Starting /dee2/code/volunteer_pipeline.sh SRR12670169 current disk space = 3055791804416 free memory = 1461962356 SRR12670169 SRAfilesize 3f2c5db7dc422ba2a7cc6a2661859d84 SRR12670169.sra SRR12670169.sra file validated SRR12670169 is paired end SRR12670169 is conventional basespace SRR12670169 read1 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR12670169_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 45 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 36.648 37.0 37.0 37.0 37.0 37.0 2 36.4575 37.0 37.0 37.0 37.0 37.0 3 36.5845 37.0 37.0 37.0 37.0 37.0 4 36.627 37.0 37.0 37.0 37.0 37.0 5 36.6715 37.0 37.0 37.0 37.0 37.0 6 36.6525 37.0 37.0 37.0 37.0 37.0 7 36.533 37.0 37.0 37.0 37.0 37.0 8 36.576 37.0 37.0 37.0 37.0 37.0 9 36.5145 37.0 37.0 37.0 37.0 37.0 10-14 36.6088 37.0 37.0 37.0 37.0 37.0 15-19 36.585699999999996 37.0 37.0 37.0 37.0 37.0 20-24 36.5081 37.0 37.0 37.0 37.0 37.0 25-29 36.5213 37.0 37.0 37.0 37.0 37.0 30-34 36.5214 37.0 37.0 37.0 37.0 37.0 35-39 36.4752 37.0 37.0 37.0 37.0 37.0 40-44 36.472 37.0 37.0 37.0 37.0 37.0 45-49 36.4307 37.0 37.0 37.0 37.0 37.0 50-54 36.365300000000005 37.0 37.0 37.0 37.0 37.0 55-59 36.373599999999996 37.0 37.0 37.0 37.0 37.0 60-64 36.385000000000005 37.0 37.0 37.0 37.0 37.0 65-69 36.3941 37.0 37.0 37.0 37.0 37.0 70-74 36.2672 37.0 37.0 37.0 37.0 37.0 75-79 36.297399999999996 37.0 37.0 37.0 37.0 37.0 80-84 36.2539 37.0 37.0 37.0 37.0 37.0 85-89 36.2378 37.0 37.0 37.0 37.0 37.0 90-94 36.2051 37.0 37.0 37.0 37.0 37.0 95-99 36.137 37.0 37.0 37.0 37.0 37.0 100-104 36.23049999999999 37.0 37.0 37.0 37.0 37.0 105-109 36.1958 37.0 37.0 37.0 37.0 37.0 110-114 36.023399999999995 37.0 37.0 37.0 37.0 37.0 115-119 36.054899999999996 37.0 37.0 37.0 37.0 37.0 120-124 35.9107 37.0 37.0 37.0 37.0 37.0 125-129 35.7538 37.0 37.0 37.0 37.0 37.0 130-134 35.5815 37.0 37.0 37.0 37.0 37.0 135-139 35.396 37.0 37.0 37.0 37.0 37.0 140-144 35.0498 37.0 37.0 37.0 32.2 37.0 145-149 34.7327 37.0 37.0 37.0 25.0 37.0 150-151 34.31925 37.0 37.0 37.0 25.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 23 1.0 24 2.0 25 1.0 26 6.0 27 10.0 28 11.0 29 24.0 30 31.0 31 30.0 32 80.0 33 113.0 34 157.0 35 356.0 36 2771.0 37 407.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 44.275 11.375 5.075 39.275 2 18.15222834251377 12.343515272909364 38.83324987481222 30.67100650976465 3 16.325 18.25 29.549999999999997 35.875 4 21.675 25.025 23.425 29.875 5 24.099999999999998 31.624999999999996 24.125 20.150000000000002 6 21.95 36.4 21.475 20.175 7 14.95 29.425 39.574999999999996 16.05 8 17.575 26.0 32.574999999999996 23.849999999999998 9 18.25 22.5 35.85 23.400000000000002 10-14 20.65 29.75 27.015 22.585 15-19 20.205000000000002 28.4 27.365000000000002 24.03 20-24 20.61 28.199999999999996 27.189999999999998 24.0 25-29 20.565 28.439999999999998 27.575 23.419999999999998 30-34 20.395 28.389999999999997 28.035 23.18 35-39 20.380000000000003 27.73 28.21 23.68 40-44 20.365 28.455000000000002 27.560000000000002 23.62 45-49 20.495 28.21 28.139999999999997 23.155 50-54 20.625 28.499999999999996 27.355 23.52 55-59 20.14 28.575 28.050000000000004 23.235 60-64 20.615 28.92 26.939999999999998 23.525 65-69 20.715 28.185 27.944999999999997 23.155 70-74 20.575 28.549999999999997 27.205000000000002 23.669999999999998 75-79 20.77 27.865000000000002 27.555000000000003 23.810000000000002 80-84 21.17 27.975 27.365000000000002 23.49 85-89 20.715 29.625 26.555 23.105 90-94 21.065 28.48 26.875 23.580000000000002 95-99 20.849999999999998 28.87 26.995 23.285 100-104 21.3 28.549999999999997 26.505000000000003 23.645 105-109 21.775 28.845 25.865 23.515 110-114 21.69 28.32 26.235000000000003 23.755000000000003 115-119 21.52 28.98 25.465 24.035 120-124 21.45 28.384999999999998 26.21 23.955000000000002 125-129 21.560000000000002 28.694999999999997 25.395 24.349999999999998 130-134 21.88 28.395 25.27 24.455 135-139 22.259999999999998 28.754999999999995 24.94 24.044999999999998 140-144 22.325 28.000000000000004 25.180000000000003 24.495 145-149 22.939999999999998 27.950000000000003 24.435000000000002 24.675 150-151 22.7625 27.8375 24.087500000000002 25.3125 >>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 0.5 6 0.5 7 0.0 8 0.0 9 0.0 10 0.0 11 0.0 12 0.0 13 0.0 14 0.5 15 0.5 16 0.5 17 0.5 18 1.0 19 1.5 20 0.5 21 0.5 22 1.0 23 1.0 24 1.0 25 2.0 26 2.0 27 3.0 28 6.5 29 9.5 30 19.0 31 30.5 32 36.0 33 43.0 34 56.0 35 61.0 36 84.5 37 120.0 38 143.0 39 162.0 40 181.0 41 203.0 42 216.5 43 235.5 44 247.0 45 246.5 46 247.5 47 244.5 48 227.0 49 206.0 50 191.5 51 170.0 52 130.0 53 101.5 54 87.0 55 66.5 56 61.5 57 47.5 58 25.0 59 24.0 60 24.0 61 11.5 62 6.0 63 5.5 64 2.5 65 1.5 66 0.5 67 0.5 68 1.0 69 0.5 70 0.0 71 0.0 72 0.0 73 0.0 74 0.0 75 0.0 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 0.15 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 83.825 #Duplication Level Percentage of deduplicated Percentage of total 1 85.14762898896511 71.375 2 11.601550849985088 19.45 3 2.445571130331047 6.15 4 0.5368326871458395 1.7999999999999998 5 0.14912019087384432 0.625 6 0.11929615269907547 0.6 7 0.0 0.0 8 0.0 0.0 9 0.0 0.0 >10 0.0 0.0 >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 GCTGTGTACTTTTTCAGTCTCAATTTCTTCCCACTAAGAAAAGAAGCCTT 6 0.15 No Hit GGCGGCAGCATCATCCATTGATCAAATCAATCGTCGCCGTCCAAAATAAA 6 0.15 No Hit GTTCCATCTCCAGTTACAGCAACAACATGTCCCCTCTTTTTCAAAGCTTG 6 0.15 No Hit GCTTGCTTAATGACCGCATGTGCAGGTAGTGCAAGTGCAGCCAGTACCGC 6 0.15 No Hit GGATGGGAAAGTGGCGGAGAAGGAGAGGTTGAGGGGCTTTGGGGAGGTGA 5 0.125 No Hit CATCGTGTCCACAAGAACTAACCACAATCTTAGCCTCCATGACATTAGGG 5 0.125 No Hit CACAGAGTTTCCCCAAGCAAGTACTGTAAGCCCAAGGAGAGATGGGGGCA 5 0.125 No Hit GTTCACTCTTATCCTGTTTCCTAGGGGTTTCAATCCTCTCTTTAGCTGGA 5 0.125 No Hit GTTCTGGTATGTTTTGAGTGCAGACTCCAAGAGATCATCAAAATCGCTGG 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 0.025 0.0 0.0 0.0 0.0 50-51 0.037500000000000006 0.0 0.0 0.0 0.0 52-53 0.1 0.0 0.0 0.0 0.0 54-55 0.125 0.0 0.0 0.0 0.0 56-57 0.15 0.0 0.0 0.0 0.0 58-59 0.175 0.0 0.0 0.0 0.0 60-61 0.1875 0.0 0.0 0.0 0.0 62-63 0.25 0.0 0.0 0.0 0.0 64-65 0.4125 0.0 0.0 0.0 0.0 66-67 0.48750000000000004 0.0 0.0 0.0 0.0 68-69 0.5874999999999999 0.0 0.0 0.0 0.0 70-71 0.6875 0.0 0.0 0.0 0.0 72-73 0.9125 0.0 0.0 0.0 0.0 74-75 1.0875 0.0 0.0 0.0 0.0 76-77 1.2625000000000002 0.0 0.0 0.0 0.0 78-79 1.5125000000000002 0.0 0.0 0.0 0.0 80-81 1.775 0.0 0.0 0.0 0.0 82-83 2.1125 0.0 0.0 0.0 0.0 84-85 2.5625 0.0 0.0 0.0 0.0 86-87 3.1 0.0 0.0 0.0 0.0 88-89 3.475 0.0 0.0 0.0 0.0 90-91 4.074999999999999 0.0 0.0 0.0 0.0 92-93 4.5875 0.0 0.0 0.0 0.0 94-95 5.1 0.0 0.0 0.0 0.0 96-97 5.8125 0.0 0.0 0.0 0.0 98-99 6.4375 0.0 0.0 0.0 0.0 100-101 7.525 0.0 0.0 0.0 0.0 102-103 8.7625 0.0 0.0 0.0 0.0 104-105 9.825 0.0 0.0 0.0 0.0 106-107 10.6875 0.0 0.0 0.0 0.0 108-109 11.9875 0.0 0.0 0.0 0.0 110-111 12.837499999999999 0.0 0.0 0.0 0.0 112-113 13.7375 0.0 0.0 0.0 0.0 114-115 15.0 0.0 0.0 0.0 0.0 116-117 16.2125 0.0 0.0 0.0 0.0 118-119 17.15 0.0 0.0 0.0 0.0 120-121 18.15 0.0 0.0 0.0 0.0 122-123 19.2625 0.0 0.0 0.0 0.0 124-125 20.5625 0.0 0.0 0.0 0.0 126-127 21.95 0.0 0.0 0.0 0.0 128-129 23.15 0.0 0.0 0.0 0.0 130-131 24.299999999999997 0.0 0.0 0.0 0.0 132-133 25.4125 0.0 0.0 0.0 0.0 134-135 26.950000000000003 0.0 0.0 0.0 0.0 136-137 28.0625 0.0 0.0 0.0 0.0 138-139 29.049999999999997 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position ACTGAAG 10 0.006830828 145.0 5 CACTGAA 10 0.006830828 145.0 4 TGGATAT 10 0.006830828 145.0 3 GCGTAGG 10 0.006830828 145.0 145 >>END_MODULE SRR12670169 read2 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR12670169_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 45 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 36.346 37.0 37.0 37.0 37.0 37.0 2 36.2465 37.0 37.0 37.0 37.0 37.0 3 36.325 37.0 37.0 37.0 37.0 37.0 4 36.354 37.0 37.0 37.0 37.0 37.0 5 36.3785 37.0 37.0 37.0 37.0 37.0 6 36.4425 37.0 37.0 37.0 37.0 37.0 7 36.3405 37.0 37.0 37.0 37.0 37.0 8 36.4025 37.0 37.0 37.0 37.0 37.0 9 36.3825 37.0 37.0 37.0 37.0 37.0 10-14 36.446099999999994 37.0 37.0 37.0 37.0 37.0 15-19 36.4246 37.0 37.0 37.0 37.0 37.0 20-24 36.3555 37.0 37.0 37.0 37.0 37.0 25-29 36.3441 37.0 37.0 37.0 37.0 37.0 30-34 36.3125 37.0 37.0 37.0 37.0 37.0 35-39 36.2477 37.0 37.0 37.0 37.0 37.0 40-44 36.24130000000001 37.0 37.0 37.0 37.0 37.0 45-49 36.2699 37.0 37.0 37.0 37.0 37.0 50-54 36.2626 37.0 37.0 37.0 37.0 37.0 55-59 36.226000000000006 37.0 37.0 37.0 37.0 37.0 60-64 36.1911 37.0 37.0 37.0 37.0 37.0 65-69 36.2089 37.0 37.0 37.0 37.0 37.0 70-74 36.184999999999995 37.0 37.0 37.0 37.0 37.0 75-79 36.121500000000005 37.0 37.0 37.0 37.0 37.0 80-84 36.0855 37.0 37.0 37.0 37.0 37.0 85-89 36.062 37.0 37.0 37.0 37.0 37.0 90-94 36.0661 37.0 37.0 37.0 37.0 37.0 95-99 35.959500000000006 37.0 37.0 37.0 37.0 37.0 100-104 35.8856 37.0 37.0 37.0 37.0 37.0 105-109 35.8146 37.0 37.0 37.0 37.0 37.0 110-114 35.792100000000005 37.0 37.0 37.0 37.0 37.0 115-119 35.7287 37.0 37.0 37.0 37.0 37.0 120-124 35.561899999999994 37.0 37.0 37.0 37.0 37.0 125-129 35.394499999999994 37.0 37.0 37.0 37.0 37.0 130-134 35.2166 37.0 37.0 37.0 32.2 37.0 135-139 35.004000000000005 37.0 37.0 37.0 25.0 37.0 140-144 34.6657 37.0 37.0 37.0 25.0 37.0 145-149 34.2699 37.0 37.0 37.0 25.0 37.0 150-151 33.844 37.0 37.0 37.0 25.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 12 1.0 13 2.0 14 4.0 15 2.0 16 1.0 17 1.0 18 0.0 19 0.0 20 1.0 21 4.0 22 3.0 23 3.0 24 5.0 25 3.0 26 7.0 27 8.0 28 9.0 29 18.0 30 18.0 31 56.0 32 88.0 33 105.0 34 227.0 35 517.0 36 2586.0 37 331.0 >>END_MODULE >>Per base sequence content warn #Base G A T C 1 39.775 22.725 9.375 28.125 2 25.424999999999997 25.924999999999997 32.1 16.55 3 20.150000000000002 27.474999999999998 33.125 19.25 4 23.175 35.075 21.65 20.1 5 25.5 36.65 21.875 15.975 6 21.575 38.7 21.9 17.825 7 19.475 23.95 37.125 19.45 8 20.9 24.65 29.475 24.975 9 21.625 23.025000000000002 31.125000000000004 24.224999999999998 10-14 23.06 29.404999999999998 26.57 20.965 15-19 22.465 27.150000000000002 28.565 21.82 20-24 22.425 28.515 27.845 21.215 25-29 22.2 27.779999999999998 28.475 21.545 30-34 22.795 28.000000000000004 28.355000000000004 20.849999999999998 35-39 22.830000000000002 27.794999999999998 28.59 20.785 40-44 23.03 27.61 28.23 21.13 45-49 22.745 27.639999999999997 28.76 20.855 50-54 22.195 28.22 28.29 21.295 55-59 23.44 27.625 27.805000000000003 21.13 60-64 22.830000000000002 27.644999999999996 27.685 21.84 65-69 23.13 27.36 27.99 21.52 70-74 23.535 27.955000000000002 27.605 20.905 75-79 22.985 27.544999999999998 27.76 21.709999999999997 80-84 23.39 28.225 27.73 20.655 85-89 24.03 28.544999999999998 27.200000000000003 20.225 90-94 23.990000000000002 28.599999999999998 26.779999999999998 20.630000000000003 95-99 24.465 28.03 26.915 20.59 100-104 25.22 27.365000000000002 26.8 20.615 105-109 25.55 27.675 26.69 20.085 110-114 26.150000000000002 28.299999999999997 25.715 19.835 115-119 26.165 27.98 26.805 19.05 120-124 27.73 28.16 25.785000000000004 18.325 125-129 27.985 28.13 25.395 18.490000000000002 130-134 28.449999999999996 28.075 25.705 17.77 135-139 29.64 26.87 25.345000000000002 18.145 140-144 30.84 26.400000000000002 25.215 17.544999999999998 145-149 32.605000000000004 26.115 24.154999999999998 17.125 150-151 31.8 25.887500000000003 24.7375 17.575 >>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 0.5 10 0.5 11 0.0 12 0.0 13 0.0 14 1.0 15 1.0 16 0.5 17 1.0 18 1.0 19 1.0 20 1.5 21 1.0 22 1.0 23 1.0 24 2.0 25 3.5 26 2.5 27 2.5 28 6.5 29 13.0 30 16.0 31 16.0 32 26.0 33 44.0 34 55.5 35 68.5 36 87.0 37 115.5 38 147.0 39 168.5 40 171.0 41 216.0 42 251.5 43 263.0 44 280.5 45 265.0 46 254.0 47 244.5 48 220.0 49 190.5 50 173.5 51 143.5 52 108.0 53 91.0 54 77.5 55 69.0 56 51.0 57 39.0 58 35.0 59 21.0 60 15.0 61 11.0 62 10.5 63 5.5 64 0.5 65 1.0 66 1.5 67 0.5 68 0.0 69 0.0 70 0.0 71 0.0 72 0.5 73 0.5 74 0.0 75 0.5 76 0.5 77 0.0 78 0.0 79 0.0 80 0.0 81 0.5 82 0.5 83 0.0 84 0.0 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 0.0 100 0.5 >>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 10-14 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 83.92500000000001 #Duplication Level Percentage of deduplicated Percentage of total 1 85.43342269883824 71.7 2 11.379207625856418 19.1 3 2.234137622877569 5.625 4 0.7149240393208222 2.4 5 0.11915400655347036 0.5 6 0.05957700327673518 0.3 7 0.02978850163836759 0.17500000000000002 8 0.02978850163836759 0.2 9 0.0 0.0 >10 0.0 0.0 >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 CAAACGCTTCGGAAGAAAATCTTTTGGCCACAAAAATGGCTTCTGTTTGT 8 0.2 No Hit GAGAACACATTCATACTCCAAGTCTTTTAGTTCATCCATTTAAGCTTAAT 7 0.17500000000000002 No Hit GCAGAAGATGCTGTGGAGCCTAATGTTATTGAAGGAAGAGTGTTTCGTAA 6 0.15 No Hit GTGTAAGGTGGGCGAGTGCGTGAAGATGATTAAGAACGTTGACTCTGATG 6 0.15 No Hit AACAGAAGAAAAAAACTCTCCACCGCCCCATCTCTCTCCACGATTGCTGG 5 0.125 No Hit CAGAGAACACATTCATACTCCAAGTCTTTTAGTTCATCCATTTAAGCTTA 5 0.125 No Hit TATGACGAGGCAGATAACTATGTGGTTATCAAGCATGCAGCTTTGTTCAC 5 0.125 No Hit CAAAGAACGAGCAAATATCAGTGGTGCTTGTGGCATTTGTAATGAGTGTC 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 0.05 0.0 0.0 0.0 0.0 48-49 0.05 0.0 0.0 0.0 0.0 50-51 0.0625 0.0 0.0 0.0 0.0 52-53 0.125 0.0 0.0 0.0 0.0 54-55 0.15 0.0 0.0 0.0 0.0 56-57 0.175 0.0 0.0 0.0 0.0 58-59 0.2 0.0 0.0 0.0 0.0 60-61 0.21250000000000002 0.0 0.0 0.0 0.0 62-63 0.275 0.0 0.0 0.0 0.0 64-65 0.4375 0.0 0.0 0.0 0.0 66-67 0.5125 0.0 0.0 0.0 0.0 68-69 0.6125 0.0 0.0 0.0 0.0 70-71 0.7125 0.0 0.0 0.0 0.0 72-73 0.9375 0.0 0.0 0.0 0.0 74-75 1.1124999999999998 0.0 0.0 0.0 0.0 76-77 1.2875 0.0 0.0 0.0 0.0 78-79 1.5375 0.0 0.0 0.0 0.0 80-81 1.7999999999999998 0.0 0.0 0.0 0.0 82-83 2.1375 0.0 0.0 0.0 0.0 84-85 2.5875 0.0 0.0 0.0 0.0 86-87 3.125 0.0 0.0 0.0 0.0 88-89 3.5 0.0 0.0 0.0 0.0 90-91 4.1 0.0 0.0 0.0 0.0 92-93 4.625 0.0 0.0 0.0 0.0 94-95 5.15 0.0 0.0 0.0 0.0 96-97 5.875 0.0 0.0 0.0 0.0 98-99 6.575 0.0 0.0 0.0 0.0 100-101 7.675000000000001 0.0 0.0 0.0 0.0 102-103 8.912500000000001 0.0 0.0 0.0 0.0 104-105 9.975 0.0 0.0 0.0 0.0 106-107 10.8375 0.0 0.0 0.0 0.0 108-109 12.149999999999999 0.0 0.0 0.0 0.0 110-111 13.0 0.0 0.0 0.0 0.0 112-113 13.9 0.0 0.0 0.0 0.0 114-115 15.1375 0.0 0.0 0.0 0.0 116-117 16.3125 0.0 0.0 0.0 0.0 118-119 17.225 0.0 0.0 0.0 0.0 120-121 18.275 0.0 0.0 0.0 0.0 122-123 19.3625 0.0 0.0 0.0 0.0 124-125 20.6625 0.0 0.0 0.0 0.0 126-127 22.025 0.0 0.0 0.0 0.0 128-129 23.262500000000003 0.0 0.0 0.0 0.0 130-131 24.424999999999997 0.0 0.0 0.0 0.0 132-133 25.5375 0.0 0.0 0.0 0.0 134-135 27.125 0.0 0.0 0.0 0.0 136-137 28.2875 0.0 0.0 0.0 0.0 138-139 29.275 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position TTCCAAA 10 0.006830828 145.0 6 GCATTGG 10 0.006830828 145.0 145 CATACCA 10 0.006830828 145.0 8 CCCCCCC 20 0.00593511 29.0 55-59 GGGGGGG 90 0.0048656333 16.11111 145 >>END_MODULE Read 577413 spots for SRR12670169.sra Written 577413 spots for SRR12670169.sra Read 577413 spots for SRR12670169.sra Written 577413 spots for SRR12670169.sra Read 577413 spots for SRR12670169.sra Written 577413 spots for SRR12670169.sra Read 577413 spots for SRR12670169.sra Written 577413 spots for SRR12670169.sra Read 577413 spots for SRR12670169.sra Written 577413 spots for SRR12670169.sra Read 577413 spots for SRR12670169.sra Written 577413 spots for SRR12670169.sra Read 577413 spots for SRR12670169.sra Written 577413 spots for SRR12670169.sra Read 577413 spots for SRR12670169.sra Written 577413 spots for SRR12670169.sra Read 577413 spots for SRR12670169.sra Written 577413 spots for SRR12670169.sra Read 577416 spots for SRR12670169.sra Written 577416 spots for SRR12670169.sra Read 577413 spots for SRR12670169.sra Written 577413 spots for SRR12670169.sra Read 577413 spots for SRR12670169.sra Written 577413 spots for SRR12670169.sra Read 577413 spots for SRR12670169.sra Written 577413 spots for SRR12670169.sra Read 577413 spots for SRR12670169.sra Written 577413 spots for SRR12670169.sra Read 577413 spots for SRR12670169.sra Written 577413 spots for SRR12670169.sra Read 577413 spots for SRR12670169.sra Written 577413 spots for SRR12670169.sra Read 577413 spots for SRR12670169.sra Written 577413 spots for SRR12670169.sra Read 577413 spots for SRR12670169.sra Written 577413 spots for SRR12670169.sra Read 577413 spots for SRR12670169.sra Written 577413 spots for SRR12670169.sra Read 577413 spots for SRR12670169.sra Written 577413 spots for SRR12670169.sra SRR ids: ['SRR12670169.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_ksysjix3 SRR12670169.sra spots: 11548263 blocks: [[1, 577413], [577414, 1154826], [1154827, 1732239], [1732240, 2309652], [2309653, 2887065], [2887066, 3464478], [3464479, 4041891], [4041892, 4619304], [4619305, 5196717], [5196718, 5774130], [5774131, 6351543], [6351544, 6928956], [6928957, 7506369], [7506370, 8083782], [8083783, 8661195], [8661196, 9238608], [9238609, 9816021], [9816022, 10393434], [10393435, 10970847], [10970848, 11548263]] SRR12670169 file size 3902904 SRR12670169 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 SRR12670169 SRR12670169_1.fastq SRR12670169_2.fastq Input file: SRR12670169_1.fastq Paired file: SRR12670169_2.fastq trimmed: SRR12670169-trimmed-pair1.fastq, SRR12670169-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 Tue Feb 11 08:09:29 2025 >> started Tue Feb 11 08:09:42 2025 >> done (13.516s) 11548263 read pairs processed; of these: 52 ( 0.00%) short read pairs filtered out after trimming by size control 3229 ( 0.03%) empty read pairs filtered out after trimming by size control 11544982 (99.97%) read pairs available; of these: 3923919 (33.99%) trimmed read pairs available after processing 7621063 (66.01%) untrimmed read pairs available after processing Length distribution of reads after trimming: length count percentage 18 5 0.00% 19 9 0.00% 20 8 0.00% 21 15 0.00% 22 12 0.00% 23 17 0.00% 24 24 0.00% 25 32 0.00% 26 24 0.00% 27 45 0.00% 28 46 0.00% 29 51 0.00% 30 54 0.00% 31 74 0.00% 32 62 0.00% 33 96 0.00% 34 85 0.00% 35 106 0.00% 36 111 0.00% 37 134 0.00% 38 139 0.00% 39 165 0.00% 40 205 0.00% 41 206 0.00% 42 237 0.00% 43 264 0.00% 44 287 0.00% 45 282 0.00% 46 335 0.00% 47 401 0.00% 48 530 0.00% 49 611 0.01% 50 702 0.01% 51 878 0.01% 52 863 0.01% 53 962 0.01% 54 1009 0.01% 55 1097 0.01% 56 1239 0.01% 57 1464 0.01% 58 1738 0.02% 59 2158 0.02% 60 2525 0.02% 61 2858 0.02% 62 3141 0.03% 63 3518 0.03% 64 3903 0.03% 65 4168 0.04% 66 4638 0.04% 67 5132 0.04% 68 5634 0.05% 69 6549 0.06% 70 7624 0.07% 71 8787 0.08% 72 9852 0.09% 73 11123 0.10% 74 12245 0.11% 75 12819 0.11% 76 13940 0.12% 77 15034 0.13% 78 16234 0.14% 79 17960 0.16% 80 19110 0.17% 81 21589 0.19% 82 23555 0.20% 83 25290 0.22% 84 27857 0.24% 85 29463 0.26% 86 30751 0.27% 87 31838 0.28% 88 32996 0.29% 89 34323 0.30% 90 36556 0.32% 91 38715 0.34% 92 40570 0.35% 93 42765 0.37% 94 44891 0.39% 95 47439 0.41% 96 47504 0.41% 97 48128 0.42% 98 48915 0.42% 99 49553 0.43% 100 50929 0.44% 101 51415 0.45% 102 53485 0.46% 103 54979 0.48% 104 56492 0.49% 105 57059 0.49% 106 57917 0.50% 107 58473 0.51% 108 57709 0.50% 109 58367 0.51% 110 57237 0.50% 111 57695 0.50% 112 59558 0.52% 113 59609 0.52% 114 60947 0.53% 115 61607 0.53% 116 61906 0.54% 117 62736 0.54% 118 62171 0.54% 119 60993 0.53% 120 61091 0.53% 121 61049 0.53% 122 61250 0.53% 123 61890 0.54% 124 61702 0.53% 125 61619 0.53% 126 62716 0.54% 127 62159 0.54% 128 61342 0.53% 129 61595 0.53% 130 60504 0.52% 131 59721 0.52% 132 59542 0.52% 133 60002 0.52% 134 60423 0.52% 135 60681 0.53% 136 60663 0.53% 137 60146 0.52% 138 59775 0.52% 139 60003 0.52% 140 58732 0.51% 141 58763 0.51% 142 58401 0.51% 143 57833 0.50% 144 58495 0.51% 145 58021 0.50% 146 58097 0.50% 147 57795 0.50% 148 58211 0.50% 149 56985 0.49% 150 57155 0.50% 151 7621063 66.01% 11544982 reads passed initial QC criterion=sequence-density sequence-density=0.43 sequence-density-rank=1 fanout-score=1.95 fanout-score-rank=29 prefix-density=0.44 prefix-fanout=1.9 sequence=CGGTAGACCCAACCTTTCTCCAACTCGAATTCCAAGCAAGGAACCCACTTCGAGCGAAGAAGGTAATCAATTTCCTTGGCCAATTCCTCCTCTGTGAGATCTGGAAGGTAAGAAAGAGTCTCGAACTTCTTCAATCCAGTTGGTGGCCACACCTGCATGCATTGAACTCGTCCACCATTGCTTGCAATGGAAGTAATGTCATTAGCCTTTCT criterion=fanout-score sequence-density=0.01 sequence-density-rank=30 fanout-score=61.75 fanout-score-rank=1 prefix-density=0.06 prefix-fanout=5.8 sequence=AAACAGAATATTTACTTTTAGCGCAAGTTTCAATTCATGAGCTCGTTACATCACAAGTTAACATTACAAGCCAATAGTCCCAGCACAGAAAAAACTCTTTTGTTGCTCACTTTCCGGGAACGAAGTTTGTGGCATATGCCCAGGCGTTGTTGTTTACTGGGTCAGAAAGGTGGTCAGCCAGGTTCTCCAGTGGTCCCTTTCCGGTCACAATGGCCTGGACAAAGAATCCGAACATTGAGAACATAGCCAA criterion=sequence-density sequence-density=0.56 sequence-density-rank=1 fanout-score=2.03 fanout-score-rank=24 prefix-density=0.56 prefix-fanout=2.0 sequence=TGTAAGAGATGGCTTCCTC criterion=fanout-score sequence-density=0.13 sequence-density-rank=25 fanout-score=29.12 fanout-score-rank=1 prefix-density=0.35 prefix-fanout=11.0 sequence=AAAGAAAAGAAAA SRR12670169 testing PE reads STAR mapping to Ensembl genome Started job on | Feb 11 08:10:25 Started mapping on | Feb 11 08:10:25 Finished on | Feb 11 08:11:41 Mapping speed, Million of reads per hour | 546.87 Number of input reads | 11544982 Average input read length | 278 UNIQUE READS: Uniquely mapped reads number | 10854366 Uniquely mapped reads % | 94.02% Average mapped length | 276.85 Number of splices: Total | 10014892 Number of splices: Annotated (sjdb) | 9789965 Number of splices: GT/AG | 9808137 Number of splices: GC/AG | 162683 Number of splices: AT/AC | 6217 Number of splices: Non-canonical | 37855 Mismatch rate per base, % | 0.33% Deletion rate per base | 0.03% Deletion average length | 2.92 Insertion rate per base | 0.02% Insertion average length | 2.37 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 255760 % of reads mapped to multiple loci | 2.22% Number of reads mapped to too many loci | 20064 % of reads mapped to too many loci | 0.17% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 3.51% % of reads unmapped: other | 0.08% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 434856 434856 434856 N_multimapping 255760 255760 255760 N_noFeature 426828 10679796 512484 N_ambiguous 153262 665 63928 UnstrandedReadsAssigned:10274276 PositiveStrandReadsAssigned:173905 NegativeStrandReadsAssigned:10277954 Dataset is classified negative stranded MeadianReadLen=151 20thPercentileLength=123 echo kmer=119 SRR12670169 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: 52,400 [index] number of k-mers: 62,057,036 [index] number of equivalence classes: 130,681 [quant] running in paired-end mode [quant] will process pair 1: SRR12670169-trimmed-pair1.fastq SRR12670169-trimmed-pair2.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 11,544,982 reads, 10,285,443 reads pseudoaligned [quant] estimated average fragment length: 189.865 [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,095 rounds 52401 SRR12670169.ke.tsv 34699 SRR12670169.se.tsv 87100 total ==> SRR12670169.ke.tsv <== target_id length eff_length est_counts tpm Potri.005G200100.1.v4.1 2018 1829.13 340 17.6888 Potri.005G024800.1.v4.1 1035 846.135 131 14.7332 Potri.004G059700.1.v4.1 961 772.217 8 0.985863 Potri.007G009000.2.v4.1 1416 1227.13 0 0 Potri.003G141000.2.v4.1 2943 2754.13 591.99 20.4548 Potri.016G087400.1.v4.1 270 116.211 559 457.753 Potri.015G069301.1.v4.1 564 380.825 0 0 Potri.010G195200.1.v4.1 1773 1584.13 79 4.7457 Potri.012G127500.1.v4.1 977 788.164 88 10.6251 ==> SRR12670169.se.tsv <== Potri.001G166300.v4.1 0 Potri.001G448400.v4.1 195 Potri.001G233950.v4.1 0 Potri.001G122700.v4.1 196 Potri.001G212900.v4.1 1 Potri.001G182400.v4.1 0 Potri.001G256600.v4.1 0 Potri.001G040500.v4.1 3 Potri.001G416900.v4.1 0 Potri.001G452600.v4.1 5 SRR12670169 completed mapping pipeline successfully