Starting /dee2/code/volunteer_pipeline.sh ERR6133546 current disk space = 1544531177472 free memory = 1450670488 ERR6133546 SRAfilesize 5d8a8e7f5a2b52e54c16ef4de3c450bf ERR6133546.sra ERR6133546.sra file validated ERR6133546 is single end ERR6133546 is conventional basespace ERR6133546 read1 length is 70-93 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename ERR6133546_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 46 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 33.95925 37.0 33.0 37.0 27.0 37.0 2 35.985 37.0 37.0 37.0 33.0 37.0 3 35.1555 37.0 33.0 37.0 33.0 37.0 4 35.227 37.0 37.0 37.0 33.0 37.0 5 35.2095 37.0 37.0 37.0 33.0 37.0 6 35.51525 37.0 37.0 37.0 33.0 37.0 7 37.28775 37.0 37.0 40.0 33.0 40.0 8 37.33 37.0 37.0 40.0 33.0 40.0 9 37.4235 37.0 37.0 40.0 33.0 40.0 10-11 37.40975 37.0 37.0 40.0 33.0 40.0 12-13 37.3635 37.0 37.0 40.0 33.0 40.0 14-15 37.38125 37.0 37.0 40.0 33.0 40.0 16-17 37.29575 37.0 37.0 40.0 33.0 40.0 18-19 37.19 37.0 37.0 40.0 33.0 40.0 20-21 37.135374999999996 37.0 37.0 40.0 33.0 40.0 22-23 37.0655 37.0 37.0 40.0 33.0 40.0 24-25 37.093625 37.0 37.0 40.0 33.0 40.0 26-27 37.151624999999996 37.0 37.0 40.0 33.0 40.0 28-29 37.044375 37.0 37.0 40.0 33.0 40.0 30-31 36.892375 37.0 37.0 40.0 33.0 40.0 32-33 36.855125 37.0 37.0 40.0 33.0 40.0 34-35 36.65975 37.0 37.0 40.0 33.0 40.0 36-37 36.506625 37.0 37.0 40.0 33.0 40.0 38-39 36.450625 37.0 37.0 40.0 33.0 40.0 40-41 36.15025 37.0 37.0 40.0 33.0 40.0 42-43 36.058125 37.0 37.0 40.0 33.0 40.0 44-45 35.785 37.0 35.0 38.5 33.0 40.0 46-47 35.461875 37.0 33.0 37.0 33.0 40.0 48-49 35.44475 37.0 33.0 37.0 33.0 40.0 50-51 35.3825 37.0 33.0 37.0 33.0 40.0 52-53 35.150375 37.0 33.0 37.0 33.0 40.0 54-55 35.08175 37.0 33.0 37.0 30.0 40.0 56-57 34.927375 37.0 33.0 37.0 33.0 37.0 58-59 34.24925 37.0 33.0 37.0 27.0 37.0 60-61 34.5165 37.0 33.0 37.0 27.0 37.0 62-63 34.396125 37.0 33.0 37.0 27.0 37.0 64-65 34.459125 37.0 33.0 37.0 27.0 37.0 66-67 34.518125 37.0 33.0 37.0 30.0 37.0 68-69 33.6335 35.0 33.0 37.0 27.0 37.0 70-71 33.76435746492986 35.0 33.0 37.0 27.0 37.0 72-73 34.172726961721295 37.0 33.0 37.0 27.0 37.0 74-75 34.1781710653822 37.0 33.0 37.0 27.0 37.0 76-77 34.01413918143881 37.0 33.0 37.0 27.0 37.0 78-79 34.08897243845185 37.0 33.0 37.0 27.0 37.0 80-81 34.08892495617696 37.0 33.0 37.0 27.0 37.0 82-83 33.8348289933011 37.0 33.0 37.0 27.0 37.0 84-85 33.75249102708568 37.0 33.0 37.0 27.0 37.0 86-87 33.683282208588956 37.0 33.0 37.0 27.0 37.0 88-89 33.85352760736197 37.0 33.0 37.0 27.0 37.0 90-91 33.485429447852766 37.0 33.0 37.0 27.0 37.0 92-93 33.38982617586912 37.0 33.0 37.0 27.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 20 14.0 21 13.0 22 16.0 23 20.0 24 29.0 25 37.0 26 31.0 27 53.0 28 53.0 29 79.0 30 74.0 31 111.0 32 149.0 33 157.0 34 243.0 35 405.0 36 937.0 37 940.0 38 627.0 39 12.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 88.14999999999999 2.35 3.5749999999999997 5.925 2 73.175 16.375 6.575 3.875 3 37.25 38.324999999999996 14.399999999999999 10.025 4 33.825 26.674999999999997 18.05 21.45 5 26.450000000000003 30.525000000000002 25.374999999999996 17.65 6 19.925 37.775 26.025 16.275000000000002 7 36.925000000000004 28.7 18.224999999999998 16.150000000000002 8 29.875 30.225 23.45 16.45 9 25.7 29.25 27.375 17.675 10-11 24.6125 28.475 27.3125 19.6 12-13 27.712500000000002 26.8375 25.775 19.675 14-15 22.0 31.05 28.825 18.125 16-17 25.324999999999996 30.599999999999998 24.5625 19.5125 18-19 24.45 27.400000000000002 26.8 21.349999999999998 20-21 25.3125 27.437499999999996 26.8625 20.3875 22-23 27.6375 23.3625 27.037499999999998 21.9625 24-25 25.6 24.375 29.2875 20.7375 26-27 25.087500000000002 25.5125 30.375000000000004 19.025 28-29 25.474999999999998 28.125 26.875 19.525000000000002 30-31 27.975 25.837500000000002 25.224999999999998 20.962500000000002 32-33 24.275 26.087500000000002 28.037499999999998 21.6 34-35 24.818613960470355 27.445584188141105 26.582436827620715 21.153365023767826 36-37 25.5625 22.925 28.499999999999996 23.0125 38-39 28.000000000000004 24.5375 29.775000000000002 17.6875 40-41 26.18809404702351 24.73736868434217 26.550775387693847 22.52376188094047 42-43 25.228381929670878 28.444500062570395 25.653860593167316 20.673257414591415 44-45 23.799399699849925 25.012506253126567 29.57728864432216 21.61080540270135 46-47 25.1875 22.825 27.35 24.637500000000003 48-49 24.8625 24.75 30.3 20.0875 50-51 24.825 26.325 28.575 20.275000000000002 52-53 25.65032516258129 26.550775387693847 26.088044022011005 21.710855427713856 54-55 23.9 28.349999999999998 28.025 19.725 56-57 26.5 25.724999999999998 27.925 19.85 58-59 24.1375 24.775 29.5375 21.55 60-61 25.3 24.2875 29.462500000000002 20.95 62-63 21.85 29.325000000000003 31.2125 17.6125 64-65 23.6375 27.775 28.9375 19.650000000000002 66-67 25.5625 27.9375 27.3 19.2 68-69 22.787499999999998 27.3125 27.037499999999998 22.8625 70-71 25.33783783783784 25.375375375375377 26.626626626626624 22.66016016016016 72-73 26.556224899598398 24.058734939759034 28.790160642570285 20.59487951807229 74-75 23.581225619730716 27.393985151629547 29.407323518308797 19.617465710330944 76-77 22.990536277602523 25.652996845425868 28.858044164037857 22.498422712933756 78-79 23.77339403136065 24.241274658573598 31.057157309054123 20.928174001011634 80-81 23.570432357043238 30.1382021047293 27.906681881577278 18.384683656650182 82-83 25.047703854471443 24.895051520162827 28.67319679430098 21.384047831064752 84-85 23.965781409601632 23.084780388151174 32.03524004085802 20.914198161389173 86-87 22.903885480572598 25.434560327198362 32.285276073619634 19.37627811860941 88-89 20.60327198364008 29.141104294478527 31.007157464212682 19.24846625766871 90-91 27.006646216768914 25.524028629856847 28.540388548057262 18.928936605316974 92-93 22.188139059304703 29.11554192229039 29.460633946830267 19.235685071574643 >>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 0.5 17 8.5 18 10.0 19 3.0 20 1.5 21 2.0 22 3.0 23 9.5 24 11.0 25 5.0 26 5.5 27 9.0 28 17.5 29 24.5 30 26.5 31 29.5 32 41.5 33 58.5 34 69.5 35 75.5 36 87.0 37 125.5 38 162.0 39 161.5 40 164.5 41 188.0 42 218.5 43 235.0 44 204.5 45 173.5 46 215.5 47 210.0 48 152.0 49 156.5 50 170.5 51 171.5 52 162.0 53 169.0 54 160.5 55 101.5 56 70.0 57 72.5 58 67.5 59 50.5 60 36.0 61 34.0 62 37.5 63 37.5 64 27.0 65 27.0 66 28.0 67 21.5 68 14.0 69 9.0 70 9.0 71 7.0 72 4.5 73 1.5 74 0.5 75 0.5 76 0.5 77 0.5 78 0.5 79 0.0 80 1.0 81 1.0 82 0.0 83 0.0 84 0.0 85 0.0 86 0.0 87 0.5 88 0.5 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 0.075 36-37 0.0 38-39 0.0 40-41 0.05 42-43 0.11249999999999999 44-45 0.05 46-47 0.0 48-49 0.0 50-51 0.0 52-53 0.05 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 8.0 71 5.0 72 6.0 73 6.0 74 3.0 75 8.0 76 3.0 77 3.0 78 8.0 79 3.0 80 7.0 81 5.0 82 9.0 83 6.0 84 8.0 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 3912.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 71.7 #Duplication Level Percentage of deduplicated Percentage of total 1 89.43514644351464 64.125 2 5.788005578800558 8.3 3 1.9874476987447698 4.275 4 0.8368200836820083 2.4 5 0.3486750348675035 1.25 6 0.24407252440725244 1.05 7 0.24407252440725244 1.225 8 0.1394700139470014 0.8 9 0.0697350069735007 0.44999999999999996 >10 0.8019525801952581 11.5 >50 0.10460251046025104 4.625 >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 76 1.9 No Hit GGGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGT 58 1.4500000000000002 No Hit GGGATGATTCTGTATTACAATTTGGTGGAGGAACTTTAGGACATCCTTGG 51 1.275 No Hit GGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCTTGG 38 0.95 No Hit GGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGTG 36 0.8999999999999999 No Hit GGACATCCTTGGGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTT 33 0.8250000000000001 No Hit GGGCGCGATCTTGCTCGTGAAGGTAATGAAATTATCCGAGCAGCTTGCAA 32 0.8 No Hit GGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAA 32 0.8 No Hit GGGGATGATTCTGTATTACAATTTGGTGGAGGAACTTTAGGACATCCTTG 30 0.75 No Hit GGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGTGTACAAGCTCGTAA 26 0.65 No Hit TACCTAGGCACCCAGAGACGAGGAAGGGCGTAGCAAGCGACGAAATGCTT 22 0.5499999999999999 No Hit GGTAATGAAATTATCCGAGCAGCTTGCAAATGGAGTCCTGAACTAGCCGC 22 0.5499999999999999 No Hit GGCGTTCAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTC 19 0.475 No Hit GGAGTATCCTTGATATATAAATATATAGATAAATAGATTTAAATGGAAAA 17 0.42500000000000004 No Hit GGAGGAACTTTAGGACATCCTTGGGGAAATGCACCTGGTGCAGCAGCTAA 17 0.42500000000000004 No Hit GGATGATTCTGTATTACAATTTGGTGGAGGAACTTTAGGACATCCTTGGG 16 0.4 No Hit GGAGTCCCATATATATATGTATAAGATGCCAGCCCGGTTTCGTCAACCAT 15 0.375 No Hit GGGATGGAGCGACAGAAGTATGGAAATAGGATAAGGTAGCGGCGAGACGA 13 0.325 No Hit GGCGCGATCTTGCTCGTGAAGGTAATGAAATTATCCGAGCAGCTTGCAAA 13 0.325 No Hit GGGAGTATTATGAAAGGAGATTAATCATAGATTATCAAAAACCCTAGAAA 13 0.325 No Hit GAAGGTAATGAAATTATCCGAGCAGCTTGCAAATGGAGTCCTGAACTAGC 13 0.325 No Hit GGGCTCGAGGAGCATATGTACATTTGAACCCTGACTACACATATACACAC 12 0.3 No Hit CAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAGGTC 11 0.27499999999999997 No Hit GGAGTCCTGAACTAGCCGCAGCTTGTGAAGTATGGAAGGCGATCAAATTC 10 0.25 No Hit GGGAATCGATCGTGATTTAGAACCTGTTCTTTACATGAACCCTCTTAACT 10 0.25 No Hit GGTTTTGAAAAGGGAATCGATCGTGATTTAGAACCTGTTCTTTACATGAA 10 0.25 No Hit GGGCTGATATCATCAACCGTGCTAATCTTGGTATGGAAGTAATGCACGAA 9 0.22499999999999998 No Hit GTACAAGCTCGTAACGAAGGGCGCGATCTTGCTCGTGAAGGTAATGAAAT 9 0.22499999999999998 No Hit GGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGTGT 8 0.2 No Hit GGAGTTGAAAATAAGCATAGATCCGGAGATTCCCAAATAGGTCAACCTTT 8 0.2 No Hit GGGAAACAACGACGTCATCATCGACATGATATATTGCTGCTATTTTCCAC 8 0.2 No Hit GGGACGCATGCAACGACCATCTACATATAGCTACTCGATCTACCGCTACC 8 0.2 No Hit GGAACTTTAGGACATCCTTGGGGAAATGCACCTGGTGCAGCAGCTAATCG 7 0.17500000000000002 No Hit GTAGTAGGAATCTGGTTCACTGCTTTAGGTATTAGTACTATGGCGTTCAA 7 0.17500000000000002 No Hit GGTGGAGGAACTTTAGGACATCCTTGGGGAAATGCACCTGGTGCAGCAGC 7 0.17500000000000002 No Hit GGATATCGTGTGTGTACATTTGAATGTACCGACATGGGCTCGAGGAGCAT 7 0.17500000000000002 No Hit CAAGGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCT 7 0.17500000000000002 No Hit GGAAAAGAGGGGTTACTTTTTTTCATTTTTCCCTTAAAAGATAGGCTTTG 7 0.17500000000000002 No Hit GGAAAAGAAAGCAAAAGCGATTCCCGTAGTAGCGGCGAGCGAAATGGGAG 7 0.17500000000000002 No Hit GGGGAAGAAGAATGCTGGCAAAATTAATTTGCTTTTTTTGGGGAGAATGG 6 0.15 No Hit GAAGGAACAAACGAGGATAAGATAAAATTTCTTTAAATTTATTTTGCCCA 6 0.15 No Hit GGGCTGCGAGGAATCCGGCAAGGCATAAACAACCAAGGACAGCTCCGTAT 6 0.15 No Hit GGGTTGTTTGGGAATGCAGCCCAAATCGGGCGGTAGACTCCGTCCAAGGC 6 0.15 No Hit GGATCGGTCGATCATCGGAGAAGAAGAACACTTCCTCCGTGCATATGCGT 6 0.15 No Hit CAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAATACTTGGGCTG 6 0.15 No Hit GGAGTATATGTACTCGCTATTTTCCAGTACTGCATGCCGGATGGCTCGAT 6 0.15 No Hit GGGATGGAGATGGCCGCGGAGAACGGCGGCTGCGGCTGCAGCACCTGCAA 5 0.125 No Hit GGAACAAACGAGGATAAGATAAAATTTCTTTAAATTTATTTTGCCCAAGT 5 0.125 No Hit CAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAATACTTGGGCTGATAT 5 0.125 No Hit GGGGATGGAGCGACAGAAGTATGGAAATAGGATAAGGTAGCGGCGAGACG 5 0.125 No Hit GGGGTTGTGGGAGAGCAATACAAGCGTTGTGCTGCTAGGCGAAGCGGTTG 5 0.125 No Hit GAAGGGCGCGATCTTGCTCGTGAAGGTAATGAAATTATCCGAGCAGCTTG 5 0.125 No Hit GGCATATGCCAGCTCTGACCGAAATCTTTGGGGATGATTCTGTATTACAA 5 0.125 No Hit GGGTGTCAATATATGATGATGTGTTGTTATAATGTACGCGCCTGCAAACT 5 0.125 No Hit GGGGAAGTACACCAGCGACGGCGAGGCCGCCGCCGCCAAGGAAGGCATGT 5 0.125 No Hit GTTCAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAG 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 0.025 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 0.025 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 warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position GGAGAGC 15 8.783281E-4 86.825 2 GGGAGAG 20 2.4063233E-5 86.825 1 CAATACA 15 8.783281E-4 86.825 8 AATACAA 15 8.783281E-4 86.825 9 GCAATAC 20 0.0027517793 65.11875 7 GAGCAAT 20 0.0027517793 65.11875 5 AGAGCAA 20 0.0027517793 65.11875 4 GAGAGCA 20 0.0027517793 65.11875 3 AGCAATA 20 0.0027517793 65.11875 6 GGGAAAT 25 0.0066597257 52.094997 1 >>END_MODULE Rejected 204574 READS because READLEN < 1 Read 204574 spots for ERR6133546.sra Written 204574 spots for ERR6133546.sra Rejected 204574 READS because READLEN < 1 Read 204574 spots for ERR6133546.sra Written 204574 spots for ERR6133546.sra Rejected 204574 READS because READLEN < 1 Read 204574 spots for ERR6133546.sra Written 204574 spots for ERR6133546.sra Rejected 204574 READS because READLEN < 1 Read 204574 spots for ERR6133546.sra Written 204574 spots for ERR6133546.sra Rejected 204574 READS because READLEN < 1 Read 204574 spots for ERR6133546.sra Written 204574 spots for ERR6133546.sra Rejected 204574 READS because READLEN < 1 Read 204574 spots for ERR6133546.sra Written 204574 spots for ERR6133546.sra Rejected 204574 READS because READLEN < 1 Read 204574 spots for ERR6133546.sra Written 204574 spots for ERR6133546.sra Rejected 204574 READS because READLEN < 1 Read 204574 spots for ERR6133546.sra Written 204574 spots for ERR6133546.sra Rejected 204574 READS because READLEN < 1 Read 204574 spots for ERR6133546.sra Written 204574 spots for ERR6133546.sra Rejected 204574 READS because READLEN < 1 Read 204574 spots for ERR6133546.sra Written 204574 spots for ERR6133546.sra Rejected 204574 READS because READLEN < 1 Read 204574 spots for ERR6133546.sra Written 204574 spots for ERR6133546.sra Rejected 204574 READS because READLEN < 1 Read 204574 spots for ERR6133546.sra Written 204574 spots for ERR6133546.sra Rejected 204574 READS because READLEN < 1 Read 204574 spots for ERR6133546.sra Written 204574 spots for ERR6133546.sra Rejected 204574 READS because READLEN < 1 Read 204574 spots for ERR6133546.sra Written 204574 spots for ERR6133546.sra Rejected 204574 READS because READLEN < 1 Read 204574 spots for ERR6133546.sra Written 204574 spots for ERR6133546.sra Rejected 204574 READS because READLEN < 1 Read 204574 spots for ERR6133546.sra Written 204574 spots for ERR6133546.sra Rejected 204574 READS because READLEN < 1 Read 204574 spots for ERR6133546.sra Written 204574 spots for ERR6133546.sra Rejected 204574 READS because READLEN < 1 Read 204574 spots for ERR6133546.sra Written 204574 spots for ERR6133546.sra Rejected 204574 READS because READLEN < 1 Read 204574 spots for ERR6133546.sra Written 204574 spots for ERR6133546.sra Rejected 204578 READS because READLEN < 1 Read 204578 spots for ERR6133546.sra Written 204578 spots for ERR6133546.sra SRR ids: ['ERR6133546.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_b6mx3fpm ERR6133546.sra spots: 4091484 blocks: [[1, 204574], [204575, 409148], [409149, 613722], [613723, 818296], [818297, 1022870], [1022871, 1227444], [1227445, 1432018], [1432019, 1636592], [1636593, 1841166], [1841167, 2045740], [2045741, 2250314], [2250315, 2454888], [2454889, 2659462], [2659463, 2864036], [2864037, 3068610], [3068611, 3273184], [3273185, 3477758], [3477759, 3682332], [3682333, 3886906], [3886907, 4091484]] ERR6133546 file size 906017 ERR6133546 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 ERR6133546 ERR6133546_1.fastq Input file: ERR6133546_1.fastq trimmed: ERR6133546-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 08:21:23 2024 >> started Sat Dec 7 08:21:25 2024 >> done (2.536s) 4091484 reads processed; of these: 98 ( 0.00%) short reads filtered out after trimming by size control 16 ( 0.00%) empty reads filtered out after trimming by size control 4091370 (100.00%) reads available; of these: 76539 ( 1.87%) trimmed reads available after processing 4014831 (98.13%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 25 0.00% 19 30 0.00% 20 12 0.00% 21 12 0.00% 22 9 0.00% 23 5 0.00% 24 4 0.00% 25 6 0.00% 26 5 0.00% 27 5 0.00% 28 11 0.00% 29 107 0.00% 30 6 0.00% 31 16 0.00% 32 11 0.00% 33 9 0.00% 34 12 0.00% 35 49 0.00% 36 542 0.01% 37 13 0.00% 38 12 0.00% 39 38 0.00% 40 41 0.00% 41 15 0.00% 42 8 0.00% 43 7 0.00% 44 11 0.00% 45 8 0.00% 46 9 0.00% 47 9 0.00% 48 2 0.00% 49 7 0.00% 50 13 0.00% 51 18 0.00% 52 7 0.00% 53 7 0.00% 54 5 0.00% 55 3 0.00% 56 3 0.00% 57 6 0.00% 58 6 0.00% 59 8 0.00% 60 3 0.00% 61 9 0.00% 62 3 0.00% 63 3 0.00% 64 3 0.00% 65 3 0.00% 66 9 0.00% 67 9 0.00% 68 29 0.00% 69 73 0.00% 70 7166 0.18% 71 5319 0.13% 72 5542 0.14% 73 5036 0.12% 74 5735 0.14% 75 5662 0.14% 76 4673 0.11% 77 4801 0.12% 78 5773 0.14% 79 7257 0.18% 80 6111 0.15% 81 6582 0.16% 82 7633 0.19% 83 8349 0.20% 84 6536 0.16% 85 183 0.00% 86 338 0.01% 87 537 0.01% 88 1011 0.02% 89 2040 0.05% 90 4506 0.11% 91 13258 0.32% 92 52078 1.27% 93 3923968 95.91% 4091370 reads passed initial QC criterion=sequence-density sequence-density=0.95 sequence-density-rank=1 fanout-score=2.19 fanout-score-rank=28 prefix-density=1.02 prefix-fanout=2.0 sequence=TGTACATTTGAACCCTGACTACACATATACACACATATACATGTAATATTATACAATCTGTCGAGTATGTGTTGGTTCATACTTA criterion=fanout-score sequence-density=0.01 sequence-density-rank=32 fanout-score=64.02 fanout-score-rank=1 prefix-density=0.12 prefix-fanout=5.6 sequence=AAAAGAAGGGGTGTTCCATCTCCGGACGACGATCCTGCCTGCGGAGGAAGACATGCCGGCGATCATGTCGAGCTTCAAGAAGTTCAACGACTCATTCATGGAGCAATACCAAGACTACTCCAGGCTGTGATGTGAAGAGGGAAACAACGACGTCATCATCGACATGATATATTGCTGCTATTTTCCACCAGCGATTAAAAGTTAAAAAATTTAGCTGTAAGCTGTAACTATCTTGAAGAAACTAAACTGGTTGCTGTGCTTGATATGTATAGGGAAAACATAATTTATGAGACAATCATACTGTGCAACTCTTGGCTCCATCGATTAATTAATACTCCTTGTTATTGCTTGCATGGTG Started job on | Dec 07 08:21:42 Started mapping on | Dec 07 08:21:42 Finished on | Dec 07 08:21:49 Mapping speed, Million of reads per hour | 2104.13 Number of input reads | 4091370 Average input read length | 92 UNIQUE READS: Uniquely mapped reads number | 2751927 Uniquely mapped reads % | 67.26% Average mapped length | 92.21 Number of splices: Total | 115589 Number of splices: Annotated (sjdb) | 94893 Number of splices: GT/AG | 110657 Number of splices: GC/AG | 2369 Number of splices: AT/AC | 97 Number of splices: Non-canonical | 2466 Mismatch rate per base, % | 0.40% Deletion rate per base | 0.04% Deletion average length | 1.78 Insertion rate per base | 0.03% Insertion average length | 2.39 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 1269983 % of reads mapped to multiple loci | 31.04% Number of reads mapped to too many loci | 20962 % of reads mapped to too many loci | 0.51% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 1.15% % of reads unmapped: other | 0.04% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 69460 69460 69460 N_multimapping 1269983 1269983 1269983 N_noFeature 166585 192830 2633254 N_ambiguous 102837 10456 249 UnstrandedReadsAssigned:2482505 PositiveStrandReadsAssigned:2548641 NegativeStrandReadsAssigned:118424 Dataset is classified positive stranded MeadianReadLen=93 20thPercentileLength=93 echo kmer=89 ERR6133546 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: ERR6133546-trimmed.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 4,091,370 reads, 3,427,291 reads pseudoaligned [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,058 rounds 52973 ERR6133546.ke.tsv 35125 ERR6133546.se.tsv 88098 total ==> ERR6133546.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 64 17.9062 PNS24243 293 194 1 1.97868 KQK14069 1603 1504 64 16.3346 KQK14071 474 375 0 0 ==> ERR6133546.se.tsv <== BRADI_1g14170v3 64 BRADI_1g53295v3 20 BRADI_1g59795v3 11 BRADI_1g07683v3 0 BRADI_1g00485v3 0 BRADI_1g20270v3 27 BRADI_1g74790v3 31 BRADI_1g09890v3 0 BRADI_1g77505v3 44 BRADI_1g48960v3 0 ERR6133546 completed mapping pipeline successfully