Starting /dee2/code/volunteer_pipeline.sh ERR6133353 current disk space = 1548295757824 free memory = 1604107092 ERR6133353 SRAfilesize db98e36e6c7c27f6659df0bbf3953a83 ERR6133353.sra ERR6133353.sra file validated ERR6133353 is single end ERR6133353 is conventional basespace ERR6133353 read1 length is 70-93 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename ERR6133353_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 44 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 36.44175 37.0 37.0 37.0 33.0 37.0 2 36.728 37.0 37.0 37.0 37.0 37.0 3 36.6815 37.0 37.0 37.0 37.0 37.0 4 36.41925 37.0 37.0 37.0 37.0 37.0 5 36.45725 37.0 37.0 37.0 37.0 37.0 6 36.57575 37.0 37.0 37.0 37.0 37.0 7 38.831 40.0 37.0 40.0 37.0 40.0 8 38.87075 40.0 37.0 40.0 37.0 40.0 9 38.85325 40.0 37.0 40.0 37.0 40.0 10-11 38.852 40.0 37.0 40.0 37.0 40.0 12-13 38.823625 40.0 37.0 40.0 37.0 40.0 14-15 38.851749999999996 40.0 37.0 40.0 37.0 40.0 16-17 38.794875000000005 40.0 37.0 40.0 37.0 40.0 18-19 38.736875 40.0 37.0 40.0 37.0 40.0 20-21 38.701 40.0 37.0 40.0 37.0 40.0 22-23 38.623375 40.0 37.0 40.0 37.0 40.0 24-25 38.559250000000006 40.0 37.0 40.0 37.0 40.0 26-27 38.54225 40.0 37.0 40.0 37.0 40.0 28-29 38.542874999999995 40.0 37.0 40.0 37.0 40.0 30-31 38.494125 40.0 37.0 40.0 37.0 40.0 32-33 38.421125 40.0 37.0 40.0 37.0 40.0 34-35 38.332375 40.0 37.0 40.0 37.0 40.0 36-37 38.2465 40.0 37.0 40.0 37.0 40.0 38-39 38.171125 40.0 37.0 40.0 37.0 40.0 40-41 38.046375 40.0 37.0 40.0 37.0 40.0 42-43 37.949250000000006 38.5 37.0 40.0 37.0 40.0 44-45 37.80275 37.0 37.0 40.0 37.0 40.0 46-47 37.71875 37.0 37.0 40.0 37.0 40.0 48-49 37.56175 37.0 37.0 40.0 37.0 40.0 50-51 37.335125000000005 37.0 37.0 40.0 35.0 40.0 52-53 37.20025 37.0 37.0 40.0 35.0 40.0 54-55 37.065124999999995 37.0 37.0 38.5 33.0 40.0 56-57 36.899375 37.0 37.0 37.0 33.0 40.0 58-59 36.699875000000006 37.0 37.0 37.0 33.0 40.0 60-61 36.580375000000004 37.0 37.0 37.0 33.0 40.0 62-63 36.41225 37.0 37.0 37.0 33.0 37.0 64-65 36.268 37.0 37.0 37.0 33.0 37.0 66-67 36.156125 37.0 37.0 37.0 33.0 37.0 68-69 35.321749999999994 37.0 35.0 37.0 33.0 37.0 70-71 35.53860734997478 37.0 35.0 37.0 33.0 37.0 72-73 35.90277908067542 37.0 37.0 37.0 33.0 37.0 74-75 35.84369719618728 37.0 37.0 37.0 33.0 37.0 76-77 35.8629466459772 37.0 37.0 37.0 33.0 37.0 78-79 35.86787386408124 37.0 37.0 37.0 33.0 37.0 80-81 35.809852476302375 37.0 37.0 37.0 33.0 37.0 82-83 35.70119243458562 37.0 37.0 37.0 33.0 37.0 84-85 35.67526691128786 37.0 37.0 37.0 33.0 37.0 86-87 35.637666761283 37.0 37.0 37.0 33.0 37.0 88-89 35.71884757309111 37.0 37.0 37.0 33.0 37.0 90-91 35.61212035197275 37.0 37.0 37.0 33.0 37.0 92-93 35.4409594095941 37.0 35.0 37.0 33.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 20 4.0 21 1.0 22 5.0 23 1.0 24 1.0 25 4.0 26 8.0 27 9.0 28 13.0 29 19.0 30 25.0 31 40.0 32 38.0 33 52.0 34 89.0 35 155.0 36 704.0 37 1202.0 38 1537.0 39 93.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 66.19154788697175 8.102025506376593 7.776944236059015 17.92948237059265 2 48.225 26.35 15.5 9.925 3 30.525000000000002 38.9 17.599999999999998 12.975 4 30.2 28.799999999999997 21.65 19.35 5 24.6 26.950000000000003 28.199999999999996 20.25 6 21.075 32.425 27.1 19.400000000000002 7 31.05 28.449999999999996 21.8 18.7 8 26.700000000000003 29.125 26.6 17.575 9 25.3 27.200000000000003 27.650000000000002 19.85 10-11 25.412499999999998 26.237500000000004 29.562500000000004 18.787499999999998 12-13 24.7375 28.3125 28.349999999999998 18.6 14-15 21.625 28.9875 29.6625 19.725 16-17 24.675 29.512500000000003 25.637500000000003 20.175 18-19 24.525 26.400000000000002 29.1125 19.9625 20-21 24.825 26.2125 27.775 21.1875 22-23 26.25 25.55 26.875 21.325 24-25 24.95 26.3 28.3875 20.3625 26-27 24.825 24.675 29.9 20.599999999999998 28-29 25.8 26.950000000000003 27.375 19.875 30-31 25.2875 27.3125 27.1125 20.2875 32-33 24.9 25.6 29.825000000000003 19.675 34-35 23.7625 28.0625 27.2625 20.9125 36-37 23.962500000000002 28.249999999999996 26.337500000000002 21.45 38-39 25.30316289536192 25.87823477934742 28.103512939117394 20.715089386173272 40-41 25.474999999999998 25.95 27.750000000000004 20.825 42-43 25.95 28.775000000000002 26.237500000000004 19.037499999999998 44-45 23.05 27.237499999999997 29.575000000000003 20.1375 46-47 24.65 28.175 27.175 20.0 48-49 23.5375 25.85 29.3875 21.224999999999998 50-51 22.537499999999998 28.95 29.475 19.037499999999998 52-53 25.162499999999998 28.3625 26.950000000000003 19.525000000000002 54-55 23.625 28.075 29.2 19.1 56-57 24.65 28.475 27.212500000000002 19.662499999999998 58-59 24.725 28.325 26.937499999999996 20.0125 60-61 24.75 27.900000000000002 28.349999999999998 19.0 62-63 21.95 29.1375 29.7375 19.175 64-65 22.380595148787197 30.632658164541137 28.257064266066518 18.72968242060515 66-67 23.540442555319416 28.9536192024003 27.50343792974122 20.002500312539066 68-69 21.4875 28.549999999999997 29.062500000000004 20.9 70-71 24.064775295003766 29.211649510419278 26.387145367813208 20.336429826763748 72-73 24.897907095456866 27.11842776927004 27.896886166411434 20.086778968861665 74-75 23.725084131504012 27.75045301579084 29.30365001294331 19.220812839761845 76-77 23.217094913476664 27.26796014682748 28.18563188253802 21.32931305715784 78-79 24.74693660095898 28.076718167288227 28.19659030367608 18.979754928076716 80-81 22.534450148608485 30.92407457443934 28.1545528235612 18.386922453390973 82-83 22.070581748001104 28.012131237937687 28.260270195754067 21.65701681830714 84-85 23.094297007340487 26.242236024844722 30.335968379446644 20.327498588368154 86-87 22.296338347998866 27.959125745103602 28.15782003973886 21.58671586715867 88-89 22.16860630144763 29.846721544138514 28.824865171728643 19.15980698268521 90-91 22.97757592960545 30.485381776894695 26.610843031507237 19.92619926199262 92-93 20.80613113823446 32.883905762134546 27.135963667328983 19.173999432302015 >>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 1.5 18 2.5 19 1.0 20 1.0 21 2.0 22 3.5 23 6.5 24 9.0 25 10.5 26 13.0 27 18.5 28 27.5 29 35.0 30 41.5 31 53.5 32 60.0 33 71.0 34 86.0 35 102.5 36 138.0 37 179.0 38 208.0 39 198.0 40 211.5 41 216.0 42 222.5 43 253.5 44 198.5 45 167.0 46 177.5 47 160.5 48 147.5 49 140.0 50 147.0 51 146.5 52 146.5 53 165.5 54 147.0 55 113.0 56 107.0 57 105.0 58 73.0 59 36.5 60 23.5 61 21.5 62 18.0 63 13.5 64 11.5 65 9.5 66 8.0 67 3.5 68 8.0 69 10.5 70 5.5 71 3.0 72 1.5 73 0.0 74 0.0 75 0.5 76 0.5 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 0.0125 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 0.014114326040931546 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 34.0 71 30.0 72 36.0 73 23.0 74 28.0 75 27.0 76 16.0 77 35.0 78 34.0 79 24.0 80 24.0 81 39.0 82 46.0 83 42.0 84 39.0 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 3523.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 76.6 #Duplication Level Percentage of deduplicated Percentage of total 1 91.22062663185379 69.875 2 4.3733681462141 6.7 3 1.3381201044386422 3.075 4 0.6201044386422976 1.9 5 0.6201044386422976 2.375 6 0.5874673629242819 2.7 7 0.3263707571801566 1.7500000000000002 8 0.22845953002610966 1.4000000000000001 9 0.09791122715404699 0.675 >10 0.5874673629242819 9.55 >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 GGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAA 48 1.2 No Hit GGGAGAGCAATACAAGCGTTGTGCTGCTAGGCGAAGCGGTTGAGTGCCGC 33 0.8250000000000001 No Hit CAAGGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCT 30 0.75 No Hit CAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAATACTTGGGCTGATAT 28 0.7000000000000001 No Hit GGGTTGTTTGGGAATGCAGCCCAAATCGGGCGGTAGACTCCGTCCAAGGC 26 0.65 No Hit GGAATCCCGTGTGAATCAGCAAGGACCACCTTGCAAGGCTAAATACTCCT 26 0.65 No Hit CAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAATACTTGGGCTG 25 0.625 No Hit GGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCTTGG 24 0.6 No Hit TACCTAGGCACCCAGAGACGAGGAAGGGCGTAGCAAGCGACGAAATGCTT 23 0.575 No Hit CAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAGGTC 18 0.44999999999999996 No Hit GGCGTTCAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTC 15 0.375 No Hit TCAAAAGAGGAAAGGCTTGCGGTGGATACCTAGGCACCCAGAGACGAGGA 15 0.375 No Hit GGGCGCGATCTTGCTCGTGAAGGTAATGAAATTATCCGAGCAGCTTGCAA 14 0.35000000000000003 No Hit GGGCTGATATCATCAACCGTGCTAATCTTGGTATGGAAGTAATGCACGAA 14 0.35000000000000003 No Hit GGGCACGTGGAATCCCGTGTGAATCAGCAAGGACCACCTTGCAAGGCTAA 12 0.3 No Hit GGAGTTGAAAATAAGCATAGATCCGGAGATTCCCAAATAGGTCAACCTTT 11 0.27499999999999997 No Hit GGTTCACTGCTTTAGGTATTAGTACTATGGCGTTCAACCTAAATGGATTC 10 0.25 No Hit GGGGAGTTGAAAATAAGCATAGATCCGGAGATTCCCAAATAGGTCAACCT 10 0.25 No Hit GGAAAGGCTTGCGGTGGATACCTAGGCACCCAGAGACGAGGAAGGGCGTA 9 0.22499999999999998 No Hit GCAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAATACTTGGGCT 9 0.22499999999999998 No Hit GCGTTCAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTCA 9 0.22499999999999998 No Hit GGAGTCCTGAACTAGCCGCAGCTTGTGAAGTATGGAAGGCGATCAAATTC 8 0.2 No Hit GGGGCAGAGGGAATTTCCGGTGGAGCGGTGAAATGCATTGAGATCGGAAA 8 0.2 No Hit GTAGTAGGAATCTGGTTCACTGCTTTAGGTATTAGTACTATGGCGTTCAA 8 0.2 No Hit GATTCAATTTCAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAAT 8 0.2 No Hit GGGAGTTGAAAATAAGCATAGATCCGGAGATTCCCAAATAGGTCAACCTT 8 0.2 No Hit GGGTTGTGGGAGAGCAATACAAGCGTTGTGCTGCTAGGCGAAGCGGTTGA 8 0.2 No Hit GGAAAAGAAAGCAAAAGCGATTCCCGTAGTAGCGGCGAGCGAAATGGGAG 8 0.2 No Hit GGGATGATTCTGTATTACAATTTGGTGGAGGAACTTTAGGACATCCTTGG 7 0.17500000000000002 No Hit CAACGAGTCGGGTTGTTTGGGAATGCAGCCCAAATCGGGCGGTAGACTCC 7 0.17500000000000002 No Hit CAAATCGGGCGGTAGACTCCGTCCAAGGCTAAATACAGGCGAGAGACCGATAGCGAACAAGTACCGCGAGGG 7 0.17500000000000002 No Hit GCAGCTTGCAAATGGAGTCCTGAACTAGCCGCAGCTTGTGAAGTATGGAA 7 0.17500000000000002 No Hit GTATTTAGCCTTGCAAGGTGGTCCTTGCTGATTCACACGGGATTCCACGT 7 0.17500000000000002 No Hit GTAGGAATCTGGTTCACTGCTTTAGGTATTAGTACTATGGCGTTCAACCT 7 0.17500000000000002 No Hit GGGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGT 7 0.17500000000000002 No Hit GGGTGAGAGCCCCGTCCGGCCCGGACCCTGTCGCCCCACGAGGCGCCGTC 7 0.17500000000000002 No Hit GTGGATACCTAGGCACCCAGAGACGAGGAAGGGCGTAGCAAGCGACGAAA 7 0.17500000000000002 No Hit GGGGCACGTGGAATCCCGTGTGAATCAGCAAGGACCACCTTGCAAGGCTA 7 0.17500000000000002 No Hit GGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGTG 6 0.15 No Hit CAAGCTCGTAACGAAGGGCGCGATCTTGCTCGTGAAGGTAATGAAATTAT 6 0.15 No Hit GGAAGGGCGTAGCAAGCGACGAAATGCTTCGGGGAGTTGAAAATAAGCAT 6 0.15 No Hit GGAGATTCCCAAATAGGTCAACCTTTTAAACTGCCTGCTGAATCCATGAG 6 0.15 No Hit GGATACCTAGGCACCCAGAGACGAGGAAGGGCGTAGCAAGCGACGAAATG 6 0.15 No Hit GTATGGAAGGCGATCAAATTCGAGTTCGCGCCGGTAGATACTATCGATTA 6 0.15 No Hit GTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCTTGGT 6 0.15 No Hit GGCGCGATCTTGCTCGTGAAGGTAATGAAATTATCCGAGCAGCTTGCAAA 6 0.15 No Hit CTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAGGTCGCGT 6 0.15 No Hit GATAGTCAAGGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGC 6 0.15 No Hit GATACCTAGGCACCCAGAGACGAGGAAGGGCGTAGCAAGCGACGAAATGC 6 0.15 No Hit CGGAGATTCCCAAATAGGTCAACCTTTTAAACTGCCTGCTGAATCCATGA 6 0.15 No Hit GAGGAAAGGCTTGCGGTGGATACCTAGGCACCCAGAGACGAGGAAGGGCG 6 0.15 No Hit GGAGTACGGTAGGGGCAGAGGGAATTTCCGGTGGAGCGGTGAAATGCATT 6 0.15 No Hit GAAGGGCGCGATCTTGCTCGTGAAGGTAATGAAATTATCCGAGCAGCTTG 6 0.15 No Hit GTACAAGCTCGTAACGAAGGGCGCGATCTTGCTCGTGAAGGTAATGAAAT 6 0.15 No Hit GTGGAATCCCGTGTGAATCAGCAAGGACCACCTTGCAAGGCTAAATACTC 6 0.15 No Hit GGTTGTTTGGGAATGCAGCCCAAATCGGGCGGTAGACTCCGTCCAAGGCT 6 0.15 No Hit GGAGTTTGGCTGGGGCGGCACATCTGTTAAAAGATAACGCAGGTGTCCTA 5 0.125 No Hit GGGGTTACTTTTTTTCATTTTTCCCTTAAAAGATAGGCTTTGAAATCGGA 5 0.125 No Hit GGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGTGT 5 0.125 No Hit GGGAATGCAGCCCAAATCGGGCGGTAGACTCCGTCCAAGGCTAAATACAG 5 0.125 No Hit GGGCGTAGCAAGCGACGAAATGCTTCGGGGAGTTGAAAATAAGCATAGAT 5 0.125 No Hit GGACATCCTTGGGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTT 5 0.125 No Hit GTAATGAAATTATCCGAGCAGCTTGCAAATGGAGTCCTGAACTAGCCGCA 5 0.125 No Hit CACGTGGAATCCCGTGTGAATCAGCAAGGACCACCTTGCAAGGCTAAATA 5 0.125 No Hit AGGAAAGGCTTGCGGTGGATACCTAGGCACCCAGAGACGAGGAAGGGCGT 5 0.125 No Hit GGGCCGGGTATCTCTCTGCATGTACGTATGCCTGTAATGTACGTAGCTAC 5 0.125 No Hit GGGGTTGTGGGAGAGCAATACAAGCGTTGTGCTGCTAGGCGAAGCGGTTG 5 0.125 No Hit AGTCAAGGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAA 5 0.125 No Hit CGGGGAGTTGAAAATAAGCATAGATCCGGAGATTCCCAAATAGGTCAACC 5 0.125 No Hit GGAGAGCAATACAAGCGTTGTGCTGCTAGGCGAAGCGGTTGAGTGCCGCA 5 0.125 No Hit AACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAATACTTGGGCTGA 5 0.125 No Hit GTGAAGGTAATGAAATTATCCGAGCAGCTTGCAAATGGAGTCCTGAACTA 5 0.125 No Hit GTTCAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAG 5 0.125 No Hit GGGGAGTTTGGCTGGGGCGGCACATCTGTTAAAAGATAACGCAGGTGTCC 5 0.125 No Hit GGTGGATACCTAGGCACCCAGAGACGAGGAAGGGCGTAGCAAGCGACGAA 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 0.025 0.0 0.0 0.0 0.0 2 0.025 0.0 0.0 0.0 0.0 3 0.025 0.0 0.0 0.0 0.0 4 0.05 0.0 0.0 0.0 0.0 5 0.05 0.0 0.0 0.0 0.0 6 0.05 0.0 0.0 0.0 0.0 7 0.05 0.0 0.0 0.0 0.0 8 0.05 0.0 0.0 0.0 0.0 9 0.05 0.0 0.0 0.0 0.0 10-11 0.05 0.0 0.0 0.0 0.0 12-13 0.05 0.0 0.0 0.0 0.0 14-15 0.05 0.0 0.0 0.0 0.0 16-17 0.05 0.0 0.0 0.0 0.0 18-19 0.05 0.0 0.0 0.0 0.0 20-21 0.1 0.0 0.0 0.0 0.0 22-23 0.1 0.0 0.0 0.0 0.0 24-25 0.1 0.0 0.0 0.0 0.0 26-27 0.1 0.0 0.0 0.0 0.0 28-29 0.1 0.0 0.0 0.0 0.0 30-31 0.1 0.0 0.0 0.0 0.0 32-33 0.1 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 0.1125 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 0.125 0.0 0.0 0.0 0.0 54-55 0.125 0.0 0.0 0.0 0.0 56-57 0.125 0.0 0.0 0.0 0.0 58-59 0.125 0.0 0.0 0.0 0.0 60-61 0.125 0.0 0.0 0.0 0.0 62-63 0.125 0.0 0.0 0.0 0.0 64-65 0.125 0.0 0.0 0.0 0.0 66-67 0.125 0.0 0.0 0.0 0.0 68-69 0.125 0.0 0.0 0.0 0.0 70-71 0.125 0.0 0.0 0.0 0.0 72-73 0.125 0.0 0.0 0.0 0.0 74-75 0.125 0.0 0.0 0.0 0.0 76-77 0.125 0.0 0.0 0.0 0.0 78-79 0.125 0.0 0.0 0.0 0.0 80-81 0.125 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position AAAAAAA 35 0.0071056574 27.697958 86-87 >>END_MODULE Rejected 143473 READS because READLEN < 1 Read 143473 spots for ERR6133353.sra Written 143473 spots for ERR6133353.sra Rejected 143473 READS because READLEN < 1 Read 143473 spots for ERR6133353.sra Written 143473 spots for ERR6133353.sra Rejected 143473 READS because READLEN < 1 Read 143473 spots for ERR6133353.sra Written 143473 spots for ERR6133353.sra Rejected 143473 READS because READLEN < 1 Read 143473 spots for ERR6133353.sra Written 143473 spots for ERR6133353.sra Rejected 143473 READS because READLEN < 1 Read 143473 spots for ERR6133353.sra Written 143473 spots for ERR6133353.sra Rejected 143473 READS because READLEN < 1 Read 143473 spots for ERR6133353.sra Written 143473 spots for ERR6133353.sra Rejected 143473 READS because READLEN < 1 Read 143473 spots for ERR6133353.sra Written 143473 spots for ERR6133353.sra Rejected 143473 READS because READLEN < 1 Read 143473 spots for ERR6133353.sra Written 143473 spots for ERR6133353.sra Rejected 143473 READS because READLEN < 1 Read 143473 spots for ERR6133353.sra Written 143473 spots for ERR6133353.sra Rejected 143473 READS because READLEN < 1 Read 143473 spots for ERR6133353.sra Written 143473 spots for ERR6133353.sra Rejected 143473 READS because READLEN < 1 Read 143473 spots for ERR6133353.sra Written 143473 spots for ERR6133353.sra Rejected 143473 READS because READLEN < 1 Read 143473 spots for ERR6133353.sra Written 143473 spots for ERR6133353.sra Rejected 143473 READS because READLEN < 1 Read 143473 spots for ERR6133353.sra Written 143473 spots for ERR6133353.sra Rejected 143473 READS because READLEN < 1 Read 143473 spots for ERR6133353.sra Written 143473 spots for ERR6133353.sra Rejected 143473 READS because READLEN < 1 Read 143473 spots for ERR6133353.sra Written 143473 spots for ERR6133353.sra Rejected 143473 READS because READLEN < 1 Read 143473 spots for ERR6133353.sra Written 143473 spots for ERR6133353.sra Rejected 143473 READS because READLEN < 1 Read 143473 spots for ERR6133353.sra Written 143473 spots for ERR6133353.sra Rejected 143473 READS because READLEN < 1 Read 143473 spots for ERR6133353.sra Written 143473 spots for ERR6133353.sra Rejected 143473 READS because READLEN < 1 Read 143473 spots for ERR6133353.sra Written 143473 spots for ERR6133353.sra Rejected 143477 READS because READLEN < 1 Read 143477 spots for ERR6133353.sra Written 143477 spots for ERR6133353.sra SRR ids: ['ERR6133353.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_1_vr9ojn ERR6133353.sra spots: 2869464 blocks: [[1, 143473], [143474, 286946], [286947, 430419], [430420, 573892], [573893, 717365], [717366, 860838], [860839, 1004311], [1004312, 1147784], [1147785, 1291257], [1291258, 1434730], [1434731, 1578203], [1578204, 1721676], [1721677, 1865149], [1865150, 2008622], [2008623, 2152095], [2152096, 2295568], [2295569, 2439041], [2439042, 2582514], [2582515, 2725987], [2725988, 2869464]] ERR6133353 file size 626828 ERR6133353 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 ERR6133353 ERR6133353_1.fastq Input file: ERR6133353_1.fastq trimmed: ERR6133353-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 01:16:38 2024 >> started Sat Dec 7 01:16:40 2024 >> done (1.613s) 2869464 reads processed; of these: 374 ( 0.01%) short reads filtered out after trimming by size control 8 ( 0.00%) empty reads filtered out after trimming by size control 2869082 (99.99%) reads available; of these: 18096 ( 0.63%) trimmed reads available after processing 2850986 (99.37%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 22 0.00% 19 81 0.00% 20 30 0.00% 21 31 0.00% 22 41 0.00% 23 33 0.00% 24 18 0.00% 25 17 0.00% 26 29 0.00% 27 24 0.00% 28 25 0.00% 29 135 0.00% 30 17 0.00% 31 41 0.00% 32 82 0.00% 33 37 0.00% 34 44 0.00% 35 76 0.00% 36 36 0.00% 37 25 0.00% 38 57 0.00% 39 125 0.00% 40 215 0.01% 41 52 0.00% 42 14 0.00% 43 44 0.00% 44 55 0.00% 45 25 0.00% 46 20 0.00% 47 21 0.00% 48 16 0.00% 49 13 0.00% 50 23 0.00% 51 201 0.01% 52 34 0.00% 53 11 0.00% 54 17 0.00% 55 17 0.00% 56 18 0.00% 57 50 0.00% 58 32 0.00% 59 26 0.00% 60 22 0.00% 61 42 0.00% 62 8 0.00% 63 10 0.00% 64 13 0.00% 65 16 0.00% 66 30 0.00% 67 42 0.00% 68 48 0.00% 69 133 0.00% 70 21636 0.75% 71 19712 0.69% 72 21651 0.75% 73 19911 0.69% 74 18737 0.65% 75 18294 0.64% 76 17950 0.63% 77 19609 0.68% 78 19835 0.69% 79 20200 0.70% 80 20450 0.71% 81 27094 0.94% 82 28260 0.98% 83 23155 0.81% 84 29371 1.02% 85 123 0.00% 86 160 0.01% 87 258 0.01% 88 352 0.01% 89 588 0.02% 90 1114 0.04% 91 2487 0.09% 92 8481 0.30% 93 2527360 88.09% 2869082 reads passed initial QC criterion=sequence-density sequence-density=5.02 sequence-density-rank=1 fanout-score=2.03 fanout-score-rank=34 prefix-density=5.07 prefix-fanout=2.0 sequence=CAAGGCTAAATAC criterion=fanout-score sequence-density=0.01 sequence-density-rank=41 fanout-score=52.13 fanout-score-rank=1 prefix-density=0.07 prefix-fanout=4.0 sequence=GAGGAAGAGACTTATAATATTGTGGCTGCTCATGGTTATTTTGGCCGATTAATCTTCCAATATGCTAGTTTCAACAACTCTCGTTCTTTACACTTCTTCTTGGCTGCTTGGCCTGTAGTAGGAATCTGGTTCACTGCTTTAGGTATTAGTACTATGGCGTTCAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCTTGGTATGGAAGTAATGCACGAACGTAATGCTCACAACTTCCCTCTAGATCTAGCTGCTCTTGAAGTTCCCGCTATTAATGGATAAGGTTTTTCCGCTAACATA 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 01:17:04 Started mapping on | Dec 07 01:17:04 Finished on | Dec 07 01:17:10 Mapping speed, Million of reads per hour | 1721.45 Number of input reads | 2869082 Average input read length | 91 UNIQUE READS: Uniquely mapped reads number | 1483979 Uniquely mapped reads % | 51.72% Average mapped length | 90.27 Number of splices: Total | 45824 Number of splices: Annotated (sjdb) | 36693 Number of splices: GT/AG | 43373 Number of splices: GC/AG | 1160 Number of splices: AT/AC | 61 Number of splices: Non-canonical | 1230 Mismatch rate per base, % | 0.42% Deletion rate per base | 0.04% Deletion average length | 1.72 Insertion rate per base | 0.02% Insertion average length | 1.69 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 1144451 % of reads mapped to multiple loci | 39.89% Number of reads mapped to too many loci | 153090 % of reads mapped to too many loci | 5.34% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 2.78% % of reads unmapped: other | 0.27% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 240652 240652 240652 N_multimapping 1144451 1144451 1144451 N_noFeature 136682 151696 1421815 N_ambiguous 55741 8539 308 UnstrandedReadsAssigned:1291556 PositiveStrandReadsAssigned:1323744 NegativeStrandReadsAssigned:61856 Dataset is classified positive stranded MeadianReadLen=93 20thPercentileLength=93 echo kmer=89 ERR6133353 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: ERR6133353-trimmed.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 2,869,082 reads, 1,929,251 reads pseudoaligned [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 936 rounds 52973 ERR6133353.ke.tsv 35125 ERR6133353.se.tsv 88098 total ==> ERR6133353.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 37 18.917 PNS24243 293 194 0 0 KQK14069 1603 1504 33 15.3911 KQK14071 474 375 0 0 ==> ERR6133353.se.tsv <== BRADI_1g14170v3 33 BRADI_1g53295v3 4 BRADI_1g59795v3 15 BRADI_1g07683v3 0 BRADI_1g00485v3 0 BRADI_1g20270v3 14 BRADI_1g74790v3 17 BRADI_1g09890v3 0 BRADI_1g77505v3 30 BRADI_1g48960v3 0 ERR6133353 completed mapping pipeline successfully