Starting /dee2/code/volunteer_pipeline.sh ERR6133344 current disk space = 1548112703488 free memory = 1603592924 ERR6133344 SRAfilesize f5585329378ed72f1a767eaaa555b502 ERR6133344.sra ERR6133344.sra file validated ERR6133344 is single end ERR6133344 is conventional basespace ERR6133344 read1 length is 70-93 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename ERR6133344_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 36.414 37.0 37.0 37.0 37.0 37.0 2 36.58175 37.0 37.0 37.0 37.0 37.0 3 36.463 37.0 37.0 37.0 37.0 37.0 4 36.377 37.0 37.0 37.0 37.0 37.0 5 36.427 37.0 37.0 37.0 37.0 37.0 6 36.47025 37.0 37.0 37.0 37.0 37.0 7 38.55175 40.0 37.0 40.0 37.0 40.0 8 38.667 40.0 37.0 40.0 37.0 40.0 9 38.67 40.0 37.0 40.0 37.0 40.0 10-11 38.727125 40.0 37.0 40.0 37.0 40.0 12-13 38.7285 40.0 37.0 40.0 37.0 40.0 14-15 38.654875000000004 40.0 37.0 40.0 37.0 40.0 16-17 38.628249999999994 40.0 37.0 40.0 37.0 40.0 18-19 38.671499999999995 40.0 37.0 40.0 37.0 40.0 20-21 38.397125 40.0 37.0 40.0 37.0 40.0 22-23 38.5515 40.0 37.0 40.0 37.0 40.0 24-25 38.5145 40.0 37.0 40.0 37.0 40.0 26-27 38.42475 40.0 37.0 40.0 37.0 40.0 28-29 38.399249999999995 40.0 37.0 40.0 37.0 40.0 30-31 38.363749999999996 40.0 37.0 40.0 37.0 40.0 32-33 38.342625 40.0 37.0 40.0 37.0 40.0 34-35 38.257875 40.0 37.0 40.0 37.0 40.0 36-37 38.135 40.0 37.0 40.0 37.0 40.0 38-39 37.888625000000005 40.0 37.0 40.0 35.0 40.0 40-41 37.800124999999994 37.0 37.0 40.0 35.0 40.0 42-43 37.695 37.0 37.0 40.0 35.0 40.0 44-45 37.458 37.0 37.0 40.0 33.0 40.0 46-47 37.304249999999996 37.0 37.0 40.0 33.0 40.0 48-49 37.167625 37.0 37.0 40.0 33.0 40.0 50-51 36.956125 37.0 37.0 40.0 33.0 40.0 52-53 36.820375 37.0 37.0 38.5 33.0 40.0 54-55 36.629875 37.0 37.0 37.0 33.0 40.0 56-57 36.46025 37.0 37.0 37.0 33.0 40.0 58-59 36.230875 37.0 37.0 37.0 33.0 40.0 60-61 36.019125 37.0 37.0 37.0 33.0 37.0 62-63 35.475625 37.0 33.0 37.0 33.0 37.0 64-65 35.246750000000006 37.0 33.0 37.0 33.0 37.0 66-67 35.115375 37.0 33.0 37.0 33.0 37.0 68-69 33.746125 35.0 33.0 37.0 30.0 37.0 70-71 33.606463512833415 33.0 33.0 37.0 30.0 37.0 72-73 34.05257258064307 33.0 33.0 37.0 33.0 37.0 74-75 33.963620803595035 33.0 33.0 37.0 33.0 37.0 76-77 33.72228188770441 33.0 33.0 37.0 30.0 37.0 78-79 33.39395415976669 33.0 33.0 37.0 27.0 37.0 80-81 33.08788113687675 33.0 33.0 37.0 27.0 37.0 82-83 33.00142254185124 33.0 33.0 37.0 27.0 37.0 84-85 32.319849150056726 33.0 33.0 35.0 27.0 37.0 86-87 32.00292153589315 33.0 33.0 33.0 27.0 37.0 88-89 32.10267111853088 33.0 33.0 33.0 27.0 37.0 90-91 31.462715637173066 33.0 30.0 33.0 24.5 37.0 92-93 30.398720089037283 33.0 27.0 33.0 22.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 20 1.0 21 1.0 22 3.0 23 3.0 24 9.0 25 8.0 26 14.0 27 13.0 28 14.0 29 19.0 30 30.0 31 53.0 32 58.0 33 126.0 34 233.0 35 582.0 36 1094.0 37 1442.0 38 282.0 39 15.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 66.125 8.649999999999999 8.075000000000001 17.150000000000002 2 48.325 26.375 15.174999999999999 10.125 3 31.0 37.325 18.45 13.225000000000001 4 32.85 24.224999999999998 23.325000000000003 19.6 5 24.0 27.075 28.849999999999998 20.075000000000003 6 21.05 33.175 28.549999999999997 17.224999999999998 7 31.374999999999996 28.675 22.475 17.474999999999998 8 28.599999999999998 27.250000000000004 26.35 17.8 9 24.0 25.624999999999996 30.925000000000004 19.45 10-11 24.2375 26.974999999999998 28.95 19.8375 12-13 24.55 28.425 28.287499999999998 18.7375 14-15 22.875 27.400000000000002 31.574999999999996 18.15 16-17 23.549999999999997 29.7875 26.9125 19.75 18-19 23.0375 26.1 30.312499999999996 20.549999999999997 20-21 24.587500000000002 25.8 28.487499999999997 21.125 22-23 25.8625 24.9375 27.3125 21.8875 24-25 25.55 26.924999999999997 28.725 18.8 26-27 23.225 26.937499999999996 30.4375 19.400000000000002 28-29 25.25 27.900000000000002 27.200000000000003 19.650000000000002 30-31 24.637500000000003 26.950000000000003 27.8125 20.599999999999998 32-33 23.825 27.0625 28.775000000000002 20.3375 34-35 23.925 27.35 27.85 20.875 36-37 24.125 26.75 27.075 22.05 38-39 24.5375 25.687500000000004 29.975 19.8 40-41 25.7875 24.887500000000003 27.625 21.7 42-43 24.6875 29.4375 26.8625 19.0125 44-45 22.1875 28.575 28.5875 20.65 46-47 23.75 27.3625 28.1 20.7875 48-49 22.4625 26.974999999999998 30.725 19.8375 50-51 23.5875 26.7125 30.362499999999997 19.3375 52-53 24.65 28.6875 27.625 19.037499999999998 54-55 23.8375 28.7 29.1875 18.275 56-57 24.0625 27.437499999999996 29.062500000000004 19.4375 58-59 24.275 27.2625 28.012500000000003 20.45 60-61 24.6125 27.3125 28.6375 19.4375 62-63 21.987499999999997 30.049999999999997 29.599999999999998 18.3625 64-65 22.475 29.812499999999996 28.549999999999997 19.162499999999998 66-67 23.4875 28.4375 28.4 19.675 68-69 21.4875 28.6125 29.7875 20.1125 70-71 24.73037371457236 27.2385252069225 28.078755956859798 19.952345121645347 72-73 24.500953591862682 27.908455181182457 28.74761602034329 18.84297520661157 74-75 23.30933401902803 28.06634096168681 28.90203137053227 19.722293648752892 76-77 22.45481731894422 28.474840722922895 29.38499544922637 19.685346508906516 78-79 22.62580900805706 27.44683661339321 30.933826443006208 18.993527935543522 80-81 23.03468595152002 30.76201955269854 27.721976697468865 18.481317798312574 82-83 22.284236319085217 27.66131227879118 28.532534712768854 21.52191668935475 84-85 22.206820072082063 27.64069864153036 30.56556695314666 19.58691433324092 86-87 21.8141346688926 29.674457429048413 29.604897050639956 18.906510851419032 88-89 20.909849749582637 31.649972175848635 28.811908736783526 18.6282693377852 90-91 22.30105731775181 29.744017807456874 28.742348358375068 19.21257651641625 92-93 21.00723427935448 32.54034501947691 27.657206455203116 18.795214245965497 >>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 1.0 18 1.5 19 2.5 20 1.5 21 2.0 22 4.0 23 5.0 24 5.5 25 9.0 26 14.5 27 15.5 28 22.5 29 32.0 30 40.5 31 49.0 32 57.5 33 71.0 34 84.0 35 109.5 36 152.5 37 199.0 38 213.0 39 197.5 40 215.5 41 227.0 42 236.0 43 255.5 44 217.0 45 194.0 46 196.0 47 166.0 48 153.0 49 182.5 50 178.5 51 151.0 52 145.0 53 137.0 54 112.0 55 84.0 56 74.5 57 66.5 58 48.5 59 24.5 60 18.0 61 17.0 62 10.5 63 5.5 64 7.0 65 6.5 66 2.5 67 4.0 68 4.0 69 3.0 70 2.0 71 1.0 72 0.5 73 0.0 74 0.5 75 0.5 76 0.0 77 0.0 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 0.0 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 0.025706940874035987 76-77 0.02599766021058105 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 26.0 71 26.0 72 31.0 73 17.0 74 20.0 75 23.0 76 21.0 77 35.0 78 31.0 79 25.0 80 23.0 81 32.0 82 34.0 83 36.0 84 26.0 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 3594.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 75.75 #Duplication Level Percentage of deduplicated Percentage of total 1 89.20792079207921 67.575 2 5.37953795379538 8.15 3 1.881188118811881 4.275 4 1.221122112211221 3.6999999999999997 5 0.49504950495049505 1.875 6 0.594059405940594 2.7 7 0.23102310231023102 1.225 8 0.033003300330033 0.2 9 0.16501650165016502 1.125 >10 0.7920792079207921 9.175 >50 0.0 0.0 >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 warn #Sequence Count Percentage Possible Source GGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCTTGG 30 0.75 No Hit CAAGGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCT 27 0.675 No Hit GGGTTGTTTGGGAATGCAGCCCAAATCGGGCGGTAGACTCCGTCCAAGGC 25 0.625 No Hit GGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGTG 22 0.5499999999999999 No Hit GGGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGT 20 0.5 No Hit GGGCGCGATCTTGCTCGTGAAGGTAATGAAATTATCCGAGCAGCTTGCAA 19 0.475 No Hit GGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAA 17 0.42500000000000004 No Hit TACCTAGGCACCCAGAGACGAGGAAGGGCGTAGCAAGCGACGAAATGCTT 16 0.4 No Hit CAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAATACTTGGGCTG 16 0.4 No Hit GGAGTCCTGAACTAGCCGCAGCTTGTGAAGTATGGAAGGCGATCAAATTC 14 0.35000000000000003 No Hit CAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAATACTTGGGCTGATAT 14 0.35000000000000003 No Hit TCAAAAGAGGAAAGGCTTGCGGTGGATACCTAGGCACCCAGAGACGAGGA 14 0.35000000000000003 No Hit GGCGTTCAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTC 12 0.3 No Hit GGGATGATTCTGTATTACAATTTGGTGGAGGAACTTTAGGACATCCTTGG 12 0.3 No Hit GGAGTTGAAAATAAGCATAGATCCGGAGATTCCCAAATAGGTCAACCTTT 12 0.3 No Hit GAAGGGCGCGATCTTGCTCGTGAAGGTAATGAAATTATCCGAGCAGCTTG 12 0.3 No Hit GGAGGAACTTTAGGACATCCTTGGGGAAATGCACCTGGTGCAGCAGCTAA 12 0.3 No Hit GGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGTGTACAAGCTCGTAA 11 0.27499999999999997 No Hit GGAATCCCGTGTGAATCAGCAAGGACCACCTTGCAAGGCTAAATACTCCT 11 0.27499999999999997 No Hit GGGGATGATTCTGTATTACAATTTGGTGGAGGAACTTTAGGACATCCTTG 11 0.27499999999999997 No Hit GTATGGAAGGCGATCAAATTCGAGTTCGCGCCGGTAGATACTATCGATTA 10 0.25 No Hit GCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGTGTACAAGCTCGTAACGA 10 0.25 No Hit GGGCTGATATCATCAACCGTGCTAATCTTGGTATGGAAGTAATGCACGAA 10 0.25 No Hit GGTAATGAAATTATCCGAGCAGCTTGCAAATGGAGTCCTGAACTAGCCGC 10 0.25 No Hit GGGCACGTGGAATCCCGTGTGAATCAGCAAGGACCACCTTGCAAGGCTAA 9 0.22499999999999998 No Hit GGACATCCTTGGGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTT 9 0.22499999999999998 No Hit AGTCAAGGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAA 9 0.22499999999999998 No Hit GTGGAATCCCGTGTGAATCAGCAAGGACCACCTTGCAAGGCTAAATACTC 9 0.22499999999999998 No Hit GAAGGTAATGAAATTATCCGAGCAGCTTGCAAATGGAGTCCTGAACTAGC 9 0.22499999999999998 No Hit CAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAGGTC 8 0.2 No Hit GGAACTTTAGGACATCCTTGGGGAAATGCACCTGGTGCAGCAGCTAATCG 7 0.17500000000000002 No Hit GTAGTAGGAATCTGGTTCACTGCTTTAGGTATTAGTACTATGGCGTTCAA 7 0.17500000000000002 No Hit GGATATCGTGTGTGTACATTTGAATGTACCGACATGGGCTCGAGGAGCAT 7 0.17500000000000002 No Hit AGGAAAGGCTTGCGGTGGATACCTAGGCACCCAGAGACGAGGAAGGGCGT 7 0.17500000000000002 No Hit GCAGCTTGTGAAGTATGGAAGGCGATCAAATTCGAGTTCGCGCCGGTAGA 7 0.17500000000000002 No Hit GTATTAGTACTATGGCGTTCAACCTAAATGGATTCAATTTCAACCAATCT 7 0.17500000000000002 No Hit GGGAGAGCAATACAAGCGTTGTGCTGCTAGGCGAAGCGGTTGAGTGCCGC 7 0.17500000000000002 No Hit GCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCTTGGTATG 6 0.15 No Hit CAGCTAATCGAGTGGCTTTAGAAGCCTGTGTACAAGCTCGTAACGAAGGG 6 0.15 No Hit GGCTTTAGAAGCCTGTGTACAAGCTCGTAACGAAGGGCGCGATCTTGCTC 6 0.15 No Hit GGATGATTCTGTATTACAATTTGGTGGAGGAACTTTAGGACATCCTTGGG 6 0.15 No Hit CAAGCTCGTAACGAAGGGCGCGATCTTGCTCGTGAAGGTAATGAAATTAT 6 0.15 No Hit GGGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCTTG 6 0.15 No Hit GCAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAATACTTGGGCT 6 0.15 No Hit GGATACCTAGGCACCCAGAGACGAGGAAGGGCGTAGCAAGCGACGAAATG 6 0.15 No Hit AACGTAATGCTCACAACTTCCCTCTAGATCTAGCTGCTCTTGAAGTTCCC 6 0.15 No Hit GCAGCTTGCAAATGGAGTCCTGAACTAGCCGCAGCTTGTGAAGTATGGAA 6 0.15 No Hit GCAAATGGAGTCCTGAACTAGCCGCAGCTTGTGAAGTATGGAAGGCGATC 6 0.15 No Hit GGAGTCCCATATATATATGTATAAGATGCCAGCCCGGTTTCGTCAACCAT 6 0.15 No Hit GTCCTGAACTAGCCGCAGCTTGTGAAGTATGGAAGGCGATCAAATTCGAG 6 0.15 No Hit CACCTGGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGTGTACAAGCT 6 0.15 No Hit GATCTTGCTCGTGAAGGTAATGAAATTATCCGAGCAGCTTGCAAATGGAG 6 0.15 No Hit GGGGAGTTGAAAATAAGCATAGATCCGGAGATTCCCAAATAGGTCAACCT 6 0.15 No Hit CGTTCAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTCAA 6 0.15 No Hit GGTGGATACCTAGGCACCCAGAGACGAGGAAGGGCGTAGCAAGCGACGAA 6 0.15 No Hit TAGTCAAGGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTA 5 0.125 No Hit CAATTTCAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAATACTT 5 0.125 No Hit TATGGCGTTCAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATA 5 0.125 No Hit CAAATAGGTCAACCTTTTAAACTGCCTGCTGAATCCATGAGCAGGCAAGA 5 0.125 No Hit GGGCGTAGCAAGCGACGAAATGCTTCGGGGAGTTGAAAATAAGCATAGAT 5 0.125 No Hit GGAAAGGCTTGCGGTGGATACCTAGGCACCCAGAGACGAGGAAGGGCGTA 5 0.125 No Hit GGAGTGACGACGGCAGCTGCCTTTACACCTTTTAAGCATGCCACTTTAAT 5 0.125 No Hit GGCGCGATCTTGCTCGTGAAGGTAATGAAATTATCCGAGCAGCTTGCAAA 5 0.125 No Hit GGGGATGGAGCGACAGAAGTATGGAAATAGGATAAGGTAGCGGCGAGACG 5 0.125 No Hit GAACTAGCCGCAGCTTGTGAAGTATGGAAGGCGATCAAATTCGAGTTCGC 5 0.125 No Hit GTAGTTGATAGTCAAGGTCGCGTTATTAATACTTGGGCTGATATCATCAA 5 0.125 No Hit GTAGGAATCTGGTTCACTGCTTTAGGTATTAGTACTATGGCGTTCAACCT 5 0.125 No Hit GTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCTTGGTATGGA 5 0.125 No Hit AAGGTAATGAAATTATCCGAGCAGCTTGCAAATGGAGTCCTGAACTAGCC 5 0.125 No Hit GGGGCACGTGGAATCCCGTGTGAATCAGCAAGGACCACCTTGCAAGGCTA 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 0.025 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 0.05 0.0 0.0 0.0 0.0 22-23 0.05 0.0 0.0 0.0 0.0 24-25 0.05 0.0 0.0 0.0 0.0 26-27 0.05 0.0 0.0 0.0 0.0 28-29 0.05 0.0 0.0 0.0 0.0 30-31 0.05 0.0 0.0 0.0 0.0 32-33 0.05 0.0 0.0 0.0 0.0 34-35 0.05 0.0 0.0 0.0 0.0 36-37 0.05 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 warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position AAAAAAA 25 0.0016132011 37.506847 86-87 >>END_MODULE Rejected 87402 READS because READLEN < 1 Read 87402 spots for ERR6133344.sra Written 87402 spots for ERR6133344.sra Rejected 87402 READS because READLEN < 1 Read 87402 spots for ERR6133344.sra Written 87402 spots for ERR6133344.sra Rejected 87402 READS because READLEN < 1 Read 87402 spots for ERR6133344.sra Written 87402 spots for ERR6133344.sra Rejected 87402 READS because READLEN < 1 Read 87402 spots for ERR6133344.sra Written 87402 spots for ERR6133344.sra Rejected 87402 READS because READLEN < 1 Read 87402 spots for ERR6133344.sra Written 87402 spots for ERR6133344.sra Rejected 87402 READS because READLEN < 1 Read 87402 spots for ERR6133344.sra Written 87402 spots for ERR6133344.sra Rejected 87402 READS because READLEN < 1 Read 87402 spots for ERR6133344.sra Written 87402 spots for ERR6133344.sra Rejected 87402 READS because READLEN < 1 Read 87402 spots for ERR6133344.sra Written 87402 spots for ERR6133344.sra Rejected 87402 READS because READLEN < 1 Read 87402 spots for ERR6133344.sra Written 87402 spots for ERR6133344.sra Rejected 87402 READS because READLEN < 1 Read 87402 spots for ERR6133344.sra Written 87402 spots for ERR6133344.sra Rejected 87402 READS because READLEN < 1 Read 87402 spots for ERR6133344.sra Written 87402 spots for ERR6133344.sra Rejected 87402 READS because READLEN < 1 Read 87402 spots for ERR6133344.sra Written 87402 spots for ERR6133344.sra Rejected 87402 READS because READLEN < 1 Read 87402 spots for ERR6133344.sra Written 87402 spots for ERR6133344.sra Rejected 87402 READS because READLEN < 1 Read 87402 spots for ERR6133344.sra Written 87402 spots for ERR6133344.sra Rejected 87418 READS because READLEN < 1 Read 87418 spots for ERR6133344.sra Written 87418 spots for ERR6133344.sra Rejected 87402 READS because READLEN < 1 Read 87402 spots for ERR6133344.sra Written 87402 spots for ERR6133344.sra Rejected 87402 READS because READLEN < 1 Read 87402 spots for ERR6133344.sra Written 87402 spots for ERR6133344.sra Rejected 87402 READS because READLEN < 1 Read 87402 spots for ERR6133344.sra Written 87402 spots for ERR6133344.sra Rejected 87402 READS because READLEN < 1 Read 87402 spots for ERR6133344.sra Written 87402 spots for ERR6133344.sra Rejected 87402 READS because READLEN < 1 Read 87402 spots for ERR6133344.sra Written 87402 spots for ERR6133344.sra SRR ids: ['ERR6133344.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_a3_c0b3x ERR6133344.sra spots: 1748056 blocks: [[1, 87402], [87403, 174804], [174805, 262206], [262207, 349608], [349609, 437010], [437011, 524412], [524413, 611814], [611815, 699216], [699217, 786618], [786619, 874020], [874021, 961422], [961423, 1048824], [1048825, 1136226], [1136227, 1223628], [1223629, 1311030], [1311031, 1398432], [1398433, 1485834], [1485835, 1573236], [1573237, 1660638], [1660639, 1748056]] ERR6133344 file size 381465 ERR6133344 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 ERR6133344 ERR6133344_1.fastq Input file: ERR6133344_1.fastq trimmed: ERR6133344-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 01:05:46 2024 >> started Sat Dec 7 01:05:47 2024 >> done (1.040s) 1748056 reads processed; of these: 339 ( 0.02%) short reads filtered out after trimming by size control 11 ( 0.00%) empty reads filtered out after trimming by size control 1747706 (99.98%) reads available; of these: 24856 ( 1.42%) trimmed reads available after processing 1722850 (98.58%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 28 0.00% 19 25 0.00% 20 35 0.00% 21 14 0.00% 22 12 0.00% 23 14 0.00% 24 14 0.00% 25 8 0.00% 26 19 0.00% 27 18 0.00% 28 25 0.00% 29 12 0.00% 30 20 0.00% 31 14 0.00% 32 25 0.00% 33 9 0.00% 34 15 0.00% 35 30 0.00% 36 14 0.00% 37 13 0.00% 38 24 0.00% 39 27 0.00% 40 38 0.00% 41 10 0.00% 42 8 0.00% 43 16 0.00% 44 15 0.00% 45 14 0.00% 46 9 0.00% 47 4 0.00% 48 13 0.00% 49 9 0.00% 50 16 0.00% 51 40 0.00% 52 10 0.00% 53 10 0.00% 54 7 0.00% 55 10 0.00% 56 5 0.00% 57 10 0.00% 58 9 0.00% 59 5 0.00% 60 12 0.00% 61 4 0.00% 62 1 0.00% 63 0 0.00% 64 3 0.00% 65 2 0.00% 66 1 0.00% 67 6 0.00% 68 19 0.00% 69 50 0.00% 70 12495 0.71% 71 11140 0.64% 72 11992 0.69% 73 11437 0.65% 74 11159 0.64% 75 10621 0.61% 76 10179 0.58% 77 10921 0.62% 78 11526 0.66% 79 12259 0.70% 80 11623 0.67% 81 13694 0.78% 82 14843 0.85% 83 13631 0.78% 84 14235 0.81% 85 18 0.00% 86 42 0.00% 87 59 0.00% 88 150 0.01% 89 383 0.02% 90 909 0.05% 91 2965 0.17% 92 18340 1.05% 93 1542314 88.25% 1747706 reads passed initial QC criterion=sequence-density sequence-density=3.09 sequence-density-rank=1 fanout-score=2.00 fanout-score-rank=25 prefix-density=3.12 prefix-fanout=2.0 sequence=CAAGGCTAAATAC criterion=fanout-score sequence-density=0.04 sequence-density-rank=20 fanout-score=40.75 fanout-score-rank=1 prefix-density=0.79 prefix-fanout=2.2 sequence=TTAAAAGATTTATTAGATAATCGAAAACAGAGGATCTTGAGTACTATTCGAAATTCGGAAGAATTGCGTAGAGGGACCTTTGAGCAGCTCGAAAAAGCTCGGATTCGATTACAGAAAGTCGAACTAGAAGCGGATGAGTATCGAATGAATGGATACTCTGAGATAGAACGAGAAAAAGAAAATTTGATTAATGCTACTTCTATTAGTTTGGAACAATTAGAAAAGTCTAAAAACGAAACCCTTTATTTTG 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 01:06:00 Started mapping on | Dec 07 01:06:00 Finished on | Dec 07 01:06:05 Mapping speed, Million of reads per hour | 1258.35 Number of input reads | 1747706 Average input read length | 91 UNIQUE READS: Uniquely mapped reads number | 949731 Uniquely mapped reads % | 54.34% Average mapped length | 90.34 Number of splices: Total | 33689 Number of splices: Annotated (sjdb) | 27034 Number of splices: GT/AG | 31854 Number of splices: GC/AG | 726 Number of splices: AT/AC | 60 Number of splices: Non-canonical | 1049 Mismatch rate per base, % | 0.57% Deletion rate per base | 0.06% Deletion average length | 1.85 Insertion rate per base | 0.04% Insertion average length | 2.02 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 699796 % of reads mapped to multiple loci | 40.04% Number of reads mapped to too many loci | 52764 % of reads mapped to too many loci | 3.02% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 2.46% % of reads unmapped: other | 0.14% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 98179 98179 98179 N_multimapping 699796 699796 699796 N_noFeature 76304 84793 910633 N_ambiguous 36629 6027 189 UnstrandedReadsAssigned:836798 PositiveStrandReadsAssigned:858911 NegativeStrandReadsAssigned:38909 Dataset is classified positive stranded MeadianReadLen=93 20thPercentileLength=93 echo kmer=89 ERR6133344 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: ERR6133344-trimmed.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 1,747,706 reads, 1,324,737 reads pseudoaligned [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 892 rounds 52973 ERR6133344.ke.tsv 35125 ERR6133344.se.tsv 88098 total ==> ERR6133344.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 8 5.95985 PNS24243 293 194 0 0 KQK14069 1603 1504 13 8.83476 KQK14071 474 375 0 0 ==> ERR6133344.se.tsv <== BRADI_1g14170v3 13 BRADI_1g53295v3 16 BRADI_1g59795v3 4 BRADI_1g07683v3 0 BRADI_1g00485v3 0 BRADI_1g20270v3 9 BRADI_1g74790v3 4 BRADI_1g09890v3 0 BRADI_1g77505v3 14 BRADI_1g48960v3 0 ERR6133344 completed mapping pipeline successfully