Starting /dee2/code/volunteer_pipeline.sh ERR6133518 current disk space = 1544465473536 free memory = 1604079532 ERR6133518 SRAfilesize 86028cf8831e45e7d9132be334110502 ERR6133518.sra ERR6133518.sra file validated ERR6133518 is single end ERR6133518 is conventional basespace ERR6133518 read1 length is 70-93 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename ERR6133518_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 44 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 36.63925 37.0 37.0 37.0 37.0 37.0 2 36.83975 37.0 37.0 37.0 37.0 37.0 3 36.57625 37.0 37.0 37.0 37.0 37.0 4 35.9265 37.0 37.0 37.0 33.0 37.0 5 36.0355 37.0 37.0 37.0 33.0 37.0 6 36.30025 37.0 37.0 37.0 33.0 37.0 7 38.31825 40.0 37.0 40.0 37.0 40.0 8 38.398 40.0 37.0 40.0 37.0 40.0 9 38.388 40.0 37.0 40.0 37.0 40.0 10-11 38.435375 40.0 37.0 40.0 37.0 40.0 12-13 38.26925 40.0 37.0 40.0 37.0 40.0 14-15 38.238749999999996 40.0 37.0 40.0 37.0 40.0 16-17 38.16375 40.0 37.0 40.0 37.0 40.0 18-19 38.07575 40.0 37.0 40.0 37.0 40.0 20-21 38.020625 40.0 37.0 40.0 37.0 40.0 22-23 38.15175 40.0 37.0 40.0 37.0 40.0 24-25 38.049125000000004 40.0 37.0 40.0 37.0 40.0 26-27 37.998125 40.0 37.0 40.0 37.0 40.0 28-29 38.036249999999995 40.0 37.0 40.0 37.0 40.0 30-31 38.079875 40.0 37.0 40.0 37.0 40.0 32-33 38.108125 40.0 37.0 40.0 37.0 40.0 34-35 37.994375000000005 40.0 37.0 40.0 37.0 40.0 36-37 37.9805 37.0 37.0 40.0 37.0 40.0 38-39 37.788375 37.0 37.0 40.0 37.0 40.0 40-41 37.71525 37.0 37.0 40.0 37.0 40.0 42-43 37.657250000000005 37.0 37.0 40.0 37.0 40.0 44-45 37.34425 37.0 37.0 40.0 35.0 40.0 46-47 37.215875 37.0 37.0 40.0 33.0 40.0 48-49 37.0685 37.0 37.0 38.5 33.0 40.0 50-51 36.838875 37.0 37.0 37.0 33.0 40.0 52-53 36.40475 37.0 37.0 37.0 33.0 40.0 54-55 36.483000000000004 37.0 37.0 37.0 33.0 40.0 56-57 36.337875 37.0 37.0 37.0 33.0 38.5 58-59 35.9865 37.0 37.0 37.0 33.0 37.0 60-61 36.082750000000004 37.0 37.0 37.0 33.0 37.0 62-63 35.965875 37.0 37.0 37.0 33.0 37.0 64-65 35.865750000000006 37.0 37.0 37.0 33.0 37.0 66-67 35.84075 37.0 37.0 37.0 33.0 37.0 68-69 34.938625 35.0 35.0 37.0 33.0 37.0 70-71 35.2199531445753 37.0 33.0 37.0 33.0 37.0 72-73 35.65266176194767 37.0 35.0 37.0 33.0 37.0 74-75 35.61514592474088 37.0 35.0 37.0 33.0 37.0 76-77 35.55164247271466 37.0 33.0 37.0 33.0 37.0 78-79 35.4345638157067 37.0 33.0 37.0 33.0 37.0 80-81 35.44175140356079 37.0 33.0 37.0 33.0 37.0 82-83 35.28454013149376 37.0 33.0 37.0 33.0 37.0 84-85 35.14098127001594 37.0 33.0 37.0 33.0 37.0 86-87 35.04459007967104 37.0 33.0 37.0 33.0 37.0 88-89 35.02929838087895 37.0 33.0 37.0 33.0 37.0 90-91 35.041249036237474 37.0 33.0 37.0 33.0 37.0 92-93 34.95990747879722 37.0 33.0 37.0 33.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 20 5.0 21 5.0 22 3.0 23 5.0 24 1.0 25 9.0 26 9.0 27 12.0 28 16.0 29 20.0 30 25.0 31 32.0 32 51.0 33 61.0 34 116.0 35 265.0 36 1112.0 37 1398.0 38 844.0 39 11.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 87.425 2.6 2.775 7.199999999999999 2 70.975 17.150000000000002 7.5 4.375 3 36.275 39.85 12.875 11.0 4 34.125 27.725 19.8 18.35 5 25.6 30.3 27.375 16.725 6 18.275 39.074999999999996 25.324999999999996 17.325 7 36.199999999999996 28.9 19.650000000000002 15.25 8 29.125 31.7 22.2 16.975 9 24.95 30.45 27.375 17.224999999999998 10-11 24.75 28.425 28.125 18.7 12-13 26.325 27.6375 27.625 18.4125 14-15 21.675 32.725 27.462500000000002 18.1375 16-17 23.599999999999998 31.412499999999998 24.8625 20.125 18-19 23.9 27.950000000000003 28.975 19.175 20-21 24.371324909295634 25.960215188289755 29.137995746277994 20.530464156136617 22-23 27.762500000000003 23.325000000000003 28.262500000000003 20.65 24-25 25.3 25.587500000000002 28.275 20.837500000000002 26-27 24.025 26.6125 32.0375 17.325 28-29 25.162499999999998 28.487499999999997 27.325 19.025 30-31 26.865858232279034 27.740967620952617 26.940867608451057 18.45230653831729 32-33 24.3875 26.9125 28.299999999999997 20.4 34-35 24.212500000000002 28.6875 26.737499999999997 20.3625 36-37 25.35 25.8 27.700000000000003 21.15 38-39 26.987499999999997 25.15 30.4875 17.375 40-41 26.637499999999996 25.587500000000002 27.275 20.5 42-43 25.7875 29.1875 26.55 18.475 44-45 23.799999999999997 26.087500000000002 29.362500000000004 20.75 46-47 24.375 25.0375 28.287499999999998 22.3 48-49 24.675 25.025 30.337500000000002 19.9625 50-51 23.4125 28.325 28.712500000000002 19.55 52-53 23.790373256252355 27.196179464622343 27.422395375141384 21.591051903983914 54-55 24.437218609304654 29.364682341170585 28.58929464732366 17.608804402201102 56-57 26.75 26.3125 27.6 19.3375 58-59 24.325 25.5 28.237499999999997 21.9375 60-61 26.0375 25.7875 29.212500000000002 18.9625 62-63 20.525 29.299999999999997 32.337500000000006 17.837500000000002 64-65 22.3375 31.15 28.525 17.9875 66-67 24.8125 28.462500000000002 29.1125 17.6125 68-69 21.325 27.5875 28.175 22.912499999999998 70-71 23.98948817419597 27.931422850707044 27.943936929045176 20.135152046051807 72-73 26.067839195979897 25.66582914572864 27.98994974874372 20.276381909547737 74-75 24.24051430732384 27.820496659523506 29.05584268246565 18.883146350687003 76-77 22.89796434441775 26.122139334934886 28.42331521051966 22.556581110127702 78-79 23.22784810126582 26.50632911392405 31.430379746835442 18.835443037974684 80-81 21.794383021985002 31.630448595755496 28.694878637692213 17.88028974456729 82-83 22.915601023017903 26.38107416879795 28.964194373401536 21.73913043478261 84-85 23.073959938366716 24.60195172059579 31.856702619414484 20.46738572162301 86-87 21.318427139552814 28.05191467489077 30.53199691595991 20.097661269596504 88-89 19.8278077615009 29.503983551786174 30.24929324081213 20.418915445900794 90-91 25.44333076329992 27.3580056540735 28.617322025186326 18.581341557440247 92-93 21.781033153430997 30.40349524543819 28.900025700334105 18.91544590079671 >>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 0.0 17 3.0 18 4.0 19 3.0 20 2.5 21 2.0 22 2.0 23 4.5 24 8.0 25 7.5 26 8.5 27 10.5 28 17.5 29 23.5 30 30.5 31 39.0 32 45.5 33 63.5 34 72.0 35 82.0 36 113.5 37 152.5 38 204.5 39 192.5 40 193.5 41 219.5 42 217.0 43 233.0 44 209.0 45 198.0 46 220.0 47 202.5 48 176.0 49 169.0 50 156.5 51 169.0 52 164.0 53 167.0 54 166.0 55 102.5 56 58.0 57 47.5 58 39.0 59 25.0 60 19.0 61 13.5 62 9.0 63 13.5 64 13.0 65 7.5 66 5.0 67 3.0 68 4.0 69 7.0 70 4.0 71 1.0 72 2.0 73 2.0 74 0.5 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 0.08750000000000001 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 0.0 42-43 0.0 44-45 0.0 46-47 0.0 48-49 0.0 50-51 0.0 52-53 0.5375 54-55 0.05 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 0.012786088735455826 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 9.0 71 8.0 72 6.0 73 7.0 74 7.0 75 7.0 76 3.0 77 2.0 78 2.0 79 10.0 80 9.0 81 14.0 82 11.0 83 8.0 84 6.0 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 3891.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 70.95 #Duplication Level Percentage of deduplicated Percentage of total 1 91.12050739957716 64.64999999999999 2 4.404510218463707 6.25 3 1.4799154334038054 3.15 4 0.810429880197322 2.3 5 0.3523608174770966 1.25 6 0.42283298097251587 1.7999999999999998 7 0.21141649048625794 1.05 8 0.14094432699083861 0.8 9 0.21141649048625794 1.35 >10 0.7751937984496124 13.425 >50 0.07047216349541931 3.975 >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 85 2.125 No Hit GGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAA 74 1.8499999999999999 No Hit GGGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGT 50 1.25 No Hit GGCGTTCAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTC 47 1.175 No Hit GGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCTTGG 47 1.175 No Hit GGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGTG 33 0.8250000000000001 No Hit GGGATGATTCTGTATTACAATTTGGTGGAGGAACTTTAGGACATCCTTGG 32 0.8 No Hit GGGCGCGATCTTGCTCGTGAAGGTAATGAAATTATCCGAGCAGCTTGCAA 32 0.8 No Hit GTAGTAGGAATCTGGTTCACTGCTTTAGGTATTAGTACTATGGCGTTCAA 31 0.775 No Hit TACCTAGGCACCCAGAGACGAGGAAGGGCGTAGCAAGCGACGAAATGCTT 30 0.75 No Hit GGCCTGTAGTAGGAATCTGGTTCACTGCTTTAGGTATTAGTACTATGGCG 26 0.65 No Hit GGAGGAACTTTAGGACATCCTTGGGGAAATGCACCTGGTGCAGCAGCTAA 24 0.6 No Hit GGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGTGTACAAGCTCGTAA 22 0.5499999999999999 No Hit GGAGTTGAAAATAAGCATAGATCCGGAGATTCCCAAATAGGTCAACCTTT 20 0.5 No Hit GGGGATGATTCTGTATTACAATTTGGTGGAGGAACTTTAGGACATCCTTG 20 0.5 No Hit GGACATCCTTGGGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTT 19 0.475 No Hit GGATGATTCTGTATTACAATTTGGTGGAGGAACTTTAGGACATCCTTGGG 18 0.44999999999999996 No Hit CAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAGGTC 17 0.42500000000000004 No Hit CAAGGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCT 16 0.4 No Hit GGTTTTGAAAAGGGAATCGATCGTGATTTAGAACCTGTTCTTTACATGAA 12 0.3 No Hit GAGGAAAGGCTTGCGGTGGATACCTAGGCACCCAGAGACGAGGAAGGGCG 11 0.27499999999999997 No Hit GAGGAAGGGCGTAGCAAGCGACGAAATGCTTCGGGGAGTTGAAAATAAGC 10 0.25 No Hit GGGATGGAGCGACAGAAGTATGGAAATAGGATAAGGTAGCGGCGAGACGA 10 0.25 No Hit GGAGTCCCATATATATATGTATAAGATGCCAGCCCGGTTTCGTCAACCAT 10 0.25 No Hit GGGAAAAGAGGGGTTACTTTTTTTCATTTTTCCCTTAAAAGATAGGCTTT 9 0.22499999999999998 No Hit GGCGCGATCTTGCTCGTGAAGGTAATGAAATTATCCGAGCAGCTTGCAAA 9 0.22499999999999998 No Hit GGGGATGGAGCGACAGAAGTATGGAAATAGGATAAGGTAGCGGCGAGACG 9 0.22499999999999998 No Hit GGGCTGATATCATCAACCGTGCTAATCTTGGTATGGAAGTAATGCACGAA 9 0.22499999999999998 No Hit GGAGTATCCTTGATATATAAATATATAGATAAATAGATTTAAATGGAAAA 9 0.22499999999999998 No Hit GGAAAAGAGGGGTTACTTTTTTTCATTTTTCCCTTAAAAGATAGGCTTTG 9 0.22499999999999998 No Hit GGTTCACTGCTTTAGGTATTAGTACTATGGCGTTCAACCTAAATGGATTC 8 0.2 No Hit GCAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAATACTTGGGCT 8 0.2 No Hit GGATACCTAGGCACCCAGAGACGAGGAAGGGCGTAGCAAGCGACGAAATG 8 0.2 No Hit GGAGCGACAGAAGTATGGAAATAGGATAAGGTAGCGGCGAGACGAGCCGT 8 0.2 No Hit GGAACTTTAGGACATCCTTGGGGAAATGCACCTGGTGCAGCAGCTAATCG 7 0.17500000000000002 No Hit CAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAATACTTGGGCTGATAT 7 0.17500000000000002 No Hit GGAATCCCGTGTGAATCAGCAAGGACCACCTTGCAAGGCTAAATACTCCT 7 0.17500000000000002 No Hit GGGGTTGTGGGAGAGCAATACAAGCGTTGTGCTGCTAGGCGAAGCGGTTG 7 0.17500000000000002 No Hit GGATTTGAAGAAAAAAAAGACTTCGATTCATTTTCTATTTATTTCGTTAG 7 0.17500000000000002 No Hit CAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAATACTTGGGCTG 7 0.17500000000000002 No Hit GGAGTCCTGAACTAGCCGCAGCTTGTGAAGTATGGAAGGCGATCAAATTC 6 0.15 No Hit GCAAGGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATC 6 0.15 No Hit GTACTATGGCGTTCAACCTAAATGGATTCAATTTCAACCAATCTGTAGTT 6 0.15 No Hit AACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAGGTCG 6 0.15 No Hit GGGCGTGGCGTTCATGAACAAGTGAAACCTTATGGCTGGATGGGTCATCG 6 0.15 No Hit GGAAGAGCCCGAGCTGCTGCAGCAGGTTTTGAAAAGGGAATCGATCGTGA 6 0.15 No Hit GGAATAAGAATAAATCGCAACTCCTTTCCACTACACATAAAAATTGATTT 6 0.15 No Hit GTAGGAATCTGGTTCACTGCTTTAGGTATTAGTACTATGGCGTTCAACCT 6 0.15 No Hit GGGGGTGCCATACGCAAAAAGGAAGCGACTCATAGAATGGCAGAGGCAAA 6 0.15 No Hit GGAGAGCAATACAAGCGTTGTGCTGCTAGGCGAAGCGGTTGAGTGCCGCA 6 0.15 No Hit GGGGAGTTGAAAATAAGCATAGATCCGGAGATTCCCAAATAGGTCAACCT 6 0.15 No Hit GGTAATGAAATTATCCGAGCAGCTTGCAAATGGAGTCCTGAACTAGCCGC 6 0.15 No Hit GGGCACGTGGAATCCCGTGTGAATCAGCAAGGACCACCTTGCAAGGCTAA 5 0.125 No Hit CAGCTAATCGAGTGGCTTTAGAAGCCTGTGTACAAGCTCGTAACGAAGGG 5 0.125 No Hit GGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGTGT 5 0.125 No Hit GGGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCTTG 5 0.125 No Hit GGAAAGGCTTGCGGTGGATACCTAGGCACCCAGAGACGAGGAAGGGCGTA 5 0.125 No Hit GGGCCGGGTATCTCTCTGCATGTACGTATGCCTGTAATGTACGTAGCTAC 5 0.125 No Hit GATACCTAGGCACCCAGAGACGAGGAAGGGCGTAGCAAGCGACGAAATGC 5 0.125 No Hit GTAGTTGATAGTCAAGGTCGCGTTATTAATACTTGGGCTGATATCATCAA 5 0.125 No Hit GGGTTACTTTTTTTCATTTTTCCCTTAAAAGATAGGCTTTGAAATCGGAG 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 0.0125 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 0.025 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 warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position AAAATAA 30 0.00611513 28.6125 60-61 >>END_MODULE Rejected 144711 READS because READLEN < 1 Read 144711 spots for ERR6133518.sra Written 144711 spots for ERR6133518.sra Rejected 144711 READS because READLEN < 1 Read 144711 spots for ERR6133518.sra Written 144711 spots for ERR6133518.sra Rejected 144711 READS because READLEN < 1 Read 144711 spots for ERR6133518.sra Written 144711 spots for ERR6133518.sra Rejected 144711 READS because READLEN < 1 Read 144711 spots for ERR6133518.sra Written 144711 spots for ERR6133518.sra Rejected 144711 READS because READLEN < 1 Read 144711 spots for ERR6133518.sra Written 144711 spots for ERR6133518.sra Rejected 144711 READS because READLEN < 1 Read 144711 spots for ERR6133518.sra Written 144711 spots for ERR6133518.sra Rejected 144711 READS because READLEN < 1 Read 144711 spots for ERR6133518.sra Written 144711 spots for ERR6133518.sra Rejected 144711 READS because READLEN < 1 Read 144711 spots for ERR6133518.sra Written 144711 spots for ERR6133518.sra Rejected 144711 READS because READLEN < 1 Read 144711 spots for ERR6133518.sra Written 144711 spots for ERR6133518.sra Rejected 144711 READS because READLEN < 1 Read 144711 spots for ERR6133518.sra Written 144711 spots for ERR6133518.sra Rejected 144711 READS because READLEN < 1 Read 144711 spots for ERR6133518.sra Written 144711 spots for ERR6133518.sra Rejected 144711 READS because READLEN < 1 Read 144711 spots for ERR6133518.sra Written 144711 spots for ERR6133518.sra Rejected 144711 READS because READLEN < 1 Read 144711 spots for ERR6133518.sra Written 144711 spots for ERR6133518.sra Rejected 144711 READS because READLEN < 1 Read 144711 spots for ERR6133518.sra Written 144711 spots for ERR6133518.sra Rejected 144711 READS because READLEN < 1 Read 144711 spots for ERR6133518.sra Written 144711 spots for ERR6133518.sra Rejected 144711 READS because READLEN < 1 Read 144711 spots for ERR6133518.sra Written 144711 spots for ERR6133518.sra Rejected 144711 READS because READLEN < 1 Read 144711 spots for ERR6133518.sra Written 144711 spots for ERR6133518.sra Rejected 144715 READS because READLEN < 1 Read 144715 spots for ERR6133518.sra Written 144715 spots for ERR6133518.sra Rejected 144711 READS because READLEN < 1 Read 144711 spots for ERR6133518.sra Written 144711 spots for ERR6133518.sra Rejected 144711 READS because READLEN < 1 Read 144711 spots for ERR6133518.sra Written 144711 spots for ERR6133518.sra SRR ids: ['ERR6133518.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_xrsx1c95 ERR6133518.sra spots: 2894224 blocks: [[1, 144711], [144712, 289422], [289423, 434133], [434134, 578844], [578845, 723555], [723556, 868266], [868267, 1012977], [1012978, 1157688], [1157689, 1302399], [1302400, 1447110], [1447111, 1591821], [1591822, 1736532], [1736533, 1881243], [1881244, 2025954], [2025955, 2170665], [2170666, 2315376], [2315377, 2460087], [2460088, 2604798], [2604799, 2749509], [2749510, 2894224]] ERR6133518 file size 639728 ERR6133518 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 ERR6133518 ERR6133518_1.fastq Input file: ERR6133518_1.fastq trimmed: ERR6133518-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 07:47:48 2024 >> started Sat Dec 7 07:47:50 2024 >> done (1.728s) 2894224 reads processed; of these: 331 ( 0.01%) short reads filtered out after trimming by size control 20 ( 0.00%) empty reads filtered out after trimming by size control 2893873 (99.99%) reads available; of these: 12997 ( 0.45%) trimmed reads available after processing 2880876 (99.55%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 65 0.00% 19 163 0.01% 20 42 0.00% 21 29 0.00% 22 61 0.00% 23 13 0.00% 24 14 0.00% 25 5 0.00% 26 16 0.00% 27 18 0.00% 28 26 0.00% 29 169 0.01% 30 10 0.00% 31 31 0.00% 32 54 0.00% 33 14 0.00% 34 27 0.00% 35 188 0.01% 36 338 0.01% 37 29 0.00% 38 55 0.00% 39 115 0.00% 40 212 0.01% 41 55 0.00% 42 7 0.00% 43 21 0.00% 44 34 0.00% 45 14 0.00% 46 5 0.00% 47 7 0.00% 48 14 0.00% 49 10 0.00% 50 11 0.00% 51 144 0.00% 52 29 0.00% 53 11 0.00% 54 7 0.00% 55 6 0.00% 56 5 0.00% 57 20 0.00% 58 17 0.00% 59 4 0.00% 60 16 0.00% 61 11 0.00% 62 1 0.00% 63 1 0.00% 64 2 0.00% 65 2 0.00% 66 8 0.00% 67 4 0.00% 68 7 0.00% 69 41 0.00% 70 5769 0.20% 71 4694 0.16% 72 5133 0.18% 73 4785 0.17% 74 5013 0.17% 75 4998 0.17% 76 4373 0.15% 77 4552 0.16% 78 5043 0.17% 79 5999 0.21% 80 5285 0.18% 81 6587 0.23% 82 7473 0.26% 83 6499 0.22% 84 6291 0.22% 85 36 0.00% 86 55 0.00% 87 101 0.00% 88 209 0.01% 89 324 0.01% 90 729 0.03% 91 1755 0.06% 92 7188 0.25% 93 2798774 96.71% 2893873 reads passed initial QC criterion=sequence-density sequence-density=0.68 sequence-density-rank=1 fanout-score=1.99 fanout-score-rank=31 prefix-density=0.68 prefix-fanout=2.0 sequence=CAAGGCTAAATAC criterion=fanout-score sequence-density=0.01 sequence-density-rank=25 fanout-score=58.09 fanout-score-rank=1 prefix-density=0.12 prefix-fanout=6.7 sequence=AAAAGAAGGGGTGTTCCATCTCCGGACGACGATCCTGCCTGCAGAGGAAGACATGCCGGCGATCATGTCGAGCTTCAAGAAGTTCAACGACTCATTCATGGAGCAATACCAAGACTACTCCAGGCTGTGATGTGAAGAGGGAAACAACGAGGTCATCATCGACATGATATATTGCTGCTATTTTCCACCAGCGATTAAAAGTTAAAAAATTTAGCTGTAAGCTGTAACTATCTTGAAGAAACTAAACTGGTTGCTGTGCTTGATATGTATAGGGAAAACATAATTTATGAGACAATCATACTGTGCAACTCTTGGCTCCATCGATTAATTAATACTCCTTGTTATTGCTTGCATGGTGG Started job on | Dec 07 07:48:04 Started mapping on | Dec 07 07:48:04 Finished on | Dec 07 07:48:09 Mapping speed, Million of reads per hour | 2083.59 Number of input reads | 2893873 Average input read length | 92 UNIQUE READS: Uniquely mapped reads number | 1750482 Uniquely mapped reads % | 60.49% Average mapped length | 92.10 Number of splices: Total | 86831 Number of splices: Annotated (sjdb) | 71328 Number of splices: GT/AG | 83282 Number of splices: GC/AG | 1910 Number of splices: AT/AC | 49 Number of splices: Non-canonical | 1590 Mismatch rate per base, % | 0.43% Deletion rate per base | 0.05% Deletion average length | 1.87 Insertion rate per base | 0.03% Insertion average length | 1.90 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 1064513 % of reads mapped to multiple loci | 36.79% Number of reads mapped to too many loci | 25435 % of reads mapped to too many loci | 0.88% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 1.81% % of reads unmapped: other | 0.04% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 78878 78878 78878 N_multimapping 1064513 1064513 1064513 N_noFeature 160580 177096 1672460 N_ambiguous 71833 10373 334 UnstrandedReadsAssigned:1518069 PositiveStrandReadsAssigned:1563013 NegativeStrandReadsAssigned:77688 Dataset is classified positive stranded MeadianReadLen=93 20thPercentileLength=93 echo kmer=89 ERR6133518 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: ERR6133518-trimmed.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 2,893,873 reads, 2,296,942 reads pseudoaligned [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 976 rounds 52973 ERR6133518.ke.tsv 35125 ERR6133518.se.tsv 88098 total ==> ERR6133518.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 76 31.8926 PNS24243 293 194 0 0 KQK14069 1603 1504 108 41.3435 KQK14071 474 375 0 0 ==> ERR6133518.se.tsv <== BRADI_1g14170v3 108 BRADI_1g53295v3 26 BRADI_1g59795v3 18 BRADI_1g07683v3 0 BRADI_1g00485v3 0 BRADI_1g20270v3 13 BRADI_1g74790v3 12 BRADI_1g09890v3 0 BRADI_1g77505v3 40 BRADI_1g48960v3 0 ERR6133518 completed mapping pipeline successfully