Starting /dee2/code/volunteer_pipeline.sh ERR6133325 current disk space = 1548224827392 free memory = 1602452708 ERR6133325 SRAfilesize 0b0c06d16c7b40374d5c0f1f45072e0f ERR6133325.sra ERR6133325.sra file validated ERR6133325 is single end ERR6133325 is conventional basespace ERR6133325 read1 length is 70-93 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename ERR6133325_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 36.2335 37.0 37.0 37.0 33.0 37.0 2 36.6225 37.0 37.0 37.0 37.0 37.0 3 36.57775 37.0 37.0 37.0 37.0 37.0 4 36.31775 37.0 37.0 37.0 37.0 37.0 5 36.32875 37.0 37.0 37.0 37.0 37.0 6 36.5015 37.0 37.0 37.0 37.0 37.0 7 38.73825 40.0 37.0 40.0 37.0 40.0 8 38.7935 40.0 37.0 40.0 37.0 40.0 9 38.8125 40.0 37.0 40.0 37.0 40.0 10-11 38.82525 40.0 37.0 40.0 37.0 40.0 12-13 38.761375 40.0 37.0 40.0 37.0 40.0 14-15 38.74275 40.0 37.0 40.0 37.0 40.0 16-17 38.69425 40.0 37.0 40.0 37.0 40.0 18-19 38.655125 40.0 37.0 40.0 37.0 40.0 20-21 38.651624999999996 40.0 37.0 40.0 37.0 40.0 22-23 38.516375 40.0 37.0 40.0 37.0 40.0 24-25 38.435375 40.0 37.0 40.0 37.0 40.0 26-27 38.449375 40.0 37.0 40.0 37.0 40.0 28-29 38.489125 40.0 37.0 40.0 37.0 40.0 30-31 38.43575 40.0 37.0 40.0 37.0 40.0 32-33 38.326375 40.0 37.0 40.0 37.0 40.0 34-35 38.221000000000004 40.0 37.0 40.0 37.0 40.0 36-37 38.129999999999995 40.0 37.0 40.0 37.0 40.0 38-39 38.098124999999996 40.0 37.0 40.0 37.0 40.0 40-41 37.942125 40.0 37.0 40.0 37.0 40.0 42-43 37.8255 37.0 37.0 40.0 37.0 40.0 44-45 37.695625 37.0 37.0 40.0 37.0 40.0 46-47 37.521 37.0 37.0 40.0 35.0 40.0 48-49 37.307874999999996 37.0 37.0 40.0 33.0 40.0 50-51 37.117875 37.0 37.0 40.0 33.0 40.0 52-53 36.965 37.0 37.0 38.5 33.0 40.0 54-55 36.81425 37.0 37.0 37.0 33.0 40.0 56-57 36.653875 37.0 37.0 37.0 33.0 40.0 58-59 36.480374999999995 37.0 37.0 37.0 33.0 40.0 60-61 36.404250000000005 37.0 37.0 37.0 33.0 40.0 62-63 36.24225 37.0 37.0 37.0 33.0 37.0 64-65 36.121375 37.0 37.0 37.0 33.0 37.0 66-67 35.9625 37.0 37.0 37.0 33.0 37.0 68-69 35.1495 35.0 35.0 37.0 33.0 37.0 70-71 35.39044979869149 37.0 35.0 37.0 33.0 37.0 72-73 35.822728073966246 37.0 37.0 37.0 33.0 37.0 74-75 35.74343234915118 37.0 37.0 37.0 33.0 37.0 76-77 35.77442493675932 37.0 37.0 37.0 33.0 37.0 78-79 35.74946726527135 37.0 37.0 37.0 33.0 37.0 80-81 35.668895129549725 37.0 37.0 37.0 33.0 37.0 82-83 35.60151410925828 37.0 35.0 37.0 33.0 37.0 84-85 35.5316247662009 37.0 35.0 37.0 33.0 37.0 86-87 35.48219332956472 37.0 33.0 37.0 33.0 37.0 88-89 35.526710005652916 37.0 33.0 37.0 33.0 37.0 90-91 35.41266252119841 37.0 33.0 37.0 33.0 37.0 92-93 35.319954776710006 37.0 33.0 37.0 33.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 20 2.0 21 2.0 22 4.0 23 3.0 24 9.0 25 4.0 26 8.0 27 15.0 28 15.0 29 20.0 30 31.0 31 44.0 32 40.0 33 67.0 34 93.0 35 181.0 36 724.0 37 1207.0 38 1464.0 39 67.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 65.64999999999999 9.175 9.6 15.575 2 47.8 26.224999999999998 14.85 11.125 3 30.9 36.025 17.474999999999998 15.6 4 31.874999999999996 26.25 21.075 20.8 5 24.875 27.775 27.750000000000004 19.6 6 20.275000000000002 35.6 25.674999999999997 18.45 7 34.925 27.125 21.45 16.5 8 27.725 28.15 25.724999999999998 18.4 9 25.874999999999996 26.325 26.700000000000003 21.099999999999998 10-11 25.0125 28.212500000000002 26.5125 20.2625 12-13 25.587500000000002 27.125 27.125 20.1625 14-15 22.662499999999998 28.599999999999998 28.512500000000003 20.225 16-17 25.0125 29.975 24.5375 20.474999999999998 18-19 24.6125 26.5 27.950000000000003 20.9375 20-21 26.5625 26.424999999999997 26.187500000000004 20.825 22-23 28.000000000000004 25.324999999999996 25.75 20.925 24-25 24.925 26.400000000000002 27.762500000000003 20.9125 26-27 25.4375 26.0 28.3375 20.225 28-29 24.4 27.450000000000003 26.55 21.6 30-31 26.187500000000004 25.7125 27.712500000000002 20.3875 32-33 25.525 27.025 27.224999999999998 20.225 34-35 25.112499999999997 28.212500000000002 25.674999999999997 21.0 36-37 25.25 27.474999999999998 24.6625 22.6125 38-39 26.450000000000003 25.825 27.1375 20.5875 40-41 26.025 26.1 26.8375 21.0375 42-43 25.825 29.6875 25.825 18.6625 44-45 22.287499999999998 28.3625 28.4375 20.9125 46-47 25.575 27.1 25.6125 21.712500000000002 48-49 24.1875 26.4125 28.525 20.875 50-51 22.8625 28.349999999999998 28.6875 20.1 52-53 26.75 27.287499999999998 26.700000000000003 19.2625 54-55 25.025 28.725 26.474999999999998 19.775000000000002 56-57 24.7375 28.1 26.900000000000002 20.2625 58-59 24.8 27.787499999999998 26.974999999999998 20.4375 60-61 25.825 28.1 26.674999999999997 19.400000000000002 62-63 22.7375 29.975 28.5625 18.725 64-65 23.025000000000002 31.2375 27.037499999999998 18.7 66-67 24.5625 30.55 26.424999999999997 18.462500000000002 68-69 22.3375 28.812500000000004 26.8625 21.987499999999997 70-71 24.630047654878354 28.95660897918234 26.686731878605467 19.726611487333834 72-73 26.75394001016777 27.541942043721402 27.1733604473818 18.530757498729027 74-75 24.26347613534028 28.70191689180497 28.12298983661392 18.91161713624083 76-77 24.368653996355118 26.881020567560533 27.11533454829472 21.634990887789638 78-79 25.498481447246796 27.096263039746464 27.84893701307276 19.556318499933976 80-81 23.933234621079553 31.027056131377034 26.679230044420514 18.3604792031229 82-83 23.17608337904553 27.811300054854637 26.94733955019199 22.065277015907846 84-85 22.350295192578017 26.834411020522914 29.983131852684846 20.832161934214223 86-87 22.724703222159413 29.084228377614473 27.741661955907293 20.449406444318825 88-89 21.368004522329 32.433578292820805 27.204635387224418 18.99378179762578 90-91 24.039005087620126 31.514980214810628 25.1695873374788 19.276427360090448 92-93 20.915771622385527 34.53928773318259 25.226116449971737 19.318824194460145 >>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 1.0 20 2.0 21 4.5 22 5.0 23 6.0 24 8.0 25 10.0 26 13.5 27 17.0 28 25.5 29 31.0 30 29.5 31 36.5 32 55.0 33 73.0 34 81.5 35 89.0 36 115.5 37 166.0 38 198.5 39 183.0 40 198.0 41 205.5 42 180.5 43 180.5 44 184.5 45 180.0 46 166.5 47 154.5 48 138.5 49 155.5 50 192.5 51 196.5 52 183.5 53 193.0 54 179.0 55 120.5 56 86.0 57 77.5 58 61.5 59 37.0 60 26.0 61 27.5 62 21.0 63 14.0 64 12.5 65 13.0 66 10.0 67 6.5 68 13.0 69 16.5 70 8.5 71 1.0 72 1.0 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 0.0 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 26.0 71 22.0 72 36.0 73 20.0 74 19.0 75 25.0 76 22.0 77 28.0 78 31.0 79 43.0 80 27.0 81 33.0 82 44.0 83 48.0 84 38.0 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 3538.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 73.925 #Duplication Level Percentage of deduplicated Percentage of total 1 89.7193101115996 66.325 2 5.2417991207304695 7.75 3 1.8261751775448092 4.05 4 0.9469056476158269 2.8000000000000003 5 0.3381805884342239 1.25 6 0.4058167061210686 1.7999999999999998 7 0.3043625295908015 1.575 8 0.16909029421711194 1.0 9 0.13527223537368954 0.8999999999999999 >10 0.9130875887724046 12.55 >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 fail #Sequence Count Percentage Possible Source GGGAGAGCAATACAAGCGTTGTGCTGCTAGGCGAAGCGGTTGAGTGCCGC 50 1.25 No Hit TACCTAGGCACCCAGAGACGAGGAAGGGCGTAGCAAGCGACGAAATGCTT 47 1.175 No Hit GGGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGT 30 0.75 No Hit GGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAA 29 0.7250000000000001 No Hit TCAAAAGAGGAAAGGCTTGCGGTGGATACCTAGGCACCCAGAGACGAGGA 27 0.675 No Hit GGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCTTGG 26 0.65 No Hit GGGCGCGATCTTGCTCGTGAAGGTAATGAAATTATCCGAGCAGCTTGCAA 24 0.6 No Hit CAAGGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCT 19 0.475 No Hit GGAATCCCGTGTGAATCAGCAAGGACCACCTTGCAAGGCTAAATACTCCT 18 0.44999999999999996 No Hit CAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAATACTTGGGCTG 17 0.42500000000000004 No Hit GGGCACGTGGAATCCCGTGTGAATCAGCAAGGACCACCTTGCAAGGCTAA 16 0.4 No Hit GGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGTGTACAAGCTCGTAA 16 0.4 No Hit GGGTTGTTTGGGAATGCAGCCCAAATCGGGCGGTAGACTCCGTCCAAGGC 16 0.4 No Hit GGAGTCCTGAACTAGCCGCAGCTTGTGAAGTATGGAAGGCGATCAAATTC 15 0.375 No Hit CAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAATACTTGGGCTGATAT 14 0.35000000000000003 No Hit GGCGTTCAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTC 13 0.325 No Hit GGACATCCTTGGGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTT 13 0.325 No Hit GGAAAAGAAAGCAAAAGCGATTCCCGTAGTAGCGGCGAGCGAAATGGGAG 13 0.325 No Hit GTGGAATCCCGTGTGAATCAGCAAGGACCACCTTGCAAGGCTAAATACTC 12 0.3 No Hit GAAGGTAATGAAATTATCCGAGCAGCTTGCAAATGGAGTCCTGAACTAGC 12 0.3 No Hit GTAGTAGGAATCTGGTTCACTGCTTTAGGTATTAGTACTATGGCGTTCAA 11 0.27499999999999997 No Hit GGAGTTGAAAATAAGCATAGATCCGGAGATTCCCAAATAGGTCAACCTTT 11 0.27499999999999997 No Hit CAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAGGTC 11 0.27499999999999997 No Hit GGAGGAACTTTAGGACATCCTTGGGGAAATGCACCTGGTGCAGCAGCTAA 11 0.27499999999999997 No Hit GGGTGAGAGCCCCGTCCGGCCCGGACCCTGTCGCCCCACGAGGCGCCGTC 11 0.27499999999999997 No Hit GGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGTG 10 0.25 No Hit GGGCTGATATCATCAACCGTGCTAATCTTGGTATGGAAGTAATGCACGAA 10 0.25 No Hit GGGATGATTCTGTATTACAATTTGGTGGAGGAACTTTAGGACATCCTTGG 9 0.22499999999999998 No Hit GGCGCGATCTTGCTCGTGAAGGTAATGAAATTATCCGAGCAGCTTGCAAA 9 0.22499999999999998 No Hit GCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGTGTACAAGCTCGTAACGA 9 0.22499999999999998 No Hit CACGAACGTAATGCTCACAACTTCCCTCTAGATCTAGCTGCTCTTGAAGT 9 0.22499999999999998 No Hit GTATGGAAGGCGATCAAATTCGAGTTCGCGCCGGTAGATACTATCGATTA 8 0.2 No Hit GTACAAGCTCGTAACGAAGGGCGCGATCTTGCTCGTGAAGGTAATGAAAT 8 0.2 No Hit CAAAAGAGGAAAGGCTTGCGGTGGATACCTAGGCACCCAGAGACGAGGAA 8 0.2 No Hit GGGGATGATTCTGTATTACAATTTGGTGGAGGAACTTTAGGACATCCTTG 8 0.2 No Hit GGGGCACGTGGAATCCCGTGTGAATCAGCAAGGACCACCTTGCAAGGCTA 8 0.2 No Hit GGAGGGTGAGAGCCCCGTCCGGCCCGGACCCTGTCGCCCCACGAGGCGCC 7 0.17500000000000002 No Hit GGTGGAGGAACTTTAGGACATCCTTGGGGAAATGCACCTGGTGCAGCAGC 7 0.17500000000000002 No Hit GTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCTTGGT 7 0.17500000000000002 No Hit CAACGAGTCGGGTTGTTTGGGAATGCAGCCCAAATCGGGCGGTAGACTCC 7 0.17500000000000002 No Hit GATACCTAGGCACCCAGAGACGAGGAAGGGCGTAGCAAGCGACGAAATGC 7 0.17500000000000002 No Hit GTAGTTGATAGTCAAGGTCGCGTTATTAATACTTGGGCTGATATCATCAA 7 0.17500000000000002 No Hit GTATTAGTACTATGGCGTTCAACCTAAATGGATTCAATTTCAACCAATCT 7 0.17500000000000002 No Hit TCAGTGTCGGCCCAGCAGAGTGCTTTCGCCGTTGGTGTTCTTTCCGATCT 7 0.17500000000000002 No Hit GGTGGATACCTAGGCACCCAGAGACGAGGAAGGGCGTAGCAAGCGACGAA 7 0.17500000000000002 No Hit GCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCTTGGTATG 6 0.15 No Hit GAGGAAGGGCGTAGCAAGCGACGAAATGCTTCGGGGAGTTGAAAATAAGC 6 0.15 No Hit GGAAGGGCGTAGCAAGCGACGAAATGCTTCGGGGAGTTGAAAATAAGCAT 6 0.15 No Hit GGATACCTAGGCACCCAGAGACGAGGAAGGGCGTAGCAAGCGACGAAATG 6 0.15 No Hit GGGGATGGAGCGACAGAAGTATGGAAATAGGATAAGGTAGCGGCGAGACG 6 0.15 No Hit GGCCTGTAGTAGGAATCTGGTTCACTGCTTTAGGTATTAGTACTATGGCG 6 0.15 No Hit GAAGTATGGAAGGCGATCAAATTCGAGTTCGCGCCGGTAGATACTATCGA 6 0.15 No Hit GAAATTATCCGAGCAGCTTGCAAATGGAGTCCTGAACTAGCCGCAGCTTG 6 0.15 No Hit GTATTTAGCCTTGCAAGGTGGTCCTTGCTGATTCACACGGGATTCCACGT 6 0.15 No Hit GAAGGGCGCGATCTTGCTCGTGAAGGTAATGAAATTATCCGAGCAGCTTG 6 0.15 No Hit GTTGTTTGGGAATGCAGCCCAAATCGGGCGGTAGACTCCGTCCAAGGCTA 6 0.15 No Hit GGTAATGAAATTATCCGAGCAGCTTGCAAATGGAGTCCTGAACTAGCCGC 6 0.15 No Hit CAATTTCAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAATACTT 5 0.125 No Hit GGATGATTCTGTATTACAATTTGGTGGAGGAACTTTAGGACATCCTTGGG 5 0.125 No Hit GCAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAATACTTGGGCT 5 0.125 No Hit GCAGCTTGCAAATGGAGTCCTGAACTAGCCGCAGCTTGTGAAGTATGGAA 5 0.125 No Hit GGGGTTGTGGGAGAGCAATACAAGCGTTGTGCTGCTAGGCGAAGCGGTTG 5 0.125 No Hit CGGGGAGTTGAAAATAAGCATAGATCCGGAGATTCCCAAATAGGTCAACC 5 0.125 No Hit GGCCCGGACCCTGTCGCCCCACGAGGCGCCGTCAACGAGTCGGGTTGTTT 5 0.125 No Hit GGAGAGCAATACAAGCGTTGTGCTGCTAGGCGAAGCGGTTGAGTGCCGCA 5 0.125 No Hit GGGGAGTTGAAAATAAGCATAGATCCGGAGATTCCCAAATAGGTCAACCT 5 0.125 No Hit GTTCAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAG 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 0.025 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 0.075 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 0.1125 0.0 0.0 0.0 0.0 42-43 0.125 0.0 0.0 0.0 0.0 44-45 0.125 0.0 0.0 0.0 0.0 46-47 0.125 0.0 0.0 0.0 0.0 48-49 0.125 0.0 0.0 0.0 0.0 50-51 0.125 0.0 0.0 0.0 0.0 52-53 0.1375 0.0 0.0 0.0 0.0 54-55 0.15 0.0 0.0 0.0 0.0 56-57 0.16249999999999998 0.0 0.0 0.0 0.0 58-59 0.175 0.0 0.0 0.0 0.0 60-61 0.175 0.0 0.0 0.0 0.0 62-63 0.175 0.0 0.0 0.0 0.0 64-65 0.175 0.0 0.0 0.0 0.0 66-67 0.2 0.0 0.0 0.0 0.0 68-69 0.2 0.0 0.0 0.0 0.0 70-71 0.2 0.0 0.0 0.0 0.0 72-73 0.2 0.0 0.0 0.0 0.0 74-75 0.2 0.0 0.0 0.0 0.0 76-77 0.2 0.0 0.0 0.0 0.0 78-79 0.2 0.0 0.0 0.0 0.0 80-81 0.2 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position TGAAGGT 30 0.0048568323 29.978355 84-85 AAGGTAA 30 0.0048568323 29.978355 86-87 CGTGAAG 30 0.0048568323 29.978355 82-83 CTCGTGA 30 0.0048568323 29.978355 80-81 AGGGCGC 30 0.005868829 28.854168 66-67 >>END_MODULE Rejected 70505 READS because READLEN < 1 Read 70505 spots for ERR6133325.sra Written 70505 spots for ERR6133325.sra Rejected 70505 READS because READLEN < 1 Read 70505 spots for ERR6133325.sra Written 70505 spots for ERR6133325.sra Rejected 70505 READS because READLEN < 1 Read 70505 spots for ERR6133325.sra Written 70505 spots for ERR6133325.sra Rejected 70505 READS because READLEN < 1 Read 70505 spots for ERR6133325.sra Written 70505 spots for ERR6133325.sra Rejected 70505 READS because READLEN < 1 Read 70505 spots for ERR6133325.sra Written 70505 spots for ERR6133325.sra Rejected 70505 READS because READLEN < 1 Read 70505 spots for ERR6133325.sra Written 70505 spots for ERR6133325.sra Rejected 70505 READS because READLEN < 1 Read 70505 spots for ERR6133325.sra Written 70505 spots for ERR6133325.sra Rejected 70505 READS because READLEN < 1 Read 70505 spots for ERR6133325.sra Written 70505 spots for ERR6133325.sra Rejected 70505 READS because READLEN < 1 Read 70505 spots for ERR6133325.sra Written 70505 spots for ERR6133325.sra Rejected 70505 READS because READLEN < 1 Read 70505 spots for ERR6133325.sra Written 70505 spots for ERR6133325.sra Rejected 70505 READS because READLEN < 1 Read 70505 spots for ERR6133325.sra Written 70505 spots for ERR6133325.sra Rejected 70505 READS because READLEN < 1 Read 70505 spots for ERR6133325.sra Written 70505 spots for ERR6133325.sra Rejected 70505 READS because READLEN < 1 Read 70505 spots for ERR6133325.sra Written 70505 spots for ERR6133325.sra Rejected 70505 READS because READLEN < 1 Read 70505 spots for ERR6133325.sra Written 70505 spots for ERR6133325.sra Rejected 70505 READS because READLEN < 1 Read 70505 spots for ERR6133325.sra Written 70505 spots for ERR6133325.sra Rejected 70505 READS because READLEN < 1 Read 70505 spots for ERR6133325.sra Written 70505 spots for ERR6133325.sra Rejected 70505 READS because READLEN < 1 Read 70505 spots for ERR6133325.sra Written 70505 spots for ERR6133325.sra Rejected 70520 READS because READLEN < 1 Read 70520 spots for ERR6133325.sra Written 70520 spots for ERR6133325.sra Rejected 70505 READS because READLEN < 1 Read 70505 spots for ERR6133325.sra Written 70505 spots for ERR6133325.sra Rejected 70505 READS because READLEN < 1 Read 70505 spots for ERR6133325.sra Written 70505 spots for ERR6133325.sra SRR ids: ['ERR6133325.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_s0hknf2q ERR6133325.sra spots: 1410115 blocks: [[1, 70505], [70506, 141010], [141011, 211515], [211516, 282020], [282021, 352525], [352526, 423030], [423031, 493535], [493536, 564040], [564041, 634545], [634546, 705050], [705051, 775555], [775556, 846060], [846061, 916565], [916566, 987070], [987071, 1057575], [1057576, 1128080], [1128081, 1198585], [1198586, 1269090], [1269091, 1339595], [1339596, 1410115]] ERR6133325 file size 306693 ERR6133325 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 ERR6133325 ERR6133325_1.fastq Input file: ERR6133325_1.fastq trimmed: ERR6133325-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 00:40:45 2024 >> started Sat Dec 7 00:40:46 2024 >> done (0.988s) 1410115 reads processed; of these: 274 ( 0.02%) short reads filtered out after trimming by size control 13 ( 0.00%) empty reads filtered out after trimming by size control 1409828 (99.98%) reads available; of these: 10277 ( 0.73%) trimmed reads available after processing 1399551 (99.27%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 23 0.00% 19 56 0.00% 20 28 0.00% 21 15 0.00% 22 23 0.00% 23 19 0.00% 24 19 0.00% 25 24 0.00% 26 26 0.00% 27 18 0.00% 28 51 0.00% 29 339 0.02% 30 23 0.00% 31 23 0.00% 32 61 0.00% 33 24 0.00% 34 26 0.00% 35 55 0.00% 36 22 0.00% 37 18 0.00% 38 28 0.00% 39 67 0.00% 40 111 0.01% 41 34 0.00% 42 12 0.00% 43 36 0.00% 44 28 0.00% 45 17 0.00% 46 18 0.00% 47 10 0.00% 48 18 0.00% 49 9 0.00% 50 19 0.00% 51 112 0.01% 52 32 0.00% 53 17 0.00% 54 13 0.00% 55 16 0.00% 56 13 0.00% 57 53 0.00% 58 34 0.00% 59 25 0.00% 60 29 0.00% 61 22 0.00% 62 6 0.00% 63 10 0.00% 64 4 0.00% 65 7 0.00% 66 9 0.00% 67 18 0.00% 68 31 0.00% 69 70 0.00% 70 11276 0.80% 71 10208 0.72% 72 10810 0.77% 73 10688 0.76% 74 10073 0.71% 75 9429 0.67% 76 9334 0.66% 77 9912 0.70% 78 10322 0.73% 79 10804 0.77% 80 10573 0.75% 81 13378 0.95% 82 14103 1.00% 83 12055 0.86% 84 14220 1.01% 85 51 0.00% 86 84 0.01% 87 135 0.01% 88 185 0.01% 89 315 0.02% 90 616 0.04% 91 1342 0.10% 92 4571 0.32% 93 1233523 87.49% 1409828 reads passed initial QC criterion=sequence-density sequence-density=4.57 sequence-density-rank=1 fanout-score=2.03 fanout-score-rank=26 prefix-density=4.62 prefix-fanout=2.0 sequence=CAAGGCTAAATAC criterion=fanout-score sequence-density=0.01 sequence-density-rank=36 fanout-score=55.75 fanout-score-rank=1 prefix-density=0.47 prefix-fanout=1.0 sequence=GTAGCTACCGAGATCAATGCAGTTAATTATGTCTCTCCTAGAAGTTGGTTATCGACTTCTCATTTTGTTCTAGGATTCTTCTTTTTTGTGGGCCATTTGTGGCATGCAGGAAGAGCCCGAGCTGCTGCAGCAGGTTTTGAAAAGGGAATCGATCGTGATTTAGAACCTGTTCTTTACATGAACCCTCTTAACTAAGATTTTCTTATTTATACCTGTTCTACTTCTACTGTTTTTTTCTGCTCTGGCTCGGTTATTTCATTTAGCCGAGCCATTCATTCCTTTTTCTGAATGAAAGATAAGGGGACAGAA 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 00:41:01 Started mapping on | Dec 07 00:41:01 Finished on | Dec 07 00:41:05 Mapping speed, Million of reads per hour | 1268.85 Number of input reads | 1409828 Average input read length | 91 UNIQUE READS: Uniquely mapped reads number | 700441 Uniquely mapped reads % | 49.68% Average mapped length | 89.92 Number of splices: Total | 22313 Number of splices: Annotated (sjdb) | 17827 Number of splices: GT/AG | 21211 Number of splices: GC/AG | 524 Number of splices: AT/AC | 44 Number of splices: Non-canonical | 534 Mismatch rate per base, % | 0.42% Deletion rate per base | 0.04% Deletion average length | 1.68 Insertion rate per base | 0.02% Insertion average length | 1.82 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 599207 % of reads mapped to multiple loci | 42.50% Number of reads mapped to too many loci | 69001 % of reads mapped to too many loci | 4.89% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 2.67% % of reads unmapped: other | 0.25% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 110180 110180 110180 N_multimapping 599207 599207 599207 N_noFeature 55785 61960 672092 N_ambiguous 25679 3456 133 UnstrandedReadsAssigned:618977 PositiveStrandReadsAssigned:635025 NegativeStrandReadsAssigned:28216 Dataset is classified positive stranded MeadianReadLen=93 20thPercentileLength=93 echo kmer=89 ERR6133325 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: ERR6133325-trimmed.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 1,409,828 reads, 957,164 reads pseudoaligned [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 931 rounds 52973 ERR6133325.ke.tsv 35125 ERR6133325.se.tsv 88098 total ==> ERR6133325.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 20 20.541 PNS24243 293 194 0 0 KQK14069 1603 1504 5 4.68454 KQK14071 474 375 0 0 ==> ERR6133325.se.tsv <== BRADI_1g14170v3 5 BRADI_1g53295v3 4 BRADI_1g59795v3 5 BRADI_1g07683v3 0 BRADI_1g00485v3 0 BRADI_1g20270v3 3 BRADI_1g74790v3 3 BRADI_1g09890v3 0 BRADI_1g77505v3 14 BRADI_1g48960v3 0 ERR6133325 completed mapping pipeline successfully