Starting /dee2/code/volunteer_pipeline.sh ERR6133360 current disk space = 1548199227392 free memory = 1405178424 ERR6133360 SRAfilesize 309e0d64c300f4e2929893f5d1748823 ERR6133360.sra ERR6133360.sra file validated ERR6133360 is single end ERR6133360 is conventional basespace ERR6133360 read1 length is 70-93 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename ERR6133360_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 36.3665 37.0 37.0 37.0 33.0 37.0 2 36.7725 37.0 37.0 37.0 37.0 37.0 3 36.73275 37.0 37.0 37.0 37.0 37.0 4 36.44525 37.0 37.0 37.0 37.0 37.0 5 36.505 37.0 37.0 37.0 37.0 37.0 6 36.65525 37.0 37.0 37.0 37.0 37.0 7 38.899 40.0 37.0 40.0 37.0 40.0 8 38.935 40.0 37.0 40.0 37.0 40.0 9 38.944 40.0 37.0 40.0 37.0 40.0 10-11 38.915375 40.0 37.0 40.0 37.0 40.0 12-13 38.909375 40.0 37.0 40.0 37.0 40.0 14-15 38.919250000000005 40.0 37.0 40.0 37.0 40.0 16-17 38.85325 40.0 37.0 40.0 37.0 40.0 18-19 38.811875 40.0 37.0 40.0 37.0 40.0 20-21 38.760999999999996 40.0 37.0 40.0 37.0 40.0 22-23 38.699625 40.0 37.0 40.0 37.0 40.0 24-25 38.6485 40.0 37.0 40.0 37.0 40.0 26-27 38.65725 40.0 37.0 40.0 37.0 40.0 28-29 38.687124999999995 40.0 37.0 40.0 37.0 40.0 30-31 38.600750000000005 40.0 37.0 40.0 37.0 40.0 32-33 38.506875 40.0 37.0 40.0 37.0 40.0 34-35 38.40825 40.0 37.0 40.0 37.0 40.0 36-37 38.342875 40.0 37.0 40.0 37.0 40.0 38-39 38.304249999999996 40.0 37.0 40.0 37.0 40.0 40-41 38.205375000000004 40.0 37.0 40.0 37.0 40.0 42-43 38.059375 40.0 37.0 40.0 37.0 40.0 44-45 37.91225 37.0 37.0 40.0 37.0 40.0 46-47 37.775125 37.0 37.0 40.0 37.0 40.0 48-49 37.6395 37.0 37.0 40.0 37.0 40.0 50-51 37.47675 37.0 37.0 40.0 37.0 40.0 52-53 37.290000000000006 37.0 37.0 40.0 35.0 40.0 54-55 37.110749999999996 37.0 37.0 38.5 33.0 40.0 56-57 36.95125 37.0 37.0 37.0 33.0 40.0 58-59 36.763875 37.0 37.0 37.0 33.0 40.0 60-61 36.649375 37.0 37.0 37.0 33.0 40.0 62-63 36.428625 37.0 37.0 37.0 33.0 37.0 64-65 36.278 37.0 37.0 37.0 33.0 37.0 66-67 36.16475 37.0 37.0 37.0 33.0 37.0 68-69 35.241625 35.0 35.0 37.0 33.0 37.0 70-71 35.44743327469213 37.0 35.0 37.0 33.0 37.0 72-73 35.957042914102146 37.0 37.0 37.0 33.0 37.0 74-75 35.92767352898302 37.0 37.0 37.0 33.0 37.0 76-77 35.87037163130603 37.0 37.0 37.0 33.0 37.0 78-79 35.90900248854638 37.0 37.0 37.0 33.0 37.0 80-81 35.83445041525137 37.0 37.0 37.0 33.0 37.0 82-83 35.778561540561924 37.0 37.0 37.0 33.0 37.0 84-85 35.732259048979074 37.0 37.0 37.0 33.0 37.0 86-87 35.57249931861543 37.0 37.0 37.0 33.0 37.0 88-89 35.66107931316435 37.0 37.0 37.0 33.0 37.0 90-91 35.58435541019351 37.0 37.0 37.0 33.0 37.0 92-93 35.47219950940311 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 2.0 23 5.0 24 4.0 25 3.0 26 5.0 27 9.0 28 13.0 29 13.0 30 13.0 31 39.0 32 37.0 33 59.0 34 81.0 35 166.0 36 700.0 37 1131.0 38 1646.0 39 71.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 64.36609152288072 8.902225556389096 8.452113028257065 18.27956989247312 2 47.4 27.950000000000003 14.85 9.8 3 30.0 38.175 17.849999999999998 13.975000000000001 4 32.425 26.200000000000003 20.625 20.75 5 26.125 27.200000000000003 26.924999999999997 19.75 6 20.325 33.725 27.725 18.224999999999998 7 33.1 26.825 22.55 17.525 8 28.000000000000004 28.849999999999998 26.375 16.775000000000002 9 24.275 27.250000000000004 30.075000000000003 18.4 10-11 24.587500000000002 28.4125 27.474999999999998 19.525000000000002 12-13 24.1625 29.125 28.4 18.3125 14-15 21.8 28.15 29.912499999999998 20.1375 16-17 24.637500000000003 29.099999999999998 25.624999999999996 20.6375 18-19 23.8875 26.187500000000004 29.525000000000002 20.4 20-21 25.1 26.674999999999997 27.487499999999997 20.7375 22-23 27.712500000000002 23.825 26.987499999999997 21.475 24-25 24.9125 26.6 27.8125 20.674999999999997 26-27 24.474999999999998 25.900000000000002 29.799999999999997 19.825 28-29 23.875 27.6875 27.537499999999998 20.9 30-31 25.0625 27.375 27.55 20.0125 32-33 24.5 25.5 29.6375 20.3625 34-35 23.3 28.3875 26.974999999999998 21.337500000000002 36-37 23.974999999999998 27.187499999999996 25.912499999999998 22.925 38-39 25.900000000000002 25.637500000000003 27.6875 20.775 40-41 25.650000000000002 26.35 26.937499999999996 21.0625 42-43 24.6875 29.325000000000003 27.0 18.987499999999997 44-45 22.925 28.225 28.537499999999998 20.3125 46-47 24.099999999999998 26.625 27.950000000000003 21.325 48-49 23.400000000000002 26.875 29.049999999999997 20.674999999999997 50-51 23.0875 27.437499999999996 28.1375 21.337500000000002 52-53 24.975 27.0125 27.975 20.0375 54-55 25.137500000000003 28.475 27.925 18.462500000000002 56-57 24.075 28.025 28.65 19.25 58-59 24.5375 28.037499999999998 27.750000000000004 19.675 60-61 25.9875 27.787499999999998 27.375 18.85 62-63 22.3875 28.65 29.562500000000004 19.400000000000002 64-65 23.8375 30.275000000000002 27.6875 18.2 66-67 24.15 28.15 28.0875 19.6125 68-69 22.2125 29.1625 27.8625 20.7625 70-71 24.902870033838827 27.346785311442535 27.10866023311192 20.64168442160672 72-73 24.65528146742568 28.349146110056928 28.260594560404805 18.734977862112586 74-75 24.29082545361615 27.229746997188858 28.251980577561973 20.227446971633018 76-77 22.343991748323877 28.442496132026818 28.236204228984015 20.97730789066529 78-79 24.219464402351402 27.51143043762247 28.608752449379494 19.660352710646638 80-81 22.674418604651162 30.40433403805497 27.180232558139533 19.741014799154332 82-83 21.609318516535012 29.615745079662602 27.420002677734633 21.354933726067745 84-85 22.211656024996604 26.92568944436897 30.07743513109632 20.785219399538107 86-87 22.594712455710003 28.550013627691467 28.454619787408014 20.400654129190514 88-89 21.886072499318615 29.149632052330336 28.27745979831017 20.686835650040884 90-91 23.09893704006541 29.040610520577815 26.80566911965113 21.054783319705642 92-93 21.62714636140638 30.75769964568002 26.95557372581085 20.659580267102754 >>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 0.0 18 0.0 19 1.0 20 2.5 21 1.5 22 3.0 23 7.5 24 9.0 25 8.5 26 10.5 27 17.5 28 29.5 29 35.0 30 40.0 31 49.0 32 57.0 33 74.0 34 81.5 35 93.5 36 121.0 37 144.0 38 166.0 39 179.5 40 218.5 41 228.5 42 256.5 43 306.0 44 248.5 45 198.0 46 190.5 47 181.5 48 160.5 49 145.5 50 153.0 51 153.0 52 135.0 53 129.5 54 130.0 55 97.0 56 80.0 57 88.0 58 66.0 59 32.5 60 23.0 61 23.0 62 23.0 63 16.0 64 9.0 65 9.5 66 7.0 67 6.5 68 18.0 69 20.0 70 8.5 71 3.0 72 2.0 73 0.5 74 0.0 75 0.0 76 0.5 77 0.5 78 0.0 79 0.0 80 0.5 81 0.5 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 0.0 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 21.0 71 18.0 72 17.0 73 20.0 74 22.0 75 15.0 76 18.0 77 26.0 78 31.0 79 18.0 80 20.0 81 22.0 82 35.0 83 25.0 84 23.0 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 3669.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 75.425 #Duplication Level Percentage of deduplicated Percentage of total 1 90.95127610208816 68.60000000000001 2 4.275770633079218 6.45 3 1.3921113689095126 3.15 4 0.8617832283725556 2.6 5 0.6297646668876367 2.375 6 0.39774610540271793 1.7999999999999998 7 0.39774610540271793 2.1 8 0.1325820351342393 0.8 9 0.23201856148491878 1.575 >10 0.7292011932383162 10.549999999999999 >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 GGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCTTGG 47 1.175 No Hit CAAGGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCT 41 1.0250000000000001 No Hit GGGAGAGCAATACAAGCGTTGTGCTGCTAGGCGAAGCGGTTGAGTGCCGC 36 0.8999999999999999 No Hit TACCTAGGCACCCAGAGACGAGGAAGGGCGTAGCAAGCGACGAAATGCTT 30 0.75 No Hit CAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAATACTTGGGCTG 30 0.75 No Hit GGGCGCGATCTTGCTCGTGAAGGTAATGAAATTATCCGAGCAGCTTGCAA 24 0.6 No Hit GAAGGTAATGAAATTATCCGAGCAGCTTGCAAATGGAGTCCTGAACTAGC 23 0.575 No Hit GGGTGAGAGCCCCGTCCGGCCCGGACCCTGTCGCCCCACGAGGCGCCGTC 20 0.5 No Hit GGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAA 17 0.42500000000000004 No Hit CAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAATACTTGGGCTGATAT 14 0.35000000000000003 No Hit GTAGTTGATAGTCAAGGTCGCGTTATTAATACTTGGGCTGATATCATCAA 14 0.35000000000000003 No Hit GGGTTGTTTGGGAATGCAGCCCAAATCGGGCGGTAGACTCCGTCCAAGGC 13 0.325 No Hit GGAGATTCCCAAATAGGTCAACCTTTTAAACTGCCTGCTGAATCCATGAG 13 0.325 No Hit GTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCTTGGT 13 0.325 No Hit TCAAAAGAGGAAAGGCTTGCGGTGGATACCTAGGCACCCAGAGACGAGGA 13 0.325 No Hit GGAAAAGAAAGCAAAAGCGATTCCCGTAGTAGCGGCGAGCGAAATGGGAG 12 0.3 No Hit GAGGAAGGGCGTAGCAAGCGACGAAATGCTTCGGGGAGTTGAAAATAAGC 11 0.27499999999999997 No Hit GGTAATGAAATTATCCGAGCAGCTTGCAAATGGAGTCCTGAACTAGCCGC 11 0.27499999999999997 No Hit GGATACCTAGGCACCCAGAGACGAGGAAGGGCGTAGCAAGCGACGAAATG 10 0.25 No Hit GGAATCCCGTGTGAATCAGCAAGGACCACCTTGCAAGGCTAAATACTCCT 10 0.25 No Hit AGGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCTTG 10 0.25 No Hit CAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAGGTC 10 0.25 No Hit GGCGTTCAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTC 9 0.22499999999999998 No Hit GGGCGTAGCAAGCGACGAAATGCTTCGGGGAGTTGAAAATAAGCATAGAT 9 0.22499999999999998 No Hit GTAGTAGGAATCTGGTTCACTGCTTTAGGTATTAGTACTATGGCGTTCAA 9 0.22499999999999998 No Hit GGAGTTGAAAATAAGCATAGATCCGGAGATTCCCAAATAGGTCAACCTTT 9 0.22499999999999998 No Hit GATCTTGCTCGTGAAGGTAATGAAATTATCCGAGCAGCTTGCAAATGGAG 9 0.22499999999999998 No Hit AAGGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCTT 9 0.22499999999999998 No Hit CTGTAGTTGATAGTCAAGGTCGCGTTATTAATACTTGGGCTGATATCATC 9 0.22499999999999998 No Hit GGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGTG 8 0.2 No Hit GGGCTGATATCATCAACCGTGCTAATCTTGGTATGGAAGTAATGCACGAA 8 0.2 No Hit GGTGGATACCTAGGCACCCAGAGACGAGGAAGGGCGTAGCAAGCGACGAA 8 0.2 No Hit GGGGCACGTGGAATCCCGTGTGAATCAGCAAGGACCACCTTGCAAGGCTA 8 0.2 No Hit GCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCTTGGTATG 7 0.17500000000000002 No Hit GGGCACGTGGAATCCCGTGTGAATCAGCAAGGACCACCTTGCAAGGCTAA 7 0.17500000000000002 No Hit GGAGTCCTGAACTAGCCGCAGCTTGTGAAGTATGGAAGGCGATCAAATTC 7 0.17500000000000002 No Hit GGAGGGTGAGAGCCCCGTCCGGCCCGGACCCTGTCGCCCCACGAGGCGCC 7 0.17500000000000002 No Hit GTAGCAAGCGACGAAATGCTTCGGGGAGTTGAAAATAAGCATAGATCCGG 7 0.17500000000000002 No Hit GGCGCGATCTTGCTCGTGAAGGTAATGAAATTATCCGAGCAGCTTGCAAA 7 0.17500000000000002 No Hit GTTGATAGTCAAGGTCGCGTTATTAATACTTGGGCTGATATCATCAACCG 7 0.17500000000000002 No Hit GGCACCCAGAGACGAGGAAGGGCGTAGCAAGCGACGAAATGCTTCGGGGA 7 0.17500000000000002 No Hit GGAGCAGCCTAAACCGTGAAAACGGGGTTGTGGGAGAGCAATACAAGCGT 7 0.17500000000000002 No Hit GTGGAATCCCGTGTGAATCAGCAAGGACCACCTTGCAAGGCTAAATACTC 7 0.17500000000000002 No Hit GGGGAGTTGAAAATAAGCATAGATCCGGAGATTCCCAAATAGGTCAACCT 7 0.17500000000000002 No Hit GGGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGT 7 0.17500000000000002 No Hit GCAAGGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATC 6 0.15 No Hit CAAATAGGTCAACCTTTTAAACTGCCTGCTGAATCCATGAGCAGGCAAGA 6 0.15 No Hit GGGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCTTG 6 0.15 No Hit GTACTATGGCGTTCAACCTAAATGGATTCAATTTCAACCAATCTGTAGTT 6 0.15 No Hit GTAATGAAATTATCCGAGCAGCTTGCAAATGGAGTCCTGAACTAGCCGCA 6 0.15 No Hit GGGAATTTCCGGTGGAGCGGTGAAATGCATTGAGATCGGAAAGAACACCA 6 0.15 No Hit GCAGCTTGCAAATGGAGTCCTGAACTAGCCGCAGCTTGTGAAGTATGGAA 6 0.15 No Hit GAGGAAAGGCTTGCGGTGGATACCTAGGCACCCAGAGACGAGGAAGGGCG 6 0.15 No Hit AGTCAAGGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAA 6 0.15 No Hit GGGGATGATTCTGTATTACAATTTGGTGGAGGAACTTTAGGACATCCTTG 6 0.15 No Hit GGAGAGCAATACAAGCGTTGTGCTGCTAGGCGAAGCGGTTGAGTGCCGCA 6 0.15 No Hit GGGACGCATGCAACGACCATCTACATATAGCTACTCGATCTACCGCTACC 6 0.15 No Hit GGCTGATATCATCAACCGTGCTAATCTTGGTATGGAAGTAATGCACGAAC 5 0.125 No Hit CGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCTTGGTAT 5 0.125 No Hit CAATTTCAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAATACTT 5 0.125 No Hit GGGGCAGAGGGAATTTCCGGTGGAGCGGTGAAATGCATTGAGATCGGAAA 5 0.125 No Hit GGGATGGAGCGACAGAAGTATGGAAATAGGATAAGGTAGCGGCGAGACGA 5 0.125 No Hit CGAGTCGGGTTGTTTGGGAATGCAGCCCAAATCGGGCGGTAGACTCCGTC 5 0.125 No Hit GGGATGATTCTGTATTACAATTTGGTGGAGGAACTTTAGGACATCCTTGG 5 0.125 No Hit GGTCAACCTTTTAAACTGCCTGCTGAATCCATGAGCAGGCAAGAGACAAC 5 0.125 No Hit GCAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAATACTTGGGCT 5 0.125 No Hit CAACGAGTCGGGTTGTTTGGGAATGCAGCCCAAATCGGGCGGTAGACTCC 5 0.125 No Hit GATAGTCAAGGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGC 5 0.125 No Hit GGAGTACGGTAGGGGCAGAGGGAATTTCCGGTGGAGCGGTGAAATGCATT 5 0.125 No Hit CGAGGAAGGGCGTAGCAAGCGACGAAATGCTTCGGGGAGTTGAAAATAAG 5 0.125 No Hit GTTGTTTGGGAATGCAGCCCAAATCGGGCGGTAGACTCCGTCCAAGGCTA 5 0.125 No Hit CGGGGAGTTGAAAATAAGCATAGATCCGGAGATTCCCAAATAGGTCAACC 5 0.125 No Hit CGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCTTGGTATGG 5 0.125 No Hit CACGAACGTAATGCTCACAACTTCCCTCTAGATCTAGCTGCTCTTGAAGT 5 0.125 No Hit GGTTGAGTGCCGCACCCTAGATGGCTAAAGTCCAGTAGCCGAAAGCATCA 5 0.125 No Hit CGTAATGCTCACAACTTCCCTCTAGATCTAGCTGCTCTTGAAGTTCCCGC 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 0.025 0.0 0.0 0.0 0.0 60-61 0.025 0.0 0.0 0.0 0.0 62-63 0.025 0.0 0.0 0.0 0.0 64-65 0.025 0.0 0.0 0.0 0.0 66-67 0.025 0.0 0.0 0.0 0.0 68-69 0.025 0.0 0.0 0.0 0.0 70-71 0.025 0.0 0.0 0.0 0.0 72-73 0.025 0.0 0.0 0.0 0.0 74-75 0.025 0.0 0.0 0.0 0.0 76-77 0.025 0.0 0.0 0.0 0.0 78-79 0.025 0.0 0.0 0.0 0.0 80-81 0.025 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content pass >>END_MODULE Rejected 151854 READS because READLEN < 1 Read 151854 spots for ERR6133360.sra Written 151854 spots for ERR6133360.sra Rejected 151854 READS because READLEN < 1 Read 151854 spots for ERR6133360.sra Written 151854 spots for ERR6133360.sra Rejected 151854 READS because READLEN < 1 Read 151854 spots for ERR6133360.sra Written 151854 spots for ERR6133360.sra Rejected 151854 READS because READLEN < 1 Read 151854 spots for ERR6133360.sra Written 151854 spots for ERR6133360.sra Rejected 151873 READS because READLEN < 1 Read 151873 spots for ERR6133360.sra Written 151873 spots for ERR6133360.sra Rejected 151854 READS because READLEN < 1 Read 151854 spots for ERR6133360.sra Written 151854 spots for ERR6133360.sra Rejected 151854 READS because READLEN < 1 Read 151854 spots for ERR6133360.sra Written 151854 spots for ERR6133360.sra Rejected 151854 READS because READLEN < 1 Read 151854 spots for ERR6133360.sra Written 151854 spots for ERR6133360.sra Rejected 151854 READS because READLEN < 1 Read 151854 spots for ERR6133360.sra Written 151854 spots for ERR6133360.sra Rejected 151854 READS because READLEN < 1 Read 151854 spots for ERR6133360.sra Written 151854 spots for ERR6133360.sra Rejected 151854 READS because READLEN < 1 Read 151854 spots for ERR6133360.sra Written 151854 spots for ERR6133360.sra Rejected 151854 READS because READLEN < 1 Read 151854 spots for ERR6133360.sra Written 151854 spots for ERR6133360.sra Rejected 151854 READS because READLEN < 1 Read 151854 spots for ERR6133360.sra Written 151854 spots for ERR6133360.sra Rejected 151854 READS because READLEN < 1 Read 151854 spots for ERR6133360.sra Written 151854 spots for ERR6133360.sra Rejected 151854 READS because READLEN < 1 Read 151854 spots for ERR6133360.sra Written 151854 spots for ERR6133360.sra Rejected 151854 READS because READLEN < 1 Read 151854 spots for ERR6133360.sra Written 151854 spots for ERR6133360.sra Rejected 151854 READS because READLEN < 1 Read 151854 spots for ERR6133360.sra Written 151854 spots for ERR6133360.sra Rejected 151854 READS because READLEN < 1 Read 151854 spots for ERR6133360.sra Written 151854 spots for ERR6133360.sra Rejected 151854 READS because READLEN < 1 Read 151854 spots for ERR6133360.sra Written 151854 spots for ERR6133360.sra Rejected 151854 READS because READLEN < 1 Read 151854 spots for ERR6133360.sra Written 151854 spots for ERR6133360.sra SRR ids: ['ERR6133360.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_mergutmf ERR6133360.sra spots: 3037099 blocks: [[1, 151854], [151855, 303708], [303709, 455562], [455563, 607416], [607417, 759270], [759271, 911124], [911125, 1062978], [1062979, 1214832], [1214833, 1366686], [1366687, 1518540], [1518541, 1670394], [1670395, 1822248], [1822249, 1974102], [1974103, 2125956], [2125957, 2277810], [2277811, 2429664], [2429665, 2581518], [2581519, 2733372], [2733373, 2885226], [2885227, 3037099]] ERR6133360 file size 667141 ERR6133360 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 ERR6133360 ERR6133360_1.fastq Input file: ERR6133360_1.fastq trimmed: ERR6133360-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 01:27:07 2024 >> started Sat Dec 7 01:27:12 2024 >> done (4.496s) 3037099 reads processed; of these: 307 ( 0.01%) short reads filtered out after trimming by size control 10 ( 0.00%) empty reads filtered out after trimming by size control 3036782 (99.99%) reads available; of these: 16536 ( 0.54%) trimmed reads available after processing 3020246 (99.46%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 15 0.00% 19 57 0.00% 20 34 0.00% 21 13 0.00% 22 30 0.00% 23 18 0.00% 24 18 0.00% 25 8 0.00% 26 20 0.00% 27 14 0.00% 28 37 0.00% 29 182 0.01% 30 7 0.00% 31 18 0.00% 32 63 0.00% 33 22 0.00% 34 14 0.00% 35 70 0.00% 36 14 0.00% 37 23 0.00% 38 33 0.00% 39 89 0.00% 40 117 0.00% 41 44 0.00% 42 12 0.00% 43 31 0.00% 44 39 0.00% 45 19 0.00% 46 12 0.00% 47 12 0.00% 48 11 0.00% 49 10 0.00% 50 17 0.00% 51 114 0.00% 52 16 0.00% 53 10 0.00% 54 10 0.00% 55 13 0.00% 56 10 0.00% 57 37 0.00% 58 23 0.00% 59 27 0.00% 60 24 0.00% 61 22 0.00% 62 11 0.00% 63 10 0.00% 64 8 0.00% 65 18 0.00% 66 22 0.00% 67 39 0.00% 68 62 0.00% 69 123 0.00% 70 14887 0.49% 71 13639 0.45% 72 14438 0.48% 73 13552 0.45% 74 13108 0.43% 75 12548 0.41% 76 12401 0.41% 77 13837 0.46% 78 13770 0.45% 79 14575 0.48% 80 15154 0.50% 81 19401 0.64% 82 20180 0.66% 83 16945 0.56% 84 20217 0.67% 85 133 0.00% 86 182 0.01% 87 239 0.01% 88 356 0.01% 89 634 0.02% 90 1068 0.04% 91 2438 0.08% 92 8044 0.26% 93 2793314 91.98% 3036782 reads passed initial QC criterion=sequence-density sequence-density=3.48 sequence-density-rank=1 fanout-score=2.04 fanout-score-rank=30 prefix-density=3.54 prefix-fanout=2.0 sequence=CAAGGCTAAATAC criterion=fanout-score sequence-density=0.01 sequence-density-rank=32 fanout-score=60.00 fanout-score-rank=1 prefix-density=0.08 prefix-fanout=4.3 sequence=GAAGAAATTAGAGTGCTCAAAGCAAGCCATCGCTCTGGATACATTAGCATGGGATAACATCATAGGATTCCGGTCCTATTGTGTTGGCCTTCGGGATCGGAGTAATGATTAATAGGGACAGTCGGGGGCATTCGTATTTCATAGTCAGAGGTGAAATTCTTGGATTTATGAAAGACGAACAACTGCGAAAGCATTTGCCAAGGATGTTTTCATTAATCAAGAACGAAAGTTGGGGGCTCGAAGACGATCAGATACCGT 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 01:28:30 Started mapping on | Dec 07 01:28:31 Finished on | Dec 07 01:28:38 Mapping speed, Million of reads per hour | 1561.77 Number of input reads | 3036782 Average input read length | 91 UNIQUE READS: Uniquely mapped reads number | 1483822 Uniquely mapped reads % | 48.86% Average mapped length | 91.04 Number of splices: Total | 44437 Number of splices: Annotated (sjdb) | 35888 Number of splices: GT/AG | 42857 Number of splices: GC/AG | 959 Number of splices: AT/AC | 60 Number of splices: Non-canonical | 561 Mismatch rate per base, % | 0.25% Deletion rate per base | 0.03% Deletion average length | 1.42 Insertion rate per base | 0.00% Insertion average length | 1.39 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 1342246 % of reads mapped to multiple loci | 44.20% Number of reads mapped to too many loci | 139287 % of reads mapped to too many loci | 4.59% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 2.16% % of reads unmapped: other | 0.20% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 210714 210714 210714 N_multimapping 1342246 1342246 1342246 N_noFeature 122298 137477 1418997 N_ambiguous 59640 10091 239 UnstrandedReadsAssigned:1301884 PositiveStrandReadsAssigned:1336254 NegativeStrandReadsAssigned:64586 Dataset is classified positive stranded MeadianReadLen=93 20thPercentileLength=93 echo kmer=89 ERR6133360 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: ERR6133360-trimmed.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 3,036,782 reads, 2,096,476 reads pseudoaligned [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 927 rounds 52973 ERR6133360.ke.tsv 35125 ERR6133360.se.tsv 88098 total ==> ERR6133360.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 32 14.9403 PNS24243 293 194 0 0 KQK14069 1603 1504 179.157 76.3046 KQK14071 474 375 0 0 ==> ERR6133360.se.tsv <== BRADI_1g14170v3 192 BRADI_1g53295v3 11 BRADI_1g59795v3 10 BRADI_1g07683v3 0 BRADI_1g00485v3 0 BRADI_1g20270v3 13 BRADI_1g74790v3 7 BRADI_1g09890v3 0 BRADI_1g77505v3 29 BRADI_1g48960v3 0 ERR6133360 completed mapping pipeline successfully