Starting /dee2/code/volunteer_pipeline.sh ERR6133537 current disk space = 1544519544832 free memory = 1601269036 ERR6133537 SRAfilesize 8b3654ee0efa78ca9bf157f91683a997 ERR6133537.sra ERR6133537.sra file validated ERR6133537 is single end ERR6133537 is conventional basespace ERR6133537 read1 length is 70-93 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename ERR6133537_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 33.9085 37.0 33.0 37.0 27.0 37.0 2 36.07875 37.0 37.0 37.0 33.0 37.0 3 35.22475 37.0 33.0 37.0 33.0 37.0 4 35.2745 37.0 37.0 37.0 33.0 37.0 5 35.253 37.0 37.0 37.0 33.0 37.0 6 35.61575 37.0 37.0 37.0 33.0 37.0 7 37.4055 37.0 37.0 40.0 33.0 40.0 8 37.39375 37.0 37.0 40.0 33.0 40.0 9 37.40325 37.0 37.0 40.0 33.0 40.0 10-11 37.488625 37.0 37.0 40.0 33.0 40.0 12-13 37.378 37.0 37.0 40.0 33.0 40.0 14-15 37.3765 37.0 37.0 40.0 33.0 40.0 16-17 37.316625 37.0 37.0 40.0 33.0 40.0 18-19 37.228750000000005 37.0 37.0 40.0 33.0 40.0 20-21 37.1725 37.0 37.0 40.0 33.0 40.0 22-23 37.128625 37.0 37.0 40.0 33.0 40.0 24-25 37.257625000000004 37.0 37.0 40.0 33.0 40.0 26-27 37.277249999999995 37.0 37.0 40.0 33.0 40.0 28-29 37.139250000000004 37.0 37.0 40.0 33.0 40.0 30-31 37.094 37.0 37.0 40.0 33.0 40.0 32-33 36.934 37.0 37.0 40.0 33.0 40.0 34-35 36.748625000000004 37.0 37.0 40.0 33.0 40.0 36-37 36.642250000000004 37.0 37.0 40.0 33.0 40.0 38-39 36.608625 37.0 37.0 40.0 33.0 40.0 40-41 36.391999999999996 37.0 37.0 40.0 33.0 40.0 42-43 36.29025 37.0 37.0 40.0 33.0 40.0 44-45 35.962999999999994 37.0 35.0 40.0 33.0 40.0 46-47 35.6275 37.0 33.0 37.0 33.0 40.0 48-49 35.701875 37.0 33.0 37.0 33.0 40.0 50-51 35.5905 37.0 33.0 37.0 33.0 40.0 52-53 35.339124999999996 37.0 33.0 37.0 33.0 40.0 54-55 35.360749999999996 37.0 33.0 37.0 33.0 40.0 56-57 35.153625000000005 37.0 33.0 37.0 33.0 38.5 58-59 34.45775 37.0 33.0 37.0 27.0 37.0 60-61 34.622625 37.0 33.0 37.0 27.0 37.0 62-63 34.549875 37.0 33.0 37.0 27.0 37.0 64-65 34.6425 37.0 33.0 37.0 30.0 37.0 66-67 34.5995 37.0 33.0 37.0 33.0 37.0 68-69 33.785375 35.0 33.0 37.0 27.0 37.0 70-71 33.8473334377349 35.0 33.0 37.0 27.0 37.0 72-73 34.262508160967094 37.0 33.0 37.0 27.0 37.0 74-75 34.16073704025952 37.0 33.0 37.0 27.0 37.0 76-77 34.064335811554145 37.0 33.0 37.0 27.0 37.0 78-79 34.12714440496306 37.0 33.0 37.0 27.0 37.0 80-81 34.154769315804174 37.0 33.0 37.0 27.0 37.0 82-83 34.070471316161644 37.0 33.0 37.0 27.0 37.0 84-85 33.90227847632264 37.0 33.0 37.0 27.0 37.0 86-87 33.85138004246285 37.0 33.0 37.0 27.0 37.0 88-89 33.95581210191083 37.0 33.0 37.0 27.0 37.0 90-91 33.71257961783439 37.0 33.0 37.0 27.0 37.0 92-93 33.5786889596603 37.0 33.0 37.0 27.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 20 12.0 21 16.0 22 11.0 23 17.0 24 30.0 25 29.0 26 34.0 27 46.0 28 54.0 29 62.0 30 99.0 31 108.0 32 128.0 33 168.0 34 203.0 35 393.0 36 879.0 37 946.0 38 750.0 39 15.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 88.14999999999999 2.1999999999999997 2.175 7.475 2 71.175 17.1 7.6 4.125 3 36.075 38.475 14.7 10.75 4 33.900000000000006 27.500000000000004 20.175 18.425 5 23.95 30.7 26.224999999999998 19.125 6 21.125 36.375 25.775 16.725 7 35.225 28.625 20.375 15.775 8 30.8 31.0 24.15 14.05 9 26.625 28.675 29.349999999999998 15.35 10-11 26.137500000000003 27.275 29.175 17.4125 12-13 27.075 25.95 29.862499999999997 17.1125 14-15 22.125 29.012500000000003 30.2625 18.6 16-17 23.2625 32.237500000000004 26.137500000000003 18.3625 18-19 23.724999999999998 27.2625 29.012500000000003 20.0 20-21 23.45 25.55 28.9125 22.0875 22-23 25.837500000000002 24.3125 27.425 22.425 24-25 24.7875 24.55 30.0875 20.575 26-27 23.6375 26.0375 31.4 18.925 28-29 25.2875 26.2875 29.4125 19.0125 30-31 24.5375 25.900000000000002 29.762499999999996 19.8 32-33 24.224999999999998 25.95 30.049999999999997 19.775000000000002 34-35 24.762262262262265 27.127127127127125 28.203203203203202 19.90740740740741 36-37 24.0125 25.7875 28.8625 21.337500000000002 38-39 24.925 26.224999999999998 29.7125 19.1375 40-41 25.969477107830873 24.768576432324245 27.90843132349262 21.353515136352264 42-43 25.58808808808809 26.326326326326328 28.716216216216218 19.36936936936937 44-45 22.71703777833375 25.594195646735052 31.198398799099326 20.490367775831874 46-47 23.962500000000002 25.6 29.725 20.7125 48-49 23.668417104276067 24.85621405351338 31.895473868467118 19.579894973743436 50-51 22.6875 27.275 30.15 19.8875 52-53 24.04904904904905 27.815315315315313 28.553553553553552 19.582082082082085 54-55 23.25 27.425 30.7875 18.5375 56-57 25.6125 25.324999999999996 29.612500000000004 19.45 58-59 24.875 25.0625 28.9375 21.125 60-61 24.4125 25.974999999999998 30.562499999999996 19.05 62-63 22.125 28.537499999999998 31.65 17.6875 64-65 22.4375 28.4375 30.25 18.875 66-67 23.7875 26.637499999999996 30.65 18.925 68-69 21.087500000000002 27.700000000000003 30.0375 21.175 70-71 23.68915029408084 27.76873983231135 29.458140407958954 19.083969465648856 72-73 24.451450189155107 25.37200504413619 29.91172761664565 20.264817150063053 74-75 23.575688364420756 26.494099733536352 30.148458317472404 19.781753584570485 76-77 23.205833439938594 27.094793399002175 29.47422284763976 20.22515031341947 78-79 21.894329896907216 26.108247422680414 32.19072164948454 19.806701030927833 80-81 22.043150506888484 28.74967507148427 30.81622043150507 18.39095399012217 82-83 22.334426229508196 26.334426229508196 31.278688524590166 20.052459016393442 84-85 22.99337748344371 23.576158940397352 33.40397350993378 20.026490066225165 86-87 22.06740976645435 26.526008492569 32.3911889596603 19.015392781316347 88-89 20.873142250530783 28.41029723991507 31.35615711252654 19.3604033970276 90-91 24.522292993630572 27.202760084925693 29.259554140127385 19.015392781316347 92-93 21.589702760084926 31.011146496815282 30.241507430997878 17.15764331210191 >>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 0.5 17 2.0 18 2.0 19 1.5 20 2.5 21 3.0 22 2.5 23 2.0 24 3.5 25 6.0 26 10.5 27 11.5 28 15.0 29 23.0 30 30.0 31 42.5 32 69.5 33 91.5 34 96.5 35 116.0 36 148.5 37 174.0 38 210.5 39 213.0 40 199.5 41 209.0 42 235.0 43 259.0 44 224.0 45 211.0 46 208.5 47 174.5 48 161.0 49 162.5 50 145.5 51 126.0 52 115.0 53 112.5 54 100.0 55 62.0 56 48.0 57 51.5 58 49.0 59 41.0 60 33.5 61 26.5 62 19.5 63 18.5 64 18.0 65 15.5 66 12.5 67 14.5 68 16.5 69 10.0 70 6.5 71 7.0 72 5.5 73 2.0 74 0.5 75 0.5 76 0.0 77 0.5 78 0.5 79 0.0 80 0.0 81 0.0 82 0.5 83 0.5 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 0.1 36-37 0.0 38-39 0.0 40-41 0.075 42-43 0.1 44-45 0.075 46-47 0.0 48-49 0.025 50-51 0.0 52-53 0.1 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 9.0 71 19.0 72 14.0 73 12.0 74 11.0 75 17.0 76 19.0 77 12.0 78 14.0 79 18.0 80 16.0 81 18.0 82 17.0 83 22.0 84 14.0 85 0.0 86 0.0 87 0.0 88 0.0 89 0.0 90 0.0 91 0.0 92 0.0 93 3768.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 82.125 #Duplication Level Percentage of deduplicated Percentage of total 1 93.2420091324201 76.575 2 3.713850837138508 6.1 3 1.06544901065449 2.625 4 0.578386605783866 1.9 5 0.30441400304414 1.25 6 0.15220700152207 0.75 7 0.213089802130898 1.225 8 0.12176560121765602 0.8 9 0.091324200913242 0.675 >10 0.4870624048706241 6.550000000000001 >50 0.030441400304414005 1.55 >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 62 1.55 No Hit GGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCTTGG 41 1.0250000000000001 No Hit GGGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGT 27 0.675 No Hit GGCGTTCAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTC 27 0.675 No Hit GGGCTGATATCATCAACCGTGCTAATCTTGGTATGGAAGTAATGCACGAA 17 0.42500000000000004 No Hit GTAGTAGGAATCTGGTTCACTGCTTTAGGTATTAGTACTATGGCGTTCAA 16 0.4 No Hit GGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGTGTACAAGCTCGTAA 16 0.4 No Hit GGTAATGAAATTATCCGAGCAGCTTGCAAATGGAGTCCTGAACTAGCCGC 14 0.35000000000000003 No Hit GGAGTTGAAAATAAGCATAGATCCGGAGATTCCCAAATAGGTCAACCTTT 13 0.325 No Hit GGGAATCGATCGTGATTTAGAACCTGTTCTTTACATGAACCCTCTTAACT 13 0.325 No Hit GGGAGAGCAATACAAGCGTTGTGCTGCTAGGCGAAGCGGTTGAGTGCCGC 13 0.325 No Hit CAAGGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCT 12 0.3 No Hit CAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAGGTC 11 0.27499999999999997 No Hit GGGATGATTCTGTATTACAATTTGGTGGAGGAACTTTAGGACATCCTTGG 11 0.27499999999999997 No Hit GGGCGCGATCTTGCTCGTGAAGGTAATGAAATTATCCGAGCAGCTTGCAA 11 0.27499999999999997 No Hit CAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAATACTTGGGCTGATAT 10 0.25 No Hit GGGTTGTTTGGGAATGCAGCCCAAATCGGGCGGTAGACTCCGTCCAAGGC 10 0.25 No Hit GGCCTGTAGTAGGAATCTGGTTCACTGCTTTAGGTATTAGTACTATGGCG 9 0.22499999999999998 No Hit GGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGTG 9 0.22499999999999998 No Hit GGAGGAACTTTAGGACATCCTTGGGGAAATGCACCTGGTGCAGCAGCTAA 9 0.22499999999999998 No Hit GGCGCGATCTTGCTCGTGAAGGTAATGAAATTATCCGAGCAGCTTGCAAA 8 0.2 No Hit GGAAGAGCCCGAGCTGCTGCAGCAGGTTTTGAAAAGGGAATCGATCGTGA 8 0.2 No Hit TACCTAGGCACCCAGAGACGAGGAAGGGCGTAGCAAGCGACGAAATGCTT 8 0.2 No Hit GGTTTTGAAAAGGGAATCGATCGTGATTTAGAACCTGTTCTTTACATGAA 8 0.2 No Hit GGCTTTAGAAGCCTGTGTACAAGCTCGTAACGAAGGGCGCGATCTTGCTC 7 0.17500000000000002 No Hit GGACATCCTTGGGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTT 7 0.17500000000000002 No Hit GGAGTAAACTAGCATAAATAATTTGTTTGATGCCGTCATCAAGGTTGAGT 7 0.17500000000000002 No Hit GGGGAGTTGAAAATAAGCATAGATCCGGAGATTCCCAAATAGGTCAACCT 7 0.17500000000000002 No Hit GGGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCTTG 7 0.17500000000000002 No Hit GTATGGAAGGCGATCAAATTCGAGTTCGCGCCGGTAGATACTATCGATTA 7 0.17500000000000002 No Hit GGGCACTGTAGCCAGTGTGTCAGTCGTTGTTAAATTACAGGTTGAGATCA 7 0.17500000000000002 No Hit GGGATGGAGCGACAGAAGTATGGAAATAGGATAAGGTAGCGGCGAGACGA 6 0.15 No Hit GGGGATGGAGCGACAGAAGTATGGAAATAGGATAAGGTAGCGGCGAGACG 6 0.15 No Hit GAAGTATGGAAGGCGATCAAATTCGAGTTCGCGCCGGTAGATACTATCGA 6 0.15 No Hit GGGCACGTGGAATCCCGTGTGAATCAGCAAGGACCACCTTGCAAGGCTAA 6 0.15 No Hit GGGGATGATTCTGTATTACAATTTGGTGGAGGAACTTTAGGACATCCTTG 6 0.15 No Hit GGGAAAAGAGGGGTTACTTTTTTTCATTTTTCCCTTAAAAGATAGGCTTT 5 0.125 No Hit GGGAAACAACGACGTCATCATCGACATGATATATTGCTGCTATTTTCCAC 5 0.125 No Hit GGGAGTATTATGAAAGGAGATTAATCATAGATTATCAAAAACCCTAGAAA 5 0.125 No Hit GGGAAATAGCTAATGTAGAATTTATCTGATATAGAACACTCATATCGATA 5 0.125 No Hit GCAAGGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATC 5 0.125 No Hit GTACTATGGCGTTCAACCTAAATGGATTCAATTTCAACCAATCTGTAGTT 5 0.125 No Hit GGAATCGATCGTGATTTAGAACCTGTTCTTTACATGAACCCTCTTAACTA 5 0.125 No Hit GGGAAATTAACAGTTGGAAAGGGCGATCGGTCTTGATCCCTCTGTGTTTC 5 0.125 No Hit GGAATCCCGTGTGAATCAGCAAGGACCACCTTGCAAGGCTAAATACTCCT 5 0.125 No Hit GGAAAAGAGGGGTTACTTTTTTTCATTTTTCCCTTAAAAGATAGGCTTTG 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 0.025 0.0 0.0 0.0 0.0 9 0.025 0.0 0.0 0.0 0.0 10-11 0.025 0.0 0.0 0.0 0.0 12-13 0.025 0.0 0.0 0.0 0.0 14-15 0.025 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 0.025 0.0 0.0 0.0 0.0 30-31 0.025 0.0 0.0 0.0 0.0 32-33 0.025 0.0 0.0 0.0 0.0 34-35 0.025 0.0 0.0 0.0 0.0 36-37 0.037500000000000006 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 pass >>END_MODULE Rejected 254146 READS because READLEN < 1 Read 254146 spots for ERR6133537.sra Written 254146 spots for ERR6133537.sra Rejected 254146 READS because READLEN < 1 Read 254146 spots for ERR6133537.sra Written 254146 spots for ERR6133537.sra Rejected 254146 READS because READLEN < 1 Read 254146 spots for ERR6133537.sra Written 254146 spots for ERR6133537.sra Rejected 254146 READS because READLEN < 1 Read 254146 spots for ERR6133537.sra Written 254146 spots for ERR6133537.sra Rejected 254146 READS because READLEN < 1 Read 254146 spots for ERR6133537.sra Written 254146 spots for ERR6133537.sra Rejected 254146 READS because READLEN < 1 Read 254146 spots for ERR6133537.sra Written 254146 spots for ERR6133537.sra Rejected 254146 READS because READLEN < 1 Read 254146 spots for ERR6133537.sra Written 254146 spots for ERR6133537.sra Rejected 254146 READS because READLEN < 1 Read 254146 spots for ERR6133537.sra Written 254146 spots for ERR6133537.sra Rejected 254146 READS because READLEN < 1 Read 254146 spots for ERR6133537.sra Written 254146 spots for ERR6133537.sra Rejected 254146 READS because READLEN < 1 Read 254146 spots for ERR6133537.sra Written 254146 spots for ERR6133537.sra Rejected 254146 READS because READLEN < 1 Read 254146 spots for ERR6133537.sra Written 254146 spots for ERR6133537.sra Rejected 254146 READS because READLEN < 1 Read 254146 spots for ERR6133537.sra Written 254146 spots for ERR6133537.sra Rejected 254146 READS because READLEN < 1 Read 254146 spots for ERR6133537.sra Written 254146 spots for ERR6133537.sra Rejected 254146 READS because READLEN < 1 Read 254146 spots for ERR6133537.sra Written 254146 spots for ERR6133537.sra Rejected 254146 READS because READLEN < 1 Read 254146 spots for ERR6133537.sra Written 254146 spots for ERR6133537.sra Rejected 254146 READS because READLEN < 1 Read 254146 spots for ERR6133537.sra Written 254146 spots for ERR6133537.sra Rejected 254146 READS because READLEN < 1 Read 254146 spots for ERR6133537.sra Written 254146 spots for ERR6133537.sra Rejected 254146 READS because READLEN < 1 Read 254146 spots for ERR6133537.sra Written 254146 spots for ERR6133537.sra Rejected 254146 READS because READLEN < 1 Read 254146 spots for ERR6133537.sra Written 254146 spots for ERR6133537.sra Rejected 254156 READS because READLEN < 1 Read 254156 spots for ERR6133537.sra Written 254156 spots for ERR6133537.sra SRR ids: ['ERR6133537.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_oaumi5u8 ERR6133537.sra spots: 5082930 blocks: [[1, 254146], [254147, 508292], [508293, 762438], [762439, 1016584], [1016585, 1270730], [1270731, 1524876], [1524877, 1779022], [1779023, 2033168], [2033169, 2287314], [2287315, 2541460], [2541461, 2795606], [2795607, 3049752], [3049753, 3303898], [3303899, 3558044], [3558045, 3812190], [3812191, 4066336], [4066337, 4320482], [4320483, 4574628], [4574629, 4828774], [4828775, 5082930]] ERR6133537 file size 1120028 ERR6133537 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 ERR6133537 ERR6133537_1.fastq Input file: ERR6133537_1.fastq trimmed: ERR6133537-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 08:09:47 2024 >> started Sat Dec 7 08:09:51 2024 >> done (3.599s) 5082930 reads processed; of these: 65 ( 0.00%) short reads filtered out after trimming by size control 11 ( 0.00%) empty reads filtered out after trimming by size control 5082854 (100.00%) reads available; of these: 83837 ( 1.65%) trimmed reads available after processing 4999017 (98.35%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 1 0.00% 19 22 0.00% 20 5 0.00% 21 1 0.00% 22 7 0.00% 23 3 0.00% 24 3 0.00% 25 3 0.00% 26 2 0.00% 27 4 0.00% 28 7 0.00% 29 23 0.00% 30 5 0.00% 31 11 0.00% 32 16 0.00% 33 8 0.00% 34 10 0.00% 35 27 0.00% 36 509 0.01% 37 14 0.00% 38 18 0.00% 39 23 0.00% 40 37 0.00% 41 15 0.00% 42 6 0.00% 43 15 0.00% 44 8 0.00% 45 13 0.00% 46 10 0.00% 47 8 0.00% 48 11 0.00% 49 8 0.00% 50 4 0.00% 51 22 0.00% 52 7 0.00% 53 4 0.00% 54 4 0.00% 55 2 0.00% 56 9 0.00% 57 9 0.00% 58 10 0.00% 59 8 0.00% 60 6 0.00% 61 16 0.00% 62 13 0.00% 63 11 0.00% 64 5 0.00% 65 14 0.00% 66 21 0.00% 67 38 0.00% 68 85 0.00% 69 255 0.01% 70 20253 0.40% 71 18885 0.37% 72 19924 0.39% 73 18974 0.37% 74 19486 0.38% 75 19282 0.38% 76 17795 0.35% 77 18165 0.36% 78 20311 0.40% 79 21345 0.42% 80 20592 0.41% 81 23733 0.47% 82 25344 0.50% 83 24440 0.48% 84 24255 0.48% 85 176 0.00% 86 295 0.01% 87 548 0.01% 88 1002 0.02% 89 1973 0.04% 90 4543 0.09% 91 13131 0.26% 92 56950 1.12% 93 4690056 92.27% 5082854 reads passed initial QC criterion=sequence-density sequence-density=0.95 sequence-density-rank=1 fanout-score=2.00 fanout-score-rank=32 prefix-density=0.95 prefix-fanout=2.0 sequence=CAAGGCTAAATAC criterion=fanout-score sequence-density=0.01 sequence-density-rank=26 fanout-score=263.47 fanout-score-rank=1 prefix-density=0.55 prefix-fanout=6.5 sequence=GAAGAAGAAAAGTTTTCTCAACATGGGGAGGAAGTCCCTCCGAAATTTGATTTGTTATTGTATTGTAAGGGGCTTTTTTAGTATTTATCTAAAGGAAGGAACAAACGAGGATAAGATAAAATTGCTTTAAATTTATTTTGCCCAAGTGGGATATATGGCATACTATTCTTTCCATTTTCATCTTTTTTTCTATTCCACTCCATCTAGATATAAGAAAGAACCCAATGCAATGAAATTCCACTAATATACAATACAAAAAAGAAGAATAGATACAGGGTCTCAAACCTTGCTATAGAGTTTTTGC Started job on | Dec 07 08:10:04 Started mapping on | Dec 07 08:10:05 Finished on | Dec 07 08:10:12 Mapping speed, Million of reads per hour | 2614.04 Number of input reads | 5082854 Average input read length | 92 UNIQUE READS: Uniquely mapped reads number | 3688033 Uniquely mapped reads % | 72.56% Average mapped length | 91.39 Number of splices: Total | 124641 Number of splices: Annotated (sjdb) | 101304 Number of splices: GT/AG | 117273 Number of splices: GC/AG | 3274 Number of splices: AT/AC | 147 Number of splices: Non-canonical | 3947 Mismatch rate per base, % | 0.60% Deletion rate per base | 0.06% Deletion average length | 1.77 Insertion rate per base | 0.04% Insertion average length | 1.92 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 1224021 % of reads mapped to multiple loci | 24.08% Number of reads mapped to too many loci | 77110 % of reads mapped to too many loci | 1.52% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 1.75% % of reads unmapped: other | 0.10% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 170800 170800 170800 N_multimapping 1224021 1224021 1224021 N_noFeature 271193 305215 3519533 N_ambiguous 150590 15947 521 UnstrandedReadsAssigned:3266250 PositiveStrandReadsAssigned:3366871 NegativeStrandReadsAssigned:167979 Dataset is classified positive stranded MeadianReadLen=93 20thPercentileLength=93 echo kmer=89 ERR6133537 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: ERR6133537-trimmed.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 5,082,854 reads, 4,184,757 reads pseudoaligned [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,070 rounds 52973 ERR6133537.ke.tsv 35125 ERR6133537.se.tsv 88098 total ==> ERR6133537.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 109 25.8614 PNS24243 293 194 0 0 KQK14069 1603 1504 167 36.145 KQK14071 474 375 0 0 ==> ERR6133537.se.tsv <== BRADI_1g14170v3 167 BRADI_1g53295v3 133 BRADI_1g59795v3 6 BRADI_1g07683v3 0 BRADI_1g00485v3 2 BRADI_1g20270v3 55 BRADI_1g74790v3 28 BRADI_1g09890v3 1 BRADI_1g77505v3 150 BRADI_1g48960v3 0 ERR6133537 completed mapping pipeline successfully