Starting /dee2/code/volunteer_pipeline.sh ERR6133489 current disk space = 1544626266112 free memory = 1421015764 ERR6133489 SRAfilesize 217aa2d1c5f2c6c483813d8afe7bb03e ERR6133489.sra ERR6133489.sra file validated ERR6133489 is single end ERR6133489 is conventional basespace ERR6133489 read1 length is 70-93 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename ERR6133489_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 35.522 37.0 33.0 37.0 33.0 37.0 2 36.447 37.0 37.0 37.0 37.0 37.0 3 35.78975 37.0 37.0 37.0 33.0 37.0 4 35.271 37.0 37.0 37.0 33.0 37.0 5 35.25775 37.0 37.0 37.0 33.0 37.0 6 35.6145 37.0 37.0 37.0 33.0 37.0 7 37.4265 37.0 37.0 40.0 33.0 40.0 8 37.4265 37.0 37.0 40.0 33.0 40.0 9 37.36325 37.0 37.0 40.0 33.0 40.0 10-11 37.399249999999995 37.0 37.0 40.0 33.0 40.0 12-13 37.33475 37.0 37.0 40.0 33.0 40.0 14-15 37.322 37.0 37.0 40.0 33.0 40.0 16-17 37.131375000000006 37.0 37.0 40.0 33.0 40.0 18-19 37.097625 37.0 37.0 40.0 33.0 40.0 20-21 36.828625 37.0 37.0 40.0 33.0 40.0 22-23 36.797875000000005 37.0 37.0 40.0 33.0 40.0 24-25 36.679874999999996 37.0 37.0 40.0 33.0 40.0 26-27 37.034625 37.0 37.0 40.0 33.0 40.0 28-29 37.01275 37.0 37.0 40.0 33.0 40.0 30-31 36.882374999999996 37.0 37.0 40.0 33.0 40.0 32-33 36.806375 37.0 37.0 40.0 33.0 40.0 34-35 36.737375 37.0 37.0 40.0 33.0 40.0 36-37 36.631874999999994 37.0 37.0 40.0 33.0 40.0 38-39 36.519875 37.0 37.0 40.0 33.0 40.0 40-41 36.31 37.0 37.0 40.0 33.0 40.0 42-43 36.373 37.0 37.0 40.0 33.0 40.0 44-45 36.323625 37.0 37.0 40.0 33.0 40.0 46-47 36.161625 37.0 37.0 40.0 33.0 40.0 48-49 36.142250000000004 37.0 37.0 37.0 33.0 40.0 50-51 36.031125 37.0 37.0 37.0 33.0 40.0 52-53 35.677125000000004 37.0 33.0 37.0 33.0 40.0 54-55 35.55225 37.0 33.0 37.0 33.0 40.0 56-57 35.3815 37.0 33.0 37.0 33.0 40.0 58-59 34.476 37.0 33.0 37.0 30.0 37.0 60-61 34.8775 37.0 33.0 37.0 33.0 37.0 62-63 34.79875 37.0 33.0 37.0 33.0 37.0 64-65 34.7435 37.0 33.0 37.0 33.0 37.0 66-67 34.693125 37.0 33.0 37.0 33.0 37.0 68-69 33.90075 35.0 33.0 37.0 30.0 37.0 70-71 34.04796512942951 35.0 33.0 37.0 27.0 37.0 72-73 34.41907236813637 37.0 33.0 37.0 33.0 37.0 74-75 34.38179473075853 37.0 33.0 37.0 33.0 37.0 76-77 34.32871096952519 37.0 33.0 37.0 30.0 37.0 78-79 34.34839910972506 37.0 33.0 37.0 30.0 37.0 80-81 34.17375448004618 37.0 33.0 37.0 27.0 37.0 82-83 34.03248741837159 37.0 33.0 37.0 27.0 37.0 84-85 33.91998320497663 37.0 33.0 37.0 27.0 37.0 86-87 33.82340136054422 37.0 33.0 37.0 27.0 37.0 88-89 33.83333333333333 37.0 33.0 37.0 27.0 37.0 90-91 33.63210884353742 37.0 33.0 37.0 27.0 37.0 92-93 33.50693877551021 37.0 33.0 37.0 27.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 20 7.0 21 14.0 22 6.0 23 10.0 24 23.0 25 23.0 26 34.0 27 40.0 28 50.0 29 64.0 30 104.0 31 91.0 32 145.0 33 166.0 34 247.0 35 436.0 36 878.0 37 934.0 38 700.0 39 28.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 87.45 2.9000000000000004 2.75 6.9 2 69.125 17.0 7.95 5.925 3 36.025 38.025 15.225 10.725 4 33.7 27.875 19.35 19.075 5 25.3 30.599999999999998 25.0 19.1 6 20.75 37.8 26.325 15.125 7 36.199999999999996 28.975 19.8 15.024999999999999 8 29.675 30.725 23.525 16.075 9 25.275 29.599999999999998 27.750000000000004 17.375 10-11 25.3 27.775 28.7 18.224999999999998 12-13 27.2625 26.2625 28.775000000000002 17.7 14-15 21.725 28.812500000000004 30.7125 18.75 16-17 24.1875 30.6375 26.775 18.4 18-19 24.4875 26.337500000000002 28.799999999999997 20.375 20-21 24.415551943992998 25.61570196274534 30.291286410801348 19.67745968246031 22-23 26.674999999999997 23.5875 28.237499999999997 21.5 24-25 25.3125 25.4375 28.712500000000002 20.5375 26-27 24.15 25.2 30.7 19.950000000000003 28-29 24.5375 27.6375 29.275000000000002 18.55 30-31 26.974999999999998 26.9625 26.450000000000003 19.6125 32-33 25.2 25.5375 28.212500000000002 21.05 34-35 24.5375 26.6 28.5625 20.3 36-37 24.175 25.0125 28.925 21.8875 38-39 26.189283925888834 25.863795693540307 30.182774161241866 17.764146219328993 40-41 25.056292219164373 25.8443832874656 28.371278458844134 20.728046034525892 42-43 24.59672377141428 28.61072902338377 27.64786795048143 19.144679254720522 44-45 23.7625 25.624999999999996 30.337500000000002 20.275000000000002 46-47 24.762500000000003 25.2125 28.050000000000004 21.975 48-49 23.974999999999998 25.874999999999996 30.7375 19.412499999999998 50-51 23.150000000000002 27.5875 29.912499999999998 19.35 52-53 23.98195714822704 27.327402581130183 28.166896378899885 20.52374389174289 54-55 23.50587646911728 27.85696424106027 30.220055013753438 18.41710427606902 56-57 24.58114528632158 26.506626656664167 28.60715178794699 20.305076269067268 58-59 22.5625 26.3125 30.025000000000002 21.099999999999998 60-61 24.1125 26.437500000000004 29.775000000000002 19.675 62-63 22.55 28.287499999999998 31.175000000000004 17.9875 64-65 22.5875 28.975 29.5875 18.85 66-67 24.212500000000002 28.762500000000003 28.999999999999996 18.025 68-69 23.150000000000002 26.900000000000002 29.275000000000002 20.674999999999997 70-71 24.313823787442036 25.39165308935957 28.637673893971677 21.656849229226722 72-73 25.376344086021508 26.05945604048071 29.386464263124605 19.17773561037318 74-75 23.171355498721226 27.915601023017906 29.641943734015346 19.271099744245525 76-77 23.288555928700593 26.34978041849651 30.495995866701108 19.86566778610178 78-79 23.30984077264422 26.12894805533803 31.362568519968676 19.198642652049074 80-81 23.30777366472766 29.204124801692227 29.74616604970915 17.741935483870968 82-83 22.960482250502345 26.376423308774278 29.631614199598122 21.03148024112525 84-85 22.146831320396252 26.258651105984534 31.089700094992534 20.50481747862668 86-87 21.877551020408163 27.29251700680272 30.843537414965986 19.98639455782313 88-89 21.25170068027211 29.006802721088437 29.986394557823132 19.75510204081633 90-91 24.74829931972789 29.156462585034014 27.6734693877551 18.421768707482993 92-93 21.63265306122449 30.571428571428573 28.10884353741497 19.687074829931973 >>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 2.5 18 5.0 19 3.0 20 1.5 21 2.0 22 1.0 23 3.0 24 4.5 25 3.0 26 9.0 27 18.5 28 22.5 29 24.5 30 32.5 31 45.5 32 60.0 33 87.0 34 106.5 35 120.0 36 148.0 37 180.0 38 192.0 39 182.0 40 196.5 41 231.5 42 242.5 43 237.0 44 210.5 45 187.5 46 192.0 47 171.0 48 149.5 49 160.0 50 157.0 51 133.5 52 116.0 53 122.0 54 133.5 55 95.0 56 58.5 57 59.0 58 47.5 59 34.0 60 30.5 61 28.0 62 25.5 63 24.0 64 22.0 65 18.5 66 14.5 67 11.0 68 7.5 69 8.0 70 8.0 71 6.0 72 6.0 73 4.5 74 4.0 75 3.0 76 1.0 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 0.0 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 0.0125 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 0.15 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 0.2375 54-55 0.025 56-57 0.025 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 15.0 72 23.0 73 18.0 74 26.0 75 16.0 76 20.0 77 16.0 78 28.0 79 25.0 80 20.0 81 28.0 82 23.0 83 27.0 84 19.0 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 3675.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 83.05 #Duplication Level Percentage of deduplicated Percentage of total 1 93.61830222757375 77.75 2 3.521974714027694 5.8500000000000005 3 1.2040939193257074 3.0 4 0.45153521974714034 1.5 5 0.1806140878988561 0.75 6 0.09030704394942805 0.44999999999999996 7 0.060204695966285374 0.35000000000000003 8 0.2408187838651415 1.6 9 0.1806140878988561 1.35 >10 0.4214328717639976 5.8999999999999995 >50 0.030102347983142687 1.5 >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 60 1.5 No Hit GGGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGT 35 0.8750000000000001 No Hit GGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCTTGG 22 0.5499999999999999 No Hit GGGATGATTCTGTATTACAATTTGGTGGAGGAACTTTAGGACATCCTTGG 21 0.525 No Hit GGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAA 20 0.5 No Hit GGGCGCGATCTTGCTCGTGAAGGTAATGAAATTATCCGAGCAGCTTGCAA 19 0.475 No Hit GGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGTG 18 0.44999999999999996 No Hit GGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGTGTACAAGCTCGTAA 16 0.4 No Hit GGACATCCTTGGGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTT 14 0.35000000000000003 No Hit GGTAATGAAATTATCCGAGCAGCTTGCAAATGGAGTCCTGAACTAGCCGC 14 0.35000000000000003 No Hit GGCGCGATCTTGCTCGTGAAGGTAATGAAATTATCCGAGCAGCTTGCAAA 13 0.325 No Hit GTATGGAAGGCGATCAAATTCGAGTTCGCGCCGGTAGATACTATCGATTA 12 0.3 No Hit GGCGTTCAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTC 11 0.27499999999999997 No Hit GGGCTGATATCATCAACCGTGCTAATCTTGGTATGGAAGTAATGCACGAA 11 0.27499999999999997 No Hit GGAGGAACTTTAGGACATCCTTGGGGAAATGCACCTGGTGCAGCAGCTAA 10 0.25 No Hit GGAGTCCTGAACTAGCCGCAGCTTGTGAAGTATGGAAGGCGATCAAATTC 9 0.22499999999999998 No Hit GGGAGTATTATGAAAGGAGATTAATCATAGATTATCAAAAACCCTAGAAA 9 0.22499999999999998 No Hit TACCTAGGCACCCAGAGACGAGGAAGGGCGTAGCAAGCGACGAAATGCTT 9 0.22499999999999998 No Hit CAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAGGTC 9 0.22499999999999998 No Hit GAAGGTAATGAAATTATCCGAGCAGCTTGCAAATGGAGTCCTGAACTAGC 9 0.22499999999999998 No Hit GGAGTTGAAAATAAGCATAGATCCGGAGATTCCCAAATAGGTCAACCTTT 9 0.22499999999999998 No Hit GGGAAAAGAGGGGTTACTTTTTTTCATTTTTCCCTTAAAAGATAGGCTTT 8 0.2 No Hit GAAGTATGGAAGGCGATCAAATTCGAGTTCGCGCCGGTAGATACTATCGA 8 0.2 No Hit GGAGTATCCTTGATATATAAATATATAGATAAATAGATTTAAATGGAAAA 8 0.2 No Hit GGATGATTCTGTATTACAATTTGGTGGAGGAACTTTAGGACATCCTTGGG 8 0.2 No Hit GGGTTGTTTGGGAATGCAGCCCAAATCGGGCGGTAGACTCCGTCCAAGGC 8 0.2 No Hit GGGCCGGGTATCTCTCTGCATGTACGTATGCCTGTAATGTACGTAGCTAC 8 0.2 No Hit GGAGATCGAGTTGTTACTTGAGAGTTTGTAACCCTTTATCATGCCATGTC 8 0.2 No Hit GGAAAAGAGGGGTTACTTTTTTTCATTTTTCCCTTAAAAGATAGGCTTTG 8 0.2 No Hit GGGGATGATTCTGTATTACAATTTGGTGGAGGAACTTTAGGACATCCTTG 7 0.17500000000000002 No Hit GGTTTTGAAAAGGGAATCGATCGTGATTTAGAACCTGTTCTTTACATGAA 7 0.17500000000000002 No Hit GGAACTTTAGGACATCCTTGGGGAAATGCACCTGGTGCAGCAGCTAATCG 6 0.15 No Hit GGGTTACTTTTTTTCATTTTTCCCTTAAAAGATAGGCTTTGAAATCGGAG 6 0.15 No Hit CAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAATACTTGGGCTG 6 0.15 No Hit GGCTTTAGAAGCCTGTGTACAAGCTCGTAACGAAGGGCGCGATCTTGCTC 5 0.125 No Hit CAAGGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCT 5 0.125 No Hit GGGGAGTTGAAAATAAGCATAGATCCGGAGATTCCCAAATAGGTCAACCT 5 0.125 No Hit GGTGGGGCAATGGGCATTCCGTTGAGTTTGTATGGTGGGTGCTGTTTTGC 5 0.125 No Hit GGAAGGCGATCAAATTCGAGTTCGCGCCGGTAGATACTATCGATTAATAG 5 0.125 No Hit GGAAAAGAAAGCAAAAGCGATTCCCGTAGTAGCGGCGAGCGAAATGGGAG 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 0.0 0.0 0.0 0.0 0.0 60-61 0.0 0.0 0.0 0.0 0.0 62-63 0.0 0.0 0.0 0.0 0.0 64-65 0.0 0.0 0.0 0.0 0.0 66-67 0.0 0.0 0.0 0.0 0.0 68-69 0.0 0.0 0.0 0.0 0.0 70-71 0.0 0.0 0.0 0.0 0.0 72-73 0.037500000000000006 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 0.075 0.0 0.0 0.0 0.0 80-81 0.075 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position GGAAAAG 20 0.003095157 63.215626 1 >>END_MODULE Rejected 260593 READS because READLEN < 1 Read 260593 spots for ERR6133489.sra Written 260593 spots for ERR6133489.sra Rejected 260593 READS because READLEN < 1 Read 260593 spots for ERR6133489.sra Written 260593 spots for ERR6133489.sra Rejected 260593 READS because READLEN < 1 Read 260593 spots for ERR6133489.sra Written 260593 spots for ERR6133489.sra Rejected 260593 READS because READLEN < 1 Read 260593 spots for ERR6133489.sra Written 260593 spots for ERR6133489.sra Rejected 260593 READS because READLEN < 1 Read 260593 spots for ERR6133489.sra Written 260593 spots for ERR6133489.sra Rejected 260593 READS because READLEN < 1 Read 260593 spots for ERR6133489.sra Written 260593 spots for ERR6133489.sra Rejected 260593 READS because READLEN < 1 Read 260593 spots for ERR6133489.sra Written 260593 spots for ERR6133489.sra Rejected 260593 READS because READLEN < 1 Read 260593 spots for ERR6133489.sra Written 260593 spots for ERR6133489.sra Rejected 260610 READS because READLEN < 1 Read 260610 spots for ERR6133489.sra Written 260610 spots for ERR6133489.sra Rejected 260593 READS because READLEN < 1 Read 260593 spots for ERR6133489.sra Written 260593 spots for ERR6133489.sra Rejected 260593 READS because READLEN < 1 Read 260593 spots for ERR6133489.sra Written 260593 spots for ERR6133489.sra Rejected 260593 READS because READLEN < 1 Read 260593 spots for ERR6133489.sra Written 260593 spots for ERR6133489.sra Rejected 260593 READS because READLEN < 1 Read 260593 spots for ERR6133489.sra Written 260593 spots for ERR6133489.sra Rejected 260593 READS because READLEN < 1 Read 260593 spots for ERR6133489.sra Written 260593 spots for ERR6133489.sra Rejected 260593 READS because READLEN < 1 Read 260593 spots for ERR6133489.sra Written 260593 spots for ERR6133489.sra Rejected 260593 READS because READLEN < 1 Read 260593 spots for ERR6133489.sra Written 260593 spots for ERR6133489.sra Rejected 260593 READS because READLEN < 1 Read 260593 spots for ERR6133489.sra Written 260593 spots for ERR6133489.sra Rejected 260593 READS because READLEN < 1 Read 260593 spots for ERR6133489.sra Written 260593 spots for ERR6133489.sra Rejected 260593 READS because READLEN < 1 Read 260593 spots for ERR6133489.sra Written 260593 spots for ERR6133489.sra Rejected 260593 READS because READLEN < 1 Read 260593 spots for ERR6133489.sra Written 260593 spots for ERR6133489.sra SRR ids: ['ERR6133489.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_dtkcr3z6 ERR6133489.sra spots: 5211877 blocks: [[1, 260593], [260594, 521186], [521187, 781779], [781780, 1042372], [1042373, 1302965], [1302966, 1563558], [1563559, 1824151], [1824152, 2084744], [2084745, 2345337], [2345338, 2605930], [2605931, 2866523], [2866524, 3127116], [3127117, 3387709], [3387710, 3648302], [3648303, 3908895], [3908896, 4169488], [4169489, 4430081], [4430082, 4690674], [4690675, 4951267], [4951268, 5211877]] ERR6133489 file size 1143390 ERR6133489 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 ERR6133489 ERR6133489_1.fastq Input file: ERR6133489_1.fastq trimmed: ERR6133489-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 07:09:59 2024 >> started Sat Dec 7 07:10:02 2024 >> done (3.022s) 5211877 reads processed; of these: 240 ( 0.00%) short reads filtered out after trimming by size control 36 ( 0.00%) empty reads filtered out after trimming by size control 5211601 (99.99%) reads available; of these: 82428 ( 1.58%) trimmed reads available after processing 5129173 (98.42%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 56 0.00% 19 106 0.00% 20 36 0.00% 21 26 0.00% 22 32 0.00% 23 9 0.00% 24 16 0.00% 25 10 0.00% 26 15 0.00% 27 17 0.00% 28 40 0.00% 29 71 0.00% 30 20 0.00% 31 30 0.00% 32 41 0.00% 33 35 0.00% 34 21 0.00% 35 306 0.01% 36 704 0.01% 37 45 0.00% 38 74 0.00% 39 165 0.00% 40 199 0.00% 41 64 0.00% 42 21 0.00% 43 42 0.00% 44 37 0.00% 45 27 0.00% 46 13 0.00% 47 20 0.00% 48 15 0.00% 49 19 0.00% 50 17 0.00% 51 119 0.00% 52 27 0.00% 53 13 0.00% 54 25 0.00% 55 15 0.00% 56 12 0.00% 57 21 0.00% 58 20 0.00% 59 21 0.00% 60 25 0.00% 61 24 0.00% 62 2 0.00% 63 6 0.00% 64 11 0.00% 65 8 0.00% 66 19 0.00% 67 37 0.00% 68 72 0.00% 69 277 0.01% 70 33042 0.63% 71 28785 0.55% 72 32223 0.62% 73 29361 0.56% 74 30178 0.58% 75 31129 0.60% 76 26778 0.51% 77 28183 0.54% 78 31866 0.61% 79 35549 0.68% 80 31298 0.60% 81 34279 0.66% 82 38408 0.74% 83 42201 0.81% 84 32456 0.62% 85 148 0.00% 86 268 0.01% 87 428 0.01% 88 843 0.02% 89 1502 0.03% 90 3389 0.07% 91 10909 0.21% 92 54623 1.05% 93 4650652 89.24% 5211601 reads passed initial QC criterion=sequence-density sequence-density=0.85 sequence-density-rank=1 fanout-score=1.98 fanout-score-rank=29 prefix-density=0.84 prefix-fanout=2.0 sequence=CAAGGCTAAATAC criterion=fanout-score sequence-density=0.01 sequence-density-rank=27 fanout-score=296.17 fanout-score-rank=1 prefix-density=0.51 prefix-fanout=7.8 sequence=GAAGAAGAAAAGTTTTCTCAACATGGGGAGGAAGTCCCTCCGAAATTTGATTTGTTATTGTATTGTAAGGGGCTTTTTTAGTATTTATCTAAAGGAAGGAACAAACGAGGATAAGATAAAATTTCTTTAAATTTATTTTGCCCAAGTGGGATATATGGCATACTATTCTTTCCATTTTCATCTTTTTTTCTATTCCACTCCATCTAGATATAAGAAAGAACCCAATGCAATGAAATTCCACTAATATACAATACAAAAAAGAAGAATAGATACAGGGTCTCAAACCTTGCTATAGAGTTTTTGCTT Started job on | Dec 07 07:10:19 Started mapping on | Dec 07 07:10:19 Finished on | Dec 07 07:10:27 Mapping speed, Million of reads per hour | 2345.22 Number of input reads | 5211601 Average input read length | 91 UNIQUE READS: Uniquely mapped reads number | 3787751 Uniquely mapped reads % | 72.68% Average mapped length | 90.85 Number of splices: Total | 157618 Number of splices: Annotated (sjdb) | 131448 Number of splices: GT/AG | 149573 Number of splices: GC/AG | 4495 Number of splices: AT/AC | 66 Number of splices: Non-canonical | 3484 Mismatch rate per base, % | 0.53% Deletion rate per base | 0.05% Deletion average length | 1.85 Insertion rate per base | 0.03% Insertion average length | 1.76 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 1274695 % of reads mapped to multiple loci | 24.46% Number of reads mapped to too many loci | 57783 % of reads mapped to too many loci | 1.11% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 1.68% % of reads unmapped: other | 0.07% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 149155 149155 149155 N_multimapping 1274695 1274695 1274695 N_noFeature 266970 302593 3606566 N_ambiguous 162630 16924 802 UnstrandedReadsAssigned:3358151 PositiveStrandReadsAssigned:3468234 NegativeStrandReadsAssigned:180383 Dataset is classified positive stranded MeadianReadLen=93 20thPercentileLength=93 echo kmer=89 ERR6133489 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: ERR6133489-trimmed.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 5,211,601 reads, 4,265,101 reads pseudoaligned [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,114 rounds 52973 ERR6133489.ke.tsv 35125 ERR6133489.se.tsv 88098 total ==> ERR6133489.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 25.7738 PNS24243 293 194 0 0 KQK14069 1603 1504 41 8.84388 KQK14071 474 375 0 0 ==> ERR6133489.se.tsv <== BRADI_1g14170v3 41 BRADI_1g53295v3 46 BRADI_1g59795v3 48 BRADI_1g07683v3 0 BRADI_1g00485v3 2 BRADI_1g20270v3 83 BRADI_1g74790v3 18 BRADI_1g09890v3 0 BRADI_1g77505v3 110 BRADI_1g48960v3 0 ERR6133489 completed mapping pipeline successfully