Starting /dee2/code/volunteer_pipeline.sh ERR6133463 current disk space = 1545196613632 free memory = 1422019364 ERR6133463 SRAfilesize 0a97824c2483cecebbb562c978cb2fe7 ERR6133463.sra ERR6133463.sra file validated ERR6133463 is single end ERR6133463 is conventional basespace ERR6133463 read1 length is 70-93 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename ERR6133463_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 34.96075 37.0 33.0 37.0 33.0 37.0 2 36.2255 37.0 37.0 37.0 33.0 37.0 3 35.31975 37.0 33.0 37.0 33.0 37.0 4 34.86525 37.0 33.0 37.0 33.0 37.0 5 34.639 37.0 33.0 37.0 27.0 37.0 6 35.14125 37.0 37.0 37.0 33.0 37.0 7 36.56775 37.0 37.0 40.0 33.0 40.0 8 36.842 37.0 37.0 40.0 33.0 40.0 9 37.047 37.0 37.0 40.0 33.0 40.0 10-11 36.952375 37.0 37.0 40.0 33.0 40.0 12-13 36.784625000000005 37.0 37.0 40.0 33.0 40.0 14-15 36.769000000000005 37.0 37.0 40.0 33.0 40.0 16-17 36.675250000000005 37.0 37.0 40.0 33.0 40.0 18-19 36.35575 37.0 37.0 40.0 33.0 40.0 20-21 36.22525 37.0 37.0 40.0 33.0 40.0 22-23 35.87925 37.0 33.0 40.0 33.0 40.0 24-25 36.08625000000001 37.0 35.0 40.0 33.0 40.0 26-27 36.341499999999996 37.0 37.0 40.0 33.0 40.0 28-29 36.174 37.0 37.0 40.0 33.0 40.0 30-31 36.293875 37.0 37.0 40.0 33.0 40.0 32-33 36.151125 37.0 37.0 40.0 33.0 40.0 34-35 36.073499999999996 37.0 33.0 40.0 33.0 40.0 36-37 36.046 37.0 35.0 40.0 33.0 40.0 38-39 35.99925 37.0 35.0 40.0 33.0 40.0 40-41 35.844750000000005 37.0 33.0 40.0 33.0 40.0 42-43 35.723375000000004 37.0 33.0 40.0 33.0 40.0 44-45 35.501999999999995 37.0 33.0 38.5 33.0 40.0 46-47 35.556125 37.0 33.0 37.0 33.0 40.0 48-49 35.4945 37.0 33.0 37.0 33.0 40.0 50-51 35.304249999999996 37.0 33.0 37.0 33.0 40.0 52-53 35.048874999999995 37.0 33.0 37.0 33.0 40.0 54-55 34.985 37.0 33.0 37.0 33.0 40.0 56-57 34.833625 37.0 33.0 37.0 33.0 37.0 58-59 34.301125 37.0 33.0 37.0 27.0 37.0 60-61 34.484375 37.0 33.0 37.0 27.0 37.0 62-63 34.39475 37.0 33.0 37.0 27.0 37.0 64-65 34.3305 37.0 33.0 37.0 27.0 37.0 66-67 34.080749999999995 37.0 33.0 37.0 27.0 37.0 68-69 33.229875 35.0 33.0 37.0 27.0 37.0 70-71 33.35863090007532 35.0 33.0 37.0 27.0 37.0 72-73 33.700707185086905 37.0 33.0 37.0 27.0 37.0 74-75 33.778324843058556 37.0 33.0 37.0 27.0 37.0 76-77 33.829958419898816 37.0 33.0 37.0 27.0 37.0 78-79 33.8463441136706 37.0 33.0 37.0 27.0 37.0 80-81 33.81442238148022 37.0 33.0 37.0 27.0 37.0 82-83 33.65487593664726 37.0 33.0 37.0 27.0 37.0 84-85 33.361073627488516 35.0 33.0 37.0 27.0 37.0 86-87 33.17618292360561 33.0 33.0 37.0 27.0 37.0 88-89 33.371530531324346 33.0 33.0 37.0 27.0 37.0 90-91 33.12040708432461 33.0 33.0 37.0 27.0 37.0 92-93 33.2065820777161 33.0 33.0 37.0 27.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 20 10.0 21 10.0 22 23.0 23 23.0 24 25.0 25 25.0 26 41.0 27 59.0 28 78.0 29 71.0 30 96.0 31 152.0 32 182.0 33 225.0 34 316.0 35 472.0 36 839.0 37 894.0 38 450.0 39 9.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 86.925 2.875 2.4250000000000003 7.775 2 71.25 17.549999999999997 7.175 4.025 3 37.425000000000004 37.95 13.625000000000002 11.0 4 33.35 29.175 19.1 18.375 5 25.924999999999997 30.7 25.75 17.625 6 18.375 40.025 27.075 14.524999999999999 7 37.8 28.000000000000004 19.225 14.975 8 28.475 30.349999999999998 22.1 19.075 9 25.474999999999998 30.675 27.825 16.025 10-11 24.25 29.2375 29.312500000000004 17.2 12-13 26.075 28.962500000000002 26.950000000000003 18.0125 14-15 20.45 32.3125 29.1625 18.075 16-17 24.9375 30.5375 24.8 19.725 18-19 25.065633204150515 26.815851981497683 29.453681710213775 18.66483310413802 20-21 25.456364091022753 24.593648412103025 30.23255813953488 19.717429357339338 22-23 26.787499999999998 24.375 28.0625 20.775 24-25 24.224999999999998 24.95 29.9 20.925 26-27 25.087500000000002 25.1 30.837500000000002 18.975 28-29 23.9125 28.325 29.2 18.5625 30-31 27.987499999999997 25.7125 27.462500000000002 18.8375 32-33 24.775 24.9125 28.6875 21.625 34-35 24.7375 29.099999999999998 26.55 19.6125 36-37 24.62807850981373 26.35329416177022 27.140892611576444 21.877734716839605 38-39 27.778472309038634 24.8906113264158 29.391173896737094 17.939742467808475 40-41 25.75 24.775 29.9875 19.4875 42-43 25.34735260983853 28.839654524971834 27.80072599824759 18.012266866942046 44-45 24.325 25.7375 30.162499999999998 19.775000000000002 46-47 25.587500000000002 24.462500000000002 28.075 21.875 48-49 24.887500000000003 25.087500000000002 30.4875 19.537499999999998 50-51 22.175 27.750000000000004 29.275000000000002 20.8 52-53 22.22640090259496 27.566754418954492 27.61689858342735 22.58994609502319 54-55 22.66816704176044 26.44411102775694 30.782695673918482 20.10502625656414 56-57 25.775 26.950000000000003 27.987499999999997 19.287499999999998 58-59 22.9375 26.2125 30.675 20.175 60-61 27.187499999999996 24.55 29.375 18.8875 62-63 20.775 27.6 32.5625 19.0625 64-65 22.125 31.2625 28.7 17.9125 66-67 24.0 29.212500000000002 28.712500000000002 18.075 68-69 21.752719089886234 26.428303537942245 29.416177022127766 22.402800350043755 70-71 23.600150319428785 27.558561944131277 27.871727420769133 20.9695603156708 72-73 26.518779934459292 25.157549785732293 29.291656163347618 19.0320141164608 74-75 25.10778594978443 27.491757545016487 28.594978442810042 18.805478062389046 76-77 22.897255902999362 24.097000638162093 29.610721123165284 23.39502233567326 78-79 23.541506039578515 27.24235415060396 29.915188897455668 19.300950912361863 80-81 21.27935642922019 32.52886985857013 29.181263786168422 17.010509926041262 82-83 24.25826689321657 26.41484773232257 28.04862109528166 21.278264279179194 84-85 22.33509234828496 24.70976253298153 32.33509234828496 20.62005277044855 86-87 22.17816547713455 28.11260904044409 29.579698651863602 20.129526830557758 88-89 21.20010573618821 27.557494052339415 31.04678826328311 20.195611948189267 90-91 25.337034099920697 27.53106000528681 29.302141157811263 17.829764736981232 92-93 20.539254559873115 29.830822098863337 30.676711604546657 18.95321173671689 >>END_MODULE >>Per sequence GC content fail #GC Content Count 0 0.0 1 0.0 2 0.0 3 0.0 4 0.0 5 0.0 6 0.0 7 0.0 8 0.0 9 0.0 10 0.0 11 0.0 12 0.0 13 0.0 14 0.0 15 0.0 16 0.0 17 6.5 18 7.0 19 0.5 20 0.5 21 1.0 22 1.0 23 4.0 24 8.5 25 10.0 26 17.5 27 20.5 28 20.0 29 24.0 30 30.0 31 41.5 32 57.5 33 80.5 34 101.5 35 113.5 36 129.5 37 159.5 38 188.0 39 202.0 40 230.0 41 226.0 42 203.0 43 207.0 44 186.0 45 187.0 46 176.5 47 147.0 48 152.5 49 154.0 50 135.0 51 119.5 52 119.0 53 135.5 54 179.5 55 144.5 56 72.0 57 62.5 58 55.0 59 38.0 60 30.0 61 27.5 62 16.5 63 14.0 64 19.0 65 18.0 66 15.0 67 9.0 68 8.5 69 8.5 70 6.5 71 7.0 72 6.5 73 3.5 74 0.5 75 0.0 76 0.5 77 0.5 78 0.0 79 0.0 80 0.0 81 0.0 82 0.0 83 0.5 84 0.5 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 0.0125 20-21 0.025 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 0.0125 38-39 0.0125 40-41 0.0 42-43 0.13749999999999998 44-45 0.0 46-47 0.0 48-49 0.0 50-51 0.0 52-53 0.2875 54-55 0.025 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 0.0125 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 17.0 71 9.0 72 14.0 73 10.0 74 14.0 75 12.0 76 13.0 77 12.0 78 16.0 79 23.0 80 13.0 81 13.0 82 17.0 83 20.0 84 14.0 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 3783.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 77.825 #Duplication Level Percentage of deduplicated Percentage of total 1 92.48313523931898 71.975 2 4.143912624477995 6.45 3 1.156440732412464 2.7 4 0.7067137809187279 2.1999999999999997 5 0.19274012206874397 0.75 6 0.22486347574686796 1.05 7 0.19274012206874397 1.05 8 0.09637006103437198 0.6 9 0.128493414712496 0.8999999999999999 >10 0.6424670735624799 8.75 >50 0.0 0.0 >100 0.032123353678124 3.5749999999999997 >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 143 3.5749999999999997 No Hit GGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAA 45 1.125 No Hit GGCGTTCAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTC 37 0.9249999999999999 No Hit GGGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGT 36 0.8999999999999999 No Hit GGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCTTGG 32 0.8 No Hit GGAGTTGAAAATAAGCATAGATCCGGAGATTCCCAAATAGGTCAACCTTT 23 0.575 No Hit CAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAATACTTGGGCTGATAT 15 0.375 No Hit GGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGTG 15 0.375 No Hit GGACATCCTTGGGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTT 13 0.325 No Hit GGAGTATCCTTGATATATAAATATATAGATAAATAGATTTAAATGGAAAA 13 0.325 No Hit GTAGTAGGAATCTGGTTCACTGCTTTAGGTATTAGTACTATGGCGTTCAA 12 0.3 No Hit GGGGTTGTGGGAGAGCAATACAAGCGTTGTGCTGCTAGGCGAAGCGGTTG 12 0.3 No Hit CAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAGGTC 12 0.3 No Hit GGGCTGATATCATCAACCGTGCTAATCTTGGTATGGAAGTAATGCACGAA 12 0.3 No Hit GGGGATGGAGCGACAGAAGTATGGAAATAGGATAAGGTAGCGGCGAGACG 11 0.27499999999999997 No Hit GGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGTGTACAAGCTCGTAA 11 0.27499999999999997 No Hit GGGTTGTTTGGGAATGCAGCCCAAATCGGGCGGTAGACTCCGTCCAAGGC 11 0.27499999999999997 No Hit GGGAAAAGAGGGGTTACTTTTTTTCATTTTTCCCTTAAAAGATAGGCTTT 10 0.25 No Hit TACCTAGGCACCCAGAGACGAGGAAGGGCGTAGCAAGCGACGAAATGCTT 10 0.25 No Hit GGGCACGTGGAATCCCGTGTGAATCAGCAAGGACCACCTTGCAAGGCTAA 10 0.25 No Hit GGGCGCGATCTTGCTCGTGAAGGTAATGAAATTATCCGAGCAGCTTGCAA 10 0.25 No Hit GGGAGTATTATGAAAGGAGATTAATCATAGATTATCAAAAACCCTAGAAA 9 0.22499999999999998 No Hit GGAAGAGCCCGAGCTGCTGCAGCAGGTTTTGAAAAGGGAATCGATCGTGA 9 0.22499999999999998 No Hit GGTAATGAAATTATCCGAGCAGCTTGCAAATGGAGTCCTGAACTAGCCGC 9 0.22499999999999998 No Hit GGAGGAACTTTAGGACATCCTTGGGGAAATGCACCTGGTGCAGCAGCTAA 9 0.22499999999999998 No Hit CAAGGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCT 8 0.2 No Hit GAAGGTAATGAAATTATCCGAGCAGCTTGCAAATGGAGTCCTGAACTAGC 8 0.2 No Hit GGTTCACTGCTTTAGGTATTAGTACTATGGCGTTCAACCTAAATGGATTC 8 0.2 No Hit GGGATGGAGCGACAGAAGTATGGAAATAGGATAAGGTAGCGGCGAGACGA 7 0.17500000000000002 No Hit GGCCTGTAGTAGGAATCTGGTTCACTGCTTTAGGTATTAGTACTATGGCG 7 0.17500000000000002 No Hit GGGTTGTGGGAGAGCAATACAAGCGTTGTGCTGCTAGGCGAAGCGGTTGA 7 0.17500000000000002 No Hit GGGGTTACTTTTTTTCATTTTTCCCTTAAAAGATAGGCTTTGAAATCGGA 7 0.17500000000000002 No Hit GGTATTAGTACTATGGCGTTCAACCTAAATGGATTCAATTTCAACCAATC 7 0.17500000000000002 No Hit GGAAAAGAGGGGTTACTTTTTTTCATTTTTCCCTTAAAAGATAGGCTTTG 7 0.17500000000000002 No Hit GGACATTTCTTCGAAAAAATTCGAATAGTGAGACGCATTAAAACGCAATT 6 0.15 No Hit GGGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTA 6 0.15 No Hit GGAATAAGAATAAATCGCAACTCCTTTCCACTACACATAAAAATTGATTT 6 0.15 No Hit GGAGAGCAATACAAGCGTTGTGCTGCTAGGCGAAGCGGTTGAGTGCCGCA 6 0.15 No Hit GGATACCTAGGCACCCAGAGACGAGGAAGGGCGTAGCAAGCGACGAAATG 6 0.15 No Hit GGGGATGATTCTGTATTACAATTTGGTGGAGGAACTTTAGGACATCCTTG 6 0.15 No Hit CACGAACGTAATGCTCACAACTTCCCTCTAGATCTAGCTGCTCTTGAAGT 6 0.15 No Hit GGAGAAGTACAAGTGCGGATCCAACGTCTTCTGGAAATGGTGAAGATGAT 5 0.125 No Hit GGATGATTCTGTATTACAATTTGGTGGAGGAACTTTAGGACATCCTTGGG 5 0.125 No Hit GGGGAGAGCAATACAAGCGTTGTGCTGCTAGGCGAAGCGGTTGAGTGCCG 5 0.125 No Hit GTATGGAAGGCGATCAAATTCGAGTTCGCGCCGGTAGATACTATCGATTA 5 0.125 No Hit GGGAATCGATCGTGATTTAGAACCTGTTCTTTACATGAACCCTCTTAACT 5 0.125 No Hit CAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAATACTTGGGCTG 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 0.0125 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 0.025 0.0 0.0 0.0 0.0 40-41 0.025 0.0 0.0 0.0 0.0 42-43 0.025 0.0 0.0 0.0 0.0 44-45 0.025 0.0 0.0 0.0 0.0 46-47 0.025 0.0 0.0 0.0 0.0 48-49 0.025 0.0 0.0 0.0 0.0 50-51 0.025 0.0 0.0 0.0 0.0 52-53 0.025 0.0 0.0 0.0 0.0 54-55 0.025 0.0 0.0 0.0 0.0 56-57 0.025 0.0 0.0 0.0 0.0 58-59 0.025 0.0 0.0 0.0 0.0 60-61 0.025 0.0 0.0 0.0 0.0 62-63 0.025 0.0 0.0 0.0 0.0 64-65 0.025 0.0 0.0 0.0 0.0 66-67 0.025 0.0 0.0 0.0 0.0 68-69 0.025 0.0 0.0 0.0 0.0 70-71 0.025 0.0 0.0 0.0 0.0 72-73 0.037500000000000006 0.0 0.0 0.0 0.0 74-75 0.05 0.0 0.0 0.0 0.0 76-77 0.05 0.0 0.0 0.0 0.0 78-79 0.05 0.0 0.0 0.0 0.0 80-81 0.0625 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position GGAGAGC 25 7.945628E-5 68.240005 2 GCAATAC 25 7.945628E-5 68.240005 7 GGGAGAG 25 7.945628E-5 68.240005 1 AGAGCAA 25 7.945628E-5 68.240005 4 GAGAGCA 25 7.945628E-5 68.240005 3 AGCAATA 25 7.945628E-5 68.240005 6 CAATACA 30 1.9591147E-4 56.866665 8 GAGCAAT 30 1.9591147E-4 56.866665 5 AATACAA 30 1.9591147E-4 56.866665 9 ATCACTA 20 5.0957873E-4 47.38889 84-85 AGCATCA 20 5.0957873E-4 47.38889 80-81 CACTAGC 20 5.0957873E-4 47.38889 86-87 TCACTAG 20 5.0957873E-4 47.38889 84-85 ACTAGCT 20 5.0957873E-4 47.38889 86-87 AAAGCAT 20 5.0957873E-4 47.38889 78-79 GAAAGCA 20 5.0957873E-4 47.38889 78-79 AAGCATC 20 5.0957873E-4 47.38889 80-81 AGTAGCC 20 6.24908E-4 45.493336 70-71 CAGTAGC 20 6.24908E-4 45.493336 70-71 TAGCCGA 20 6.24908E-4 45.493336 72-73 >>END_MODULE Rejected 152452 READS because READLEN < 1 Read 152452 spots for ERR6133463.sra Written 152452 spots for ERR6133463.sra Rejected 152452 READS because READLEN < 1 Read 152452 spots for ERR6133463.sra Written 152452 spots for ERR6133463.sra Rejected 152452 READS because READLEN < 1 Read 152452 spots for ERR6133463.sra Written 152452 spots for ERR6133463.sra Rejected 152452 READS because READLEN < 1 Read 152452 spots for ERR6133463.sra Written 152452 spots for ERR6133463.sra Rejected 152452 READS because READLEN < 1 Read 152452 spots for ERR6133463.sra Written 152452 spots for ERR6133463.sra Rejected 152452 READS because READLEN < 1 Read 152452 spots for ERR6133463.sra Written 152452 spots for ERR6133463.sra Rejected 152452 READS because READLEN < 1 Read 152452 spots for ERR6133463.sra Written 152452 spots for ERR6133463.sra Rejected 152452 READS because READLEN < 1 Read 152452 spots for ERR6133463.sra Written 152452 spots for ERR6133463.sra Rejected 152452 READS because READLEN < 1 Read 152452 spots for ERR6133463.sra Written 152452 spots for ERR6133463.sra Rejected 152452 READS because READLEN < 1 Read 152452 spots for ERR6133463.sra Written 152452 spots for ERR6133463.sra Rejected 152452 READS because READLEN < 1 Read 152452 spots for ERR6133463.sra Written 152452 spots for ERR6133463.sra Rejected 152452 READS because READLEN < 1 Read 152452 spots for ERR6133463.sra Written 152452 spots for ERR6133463.sra Rejected 152452 READS because READLEN < 1 Read 152452 spots for ERR6133463.sra Written 152452 spots for ERR6133463.sra Rejected 152452 READS because READLEN < 1 Read 152452 spots for ERR6133463.sra Written 152452 spots for ERR6133463.sra Rejected 152452 READS because READLEN < 1 Read 152452 spots for ERR6133463.sra Written 152452 spots for ERR6133463.sra Rejected 152452 READS because READLEN < 1 Read 152452 spots for ERR6133463.sra Written 152452 spots for ERR6133463.sra Rejected 152452 READS because READLEN < 1 Read 152452 spots for ERR6133463.sra Written 152452 spots for ERR6133463.sra Rejected 152471 READS because READLEN < 1 Read 152471 spots for ERR6133463.sra Written 152471 spots for ERR6133463.sra Rejected 152452 READS because READLEN < 1 Read 152452 spots for ERR6133463.sra Written 152452 spots for ERR6133463.sra Rejected 152452 READS because READLEN < 1 Read 152452 spots for ERR6133463.sra Written 152452 spots for ERR6133463.sra SRR ids: ['ERR6133463.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_a528fvws ERR6133463.sra spots: 3049059 blocks: [[1, 152452], [152453, 304904], [304905, 457356], [457357, 609808], [609809, 762260], [762261, 914712], [914713, 1067164], [1067165, 1219616], [1219617, 1372068], [1372069, 1524520], [1524521, 1676972], [1676973, 1829424], [1829425, 1981876], [1981877, 2134328], [2134329, 2286780], [2286781, 2439232], [2439233, 2591684], [2591685, 2744136], [2744137, 2896588], [2896589, 3049059]] ERR6133463 file size 671565 ERR6133463 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 ERR6133463 ERR6133463_1.fastq Input file: ERR6133463_1.fastq trimmed: ERR6133463-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 06:34:28 2024 >> started Sat Dec 7 06:34:30 2024 >> done (1.822s) 3049059 reads processed; of these: 76 ( 0.00%) short reads filtered out after trimming by size control 12 ( 0.00%) empty reads filtered out after trimming by size control 3048971 (100.00%) reads available; of these: 43125 ( 1.41%) trimmed reads available after processing 3005846 (98.59%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 11 0.00% 19 29 0.00% 20 12 0.00% 21 18 0.00% 22 14 0.00% 23 2 0.00% 24 6 0.00% 25 2 0.00% 26 7 0.00% 27 3 0.00% 28 10 0.00% 29 11 0.00% 30 13 0.00% 31 14 0.00% 32 15 0.00% 33 5 0.00% 34 8 0.00% 35 48 0.00% 36 395 0.01% 37 7 0.00% 38 30 0.00% 39 51 0.00% 40 63 0.00% 41 20 0.00% 42 9 0.00% 43 11 0.00% 44 7 0.00% 45 10 0.00% 46 6 0.00% 47 3 0.00% 48 11 0.00% 49 2 0.00% 50 6 0.00% 51 20 0.00% 52 10 0.00% 53 7 0.00% 54 3 0.00% 55 3 0.00% 56 8 0.00% 57 10 0.00% 58 13 0.00% 59 5 0.00% 60 6 0.00% 61 9 0.00% 62 3 0.00% 63 1 0.00% 64 4 0.00% 65 2 0.00% 66 8 0.00% 67 14 0.00% 68 23 0.00% 69 93 0.00% 70 10689 0.35% 71 9658 0.32% 72 10806 0.35% 73 10098 0.33% 74 10604 0.35% 75 10295 0.34% 76 9270 0.30% 77 9631 0.32% 78 10971 0.36% 79 11573 0.38% 80 11290 0.37% 81 13869 0.45% 82 14989 0.49% 83 13083 0.43% 84 13345 0.44% 85 93 0.00% 86 196 0.01% 87 307 0.01% 88 560 0.02% 89 1149 0.04% 90 2326 0.08% 91 7321 0.24% 92 28171 0.92% 93 2837576 93.07% 3048971 reads passed initial QC criterion=sequence-density sequence-density=1.34 sequence-density-rank=1 fanout-score=2.00 fanout-score-rank=31 prefix-density=1.34 prefix-fanout=2.0 sequence=CAAGGCTAAATAC criterion=fanout-score sequence-density=0.01 sequence-density-rank=34 fanout-score=126.55 fanout-score-rank=1 prefix-density=0.16 prefix-fanout=4.7 sequence=AAAAGAAGGGGTGTTCCATCTCCGGACGACGATCCTGCCTGCAGAGGAAGACATGCCGGCGATCATGTCGAGCTTCAAGAAGTTCAACGACTCATTCATGGAGCAATACCAAGACTACTCCAGGCTGTGATGTGAAGAGGGAAACAACGAGGTCATCATCGACATGATATATTGCTGCTATTTTCCACCAGCGATTAAAAGTTAAAAAATTTAGCTGTAAGCTGTAACTATCTTGAAGAAACTAAACTGGTTGCTGTGCTTGATATGTATAGGGAAAACATAATTTATGAGACAATCATACTGTGCAACTCTTGGCTCCATCGATTAATTAATACTCCTTGTTATTGCTTGCATGGTGG Started job on | Dec 07 06:34:48 Started mapping on | Dec 07 06:34:48 Finished on | Dec 07 06:34:54 Mapping speed, Million of reads per hour | 1829.38 Number of input reads | 3048971 Average input read length | 92 UNIQUE READS: Uniquely mapped reads number | 1962029 Uniquely mapped reads % | 64.35% Average mapped length | 91.50 Number of splices: Total | 71820 Number of splices: Annotated (sjdb) | 58407 Number of splices: GT/AG | 68148 Number of splices: GC/AG | 1898 Number of splices: AT/AC | 55 Number of splices: Non-canonical | 1719 Mismatch rate per base, % | 0.55% Deletion rate per base | 0.05% Deletion average length | 1.85 Insertion rate per base | 0.02% Insertion average length | 1.76 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 981571 % of reads mapped to multiple loci | 32.19% Number of reads mapped to too many loci | 49411 % of reads mapped to too many loci | 1.62% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 1.71% % of reads unmapped: other | 0.12% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 105371 105371 105371 N_multimapping 981571 981571 981571 N_noFeature 173423 193929 1873672 N_ambiguous 78180 10234 343 UnstrandedReadsAssigned:1710426 PositiveStrandReadsAssigned:1757866 NegativeStrandReadsAssigned:88014 Dataset is classified positive stranded MeadianReadLen=93 20thPercentileLength=93 echo kmer=89 ERR6133463 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: ERR6133463-trimmed.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 3,048,971 reads, 2,315,300 reads pseudoaligned [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 996 rounds 52973 ERR6133463.ke.tsv 35125 ERR6133463.se.tsv 88098 total ==> ERR6133463.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 60 25.3736 PNS24243 293 194 0 0 KQK14069 1603 1504 32 12.3449 KQK14071 474 375 0 0 ==> ERR6133463.se.tsv <== BRADI_1g14170v3 32 BRADI_1g53295v3 24 BRADI_1g59795v3 20 BRADI_1g07683v3 0 BRADI_1g00485v3 0 BRADI_1g20270v3 29 BRADI_1g74790v3 34 BRADI_1g09890v3 0 BRADI_1g77505v3 63 BRADI_1g48960v3 0 ERR6133463 completed mapping pipeline successfully