Starting /dee2/code/volunteer_pipeline.sh ERR6133501 current disk space = 1544442380288 free memory = 1424525196 ERR6133501 SRAfilesize 46ffd2505c824f3e08c649e659239a0e ERR6133501.sra ERR6133501.sra file validated ERR6133501 is single end ERR6133501 is conventional basespace ERR6133501 read1 length is 70-93 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename ERR6133501_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 35.38925 37.0 33.0 37.0 33.0 37.0 2 36.447 37.0 37.0 37.0 37.0 37.0 3 35.6115 37.0 37.0 37.0 33.0 37.0 4 35.065 37.0 37.0 37.0 33.0 37.0 5 35.11925 37.0 37.0 37.0 33.0 37.0 6 35.51125 37.0 37.0 37.0 33.0 37.0 7 37.172 37.0 37.0 40.0 33.0 40.0 8 37.25875 37.0 37.0 40.0 33.0 40.0 9 37.28125 37.0 37.0 40.0 33.0 40.0 10-11 37.29325 37.0 37.0 40.0 33.0 40.0 12-13 37.189375 37.0 37.0 40.0 33.0 40.0 14-15 37.11625 37.0 37.0 40.0 33.0 40.0 16-17 36.925250000000005 37.0 37.0 40.0 33.0 40.0 18-19 36.842124999999996 37.0 37.0 40.0 33.0 40.0 20-21 36.5225 37.0 37.0 40.0 33.0 40.0 22-23 36.603875 37.0 37.0 40.0 33.0 40.0 24-25 36.47325 37.0 37.0 40.0 33.0 40.0 26-27 36.760000000000005 37.0 37.0 40.0 33.0 40.0 28-29 36.670500000000004 37.0 37.0 40.0 33.0 40.0 30-31 36.568 37.0 37.0 40.0 33.0 40.0 32-33 36.406125 37.0 37.0 40.0 33.0 40.0 34-35 36.412 37.0 37.0 40.0 33.0 40.0 36-37 36.170249999999996 37.0 37.0 40.0 33.0 40.0 38-39 36.076875 37.0 37.0 40.0 33.0 40.0 40-41 35.831625 37.0 33.0 40.0 33.0 40.0 42-43 35.86325 37.0 33.0 40.0 33.0 40.0 44-45 35.801249999999996 37.0 35.0 40.0 33.0 40.0 46-47 35.663125 37.0 33.0 37.0 33.0 40.0 48-49 35.690124999999995 37.0 33.0 37.0 33.0 40.0 50-51 35.51775 37.0 33.0 37.0 33.0 40.0 52-53 35.2725 37.0 33.0 37.0 33.0 40.0 54-55 35.215875 37.0 33.0 37.0 33.0 40.0 56-57 35.02525 37.0 33.0 37.0 33.0 40.0 58-59 33.958 37.0 33.0 37.0 27.0 37.0 60-61 34.508375 37.0 33.0 37.0 27.0 37.0 62-63 34.44775 37.0 33.0 37.0 27.0 37.0 64-65 34.27975 37.0 33.0 37.0 27.0 37.0 66-67 34.31275 37.0 33.0 37.0 27.0 37.0 68-69 33.513 35.0 33.0 37.0 27.0 37.0 70-71 33.6911425879397 35.0 33.0 37.0 27.0 37.0 72-73 34.0435499252141 37.0 33.0 37.0 27.0 37.0 74-75 34.050643424324456 37.0 33.0 37.0 27.0 37.0 76-77 33.883004886777 37.0 33.0 37.0 27.0 37.0 78-79 33.90429566655929 37.0 33.0 37.0 27.0 37.0 80-81 33.686824754142606 37.0 33.0 37.0 27.0 37.0 82-83 33.61920725385981 37.0 33.0 37.0 27.0 37.0 84-85 33.3501358215173 37.0 33.0 37.0 27.0 37.0 86-87 33.33260453675868 37.0 33.0 37.0 27.0 37.0 88-89 33.49603716862531 37.0 33.0 37.0 27.0 37.0 90-91 33.189805957912 33.0 33.0 37.0 27.0 37.0 92-93 33.019814156873466 33.0 33.0 37.0 27.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 20 7.0 21 13.0 22 25.0 23 27.0 24 30.0 25 27.0 26 48.0 27 39.0 28 62.0 29 67.0 30 89.0 31 111.0 32 145.0 33 193.0 34 280.0 35 498.0 36 845.0 37 920.0 38 553.0 39 21.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 86.625 2.825 3.1 7.449999999999999 2 68.89999999999999 17.549999999999997 8.125 5.425 3 36.8 37.35 15.15 10.7 4 30.625000000000004 29.775000000000002 19.400000000000002 20.200000000000003 5 26.075 29.549999999999997 26.5 17.875 6 19.975 36.3 26.0 17.724999999999998 7 36.95 27.700000000000003 19.3 16.05 8 28.675 29.525000000000002 23.599999999999998 18.2 9 24.45 29.65 27.650000000000002 18.25 10-11 24.2625 29.475 27.900000000000002 18.3625 12-13 27.6 25.924999999999997 27.825 18.65 14-15 21.55 30.9 29.6625 17.8875 16-17 24.3125 30.2375 25.674999999999997 19.775000000000002 18-19 24.125 26.9125 28.65 20.3125 20-21 24.7 25.45 29.912499999999998 19.9375 22-23 26.387500000000003 23.875 28.499999999999996 21.2375 24-25 24.775 23.65 30.2125 21.3625 26-27 25.825 24.525 30.099999999999998 19.55 28-29 24.7875 28.1375 28.0625 19.0125 30-31 27.962500000000002 25.6 26.387500000000003 20.05 32-33 24.15 26.700000000000003 27.787499999999998 21.3625 34-35 24.9875 27.462500000000002 27.3375 20.2125 36-37 25.825 24.474999999999998 26.950000000000003 22.75 38-39 27.98297233003631 24.840365594090397 28.896957556028546 18.279704519844746 40-41 25.84761666458151 24.48392343300388 29.00037532841236 20.66808457400225 42-43 25.13442540952857 29.89871201700638 26.20982868575716 18.75703388770789 44-45 23.4125 26.0125 30.225 20.349999999999998 46-47 24.4 24.425 27.6375 23.5375 48-49 26.025 23.7875 29.9625 20.225 50-51 23.7625 27.287499999999998 28.075 20.875 52-53 23.68949084524705 27.200902934537247 27.13819914722849 21.97140707298721 54-55 22.162499999999998 29.062500000000004 28.812500000000004 19.9625 56-57 25.2375 27.3375 27.987499999999997 19.4375 58-59 22.625 26.237500000000004 30.45 20.6875 60-61 26.200000000000003 24.9875 28.575 20.2375 62-63 22.0 28.537499999999998 31.0625 18.4 64-65 23.5375 29.4 28.65 18.4125 66-67 24.5375 29.525000000000002 28.275 17.6625 68-69 21.7375 27.3875 29.099999999999998 21.775 70-71 23.671679197994987 26.44110275689223 28.195488721804512 21.69172932330827 72-73 25.548370736655258 25.637124381894257 28.705464688728288 20.1090401927222 74-75 23.391963024778534 27.808447811015537 29.451790987289765 19.347798176916164 76-77 22.530824140168722 25.90525632706035 29.318624269954576 22.245295262816352 78-79 24.472684396698547 25.44215904624656 30.76116860998297 19.323987947071924 80-81 23.260754115772702 30.868295273499736 28.053637812002126 17.81731279872544 82-83 24.123101733637952 26.62276575729069 28.033866415804326 21.220266093267036 84-85 22.316076294277927 25.367847411444146 31.103542234332426 21.212534059945504 86-87 21.371959551790106 27.671494943973762 30.705110685979776 20.251434818256353 88-89 20.333424432905165 29.830554796392455 29.721235310194043 20.114785460508337 90-91 25.252801311833835 29.092648264553155 27.657830008198964 17.996720415414046 92-93 20.852691992347637 31.07406395189943 28.395736540038264 19.677507515714677 >>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 4.5 18 6.5 19 2.5 20 1.0 21 1.0 22 1.0 23 0.5 24 3.5 25 7.5 26 12.0 27 15.0 28 22.5 29 31.5 30 40.5 31 53.0 32 68.5 33 80.5 34 90.0 35 108.0 36 133.0 37 169.5 38 195.0 39 183.0 40 189.5 41 201.5 42 200.0 43 206.0 44 202.0 45 181.5 46 184.0 47 178.0 48 150.0 49 161.0 50 150.0 51 132.5 52 125.0 53 132.0 54 153.0 55 117.5 56 62.0 57 45.0 58 51.5 59 48.5 60 40.0 61 38.5 62 34.5 63 31.0 64 22.0 65 16.5 66 12.0 67 11.5 68 14.0 69 10.0 70 10.5 71 12.0 72 7.5 73 4.0 74 3.5 75 1.5 76 1.0 77 1.0 78 1.0 79 0.5 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 0.1625 40-41 0.08750000000000001 42-43 0.0375 44-45 0.0 46-47 0.0 48-49 0.0 50-51 0.0 52-53 0.325 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 20.0 71 25.0 72 23.0 73 25.0 74 25.0 75 21.0 76 17.0 77 15.0 78 25.0 79 26.0 80 24.0 81 23.0 82 21.0 83 29.0 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 3659.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 76.35 #Duplication Level Percentage of deduplicated Percentage of total 1 91.0936476751801 69.55 2 4.944335297969875 7.55 3 1.5717092337917484 3.5999999999999996 4 0.7858546168958742 2.4 5 0.3601833660772757 1.375 6 0.19646365422396855 0.8999999999999999 7 0.13097576948264572 0.7000000000000001 8 0.06548788474132286 0.4 9 0.0 0.0 >10 0.8185985592665358 10.925 >50 0.0 0.0 >100 0.03274394237066143 2.6 >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 104 2.6 No Hit GGGATGATTCTGTATTACAATTTGGTGGAGGAACTTTAGGACATCCTTGG 42 1.05 No Hit GGGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGT 32 0.8 No Hit GGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCTTGG 31 0.775 No Hit GGGCGCGATCTTGCTCGTGAAGGTAATGAAATTATCCGAGCAGCTTGCAA 28 0.7000000000000001 No Hit GGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGTG 21 0.525 No Hit GGACATCCTTGGGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTT 20 0.5 No Hit TACCTAGGCACCCAGAGACGAGGAAGGGCGTAGCAAGCGACGAAATGCTT 20 0.5 No Hit GGCGTTCAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTC 18 0.44999999999999996 No Hit GGATGATTCTGTATTACAATTTGGTGGAGGAACTTTAGGACATCCTTGGG 18 0.44999999999999996 No Hit GGAGTCCTGAACTAGCCGCAGCTTGTGAAGTATGGAAGGCGATCAAATTC 17 0.42500000000000004 No Hit GGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGTGTACAAGCTCGTAA 17 0.42500000000000004 No Hit GGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAA 17 0.42500000000000004 No Hit GGTAATGAAATTATCCGAGCAGCTTGCAAATGGAGTCCTGAACTAGCCGC 16 0.4 No Hit GGAAAAGAAAGCAAAAGCGATTCCCGTAGTAGCGGCGAGCGAAATGGGAG 15 0.375 No Hit GGAAGAGCCCGAGCTGCTGCAGCAGGTTTTGAAAAGGGAATCGATCGTGA 14 0.35000000000000003 No Hit GGATATCGTGTGTGTACATTTGAATGTACCGACATGGGCTCGAGGAGCAT 13 0.325 No Hit GGGGATGATTCTGTATTACAATTTGGTGGAGGAACTTTAGGACATCCTTG 13 0.325 No Hit GGGCTGATATCATCAACCGTGCTAATCTTGGTATGGAAGTAATGCACGAA 12 0.3 No Hit GGAGGAACTTTAGGACATCCTTGGGGAAATGCACCTGGTGCAGCAGCTAA 12 0.3 No Hit GAAGGTAATGAAATTATCCGAGCAGCTTGCAAATGGAGTCCTGAACTAGC 11 0.27499999999999997 No Hit GGTGGAGGAACTTTAGGACATCCTTGGGGAAATGCACCTGGTGCAGCAGC 10 0.25 No Hit GGAGTTGAAAATAAGCATAGATCCGGAGATTCCCAAATAGGTCAACCTTT 10 0.25 No Hit CAAGGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCT 10 0.25 No Hit GGAGTATCCTTGATATATAAATATATAGATAAATAGATTTAAATGGAAAA 10 0.25 No Hit GGTTTTGAAAAGGGAATCGATCGTGATTTAGAACCTGTTCTTTACATGAA 10 0.25 No Hit GGGCACGTGGAATCCCGTGTGAATCAGCAAGGACCACCTTGCAAGGCTAA 8 0.2 No Hit GTATGGAAGGCGATCAAATTCGAGTTCGCGCCGGTAGATACTATCGATTA 8 0.2 No Hit GGGAAAAGAGGGGTTACTTTTTTTCATTTTTCCCTTAAAAGATAGGCTTT 7 0.17500000000000002 No Hit GGGCTCGAGGAGCATATGTACATTTGAACCCTGACTACACATATACACAC 7 0.17500000000000002 No Hit GGCCTGTAGTAGGAATCTGGTTCACTGCTTTAGGTATTAGTACTATGGCG 7 0.17500000000000002 No Hit GTACAAGCTCGTAACGAAGGGCGCGATCTTGCTCGTGAAGGTAATGAAAT 7 0.17500000000000002 No Hit GGTGGGGCAATGGGCATTCCGTTGAGTTTGTATGGTGGGTGCTGTTTTGC 6 0.15 No Hit GTAGTAGGAATCTGGTTCACTGCTTTAGGTATTAGTACTATGGCGTTCAA 6 0.15 No Hit GGAGTCCCATATATATATGTATAAGATGCCAGCCCGGTTTCGTCAACCAT 6 0.15 No Hit GGGAGTATTATGAAAGGAGATTAATCATAGATTATCAAAAACCCTAGAAA 6 0.15 No Hit CAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAGGTC 6 0.15 No Hit GGGTTACTTTTTTTCATTTTTCCCTTAAAAGATAGGCTTTGAAATCGGAG 6 0.15 No Hit GGGGTTACTTTTTTTCATTTTTCCCTTAAAAGATAGGCTTTGAAATCGGA 5 0.125 No Hit GGGATGGAGATGGCCGCGGAGAACGGCGGCTGCGGCTGCAGCACCTGCAA 5 0.125 No Hit GGAACTTTAGGACATCCTTGGGGAAATGCACCTGGTGCAGCAGCTAATCG 5 0.125 No Hit GGGTTGTTTGGGAATGCAGCCCAAATCGGGCGGTAGACTCCGTCCAAGGC 5 0.125 No Hit GGAAGGCGATCAAATTCGAGTTCGCGCCGGTAGATACTATCGATTAATAG 5 0.125 No Hit GGCGCGATCTTGCTCGTGAAGGTAATGAAATTATCCGAGCAGCTTGCAAA 5 0.125 No Hit GGGGATGGAGCGACAGAAGTATGGAAATAGGATAAGGTAGCGGCGAGACG 5 0.125 No Hit GAAGTATGGAAGGCGATCAAATTCGAGTTCGCGCCGGTAGATACTATCGA 5 0.125 No Hit GGAATCCCGTGTGAATCAGCAAGGACCACCTTGCAAGGCTAAATACTCCT 5 0.125 No Hit GGAGCAGCCTAAACCGTGAAAACGGGGTTGTGGGAGAGCAATACAAGCGT 5 0.125 No Hit GGGCACTGTAGCCAGTGTGTCAGTCGTTGTTAAATTACAGGTTGAGATCA 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 0.0 0.0 0.0 0.0 0.0 42-43 0.0 0.0 0.0 0.0 0.0 44-45 0.0 0.0 0.0 0.0 0.0 46-47 0.0 0.0 0.0 0.0 0.0 48-49 0.0 0.0 0.0 0.0 0.0 50-51 0.0 0.0 0.0 0.0 0.0 52-53 0.0 0.0 0.0 0.0 0.0 54-55 0.0 0.0 0.0 0.0 0.0 56-57 0.0 0.0 0.0 0.0 0.0 58-59 0.0 0.0 0.0 0.0 0.0 60-61 0.0 0.0 0.0 0.0 0.0 62-63 0.0 0.0 0.0 0.0 0.0 64-65 0.0 0.0 0.0 0.0 0.0 66-67 0.0 0.0 0.0 0.0 0.0 68-69 0.0 0.0 0.0 0.0 0.0 70-71 0.0 0.0 0.0 0.0 0.0 72-73 0.0 0.0 0.0 0.0 0.0 74-75 0.0 0.0 0.0 0.0 0.0 76-77 0.0 0.0 0.0 0.0 0.0 78-79 0.0 0.0 0.0 0.0 0.0 80-81 0.0 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content pass >>END_MODULE Rejected 272840 READS because READLEN < 1 Read 272840 spots for ERR6133501.sra Written 272840 spots for ERR6133501.sra Rejected 272840 READS because READLEN < 1 Read 272840 spots for ERR6133501.sra Written 272840 spots for ERR6133501.sra Rejected 272847 READS because READLEN < 1 Read 272847 spots for ERR6133501.sra Written 272847 spots for ERR6133501.sra Rejected 272840 READS because READLEN < 1 Read 272840 spots for ERR6133501.sra Written 272840 spots for ERR6133501.sra Rejected 272840 READS because READLEN < 1 Read 272840 spots for ERR6133501.sra Written 272840 spots for ERR6133501.sra Rejected 272840 READS because READLEN < 1 Read 272840 spots for ERR6133501.sra Written 272840 spots for ERR6133501.sra Rejected 272840 READS because READLEN < 1 Read 272840 spots for ERR6133501.sra Written 272840 spots for ERR6133501.sra Rejected 272840 READS because READLEN < 1 Read 272840 spots for ERR6133501.sra Written 272840 spots for ERR6133501.sra Rejected 272840 READS because READLEN < 1 Read 272840 spots for ERR6133501.sra Written 272840 spots for ERR6133501.sra Rejected 272840 READS because READLEN < 1 Read 272840 spots for ERR6133501.sra Written 272840 spots for ERR6133501.sra Rejected 272840 READS because READLEN < 1 Read 272840 spots for ERR6133501.sra Written 272840 spots for ERR6133501.sra Rejected 272840 READS because READLEN < 1 Read 272840 spots for ERR6133501.sra Written 272840 spots for ERR6133501.sra Rejected 272840 READS because READLEN < 1 Read 272840 spots for ERR6133501.sra Written 272840 spots for ERR6133501.sra Rejected 272840 READS because READLEN < 1 Read 272840 spots for ERR6133501.sra Written 272840 spots for ERR6133501.sra Rejected 272840 READS because READLEN < 1 Read 272840 spots for ERR6133501.sra Written 272840 spots for ERR6133501.sra Rejected 272840 READS because READLEN < 1 Read 272840 spots for ERR6133501.sra Written 272840 spots for ERR6133501.sra Rejected 272840 READS because READLEN < 1 Read 272840 spots for ERR6133501.sra Written 272840 spots for ERR6133501.sra Rejected 272840 READS because READLEN < 1 Read 272840 spots for ERR6133501.sra Written 272840 spots for ERR6133501.sra Rejected 272840 READS because READLEN < 1 Read 272840 spots for ERR6133501.sra Written 272840 spots for ERR6133501.sra Rejected 272840 READS because READLEN < 1 Read 272840 spots for ERR6133501.sra Written 272840 spots for ERR6133501.sra SRR ids: ['ERR6133501.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_8qxoatv_ ERR6133501.sra spots: 5456807 blocks: [[1, 272840], [272841, 545680], [545681, 818520], [818521, 1091360], [1091361, 1364200], [1364201, 1637040], [1637041, 1909880], [1909881, 2182720], [2182721, 2455560], [2455561, 2728400], [2728401, 3001240], [3001241, 3274080], [3274081, 3546920], [3546921, 3819760], [3819761, 4092600], [4092601, 4365440], [4365441, 4638280], [4638281, 4911120], [4911121, 5183960], [5183961, 5456807]] ERR6133501 file size 1195529 ERR6133501 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 ERR6133501 ERR6133501_1.fastq Input file: ERR6133501_1.fastq trimmed: ERR6133501-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 07:25:30 2024 >> started Sat Dec 7 07:25:37 2024 >> done (7.206s) 5456807 reads processed; of these: 524 ( 0.01%) short reads filtered out after trimming by size control 80 ( 0.00%) empty reads filtered out after trimming by size control 5456203 (99.99%) reads available; of these: 96752 ( 1.77%) trimmed reads available after processing 5359451 (98.23%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 202 0.00% 19 268 0.00% 20 117 0.00% 21 75 0.00% 22 82 0.00% 23 35 0.00% 24 34 0.00% 25 30 0.00% 26 26 0.00% 27 51 0.00% 28 87 0.00% 29 38 0.00% 30 42 0.00% 31 73 0.00% 32 99 0.00% 33 60 0.00% 34 65 0.00% 35 381 0.01% 36 1076 0.02% 37 70 0.00% 38 168 0.00% 39 388 0.01% 40 418 0.01% 41 116 0.00% 42 47 0.00% 43 47 0.00% 44 66 0.00% 45 48 0.00% 46 32 0.00% 47 34 0.00% 48 22 0.00% 49 25 0.00% 50 49 0.00% 51 250 0.00% 52 60 0.00% 53 29 0.00% 54 19 0.00% 55 34 0.00% 56 32 0.00% 57 52 0.00% 58 47 0.00% 59 27 0.00% 60 55 0.00% 61 31 0.00% 62 7 0.00% 63 5 0.00% 64 11 0.00% 65 18 0.00% 66 13 0.00% 67 37 0.00% 68 76 0.00% 69 316 0.01% 70 41494 0.76% 71 34394 0.63% 72 37674 0.69% 73 33288 0.61% 74 36333 0.67% 75 36348 0.67% 76 28474 0.52% 77 30568 0.56% 78 37008 0.68% 79 43947 0.81% 80 34530 0.63% 81 38730 0.71% 82 44033 0.81% 83 48028 0.88% 84 35029 0.64% 85 162 0.00% 86 300 0.01% 87 520 0.01% 88 950 0.02% 89 1984 0.04% 90 4047 0.07% 91 12767 0.23% 92 62046 1.14% 93 4808059 88.12% 5456203 reads passed initial QC criterion=sequence-density sequence-density=1.02 sequence-density-rank=1 fanout-score=1.97 fanout-score-rank=30 prefix-density=1.02 prefix-fanout=2.0 sequence=CAAGGCTAAATAC criterion=fanout-score sequence-density=0.05 sequence-density-rank=17 fanout-score=59.16 fanout-score-rank=1 prefix-density=0.20 prefix-fanout=16.2 sequence=TTTTTTTTTTAAGAATCCTCCATTTTTGTTCTTCCACCCATGCAATAGAGAGCAAATGGGAAAAGAGGGGTTACTTTTTTTCATTTTTCCCTTAAAAGATAGGCTTTGAAATCGGAGTCATGGAATAATGGTGAATTCAAATGTTTAGTTCTTTAGTATAAGAAGTATAAGAA Started job on | Dec 07 07:26:15 Started mapping on | Dec 07 07:26:16 Finished on | Dec 07 07:26:40 Mapping speed, Million of reads per hour | 818.43 Number of input reads | 5456203 Average input read length | 91 UNIQUE READS: Uniquely mapped reads number | 3599553 Uniquely mapped reads % | 65.97% Average mapped length | 90.64 Number of splices: Total | 135346 Number of splices: Annotated (sjdb) | 111517 Number of splices: GT/AG | 130063 Number of splices: GC/AG | 2359 Number of splices: AT/AC | 116 Number of splices: Non-canonical | 2808 Mismatch rate per base, % | 0.43% Deletion rate per base | 0.04% Deletion average length | 1.80 Insertion rate per base | 0.02% Insertion average length | 2.21 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 1718450 % of reads mapped to multiple loci | 31.50% Number of reads mapped to too many loci | 52983 % of reads mapped to too many loci | 0.97% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 1.50% % of reads unmapped: other | 0.06% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 138200 138200 138200 N_multimapping 1718450 1718450 1718450 N_noFeature 251323 284114 3449409 N_ambiguous 132977 15357 682 UnstrandedReadsAssigned:3215253 PositiveStrandReadsAssigned:3300082 NegativeStrandReadsAssigned:149462 Dataset is classified positive stranded MeadianReadLen=93 20thPercentileLength=93 echo kmer=89 ERR6133501 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: ERR6133501-trimmed.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 5,456,203 reads, 4,429,487 reads pseudoaligned [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,075 rounds 52973 ERR6133501.ke.tsv 35125 ERR6133501.se.tsv 88098 total ==> ERR6133501.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 42 9.37057 PNS24243 293 194 0 0 KQK14069 1603 1504 10 2.03528 KQK14071 474 375 0 0 ==> ERR6133501.se.tsv <== BRADI_1g14170v3 10 BRADI_1g53295v3 14 BRADI_1g59795v3 31 BRADI_1g07683v3 0 BRADI_1g00485v3 0 BRADI_1g20270v3 54 BRADI_1g74790v3 43 BRADI_1g09890v3 0 BRADI_1g77505v3 63 BRADI_1g48960v3 0 ERR6133501 completed mapping pipeline successfully