Starting /dee2/code/volunteer_pipeline.sh ERR6133303 current disk space = 1547846434816 free memory = 1596802084 ERR6133303 SRAfilesize 3e486be701f0da6451bb3d9c62ba83ae ERR6133303.sra ERR6133303.sra file validated ERR6133303 is single end ERR6133303 is conventional basespace ERR6133303 read1 length is 70-93 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename ERR6133303_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 35.14825 37.0 33.0 37.0 33.0 37.0 2 36.26625 37.0 37.0 37.0 33.0 37.0 3 35.98975 37.0 37.0 37.0 33.0 37.0 4 35.65425 37.0 37.0 37.0 33.0 37.0 5 35.56475 37.0 37.0 37.0 33.0 37.0 6 35.86675 37.0 37.0 37.0 33.0 37.0 7 37.58375 40.0 37.0 40.0 33.0 40.0 8 37.58475 40.0 37.0 40.0 33.0 40.0 9 37.7045 40.0 37.0 40.0 33.0 40.0 10-11 37.525125 40.0 37.0 40.0 33.0 40.0 12-13 37.509125 40.0 37.0 40.0 33.0 40.0 14-15 37.543 40.0 37.0 40.0 33.0 40.0 16-17 37.347375 40.0 37.0 40.0 33.0 40.0 18-19 37.27075 37.0 37.0 40.0 33.0 40.0 20-21 37.080625 37.0 37.0 40.0 33.0 40.0 22-23 37.06175 37.0 37.0 40.0 33.0 40.0 24-25 37.171375 37.0 37.0 40.0 33.0 40.0 26-27 37.17 37.0 37.0 40.0 33.0 40.0 28-29 37.09462499999999 37.0 37.0 40.0 33.0 40.0 30-31 37.016375 37.0 37.0 40.0 33.0 40.0 32-33 36.82575 37.0 37.0 40.0 33.0 40.0 34-35 36.728125 37.0 37.0 40.0 33.0 40.0 36-37 36.51325 37.0 37.0 40.0 33.0 40.0 38-39 36.228625 37.0 37.0 40.0 33.0 40.0 40-41 36.098875 37.0 37.0 40.0 33.0 40.0 42-43 35.814125000000004 37.0 35.0 40.0 30.0 40.0 44-45 35.437375 37.0 33.0 40.0 27.0 40.0 46-47 35.199749999999995 37.0 33.0 37.0 27.0 40.0 48-49 35.051500000000004 37.0 33.0 37.0 27.0 40.0 50-51 34.9525 37.0 33.0 37.0 27.0 40.0 52-53 34.630624999999995 37.0 33.0 37.0 27.0 40.0 54-55 34.55525 37.0 33.0 37.0 27.0 40.0 56-57 34.289875 37.0 33.0 37.0 27.0 40.0 58-59 31.832625 33.0 30.0 37.0 22.0 37.0 60-61 33.52475 37.0 33.0 37.0 27.0 37.0 62-63 33.715500000000006 37.0 33.0 37.0 27.0 37.0 64-65 33.505750000000006 37.0 33.0 37.0 27.0 37.0 66-67 33.340625 37.0 33.0 37.0 27.0 37.0 68-69 32.751125 35.0 33.0 37.0 27.0 37.0 70-71 32.85755286412635 35.0 33.0 37.0 27.0 37.0 72-73 33.1411539206306 37.0 33.0 37.0 27.0 37.0 74-75 33.20446327771178 37.0 33.0 37.0 27.0 37.0 76-77 33.306128599005724 37.0 33.0 37.0 27.0 37.0 78-79 33.145278663353324 37.0 33.0 37.0 27.0 37.0 80-81 32.99072882780584 35.0 33.0 37.0 27.0 37.0 82-83 32.8169391018139 33.0 33.0 37.0 27.0 37.0 84-85 32.652778573135876 33.0 33.0 37.0 27.0 37.0 86-87 32.64754746835443 33.0 33.0 37.0 27.0 37.0 88-89 32.71624472573839 33.0 33.0 37.0 27.0 37.0 90-91 32.52228375527426 33.0 33.0 37.0 24.5 37.0 92-93 32.49446202531645 33.0 33.0 37.0 27.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 20 19.0 21 27.0 22 27.0 23 33.0 24 44.0 25 23.0 26 54.0 27 57.0 28 65.0 29 70.0 30 110.0 31 142.0 32 166.0 33 196.0 34 254.0 35 418.0 36 773.0 37 909.0 38 597.0 39 16.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 81.325 3.65 6.325 8.7 2 60.475 22.525000000000002 11.35 5.65 3 29.375 37.625 18.425 14.575 4 30.825000000000003 27.025 19.650000000000002 22.5 5 22.625 29.15 31.0 17.224999999999998 6 19.650000000000002 37.574999999999996 26.075 16.7 7 36.375 27.175 21.175 15.275 8 29.125 29.599999999999998 24.85 16.425 9 23.95 26.174999999999997 29.325000000000003 20.549999999999997 10-11 23.225 27.525 30.3 18.95 12-13 24.55 26.687499999999996 28.599999999999998 20.1625 14-15 20.825 29.9375 30.575000000000003 18.6625 16-17 23.7 32.4375 23.8375 20.025000000000002 18-19 22.412499999999998 27.287499999999998 29.549999999999997 20.75 20-21 25.474999999999998 25.5125 29.0875 19.925 22-23 29.225 21.475 28.537499999999998 20.7625 24-25 25.337500000000002 26.75 28.225 19.6875 26-27 26.174999999999997 25.0125 30.362499999999997 18.45 28-29 25.6125 27.9375 26.987499999999997 19.4625 30-31 26.474999999999998 26.2125 27.8375 19.475 32-33 24.3875 26.6125 29.262500000000003 19.7375 34-35 23.400000000000002 29.549999999999997 26.937499999999996 20.1125 36-37 24.712500000000002 25.924999999999997 27.175 22.1875 38-39 27.037499999999998 25.3125 29.2 18.45 40-41 25.174999999999997 24.6875 28.0875 22.05 42-43 25.874999999999996 28.95 26.75 18.425 44-45 22.877859732466558 28.166020752594072 29.1911488936117 19.764970621327667 46-47 24.228028503562946 25.315664458057256 28.816102012751593 21.640205025628205 48-49 24.55 24.0 31.137500000000003 20.3125 50-51 23.371264224084033 25.997248968363134 29.823683881455548 20.807802926097285 52-53 25.431789737171464 27.121401752190238 26.307884856070086 21.13892365456821 54-55 25.8 26.0 30.025000000000002 18.175 56-57 25.2875 27.462500000000002 28.1625 19.0875 58-59 23.025000000000002 25.087500000000002 31.6875 20.200000000000003 60-61 25.474999999999998 26.775 29.1875 18.5625 62-63 22.3875 29.925 29.8875 17.8 64-65 22.475 28.5875 30.9875 17.95 66-67 24.474999999999998 28.8875 27.825 18.8125 68-69 22.425 27.3875 28.275 21.912499999999998 70-71 24.25835523845287 27.087244961822503 29.177619226436352 19.47678057328827 72-73 24.647532729103727 25.74269889224572 29.85901309164149 19.750755287009063 74-75 23.105149943059597 28.217132734404654 28.875110717449072 19.802606605086677 76-77 22.420382165605098 26.484076433121018 27.745222929936308 23.35031847133758 78-79 25.55726364335127 25.36510376633359 29.964130156290032 19.113502434025108 80-81 23.770809136662795 29.74577364821267 28.894050845270357 17.589366369854176 82-83 22.72254034357106 27.43362831858407 30.07548152004165 19.768349817803227 84-85 22.735042735042736 23.86587771203156 32.22879684418146 21.17028270874425 86-87 21.96729957805907 25.395569620253166 30.762130801687764 21.875 88-89 20.622362869198312 29.957805907172997 29.338080168776372 20.08175105485232 90-91 25.90981012658228 27.584388185654007 27.83491561181435 18.670886075949365 92-93 21.571729957805907 30.155590717299578 29.52267932489451 18.75 >>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 1.5 17 10.5 18 11.0 19 2.5 20 1.5 21 1.5 22 4.0 23 6.0 24 5.5 25 4.5 26 5.5 27 10.5 28 21.0 29 32.0 30 38.0 31 41.0 32 53.5 33 69.5 34 86.0 35 101.5 36 117.5 37 186.0 38 216.5 39 178.5 40 198.5 41 207.5 42 209.5 43 236.0 44 217.0 45 189.0 46 195.5 47 187.5 48 158.0 49 165.0 50 188.5 51 175.0 52 136.0 53 122.0 54 119.0 55 87.5 56 62.5 57 65.5 58 48.0 59 28.5 60 26.5 61 19.0 62 15.0 63 17.5 64 16.0 65 11.5 66 10.5 67 10.5 68 6.5 69 5.5 70 7.5 71 9.0 72 9.0 73 8.0 74 5.5 75 4.0 76 3.5 77 2.0 78 1.5 79 1.5 80 0.5 81 0.0 82 0.0 83 0.0 84 0.0 85 0.0 86 0.0 87 0.5 88 0.5 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 0.0125 46-47 0.0125 48-49 0.0 50-51 0.0375 52-53 0.125 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 11.0 71 10.0 72 14.0 73 9.0 74 9.0 75 18.0 76 8.0 77 10.0 78 16.0 79 13.0 80 15.0 81 16.0 82 18.0 83 20.0 84 21.0 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 3792.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 77.14999999999999 #Duplication Level Percentage of deduplicated Percentage of total 1 93.48671419313025 72.125 2 3.0784186649384315 4.75 3 1.3285806869734285 3.075 4 0.356448476992871 1.0999999999999999 5 0.356448476992871 1.375 6 0.16202203499675957 0.75 7 0.22683084899546338 1.225 8 0.19442644199611148 1.2 9 0.0 0.0 >10 0.7453013609850939 10.575 >50 0.06480881399870382 3.8249999999999997 >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 TACCTAGGCACCCAGAGACGAGGAAGGGCGTAGCAAGCGACGAAATGCTT 93 2.325 No Hit GGGAGAGCAATACAAGCGTTGTGCTGCTAGGCGAAGCGGTTGAGTGCCGC 60 1.5 No Hit GGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCTTGG 48 1.2 No Hit GGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAA 44 1.0999999999999999 No Hit GGGATGATTCTGTATTACAATTTGGTGGAGGAACTTTAGGACATCCTTGG 34 0.8500000000000001 No Hit GGGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGT 25 0.625 No Hit GGTAATGAAATTATCCGAGCAGCTTGCAAATGGAGTCCTGAACTAGCCGC 23 0.575 No Hit GGAGTATCCTTGATATATAAATATATAGATAAATAGATTTAAATGGAAAA 21 0.525 No Hit GGACATCCTTGGGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTT 19 0.475 No Hit GGATGATTCTGTATTACAATTTGGTGGAGGAACTTTAGGACATCCTTGGG 18 0.44999999999999996 No Hit GGCGTTCAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTC 17 0.42500000000000004 No Hit CAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAGGTC 15 0.375 No Hit GGGCGCGATCTTGCTCGTGAAGGTAATGAAATTATCCGAGCAGCTTGCAA 15 0.375 No Hit GAAGCCTGTGTACAAGCTCGTAACGAAGGGCGCGATCTTGCTCGTGAAGG 14 0.35000000000000003 No Hit GGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGTG 14 0.35000000000000003 No Hit GGAGTTGAAAATAAGCATAGATCCGGAGATTCCCAAATAGGTCAACCTTT 14 0.35000000000000003 No Hit GTATTTAGCCTTGCAAGGTGGTCCTTGCTGATTCACACGGGATTCCACGT 13 0.325 No Hit GTAGTAGGAATCTGGTTCACTGCTTTAGGTATTAGTACTATGGCGTTCAA 12 0.3 No Hit CAAGGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCT 12 0.3 No Hit GGAATCCCGTGTGAATCAGCAAGGACCACCTTGCAAGGCTAAATACTCCT 12 0.3 No Hit GGGATGGAGCGACAGAAGTATGGAAATAGGATAAGGTAGCGGCGAGACGA 11 0.27499999999999997 No Hit GGGCATTCGTATTTCATAGTCAGAGGTGAAATTCTTGGATTTATGAAAGA 11 0.27499999999999997 No Hit GGGTTGTTTGGGAATGCAGCCCAAATCGGGCGGTAGACTCCGTCCAAGGC 11 0.27499999999999997 No Hit GGAGTCCTGAACTAGCCGCAGCTTGTGAAGTATGGAAGGCGATCAAATTC 10 0.25 No Hit GTACAAGCTCGTAACGAAGGGCGCGATCTTGCTCGTGAAGGTAATGAAAT 10 0.25 No Hit GGTCTTGATCCCTCTGTGTTTCCCGTGTAACGGCTACTGATCCAGTGGTT 8 0.2 No Hit GGCGCGATCTTGCTCGTGAAGGTAATGAAATTATCCGAGCAGCTTGCAAA 8 0.2 No Hit GGCCTGTAGTAGGAATCTGGTTCACTGCTTTAGGTATTAGTACTATGGCG 8 0.2 No Hit GTAGGAATCTGGTTCACTGCTTTAGGTATTAGTACTATGGCGTTCAACCT 8 0.2 No Hit GAAGGTAATGAAATTATCCGAGCAGCTTGCAAATGGAGTCCTGAACTAGC 8 0.2 No Hit GGGTGAGAGCCCCGTCCGGCCCGGACCCTGTCGCCCCACGAGGCGCCGTC 8 0.2 No Hit GGGGATGGAGCGACAGAAGTATGGAAATAGGATAAGGTAGCGGCGAGACG 7 0.17500000000000002 No Hit GGGAGTATTATGAAAGGAGATTAATCATAGATTATCAAAAACCCTAGAAA 7 0.17500000000000002 No Hit GGGGAGTTGAAAATAAGCATAGATCCGGAGATTCCCAAATAGGTCAACCT 7 0.17500000000000002 No Hit GTATGGAAGGCGATCAAATTCGAGTTCGCGCCGGTAGATACTATCGATTA 7 0.17500000000000002 No Hit GATACCTAGGCACCCAGAGACGAGGAAGGGCGTAGCAAGCGACGAAATGC 7 0.17500000000000002 No Hit GGAGGAACTTTAGGACATCCTTGGGGAAATGCACCTGGTGCAGCAGCTAA 7 0.17500000000000002 No Hit AAGGTAATGAAATTATCCGAGCAGCTTGCAAATGGAGTCCTGAACTAGCC 7 0.17500000000000002 No Hit GGAACTTTAGGACATCCTTGGGGAAATGCACCTGGTGCAGCAGCTAATCG 6 0.15 No Hit GGTGGAGGAACTTTAGGACATCCTTGGGGAAATGCACCTGGTGCAGCAGC 6 0.15 No Hit GGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGTGTACAAGCTCGTAA 6 0.15 No Hit GGGCTGATATCATCAACCGTGCTAATCTTGGTATGGAAGTAATGCACGAA 6 0.15 No Hit GGAAAAGAGGGGTTACTTTTTTTCATTTTTCCCTTAAAAGATAGGCTTTG 6 0.15 No Hit CACCCAGAGACGAGGAAGGGCGTAGCAAGCGACGAAATGCTTCGGGGAGT 5 0.125 No Hit GGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTTTTAA 5 0.125 No Hit CAACATAGGTCATCGAAAAGATCTCGGACGACTCACCAAAGCACGAAAGC 5 0.125 No Hit GGAGTGGGGGTGCCATACGCAAAAAGGAAGCGACTCATAGAATGGCAGAG 5 0.125 No Hit GTAACGAAGGGCGCGATCTTGCTCGTGAAGGTAATGAAATTATCCGAGCA 5 0.125 No Hit GTAATGAAATTATCCGAGCAGCTTGCAAATGGAGTCCTGAACTAGCCGCA 5 0.125 No Hit CATTACTGATGGAGTGATGGTCCATAGAGCATTAGTTTCACTACCTTCGC 5 0.125 No Hit GGGCCGGGTATCTCTCTGCATGTACGTATGCCTGTAATGTACGTAGCTAC 5 0.125 No Hit GGGGATGATTCTGTATTACAATTTGGTGGAGGAACTTTAGGACATCCTTG 5 0.125 No Hit GGGGCATTCGTATTTCATAGTCAGAGGTGAAATTCTTGGATTTATGAAAG 5 0.125 No Hit GGAAATTAACAGTTGGAAAGGGCGATCGGTCTTGATCCCTCTGTGTTTCC 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 0.05 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 0.0625 0.0 0.0 0.0 0.0 68-69 0.075 0.0 0.0 0.0 0.0 70-71 0.075 0.0 0.0 0.0 0.0 72-73 0.0875 0.0 0.0 0.0 0.0 74-75 0.1 0.0 0.0 0.0 0.0 76-77 0.1 0.0 0.0 0.0 0.0 78-79 0.1 0.0 0.0 0.0 0.0 80-81 0.1 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position GGAGAGC 15 9.0703985E-4 86.125 2 GCAATAC 15 9.0703985E-4 86.125 7 CAATACA 15 9.0703985E-4 86.125 8 AGCAATA 15 9.0703985E-4 86.125 6 GAGAGCA 20 0.00284153 64.59375 3 AATACAA 20 0.00284153 64.59375 9 GAGCAAT 25 0.0068764486 51.675 5 >>END_MODULE Rejected 190833 READS because READLEN < 1 Read 190833 spots for ERR6133303.sra Written 190833 spots for ERR6133303.sra Rejected 190833 READS because READLEN < 1 Read 190833 spots for ERR6133303.sra Written 190833 spots for ERR6133303.sra Rejected 190833 READS because READLEN < 1 Read 190833 spots for ERR6133303.sra Written 190833 spots for ERR6133303.sra Rejected 190833 READS because READLEN < 1 Read 190833 spots for ERR6133303.sra Written 190833 spots for ERR6133303.sra Rejected 190833 READS because READLEN < 1 Read 190833 spots for ERR6133303.sra Written 190833 spots for ERR6133303.sra Rejected 190833 READS because READLEN < 1 Read 190833 spots for ERR6133303.sra Written 190833 spots for ERR6133303.sra Rejected 190833 READS because READLEN < 1 Read 190833 spots for ERR6133303.sra Written 190833 spots for ERR6133303.sra Rejected 190833 READS because READLEN < 1 Read 190833 spots for ERR6133303.sra Written 190833 spots for ERR6133303.sra Rejected 190833 READS because READLEN < 1 Read 190833 spots for ERR6133303.sra Written 190833 spots for ERR6133303.sra Rejected 190833 READS because READLEN < 1 Read 190833 spots for ERR6133303.sra Written 190833 spots for ERR6133303.sra Rejected 190833 READS because READLEN < 1 Read 190833 spots for ERR6133303.sra Written 190833 spots for ERR6133303.sra Rejected 190833 READS because READLEN < 1 Read 190833 spots for ERR6133303.sra Written 190833 spots for ERR6133303.sra Rejected 190833 READS because READLEN < 1 Read 190833 spots for ERR6133303.sra Written 190833 spots for ERR6133303.sra Rejected 190833 READS because READLEN < 1 Read 190833 spots for ERR6133303.sra Written 190833 spots for ERR6133303.sra Rejected 190833 READS because READLEN < 1 Read 190833 spots for ERR6133303.sra Written 190833 spots for ERR6133303.sra Rejected 190841 READS because READLEN < 1 Read 190841 spots for ERR6133303.sra Written 190841 spots for ERR6133303.sra Rejected 190833 READS because READLEN < 1 Read 190833 spots for ERR6133303.sra Written 190833 spots for ERR6133303.sra Rejected 190833 READS because READLEN < 1 Read 190833 spots for ERR6133303.sra Written 190833 spots for ERR6133303.sra Rejected 190833 READS because READLEN < 1 Read 190833 spots for ERR6133303.sra Written 190833 spots for ERR6133303.sra Rejected 190833 READS because READLEN < 1 Read 190833 spots for ERR6133303.sra Written 190833 spots for ERR6133303.sra SRR ids: ['ERR6133303.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_swa4wty5 ERR6133303.sra spots: 3816668 blocks: [[1, 190833], [190834, 381666], [381667, 572499], [572500, 763332], [763333, 954165], [954166, 1144998], [1144999, 1335831], [1335832, 1526664], [1526665, 1717497], [1717498, 1908330], [1908331, 2099163], [2099164, 2289996], [2289997, 2480829], [2480830, 2671662], [2671663, 2862495], [2862496, 3053328], [3053329, 3244161], [3244162, 3434994], [3434995, 3625827], [3625828, 3816668]] ERR6133303 file size 841128 ERR6133303 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 ERR6133303 ERR6133303_1.fastq Input file: ERR6133303_1.fastq trimmed: ERR6133303-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 00:09:50 2024 >> started Sat Dec 7 00:09:52 2024 >> done (2.053s) 3816668 reads processed; of these: 478 ( 0.01%) short reads filtered out after trimming by size control 35 ( 0.00%) empty reads filtered out after trimming by size control 3816155 (99.99%) reads available; of these: 63795 ( 1.67%) trimmed reads available after processing 3752360 (98.33%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 68 0.00% 19 120 0.00% 20 113 0.00% 21 127 0.00% 22 131 0.00% 23 38 0.00% 24 56 0.00% 25 36 0.00% 26 36 0.00% 27 60 0.00% 28 122 0.00% 29 131 0.00% 30 121 0.00% 31 172 0.00% 32 76 0.00% 33 55 0.00% 34 77 0.00% 35 687 0.02% 36 402 0.01% 37 74 0.00% 38 88 0.00% 39 520 0.01% 40 183 0.00% 41 278 0.01% 42 21 0.00% 43 25 0.00% 44 20 0.00% 45 12 0.00% 46 21 0.00% 47 12 0.00% 48 17 0.00% 49 14 0.00% 50 24 0.00% 51 40 0.00% 52 16 0.00% 53 13 0.00% 54 18 0.00% 55 14 0.00% 56 19 0.00% 57 30 0.00% 58 22 0.00% 59 10 0.00% 60 23 0.00% 61 27 0.00% 62 3 0.00% 63 9 0.00% 64 6 0.00% 65 8 0.00% 66 7 0.00% 67 14 0.00% 68 43 0.00% 69 156 0.00% 70 13072 0.34% 71 12121 0.32% 72 14628 0.38% 73 12348 0.32% 74 12656 0.33% 75 13693 0.36% 76 11508 0.30% 77 11771 0.31% 78 13482 0.35% 79 15269 0.40% 80 14516 0.38% 81 16589 0.43% 82 18630 0.49% 83 17972 0.47% 84 16428 0.43% 85 193 0.01% 86 377 0.01% 87 552 0.01% 88 1006 0.03% 89 1674 0.04% 90 3613 0.09% 91 10652 0.28% 92 38856 1.02% 93 3540134 92.77% 3816155 reads passed initial QC criterion=sequence-density sequence-density=0.42 sequence-density-rank=1 fanout-score=5.18 fanout-score-rank=23 prefix-density=1.19 prefix-fanout=1.9 sequence=AGGCTAAATACTCCTGGGTGACCGATAGCG criterion=fanout-score sequence-density=0.01 sequence-density-rank=29 fanout-score=243.87 fanout-score-rank=1 prefix-density=0.50 prefix-fanout=6.1 sequence=GAAGAAGAAAAGTTTTCTCAACATGGGGAGGAAGTCCCTCCGAAATTTGATTTGTTATTGTATTGTAAGGGGCTTTTTTAGTATTTATCTAAAGGAAGGAACAAACGAGGATAAGATAAAATTTCTTTAAATTTATTTTGCCCAAGTGGGATATATGGCATACTATTCTTTCCATTTTCATCTTTTTTTCTATTCCACTCCATCTAGATATAAGAAAGAACCCAATGCAATGAAATTCCACTAATATACAATACAAAAAAGAAGAATAGATACAGGGTCTCAAACCTTGCTATAGAGTTTTTGCTTTAAAG Started job on | Dec 07 00:10:07 Started mapping on | Dec 07 00:10:07 Finished on | Dec 07 00:10:13 Mapping speed, Million of reads per hour | 2289.69 Number of input reads | 3816155 Average input read length | 92 UNIQUE READS: Uniquely mapped reads number | 2341928 Uniquely mapped reads % | 61.37% Average mapped length | 91.46 Number of splices: Total | 80974 Number of splices: Annotated (sjdb) | 63774 Number of splices: GT/AG | 75985 Number of splices: GC/AG | 1895 Number of splices: AT/AC | 48 Number of splices: Non-canonical | 3046 Mismatch rate per base, % | 0.47% Deletion rate per base | 0.04% Deletion average length | 1.75 Insertion rate per base | 0.03% Insertion average length | 1.70 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 1284797 % of reads mapped to multiple loci | 33.67% Number of reads mapped to too many loci | 117982 % of reads mapped to too many loci | 3.09% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 1.65% % of reads unmapped: other | 0.22% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 189430 189430 189430 N_multimapping 1284797 1284797 1284797 N_noFeature 182630 208392 2232380 N_ambiguous 96872 13044 369 UnstrandedReadsAssigned:2062426 PositiveStrandReadsAssigned:2120492 NegativeStrandReadsAssigned:109179 Dataset is classified positive stranded MeadianReadLen=93 20thPercentileLength=93 echo kmer=89 ERR6133303 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: ERR6133303-trimmed.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 3,816,155 reads, 2,962,079 reads pseudoaligned [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,024 rounds 52973 ERR6133303.ke.tsv 35125 ERR6133303.se.tsv 88098 total ==> ERR6133303.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 65 21.4345 PNS24243 293 194 0 0 KQK14069 1603 1504 17 5.11394 KQK14071 474 375 0 0 ==> ERR6133303.se.tsv <== BRADI_1g14170v3 17 BRADI_1g53295v3 126 BRADI_1g59795v3 12 BRADI_1g07683v3 0 BRADI_1g00485v3 0 BRADI_1g20270v3 33 BRADI_1g74790v3 41 BRADI_1g09890v3 0 BRADI_1g77505v3 57 BRADI_1g48960v3 0 ERR6133303 completed mapping pipeline successfully