Starting /dee2/code/volunteer_pipeline.sh ERR6133523 current disk space = 1544434749440 free memory = 1598954824 ERR6133523 SRAfilesize 8b4f9d1c12ee7a87c7573d4ebec2b0b6 ERR6133523.sra ERR6133523.sra file validated ERR6133523 is single end ERR6133523 is conventional basespace ERR6133523 read1 length is 70-93 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename ERR6133523_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 36.64675 37.0 37.0 37.0 37.0 37.0 2 36.8045 37.0 37.0 37.0 37.0 37.0 3 36.552 37.0 37.0 37.0 37.0 37.0 4 35.976 37.0 37.0 37.0 33.0 37.0 5 36.0105 37.0 37.0 37.0 33.0 37.0 6 36.303 37.0 37.0 37.0 33.0 37.0 7 38.33225 40.0 37.0 40.0 37.0 40.0 8 38.334 40.0 37.0 40.0 37.0 40.0 9 38.45175 40.0 37.0 40.0 37.0 40.0 10-11 38.38825 40.0 37.0 40.0 37.0 40.0 12-13 38.29075 40.0 37.0 40.0 37.0 40.0 14-15 38.240624999999994 40.0 37.0 40.0 37.0 40.0 16-17 38.17775 40.0 37.0 40.0 37.0 40.0 18-19 38.109375 40.0 37.0 40.0 37.0 40.0 20-21 38.05825 40.0 37.0 40.0 37.0 40.0 22-23 38.214625 40.0 37.0 40.0 37.0 40.0 24-25 38.11425 40.0 37.0 40.0 37.0 40.0 26-27 38.07275 40.0 37.0 40.0 37.0 40.0 28-29 38.060125 40.0 37.0 40.0 37.0 40.0 30-31 38.125249999999994 40.0 37.0 40.0 37.0 40.0 32-33 38.142375 40.0 37.0 40.0 37.0 40.0 34-35 38.02975 40.0 37.0 40.0 37.0 40.0 36-37 37.97 37.0 37.0 40.0 37.0 40.0 38-39 37.84125 37.0 37.0 40.0 37.0 40.0 40-41 37.649249999999995 37.0 37.0 40.0 37.0 40.0 42-43 37.660250000000005 37.0 37.0 40.0 37.0 40.0 44-45 37.436125000000004 37.0 37.0 40.0 35.0 40.0 46-47 37.295 37.0 37.0 40.0 33.0 40.0 48-49 37.108625 37.0 37.0 38.5 33.0 40.0 50-51 36.893125 37.0 37.0 37.0 33.0 40.0 52-53 36.531375 37.0 37.0 37.0 33.0 40.0 54-55 36.512125 37.0 37.0 37.0 33.0 40.0 56-57 36.378 37.0 37.0 37.0 33.0 38.5 58-59 36.061625 37.0 37.0 37.0 33.0 37.0 60-61 36.125 37.0 37.0 37.0 33.0 37.0 62-63 35.922875 37.0 37.0 37.0 33.0 37.0 64-65 35.921375 37.0 37.0 37.0 33.0 37.0 66-67 35.91125 37.0 37.0 37.0 33.0 37.0 68-69 34.965999999999994 35.0 35.0 37.0 33.0 37.0 70-71 35.193830117764975 37.0 33.0 37.0 33.0 37.0 72-73 35.64216055362232 37.0 35.0 37.0 33.0 37.0 74-75 35.579766618970766 37.0 33.0 37.0 33.0 37.0 76-77 35.60512618090715 37.0 35.0 37.0 33.0 37.0 78-79 35.53844478480472 37.0 33.0 37.0 33.0 37.0 80-81 35.41744084127389 37.0 33.0 37.0 33.0 37.0 82-83 35.297997907474695 37.0 33.0 37.0 33.0 37.0 84-85 35.07718825830831 37.0 33.0 37.0 33.0 37.0 86-87 35.07298503544237 37.0 33.0 37.0 33.0 37.0 88-89 35.06130217904962 37.0 33.0 37.0 33.0 37.0 90-91 34.9787345760042 37.0 33.0 37.0 33.0 37.0 92-93 34.96035704909425 37.0 33.0 37.0 33.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 21 1.0 22 2.0 23 3.0 24 3.0 25 11.0 26 10.0 27 12.0 28 12.0 29 18.0 30 28.0 31 37.0 32 51.0 33 62.0 34 113.0 35 273.0 36 1098.0 37 1414.0 38 834.0 39 18.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 88.3 2.45 2.775 6.4750000000000005 2 72.875 16.05 6.7 4.375 3 35.15 38.975 14.499999999999998 11.375 4 33.925 28.549999999999997 18.2 19.325 5 25.025 30.525000000000002 26.724999999999998 17.724999999999998 6 20.525 37.25 26.875 15.35 7 36.025 29.375 19.175 15.425 8 27.925 31.424999999999997 24.325 16.325 9 26.174999999999997 28.849999999999998 27.975 17.0 10-11 24.975 28.449999999999996 27.8625 18.712500000000002 12-13 26.687499999999996 27.025 27.8625 18.425 14-15 22.85 31.35 28.7 17.1 16-17 23.925 31.424999999999997 25.4625 19.1875 18-19 23.2125 27.5875 27.650000000000002 21.55 20-21 24.593648412103025 27.44436109027257 28.132033008252062 19.829957489372344 22-23 26.875 24.15 27.900000000000002 21.075 24-25 26.700000000000003 25.025 27.987499999999997 20.2875 26-27 25.3125 25.9625 31.087500000000002 17.6375 28-29 25.662499999999998 27.975 27.375 18.987499999999997 30-31 27.2625 25.7875 27.2625 19.6875 32-33 24.625 27.9125 27.375 20.0875 34-35 25.55 27.500000000000004 26.875 20.075000000000003 36-37 23.775 25.7125 29.299999999999997 21.212500000000002 38-39 25.775 25.05 31.4625 17.712500000000002 40-41 26.338169084542272 26.425712856428213 27.188594297148573 20.04752376188094 42-43 24.943735933983497 29.382345586396596 26.619154788697173 19.05476369092273 44-45 23.525 26.424999999999997 29.612500000000004 20.4375 46-47 24.575 24.712500000000002 27.8375 22.875 48-49 24.5125 24.349999999999998 32.1 19.037499999999998 50-51 24.575 27.487499999999997 29.0875 18.85 52-53 25.03763171098846 28.537380832915204 26.342197691921726 20.08278976417461 54-55 24.2625 28.825 28.675 18.2375 56-57 26.375 25.7875 27.4125 20.424999999999997 58-59 22.6875 25.874999999999996 29.849999999999998 21.587500000000002 60-61 24.6 25.674999999999997 30.2875 19.4375 62-63 21.4375 28.499999999999996 31.95 18.1125 64-65 23.3375 28.599999999999998 28.8875 19.175 66-67 25.5125 28.5625 27.437499999999996 18.4875 68-69 22.2625 27.762500000000003 27.8375 22.1375 70-71 25.153297459642097 26.442247528469526 27.81879614566387 20.585658866224502 72-73 26.149968494013866 25.721487082545686 28.128544423440456 20.0 74-75 24.21934501142422 27.887788778877887 28.535161208428534 19.357705001269355 76-77 23.077905491698594 26.500638569604085 29.01660280970626 21.40485312899106 78-79 23.608617594254937 25.75019235701462 30.443703513721466 20.197486535008977 80-81 24.058307533539733 29.411764705882355 29.36016511867905 17.169762641898863 82-83 23.09892109710126 26.03665670089692 29.676329130378264 21.188093071623555 84-85 23.158584534731325 24.390563564875492 31.585845347313235 20.865006553079947 86-87 22.880021002887897 26.98871094775532 31.2417957469152 18.889472302441586 88-89 21.08164872669992 29.325282226306115 31.071147282751376 18.52192176424258 90-91 26.12234182200053 27.02809136256235 28.682068784457865 18.16749803097926 92-93 22.8143869782095 30.283538986610658 28.196377001837753 18.705697033342084 >>END_MODULE >>Per sequence GC content pass #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 6.5 18 7.5 19 3.0 20 1.0 21 2.5 22 5.0 23 4.5 24 4.0 25 4.5 26 6.5 27 11.0 28 23.0 29 32.5 30 34.5 31 34.5 32 36.0 33 48.5 34 65.5 35 90.0 36 114.5 37 144.5 38 176.0 39 184.0 40 197.5 41 202.5 42 209.0 43 223.5 44 218.0 45 219.0 46 238.5 47 200.5 48 167.0 49 189.5 50 178.5 51 172.5 52 170.5 53 176.5 54 165.0 55 98.0 56 54.0 57 48.0 58 38.5 59 24.5 60 21.5 61 20.0 62 13.0 63 11.0 64 10.5 65 7.5 66 7.0 67 8.5 68 5.5 69 3.5 70 3.5 71 2.0 72 2.0 73 1.0 74 1.0 75 1.0 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 0.025 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 0.0 38-39 0.0 40-41 0.05 42-43 0.025 44-45 0.0 46-47 0.0 48-49 0.0 50-51 0.0 52-53 0.35000000000000003 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 9.0 71 15.0 72 17.0 73 12.0 74 16.0 75 11.0 76 10.0 77 8.0 78 6.0 79 12.0 80 16.0 81 15.0 82 13.0 83 19.0 84 12.0 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 3809.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 76.35 #Duplication Level Percentage of deduplicated Percentage of total 1 92.07596594629993 70.3 2 4.551407989521938 6.950000000000001 3 1.1787819253438114 2.7 4 0.4911591355599214 1.5 5 0.3274394237066143 1.25 6 0.3929273084479371 1.7999999999999998 7 0.09823182711198428 0.525 8 0.16371971185330714 1.0 9 0.0 0.0 >10 0.68762278978389 12.375 >50 0.03274394237066143 1.6 >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 GGGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGT 64 1.6 No Hit GGGAGAGCAATACAAGCGTTGTGCTGCTAGGCGAAGCGGTTGAGTGCCGC 49 1.225 No Hit GGGATGATTCTGTATTACAATTTGGTGGAGGAACTTTAGGACATCCTTGG 47 1.175 No Hit GGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAA 39 0.975 No Hit GGCGTTCAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTC 37 0.9249999999999999 No Hit GGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCTTGG 37 0.9249999999999999 No Hit TACCTAGGCACCCAGAGACGAGGAAGGGCGTAGCAAGCGACGAAATGCTT 28 0.7000000000000001 No Hit GGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGTG 27 0.675 No Hit GGACATCCTTGGGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTT 27 0.675 No Hit GGAGTTGAAAATAAGCATAGATCCGGAGATTCCCAAATAGGTCAACCTTT 24 0.6 No Hit GGAGGAACTTTAGGACATCCTTGGGGAAATGCACCTGGTGCAGCAGCTAA 23 0.575 No Hit GGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGTGTACAAGCTCGTAA 20 0.5 No Hit GGGGATGATTCTGTATTACAATTTGGTGGAGGAACTTTAGGACATCCTTG 18 0.44999999999999996 No Hit CAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAGGTC 17 0.42500000000000004 No Hit GGATGATTCTGTATTACAATTTGGTGGAGGAACTTTAGGACATCCTTGGG 16 0.4 No Hit GGCCTGTAGTAGGAATCTGGTTCACTGCTTTAGGTATTAGTACTATGGCG 16 0.4 No Hit GGGCGCGATCTTGCTCGTGAAGGTAATGAAATTATCCGAGCAGCTTGCAA 14 0.35000000000000003 No Hit GGGCTGATATCATCAACCGTGCTAATCTTGGTATGGAAGTAATGCACGAA 13 0.325 No Hit GGAGTATCCTTGATATATAAATATATAGATAAATAGATTTAAATGGAAAA 12 0.3 No Hit GGGAGTATTATGAAAGGAGATTAATCATAGATTATCAAAAACCCTAGAAA 11 0.27499999999999997 No Hit GGAACTTTAGGACATCCTTGGGGAAATGCACCTGGTGCAGCAGCTAATCG 10 0.25 No Hit CAAGGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCT 10 0.25 No Hit GGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGTGT 8 0.2 No Hit GGGTTGTTTGGGAATGCAGCCCAAATCGGGCGGTAGACTCCGTCCAAGGC 8 0.2 No Hit GTAGTAGGAATCTGGTTCACTGCTTTAGGTATTAGTACTATGGCGTTCAA 8 0.2 No Hit GGTGGAGGAACTTTAGGACATCCTTGGGGAAATGCACCTGGTGCAGCAGC 8 0.2 No Hit GAAGGTAATGAAATTATCCGAGCAGCTTGCAAATGGAGTCCTGAACTAGC 8 0.2 No Hit GGGATGGAGCGACAGAAGTATGGAAATAGGATAAGGTAGCGGCGAGACGA 7 0.17500000000000002 No Hit GGGGATGGAGCGACAGAAGTATGGAAATAGGATAAGGTAGCGGCGAGACG 7 0.17500000000000002 No Hit GGAATCCCGTGTGAATCAGCAAGGACCACCTTGCAAGGCTAAATACTCCT 7 0.17500000000000002 No Hit GGGCACGTGGAATCCCGTGTGAATCAGCAAGGACCACCTTGCAAGGCTAA 6 0.15 No Hit GGGAAAAGAGGGGTTACTTTTTTTCATTTTTCCCTTAAAAGATAGGCTTT 6 0.15 No Hit GGTGGGGCAATGGGCATTCCGTTGAGTTTGTATGGTGGGTGCTGTTTTGC 6 0.15 No Hit GGAGTGGGGGTGCCATACGCAAAAAGGAAGCGACTCATAGAATGGCAGAG 6 0.15 No Hit GTAGCAAGCGACGAAATGCTTCGGGGAGTTGAAAATAAGCATAGATCCGG 6 0.15 No Hit GTATGGAAGGCGATCAAATTCGAGTTCGCGCCGGTAGATACTATCGATTA 6 0.15 No Hit GGAATAAGAATAAATCGCAACTCCTTTCCACTACACATAAAAATTGATTT 6 0.15 No Hit CACCTGGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGTGTACAAGCT 6 0.15 No Hit GGAAAAGAGGGGTTACTTTTTTTCATTTTTCCCTTAAAAGATAGGCTTTG 6 0.15 No Hit GGGGAGTTGAAAATAAGCATAGATCCGGAGATTCCCAAATAGGTCAACCT 6 0.15 No Hit GGTAATGAAATTATCCGAGCAGCTTGCAAATGGAGTCCTGAACTAGCCGC 6 0.15 No Hit GTTCAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAG 6 0.15 No Hit GGAAGAGACTTATAATATTGTGGCTGCTCATGGTTATTTTGGCCGATTAA 5 0.125 No Hit GGTTCACTGCTTTAGGTATTAGTACTATGGCGTTCAACCTAAATGGATTC 5 0.125 No Hit GCAAGGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATC 5 0.125 No Hit GGATCGGTCGATCATCGGAGAAAAAGAACACTTCCTCCGTGCATATGCGT 5 0.125 No Hit CAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAATACTTGGGCTGATAT 5 0.125 No Hit GGAAAGGCTTGCGGTGGATACCTAGGCACCCAGAGACGAGGAAGGGCGTA 5 0.125 No Hit GGAAGGGCGTAGCAAGCGACGAAATGCTTCGGGGAGTTGAAAATAAGCAT 5 0.125 No Hit GGGCCGGGTATCTCTCTGCATGTACGTATGCCTGTAATGTACGTAGCTAC 5 0.125 No Hit GGGCGTGGCGTTCATGAACAAGTGAAACCTTATGGCTGGATGGGTCATCG 5 0.125 No Hit GGGCTTGGCTACAATTCCGAATACGCTATTACATGTTTGCGCTAGTTTTT 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 0.0125 0.0 0.0 0.0 0.0 34-35 0.05 0.0 0.0 0.0 0.0 36-37 0.0625 0.0 0.0 0.0 0.0 38-39 0.075 0.0 0.0 0.0 0.0 40-41 0.075 0.0 0.0 0.0 0.0 42-43 0.075 0.0 0.0 0.0 0.0 44-45 0.075 0.0 0.0 0.0 0.0 46-47 0.075 0.0 0.0 0.0 0.0 48-49 0.075 0.0 0.0 0.0 0.0 50-51 0.075 0.0 0.0 0.0 0.0 52-53 0.075 0.0 0.0 0.0 0.0 54-55 0.075 0.0 0.0 0.0 0.0 56-57 0.075 0.0 0.0 0.0 0.0 58-59 0.075 0.0 0.0 0.0 0.0 60-61 0.075 0.0 0.0 0.0 0.0 62-63 0.075 0.0 0.0 0.0 0.0 64-65 0.075 0.0 0.0 0.0 0.0 66-67 0.075 0.0 0.0 0.0 0.0 68-69 0.075 0.0 0.0 0.0 0.0 70-71 0.075 0.0 0.0 0.0 0.0 72-73 0.075 0.0 0.0 0.0 0.0 74-75 0.075 0.0 0.0 0.0 0.0 76-77 0.075 0.0 0.0 0.0 0.0 78-79 0.075 0.0 0.0 0.0 0.0 80-81 0.075 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content pass >>END_MODULE Rejected 149188 READS because READLEN < 1 Read 149188 spots for ERR6133523.sra Written 149188 spots for ERR6133523.sra Rejected 149188 READS because READLEN < 1 Read 149188 spots for ERR6133523.sra Written 149188 spots for ERR6133523.sra Rejected 149188 READS because READLEN < 1 Read 149188 spots for ERR6133523.sra Written 149188 spots for ERR6133523.sra Rejected 149188 READS because READLEN < 1 Read 149188 spots for ERR6133523.sra Written 149188 spots for ERR6133523.sra Rejected 149188 READS because READLEN < 1 Read 149188 spots for ERR6133523.sra Written 149188 spots for ERR6133523.sra Rejected 149188 READS because READLEN < 1 Read 149188 spots for ERR6133523.sra Written 149188 spots for ERR6133523.sra Rejected 149188 READS because READLEN < 1 Read 149188 spots for ERR6133523.sra Written 149188 spots for ERR6133523.sra Rejected 149188 READS because READLEN < 1 Read 149188 spots for ERR6133523.sra Written 149188 spots for ERR6133523.sra Rejected 149201 READS because READLEN < 1 Read 149201 spots for ERR6133523.sra Written 149201 spots for ERR6133523.sra Rejected 149188 READS because READLEN < 1 Read 149188 spots for ERR6133523.sra Written 149188 spots for ERR6133523.sra Rejected 149188 READS because READLEN < 1 Read 149188 spots for ERR6133523.sra Written 149188 spots for ERR6133523.sra Rejected 149188 READS because READLEN < 1 Read 149188 spots for ERR6133523.sra Written 149188 spots for ERR6133523.sra Rejected 149188 READS because READLEN < 1 Read 149188 spots for ERR6133523.sra Written 149188 spots for ERR6133523.sra Rejected 149188 READS because READLEN < 1 Read 149188 spots for ERR6133523.sra Written 149188 spots for ERR6133523.sra Rejected 149188 READS because READLEN < 1 Read 149188 spots for ERR6133523.sra Written 149188 spots for ERR6133523.sra Rejected 149188 READS because READLEN < 1 Read 149188 spots for ERR6133523.sra Written 149188 spots for ERR6133523.sra Rejected 149188 READS because READLEN < 1 Read 149188 spots for ERR6133523.sra Written 149188 spots for ERR6133523.sra Rejected 149188 READS because READLEN < 1 Read 149188 spots for ERR6133523.sra Written 149188 spots for ERR6133523.sra Rejected 149188 READS because READLEN < 1 Read 149188 spots for ERR6133523.sra Written 149188 spots for ERR6133523.sra Rejected 149188 READS because READLEN < 1 Read 149188 spots for ERR6133523.sra Written 149188 spots for ERR6133523.sra SRR ids: ['ERR6133523.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd__5fzg2ao ERR6133523.sra spots: 2983773 blocks: [[1, 149188], [149189, 298376], [298377, 447564], [447565, 596752], [596753, 745940], [745941, 895128], [895129, 1044316], [1044317, 1193504], [1193505, 1342692], [1342693, 1491880], [1491881, 1641068], [1641069, 1790256], [1790257, 1939444], [1939445, 2088632], [2088633, 2237820], [2237821, 2387008], [2387009, 2536196], [2536197, 2685384], [2685385, 2834572], [2834573, 2983773]] ERR6133523 file size 657817 ERR6133523 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 ERR6133523 ERR6133523_1.fastq Input file: ERR6133523_1.fastq trimmed: ERR6133523-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 07:52:30 2024 >> started Sat Dec 7 07:52:32 2024 >> done (1.741s) 2983773 reads processed; of these: 610 ( 0.02%) short reads filtered out after trimming by size control 22 ( 0.00%) empty reads filtered out after trimming by size control 2983141 (99.98%) reads available; of these: 14587 ( 0.49%) trimmed reads available after processing 2968554 (99.51%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 70 0.00% 19 151 0.01% 20 58 0.00% 21 59 0.00% 22 64 0.00% 23 23 0.00% 24 32 0.00% 25 21 0.00% 26 23 0.00% 27 31 0.00% 28 28 0.00% 29 37 0.00% 30 36 0.00% 31 35 0.00% 32 42 0.00% 33 24 0.00% 34 47 0.00% 35 281 0.01% 36 403 0.01% 37 32 0.00% 38 69 0.00% 39 170 0.01% 40 174 0.01% 41 78 0.00% 42 12 0.00% 43 25 0.00% 44 27 0.00% 45 15 0.00% 46 11 0.00% 47 14 0.00% 48 19 0.00% 49 13 0.00% 50 15 0.00% 51 88 0.00% 52 26 0.00% 53 14 0.00% 54 6 0.00% 55 7 0.00% 56 9 0.00% 57 8 0.00% 58 18 0.00% 59 12 0.00% 60 22 0.00% 61 11 0.00% 62 2 0.00% 63 3 0.00% 64 1 0.00% 65 1 0.00% 66 12 0.00% 67 14 0.00% 68 14 0.00% 69 88 0.00% 70 9670 0.32% 71 8990 0.30% 72 9586 0.32% 73 8773 0.29% 74 8749 0.29% 75 8631 0.29% 76 7735 0.26% 77 7774 0.26% 78 8800 0.29% 79 9998 0.34% 80 8842 0.30% 81 10723 0.36% 82 12075 0.40% 83 11072 0.37% 84 10116 0.34% 85 51 0.00% 86 81 0.00% 87 129 0.00% 88 215 0.01% 89 352 0.01% 90 770 0.03% 91 2042 0.07% 92 7840 0.26% 93 2827632 94.79% 2983141 reads passed initial QC criterion=sequence-density sequence-density=0.83 sequence-density-rank=1 fanout-score=2.05 fanout-score-rank=31 prefix-density=0.84 prefix-fanout=2.0 sequence=CAAGGCTAAATAC criterion=fanout-score sequence-density=0.01 sequence-density-rank=26 fanout-score=104.36 fanout-score-rank=1 prefix-density=0.16 prefix-fanout=8.4 sequence=AAAAGAAGGGGTGTTCCATCTCCGGACGACGATCCTGCCTGCAGAGGAAGACATGCCGGCGATCATGTCGAGCTTCAAGAAGTTCAACGACTCATTCATGGAGCAATACCAAGACTACTCCAGGCTGTGATGTGAAGAGGGAAACAACGAGGTCATCATCGACATGATATATTGCTGCTATTTTCCACCAGCGATTAAAAGTTAAAAAATTTAGCTGTAAGCTGTAACTATCTTGAAGAAACTAAACTGGTTGCTGTGCTTGATATGTAT Started job on | Dec 07 07:52:44 Started mapping on | Dec 07 07:52:44 Finished on | Dec 07 07:52:48 Mapping speed, Million of reads per hour | 2684.83 Number of input reads | 2983141 Average input read length | 92 UNIQUE READS: Uniquely mapped reads number | 1974503 Uniquely mapped reads % | 66.19% Average mapped length | 91.77 Number of splices: Total | 117852 Number of splices: Annotated (sjdb) | 99374 Number of splices: GT/AG | 113681 Number of splices: GC/AG | 2230 Number of splices: AT/AC | 43 Number of splices: Non-canonical | 1898 Mismatch rate per base, % | 0.38% Deletion rate per base | 0.04% Deletion average length | 1.79 Insertion rate per base | 0.02% Insertion average length | 1.86 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 914855 % of reads mapped to multiple loci | 30.67% Number of reads mapped to too many loci | 28994 % of reads mapped to too many loci | 0.97% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 2.13% % of reads unmapped: other | 0.04% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 93783 93783 93783 N_multimapping 914855 914855 914855 N_noFeature 141280 160293 1886310 N_ambiguous 79459 10281 258 UnstrandedReadsAssigned:1753764 PositiveStrandReadsAssigned:1803929 NegativeStrandReadsAssigned:87935 Dataset is classified positive stranded MeadianReadLen=93 20thPercentileLength=93 echo kmer=89 ERR6133523 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: ERR6133523-trimmed.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 2,983,141 reads, 2,438,852 reads pseudoaligned [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 984 rounds 52973 ERR6133523.ke.tsv 35125 ERR6133523.se.tsv 88098 total ==> ERR6133523.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 81 31.8406 PNS24243 293 194 0 0 KQK14069 1603 1504 24 8.60624 KQK14071 474 375 0 0 ==> ERR6133523.se.tsv <== BRADI_1g14170v3 24 BRADI_1g53295v3 55 BRADI_1g59795v3 17 BRADI_1g07683v3 0 BRADI_1g00485v3 0 BRADI_1g20270v3 16 BRADI_1g74790v3 24 BRADI_1g09890v3 0 BRADI_1g77505v3 61 BRADI_1g48960v3 0 ERR6133523 completed mapping pipeline successfully