Starting /dee2/code/volunteer_pipeline.sh ERR6133355 current disk space = 1548266782720 free memory = 1602914008 ERR6133355 SRAfilesize 602abfcc2ae1576bc814ee5604f990e2 ERR6133355.sra ERR6133355.sra file validated ERR6133355 is single end ERR6133355 is conventional basespace ERR6133355 read1 length is 70-93 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename ERR6133355_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 36.3875 37.0 37.0 37.0 33.0 37.0 2 36.66525 37.0 37.0 37.0 37.0 37.0 3 36.608 37.0 37.0 37.0 37.0 37.0 4 36.26625 37.0 37.0 37.0 37.0 37.0 5 36.34275 37.0 37.0 37.0 37.0 37.0 6 36.4905 37.0 37.0 37.0 37.0 37.0 7 38.572 40.0 37.0 40.0 37.0 40.0 8 38.59275 40.0 37.0 40.0 37.0 40.0 9 38.604 40.0 37.0 40.0 37.0 40.0 10-11 38.626375 40.0 37.0 40.0 37.0 40.0 12-13 38.653125 40.0 37.0 40.0 37.0 40.0 14-15 38.615375 40.0 37.0 40.0 37.0 40.0 16-17 38.570125000000004 40.0 37.0 40.0 37.0 40.0 18-19 38.449375 40.0 37.0 40.0 37.0 40.0 20-21 38.42775 40.0 37.0 40.0 37.0 40.0 22-23 38.408125 40.0 37.0 40.0 37.0 40.0 24-25 38.31975 40.0 37.0 40.0 37.0 40.0 26-27 38.3285 40.0 37.0 40.0 37.0 40.0 28-29 38.340875 40.0 37.0 40.0 37.0 40.0 30-31 38.290875 40.0 37.0 40.0 37.0 40.0 32-33 38.0905 40.0 37.0 40.0 37.0 40.0 34-35 38.10575 40.0 37.0 40.0 37.0 40.0 36-37 37.998625000000004 40.0 37.0 40.0 37.0 40.0 38-39 37.9155 38.5 37.0 40.0 37.0 40.0 40-41 37.75475 37.0 37.0 40.0 37.0 40.0 42-43 37.678375 37.0 37.0 40.0 37.0 40.0 44-45 37.482875 37.0 37.0 40.0 33.0 40.0 46-47 37.392125 37.0 37.0 40.0 33.0 40.0 48-49 37.245000000000005 37.0 37.0 40.0 33.0 40.0 50-51 37.084875 37.0 37.0 40.0 33.0 40.0 52-53 36.92875 37.0 37.0 38.5 33.0 40.0 54-55 36.809125 37.0 37.0 37.0 33.0 40.0 56-57 36.674375 37.0 37.0 37.0 33.0 40.0 58-59 36.4455 37.0 37.0 37.0 33.0 40.0 60-61 36.308125 37.0 37.0 37.0 33.0 37.0 62-63 36.183375 37.0 37.0 37.0 33.0 37.0 64-65 36.063874999999996 37.0 37.0 37.0 33.0 37.0 66-67 35.977125 37.0 37.0 37.0 33.0 37.0 68-69 35.103375 35.0 35.0 37.0 33.0 37.0 70-71 35.29268927405174 37.0 33.0 37.0 33.0 37.0 72-73 35.740586949774666 37.0 37.0 37.0 33.0 37.0 74-75 35.73141731106121 37.0 37.0 37.0 33.0 37.0 76-77 35.716591461298165 37.0 37.0 37.0 33.0 37.0 78-79 35.73557435294492 37.0 37.0 37.0 33.0 37.0 80-81 35.66200457026508 37.0 37.0 37.0 33.0 37.0 82-83 35.667053923753066 37.0 37.0 37.0 33.0 37.0 84-85 35.592673189468755 37.0 37.0 37.0 33.0 37.0 86-87 35.488694481830414 37.0 37.0 37.0 33.0 37.0 88-89 35.59892328398385 37.0 37.0 37.0 33.0 37.0 90-91 35.485329744279944 37.0 37.0 37.0 33.0 37.0 92-93 35.30807537012113 37.0 33.0 37.0 33.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 20 2.0 21 4.0 22 6.0 23 3.0 24 8.0 25 7.0 26 10.0 27 20.0 28 9.0 29 24.0 30 31.0 31 40.0 32 40.0 33 77.0 34 87.0 35 189.0 36 866.0 37 1095.0 38 1425.0 39 57.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 71.5 6.775 7.375 14.35 2 53.849999999999994 25.674999999999997 12.525 7.95 3 33.225 35.625 17.349999999999998 13.8 4 30.75 27.750000000000004 19.7 21.8 5 29.2 26.400000000000002 26.150000000000002 18.25 6 19.075 38.05 25.775 17.1 7 39.125 25.124999999999996 19.0 16.75 8 27.975 27.6 25.45 18.975 9 22.75 29.875 27.750000000000004 19.625 10-11 23.200000000000003 30.575000000000003 27.85 18.375 12-13 22.95 29.1625 27.1375 20.75 14-15 20.4625 32.975 28.6875 17.875 16-17 25.112499999999997 30.9625 22.25 21.675 18-19 24.474999999999998 25.674999999999997 30.049999999999997 19.8 20-21 26.9125 24.375 28.9 19.8125 22-23 30.825000000000003 22.112499999999997 26.974999999999998 20.0875 24-25 23.2875 26.137500000000003 28.487499999999997 22.0875 26-27 26.0375 24.337500000000002 28.175 21.45 28-29 24.275 27.962500000000002 28.549999999999997 19.2125 30-31 27.275 26.6 26.5125 19.6125 32-33 25.825 23.9375 27.425 22.8125 34-35 22.1875 32.6375 25.112499999999997 20.0625 36-37 25.2375 27.3625 22.900000000000002 24.5 38-39 29.336001000375138 24.59672377141428 25.82218331874453 20.24509190946605 40-41 25.2375 25.112499999999997 29.549999999999997 20.1 42-43 26.937499999999996 29.9375 25.324999999999996 17.8 44-45 23.200000000000003 28.037499999999998 29.512500000000003 19.25 46-47 26.737499999999997 25.412499999999998 26.1125 21.7375 48-49 23.9 24.725 28.4 22.975 50-51 21.099999999999998 27.800000000000004 28.849999999999998 22.25 52-53 25.0375 26.224999999999998 26.087500000000002 22.650000000000002 54-55 25.2875 27.3 26.775 20.6375 56-57 25.837500000000002 29.9375 25.7875 18.4375 58-59 23.825 28.3625 28.925 18.8875 60-61 29.6375 27.325 24.875 18.1625 62-63 20.9125 28.475 30.7875 19.825 64-65 21.37853390042532 34.48836627470603 26.782586940205157 17.350512884663498 66-67 25.2625 29.75 25.6 19.3875 68-69 21.462500000000002 27.237499999999997 27.725 23.575 70-71 25.435409096604435 28.643027189575243 24.445558200726726 21.476005513093597 72-73 26.740947075208915 27.525955938212203 27.563940238034945 18.169156748543934 74-75 25.667561006771432 29.21936885141178 27.290149482560366 17.822920659256418 76-77 22.911294481691595 25.747808148530172 25.9412068076328 25.399690562145437 78-79 25.923997917751173 28.14940135346174 27.056220718375844 18.870380010411246 80-81 20.83006022518984 34.524744697564806 25.752814873003405 18.89238020424195 82-83 22.125066242713302 29.358770535241124 25.410704822469526 23.105458399576044 84-85 21.038507983362404 26.807996779820208 30.01475915738629 22.1387360794311 86-87 20.659488559892328 30.02691790040377 25.464333781965003 23.849259757738896 88-89 20.242261103633915 29.192462987886948 28.977119784656796 21.58815612382234 90-91 24.441453566621803 30.16150740242261 24.72409152086137 20.672947510094215 92-93 20.686406460296098 30.901749663526246 27.550471063257064 20.861372812920592 >>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 1.0 18 1.0 19 2.0 20 2.5 21 2.5 22 2.5 23 5.0 24 6.5 25 7.0 26 9.0 27 10.0 28 20.5 29 29.5 30 29.0 31 29.5 32 45.5 33 67.5 34 74.0 35 86.0 36 109.0 37 138.5 38 167.0 39 179.0 40 219.0 41 221.5 42 236.0 43 286.5 44 224.5 45 175.0 46 186.5 47 160.0 48 134.5 49 140.0 50 161.0 51 163.0 52 138.0 53 145.0 54 214.5 55 180.5 56 88.5 57 80.0 58 56.0 59 28.5 60 24.0 61 20.0 62 15.5 63 13.5 64 11.0 65 10.5 66 8.5 67 8.5 68 22.0 69 27.0 70 10.5 71 0.0 72 0.0 73 1.5 74 2.0 75 0.5 76 0.5 77 0.5 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 0.0375 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 0.075 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 19.0 71 23.0 72 18.0 73 18.0 74 17.0 75 19.0 76 16.0 77 21.0 78 14.0 79 9.0 80 14.0 81 25.0 82 26.0 83 23.0 84 23.0 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 3715.0 >>END_MODULE >>Sequence Duplication Levels warn #Total Deduplicated Percentage 67.875 #Duplication Level Percentage of deduplicated Percentage of total 1 89.98158379373848 61.075 2 4.567219152854512 6.2 3 1.9152854511970532 3.9 4 1.0681399631675874 2.9000000000000004 5 0.40515653775322286 1.375 6 0.2578268876611418 1.05 7 0.3683241252302026 1.7500000000000002 8 0.22099447513812157 1.2 9 0.22099447513812157 1.35 >10 0.847145488029466 9.475 >50 0.11049723756906078 5.0 >100 0.036832412523020254 4.725 >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 189 4.725 No Hit GGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCTTGG 78 1.95 No Hit CAAGGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCT 63 1.575 No Hit TACCTAGGCACCCAGAGACGAGGAAGGGCGTAGCAAGCGACGAAATGCTT 59 1.4749999999999999 No Hit CAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAATACTTGGGCTGATAT 26 0.65 No Hit GGGCTGATATCATCAACCGTGCTAATCTTGGTATGGAAGTAATGCACGAA 26 0.65 No Hit GGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAA 26 0.65 No Hit GGGTGAGAGCCCCGTCCGGCCCGGACCCTGTCGCCCCACGAGGCGCCGTC 24 0.6 No Hit GGGCGCGATCTTGCTCGTGAAGGTAATGAAATTATCCGAGCAGCTTGCAA 23 0.575 No Hit GGAAAAGAAAGCAAAAGCGATTCCCGTAGTAGCGGCGAGCGAAATGGGAG 22 0.5499999999999999 No Hit GGGCACGTGGAATCCCGTGTGAATCAGCAAGGACCACCTTGCAAGGCTAA 18 0.44999999999999996 No Hit GGAGTTGAAAATAAGCATAGATCCGGAGATTCCCAAATAGGTCAACCTTT 17 0.42500000000000004 No Hit CAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAGGTC 17 0.42500000000000004 No Hit CAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAATACTTGGGCTG 17 0.42500000000000004 No Hit GGAATCCCGTGTGAATCAGCAAGGACCACCTTGCAAGGCTAAATACTCCT 16 0.4 No Hit GGCGTTCAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTC 15 0.375 No Hit GGGTTGTTTGGGAATGCAGCCCAAATCGGGCGGTAGACTCCGTCCAAGGC 15 0.375 No Hit GTAGTTGATAGTCAAGGTCGCGTTATTAATACTTGGGCTGATATCATCAA 15 0.375 No Hit GGGGAGTTGAAAATAAGCATAGATCCGGAGATTCCCAAATAGGTCAACCT 13 0.325 No Hit GTTCAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAG 13 0.325 No Hit GGAGGGTGAGAGCCCCGTCCGGCCCGGACCCTGTCGCCCCACGAGGCGCC 12 0.3 No Hit GTAGTAGGAATCTGGTTCACTGCTTTAGGTATTAGTACTATGGCGTTCAA 12 0.3 No Hit GTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCTTGGT 11 0.27499999999999997 No Hit GAAGGGCGCGATCTTGCTCGTGAAGGTAATGAAATTATCCGAGCAGCTTG 11 0.27499999999999997 No Hit GGAAGGGCGTAGCAAGCGACGAAATGCTTCGGGGAGTTGAAAATAAGCAT 10 0.25 No Hit GCAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAATACTTGGGCT 10 0.25 No Hit GGCGCGATCTTGCTCGTGAAGGTAATGAAATTATCCGAGCAGCTTGCAAA 10 0.25 No Hit GCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCTTGGTATG 9 0.22499999999999998 No Hit GAGGAAGGGCGTAGCAAGCGACGAAATGCTTCGGGGAGTTGAAAATAAGC 9 0.22499999999999998 No Hit GCAAGGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATC 9 0.22499999999999998 No Hit GGGCGTAGCAAGCGACGAAATGCTTCGGGGAGTTGAAAATAAGCATAGAT 9 0.22499999999999998 No Hit GGTAATGAAATTATCCGAGCAGCTTGCAAATGGAGTCCTGAACTAGCCGC 9 0.22499999999999998 No Hit TCAAAAGAGGAAAGGCTTGCGGTGGATACCTAGGCACCCAGAGACGAGGA 9 0.22499999999999998 No Hit GGGGAGAGCAATACAAGCGTTGTGCTGCTAGGCGAAGCGGTTGAGTGCCG 8 0.2 No Hit GGGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCTTG 8 0.2 No Hit GGATACCTAGGCACCCAGAGACGAGGAAGGGCGTAGCAAGCGACGAAATG 8 0.2 No Hit GATACCTAGGCACCCAGAGACGAGGAAGGGCGTAGCAAGCGACGAAATGC 8 0.2 No Hit GTATTAGTACTATGGCGTTCAACCTAAATGGATTCAATTTCAACCAATCT 8 0.2 No Hit GGGGCACGTGGAATCCCGTGTGAATCAGCAAGGACCACCTTGCAAGGCTA 8 0.2 No Hit GGAGTCCTGAACTAGCCGCAGCTTGTGAAGTATGGAAGGCGATCAAATTC 7 0.17500000000000002 No Hit GGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGTG 7 0.17500000000000002 No Hit GATTCAATTTCAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAAT 7 0.17500000000000002 No Hit GGCCTGTAGTAGGAATCTGGTTCACTGCTTTAGGTATTAGTACTATGGCG 7 0.17500000000000002 No Hit GGGGTTGTGGGAGAGCAATACAAGCGTTGTGCTGCTAGGCGAAGCGGTTG 7 0.17500000000000002 No Hit AGTCAAGGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAA 7 0.17500000000000002 No Hit CGAGGAAGGGCGTAGCAAGCGACGAAATGCTTCGGGGAGTTGAAAATAAG 7 0.17500000000000002 No Hit GTGGAATCCCGTGTGAATCAGCAAGGACCACCTTGCAAGGCTAAATACTC 7 0.17500000000000002 No Hit GAAGGTAATGAAATTATCCGAGCAGCTTGCAAATGGAGTCCTGAACTAGC 7 0.17500000000000002 No Hit GGGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGT 7 0.17500000000000002 No Hit CGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCTTGGTAT 6 0.15 No Hit GGGATGATTCTGTATTACAATTTGGTGGAGGAACTTTAGGACATCCTTGG 6 0.15 No Hit CACCCAGAGACGAGGAAGGGCGTAGCAAGCGACGAAATGCTTCGGGGAGT 6 0.15 No Hit GGCGTAGCAAGCGACGAAATGCTTCGGGGAGTTGAAAATAAGCATAGATC 6 0.15 No Hit GATCTTGCTCGTGAAGGTAATGAAATTATCCGAGCAGCTTGCAAATGGAG 6 0.15 No Hit GTCAAGGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAAT 6 0.15 No Hit CACGAACGTAATGCTCACAACTTCCCTCTAGATCTAGCTGCTCTTGAAGT 6 0.15 No Hit CAATTTCAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAATACTT 5 0.125 No Hit GGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGTGTACAAGCTCGTAA 5 0.125 No Hit CACCCTAGATGGCTAAAGTCCAGTAGCCGAAAGCATCACTAGCTTACGCT 5 0.125 No Hit GGACATCCTTGGGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTT 5 0.125 No Hit AGGAAAGGCTTGCGGTGGATACCTAGGCACCCAGAGACGAGGAAGGGCGT 5 0.125 No Hit GGGCCGGGTATCTCTCTGCATGTACGTATGCCTGTAATGTACGTAGCTAC 5 0.125 No Hit GGGAGGGTGAGAGCCCCGTCCGGCCCGGACCCTGTCGCCCCACGAGGCGC 5 0.125 No Hit GTACAAGCTCGTAACGAAGGGCGCGATCTTGCTCGTGAAGGTAATGAAAT 5 0.125 No Hit AAGGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCTT 5 0.125 No Hit GCACCCTAGATGGCTAAAGTCCAGTAGCCGAAAGCATCACTAGCTTACGC 5 0.125 No Hit TCAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAATACTTGGGCT 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 0.025 0.0 0.0 0.0 0.0 3 0.025 0.0 0.0 0.0 0.0 4 0.025 0.0 0.0 0.0 0.0 5 0.025 0.0 0.0 0.0 0.0 6 0.025 0.0 0.0 0.0 0.0 7 0.025 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 0.025 0.0 0.0 0.0 0.0 38-39 0.037500000000000006 0.0 0.0 0.0 0.0 40-41 0.0625 0.0 0.0 0.0 0.0 42-43 0.0875 0.0 0.0 0.0 0.0 44-45 0.1 0.0 0.0 0.0 0.0 46-47 0.1 0.0 0.0 0.0 0.0 48-49 0.1 0.0 0.0 0.0 0.0 50-51 0.1 0.0 0.0 0.0 0.0 52-53 0.1 0.0 0.0 0.0 0.0 54-55 0.1 0.0 0.0 0.0 0.0 56-57 0.1 0.0 0.0 0.0 0.0 58-59 0.1 0.0 0.0 0.0 0.0 60-61 0.1 0.0 0.0 0.0 0.0 62-63 0.1 0.0 0.0 0.0 0.0 64-65 0.1 0.0 0.0 0.0 0.0 66-67 0.1 0.0 0.0 0.0 0.0 68-69 0.1 0.0 0.0 0.0 0.0 70-71 0.1 0.0 0.0 0.0 0.0 72-73 0.1 0.0 0.0 0.0 0.0 74-75 0.1 0.0 0.0 0.0 0.0 76-77 0.1125 0.0 0.0 0.0 0.0 78-79 0.125 0.0 0.0 0.0 0.0 80-81 0.125 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position GCAATAC 20 0.0028794508 64.37813 7 AATACAA 20 0.0028794508 64.37813 9 AGCAATA 20 0.0028794508 64.37813 6 GGAGAGC 25 0.00696801 51.5025 2 GGGAGAG 25 0.00696801 51.5025 1 CAATACA 25 0.00696801 51.5025 8 GAGCAAT 25 0.00696801 51.5025 5 AGAGCAA 25 0.00696801 51.5025 4 GAGAGCA 25 0.00696801 51.5025 3 ATCACTA 20 5.665551E-4 46.398647 84-85 CACTAGC 20 5.665551E-4 46.398647 86-87 AAGCATC 20 5.665551E-4 46.398647 80-81 CCGAAAG 20 6.472884E-4 45.17763 76-77 CAGTAGC 20 6.9094123E-4 44.590908 70-71 GTAGCCG 20 6.9094123E-4 44.590908 72-73 TCCAGTA 20 7.368997E-4 44.01923 68-69 AGTCCAG 20 7.607711E-4 43.738853 66-67 AAAGTCC 20 8.1035483E-4 43.18868 64-65 GCTAGGC 20 8.360902E-4 42.91875 26-27 GCGGTTG 20 8.360902E-4 42.91875 36-37 >>END_MODULE Rejected 177922 READS because READLEN < 1 Read 177922 spots for ERR6133355.sra Written 177922 spots for ERR6133355.sra Rejected 177922 READS because READLEN < 1 Read 177922 spots for ERR6133355.sra Written 177922 spots for ERR6133355.sra Rejected 177922 READS because READLEN < 1 Read 177922 spots for ERR6133355.sra Written 177922 spots for ERR6133355.sra Rejected 177922 READS because READLEN < 1 Read 177922 spots for ERR6133355.sra Written 177922 spots for ERR6133355.sra Rejected 177922 READS because READLEN < 1 Read 177922 spots for ERR6133355.sra Written 177922 spots for ERR6133355.sra Rejected 177922 READS because READLEN < 1 Read 177922 spots for ERR6133355.sra Written 177922 spots for ERR6133355.sra Rejected 177922 READS because READLEN < 1 Read 177922 spots for ERR6133355.sra Written 177922 spots for ERR6133355.sra Rejected 177922 READS because READLEN < 1 Read 177922 spots for ERR6133355.sra Written 177922 spots for ERR6133355.sra Rejected 177922 READS because READLEN < 1 Read 177922 spots for ERR6133355.sra Written 177922 spots for ERR6133355.sra Rejected 177922 READS because READLEN < 1 Read 177922 spots for ERR6133355.sra Written 177922 spots for ERR6133355.sra Rejected 177922 READS because READLEN < 1 Read 177922 spots for ERR6133355.sra Written 177922 spots for ERR6133355.sra Rejected 177922 READS because READLEN < 1 Read 177922 spots for ERR6133355.sra Written 177922 spots for ERR6133355.sra Rejected 177922 READS because READLEN < 1 Read 177922 spots for ERR6133355.sra Written 177922 spots for ERR6133355.sra Rejected 177922 READS because READLEN < 1 Read 177922 spots for ERR6133355.sra Written 177922 spots for ERR6133355.sra Rejected 177922 READS because READLEN < 1 Read 177922 spots for ERR6133355.sra Written 177922 spots for ERR6133355.sra Rejected 177922 READS because READLEN < 1 Read 177922 spots for ERR6133355.sra Written 177922 spots for ERR6133355.sra Rejected 177922 READS because READLEN < 1 Read 177922 spots for ERR6133355.sra Written 177922 spots for ERR6133355.sra Rejected 177931 READS because READLEN < 1 Read 177931 spots for ERR6133355.sra Written 177931 spots for ERR6133355.sra Rejected 177922 READS because READLEN < 1 Read 177922 spots for ERR6133355.sra Written 177922 spots for ERR6133355.sra Rejected 177922 READS because READLEN < 1 Read 177922 spots for ERR6133355.sra Written 177922 spots for ERR6133355.sra SRR ids: ['ERR6133355.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_m_es3emd ERR6133355.sra spots: 3558449 blocks: [[1, 177922], [177923, 355844], [355845, 533766], [533767, 711688], [711689, 889610], [889611, 1067532], [1067533, 1245454], [1245455, 1423376], [1423377, 1601298], [1601299, 1779220], [1779221, 1957142], [1957143, 2135064], [2135065, 2312986], [2312987, 2490908], [2490909, 2668830], [2668831, 2846752], [2846753, 3024674], [3024675, 3202596], [3202597, 3380518], [3380519, 3558449]] ERR6133355 file size 782305 ERR6133355 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 ERR6133355 ERR6133355_1.fastq Input file: ERR6133355_1.fastq trimmed: ERR6133355-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 01:19:47 2024 >> started Sat Dec 7 01:19:49 2024 >> done (2.103s) 3558449 reads processed; of these: 505 ( 0.01%) short reads filtered out after trimming by size control 7 ( 0.00%) empty reads filtered out after trimming by size control 3557937 (99.99%) reads available; of these: 21011 ( 0.59%) trimmed reads available after processing 3536926 (99.41%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 30 0.00% 19 55 0.00% 20 34 0.00% 21 23 0.00% 22 30 0.00% 23 29 0.00% 24 23 0.00% 25 24 0.00% 26 40 0.00% 27 28 0.00% 28 42 0.00% 29 168 0.00% 30 22 0.00% 31 24 0.00% 32 62 0.00% 33 31 0.00% 34 21 0.00% 35 58 0.00% 36 17 0.00% 37 25 0.00% 38 44 0.00% 39 77 0.00% 40 129 0.00% 41 35 0.00% 42 18 0.00% 43 35 0.00% 44 37 0.00% 45 22 0.00% 46 12 0.00% 47 14 0.00% 48 16 0.00% 49 16 0.00% 50 23 0.00% 51 105 0.00% 52 26 0.00% 53 12 0.00% 54 12 0.00% 55 14 0.00% 56 10 0.00% 57 29 0.00% 58 22 0.00% 59 21 0.00% 60 23 0.00% 61 19 0.00% 62 10 0.00% 63 10 0.00% 64 3 0.00% 65 29 0.00% 66 26 0.00% 67 44 0.00% 68 66 0.00% 69 146 0.00% 70 17104 0.48% 71 15111 0.42% 72 16386 0.46% 73 15030 0.42% 74 14696 0.41% 75 14210 0.40% 76 13940 0.39% 77 15334 0.43% 78 15962 0.45% 79 17158 0.48% 80 17098 0.48% 81 22603 0.64% 82 22972 0.65% 83 18765 0.53% 84 22633 0.64% 85 116 0.00% 86 190 0.01% 87 297 0.01% 88 484 0.01% 89 721 0.02% 90 1354 0.04% 91 3292 0.09% 92 10535 0.30% 93 3280055 92.19% 3557937 reads passed initial QC criterion=sequence-density sequence-density=3.76 sequence-density-rank=1 fanout-score=2.03 fanout-score-rank=30 prefix-density=3.80 prefix-fanout=2.0 sequence=CAAGGCTAAATAC criterion=fanout-score sequence-density=0.01 sequence-density-rank=34 fanout-score=33.54 fanout-score-rank=1 prefix-density=0.05 prefix-fanout=4.9 sequence=GTATCTTTTTCACTCAGGACTGGGTATCCATGCCAGGTGTTATACCAGTAGCTTCAGGTGGTATTCATGTTTGGCATATGCCAGCTCTGACCGAAATCTTTGGGGATGATTCTGTATTACAATTTGGTGGAGGAACTTTAGGACATCCTTGGGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGTGTACAAGCTCGTAACGAAGGGCGCGATCTTGCTCGTGAAGGTAATGAAATTATCCGAGCAGCTTGCAAATGGAGTCCTGAACTAGCCGCAGCTTGTGAAGTATGGAAGGCGATCAAATTCGAGTTCGCGCCGGTAGATACTATCGATTAATAGATAAAACTAAATATGAAGAAGGTCTAAA 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 01:20:03 Started mapping on | Dec 07 01:20:03 Finished on | Dec 07 01:20:11 Mapping speed, Million of reads per hour | 1601.07 Number of input reads | 3557937 Average input read length | 91 UNIQUE READS: Uniquely mapped reads number | 1598447 Uniquely mapped reads % | 44.93% Average mapped length | 90.88 Number of splices: Total | 59048 Number of splices: Annotated (sjdb) | 49489 Number of splices: GT/AG | 56540 Number of splices: GC/AG | 1148 Number of splices: AT/AC | 74 Number of splices: Non-canonical | 1286 Mismatch rate per base, % | 0.42% Deletion rate per base | 0.05% Deletion average length | 1.76 Insertion rate per base | 0.02% Insertion average length | 1.68 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 1704965 % of reads mapped to multiple loci | 47.92% Number of reads mapped to too many loci | 157140 % of reads mapped to too many loci | 4.42% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 2.52% % of reads unmapped: other | 0.22% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 254525 254525 254525 N_multimapping 1704965 1704965 1704965 N_noFeature 137245 152539 1531019 N_ambiguous 62865 10774 287 UnstrandedReadsAssigned:1398337 PositiveStrandReadsAssigned:1435134 NegativeStrandReadsAssigned:67141 Dataset is classified positive stranded MeadianReadLen=93 20thPercentileLength=93 echo kmer=89 ERR6133355 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: ERR6133355-trimmed.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 3,557,937 reads, 2,363,544 reads pseudoaligned [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 934 rounds 52973 ERR6133355.ke.tsv 35125 ERR6133355.se.tsv 88098 total ==> ERR6133355.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 45 18.569 PNS24243 293 194 0 0 KQK14069 1603 1504 67 25.2207 KQK14071 474 375 0 0 ==> ERR6133355.se.tsv <== BRADI_1g14170v3 67 BRADI_1g53295v3 37 BRADI_1g59795v3 11 BRADI_1g07683v3 0 BRADI_1g00485v3 0 BRADI_1g20270v3 15 BRADI_1g74790v3 14 BRADI_1g09890v3 0 BRADI_1g77505v3 33 BRADI_1g48960v3 0 ERR6133355 completed mapping pipeline successfully