Starting /dee2/code/volunteer_pipeline.sh ERR6133406 current disk space = 1547250089984 free memory = 1598104784 ERR6133406 SRAfilesize c31f9bb960dea887b34f49fae511f487 ERR6133406.sra ERR6133406.sra file validated ERR6133406 is single end ERR6133406 is conventional basespace ERR6133406 read1 length is 70-93 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename ERR6133406_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 fail #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 28.9905 33.0 27.0 33.0 15.0 37.0 2 33.5765 33.0 33.0 37.0 27.0 37.0 3 33.78575 37.0 33.0 37.0 27.0 37.0 4 33.8285 37.0 33.0 37.0 27.0 37.0 5 34.0145 37.0 33.0 37.0 27.0 37.0 6 34.354 37.0 33.0 37.0 27.0 37.0 7 35.3365 37.0 33.0 40.0 27.0 40.0 8 35.47225 37.0 33.0 40.0 33.0 40.0 9 35.56875 37.0 33.0 40.0 33.0 40.0 10-11 35.39975 37.0 33.0 40.0 30.0 40.0 12-13 35.175125 37.0 33.0 38.5 27.0 40.0 14-15 35.205875 37.0 33.0 37.0 27.0 40.0 16-17 34.951 37.0 33.0 37.0 27.0 40.0 18-19 34.7745 37.0 33.0 37.0 27.0 40.0 20-21 33.912499999999994 37.0 33.0 37.0 27.0 40.0 22-23 33.733875 37.0 33.0 37.0 24.5 40.0 24-25 33.35 37.0 33.0 37.0 22.0 40.0 26-27 33.390375 37.0 33.0 37.0 22.0 40.0 28-29 32.7715 37.0 33.0 37.0 22.0 40.0 30-31 32.699625 37.0 33.0 37.0 22.0 40.0 32-33 32.281 33.0 33.0 37.0 22.0 40.0 34-35 31.55625 33.0 27.0 37.0 18.5 40.0 36-37 31.174750000000003 33.0 27.0 37.0 15.0 37.0 38-39 31.3305 33.0 27.0 37.0 22.0 37.0 40-41 31.41 33.0 27.0 37.0 22.0 38.5 42-43 31.009875 33.0 27.0 37.0 15.0 40.0 44-45 30.810125 33.0 27.0 37.0 15.0 37.0 46-47 30.09925 33.0 27.0 37.0 15.0 37.0 48-49 30.093875 33.0 27.0 37.0 15.0 37.0 50-51 29.598375 33.0 27.0 37.0 15.0 37.0 52-53 29.365625 33.0 27.0 37.0 15.0 37.0 54-55 29.25475 33.0 27.0 37.0 15.0 37.0 56-57 28.433625 33.0 24.5 33.0 15.0 37.0 58-59 28.17275 33.0 27.0 33.0 15.0 37.0 60-61 28.031125 33.0 24.5 33.0 15.0 37.0 62-63 27.525375 33.0 22.0 33.0 15.0 37.0 64-65 27.067125 33.0 22.0 33.0 10.5 37.0 66-67 26.5415 30.0 22.0 33.0 6.0 37.0 68-69 26.271375 27.0 22.0 33.0 10.5 35.0 70-71 28.152056629834256 33.0 27.0 33.0 15.0 37.0 72-73 28.651458734416792 33.0 27.0 33.0 15.0 37.0 74-75 28.513696814145526 33.0 27.0 33.0 15.0 37.0 76-77 28.16847870997038 33.0 27.0 33.0 15.0 37.0 78-79 27.548423904941178 33.0 27.0 33.0 10.5 37.0 80-81 26.707244131094907 33.0 22.0 33.0 6.0 37.0 82-83 26.0955661591711 33.0 22.0 33.0 2.0 37.0 84-85 25.361244152059747 33.0 18.5 33.0 2.0 37.0 86-87 24.439890710382514 33.0 15.0 33.0 2.0 35.0 88-89 23.733879781420764 30.0 10.5 33.0 2.0 35.0 90-91 22.62349726775956 27.0 2.0 33.0 2.0 35.0 92-93 21.311475409836063 27.0 2.0 33.0 2.0 33.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 20 99.0 21 104.0 22 142.0 23 158.0 24 164.0 25 211.0 26 210.0 27 247.0 28 251.0 29 270.0 30 257.0 31 270.0 32 288.0 33 284.0 34 295.0 35 306.0 36 251.0 37 156.0 38 37.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 68.475 8.25 8.4 14.875 2 50.64999999999999 23.95 14.325 11.075 3 33.25 34.8 17.9 14.05 4 27.375 28.749999999999996 21.725 22.15 5 26.150000000000002 26.424999999999997 27.700000000000003 19.725 6 18.3 36.175000000000004 26.3 19.225 7 35.275 26.424999999999997 21.6 16.7 8 25.5 28.799999999999997 25.724999999999998 19.975 9 22.3 29.375 28.9 19.425 10-11 22.975 28.3125 30.4375 18.275 12-13 22.3375 29.65 27.6625 20.349999999999998 14-15 19.825 31.275 29.125 19.775000000000002 16-17 24.575 29.15 23.925 22.35 18-19 23.3625 25.087500000000002 31.362499999999997 20.1875 20-21 25.112499999999997 24.887500000000003 30.162499999999998 19.8375 22-23 28.8875 22.8125 28.225 20.075000000000003 24-25 23.7125 26.400000000000002 28.575 21.3125 26-27 25.025 24.675 29.4125 20.8875 28-29 23.6125 27.712500000000002 29.325000000000003 19.35 30-31 28.4375 26.775 25.0 19.787499999999998 32-33 25.7625 24.4875 28.4375 21.3125 34-35 22.75 32.2625 25.825 19.162499999999998 36-37 25.55 25.7125 25.2125 23.525 38-39 29.3875 23.8875 27.125 19.6 40-41 24.1375 25.424999999999997 30.6875 19.75 42-43 26.237500000000004 29.025000000000002 26.5375 18.2 44-45 23.7 27.150000000000002 29.849999999999998 19.3 46-47 26.1625 25.112499999999997 26.387500000000003 22.3375 48-49 24.7375 25.074999999999996 28.5625 21.625 50-51 21.0375 29.849999999999998 27.325 21.7875 52-53 23.7 27.3625 25.5125 23.425 54-55 23.0125 26.4625 29.975 20.549999999999997 56-57 25.724999999999998 28.8875 26.900000000000002 18.4875 58-59 22.475 29.512500000000003 27.8125 20.200000000000003 60-61 28.8625 26.1625 25.874999999999996 19.1 62-63 21.775 27.325 29.362500000000004 21.5375 64-65 20.9 33.7375 27.0 18.3625 66-67 24.8125 29.812499999999996 25.775 19.6 68-69 20.2125 28.1375 28.1 23.549999999999997 70-71 23.66574793284891 29.20320721623653 25.770483588073162 21.360561262841394 72-73 25.288376220053237 26.492584611484343 30.029154518950435 18.189884649511978 74-75 25.0864387245486 29.004994237418362 27.570751696760148 18.33781534127289 76-77 22.7278603749192 25.921137685843572 26.464124111182937 24.8868778280543 78-79 25.133899412148924 27.759634225996084 27.563683866753756 19.542782495101243 80-81 21.274626470977125 34.1795583763057 26.52386619066508 18.021948962052097 82-83 23.66871822317367 27.48193738292748 25.515119079475518 23.334225314423335 84-85 21.432454471323727 25.727099755368304 32.277792878499596 20.562652894808373 86-87 21.625683060109292 29.890710382513664 25.997267759562842 22.486338797814206 88-89 20.423497267759565 29.4672131147541 28.72950819672131 21.379781420765028 90-91 24.69945355191257 30.92896174863388 25.437158469945352 18.934426229508198 92-93 19.76775956284153 33.060109289617486 26.475409836065573 20.69672131147541 >>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 0.5 16 1.5 17 2.5 18 3.5 19 3.0 20 2.0 21 2.5 22 3.5 23 5.5 24 5.0 25 5.5 26 13.5 27 18.5 28 15.5 29 15.0 30 30.5 31 49.0 32 56.5 33 64.5 34 71.0 35 88.0 36 122.0 37 180.5 38 222.0 39 198.0 40 209.0 41 234.5 42 232.0 43 238.0 44 207.0 45 177.5 46 168.0 47 137.5 48 127.0 49 128.0 50 134.5 51 137.5 52 119.0 53 130.5 54 198.5 55 194.0 56 109.5 57 81.0 58 72.0 59 48.5 60 29.0 61 18.5 62 9.5 63 8.0 64 9.0 65 8.0 66 7.5 67 6.5 68 10.5 69 13.5 70 10.5 71 9.0 72 5.0 73 1.5 74 2.0 75 1.0 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 18.0 71 24.0 72 27.0 73 20.0 74 13.0 75 19.0 76 23.0 77 17.0 78 23.0 79 27.0 80 15.0 81 26.0 82 22.0 83 28.0 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 3660.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 72.55 #Duplication Level Percentage of deduplicated Percentage of total 1 91.62646450723639 66.475 2 3.9283252929014476 5.7 3 1.0337698139214335 2.25 4 0.9993108201240523 2.9000000000000004 5 0.6202618883528601 2.25 6 0.2412129565816678 1.05 7 0.2756719503790489 1.4000000000000001 8 0.13783597518952445 0.8 9 0.2412129565816678 1.575 >10 0.861474844934528 11.525 >50 0.0 0.0 >100 0.03445899379738111 4.075 >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 163 4.075 No Hit GGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCTTGG 44 1.0999999999999999 No Hit GGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAA 41 1.0250000000000001 No Hit CAAGGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCT 29 0.7250000000000001 No Hit GGGCTGATATCATCAACCGTGCTAATCTTGGTATGGAAGTAATGCACGAA 24 0.6 No Hit TACCTAGGCACCCAGAGACGAGGAAGGGCGTAGCAAGCGACGAAATGCTT 24 0.6 No Hit CAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAATACTTGGGCTGATAT 23 0.575 No Hit CAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAGGTC 23 0.575 No Hit CAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAATACTTGGGCTG 21 0.525 No Hit GGCGTTCAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTC 19 0.475 No Hit GGGCGCGATCTTGCTCGTGAAGGTAATGAAATTATCCGAGCAGCTTGCAA 18 0.44999999999999996 No Hit TCAAAAGAGGAAAGGCTTGCGGTGGATACCTAGGCACCCAGAGACGAGGA 18 0.44999999999999996 No Hit GGGCACGTGGAATCCCGTGTGAATCAGCAAGGACCACCTTGCAAGGCTAA 17 0.42500000000000004 No Hit GGGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGT 17 0.42500000000000004 No Hit GGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGTG 14 0.35000000000000003 No Hit GGGTTGTTTGGGAATGCAGCCCAAATCGGGCGGTAGACTCCGTCCAAGGC 14 0.35000000000000003 No Hit GGGATGATTCTGTATTACAATTTGGTGGAGGAACTTTAGGACATCCTTGG 13 0.325 No Hit GTTCAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAG 13 0.325 No Hit GGGTGAGAGCCCCGTCCGGCCCGGACCCTGTCGCCCCACGAGGCGCCGTC 13 0.325 No Hit GCAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAATACTTGGGCT 12 0.3 No Hit GCAGCTTGCAAATGGAGTCCTGAACTAGCCGCAGCTTGTGAAGTATGGAA 12 0.3 No Hit GGAATCTGGTTCACTGCTTTAGGTATTAGTACTATGGCGTTCAACCTAAA 12 0.3 No Hit CAATTTCAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAATACTT 10 0.25 No Hit GGGGAGAGCAATACAAGCGTTGTGCTGCTAGGCGAAGCGGTTGAGTGCCG 10 0.25 No Hit GATTCAATTTCAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAAT 10 0.25 No Hit GAAGGTAATGAAATTATCCGAGCAGCTTGCAAATGGAGTCCTGAACTAGC 10 0.25 No Hit GCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCTTGGTATG 9 0.22499999999999998 No Hit GTATTAGTACTATGGCGTTCAACCTAAATGGATTCAATTTCAACCAATCT 9 0.22499999999999998 No Hit GTAGGAATCTGGTTCACTGCTTTAGGTATTAGTACTATGGCGTTCAACCT 9 0.22499999999999998 No Hit GTGGAATCCCGTGTGAATCAGCAAGGACCACCTTGCAAGGCTAAATACTC 9 0.22499999999999998 No Hit TCTCATGGAGAGTTCGATCCTGGCTCAGGATGAACGCTGGCGGCATGCTT 9 0.22499999999999998 No Hit GGATTTGTTAAATCAAATCCTTGGTTTAATAACGAACGGTGTTAACTTAC 9 0.22499999999999998 No Hit GGGGCACGTGGAATCCCGTGTGAATCAGCAAGGACCACCTTGCAAGGCTA 9 0.22499999999999998 No Hit GTAGTAGGAATCTGGTTCACTGCTTTAGGTATTAGTACTATGGCGTTCAA 8 0.2 No Hit GTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCTTGGT 8 0.2 No Hit GGAGCAGCCTAAACCGTGAAAACGGGGTTGTGGGAGAGCAATACAAGCGT 8 0.2 No Hit GGAAAAGAAAGCAAAAGCGATTCCCGTAGTAGCGGCGAGCGAAATGGGAG 8 0.2 No Hit GGTTCACTGCTTTAGGTATTAGTACTATGGCGTTCAACCTAAATGGATTC 7 0.17500000000000002 No Hit GGGAATGCAGCCCAAATCGGGCGGTAGACTCCGTCCAAGGCTAAATACAG 7 0.17500000000000002 No Hit GGGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCTTG 7 0.17500000000000002 No Hit GGAGTTGAAAATAAGCATAGATCCGGAGATTCCCAAATAGGTCAACCTTT 7 0.17500000000000002 No Hit GTAGTTGATAGTCAAGGTCGCGTTATTAATACTTGGGCTGATATCATCAA 7 0.17500000000000002 No Hit GGAGAGCAATACAAGCGTTGTGCTGCTAGGCGAAGCGGTTGAGTGCCGCA 7 0.17500000000000002 No Hit AACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAATACTTGGGCTGA 7 0.17500000000000002 No Hit GGTAATGAAATTATCCGAGCAGCTTGCAAATGGAGTCCTGAACTAGCCGC 7 0.17500000000000002 No Hit GGATACCTAGGCACCCAGAGACGAGGAAGGGCGTAGCAAGCGACGAAATG 6 0.15 No Hit CTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAGGTCGCGT 6 0.15 No Hit GGAATCCCGTGTGAATCAGCAAGGACCACCTTGCAAGGCTAAATACTCCT 6 0.15 No Hit GGGGTTGTGGGAGAGCAATACAAGCGTTGTGCTGCTAGGCGAAGCGGTTG 6 0.15 No Hit GGGTTGTGGGAGAGCAATACAAGCGTTGTGCTGCTAGGCGAAGCGGTTGA 6 0.15 No Hit GCAATTTCAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAATACT 6 0.15 No Hit GGGGAGTTGAAAATAAGCATAGATCCGGAGATTCCCAAATAGGTCAACCT 6 0.15 No Hit GGAGTCCTGAACTAGCCGCAGCTTGTGAAGTATGGAAGGCGATCAAATTC 5 0.125 No Hit GAGGAAGGGCGTAGCAAGCGACGAAATGCTTCGGGGAGTTGAAAATAAGC 5 0.125 No Hit GTACTATGGCGTTCAACCTAAATGGATTCAATTTCAACCAATCTGTAGTT 5 0.125 No Hit GTATGGAAGGCGATCAAATTCGAGTTCGCGCCGGTAGATACTATCGATTA 5 0.125 No Hit GGCCTGTAGTAGGAATCTGGTTCACTGCTTTAGGTATTAGTACTATGGCG 5 0.125 No Hit GGGCAGAGGGAATTTCCGGTGGAGCGGTGAAATGCATTGAGATCGGAAAG 5 0.125 No Hit GGGAGGGTGAGAGCCCCGTCCGGCCCGGACCCTGTCGCCCCACGAGGCGC 5 0.125 No Hit GTAATGCACGAACGTAATGCTCACAACTTCCCTCTAGATCTAGCTGCTCT 5 0.125 No Hit AGTCAAGGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAA 5 0.125 No Hit GATCCGGAGATTCCCAAATAGGTCAACCTTTTAAACTGCCTGCTGAATCC 5 0.125 No Hit CGAGGAAGGGCGTAGCAAGCGACGAAATGCTTCGGGGAGTTGAAAATAAG 5 0.125 No Hit TATTAATACTTGGGCTGATATCATCAACCGTGCTAATCTTGGTATGGAAG 5 0.125 No Hit GGCCCGGACCCTGTCGCCCCACGAGGCGCCGTCAACGAGTCGGGTTGTTT 5 0.125 No Hit GCGTTCAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTCA 5 0.125 No Hit GGAGTATCCTTGATATATAAATATATAGATAAATAGATTTAAATGGAAAA 5 0.125 No Hit CGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCTTGGTATGG 5 0.125 No Hit GGTGGATACCTAGGCACCCAGAGACGAGGAAGGGCGTAGCAAGCGACGAA 5 0.125 No Hit GGTTGTTTGGGAATGCAGCCCAAATCGGGCGGTAGACTCCGTCCAAGGCT 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 0.025 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 0.05 0.0 0.0 0.0 0.0 28-29 0.05 0.0 0.0 0.0 0.0 30-31 0.05 0.0 0.0 0.0 0.0 32-33 0.05 0.0 0.0 0.0 0.0 34-35 0.05 0.0 0.0 0.0 0.0 36-37 0.05 0.0 0.0 0.0 0.0 38-39 0.05 0.0 0.0 0.0 0.0 40-41 0.05 0.0 0.0 0.0 0.0 42-43 0.05 0.0 0.0 0.0 0.0 44-45 0.05 0.0 0.0 0.0 0.0 46-47 0.05 0.0 0.0 0.0 0.0 48-49 0.05 0.0 0.0 0.0 0.0 50-51 0.05 0.0 0.0 0.0 0.0 52-53 0.05 0.0 0.0 0.0 0.0 54-55 0.05 0.0 0.0 0.0 0.0 56-57 0.05 0.0 0.0 0.0 0.0 58-59 0.05 0.0 0.0 0.0 0.0 60-61 0.05 0.0 0.0 0.0 0.0 62-63 0.05 0.0 0.0 0.0 0.0 64-65 0.05 0.0 0.0 0.0 0.0 66-67 0.05 0.0 0.0 0.0 0.0 68-69 0.05 0.0 0.0 0.0 0.0 70-71 0.05 0.0 0.0 0.0 0.0 72-73 0.05 0.0 0.0 0.0 0.0 74-75 0.05 0.0 0.0 0.0 0.0 76-77 0.05 0.0 0.0 0.0 0.0 78-79 0.05 0.0 0.0 0.0 0.0 80-81 0.05 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content fail #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position GGAGAGC 35 5.620677E-10 84.9875 2 GCAATAC 35 5.620677E-10 84.9875 7 CAATACA 35 5.620677E-10 84.9875 8 GAGCAAT 35 5.620677E-10 84.9875 5 AGAGCAA 35 5.620677E-10 84.9875 4 GAGAGCA 35 5.620677E-10 84.9875 3 AATACAA 35 5.620677E-10 84.9875 9 AGCAATA 35 5.620677E-10 84.9875 6 GGGAGAG 40 1.6189006E-9 74.36406 1 CCGAAAG 35 6.8712325E-8 47.21528 76-77 AGCCGAA 35 7.679955E-8 46.568493 74-75 GCCGAAA 35 7.679955E-8 46.568493 74-75 TAGCCGA 35 9.5495125E-8 45.326668 72-73 GTTGAGT 30 2.8294598E-6 42.49375 38-39 GCTAGGC 30 2.8294598E-6 42.49375 26-27 GAAGCGG 30 2.8294598E-6 42.49375 32-33 GCGGTTG 30 2.8294598E-6 42.49375 36-37 GCGAAGC 30 2.8294598E-6 42.49375 30-31 TGCTGCT 35 1.6050035E-7 42.49375 22-23 CGAAGCG 30 2.8294598E-6 42.49375 32-33 >>END_MODULE Rejected 47787 READS because READLEN < 1 Read 47787 spots for ERR6133406.sra Written 47787 spots for ERR6133406.sra Rejected 47787 READS because READLEN < 1 Read 47787 spots for ERR6133406.sra Written 47787 spots for ERR6133406.sra Rejected 47787 READS because READLEN < 1 Read 47787 spots for ERR6133406.sra Written 47787 spots for ERR6133406.sra Rejected 47787 READS because READLEN < 1 Read 47787 spots for ERR6133406.sra Written 47787 spots for ERR6133406.sra Rejected 47787 READS because READLEN < 1 Read 47787 spots for ERR6133406.sra Written 47787 spots for ERR6133406.sra Rejected 47787 READS because READLEN < 1 Read 47787 spots for ERR6133406.sra Written 47787 spots for ERR6133406.sra Rejected 47787 READS because READLEN < 1 Read 47787 spots for ERR6133406.sra Written 47787 spots for ERR6133406.sra Rejected 47787 READS because READLEN < 1 Read 47787 spots for ERR6133406.sra Written 47787 spots for ERR6133406.sra Rejected 47787 READS because READLEN < 1 Read 47787 spots for ERR6133406.sra Written 47787 spots for ERR6133406.sra Rejected 47787 READS because READLEN < 1 Read 47787 spots for ERR6133406.sra Written 47787 spots for ERR6133406.sra Rejected 47787 READS because READLEN < 1 Read 47787 spots for ERR6133406.sra Written 47787 spots for ERR6133406.sra Rejected 47787 READS because READLEN < 1 Read 47787 spots for ERR6133406.sra Written 47787 spots for ERR6133406.sra Rejected 47787 READS because READLEN < 1 Read 47787 spots for ERR6133406.sra Written 47787 spots for ERR6133406.sra Rejected 47787 READS because READLEN < 1 Read 47787 spots for ERR6133406.sra Written 47787 spots for ERR6133406.sra Rejected 47787 READS because READLEN < 1 Read 47787 spots for ERR6133406.sra Written 47787 spots for ERR6133406.sra Rejected 47787 READS because READLEN < 1 Read 47787 spots for ERR6133406.sra Written 47787 spots for ERR6133406.sra Rejected 47787 READS because READLEN < 1 Read 47787 spots for ERR6133406.sra Written 47787 spots for ERR6133406.sra Rejected 47787 READS because READLEN < 1 Read 47787 spots for ERR6133406.sra Written 47787 spots for ERR6133406.sra Rejected 47787 READS because READLEN < 1 Read 47787 spots for ERR6133406.sra Written 47787 spots for ERR6133406.sra Rejected 47800 READS because READLEN < 1 Read 47800 spots for ERR6133406.sra Written 47800 spots for ERR6133406.sra SRR ids: ['ERR6133406.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_ik4flynx ERR6133406.sra spots: 955753 blocks: [[1, 47787], [47788, 95574], [95575, 143361], [143362, 191148], [191149, 238935], [238936, 286722], [286723, 334509], [334510, 382296], [382297, 430083], [430084, 477870], [477871, 525657], [525658, 573444], [573445, 621231], [621232, 669018], [669019, 716805], [716806, 764592], [764593, 812379], [812380, 860166], [860167, 907953], [907954, 955753]] ERR6133406 file size 208254 ERR6133406 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 ERR6133406 ERR6133406_1.fastq Input file: ERR6133406_1.fastq trimmed: ERR6133406-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 04:23:14 2024 >> started Sat Dec 7 04:23:21 2024 >> done (7.015s) 955753 reads processed; of these: 28 ( 0.00%) short reads filtered out after trimming by size control 7 ( 0.00%) empty reads filtered out after trimming by size control 955718 (100.00%) reads available; of these: 244462 (25.58%) trimmed reads available after processing 711256 (74.42%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 7 0.00% 19 15 0.00% 20 3 0.00% 21 4 0.00% 22 6 0.00% 23 3 0.00% 24 1 0.00% 25 2 0.00% 26 1 0.00% 27 1 0.00% 28 15 0.00% 29 97 0.01% 30 4 0.00% 31 5 0.00% 32 12 0.00% 33 5 0.00% 34 3 0.00% 35 8 0.00% 36 8 0.00% 37 6 0.00% 38 11 0.00% 39 12 0.00% 40 24 0.00% 41 14 0.00% 42 13 0.00% 43 19 0.00% 44 14 0.00% 45 22 0.00% 46 34 0.00% 47 40 0.00% 48 64 0.01% 49 98 0.01% 50 129 0.01% 51 165 0.02% 52 222 0.02% 53 290 0.03% 54 374 0.04% 55 551 0.06% 56 697 0.07% 57 1119 0.12% 58 755 0.08% 59 929 0.10% 60 1053 0.11% 61 1270 0.13% 62 1417 0.15% 63 1442 0.15% 64 1617 0.17% 65 1758 0.18% 66 1811 0.19% 67 1834 0.19% 68 1688 0.18% 69 1730 0.18% 70 6764 0.71% 71 6872 0.72% 72 7951 0.83% 73 8440 0.88% 74 8457 0.88% 75 9197 0.96% 76 9418 0.99% 77 10525 1.10% 78 11163 1.17% 79 11971 1.25% 80 12330 1.29% 81 14671 1.54% 82 15661 1.64% 83 15669 1.64% 84 17123 1.79% 85 12332 1.29% 86 12583 1.32% 87 13885 1.45% 88 16692 1.75% 89 17733 1.86% 90 18934 1.98% 91 20700 2.17% 92 17301 1.81% 93 637924 66.75% 955718 reads passed initial QC criterion=sequence-density sequence-density=4.36 sequence-density-rank=1 fanout-score=2.05 fanout-score-rank=24 prefix-density=4.46 prefix-fanout=2.0 sequence=CAAGGCTAAATAC criterion=fanout-score sequence-density=0.01 sequence-density-rank=43 fanout-score=25.49 fanout-score-rank=1 prefix-density=0.22 prefix-fanout=1.3 sequence=GAAATAGGATCTAAACAAGGAAGAGCACTTGCCATTCGTTGGTTATTAGAAGCATCCCAAAAGCGTCCGGGTCGAAATATGGCTTTCAAATTAAGTTCCGAATTAGTAGATGCTGCCAAAGGGAGTGGGGGTGCCATACGCAAAAAGGAAGCGACTCATAGAATGGCAGAGGCAAATAGAGCTCTTGCACATTTTCGTTAATCCATGAACAGAATCTAGGTATGTAGACACATGGATCCATACATCTCGATCGGAAAAGAATCAATAGAAGGAGAATCGGACGATATCTTTCTCGAAACAAAC 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 04:25:40 Started mapping on | Dec 07 04:25:41 Finished on | Dec 07 04:26:05 Mapping speed, Million of reads per hour | 143.36 Number of input reads | 955718 Average input read length | 89 UNIQUE READS: Uniquely mapped reads number | 381192 Uniquely mapped reads % | 39.89% Average mapped length | 88.32 Number of splices: Total | 13565 Number of splices: Annotated (sjdb) | 10565 Number of splices: GT/AG | 12724 Number of splices: GC/AG | 294 Number of splices: AT/AC | 15 Number of splices: Non-canonical | 532 Mismatch rate per base, % | 0.81% Deletion rate per base | 0.03% Deletion average length | 1.76 Insertion rate per base | 0.02% Insertion average length | 1.79 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 477887 % of reads mapped to multiple loci | 50.00% Number of reads mapped to too many loci | 42525 % of reads mapped to too many loci | 4.45% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 4.90% % of reads unmapped: other | 0.76% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 96639 96639 96639 N_multimapping 477887 477887 477887 N_noFeature 35666 39709 364507 N_ambiguous 15409 2739 86 UnstrandedReadsAssigned:330117 PositiveStrandReadsAssigned:338744 NegativeStrandReadsAssigned:16599 Dataset is classified positive stranded MeadianReadLen=93 20thPercentileLength=85 echo kmer=81 ERR6133406 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: ERR6133406-trimmed.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 955,718 reads, 607,771 reads pseudoaligned [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 840 rounds 52973 ERR6133406.ke.tsv 35125 ERR6133406.se.tsv 88098 total ==> ERR6133406.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 3 4.7636 PNS24243 293 194 0 0 KQK14069 1603 1504 1 1.44851 KQK14071 474 375 0 0 ==> ERR6133406.se.tsv <== BRADI_1g14170v3 1 BRADI_1g53295v3 5 BRADI_1g59795v3 3 BRADI_1g07683v3 0 BRADI_1g00485v3 0 BRADI_1g20270v3 4 BRADI_1g74790v3 3 BRADI_1g09890v3 0 BRADI_1g77505v3 8 BRADI_1g48960v3 0 ERR6133406 completed mapping pipeline successfully