Starting /dee2/code/volunteer_pipeline.sh ERR6133407 current disk space = 1547624972288 free memory = 1407038080 ERR6133407 SRAfilesize 1f1b3fed0d3268fec17265780975ce60 ERR6133407.sra ERR6133407.sra file validated ERR6133407 is single end ERR6133407 is conventional basespace ERR6133407 read1 length is 70-93 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename ERR6133407_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 46 >>END_MODULE >>Per base sequence quality fail #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 29.35975 33.0 27.0 33.0 15.0 37.0 2 33.598 37.0 33.0 37.0 27.0 37.0 3 33.63475 37.0 33.0 37.0 27.0 37.0 4 33.6385 37.0 33.0 37.0 27.0 37.0 5 33.8555 37.0 33.0 37.0 27.0 37.0 6 33.81 37.0 33.0 37.0 27.0 37.0 7 35.074 37.0 33.0 37.0 27.0 40.0 8 34.9855 37.0 33.0 37.0 27.0 40.0 9 35.1825 37.0 33.0 37.0 27.0 40.0 10-11 35.189375 37.0 33.0 37.0 27.0 40.0 12-13 34.92375 37.0 33.0 37.0 27.0 40.0 14-15 34.96625 37.0 33.0 37.0 27.0 40.0 16-17 34.707 37.0 33.0 37.0 27.0 40.0 18-19 34.585625 37.0 33.0 37.0 27.0 40.0 20-21 33.71025 37.0 33.0 37.0 24.5 40.0 22-23 33.588875 37.0 33.0 37.0 24.5 40.0 24-25 33.474375 37.0 33.0 37.0 24.5 40.0 26-27 33.284625000000005 37.0 33.0 37.0 22.0 40.0 28-29 32.838499999999996 35.0 33.0 37.0 22.0 40.0 30-31 32.792 33.0 33.0 37.0 22.0 40.0 32-33 32.11575 33.0 33.0 37.0 22.0 40.0 34-35 31.223 33.0 27.0 37.0 15.0 40.0 36-37 30.86475 33.0 27.0 37.0 15.0 37.0 38-39 31.402625 33.0 27.0 37.0 22.0 37.0 40-41 30.8185 33.0 27.0 37.0 15.0 37.0 42-43 30.790625 33.0 27.0 37.0 15.0 37.0 44-45 30.689 33.0 27.0 37.0 18.5 37.0 46-47 30.1005 33.0 27.0 37.0 15.0 37.0 48-49 29.912 33.0 27.0 37.0 15.0 37.0 50-51 29.287375 33.0 27.0 37.0 15.0 37.0 52-53 29.280375 33.0 27.0 37.0 15.0 37.0 54-55 29.286375 33.0 27.0 37.0 15.0 37.0 56-57 28.619999999999997 33.0 27.0 33.0 15.0 37.0 58-59 28.416125 33.0 27.0 33.0 15.0 37.0 60-61 28.164375 33.0 27.0 33.0 15.0 37.0 62-63 27.788249999999998 33.0 22.0 33.0 15.0 37.0 64-65 27.350499999999997 33.0 22.0 33.0 15.0 37.0 66-67 27.03125 33.0 22.0 33.0 15.0 37.0 68-69 26.339624999999998 27.0 22.0 33.0 10.5 35.0 70-71 28.363848247927656 33.0 27.0 33.0 15.0 35.0 72-73 28.583375835421037 33.0 27.0 33.0 15.0 37.0 74-75 28.63927538499383 33.0 27.0 33.0 15.0 37.0 76-77 28.405293010957852 33.0 27.0 33.0 15.0 37.0 78-79 27.576723823233714 33.0 27.0 33.0 10.5 37.0 80-81 26.649527215654842 33.0 22.0 33.0 6.0 37.0 82-83 26.141790271692088 33.0 22.0 33.0 4.0 37.0 84-85 25.496079183704936 33.0 22.0 33.0 2.0 37.0 86-87 24.69707835325365 33.0 15.0 33.0 2.0 37.0 88-89 24.10265604249668 33.0 15.0 33.0 2.0 35.0 90-91 22.727091633466134 27.0 2.0 33.0 2.0 35.0 92-93 21.252589641434263 27.0 2.0 33.0 2.0 33.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 20 81.0 21 119.0 22 128.0 23 152.0 24 171.0 25 222.0 26 229.0 27 265.0 28 240.0 29 271.0 30 284.0 31 255.0 32 287.0 33 295.0 34 279.0 35 296.0 36 258.0 37 145.0 38 23.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 72.725 6.8500000000000005 7.575 12.85 2 57.175 21.775 11.55 9.5 3 37.175000000000004 33.975 17.5 11.35 4 24.725 33.45 19.475 22.35 5 34.225 22.95 25.674999999999997 17.150000000000002 6 17.625 40.525 25.0 16.85 7 40.8 25.124999999999996 19.15 14.924999999999999 8 25.624999999999996 22.7 25.775 25.900000000000002 9 20.075000000000003 35.65 27.175 17.1 10-11 20.9 31.137500000000003 31.974999999999998 15.987499999999999 12-13 19.0875 32.337500000000006 26.937499999999996 21.637500000000003 14-15 16.4375 36.762499999999996 27.737499999999997 19.0625 16-17 25.4875 29.5875 21.0375 23.8875 18-19 24.95 21.775 34.4 18.875 20-21 27.8125 21.175 32.0 19.0125 22-23 31.337500000000002 18.9375 30.8 18.925 24-25 22.05 23.3875 30.7875 23.775 26-27 26.05 21.2625 28.749999999999996 23.9375 28-29 22.25 29.799999999999997 31.075000000000003 16.875 30-31 34.1875 25.0375 24.525 16.25 32-33 27.8625 22.650000000000002 25.35 24.1375 34-35 19.625 39.4875 23.599999999999998 17.2875 36-37 27.35 24.725 21.2625 26.6625 38-39 36.162499999999994 21.5625 24.6875 17.5875 40-41 23.400000000000002 21.875 35.325 19.400000000000002 42-43 28.825 30.7 24.712500000000002 15.7625 44-45 24.575 25.5375 31.7375 18.15 46-47 28.249999999999996 22.175 24.5375 25.0375 48-49 27.125 21.925 26.0125 24.9375 50-51 19.225 31.05 25.924999999999997 23.799999999999997 52-53 22.2 24.65 23.6375 29.512500000000003 54-55 20.5 25.8625 31.0 22.6375 56-57 27.375 30.837500000000002 24.375 17.4125 58-59 20.9 30.375000000000004 29.512500000000003 19.2125 60-61 33.5875 26.650000000000002 22.537499999999998 17.224999999999998 62-63 20.549999999999997 24.75 31.924999999999997 22.775000000000002 64-65 19.6 38.9375 24.2 17.2625 66-67 25.9625 31.525 24.0 18.512500000000003 68-69 18.7375 24.5125 28.537499999999998 28.212500000000002 70-71 22.528505199849644 29.2695150983586 23.480766821200348 24.721212880591402 72-73 25.80482262340614 26.03206665825022 30.804191389976015 17.35891932836763 74-75 28.694878637692213 30.4104714703266 24.920574405896556 15.974075486084635 76-77 21.382924335378323 24.143660531697343 23.824130879345603 30.649284253578735 78-79 27.286761868004632 29.306574038337835 26.50199408207899 16.904670011578542 80-81 18.451996381961493 39.255717792996506 24.783563767928673 17.50872205711332 82-83 24.268547544409614 24.751828631138974 24.21630094043887 26.763322884012542 84-85 18.596955658504303 28.69622766379881 30.57577763070814 22.13103904698875 86-87 18.220451527224434 31.314741035856574 24.701195219123505 25.763612217795483 88-89 20.132802124833997 24.741035856573706 31.314741035856574 23.811420982735722 90-91 26.82602921646746 31.992031872509962 22.416998671978753 18.764940239043824 92-93 17.795484727755646 30.199203187250994 28.605577689243027 23.399734395750333 >>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 0.0 17 1.5 18 2.5 19 2.5 20 3.0 21 3.0 22 4.0 23 7.0 24 6.5 25 6.5 26 10.5 27 13.5 28 18.0 29 20.5 30 31.0 31 59.0 32 68.5 33 55.5 34 58.5 35 74.0 36 90.5 37 128.5 38 179.0 39 180.0 40 173.0 41 191.0 42 227.5 43 265.5 44 231.5 45 195.5 46 184.0 47 146.5 48 108.5 49 98.5 50 99.0 51 106.0 52 111.5 53 143.5 54 312.0 55 318.0 56 147.0 57 96.5 58 76.0 59 42.0 60 24.0 61 14.5 62 9.0 63 10.5 64 10.0 65 13.5 66 11.0 67 7.0 68 6.5 69 9.5 70 9.5 71 5.0 72 4.5 73 2.5 74 1.0 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 0.0 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 15.0 73 12.0 74 13.0 75 12.0 76 8.0 77 14.0 78 15.0 79 4.0 80 11.0 81 25.0 82 22.0 83 27.0 84 25.0 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 3765.0 >>END_MODULE >>Sequence Duplication Levels warn #Total Deduplicated Percentage 63.125 #Duplication Level Percentage of deduplicated Percentage of total 1 90.41584158415841 57.074999999999996 2 4.237623762376238 5.35 3 1.3465346534653466 2.55 4 1.0693069306930694 2.7 5 0.6336633663366337 2.0 6 0.4356435643564357 1.6500000000000001 7 0.4356435643564357 1.925 8 0.15841584158415842 0.8 9 0.1188118811881188 0.675 >10 1.0297029702970297 11.725 >50 0.07920792079207921 3.25 >100 0.039603960396039604 10.299999999999999 >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 412 10.299999999999999 No Hit GGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCTTGG 69 1.725 No Hit GGGCTGATATCATCAACCGTGCTAATCTTGGTATGGAAGTAATGCACGAA 61 1.525 No Hit TCTCATGGAGAGTTCGATCCTGGCTCAGGATGAACGCTGGCGGCATGCTT 50 1.25 No Hit CAAGGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCT 44 1.0999999999999999 No Hit GGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAA 44 1.0999999999999999 No Hit GGATTTGTTAAATCAAATCCTTGGTTTAATAACGAACGGTGTTAACTTAC 33 0.8250000000000001 No Hit TACCTAGGCACCCAGAGACGAGGAAGGGCGTAGCAAGCGACGAAATGCTT 23 0.575 No Hit CAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAATACTTGGGCTG 23 0.575 No Hit GGGTTGTTTGGGAATGCAGCCCAAATCGGGCGGTAGACTCCGTCCAAGGC 19 0.475 No Hit GCAAGGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATC 17 0.42500000000000004 No Hit GGGGAGAGCAATACAAGCGTTGTGCTGCTAGGCGAAGCGGTTGAGTGCCG 17 0.42500000000000004 No Hit CAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAATACTTGGGCTGATAT 17 0.42500000000000004 No Hit GGTAATGAAATTATCCGAGCAGCTTGCAAATGGAGTCCTGAACTAGCCGC 15 0.375 No Hit GGAGTTGAAAATAAGCATAGATCCGGAGATTCCCAAATAGGTCAACCTTT 14 0.35000000000000003 No Hit GGCGTTCAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTC 13 0.325 No Hit GGGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCTTG 12 0.3 No Hit GGGCGCGATCTTGCTCGTGAAGGTAATGAAATTATCCGAGCAGCTTGCAA 12 0.3 No Hit GGGCACGTGGAATCCCGTGTGAATCAGCAAGGACCACCTTGCAAGGCTAA 11 0.27499999999999997 No Hit GGGATGATTCTGTATTACAATTTGGTGGAGGAACTTTAGGACATCCTTGG 11 0.27499999999999997 No Hit GCAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAATACTTGGGCT 11 0.27499999999999997 No Hit GATTCAATTTCAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAAT 11 0.27499999999999997 No Hit GGAATCCCGTGTGAATCAGCAAGGACCACCTTGCAAGGCTAAATACTCCT 11 0.27499999999999997 No Hit TCAAAAGAGGAAAGGCTTGCGGTGGATACCTAGGCACCCAGAGACGAGGA 11 0.27499999999999997 No Hit GGAATCTGGTTCACTGCTTTAGGTATTAGTACTATGGCGTTCAACCTAAA 10 0.25 No Hit CAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAGGTC 10 0.25 No Hit GAAGGTAATGAAATTATCCGAGCAGCTTGCAAATGGAGTCCTGAACTAGC 10 0.25 No Hit GGGGCACGTGGAATCCCGTGTGAATCAGCAAGGACCACCTTGCAAGGCTA 10 0.25 No Hit GGAAAAGAAAGCAAAAGCGATTCCCGTAGTAGCGGCGAGCGAAATGGGAG 10 0.25 No Hit GGGTTGTGGGAGAGCAATACAAGCGTTGTGCTGCTAGGCGAAGCGGTTGA 9 0.22499999999999998 No Hit CACGAACGTAATGCTCACAACTTCCCTCTAGATCTAGCTGCTCTTGAAGT 9 0.22499999999999998 No Hit GTTCAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAG 9 0.22499999999999998 No Hit GGTTCACTGCTTTAGGTATTAGTACTATGGCGTTCAACCTAAATGGATTC 8 0.2 No Hit GGAGGGTGAGAGCCCCGTCCGGCCCGGACCCTGTCGCCCCACGAGGCGCC 8 0.2 No Hit TGGGCTGATATCATCAACCGTGCTAATCTTGGTATGGAAGTAATGCACGA 8 0.2 No Hit GGGGAGTTGAAAATAAGCATAGATCCGGAGATTCCCAAATAGGTCAACCT 8 0.2 No Hit GGATGATTCTGTATTACAATTTGGTGGAGGAACTTTAGGACATCCTTGGG 7 0.17500000000000002 No Hit GGGTGAGTAACGCGTAAGAACCTGCCCTTGGGAGGGGAACAACAACTGGA 7 0.17500000000000002 No Hit GTAGTAGGAATCTGGTTCACTGCTTTAGGTATTAGTACTATGGCGTTCAA 7 0.17500000000000002 No Hit GTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCTTGGT 7 0.17500000000000002 No Hit GGCCTGTAGTAGGAATCTGGTTCACTGCTTTAGGTATTAGTACTATGGCG 7 0.17500000000000002 No Hit AGTCAAGGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAA 7 0.17500000000000002 No Hit GAAGGGCGCGATCTTGCTCGTGAAGGTAATGAAATTATCCGAGCAGCTTG 7 0.17500000000000002 No Hit GTAGGAATCTGGTTCACTGCTTTAGGTATTAGTACTATGGCGTTCAACCT 7 0.17500000000000002 No Hit GGCCCGGACCCTGTCGCCCCACGAGGCGCCGTCAACGAGTCGGGTTGTTT 7 0.17500000000000002 No Hit GTCAAGGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAAT 7 0.17500000000000002 No Hit AACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAATACTTGGGCTGA 7 0.17500000000000002 No Hit GGCTGATATCATCAACCGTGCTAATCTTGGTATGGAAGTAATGCACGAAC 6 0.15 No Hit CGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCTTGGTAT 6 0.15 No Hit GGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGTG 6 0.15 No Hit GGGAGAGCAATACAAGCGTTGTGCTGCTAGGCGAAGCGGGTGAGTGCCGC 6 0.15 No Hit GGAAGGGCGTAGCAAGCGACGAAATGCTTCGGGGAGTTGAAAATAAGCAT 6 0.15 No Hit GGGAGAGCAATACAAGCGTTGTGCTGCTAGGCGAAGCGGTTGAGTGCAGC 6 0.15 No Hit GGGAGAGCAATACAAGCGTTGTGCTGCTAGGCGAAGCGGTTGAGGGCCGC 6 0.15 No Hit GATATCATCAACCGTGCTAATCTTGGTATGGAAGTAATGCACGAACGTAA 6 0.15 No Hit GGAGAGCAATACAAGCGTTGTGCTGCTAGGCGAAGCGGTTGAGTGCCGCA 6 0.15 No Hit GGGTGAGAGCCCCGTCCGGCCCGGACCCTGTCGCCCCACGAGGCGCCGTC 6 0.15 No Hit GAACGTAATGCTCACAACTTCCCTCTAGATCTAGCTGCTCTTGAAGTTCC 6 0.15 No Hit GGGAGAGCAATACAAGCGTTGTGCTGCTAGGCGCAGCGGTTGAGTGCCGC 5 0.125 No Hit GCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCTTGGTATG 5 0.125 No Hit GGAGTCCTGAACTAGCCGCAGCTTGTGAAGTATGGAAGGCGATCAAATTC 5 0.125 No Hit CAACTCTCGTTCTTTACACTTCTTCTTGGCTGCTTGGCCTGTAGTAGGAA 5 0.125 No Hit CACCCTAGATGGCTAAAGTCCAGTAGCCGAAAGCATCACTAGCTTACGCT 5 0.125 No Hit GGGGCAGAGGGAATTTCCGGTGGAGCGGTGAAATGCATTGAGATCGGAAA 5 0.125 No Hit GTAATGAAATTATCCGAGCAGCTTGCAAATGGAGTCCTGAACTAGCCGCA 5 0.125 No Hit GGCTGCTTGGCCTGTAGTAGGAATCTGGTTCACTGCTTTAGGTATTAGTA 5 0.125 No Hit GACCCGAGTAGCATGGGGCACGTGGAATCCCGTGTGAATCAGCAAGGACC 5 0.125 No Hit AACGTAATGCTCACAACTTCCCTCTAGATCTAGCTGCTCTTGAAGTTCCC 5 0.125 No Hit GTATGGAAGGCGATCAAATTCGAGTTCGCGCCGGTAGATACTATCGATTA 5 0.125 No Hit CTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAGGTCGCGT 5 0.125 No Hit AACCGTGCTAATCTTGGTATGGAAGTAATGCACGAACGTAATGCTCACAA 5 0.125 No Hit GGGAGTATTATGAAAGGAGATTAATCATAGATTATCAAAAACCCTAGAAA 5 0.125 No Hit GTATTAGTACTATGGCGTTCAACCTAAATGGATTCAATTTCAACCAATCT 5 0.125 No Hit GGAGCAGCCTAAACCGTGAAAACGGGGTTGTGGGAGAGCAATACAAGCGT 5 0.125 No Hit >>END_MODULE >>Adapter Content pass #Position Illumina Universal Adapter Illumina Small RNA 3' Adapter Illumina Small RNA 5' Adapter Nextera Transposase Sequence SOLID Small RNA Adapter 1 0.0 0.0 0.0 0.0 0.0 2 0.0 0.0 0.0 0.0 0.0 3 0.0 0.0 0.0 0.0 0.0 4 0.0 0.0 0.0 0.0 0.0 5 0.0 0.0 0.0 0.0 0.0 6 0.0 0.0 0.0 0.0 0.0 7 0.0 0.0 0.0 0.0 0.0 8 0.0 0.0 0.0 0.0 0.0 9 0.0 0.0 0.0 0.0 0.0 10-11 0.0 0.0 0.0 0.0 0.0 12-13 0.0 0.0 0.0 0.0 0.0 14-15 0.0 0.0 0.0 0.0 0.0 16-17 0.0 0.0 0.0 0.0 0.0 18-19 0.0 0.0 0.0 0.0 0.0 20-21 0.0 0.0 0.0 0.0 0.0 22-23 0.0 0.0 0.0 0.0 0.0 24-25 0.0 0.0 0.0 0.0 0.0 26-27 0.0 0.0 0.0 0.0 0.0 28-29 0.0 0.0 0.0 0.0 0.0 30-31 0.0 0.0 0.0 0.0 0.0 32-33 0.0 0.0 0.0 0.0 0.0 34-35 0.0 0.0 0.0 0.0 0.0 36-37 0.0 0.0 0.0 0.0 0.0 38-39 0.0 0.0 0.0 0.0 0.0 40-41 0.0 0.0 0.0 0.0 0.0 42-43 0.0 0.0 0.0 0.0 0.0 44-45 0.0 0.0 0.0 0.0 0.0 46-47 0.0 0.0 0.0 0.0 0.0 48-49 0.0 0.0 0.0 0.0 0.0 50-51 0.0 0.0 0.0 0.0 0.0 52-53 0.0 0.0 0.0 0.0 0.0 54-55 0.0 0.0 0.0 0.0 0.0 56-57 0.0 0.0 0.0 0.0 0.0 58-59 0.0 0.0 0.0 0.0 0.0 60-61 0.0 0.0 0.0 0.0 0.0 62-63 0.0 0.0 0.0 0.0 0.0 64-65 0.0 0.0 0.0 0.0 0.0 66-67 0.0 0.0 0.0 0.0 0.0 68-69 0.0 0.0 0.0 0.0 0.0 70-71 0.0 0.0 0.0 0.0 0.0 72-73 0.0 0.0 0.0 0.0 0.0 74-75 0.0 0.0 0.0 0.0 0.0 76-77 0.0 0.0 0.0 0.0 0.0 78-79 0.0 0.0 0.0 0.0 0.0 80-81 0.0 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position GGAGAGT 15 9.3584583E-4 85.450005 7 AGAGTTC 15 9.3584583E-4 85.450005 9 GAGAGTT 15 9.3584583E-4 85.450005 8 CATGGAG 15 9.3584583E-4 85.450005 4 CTCATGG 15 9.3584583E-4 85.450005 2 TCTCATG 15 9.3584583E-4 85.450005 1 GGGAGAG 90 0.0 75.95555 1 GGAGAGC 95 0.0 71.95789 2 GCAATAC 95 0.0 71.95789 7 CAATACA 95 0.0 71.95789 8 GAGCAAT 95 0.0 71.95789 5 AGAGCAA 95 0.0 71.95789 4 GAGAGCA 95 0.0 71.95789 3 AGCAATA 95 0.0 71.95789 6 AATACAA 100 0.0 68.36 9 TGGAGAG 20 0.002931568 64.0875 6 TCATGGA 20 0.002931568 64.0875 3 ATGGAGA 25 0.0070938445 51.27 5 AGTGGCG 15 0.009939472 47.472225 84-85 AGTGAAA 15 0.009939472 47.472225 84-85 >>END_MODULE Rejected 59647 READS because READLEN < 1 Read 59647 spots for ERR6133407.sra Written 59647 spots for ERR6133407.sra Rejected 59647 READS because READLEN < 1 Read 59647 spots for ERR6133407.sra Written 59647 spots for ERR6133407.sra Rejected 59647 READS because READLEN < 1 Read 59647 spots for ERR6133407.sra Written 59647 spots for ERR6133407.sra Rejected 59647 READS because READLEN < 1 Read 59647 spots for ERR6133407.sra Written 59647 spots for ERR6133407.sra Rejected 59647 READS because READLEN < 1 Read 59647 spots for ERR6133407.sra Written 59647 spots for ERR6133407.sra Rejected 59647 READS because READLEN < 1 Read 59647 spots for ERR6133407.sra Written 59647 spots for ERR6133407.sra Rejected 59647 READS because READLEN < 1 Read 59647 spots for ERR6133407.sra Written 59647 spots for ERR6133407.sra Rejected 59647 READS because READLEN < 1 Read 59647 spots for ERR6133407.sra Written 59647 spots for ERR6133407.sra Rejected 59647 READS because READLEN < 1 Read 59647 spots for ERR6133407.sra Written 59647 spots for ERR6133407.sra Rejected 59647 READS because READLEN < 1 Read 59647 spots for ERR6133407.sra Written 59647 spots for ERR6133407.sra Rejected 59647 READS because READLEN < 1 Read 59647 spots for ERR6133407.sra Written 59647 spots for ERR6133407.sra Rejected 59647 READS because READLEN < 1 Read 59647 spots for ERR6133407.sra Written 59647 spots for ERR6133407.sra Rejected 59647 READS because READLEN < 1 Read 59647 spots for ERR6133407.sra Written 59647 spots for ERR6133407.sra Rejected 59647 READS because READLEN < 1 Read 59647 spots for ERR6133407.sra Written 59647 spots for ERR6133407.sra Rejected 59647 READS because READLEN < 1 Read 59647 spots for ERR6133407.sra Written 59647 spots for ERR6133407.sra Rejected 59647 READS because READLEN < 1 Read 59647 spots for ERR6133407.sra Written 59647 spots for ERR6133407.sra Rejected 59647 READS because READLEN < 1 Read 59647 spots for ERR6133407.sra Written 59647 spots for ERR6133407.sra Rejected 59647 READS because READLEN < 1 Read 59647 spots for ERR6133407.sra Written 59647 spots for ERR6133407.sra Rejected 59647 READS because READLEN < 1 Read 59647 spots for ERR6133407.sra Written 59647 spots for ERR6133407.sra Rejected 59657 READS because READLEN < 1 Read 59657 spots for ERR6133407.sra Written 59657 spots for ERR6133407.sra SRR ids: ['ERR6133407.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_ta8dhcoh ERR6133407.sra spots: 1192950 blocks: [[1, 59647], [59648, 119294], [119295, 178941], [178942, 238588], [238589, 298235], [298236, 357882], [357883, 417529], [417530, 477176], [477177, 536823], [536824, 596470], [596471, 656117], [656118, 715764], [715765, 775411], [775412, 835058], [835059, 894705], [894706, 954352], [954353, 1013999], [1014000, 1073646], [1073647, 1133293], [1133294, 1192950]] ERR6133407 file size 261268 ERR6133407 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 ERR6133407 ERR6133407_1.fastq Input file: ERR6133407_1.fastq trimmed: ERR6133407-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 03:25:35 2024 >> started Sat Dec 7 03:25:36 2024 >> done (0.843s) 1192950 reads processed; of these: 12 ( 0.00%) short reads filtered out after trimming by size control 1 ( 0.00%) empty reads filtered out after trimming by size control 1192937 (100.00%) reads available; of these: 311383 (26.10%) trimmed reads available after processing 881554 (73.90%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 19 7 0.00% 20 0 0.00% 21 4 0.00% 22 4 0.00% 23 1 0.00% 24 1 0.00% 25 2 0.00% 26 0 0.00% 27 0 0.00% 28 8 0.00% 29 64 0.01% 30 0 0.00% 31 4 0.00% 32 3 0.00% 33 2 0.00% 34 2 0.00% 35 4 0.00% 36 2 0.00% 37 2 0.00% 38 3 0.00% 39 13 0.00% 40 15 0.00% 41 4 0.00% 42 8 0.00% 43 17 0.00% 44 14 0.00% 45 18 0.00% 46 37 0.00% 47 56 0.00% 48 72 0.01% 49 89 0.01% 50 132 0.01% 51 155 0.01% 52 224 0.02% 53 326 0.03% 54 464 0.04% 55 606 0.05% 56 903 0.08% 57 1277 0.11% 58 956 0.08% 59 1078 0.09% 60 1418 0.12% 61 1664 0.14% 62 1821 0.15% 63 1877 0.16% 64 2037 0.17% 65 2267 0.19% 66 2309 0.19% 67 2535 0.21% 68 2210 0.19% 69 2095 0.18% 70 6579 0.55% 71 6760 0.57% 72 8145 0.68% 73 8392 0.70% 74 9043 0.76% 75 9532 0.80% 76 10459 0.88% 77 12186 1.02% 78 12502 1.05% 79 12901 1.08% 80 13801 1.16% 81 16121 1.35% 82 17506 1.47% 83 18131 1.52% 84 20402 1.71% 85 15873 1.33% 86 16030 1.34% 87 17932 1.50% 88 22083 1.85% 89 23075 1.93% 90 24216 2.03% 91 26083 2.19% 92 22672 1.90% 93 815703 68.38% 1192937 reads passed initial QC criterion=sequence-density sequence-density=4.00 sequence-density-rank=1 fanout-score=2.09 fanout-score-rank=23 prefix-density=4.12 prefix-fanout=2.0 sequence=CAAGGCTAAATAC criterion=fanout-score sequence-density=0.13 sequence-density-rank=20 fanout-score=113.10 fanout-score-rank=1 prefix-density=13.49 prefix-fanout=1.1 sequence=CTAGATGGCTACAGTCCAGTAGC 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 03:25:52 Started mapping on | Dec 07 03:25:52 Finished on | Dec 07 03:25:58 Mapping speed, Million of reads per hour | 715.76 Number of input reads | 1192937 Average input read length | 89 UNIQUE READS: Uniquely mapped reads number | 412847 Uniquely mapped reads % | 34.61% Average mapped length | 88.67 Number of splices: Total | 13881 Number of splices: Annotated (sjdb) | 10856 Number of splices: GT/AG | 13218 Number of splices: GC/AG | 243 Number of splices: AT/AC | 17 Number of splices: Non-canonical | 403 Mismatch rate per base, % | 0.83% Deletion rate per base | 0.03% Deletion average length | 1.67 Insertion rate per base | 0.02% Insertion average length | 1.88 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 679242 % of reads mapped to multiple loci | 56.94% Number of reads mapped to too many loci | 46804 % of reads mapped to too many loci | 3.92% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 3.89% % of reads unmapped: other | 0.64% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 100848 100848 100848 N_multimapping 679242 679242 679242 N_noFeature 40275 45280 393590 N_ambiguous 16929 2664 79 UnstrandedReadsAssigned:355643 PositiveStrandReadsAssigned:364903 NegativeStrandReadsAssigned:19178 Dataset is classified positive stranded MeadianReadLen=93 20thPercentileLength=86 echo kmer=81 ERR6133407 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: ERR6133407-trimmed.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 1,192,937 reads, 693,257 reads pseudoaligned [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 957 rounds 52973 ERR6133407.ke.tsv 35125 ERR6133407.se.tsv 88098 total ==> ERR6133407.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 1 1.33504 PNS24243 293 194 0 0 KQK14069 1603 1504 1 1.21787 KQK14071 474 375 0 0 ==> ERR6133407.se.tsv <== BRADI_1g14170v3 1 BRADI_1g53295v3 8 BRADI_1g59795v3 3 BRADI_1g07683v3 0 BRADI_1g00485v3 0 BRADI_1g20270v3 4 BRADI_1g74790v3 4 BRADI_1g09890v3 0 BRADI_1g77505v3 8 BRADI_1g48960v3 0 ERR6133407 completed mapping pipeline successfully