Starting /dee2/code/volunteer_pipeline.sh ERR6133410 current disk space = 1547441713152 free memory = 1603206044 ERR6133410 SRAfilesize d91510c2d91cb81dd42cb357937e4df0 ERR6133410.sra ERR6133410.sra file validated ERR6133410 is single end ERR6133410 is conventional basespace ERR6133410 read1 length is 70-93 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename ERR6133410_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 fail #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 29.79875 33.0 27.0 33.0 15.0 37.0 2 33.70875 37.0 33.0 37.0 27.0 37.0 3 33.7465 37.0 33.0 37.0 27.0 37.0 4 33.83675 37.0 33.0 37.0 27.0 37.0 5 34.05775 37.0 33.0 37.0 27.0 37.0 6 34.22375 37.0 33.0 37.0 27.0 37.0 7 35.2005 37.0 33.0 40.0 27.0 40.0 8 35.178 37.0 33.0 40.0 27.0 40.0 9 35.44075 37.0 33.0 40.0 33.0 40.0 10-11 35.350875 37.0 33.0 40.0 30.0 40.0 12-13 35.21425 37.0 33.0 38.5 30.0 40.0 14-15 35.102000000000004 37.0 33.0 37.0 27.0 40.0 16-17 34.818 37.0 33.0 37.0 27.0 40.0 18-19 34.703625 37.0 33.0 37.0 27.0 40.0 20-21 34.07125 37.0 33.0 37.0 27.0 40.0 22-23 33.908249999999995 37.0 33.0 37.0 27.0 40.0 24-25 33.386250000000004 37.0 33.0 37.0 24.5 40.0 26-27 33.183875 37.0 33.0 37.0 22.0 40.0 28-29 32.893625 37.0 33.0 37.0 22.0 40.0 30-31 32.860375 37.0 33.0 37.0 22.0 40.0 32-33 32.34225 33.0 33.0 37.0 22.0 40.0 34-35 31.433500000000002 33.0 27.0 37.0 18.5 40.0 36-37 30.99975 33.0 27.0 37.0 15.0 37.0 38-39 31.435875 33.0 27.0 37.0 22.0 38.5 40-41 31.3795 33.0 27.0 37.0 22.0 40.0 42-43 30.85 33.0 27.0 37.0 15.0 38.5 44-45 30.725125 33.0 27.0 37.0 15.0 37.0 46-47 30.27375 33.0 27.0 37.0 15.0 37.0 48-49 29.90725 33.0 27.0 37.0 15.0 37.0 50-51 29.686 33.0 27.0 37.0 15.0 37.0 52-53 29.377625000000002 33.0 27.0 37.0 15.0 37.0 54-55 29.238374999999998 33.0 27.0 37.0 15.0 37.0 56-57 28.4105 33.0 24.5 35.0 15.0 37.0 58-59 28.1725 33.0 27.0 33.0 15.0 37.0 60-61 28.2095 33.0 27.0 33.0 15.0 37.0 62-63 27.76525 33.0 22.0 33.0 15.0 37.0 64-65 27.3135 33.0 22.0 33.0 10.5 37.0 66-67 26.750875 30.0 22.0 33.0 6.0 37.0 68-69 26.276874999999997 27.0 22.0 33.0 10.5 35.0 70-71 28.169762967847277 33.0 27.0 33.0 15.0 37.0 72-73 28.528490455287873 33.0 27.0 33.0 15.0 37.0 74-75 28.285767487773143 33.0 27.0 33.0 15.0 37.0 76-77 28.025793205348336 33.0 27.0 33.0 15.0 37.0 78-79 27.35907012189439 33.0 27.0 33.0 6.0 37.0 80-81 26.61959426190164 33.0 22.0 33.0 6.0 37.0 82-83 25.779298752048547 33.0 22.0 33.0 2.0 37.0 84-85 25.317089259706577 33.0 22.0 33.0 2.0 37.0 86-87 24.232611637347766 30.0 15.0 33.0 2.0 37.0 88-89 23.794451962110962 30.0 10.5 33.0 2.0 37.0 90-91 22.52462787550744 27.0 2.0 33.0 2.0 35.0 92-93 21.06102841677943 27.0 2.0 33.0 2.0 33.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 20 94.0 21 110.0 22 142.0 23 146.0 24 180.0 25 198.0 26 240.0 27 221.0 28 275.0 29 272.0 30 271.0 31 247.0 32 258.0 33 298.0 34 295.0 35 309.0 36 262.0 37 155.0 38 26.0 39 1.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 73.875 6.675000000000001 6.550000000000001 12.9 2 55.800000000000004 21.525 13.925 8.75 3 34.150000000000006 36.8 16.35 12.7 4 28.875 29.799999999999997 20.525 20.8 5 26.700000000000003 25.650000000000002 28.975 18.675 6 18.099999999999998 38.45 25.575 17.875 7 33.675 27.875 22.35 16.1 8 26.075 26.924999999999997 25.75 21.25 9 24.425 30.725 26.474999999999998 18.375 10-11 22.225 27.775 30.6375 19.3625 12-13 22.650000000000002 29.037499999999998 27.287499999999998 21.025 14-15 21.087500000000002 32.375 27.55 18.987499999999997 16-17 24.962500000000002 27.8375 23.9375 23.2625 18-19 24.3125 23.825 31.474999999999998 20.3875 20-21 25.112499999999997 23.799999999999997 30.312499999999996 20.775 22-23 27.2625 23.3625 29.1125 20.2625 24-25 23.65 24.099999999999998 29.1625 23.0875 26-27 25.224999999999998 24.8625 28.225 21.6875 28-29 23.0625 28.8625 29.049999999999997 19.025 30-31 28.499999999999996 25.85 25.2875 20.3625 32-33 26.787499999999998 24.6 27.175 21.4375 34-35 22.0875 32.1 26.3 19.5125 36-37 25.35 26.75 24.6625 23.2375 38-39 30.125 23.1125 27.037499999999998 19.725 40-41 24.1375 24.8 31.624999999999996 19.4375 42-43 25.637500000000003 30.2875 25.75 18.325 44-45 24.212500000000002 26.2625 29.099999999999998 20.424999999999997 46-47 26.0625 25.900000000000002 24.95 23.0875 48-49 25.8125 23.9375 27.650000000000002 22.6 50-51 21.55 29.45 26.4625 22.537499999999998 52-53 23.849999999999998 26.0125 25.162499999999998 24.975 54-55 22.0 26.200000000000003 31.112499999999997 20.6875 56-57 26.5625 28.725 24.8625 19.85 58-59 21.8625 29.275000000000002 28.287499999999998 20.575 60-61 28.95 25.25 26.387500000000003 19.412499999999998 62-63 20.3625 27.125 31.2125 21.3 64-65 20.65 34.8 26.487500000000004 18.0625 66-67 25.324999999999996 29.212500000000002 25.887500000000003 19.575 68-69 21.575 26.125 27.762500000000003 24.5375 70-71 22.804159879714323 29.043979451196595 26.826212254103492 21.32564841498559 72-73 26.193483202829 25.145238696640565 30.550644102045972 18.110633998484467 74-75 26.520464108121892 29.51676654341451 25.36019380339156 18.60257554507204 76-77 22.3667267576616 24.311099665207315 27.65902652588205 25.663147051249034 78-79 24.629002863837542 28.924759177297577 26.620671700078102 19.825566258786775 80-81 21.852046169989507 34.87670514165792 26.128016789087095 17.143231899265476 82-83 24.378902617244584 25.48159957486382 25.893450245781853 24.246047562109737 84-85 22.003505460428745 25.455035728731296 31.319940676823517 21.22151813401645 86-87 22.39512855209743 30.013531799729364 25.602165087956696 21.989174560216508 88-89 21.33964817320704 27.374830852503386 29.147496617050066 22.138024357239512 90-91 26.41407307171854 30.20297699594046 24.519621109607577 18.863328822733425 92-93 20.040595399188092 30.730717185385657 27.307171853856566 21.921515561569688 >>END_MODULE >>Per sequence GC content fail #GC Content Count 0 0.0 1 0.0 2 0.0 3 0.0 4 0.0 5 0.0 6 0.0 7 0.0 8 0.0 9 0.0 10 0.0 11 0.0 12 0.0 13 0.0 14 0.0 15 0.0 16 1.0 17 4.5 18 6.0 19 2.5 20 0.5 21 1.0 22 2.5 23 5.5 24 11.5 25 12.0 26 9.0 27 13.5 28 25.0 29 32.5 30 33.0 31 44.0 32 50.0 33 52.0 34 53.5 35 63.0 36 116.0 37 188.0 38 224.0 39 214.0 40 193.5 41 198.0 42 205.0 43 200.5 44 186.0 45 167.0 46 152.0 47 145.0 48 135.5 49 121.0 50 122.5 51 121.0 52 116.0 53 152.5 54 234.0 55 218.0 56 137.0 57 115.5 58 92.5 59 55.5 60 32.0 61 22.5 62 17.0 63 13.0 64 11.0 65 11.0 66 12.0 67 10.0 68 12.5 69 14.0 70 9.0 71 5.0 72 6.5 73 5.0 74 1.0 75 0.5 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 0.0 36-37 0.0 38-39 0.0 40-41 0.0 42-43 0.0 44-45 0.0 46-47 0.0 48-49 0.0 50-51 0.0 52-53 0.0 54-55 0.0 56-57 0.0 58-59 0.0 60-61 0.0 62-63 0.0 64-65 0.0 66-67 0.0 68-69 0.0 70-71 0.0 72-73 0.0 74-75 0.0 76-77 0.0 78-79 0.0 80-81 0.0 82-83 0.0 84-85 0.0 86-87 0.0 88-89 0.0 90-91 0.0 92-93 0.0 >>END_MODULE >>Sequence Length Distribution warn #Length Count 70 19.0 71 13.0 72 18.0 73 17.0 74 23.0 75 21.0 76 12.0 77 26.0 78 20.0 79 12.0 80 14.0 81 26.0 82 31.0 83 26.0 84 27.0 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 3695.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 74.225 #Duplication Level Percentage of deduplicated Percentage of total 1 92.65746042438532 68.77499999999999 2 3.4691815426069383 5.1499999999999995 3 1.2798922196025597 2.85 4 0.6399461098012799 1.9 5 0.370495116200741 1.375 6 0.20208824520040417 0.8999999999999999 7 0.1684068710003368 0.8750000000000001 8 0.20208824520040417 1.2 9 0.20208824520040417 1.35 >10 0.7746716066015493 10.525 >50 0.0 0.0 >100 0.033681374200067365 5.1 >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 204 5.1 No Hit GGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAA 36 0.8999999999999999 No Hit CAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAGGTC 29 0.7250000000000001 No Hit GGCGTTCAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTC 27 0.675 No Hit GGTTCACTGCTTTAGGTATTAGTACTATGGCGTTCAACCTAAATGGATTC 27 0.675 No Hit GGAATCTGGTTCACTGCTTTAGGTATTAGTACTATGGCGTTCAACCTAAA 23 0.575 No Hit GGGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGT 22 0.5499999999999999 No Hit GTAGGAATCTGGTTCACTGCTTTAGGTATTAGTACTATGGCGTTCAACCT 21 0.525 No Hit GGGCTGATATCATCAACCGTGCTAATCTTGGTATGGAAGTAATGCACGAA 20 0.5 No Hit GGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCTTGG 20 0.5 No Hit CAAGGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCT 19 0.475 No Hit GTTCAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAG 19 0.475 No Hit GGGTTGTTTGGGAATGCAGCCCAAATCGGGCGGTAGACTCCGTCCAAGGC 18 0.44999999999999996 No Hit GTAGTAGGAATCTGGTTCACTGCTTTAGGTATTAGTACTATGGCGTTCAA 18 0.44999999999999996 No Hit GGGCACGTGGAATCCCGTGTGAATCAGCAAGGACCACCTTGCAAGGCTAA 17 0.42500000000000004 No Hit GGGATGATTCTGTATTACAATTTGGTGGAGGAACTTTAGGACATCCTTGG 13 0.325 No Hit GTACTATGGCGTTCAACCTAAATGGATTCAATTTCAACCAATCTGTAGTT 12 0.3 No Hit GGCCTGTAGTAGGAATCTGGTTCACTGCTTTAGGTATTAGTACTATGGCG 12 0.3 No Hit GGAATCCCGTGTGAATCAGCAAGGACCACCTTGCAAGGCTAAATACTCCT 12 0.3 No Hit GGGGTTGTGGGAGAGCAATACAAGCGTTGTGCTGCTAGGCGAAGCGGTTG 12 0.3 No Hit TCAAAAGAGGAAAGGCTTGCGGTGGATACCTAGGCACCCAGAGACGAGGA 12 0.3 No Hit GGAGTTGAAAATAAGCATAGATCCGGAGATTCCCAAATAGGTCAACCTTT 11 0.27499999999999997 No Hit GGAGAGCAATACAAGCGTTGTGCTGCTAGGCGAAGCGGTTGAGTGCCGCA 11 0.27499999999999997 No Hit GGGTGAGAGCCCCGTCCGGCCCGGACCCTGTCGCCCCACGAGGCGCCGTC 10 0.25 No Hit GGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGTG 9 0.22499999999999998 No Hit GGATGATTCTGTATTACAATTTGGTGGAGGAACTTTAGGACATCCTTGGG 9 0.22499999999999998 No Hit CAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAATACTTGGGCTGATAT 9 0.22499999999999998 No Hit GCAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAATACTTGGGCT 9 0.22499999999999998 No Hit GTATTAGTACTATGGCGTTCAACCTAAATGGATTCAATTTCAACCAATCT 9 0.22499999999999998 No Hit GAACGTAATGCTCACAACTTCCCTCTAGATCTAGCTGCTCTTGAAGTTCC 9 0.22499999999999998 No Hit GGTATTAGTACTATGGCGTTCAACCTAAATGGATTCAATTTCAACCAATC 8 0.2 No Hit GGTGGAGGAACTTTAGGACATCCTTGGGGAAATGCACCTGGTGCAGCAGC 8 0.2 No Hit TACCTAGGCACCCAGAGACGAGGAAGGGCGTAGCAAGCGACGAAATGCTT 8 0.2 No Hit GTTGTTTGGGAATGCAGCCCAAATCGGGCGGTAGACTCCGTCCAAGGCTA 8 0.2 No Hit GGAGTATCCTTGATATATAAATATATAGATAAATAGATTTAAATGGAAAA 8 0.2 No Hit CAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAATACTTGGGCTG 8 0.2 No Hit GGAGGGTGAGAGCCCCGTCCGGCCCGGACCCTGTCGCCCCACGAGGCGCC 7 0.17500000000000002 No Hit GGTCAACCTTTTAAACTGCCTGCTGAATCCATGAGCAGGCAAGAGACAAC 7 0.17500000000000002 No Hit GATTCAATTTCAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAAT 7 0.17500000000000002 No Hit GTGGAATCCCGTGTGAATCAGCAAGGACCACCTTGCAAGGCTAAATACTC 7 0.17500000000000002 No Hit GCGTTCAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTCA 7 0.17500000000000002 No Hit GGGAATGCAGCCCAAATCGGGCGGTAGACTCCGTCCAAGGCTAAATACAG 6 0.15 No Hit GGGGAGAGCAATACAAGCGTTGTGCTGCTAGGCGAAGCGGTTGAGTGCCG 6 0.15 No Hit GAATCTGGTTCACTGCTTTAGGTATTAGTACTATGGCGTTCAACCTAAAT 6 0.15 No Hit GACCCGAGTAGCATGGGGCACGTGGAATCCCGTGTGAATCAGCAAGGACC 6 0.15 No Hit GGAGCAGCCTAAACCGTGAAAACGGGGTTGTGGGAGAGCAATACAAGCGT 6 0.15 No Hit GGATTTGTTAAATCAAATCCTTGGTTTAATAACGAACGGTGTTAACTTAC 6 0.15 No Hit GCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCTTGGTATG 5 0.125 No Hit GGAGTCCTGAACTAGCCGCAGCTTGTGAAGTATGGAAGGCGATCAAATTC 5 0.125 No Hit CAATTTCAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAATACTT 5 0.125 No Hit CGAGTCGGGTTGTTTGGGAATGCAGCCCAAATCGGGCGGTAGACTCCGTC 5 0.125 No Hit GGAGATTCCCAAATAGGTCAACCTTTTAAACTGCCTGCTGAATCCATGAG 5 0.125 No Hit GTATGGAAGGCGATCAAATTCGAGTTCGCGCCGGTAGATACTATCGATTA 5 0.125 No Hit AGTCAAGGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAA 5 0.125 No Hit GGGTTGTGGGAGAGCAATACAAGCGTTGTGCTGCTAGGCGAAGCGGTTGA 5 0.125 No Hit GGTAGTAGGAATCTGGTTCACTGCTTTAGGTATTAGTACTATGGCGTTCA 5 0.125 No Hit GAATCCCGTGTGAATCAGCAAGGACCACCTTGCAAGGCTAAATACTCCTG 5 0.125 No Hit GGAAAAGAAAGCAAAAGCGATTCCCGTAGTAGCGGCGAGCGAAATGGGAG 5 0.125 No Hit >>END_MODULE >>Adapter Content pass #Position Illumina Universal Adapter Illumina Small RNA 3' Adapter Illumina Small RNA 5' Adapter Nextera Transposase Sequence SOLID Small RNA Adapter 1 0.0 0.0 0.0 0.0 0.0 2 0.0 0.0 0.0 0.0 0.0 3 0.0 0.0 0.0 0.0 0.0 4 0.0 0.0 0.0 0.0 0.0 5 0.0 0.0 0.0 0.0 0.0 6 0.0 0.0 0.0 0.0 0.0 7 0.0 0.0 0.0 0.0 0.0 8 0.0 0.0 0.0 0.0 0.0 9 0.0 0.0 0.0 0.0 0.0 10-11 0.0 0.0 0.0 0.0 0.0 12-13 0.0 0.0 0.0 0.0 0.0 14-15 0.0 0.0 0.0 0.0 0.0 16-17 0.0 0.0 0.0 0.0 0.0 18-19 0.0 0.0 0.0 0.0 0.0 20-21 0.0 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 0.025 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 0.025 0.0 0.0 0.0 0.0 74-75 0.025 0.0 0.0 0.0 0.0 76-77 0.025 0.0 0.0 0.0 0.0 78-79 0.025 0.0 0.0 0.0 0.0 80-81 0.025 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content fail #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position GGGAGAG 35 5.0676827E-6 61.53571 1 GGAGAGC 40 1.1188355E-5 53.84375 2 GCAATAC 40 1.1188355E-5 53.84375 7 CAATACA 40 1.1188355E-5 53.84375 8 GAGCAAT 40 1.1188355E-5 53.84375 5 AGAGCAA 40 1.1188355E-5 53.84375 4 GAGAGCA 40 1.1188355E-5 53.84375 3 AATACAA 40 1.1188355E-5 53.84375 9 AGCAATA 40 1.1188355E-5 53.84375 6 CATCACT 30 1.7976927E-6 45.342106 82-83 TCACTAG 30 1.7976927E-6 45.342106 84-85 ACTAGCT 30 1.7976927E-6 45.342106 86-87 CGAAAGC 35 9.54733E-8 45.342102 76-77 GCCGAAA 35 9.54733E-8 45.342102 74-75 TAGCCGA 35 1.1174052E-7 44.464516 72-73 CCGCACC 30 2.576875E-6 43.075 46-47 TGGCTAA 30 2.576875E-6 43.075 58-59 GATGGCT 35 1.4424222E-7 43.074997 56-57 TGCCGCA 35 1.4424222E-7 43.074997 44-45 AGTGCCG 35 1.4424222E-7 43.074997 42-43 >>END_MODULE Rejected 71600 READS because READLEN < 1 Read 71600 spots for ERR6133410.sra Written 71600 spots for ERR6133410.sra Rejected 71600 READS because READLEN < 1 Read 71600 spots for ERR6133410.sra Written 71600 spots for ERR6133410.sra Rejected 71600 READS because READLEN < 1 Read 71600 spots for ERR6133410.sra Written 71600 spots for ERR6133410.sra Rejected 71600 READS because READLEN < 1 Read 71600 spots for ERR6133410.sra Written 71600 spots for ERR6133410.sra Rejected 71600 READS because READLEN < 1 Read 71600 spots for ERR6133410.sra Written 71600 spots for ERR6133410.sra Rejected 71600 READS because READLEN < 1 Read 71600 spots for ERR6133410.sra Written 71600 spots for ERR6133410.sra Rejected 71600 READS because READLEN < 1 Read 71600 spots for ERR6133410.sra Written 71600 spots for ERR6133410.sra Rejected 71600 READS because READLEN < 1 Read 71600 spots for ERR6133410.sra Written 71600 spots for ERR6133410.sra Rejected 71600 READS because READLEN < 1 Read 71600 spots for ERR6133410.sra Written 71600 spots for ERR6133410.sra Rejected 71600 READS because READLEN < 1 Read 71600 spots for ERR6133410.sra Written 71600 spots for ERR6133410.sra Rejected 71600 READS because READLEN < 1 Read 71600 spots for ERR6133410.sra Written 71600 spots for ERR6133410.sra Rejected 71600 READS because READLEN < 1 Read 71600 spots for ERR6133410.sra Written 71600 spots for ERR6133410.sra Rejected 71600 READS because READLEN < 1 Read 71600 spots for ERR6133410.sra Written 71600 spots for ERR6133410.sra Rejected 71600 READS because READLEN < 1 Read 71600 spots for ERR6133410.sra Written 71600 spots for ERR6133410.sra Rejected 71600 READS because READLEN < 1 Read 71600 spots for ERR6133410.sra Written 71600 spots for ERR6133410.sra Rejected 71600 READS because READLEN < 1 Read 71600 spots for ERR6133410.sra Written 71600 spots for ERR6133410.sra Rejected 71600 READS because READLEN < 1 Read 71600 spots for ERR6133410.sra Written 71600 spots for ERR6133410.sra Rejected 71616 READS because READLEN < 1 Read 71616 spots for ERR6133410.sra Written 71616 spots for ERR6133410.sra Rejected 71600 READS because READLEN < 1 Read 71600 spots for ERR6133410.sra Written 71600 spots for ERR6133410.sra Rejected 71600 READS because READLEN < 1 Read 71600 spots for ERR6133410.sra Written 71600 spots for ERR6133410.sra SRR ids: ['ERR6133410.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_wwps9f94 ERR6133410.sra spots: 1432016 blocks: [[1, 71600], [71601, 143200], [143201, 214800], [214801, 286400], [286401, 358000], [358001, 429600], [429601, 501200], [501201, 572800], [572801, 644400], [644401, 716000], [716001, 787600], [787601, 859200], [859201, 930800], [930801, 1002400], [1002401, 1074000], [1074001, 1145600], [1145601, 1217200], [1217201, 1288800], [1288801, 1360400], [1360401, 1432016]] ERR6133410 file size 313477 ERR6133410 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 ERR6133410 ERR6133410_1.fastq Input file: ERR6133410_1.fastq trimmed: ERR6133410-trimmed.fastq Parameters used: -- 3' end adapter sequence (-x): AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC -- maximum error ratio allowed (-r): 0.100 -- maximum indel error ratio allowed (-d): 0.030 -- end quality threshold (-q): 10 -- minimum read length allowed after trimming (-l): 18 -- file format (-f): Sanger/Illumina 1.8+ FASTQ -- minimum overlap length for adapter detection (-k): inf -- number of concurrent threads (-t): 20 Sat Dec 7 03:38:33 2024 >> started Sat Dec 7 03:38:34 2024 >> done (0.878s) 1432016 reads processed; of these: 60 ( 0.00%) short reads filtered out after trimming by size control 3 ( 0.00%) empty reads filtered out after trimming by size control 1431953 (100.00%) reads available; of these: 376734 (26.31%) trimmed reads available after processing 1055219 (73.69%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 5 0.00% 19 8 0.00% 20 1 0.00% 21 5 0.00% 22 1 0.00% 23 1 0.00% 24 1 0.00% 25 3 0.00% 26 1 0.00% 27 3 0.00% 28 7 0.00% 29 23 0.00% 30 1 0.00% 31 4 0.00% 32 14 0.00% 33 6 0.00% 34 3 0.00% 35 7 0.00% 36 6 0.00% 37 6 0.00% 38 16 0.00% 39 32 0.00% 40 27 0.00% 41 16 0.00% 42 22 0.00% 43 42 0.00% 44 28 0.00% 45 49 0.00% 46 49 0.00% 47 67 0.00% 48 89 0.01% 49 123 0.01% 50 187 0.01% 51 273 0.02% 52 319 0.02% 53 455 0.03% 54 655 0.05% 55 880 0.06% 56 1187 0.08% 57 1735 0.12% 58 1305 0.09% 59 1504 0.11% 60 1724 0.12% 61 2103 0.15% 62 2118 0.15% 63 2377 0.17% 64 2510 0.18% 65 2704 0.19% 66 2754 0.19% 67 2829 0.20% 68 2595 0.18% 69 2606 0.18% 70 9172 0.64% 71 9709 0.68% 72 11316 0.79% 73 11876 0.83% 74 11997 0.84% 75 13236 0.92% 76 13792 0.96% 77 15439 1.08% 78 16067 1.12% 79 16620 1.16% 80 18017 1.26% 81 21037 1.47% 82 22503 1.57% 83 22272 1.56% 84 25381 1.77% 85 18721 1.31% 86 19807 1.38% 87 21629 1.51% 88 25621 1.79% 89 27312 1.91% 90 28962 2.02% 91 30811 2.15% 92 26424 1.85% 93 960746 67.09% 1431953 reads passed initial QC criterion=sequence-density sequence-density=3.78 sequence-density-rank=1 fanout-score=2.08 fanout-score-rank=28 prefix-density=3.88 prefix-fanout=2.0 sequence=CAAGGCTAAATAC criterion=fanout-score sequence-density=0.11 sequence-density-rank=21 fanout-score=77.06 fanout-score-rank=1 prefix-density=8.40 prefix-fanout=1.1 sequence=CCGCACCCTAGCTGGCTAAAGTC Potential 3prime adapter identified. Now checking if in reference sequence Warning: gzbuffer added in zlib v1.2.3.5. Unable to change buffer size from default of 8192. 1 reads; of these: 1 (100.00%) were unpaired; of these: 0 (0.00%) aligned 0 times 0 (0.00%) aligned exactly 1 time 1 (100.00%) aligned >1 times 100.00% overall alignment rate Potential adapter found in reference sequence. Continuing without clipping. Started job on | Dec 07 03:38:48 Started mapping on | Dec 07 03:38:49 Finished on | Dec 07 03:38:55 Mapping speed, Million of reads per hour | 859.17 Number of input reads | 1431953 Average input read length | 89 UNIQUE READS: Uniquely mapped reads number | 627249 Uniquely mapped reads % | 43.80% Average mapped length | 88.47 Number of splices: Total | 36482 Number of splices: Annotated (sjdb) | 29732 Number of splices: GT/AG | 35112 Number of splices: GC/AG | 636 Number of splices: AT/AC | 25 Number of splices: Non-canonical | 709 Mismatch rate per base, % | 0.85% Deletion rate per base | 0.04% Deletion average length | 1.73 Insertion rate per base | 0.02% Insertion average length | 1.78 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 675844 % of reads mapped to multiple loci | 47.20% Number of reads mapped to too many loci | 58672 % of reads mapped to too many loci | 4.10% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 4.19% % of reads unmapped: other | 0.71% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 128860 128860 128860 N_multimapping 675844 675844 675844 N_noFeature 56311 62660 600319 N_ambiguous 24730 4137 107 UnstrandedReadsAssigned:546208 PositiveStrandReadsAssigned:560452 NegativeStrandReadsAssigned:26823 Dataset is classified positive stranded MeadianReadLen=93 20thPercentileLength=84 echo kmer=79 ERR6133410 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: ERR6133410-trimmed.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 1,431,953 reads, 920,066 reads pseudoaligned [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 917 rounds 52973 ERR6133410.ke.tsv 35125 ERR6133410.se.tsv 88098 total ==> ERR6133410.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 20 20.6645 PNS24243 293 194 0 0 KQK14069 1603 1504 23 21.6785 KQK14071 474 375 0 0 ==> ERR6133410.se.tsv <== BRADI_1g14170v3 23 BRADI_1g53295v3 6 BRADI_1g59795v3 9 BRADI_1g07683v3 0 BRADI_1g00485v3 0 BRADI_1g20270v3 13 BRADI_1g74790v3 5 BRADI_1g09890v3 1 BRADI_1g77505v3 13 BRADI_1g48960v3 0 ERR6133410 completed mapping pipeline successfully