Starting /dee2/code/volunteer_pipeline.sh ERR6133423 current disk space = 1546945880064 free memory = 1421056124 ERR6133423 SRAfilesize faef2d6ed7a33f7281fffbfb3ff82176 ERR6133423.sra ERR6133423.sra file validated ERR6133423 is single end ERR6133423 is conventional basespace ERR6133423 read1 length is 70-93 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename ERR6133423_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 pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 34.95675 37.0 33.0 37.0 33.0 37.0 2 36.3585 37.0 37.0 37.0 33.0 37.0 3 35.69925 37.0 37.0 37.0 33.0 37.0 4 35.44825 37.0 37.0 37.0 33.0 37.0 5 35.39975 37.0 37.0 37.0 33.0 37.0 6 35.66 37.0 37.0 37.0 33.0 37.0 7 37.31625 37.0 37.0 40.0 33.0 40.0 8 37.2975 37.0 37.0 40.0 33.0 40.0 9 37.3235 37.0 37.0 40.0 33.0 40.0 10-11 37.247375 37.0 37.0 40.0 33.0 40.0 12-13 37.179 37.0 37.0 40.0 33.0 40.0 14-15 37.178 37.0 37.0 40.0 33.0 40.0 16-17 36.993875 37.0 37.0 40.0 33.0 40.0 18-19 37.149 37.0 37.0 40.0 33.0 40.0 20-21 37.308625 37.0 37.0 40.0 33.0 40.0 22-23 37.2025 37.0 37.0 40.0 33.0 40.0 24-25 37.238875 37.0 37.0 40.0 33.0 40.0 26-27 37.105875 37.0 37.0 40.0 33.0 40.0 28-29 37.243875 37.0 37.0 40.0 33.0 40.0 30-31 37.173375 37.0 37.0 40.0 33.0 40.0 32-33 37.05275 37.0 37.0 40.0 33.0 40.0 34-35 36.811375 37.0 37.0 40.0 33.0 40.0 36-37 36.880125 37.0 37.0 40.0 33.0 40.0 38-39 36.669375 37.0 37.0 40.0 33.0 40.0 40-41 36.62075 37.0 37.0 40.0 33.0 40.0 42-43 36.45325 37.0 37.0 40.0 33.0 40.0 44-45 36.22725 37.0 37.0 40.0 33.0 40.0 46-47 36.163 37.0 37.0 37.0 33.0 40.0 48-49 35.906375 37.0 35.0 37.0 33.0 40.0 50-51 35.74375 37.0 35.0 37.0 33.0 40.0 52-53 35.656000000000006 37.0 33.0 37.0 33.0 40.0 54-55 35.48925 37.0 33.0 37.0 33.0 38.5 56-57 35.416375 37.0 33.0 37.0 33.0 37.0 58-59 34.920375 37.0 33.0 37.0 33.0 37.0 60-61 34.81275 37.0 33.0 37.0 33.0 37.0 62-63 34.819375 37.0 33.0 37.0 33.0 37.0 64-65 34.47275 37.0 33.0 37.0 33.0 37.0 66-67 34.398875 37.0 33.0 37.0 33.0 37.0 68-69 33.11825 35.0 33.0 35.0 30.0 37.0 70-71 33.37636550989727 33.0 33.0 37.0 27.0 37.0 72-73 34.04997436392861 37.0 33.0 37.0 27.0 37.0 74-75 34.363043389244005 37.0 33.0 37.0 33.0 37.0 76-77 34.254115140021156 37.0 33.0 37.0 33.0 37.0 78-79 34.237011682976146 37.0 33.0 37.0 30.0 37.0 80-81 34.351015667518226 37.0 33.0 37.0 33.0 37.0 82-83 33.93746002505911 37.0 33.0 37.0 30.0 37.0 84-85 34.06083209699517 37.0 33.0 37.0 33.0 37.0 86-87 33.95108005082592 37.0 33.0 37.0 27.0 37.0 88-89 33.89161372299873 37.0 33.0 37.0 27.0 37.0 90-91 33.693646759847525 35.0 33.0 37.0 27.0 37.0 92-93 33.3010165184244 33.0 33.0 37.0 27.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 20 10.0 21 8.0 22 12.0 23 17.0 24 28.0 25 20.0 26 20.0 27 24.0 28 39.0 29 55.0 30 68.0 31 103.0 32 151.0 33 160.0 34 253.0 35 520.0 36 1008.0 37 1098.0 38 405.0 39 1.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 88.675 2.85 2.475 6.0 2 74.52452452452452 15.14014014014014 5.9309309309309315 4.404404404404405 3 39.25 36.75 13.375 10.625 4 34.150000000000006 27.6 18.6 19.650000000000002 5 25.15 31.924999999999997 23.849999999999998 19.075 6 20.1 38.175 23.724999999999998 18.0 7 35.625 30.325000000000003 18.85 15.2 8 31.624999999999996 29.375 23.799999999999997 15.2 9 27.925 26.85 26.174999999999997 19.05 10-11 26.3125 27.0625 26.125 20.5 12-13 29.2375 24.9 26.075 19.787499999999998 14-15 22.725 28.537499999999998 29.599999999999998 19.1375 16-17 24.4875 30.7125 25.937500000000004 18.862499999999997 18-19 24.55 26.950000000000003 26.325 22.175 20-21 24.8 26.825 26.6625 21.712500000000002 22-23 26.775 23.925 27.037499999999998 22.2625 24-25 27.025 24.5625 27.825 20.5875 26-27 24.837500000000002 26.0125 30.6875 18.462500000000002 28-29 25.1 27.5875 27.075 20.2375 30-31 27.075 25.2875 25.8625 21.775 32-33 24.6625 26.7625 27.950000000000003 20.625 34-35 24.887500000000003 23.549999999999997 28.6375 22.925 36-37 25.05 24.1625 28.512500000000003 22.275 38-39 25.474999999999998 25.162499999999998 30.312499999999996 19.05 40-41 26.387500000000003 25.650000000000002 26.625 21.337500000000002 42-43 24.75 28.1 26.137500000000003 21.0125 44-45 23.799999999999997 25.6 28.9 21.7 46-47 23.325000000000003 23.525 28.249999999999996 24.9 48-49 24.337500000000002 25.637500000000003 31.0375 18.987499999999997 50-51 26.237500000000004 25.5625 29.175 19.025 52-53 25.2375 27.625 27.212500000000002 19.925 54-55 23.4625 29.9 27.6375 19.0 56-57 26.424999999999997 24.5125 28.925 20.1375 58-59 24.1125 23.1125 29.462500000000002 23.3125 60-61 24.4375 23.45 29.625 22.4875 62-63 21.7875 28.4125 31.6 18.2 64-65 24.462500000000002 26.224999999999998 29.1125 20.200000000000003 66-67 24.95 26.187500000000004 28.9125 19.950000000000003 68-69 23.9375 25.7 28.599999999999998 21.762500000000003 70-71 26.56738831185083 24.465023151044925 27.305718933800527 21.661869603303714 72-73 26.446592192795283 24.789757750721726 27.676666248274127 21.086983808208863 74-75 23.333333333333332 26.81761006289308 29.157232704402514 20.69182389937107 76-77 23.181646287659145 26.169166771713098 29.282742972393798 21.36644396823396 78-79 23.052644868072214 23.835374321424062 30.85469006438581 22.257290746117913 80-81 23.873987854251013 27.416497975708502 30.528846153846157 18.180668016194332 82-83 23.45929495308141 25.031701749936598 30.814100938371798 20.694902358610197 84-85 23.926302414231255 23.913595933926302 30.50825921219822 21.651842439644216 86-87 23.86277001270648 25.12071156289708 31.95679796696315 19.05972045743329 88-89 22.07115628970775 29.669631512071152 29.364675984752225 18.894536213468868 90-91 27.9415501905972 24.358322744599743 28.42439644218551 19.275730622617534 92-93 23.44345616264295 28.602287166454893 29.008894536213468 18.945362134688693 >>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 2.5 18 2.0 19 0.5 20 0.0 21 3.0 22 3.5 23 3.0 24 5.5 25 6.0 26 6.5 27 9.0 28 11.5 29 10.5 30 17.0 31 30.5 32 38.5 33 51.0 34 60.5 35 65.5 36 93.5 37 120.0 38 146.0 39 167.0 40 182.5 41 191.5 42 213.0 43 240.0 44 207.5 45 188.5 46 221.5 47 222.0 48 189.5 49 192.5 50 178.0 51 164.5 52 168.5 53 170.0 54 139.5 55 75.0 56 51.0 57 47.5 58 54.0 59 52.5 60 43.5 61 43.0 62 44.5 63 39.0 64 31.5 65 27.5 66 24.5 67 19.5 68 10.0 69 7.0 70 5.0 71 2.0 72 2.0 73 2.5 74 2.5 75 1.5 76 1.0 77 0.5 78 0.5 79 0.5 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 0.1 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 0.038104915534103896 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 9.0 71 5.0 72 5.0 73 4.0 74 4.0 75 6.0 76 1.0 77 4.0 78 3.0 79 5.0 80 4.0 81 4.0 82 6.0 83 2.0 84 3.0 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 3935.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 77.725 #Duplication Level Percentage of deduplicated Percentage of total 1 90.47925377935027 70.325 2 5.467996140238018 8.5 3 2.0585397233837246 4.8 4 0.6111289803795433 1.9 5 0.3859761981344484 1.5 6 0.1929880990672242 0.8999999999999999 7 0.0 0.0 8 0.0643293663557414 0.4 9 0.1286587327114828 0.8999999999999999 >10 0.5789642972016726 8.825 >50 0.0321646831778707 1.95 >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 GGGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGT 78 1.95 No Hit GGGATGATTCTGTATTACAATTTGGTGGAGGAACTTTAGGACATCCTTGG 49 1.225 No Hit GGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGTG 38 0.95 No Hit GGGCGCGATCTTGCTCGTGAAGGTAATGAAATTATCCGAGCAGCTTGCAA 34 0.8500000000000001 No Hit GGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGTGTACAAGCTCGTAA 26 0.65 No Hit GGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAA 25 0.625 No Hit GGGGATGATTCTGTATTACAATTTGGTGGAGGAACTTTAGGACATCCTTG 22 0.5499999999999999 No Hit GGACATCCTTGGGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTT 21 0.525 No Hit GGAGTCCCATATATATATGTATAAGATGCCAGCCCGGTTTCGTCAACCAT 16 0.4 No Hit GGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCTTGG 16 0.4 No Hit GGATGATTCTGTATTACAATTTGGTGGAGGAACTTTAGGACATCCTTGGG 16 0.4 No Hit GGAGGAACTTTAGGACATCCTTGGGGAAATGCACCTGGTGCAGCAGCTAA 15 0.375 No Hit TACCTAGGCACCCAGAGACGAGGAAGGGCGTAGCAAGCGACGAAATGCTT 12 0.3 No Hit GGAACTTTAGGACATCCTTGGGGAAATGCACCTGGTGCAGCAGCTAATCG 11 0.27499999999999997 No Hit GGAAGAGCCCGAGCTGCTGCAGCAGGTTTTGAAAAGGGAATCGATCGTGA 11 0.27499999999999997 No Hit GGCGTTCAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTC 11 0.27499999999999997 No Hit GGGAGTATTATGAAAGGAGATTAATCATAGATTATCAAAAACCCTAGAAA 10 0.25 No Hit GAAGGTAATGAAATTATCCGAGCAGCTTGCAAATGGAGTCCTGAACTAGC 10 0.25 No Hit GGAGTTGAAAATAAGCATAGATCCGGAGATTCCCAAATAGGTCAACCTTT 10 0.25 No Hit GTAGTAGGAATCTGGTTCACTGCTTTAGGTATTAGTACTATGGCGTTCAA 9 0.22499999999999998 No Hit GGTAATGAAATTATCCGAGCAGCTTGCAAATGGAGTCCTGAACTAGCCGC 9 0.22499999999999998 No Hit GGAGTGGGGGTGCCATACGCAAAAAGGAAGCGACTCATAGAATGGCAGAG 9 0.22499999999999998 No Hit GGGAGAGCAATACAAGCGTTGTGCTGCTAGGCGAAGCGGTTGAGTGCCGC 9 0.22499999999999998 No Hit GGCTTTAGAAGCCTGTGTACAAGCTCGTAACGAAGGGCGCGATCTTGCTC 8 0.2 No Hit GGCGCGATCTTGCTCGTGAAGGTAATGAAATTATCCGAGCAGCTTGCAAA 8 0.2 No Hit GAGGAACTTTAGGACATCCTTGGGGAAATGCACCTGGTGCAGCAGCTAAT 6 0.15 No Hit GTAGTTGATAGTCAAGGTCGCGTTATTAATACTTGGGCTGATATCATCAA 6 0.15 No Hit GGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGTGT 6 0.15 No Hit GTACAAGCTCGTAACGAAGGGCGCGATCTTGCTCGTGAAGGTAATGAAAT 6 0.15 No Hit GGGAATCGATCGTGATTTAGAACCTGTTCTTTACATGAACCCTCTTAACT 6 0.15 No Hit GGTTTTGAAAAGGGAATCGATCGTGATTTAGAACCTGTTCTTTACATGAA 6 0.15 No Hit GGAGTCCTGAACTAGCCGCAGCTTGTGAAGTATGGAAGGCGATCAAATTC 5 0.125 No Hit GGGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTA 5 0.125 No Hit GTATTAAGATGGACCATATATAAAGTGTCAGCTCAGTTTTGTCAACTCTG 5 0.125 No Hit GGATTTGAAGAAAAAAAAGACTTCGATTCATTTTCTATTTATTTCGTTAG 5 0.125 No Hit GGGCAAGGAGAAGTACAAGTGCGGATCCAACGTCTTCTGGAAATGGTGAA 5 0.125 No Hit GGAGAAGTACAAGTGCGGATCCAACGTCTTCTGGAAATGGTGAAGATGAT 5 0.125 No Hit CAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAGGTC 5 0.125 No Hit GGGAGTGGGGGTGCCATACGCAAAAAGGAAGCGACTCATAGAATGGCAGA 5 0.125 No Hit GAATCAAGTCATCTCATTCTCATCTATGCAATTGCAAACACAACACAGGG 5 0.125 No Hit GGGCCGGGTATCTCTCTGCATGTACGTATGCCTGTAATGTACGTAGCTAC 5 0.125 No Hit GGGCAATGGGGGATGTGAAGGCTTGTGGTGCCTGTGTGGGCTTGGTGTAG 5 0.125 No Hit GGAAATGGTGAAGATGATACGAATATGCCGGCCGGGTGCTGATATTGTGA 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 0.025 0.0 0.0 0.0 0.0 8 0.025 0.0 0.0 0.0 0.0 9 0.05 0.0 0.0 0.0 0.0 10-11 0.05 0.0 0.0 0.0 0.0 12-13 0.0625 0.0 0.0 0.0 0.0 14-15 0.075 0.0 0.0 0.0 0.0 16-17 0.075 0.0 0.0 0.0 0.0 18-19 0.075 0.0 0.0 0.0 0.0 20-21 0.075 0.0 0.0 0.0 0.0 22-23 0.075 0.0 0.0 0.0 0.0 24-25 0.075 0.0 0.0 0.0 0.0 26-27 0.075 0.0 0.0 0.0 0.0 28-29 0.075 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 0.075 0.0 0.0 0.0 0.0 36-37 0.075 0.0 0.0 0.0 0.0 38-39 0.075 0.0 0.0 0.0 0.0 40-41 0.075 0.0 0.0 0.0 0.0 42-43 0.075 0.0 0.0 0.0 0.0 44-45 0.075 0.0 0.0 0.0 0.0 46-47 0.075 0.0 0.0 0.0 0.0 48-49 0.075 0.0 0.0 0.0 0.0 50-51 0.075 0.0 0.0 0.0 0.0 52-53 0.075 0.0 0.0 0.0 0.0 54-55 0.075 0.0 0.0 0.0 0.0 56-57 0.075 0.0 0.0 0.0 0.0 58-59 0.075 0.0 0.0 0.0 0.0 60-61 0.075 0.0 0.0 0.0 0.0 62-63 0.075 0.0 0.0 0.0 0.0 64-65 0.075 0.0 0.0 0.0 0.0 66-67 0.075 0.0 0.0 0.0 0.0 68-69 0.075 0.0 0.0 0.0 0.0 70-71 0.075 0.0 0.0 0.0 0.0 72-73 0.075 0.0 0.0 0.0 0.0 74-75 0.075 0.0 0.0 0.0 0.0 76-77 0.075 0.0 0.0 0.0 0.0 78-79 0.075 0.0 0.0 0.0 0.0 80-81 0.075 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content pass >>END_MODULE Rejected 155771 READS because READLEN < 1 Read 155771 spots for ERR6133423.sra Written 155771 spots for ERR6133423.sra Rejected 155771 READS because READLEN < 1 Read 155771 spots for ERR6133423.sra Written 155771 spots for ERR6133423.sra Rejected 155771 READS because READLEN < 1 Read 155771 spots for ERR6133423.sra Written 155771 spots for ERR6133423.sra Rejected 155771 READS because READLEN < 1 Read 155771 spots for ERR6133423.sra Written 155771 spots for ERR6133423.sra Rejected 155771 READS because READLEN < 1 Read 155771 spots for ERR6133423.sra Written 155771 spots for ERR6133423.sra Rejected 155771 READS because READLEN < 1 Read 155771 spots for ERR6133423.sra Written 155771 spots for ERR6133423.sra Rejected 155771 READS because READLEN < 1 Read 155771 spots for ERR6133423.sra Written 155771 spots for ERR6133423.sra Rejected 155771 READS because READLEN < 1 Read 155771 spots for ERR6133423.sra Written 155771 spots for ERR6133423.sra Rejected 155771 READS because READLEN < 1 Read 155771 spots for ERR6133423.sra Written 155771 spots for ERR6133423.sra Rejected 155771 READS because READLEN < 1 Read 155771 spots for ERR6133423.sra Written 155771 spots for ERR6133423.sra Rejected 155771 READS because READLEN < 1 Read 155771 spots for ERR6133423.sra Written 155771 spots for ERR6133423.sra Rejected 155771 READS because READLEN < 1 Read 155771 spots for ERR6133423.sra Written 155771 spots for ERR6133423.sra Rejected 155788 READS because READLEN < 1 Read 155788 spots for ERR6133423.sra Written 155788 spots for ERR6133423.sra Rejected 155771 READS because READLEN < 1 Read 155771 spots for ERR6133423.sra Written 155771 spots for ERR6133423.sra Rejected 155771 READS because READLEN < 1 Read 155771 spots for ERR6133423.sra Written 155771 spots for ERR6133423.sra Rejected 155771 READS because READLEN < 1 Read 155771 spots for ERR6133423.sra Written 155771 spots for ERR6133423.sra Rejected 155771 READS because READLEN < 1 Read 155771 spots for ERR6133423.sra Written 155771 spots for ERR6133423.sra Rejected 155771 READS because READLEN < 1 Read 155771 spots for ERR6133423.sra Written 155771 spots for ERR6133423.sra Rejected 155771 READS because READLEN < 1 Read 155771 spots for ERR6133423.sra Written 155771 spots for ERR6133423.sra Rejected 155771 READS because READLEN < 1 Read 155771 spots for ERR6133423.sra Written 155771 spots for ERR6133423.sra SRR ids: ['ERR6133423.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd__ho4gxqu ERR6133423.sra spots: 3115437 blocks: [[1, 155771], [155772, 311542], [311543, 467313], [467314, 623084], [623085, 778855], [778856, 934626], [934627, 1090397], [1090398, 1246168], [1246169, 1401939], [1401940, 1557710], [1557711, 1713481], [1713482, 1869252], [1869253, 2025023], [2025024, 2180794], [2180795, 2336565], [2336566, 2492336], [2492337, 2648107], [2648108, 2803878], [2803879, 2959649], [2959650, 3115437]] ERR6133423 file size 689887 ERR6133423 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 ERR6133423 ERR6133423_1.fastq Input file: ERR6133423_1.fastq trimmed: ERR6133423-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 04:48:54 2024 >> started Sat Dec 7 04:48:55 2024 >> done (1.689s) 3115437 reads processed; of these: 1551 ( 0.05%) short reads filtered out after trimming by size control 19 ( 0.00%) empty reads filtered out after trimming by size control 3113867 (99.95%) reads available; of these: 43874 ( 1.41%) trimmed reads available after processing 3069993 (98.59%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 35 0.00% 19 27 0.00% 20 22 0.00% 21 14 0.00% 22 12 0.00% 23 11 0.00% 24 11 0.00% 25 11 0.00% 26 7 0.00% 27 6 0.00% 28 7 0.00% 29 40 0.00% 30 3 0.00% 31 4 0.00% 32 5 0.00% 33 5 0.00% 34 4 0.00% 35 6 0.00% 36 4 0.00% 37 8 0.00% 38 9 0.00% 39 15 0.00% 40 19 0.00% 41 14 0.00% 42 20 0.00% 43 17 0.00% 44 18 0.00% 45 25 0.00% 46 23 0.00% 47 25 0.00% 48 33 0.00% 49 27 0.00% 50 25 0.00% 51 19 0.00% 52 20 0.00% 53 17 0.00% 54 22 0.00% 55 20 0.00% 56 17 0.00% 57 13 0.00% 58 16 0.00% 59 18 0.00% 60 16 0.00% 61 16 0.00% 62 1 0.00% 63 3 0.00% 64 4 0.00% 65 4 0.00% 66 2 0.00% 67 9 0.00% 68 18 0.00% 69 38 0.00% 70 4285 0.14% 71 3038 0.10% 72 3278 0.11% 73 2882 0.09% 74 3249 0.10% 75 3319 0.11% 76 2638 0.08% 77 2713 0.09% 78 3278 0.11% 79 4073 0.13% 80 3267 0.10% 81 3495 0.11% 82 3897 0.13% 83 4669 0.15% 84 3274 0.11% 85 77 0.00% 86 187 0.01% 87 262 0.01% 88 496 0.02% 89 1143 0.04% 90 2545 0.08% 91 7498 0.24% 92 30143 0.97% 93 3019376 96.97% 3113867 reads passed initial QC criterion=sequence-density sequence-density=0.53 sequence-density-rank=1 fanout-score=2.42 fanout-score-rank=29 prefix-density=0.60 prefix-fanout=2.1 sequence=TGTACATTTGAA criterion=fanout-score sequence-density=0.06 sequence-density-rank=16 fanout-score=39.35 fanout-score-rank=1 prefix-density=0.18 prefix-fanout=12.6 sequence=TTTTTTTTTTAAGAATCCTCCATTTTTGTTCTTCCACCCATGCAATAGAGAGCAAATGGGAAAAGAGGGGTTACTTTTTTTCATTTTTCCCTTAAAAGATAGGCTTTGAAATCGGAGTCATGGAATAATGGTGAATTCAAATGTTTAGTTCTTTAGTATAAGAAGTATAAGAA Started job on | Dec 07 04:50:11 Started mapping on | Dec 07 04:50:11 Finished on | Dec 07 04:50:17 Mapping speed, Million of reads per hour | 1868.32 Number of input reads | 3113867 Average input read length | 92 UNIQUE READS: Uniquely mapped reads number | 2226778 Uniquely mapped reads % | 71.51% Average mapped length | 92.35 Number of splices: Total | 109866 Number of splices: Annotated (sjdb) | 90584 Number of splices: GT/AG | 105161 Number of splices: GC/AG | 2808 Number of splices: AT/AC | 50 Number of splices: Non-canonical | 1847 Mismatch rate per base, % | 0.47% Deletion rate per base | 0.05% Deletion average length | 1.85 Insertion rate per base | 0.02% Insertion average length | 1.87 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 823485 % of reads mapped to multiple loci | 26.45% Number of reads mapped to too many loci | 8427 % of reads mapped to too many loci | 0.27% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 1.75% % of reads unmapped: other | 0.02% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 63604 63604 63604 N_multimapping 823485 823485 823485 N_noFeature 119705 138595 2126452 N_ambiguous 89687 8317 263 UnstrandedReadsAssigned:2017386 PositiveStrandReadsAssigned:2079866 NegativeStrandReadsAssigned:100063 Dataset is classified positive stranded MeadianReadLen=93 20thPercentileLength=93 echo kmer=89 ERR6133423 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: ERR6133423-trimmed.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 3,113,867 reads, 2,721,698 reads pseudoaligned [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 973 rounds 52973 ERR6133423.ke.tsv 35125 ERR6133423.se.tsv 88098 total ==> ERR6133423.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 59 21.0681 PNS24243 293 194 0 0 KQK14069 1603 1504 86 28.0142 KQK14071 474 375 0 0 ==> ERR6133423.se.tsv <== BRADI_1g14170v3 85 BRADI_1g53295v3 24 BRADI_1g59795v3 6 BRADI_1g07683v3 0 BRADI_1g00485v3 0 BRADI_1g20270v3 23 BRADI_1g74790v3 25 BRADI_1g09890v3 0 BRADI_1g77505v3 47 BRADI_1g48960v3 0 ERR6133423 completed mapping pipeline successfully