Starting /dee2/code/volunteer_pipeline.sh SRR12682231 current disk space = 1547420729344 free memory = 1603538660 SRR12682231 SRAfilesize cc1984671fdb8121b86cbb0482eb2278 SRR12682231.sra SRR12682231.sra file validated SRR12682231 is single end SRR12682231 is conventional basespace SRR12682231 read1 length is 35-150 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR12682231_1.fastq File type Conventional base calls Encoding Sanger / Illumina 1.9 Total Sequences 4000 Sequences flagged as poor quality 0 Sequence length 35-150 %GC 51 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 31.54875 32.0 32.0 32.0 32.0 32.0 2 31.522 32.0 32.0 32.0 32.0 32.0 3 31.6075 32.0 32.0 32.0 32.0 32.0 4 31.6265 32.0 32.0 32.0 32.0 32.0 5 31.596 32.0 32.0 32.0 32.0 32.0 6 34.84525 36.0 36.0 36.0 36.0 36.0 7 35.27925 36.0 36.0 36.0 36.0 36.0 8 35.11575 36.0 36.0 36.0 36.0 36.0 9 35.25075 36.0 36.0 36.0 36.0 36.0 10-14 35.13745 36.0 36.0 36.0 36.0 36.0 15-19 35.08925 36.0 36.0 36.0 36.0 36.0 20-24 35.04785 36.0 36.0 36.0 36.0 36.0 25-29 34.87025 36.0 36.0 36.0 33.6 36.0 30-34 34.869899999999994 36.0 36.0 36.0 34.4 36.0 35-39 34.8514980097185 36.0 36.0 36.0 33.6 36.0 40-44 34.780523641390815 36.0 36.0 36.0 33.6 36.0 45-49 34.56030627885451 36.0 36.0 36.0 32.0 36.0 50-54 34.510513227835794 36.0 36.0 36.0 32.0 36.0 55-59 34.464674001831284 36.0 36.0 36.0 32.0 36.0 60-64 34.344860453055105 36.0 36.0 36.0 32.0 36.0 65-69 34.24467959522157 36.0 36.0 36.0 32.0 36.0 70-74 34.26079706544347 36.0 36.0 36.0 32.0 36.0 75-79 34.079116783525606 36.0 36.0 36.0 32.0 36.0 80-84 34.04375827984114 36.0 36.0 36.0 30.0 36.0 85-89 33.98783135126657 36.0 36.0 36.0 31.0 36.0 90-94 33.99477292494663 36.0 36.0 36.0 31.0 36.0 95-99 33.947691812999025 36.0 36.0 36.0 29.0 36.0 100-104 33.78205085348162 36.0 36.0 36.0 27.0 36.0 105-109 33.52970700980277 36.0 33.6 36.0 27.0 36.0 110-114 33.39579013672774 36.0 32.8 36.0 27.0 36.0 115-119 33.01764275379041 36.0 32.0 36.0 27.0 36.0 120-124 32.38599937503974 34.4 32.0 36.0 25.8 36.0 125-129 32.32205267057067 34.4 32.0 36.0 25.8 36.0 130-134 31.90432771702358 33.6 32.0 36.0 24.6 36.0 135-139 31.819859539174814 33.6 32.0 36.0 24.6 36.0 140-144 31.956586925092843 35.2 32.0 36.0 23.4 36.0 145-149 31.81139864789096 33.6 32.0 36.0 21.0 36.0 150 26.3755905511811 27.0 14.0 32.0 14.0 36.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 2 2.0 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 0.0 18 0.0 19 2.0 20 0.0 21 3.0 22 4.0 23 8.0 24 21.0 25 16.0 26 27.0 27 59.0 28 82.0 29 104.0 30 124.0 31 149.0 32 231.0 33 378.0 34 846.0 35 1944.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 29.48974487243622 11.080540270135067 6.4282141070535275 53.001500750375186 2 22.061030515257627 14.157078539269635 33.84192096048024 29.939969984992498 3 21.085542771385693 15.957978989494748 21.210605302651324 41.74587293646824 4 26.538269134567283 23.836918459229615 18.98449224612306 30.64032016008004 5 26.263131565782892 29.214607303651825 22.386193096548272 22.136068034017008 6 20.843860535624053 32.895401718039416 24.153612935826175 22.10712481051036 7 18.10905452726363 21.53576788394197 38.744372186093045 21.61080540270135 8 19.909954977488745 19.909954977488745 32.7663831915958 27.41370685342671 9 19.484742371185593 19.959979989995 34.167083541770886 26.388194097048522 10-14 23.29664832416208 25.587793896948476 24.537268634317158 26.578289144572288 15-19 22.991495747873934 23.96698349174587 25.68784392196098 27.35367683841921 20-24 23.971985992996498 24.73736868434217 25.062531265632813 26.228114057028513 25-29 22.867577167442093 24.8336585121817 24.603531942568413 27.695232377807795 30-34 23.367525644233176 24.143107330497873 24.73855391543658 27.75081310983237 35-39 24.04043436921383 23.80523444928189 25.11634889656208 27.037982284942203 40-44 24.092343131854374 24.142420752165858 24.643196955280686 27.122039160699085 45-49 23.49222277972905 24.385348720521826 25.218263923733065 26.904164576016054 50-54 23.09393375885812 24.973614112680302 25.028898828969194 26.903553299492383 55-59 23.63132712163183 24.114832535885167 24.835054142533366 27.418786199949636 60-64 23.20905324845913 22.961503485904817 26.336263514196222 27.49317975143983 65-69 23.26785442363332 24.399776661083195 25.486015938277244 26.846352977006244 70-74 24.407884683950492 24.209239545662914 24.499567055467836 26.88330871491876 75-79 24.40188931101756 24.463497278981414 23.796077626039636 27.338535783961394 80-84 24.679437263146966 22.94554326948035 24.700202460675907 27.674817006696777 85-89 24.229610444526667 23.907183254928906 24.985464348009938 26.87774195253449 90-94 24.367704280155642 23.881322957198446 24.45417207090359 27.296800691742323 95-99 23.261483903141798 24.23117415636948 24.951515487338614 27.555826453150107 100-104 23.97111085635676 24.074286369368338 24.401008827238336 27.55359394703657 105-109 24.01053829112029 23.926710975390694 25.190108376743908 26.872642356745107 110-114 24.51356967445375 24.10427554939865 24.469491845601663 26.912662930545935 115-119 24.8252688172043 23.42069892473118 25.228494623655912 26.525537634408604 120-124 24.098278694378973 23.64831083494036 24.89822155560317 27.355188915077495 125-129 24.26284751474305 24.454315692731868 23.267212989201195 28.015623803323887 130-134 23.969541466644596 23.93643436517133 24.598576394636652 27.495447773547426 135-139 24.53753112771256 23.577018854500178 24.88438278192814 27.00106723585913 140-144 24.373445571073272 24.660417065238185 24.16299980868567 26.80313755500287 145-149 25.584826132771337 22.486828240252898 24.383561643835616 27.544783983140146 150 25.905511811023622 0.0 33.54330708661417 40.55118110236221 >>END_MODULE >>Per sequence GC content warn #GC Content Count 0 2.0 1 1.0 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 0.0 18 0.0 19 0.0 20 0.0 21 0.0 22 0.0 23 0.0 24 0.0 25 0.0 26 0.0 27 0.5 28 1.5 29 4.0 30 5.5 31 6.0 32 8.5 33 13.0 34 18.5 35 25.0 36 43.0 37 60.0 38 67.0 39 86.5 40 100.5 41 106.0 42 107.5 43 123.5 44 136.0 45 150.0 46 176.0 47 192.5 48 212.0 49 213.0 50 199.5 51 186.0 52 171.0 53 164.5 54 167.5 55 165.5 56 156.0 57 127.5 58 100.5 59 88.0 60 82.5 61 70.5 62 62.0 63 69.0 64 58.5 65 45.5 66 40.0 67 43.5 68 46.0 69 34.5 70 32.5 71 32.5 72 27.5 73 21.0 74 13.0 75 14.0 76 13.5 77 6.0 78 4.5 79 5.0 80 4.0 81 1.5 82 0.0 83 0.5 84 0.5 85 0.5 86 0.5 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 0.5 100 1.0 >>END_MODULE >>Per base N content pass #Base N-Count 1 0.05 2 0.05 3 0.05 4 0.05 5 0.05 6 1.05 7 0.05 8 0.05 9 0.05 10-14 0.05 15-19 0.05 20-24 0.05 25-29 0.055 30-34 0.075 35-39 0.015010507355148604 40-44 0.0 45-49 0.0 50-54 0.0 55-59 0.0 60-64 0.0 65-69 0.0 70-74 0.0 75-79 0.0 80-84 0.0 85-89 0.0 90-94 0.0 95-99 0.0 100-104 0.0 105-109 0.0 110-114 0.0 115-119 0.0 120-124 0.0 125-129 0.0 130-134 0.0 135-139 0.0 140-144 0.0 145-149 0.0 150 0.0 >>END_MODULE >>Sequence Length Distribution warn #Length Count 35-39 4.0 40-44 8.0 45-49 5.0 50-54 9.0 55-59 10.0 60-64 16.0 65-69 15.0 70-74 23.0 75-79 36.0 80-84 56.0 85-89 80.0 90-94 85.0 95-99 109.0 100-104 144.0 105-109 152.0 110-114 197.0 115-119 173.0 120-124 193.0 125-129 198.0 130-134 179.0 135-139 153.0 140-144 152.0 145-149 733.0 150-151 1270.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 85.0 #Duplication Level Percentage of deduplicated Percentage of total 1 91.61764705882352 77.875 2 4.5 7.6499999999999995 3 1.7941176470588234 4.575 4 0.7941176470588235 2.7 5 0.5294117647058824 2.25 6 0.3235294117647059 1.6500000000000001 7 0.17647058823529413 1.05 8 0.02941176470588235 0.2 9 0.1176470588235294 0.8999999999999999 >10 0.1176470588235294 1.15 >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 warn #Sequence Count Percentage Possible Source CCCGACTGTCCCTATTAATCATTACTCCGATCCCGAAGGCCAACACAATA 13 0.325 No Hit CCTAATTCTCCGTCACCCGTCACCACCATGGTAGGCCCCTATCCTACCAT 11 0.27499999999999997 No Hit CCCAACTTTCGTTCTTGATTAATGAAAACATCCTTGGCAAATGCTTTCGC 11 0.27499999999999997 No Hit CAACAACTTAAATATACGCTATTGGAGCTGGAATTACCGCGGCTGCTGGC 11 0.27499999999999997 No Hit CTCAGAGCCAATCCTTTTCCCGAAGTTACGGATCCGTTTTGCCGACTTCC 9 0.22499999999999998 No Hit CCCCAACTTTCGTTCTTGATTAATGAAAACATCCTTGGCAAATGCTTTCG 9 0.22499999999999998 No Hit CGTTAACGGAATTAACCAGACAAATCGCTCCACCAACTAAGAACGGCCAT 9 0.22499999999999998 No Hit ATCACGATGAAATTTCCCAAGATTACCCGGGCCTGTCGGCCAAGGCTATA 9 0.22499999999999998 No Hit CTCGTTGAAGACCAACAATTGCAATGATCTATCCCCATCACGATGAAATT 8 0.2 No Hit GTAGCGCGCGTGCGGCCCAGAACATCTAAGGGCATCACAGACCTGTTATT 7 0.17500000000000002 No Hit GCTGGAATTACCGCGGCTGCTGGCACCAGACTTGCCCTCCAATGGATCCT 7 0.17500000000000002 No Hit CTCTAAGAAGCTAGCTGCGGAGGGATGGCTCCGCATAGCTAGTTAGCAGG 7 0.17500000000000002 No Hit CCGACATCGAAGGATCAAAAAGCAACGTCGCTATGAACGCTTGGCTGCCA 7 0.17500000000000002 No Hit GTCAATTCCTTTAAGTTTCAGCCTTGCGACCATACTCCCCCCGGAACCCA 7 0.17500000000000002 No Hit GTCGAGTTATCATGAATCATCGGATCAGCGAGCAAAGCCCGCGTCAGCCT 7 0.17500000000000002 No Hit GTCCCTCTAAGAAGCTAGCTGCGGAGGGATGGCTCCGCATAGCTAGTTAG 6 0.15 No Hit ATCCGAGTAGCACGTACCATCAAACAAACTATAACTGATTTAATGAGCCA 6 0.15 No Hit ATTCAATCGGTAGGAGCGACGGGCGGTGTGTACAAAGGGCAGGGACGTAG 6 0.15 No Hit CCGGAACCCAAAGACTTTGATTTCTCATAAGGTGCCGGCGGAGTCCTATA 6 0.15 No Hit CTCTGACTATGAAATACGAATGCCCCCGACTGTCCCTATTAATCATTACT 6 0.15 No Hit CAGCCTTTTATCTAATAAATGCGCCCCTCCCAGAAGTCGGGGTTTGTTGC 6 0.15 No Hit CGTCAATTCCTTTAAGTTTCAGCCTTGCGACCATACTCCCCCCGGAACCC 6 0.15 No Hit CTCATTCCAATTACCAGACACTAATGTGCCCGGTATTGTTATTTATTGTC 6 0.15 No Hit CCTCGCGGTACTTGTTCGCTATCGGTCTCTCGCCTGTATTTAGCCTTGGA 6 0.15 No Hit CACGCTTTCACGGTTCGTATTCGTACTGGAAATCAGAATCAAACGAGCTT 6 0.15 No Hit CCCCGACTGTCCCTATTAATCATTACTCCGATCCCGAAGGCCAACACAAT 6 0.15 No Hit CTGACTATGAAATACGAATGCCCCCGACTGTCCCTATTAATCATTACTCC 5 0.125 No Hit CTTGGCAAATGCTTTCGCAGTTGTTCGTCTTTCATAAATCCAAGAATTTC 5 0.125 No Hit CTTGTTACGACTTCTCCTTCCTCTAAATGATAAGGTTCAATGGACTTCTC 5 0.125 No Hit GGGAAACTTCGGAGGGAACCAGCTACTAGATGGTTCGATTAGTCTTTCGC 5 0.125 No Hit CTGTTATTGCCTCAAACTTCCGTCGCCTAAACGGCGATAGTCCCTCTAAG 5 0.125 No Hit GCCGACTTCCCTTGCCTACATTGTTCCATTGGCCAGAGGCTGTTCACCTT 5 0.125 No Hit CCTCTAAGAAGCTAGCTGCGGAGGGATGGCTCCGCATAGCTAGTTAGCAG 5 0.125 No Hit GTCAGGATTGGGTAATTTGCGCGCCTGCTGCCTTCCTTGGATGTGGTAGC 5 0.125 No Hit CTCCCCGTGTCAGGATTGGGTAATTTGCGCGCCTGCTGCCTTCCTTGGAT 5 0.125 No Hit CTTCGAGCCCCCAACTTTCGTTCTTGATTAATGAAAACATCCTTGGCAAA 5 0.125 No Hit CTCGTTGAATACATCAGTGTAGCGCGCGTGCGGCCCAGAACATCTAAGGG 5 0.125 No Hit CATCAGTGTAGCGCGCGTGCGGCCCAGAACATCTAAGGGCATCACAGACC 5 0.125 No Hit CCTGTGGTAACTTTTCTGACACCTCTAGCTTCAAACTCCGAAGATCTAAA 5 0.125 No Hit CCCGAAGTTACGGATCCGTTTTGCCGACTTCCCTTGCCTACATTGTTCCA 5 0.125 No Hit CTTTTATCTAATAAATGCGCCCCTCCCAGAAGTCGGGGTTTGTTGCACGT 5 0.125 No Hit CGGCAATTTCAAGCACTCTTTGACTCTCTTTTCAAAGTCCTTTTCATCTT 5 0.125 No Hit CTCAAACTTCCGTCGCCTAAACGGCGATAGTCCCTCTAAGAAGCTAGCTG 5 0.125 No Hit CATGAATCATCGGATCAGCGAGCAAAGCCCGCGTCAGCCTTTTATCTAAT 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 82-83 0.0 0.0 0.0 0.0 0.0 84-85 0.0 0.0 0.0 0.0 0.0 86-87 0.0 0.0 0.0 0.0 0.0 88-89 0.0 0.0 0.0 0.0 0.0 90-91 0.0 0.0 0.0 0.0 0.0 92-93 0.0 0.0 0.0 0.0 0.0 94-95 0.0 0.0 0.0 0.0 0.0 96-97 0.0 0.0 0.0 0.0 0.0 98-99 0.0 0.0 0.0 0.0 0.0 100-101 0.0 0.0 0.0 0.0 0.0 102-103 0.0 0.0 0.0 0.0 0.0 104-105 0.0 0.0 0.0 0.0 0.0 106-107 0.0 0.0 0.0 0.0 0.0 108-109 0.0 0.0 0.0 0.0 0.0 110-111 0.0 0.0 0.0 0.0 0.0 112-113 0.0 0.0 0.0 0.0 0.0 114-115 0.0 0.0 0.0 0.0 0.0 116-117 0.0 0.0 0.0 0.0 0.0 118-119 0.0 0.0 0.0 0.0 0.0 120-121 0.0 0.0 0.0 0.0 0.0 122-123 0.0 0.0 0.0 0.0 0.0 124-125 0.0 0.0 0.0 0.0 0.0 126-127 0.0 0.0 0.0 0.0 0.0 128-129 0.0 0.0 0.0 0.0 0.0 130-131 0.0 0.0 0.0 0.0 0.0 132-133 0.0 0.0 0.0 0.0 0.0 134-135 0.0 0.0 0.0 0.0 0.0 136-137 0.0 0.0 0.0 0.0 0.0 138 0.0 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content pass >>END_MODULE Rejected 1645765 READS because READLEN < 1 Read 1645765 spots for SRR12682231.sra Written 1645765 spots for SRR12682231.sra Rejected 1645765 READS because READLEN < 1 Read 1645765 spots for SRR12682231.sra Written 1645765 spots for SRR12682231.sra Rejected 1645771 READS because READLEN < 1 Read 1645771 spots for SRR12682231.sra Written 1645771 spots for SRR12682231.sra Rejected 1645765 READS because READLEN < 1 Read 1645765 spots for SRR12682231.sra Written 1645765 spots for SRR12682231.sra Rejected 1645765 READS because READLEN < 1 Read 1645765 spots for SRR12682231.sra Written 1645765 spots for SRR12682231.sra Rejected 1645765 READS because READLEN < 1 Read 1645765 spots for SRR12682231.sra Written 1645765 spots for SRR12682231.sra Rejected 1645765 READS because READLEN < 1 Read 1645765 spots for SRR12682231.sra Written 1645765 spots for SRR12682231.sra Rejected 1645765 READS because READLEN < 1 Read 1645765 spots for SRR12682231.sra Written 1645765 spots for SRR12682231.sra Rejected 1645765 READS because READLEN < 1 Read 1645765 spots for SRR12682231.sra Written 1645765 spots for SRR12682231.sra Rejected 1645765 READS because READLEN < 1 Read 1645765 spots for SRR12682231.sra Written 1645765 spots for SRR12682231.sra Rejected 1645765 READS because READLEN < 1 Read 1645765 spots for SRR12682231.sra Written 1645765 spots for SRR12682231.sra Rejected 1645765 READS because READLEN < 1 Read 1645765 spots for SRR12682231.sra Written 1645765 spots for SRR12682231.sra Rejected 1645765 READS because READLEN < 1 Read 1645765 spots for SRR12682231.sra Written 1645765 spots for SRR12682231.sra Rejected 1645765 READS because READLEN < 1 Read 1645765 spots for SRR12682231.sra Written 1645765 spots for SRR12682231.sra Rejected 1645765 READS because READLEN < 1 Read 1645765 spots for SRR12682231.sra Written 1645765 spots for SRR12682231.sra Rejected 1645765 READS because READLEN < 1 Read 1645765 spots for SRR12682231.sra Written 1645765 spots for SRR12682231.sra Rejected 1645765 READS because READLEN < 1 Read 1645765 spots for SRR12682231.sra Written 1645765 spots for SRR12682231.sra Rejected 1645765 READS because READLEN < 1 Read 1645765 spots for SRR12682231.sra Written 1645765 spots for SRR12682231.sra Rejected 1645765 READS because READLEN < 1 Read 1645765 spots for SRR12682231.sra Written 1645765 spots for SRR12682231.sra Rejected 1645765 READS because READLEN < 1 Read 1645765 spots for SRR12682231.sra Written 1645765 spots for SRR12682231.sra SRR ids: ['SRR12682231.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_tu91lzfl SRR12682231.sra spots: 32915306 blocks: [[1, 1645765], [1645766, 3291530], [3291531, 4937295], [4937296, 6583060], [6583061, 8228825], [8228826, 9874590], [9874591, 11520355], [11520356, 13166120], [13166121, 14811885], [14811886, 16457650], [16457651, 18103415], [18103416, 19749180], [19749181, 21394945], [21394946, 23040710], [23040711, 24686475], [24686476, 26332240], [26332241, 27978005], [27978006, 29623770], [29623771, 31269535], [31269536, 32915306]] SRR12682231 file size 9893405 SRR12682231 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 SRR12682231 SRR12682231_1.fastq Input file: SRR12682231_1.fastq trimmed: SRR12682231-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 03:43:08 2024 >> started Sat Dec 7 03:43:26 2024 >> done (18.061s) 32915306 reads processed; of these: 2 ( 0.00%) short reads filtered out after trimming by size control 9895 ( 0.03%) empty reads filtered out after trimming by size control 32905409 (99.97%) reads available; of these: 29209 ( 0.09%) trimmed reads available after processing 32876200 (99.91%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 22 45 0.00% 23 69 0.00% 24 103 0.00% 25 179 0.00% 26 295 0.00% 27 429 0.00% 28 709 0.00% 29 719 0.00% 30 930 0.00% 31 1023 0.00% 32 1221 0.00% 33 1422 0.00% 34 1696 0.01% 35 1953 0.01% 36 2290 0.01% 37 2659 0.01% 38 3469 0.01% 39 4075 0.01% 40 4712 0.01% 41 5242 0.02% 42 5120 0.02% 43 5260 0.02% 44 5250 0.02% 45 5574 0.02% 46 5970 0.02% 47 7215 0.02% 48 8588 0.03% 49 9972 0.03% 50 10866 0.03% 51 11814 0.04% 52 12403 0.04% 53 12236 0.04% 54 12274 0.04% 55 12997 0.04% 56 13533 0.04% 57 15366 0.05% 58 18146 0.06% 59 19071 0.06% 60 20759 0.06% 61 22303 0.07% 62 24401 0.07% 63 24806 0.08% 64 25207 0.08% 65 26438 0.08% 66 28548 0.09% 67 30971 0.09% 68 32198 0.10% 69 34592 0.11% 70 35568 0.11% 71 42007 0.13% 72 45684 0.14% 73 48560 0.15% 74 50422 0.15% 75 53749 0.16% 76 58258 0.18% 77 59577 0.18% 78 62964 0.19% 79 69459 0.21% 80 73401 0.22% 81 77490 0.24% 82 85050 0.26% 83 88640 0.27% 84 94728 0.29% 85 107687 0.33% 86 118652 0.36% 87 122852 0.37% 88 125957 0.38% 89 131269 0.40% 90 139658 0.42% 91 141489 0.43% 92 158160 0.48% 93 166864 0.51% 94 167816 0.51% 95 185377 0.56% 96 192255 0.58% 97 199857 0.61% 98 217140 0.66% 99 214479 0.65% 100 219506 0.67% 101 222625 0.68% 102 232397 0.71% 103 247676 0.75% 104 252134 0.77% 105 252794 0.77% 106 258070 0.78% 107 270611 0.82% 108 260559 0.79% 109 276551 0.84% 110 272318 0.83% 111 284922 0.87% 112 302493 0.92% 113 291103 0.88% 114 307427 0.93% 115 320586 0.97% 116 322520 0.98% 117 303526 0.92% 118 299023 0.91% 119 309259 0.94% 120 327168 0.99% 121 307051 0.93% 122 325800 0.99% 123 332087 1.01% 124 311715 0.95% 125 311555 0.95% 126 314504 0.96% 127 303254 0.92% 128 306073 0.93% 129 315753 0.96% 130 300308 0.91% 131 299612 0.91% 132 297879 0.91% 133 302860 0.92% 134 288445 0.88% 135 288762 0.88% 136 296746 0.90% 137 290930 0.88% 138 272692 0.83% 139 279558 0.85% 140 273140 0.83% 141 260565 0.79% 142 256413 0.78% 143 255703 0.78% 144 262353 0.80% 145 250823 0.76% 146 303844 0.92% 147 509179 1.55% 148 1108514 3.37% 149 3700064 11.24% 150 10315772 31.35% 32905409 reads passed initial QC criterion=sequence-density sequence-density=0.63 sequence-density-rank=1 fanout-score=2.77 fanout-score-rank=28 prefix-density=1.72 prefix-fanout=1.0 sequence=CTTGGATGTGGCAGCCGTTTCTC criterion=fanout-score sequence-density=0.06 sequence-density-rank=22 fanout-score=37.37 fanout-score-rank=1 prefix-density=0.88 prefix-fanout=2.4 sequence=CGGCGGCGGCGG Started job on | Dec 07 03:43:45 Started mapping on | Dec 07 03:43:45 Finished on | Dec 07 03:45:07 Mapping speed, Million of reads per hour | 1444.63 Number of input reads | 32905409 Average input read length | 131 UNIQUE READS: Uniquely mapped reads number | 17853419 Uniquely mapped reads % | 54.26% Average mapped length | 131.46 Number of splices: Total | 7310446 Number of splices: Annotated (sjdb) | 6918853 Number of splices: GT/AG | 7213517 Number of splices: GC/AG | 86385 Number of splices: AT/AC | 5465 Number of splices: Non-canonical | 5079 Mismatch rate per base, % | 0.22% Deletion rate per base | 0.01% Deletion average length | 1.56 Insertion rate per base | 0.00% Insertion average length | 1.12 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 829251 % of reads mapped to multiple loci | 2.52% Number of reads mapped to too many loci | 12234264 % of reads mapped to too many loci | 37.18% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 1.73% % of reads unmapped: other | 4.32% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 14222739 14222739 14222739 N_multimapping 829251 829251 829251 N_noFeature 759221 17424957 909714 N_ambiguous 323954 1754 46821 UnstrandedReadsAssigned:16770244 PositiveStrandReadsAssigned:426708 NegativeStrandReadsAssigned:16896884 Dataset is classified negative stranded MeadianReadLen=144 20thPercentileLength=110 echo kmer=105 SRR12682231 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: SRR12682231-trimmed.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 32,905,409 reads, 17,175,532 reads pseudoaligned [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,112 rounds 52973 SRR12682231.ke.tsv 35125 SRR12682231.se.tsv 88098 total ==> SRR12682231.ke.tsv <== target_id length eff_length est_counts tpm PNS24245 936 837 27.4245 3.02496 PNS24247 1044 945 40.3587 3.94287 PNS24249 1928 1829 158.467 7.99893 PNS24246 1044 945 40.3587 3.94287 PNS24248 1044 945 40.3587 3.94287 PNS24244 1471 1372 139.032 9.35554 PNS24243 293 194 0 0 KQK14069 1603 1504 4549.53 279.271 KQK14071 474 375 368.512 90.7249 ==> SRR12682231.se.tsv <== BRADI_1g14170v3 5431 BRADI_1g53295v3 77 BRADI_1g59795v3 276 BRADI_1g07683v3 0 BRADI_1g00485v3 11 BRADI_1g20270v3 1183 BRADI_1g74790v3 359 BRADI_1g09890v3 0 BRADI_1g77505v3 162 BRADI_1g48960v3 0 SRR12682231 completed mapping pipeline successfully