Starting /dee2/code/volunteer_pipeline.sh ERR6133508 current disk space = 1544438857728 free memory = 1604475716 ERR6133508 SRAfilesize 04eedd492c117d80be559e0251bbf995 ERR6133508.sra ERR6133508.sra file validated ERR6133508 is single end ERR6133508 is conventional basespace ERR6133508 read1 length is 70-93 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename ERR6133508_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 36.62575 37.0 37.0 37.0 37.0 37.0 2 36.83 37.0 37.0 37.0 37.0 37.0 3 36.515 37.0 37.0 37.0 37.0 37.0 4 35.85225 37.0 37.0 37.0 33.0 37.0 5 35.93975 37.0 37.0 37.0 33.0 37.0 6 36.2495 37.0 37.0 37.0 33.0 37.0 7 38.2405 40.0 37.0 40.0 37.0 40.0 8 38.25375 40.0 37.0 40.0 37.0 40.0 9 38.24 40.0 37.0 40.0 37.0 40.0 10-11 38.233374999999995 40.0 37.0 40.0 37.0 40.0 12-13 38.153875 40.0 37.0 40.0 37.0 40.0 14-15 38.13225 40.0 37.0 40.0 37.0 40.0 16-17 38.086124999999996 40.0 37.0 40.0 37.0 40.0 18-19 37.990125 40.0 37.0 40.0 37.0 40.0 20-21 37.977000000000004 40.0 37.0 40.0 35.0 40.0 22-23 38.097625 40.0 37.0 40.0 37.0 40.0 24-25 37.9915 40.0 37.0 40.0 37.0 40.0 26-27 37.968 40.0 37.0 40.0 37.0 40.0 28-29 37.90537500000001 40.0 37.0 40.0 35.0 40.0 30-31 37.956625 40.0 37.0 40.0 37.0 40.0 32-33 37.9765 40.0 37.0 40.0 37.0 40.0 34-35 37.87925 38.5 37.0 40.0 37.0 40.0 36-37 37.8375 37.0 37.0 40.0 37.0 40.0 38-39 37.716625 37.0 37.0 40.0 37.0 40.0 40-41 37.493750000000006 37.0 37.0 40.0 33.0 40.0 42-43 37.497875 37.0 37.0 40.0 35.0 40.0 44-45 37.2775 37.0 37.0 40.0 35.0 40.0 46-47 37.117625000000004 37.0 37.0 40.0 33.0 40.0 48-49 36.998125 37.0 37.0 37.0 33.0 40.0 50-51 36.826 37.0 37.0 37.0 33.0 40.0 52-53 36.432375 37.0 37.0 37.0 33.0 40.0 54-55 36.419 37.0 37.0 37.0 33.0 40.0 56-57 36.263999999999996 37.0 37.0 37.0 33.0 38.5 58-59 35.878875 37.0 37.0 37.0 33.0 37.0 60-61 36.036 37.0 37.0 37.0 33.0 37.0 62-63 35.91625 37.0 37.0 37.0 33.0 37.0 64-65 35.786500000000004 37.0 37.0 37.0 33.0 37.0 66-67 35.744875 37.0 37.0 37.0 33.0 37.0 68-69 34.881875 35.0 35.0 37.0 33.0 37.0 70-71 35.036931633291616 37.0 33.0 37.0 33.0 37.0 72-73 35.551107447303636 37.0 33.0 37.0 33.0 37.0 74-75 35.53629888914298 37.0 33.0 37.0 33.0 37.0 76-77 35.52293985241861 37.0 33.0 37.0 33.0 37.0 78-79 35.47621207029985 37.0 33.0 37.0 33.0 37.0 80-81 35.30007303741026 37.0 33.0 37.0 33.0 37.0 82-83 35.22421853007263 37.0 33.0 37.0 33.0 37.0 84-85 35.091113687935554 37.0 33.0 37.0 33.0 37.0 86-87 34.99556175500888 37.0 33.0 37.0 33.0 37.0 88-89 34.951306112097384 37.0 33.0 37.0 33.0 37.0 90-91 34.9332995181334 37.0 33.0 37.0 33.0 37.0 92-93 34.92683236114634 37.0 33.0 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 6.0 24 5.0 25 5.0 26 11.0 27 16.0 28 19.0 29 25.0 30 19.0 31 39.0 32 60.0 33 66.0 34 109.0 35 300.0 36 1156.0 37 1399.0 38 748.0 39 7.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 89.2 2.45 2.725 5.625 2 75.14999999999999 14.85 6.0249999999999995 3.975 3 37.5 38.35 13.725000000000001 10.424999999999999 4 32.925 29.475 18.9 18.7 5 25.55 29.225 27.875 17.349999999999998 6 19.675 39.85 24.474999999999998 16.0 7 36.775000000000006 28.525 19.3 15.4 8 30.575000000000003 30.475 21.525 17.424999999999997 9 25.825 30.85 26.275 17.05 10-11 25.2625 28.625 28.325 17.7875 12-13 26.8125 28.6875 26.25 18.25 14-15 22.025 31.7 27.6875 18.587500000000002 16-17 24.4875 30.562499999999996 24.525 20.424999999999997 18-19 23.25 28.3625 27.900000000000002 20.4875 20-21 25.365853658536587 25.278298936835526 29.118198874296436 20.237648530331455 22-23 28.1625 23.8875 27.487499999999997 20.4625 24-25 25.662499999999998 24.887500000000003 28.1625 21.2875 26-27 25.112499999999997 25.924999999999997 31.137500000000003 17.825 28-29 24.725 28.212500000000002 26.75 20.3125 30-31 27.994498624656167 25.84396099024756 26.79419854963741 19.367341835458866 32-33 24.9875 26.85 26.987499999999997 21.175 34-35 23.8875 28.7375 26.525 20.849999999999998 36-37 24.962500000000002 26.0625 27.037499999999998 21.9375 38-39 27.6625 24.975 28.5875 18.775 40-41 27.370527895921942 24.706029522141606 27.60820615461596 20.31523642732049 42-43 25.847192697261473 28.973365011879455 25.82218331874453 19.357258972114543 44-45 24.8625 25.5 28.5625 21.075 46-47 24.712500000000002 24.0625 28.65 22.575 48-49 24.25 25.474999999999998 31.0625 19.2125 50-51 23.6625 27.437499999999996 29.099999999999998 19.8 52-53 24.793077501881115 27.163280662151994 25.670930524203662 22.37271131176323 54-55 23.2375 27.787499999999998 29.5 19.475 56-57 27.462500000000002 25.874999999999996 27.325 19.3375 58-59 24.275 24.5625 29.9875 21.175 60-61 25.837500000000002 25.087500000000002 29.212500000000002 19.8625 62-63 21.525 27.950000000000003 31.424999999999997 19.1 64-65 22.7125 30.025000000000002 28.3125 18.95 66-67 24.3625 27.400000000000002 28.825 19.412499999999998 68-69 22.225 27.400000000000002 28.225 22.15 70-71 23.26454033771107 27.629768605378363 28.055034396497813 21.05065666041276 72-73 26.31513026052104 24.524048096192384 28.632264529058116 20.52855711422846 74-75 23.87460815047022 28.78996865203762 28.70219435736677 18.633228840125394 76-77 23.01796708129162 25.141349415755748 28.646814926498305 23.193868576454328 78-79 24.21344072489303 26.31512710797886 30.090611628492326 19.380820538635792 80-81 23.031297324583544 30.24987380111055 29.05098435133771 17.6678445229682 82-83 23.359048943973697 25.48374857721007 28.708739091943848 22.44846338687239 84-85 23.292358382967937 23.900646305918137 32.264605246483335 20.54239006463059 86-87 22.97742835404514 26.274410347451177 31.283286837433426 19.46487446107025 88-89 21.45574435708851 27.82145574435709 31.3086482373827 19.414151661171697 90-91 25.957392848085213 26.05883844788232 28.68374334263251 19.30002536139995 92-93 22.077098655845802 29.5333502409333 29.279736241440528 19.109814861780368 >>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 0.5 16 0.5 17 4.5 18 5.5 19 1.5 20 1.5 21 2.0 22 1.5 23 4.0 24 6.0 25 3.5 26 4.5 27 6.5 28 13.0 29 20.5 30 23.5 31 29.0 32 35.0 33 45.0 34 58.5 35 67.0 36 100.0 37 148.0 38 192.0 39 194.5 40 186.5 41 192.0 42 203.0 43 225.0 44 209.0 45 200.5 46 233.0 47 231.5 48 195.5 49 184.5 50 173.5 51 167.0 52 159.5 53 154.0 54 171.0 55 117.5 56 56.5 57 61.5 58 49.5 59 30.5 60 20.0 61 15.0 62 18.5 63 19.5 64 16.5 65 15.5 66 10.5 67 9.0 68 8.0 69 5.0 70 4.5 71 4.0 72 3.0 73 1.5 74 1.5 75 2.0 76 1.0 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 0.0625 22-23 0.0 24-25 0.0 26-27 0.0 28-29 0.0 30-31 0.025 32-33 0.0 34-35 0.0 36-37 0.0 38-39 0.0 40-41 0.075 42-43 0.0375 44-45 0.0 46-47 0.0 48-49 0.0 50-51 0.0 52-53 0.325 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 5.0 71 2.0 72 2.0 73 3.0 74 1.0 75 5.0 76 5.0 77 3.0 78 2.0 79 7.0 80 6.0 81 4.0 82 3.0 83 4.0 84 5.0 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 3943.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 77.375 #Duplication Level Percentage of deduplicated Percentage of total 1 92.34248788368336 71.45 2 4.458804523424878 6.9 3 1.1954765751211631 2.775 4 0.6462035541195477 2.0 5 0.32310177705977383 1.25 6 0.12924071082390953 0.6 7 0.12924071082390953 0.7000000000000001 8 0.03231017770597738 0.2 9 0.12924071082390953 0.8999999999999999 >10 0.5492730210016155 9.049999999999999 >50 0.06462035541195477 4.175 >100 0.0 0.0 >500 0.0 0.0 >1k 0.0 0.0 >5k 0.0 0.0 >10k+ 0.0 0.0 >>END_MODULE >>Overrepresented sequences fail #Sequence Count Percentage Possible Source GGGAGAGCAATACAAGCGTTGTGCTGCTAGGCGAAGCGGTTGAGTGCCGC 97 2.4250000000000003 No Hit GGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAA 70 1.7500000000000002 No Hit GGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCTTGG 38 0.95 No Hit GGGATGATTCTGTATTACAATTTGGTGGAGGAACTTTAGGACATCCTTGG 37 0.9249999999999999 No Hit GGCGTTCAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTC 34 0.8500000000000001 No Hit GGGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGT 30 0.75 No Hit GGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGTG 28 0.7000000000000001 No Hit TACCTAGGCACCCAGAGACGAGGAAGGGCGTAGCAAGCGACGAAATGCTT 24 0.6 No Hit GGAGGAACTTTAGGACATCCTTGGGGAAATGCACCTGGTGCAGCAGCTAA 23 0.575 No Hit GGATGATTCTGTATTACAATTTGGTGGAGGAACTTTAGGACATCCTTGGG 21 0.525 No Hit GGCCTGTAGTAGGAATCTGGTTCACTGCTTTAGGTATTAGTACTATGGCG 20 0.5 No Hit GTAGTAGGAATCTGGTTCACTGCTTTAGGTATTAGTACTATGGCGTTCAA 17 0.42500000000000004 No Hit CAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAGGTC 17 0.42500000000000004 No Hit GGGGATGATTCTGTATTACAATTTGGTGGAGGAACTTTAGGACATCCTTG 14 0.35000000000000003 No Hit GGTATTAGTACTATGGCGTTCAACCTAAATGGATTCAATTTCAACCAATC 13 0.325 No Hit GGAGTTGAAAATAAGCATAGATCCGGAGATTCCCAAATAGGTCAACCTTT 13 0.325 No Hit GGAAGAGACTTATAATATTGTGGCTGCTCATGGTTATTTTGGCCGATTAA 12 0.3 No Hit GGACATCCTTGGGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTT 11 0.27499999999999997 No Hit GGTTCACTGCTTTAGGTATTAGTACTATGGCGTTCAACCTAAATGGATTC 10 0.25 No Hit GGGAAAAGAGGGGTTACTTTTTTTCATTTTTCCCTTAAAAGATAGGCTTT 9 0.22499999999999998 No Hit GGAGTATCCTTGATATATAAATATATAGATAAATAGATTTAAATGGAAAA 9 0.22499999999999998 No Hit GGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGTGTACAAGCTCGTAA 9 0.22499999999999998 No Hit GGGCTGATATCATCAACCGTGCTAATCTTGGTATGGAAGTAATGCACGAA 9 0.22499999999999998 No Hit CAAGGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCT 8 0.2 No Hit GGGGATGGAGCGACAGAAGTATGGAAATAGGATAAGGTAGCGGCGAGACG 7 0.17500000000000002 No Hit GGGAGTATTATGAAAGGAGATTAATCATAGATTATCAAAAACCCTAGAAA 7 0.17500000000000002 No Hit GGAATCTGGTTCACTGCTTTAGGTATTAGTACTATGGCGTTCAACCTAAA 7 0.17500000000000002 No Hit GGGCCGGGTATCTCTCTGCATGTACGTATGCCTGTAATGTACGTAGCTAC 7 0.17500000000000002 No Hit GGGATGGAGCGACAGAAGTATGGAAATAGGATAAGGTAGCGGCGAGACGA 6 0.15 No Hit GGAATAAGAATAAATCGCAACTCCTTTCCACTACACATAAAAATTGATTT 6 0.15 No Hit GGGGAGTTGAAAATAAGCATAGATCCGGAGATTCCCAAATAGGTCAACCT 6 0.15 No Hit GGGAATCGATCGTGATTTAGAACCTGTTCTTTACATGAACCCTCTTAACT 6 0.15 No Hit GGAACTTTAGGACATCCTTGGGGAAATGCACCTGGTGCAGCAGCTAATCG 5 0.125 No Hit GGGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTA 5 0.125 No Hit GAGGAACTTTAGGACATCCTTGGGGAAATGCACCTGGTGCAGCAGCTAAT 5 0.125 No Hit GGAAGAGCCCGAGCTGCTGCAGCAGGTTTTGAAAAGGGAATCGATCGTGA 5 0.125 No Hit GGAACAAACGAGGATAAGATAAAATTTCTTTAAATTTATTTTGCCCAAGT 5 0.125 No Hit GGAGTGGGGGTGCCATACGCAAAAAGGAAGCGACTCATAGAATGGCAGAG 5 0.125 No Hit GTACTATGGCGTTCAACCTAAATGGATTCAATTTCAACCAATCTGTAGTT 5 0.125 No Hit GGGATTACGACGAGAAAGAAGAAGAAGAAGAAACGCATGGTGCCCTGCTT 5 0.125 No Hit GGTAGTAGGAATCTGGTTCACTGCTTTAGGTATTAGTACTATGGCGTTCA 5 0.125 No Hit GGGCCATTTGTGGCATGCAGGAAGAGCCCGAGCTGCTGCAGCAGGTTTTG 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 0.025 0.0 0.0 0.0 0.0 18-19 0.025 0.0 0.0 0.0 0.0 20-21 0.025 0.0 0.0 0.0 0.0 22-23 0.025 0.0 0.0 0.0 0.0 24-25 0.025 0.0 0.0 0.0 0.0 26-27 0.025 0.0 0.0 0.0 0.0 28-29 0.037500000000000006 0.0 0.0 0.0 0.0 30-31 0.0875 0.0 0.0 0.0 0.0 32-33 0.1 0.0 0.0 0.0 0.0 34-35 0.1125 0.0 0.0 0.0 0.0 36-37 0.125 0.0 0.0 0.0 0.0 38-39 0.125 0.0 0.0 0.0 0.0 40-41 0.1375 0.0 0.0 0.0 0.0 42-43 0.15 0.0 0.0 0.0 0.0 44-45 0.15 0.0 0.0 0.0 0.0 46-47 0.15 0.0 0.0 0.0 0.0 48-49 0.15 0.0 0.0 0.0 0.0 50-51 0.15 0.0 0.0 0.0 0.0 52-53 0.15 0.0 0.0 0.0 0.0 54-55 0.15 0.0 0.0 0.0 0.0 56-57 0.15 0.0 0.0 0.0 0.0 58-59 0.15 0.0 0.0 0.0 0.0 60-61 0.15 0.0 0.0 0.0 0.0 62-63 0.15 0.0 0.0 0.0 0.0 64-65 0.15 0.0 0.0 0.0 0.0 66-67 0.15 0.0 0.0 0.0 0.0 68-69 0.15 0.0 0.0 0.0 0.0 70-71 0.15 0.0 0.0 0.0 0.0 72-73 0.15 0.0 0.0 0.0 0.0 74-75 0.15 0.0 0.0 0.0 0.0 76-77 0.15 0.0 0.0 0.0 0.0 78-79 0.15 0.0 0.0 0.0 0.0 80-81 0.15 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position GGAGGAG 20 2.3823906E-5 87.0 1 >>END_MODULE Rejected 94285 READS because READLEN < 1 Read 94285 spots for ERR6133508.sra Written 94285 spots for ERR6133508.sra Rejected 94285 READS because READLEN < 1 Read 94285 spots for ERR6133508.sra Written 94285 spots for ERR6133508.sra Rejected 94285 READS because READLEN < 1 Read 94285 spots for ERR6133508.sra Written 94285 spots for ERR6133508.sra Rejected 94285 READS because READLEN < 1 Read 94285 spots for ERR6133508.sra Written 94285 spots for ERR6133508.sra Rejected 94285 READS because READLEN < 1 Read 94285 spots for ERR6133508.sra Written 94285 spots for ERR6133508.sra Rejected 94285 READS because READLEN < 1 Read 94285 spots for ERR6133508.sra Written 94285 spots for ERR6133508.sra Rejected 94285 READS because READLEN < 1 Read 94285 spots for ERR6133508.sra Written 94285 spots for ERR6133508.sra Rejected 94285 READS because READLEN < 1 Read 94285 spots for ERR6133508.sra Written 94285 spots for ERR6133508.sra Rejected 94285 READS because READLEN < 1 Read 94285 spots for ERR6133508.sra Written 94285 spots for ERR6133508.sra Rejected 94285 READS because READLEN < 1 Read 94285 spots for ERR6133508.sra Written 94285 spots for ERR6133508.sra Rejected 94285 READS because READLEN < 1 Read 94285 spots for ERR6133508.sra Written 94285 spots for ERR6133508.sra Rejected 94285 READS because READLEN < 1 Read 94285 spots for ERR6133508.sra Written 94285 spots for ERR6133508.sra Rejected 94294 READS because READLEN < 1 Read 94294 spots for ERR6133508.sra Written 94294 spots for ERR6133508.sra Rejected 94285 READS because READLEN < 1 Read 94285 spots for ERR6133508.sra Written 94285 spots for ERR6133508.sra Rejected 94285 READS because READLEN < 1 Read 94285 spots for ERR6133508.sra Written 94285 spots for ERR6133508.sra Rejected 94285 READS because READLEN < 1 Read 94285 spots for ERR6133508.sra Written 94285 spots for ERR6133508.sra Rejected 94285 READS because READLEN < 1 Read 94285 spots for ERR6133508.sra Written 94285 spots for ERR6133508.sra Rejected 94285 READS because READLEN < 1 Read 94285 spots for ERR6133508.sra Written 94285 spots for ERR6133508.sra Rejected 94285 READS because READLEN < 1 Read 94285 spots for ERR6133508.sra Written 94285 spots for ERR6133508.sra Rejected 94285 READS because READLEN < 1 Read 94285 spots for ERR6133508.sra Written 94285 spots for ERR6133508.sra SRR ids: ['ERR6133508.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_pp4lsomt ERR6133508.sra spots: 1885709 blocks: [[1, 94285], [94286, 188570], [188571, 282855], [282856, 377140], [377141, 471425], [471426, 565710], [565711, 659995], [659996, 754280], [754281, 848565], [848566, 942850], [942851, 1037135], [1037136, 1131420], [1131421, 1225705], [1225706, 1319990], [1319991, 1414275], [1414276, 1508560], [1508561, 1602845], [1602846, 1697130], [1697131, 1791415], [1791416, 1885709]] ERR6133508 file size 416718 ERR6133508 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 ERR6133508 ERR6133508_1.fastq Input file: ERR6133508_1.fastq trimmed: ERR6133508-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 07:35:25 2024 >> started Sat Dec 7 07:35:26 2024 >> done (1.379s) 1885709 reads processed; of these: 303 ( 0.02%) short reads filtered out after trimming by size control 16 ( 0.00%) empty reads filtered out after trimming by size control 1885390 (99.98%) reads available; of these: 9801 ( 0.52%) trimmed reads available after processing 1875589 (99.48%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 37 0.00% 19 59 0.00% 20 26 0.00% 21 30 0.00% 22 21 0.00% 23 17 0.00% 24 13 0.00% 25 6 0.00% 26 13 0.00% 27 50 0.00% 28 277 0.01% 29 150 0.01% 30 25 0.00% 31 21 0.00% 32 45 0.00% 33 53 0.00% 34 29 0.00% 35 68 0.00% 36 423 0.02% 37 19 0.00% 38 21 0.00% 39 49 0.00% 40 53 0.00% 41 15 0.00% 42 15 0.00% 43 69 0.00% 44 13 0.00% 45 34 0.00% 46 11 0.00% 47 5 0.00% 48 13 0.00% 49 6 0.00% 50 8 0.00% 51 19 0.00% 52 9 0.00% 53 7 0.00% 54 4 0.00% 55 9 0.00% 56 12 0.00% 57 4 0.00% 58 12 0.00% 59 7 0.00% 60 5 0.00% 61 6 0.00% 62 0 0.00% 63 0 0.00% 64 0 0.00% 65 0 0.00% 66 4 0.00% 67 1 0.00% 68 5 0.00% 69 25 0.00% 70 2222 0.12% 71 2044 0.11% 72 1999 0.11% 73 1891 0.10% 74 1998 0.11% 75 1806 0.10% 76 1830 0.10% 77 1905 0.10% 78 2010 0.11% 79 2186 0.12% 80 2097 0.11% 81 2353 0.12% 82 2599 0.14% 83 2312 0.12% 84 2184 0.12% 85 28 0.00% 86 54 0.00% 87 91 0.00% 88 129 0.01% 89 269 0.01% 90 496 0.03% 91 1328 0.07% 92 5358 0.28% 93 1844378 97.82% 1885390 reads passed initial QC criterion=sequence-density sequence-density=0.26 sequence-density-rank=1 fanout-score=2.18 fanout-score-rank=28 prefix-density=0.27 prefix-fanout=2.1 sequence=CAAGGCTAAATAC criterion=fanout-score sequence-density=0.01 sequence-density-rank=29 fanout-score=82.64 fanout-score-rank=1 prefix-density=0.17 prefix-fanout=6.9 sequence=AGGAAGAGGAGGATGCAGTCAGGGCTCACAAACAACCTGCCACTGCCGCCATTGGCCTTCTAAAACAGGAGAGGAGGGGTTAGATAGTTTCGATCTGCAAGGGGGTGGGGCAATGGGCATTCCGTTGAGTTTGTATGGTGGGTGCTGTTTTGCAGAAGCTGTATGCTTATGAGCAGCTATGGTACTTATCGAGGACAGTAGCGTACTTGAGGTGTTGTATTTTTATTTATTT Started job on | Dec 07 07:35:40 Started mapping on | Dec 07 07:35:40 Finished on | Dec 07 07:35:43 Mapping speed, Million of reads per hour | 2262.47 Number of input reads | 1885390 Average input read length | 92 UNIQUE READS: Uniquely mapped reads number | 1249856 Uniquely mapped reads % | 66.29% Average mapped length | 92.34 Number of splices: Total | 86609 Number of splices: Annotated (sjdb) | 73823 Number of splices: GT/AG | 83853 Number of splices: GC/AG | 1695 Number of splices: AT/AC | 41 Number of splices: Non-canonical | 1020 Mismatch rate per base, % | 0.38% Deletion rate per base | 0.04% Deletion average length | 1.85 Insertion rate per base | 0.03% Insertion average length | 2.12 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 569814 % of reads mapped to multiple loci | 30.22% Number of reads mapped to too many loci | 9862 % of reads mapped to too many loci | 0.52% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 2.93% % of reads unmapped: other | 0.03% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 65720 65720 65720 N_multimapping 569814 569814 569814 N_noFeature 87756 99267 1196631 N_ambiguous 47758 5964 202 UnstrandedReadsAssigned:1114342 PositiveStrandReadsAssigned:1144625 NegativeStrandReadsAssigned:53023 Dataset is classified positive stranded MeadianReadLen=93 20thPercentileLength=93 echo kmer=89 ERR6133508 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: ERR6133508-trimmed.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 1,885,390 reads, 1,524,497 reads pseudoaligned [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 910 rounds 52973 ERR6133508.ke.tsv 35125 ERR6133508.se.tsv 88098 total ==> ERR6133508.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 50 31.2525 PNS24243 293 194 0 0 KQK14069 1603 1504 39 22.2375 KQK14071 474 375 0 0 ==> ERR6133508.se.tsv <== BRADI_1g14170v3 40 BRADI_1g53295v3 10 BRADI_1g59795v3 12 BRADI_1g07683v3 0 BRADI_1g00485v3 0 BRADI_1g20270v3 12 BRADI_1g74790v3 17 BRADI_1g09890v3 0 BRADI_1g77505v3 39 BRADI_1g48960v3 0 ERR6133508 completed mapping pipeline successfully