Starting /dee2/code/volunteer_pipeline.sh ERR6133398 current disk space = 1547668152320 free memory = 1603274732 ERR6133398 SRAfilesize 3e305ec3126f267c580596ad142aebd2 ERR6133398.sra ERR6133398.sra file validated ERR6133398 is single end ERR6133398 is conventional basespace ERR6133398 read1 length is 70-93 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename ERR6133398_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 fail #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 29.28525 33.0 27.0 33.0 15.0 37.0 2 33.58375 33.0 33.0 37.0 27.0 37.0 3 33.7495 37.0 33.0 37.0 27.0 37.0 4 33.8755 37.0 33.0 37.0 27.0 37.0 5 34.106 37.0 33.0 37.0 27.0 37.0 6 34.29525 37.0 33.0 37.0 27.0 37.0 7 35.36775 37.0 33.0 40.0 27.0 40.0 8 35.179 37.0 33.0 40.0 27.0 40.0 9 35.354 37.0 33.0 40.0 27.0 40.0 10-11 35.313375 37.0 33.0 37.0 30.0 40.0 12-13 35.113625 37.0 33.0 37.0 27.0 40.0 14-15 35.186125000000004 37.0 33.0 37.0 27.0 40.0 16-17 34.78 37.0 33.0 37.0 27.0 40.0 18-19 34.662375 37.0 33.0 37.0 27.0 40.0 20-21 33.96025 37.0 33.0 37.0 24.5 40.0 22-23 33.788 37.0 33.0 37.0 27.0 40.0 24-25 33.262125 37.0 33.0 37.0 22.0 40.0 26-27 33.241625 37.0 33.0 37.0 22.0 40.0 28-29 32.74575 37.0 33.0 37.0 22.0 40.0 30-31 32.591875 35.0 33.0 37.0 22.0 40.0 32-33 32.106625 33.0 33.0 37.0 22.0 40.0 34-35 31.361125 33.0 27.0 37.0 15.0 40.0 36-37 31.021875 33.0 27.0 37.0 15.0 37.0 38-39 31.342750000000002 33.0 27.0 37.0 22.0 38.5 40-41 31.318375000000003 33.0 27.0 37.0 22.0 38.5 42-43 31.03975 33.0 27.0 37.0 15.0 40.0 44-45 30.679875 33.0 27.0 37.0 15.0 38.5 46-47 30.154 33.0 27.0 37.0 15.0 37.0 48-49 29.98475 33.0 27.0 37.0 15.0 37.0 50-51 29.492125 33.0 27.0 37.0 15.0 37.0 52-53 29.251625 33.0 27.0 37.0 15.0 37.0 54-55 29.225875000000002 33.0 27.0 37.0 15.0 37.0 56-57 28.536875 33.0 27.0 35.0 15.0 37.0 58-59 28.30325 33.0 27.0 33.0 15.0 37.0 60-61 28.089624999999998 33.0 27.0 33.0 15.0 37.0 62-63 27.596375000000002 33.0 22.0 33.0 15.0 37.0 64-65 27.12325 33.0 22.0 33.0 10.5 37.0 66-67 26.819625000000002 30.0 22.0 33.0 10.5 37.0 68-69 26.394125000000003 27.0 22.0 33.0 10.5 35.0 70-71 28.09386884267404 33.0 27.0 33.0 15.0 37.0 72-73 28.692402572519768 33.0 27.0 33.0 15.0 37.0 74-75 28.664572953086044 33.0 27.0 33.0 15.0 37.0 76-77 28.199389659746842 33.0 27.0 33.0 15.0 37.0 78-79 27.40382583788673 33.0 24.5 33.0 10.5 37.0 80-81 26.7442753699045 33.0 22.0 33.0 6.0 37.0 82-83 26.168161510473723 33.0 22.0 33.0 2.0 37.0 84-85 25.284362887914817 33.0 18.5 33.0 2.0 37.0 86-87 24.24477895307838 30.0 15.0 33.0 2.0 37.0 88-89 23.723216707350147 30.0 10.5 33.0 2.0 37.0 90-91 22.66870084079197 27.0 2.0 33.0 2.0 37.0 92-93 21.249389747762407 27.0 2.0 33.0 2.0 33.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 20 80.0 21 108.0 22 137.0 23 153.0 24 209.0 25 220.0 26 210.0 27 237.0 28 236.0 29 263.0 30 283.0 31 270.0 32 296.0 33 276.0 34 298.0 35 269.0 36 234.0 37 181.0 38 40.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 70.72500000000001 7.675 6.7250000000000005 14.875 2 53.075 24.2 14.7 8.025 3 32.125 36.75 18.05 13.075000000000001 4 27.500000000000004 28.7 22.625 21.175 5 26.474999999999998 25.6 29.4 18.525 6 17.375 37.824999999999996 26.3 18.5 7 35.15 26.700000000000003 21.525 16.625 8 23.849999999999998 27.250000000000004 27.375 21.525 9 21.7 32.85 28.275 17.175 10-11 22.7125 28.487499999999997 30.8125 17.9875 12-13 21.1625 30.062499999999996 27.9375 20.837500000000002 14-15 19.725 33.3625 27.9375 18.975 16-17 24.3125 28.3875 24.3625 22.9375 18-19 23.400000000000002 24.5 32.6875 19.412499999999998 20-21 25.45 23.6625 30.9625 19.925 22-23 27.975 23.1625 28.625 20.2375 24-25 22.4625 25.6125 29.5875 22.3375 26-27 24.1625 24.5 29.9375 21.4 28-29 22.475 28.775000000000002 29.562500000000004 19.1875 30-31 28.4125 26.387500000000003 26.3625 18.8375 32-33 26.05 23.7 28.4 21.85 34-35 21.6875 33.650000000000006 25.5375 19.125 36-37 25.387500000000003 26.05 25.337500000000002 23.225 38-39 30.125 23.425 27.3625 19.0875 40-41 23.3875 24.2875 32.875 19.45 42-43 26.0 29.375 26.75 17.875 44-45 23.9875 26.7125 30.2125 19.0875 46-47 25.162499999999998 25.412499999999998 25.900000000000002 23.525 48-49 24.175 25.525 28.3375 21.9625 50-51 22.0625 29.575000000000003 26.087500000000002 22.275 52-53 21.7375 27.0625 26.0 25.2 54-55 21.925 26.0 31.112499999999997 20.962500000000002 56-57 25.412499999999998 30.075000000000003 25.837500000000002 18.675 58-59 22.4625 28.9 28.6125 20.025000000000002 60-61 27.925 26.974999999999998 27.3375 17.7625 62-63 20.5875 26.924999999999997 31.374999999999996 21.1125 64-65 20.5 35.3 26.474999999999998 17.724999999999998 66-67 24.45 29.049999999999997 27.275 19.225 68-69 19.9875 27.55 28.425 24.0375 70-71 22.458954756235116 28.6878054894097 27.045995738814387 21.807244015540796 72-73 24.564063684609554 26.29517311094263 30.224917867071017 18.915845337376798 74-75 25.379415890830252 29.28197933936998 26.42520086723632 18.91340390256345 76-77 21.807415036045313 25.16735324407827 26.544799176107105 26.48043254376931 78-79 24.084653336795636 28.551025707608414 27.888860036354195 19.475460919241755 80-81 20.089461912906195 35.718984344165236 27.035916326799104 17.15563741612946 82-83 23.427505330490405 26.945628997867804 25.652985074626866 23.973880597014926 84-85 20.76414202781153 26.04293236127987 32.334278385311194 20.85864722559741 86-87 20.88418768646596 29.888798481149987 26.471385950637377 22.755627881746676 88-89 19.9484675888256 28.044480607540006 29.509085977759696 22.497965825874694 90-91 24.003254678600488 32.072145375644155 25.07458638459452 18.850013561160836 92-93 19.338215351234066 31.1364252780038 28.22077569839978 21.304583672362355 >>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 1.0 17 3.5 18 3.5 19 2.0 20 3.0 21 4.5 22 5.5 23 5.0 24 7.5 25 9.5 26 10.0 27 16.5 28 29.5 29 35.0 30 35.5 31 50.0 32 63.0 33 59.5 34 76.5 35 99.0 36 119.5 37 191.0 38 231.0 39 208.0 40 216.5 41 211.5 42 210.5 43 236.5 44 219.0 45 191.5 46 174.5 47 146.5 48 116.5 49 113.0 50 114.0 51 107.0 52 112.5 53 132.0 54 226.5 55 216.5 56 102.0 57 76.0 58 55.0 59 34.0 60 23.5 61 17.5 62 13.5 63 8.0 64 11.0 65 10.5 66 7.0 67 3.5 68 4.0 69 7.5 70 5.5 71 3.0 72 3.0 73 3.0 74 2.0 75 0.5 76 0.0 77 0.0 78 0.5 79 0.5 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 21.0 71 15.0 72 14.0 73 16.0 74 27.0 75 13.0 76 20.0 77 15.0 78 16.0 79 34.0 80 17.0 81 25.0 82 30.0 83 17.0 84 33.0 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 3687.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 72.425 #Duplication Level Percentage of deduplicated Percentage of total 1 91.81912323092854 66.5 2 3.8660683465654127 5.6000000000000005 3 1.2426648256817396 2.7 4 0.9319986192613048 2.7 5 0.3451846738004833 1.25 6 0.3451846738004833 1.5 7 0.1380738695201933 0.7000000000000001 8 0.3106662064204349 1.7999999999999998 9 0.2416292716603383 1.575 >10 0.7248878149810148 10.100000000000001 >50 0.0 0.0 >100 0.03451846738004832 5.575 >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 223 5.575 No Hit GGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCTTGG 46 1.15 No Hit GGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAA 41 1.0250000000000001 No Hit CAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAGGTC 27 0.675 No Hit GGCGTTCAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTC 26 0.65 No Hit GGGCTGATATCATCAACCGTGCTAATCTTGGTATGGAAGTAATGCACGAA 25 0.625 No Hit CAAGGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCT 23 0.575 No Hit GGTTCACTGCTTTAGGTATTAGTACTATGGCGTTCAACCTAAATGGATTC 19 0.475 No Hit CAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAATACTTGGGCTGATAT 18 0.44999999999999996 No Hit CAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAATACTTGGGCTG 18 0.44999999999999996 No Hit GGGCACGTGGAATCCCGTGTGAATCAGCAAGGACCACCTTGCAAGGCTAA 17 0.42500000000000004 No Hit GTTCAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAG 17 0.42500000000000004 No Hit GGGTTGTTTGGGAATGCAGCCCAAATCGGGCGGTAGACTCCGTCCAAGGC 15 0.375 No Hit GGAATCTGGTTCACTGCTTTAGGTATTAGTACTATGGCGTTCAACCTAAA 15 0.375 No Hit GGCCTGTAGTAGGAATCTGGTTCACTGCTTTAGGTATTAGTACTATGGCG 14 0.35000000000000003 No Hit GGAATCCCGTGTGAATCAGCAAGGACCACCTTGCAAGGCTAAATACTCCT 13 0.325 No Hit GTAGGAATCTGGTTCACTGCTTTAGGTATTAGTACTATGGCGTTCAACCT 13 0.325 No Hit GTACTATGGCGTTCAACCTAAATGGATTCAATTTCAACCAATCTGTAGTT 12 0.3 No Hit GTAGTAGGAATCTGGTTCACTGCTTTAGGTATTAGTACTATGGCGTTCAA 12 0.3 No Hit GGGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGT 12 0.3 No Hit GGAGAGCAATACAAGCGTTGTGCTGCTAGGCGAAGCGGTTGAGTGCCGCA 11 0.27499999999999997 No Hit GGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGTG 10 0.25 No Hit GCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCTTGGTATG 9 0.22499999999999998 No Hit GGGGAGAGCAATACAAGCGTTGTGCTGCTAGGCGAAGCGGTTGAGTGCCG 9 0.22499999999999998 No Hit GCAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAATACTTGGGCT 9 0.22499999999999998 No Hit GGGCGCGATCTTGCTCGTGAAGGTAATGAAATTATCCGAGCAGCTTGCAA 9 0.22499999999999998 No Hit AACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAGGTCG 9 0.22499999999999998 No Hit GTGGGAGAGCAATACAAGCGTTGTGCTGCTAGGCGAAGCGGTTGAGTGCC 9 0.22499999999999998 No Hit GGATTTGTTAAATCAAATCCTTGGTTTAATAACGAACGGTGTTAACTTAC 9 0.22499999999999998 No Hit GGTATTAGTACTATGGCGTTCAACCTAAATGGATTCAATTTCAACCAATC 8 0.2 No Hit GGGAATGCAGCCCAAATCGGGCGGTAGACTCCGTCCAAGGCTAAATACAG 8 0.2 No Hit GGAGTTGAAAATAAGCATAGATCCGGAGATTCCCAAATAGGTCAACCTTT 8 0.2 No Hit GGGGTTGTGGGAGAGCAATACAAGCGTTGTGCTGCTAGGCGAAGCGGTTG 8 0.2 No Hit GTATTAGTACTATGGCGTTCAACCTAAATGGATTCAATTTCAACCAATCT 8 0.2 No Hit TACCTAGGCACCCAGAGACGAGGAAGGGCGTAGCAAGCGACGAAATGCTT 8 0.2 No Hit GGTAATGAAATTATCCGAGCAGCTTGCAAATGGAGTCCTGAACTAGCCGC 8 0.2 No Hit GGGTGAGAGCCCCGTCCGGCCCGGACCCTGTCGCCCCACGAGGCGCCGTC 8 0.2 No Hit GGGGCACGTGGAATCCCGTGTGAATCAGCAAGGACCACCTTGCAAGGCTA 8 0.2 No Hit CACGAACGTAATGCTCACAACTTCCCTCTAGATCTAGCTGCTCTTGAAGT 7 0.17500000000000002 No Hit GGAGGAACTTTAGGACATCCTTGGGGAAATGCACCTGGTGCAGCAGCTAA 7 0.17500000000000002 No Hit TCAAAAGAGGAAAGGCTTGCGGTGGATACCTAGGCACCCAGAGACGAGGA 7 0.17500000000000002 No Hit GGAAAAGAAAGCAAAAGCGATTCCCGTAGTAGCGGCGAGCGAAATGGGAG 7 0.17500000000000002 No Hit GGAGTCCTGAACTAGCCGCAGCTTGTGAAGTATGGAAGGCGATCAAATTC 6 0.15 No Hit CGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCTTGGTAT 6 0.15 No Hit CAATTTCAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAATACTT 6 0.15 No Hit GGGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCTTG 6 0.15 No Hit TATTAATACTTGGGCTGATATCATCAACCGTGCTAATCTTGGTATGGAAG 6 0.15 No Hit GGGTTGTGGGAGAGCAATACAAGCGTTGTGCTGCTAGGCGAAGCGGTTGA 6 0.15 No Hit GGAGTATCCTTGATATATAAATATATAGATAAATAGATTTAAATGGAAAA 6 0.15 No Hit GTCAAGGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAAT 6 0.15 No Hit GGGGAGTTGAAAATAAGCATAGATCCGGAGATTCCCAAATAGGTCAACCT 6 0.15 No Hit GAACGTAATGCTCACAACTTCCCTCTAGATCTAGCTGCTCTTGAAGTTCC 6 0.15 No Hit GCAAGGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATC 5 0.125 No Hit GGGTGAGTAACGCGTAAGAACCTGCCCTTGGGAGGGGAACAACAACTGGA 5 0.125 No Hit GGAGGGTGAGAGCCCCGTCCGGCCCGGACCCTGTCGCCCCACGAGGCGCC 5 0.125 No Hit GAATCTGGTTCACTGCTTTAGGTATTAGTACTATGGCGTTCAACCTAAAT 5 0.125 No Hit GTAATGAAATTATCCGAGCAGCTTGCAAATGGAGTCCTGAACTAGCCGCA 5 0.125 No Hit TGGGCTGATATCATCAACCGTGCTAATCTTGGTATGGAAGTAATGCACGA 5 0.125 No Hit GCGTTCAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTCA 5 0.125 No Hit GAATCCCGTGTGAATCAGCAAGGACCACCTTGCAAGGCTAAATACTCCTG 5 0.125 No Hit CAACCGTGCTAATCTTGGTATGGAAGTAATGCACGAACGTAATGCTCACA 5 0.125 No Hit TCTCATGGAGAGTTCGATCCTGGCTCAGGATGAACGCTGGCGGCATGCTT 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 0.0125 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 fail #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position GCAATAC 50 6.8852205E-7 51.1725 7 CAATACA 50 6.8852205E-7 51.1725 8 AGCAATA 50 6.8852205E-7 51.1725 6 ATCACTA 25 2.1884507E-5 48.735714 84-85 AGTTGAA 15 0.008949027 48.735714 82-83 CACTAGC 30 1.0802269E-6 48.735714 86-87 ACTAGCT 25 2.1884507E-5 48.735714 86-87 GCATCAC 30 1.0802269E-6 48.735714 82-83 GGAGTTG 15 0.008949027 48.735714 80-81 GGGGAGT 15 0.00920708 48.390068 78-79 GGAGAGC 45 2.3852977E-5 47.381943 2 GGGAGAG 45 2.3852977E-5 47.381943 1 GAGCAAT 55 1.3292338E-6 46.520454 5 AATACAA 55 1.3292338E-6 46.520454 9 GAGAGCA 50 4.446852E-5 42.643753 3 AAGCATC 35 3.1242216E-6 41.77347 80-81 CATCACT 30 6.425731E-5 40.613094 82-83 AGCATCA 30 6.425731E-5 40.613094 80-81 CCGAAAG 35 4.195088E-6 40.05675 76-77 TCACTAG 25 0.0013295984 38.98857 84-85 >>END_MODULE Rejected 67764 READS because READLEN < 1 Read 67764 spots for ERR6133398.sra Written 67764 spots for ERR6133398.sra Rejected 67764 READS because READLEN < 1 Read 67764 spots for ERR6133398.sra Written 67764 spots for ERR6133398.sra Rejected 67764 READS because READLEN < 1 Read 67764 spots for ERR6133398.sra Written 67764 spots for ERR6133398.sra Rejected 67764 READS because READLEN < 1 Read 67764 spots for ERR6133398.sra Written 67764 spots for ERR6133398.sra Rejected 67764 READS because READLEN < 1 Read 67764 spots for ERR6133398.sra Written 67764 spots for ERR6133398.sra Rejected 67764 READS because READLEN < 1 Read 67764 spots for ERR6133398.sra Written 67764 spots for ERR6133398.sra Rejected 67764 READS because READLEN < 1 Read 67764 spots for ERR6133398.sra Written 67764 spots for ERR6133398.sra Rejected 67767 READS because READLEN < 1 Read 67767 spots for ERR6133398.sra Written 67767 spots for ERR6133398.sra Rejected 67764 READS because READLEN < 1 Read 67764 spots for ERR6133398.sra Written 67764 spots for ERR6133398.sra Rejected 67764 READS because READLEN < 1 Read 67764 spots for ERR6133398.sra Written 67764 spots for ERR6133398.sra Rejected 67764 READS because READLEN < 1 Read 67764 spots for ERR6133398.sra Written 67764 spots for ERR6133398.sra Rejected 67764 READS because READLEN < 1 Read 67764 spots for ERR6133398.sra Written 67764 spots for ERR6133398.sra Rejected 67764 READS because READLEN < 1 Read 67764 spots for ERR6133398.sra Written 67764 spots for ERR6133398.sra Rejected 67764 READS because READLEN < 1 Read 67764 spots for ERR6133398.sra Written 67764 spots for ERR6133398.sra Rejected 67764 READS because READLEN < 1 Read 67764 spots for ERR6133398.sra Written 67764 spots for ERR6133398.sra Rejected 67764 READS because READLEN < 1 Read 67764 spots for ERR6133398.sra Written 67764 spots for ERR6133398.sra Rejected 67764 READS because READLEN < 1 Read 67764 spots for ERR6133398.sra Written 67764 spots for ERR6133398.sra Rejected 67764 READS because READLEN < 1 Read 67764 spots for ERR6133398.sra Written 67764 spots for ERR6133398.sra Rejected 67764 READS because READLEN < 1 Read 67764 spots for ERR6133398.sra Written 67764 spots for ERR6133398.sra Rejected 67764 READS because READLEN < 1 Read 67764 spots for ERR6133398.sra Written 67764 spots for ERR6133398.sra SRR ids: ['ERR6133398.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_stp_fuss ERR6133398.sra spots: 1355283 blocks: [[1, 67764], [67765, 135528], [135529, 203292], [203293, 271056], [271057, 338820], [338821, 406584], [406585, 474348], [474349, 542112], [542113, 609876], [609877, 677640], [677641, 745404], [745405, 813168], [813169, 880932], [880933, 948696], [948697, 1016460], [1016461, 1084224], [1084225, 1151988], [1151989, 1219752], [1219753, 1287516], [1287517, 1355283]] ERR6133398 file size 296259 ERR6133398 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 ERR6133398 ERR6133398_1.fastq Input file: ERR6133398_1.fastq trimmed: ERR6133398-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 03:11:51 2024 >> started Sat Dec 7 03:11:52 2024 >> done (1.037s) 1355283 reads processed; of these: 19 ( 0.00%) short reads filtered out after trimming by size control 3 ( 0.00%) empty reads filtered out after trimming by size control 1355261 (100.00%) reads available; of these: 344873 (25.45%) trimmed reads available after processing 1010388 (74.55%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 2 0.00% 19 18 0.00% 20 4 0.00% 21 2 0.00% 22 4 0.00% 23 0 0.00% 24 1 0.00% 25 4 0.00% 26 2 0.00% 27 2 0.00% 28 14 0.00% 29 28 0.00% 30 5 0.00% 31 0 0.00% 32 11 0.00% 33 1 0.00% 34 6 0.00% 35 1 0.00% 36 4 0.00% 37 4 0.00% 38 15 0.00% 39 18 0.00% 40 17 0.00% 41 9 0.00% 42 11 0.00% 43 19 0.00% 44 18 0.00% 45 32 0.00% 46 39 0.00% 47 63 0.00% 48 103 0.01% 49 125 0.01% 50 183 0.01% 51 232 0.02% 52 295 0.02% 53 415 0.03% 54 564 0.04% 55 747 0.06% 56 1001 0.07% 57 1484 0.11% 58 1053 0.08% 59 1267 0.09% 60 1478 0.11% 61 1769 0.13% 62 1952 0.14% 63 2113 0.16% 64 2308 0.17% 65 2452 0.18% 66 2416 0.18% 67 2637 0.19% 68 2320 0.17% 69 2361 0.17% 70 9054 0.67% 71 9544 0.70% 72 10868 0.80% 73 11412 0.84% 74 11717 0.86% 75 12576 0.93% 76 13480 0.99% 77 14919 1.10% 78 15422 1.14% 79 16178 1.19% 80 17232 1.27% 81 20185 1.49% 82 21366 1.58% 83 21400 1.58% 84 24436 1.80% 85 17399 1.28% 86 17979 1.33% 87 20097 1.48% 88 23948 1.77% 89 25158 1.86% 90 26490 1.95% 91 28454 2.10% 92 24613 1.82% 93 911705 67.27% 1355261 reads passed initial QC criterion=sequence-density sequence-density=3.96 sequence-density-rank=1 fanout-score=2.04 fanout-score-rank=26 prefix-density=4.06 prefix-fanout=2.0 sequence=CAAGGCTAAATAC criterion=fanout-score sequence-density=0.12 sequence-density-rank=15 fanout-score=76.44 fanout-score-rank=1 prefix-density=8.84 prefix-fanout=1.1 sequence=CCGCACCCTAGCTGGCTAAAGTC 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 03:12:17 Started mapping on | Dec 07 03:12:17 Finished on | Dec 07 03:12:24 Mapping speed, Million of reads per hour | 696.99 Number of input reads | 1355261 Average input read length | 89 UNIQUE READS: Uniquely mapped reads number | 551610 Uniquely mapped reads % | 40.70% Average mapped length | 88.32 Number of splices: Total | 22538 Number of splices: Annotated (sjdb) | 18231 Number of splices: GT/AG | 21533 Number of splices: GC/AG | 455 Number of splices: AT/AC | 23 Number of splices: Non-canonical | 527 Mismatch rate per base, % | 0.84% Deletion rate per base | 0.04% Deletion average length | 1.70 Insertion rate per base | 0.02% Insertion average length | 1.88 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 677191 % of reads mapped to multiple loci | 49.97% Number of reads mapped to too many loci | 51621 % of reads mapped to too many loci | 3.81% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 4.88% % of reads unmapped: other | 0.65% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 126460 126460 126460 N_multimapping 677191 677191 677191 N_noFeature 53242 59260 527225 N_ambiguous 22440 4047 121 UnstrandedReadsAssigned:475928 PositiveStrandReadsAssigned:488303 NegativeStrandReadsAssigned:24264 Dataset is classified positive stranded MeadianReadLen=93 20thPercentileLength=84 echo kmer=79 ERR6133398 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: ERR6133398-trimmed.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 1,355,261 reads, 866,478 reads pseudoaligned [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 848 rounds 52973 ERR6133398.ke.tsv 35125 ERR6133398.se.tsv 88098 total ==> ERR6133398.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 6 6.62205 PNS24243 293 194 0 0 KQK14069 1603 1504 5 5.03405 KQK14071 474 375 0 0 ==> ERR6133398.se.tsv <== BRADI_1g14170v3 5 BRADI_1g53295v3 7 BRADI_1g59795v3 8 BRADI_1g07683v3 0 BRADI_1g00485v3 0 BRADI_1g20270v3 12 BRADI_1g74790v3 4 BRADI_1g09890v3 0 BRADI_1g77505v3 14 BRADI_1g48960v3 0 ERR6133398 completed mapping pipeline successfully