Starting /dee2/code/volunteer_pipeline.sh ERR6133565 current disk space = 1544520458240 free memory = 1596960452 ERR6133565 SRAfilesize 605c32c5411749661aaec2d1508de2ac ERR6133565.sra ERR6133565.sra file validated ERR6133565 is single end ERR6133565 is conventional basespace ERR6133565 read1 length is 70-93 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename ERR6133565_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 35.66375 37.0 33.0 37.0 33.0 37.0 2 36.475 37.0 37.0 37.0 37.0 37.0 3 36.0365 37.0 37.0 37.0 33.0 37.0 4 35.5015 37.0 37.0 37.0 33.0 37.0 5 35.24075 37.0 37.0 37.0 33.0 37.0 6 35.6445 37.0 37.0 37.0 33.0 37.0 7 37.4465 40.0 37.0 40.0 33.0 40.0 8 37.567 40.0 37.0 40.0 33.0 40.0 9 37.60125 40.0 37.0 40.0 33.0 40.0 10-11 37.521625 38.5 37.0 40.0 33.0 40.0 12-13 37.478375 38.5 37.0 40.0 33.0 40.0 14-15 37.424125000000004 37.0 37.0 40.0 33.0 40.0 16-17 37.275625000000005 37.0 37.0 40.0 33.0 40.0 18-19 37.33425 37.0 37.0 40.0 33.0 40.0 20-21 37.21425 37.0 37.0 40.0 33.0 40.0 22-23 37.201375 37.0 37.0 40.0 33.0 40.0 24-25 37.270250000000004 37.0 37.0 40.0 33.0 40.0 26-27 37.251 37.0 37.0 40.0 33.0 40.0 28-29 37.17125 37.0 37.0 40.0 33.0 40.0 30-31 37.02375 37.0 37.0 40.0 33.0 40.0 32-33 36.961375000000004 37.0 37.0 40.0 33.0 40.0 34-35 36.911625 37.0 37.0 40.0 33.0 40.0 36-37 36.718 37.0 37.0 40.0 33.0 40.0 38-39 36.429125 37.0 37.0 40.0 33.0 40.0 40-41 36.312875000000005 37.0 37.0 40.0 33.0 40.0 42-43 36.1965 37.0 37.0 40.0 33.0 40.0 44-45 35.9865 37.0 35.0 40.0 33.0 40.0 46-47 35.658875 37.0 33.0 38.5 33.0 40.0 48-49 35.585375 37.0 33.0 37.0 33.0 40.0 50-51 35.53 37.0 33.0 37.0 33.0 40.0 52-53 35.177625 37.0 33.0 37.0 33.0 40.0 54-55 35.125 37.0 33.0 37.0 30.0 40.0 56-57 34.934625 37.0 33.0 37.0 30.0 38.5 58-59 33.77725 37.0 33.0 37.0 27.0 37.0 60-61 34.261625 37.0 33.0 37.0 27.0 37.0 62-63 34.40775 37.0 33.0 37.0 27.0 37.0 64-65 34.244 37.0 33.0 37.0 27.0 37.0 66-67 34.2565 37.0 33.0 37.0 27.0 37.0 68-69 33.62925 35.0 33.0 37.0 27.0 37.0 70-71 33.685913442273986 35.0 33.0 37.0 27.0 37.0 72-73 34.03300337556253 37.0 33.0 37.0 27.0 37.0 74-75 33.79244528547151 37.0 33.0 37.0 27.0 37.0 76-77 33.94587199755853 37.0 33.0 37.0 27.0 37.0 78-79 33.99903391359267 37.0 33.0 37.0 27.0 37.0 80-81 33.799688481480175 37.0 33.0 37.0 27.0 37.0 82-83 33.675399967089206 37.0 33.0 37.0 27.0 37.0 84-85 33.62694612987967 37.0 33.0 37.0 27.0 37.0 86-87 33.53682682154171 37.0 33.0 37.0 27.0 37.0 88-89 33.784186906019 37.0 33.0 37.0 27.0 37.0 90-91 33.56032206969377 37.0 33.0 37.0 27.0 37.0 92-93 33.359028511087644 37.0 33.0 37.0 27.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 20 12.0 21 14.0 22 22.0 23 19.0 24 24.0 25 34.0 26 39.0 27 45.0 28 53.0 29 67.0 30 79.0 31 119.0 32 109.0 33 178.0 34 241.0 35 430.0 36 875.0 37 903.0 38 716.0 39 21.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 87.35000000000001 2.9000000000000004 3.2 6.550000000000001 2 69.0 17.525 8.1 5.375 3 34.599999999999994 38.550000000000004 15.675 11.175 4 33.875 27.900000000000002 19.6 18.625 5 25.900000000000002 30.45 25.2 18.45 6 19.900000000000002 37.724999999999994 25.8 16.575 7 36.325 28.199999999999996 21.15 14.325 8 29.825000000000003 29.325000000000003 23.65 17.2 9 26.05 27.375 29.2 17.375 10-11 25.0375 28.749999999999996 27.825 18.387500000000003 12-13 26.487500000000004 27.575 27.05 18.8875 14-15 22.537499999999998 30.312499999999996 29.3875 17.7625 16-17 24.9875 30.275000000000002 25.924999999999997 18.8125 18-19 23.775 26.687499999999996 28.625 20.9125 20-21 25.525 25.7125 28.975 19.787499999999998 22-23 27.3375 23.7625 28.237499999999997 20.6625 24-25 25.5 24.625 28.925 20.95 26-27 25.424999999999997 25.3125 29.849999999999998 19.412499999999998 28-29 25.7875 27.187499999999996 27.5625 19.4625 30-31 26.8125 25.912499999999998 28.1 19.175 32-33 23.724999999999998 26.85 29.062500000000004 20.3625 34-35 25.337500000000002 26.674999999999997 27.650000000000002 20.3375 36-37 25.0625 25.2625 27.987499999999997 21.6875 38-39 26.486418825885593 25.873075478783324 29.528101139066216 18.112404556264863 40-41 25.761182809171785 25.498057887482773 27.778473875454203 20.962285427891242 42-43 24.434162811054144 28.710766537451544 26.710016256096036 20.145054395398272 44-45 23.3375 26.687499999999996 29.349999999999998 20.625 46-47 24.5125 25.275 28.875 21.337500000000002 48-49 25.0375 25.7875 30.5 18.675 50-51 24.175 26.950000000000003 28.799999999999997 20.075000000000003 52-53 25.46023794614903 26.825297432686284 26.24921728240451 21.465247338760175 54-55 24.075 27.800000000000004 29.95 18.175 56-57 26.137500000000003 26.387500000000003 28.4375 19.037499999999998 58-59 25.224999999999998 25.924999999999997 28.9125 19.9375 60-61 25.5125 25.412499999999998 29.1125 19.9625 62-63 22.7125 28.9875 30.5375 17.7625 64-65 23.549999999999997 28.487499999999997 29.1125 18.85 66-67 24.7 28.3875 28.1 18.8125 68-69 22.55 26.7125 28.712500000000002 22.025 70-71 24.33379206805955 26.84849243087702 27.711747779306894 21.10596772175654 72-73 26.00654252642174 25.84297936587821 29.428787116255663 18.72169099144439 74-75 23.52941176470588 27.649594320486813 29.63995943204868 19.181034482758623 76-77 22.59959141981614 26.212972420837588 28.894279877425944 22.293156281920325 78-79 24.533401982237095 25.447290513579613 30.930621701634703 19.088685802548593 80-81 23.24226336915706 29.39272303508999 28.965427942509386 18.39958565324356 82-83 23.777138373005492 26.497515040544073 29.322521579911065 20.402825006539366 84-85 23.316198761038617 23.777514168973244 32.77975484381178 20.126532226176355 86-87 22.78247096092925 27.230728616684267 30.491024287222807 19.495776135163677 88-89 21.40971488912355 29.157866948257656 30.1610348468849 19.271383315733896 90-91 24.78880675818374 26.517951425554383 29.23706441393875 19.456177402323124 92-93 22.980464625131997 30.095036958817317 27.732312565997887 19.192185850052798 >>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 1.0 17 11.0 18 11.5 19 1.5 20 1.0 21 2.0 22 1.5 23 4.5 24 7.0 25 7.0 26 9.5 27 16.5 28 20.0 29 18.5 30 25.5 31 45.5 32 62.5 33 74.0 34 84.5 35 99.5 36 122.0 37 144.5 38 172.0 39 175.0 40 183.0 41 197.0 42 214.0 43 239.0 44 229.0 45 204.5 46 200.5 47 195.5 48 173.0 49 160.5 50 158.5 51 149.0 52 125.5 53 122.0 54 118.0 55 87.5 56 65.5 57 61.0 58 63.0 59 51.5 60 32.5 61 28.5 62 28.0 63 21.0 64 21.0 65 23.0 66 21.5 67 17.5 68 12.5 69 13.5 70 10.0 71 6.0 72 5.0 73 3.0 74 3.5 75 3.0 76 0.5 77 0.0 78 1.0 79 1.0 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 0.13749999999999998 40-41 0.2375 42-43 0.0375 44-45 0.0 46-47 0.0 48-49 0.0 50-51 0.0 52-53 0.1875 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 7.0 71 12.0 72 14.0 73 14.0 74 18.0 75 13.0 76 12.0 77 15.0 78 21.0 79 7.0 80 11.0 81 25.0 82 16.0 83 16.0 84 11.0 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 3788.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 81.5 #Duplication Level Percentage of deduplicated Percentage of total 1 93.03680981595092 75.825 2 3.9877300613496933 6.5 3 1.0736196319018405 2.625 4 0.5214723926380368 1.7000000000000002 5 0.3374233128834356 1.375 6 0.18404907975460122 0.8999999999999999 7 0.15337423312883436 0.8750000000000001 8 0.06134969325153375 0.4 9 0.06134969325153375 0.44999999999999996 >10 0.5828220858895705 9.35 >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 fail #Sequence Count Percentage Possible Source GGGAGAGCAATACAAGCGTTGTGCTGCTAGGCGAAGCGGTTGAGTGCCGC 44 1.0999999999999999 No Hit GGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCTTGG 34 0.8500000000000001 No Hit GGGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGT 28 0.7000000000000001 No Hit TACCTAGGCACCCAGAGACGAGGAAGGGCGTAGCAAGCGACGAAATGCTT 27 0.675 No Hit GGGATGATTCTGTATTACAATTTGGTGGAGGAACTTTAGGACATCCTTGG 27 0.675 No Hit GGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAA 24 0.6 No Hit GGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGTG 21 0.525 No Hit GGAGTATCCTTGATATATAAATATATAGATAAATAGATTTAAATGGAAAA 19 0.475 No Hit GGCGTTCAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTC 19 0.475 No Hit GGGCGCGATCTTGCTCGTGAAGGTAATGAAATTATCCGAGCAGCTTGCAA 19 0.475 No Hit GAAGGTAATGAAATTATCCGAGCAGCTTGCAAATGGAGTCCTGAACTAGC 18 0.44999999999999996 No Hit GGTAATGAAATTATCCGAGCAGCTTGCAAATGGAGTCCTGAACTAGCCGC 15 0.375 No Hit GGATGATTCTGTATTACAATTTGGTGGAGGAACTTTAGGACATCCTTGGG 13 0.325 No Hit GGACATCCTTGGGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTT 12 0.3 No Hit GGAGGAACTTTAGGACATCCTTGGGGAAATGCACCTGGTGCAGCAGCTAA 12 0.3 No Hit GGGAGTATTATGAAAGGAGATTAATCATAGATTATCAAAAACCCTAGAAA 11 0.27499999999999997 No Hit GGAGTTGAAAATAAGCATAGATCCGGAGATTCCCAAATAGGTCAACCTTT 11 0.27499999999999997 No Hit GGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGTGTACAAGCTCGTAA 10 0.25 No Hit GTATGGAAGGCGATCAAATTCGAGTTCGCGCCGGTAGATACTATCGATTA 10 0.25 No Hit GGGGATGATTCTGTATTACAATTTGGTGGAGGAACTTTAGGACATCCTTG 9 0.22499999999999998 No Hit GGAAAAGAAAGCAAAAGCGATTCCCGTAGTAGCGGCGAGCGAAATGGGAG 9 0.22499999999999998 No Hit GGGAAAAGAGGGGTTACTTTTTTTCATTTTTCCCTTAAAAGATAGGCTTT 8 0.2 No Hit GGCGCGATCTTGCTCGTGAAGGTAATGAAATTATCCGAGCAGCTTGCAAA 8 0.2 No Hit GGAGTCCTGAACTAGCCGCAGCTTGTGAAGTATGGAAGGCGATCAAATTC 7 0.17500000000000002 No Hit GGGGATGGAGCGACAGAAGTATGGAAATAGGATAAGGTAGCGGCGAGACG 7 0.17500000000000002 No Hit GCAGCTTGCAAATGGAGTCCTGAACTAGCCGCAGCTTGTGAAGTATGGAA 7 0.17500000000000002 No Hit CAAGGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCT 7 0.17500000000000002 No Hit GGAAAAGAGGGGTTACTTTTTTTCATTTTTCCCTTAAAAGATAGGCTTTG 7 0.17500000000000002 No Hit CAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAATACTTGGGCTGATAT 6 0.15 No Hit GGTGGAGGAACTTTAGGACATCCTTGGGGAAATGCACCTGGTGCAGCAGC 6 0.15 No Hit GGGCTGATATCATCAACCGTGCTAATCTTGGTATGGAAGTAATGCACGAA 6 0.15 No Hit GATACCTAGGCACCCAGAGACGAGGAAGGGCGTAGCAAGCGACGAAATGC 6 0.15 No Hit GAAATCTTTGGGGATGATTCTGTATTACAATTTGGTGGAGGAACTTTAGG 6 0.15 No Hit TTCACAAGTCTGGTTCAGGGTGTCCTCCGGTGGAGTTGTCGCGTGTCTGA 6 0.15 No Hit GACCACAGCGCATTCCCAATTAGCATCTAAGCTCTCGTTGACATTTCCTT 5 0.125 No Hit GGAACTTTAGGACATCCTTGGGGAAATGCACCTGGTGCAGCAGCTAATCG 5 0.125 No Hit GGGATGGAGCGACAGAAGTATGGAAATAGGATAAGGTAGCGGCGAGACGA 5 0.125 No Hit GGCCTGTAGTAGGAATCTGGTTCACTGCTTTAGGTATTAGTACTATGGCG 5 0.125 No Hit GAAGTATGGAAGGCGATCAAATTCGAGTTCGCGCCGGTAGATACTATCGA 5 0.125 No Hit GGAATAAGAATAAATCGCAACTCCTTTCCACTACACATAAAAATTGATTT 5 0.125 No Hit CAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAGGTC 5 0.125 No Hit GGGGAGTTGAAAATAAGCATAGATCCGGAGATTCCCAAATAGGTCAACCT 5 0.125 No Hit GGAGTGGGGGTGCCATACGCAAAAAGGAAGCGACTCATAGAATGGCAGAG 5 0.125 No Hit GGATACCTAGGCACCCAGAGACGAGGAAGGGCGTAGCAAGCGACGAAATG 5 0.125 No Hit GGGACGCATGCAACGACCATCTACATATAGCTACTCGATCTACCGCTACC 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 0.0125 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 0.025 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 pass >>END_MODULE Rejected 440827 READS because READLEN < 1 Read 440827 spots for ERR6133565.sra Written 440827 spots for ERR6133565.sra Rejected 440827 READS because READLEN < 1 Read 440827 spots for ERR6133565.sra Written 440827 spots for ERR6133565.sra Rejected 440827 READS because READLEN < 1 Read 440827 spots for ERR6133565.sra Written 440827 spots for ERR6133565.sra Rejected 440827 READS because READLEN < 1 Read 440827 spots for ERR6133565.sra Written 440827 spots for ERR6133565.sra Rejected 440827 READS because READLEN < 1 Read 440827 spots for ERR6133565.sra Written 440827 spots for ERR6133565.sra Rejected 440827 READS because READLEN < 1 Read 440827 spots for ERR6133565.sra Written 440827 spots for ERR6133565.sra Rejected 440827 READS because READLEN < 1 Read 440827 spots for ERR6133565.sra Written 440827 spots for ERR6133565.sra Rejected 440844 READS because READLEN < 1 Read 440844 spots for ERR6133565.sra Written 440844 spots for ERR6133565.sra Rejected 440827 READS because READLEN < 1 Read 440827 spots for ERR6133565.sra Written 440827 spots for ERR6133565.sra Rejected 440827 READS because READLEN < 1 Read 440827 spots for ERR6133565.sra Written 440827 spots for ERR6133565.sra Rejected 440827 READS because READLEN < 1 Read 440827 spots for ERR6133565.sra Written 440827 spots for ERR6133565.sra Rejected 440827 READS because READLEN < 1 Read 440827 spots for ERR6133565.sra Written 440827 spots for ERR6133565.sra Rejected 440827 READS because READLEN < 1 Read 440827 spots for ERR6133565.sra Written 440827 spots for ERR6133565.sra Rejected 440827 READS because READLEN < 1 Read 440827 spots for ERR6133565.sra Written 440827 spots for ERR6133565.sra Rejected 440827 READS because READLEN < 1 Read 440827 spots for ERR6133565.sra Written 440827 spots for ERR6133565.sra Rejected 440827 READS because READLEN < 1 Read 440827 spots for ERR6133565.sra Written 440827 spots for ERR6133565.sra Rejected 440827 READS because READLEN < 1 Read 440827 spots for ERR6133565.sra Written 440827 spots for ERR6133565.sra Rejected 440827 READS because READLEN < 1 Read 440827 spots for ERR6133565.sra Written 440827 spots for ERR6133565.sra Rejected 440827 READS because READLEN < 1 Read 440827 spots for ERR6133565.sra Written 440827 spots for ERR6133565.sra Rejected 440827 READS because READLEN < 1 Read 440827 spots for ERR6133565.sra Written 440827 spots for ERR6133565.sra SRR ids: ['ERR6133565.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_2fde20tu ERR6133565.sra spots: 8816557 blocks: [[1, 440827], [440828, 881654], [881655, 1322481], [1322482, 1763308], [1763309, 2204135], [2204136, 2644962], [2644963, 3085789], [3085790, 3526616], [3526617, 3967443], [3967444, 4408270], [4408271, 4849097], [4849098, 5289924], [5289925, 5730751], [5730752, 6171578], [6171579, 6612405], [6612406, 7053232], [7053233, 7494059], [7494060, 7934886], [7934887, 8375713], [8375714, 8816557]] ERR6133565 file size 1947634 ERR6133565 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 ERR6133565 ERR6133565_1.fastq Input file: ERR6133565_1.fastq trimmed: ERR6133565-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 08:44:46 2024 >> started Sat Dec 7 08:44:50 2024 >> done (4.310s) 8816557 reads processed; of these: 195 ( 0.00%) short reads filtered out after trimming by size control 45 ( 0.00%) empty reads filtered out after trimming by size control 8816317 (100.00%) reads available; of these: 166389 ( 1.89%) trimmed reads available after processing 8649928 (98.11%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 44 0.00% 19 57 0.00% 20 35 0.00% 21 31 0.00% 22 44 0.00% 23 10 0.00% 24 13 0.00% 25 18 0.00% 26 6 0.00% 27 17 0.00% 28 34 0.00% 29 32 0.00% 30 20 0.00% 31 32 0.00% 32 31 0.00% 33 36 0.00% 34 38 0.00% 35 278 0.00% 36 1000 0.01% 37 32 0.00% 38 60 0.00% 39 149 0.00% 40 106 0.00% 41 70 0.00% 42 19 0.00% 43 20 0.00% 44 19 0.00% 45 25 0.00% 46 13 0.00% 47 22 0.00% 48 27 0.00% 49 16 0.00% 50 16 0.00% 51 36 0.00% 52 24 0.00% 53 21 0.00% 54 14 0.00% 55 8 0.00% 56 14 0.00% 57 20 0.00% 58 20 0.00% 59 19 0.00% 60 23 0.00% 61 25 0.00% 62 8 0.00% 63 6 0.00% 64 12 0.00% 65 9 0.00% 66 19 0.00% 67 30 0.00% 68 86 0.00% 69 253 0.00% 70 26890 0.31% 71 26360 0.30% 72 28763 0.33% 73 26228 0.30% 74 27226 0.31% 75 27210 0.31% 76 24268 0.28% 77 25069 0.28% 78 28388 0.32% 79 32515 0.37% 80 28921 0.33% 81 30640 0.35% 82 34447 0.39% 83 36284 0.41% 84 30825 0.35% 85 297 0.00% 86 594 0.01% 87 976 0.01% 88 1868 0.02% 89 3498 0.04% 90 7393 0.08% 91 21881 0.25% 92 122365 1.39% 93 8220394 93.24% 8816317 reads passed initial QC criterion=sequence-density sequence-density=0.40 sequence-density-rank=1 fanout-score=6.71 fanout-score-rank=22 prefix-density=0.60 prefix-fanout=4.5 sequence=ATGCATGCATGC criterion=fanout-score sequence-density=0.02 sequence-density-rank=33 fanout-score=212.74 fanout-score-rank=1 prefix-density=0.87 prefix-fanout=5.1 sequence=GAAGAAGAAAAGTTTTCTCAACATGGGGAGGAAGTCCCTCCGAAATTTGATTTGTTATTGTATTGTAAGGGGCTTTTTTAGTATTTATCTAAAGGAAGGAACAAACGAGGATAAGATAAAATTTCTTTAAATTTATTTTGCCCAAGTGGGATATATGGCATACTATTCTTTCCATTTTCATCTTTTTTTCTATTCCACTCCATCTAGATATAAGAAAGAACCCAATGCAATGAAATTCCACTAATATACAATACAAAAAAGAAGAATAGATACAGGGTCTCAAACCTTGCTATAGAGTTTTTGCTT Started job on | Dec 07 08:45:04 Started mapping on | Dec 07 08:45:05 Finished on | Dec 07 08:45:17 Mapping speed, Million of reads per hour | 2644.90 Number of input reads | 8816317 Average input read length | 92 UNIQUE READS: Uniquely mapped reads number | 6167565 Uniquely mapped reads % | 69.96% Average mapped length | 91.71 Number of splices: Total | 260929 Number of splices: Annotated (sjdb) | 214520 Number of splices: GT/AG | 249118 Number of splices: GC/AG | 5771 Number of splices: AT/AC | 130 Number of splices: Non-canonical | 5910 Mismatch rate per base, % | 0.42% Deletion rate per base | 0.04% Deletion average length | 1.75 Insertion rate per base | 0.02% Insertion average length | 2.08 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 2419424 % of reads mapped to multiple loci | 27.44% Number of reads mapped to too many loci | 93356 % of reads mapped to too many loci | 1.06% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 1.48% % of reads unmapped: other | 0.06% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 229328 229328 229328 N_multimapping 2419424 2419424 2419424 N_noFeature 412783 479301 5892720 N_ambiguous 239907 31492 887 UnstrandedReadsAssigned:5514875 PositiveStrandReadsAssigned:5656772 NegativeStrandReadsAssigned:273958 Dataset is classified positive stranded MeadianReadLen=93 20thPercentileLength=93 echo kmer=89 ERR6133565 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: ERR6133565-trimmed.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 8,816,317 reads, 7,297,937 reads pseudoaligned [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,085 rounds 52973 ERR6133565.ke.tsv 35125 ERR6133565.se.tsv 88098 total ==> ERR6133565.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 168 22.6627 PNS24243 293 194 0 0 KQK14069 1603 1504 59 7.26041 KQK14071 474 375 0 0 ==> ERR6133565.se.tsv <== BRADI_1g14170v3 59 BRADI_1g53295v3 152 BRADI_1g59795v3 52 BRADI_1g07683v3 0 BRADI_1g00485v3 1 BRADI_1g20270v3 110 BRADI_1g74790v3 118 BRADI_1g09890v3 0 BRADI_1g77505v3 121 BRADI_1g48960v3 2 ERR6133565 completed mapping pipeline successfully