Starting /dee2/code/volunteer_pipeline.sh ERR6133341 current disk space = 1548165705728 free memory = 1387928316 ERR6133341 SRAfilesize da7ffcb72f429b716bf4d36dbd4719a8 ERR6133341.sra ERR6133341.sra file validated ERR6133341 is single end ERR6133341 is conventional basespace ERR6133341 read1 length is 70-93 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename ERR6133341_1.fastq File type Conventional base calls Encoding Sanger / Illumina 1.9 Total Sequences 4000 Sequences flagged as poor quality 0 Sequence length 70-93 %GC 46 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 36.03225 37.0 37.0 37.0 33.0 37.0 2 36.564 37.0 37.0 37.0 37.0 37.0 3 36.59 37.0 37.0 37.0 37.0 37.0 4 36.3565 37.0 37.0 37.0 37.0 37.0 5 36.3685 37.0 37.0 37.0 37.0 37.0 6 36.473 37.0 37.0 37.0 37.0 37.0 7 38.58425 40.0 37.0 40.0 37.0 40.0 8 38.63875 40.0 37.0 40.0 37.0 40.0 9 38.641 40.0 37.0 40.0 37.0 40.0 10-11 38.670249999999996 40.0 37.0 40.0 37.0 40.0 12-13 38.67175 40.0 37.0 40.0 37.0 40.0 14-15 38.665625000000006 40.0 37.0 40.0 37.0 40.0 16-17 38.602125 40.0 37.0 40.0 37.0 40.0 18-19 38.519999999999996 40.0 37.0 40.0 37.0 40.0 20-21 38.40225 40.0 37.0 40.0 37.0 40.0 22-23 38.409875 40.0 37.0 40.0 37.0 40.0 24-25 38.323 40.0 37.0 40.0 37.0 40.0 26-27 38.292249999999996 40.0 37.0 40.0 37.0 40.0 28-29 38.371375 40.0 37.0 40.0 37.0 40.0 30-31 38.299625000000006 40.0 37.0 40.0 37.0 40.0 32-33 38.258875 40.0 37.0 40.0 37.0 40.0 34-35 38.046375 40.0 37.0 40.0 37.0 40.0 36-37 37.954499999999996 40.0 37.0 40.0 37.0 40.0 38-39 37.982375000000005 38.5 37.0 40.0 37.0 40.0 40-41 37.817 37.0 37.0 40.0 35.0 40.0 42-43 37.703375 37.0 37.0 40.0 37.0 40.0 44-45 37.51 37.0 37.0 40.0 35.0 40.0 46-47 37.43237499999999 37.0 37.0 40.0 33.0 40.0 48-49 37.310500000000005 37.0 37.0 40.0 33.0 40.0 50-51 37.170249999999996 37.0 37.0 40.0 35.0 40.0 52-53 37.044125 37.0 37.0 40.0 33.0 40.0 54-55 36.87325 37.0 37.0 37.0 33.0 40.0 56-57 36.746 37.0 37.0 37.0 33.0 40.0 58-59 36.534625 37.0 37.0 37.0 33.0 40.0 60-61 36.453875 37.0 37.0 37.0 33.0 40.0 62-63 36.244875 37.0 37.0 37.0 33.0 37.0 64-65 36.12325 37.0 37.0 37.0 33.0 37.0 66-67 35.959374999999994 37.0 37.0 37.0 33.0 37.0 68-69 35.027625 35.0 35.0 37.0 33.0 37.0 70-71 35.29182796375535 37.0 33.0 37.0 33.0 37.0 72-73 35.746368125683446 37.0 37.0 37.0 33.0 37.0 74-75 35.67905899828678 37.0 37.0 37.0 33.0 37.0 76-77 35.74954959131013 37.0 37.0 37.0 33.0 37.0 78-79 35.69460279864795 37.0 37.0 37.0 33.0 37.0 80-81 35.69587484374711 37.0 37.0 37.0 33.0 37.0 82-83 35.58742935552328 37.0 37.0 37.0 33.0 37.0 84-85 35.56298246407442 37.0 37.0 37.0 33.0 37.0 86-87 35.47947338618347 37.0 33.0 37.0 33.0 37.0 88-89 35.55648357870895 37.0 35.0 37.0 33.0 37.0 90-91 35.425113250283125 37.0 33.0 37.0 33.0 37.0 92-93 35.38221970554926 37.0 33.0 37.0 33.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 20 2.0 21 5.0 22 2.0 23 4.0 24 4.0 25 5.0 26 12.0 27 9.0 28 12.0 29 27.0 30 21.0 31 41.0 32 49.0 33 51.0 34 104.0 35 216.0 36 884.0 37 1166.0 38 1313.0 39 73.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 66.425 9.4 8.525 15.65 2 50.025 25.3 14.6 10.075000000000001 3 34.1 35.475 16.75 13.675 4 30.375000000000004 29.475 20.45 19.7 5 27.925 26.400000000000002 26.55 19.125 6 19.25 39.1 24.75 16.900000000000002 7 37.7 25.05 21.55 15.7 8 26.674999999999997 25.374999999999996 26.3 21.65 9 24.725 30.625000000000004 25.35 19.3 10-11 24.05 28.65 28.7 18.6 12-13 22.9625 30.099999999999998 25.95 20.9875 14-15 21.4 32.9625 27.5875 18.05 16-17 26.775 28.075 22.400000000000002 22.75 18-19 26.325 24.5375 30.4 18.7375 20-21 28.249999999999996 23.7375 27.737499999999997 20.275000000000002 22-23 29.65 23.3625 26.900000000000002 20.0875 24-25 24.1625 25.05 28.8875 21.9 26-27 27.450000000000003 23.8625 26.875 21.8125 28-29 23.8875 27.750000000000004 28.012500000000003 20.349999999999998 30-31 29.3875 25.575 25.674999999999997 19.3625 32-33 27.275 24.525 26.400000000000002 21.8 34-35 22.625 32.7875 24.4375 20.150000000000002 36-37 26.737499999999997 25.9875 22.725 24.55 38-39 30.26628328541068 23.627953494186773 25.640705088136016 20.465058132266535 40-41 24.1375 24.5125 31.162499999999998 20.1875 42-43 27.6 30.725 24.55 17.125 44-45 24.212500000000002 28.037499999999998 28.9 18.85 46-47 27.35 25.7875 24.725 22.1375 48-49 26.075 24.962500000000002 26.2625 22.7 50-51 22.125 29.1875 26.825 21.8625 52-53 24.55 27.525 24.05 23.875 54-55 24.0375 26.8 28.299999999999997 20.8625 56-57 26.3125 30.1875 24.85 18.65 58-59 22.8875 30.062499999999996 28.299999999999997 18.75 60-61 31.275 27.0 23.0125 18.712500000000002 62-63 21.4 29.025000000000002 29.0875 20.4875 64-65 21.91797949487372 35.483870967741936 25.78144536134033 16.816704176044013 66-67 26.5 31.1875 23.4375 18.875 68-69 21.6875 27.6125 27.35 23.35 70-71 24.219239934779882 29.82566160792675 24.570425184999372 21.38467327229399 72-73 26.669210225104923 28.004578405188855 28.004578405188855 17.32163296451736 74-75 26.639979338842974 29.274276859504134 26.162190082644628 17.923553719008265 76-77 22.57599580712788 24.81656184486373 25.45859538784067 27.148846960167717 78-79 27.636990845163854 29.42815443810535 25.540666047499005 17.394188669231788 80-81 23.46594740391099 35.65745111260957 23.70869858395145 17.167902899527984 82-83 24.33063298091446 27.83193738843883 24.110943292599206 23.726486338047508 84-85 20.666385491353857 27.316181639252076 30.63405033038099 21.383382539013073 86-87 20.61155152887882 31.936579841449603 23.867497168742922 23.58437146092865 88-89 20.724801812004532 30.365232163080407 27.10928652321631 21.800679501698756 90-91 24.731030577576444 33.960928652321634 22.76330690826727 18.544733861834654 92-93 20.257644394110986 32.913363533408834 26.174971687429217 20.654020385050963 >>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 0.0 17 0.0 18 0.0 19 0.0 20 0.5 21 1.5 22 3.5 23 7.0 24 6.5 25 5.0 26 9.5 27 14.0 28 25.0 29 37.0 30 35.0 31 29.5 32 37.5 33 59.5 34 71.5 35 79.5 36 114.5 37 170.5 38 183.5 39 162.0 40 187.5 41 204.0 42 206.5 43 227.0 44 199.0 45 175.5 46 165.0 47 136.5 48 127.5 49 141.0 50 169.5 51 181.5 52 164.0 53 162.5 54 262.5 55 249.0 56 124.0 57 97.0 58 69.0 59 30.5 60 18.0 61 17.5 62 14.0 63 10.5 64 7.5 65 7.0 66 7.0 67 7.0 68 11.0 69 16.0 70 10.5 71 3.0 72 2.5 73 1.5 74 0.5 75 0.0 76 0.0 77 0.0 78 0.5 79 0.5 80 0.0 81 0.0 82 0.0 83 0.0 84 0.0 85 0.0 86 0.0 87 0.0 88 0.0 89 0.0 90 0.0 91 0.0 92 0.0 93 0.0 94 0.0 95 0.0 96 0.0 97 0.0 98 0.0 99 0.0 100 0.0 >>END_MODULE >>Per base N content pass #Base N-Count 1 0.0 2 0.0 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 0.025 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 27.0 71 27.0 72 29.0 73 32.0 74 26.0 75 34.0 76 18.0 77 21.0 78 35.0 79 29.0 80 29.0 81 30.0 82 43.0 83 39.0 84 49.0 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 3532.0 >>END_MODULE >>Sequence Duplication Levels warn #Total Deduplicated Percentage 66.525 #Duplication Level Percentage of deduplicated Percentage of total 1 89.21458098459226 59.35 2 4.547162720781661 6.05 3 2.1796317173994737 4.35 4 0.9394964299135663 2.5 5 0.864336715520481 2.875 6 0.5261180007515971 2.1 7 0.3006388575723412 1.4000000000000001 8 0.26305900037579855 1.4000000000000001 9 0.11273957158962795 0.675 >10 0.977076287110109 11.799999999999999 >50 0.03757985719654265 1.375 >100 0.03757985719654265 6.125 >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 245 6.125 No Hit TACCTAGGCACCCAGAGACGAGGAAGGGCGTAGCAAGCGACGAAATGCTT 55 1.375 No Hit GGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCTTGG 39 0.975 No Hit CAAGGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCT 34 0.8500000000000001 No Hit GGGCACGTGGAATCCCGTGTGAATCAGCAAGGACCACCTTGCAAGGCTAA 31 0.775 No Hit GGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAA 28 0.7000000000000001 No Hit GGGTTGTTTGGGAATGCAGCCCAAATCGGGCGGTAGACTCCGTCCAAGGC 27 0.675 No Hit TCAAAAGAGGAAAGGCTTGCGGTGGATACCTAGGCACCCAGAGACGAGGA 26 0.65 No Hit GGAATCCCGTGTGAATCAGCAAGGACCACCTTGCAAGGCTAAATACTCCT 25 0.625 No Hit CAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAATACTTGGGCTGATAT 24 0.6 No Hit CAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAATACTTGGGCTG 24 0.6 No Hit CAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAGGTC 20 0.5 No Hit GGCGTTCAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTC 17 0.42500000000000004 No Hit GGAAAAGAAAGCAAAAGCGATTCCCGTAGTAGCGGCGAGCGAAATGGGAG 17 0.42500000000000004 No Hit GGGGCACGTGGAATCCCGTGTGAATCAGCAAGGACCACCTTGCAAGGCTA 15 0.375 No Hit GGGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGT 13 0.325 No Hit GGTAATGAAATTATCCGAGCAGCTTGCAAATGGAGTCCTGAACTAGCCGC 13 0.325 No Hit GGGCGCGATCTTGCTCGTGAAGGTAATGAAATTATCCGAGCAGCTTGCAA 12 0.3 No Hit GGAGAGCAATACAAGCGTTGTGCTGCTAGGCGAAGCGGTTGAGTGCCGCA 12 0.3 No Hit GCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCTTGGTATG 11 0.27499999999999997 No Hit GCAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAATACTTGGGCT 11 0.27499999999999997 No Hit GTGGAATCCCGTGTGAATCAGCAAGGACCACCTTGCAAGGCTAAATACTC 11 0.27499999999999997 No Hit AACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAATACTTGGGCTGA 11 0.27499999999999997 No Hit GGGGAGTTGAAAATAAGCATAGATCCGGAGATTCCCAAATAGGTCAACCT 11 0.27499999999999997 No Hit GGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGTG 10 0.25 No Hit GGGAATGCAGCCCAAATCGGGCGGTAGACTCCGTCCAAGGCTAAATACAG 10 0.25 No Hit GTACTATGGCGTTCAACCTAAATGGATTCAATTTCAACCAATCTGTAGTT 10 0.25 No Hit GGGCTGATATCATCAACCGTGCTAATCTTGGTATGGAAGTAATGCACGAA 10 0.25 No Hit GGGGCAGAGGGAATTTCCGGTGGAGCGGTGAAATGCATTGAGATCGGAAA 9 0.22499999999999998 No Hit AGTCAAGGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAA 9 0.22499999999999998 No Hit GTTGTTTGGGAATGCAGCCCAAATCGGGCGGTAGACTCCGTCCAAGGCTA 9 0.22499999999999998 No Hit GGAGGGTGAGAGCCCCGTCCGGCCCGGACCCTGTCGCCCCACGAGGCGCC 8 0.2 No Hit GTAGTAGGAATCTGGTTCACTGCTTTAGGTATTAGTACTATGGCGTTCAA 8 0.2 No Hit GGCGCGATCTTGCTCGTGAAGGTAATGAAATTATCCGAGCAGCTTGCAAA 8 0.2 No Hit GAAATTATCCGAGCAGCTTGCAAATGGAGTCCTGAACTAGCCGCAGCTTG 8 0.2 No Hit GTAGTTGATAGTCAAGGTCGCGTTATTAATACTTGGGCTGATATCATCAA 8 0.2 No Hit CACGAACGTAATGCTCACAACTTCCCTCTAGATCTAGCTGCTCTTGAAGT 8 0.2 No Hit GAAGGTAATGAAATTATCCGAGCAGCTTGCAAATGGAGTCCTGAACTAGC 8 0.2 No Hit CAATTTCAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAATACTT 7 0.17500000000000002 No Hit CAACGAGTCGGGTTGTTTGGGAATGCAGCCCAAATCGGGCGGTAGACTCC 7 0.17500000000000002 No Hit CTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAGGTCGCGT 7 0.17500000000000002 No Hit GGGGTTGTGGGAGAGCAATACAAGCGTTGTGCTGCTAGGCGAAGCGGTTG 7 0.17500000000000002 No Hit GTATTAGTACTATGGCGTTCAACCTAAATGGATTCAATTTCAACCAATCT 7 0.17500000000000002 No Hit CGGGTTGTTTGGGAATGCAGCCCAAATCGGGCGGTAGACTCCGTCCAAGG 7 0.17500000000000002 No Hit GGGTGAGAGCCCCGTCCGGCCCGGACCCTGTCGCCCCACGAGGCGCCGTC 7 0.17500000000000002 No Hit GAACGTAATGCTCACAACTTCCCTCTAGATCTAGCTGCTCTTGAAGTTCC 7 0.17500000000000002 No Hit GGCGCCGTCAACGAGTCGGGTTGTTTGGGAATGCAGCCCAAATCGGGCGG 6 0.15 No Hit GAGGAAGGGCGTAGCAAGCGACGAAATGCTTCGGGGAGTTGAAAATAAGC 6 0.15 No Hit GGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGTGTACAAGCTCGTAA 6 0.15 No Hit GGAAAGGCTTGCGGTGGATACCTAGGCACCCAGAGACGAGGAAGGGCGTA 6 0.15 No Hit CGAGTCGGGTTGTTTGGGAATGCAGCCCAAATCGGGCGGTAGACTCCGTC 6 0.15 No Hit GGTTGTGGGAGAGCAATACAAGCGTTGTGCTGCTAGGCGAAGCGGTTGAG 6 0.15 No Hit GGTCAACCTTTTAAACTGCCTGCTGAATCCATGAGCAGGCAAGAGACAAC 6 0.15 No Hit GTAATGAAATTATCCGAGCAGCTTGCAAATGGAGTCCTGAACTAGCCGCA 6 0.15 No Hit GTATGGAAGGCGATCAAATTCGAGTTCGCGCCGGTAGATACTATCGATTA 6 0.15 No Hit GATACCTAGGCACCCAGAGACGAGGAAGGGCGTAGCAAGCGACGAAATGC 6 0.15 No Hit GTACAAGCTCGTAACGAAGGGCGCGATCTTGCTCGTGAAGGTAATGAAAT 6 0.15 No Hit CGGGGAGTTGAAAATAAGCATAGATCCGGAGATTCCCAAATAGGTCAACC 6 0.15 No Hit AACGAAGGGCGCGATCTTGCTCGTGAAGGTAATGAAATTATCCGAGCAGC 6 0.15 No Hit GTTCAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAG 6 0.15 No Hit GGGAAAAGAGGGGTTACTTTTTTTCATTTTTCCCTTAAAAGATAGGCTTT 5 0.125 No Hit GGAGTCCTGAACTAGCCGCAGCTTGTGAAGTATGGAAGGCGATCAAATTC 5 0.125 No Hit GCAAGGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATC 5 0.125 No Hit GCCGCAGCTTGTGAAGTATGGAAGGCGATCAAATTCGAGTTCGCGCCGGT 5 0.125 No Hit TATGGCGTTCAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATA 5 0.125 No Hit CAAATAGGTCAACCTTTTAAACTGCCTGCTGAATCCATGAGCAGGCAAGA 5 0.125 No Hit GGAGATTCCCAAATAGGTCAACCTTTTAAACTGCCTGCTGAATCCATGAG 5 0.125 No Hit GGATACCTAGGCACCCAGAGACGAGGAAGGGCGTAGCAAGCGACGAAATG 5 0.125 No Hit AACGTAATGCTCACAACTTCCCTCTAGATCTAGCTGCTCTTGAAGTTCCC 5 0.125 No Hit CACCCAGAGACGAGGAAGGGCGTAGCAAGCGACGAAATGCTTCGGGGAGT 5 0.125 No Hit GTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCTTGGT 5 0.125 No Hit GATTCAATTTCAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAAT 5 0.125 No Hit AGGTAATGAAATTATCCGAGCAGCTTGCAAATGGAGTCCTGAACTAGCCG 5 0.125 No Hit GGCCTGTAGTAGGAATCTGGTTCACTGCTTTAGGTATTAGTACTATGGCG 5 0.125 No Hit GCAGCTTGCAAATGGAGTCCTGAACTAGCCGCAGCTTGTGAAGTATGGAA 5 0.125 No Hit GGGAGGGTGAGAGCCCCGTCCGGCCCGGACCCTGTCGCCCCACGAGGCGC 5 0.125 No Hit ACGAACGTAATGCTCACAACTTCCCTCTAGATCTAGCTGCTCTTGAAGTT 5 0.125 No Hit TCTGTAGTTGATAGTCAAGGTCGCGTTATTAATACTTGGGCTGATATCAT 5 0.125 No Hit CGAGGAAGGGCGTAGCAAGCGACGAAATGCTTCGGGGAGTTGAAAATAAG 5 0.125 No Hit GTAGGAATCTGGTTCACTGCTTTAGGTATTAGTACTATGGCGTTCAACCT 5 0.125 No Hit ATAGGTCAACCTTTTAAACTGCCTGCTGAATCCATGAGCAGGCAAGAGAC 5 0.125 No Hit GGTTGAGTGCCGCACCCTAGATGGCTAAAGTCCAGTAGCCGAAAGCATCA 5 0.125 No Hit AAGGTAATGAAATTATCCGAGCAGCTTGCAAATGGAGTCCTGAACTAGCC 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 0.0 0.0 28-29 0.0 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 0.1 0.0 0.0 0.0 0.0 36-37 0.1 0.0 0.0 0.0 0.0 38-39 0.1 0.0 0.0 0.0 0.0 40-41 0.1 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 0.1125 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position GGGAGAG 20 2.6199332E-5 85.35 1 GCAATAC 25 7.9225945E-5 68.28 7 CAATACA 25 7.9225945E-5 68.28 8 GAGCAAT 25 7.9225945E-5 68.28 5 AGAGCAA 25 7.9225945E-5 68.28 4 AATACAA 25 7.9225945E-5 68.28 9 GGAGAGC 30 1.9534459E-4 56.9 2 GAGAGCA 30 1.9534459E-4 56.9 3 AGCAATA 35 4.183728E-4 48.771427 6 CATCACT 25 2.3732586E-5 48.084507 82-83 AGCATCA 25 2.3732586E-5 48.084507 80-81 ACTAGCT 25 2.3732586E-5 48.084507 86-87 GCCGAAA 25 3.5731442E-5 44.921055 74-75 TAGCCGA 25 3.7166566E-5 44.62745 72-73 CCAGTAG 25 4.176128E-5 43.76923 68-69 GTCCAGT 25 4.176128E-5 43.76923 66-67 GATGGCT 25 4.861009E-5 42.675 56-57 TGCCGCA 25 4.861009E-5 42.675 44-45 GCGAAGC 25 4.861009E-5 42.675 30-31 AGGCGAA 25 4.861009E-5 42.675 28-29 >>END_MODULE Rejected 32120 READS because READLEN < 1 Read 32120 spots for ERR6133341.sra Written 32120 spots for ERR6133341.sra Rejected 32120 READS because READLEN < 1 Read 32120 spots for ERR6133341.sra Written 32120 spots for ERR6133341.sra Rejected 32120 READS because READLEN < 1 Read 32120 spots for ERR6133341.sra Written 32120 spots for ERR6133341.sra Rejected 32120 READS because READLEN < 1 Read 32120 spots for ERR6133341.sra Written 32120 spots for ERR6133341.sra Rejected 32120 READS because READLEN < 1 Read 32120 spots for ERR6133341.sra Written 32120 spots for ERR6133341.sra Rejected 32120 READS because READLEN < 1 Read 32120 spots for ERR6133341.sra Written 32120 spots for ERR6133341.sra Rejected 32120 READS because READLEN < 1 Read 32120 spots for ERR6133341.sra Written 32120 spots for ERR6133341.sra Rejected 32120 READS because READLEN < 1 Read 32120 spots for ERR6133341.sra Written 32120 spots for ERR6133341.sra Rejected 32120 READS because READLEN < 1 Read 32120 spots for ERR6133341.sra Written 32120 spots for ERR6133341.sra Rejected 32120 READS because READLEN < 1 Read 32120 spots for ERR6133341.sra Written 32120 spots for ERR6133341.sra Rejected 32120 READS because READLEN < 1 Read 32120 spots for ERR6133341.sra Written 32120 spots for ERR6133341.sra Rejected 32120 READS because READLEN < 1 Read 32120 spots for ERR6133341.sra Written 32120 spots for ERR6133341.sra Rejected 32120 READS because READLEN < 1 Read 32120 spots for ERR6133341.sra Written 32120 spots for ERR6133341.sra Rejected 32120 READS because READLEN < 1 Read 32120 spots for ERR6133341.sra Written 32120 spots for ERR6133341.sra Rejected 32120 READS because READLEN < 1 Read 32120 spots for ERR6133341.sra Written 32120 spots for ERR6133341.sra Rejected 32120 READS because READLEN < 1 Read 32120 spots for ERR6133341.sra Written 32120 spots for ERR6133341.sra Rejected 32135 READS because READLEN < 1 Read 32135 spots for ERR6133341.sra Written 32135 spots for ERR6133341.sra Rejected 32120 READS because READLEN < 1 Read 32120 spots for ERR6133341.sra Written 32120 spots for ERR6133341.sra Rejected 32120 READS because READLEN < 1 Read 32120 spots for ERR6133341.sra Written 32120 spots for ERR6133341.sra Rejected 32120 READS because READLEN < 1 Read 32120 spots for ERR6133341.sra Written 32120 spots for ERR6133341.sra SRR ids: ['ERR6133341.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_4sif7645 ERR6133341.sra spots: 642415 blocks: [[1, 32120], [32121, 64240], [64241, 96360], [96361, 128480], [128481, 160600], [160601, 192720], [192721, 224840], [224841, 256960], [256961, 289080], [289081, 321200], [321201, 353320], [353321, 385440], [385441, 417560], [417561, 449680], [449681, 481800], [481801, 513920], [513921, 546040], [546041, 578160], [578161, 610280], [610281, 642415]] ERR6133341 file size 138945 ERR6133341 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 ERR6133341 ERR6133341_1.fastq Input file: ERR6133341_1.fastq trimmed: ERR6133341-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 01:01:29 2024 >> started Sat Dec 7 01:01:29 2024 >> done (0.523s) 642415 reads processed; of these: 60 ( 0.01%) short reads filtered out after trimming by size control 1 ( 0.00%) empty reads filtered out after trimming by size control 642354 (99.99%) reads available; of these: 5233 ( 0.81%) trimmed reads available after processing 637121 (99.19%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 7 0.00% 19 14 0.00% 20 9 0.00% 21 11 0.00% 22 9 0.00% 23 6 0.00% 24 7 0.00% 25 8 0.00% 26 7 0.00% 27 6 0.00% 28 18 0.00% 29 78 0.01% 30 6 0.00% 31 13 0.00% 32 21 0.00% 33 1292 0.20% 34 6 0.00% 35 24 0.00% 36 8 0.00% 37 12 0.00% 38 13 0.00% 39 32 0.00% 40 31 0.00% 41 15 0.00% 42 10 0.00% 43 17 0.00% 44 10 0.00% 45 10 0.00% 46 8 0.00% 47 8 0.00% 48 8 0.00% 49 5 0.00% 50 7 0.00% 51 41 0.01% 52 12 0.00% 53 4 0.00% 54 5 0.00% 55 6 0.00% 56 4 0.00% 57 18 0.00% 58 6 0.00% 59 3 0.00% 60 8 0.00% 61 10 0.00% 62 3 0.00% 63 2 0.00% 64 2 0.00% 65 5 0.00% 66 7 0.00% 67 8 0.00% 68 15 0.00% 69 37 0.01% 70 5609 0.87% 71 5319 0.83% 72 5797 0.90% 73 5435 0.85% 74 5030 0.78% 75 4845 0.75% 76 4710 0.73% 77 5203 0.81% 78 5210 0.81% 79 5543 0.86% 80 5437 0.85% 81 7069 1.10% 82 7379 1.15% 83 6107 0.95% 84 7221 1.12% 85 21 0.00% 86 44 0.01% 87 48 0.01% 88 98 0.02% 89 123 0.02% 90 217 0.03% 91 507 0.08% 92 1664 0.26% 93 551786 85.90% 642354 reads passed initial QC criterion=sequence-density sequence-density=5.78 sequence-density-rank=1 fanout-score=2.04 fanout-score-rank=17 prefix-density=5.92 prefix-fanout=2.0 sequence=CAAGGCTAAATAC criterion=fanout-score sequence-density=0.02 sequence-density-rank=28 fanout-score=77.71 fanout-score-rank=1 prefix-density=0.82 prefix-fanout=1.8 sequence=TTAAAAGATTTATTAGATAATCGAAAACAGAGGATCTTGAGTACTATTCGAAATTCGGAAGAATTGCGTAGAGGGACCTTTGAGCAGCTCGAAAAAGCTCGGATTCGATTACAGAAAGTCGAACTAGAAGCGGATGAGTATCGAATGAATGGATACTCTGAGATAGAACGA 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 01:01:46 Started mapping on | Dec 07 01:01:46 Finished on | Dec 07 01:01:51 Mapping speed, Million of reads per hour | 462.49 Number of input reads | 642354 Average input read length | 90 UNIQUE READS: Uniquely mapped reads number | 279988 Uniquely mapped reads % | 43.59% Average mapped length | 89.25 Number of splices: Total | 9487 Number of splices: Annotated (sjdb) | 7850 Number of splices: GT/AG | 8987 Number of splices: GC/AG | 167 Number of splices: AT/AC | 8 Number of splices: Non-canonical | 325 Mismatch rate per base, % | 0.44% Deletion rate per base | 0.04% Deletion average length | 1.69 Insertion rate per base | 0.02% Insertion average length | 1.90 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 303378 % of reads mapped to multiple loci | 47.23% Number of reads mapped to too many loci | 34783 % of reads mapped to too many loci | 5.41% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 3.50% % of reads unmapped: other | 0.27% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 58988 58988 58988 N_multimapping 303378 303378 303378 N_noFeature 24110 27057 267743 N_ambiguous 10798 1462 76 UnstrandedReadsAssigned:245080 PositiveStrandReadsAssigned:251469 NegativeStrandReadsAssigned:12169 Dataset is classified positive stranded MeadianReadLen=93 20thPercentileLength=93 echo kmer=89 ERR6133341 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: ERR6133341-trimmed.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 642,354 reads, 380,571 reads pseudoaligned [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 820 rounds 52973 ERR6133341.ke.tsv 35125 ERR6133341.se.tsv 88098 total ==> ERR6133341.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 9 23.4802 PNS24243 293 194 0 0 KQK14069 1603 1504 6 14.2797 KQK14071 474 375 0 0 ==> ERR6133341.se.tsv <== BRADI_1g14170v3 6 BRADI_1g53295v3 6 BRADI_1g59795v3 1 BRADI_1g07683v3 0 BRADI_1g00485v3 0 BRADI_1g20270v3 6 BRADI_1g74790v3 4 BRADI_1g09890v3 0 BRADI_1g77505v3 2 BRADI_1g48960v3 0 ERR6133341 completed mapping pipeline successfully