Starting /dee2/code/volunteer_pipeline.sh ERR6133408 current disk space = 1547593469952 free memory = 1459109752 ERR6133408 SRAfilesize 157f6484db48aeec19a530a33a90afbd ERR6133408.sra ERR6133408.sra file validated ERR6133408 is single end ERR6133408 is conventional basespace ERR6133408 read1 length is 70-93 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename ERR6133408_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 fail #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 29.81125 33.0 27.0 33.0 15.0 37.0 2 33.883 37.0 33.0 37.0 27.0 37.0 3 33.94025 37.0 33.0 37.0 27.0 37.0 4 34.047 37.0 33.0 37.0 27.0 37.0 5 34.25825 37.0 33.0 37.0 27.0 37.0 6 34.1675 37.0 33.0 37.0 27.0 37.0 7 35.4455 37.0 33.0 40.0 27.0 40.0 8 35.184 37.0 33.0 40.0 27.0 40.0 9 35.57775 37.0 33.0 40.0 33.0 40.0 10-11 35.39925 37.0 33.0 40.0 30.0 40.0 12-13 35.326875 37.0 33.0 40.0 30.0 40.0 14-15 35.211875000000006 37.0 33.0 40.0 27.0 40.0 16-17 34.895250000000004 37.0 33.0 37.0 27.0 40.0 18-19 34.78425 37.0 33.0 37.0 27.0 40.0 20-21 34.083 37.0 33.0 37.0 24.5 40.0 22-23 33.997875 37.0 33.0 37.0 27.0 40.0 24-25 33.730625 37.0 33.0 37.0 24.5 40.0 26-27 33.261250000000004 37.0 33.0 37.0 22.0 40.0 28-29 32.956125 37.0 33.0 37.0 22.0 40.0 30-31 32.931375 37.0 33.0 37.0 22.0 40.0 32-33 32.375625 35.0 33.0 37.0 22.0 40.0 34-35 31.54975 33.0 27.0 37.0 18.5 40.0 36-37 31.243375 33.0 27.0 37.0 15.0 38.5 38-39 31.668 33.0 27.0 37.0 22.0 40.0 40-41 31.620375000000003 33.0 27.0 37.0 22.0 40.0 42-43 31.074624999999997 33.0 27.0 37.0 15.0 40.0 44-45 30.942125 33.0 27.0 37.0 18.5 40.0 46-47 30.389375 33.0 27.0 37.0 15.0 37.0 48-49 30.175874999999998 33.0 27.0 37.0 15.0 37.0 50-51 29.622 33.0 27.0 37.0 15.0 37.0 52-53 29.62975 33.0 27.0 37.0 15.0 37.0 54-55 29.460124999999998 33.0 27.0 37.0 15.0 37.0 56-57 28.661250000000003 33.0 27.0 35.0 15.0 37.0 58-59 28.47175 33.0 27.0 33.0 15.0 37.0 60-61 28.313125 33.0 27.0 33.0 15.0 37.0 62-63 27.918375 33.0 22.0 33.0 15.0 37.0 64-65 27.394 33.0 22.0 33.0 10.5 37.0 66-67 26.831125 30.0 22.0 33.0 10.5 37.0 68-69 26.518124999999998 27.0 22.0 33.0 10.5 35.0 70-71 28.303832800351138 33.0 27.0 33.0 15.0 37.0 72-73 28.641029520143952 33.0 27.0 33.0 15.0 37.0 74-75 28.54809831907611 33.0 27.0 33.0 15.0 37.0 76-77 28.42604638160629 33.0 27.0 33.0 15.0 37.0 78-79 27.92041712865918 33.0 27.0 33.0 10.5 37.0 80-81 27.057940315609883 33.0 24.5 33.0 6.0 37.0 82-83 26.311916820809728 33.0 22.0 33.0 4.0 37.0 84-85 25.537007581768254 33.0 22.0 33.0 2.0 37.0 86-87 24.405275467775468 30.0 15.0 33.0 2.0 37.0 88-89 23.912551975051976 30.0 15.0 33.0 2.0 37.0 90-91 22.943217255717258 27.0 4.0 33.0 2.0 37.0 92-93 21.525467775467774 27.0 2.0 33.0 2.0 33.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 20 95.0 21 84.0 22 147.0 23 149.0 24 167.0 25 195.0 26 221.0 27 250.0 28 244.0 29 269.0 30 286.0 31 243.0 32 289.0 33 263.0 34 310.0 35 308.0 36 273.0 37 175.0 38 32.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 69.6 8.674999999999999 7.1499999999999995 14.575 2 52.800000000000004 22.1 15.25 9.85 3 34.175 35.65 16.85 13.325000000000001 4 26.3 30.575000000000003 22.400000000000002 20.724999999999998 5 25.900000000000002 26.375 28.375 19.35 6 17.599999999999998 38.6 26.400000000000002 17.4 7 34.449999999999996 26.3 21.85 17.4 8 23.674999999999997 26.325 26.900000000000002 23.1 9 24.0 31.45 26.275 18.275 10-11 21.9625 29.062500000000004 29.762499999999996 19.2125 12-13 21.5375 30.1875 27.287499999999998 20.9875 14-15 21.6125 32.6375 27.224999999999998 18.525 16-17 25.374999999999996 27.187499999999996 24.0 23.4375 18-19 24.05 24.85 31.6875 19.412499999999998 20-21 25.8625 24.4375 30.412499999999998 19.287499999999998 22-23 28.199999999999996 21.912499999999998 29.425 20.4625 24-25 23.4625 24.2625 29.299999999999997 22.975 26-27 24.9875 24.4 29.5375 21.075 28-29 22.650000000000002 28.325 29.4875 19.537499999999998 30-31 29.75 25.8625 25.2625 19.125 32-33 26.5375 23.35 28.012500000000003 22.1 34-35 22.237499999999997 32.2 26.0125 19.55 36-37 24.825 26.6 24.962500000000002 23.6125 38-39 30.675 23.1375 27.037499999999998 19.15 40-41 23.9375 24.9875 32.574999999999996 18.5 42-43 26.700000000000003 29.75 25.7375 17.8125 44-45 25.6125 25.224999999999998 29.3875 19.775000000000002 46-47 26.4625 26.087500000000002 24.462500000000002 22.9875 48-49 25.95 22.9375 28.175 22.9375 50-51 21.4125 29.1125 26.825 22.650000000000002 52-53 22.6875 26.275 24.7 26.337500000000002 54-55 21.9625 24.875 31.5125 21.65 56-57 26.25 28.762500000000003 25.0375 19.950000000000003 58-59 22.025 29.299999999999997 28.925 19.75 60-61 28.7375 25.25 27.0 19.0125 62-63 19.5125 26.0375 31.95 22.5 64-65 20.9875 34.362500000000004 26.400000000000002 18.25 66-67 25.900000000000002 28.812500000000004 26.125 19.162499999999998 68-69 21.0 25.8 29.062500000000004 24.1375 70-71 22.599223738575187 28.47126580693627 26.480530862651808 22.448979591836736 72-73 26.80594009564561 23.59677825320916 30.581424616159076 19.015857034986155 74-75 25.754705065049894 30.011367942402423 26.348364279398762 17.88556271314892 76-77 20.623258170762604 24.61363060552318 27.514568026349124 27.248543197365088 78-79 25.012722646310433 29.24936386768448 27.353689567430024 18.384223918575064 80-81 22.186700767263424 34.57800511508952 26.265984654731454 16.969309462915604 82-83 24.17568263781556 25.2833590932509 25.07727975270479 25.46367851622875 84-85 21.599896279009464 26.38402696745754 31.557111370413587 20.45896538311941 86-87 22.362266112266113 29.417879417879416 25.55873180873181 22.66112266112266 88-89 20.93295218295218 26.624220374220375 30.10654885654886 22.336278586278585 90-91 25.753638253638258 29.495841995842 25.92255717255717 18.82796257796258 92-93 18.633056133056133 30.067567567567565 28.82016632016632 22.47920997920998 >>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 1.0 16 1.5 17 2.5 18 3.5 19 2.0 20 0.5 21 1.5 22 4.0 23 4.0 24 3.0 25 3.0 26 6.5 27 12.5 28 21.0 29 25.5 30 25.5 31 27.0 32 34.5 33 42.0 34 47.5 35 69.5 36 119.5 37 213.0 38 262.5 39 238.0 40 219.0 41 203.0 42 205.5 43 219.0 44 194.0 45 165.0 46 163.5 47 142.5 48 116.0 49 115.0 50 111.0 51 121.0 52 134.0 53 143.0 54 229.0 55 229.0 56 114.5 57 75.0 58 65.5 59 46.0 60 32.0 61 23.0 62 18.0 63 18.5 64 15.5 65 12.0 66 9.0 67 5.5 68 8.5 69 11.0 70 6.0 71 1.0 72 2.5 73 2.0 74 1.0 75 1.0 76 0.5 77 0.5 78 0.0 79 0.0 80 0.0 81 0.0 82 0.5 83 0.5 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 13.0 71 10.0 72 8.0 73 8.0 74 5.0 75 7.0 76 4.0 77 10.0 78 10.0 79 8.0 80 14.0 81 14.0 82 14.0 83 10.0 84 17.0 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 3848.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 71.175 #Duplication Level Percentage of deduplicated Percentage of total 1 92.41306638566913 65.77499999999999 2 2.73972602739726 3.9 3 1.8616087109237796 3.975 4 0.8078679311556024 2.3 5 0.49174569722514927 1.7500000000000002 6 0.31612223393045313 1.35 7 0.21074815595363539 1.05 8 0.14049877063575694 0.8 9 0.07024938531787847 0.44999999999999996 >10 0.91324200913242 12.65 >50 0.0 0.0 >100 0.035124692658939236 6.0 >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 240 6.0 No Hit GGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAA 47 1.175 No Hit GGTTCACTGCTTTAGGTATTAGTACTATGGCGTTCAACCTAAATGGATTC 38 0.95 No Hit GGCGTTCAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTC 34 0.8500000000000001 No Hit TCAAAAGAGGAAAGGCTTGCGGTGGATACCTAGGCACCCAGAGACGAGGA 32 0.8 No Hit CAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAGGTC 29 0.7250000000000001 No Hit GTAGTAGGAATCTGGTTCACTGCTTTAGGTATTAGTACTATGGCGTTCAA 27 0.675 No Hit GTTCAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAG 25 0.625 No Hit CAAGGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCT 20 0.5 No Hit GTATTAGTACTATGGCGTTCAACCTAAATGGATTCAATTTCAACCAATCT 20 0.5 No Hit GGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCTTGG 18 0.44999999999999996 No Hit GGAATCTGGTTCACTGCTTTAGGTATTAGTACTATGGCGTTCAACCTAAA 18 0.44999999999999996 No Hit CAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAATACTTGGGCTG 16 0.4 No Hit CAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAATACTTGGGCTGATAT 15 0.375 No Hit GGACATCCTTGGGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTT 15 0.375 No Hit GTAGGAATCTGGTTCACTGCTTTAGGTATTAGTACTATGGCGTTCAACCT 15 0.375 No Hit GGGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGT 15 0.375 No Hit GGCCTGTAGTAGGAATCTGGTTCACTGCTTTAGGTATTAGTACTATGGCG 14 0.35000000000000003 No Hit GGGCTGATATCATCAACCGTGCTAATCTTGGTATGGAAGTAATGCACGAA 14 0.35000000000000003 No Hit GTACTATGGCGTTCAACCTAAATGGATTCAATTTCAACCAATCTGTAGTT 13 0.325 No Hit GGGCACGTGGAATCCCGTGTGAATCAGCAAGGACCACCTTGCAAGGCTAA 12 0.3 No Hit GGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGTG 12 0.3 No Hit GGGTTGTTTGGGAATGCAGCCCAAATCGGGCGGTAGACTCCGTCCAAGGC 12 0.3 No Hit AACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAATACTTGGGCTGA 12 0.3 No Hit GGAAAAGAAAGCAAAAGCGATTCCCGTAGTAGCGGCGAGCGAAATGGGAG 12 0.3 No Hit GGGGTTGTGGGAGAGCAATACAAGCGTTGTGCTGCTAGGCGAAGCGGTTG 11 0.27499999999999997 No Hit GGGGAGAGCAATACAAGCGTTGTGCTGCTAGGCGAAGCGGTTGAGTGCCG 10 0.25 No Hit GAATCTGGTTCACTGCTTTAGGTATTAGTACTATGGCGTTCAACCTAAAT 9 0.22499999999999998 No Hit AGTCAAGGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAA 9 0.22499999999999998 No Hit GGAGTTGAAAATAAGCATAGATCCGGAGATTCCCAAATAGGTCAACCTTT 8 0.2 No Hit TACCTAGGCACCCAGAGACGAGGAAGGGCGTAGCAAGCGACGAAATGCTT 8 0.2 No Hit GTCAAGGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAAT 8 0.2 No Hit GGGGAGTTGAAAATAAGCATAGATCCGGAGATTCCCAAATAGGTCAACCT 8 0.2 No Hit GGTATTAGTACTATGGCGTTCAACCTAAATGGATTCAATTTCAACCAATC 7 0.17500000000000002 No Hit GGGAATGCAGCCCAAATCGGGCGGTAGACTCCGTCCAAGGCTAAATACAG 7 0.17500000000000002 No Hit GGTTGTGGGAGAGCAATACAAGCGTTGTGCTGCTAGGCGAAGCGGTTGAG 7 0.17500000000000002 No Hit GCAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAATACTTGGGCT 7 0.17500000000000002 No Hit CTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAGGTCGCGT 7 0.17500000000000002 No Hit GGAATCCCGTGTGAATCAGCAAGGACCACCTTGCAAGGCTAAATACTCCT 7 0.17500000000000002 No Hit CAATTTCAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAATACTT 6 0.15 No Hit GCAAGGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATC 6 0.15 No Hit GGCTGCTTGGCCTGTAGTAGGAATCTGGTTCACTGCTTTAGGTATTAGTA 6 0.15 No Hit GGGAATTTCCGGTGGAGCGGTGAAATGCATTGAGATCGGAAAGAACACCA 6 0.15 No Hit GGAGAGCAATACAAGCGTTGTGCTGCTAGGCGAAGCGGTTGAGTGCCGCA 6 0.15 No Hit GGGTGAGAGCCCCGTCCGGCCCGGACCCTGTCGCCCCACGAGGCGCCGTC 6 0.15 No Hit CTGTAGTAGGAATCTGGTTCACTGCTTTAGGTATTAGTACTATGGCGTTC 6 0.15 No Hit GCAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAGGT 6 0.15 No Hit GGGGCACGTGGAATCCCGTGTGAATCAGCAAGGACCACCTTGCAAGGCTA 6 0.15 No Hit GAGGAAGGGCGTAGCAAGCGACGAAATGCTTCGGGGAGTTGAAAATAAGC 5 0.125 No Hit GGATGATTCTGTATTACAATTTGGTGGAGGAACTTTAGGACATCCTTGGG 5 0.125 No Hit GGAGGGTGAGAGCCCCGTCCGGCCCGGACCCTGTCGCCCCACGAGGCGCC 5 0.125 No Hit AATGGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTAT 5 0.125 No Hit AACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAGGTCG 5 0.125 No Hit GTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCTTGGTATGGA 5 0.125 No Hit GGAGCGGTGAAATGCATTGAGATCGGAAAGAACACCAACGGCGAAAGCAC 5 0.125 No Hit ATGGCGTTCAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAG 5 0.125 No Hit TATCATCAACCGTGCTAATCTTGGTATGGAAGTAATGCACGAACGTAATG 5 0.125 No Hit GCGTTCAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTCA 5 0.125 No Hit GGGGCTGATATCATCAACCGTGCTAATCTTGGTATGGAAGTAATGCACGA 5 0.125 No Hit GAAGGTAATGAAATTATCCGAGCAGCTTGCAAATGGAGTCCTGAACTAGC 5 0.125 No Hit GGATTTGTTAAATCAAATCCTTGGTTTAATAACGAACGGTGTTAACTTAC 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 0.025 0.0 0.0 0.0 0.0 22-23 0.025 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 GCAATAC 50 4.1190964E-5 43.2 7 AATACAA 50 4.1190964E-5 43.2 9 GGGAGAG 65 3.8424514E-6 39.876923 1 GGAGAGC 55 7.230621E-5 39.27273 2 CAATACA 55 7.230621E-5 39.27273 8 GAGCAAT 55 7.230621E-5 39.27273 5 AGAGCAA 55 7.230621E-5 39.27273 4 GAGAGCA 55 7.230621E-5 39.27273 3 AGCAATA 55 7.230621E-5 39.27273 6 GCATCAC 35 5.578053E-6 38.47124 82-83 AAGCATC 35 5.578053E-6 38.47124 80-81 ATCACTA 45 7.4566924E-7 34.90909 84-85 CACTAGC 45 7.4566924E-7 34.90909 86-87 CCGAAAG 40 1.3942959E-5 33.66234 76-77 AGCCGAA 40 1.52575685E-5 33.23077 74-75 GTAGCCG 40 1.52575685E-5 33.23077 72-73 ACTAGCT 35 2.609873E-4 32.05937 86-87 TCCAGTA 50 2.086348E-6 30.622786 68-69 GGTTGAG 50 2.3065804E-6 30.24 38-39 GCTAGGC 50 2.3065804E-6 30.24 26-27 >>END_MODULE Rejected 122819 READS because READLEN < 1 Read 122819 spots for ERR6133408.sra Written 122819 spots for ERR6133408.sra Rejected 122819 READS because READLEN < 1 Read 122819 spots for ERR6133408.sra Written 122819 spots for ERR6133408.sra Rejected 122819 READS because READLEN < 1 Read 122819 spots for ERR6133408.sra Written 122819 spots for ERR6133408.sra Rejected 122819 READS because READLEN < 1 Read 122819 spots for ERR6133408.sra Written 122819 spots for ERR6133408.sra Rejected 122819 READS because READLEN < 1 Read 122819 spots for ERR6133408.sra Written 122819 spots for ERR6133408.sra Rejected 122819 READS because READLEN < 1 Read 122819 spots for ERR6133408.sra Written 122819 spots for ERR6133408.sra Rejected 122819 READS because READLEN < 1 Read 122819 spots for ERR6133408.sra Written 122819 spots for ERR6133408.sra Rejected 122819 READS because READLEN < 1 Read 122819 spots for ERR6133408.sra Written 122819 spots for ERR6133408.sra Rejected 122819 READS because READLEN < 1 Read 122819 spots for ERR6133408.sra Written 122819 spots for ERR6133408.sra Rejected 122819 READS because READLEN < 1 Read 122819 spots for ERR6133408.sra Written 122819 spots for ERR6133408.sra Rejected 122826 READS because READLEN < 1 Read 122826 spots for ERR6133408.sra Written 122826 spots for ERR6133408.sra Rejected 122819 READS because READLEN < 1 Read 122819 spots for ERR6133408.sra Written 122819 spots for ERR6133408.sra Rejected 122819 READS because READLEN < 1 Read 122819 spots for ERR6133408.sra Written 122819 spots for ERR6133408.sra Rejected 122819 READS because READLEN < 1 Read 122819 spots for ERR6133408.sra Written 122819 spots for ERR6133408.sra Rejected 122819 READS because READLEN < 1 Read 122819 spots for ERR6133408.sra Written 122819 spots for ERR6133408.sra Rejected 122819 READS because READLEN < 1 Read 122819 spots for ERR6133408.sra Written 122819 spots for ERR6133408.sra Rejected 122819 READS because READLEN < 1 Read 122819 spots for ERR6133408.sra Written 122819 spots for ERR6133408.sra Rejected 122819 READS because READLEN < 1 Read 122819 spots for ERR6133408.sra Written 122819 spots for ERR6133408.sra Rejected 122819 READS because READLEN < 1 Read 122819 spots for ERR6133408.sra Written 122819 spots for ERR6133408.sra Rejected 122819 READS because READLEN < 1 Read 122819 spots for ERR6133408.sra Written 122819 spots for ERR6133408.sra SRR ids: ['ERR6133408.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_c0v288w4 ERR6133408.sra spots: 2456387 blocks: [[1, 122819], [122820, 245638], [245639, 368457], [368458, 491276], [491277, 614095], [614096, 736914], [736915, 859733], [859734, 982552], [982553, 1105371], [1105372, 1228190], [1228191, 1351009], [1351010, 1473828], [1473829, 1596647], [1596648, 1719466], [1719467, 1842285], [1842286, 1965104], [1965105, 2087923], [2087924, 2210742], [2210743, 2333561], [2333562, 2456387]] ERR6133408 file size 541948 ERR6133408 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 ERR6133408 ERR6133408_1.fastq Input file: ERR6133408_1.fastq trimmed: ERR6133408-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 03:29:21 2024 >> started Sat Dec 7 03:29:22 2024 >> done (1.580s) 2456387 reads processed; of these: 92 ( 0.00%) short reads filtered out after trimming by size control 7 ( 0.00%) empty reads filtered out after trimming by size control 2456288 (100.00%) reads available; of these: 651131 (26.51%) trimmed reads available after processing 1805157 (73.49%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 7 0.00% 19 24 0.00% 20 4 0.00% 21 2 0.00% 22 9 0.00% 23 3 0.00% 24 0 0.00% 25 2 0.00% 26 1 0.00% 27 3 0.00% 28 11 0.00% 29 34 0.00% 30 2 0.00% 31 4 0.00% 32 12 0.00% 33 5 0.00% 34 0 0.00% 35 2 0.00% 36 4 0.00% 37 11 0.00% 38 11 0.00% 39 16 0.00% 40 24 0.00% 41 13 0.00% 42 8 0.00% 43 25 0.00% 44 22 0.00% 45 33 0.00% 46 45 0.00% 47 80 0.00% 48 105 0.00% 49 151 0.01% 50 241 0.01% 51 294 0.01% 52 474 0.02% 53 685 0.03% 54 1008 0.04% 55 1290 0.05% 56 1748 0.07% 57 2693 0.11% 58 1866 0.08% 59 2280 0.09% 60 2788 0.11% 61 3277 0.13% 62 3570 0.15% 63 3863 0.16% 64 4163 0.17% 65 4440 0.18% 66 4527 0.18% 67 4809 0.20% 68 4281 0.17% 69 3968 0.16% 70 9410 0.38% 71 11088 0.45% 72 13262 0.54% 73 14976 0.61% 74 15590 0.63% 75 17435 0.71% 76 18652 0.76% 77 21312 0.87% 78 22328 0.91% 79 23991 0.98% 80 26097 1.06% 81 30123 1.23% 82 32807 1.34% 83 33741 1.37% 84 38966 1.59% 85 33081 1.35% 86 34670 1.41% 87 38087 1.55% 88 45534 1.85% 89 48318 1.97% 90 50873 2.07% 91 54928 2.24% 92 48555 1.98% 93 1719526 70.01% 2456288 reads passed initial QC criterion=sequence-density sequence-density=2.34 sequence-density-rank=1 fanout-score=2.11 fanout-score-rank=32 prefix-density=2.42 prefix-fanout=2.0 sequence=CAAGGCTAAATAC criterion=fanout-score sequence-density=0.13 sequence-density-rank=15 fanout-score=94.30 fanout-score-rank=1 prefix-density=11.99 prefix-fanout=1.0 sequence=GATAGTCAAGGGCGCGTTATTAA 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 03:29:39 Started mapping on | Dec 07 03:29:40 Finished on | Dec 07 03:29:50 Mapping speed, Million of reads per hour | 884.26 Number of input reads | 2456288 Average input read length | 89 UNIQUE READS: Uniquely mapped reads number | 1045410 Uniquely mapped reads % | 42.56% Average mapped length | 89.05 Number of splices: Total | 59794 Number of splices: Annotated (sjdb) | 48964 Number of splices: GT/AG | 57905 Number of splices: GC/AG | 981 Number of splices: AT/AC | 64 Number of splices: Non-canonical | 844 Mismatch rate per base, % | 0.81% Deletion rate per base | 0.03% Deletion average length | 1.72 Insertion rate per base | 0.02% Insertion average length | 1.78 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 1238073 % of reads mapped to multiple loci | 50.40% Number of reads mapped to too many loci | 76387 % of reads mapped to too many loci | 3.11% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 3.39% % of reads unmapped: other | 0.54% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 172805 172805 172805 N_multimapping 1238073 1238073 1238073 N_noFeature 89270 99689 1000000 N_ambiguous 41105 6072 196 UnstrandedReadsAssigned:915035 PositiveStrandReadsAssigned:939649 NegativeStrandReadsAssigned:45214 Dataset is classified positive stranded MeadianReadLen=93 20thPercentileLength=87 echo kmer=83 ERR6133408 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: ERR6133408-trimmed.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 2,456,288 reads, 1,652,373 reads pseudoaligned [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 942 rounds 52973 ERR6133408.ke.tsv 35125 ERR6133408.se.tsv 88098 total ==> ERR6133408.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 41 23.2919 PNS24243 293 194 0 0 KQK14069 1603 1504 22 11.4012 KQK14071 474 375 0 0 ==> ERR6133408.se.tsv <== BRADI_1g14170v3 22 BRADI_1g53295v3 9 BRADI_1g59795v3 11 BRADI_1g07683v3 0 BRADI_1g00485v3 1 BRADI_1g20270v3 17 BRADI_1g74790v3 12 BRADI_1g09890v3 0 BRADI_1g77505v3 24 BRADI_1g48960v3 0 ERR6133408 completed mapping pipeline successfully