Starting /dee2/code/volunteer_pipeline.sh ERR6133342 current disk space = 1548143235072 free memory = 1375560636 ERR6133342 SRAfilesize 15eaee77eb248dbba47cb8b0b2f72558 ERR6133342.sra ERR6133342.sra file validated ERR6133342 is single end ERR6133342 is conventional basespace ERR6133342 read1 length is 70-93 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename ERR6133342_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 43 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 36.40075 37.0 37.0 37.0 37.0 37.0 2 36.605 37.0 37.0 37.0 37.0 37.0 3 36.37875 37.0 37.0 37.0 37.0 37.0 4 36.394 37.0 37.0 37.0 37.0 37.0 5 36.45275 37.0 37.0 37.0 37.0 37.0 6 36.43825 37.0 37.0 37.0 37.0 37.0 7 38.514 40.0 37.0 40.0 37.0 40.0 8 38.653 40.0 37.0 40.0 37.0 40.0 9 38.7365 40.0 37.0 40.0 37.0 40.0 10-11 38.731 40.0 37.0 40.0 37.0 40.0 12-13 38.663375 40.0 37.0 40.0 37.0 40.0 14-15 38.6035 40.0 37.0 40.0 37.0 40.0 16-17 38.609625 40.0 37.0 40.0 37.0 40.0 18-19 38.67 40.0 37.0 40.0 37.0 40.0 20-21 38.237375 40.0 37.0 40.0 37.0 40.0 22-23 38.478 40.0 37.0 40.0 37.0 40.0 24-25 38.47325 40.0 37.0 40.0 37.0 40.0 26-27 38.355000000000004 40.0 37.0 40.0 37.0 40.0 28-29 38.342124999999996 40.0 37.0 40.0 37.0 40.0 30-31 38.371625 40.0 37.0 40.0 37.0 40.0 32-33 38.35375 40.0 37.0 40.0 37.0 40.0 34-35 38.308875 40.0 37.0 40.0 37.0 40.0 36-37 38.111125 40.0 37.0 40.0 37.0 40.0 38-39 37.79875 40.0 37.0 40.0 37.0 40.0 40-41 37.76875 38.5 37.0 40.0 35.0 40.0 42-43 37.79625 37.0 37.0 40.0 37.0 40.0 44-45 37.53675 37.0 37.0 40.0 33.0 40.0 46-47 37.343374999999995 37.0 37.0 40.0 33.0 40.0 48-49 37.287000000000006 37.0 37.0 40.0 33.0 40.0 50-51 37.001875 37.0 37.0 40.0 33.0 40.0 52-53 36.832499999999996 37.0 37.0 40.0 33.0 40.0 54-55 36.594750000000005 37.0 37.0 37.0 33.0 40.0 56-57 36.369875 37.0 37.0 37.0 33.0 40.0 58-59 36.0805 37.0 37.0 37.0 33.0 40.0 60-61 35.939 37.0 37.0 37.0 33.0 37.0 62-63 35.371375 37.0 33.0 37.0 33.0 37.0 64-65 35.134125 37.0 33.0 37.0 33.0 37.0 66-67 35.01375 37.0 33.0 37.0 33.0 37.0 68-69 33.5565 35.0 33.0 37.0 30.0 37.0 70-71 33.44422467279134 33.0 33.0 37.0 30.0 37.0 72-73 33.83768486334263 33.0 33.0 37.0 33.0 37.0 74-75 33.76005580466635 33.0 33.0 37.0 30.0 37.0 76-77 33.51138844681422 33.0 33.0 37.0 27.0 37.0 78-79 33.2110740457117 33.0 33.0 37.0 27.0 37.0 80-81 32.89271304541739 33.0 33.0 37.0 27.0 37.0 82-83 32.815089115236084 33.0 33.0 37.0 27.0 37.0 84-85 32.23513848925525 33.0 33.0 33.0 27.0 37.0 86-87 32.10247686445291 33.0 33.0 33.0 27.0 37.0 88-89 32.1254763200871 33.0 33.0 33.0 27.0 37.0 90-91 31.305389221556887 33.0 30.0 33.0 24.5 37.0 92-93 30.47563962983125 33.0 27.0 33.0 22.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 20 2.0 21 2.0 22 3.0 23 2.0 24 11.0 25 10.0 26 5.0 27 22.0 28 17.0 29 34.0 30 33.0 31 57.0 32 67.0 33 111.0 34 244.0 35 558.0 36 1126.0 37 1428.0 38 252.0 39 16.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 64.075 9.4 9.375 17.150000000000002 2 44.7 28.299999999999997 16.825000000000003 10.174999999999999 3 28.799999999999997 37.475 18.65 15.075 4 29.075 26.825 23.0 21.099999999999998 5 24.25 26.275 28.999999999999996 20.474999999999998 6 19.725 34.875 27.075 18.325 7 32.824999999999996 26.6 23.150000000000002 17.424999999999997 8 26.875 27.450000000000003 27.750000000000004 17.925 9 23.225 28.375 28.375 20.025000000000002 10-11 23.8875 28.425 28.9375 18.75 12-13 23.4125 27.962500000000002 28.9875 19.6375 14-15 22.825 28.275 30.5125 18.387500000000003 16-17 24.525 29.262500000000003 26.400000000000002 19.8125 18-19 23.5625 25.362499999999997 30.875000000000004 20.200000000000003 20-21 24.825 26.200000000000003 29.2375 19.7375 22-23 26.5 24.0125 28.349999999999998 21.1375 24-25 24.575 26.450000000000003 28.8875 20.0875 26-27 24.7875 25.724999999999998 30.275000000000002 19.2125 28-29 24.212500000000002 26.450000000000003 29.15 20.1875 30-31 25.45 26.275 28.799999999999997 19.475 32-33 23.849999999999998 26.35 29.125 20.674999999999997 34-35 21.475 30.9875 26.787499999999998 20.75 36-37 23.3875 26.5625 28.3375 21.712500000000002 38-39 25.637500000000003 25.025 29.1375 20.200000000000003 40-41 24.5125 25.825 29.1875 20.474999999999998 42-43 25.087500000000002 28.262500000000003 28.799999999999997 17.849999999999998 44-45 22.375 27.737499999999997 29.075 20.8125 46-47 25.25 27.400000000000002 27.8375 19.5125 48-49 23.150000000000002 25.112499999999997 30.587500000000002 21.15 50-51 21.712500000000002 28.4125 30.0875 19.787499999999998 52-53 24.575 27.425 28.3625 19.6375 54-55 23.7875 27.400000000000002 29.525000000000002 19.287499999999998 56-57 25.2 27.6875 28.175 18.9375 58-59 23.962500000000002 27.1375 29.762499999999996 19.1375 60-61 24.825 27.6 28.975 18.6 62-63 21.587500000000002 28.6875 30.7375 18.987499999999997 64-65 21.95 31.574999999999996 28.812500000000004 17.6625 66-67 23.05 29.25 28.375 19.325 68-69 20.95 28.6375 29.45 20.962500000000002 70-71 23.328734478866174 28.546343910698607 28.320581964128934 19.804339646306286 72-73 24.584759731203246 27.868644605046278 29.18727019145429 18.359325472296185 74-75 24.429925698180888 28.324365872405842 29.041762746605176 18.203945682808094 76-77 21.622670807453417 27.212732919254655 28.59730848861284 22.56728778467909 78-79 24.393108848864525 27.721221613155834 29.757243539545808 18.128425998433826 80-81 22.688299696609945 32.05381875741987 27.56892230576441 17.68895924020578 82-83 21.62089752176825 28.265237776289347 28.546550569323507 21.56731413261889 84-85 21.19402985074627 26.526458616010856 32.13025780189959 20.149253731343283 86-87 20.18236254763201 29.776810016330973 27.35438214480131 22.68644529123571 88-89 20.223189983669027 29.926510615133367 29.463799673380514 20.386499727817093 90-91 22.56396298312466 29.858464888405006 27.694610778443113 19.882961350027216 92-93 20.18236254763201 31.260206859009255 27.91235710397387 20.645073489384867 >>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 0.0 17 1.0 18 1.0 19 1.5 20 3.0 21 3.0 22 3.5 23 4.5 24 4.5 25 7.5 26 11.0 27 17.5 28 27.0 29 30.0 30 35.5 31 49.0 32 55.5 33 64.0 34 81.0 35 99.5 36 140.0 37 196.5 38 235.0 39 221.0 40 233.0 41 252.0 42 262.5 43 295.0 44 250.5 45 197.5 46 160.0 47 139.5 48 148.5 49 142.5 50 149.5 51 151.5 52 136.5 53 135.5 54 144.0 55 119.5 56 81.0 57 66.0 58 42.0 59 17.0 60 12.0 61 8.5 62 6.5 63 4.0 64 1.5 65 2.0 66 2.5 67 2.0 68 1.0 69 3.0 70 3.0 71 1.0 72 1.0 73 1.0 74 0.5 75 0.0 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 0.05121638924455826 76-77 0.0646579593948015 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 27.0 71 19.0 72 21.0 73 17.0 74 22.0 75 17.0 76 21.0 77 15.0 78 20.0 79 19.0 80 23.0 81 34.0 82 25.0 83 24.0 84 22.0 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 3674.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 74.225 #Duplication Level Percentage of deduplicated Percentage of total 1 91.68070057258336 68.05 2 3.5702256652071407 5.3 3 1.4146177164028293 3.15 4 0.9430784776018861 2.8000000000000003 5 0.5389019872010778 2.0 6 0.47153923880094306 2.1 7 0.370495116200741 1.925 8 0.10104412260020208 0.6 9 0.10104412260020208 0.675 >10 0.7746716066015493 11.35 >50 0.033681374200067365 2.0500000000000003 >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 82 2.0500000000000003 No Hit TACCTAGGCACCCAGAGACGAGGAAGGGCGTAGCAAGCGACGAAATGCTT 50 1.25 No Hit CAAGGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCT 42 1.05 No Hit GGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCTTGG 36 0.8999999999999999 No Hit GGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAA 33 0.8250000000000001 No Hit TCAAAAGAGGAAAGGCTTGCGGTGGATACCTAGGCACCCAGAGACGAGGA 29 0.7250000000000001 No Hit GGCGTTCAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTC 28 0.7000000000000001 No Hit CAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAATACTTGGGCTG 24 0.6 No Hit CAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAATACTTGGGCTGATAT 21 0.525 No Hit GTTCAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAG 17 0.42500000000000004 No Hit GTAGTAGGAATCTGGTTCACTGCTTTAGGTATTAGTACTATGGCGTTCAA 16 0.4 No Hit GTATTAGTACTATGGCGTTCAACCTAAATGGATTCAATTTCAACCAATCT 16 0.4 No Hit CAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAGGTC 16 0.4 No Hit GGGTTGTTTGGGAATGCAGCCCAAATCGGGCGGTAGACTCCGTCCAAGGC 15 0.375 No Hit GCAAGGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATC 14 0.35000000000000003 No Hit GGAGTTGAAAATAAGCATAGATCCGGAGATTCCCAAATAGGTCAACCTTT 12 0.3 No Hit GGAATCCCGTGTGAATCAGCAAGGACCACCTTGCAAGGCTAAATACTCCT 12 0.3 No Hit GGGCACGTGGAATCCCGTGTGAATCAGCAAGGACCACCTTGCAAGGCTAA 11 0.27499999999999997 No Hit GGATACCTAGGCACCCAGAGACGAGGAAGGGCGTAGCAAGCGACGAAATG 11 0.27499999999999997 No Hit GGGGAGTTGAAAATAAGCATAGATCCGGAGATTCCCAAATAGGTCAACCT 11 0.27499999999999997 No Hit CGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCTTGGTAT 10 0.25 No Hit GTACTATGGCGTTCAACCTAAATGGATTCAATTTCAACCAATCTGTAGTT 10 0.25 No Hit GTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCTTGGT 10 0.25 No Hit GGGCTGATATCATCAACCGTGCTAATCTTGGTATGGAAGTAATGCACGAA 10 0.25 No Hit GCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCTTGGTATG 9 0.22499999999999998 No Hit GGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGTG 9 0.22499999999999998 No Hit GTGGAATCCCGTGTGAATCAGCAAGGACCACCTTGCAAGGCTAAATACTC 9 0.22499999999999998 No Hit GGAGTCCTGAACTAGCCGCAGCTTGTGAAGTATGGAAGGCGATCAAATTC 8 0.2 No Hit AACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAATACTTGGGCTGA 8 0.2 No Hit CGTTCAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTCAA 8 0.2 No Hit TAGTCAAGGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTA 7 0.17500000000000002 No Hit GAGGAAGGGCGTAGCAAGCGACGAAATGCTTCGGGGAGTTGAAAATAAGC 7 0.17500000000000002 No Hit TATGGCGTTCAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATA 7 0.17500000000000002 No Hit GGGCGCGATCTTGCTCGTGAAGGTAATGAAATTATCCGAGCAGCTTGCAA 7 0.17500000000000002 No Hit AGGAAAGGCTTGCGGTGGATACCTAGGCACCCAGAGACGAGGAAGGGCGT 7 0.17500000000000002 No Hit GTAGTTGATAGTCAAGGTCGCGTTATTAATACTTGGGCTGATATCATCAA 7 0.17500000000000002 No Hit GTAGGAATCTGGTTCACTGCTTTAGGTATTAGTACTATGGCGTTCAACCT 7 0.17500000000000002 No Hit GAAGGTAATGAAATTATCCGAGCAGCTTGCAAATGGAGTCCTGAACTAGC 7 0.17500000000000002 No Hit GGAGGAACTTTAGGACATCCTTGGGGAAATGCACCTGGTGCAGCAGCTAA 7 0.17500000000000002 No Hit GGGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGT 7 0.17500000000000002 No Hit GAACGTAATGCTCACAACTTCCCTCTAGATCTAGCTGCTCTTGAAGTTCC 7 0.17500000000000002 No Hit CAATTTCAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAATACTT 6 0.15 No Hit CAAATAGGTCAACCTTTTAAACTGCCTGCTGAATCCATGAGCAGGCAAGA 6 0.15 No Hit GCAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAATACTTGGGCT 6 0.15 No Hit GTAGCAAGCGACGAAATGCTTCGGGGAGTTGAAAATAAGCATAGATCCGG 6 0.15 No Hit GTATGGAAGGCGATCAAATTCGAGTTCGCGCCGGTAGATACTATCGATTA 6 0.15 No Hit GATAGTCAAGGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGC 6 0.15 No Hit AATGGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTAT 6 0.15 No Hit GGAAGAGCCCGAGCTGCTGCAGCAGGTTTTGAAAAGGGAATCGATCGTGA 6 0.15 No Hit AGTCAAGGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAA 6 0.15 No Hit GTCAAGGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAAT 6 0.15 No Hit GAAGCGGTTGAGTGCCGCACCCTAGATGGCTAAAGTCCAGTAGCCGAAAG 6 0.15 No Hit GGTAATGAAATTATCCGAGCAGCTTGCAAATGGAGTCCTGAACTAGCCGC 6 0.15 No Hit GGTGGATACCTAGGCACCCAGAGACGAGGAAGGGCGTAGCAAGCGACGAA 6 0.15 No Hit TCAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAATACTTGGGCT 6 0.15 No Hit GGTTCACTGCTTTAGGTATTAGTACTATGGCGTTCAACCTAAATGGATTC 5 0.125 No Hit GGGAAAAGAGGGGTTACTTTTTTTCATTTTTCCCTTAAAAGATAGGCTTT 5 0.125 No Hit AAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTA 5 0.125 No Hit GATTCAATTTCAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAAT 5 0.125 No Hit GCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGTGTACAAGCTCGTAACGA 5 0.125 No Hit GAAGCCTGTGTACAAGCTCGTAACGAAGGGCGCGATCTTGCTCGTGAAGG 5 0.125 No Hit GTTGATAGTCAAGGTCGCGTTATTAATACTTGGGCTGATATCATCAACCG 5 0.125 No Hit GAGGAAAGGCTTGCGGTGGATACCTAGGCACCCAGAGACGAGGAAGGGCG 5 0.125 No Hit GGAGTACGGTAGGGGCAGAGGGAATTTCCGGTGGAGCGGTGAAATGCATT 5 0.125 No Hit GAAGGGCGCGATCTTGCTCGTGAAGGTAATGAAATTATCCGAGCAGCTTG 5 0.125 No Hit CGAGGAAGGGCGTAGCAAGCGACGAAATGCTTCGGGGAGTTGAAAATAAG 5 0.125 No Hit GGGAATCGATCGTGATTTAGAACCTGTTCTTTACATGAACCCTCTTAACT 5 0.125 No Hit GAATCCCGTGTGAATCAGCAAGGACCACCTTGCAAGGCTAAATACTCCTG 5 0.125 No Hit GGTTTTGAAAAGGGAATCGATCGTGATTTAGAACCTGTTCTTTACATGAA 5 0.125 No Hit AAGGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCTT 5 0.125 No Hit CTGTAGTTGATAGTCAAGGTCGCGTTATTAATACTTGGGCTGATATCATC 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 0.0125 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 0.025 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 0.05 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content pass >>END_MODULE Rejected 136841 READS because READLEN < 1 Read 136841 spots for ERR6133342.sra Written 136841 spots for ERR6133342.sra Rejected 136841 READS because READLEN < 1 Read 136841 spots for ERR6133342.sra Written 136841 spots for ERR6133342.sra Rejected 136841 READS because READLEN < 1 Read 136841 spots for ERR6133342.sra Written 136841 spots for ERR6133342.sra Rejected 136841 READS because READLEN < 1 Read 136841 spots for ERR6133342.sra Written 136841 spots for ERR6133342.sra Rejected 136841 READS because READLEN < 1 Read 136841 spots for ERR6133342.sra Written 136841 spots for ERR6133342.sra Rejected 136841 READS because READLEN < 1 Read 136841 spots for ERR6133342.sra Written 136841 spots for ERR6133342.sra Rejected 136841 READS because READLEN < 1 Read 136841 spots for ERR6133342.sra Written 136841 spots for ERR6133342.sra Rejected 136841 READS because READLEN < 1 Read 136841 spots for ERR6133342.sra Written 136841 spots for ERR6133342.sra Rejected 136841 READS because READLEN < 1 Read 136841 spots for ERR6133342.sra Written 136841 spots for ERR6133342.sra Rejected 136841 READS because READLEN < 1 Read 136841 spots for ERR6133342.sra Written 136841 spots for ERR6133342.sra Rejected 136841 READS because READLEN < 1 Read 136841 spots for ERR6133342.sra Written 136841 spots for ERR6133342.sra Rejected 136841 READS because READLEN < 1 Read 136841 spots for ERR6133342.sra Written 136841 spots for ERR6133342.sra Rejected 136841 READS because READLEN < 1 Read 136841 spots for ERR6133342.sra Written 136841 spots for ERR6133342.sra Rejected 136841 READS because READLEN < 1 Read 136841 spots for ERR6133342.sra Written 136841 spots for ERR6133342.sra Rejected 136841 READS because READLEN < 1 Read 136841 spots for ERR6133342.sra Written 136841 spots for ERR6133342.sra Rejected 136841 READS because READLEN < 1 Read 136841 spots for ERR6133342.sra Written 136841 spots for ERR6133342.sra Rejected 136851 READS because READLEN < 1 Read 136851 spots for ERR6133342.sra Written 136851 spots for ERR6133342.sra Rejected 136841 READS because READLEN < 1 Read 136841 spots for ERR6133342.sra Written 136841 spots for ERR6133342.sra Rejected 136841 READS because READLEN < 1 Read 136841 spots for ERR6133342.sra Written 136841 spots for ERR6133342.sra Rejected 136841 READS because READLEN < 1 Read 136841 spots for ERR6133342.sra Written 136841 spots for ERR6133342.sra SRR ids: ['ERR6133342.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_oknwvvs9 ERR6133342.sra spots: 2736830 blocks: [[1, 136841], [136842, 273682], [273683, 410523], [410524, 547364], [547365, 684205], [684206, 821046], [821047, 957887], [957888, 1094728], [1094729, 1231569], [1231570, 1368410], [1368411, 1505251], [1505252, 1642092], [1642093, 1778933], [1778934, 1915774], [1915775, 2052615], [2052616, 2189456], [2189457, 2326297], [2326298, 2463138], [2463139, 2599979], [2599980, 2736830]] ERR6133342 file size 600416 ERR6133342 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 ERR6133342 ERR6133342_1.fastq Input file: ERR6133342_1.fastq trimmed: ERR6133342-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 01:03:55 2024 >> started Sat Dec 7 01:03:57 2024 >> done (1.628s) 2736830 reads processed; of these: 380 ( 0.01%) short reads filtered out after trimming by size control 7 ( 0.00%) empty reads filtered out after trimming by size control 2736443 (99.99%) reads available; of these: 38013 ( 1.39%) trimmed reads available after processing 2698430 (98.61%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 37 0.00% 19 50 0.00% 20 28 0.00% 21 20 0.00% 22 25 0.00% 23 17 0.00% 24 16 0.00% 25 7 0.00% 26 21 0.00% 27 17 0.00% 28 31 0.00% 29 25 0.00% 30 12 0.00% 31 27 0.00% 32 34 0.00% 33 11 0.00% 34 20 0.00% 35 36 0.00% 36 22 0.00% 37 15 0.00% 38 18 0.00% 39 34 0.00% 40 50 0.00% 41 29 0.00% 42 18 0.00% 43 10 0.00% 44 21 0.00% 45 9 0.00% 46 12 0.00% 47 6 0.00% 48 21 0.00% 49 14 0.00% 50 13 0.00% 51 57 0.00% 52 12 0.00% 53 11 0.00% 54 12 0.00% 55 10 0.00% 56 11 0.00% 57 18 0.00% 58 16 0.00% 59 9 0.00% 60 6 0.00% 61 11 0.00% 62 0 0.00% 63 2 0.00% 64 5 0.00% 65 5 0.00% 66 2 0.00% 67 6 0.00% 68 17 0.00% 69 73 0.00% 70 13630 0.50% 71 13370 0.49% 72 14004 0.51% 73 13643 0.50% 74 13022 0.48% 75 12738 0.47% 76 12633 0.46% 77 13929 0.51% 78 13867 0.51% 79 14661 0.54% 80 14814 0.54% 81 18419 0.67% 82 19516 0.71% 83 16459 0.60% 84 19307 0.71% 85 27 0.00% 86 55 0.00% 87 99 0.00% 88 211 0.01% 89 510 0.02% 90 1290 0.05% 91 4491 0.16% 92 28712 1.05% 93 2476027 90.48% 2736443 reads passed initial QC criterion=sequence-density sequence-density=2.91 sequence-density-rank=1 fanout-score=2.04 fanout-score-rank=26 prefix-density=2.99 prefix-fanout=2.0 sequence=CAAGGCTAAATAC criterion=fanout-score sequence-density=0.01 sequence-density-rank=40 fanout-score=51.52 fanout-score-rank=1 prefix-density=0.08 prefix-fanout=3.4 sequence=GTATTTATGTTAATGCACTTTCTAATGATACGTAAGCAAGGTATTTCGGGTCCTTTATAGGGAAGGCATATCATAGAGAATTAGAATTCTCATATATAATATTGGGTAGGTTGTGGTATTTCATTGCTACAAACATGGGTTATTGTAAAATAACACATGTCATTTGGATACTTCTCTTCAACTCCGAAGTATTTTGATATAATACAAATAGTTGAAGTTAATTTTACAAA 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 01:04:26 Started mapping on | Dec 07 01:04:27 Finished on | Dec 07 01:04:33 Mapping speed, Million of reads per hour | 1641.87 Number of input reads | 2736443 Average input read length | 91 UNIQUE READS: Uniquely mapped reads number | 1421513 Uniquely mapped reads % | 51.95% Average mapped length | 90.72 Number of splices: Total | 43526 Number of splices: Annotated (sjdb) | 34648 Number of splices: GT/AG | 41057 Number of splices: GC/AG | 965 Number of splices: AT/AC | 52 Number of splices: Non-canonical | 1452 Mismatch rate per base, % | 0.41% Deletion rate per base | 0.04% Deletion average length | 1.68 Insertion rate per base | 0.02% Insertion average length | 1.70 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 1188957 % of reads mapped to multiple loci | 43.45% Number of reads mapped to too many loci | 73597 % of reads mapped to too many loci | 2.69% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 1.78% % of reads unmapped: other | 0.14% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 125973 125973 125973 N_multimapping 1188957 1188957 1188957 N_noFeature 130768 144697 1362642 N_ambiguous 52645 7604 305 UnstrandedReadsAssigned:1238100 PositiveStrandReadsAssigned:1269212 NegativeStrandReadsAssigned:58566 Dataset is classified positive stranded MeadianReadLen=93 20thPercentileLength=93 echo kmer=89 ERR6133342 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: ERR6133342-trimmed.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 2,736,443 reads, 1,964,971 reads pseudoaligned [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 963 rounds 52973 ERR6133342.ke.tsv 35125 ERR6133342.se.tsv 88098 total ==> ERR6133342.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 36 17.7591 PNS24243 293 194 0 0 KQK14069 1603 1504 21 9.45025 KQK14071 474 375 0 0 ==> ERR6133342.se.tsv <== BRADI_1g14170v3 21 BRADI_1g53295v3 21 BRADI_1g59795v3 23 BRADI_1g07683v3 0 BRADI_1g00485v3 0 BRADI_1g20270v3 11 BRADI_1g74790v3 10 BRADI_1g09890v3 0 BRADI_1g77505v3 45 BRADI_1g48960v3 0 ERR6133342 completed mapping pipeline successfully