Starting /dee2/code/volunteer_pipeline.sh SRR13662586 current disk space = 1526816460800 free memory = 1555296736 SRR13662586 SRAfilesize 6e30c70c5adfa9403ed89f7176a02972 SRR13662586.sra SRR13662586.sra file validated SRR13662586 is paired end SRR13662586 is conventional basespace SRR13662586 read1 length is 125 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR13662586_1.fastq File type Conventional base calls Encoding Sanger / Illumina 1.9 Total Sequences 4000 Sequences flagged as poor quality 0 Sequence length 125 %GC 55 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 32.4175 33.0 33.0 34.0 31.0 34.0 2 32.22725 33.0 33.0 34.0 30.0 34.0 3 32.4065 33.0 33.0 34.0 31.0 34.0 4 32.40575 33.0 33.0 34.0 31.0 34.0 5 32.341 33.0 33.0 34.0 31.0 34.0 6 35.97 38.0 36.0 38.0 32.0 38.0 7 36.45625 38.0 37.0 38.0 34.0 38.0 8 36.6075 38.0 38.0 38.0 34.0 38.0 9 36.7135 38.0 38.0 38.0 34.0 38.0 10-11 36.688375 38.0 38.0 38.0 34.0 38.0 12-13 36.491125 38.0 38.0 38.0 34.0 38.0 14-15 36.67225 38.0 38.0 38.0 34.0 38.0 16-17 36.604 38.0 38.0 38.0 34.0 38.0 18-19 36.71875 38.0 38.0 38.0 34.5 38.0 20-21 36.582499999999996 38.0 38.0 38.0 34.0 38.0 22-23 36.66175 38.0 38.0 38.0 34.0 38.0 24-25 36.586875000000006 38.0 38.0 38.0 34.0 38.0 26-27 36.575 38.0 38.0 38.0 34.0 38.0 28-29 36.694874999999996 38.0 38.0 38.0 34.0 38.0 30-31 36.704125 38.0 38.0 38.0 34.0 38.0 32-33 36.5955 38.0 38.0 38.0 34.0 38.0 34-35 36.560625 38.0 38.0 38.0 34.0 38.0 36-37 36.53875 38.0 38.0 38.0 34.0 38.0 38-39 36.416 38.0 38.0 38.0 33.5 38.0 40-41 36.498125 38.0 38.0 38.0 34.0 38.0 42-43 36.510374999999996 38.0 38.0 38.0 34.0 38.0 44-45 36.57525 38.0 38.0 38.0 34.0 38.0 46-47 36.429874999999996 38.0 38.0 38.0 33.5 38.0 48-49 36.51875 38.0 38.0 38.0 34.0 38.0 50-51 36.6755 38.0 38.0 38.0 34.0 38.0 52-53 36.544624999999996 38.0 38.0 38.0 34.0 38.0 54-55 36.516125 38.0 38.0 38.0 34.0 38.0 56-57 36.5245 38.0 38.0 38.0 34.0 38.0 58-59 36.3005 38.0 38.0 38.0 33.5 38.0 60-61 36.29075 38.0 38.0 38.0 33.0 38.0 62-63 36.322874999999996 38.0 38.0 38.0 33.0 38.0 64-65 36.266625 38.0 38.0 38.0 33.0 38.0 66-67 36.250875 38.0 38.0 38.0 33.0 38.0 68-69 36.395125 38.0 38.0 38.0 34.0 38.0 70-71 36.44025 38.0 38.0 38.0 34.0 38.0 72-73 36.384125 38.0 38.0 38.0 33.5 38.0 74-75 36.092124999999996 38.0 38.0 38.0 33.0 38.0 76-77 36.244625 38.0 38.0 38.0 33.0 38.0 78-79 36.201499999999996 38.0 38.0 38.0 33.5 38.0 80-81 36.288375 38.0 38.0 38.0 33.5 38.0 82-83 35.955625 38.0 37.5 38.0 32.0 38.0 84-85 36.013125 38.0 37.5 38.0 32.5 38.0 86-87 35.789875 38.0 37.0 38.0 31.0 38.0 88-89 35.942125 38.0 37.5 38.0 32.0 38.0 90-91 36.057625 38.0 37.5 38.0 33.0 38.0 92-93 35.694625 38.0 37.0 38.0 31.0 38.0 94-95 35.713875 38.0 37.0 38.0 31.0 38.0 96-97 35.73425 38.0 37.0 38.0 31.0 38.0 98-99 35.341499999999996 38.0 36.0 38.0 29.0 38.0 100-101 35.45375 38.0 36.5 38.0 30.0 38.0 102-103 35.547375 38.0 36.5 38.0 30.5 38.0 104-105 35.666125 38.0 37.0 38.0 31.5 38.0 106-107 35.415625 38.0 36.5 38.0 30.5 38.0 108-109 35.326625 38.0 36.0 38.0 30.0 38.0 110-111 35.23925 38.0 36.0 38.0 29.5 38.0 112-113 35.1175 38.0 35.5 38.0 29.0 38.0 114-115 35.118125 38.0 36.0 38.0 29.5 38.0 116-117 34.664125 38.0 35.5 38.0 26.0 38.0 118-119 34.94175 38.0 36.0 38.0 28.5 38.0 120-121 34.591125000000005 38.0 35.0 38.0 26.0 38.0 122-123 34.63975 38.0 36.0 38.0 28.0 38.0 124-125 34.03875 38.0 35.5 38.0 24.5 38.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 15 2.0 16 0.0 17 6.0 18 3.0 19 6.0 20 5.0 21 9.0 22 10.0 23 6.0 24 10.0 25 23.0 26 29.0 27 39.0 28 40.0 29 59.0 30 68.0 31 115.0 32 91.0 33 128.0 34 210.0 35 315.0 36 493.0 37 2333.0 >>END_MODULE >>Per base sequence content warn #Base G A T C 1 41.625 10.8 9.950000000000001 37.625 2 34.175 15.7 26.8 23.325000000000003 3 30.675 20.9 19.475 28.95 4 32.875 26.174999999999997 15.775 25.174999999999997 5 31.825 29.075 17.9 21.2 6 24.5 33.1 19.625 22.775000000000002 7 24.0 16.475 34.5 25.025 8 23.925 19.025 25.275 31.775 9 24.825 19.475 26.25 29.45 10-11 28.3875 27.237499999999997 19.0125 25.362499999999997 12-13 27.275 20.525 24.6625 27.537499999999998 14-15 27.500000000000004 21.912499999999998 22.912499999999998 27.675 16-17 27.500000000000004 23.375 21.275 27.85 18-19 26.825 22.3625 22.912499999999998 27.900000000000002 20-21 27.6375 23.1375 22.45 26.775 22-23 28.012500000000003 22.75 22.2125 27.025 24-25 27.5875 22.662499999999998 22.325 27.425 26-27 26.974999999999998 21.9375 23.549999999999997 27.537499999999998 28-29 27.9125 22.3375 21.7875 27.962500000000002 30-31 26.650000000000002 22.6125 22.3 28.4375 32-33 27.500000000000004 23.0625 22.45 26.987499999999997 34-35 28.549999999999997 22.037499999999998 22.275 27.1375 36-37 27.400000000000002 22.35 22.037499999999998 28.212500000000002 38-39 27.35 22.1375 22.775000000000002 27.737499999999997 40-41 28.3875 21.712500000000002 22.15 27.750000000000004 42-43 27.8875 23.2625 21.349999999999998 27.500000000000004 44-45 26.6625 22.1875 22.35 28.799999999999997 46-47 28.449999999999996 22.1375 21.975 27.437499999999996 48-49 27.05 22.3375 22.5875 28.025 50-51 27.175 22.675 21.8625 28.287499999999998 52-53 27.762500000000003 22.275 22.112499999999997 27.85 54-55 27.6125 22.287499999999998 22.225 27.875 56-57 27.05 21.925 22.425 28.599999999999998 58-59 27.287499999999998 22.8625 22.15 27.700000000000003 60-61 28.249999999999996 21.25 22.6375 27.8625 62-63 28.1375 23.25 21.837500000000002 26.775 64-65 28.6375 22.5625 21.1875 27.6125 66-67 28.3125 21.875 22.1875 27.625 68-69 27.187499999999996 22.1 22.037499999999998 28.675 70-71 28.625 22.8875 21.099999999999998 27.3875 72-73 27.450000000000003 22.275 21.85 28.425 74-75 27.0875 22.325 22.2625 28.325 76-77 28.8625 20.875 22.55 27.712500000000002 78-79 27.575 21.512500000000003 21.7 29.212500000000002 80-81 27.237499999999997 21.512500000000003 23.025000000000002 28.225 82-83 28.15 22.0125 22.1375 27.700000000000003 84-85 27.875 22.15 21.675 28.299999999999997 86-87 27.787499999999998 22.45 21.712500000000002 28.050000000000004 88-89 27.775 22.400000000000002 22.412499999999998 27.4125 90-91 27.0625 22.125 22.2625 28.549999999999997 92-93 27.474999999999998 22.9375 21.6125 27.975 94-95 28.262500000000003 21.8125 22.225 27.700000000000003 96-97 28.237499999999997 22.15 21.587500000000002 28.025 98-99 28.0875 21.925 22.3375 27.650000000000002 100-101 28.237499999999997 22.925 21.825 27.0125 102-103 28.625 21.712500000000002 22.425 27.237499999999997 104-105 27.3625 22.175 21.875 28.5875 106-107 28.6875 23.2375 21.6 26.474999999999998 108-109 28.9375 22.6375 21.7375 26.687499999999996 110-111 27.6125 22.3875 22.675 27.325 112-113 28.325 22.1875 21.375 28.1125 114-115 28.15 21.712500000000002 21.9375 28.199999999999996 116-117 28.499999999999996 21.55 22.0625 27.8875 118-119 27.85 22.625 21.987499999999997 27.537499999999998 120-121 28.225 22.3 22.275 27.200000000000003 122-123 27.375 21.825 23.075000000000003 27.725 124-125 28.075 21.8125 22.1875 27.925 >>END_MODULE >>Per sequence GC content fail #GC Content Count 0 1.0 1 1.0 2 0.5 3 0.5 4 0.5 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 0.5 19 0.5 20 0.0 21 0.0 22 0.0 23 0.5 24 1.0 25 1.0 26 1.0 27 2.0 28 1.5 29 0.5 30 2.5 31 5.0 32 4.5 33 9.0 34 15.0 35 18.0 36 26.0 37 33.0 38 41.5 39 56.5 40 73.5 41 82.0 42 94.5 43 112.5 44 119.0 45 131.0 46 125.0 47 122.0 48 127.5 49 119.5 50 132.5 51 135.0 52 124.5 53 117.5 54 106.5 55 100.5 56 102.0 57 98.5 58 95.0 59 90.0 60 86.0 61 96.5 62 97.5 63 96.0 64 95.0 65 97.0 66 101.5 67 103.5 68 94.5 69 84.0 70 79.5 71 77.5 72 78.5 73 71.5 74 63.0 75 51.5 76 51.5 77 43.0 78 26.5 79 21.0 80 15.5 81 12.0 82 9.0 83 5.0 84 2.5 85 4.0 86 4.0 87 1.5 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 0.0 36-37 0.0 38-39 0.0 40-41 0.0 42-43 0.0 44-45 0.0 46-47 0.0 48-49 0.0 50-51 0.0 52-53 0.0 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 94-95 0.0 96-97 0.0 98-99 0.0 100-101 0.0 102-103 0.0 104-105 0.0 106-107 0.0 108-109 0.0 110-111 0.0 112-113 0.0 114-115 0.0 116-117 0.0 118-119 0.0 120-121 0.0 122-123 0.0 124-125 0.0 >>END_MODULE >>Sequence Length Distribution pass #Length Count 125 4000.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 99.575 #Duplication Level Percentage of deduplicated Percentage of total 1 99.57318604067285 99.15 2 0.42681395932714034 0.8500000000000001 3 0.0 0.0 4 0.0 0.0 5 0.0 0.0 6 0.0 0.0 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 pass >>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 >>END_MODULE >>Kmer Content pass >>END_MODULE SRR13662586 read2 length is 125 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR13662586_2.fastq File type Conventional base calls Encoding Sanger / Illumina 1.9 Total Sequences 4000 Sequences flagged as poor quality 0 Sequence length 125 %GC 55 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 31.384 33.0 32.0 34.0 25.0 34.0 2 31.43025 33.0 32.0 34.0 25.0 34.0 3 31.25875 33.0 32.0 34.0 25.0 34.0 4 31.15225 33.0 32.0 34.0 25.0 34.0 5 31.19675 33.0 32.0 34.0 25.0 34.0 6 34.979 38.0 36.0 38.0 27.0 38.0 7 35.03925 38.0 36.0 38.0 27.0 38.0 8 34.86575 38.0 36.0 38.0 26.0 38.0 9 35.30075 38.0 36.0 38.0 28.0 38.0 10-11 35.2 38.0 36.5 38.0 27.5 38.0 12-13 35.415125 38.0 36.5 38.0 28.5 38.0 14-15 34.898375 38.0 36.0 38.0 26.5 38.0 16-17 35.326750000000004 38.0 36.0 38.0 28.0 38.0 18-19 35.090875 38.0 36.0 38.0 27.0 38.0 20-21 34.642125 38.0 35.0 38.0 25.0 38.0 22-23 35.2145 38.0 36.0 38.0 27.0 38.0 24-25 35.247125 38.0 36.0 38.0 27.5 38.0 26-27 34.816625 38.0 35.5 38.0 26.0 38.0 28-29 35.367625000000004 38.0 36.5 38.0 27.5 38.0 30-31 35.128 38.0 36.0 38.0 27.0 38.0 32-33 35.012875 38.0 36.0 38.0 26.5 38.0 34-35 35.015875 38.0 36.0 38.0 27.0 38.0 36-37 35.030375 38.0 36.0 38.0 26.0 38.0 38-39 34.455375000000004 38.0 35.0 38.0 24.0 38.0 40-41 34.8855 38.0 35.5 38.0 26.0 38.0 42-43 35.2415 38.0 36.0 38.0 27.0 38.0 44-45 34.93775 38.0 35.5 38.0 25.5 38.0 46-47 35.513 38.0 37.0 38.0 28.0 38.0 48-49 35.489125 38.0 37.0 38.0 28.0 38.0 50-51 35.600125 38.0 37.0 38.0 29.0 38.0 52-53 35.59725 38.0 37.0 38.0 29.0 38.0 54-55 35.6255 38.0 37.0 38.0 29.0 38.0 56-57 35.73475 38.0 37.0 38.0 30.0 38.0 58-59 35.5115 38.0 37.0 38.0 29.0 38.0 60-61 35.521874999999994 38.0 36.5 38.0 28.0 38.0 62-63 35.542625 38.0 36.5 38.0 28.5 38.0 64-65 35.40675 38.0 36.0 38.0 28.5 38.0 66-67 35.4495 38.0 36.5 38.0 28.5 38.0 68-69 35.498999999999995 38.0 37.0 38.0 29.0 38.0 70-71 35.5095 38.0 36.5 38.0 29.0 38.0 72-73 35.483625 38.0 36.5 38.0 29.5 38.0 74-75 35.100125000000006 38.0 36.0 38.0 26.5 38.0 76-77 35.28125 38.0 36.0 38.0 28.0 38.0 78-79 35.382875 38.0 36.0 38.0 28.5 38.0 80-81 35.293125 38.0 36.5 38.0 28.0 38.0 82-83 35.308499999999995 38.0 36.0 38.0 28.5 38.0 84-85 35.66375 38.0 37.0 38.0 30.5 38.0 86-87 35.281125 38.0 36.5 38.0 28.5 38.0 88-89 35.317875 38.0 36.0 38.0 29.0 38.0 90-91 35.03275 38.0 36.0 38.0 27.0 38.0 92-93 35.137375000000006 38.0 36.0 38.0 28.5 38.0 94-95 34.99825 38.0 35.5 38.0 27.0 38.0 96-97 35.092749999999995 38.0 36.0 38.0 28.0 38.0 98-99 34.896249999999995 38.0 35.5 38.0 26.5 38.0 100-101 35.03125 38.0 36.0 38.0 27.5 38.0 102-103 34.897125 38.0 35.5 38.0 27.0 38.0 104-105 34.79625 38.0 35.0 38.0 26.0 38.0 106-107 34.761624999999995 38.0 35.0 38.0 26.5 38.0 108-109 34.70375 38.0 35.0 38.0 25.5 38.0 110-111 34.83175 38.0 35.5 38.0 27.5 38.0 112-113 34.67225 38.0 35.5 38.0 25.5 38.0 114-115 34.740875 38.0 35.0 38.0 27.0 38.0 116-117 34.309 38.0 35.0 38.0 24.0 38.0 118-119 34.494375000000005 38.0 35.0 38.0 25.5 38.0 120-121 34.171625 38.0 35.0 38.0 23.0 38.0 122-123 34.076875 38.0 35.0 38.0 23.5 38.0 124-125 33.595625 38.0 35.0 38.0 22.0 38.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 12 5.0 13 3.0 14 5.0 15 5.0 16 3.0 17 7.0 18 6.0 19 12.0 20 17.0 21 12.0 22 26.0 23 36.0 24 41.0 25 68.0 26 52.0 27 58.0 28 79.0 29 88.0 30 85.0 31 120.0 32 129.0 33 149.0 34 187.0 35 303.0 36 501.0 37 2003.0 >>END_MODULE >>Per base sequence content warn #Base G A T C 1 40.400000000000006 9.675 9.25 40.675 2 33.95 16.75 26.35 22.95 3 30.099999999999998 21.95 18.075 29.875 4 32.35 27.450000000000003 15.625 24.575 5 32.925 28.275 17.65 21.15 6 25.650000000000002 32.925 18.875 22.55 7 23.375 16.325 35.0 25.3 8 25.025 19.425 24.2 31.35 9 25.650000000000002 18.5 26.450000000000003 29.4 10-11 28.3375 26.275 19.8 25.587500000000002 12-13 27.175 21.1375 24.6625 27.025 14-15 26.637499999999996 21.75 23.9875 27.625 16-17 28.775000000000002 21.4375 22.7125 27.075 18-19 26.974999999999998 21.525 23.275000000000002 28.225 20-21 26.974999999999998 22.237499999999997 22.575 28.212500000000002 22-23 28.225 22.475 21.375 27.925 24-25 28.4 23.474999999999998 21.6625 26.4625 26-27 26.7125 23.9375 22.287499999999998 27.0625 28-29 27.1375 22.8 21.775 28.287499999999998 30-31 27.975 21.975 22.775000000000002 27.275 32-33 27.187499999999996 22.975 21.925 27.9125 34-35 27.462500000000002 23.3125 21.75 27.474999999999998 36-37 27.6375 22.975 21.6875 27.700000000000003 38-39 26.35 23.150000000000002 22.75 27.750000000000004 40-41 27.462500000000002 22.6875 22.7625 27.0875 42-43 27.237499999999997 22.537499999999998 22.412499999999998 27.8125 44-45 26.387500000000003 23.05 22.400000000000002 28.1625 46-47 27.6375 22.35 22.175 27.8375 48-49 28.3125 22.2625 21.712500000000002 27.712500000000002 50-51 28.1 22.5 21.6625 27.737499999999997 52-53 28.075 21.925 22.25 27.750000000000004 54-55 27.750000000000004 22.1 21.8 28.349999999999998 56-57 27.625 21.85 22.7625 27.762500000000003 58-59 28.1375 22.112499999999997 21.975 27.775 60-61 27.750000000000004 22.375 22.787499999999998 27.0875 62-63 27.2625 22.075 21.6875 28.975 64-65 27.700000000000003 22.3875 21.837500000000002 28.075 66-67 26.900000000000002 21.725 23.45 27.925 68-69 28.025 21.7 22.5625 27.712500000000002 70-71 28.5625 21.9 21.7 27.8375 72-73 27.450000000000003 22.662499999999998 22.0625 27.825 74-75 27.762500000000003 21.875 22.912499999999998 27.450000000000003 76-77 28.3375 22.5875 21.525 27.55 78-79 27.9125 22.725 20.9375 28.425 80-81 27.3875 22.6375 21.55 28.425 82-83 28.799999999999997 21.462500000000002 21.8875 27.85 84-85 27.712500000000002 23.175 21.462500000000002 27.650000000000002 86-87 27.725 22.0625 21.837500000000002 28.375 88-89 28.15 21.625 21.9 28.325 90-91 27.537499999999998 22.45 22.25 27.762500000000003 92-93 28.225 22.037499999999998 22.375 27.3625 94-95 28.675 21.712500000000002 21.525 28.0875 96-97 27.85 21.95 22.525000000000002 27.675 98-99 26.900000000000002 21.337500000000002 23.025000000000002 28.7375 100-101 27.700000000000003 22.0 22.3 28.000000000000004 102-103 28.1375 21.775 21.5625 28.525 104-105 26.987499999999997 22.425 22.3 28.287499999999998 106-107 27.700000000000003 21.8 22.25 28.249999999999996 108-109 27.800000000000004 21.7875 22.037499999999998 28.375 110-111 27.675 22.0875 22.112499999999997 28.125 112-113 27.762500000000003 22.5 21.512500000000003 28.225 114-115 28.375 22.5125 22.1 27.0125 116-117 27.250000000000004 22.0625 22.825 27.8625 118-119 27.275 22.675 21.725 28.325 120-121 28.012500000000003 22.1 22.1375 27.750000000000004 122-123 27.675 22.225 22.275 27.825 124-125 28.512500000000003 22.2625 21.65 27.575 >>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 0.5 13 0.5 14 0.0 15 0.0 16 0.0 17 0.0 18 0.0 19 0.0 20 0.0 21 1.0 22 1.0 23 0.0 24 0.0 25 0.5 26 0.5 27 0.5 28 1.0 29 1.5 30 4.0 31 4.5 32 5.5 33 8.5 34 9.0 35 16.5 36 30.5 37 38.5 38 44.0 39 53.0 40 69.0 41 86.5 42 104.0 43 114.0 44 119.5 45 124.0 46 119.5 47 135.0 48 136.0 49 124.0 50 125.0 51 124.0 52 114.0 53 109.0 54 115.5 55 104.0 56 97.5 57 107.0 58 101.5 59 94.0 60 93.5 61 80.0 62 75.0 63 94.0 64 105.5 65 98.0 66 100.5 67 103.5 68 101.5 69 103.0 70 87.5 71 74.0 72 71.5 73 70.0 74 67.0 75 55.0 76 39.0 77 33.5 78 33.0 79 22.5 80 16.5 81 12.5 82 6.5 83 5.0 84 4.5 85 2.5 86 1.0 87 0.0 88 0.0 89 0.0 90 0.0 91 0.0 92 0.0 93 0.0 94 0.0 95 0.0 96 0.0 97 0.0 98 0.0 99 0.0 100 0.0 >>END_MODULE >>Per base N content pass #Base N-Count 1 0.0 2 0.0 3 0.0 4 0.0 5 0.0 6 0.0 7 0.0 8 0.0 9 0.0 10-11 0.0 12-13 0.0 14-15 0.0 16-17 0.0 18-19 0.0 20-21 0.0 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 0.0 36-37 0.0 38-39 0.0 40-41 0.0 42-43 0.0 44-45 0.0 46-47 0.0 48-49 0.0 50-51 0.0 52-53 0.0 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 94-95 0.0 96-97 0.0 98-99 0.0 100-101 0.0 102-103 0.0 104-105 0.0 106-107 0.0 108-109 0.0 110-111 0.0 112-113 0.0 114-115 0.0 116-117 0.0 118-119 0.0 120-121 0.0 122-123 0.0 124-125 0.0 >>END_MODULE >>Sequence Length Distribution pass #Length Count 125 4000.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 99.675 #Duplication Level Percentage of deduplicated Percentage of total 1 99.67394030599448 99.35000000000001 2 0.32605969400551793 0.65 3 0.0 0.0 4 0.0 0.0 5 0.0 0.0 6 0.0 0.0 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 pass >>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 >>END_MODULE >>Kmer Content pass >>END_MODULE Read 583786 spots for SRR13662586.sra Written 583786 spots for SRR13662586.sra Read 583786 spots for SRR13662586.sra Written 583786 spots for SRR13662586.sra Read 583786 spots for SRR13662586.sra Written 583786 spots for SRR13662586.sra Read 583786 spots for SRR13662586.sra Written 583786 spots for SRR13662586.sra Read 583786 spots for SRR13662586.sra Written 583786 spots for SRR13662586.sra Read 583786 spots for SRR13662586.sra Written 583786 spots for SRR13662586.sra Read 583786 spots for SRR13662586.sra Written 583786 spots for SRR13662586.sra Read 583786 spots for SRR13662586.sra Written 583786 spots for SRR13662586.sra Read 583786 spots for SRR13662586.sra Written 583786 spots for SRR13662586.sra Read 583786 spots for SRR13662586.sra Written 583786 spots for SRR13662586.sra Read 583786 spots for SRR13662586.sra Written 583786 spots for SRR13662586.sra Read 583786 spots for SRR13662586.sra Written 583786 spots for SRR13662586.sra Read 583786 spots for SRR13662586.sra Written 583786 spots for SRR13662586.sra Read 583786 spots for SRR13662586.sra Written 583786 spots for SRR13662586.sra Read 583786 spots for SRR13662586.sra Written 583786 spots for SRR13662586.sra Read 583786 spots for SRR13662586.sra Written 583786 spots for SRR13662586.sra Read 583786 spots for SRR13662586.sra Written 583786 spots for SRR13662586.sra Read 583786 spots for SRR13662586.sra Written 583786 spots for SRR13662586.sra Read 583786 spots for SRR13662586.sra Written 583786 spots for SRR13662586.sra Read 583794 spots for SRR13662586.sra Written 583794 spots for SRR13662586.sra SRR ids: ['SRR13662586.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_ou6ziuka SRR13662586.sra spots: 11675728 blocks: [[1, 583786], [583787, 1167572], [1167573, 1751358], [1751359, 2335144], [2335145, 2918930], [2918931, 3502716], [3502717, 4086502], [4086503, 4670288], [4670289, 5254074], [5254075, 5837860], [5837861, 6421646], [6421647, 7005432], [7005433, 7589218], [7589219, 8173004], [8173005, 8756790], [8756791, 9340576], [9340577, 9924362], [9924363, 10508148], [10508149, 11091934], [11091935, 11675728]] SRR13662586 file size 3353314 SRR13662586 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 SRR13662586 SRR13662586_1.fastq SRR13662586_2.fastq Input file: SRR13662586_1.fastq Paired file: SRR13662586_2.fastq trimmed: SRR13662586-trimmed-pair1.fastq, SRR13662586-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 Dec 10 07:38:07 2024 >> started Tue Dec 10 07:38:18 2024 >> done (11.372s) 11675728 read pairs processed; of these: 0 ( 0.00%) short read pairs filtered out after trimming by size control 148 ( 0.00%) empty read pairs filtered out after trimming by size control 11675580 (100.00%) read pairs available; of these: 1547810 (13.26%) trimmed read pairs available after processing 10127770 (86.74%) untrimmed read pairs available after processing Length distribution of reads after trimming: length count percentage 26 1 0.00% 27 0 0.00% 28 0 0.00% 29 0 0.00% 30 0 0.00% 31 0 0.00% 32 0 0.00% 33 0 0.00% 34 0 0.00% 35 4 0.00% 36 0 0.00% 37 0 0.00% 38 1 0.00% 39 0 0.00% 40 0 0.00% 41 1 0.00% 42 1 0.00% 43 0 0.00% 44 0 0.00% 45 0 0.00% 46 1 0.00% 47 0 0.00% 48 0 0.00% 49 2 0.00% 50 0 0.00% 51 2 0.00% 52 1 0.00% 53 0 0.00% 54 1 0.00% 55 1 0.00% 56 1 0.00% 57 2 0.00% 58 1 0.00% 59 4 0.00% 60 1 0.00% 61 1 0.00% 62 3 0.00% 63 39 0.00% 64 68 0.00% 65 91 0.00% 66 115 0.00% 67 135 0.00% 68 167 0.00% 69 184 0.00% 70 190 0.00% 71 239 0.00% 72 305 0.00% 73 317 0.00% 74 336 0.00% 75 410 0.00% 76 383 0.00% 77 456 0.00% 78 488 0.00% 79 499 0.00% 80 566 0.00% 81 650 0.01% 82 716 0.01% 83 734 0.01% 84 836 0.01% 85 882 0.01% 86 975 0.01% 87 1009 0.01% 88 1118 0.01% 89 1294 0.01% 90 1374 0.01% 91 1492 0.01% 92 1835 0.02% 93 2196 0.02% 94 5361 0.05% 95 5532 0.05% 96 5759 0.05% 97 6012 0.05% 98 6379 0.05% 99 6575 0.06% 100 6954 0.06% 101 7095 0.06% 102 7725 0.07% 103 7772 0.07% 104 7922 0.07% 105 8500 0.07% 106 9128 0.08% 107 9593 0.08% 108 10119 0.09% 109 10895 0.09% 110 11816 0.10% 111 12906 0.11% 112 13899 0.12% 113 15239 0.13% 114 17366 0.15% 115 19632 0.17% 116 41453 0.36% 117 46535 0.40% 118 53489 0.46% 119 63731 0.55% 120 77614 0.66% 121 99460 0.85% 122 143481 1.23% 123 231044 1.98% 124 558696 4.79% 125 10127770 86.74% 11675580 reads passed initial QC criterion=sequence-density sequence-density=0.18 sequence-density-rank=1 fanout-score=4.80 fanout-score-rank=23 prefix-density=0.20 prefix-fanout=4.5 sequence=TGCCGCACTTGCAGGTGGTGCAGTCGCAGCCGCCGCT criterion=fanout-score sequence-density=0.07 sequence-density-rank=19 fanout-score=404.89 fanout-score-rank=1 prefix-density=1.22 prefix-fanout=23.5 sequence=GGCGGCGGCGAACCGCCCCCGTCGCCGCGATCCGAACACTTCACCGGACCATTCAATCGGTAGGAGCGACGGGCGGTGTGTACAAAGGGCAGGGACGTAGTCAACGCGAGCTGATGACTCGCGCTTACTAGGCATTCCTCGTTGAAGACCAACAATTGCAATGATCTATCCCCATCACGATGAAATTTCCCAAGATTACCCGGGCCTGTCGGCCAAGGCTATATACTCGTTGAATACATCAGTGTAGCGCGCGTGCGGCCCAGAACATCTAAGGGCATCACAGACCTGTTATTGCCTCAAACTTCCGTCGCCTAAACGGCGATAGTCCCTCTAAGAAGCTAGCTGCGGAGGGATGGCTCCGCATAGCTAGTTAGCAGGCTGAGGTCTCGTTCGTTAACGGAATTAACCAGACAAATCGCTCCACCAACTAAGAACGGCCATGCACCACCACCCATAGAATCAAGAAAGAGCTCTCAGTCTGTCAATCCTTGCTATGTCTGGACCTGGTAAG criterion=sequence-density sequence-density=0.18 sequence-density-rank=1 fanout-score=4.87 fanout-score-rank=22 prefix-density=0.19 prefix-fanout=4.6 sequence=TGCCGCACTTGCAGGTGGTGCAGTCGCAGCCGCCGCT criterion=fanout-score sequence-density=0.07 sequence-density-rank=19 fanout-score=435.95 fanout-score-rank=1 prefix-density=1.24 prefix-fanout=24.0 sequence=GGCGGCGGCGAACCGCCCCCGTCGCCGCGATCCGAACACTTCACCGGACCATTCAATCGGTAGGAGCGACGGGCGGTGTGTACAAAGGGCAGGGACGTAGTCAACGCGAGCTGATGACTCGCGCTTACTAGGCATTCCTCGTTGAAGACCAACAATTGCAATGATCTATCCCCATCACGATGAAATTTCCCAAGATTACCCGGGCCTGTCGGCCAAGGCTATATACTCGTTGAATACATCAGTGTAGCGCGCGTGCGGCCCAGAACATCTAAGGGCATCACAGACCTGTTATTGCCTCAAACTTCCGTCGCCTAAACGGCGATAGTCCCTCTAAGAAGCTAGCTGCGGAGGGATGGCTCCGCATAGCTAGTTAGCAGGCTGAGGTCTCGTTCGTTAACGGAATTAACCAGACAAATCGCTCCACCAACTAAGAACGGCCATGCACCACCACCCATAGAATCAAGAAAGAGCTCTCAGTCTGTCAATCCTTGCTATGTCTGGACCTGGTAAG SRR13662586 testing PE reads STAR mapping to Ensembl genome Started job on | Dec 10 07:39:04 Started mapping on | Dec 10 07:39:04 Finished on | Dec 10 07:39:48 Mapping speed, Million of reads per hour | 955.27 Number of input reads | 11675580 Average input read length | 248 UNIQUE READS: Uniquely mapped reads number | 10532484 Uniquely mapped reads % | 90.21% Average mapped length | 246.10 Number of splices: Total | 7612139 Number of splices: Annotated (sjdb) | 7189040 Number of splices: GT/AG | 7506031 Number of splices: GC/AG | 86510 Number of splices: AT/AC | 4084 Number of splices: Non-canonical | 15514 Mismatch rate per base, % | 0.33% Deletion rate per base | 0.01% Deletion average length | 2.20 Insertion rate per base | 0.01% Insertion average length | 2.08 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 278458 % of reads mapped to multiple loci | 2.38% Number of reads mapped to too many loci | 82671 % of reads mapped to too many loci | 0.71% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 2.14% % of reads unmapped: other | 4.56% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 864693 864693 864693 N_multimapping 278458 278458 278458 N_noFeature 250165 5281211 5279472 N_ambiguous 259218 19568 19776 UnstrandedReadsAssigned:10023101 PositiveStrandReadsAssigned:5231705 NegativeStrandReadsAssigned:5233236 Dataset is classified unstranded MeadianReadLen=125 20thPercentileLength=125 echo kmer=121 SRR13662586 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: SRR13662586-trimmed-pair1.fastq SRR13662586-trimmed-pair2.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 11,675,580 reads, 10,579,309 reads pseudoaligned [quant] estimated average fragment length: 195.563 [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,084 rounds 52973 SRR13662586.ke.tsv 35125 SRR13662586.se.tsv 88098 total ==> SRR13662586.ke.tsv <== target_id length eff_length est_counts tpm PNS24245 936 741.618 3.29927 0.529722 PNS24247 1044 849.437 15.7564 2.20869 PNS24249 1928 1733.44 167.501 11.5059 PNS24246 1044 849.437 15.7564 2.20869 PNS24248 1044 849.437 15.7564 2.20869 PNS24244 1471 1276.44 9.93071 0.926383 PNS24243 293 105.456 6 6.77467 KQK14069 1603 1408.44 5283.96 446.717 KQK14071 474 281.512 828.445 350.411 ==> SRR13662586.se.tsv <== BRADI_1g14170v3 6283 BRADI_1g53295v3 23 BRADI_1g59795v3 94 BRADI_1g07683v3 0 BRADI_1g00485v3 4 BRADI_1g20270v3 596 BRADI_1g74790v3 118 BRADI_1g09890v3 19 BRADI_1g77505v3 180 BRADI_1g48960v3 0 SRR13662586 completed mapping pipeline successfully