Starting /dee2/code/volunteer_pipeline.sh ERR6133323 current disk space = 1548297191424 free memory = 1395872172 ERR6133323 SRAfilesize 73a72cb9175d5ca977162815b3a2da48 ERR6133323.sra ERR6133323.sra file validated ERR6133323 is single end ERR6133323 is conventional basespace ERR6133323 read1 length is 70-93 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename ERR6133323_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 36.2525 37.0 37.0 37.0 33.0 37.0 2 36.63025 37.0 37.0 37.0 37.0 37.0 3 36.62625 37.0 37.0 37.0 37.0 37.0 4 36.37325 37.0 37.0 37.0 37.0 37.0 5 36.419 37.0 37.0 37.0 37.0 37.0 6 36.52925 37.0 37.0 37.0 37.0 37.0 7 38.73375 40.0 37.0 40.0 37.0 40.0 8 38.7495 40.0 37.0 40.0 37.0 40.0 9 38.76975 40.0 37.0 40.0 37.0 40.0 10-11 38.75875 40.0 37.0 40.0 37.0 40.0 12-13 38.771 40.0 37.0 40.0 37.0 40.0 14-15 38.749624999999995 40.0 37.0 40.0 37.0 40.0 16-17 38.711625 40.0 37.0 40.0 37.0 40.0 18-19 38.612750000000005 40.0 37.0 40.0 37.0 40.0 20-21 38.554874999999996 40.0 37.0 40.0 37.0 40.0 22-23 38.521875 40.0 37.0 40.0 37.0 40.0 24-25 38.422 40.0 37.0 40.0 37.0 40.0 26-27 38.44475 40.0 37.0 40.0 37.0 40.0 28-29 38.463875 40.0 37.0 40.0 37.0 40.0 30-31 38.402625 40.0 37.0 40.0 37.0 40.0 32-33 38.28975 40.0 37.0 40.0 37.0 40.0 34-35 38.12175 40.0 37.0 40.0 37.0 40.0 36-37 38.052375 40.0 37.0 40.0 37.0 40.0 38-39 38.063874999999996 40.0 37.0 40.0 37.0 40.0 40-41 37.967 40.0 37.0 40.0 37.0 40.0 42-43 37.867000000000004 37.0 37.0 40.0 37.0 40.0 44-45 37.668375 37.0 37.0 40.0 35.0 40.0 46-47 37.561 37.0 37.0 40.0 33.0 40.0 48-49 37.361875 37.0 37.0 40.0 33.0 40.0 50-51 37.258625 37.0 37.0 40.0 33.0 40.0 52-53 37.120375 37.0 37.0 40.0 33.0 40.0 54-55 36.98825 37.0 37.0 38.5 33.0 40.0 56-57 36.845875 37.0 37.0 37.0 33.0 40.0 58-59 36.56525 37.0 37.0 37.0 33.0 40.0 60-61 36.443375 37.0 37.0 37.0 33.0 40.0 62-63 36.25875 37.0 37.0 37.0 33.0 37.0 64-65 36.16225 37.0 37.0 37.0 33.0 37.0 66-67 36.035250000000005 37.0 37.0 37.0 33.0 37.0 68-69 35.17725 35.0 35.0 37.0 33.0 37.0 70-71 35.36333813335014 37.0 35.0 37.0 33.0 37.0 72-73 35.82710303795051 37.0 37.0 37.0 33.0 37.0 74-75 35.79287131679824 37.0 37.0 37.0 33.0 37.0 76-77 35.717408782564505 37.0 37.0 37.0 33.0 37.0 78-79 35.67212525579199 37.0 37.0 37.0 33.0 37.0 80-81 35.602619530200286 37.0 37.0 37.0 33.0 37.0 82-83 35.55075720188712 37.0 37.0 37.0 33.0 37.0 84-85 35.565010783462114 37.0 37.0 37.0 33.0 37.0 86-87 35.44846396784381 37.0 33.0 37.0 33.0 37.0 88-89 35.49138673557278 37.0 35.0 37.0 33.0 37.0 90-91 35.3917599770313 37.0 33.0 37.0 33.0 37.0 92-93 35.280648865920185 37.0 33.0 37.0 33.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 20 2.0 21 3.0 22 2.0 23 8.0 24 7.0 25 6.0 26 10.0 27 13.0 28 14.0 29 19.0 30 29.0 31 31.0 32 47.0 33 65.0 34 84.0 35 202.0 36 728.0 37 1132.0 38 1513.0 39 85.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 66.14999999999999 9.2 8.375 16.275000000000002 2 47.675 25.900000000000002 14.924999999999999 11.5 3 30.575000000000003 37.325 17.75 14.35 4 30.625000000000004 27.1 21.775 20.5 5 24.45 27.650000000000002 26.25 21.65 6 20.674999999999997 33.825 27.575 17.925 7 32.574999999999996 26.85 23.125 17.45 8 27.650000000000002 26.400000000000002 28.275 17.675 9 24.875 26.474999999999998 29.525000000000002 19.125 10-11 25.75 26.687499999999996 27.875 19.6875 12-13 24.275 28.037499999999998 28.875 18.8125 14-15 22.475 28.249999999999996 29.349999999999998 19.925 16-17 24.3625 29.762499999999996 25.674999999999997 20.200000000000003 18-19 25.1875 25.162499999999998 29.025000000000002 20.625 20-21 25.85 24.887500000000003 28.0625 21.2 22-23 27.500000000000004 24.962500000000002 26.474999999999998 21.0625 24-25 24.224999999999998 27.4125 28.1125 20.25 26-27 26.0375 24.962500000000002 28.5875 20.4125 28-29 25.3 26.7625 27.6375 20.3 30-31 25.7 26.150000000000002 27.5125 20.6375 32-33 25.412499999999998 25.137500000000003 28.762500000000003 20.6875 34-35 22.6125 28.962500000000002 27.0875 21.337500000000002 36-37 24.4875 28.025 25.75 21.7375 38-39 25.828228528566072 25.403175396924617 27.87848481060132 20.890111263907986 40-41 24.975 25.8125 28.000000000000004 21.212500000000002 42-43 24.85 28.299999999999997 27.3875 19.4625 44-45 23.775 29.125 27.950000000000003 19.15 46-47 25.55 27.5625 27.025 19.8625 48-49 24.3 25.887500000000003 28.9875 20.825 50-51 22.45 27.725 29.075 20.75 52-53 24.375 27.962500000000002 27.400000000000002 20.2625 54-55 24.75 29.512500000000003 27.55 18.1875 56-57 24.2 28.975 26.825 20.0 58-59 24.65 28.012500000000003 27.0875 20.25 60-61 27.3375 27.425 26.625 18.6125 62-63 23.125 29.212500000000002 29.0875 18.575 64-65 22.78354382893585 31.42428410653995 27.76041015380768 18.03176191071652 66-67 23.962500000000002 29.325000000000003 27.1 19.6125 68-69 22.275 29.275000000000002 28.050000000000004 20.4 70-71 24.95293083971382 28.153633739174094 27.350320070289946 19.54311535082214 72-73 26.027572121521576 27.316824100076587 27.92953791166709 18.726065866734746 74-75 24.941573617242273 27.668138145936123 28.369254739028825 19.02103349779278 76-77 23.510806536636792 27.055877701634156 27.780706378492354 21.65260938323669 78-79 25.371138157014844 27.85876688511435 27.765146449110606 19.004948508760197 80-81 23.626224156692057 30.31828073993471 27.081066376496192 18.97442872687704 82-83 22.65886287625418 28.539576365663322 27.076365663322182 21.725195094760313 84-85 22.589845978322877 26.99657729606389 29.449515116942383 20.96406160867085 86-87 21.762848119437265 29.486075222509335 26.902095894343958 21.84898076370945 88-89 22.006890611541774 30.76370944587999 27.34711455641688 19.882285386161357 90-91 23.61469997128912 31.869078380706288 25.337352856732704 19.178868791271892 92-93 20.21246052253804 33.82141831754235 27.088716623600344 18.877404536319265 >>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 0.5 16 1.0 17 1.0 18 0.5 19 0.5 20 0.5 21 1.0 22 5.0 23 10.0 24 9.5 25 5.0 26 10.0 27 22.5 28 25.5 29 22.5 30 31.5 31 51.0 32 64.0 33 71.0 34 87.0 35 110.5 36 130.5 37 164.0 38 182.5 39 180.5 40 225.0 41 234.0 42 228.5 43 253.5 44 216.0 45 187.0 46 169.5 47 141.0 48 137.0 49 130.0 50 137.5 51 149.5 52 152.5 53 159.0 54 151.5 55 125.0 56 95.0 57 81.0 58 60.5 59 42.0 60 35.5 61 22.0 62 16.5 63 16.5 64 12.0 65 13.5 66 11.5 67 5.5 68 13.0 69 22.5 70 13.5 71 1.5 72 2.0 73 2.0 74 1.5 75 1.0 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 0.0125 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 0.0375 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 33.0 71 38.0 72 24.0 73 41.0 74 26.0 75 33.0 76 22.0 77 31.0 78 27.0 79 31.0 80 36.0 81 45.0 82 50.0 83 34.0 84 46.0 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 3483.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 75.5 #Duplication Level Percentage of deduplicated Percentage of total 1 90.66225165562913 68.45 2 4.66887417218543 7.049999999999999 3 1.8543046357615895 4.2 4 0.5298013245033113 1.6 5 0.49668874172185434 1.875 6 0.33112582781456956 1.5 7 0.16556291390728478 0.8750000000000001 8 0.2980132450331126 1.7999999999999998 9 0.16556291390728478 1.125 >10 0.8278145695364238 11.525 >50 0.0 0.0 >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 warn #Sequence Count Percentage Possible Source GGGAGAGCAATACAAGCGTTGTGCTGCTAGGCGAAGCGGTTGAGTGCCGC 40 1.0 No Hit CAAGGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCT 33 0.8250000000000001 No Hit TACCTAGGCACCCAGAGACGAGGAAGGGCGTAGCAAGCGACGAAATGCTT 32 0.8 No Hit GGGTTGTTTGGGAATGCAGCCCAAATCGGGCGGTAGACTCCGTCCAAGGC 28 0.7000000000000001 No Hit CAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAATACTTGGGCTGATAT 25 0.625 No Hit GGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCTTGG 25 0.625 No Hit CAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAATACTTGGGCTG 25 0.625 No Hit GGAATCCCGTGTGAATCAGCAAGGACCACCTTGCAAGGCTAAATACTCCT 24 0.6 No Hit GGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAA 22 0.5499999999999999 No Hit GGGGCACGTGGAATCCCGTGTGAATCAGCAAGGACCACCTTGCAAGGCTA 21 0.525 No Hit GGCGTTCAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTC 19 0.475 No Hit GGGCACGTGGAATCCCGTGTGAATCAGCAAGGACCACCTTGCAAGGCTAA 16 0.4 No Hit GGAGGGTGAGAGCCCCGTCCGGCCCGGACCCTGTCGCCCCACGAGGCGCC 13 0.325 No Hit GGGAATGCAGCCCAAATCGGGCGGTAGACTCCGTCCAAGGCTAAATACAG 13 0.325 No Hit GGGCGCGATCTTGCTCGTGAAGGTAATGAAATTATCCGAGCAGCTTGCAA 13 0.325 No Hit CAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAGGTC 13 0.325 No Hit GGGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGT 13 0.325 No Hit GGGCTGATATCATCAACCGTGCTAATCTTGGTATGGAAGTAATGCACGAA 12 0.3 No Hit GTAGTTGATAGTCAAGGTCGCGTTATTAATACTTGGGCTGATATCATCAA 11 0.27499999999999997 No Hit GTGGAATCCCGTGTGAATCAGCAAGGACCACCTTGCAAGGCTAAATACTC 11 0.27499999999999997 No Hit GGGTGAGAGCCCCGTCCGGCCCGGACCCTGTCGCCCCACGAGGCGCCGTC 11 0.27499999999999997 No Hit TCAAAAGAGGAAAGGCTTGCGGTGGATACCTAGGCACCCAGAGACGAGGA 11 0.27499999999999997 No Hit GCAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAATACTTGGGCT 10 0.25 No Hit GGAGTTGAAAATAAGCATAGATCCGGAGATTCCCAAATAGGTCAACCTTT 10 0.25 No Hit GGTTGTTTGGGAATGCAGCCCAAATCGGGCGGTAGACTCCGTCCAAGGCT 10 0.25 No Hit GGGCGTAGCAAGCGACGAAATGCTTCGGGGAGTTGAAAATAAGCATAGAT 9 0.22499999999999998 No Hit AACGTAATGCTCACAACTTCCCTCTAGATCTAGCTGCTCTTGAAGTTCCC 9 0.22499999999999998 No Hit GGGAGGGTGAGAGCCCCGTCCGGCCCGGACCCTGTCGCCCCACGAGGCGC 9 0.22499999999999998 No Hit CACGAACGTAATGCTCACAACTTCCCTCTAGATCTAGCTGCTCTTGAAGT 9 0.22499999999999998 No Hit GGTGGATACCTAGGCACCCAGAGACGAGGAAGGGCGTAGCAAGCGACGAA 9 0.22499999999999998 No Hit GCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCTTGGTATG 8 0.2 No Hit GAGGAAGGGCGTAGCAAGCGACGAAATGCTTCGGGGAGTTGAAAATAAGC 8 0.2 No Hit CAAATAGGTCAACCTTTTAAACTGCCTGCTGAATCCATGAGCAGGCAAGA 8 0.2 No Hit GGATACCTAGGCACCCAGAGACGAGGAAGGGCGTAGCAAGCGACGAAATG 8 0.2 No Hit GTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCTTGGT 8 0.2 No Hit GTAGGAATCTGGTTCACTGCTTTAGGTATTAGTACTATGGCGTTCAACCT 8 0.2 No Hit CGGGTTGTTTGGGAATGCAGCCCAAATCGGGCGGTAGACTCCGTCCAAGG 8 0.2 No Hit GGCCCGGACCCTGTCGCCCCACGAGGCGCCGTCAACGAGTCGGGTTGTTT 8 0.2 No Hit GGGGAGTTGAAAATAAGCATAGATCCGGAGATTCCCAAATAGGTCAACCT 8 0.2 No Hit GGAGTTTGGCTGGGGCGGCACATCTGTTAAAAGATAACGCAGGTGTCCTA 7 0.17500000000000002 No Hit GTACTATGGCGTTCAACCTAAATGGATTCAATTTCAACCAATCTGTAGTT 7 0.17500000000000002 No Hit GGAAAGGCTTGCGGTGGATACCTAGGCACCCAGAGACGAGGAAGGGCGTA 7 0.17500000000000002 No Hit GATTCAATTTCAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAAT 7 0.17500000000000002 No Hit AACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAATACTTGGGCTGA 7 0.17500000000000002 No Hit GGTTCACTGCTTTAGGTATTAGTACTATGGCGTTCAACCTAAATGGATTC 6 0.15 No Hit GGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGTG 6 0.15 No Hit GGAAGGGCGTAGCAAGCGACGAAATGCTTCGGGGAGTTGAAAATAAGCAT 6 0.15 No Hit GGGCAGAGGGAATTTCCGGTGGAGCGGTGAAATGCATTGAGATCGGAAAG 6 0.15 No Hit AGGAAAGGCTTGCGGTGGATACCTAGGCACCCAGAGACGAGGAAGGGCGT 6 0.15 No Hit GTACAAGCTCGTAACGAAGGGCGCGATCTTGCTCGTGAAGGTAATGAAAT 6 0.15 No Hit GGAGAGCAATACAAGCGTTGTGCTGCTAGGCGAAGCGGTTGAGTGCCGCA 6 0.15 No Hit GTCAAGGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAAT 6 0.15 No Hit GGTAATGAAATTATCCGAGCAGCTTGCAAATGGAGTCCTGAACTAGCCGC 6 0.15 No Hit GGAAAAGAAAGCAAAAGCGATTCCCGTAGTAGCGGCGAGCGAAATGGGAG 6 0.15 No Hit GAAAATAAGCATAGATCCGGAGATTCCCAAATAGGTCAACCTTTTAAACT 5 0.125 No Hit CGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCTTGGTAT 5 0.125 No Hit GGTCAACCTTTTAAACTGCCTGCTGAATCCATGAGCAGGCAAGAGACAAC 5 0.125 No Hit GGAGATTCCCAAATAGGTCAACCTTTTAAACTGCCTGCTGAATCCATGAG 5 0.125 No Hit GTAGCAAGCGACGAAATGCTTCGGGGAGTTGAAAATAAGCATAGATCCGG 5 0.125 No Hit GTTGATAGTCAAGGTCGCGTTATTAATACTTGGGCTGATATCATCAACCG 5 0.125 No Hit AGTCAAGGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAA 5 0.125 No Hit GAAGGGCGCGATCTTGCTCGTGAAGGTAATGAAATTATCCGAGCAGCTTG 5 0.125 No Hit GTATTAGTACTATGGCGTTCAACCTAAATGGATTCAATTTCAACCAATCT 5 0.125 No Hit GTTGTTTGGGAATGCAGCCCAAATCGGGCGGTAGACTCCGTCCAAGGCTA 5 0.125 No Hit GAATCCCGTGTGAATCAGCAAGGACCACCTTGCAAGGCTAAATACTCCTG 5 0.125 No Hit GAAGGTAATGAAATTATCCGAGCAGCTTGCAAATGGAGTCCTGAACTAGC 5 0.125 No Hit GGGGAGTTTGGCTGGGGCGGCACATCTGTTAAAAGATAACGCAGGTGTCC 5 0.125 No Hit GAACGTAATGCTCACAACTTCCCTCTAGATCTAGCTGCTCTTGAAGTTCC 5 0.125 No Hit TCAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAATACTTGGGCT 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 0.0125 0.0 28-29 0.0 0.0 0.0 0.025 0.0 30-31 0.0 0.0 0.0 0.025 0.0 32-33 0.0 0.0 0.0 0.025 0.0 34-35 0.025 0.0 0.0 0.025 0.0 36-37 0.025 0.0 0.0 0.025 0.0 38-39 0.025 0.0 0.0 0.025 0.0 40-41 0.025 0.0 0.0 0.025 0.0 42-43 0.025 0.0 0.0 0.025 0.0 44-45 0.025 0.0 0.0 0.025 0.0 46-47 0.025 0.0 0.0 0.025 0.0 48-49 0.025 0.0 0.0 0.025 0.0 50-51 0.025 0.0 0.0 0.025 0.0 52-53 0.075 0.0 0.0 0.025 0.0 54-55 0.075 0.0 0.0 0.025 0.0 56-57 0.075 0.0 0.0 0.025 0.0 58-59 0.075 0.0 0.0 0.025 0.0 60-61 0.075 0.0 0.0 0.025 0.0 62-63 0.075 0.0 0.0 0.025 0.0 64-65 0.075 0.0 0.0 0.025 0.0 66-67 0.075 0.0 0.0 0.025 0.0 68-69 0.0875 0.0 0.0 0.025 0.0 70-71 0.1 0.0 0.0 0.025 0.0 72-73 0.125 0.0 0.0 0.025 0.0 74-75 0.125 0.0 0.0 0.025 0.0 76-77 0.125 0.0 0.0 0.025 0.0 78-79 0.125 0.0 0.0 0.025 0.0 80-81 0.125 0.0 0.0 0.025 0.0 >>END_MODULE >>Kmer Content pass >>END_MODULE Rejected 57511 READS because READLEN < 1 Read 57511 spots for ERR6133323.sra Written 57511 spots for ERR6133323.sra Rejected 57511 READS because READLEN < 1 Read 57511 spots for ERR6133323.sra Written 57511 spots for ERR6133323.sra Rejected 57511 READS because READLEN < 1 Read 57511 spots for ERR6133323.sra Written 57511 spots for ERR6133323.sra Rejected 57511 READS because READLEN < 1 Read 57511 spots for ERR6133323.sra Written 57511 spots for ERR6133323.sra Rejected 57511 READS because READLEN < 1 Read 57511 spots for ERR6133323.sra Written 57511 spots for ERR6133323.sra Rejected 57511 READS because READLEN < 1 Read 57511 spots for ERR6133323.sra Written 57511 spots for ERR6133323.sra Rejected 57511 READS because READLEN < 1 Read 57511 spots for ERR6133323.sra Written 57511 spots for ERR6133323.sra Rejected 57511 READS because READLEN < 1 Read 57511 spots for ERR6133323.sra Written 57511 spots for ERR6133323.sra Rejected 57515 READS because READLEN < 1 Read 57515 spots for ERR6133323.sra Written 57515 spots for ERR6133323.sra Rejected 57511 READS because READLEN < 1 Read 57511 spots for ERR6133323.sra Written 57511 spots for ERR6133323.sra Rejected 57511 READS because READLEN < 1 Read 57511 spots for ERR6133323.sra Written 57511 spots for ERR6133323.sra Rejected 57511 READS because READLEN < 1 Read 57511 spots for ERR6133323.sra Written 57511 spots for ERR6133323.sra Rejected 57511 READS because READLEN < 1 Read 57511 spots for ERR6133323.sra Written 57511 spots for ERR6133323.sra Rejected 57511 READS because READLEN < 1 Read 57511 spots for ERR6133323.sra Written 57511 spots for ERR6133323.sra Rejected 57511 READS because READLEN < 1 Read 57511 spots for ERR6133323.sra Written 57511 spots for ERR6133323.sra Rejected 57511 READS because READLEN < 1 Read 57511 spots for ERR6133323.sra Written 57511 spots for ERR6133323.sra Rejected 57511 READS because READLEN < 1 Read 57511 spots for ERR6133323.sra Written 57511 spots for ERR6133323.sra Rejected 57511 READS because READLEN < 1 Read 57511 spots for ERR6133323.sra Written 57511 spots for ERR6133323.sra Rejected 57511 READS because READLEN < 1 Read 57511 spots for ERR6133323.sra Written 57511 spots for ERR6133323.sra Rejected 57511 READS because READLEN < 1 Read 57511 spots for ERR6133323.sra Written 57511 spots for ERR6133323.sra SRR ids: ['ERR6133323.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_7rdaontc ERR6133323.sra spots: 1150224 blocks: [[1, 57511], [57512, 115022], [115023, 172533], [172534, 230044], [230045, 287555], [287556, 345066], [345067, 402577], [402578, 460088], [460089, 517599], [517600, 575110], [575111, 632621], [632622, 690132], [690133, 747643], [747644, 805154], [805155, 862665], [862666, 920176], [920177, 977687], [977688, 1035198], [1035199, 1092709], [1092710, 1150224]] ERR6133323 file size 249653 ERR6133323 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 ERR6133323 ERR6133323_1.fastq Input file: ERR6133323_1.fastq trimmed: ERR6133323-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 00:37:51 2024 >> started Sat Dec 7 00:37:53 2024 >> done (2.612s) 1150224 reads processed; of these: 176 ( 0.02%) short reads filtered out after trimming by size control 8 ( 0.00%) empty reads filtered out after trimming by size control 1150040 (99.98%) reads available; of these: 7389 ( 0.64%) trimmed reads available after processing 1142651 (99.36%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 3 0.00% 19 39 0.00% 20 23 0.00% 21 6 0.00% 22 12 0.00% 23 14 0.00% 24 14 0.00% 25 7 0.00% 26 16 0.00% 27 14 0.00% 28 20 0.00% 29 91 0.01% 30 15 0.00% 31 14 0.00% 32 32 0.00% 33 19 0.00% 34 10 0.00% 35 47 0.00% 36 11 0.00% 37 10 0.00% 38 27 0.00% 39 63 0.01% 40 91 0.01% 41 22 0.00% 42 10 0.00% 43 13 0.00% 44 23 0.00% 45 17 0.00% 46 9 0.00% 47 3 0.00% 48 8 0.00% 49 4 0.00% 50 10 0.00% 51 51 0.00% 52 14 0.00% 53 8 0.00% 54 7 0.00% 55 0 0.00% 56 10 0.00% 57 19 0.00% 58 11 0.00% 59 7 0.00% 60 22 0.00% 61 10 0.00% 62 3 0.00% 63 4 0.00% 64 3 0.00% 65 11 0.00% 66 7 0.00% 67 19 0.00% 68 32 0.00% 69 60 0.01% 70 8879 0.77% 71 8576 0.75% 72 9377 0.82% 73 8758 0.76% 74 8184 0.71% 75 8064 0.70% 76 7864 0.68% 77 8709 0.76% 78 8463 0.74% 79 8711 0.76% 80 8863 0.77% 81 11468 1.00% 82 12012 1.04% 83 9987 0.87% 84 12997 1.13% 85 51 0.00% 86 63 0.01% 87 94 0.01% 88 127 0.01% 89 242 0.02% 90 464 0.04% 91 1003 0.09% 92 3335 0.29% 93 1002734 87.19% 1150040 reads passed initial QC criterion=sequence-density sequence-density=5.67 sequence-density-rank=1 fanout-score=2.02 fanout-score-rank=21 prefix-density=5.73 prefix-fanout=2.0 sequence=CAAGGCTAAATAC criterion=fanout-score sequence-density=0.16 sequence-density-rank=9 fanout-score=69.94 fanout-score-rank=1 prefix-density=5.69 prefix-fanout=2.0 sequence=AAGGCTAAATAAAGGCGAGAGAC 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 00:38:16 Started mapping on | Dec 07 00:38:16 Finished on | Dec 07 00:38:42 Mapping speed, Million of reads per hour | 159.24 Number of input reads | 1150040 Average input read length | 91 UNIQUE READS: Uniquely mapped reads number | 578245 Uniquely mapped reads % | 50.28% Average mapped length | 89.82 Number of splices: Total | 16933 Number of splices: Annotated (sjdb) | 13698 Number of splices: GT/AG | 15553 Number of splices: GC/AG | 433 Number of splices: AT/AC | 13 Number of splices: Non-canonical | 934 Mismatch rate per base, % | 0.51% Deletion rate per base | 0.06% Deletion average length | 1.81 Insertion rate per base | 0.03% Insertion average length | 1.76 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 455135 % of reads mapped to multiple loci | 39.58% Number of reads mapped to too many loci | 75720 % of reads mapped to too many loci | 6.58% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 3.16% % of reads unmapped: other | 0.40% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 116660 116660 116660 N_multimapping 455135 455135 455135 N_noFeature 48666 56100 551134 N_ambiguous 22865 3206 93 UnstrandedReadsAssigned:506714 PositiveStrandReadsAssigned:518939 NegativeStrandReadsAssigned:27018 Dataset is classified positive stranded MeadianReadLen=93 20thPercentileLength=93 echo kmer=89 ERR6133323 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: ERR6133323-trimmed.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 1,150,040 reads, 747,447 reads pseudoaligned [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 869 rounds 52973 ERR6133323.ke.tsv 35125 ERR6133323.se.tsv 88098 total ==> ERR6133323.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 19 25.1894 PNS24243 293 194 0 0 KQK14069 1603 1504 4 4.83761 KQK14071 474 375 0 0 ==> ERR6133323.se.tsv <== BRADI_1g14170v3 4 BRADI_1g53295v3 16 BRADI_1g59795v3 2 BRADI_1g07683v3 0 BRADI_1g00485v3 0 BRADI_1g20270v3 18 BRADI_1g74790v3 7 BRADI_1g09890v3 0 BRADI_1g77505v3 16 BRADI_1g48960v3 0 ERR6133323 completed mapping pipeline successfully