Starting /dee2/code/volunteer_pipeline.sh ERR6133356 current disk space = 1548284342272 free memory = 1602053356 ERR6133356 SRAfilesize f652943d55752e8c00db6e0291137fec ERR6133356.sra ERR6133356.sra file validated ERR6133356 is single end ERR6133356 is conventional basespace ERR6133356 read1 length is 70-93 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename ERR6133356_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 36.356 37.0 37.0 37.0 33.0 37.0 2 36.68575 37.0 37.0 37.0 37.0 37.0 3 36.63375 37.0 37.0 37.0 37.0 37.0 4 36.35775 37.0 37.0 37.0 37.0 37.0 5 36.3355 37.0 37.0 37.0 37.0 37.0 6 36.492 37.0 37.0 37.0 37.0 37.0 7 38.65575 40.0 37.0 40.0 37.0 40.0 8 38.6685 40.0 37.0 40.0 37.0 40.0 9 38.6585 40.0 37.0 40.0 37.0 40.0 10-11 38.688625 40.0 37.0 40.0 37.0 40.0 12-13 38.652 40.0 37.0 40.0 37.0 40.0 14-15 38.695875 40.0 37.0 40.0 37.0 40.0 16-17 38.634125 40.0 37.0 40.0 37.0 40.0 18-19 38.57125 40.0 37.0 40.0 37.0 40.0 20-21 38.51025 40.0 37.0 40.0 37.0 40.0 22-23 38.448499999999996 40.0 37.0 40.0 37.0 40.0 24-25 38.34725 40.0 37.0 40.0 37.0 40.0 26-27 38.352125 40.0 37.0 40.0 37.0 40.0 28-29 38.44825 40.0 37.0 40.0 37.0 40.0 30-31 38.34675 40.0 37.0 40.0 37.0 40.0 32-33 38.253375 40.0 37.0 40.0 37.0 40.0 34-35 38.194625 40.0 37.0 40.0 37.0 40.0 36-37 38.08925 40.0 37.0 40.0 37.0 40.0 38-39 37.993750000000006 40.0 37.0 40.0 37.0 40.0 40-41 37.84375 37.0 37.0 40.0 37.0 40.0 42-43 37.674499999999995 37.0 37.0 40.0 37.0 40.0 44-45 37.547875000000005 37.0 37.0 40.0 35.0 40.0 46-47 37.45 37.0 37.0 40.0 33.0 40.0 48-49 37.32325 37.0 37.0 40.0 35.0 40.0 50-51 37.147999999999996 37.0 37.0 40.0 33.0 40.0 52-53 37.0395 37.0 37.0 38.5 33.0 40.0 54-55 36.893625 37.0 37.0 37.0 33.0 40.0 56-57 36.739125 37.0 37.0 37.0 33.0 40.0 58-59 36.497375 37.0 37.0 37.0 33.0 40.0 60-61 36.440625 37.0 37.0 37.0 33.0 38.5 62-63 36.23575 37.0 37.0 37.0 33.0 37.0 64-65 36.16575 37.0 37.0 37.0 33.0 37.0 66-67 36.06875 37.0 37.0 37.0 33.0 37.0 68-69 35.126 35.0 35.0 37.0 33.0 37.0 70-71 35.290332329317266 37.0 33.0 37.0 33.0 37.0 72-73 35.811285862426544 37.0 37.0 37.0 33.0 37.0 74-75 35.78370959162132 37.0 37.0 37.0 33.0 37.0 76-77 35.82875278074658 37.0 37.0 37.0 33.0 37.0 78-79 35.81856191964775 37.0 37.0 37.0 33.0 37.0 80-81 35.78393684864431 37.0 37.0 37.0 33.0 37.0 82-83 35.66939289927383 37.0 37.0 37.0 33.0 37.0 84-85 35.71030452035269 37.0 37.0 37.0 33.0 37.0 86-87 35.656644295302016 37.0 37.0 37.0 33.0 37.0 88-89 35.77852348993289 37.0 37.0 37.0 33.0 37.0 90-91 35.602818791946305 37.0 37.0 37.0 33.0 37.0 92-93 35.46953020134228 37.0 35.0 37.0 33.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 20 2.0 21 3.0 22 1.0 23 8.0 24 6.0 25 4.0 26 17.0 27 13.0 28 7.0 29 18.0 30 22.0 31 34.0 32 59.0 33 51.0 34 91.0 35 175.0 36 851.0 37 1145.0 38 1436.0 39 57.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 68.61715428857215 7.826956739184795 7.326831707926981 16.22905726431608 2 52.1 25.224999999999998 13.850000000000001 8.825 3 32.4 37.075 16.725 13.8 4 31.624999999999996 27.0 19.425 21.95 5 27.925 25.974999999999998 26.825 19.275000000000002 6 20.525 36.5 25.45 17.525 7 38.125 24.325 20.575 16.975 8 28.7 26.75 25.074999999999996 19.475 9 23.75 28.050000000000004 28.225 19.975 10-11 24.025 28.6375 27.925 19.412499999999998 12-13 22.775000000000002 29.1125 28.037499999999998 20.075000000000003 14-15 20.1125 30.837500000000002 29.549999999999997 19.5 16-17 24.9 29.7125 23.3875 22.0 18-19 25.15 25.324999999999996 29.95 19.575 20-21 25.937500000000004 25.224999999999998 28.3625 20.474999999999998 22-23 29.325000000000003 22.075 26.8375 21.762500000000003 24-25 24.675 25.6 28.9 20.825 26-27 26.650000000000002 23.4875 28.749999999999996 21.1125 28-29 24.462500000000002 27.987499999999997 28.1375 19.412499999999998 30-31 27.275 26.400000000000002 27.8875 18.4375 32-33 25.275 23.9375 28.749999999999996 22.037499999999998 34-35 23.0875 32.275 25.75 18.8875 36-37 24.675 26.674999999999997 24.224999999999998 24.425 38-39 28.549999999999997 24.4 26.087500000000002 20.962500000000002 40-41 25.587500000000002 24.525 28.7 21.1875 42-43 25.637500000000003 30.65 24.925 18.787499999999998 44-45 23.525 27.474999999999998 29.4875 19.5125 46-47 26.3125 26.1625 26.2875 21.2375 48-49 24.275 24.7875 28.349999999999998 22.5875 50-51 20.9875 27.2625 29.5375 22.2125 52-53 24.962500000000002 25.8625 26.825 22.35 54-55 25.2125 26.0 27.800000000000004 20.9875 56-57 25.5125 29.062500000000004 27.55 17.875 58-59 23.575 28.8875 28.7375 18.8 60-61 28.9 27.6125 24.85 18.637500000000003 62-63 20.9375 27.762500000000003 30.9375 20.3625 64-65 22.1875 33.375 26.8 17.6375 66-67 25.0 30.625000000000004 25.525 18.85 68-69 21.95 27.987499999999997 26.787499999999998 23.275000000000002 70-71 25.288076152304612 28.369238476953907 25.463426853707418 20.879258517034067 72-73 26.185958254269448 27.94433902593295 28.437697659709045 17.43200506008855 74-75 26.049240974614108 28.243398392652125 27.70761576731726 17.999744865416506 76-77 22.723765432098766 26.620370370370374 26.15740740740741 24.498456790123456 78-79 26.17936754795231 27.449455676516333 27.64385692068429 18.72731985484707 80-81 23.289284312442756 32.2648174800471 25.63129661127829 18.814601596231846 82-83 22.905915045653035 28.172555246791052 26.042080190551808 22.8794495170041 84-85 20.5406128730095 26.321423792319017 30.50983540746688 22.628127927204602 86-87 20.671140939597315 29.48993288590604 25.651006711409398 24.187919463087248 88-89 20.28187919463087 28.966442953020135 28.778523489932883 21.973154362416107 90-91 23.63758389261745 29.208053691275165 26.40268456375839 20.751677852348994 92-93 20.053691275167786 30.75167785234899 27.489932885906036 21.70469798657718 >>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 1.0 18 0.5 19 0.5 20 1.0 21 2.0 22 2.5 23 5.0 24 8.5 25 7.0 26 8.0 27 13.0 28 20.0 29 26.0 30 30.5 31 37.0 32 47.5 33 66.0 34 74.5 35 83.5 36 101.5 37 138.0 38 155.0 39 154.5 40 197.5 41 217.0 42 270.5 43 335.5 44 264.0 45 183.5 46 162.5 47 158.5 48 149.5 49 130.5 50 155.5 51 169.5 52 143.0 53 135.0 54 200.0 55 195.0 56 104.0 57 77.5 58 59.0 59 33.5 60 22.0 61 20.5 62 21.0 63 16.5 64 10.5 65 9.0 66 8.0 67 10.5 68 18.0 69 18.5 70 10.0 71 3.0 72 2.0 73 0.5 74 0.0 75 0.0 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 0.025 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 16.0 71 24.0 72 15.0 73 17.0 74 17.0 75 13.0 76 20.0 77 10.0 78 20.0 79 17.0 80 19.0 81 21.0 82 25.0 83 18.0 84 23.0 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 3725.0 >>END_MODULE >>Sequence Duplication Levels warn #Total Deduplicated Percentage 69.27499999999999 #Duplication Level Percentage of deduplicated Percentage of total 1 90.14796102490075 62.45 2 4.114038253338145 5.7 3 2.201371346084446 4.575 4 0.7578491519307109 2.1 5 0.6134969325153374 2.125 6 0.6134969325153374 2.55 7 0.21652832912306025 1.05 8 0.288704438830747 1.6 9 0.18044027426921688 1.125 >10 0.7217610970768675 8.175 >50 0.10826416456153012 4.7 >100 0.03608805485384337 3.85 >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 154 3.85 No Hit GGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCTTGG 69 1.725 No Hit CAAGGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCT 66 1.6500000000000001 No Hit TACCTAGGCACCCAGAGACGAGGAAGGGCGTAGCAAGCGACGAAATGCTT 53 1.325 No Hit GGAAAAGAAAGCAAAAGCGATTCCCGTAGTAGCGGCGAGCGAAATGGGAG 27 0.675 No Hit GGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAA 22 0.5499999999999999 No Hit CAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAATACTTGGGCTG 21 0.525 No Hit CAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAATACTTGGGCTGATAT 20 0.5 No Hit AGTCAAGGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAA 19 0.475 No Hit GTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCTTGGT 18 0.44999999999999996 No Hit GGGTTGTTTGGGAATGCAGCCCAAATCGGGCGGTAGACTCCGTCCAAGGC 17 0.42500000000000004 No Hit GGGCGCGATCTTGCTCGTGAAGGTAATGAAATTATCCGAGCAGCTTGCAA 17 0.42500000000000004 No Hit GGGCTGATATCATCAACCGTGCTAATCTTGGTATGGAAGTAATGCACGAA 17 0.42500000000000004 No Hit GAGGAAGGGCGTAGCAAGCGACGAAATGCTTCGGGGAGTTGAAAATAAGC 16 0.4 No Hit GGAATCCCGTGTGAATCAGCAAGGACCACCTTGCAAGGCTAAATACTCCT 16 0.4 No Hit GGGTGAGAGCCCCGTCCGGCCCGGACCCTGTCGCCCCACGAGGCGCCGTC 16 0.4 No Hit GTAGTTGATAGTCAAGGTCGCGTTATTAATACTTGGGCTGATATCATCAA 15 0.375 No Hit GGAGTTGAAAATAAGCATAGATCCGGAGATTCCCAAATAGGTCAACCTTT 14 0.35000000000000003 No Hit GTCAAGGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAAT 14 0.35000000000000003 No Hit GGGGCACGTGGAATCCCGTGTGAATCAGCAAGGACCACCTTGCAAGGCTA 14 0.35000000000000003 No Hit GGGCACGTGGAATCCCGTGTGAATCAGCAAGGACCACCTTGCAAGGCTAA 12 0.3 No Hit CAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAGGTC 11 0.27499999999999997 No Hit GGTTGAGTGCCGCACCCTAGATGGCTAAAGTCCAGTAGCCGAAAGCATCA 11 0.27499999999999997 No Hit GTAGTAGGAATCTGGTTCACTGCTTTAGGTATTAGTACTATGGCGTTCAA 10 0.25 No Hit GGCGTTCAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTC 9 0.22499999999999998 No Hit GGGGTTGTGGGAGAGCAATACAAGCGTTGTGCTGCTAGGCGAAGCGGTTG 9 0.22499999999999998 No Hit GGAGAGCAATACAAGCGTTGTGCTGCTAGGCGAAGCGGTTGAGTGCCGCA 9 0.22499999999999998 No Hit GAAGGTAATGAAATTATCCGAGCAGCTTGCAAATGGAGTCCTGAACTAGC 9 0.22499999999999998 No Hit GGGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGT 9 0.22499999999999998 No Hit GCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCTTGGTATG 8 0.2 No Hit GCAAGGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATC 8 0.2 No Hit GGGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCTTG 8 0.2 No Hit GGCGCGATCTTGCTCGTGAAGGTAATGAAATTATCCGAGCAGCTTGCAAA 8 0.2 No Hit GTATTTAGCCTTGCAAGGTGGTCCTTGCTGATTCACACGGGATTCCACGT 8 0.2 No Hit GGGGAGTTGAAAATAAGCATAGATCCGGAGATTCCCAAATAGGTCAACCT 8 0.2 No Hit GGTAATGAAATTATCCGAGCAGCTTGCAAATGGAGTCCTGAACTAGCCGC 8 0.2 No Hit TCAAAAGAGGAAAGGCTTGCGGTGGATACCTAGGCACCCAGAGACGAGGA 8 0.2 No Hit GGGGCAGAGGGAATTTCCGGTGGAGCGGTGAAATGCATTGAGATCGGAAA 7 0.17500000000000002 No Hit GGAAGGGCGTAGCAAGCGACGAAATGCTTCGGGGAGTTGAAAATAAGCAT 7 0.17500000000000002 No Hit GATAGTCAAGGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGC 7 0.17500000000000002 No Hit GTACAAGCTCGTAACGAAGGGCGCGATCTTGCTCGTGAAGGTAATGAAAT 7 0.17500000000000002 No Hit GGAGCAGCCTAAACCGTGAAAACGGGGTTGTGGGAGAGCAATACAAGCGT 7 0.17500000000000002 No Hit GTTCAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAG 7 0.17500000000000002 No Hit GGAGTTTGGCTGGGGCGGCACATCTGTTAAAAGATAACGCAGGTGTCCTA 6 0.15 No Hit GGTTCACTGCTTTAGGTATTAGTACTATGGCGTTCAACCTAAATGGATTC 6 0.15 No Hit TAGTCAAGGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTA 6 0.15 No Hit CGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCTTGGTAT 6 0.15 No Hit CAATTTCAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAATACTT 6 0.15 No Hit GGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGTG 6 0.15 No Hit GGAGGGTGAGAGCCCCGTCCGGCCCGGACCCTGTCGCCCCACGAGGCGCC 6 0.15 No Hit GTACTATGGCGTTCAACCTAAATGGATTCAATTTCAACCAATCTGTAGTT 6 0.15 No Hit GGGCGTAGCAAGCGACGAAATGCTTCGGGGAGTTGAAAATAAGCATAGAT 6 0.15 No Hit CGAGTCGGGTTGTTTGGGAATGCAGCCCAAATCGGGCGGTAGACTCCGTC 6 0.15 No Hit GGGATGATTCTGTATTACAATTTGGTGGAGGAACTTTAGGACATCCTTGG 6 0.15 No Hit GACCCGAGTAGCATGGGGCACGTGGAATCCCGTGTGAATCAGCAAGGACC 6 0.15 No Hit GCAGCTTGCAAATGGAGTCCTGAACTAGCCGCAGCTTGTGAAGTATGGAA 6 0.15 No Hit GATACCTAGGCACCCAGAGACGAGGAAGGGCGTAGCAAGCGACGAAATGC 6 0.15 No Hit CGAGGAAGGGCGTAGCAAGCGACGAAATGCTTCGGGGAGTTGAAAATAAG 6 0.15 No Hit GGCCCGGACCCTGTCGCCCCACGAGGCGCCGTCAACGAGTCGGGTTGTTT 6 0.15 No Hit AACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAATACTTGGGCTGA 6 0.15 No Hit GAAGGCGATCAAATTCGAGTTCGCGCCGGTAGATACTATCGATTAATAGA 5 0.125 No Hit GGTTGTGGGAGAGCAATACAAGCGTTGTGCTGCTAGGCGAAGCGGTTGAG 5 0.125 No Hit CACCCAGAGACGAGGAAGGGCGTAGCAAGCGACGAAATGCTTCGGGGAGT 5 0.125 No Hit GGCCTGTAGTAGGAATCTGGTTCACTGCTTTAGGTATTAGTACTATGGCG 5 0.125 No Hit GTTGTGGGAGAGCAATACAAGCGTTGTGCTGCTAGGCGAAGCGGTTGAGT 5 0.125 No Hit CAAAAGAGGAAAGGCTTGCGGTGGATACCTAGGCACCCAGAGACGAGGAA 5 0.125 No Hit GAAGGGCGTAGCAAGCGACGAAATGCTTCGGGGAGTTGAAAATAAGCATA 5 0.125 No Hit GCCGCACCCTAGATGGCTAAAGTCCAGTAGCCGAAAGCATCACTAGCTTA 5 0.125 No Hit GGGGATGATTCTGTATTACAATTTGGTGGAGGAACTTTAGGACATCCTTG 5 0.125 No Hit GTGGAATCCCGTGTGAATCAGCAAGGACCACCTTGCAAGGCTAAATACTC 5 0.125 No Hit TCAGTGTCGGCCCAGCAGAGTGCTTTCGCCGTTGGTGTTCTTTCCGATCT 5 0.125 No Hit AGGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCTTG 5 0.125 No Hit GGAAAAGAGGGGTTACTTTTTTTCATTTTTCCCTTAAAAGATAGGCTTTG 5 0.125 No Hit GGGGCTGATATCATCAACCGTGCTAATCTTGGTATGGAAGTAATGCACGA 5 0.125 No Hit CTGTAGTTGATAGTCAAGGTCGCGTTATTAATACTTGGGCTGATATCATC 5 0.125 No Hit GCACCCTAGATGGCTAAAGTCCAGTAGCCGAAAGCATCACTAGCTTACGC 5 0.125 No Hit GAACGTAATGCTCACAACTTCCCTCTAGATCTAGCTGCTCTTGAAGTTCC 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 0.025 0.0 0.0 0.0 0.0 10-11 0.025 0.0 0.0 0.0 0.0 12-13 0.025 0.0 0.0 0.0 0.0 14-15 0.025 0.0 0.0 0.0 0.0 16-17 0.037500000000000006 0.0 0.0 0.0 0.0 18-19 0.05 0.0 0.0 0.0 0.0 20-21 0.05 0.0 0.0 0.0 0.0 22-23 0.05 0.0 0.0 0.0 0.0 24-25 0.05 0.0 0.0 0.0 0.0 26-27 0.0625 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 0.1 0.0 0.0 0.0 0.0 44-45 0.1 0.0 0.0 0.0 0.0 46-47 0.1 0.0 0.0 0.0 0.0 48-49 0.1 0.0 0.0 0.0 0.0 50-51 0.1 0.0 0.0 0.0 0.0 52-53 0.1 0.0 0.0 0.0 0.0 54-55 0.1 0.0 0.0 0.0 0.0 56-57 0.1 0.0 0.0 0.0 0.0 58-59 0.1 0.0 0.0 0.0 0.0 60-61 0.1 0.0 0.0 0.0 0.0 62-63 0.1 0.0 0.0 0.0 0.0 64-65 0.1 0.0 0.0 0.0 0.0 66-67 0.1 0.0 0.0 0.0 0.0 68-69 0.1 0.0 0.0 0.0 0.0 70-71 0.1 0.0 0.0 0.0 0.0 72-73 0.1 0.0 0.0 0.0 0.0 74-75 0.1 0.0 0.0 0.0 0.0 76-77 0.1 0.0 0.0 0.0 0.0 78-79 0.1 0.0 0.0 0.0 0.0 80-81 0.1 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position GGCACCC 15 9.207688E-4 85.8 7 CTAGGCA 15 9.207688E-4 85.8 4 GCACCCA 15 9.207688E-4 85.8 8 TAGGCAC 15 9.207688E-4 85.8 5 GGGAGAG 35 5.5944838E-8 73.54286 1 GGAGAGC 40 1.4114266E-7 64.35 2 CAATACA 40 1.4114266E-7 64.35 8 GAGCAAT 40 1.4114266E-7 64.35 5 CACCCAG 20 0.0028844438 64.35 9 AGAGCAA 40 1.4114266E-7 64.35 4 AGGCACC 20 0.0028844438 64.35 6 GGGGCTG 20 0.0028844438 64.35 1 GAGAGCA 40 1.4114266E-7 64.35 3 AATACAA 40 1.4114266E-7 64.35 9 AGCAATA 40 1.4114266E-7 64.35 6 TACCTAG 20 0.0028844438 64.35 1 ACCTAGG 20 0.0028844438 64.35 2 CCTAGGC 20 0.0028844438 64.35 3 GCAATAC 45 3.189216E-7 57.200005 7 GAAGCGG 30 2.6501057E-6 42.9 32-33 >>END_MODULE Rejected 251159 READS because READLEN < 1 Read 251159 spots for ERR6133356.sra Written 251159 spots for ERR6133356.sra Rejected 251159 READS because READLEN < 1 Read 251159 spots for ERR6133356.sra Written 251159 spots for ERR6133356.sra Rejected 251159 READS because READLEN < 1 Read 251159 spots for ERR6133356.sra Written 251159 spots for ERR6133356.sra Rejected 251159 READS because READLEN < 1 Read 251159 spots for ERR6133356.sra Written 251159 spots for ERR6133356.sra Rejected 251159 READS because READLEN < 1 Read 251159 spots for ERR6133356.sra Written 251159 spots for ERR6133356.sra Rejected 251159 READS because READLEN < 1 Read 251159 spots for ERR6133356.sra Written 251159 spots for ERR6133356.sra Rejected 251159 READS because READLEN < 1 Read 251159 spots for ERR6133356.sra Written 251159 spots for ERR6133356.sra Rejected 251159 READS because READLEN < 1 Read 251159 spots for ERR6133356.sra Written 251159 spots for ERR6133356.sra Rejected 251159 READS because READLEN < 1 Read 251159 spots for ERR6133356.sra Written 251159 spots for ERR6133356.sra Rejected 251159 READS because READLEN < 1 Read 251159 spots for ERR6133356.sra Written 251159 spots for ERR6133356.sra Rejected 251159 READS because READLEN < 1 Read 251159 spots for ERR6133356.sra Written 251159 spots for ERR6133356.sra Rejected 251166 READS because READLEN < 1 Read 251166 spots for ERR6133356.sra Written 251166 spots for ERR6133356.sra Rejected 251159 READS because READLEN < 1 Read 251159 spots for ERR6133356.sra Written 251159 spots for ERR6133356.sra Rejected 251159 READS because READLEN < 1 Read 251159 spots for ERR6133356.sra Written 251159 spots for ERR6133356.sra Rejected 251159 READS because READLEN < 1 Read 251159 spots for ERR6133356.sra Written 251159 spots for ERR6133356.sra Rejected 251159 READS because READLEN < 1 Read 251159 spots for ERR6133356.sra Written 251159 spots for ERR6133356.sra Rejected 251159 READS because READLEN < 1 Read 251159 spots for ERR6133356.sra Written 251159 spots for ERR6133356.sra Rejected 251159 READS because READLEN < 1 Read 251159 spots for ERR6133356.sra Written 251159 spots for ERR6133356.sra Rejected 251159 READS because READLEN < 1 Read 251159 spots for ERR6133356.sra Written 251159 spots for ERR6133356.sra Rejected 251159 READS because READLEN < 1 Read 251159 spots for ERR6133356.sra Written 251159 spots for ERR6133356.sra SRR ids: ['ERR6133356.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_kmzjytwz ERR6133356.sra spots: 5023187 blocks: [[1, 251159], [251160, 502318], [502319, 753477], [753478, 1004636], [1004637, 1255795], [1255796, 1506954], [1506955, 1758113], [1758114, 2009272], [2009273, 2260431], [2260432, 2511590], [2511591, 2762749], [2762750, 3013908], [3013909, 3265067], [3265068, 3516226], [3516227, 3767385], [3767386, 4018544], [4018545, 4269703], [4269704, 4520862], [4520863, 4772021], [4772022, 5023187]] ERR6133356 file size 1105879 ERR6133356 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 ERR6133356 ERR6133356_1.fastq Input file: ERR6133356_1.fastq trimmed: ERR6133356-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 01:19:23 2024 >> started Sat Dec 7 01:19:25 2024 >> done (2.763s) 5023187 reads processed; of these: 693 ( 0.01%) short reads filtered out after trimming by size control 17 ( 0.00%) empty reads filtered out after trimming by size control 5022477 (99.99%) reads available; of these: 30694 ( 0.61%) trimmed reads available after processing 4991783 (99.39%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 41 0.00% 19 145 0.00% 20 72 0.00% 21 47 0.00% 22 60 0.00% 23 49 0.00% 24 36 0.00% 25 32 0.00% 26 68 0.00% 27 49 0.00% 28 60 0.00% 29 95 0.00% 30 38 0.00% 31 59 0.00% 32 139 0.00% 33 60 0.00% 34 56 0.00% 35 186 0.00% 36 40 0.00% 37 45 0.00% 38 85 0.00% 39 190 0.00% 40 259 0.01% 41 81 0.00% 42 28 0.00% 43 54 0.00% 44 84 0.00% 45 49 0.00% 46 19 0.00% 47 22 0.00% 48 27 0.00% 49 31 0.00% 50 36 0.00% 51 247 0.00% 52 47 0.00% 53 22 0.00% 54 23 0.00% 55 38 0.00% 56 24 0.00% 57 50 0.00% 58 34 0.00% 59 27 0.00% 60 39 0.00% 61 21 0.00% 62 8 0.00% 63 20 0.00% 64 28 0.00% 65 32 0.00% 66 31 0.00% 67 34 0.00% 68 98 0.00% 69 161 0.00% 70 22124 0.44% 71 20234 0.40% 72 21656 0.43% 73 20448 0.41% 74 19333 0.38% 75 18825 0.37% 76 18759 0.37% 77 20612 0.41% 78 20834 0.41% 79 22229 0.44% 80 22525 0.45% 81 30074 0.60% 82 30647 0.61% 83 24993 0.50% 84 30636 0.61% 85 208 0.00% 86 287 0.01% 87 389 0.01% 88 621 0.01% 89 1076 0.02% 90 2012 0.04% 91 4472 0.09% 92 15374 0.31% 93 4650783 92.60% 5022477 reads passed initial QC criterion=sequence-density sequence-density=3.54 sequence-density-rank=1 fanout-score=2.02 fanout-score-rank=29 prefix-density=3.58 prefix-fanout=2.0 sequence=CAAGGCTAAATAC criterion=fanout-score sequence-density=0.01 sequence-density-rank=39 fanout-score=51.10 fanout-score-rank=1 prefix-density=0.07 prefix-fanout=4.4 sequence=CTTTTTTCCTTAGAAAAATAACTCAATCAAAATCCAATTATTTACTCTACAAGAACGAAATGCTTGTTATGCCTAATATACTTAGTTTAACCTGTATCTGTTTTAATTGTGTTCTTTATCCGACTAGTTTTTTCTTTGCTAAACTACCCGAAGCTTATGCTATTTTCAACCCAATCGTGGATGTTATGCCTGTCATACCTCTATTCTTTTTTCTATTAGCCTTTGTTTGGCAAGCTGCTGTAAGTTTTCGATGAAATCTTTACTACTCCGTCTGCCAAATTGAATGGTCTATTCATTCCAAAACC 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 01:19:46 Started mapping on | Dec 07 01:19:46 Finished on | Dec 07 01:19:54 Mapping speed, Million of reads per hour | 2260.11 Number of input reads | 5022477 Average input read length | 91 UNIQUE READS: Uniquely mapped reads number | 2314202 Uniquely mapped reads % | 46.08% Average mapped length | 90.96 Number of splices: Total | 83951 Number of splices: Annotated (sjdb) | 68645 Number of splices: GT/AG | 79399 Number of splices: GC/AG | 1542 Number of splices: AT/AC | 76 Number of splices: Non-canonical | 2934 Mismatch rate per base, % | 0.41% Deletion rate per base | 0.04% Deletion average length | 1.72 Insertion rate per base | 0.02% Insertion average length | 1.80 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 2357899 % of reads mapped to multiple loci | 46.95% Number of reads mapped to too many loci | 229288 % of reads mapped to too many loci | 4.57% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 2.21% % of reads unmapped: other | 0.20% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 350376 350376 350376 N_multimapping 2357899 2357899 2357899 N_noFeature 209238 233192 2213227 N_ambiguous 89902 12696 444 UnstrandedReadsAssigned:2015062 PositiveStrandReadsAssigned:2068314 NegativeStrandReadsAssigned:100531 Dataset is classified positive stranded MeadianReadLen=93 20thPercentileLength=93 echo kmer=89 ERR6133356 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: ERR6133356-trimmed.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 5,022,477 reads, 3,309,254 reads pseudoaligned [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 978 rounds 52973 ERR6133356.ke.tsv 35125 ERR6133356.se.tsv 88098 total ==> ERR6133356.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 65 19.011 PNS24243 293 194 0 0 KQK14069 1603 1504 26 6.93699 KQK14071 474 375 0 0 ==> ERR6133356.se.tsv <== BRADI_1g14170v3 26 BRADI_1g53295v3 29 BRADI_1g59795v3 24 BRADI_1g07683v3 0 BRADI_1g00485v3 0 BRADI_1g20270v3 24 BRADI_1g74790v3 29 BRADI_1g09890v3 0 BRADI_1g77505v3 49 BRADI_1g48960v3 0 ERR6133356 completed mapping pipeline successfully