Starting /dee2/code/volunteer_pipeline.sh ERR6133359 current disk space = 1548280139776 free memory = 1403832472 ERR6133359 SRAfilesize a95dc1ebf345d0af83ffb518a72c6663 ERR6133359.sra ERR6133359.sra file validated ERR6133359 is single end ERR6133359 is conventional basespace ERR6133359 read1 length is 70-93 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename ERR6133359_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 36.44675 37.0 37.0 37.0 33.0 37.0 2 36.78125 37.0 37.0 37.0 37.0 37.0 3 36.72525 37.0 37.0 37.0 37.0 37.0 4 36.4605 37.0 37.0 37.0 37.0 37.0 5 36.47275 37.0 37.0 37.0 37.0 37.0 6 36.5815 37.0 37.0 37.0 37.0 37.0 7 38.8505 40.0 37.0 40.0 37.0 40.0 8 38.837 40.0 37.0 40.0 37.0 40.0 9 38.88175 40.0 37.0 40.0 37.0 40.0 10-11 38.816874999999996 40.0 37.0 40.0 37.0 40.0 12-13 38.8585 40.0 37.0 40.0 37.0 40.0 14-15 38.860125 40.0 37.0 40.0 37.0 40.0 16-17 38.81125 40.0 37.0 40.0 37.0 40.0 18-19 38.74225 40.0 37.0 40.0 37.0 40.0 20-21 38.679874999999996 40.0 37.0 40.0 37.0 40.0 22-23 38.610749999999996 40.0 37.0 40.0 37.0 40.0 24-25 38.497 40.0 37.0 40.0 37.0 40.0 26-27 38.572625 40.0 37.0 40.0 37.0 40.0 28-29 38.622 40.0 37.0 40.0 37.0 40.0 30-31 38.57225 40.0 37.0 40.0 37.0 40.0 32-33 38.408 40.0 37.0 40.0 37.0 40.0 34-35 38.348375000000004 40.0 37.0 40.0 37.0 40.0 36-37 38.239625000000004 40.0 37.0 40.0 37.0 40.0 38-39 38.212999999999994 40.0 37.0 40.0 37.0 40.0 40-41 38.06925 40.0 37.0 40.0 37.0 40.0 42-43 37.958875 37.0 37.0 40.0 37.0 40.0 44-45 37.758250000000004 37.0 37.0 40.0 37.0 40.0 46-47 37.652 37.0 37.0 40.0 37.0 40.0 48-49 37.469875 37.0 37.0 40.0 37.0 40.0 50-51 37.351 37.0 37.0 40.0 37.0 40.0 52-53 37.207875 37.0 37.0 40.0 37.0 40.0 54-55 37.055375 37.0 37.0 37.0 33.0 40.0 56-57 36.91175 37.0 37.0 37.0 33.0 40.0 58-59 36.694374999999994 37.0 37.0 37.0 33.0 40.0 60-61 36.65375 37.0 37.0 37.0 33.0 38.5 62-63 36.463875 37.0 37.0 37.0 33.0 37.0 64-65 36.29625 37.0 37.0 37.0 33.0 37.0 66-67 36.238375 37.0 37.0 37.0 33.0 37.0 68-69 35.309375 35.0 35.0 37.0 33.0 37.0 70-71 35.52983270676692 37.0 35.0 37.0 33.0 37.0 72-73 35.99511728866448 37.0 37.0 37.0 33.0 37.0 74-75 35.95959276306948 37.0 37.0 37.0 33.0 37.0 76-77 35.8652118569068 37.0 37.0 37.0 33.0 37.0 78-79 35.96379861495686 37.0 37.0 37.0 33.0 37.0 80-81 35.90737715220136 37.0 37.0 37.0 33.0 37.0 82-83 35.77983118109256 37.0 37.0 37.0 33.0 37.0 84-85 35.78921670618479 37.0 37.0 37.0 33.0 37.0 86-87 35.77037617554859 37.0 37.0 37.0 33.0 37.0 88-89 35.84430512016719 37.0 37.0 37.0 33.0 37.0 90-91 35.77716823406479 37.0 37.0 37.0 33.0 37.0 92-93 35.52925809822362 37.0 35.0 37.0 33.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 20 1.0 21 2.0 22 3.0 23 4.0 24 3.0 25 5.0 26 4.0 27 5.0 28 11.0 29 14.0 30 20.0 31 31.0 32 42.0 33 41.0 34 85.0 35 171.0 36 795.0 37 1210.0 38 1500.0 39 53.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 68.89222305576395 7.62690672668167 8.477119279819954 15.003750937734434 2 49.1 27.275 14.325 9.3 3 30.65 37.3 16.925 15.125 4 29.675 26.325 20.075000000000003 23.925 5 24.925 27.250000000000004 26.924999999999997 20.9 6 20.025000000000002 36.65 25.900000000000002 17.424999999999997 7 36.275 26.674999999999997 19.725 17.325 8 29.599999999999998 27.375 25.4 17.625 9 23.275000000000002 28.275 27.625 20.825 10-11 23.962500000000002 28.775000000000002 28.575 18.6875 12-13 24.025 27.975 27.762500000000003 20.2375 14-15 22.1875 30.1375 29.225 18.45 16-17 25.724999999999998 29.875 24.4 20.0 18-19 23.400000000000002 25.7375 30.6875 20.175 20-21 26.8 26.450000000000003 27.675 19.075 22-23 29.099999999999998 22.8375 26.8625 21.2 24-25 24.625 27.250000000000004 28.037499999999998 20.0875 26-27 26.8625 24.4 29.099999999999998 19.6375 28-29 25.4 26.8125 27.725 20.0625 30-31 28.199999999999996 25.5375 27.1375 19.125 32-33 24.3625 25.174999999999997 29.4125 21.05 34-35 21.912499999999998 32.175 25.937500000000004 19.975 36-37 24.925 26.487500000000004 25.75 22.8375 38-39 26.67833479184898 26.26578322290286 27.340917614701837 19.71496437054632 40-41 25.412499999999998 25.674999999999997 28.1875 20.724999999999998 42-43 26.4625 28.8375 26.174999999999997 18.525 44-45 23.8625 27.224999999999998 29.1875 19.725 46-47 27.175 25.6 27.037499999999998 20.1875 48-49 25.25 23.962500000000002 29.475 21.3125 50-51 21.462500000000002 28.512500000000003 29.125 20.9 52-53 25.75 26.8 25.45 22.0 54-55 26.025 26.3625 27.750000000000004 19.8625 56-57 25.5125 28.1625 27.6 18.725 58-59 23.35 28.1 28.925 19.625 60-61 27.05 29.299999999999997 25.324999999999996 18.325 62-63 20.724999999999998 28.512500000000003 30.55 20.2125 64-65 22.218054513628406 32.30807701925482 27.66941735433858 17.804451112778192 66-67 23.7375 30.55 26.075 19.6375 68-69 21.8125 27.462500000000002 26.950000000000003 23.775 70-71 23.842302878598247 28.34793491864831 27.121401752190238 20.688360450563202 72-73 26.0694514343231 27.113739305485655 28.91293407146452 17.903875188726722 74-75 25.253036437246962 28.036437246963565 28.795546558704455 17.91497975708502 76-77 21.743550641758798 26.165967721438555 26.852204854492314 25.238276782310333 78-79 26.70498084291188 25.721583652618136 28.659003831417625 18.914431673052363 80-81 22.29086229086229 32.857142857142854 26.525096525096526 18.326898326898327 82-83 22.128706461219732 29.043117959342226 26.72536579049592 22.10280978894212 84-85 21.773142112125164 25.345501955671445 31.773142112125164 21.108213820078227 86-87 21.32967607105538 28.160919540229884 27.076802507836987 23.432601880877744 88-89 19.46185997910136 30.91692789968652 28.435214211076282 21.185997910135843 90-91 23.341170323928946 28.827063740856847 27.48171368861024 20.35005224660397 92-93 20.741901776384537 31.896551724137932 27.403343782654126 19.958202716823408 >>END_MODULE >>Per sequence GC content warn #GC Content Count 0 0.0 1 0.0 2 0.0 3 0.0 4 0.0 5 0.0 6 0.0 7 0.0 8 0.0 9 0.0 10 0.0 11 0.0 12 0.0 13 0.0 14 0.0 15 0.0 16 0.0 17 2.5 18 3.5 19 1.0 20 0.5 21 3.0 22 4.5 23 7.5 24 9.0 25 6.5 26 9.5 27 13.0 28 18.5 29 23.0 30 25.5 31 35.0 32 48.5 33 62.5 34 61.5 35 68.5 36 112.5 37 165.0 38 187.0 39 186.0 40 226.0 41 242.5 42 253.0 43 285.5 44 220.5 45 160.5 46 169.5 47 173.0 48 148.5 49 129.0 50 167.0 51 183.0 52 138.0 53 142.0 54 190.0 55 151.5 56 74.5 57 53.0 58 47.0 59 31.0 60 26.0 61 28.5 62 16.0 63 10.0 64 12.0 65 14.5 66 10.0 67 5.0 68 13.0 69 13.5 70 4.5 71 0.0 72 0.0 73 0.0 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 0.0125 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 10.0 71 12.0 72 8.0 73 13.0 74 10.0 75 7.0 76 11.0 77 7.0 78 14.0 79 19.0 80 8.0 81 12.0 82 15.0 83 12.0 84 14.0 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 3828.0 >>END_MODULE >>Sequence Duplication Levels warn #Total Deduplicated Percentage 67.175 #Duplication Level Percentage of deduplicated Percentage of total 1 90.39821362113881 60.724999999999994 2 3.7960550800148867 5.1 3 1.7863788611834759 3.5999999999999996 4 1.0048381094157053 2.7 5 0.5582433941198363 1.875 6 0.5954596203944921 2.4 7 0.14886490509862302 0.7000000000000001 8 0.3721622627465575 2.0 9 0.22329735764793449 1.35 >10 1.0048381094157053 12.8 >50 0.07443245254931151 3.8 >100 0.037216226274655755 2.9499999999999997 >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 118 2.9499999999999997 No Hit TACCTAGGCACCCAGAGACGAGGAAGGGCGTAGCAAGCGACGAAATGCTT 85 2.125 No Hit GGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCTTGG 67 1.675 No Hit CAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAATACTTGGGCTG 46 1.15 No Hit CAAGGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCT 43 1.075 No Hit GGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAA 41 1.0250000000000001 No Hit CAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAATACTTGGGCTGATAT 33 0.8250000000000001 No Hit TCAAAAGAGGAAAGGCTTGCGGTGGATACCTAGGCACCCAGAGACGAGGA 32 0.8 No Hit GGCGTTCAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTC 25 0.625 No Hit CAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAGGTC 22 0.5499999999999999 No Hit GGGCGCGATCTTGCTCGTGAAGGTAATGAAATTATCCGAGCAGCTTGCAA 21 0.525 No Hit GTAGTAGGAATCTGGTTCACTGCTTTAGGTATTAGTACTATGGCGTTCAA 20 0.5 No Hit GGGCTGATATCATCAACCGTGCTAATCTTGGTATGGAAGTAATGCACGAA 20 0.5 No Hit AACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAATACTTGGGCTGA 20 0.5 No Hit AGTCAAGGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAA 16 0.4 No Hit GTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCTTGGT 14 0.35000000000000003 No Hit GGCCTGTAGTAGGAATCTGGTTCACTGCTTTAGGTATTAGTACTATGGCG 14 0.35000000000000003 No Hit GGAAAAGAAAGCAAAAGCGATTCCCGTAGTAGCGGCGAGCGAAATGGGAG 14 0.35000000000000003 No Hit GGAGTTGAAAATAAGCATAGATCCGGAGATTCCCAAATAGGTCAACCTTT 13 0.325 No Hit GGGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGT 13 0.325 No Hit GGATACCTAGGCACCCAGAGACGAGGAAGGGCGTAGCAAGCGACGAAATG 12 0.3 No Hit GGGCGTAGCAAGCGACGAAATGCTTCGGGGAGTTGAAAATAAGCATAGAT 11 0.27499999999999997 No Hit GGCCCGGACCCTGTCGCCCCACGAGGCGCCGTCAACGAGTCGGGTTGTTT 11 0.27499999999999997 No Hit GGGTGAGAGCCCCGTCCGGCCCGGACCCTGTCGCCCCACGAGGCGCCGTC 11 0.27499999999999997 No Hit GGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGTG 10 0.25 No Hit GTACTATGGCGTTCAACCTAAATGGATTCAATTTCAACCAATCTGTAGTT 10 0.25 No Hit GGGTTGTTTGGGAATGCAGCCCAAATCGGGCGGTAGACTCCGTCCAAGGC 10 0.25 No Hit GCAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAATACTTGGGCT 10 0.25 No Hit GGGGAGTTGAAAATAAGCATAGATCCGGAGATTCCCAAATAGGTCAACCT 10 0.25 No Hit GTTCAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAG 10 0.25 No Hit GCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCTTGGTATG 9 0.22499999999999998 No Hit GAGGAAGGGCGTAGCAAGCGACGAAATGCTTCGGGGAGTTGAAAATAAGC 9 0.22499999999999998 No Hit GGACATCCTTGGGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTT 9 0.22499999999999998 No Hit GGGATGATTCTGTATTACAATTTGGTGGAGGAACTTTAGGACATCCTTGG 9 0.22499999999999998 No Hit GTAGTTGATAGTCAAGGTCGCGTTATTAATACTTGGGCTGATATCATCAA 9 0.22499999999999998 No Hit GGGGATGATTCTGTATTACAATTTGGTGGAGGAACTTTAGGACATCCTTG 9 0.22499999999999998 No Hit GCAAGGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATC 8 0.2 No Hit GTAACGAAGGGCGCGATCTTGCTCGTGAAGGTAATGAAATTATCCGAGCA 8 0.2 No Hit GGGATGGAGCGACAGAAGTATGGAAATAGGATAAGGTAGCGGCGAGACGA 8 0.2 No Hit GCAGCTTGCAAATGGAGTCCTGAACTAGCCGCAGCTTGTGAAGTATGGAA 8 0.2 No Hit GATACCTAGGCACCCAGAGACGAGGAAGGGCGTAGCAAGCGACGAAATGC 8 0.2 No Hit GTATTAGTACTATGGCGTTCAACCTAAATGGATTCAATTTCAACCAATCT 8 0.2 No Hit GTACAAGCTCGTAACGAAGGGCGCGATCTTGCTCGTGAAGGTAATGAAAT 8 0.2 No Hit GTCAAGGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAAT 8 0.2 No Hit AGGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCTTG 8 0.2 No Hit TCTCATGGAGAGTTCGATCCTGGCTCAGGATGAACGCTGGCGGCATGCTT 8 0.2 No Hit GGGCACGTGGAATCCCGTGTGAATCAGCAAGGACCACCTTGCAAGGCTAA 7 0.17500000000000002 No Hit GGAAAGGCTTGCGGTGGATACCTAGGCACCCAGAGACGAGGAAGGGCGTA 7 0.17500000000000002 No Hit GGGGTTGTGGGAGAGCAATACAAGCGTTGTGCTGCTAGGCGAAGCGGTTG 7 0.17500000000000002 No Hit GTAGGAATCTGGTTCACTGCTTTAGGTATTAGTACTATGGCGTTCAACCT 7 0.17500000000000002 No Hit CGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCTTGGTAT 6 0.15 No Hit ATTTCAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAATACTTGG 6 0.15 No Hit TCAAGGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATC 6 0.15 No Hit GGAAGGGCGTAGCAAGCGACGAAATGCTTCGGGGAGTTGAAAATAAGCAT 6 0.15 No Hit GGCTGCTTGGCCTGTAGTAGGAATCTGGTTCACTGCTTTAGGTATTAGTA 6 0.15 No Hit GGGGATGGAGCGACAGAAGTATGGAAATAGGATAAGGTAGCGGCGAGACG 6 0.15 No Hit GATAGTCAAGGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGC 6 0.15 No Hit GAGGAAAAGAAAGCAAAAGCGATTCCCGTAGTAGCGGCGAGCGAAATGGG 6 0.15 No Hit GAGGAAAGGCTTGCGGTGGATACCTAGGCACCCAGAGACGAGGAAGGGCG 6 0.15 No Hit GAAGGGCGCGATCTTGCTCGTGAAGGTAATGAAATTATCCGAGCAGCTTG 6 0.15 No Hit GAAGGGCGTAGCAAGCGACGAAATGCTTCGGGGAGTTGAAAATAAGCATA 6 0.15 No Hit GGAGCAGCCTAAACCGTGAAAACGGGGTTGTGGGAGAGCAATACAAGCGT 6 0.15 No Hit GGGAATCGATCGTGATTTAGAACCTGTTCTTTACATGAACCCTCTTAACT 6 0.15 No Hit CACGAACGTAATGCTCACAACTTCCCTCTAGATCTAGCTGCTCTTGAAGT 6 0.15 No Hit GAAGGTAATGAAATTATCCGAGCAGCTTGCAAATGGAGTCCTGAACTAGC 6 0.15 No Hit GGAGGAACTTTAGGACATCCTTGGGGAAATGCACCTGGTGCAGCAGCTAA 6 0.15 No Hit GGGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCTTG 5 0.125 No Hit CTGGTTCACTGCTTTAGGTATTAGTACTATGGCGTTCAACCTAAATGGAT 5 0.125 No Hit GTAGCAAGCGACGAAATGCTTCGGGGAGTTGAAAATAAGCATAGATCCGG 5 0.125 No Hit GACGAGGAAGGGCGTAGCAAGCGACGAAATGCTTCGGGGAGTTGAAAATA 5 0.125 No Hit CACCCAGAGACGAGGAAGGGCGTAGCAAGCGACGAAATGCTTCGGGGAGT 5 0.125 No Hit GATTCAATTTCAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAAT 5 0.125 No Hit GGAGGAAGGGCGTAGCAAGCGACGAAATGCTTCGGGGAGTTGAAAATAAG 5 0.125 No Hit GAAGCCTGTGTACAAGCTCGTAACGAAGGGCGCGATCTTGCTCGTGAAGG 5 0.125 No Hit AGGAAAGGCTTGCGGTGGATACCTAGGCACCCAGAGACGAGGAAGGGCGT 5 0.125 No Hit AACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAGGTCG 5 0.125 No Hit GTATTTAGCCTTGCAAGGTGGTCCTTGCTGATTCACACGGGATTCCACGT 5 0.125 No Hit GGAAAAGAGGGGTTACTTTTTTTCATTTTTCCCTTAAAAGATAGGCTTTG 5 0.125 No Hit CGTTCAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTCAA 5 0.125 No Hit GGCACGTGGAATCCCGTGTGAATCAGCAAGGACCACCTTGCAAGGCTAAA 5 0.125 No Hit TCAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAATACTTGGGCT 5 0.125 No Hit >>END_MODULE >>Adapter Content pass #Position Illumina Universal Adapter Illumina Small RNA 3' Adapter Illumina Small RNA 5' Adapter Nextera Transposase Sequence SOLID Small RNA Adapter 1 0.0 0.0 0.0 0.0 0.0 2 0.0 0.0 0.0 0.0 0.0 3 0.0 0.0 0.0 0.0 0.0 4 0.0 0.0 0.0 0.0 0.0 5 0.0 0.0 0.0 0.0 0.0 6 0.0 0.0 0.0 0.0 0.0 7 0.0 0.0 0.0 0.0 0.0 8 0.0 0.0 0.0 0.0 0.0 9 0.0 0.0 0.0 0.0 0.0 10-11 0.0 0.0 0.0 0.0 0.0 12-13 0.0 0.0 0.0 0.0 0.0 14-15 0.0 0.0 0.0 0.0 0.0 16-17 0.0 0.0 0.0 0.0 0.0 18-19 0.0 0.0 0.0 0.0 0.0 20-21 0.0 0.0 0.0 0.0 0.0 22-23 0.0 0.0 0.0 0.0 0.0 24-25 0.0 0.0 0.0 0.0 0.0 26-27 0.0 0.0 0.0 0.0 0.0 28-29 0.0 0.0 0.0 0.0 0.0 30-31 0.0 0.0 0.0 0.0 0.0 32-33 0.0 0.0 0.0 0.0 0.0 34-35 0.0 0.0 0.0 0.0 0.0 36-37 0.0 0.0 0.0 0.0 0.0 38-39 0.0 0.0 0.0 0.0 0.0 40-41 0.0 0.0 0.0 0.0 0.0 42-43 0.0 0.0 0.0 0.0 0.0 44-45 0.0 0.0 0.0 0.0 0.0 46-47 0.0 0.0 0.0 0.0 0.0 48-49 0.0 0.0 0.0 0.0 0.0 50-51 0.0 0.0 0.0 0.0 0.0 52-53 0.0 0.0 0.0 0.0 0.0 54-55 0.0 0.0 0.0 0.0 0.0 56-57 0.0 0.0 0.0 0.0 0.0 58-59 0.0 0.0 0.0 0.0 0.0 60-61 0.0 0.0 0.0 0.0 0.0 62-63 0.0 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 fail #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position AATACAA 35 5.020411E-10 86.200005 9 GGAGAGC 40 1.4460966E-9 75.425 2 GCAATAC 40 1.4460966E-9 75.425 7 CAATACA 40 1.4460966E-9 75.425 8 AGCAATA 40 1.4460966E-9 75.425 6 GGCACCC 25 7.543009E-5 68.96 7 CTAGGCA 25 7.543009E-5 68.96 4 AGGCACC 25 7.543009E-5 68.96 6 GCACCCA 25 7.543009E-5 68.96 8 TACCTAG 25 7.543009E-5 68.96 1 CCTAGGC 25 7.543009E-5 68.96 3 TAGGCAC 25 7.543009E-5 68.96 5 GGGAGAG 45 3.6779966E-9 67.04444 1 GAGCAAT 45 3.6779966E-9 67.04444 5 AGAGCAA 45 3.6779966E-9 67.04444 4 GAGAGCA 45 3.6779966E-9 67.04444 3 CACCCAG 30 1.8600201E-4 57.466667 9 ACCTAGG 30 1.8600201E-4 57.466667 2 CATCACT 35 8.541974E-8 45.97333 82-83 ATCACTA 35 8.541974E-8 45.97333 84-85 >>END_MODULE Rejected 253831 READS because READLEN < 1 Read 253831 spots for ERR6133359.sra Written 253831 spots for ERR6133359.sra Rejected 253831 READS because READLEN < 1 Read 253831 spots for ERR6133359.sra Written 253831 spots for ERR6133359.sra Rejected 253831 READS because READLEN < 1 Read 253831 spots for ERR6133359.sra Written 253831 spots for ERR6133359.sra Rejected 253831 READS because READLEN < 1 Read 253831 spots for ERR6133359.sra Written 253831 spots for ERR6133359.sra Rejected 253831 READS because READLEN < 1 Read 253831 spots for ERR6133359.sra Written 253831 spots for ERR6133359.sra Rejected 253831 READS because READLEN < 1 Read 253831 spots for ERR6133359.sra Written 253831 spots for ERR6133359.sra Rejected 253831 READS because READLEN < 1 Read 253831 spots for ERR6133359.sra Written 253831 spots for ERR6133359.sra Rejected 253831 READS because READLEN < 1 Read 253831 spots for ERR6133359.sra Written 253831 spots for ERR6133359.sra Rejected 253831 READS because READLEN < 1 Read 253831 spots for ERR6133359.sra Written 253831 spots for ERR6133359.sra Rejected 253831 READS because READLEN < 1 Read 253831 spots for ERR6133359.sra Written 253831 spots for ERR6133359.sra Rejected 253831 READS because READLEN < 1 Read 253831 spots for ERR6133359.sra Written 253831 spots for ERR6133359.sra Rejected 253831 READS because READLEN < 1 Read 253831 spots for ERR6133359.sra Written 253831 spots for ERR6133359.sra Rejected 253831 READS because READLEN < 1 Read 253831 spots for ERR6133359.sra Written 253831 spots for ERR6133359.sra Rejected 253831 READS because READLEN < 1 Read 253831 spots for ERR6133359.sra Written 253831 spots for ERR6133359.sra Rejected 253831 READS because READLEN < 1 Read 253831 spots for ERR6133359.sra Written 253831 spots for ERR6133359.sra Rejected 253831 READS because READLEN < 1 Read 253831 spots for ERR6133359.sra Written 253831 spots for ERR6133359.sra Rejected 253831 READS because READLEN < 1 Read 253831 spots for ERR6133359.sra Written 253831 spots for ERR6133359.sra Rejected 253831 READS because READLEN < 1 Read 253831 spots for ERR6133359.sra Written 253831 spots for ERR6133359.sra Rejected 253831 READS because READLEN < 1 Read 253831 spots for ERR6133359.sra Written 253831 spots for ERR6133359.sra Rejected 253835 READS because READLEN < 1 Read 253835 spots for ERR6133359.sra Written 253835 spots for ERR6133359.sra SRR ids: ['ERR6133359.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_sdmythzy ERR6133359.sra spots: 5076624 blocks: [[1, 253831], [253832, 507662], [507663, 761493], [761494, 1015324], [1015325, 1269155], [1269156, 1522986], [1522987, 1776817], [1776818, 2030648], [2030649, 2284479], [2284480, 2538310], [2538311, 2792141], [2792142, 3045972], [3045973, 3299803], [3299804, 3553634], [3553635, 3807465], [3807466, 4061296], [4061297, 4315127], [4315128, 4568958], [4568959, 4822789], [4822790, 5076624]] ERR6133359 file size 1120886 ERR6133359 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 ERR6133359 ERR6133359_1.fastq Input file: ERR6133359_1.fastq trimmed: ERR6133359-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 01:24:02 2024 >> started Sat Dec 7 01:24:05 2024 >> done (2.704s) 5076624 reads processed; of these: 301 ( 0.01%) short reads filtered out after trimming by size control 8 ( 0.00%) empty reads filtered out after trimming by size control 5076315 (99.99%) reads available; of these: 26399 ( 0.52%) trimmed reads available after processing 5049916 (99.48%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 22 0.00% 19 65 0.00% 20 47 0.00% 21 20 0.00% 22 37 0.00% 23 26 0.00% 24 23 0.00% 25 16 0.00% 26 36 0.00% 27 18 0.00% 28 38 0.00% 29 33 0.00% 30 24 0.00% 31 25 0.00% 32 65 0.00% 33 28 0.00% 34 26 0.00% 35 126 0.00% 36 24 0.00% 37 23 0.00% 38 31 0.00% 39 98 0.00% 40 159 0.00% 41 55 0.00% 42 15 0.00% 43 29 0.00% 44 32 0.00% 45 29 0.00% 46 12 0.00% 47 13 0.00% 48 17 0.00% 49 15 0.00% 50 15 0.00% 51 155 0.00% 52 41 0.00% 53 16 0.00% 54 14 0.00% 55 12 0.00% 56 19 0.00% 57 32 0.00% 58 24 0.00% 59 16 0.00% 60 29 0.00% 61 25 0.00% 62 10 0.00% 63 9 0.00% 64 22 0.00% 65 21 0.00% 66 31 0.00% 67 54 0.00% 68 73 0.00% 69 99 0.00% 70 15560 0.31% 71 14175 0.28% 72 14922 0.29% 73 14337 0.28% 74 13972 0.28% 75 13250 0.26% 76 13210 0.26% 77 14259 0.28% 78 14488 0.29% 79 16029 0.32% 80 15635 0.31% 81 20716 0.41% 82 21563 0.42% 83 18095 0.36% 84 21305 0.42% 85 192 0.00% 86 316 0.01% 87 412 0.01% 88 629 0.01% 89 1043 0.02% 90 1808 0.04% 91 4075 0.08% 92 13749 0.27% 93 4810631 94.77% 5076315 reads passed initial QC criterion=sequence-density sequence-density=2.01 sequence-density-rank=1 fanout-score=2.04 fanout-score-rank=26 prefix-density=2.03 prefix-fanout=2.0 sequence=CAAGGCTAAATAC criterion=fanout-score sequence-density=0.01 sequence-density-rank=37 fanout-score=91.16 fanout-score-rank=1 prefix-density=0.43 prefix-fanout=1.2 sequence=GAAATAGGATCTAAACAAGGAAGAGCACTTGCCATTCGTTGGTTATTAGAAGCATCCCAAAAGCGTCCGGGTCGAAATATGGCTTTCAAATTAAGTTCCGAATTAGTAGATGCTGCCAAAGGGAGTGGGGGTGCCATACGCAAAAAGGAAGCGACTCATAGAATGGCAGAGGCAAATAGAGCTCTTGCACATTTTCGTTAATCCATGAACAGAATCTAGGTATGTAGACACATGGATCCATACATCTCGATCGGAAAAGAATCAATAGAAGGAGAATCGGACGATATCTTTCTCGAAACAAACAA 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 01:24:21 Started mapping on | Dec 07 01:24:21 Finished on | Dec 07 01:24:28 Mapping speed, Million of reads per hour | 2610.68 Number of input reads | 5076315 Average input read length | 92 UNIQUE READS: Uniquely mapped reads number | 2307841 Uniquely mapped reads % | 45.46% Average mapped length | 91.45 Number of splices: Total | 79098 Number of splices: Annotated (sjdb) | 60831 Number of splices: GT/AG | 74407 Number of splices: GC/AG | 1755 Number of splices: AT/AC | 151 Number of splices: Non-canonical | 2785 Mismatch rate per base, % | 0.39% Deletion rate per base | 0.04% Deletion average length | 1.70 Insertion rate per base | 0.02% Insertion average length | 2.04 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 2528311 % of reads mapped to multiple loci | 49.81% Number of reads mapped to too many loci | 133361 % of reads mapped to too many loci | 2.63% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 1.97% % of reads unmapped: other | 0.13% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 240163 240163 240163 N_multimapping 2528311 2528311 2528311 N_noFeature 209937 236182 2207318 N_ambiguous 85780 11448 429 UnstrandedReadsAssigned:2012124 PositiveStrandReadsAssigned:2060211 NegativeStrandReadsAssigned:100094 Dataset is classified positive stranded MeadianReadLen=93 20thPercentileLength=93 echo kmer=89 ERR6133359 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: ERR6133359-trimmed.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 5,076,315 reads, 3,491,073 reads pseudoaligned [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 979 rounds 52973 ERR6133359.ke.tsv 35125 ERR6133359.se.tsv 88098 total ==> ERR6133359.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 87 24.0661 PNS24243 293 194 0 0 KQK14069 1603 1504 132 33.3095 KQK14071 474 375 0 0 ==> ERR6133359.se.tsv <== BRADI_1g14170v3 132 BRADI_1g53295v3 18 BRADI_1g59795v3 23 BRADI_1g07683v3 0 BRADI_1g00485v3 0 BRADI_1g20270v3 11 BRADI_1g74790v3 33 BRADI_1g09890v3 0 BRADI_1g77505v3 33 BRADI_1g48960v3 0 ERR6133359 completed mapping pipeline successfully