.0 37.0 68-69 34.97 35.0 35.0 37.0 33.0 37.0 70-71 35.204916040100244 37.0 33.0 37.0 33.0 37.0 72-73 35.73343102212154 37.0 33.0 37.0 33.0 37.0 74-75 35.74842131811158 37.0 35.0 37.0 33.0 37.0 76-77 35.662877745618104 37.0 33.0 37.0 33.0 37.0 78-79 35.542188111601305 37.0 33.0 37.0 33.0 37.0 80-81 35.443437851057666 37.0 33.0 37.0 33.0 37.0 82-83 35.32301356312656 37.0 33.0 37.0 33.0 37.0 84-85 35.13687511171068 37.0 33.0 37.0 33.0 37.0 86-87 35.13752582644628 37.0 33.0 37.0 33.0 37.0 88-89 35.10524276859504 37.0 33.0 37.0 33.0 37.0 90-91 35.03693181818181 37.0 33.0 37.0 33.0 37.0 92-93 35.04338842975207 37.0 33.0 37.0 33.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 20 1.0 21 2.0 22 2.0 23 1.0 24 6.0 25 3.0 26 10.0 27 14.0 28 7.0 29 16.0 30 36.0 31 42.0 32 30.0 33 65.0 34 94.0 35 308.0 36 1166.0 37 1411.0 38 768.0 39 18.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 87.9 2.9250000000000003 3.5000000000000004 5.675 2 74.85000000000001 15.049999999999999 6.325 3.775 3 36.925000000000004 38.425 13.075000000000001 11.575000000000001 4 32.574999999999996 28.9 19.15 19.375 5 25.374999999999996 30.675 26.974999999999998 16.975 6 20.9 38.4 24.525 16.175 7 37.65 29.45 18.3 14.6 8 29.7 30.625000000000004 22.525000000000002 17.150000000000002 9 25.424999999999997 29.125 27.650000000000002 17.8 10-11 25.174999999999997 28.15 28.262500000000003 18.4125 12-13 27.287499999999998 26.85 26.950000000000003 18.912499999999998 14-15 22.05 32.125 27.8375 17.9875 16-17 24.275 32.0625 24.6875 18.975 18-19 23.3125 28.199999999999996 27.625 20.8625 20-21 24.493623405851466 27.494373593398347 28.219554888722183 19.79244811202801 22-23 28.125 23.6375 28.275 19.9625 24-25 25.837500000000002 25.8125 27.6125 20.7375 26-27 26.1625 25.374999999999996 30.775000000000002 17.6875 28-29 25.4375 28.6125 27.900000000000002 18.05 30-31 29.203650456307038 25.528191023877984 27.21590198774847 18.052256532066508 32-33 22.8375 28.325 28.4375 20.4 34-35 24.0125 27.537499999999998 27.0625 21.3875 36-37 25.837500000000002 24.7 28.325 21.1375 38-39 27.9125 25.3 29.299999999999997 17.4875 40-41 27.38184546136534 24.706176544136035 26.806701675418854 21.10527631907977 42-43 24.981245311327832 29.48237059264816 25.756439109777446 19.779944986246562 44-45 22.8875 25.95 30.325000000000003 20.837500000000002 46-47 24.075 24.2625 29.425 22.237499999999997 48-49 24.2625 25.587500000000002 30.587500000000002 19.5625 50-51 25.26565820727591 26.990873859232405 28.2410301287661 19.50243780472559 52-53 25.382109746930592 27.48684540215485 25.82059634176898 21.310448509145576 54-55 24.637500000000003 28.475 29.15 17.7375 56-57 26.625 25.8125 28.625 18.9375 58-59 22.825 25.900000000000002 29.099999999999998 22.175 60-61 24.7875 26.075 29.45 19.6875 62-63 22.237499999999997 28.4125 31.7875 17.5625 64-65 24.4875 28.375 29.65 17.4875 66-67 25.15 28.175 27.725 18.95 68-69 22.3625 26.875 27.712500000000002 23.05 70-71 24.105131414267834 26.545682102628287 27.934918648310386 21.414267834793492 72-73 26.557583385777217 24.946507237256135 28.99937067337948 19.496538703587163 74-75 22.893240682248894 28.060644346178144 30.30953885028427 18.736576121288692 76-77 22.806349206349203 25.955555555555556 28.48253968253968 22.755555555555556 78-79 25.84756563854193 24.72597501911802 30.830996686209534 18.59546265613051 80-81 23.199897685125975 31.014196188770942 28.46911369740376 17.31679242869932 82-83 24.10691338987407 25.456180930352097 29.503983551786174 20.932922127987663 84-85 24.381124290871583 23.76224858174317 31.45951521402785 20.397111913357403 86-87 22.598140495867767 26.820764462809915 31.082128099173556 19.49896694214876 88-89 21.5650826446281 29.364669421487605 29.803719008264462 19.266528925619834 90-91 26.020144628099175 27.104855371900825 27.673037190082646 19.201962809917354 92-93 22.48192148760331 30.320247933884296 28.473657024793386 18.72417355371901 >>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 9.0 18 10.0 19 2.5 20 2.0 21 2.5 22 1.5 23 5.0 24 5.5 25 2.5 26 9.0 27 12.0 28 15.0 29 21.0 30 22.0 31 25.0 32 41.5 33 59.5 34 63.5 35 77.0 36 96.0 37 127.5 38 168.5 39 176.0 40 182.5 41 191.5 42 204.5 43 220.0 44 205.0 45 198.0 46 254.5 47 248.5 48 198.5 49 191.0 50 198.5 51 194.0 52 156.5 53 149.5 54 152.5 55 114.5 56 65.0 57 53.0 58 44.0 59 28.5 60 19.5 61 17.0 62 16.0 63 11.0 64 10.0 65 11.0 66 7.5 67 6.0 68 5.5 69 5.0 70 3.5 71 2.0 72 1.5 73 0.5 74 0.5 75 0.5 76 0.0 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 0.0125 32-33 0.0 34-35 0.0 36-37 0.0 38-39 0.0 40-41 0.025 42-43 0.025 44-45 0.0 46-47 0.0 48-49 0.0 50-51 0.0125 52-53 0.22499999999999998 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 10.0 71 12.0 72 11.0 73 7.0 74 5.0 75 13.0 76 9.0 77 9.0 78 2.0 79 8.0 80 9.0 81 11.0 82 6.0 83 4.0 84 12.0 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 3872.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 75.02499999999999 #Duplication Level Percentage of deduplicated Percentage of total 1 91.5361546151283 68.675 2 4.665111629456848 7.000000000000001 3 1.599466844385205 3.5999999999999996 4 0.4998333888703766 1.5 5 0.46651116294568473 1.7500000000000002 6 0.16661112962345886 0.75 7 0.09996667777407531 0.525 8 0.09996667777407531 0.6 9 0.13328890369876709 0.8999999999999999 >10 0.6331222925691435 10.025 >50 0.09996667777407531 4.675 >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 77 1.925 No Hit GGGATGATTCTGTATTACAATTTGGTGGAGGAACTTTAGGACATCCTTGG 56 1.4000000000000001 No Hit GGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAA 54 1.35 No Hit TACCTAGGCACCCAGAGACGAGGAAGGGCGTAGCAAGCGACGAAATGCTT 39 0.975 No Hit GGGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGT 36 0.8999999999999999 No Hit GGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCTTGG 33 0.8250000000000001 No Hit GGATGATTCTGTATTACAATTTGGTGGAGGAACTTTAGGACATCCTTGGG 31 0.775 No Hit GGCGTTCAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTC 28 0.7000000000000001 No Hit GGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGTG 27 0.675 No Hit GGGGATGATTCTGTATTACAATTTGGTGGAGGAACTTTAGGACATCCTTG 24 0.6 No Hit GGGCGCGATCTTGCTCGTGAAGGTAATGAAATTATCCGAGCAGCTTGCAA 22 0.5499999999999999 No Hit GGGATGGAGCGACAGAAGTATGGAAATAGGATAAGGTAGCGGCGAGACGA 18 0.44999999999999996 No Hit GGACATCCTTGGGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTT 18 0.44999999999999996 No Hit GGAGGAACTTTAGGACATCCTTGGGGAAATGCACCTGGTGCAGCAGCTAA 17 0.42500000000000004 No Hit GGCGCGATCTTGCTCGTGAAGGTAATGAAATTATCCGAGCAGCTTGCAAA 16 0.4 No Hit GGGAATCGATCGTGATTTAGAACCTGTTCTTTACATGAACCCTCTTAACT 16 0.4 No Hit CAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAGGTC 16 0.4 No Hit GGAGTATCCTTGATATATAAATATATAGATAAATAGATTTAAATGGAAAA 15 0.375 No Hit GGGGATGGAGCGACAGAAGTATGGAAATAGGATAAGGTAGCGGCGAGACG 13 0.325 No Hit GGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGTGTACAAGCTCGTAA 12 0.3 No Hit GTAGTAGGAATCTGGTTCACTGCTTTAGGTATTAGTACTATGGCGTTCAA 10 0.25 No Hit GGCCTGTAGTAGGAATCTGGTTCACTGCTTTAGGTATTAGTACTATGGCG 10 0.25 No Hit GGTGGGGCAATGGGCATTCCGTTGAGTTTGTATGGTGGGTGCTGTTTTGC 9 0.22499999999999998 No Hit GTACTATGGCGTTCAACCTAAATGGATTCAATTTCAACCAATCTGTAGTT 9 0.22499999999999998 No Hit GGGACGCATGCAACGACCATCTACATATAGCTACTCGATCTACCGCTACC 9 0.22499999999999998 No Hit GGTTTTGAAAAGGGAATCGATCGTGATTTAGAACCTGTTCTTTACATGAA 9 0.22499999999999998 No Hit GGAACTTTAGGACATCCTTGGGGAAATGCACCTGGTGCAGCAGCTAATCG 8 0.2 No Hit CAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAATACTTGGGCTGATAT 8 0.2 No Hit GGAGTTGAAAATAAGCATAGATCCGGAGATTCCCAAATAGGTCAACCTTT 8 0.2 No Hit GGGCTGATATCATCAACCGTGCTAATCTTGGTATGGAAGTAATGCACGAA 7 0.17500000000000002 No Hit CAAGGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCT 7 0.17500000000000002 No Hit GGGAGTATTATGAAAGGAGATTAATCATAGATTATCAAAAACCCTAGAAA 7 0.17500000000000002 No Hit GGATACCTAGGCACCCAGAGACGAGGAAGGGCGTAGCAAGCGACGAAATG 6 0.15 No Hit GGTGGAGGAACTTTAGGACATCCTTGGGGAAATGCACCTGGTGCAGCAGC 6 0.15 No Hit GGGCGTGGCGTTCATGAACAAGTGAAACCTTATGGCTGGATGGGTCATCG 6 0.15 No Hit GGTAATGAAATTATCCGAGCAGCTTGCAAATGGAGTCCTGAACTAGCCGC 6 0.15 No Hit GGAAAAGAAAGCAAAAGCGATTCCCGTAGTAGCGGCGAGCGAAATGGGAG 6 0.15 No Hit GGAGTCCTGAACTAGCCGCAGCTTGTGAAGTATGGAAGGCGATCAAATTC 5 0.125 No Hit GGGAGTGGGGGTGCCATACGCAAAAAGGAAGCGACTCATAGAATGGCAGA 5 0.125 No Hit GGAGTGGGGGTGCCATACGCAAAAAGGAAGCGACTCATAGAATGGCAGAG 5 0.125 No Hit GGATCGGTCGATCATCGGAGAAGAACACTTCCTCCGTGCATATGCGTGTA 5 0.125 No Hit GGAGAAGAACACTTCCTCCGTGCATATGCGTGTACGTGGGTTGATCGGTG 5 0.125 No Hit GGAAGGGCGTAGCAAGCGACGAAATGCTTCGGGGAGTTGAAAATAAGCAT 5 0.125 No Hit GGAGCGACAGAAGTATGGAAATAGGATAAGGTAGCGGCGAGACGAGCCGT 5 0.125 No Hit GGGCCGGGTATCTCTCTGCATGTACGTATGCCTGTAATGTACGTAGCTAC 5 0.125 No Hit GTACAAGCTCGTAACGAAGGGCGCGATCTTGCTCGTGAAGGTAATGAAAT 5 0.125 No Hit GGTAGTAGGAATCTGGTTCACTGCTTTAGGTATTAGTACTATGGCGTTCA 5 0.125 No Hit GGAGAAGTACAAGTGCGGATCCAACGTCTTCTGGAAATGGTGAAGATGAT 5 0.125 No Hit GAAGGTAATGAAATTATCCGAGCAGCTTGCAAATGGAGTCCTGAACTAGC 5 0.125 No Hit GGGGAGTTGAAAATAAGCATAGATCCGGAGATTCCCAAATAGGTCAACCT 5 0.125 No Hit TCAAAAGAGGAAAGGCTTGCGGTGGATACCTAGGCACCCAGAGACGAGGA 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 0.025 0.0 0.0 0.0 0.0 14-15 0.037500000000000006 0.0 0.0 0.0 0.0 16-17 0.05 0.0 0.0 0.0 0.0 18-19 0.05 0.0 0.0 0.0 0.0 20-21 0.05 0.0 0.0 0.0 0.0 22-23 0.05 0.0 0.0 0.0 0.0 24-25 0.05 0.0 0.0 0.0 0.0 26-27 0.05 0.0 0.0 0.0 0.0 28-29 0.05 0.0 0.0 0.0 0.0 30-31 0.075 0.0 0.0 0.0 0.0 32-33 0.075 0.0 0.0 0.0 0.0 34-35 0.1 0.0 0.0 0.0 0.0 36-37 0.1375 0.0 0.0 0.0 0.0 38-39 0.175 0.0 0.0 0.0 0.0 40-41 0.175 0.0 0.0 0.0 0.0 42-43 0.175 0.0 0.0 0.0 0.0 44-45 0.175 0.0 0.0 0.0 0.0 46-47 0.175 0.0 0.0 0.0 0.0 48-49 0.175 0.0 0.0 0.0 0.0 50-51 0.175 0.0 0.0 0.0 0.0 52-53 0.175 0.0 0.0 0.0 0.0 54-55 0.175 0.0 0.0 0.0 0.0 56-57 0.175 0.0 0.0 0.0 0.0 58-59 0.175 0.0 0.0 0.0 0.0 60-61 0.175 0.0 0.0 0.0 0.0 62-63 0.175 0.0 0.0 0.0 0.0 64-65 0.175 0.0 0.0 0.0 0.0 66-67 0.175 0.0 0.0 0.0 0.0 68-69 0.175 0.0 0.0 0.0 0.0 70-71 0.175 0.0 0.0 0.0 0.0 72-73 0.175 0.0 0.0 0.0 0.0 74-75 0.175 0.0 0.0 0.0 0.0 76-77 0.175 0.0 0.0 0.0 0.0 78-79 0.175 0.0 0.0 0.0 0.0 80-81 0.175 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position GGAGAAA 15 8.8641414E-4 86.625 1 TTCTGTA 15 8.8641414E-4 86.625 8 TGATTCT 15 8.8641414E-4 86.625 5 GATGATT 15 8.8641414E-4 86.625 3 TCTGTAT 15 8.8641414E-4 86.625 9 ATTCTGT 15 8.8641414E-4 86.625 7 GGATGAT 20 0.0027770554 64.96875 2 GATTCTG 20 0.0027770554 64.96875 6 GGGATGA 20 0.0027770554 64.96875 1 TTCAATT 30 1.8153216E-4 57.75 4 CAATTTC 30 1.8153216E-4 57.75 6 TCAATTT 30 1.8153216E-4 57.75 5 GATTCAA 30 1.8153216E-4 57.75 2 ATTTCAA 30 1.8153216E-4 57.75 8 ATTCAAT 30 1.8153216E-4 57.75 3 ATGATTC 25 0.0067207636 51.975 4 AATTTCA 35 3.8884295E-4 49.499996 7 GGATTCA 35 3.8884295E-4 49.499996 1 TTTCAAC 35 3.8884295E-4 49.499996 9 AATCTTG 30 0.0051592034 29.615383 78-79 >>END_MODULE Rejected 98448 READS because READLEN < 1 Read 98448 spots for ERR6133507.sra Written 98448 spots for ERR6133507.sra Rejected 98448 READS because READLEN < 1 Read 98448 spots for ERR6133507.sra Written 98448 spots for ERR6133507.sra Rejected 98448 READS because READLEN < 1 Read 98448 spots for ERR6133507.sra Written 98448 spots for ERR6133507.sra Rejected 98448 READS because READLEN < 1 Read 98448 spots for ERR6133507.sra Written 98448 spots for ERR6133507.sra Rejected 98448 READS because READLEN < 1 Read 98448 spots for ERR6133507.sra Written 98448 spots for ERR6133507.sra Rejected 98448 READS because READLEN < 1 Read 98448 spots for ERR6133507.sra Written 98448 spots for ERR6133507.sra Rejected 98448 READS because READLEN < 1 Read 98448 spots for ERR6133507.sra Written 98448 spots for ERR6133507.sra Rejected 98448 READS because READLEN < 1 Read 98448 spots for ERR6133507.sra Written 98448 spots for ERR6133507.sra Rejected 98448 READS because READLEN < 1 Read 98448 spots for ERR6133507.sra Written 98448 spots for ERR6133507.sra Rejected 98448 READS because READLEN < 1 Read 98448 spots for ERR6133507.sra Written 98448 spots for ERR6133507.sra Rejected 98448 READS because READLEN < 1 Read 98448 spots for ERR6133507.sra Written 98448 spots for ERR6133507.sra Rejected 98448 READS because READLEN < 1 Read 98448 spots for ERR6133507.sra Written 98448 spots for ERR6133507.sra Rejected 98450 READS because READLEN < 1 Read 98450 spots for ERR6133507.sra Written 98450 spots for ERR6133507.sra Rejected 98448 READS because READLEN < 1 Read 98448 spots for ERR6133507.sra Written 98448 spots for ERR6133507.sra Rejected 98448 READS because READLEN < 1 Read 98448 spots for ERR6133507.sra Written 98448 spots for ERR6133507.sra Rejected 98448 READS because READLEN < 1 Read 98448 spots for ERR6133507.sra Written 98448 spots for ERR6133507.sra Rejected 98448 READS because READLEN < 1 Read 98448 spots for ERR6133507.sra Written 98448 spots for ERR6133507.sra Rejected 98448 READS because READLEN < 1 Read 98448 spots for ERR6133507.sra Written 98448 spots for ERR6133507.sra Rejected 98448 READS because READLEN < 1 Read 98448 spots for ERR6133507.sra Written 98448 spots for ERR6133507.sra Rejected 98448 READS because READLEN < 1 Read 98448 spots for ERR6133507.sra Written 98448 spots for ERR6133507.sra SRR ids: ['ERR6133507.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_9tj3l_b5 ERR6133507.sra spots: 1968962 blocks: [[1, 98448], [98449, 196896], [196897, 295344], [295345, 393792], [393793, 492240], [492241, 590688], [590689, 689136], [689137, 787584], [787585, 886032], [886033, 984480], [984481, 1082928], [1082929, 1181376], [1181377, 1279824], [1279825, 1378272], [1378273, 1476720], [1476721, 1575168], [1575169, 1673616], [1673617, 1772064], [1772065, 1870512], [1870513, 1968962]] ERR6133507 file size 434241 ERR6133507 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 ERR6133507 ERR6133507_1.fastq Input file: ERR6133507_1.fastq trimmed: ERR6133507-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 07:34:14 2024 >> started Sat Dec 7 07:34:16 2024 >> done (2.358s) 1968962 reads processed; of these: 235 ( 0.01%) short reads filtered out after trimming by size control 11 ( 0.00%) empty reads filtered out after trimming by size control 1968716 (99.99%) reads available; of these: 9711 ( 0.49%) trimmed reads available after processing 1959005 (99.51%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 31 0.00% 19 75 0.00% 20 23 0.00% 21 24 0.00% 22 25 0.00% 23 12 0.00% 24 12 0.00% 25 5 0.00% 26 7 0.00% 27 11 0.00% 28 49 0.00% 29 176 0.01% 30 22 0.00% 31 37 0.00% 32 28 0.00% 33 37 0.00% 34 25 0.00% 35 71 0.00% 36 472 0.02% 37 28 0.00% 38 35 0.00% 39 103 0.01% 40 73 0.00% 41 38 0.00% 42 22 0.00% 43 14 0.00% 44 40 0.00% 45 20 0.00% 46 34 0.00% 47 9 0.00% 48 13 0.00% 49 8 0.00% 50 21 0.00% 51 44 0.00% 52 12 0.00% 53 10 0.00% 54 13 0.00% 55 6 0.00% 56 9 0.00% 57 27 0.00% 58 12 0.00% 59 15 0.00% 60 12 0.00% 61 5 0.00% 62 2 0.00% 63 0 0.00% 64 0 0.00% 65 3 0.00% 66 3 0.00% 67 4 0.00% 68 6 0.00% 69 36 0.00% 70 4805 0.24% 71 4476 0.23% 72 4292 0.22% 73 4242 0.22% 74 4361 0.22% 75 4537 0.23% 76 3895 0.20% 77 3678 0.19% 78 3824 0.19% 79 3948 0.20% 80 3754 0.19% 81 4021 0.20% 82 4637 0.24% 83 4633 0.24% 84 3840 0.20% 85 28 0.00% 86 45 0.00% 87 74 0.00% 88 156 0.01% 89 238 0.01% 90 501 0.03% 91 1305 0.07% 92 5233 0.27% 93 1896374 96.33% 1968716 reads passed initial QC criterion=sequence-density sequence-density=0.29 sequence-density-rank=1 fanout-score=2.03 fanout-score-rank=32 prefix-density=0.29 prefix-fanout=2.0 sequence=CAAGGCTAAATAC criterion=fanout-score sequence-density=0.01 sequence-density-rank=30 fanout-score=76.39 fanout-score-rank=1 prefix-density=0.14 prefix-fanout=6.7 sequence=AAAAGAAGGGGTGTTCCATCTCCGGACGACGATCCTGCCTGCGGAGGAAGACATGCCGGCGATCATGTCGAGCTTCAAGAAGTTCAACGACTCATTCATGGAGCAATACCAAGACTACTCCAGGCTGTGATGTGAAGAGGGAAACAACGACGTCATCATCGACATGATATATTGCTGCTATTTTCCACCAGCGATTAAAAGTTAAAAAATTTAGCTGTAAGCTGTAACTATCTTGAAGAAACTAAACTGGTTGCTGTGCTT Started job on | Dec 07 07:34:34 Started mapping on | Dec 07 07:34:34 Finished on | Dec 07 07:34:39 Mapping speed, Million of reads per hour | 1417.48 Number of input reads | 1968716 Average input read length | 92 UNIQUE READS: Uniquely mapped reads number | 1273652 Uniquely mapped reads % | 64.69% Average mapped length | 92.23 Number of splices: Total | 63639 Number of splices: Annotated (sjdb) | 53143 Number of splices: GT/AG | 61403 Number of splices: GC/AG | 1587 Number of splices: AT/AC | 27 Number of splices: Non-canonical | 622 Mismatch rate per base, % | 0.37% Deletion rate per base | 0.05% Deletion average length | 1.88 Insertion rate per base | 0.02% Insertion average length | 1.83 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 606197 % of reads mapped to multiple loci | 30.79% Number of reads mapped to too many loci | 11720 % of reads mapped to too many loci | 0.60% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 3.88% % of reads unmapped: other | 0.04% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 88867 88867 88867 N_multimapping 606197 606197 606197 N_noFeature 95549 107326 1215945 N_ambiguous 52489 6548 167 UnstrandedReadsAssigned:1125614 PositiveStrandReadsAssigned:1159778 NegativeStrandReadsAssigned:57540 Dataset is classified positive stranded MeadianReadLen=93 20thPercentileLength=93 echo kmer=89 ERR6133507 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: ERR6133507-trimmed.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 1,968,716 reads, 1,569,683 reads pseudoaligned [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 926 rounds 52973 ERR6133507.ke.tsv 35125 ERR6133507.se.tsv 88098 total ==> ERR6133507.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 43 26.4502 PNS24243 293 194 0 0 KQK14069 1603 1504 26 14.5895 KQK14071 474 375 0 0 ==> ERR6133507.se.tsv <== BRADI_1g14170v3 26 BRADI_1g53295v3 14 BRADI_1g59795v3 8 BRADI_1g07683v3 0 BRADI_1g00485v3 0 BRADI_1g20270v3 22 BRADI_1g74790v3 19 BRADI_1g09890v3 0 BRADI_1g77505v3 34 BRADI_1g48960v3 0 ERR6133507 completed mapping pipeline successfully