Starting /dee2/code/volunteer_pipeline.sh SRR13165363 current disk space = 1541868670976 free memory = 1602314548 SRR13165363 SRAfilesize 94347294d14970aedf423ebdb8e21426 SRR13165363.sra SRR13165363.sra file validated SRR13165363 is paired end SRR13165363 is conventional basespace SRR13165363 read1 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR13165363_1.fastq File type Conventional base calls Encoding Sanger / Illumina 1.9 Total Sequences 4000 Sequences flagged as poor quality 0 Sequence length 151 %GC 52 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 36.531 37.0 37.0 37.0 37.0 37.0 2 36.09825 37.0 37.0 37.0 37.0 37.0 3 36.5175 37.0 37.0 37.0 37.0 37.0 4 36.5575 37.0 37.0 37.0 37.0 37.0 5 36.5425 37.0 37.0 37.0 37.0 37.0 6 36.56 37.0 37.0 37.0 37.0 37.0 7 36.549 37.0 37.0 37.0 37.0 37.0 8 36.5585 37.0 37.0 37.0 37.0 37.0 9 36.585 37.0 37.0 37.0 37.0 37.0 10-14 36.514300000000006 37.0 37.0 37.0 37.0 37.0 15-19 36.501599999999996 37.0 37.0 37.0 37.0 37.0 20-24 36.513600000000004 37.0 37.0 37.0 37.0 37.0 25-29 36.4388 37.0 37.0 37.0 37.0 37.0 30-34 36.4082 37.0 37.0 37.0 37.0 37.0 35-39 36.345800000000004 37.0 37.0 37.0 37.0 37.0 40-44 36.30159999999999 37.0 37.0 37.0 37.0 37.0 45-49 35.5501 37.0 37.0 37.0 37.0 37.0 50-54 35.637800000000006 37.0 37.0 37.0 37.0 37.0 55-59 35.266099999999994 37.0 37.0 37.0 37.0 37.0 60-64 35.3368 37.0 37.0 37.0 37.0 37.0 65-69 35.2089 37.0 37.0 37.0 37.0 37.0 70-74 35.5976 37.0 37.0 37.0 37.0 37.0 75-79 36.119 37.0 37.0 37.0 37.0 37.0 80-84 36.1666 37.0 37.0 37.0 37.0 37.0 85-89 36.208299999999994 37.0 37.0 37.0 37.0 37.0 90-94 36.1893 37.0 37.0 37.0 37.0 37.0 95-99 36.0779 37.0 37.0 37.0 37.0 37.0 100-104 36.0921 37.0 37.0 37.0 37.0 37.0 105-109 36.033699999999996 37.0 37.0 37.0 37.0 37.0 110-114 35.972899999999996 37.0 37.0 37.0 37.0 37.0 115-119 35.799800000000005 37.0 37.0 37.0 37.0 37.0 120-124 35.5415 37.0 37.0 37.0 37.0 37.0 125-129 35.36149999999999 37.0 37.0 37.0 37.0 37.0 130-134 35.1081 37.0 37.0 37.0 32.2 37.0 135-139 34.933899999999994 37.0 37.0 37.0 25.0 37.0 140-144 34.5003 37.0 37.0 37.0 25.0 37.0 145-149 34.0441 37.0 37.0 37.0 25.0 37.0 150-151 33.8135 37.0 37.0 37.0 25.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 22 1.0 23 1.0 24 5.0 25 5.0 26 9.0 27 8.0 28 19.0 29 27.0 30 38.0 31 42.0 32 165.0 33 280.0 34 208.0 35 417.0 36 2453.0 37 322.0 >>END_MODULE >>Per base sequence content warn #Base G A T C 1 45.550000000000004 8.9 8.450000000000001 37.1 2 24.401310814217293 15.351651121754475 27.804386186034787 32.44265187799344 3 22.1 16.325 28.025 33.550000000000004 4 25.45 22.425 20.775 31.35 5 30.025000000000002 25.825 20.4 23.75 6 30.049999999999997 30.625000000000004 20.525 18.8 7 18.85 27.35 36.05 17.75 8 21.125 28.725 25.4 24.75 9 25.3 21.775 29.175 23.75 10-14 23.49 27.755000000000003 23.185 25.569999999999997 15-19 22.78 25.775 24.66 26.784999999999997 20-24 23.200000000000003 26.51 24.305 25.985000000000003 25-29 24.310000000000002 25.874999999999996 23.325000000000003 26.490000000000002 30-34 23.125 25.740000000000002 24.39 26.745 35-39 23.06 27.229999999999997 24.275 25.435000000000002 40-44 24.0 25.119999999999997 24.990000000000002 25.89 45-49 23.875 25.445 24.55 26.13 50-54 24.93 24.63 24.515 25.924999999999997 55-59 23.82 24.865000000000002 25.36 25.955000000000002 60-64 25.759999999999998 23.865 24.9 25.474999999999998 65-69 24.759999999999998 26.745 24.14 24.355 70-74 27.505000000000003 24.7 23.18 24.615000000000002 75-79 28.115000000000002 23.665 22.67 25.55 80-84 27.83 24.325 22.99 24.855 85-89 28.060000000000002 24.895 22.55 24.495 90-94 28.599999999999998 24.855 21.65 24.895 95-99 28.04 24.495 22.195 25.27 100-104 29.01 24.725 22.055 24.21 105-109 28.58 24.235 22.095000000000002 25.09 110-114 28.27 25.03 21.224999999999998 25.474999999999998 115-119 27.834999999999997 25.465 21.58 25.119999999999997 120-124 28.29 24.7 21.185000000000002 25.825 125-129 28.62 24.065 21.85 25.465 130-134 28.98 24.035 21.825 25.16 135-139 29.175 23.49 21.465 25.869999999999997 140-144 29.244999999999997 23.200000000000003 22.125 25.430000000000003 145-149 29.865000000000002 23.165 21.615000000000002 25.355 150-151 30.337500000000002 22.175 22.275 25.2125 >>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 0.0 17 0.0 18 0.0 19 0.0 20 0.0 21 0.0 22 1.0 23 1.5 24 1.0 25 1.5 26 1.5 27 2.5 28 3.5 29 4.0 30 2.5 31 6.5 32 11.0 33 16.5 34 26.0 35 35.5 36 57.0 37 72.0 38 76.0 39 86.0 40 110.5 41 135.5 42 136.5 43 144.0 44 162.0 45 176.0 46 177.5 47 175.5 48 162.5 49 157.0 50 156.0 51 135.0 52 123.5 53 121.0 54 120.5 55 113.5 56 100.0 57 89.0 58 76.5 59 77.5 60 78.0 61 62.0 62 58.0 63 57.0 64 58.0 65 65.0 66 84.0 67 87.0 68 77.0 69 72.5 70 58.0 71 39.0 72 31.5 73 26.5 74 17.5 75 17.5 76 16.5 77 13.5 78 10.5 79 5.0 80 2.5 81 5.0 82 3.5 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 0.8250000000000001 3 0.0 4 0.0 5 0.0 6 0.0 7 0.0 8 0.0 9 0.0 10-14 0.0 15-19 0.0 20-24 0.0 25-29 0.0 30-34 0.0 35-39 0.0 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 0.0 150-151 0.0 >>END_MODULE >>Sequence Length Distribution pass #Length Count 151 4000.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 71.25 #Duplication Level Percentage of deduplicated Percentage of total 1 75.12280701754386 53.525 2 17.087719298245613 24.349999999999998 3 5.473684210526316 11.700000000000001 4 1.368421052631579 3.9 5 0.45614035087719296 1.625 6 0.14035087719298245 0.6 7 0.03508771929824561 0.17500000000000002 8 0.03508771929824561 0.2 9 0.03508771929824561 0.22499999999999998 >10 0.2456140350877193 3.6999999999999997 >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 GATCGGAAGAGCACACGTCTGAACTCCAGTCACGATTACCGATCTCGTAT 34 0.8500000000000001 TruSeq Adapter, Index 9 (97% over 38bp) GATCGGAAGAGCACACGTCTGAACTCCAGTCACGATTACCGATCTCGTTT 31 0.775 TruSeq Adapter, Index 9 (97% over 38bp) GATCGGAAGAGCACACGTCTGAACTCCAGTCACGATTACCGATCTCGGAT 23 0.575 TruSeq Adapter, Index 9 (97% over 38bp) GATCGGAAGAGCACACGTCTGAACTCCAGTCACGATTACCGATCTCGGTT 18 0.44999999999999996 TruSeq Adapter, Index 9 (97% over 38bp) GATCGGAAGAGCACACGTCTGAACTCCAGTCACGATTACCGATCGCGTAT 15 0.375 TruSeq Adapter, Index 9 (97% over 38bp) GATCGGAAGAGCACACGTCTGAACTCCAGTCACGATTACCGATCGCGTTT 14 0.35000000000000003 TruSeq Adapter, Index 9 (97% over 38bp) GATCGGAAGAGCACACGTCTGAACTCCAGTCACGATTACCGATCGCGGTT 13 0.325 TruSeq Adapter, Index 9 (97% over 38bp) GGGTTGGCAAAGCATCATTCAAAGTGGCGTCTCAAAAACATCAAATTGCA 9 0.22499999999999998 No Hit GATCGGAAGAGCACACGTCTGAACTCCAGTCACGATTACCGATCGCGGAT 8 0.2 TruSeq Adapter, Index 9 (97% over 38bp) CCACGAACTACATTGATCCACCCTGAAACGGACTGAACCACTGCATACGC 7 0.17500000000000002 No Hit AGTAGATTTGGATGGCTGAATTGCGAGGACACTCGGATCTCCTGCCGGAC 6 0.15 No Hit GACCGAGGAGGAAGTACAAAATGGGGTCTTGACTTGTCGCGCGGCACAAA 6 0.15 No Hit TGTGCATGTTCCTCATAGTAAACGCTTACTGGTTTATCCTCAAACGTCCA 6 0.15 No Hit GCCCCATCACAAAGGTCAGACCAGCGAGAATCCCAGCCATTGCCAGCCAG 6 0.15 No Hit GTCAAATCGCAGATTCTGGTGTTCAGAAACGACCATTATTGCTCAATGCT 5 0.125 No Hit GGGGGCGCGGCGGCGGAGGCCCTCACGCGGAAGCGGACGGCGGAGAAGGC 5 0.125 No Hit CTCCTTGTTCTCAGCAATCTCAAAGAAGAGCTCGATGGACTTCTTGACAA 5 0.125 No Hit CATGGTTCTATCTTTTCTTTCAATGTCCAGGTCAAGCTTTTCCTTCAATT 5 0.125 No Hit GATCGGAAGAGCACACGTCTGAACTCCAGTCACGATTACCGATCTCGGGT 5 0.125 TruSeq Adapter, Index 9 (97% over 38bp) CACTTTACAACTAGGGCTGGTCACATCAGCCATGTTTCTTTCATTTCATT 5 0.125 No Hit CGACTGCAGAACTTTTGCAACATTGAACTTGATGTTCGGCACTCTGTCCT 5 0.125 No Hit CCTGCGCATAACAACAGAAGCCATGTGCGTAAGAGCATTTGATTAAGGTA 5 0.125 No Hit GGGTGACGACCTCAGGCATAGTAGCAGCGGAATGTCTTCAACGGTACTTG 5 0.125 No Hit TGATGTCTCGCCGTGCACGGCATCTGCGAGCCCGATCGCCACCAGAACGA 5 0.125 No Hit GGGGGTGCGCGCTGTAGAGCATGGCGCGCAGCACGGCGGAGACGGTGGGG 5 0.125 No Hit CCACGTTCCAGCAGCTTTTCAGCTTGCTCCAGGAGAGACCCAGCCATGAC 5 0.125 No Hit GCACCATTCGTCTGATTACTGAACTAGTAAATCACAATAGTCCAATCATC 5 0.125 No Hit >>END_MODULE >>Adapter Content fail #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 0.0125 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 0.037500000000000006 0.0 0.0 0.0 0.0 50-51 0.05 0.0 0.0 0.0 0.0 52-53 0.07500000000000001 0.0 0.0 0.0 0.0 54-55 0.21250000000000002 0.0 0.0 0.0 0.0 56-57 0.225 0.0 0.0 0.0 0.0 58-59 0.2625 0.0 0.0 0.0 0.0 60-61 0.4 0.0 0.0 0.0 0.0 62-63 0.5625 0.0 0.0 0.0 0.0 64-65 0.7375 0.0 0.0 0.0 0.0 66-67 0.8999999999999999 0.0 0.0 0.0 0.0 68-69 1.0375 0.0 0.0 0.0 0.0 70-71 1.3375 0.0 0.0 0.0 0.0 72-73 1.65 0.0 0.0 0.0 0.0 74-75 2.0374999999999996 0.0 0.0 0.0 0.0 76-77 2.2625 0.0 0.0 0.0 0.0 78-79 2.9875 0.0 0.0 0.0 0.0 80-81 3.65 0.0 0.0 0.0 0.0 82-83 4.3375 0.0 0.0 0.0 0.0 84-85 4.7625 0.0 0.0 0.0 0.0 86-87 5.3375 0.0 0.0 0.0 0.0 88-89 6.0625 0.0 0.0 0.0 0.0 90-91 6.65 0.0 0.0 0.0 0.0 92-93 7.3625 0.0 0.0 0.0 0.0 94-95 8.2875 0.0 0.0 0.0 0.0 96-97 9.4 0.0 0.0 0.0 0.0 98-99 10.25 0.0 0.0 0.0 0.0 100-101 11.25 0.0 0.0 0.0 0.0 102-103 12.05 0.0 0.0 0.0 0.0 104-105 13.037500000000001 0.0 0.0 0.0 0.0 106-107 14.399999999999999 0.0 0.0 0.0 0.0 108-109 15.45 0.0 0.0 0.0 0.0 110-111 16.1625 0.0 0.0 0.0 0.0 112-113 17.225 0.0 0.0 0.0 0.0 114-115 17.9375 0.0 0.0 0.0 0.0 116-117 18.875 0.0 0.0 0.0 0.0 118-119 19.9 0.0 0.0 0.0 0.0 120-121 20.7125 0.0 0.0 0.0 0.0 122-123 21.6625 0.0 0.0 0.0 0.0 124-125 22.762500000000003 0.0 0.0 0.0 0.0 126-127 23.775 0.0 0.0 0.0 0.0 128-129 24.575 0.0 0.0 0.0 0.0 130-131 25.75 0.0 0.0 0.0 0.0 132-133 27.237499999999997 0.0 0.0 0.0 0.0 134-135 28.125 0.0 0.0 0.0 0.0 136-137 28.75 0.0 0.0 0.0 0.0 138-139 29.5625 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position CCCAGGT 10 0.006830828 145.0 1 TTGGAGT 10 0.006830828 145.0 7 GGAGTAA 10 0.006830828 145.0 9 ACCGATC 60 0.004491891 14.500001 130-134 TACCGAT 65 0.0076375785 13.384615 130-134 >>END_MODULE SRR13165363 read2 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR13165363_2.fastq File type Conventional base calls Encoding Sanger / Illumina 1.9 Total Sequences 4000 Sequences flagged as poor quality 0 Sequence length 151 %GC 53 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 36.08125 37.0 37.0 37.0 37.0 37.0 2 36.227 37.0 37.0 37.0 37.0 37.0 3 36.0565 37.0 37.0 37.0 37.0 37.0 4 36.1915 37.0 37.0 37.0 37.0 37.0 5 36.2945 37.0 37.0 37.0 37.0 37.0 6 36.162 37.0 37.0 37.0 37.0 37.0 7 35.9815 37.0 37.0 37.0 37.0 37.0 8 35.9175 37.0 37.0 37.0 37.0 37.0 9 35.6125 37.0 37.0 37.0 37.0 37.0 10-14 35.6867 37.0 37.0 37.0 37.0 37.0 15-19 35.5724 37.0 37.0 37.0 37.0 37.0 20-24 35.4563 37.0 37.0 37.0 37.0 37.0 25-29 35.1048 37.0 37.0 37.0 37.0 37.0 30-34 34.9706 37.0 37.0 37.0 32.2 37.0 35-39 34.8806 37.0 37.0 37.0 34.6 37.0 40-44 34.86579999999999 37.0 37.0 37.0 27.4 37.0 45-49 34.814550000000004 37.0 37.0 37.0 29.8 37.0 50-54 34.8113 37.0 37.0 37.0 25.0 37.0 55-59 34.9557 37.0 37.0 37.0 29.8 37.0 60-64 35.1077 37.0 37.0 37.0 32.2 37.0 65-69 34.922250000000005 37.0 37.0 37.0 27.4 37.0 70-74 34.7327 37.0 37.0 37.0 25.0 37.0 75-79 34.7346 37.0 37.0 37.0 25.0 37.0 80-84 34.99195 37.0 37.0 37.0 27.4 37.0 85-89 35.255399999999995 37.0 37.0 37.0 37.0 37.0 90-94 35.3827 37.0 37.0 37.0 37.0 37.0 95-99 35.463 37.0 37.0 37.0 37.0 37.0 100-104 35.396699999999996 37.0 37.0 37.0 37.0 37.0 105-109 35.398 37.0 37.0 37.0 37.0 37.0 110-114 35.268600000000006 37.0 37.0 37.0 37.0 37.0 115-119 35.155100000000004 37.0 37.0 37.0 32.2 37.0 120-124 34.926 37.0 37.0 37.0 25.0 37.0 125-129 34.83125 37.0 37.0 37.0 25.0 37.0 130-134 34.5498 37.0 37.0 37.0 25.0 37.0 135-139 34.31394999999999 37.0 37.0 37.0 25.0 37.0 140-144 33.989599999999996 37.0 37.0 37.0 25.0 37.0 145-149 33.62445 37.0 37.0 37.0 19.4 37.0 150-151 33.4185 37.0 37.0 37.0 18.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 5 1.0 6 0.0 7 0.0 8 0.0 9 0.0 10 0.0 11 0.0 12 5.0 13 12.0 14 12.0 15 13.0 16 4.0 17 7.0 18 6.0 19 7.0 20 5.0 21 14.0 22 15.0 23 7.0 24 32.0 25 28.0 26 48.0 27 52.0 28 43.0 29 20.0 30 23.0 31 51.0 32 120.0 33 122.0 34 232.0 35 543.0 36 2311.0 37 267.0 >>END_MODULE >>Per base sequence content warn #Base G A T C 1 45.08917357447878 14.066817382567196 13.539311730720923 27.304697312233106 2 37.05 17.525 23.1 22.325 3 28.349999999999998 21.6 25.525 24.525 4 33.300000000000004 27.125 18.4 21.175 5 31.65 28.599999999999998 18.7 21.05 6 28.775000000000002 29.025000000000002 20.625 21.575 7 27.55 17.974999999999998 31.825 22.650000000000002 8 30.25 20.275000000000002 21.725 27.750000000000004 9 28.275 18.925 26.275 26.525 10-14 30.330000000000002 22.865 21.645 25.16 15-19 30.94 22.755 22.59 23.715 20-24 30.259077723316995 22.726818045413623 23.196959087726317 23.817145143543065 25-29 29.70985492746373 23.536768384192097 22.291145572786395 24.462231115557778 30-34 28.96658663465386 23.249299719887954 23.809523809523807 23.974589835934374 35-39 27.858357507252173 23.482044613384016 24.86245873762129 23.797139141742523 40-44 28.406362545018006 22.939175670268106 23.279311724689876 25.37515006002401 45-49 27.58465462912019 23.023058070324616 25.85404891712099 23.5382383834342 50-54 28.11343403020906 23.732119635890765 24.682404721416425 23.472041612483746 55-59 29.85492746373187 23.921960980490244 22.23111555777889 23.991995997999 60-64 29.67890367110133 23.45703711113334 22.77183154946484 24.092227668300488 65-69 29.857464366091524 23.815953988497125 22.605651412853213 23.72093023255814 70-74 29.43471735867934 23.931965982991496 23.271635817908955 23.36168084042021 75-79 28.52140856342537 24.579831932773107 23.554421768707485 23.344337735094037 80-84 29.457364341085274 23.59089772443111 23.540885221305327 23.410852713178297 85-89 30.975487743871938 23.946973486743374 22.8064032016008 22.271135567783894 90-94 31.224367310193056 23.877163148944682 22.096628988696608 22.80184055216565 95-99 31.53446033810143 23.697109132739822 22.391717515254577 22.37671301390417 100-104 32.7663831915958 23.271635817908955 21.96098049024512 22.001000500250125 105-109 31.960980490245124 24.47223611805903 22.141070535267634 21.425712856428213 110-114 32.39471841552466 23.982194658397518 22.611783535060518 21.011303391017304 115-119 33.006503251625816 23.546773386693346 23.16658329164582 20.280140070035017 120-124 33.621810905452726 23.441720860430216 22.086043021510758 20.850425212606304 125-129 34.57055675053774 23.70566755039768 22.300035015757093 19.42374068330749 130-134 34.28557134280568 24.119471683009806 21.28276966179708 20.312187312387433 135-139 35.29441192655961 22.53739556756216 22.32227725248887 19.845915253389364 140-144 35.725717715314595 23.21696508952686 21.52145643693108 19.535860758227468 145-149 36.334984241332734 21.666916804242334 22.30226624643554 19.695832707989393 150-151 36.81511133350012 23.279959969977483 21.053289967475607 18.851638729046787 >>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 0.5 6 0.5 7 0.5 8 1.0 9 1.0 10 0.5 11 0.0 12 0.0 13 0.5 14 1.0 15 1.0 16 1.5 17 1.5 18 0.5 19 0.5 20 0.5 21 0.5 22 0.5 23 1.0 24 1.5 25 1.0 26 2.5 27 3.5 28 3.5 29 4.0 30 4.5 31 5.5 32 8.5 33 14.0 34 21.5 35 26.5 36 34.5 37 45.5 38 61.0 39 78.5 40 94.0 41 105.0 42 116.5 43 130.5 44 152.5 45 181.0 46 172.0 47 154.5 48 147.5 49 151.5 50 156.5 51 135.0 52 116.5 53 115.0 54 116.0 55 104.5 56 94.0 57 106.5 58 108.0 59 92.5 60 83.0 61 73.5 62 65.5 63 62.0 64 64.0 65 58.5 66 66.5 67 67.5 68 58.0 69 64.0 70 53.5 71 43.5 72 38.5 73 31.0 74 29.5 75 26.5 76 17.0 77 10.5 78 13.5 79 11.5 80 7.5 81 6.0 82 7.5 83 5.5 84 5.5 85 6.0 86 4.5 87 7.5 88 8.0 89 8.5 90 8.5 91 11.5 92 14.0 93 14.0 94 14.5 95 11.0 96 7.0 97 6.0 98 5.0 99 3.5 100 12.0 >>END_MODULE >>Per base N content pass #Base N-Count 1 0.475 2 0.0 3 0.0 4 0.0 5 0.0 6 0.0 7 0.0 8 0.0 9 0.0 10-14 0.0 15-19 0.0 20-24 0.03 25-29 0.05 30-34 0.04 35-39 0.03 40-44 0.04 45-49 0.034999999999999996 50-54 0.03 55-59 0.05 60-64 0.03 65-69 0.025 70-74 0.05 75-79 0.04 80-84 0.025 85-89 0.05 90-94 0.03 95-99 0.03 100-104 0.05 105-109 0.05 110-114 0.03 115-119 0.05 120-124 0.05 125-129 0.045 130-134 0.06 135-139 0.055 140-144 0.03 145-149 0.055 150-151 0.075 >>END_MODULE >>Sequence Length Distribution pass #Length Count 151 4000.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 75.325 #Duplication Level Percentage of deduplicated Percentage of total 1 77.13242615333554 58.099999999999994 2 16.06372386325921 24.2 3 5.17756388981082 11.700000000000001 4 1.0288748755393295 3.1 5 0.39827414537006306 1.5 6 0.1327580484566877 0.6 7 0.0 0.0 8 0.0 0.0 9 0.033189512114171926 0.22499999999999998 >10 0.033189512114171926 0.575 >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 GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG 23 0.575 No Hit GTCCACTTCAGCCTCTGCAAGAGGGACAACACCAAGCAGTTCCACAACTC 9 0.22499999999999998 No Hit CCCAAACTGAACAGCGTCGTCGGCCACATACTCCACTCCTCCATTCTCGT 6 0.15 No Hit CAGCAGCCTCCGACGCCGGCGCGGGCGGGGGAGCGGGACCCGGCCCCGTC 6 0.15 No Hit CTAGTCGTCGAGTTCCCGAGTCCACTGCAGCCCACGTTGTGTGCTCCCTC 6 0.15 No Hit TCTGAAGGTCTTTTGCAGCGGGTCTTGTCTGTAGGATGCATACATATTAT 6 0.15 No Hit GCTGCTGGCGGCGCTCCCTACGGCGGCTCCAGCATCGGCATGGGCCCGTA 5 0.125 No Hit AGCCTATCTGGATGAGGAAGCCTGAGGAAATTACCAAGGAGGAATATGCT 5 0.125 No Hit CTCATGGTCTGATCAGGAAGTACGGGCTCATGTGCTGCAGGCAGTGCTTC 5 0.125 No Hit GCTGAATACGCTGAAGGGCCACGTTGAGTCTGTCGTGAAGCTGAAGGGAC 5 0.125 No Hit GCGATGACTCGCGGCGACCAGAGGGAGCGGGATCGGCAGAGGGCGCAGGC 5 0.125 No Hit GTTCCACACGTCCACATCCATGTGATCCCAAGAAAGAAAGGAGATTTTGA 5 0.125 No Hit GGGAACGTGAGCCGGGAGGCAAATGGAGGCGGCGAGCGGGCGCGGCGGAT 5 0.125 No Hit GGCGGCTGGATTATCAAGGTCAAGGTCAAAGATGCGGGTGAGCTCAACTC 5 0.125 No Hit GGATAATTAGCATGAGGCAACAGCTTTTTAATGCTCTGAACATCAGAGGT 5 0.125 No Hit CGAGCTACGATGCTACCACACATTTTGAGACAACTGTGACAGACGTTCTT 5 0.125 No Hit GATAAACAACCCACATTATCTGTATCGCATGACCATCCTGCAAGCTATCT 5 0.125 No Hit CACAGGCTTCCCTTTCGGAACAAGCTGTAGGTTCTCGCCATGGAGATCCA 5 0.125 No Hit >>END_MODULE >>Adapter Content fail #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 0.0125 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 0.037500000000000006 0.0 0.0 0.0 0.0 40-41 0.05 0.0 0.0 0.0 0.0 42-43 0.05 0.0 0.0 0.0 0.0 44-45 0.05 0.0 0.0 0.0 0.0 46-47 0.05 0.0 0.0 0.0 0.0 48-49 0.0625 0.0 0.0 0.0 0.0 50-51 0.075 0.0 0.0 0.0 0.0 52-53 0.1 0.0 0.0 0.0 0.0 54-55 0.2375 0.0 0.0 0.0 0.0 56-57 0.25 0.0 0.0 0.0 0.0 58-59 0.2875 0.0 0.0 0.0 0.0 60-61 0.4375 0.0 0.0 0.0 0.0 62-63 0.5875 0.0 0.0 0.0 0.0 64-65 0.7625 0.0 0.0 0.0 0.0 66-67 0.925 0.0 0.0 0.0 0.0 68-69 1.0625 0.0 0.0 0.0 0.0 70-71 1.3875 0.0 0.0 0.0 0.0 72-73 1.7125 0.0 0.0 0.0 0.0 74-75 2.0875 0.0 0.0 0.0 0.0 76-77 2.325 0.0 0.0 0.0 0.0 78-79 3.05 0.0 0.0 0.0 0.0 80-81 3.7 0.0 0.0 0.0 0.0 82-83 4.3375 0.0 0.0 0.0 0.0 84-85 4.7625 0.0 0.0 0.0 0.0 86-87 5.324999999999999 0.0 0.0 0.0 0.0 88-89 6.0375 0.0 0.0 0.0 0.0 90-91 6.65 0.0 0.0 0.0 0.0 92-93 7.3625 0.0 0.0 0.0 0.0 94-95 8.274999999999999 0.0 0.0 0.0 0.0 96-97 9.4 0.0 0.0 0.0 0.0 98-99 10.25 0.0 0.0 0.0 0.0 100-101 11.3125 0.0 0.0 0.0 0.0 102-103 12.0875 0.0 0.0 0.0 0.0 104-105 13.0625 0.0 0.0 0.0 0.0 106-107 14.475000000000001 0.0 0.0 0.0 0.0 108-109 15.5625 0.0 0.0 0.0 0.0 110-111 16.3125 0.0 0.0 0.0 0.0 112-113 17.4 0.0 0.0 0.0 0.0 114-115 18.112499999999997 0.0 0.0 0.0 0.0 116-117 19.049999999999997 0.0 0.0 0.0 0.0 118-119 20.1125 0.0 0.0 0.0 0.0 120-121 20.9375 0.0 0.0 0.0 0.0 122-123 21.8875 0.0 0.0 0.0 0.0 124-125 23.0125 0.0 0.0 0.0 0.0 126-127 24.025 0.0 0.0 0.0 0.0 128-129 24.775 0.0 0.0 0.0 0.0 130-131 25.95 0.0 0.0 0.0 0.0 132-133 27.4625 0.0 0.0 0.0 0.0 134-135 28.3375 0.0 0.0 0.0 0.0 136-137 28.95 0.0 0.0 0.0 0.0 138-139 29.775 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position GAGTTTG 10 0.006830828 145.0 4 TCTGAGT 10 0.006830828 145.0 1 TTGACAA 10 0.006830828 145.0 8 TGAGTTT 10 0.006830828 145.0 3 GTGTGAT 80 0.0018040554 36.25 145 CCGGTGT 45 6.5511256E-4 19.333332 130-134 CGGTGTA 40 0.0076550315 18.125 130-134 ACCGGTG 50 0.0013298223 17.4 130-134 TGATTAC 55 0.0025160722 15.818182 125-129 GATTACC 55 0.0025160722 15.818182 125-129 >>END_MODULE Read 1408558 spots for SRR13165363.sra Written 1408558 spots for SRR13165363.sra Read 1408558 spots for SRR13165363.sra Written 1408558 spots for SRR13165363.sra Read 1408558 spots for SRR13165363.sra Written 1408558 spots for SRR13165363.sra Read 1408558 spots for SRR13165363.sra Written 1408558 spots for SRR13165363.sra Read 1408558 spots for SRR13165363.sra Written 1408558 spots for SRR13165363.sra Read 1408558 spots for SRR13165363.sra Written 1408558 spots for SRR13165363.sra Read 1408558 spots for SRR13165363.sra Written 1408558 spots for SRR13165363.sra Read 1408558 spots for SRR13165363.sra Written 1408558 spots for SRR13165363.sra Read 1408558 spots for SRR13165363.sra Written 1408558 spots for SRR13165363.sra Read 1408558 spots for SRR13165363.sra Written 1408558 spots for SRR13165363.sra Read 1408558 spots for SRR13165363.sra Written 1408558 spots for SRR13165363.sra Read 1408558 spots for SRR13165363.sra Written 1408558 spots for SRR13165363.sra Read 1408558 spots for SRR13165363.sra Written 1408558 spots for SRR13165363.sra Read 1408558 spots for SRR13165363.sra Written 1408558 spots for SRR13165363.sra Read 1408558 spots for SRR13165363.sra Written 1408558 spots for SRR13165363.sra Read 1408558 spots for SRR13165363.sra Written 1408558 spots for SRR13165363.sra Read 1408558 spots for SRR13165363.sra Written 1408558 spots for SRR13165363.sra Read 1408559 spots for SRR13165363.sra Written 1408559 spots for SRR13165363.sra Read 1408558 spots for SRR13165363.sra Written 1408558 spots for SRR13165363.sra Read 1408558 spots for SRR13165363.sra Written 1408558 spots for SRR13165363.sra SRR ids: ['SRR13165363.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_11wnf6to SRR13165363.sra spots: 28171161 blocks: [[1, 1408558], [1408559, 2817116], [2817117, 4225674], [4225675, 5634232], [5634233, 7042790], [7042791, 8451348], [8451349, 9859906], [9859907, 11268464], [11268465, 12677022], [12677023, 14085580], [14085581, 15494138], [15494139, 16902696], [16902697, 18311254], [18311255, 19719812], [19719813, 21128370], [21128371, 22536928], [22536929, 23945486], [23945487, 25354044], [25354045, 26762602], [26762603, 28171161]] SRR13165363 file size 9552092 SRR13165363 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 SRR13165363 SRR13165363_1.fastq SRR13165363_2.fastq Input file: SRR13165363_1.fastq Paired file: SRR13165363_2.fastq trimmed: SRR13165363-trimmed-pair1.fastq, SRR13165363-trimmed-pair2.fastq Parameters used: -- 3' end adapter sequence (-x): AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC -- paired 3' end adapter sequence (-y): AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTA -- 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 -- number of concurrent threads (-t): 20 Sat Dec 7 16:10:53 2024 >> started Sat Dec 7 16:11:23 2024 >> done (29.598s) 28171161 read pairs processed; of these: 972 ( 0.00%) short read pairs filtered out after trimming by size control 1102249 ( 3.91%) empty read pairs filtered out after trimming by size control 27067940 (96.08%) read pairs available; of these: 9732229 (35.95%) trimmed read pairs available after processing 17335711 (64.05%) untrimmed read pairs available after processing Length distribution of reads after trimming: length count percentage 18 46 0.00% 19 40 0.00% 20 50 0.00% 21 45 0.00% 22 60 0.00% 23 78 0.00% 24 91 0.00% 25 113 0.00% 26 124 0.00% 27 163 0.00% 28 202 0.00% 29 261 0.00% 30 346 0.00% 31 416 0.00% 32 494 0.00% 33 522 0.00% 34 580 0.00% 35 719 0.00% 36 745 0.00% 37 970 0.00% 38 1179 0.00% 39 1311 0.00% 40 1664 0.01% 41 1898 0.01% 42 1940 0.01% 43 2241 0.01% 44 2232 0.01% 45 2487 0.01% 46 2724 0.01% 47 3167 0.01% 48 3627 0.01% 49 4474 0.02% 50 5343 0.02% 51 5961 0.02% 52 6587 0.02% 53 6909 0.03% 54 7130 0.03% 55 7544 0.03% 56 7911 0.03% 57 8895 0.03% 58 10709 0.04% 59 11587 0.04% 60 13417 0.05% 61 15269 0.06% 62 17225 0.06% 63 18393 0.07% 64 20031 0.07% 65 20534 0.08% 66 21463 0.08% 67 23925 0.09% 68 25660 0.09% 69 28795 0.11% 70 32043 0.12% 71 36639 0.14% 72 40758 0.15% 73 44710 0.17% 74 48000 0.18% 75 49804 0.18% 76 52354 0.19% 77 55227 0.20% 78 58294 0.22% 79 63811 0.24% 80 69114 0.26% 81 75079 0.28% 82 81991 0.30% 83 87693 0.32% 84 92173 0.34% 85 96131 0.36% 86 98382 0.36% 87 99907 0.37% 88 103492 0.38% 89 107319 0.40% 90 112412 0.42% 91 117952 0.44% 92 123337 0.46% 93 128521 0.47% 94 133189 0.49% 95 136228 0.50% 96 135114 0.50% 97 135403 0.50% 98 136695 0.51% 99 135811 0.50% 100 138997 0.51% 101 142337 0.53% 102 144289 0.53% 103 147105 0.54% 104 149204 0.55% 105 148227 0.55% 106 148106 0.55% 107 147510 0.54% 108 142618 0.53% 109 144471 0.53% 110 143562 0.53% 111 143539 0.53% 112 145510 0.54% 113 145325 0.54% 114 146543 0.54% 115 146630 0.54% 116 144949 0.54% 117 142412 0.53% 118 139558 0.52% 119 137839 0.51% 120 135813 0.50% 121 136265 0.50% 122 136341 0.50% 123 136012 0.50% 124 136862 0.51% 125 135602 0.50% 126 135264 0.50% 127 133182 0.49% 128 131512 0.49% 129 128475 0.47% 130 126803 0.47% 131 125538 0.46% 132 124929 0.46% 133 125015 0.46% 134 124242 0.46% 135 124583 0.46% 136 122683 0.45% 137 122053 0.45% 138 120105 0.44% 139 119725 0.44% 140 116690 0.43% 141 116311 0.43% 142 116028 0.43% 143 114754 0.42% 144 116193 0.43% 145 115735 0.43% 146 114434 0.42% 147 113602 0.42% 148 112103 0.41% 149 111118 0.41% 150 109646 0.41% 151 17335711 64.05% 27067940 reads passed initial QC criterion=sequence-density sequence-density=0.57 sequence-density-rank=1 fanout-score=34.55 fanout-score-rank=4 prefix-density=0.60 prefix-fanout=33.1 sequence=GGATCGGAAGAGCACACGTCTGAACTCCAGTCACGATTACCGATCTCGTATGCCGTCTTCTGCTTGAAAA criterion=fanout-score sequence-density=0.03 sequence-density-rank=32 fanout-score=415.21 fanout-score-rank=1 prefix-density=0.60 prefix-fanout=21.3 sequence=GGCGGCGGCGAACCGCCCCCGTCGCCGCGATCCGAACACTTCACCGGACCATTCAATCGGTAGGAGCGACGGGCGGTGTGTACAAAGGGCAGGGACGTAGTCAACGCGAGCTGATGACTCGCGCTTACTAGGCATTCCTCGTTGAAGACCAACAATTGCAATGATCTATCCCCATCACGATGAAATTTCCCAAGATTACCCGGGCCTGTCGGCCAAGGCTATATACTCGTTGAATACATCAGTGTAGCGCGCGTGCGGCCCAGAACATCTAAGGGCATCACAGACCTGTTATTGCCTCAAACTTCCGTCGCCTAAACGGCGATAGTCCCTCTAAGAAGCTAGCTGCGGAGGGATGGCTCCGCATAGCTAGTTAGCAGGCTGAGGTCTCGTTCGTTAACGGAATTAACCAGACAAATCGCTCCACCAACTAAGAACGGCCATGCACCACCACCCATAGAATCAAGAAAGAGCTCTCAGTCTGTCAATCCTTGCTATGTCTGGACCTGGTAAG criterion=sequence-density sequence-density=0.18 sequence-density-rank=1 fanout-score=10.05 fanout-score-rank=18 prefix-density=0.27 prefix-fanout=6.5 sequence=GGCAAGACCATCACCCTTGAGGT criterion=fanout-score sequence-density=0.09 sequence-density-rank=23 fanout-score=221.22 fanout-score-rank=1 prefix-density=0.94 prefix-fanout=21.1 sequence=CGCCGCCGCCGTC SRR13165363 testing PE reads STAR mapping to Ensembl genome Started job on | Dec 07 16:12:11 Started mapping on | Dec 07 16:12:11 Finished on | Dec 07 16:14:55 Mapping speed, Million of reads per hour | 594.17 Number of input reads | 27067940 Average input read length | 273 UNIQUE READS: Uniquely mapped reads number | 24861475 Uniquely mapped reads % | 91.85% Average mapped length | 271.28 Number of splices: Total | 20142252 Number of splices: Annotated (sjdb) | 18795531 Number of splices: GT/AG | 19878126 Number of splices: GC/AG | 211492 Number of splices: AT/AC | 13468 Number of splices: Non-canonical | 39166 Mismatch rate per base, % | 0.22% Deletion rate per base | 0.01% Deletion average length | 2.52 Insertion rate per base | 0.01% Insertion average length | 2.17 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 285616 % of reads mapped to multiple loci | 1.06% Number of reads mapped to too many loci | 72183 % of reads mapped to too many loci | 0.27% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 5.96% % of reads unmapped: other | 0.87% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 1921111 1921111 1921111 N_multimapping 285616 285616 285616 N_noFeature 748317 24137321 1020847 N_ambiguous 507141 2950 56094 UnstrandedReadsAssigned:23606017 PositiveStrandReadsAssigned:721204 NegativeStrandReadsAssigned:23784534 Dataset is classified negative stranded MeadianReadLen=151 20thPercentileLength=117 echo kmer=113 SRR13165363 Starting Kallisto paired end mapping to ensembl reference transcriptome [quant] fragment length distribution will be estimated from the data [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 paired-end mode [quant] will process pair 1: SRR13165363-trimmed-pair1.fastq SRR13165363-trimmed-pair2.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 27,067,940 reads, 24,389,319 reads pseudoaligned [quant] estimated average fragment length: 199.788 [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,233 rounds 52973 SRR13165363.ke.tsv 35125 SRR13165363.se.tsv 88098 total ==> SRR13165363.ke.tsv <== target_id length eff_length est_counts tpm PNS24245 936 737.596 0 0 PNS24247 1044 845.212 32.5914 2.35804 PNS24249 1928 1729.21 190.151 6.72457 PNS24246 1044 845.212 32.5914 2.35804 PNS24248 1044 845.212 32.5914 2.35804 PNS24244 1471 1272.21 71.075 3.41642 PNS24243 293 136.061 1 0.449448 KQK14069 1603 1404.21 28 1.21938 KQK14071 474 288.494 0 0 ==> SRR13165363.se.tsv <== BRADI_1g14170v3 28 BRADI_1g53295v3 48 BRADI_1g59795v3 509 BRADI_1g07683v3 0 BRADI_1g00485v3 241 BRADI_1g20270v3 5801 BRADI_1g74790v3 43 BRADI_1g09890v3 30 BRADI_1g77505v3 242 BRADI_1g48960v3 0 SRR13165363 completed mapping pipeline successfully