Starting /dee2/code/volunteer_pipeline.sh ERR9452527 current disk space = 1547612491776 free memory = 1398305256 ERR9452527 SRAfilesize d33d370e511c16348976d3067ad5094f ERR9452527.sra ERR9452527.sra file validated ERR9452527 is paired end ERR9452527 is conventional basespace ERR9452527 read1 length is 150 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename ERR9452527_1.fastq File type Conventional base calls Encoding Sanger / Illumina 1.9 Total Sequences 4000 Sequences flagged as poor quality 0 Sequence length 150 %GC 55 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 35.867 37.0 37.0 37.0 37.0 37.0 2 35.7785 37.0 37.0 37.0 37.0 37.0 3 36.1545 37.0 37.0 37.0 37.0 37.0 4 36.218 37.0 37.0 37.0 37.0 37.0 5 36.29 37.0 37.0 37.0 37.0 37.0 6 36.2035 37.0 37.0 37.0 37.0 37.0 7 36.1055 37.0 37.0 37.0 37.0 37.0 8 36.1865 37.0 37.0 37.0 37.0 37.0 9 36.3855 37.0 37.0 37.0 37.0 37.0 10-14 36.262899999999995 37.0 37.0 37.0 37.0 37.0 15-19 36.22430000000001 37.0 37.0 37.0 37.0 37.0 20-24 36.2162 37.0 37.0 37.0 37.0 37.0 25-29 36.181200000000004 37.0 37.0 37.0 37.0 37.0 30-34 36.1163 37.0 37.0 37.0 37.0 37.0 35-39 36.1006 37.0 37.0 37.0 37.0 37.0 40-44 36.022800000000004 37.0 37.0 37.0 37.0 37.0 45-49 35.9636 37.0 37.0 37.0 37.0 37.0 50-54 36.055600000000005 37.0 37.0 37.0 37.0 37.0 55-59 35.9642 37.0 37.0 37.0 37.0 37.0 60-64 35.9341 37.0 37.0 37.0 37.0 37.0 65-69 35.95790000000001 37.0 37.0 37.0 37.0 37.0 70-74 35.9423 37.0 37.0 37.0 37.0 37.0 75-79 35.8771 37.0 37.0 37.0 37.0 37.0 80-84 35.8058 37.0 37.0 37.0 37.0 37.0 85-89 35.7407 37.0 37.0 37.0 37.0 37.0 90-94 35.7633 37.0 37.0 37.0 37.0 37.0 95-99 35.757600000000004 37.0 37.0 37.0 37.0 37.0 100-104 35.713800000000006 37.0 37.0 37.0 37.0 37.0 105-109 35.665099999999995 37.0 37.0 37.0 37.0 37.0 110-114 35.6679 37.0 37.0 37.0 37.0 37.0 115-119 35.6069 37.0 37.0 37.0 37.0 37.0 120-124 35.504599999999996 37.0 37.0 37.0 37.0 37.0 125-129 35.6234 37.0 37.0 37.0 37.0 37.0 130-134 35.4972 37.0 37.0 37.0 37.0 37.0 135-139 35.2457 37.0 37.0 37.0 27.4 37.0 140-144 35.408 37.0 37.0 37.0 34.6 37.0 145-149 35.55459999999999 37.0 37.0 37.0 37.0 37.0 150 35.4945 37.0 37.0 37.0 37.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 20 2.0 21 3.0 22 0.0 23 3.0 24 1.0 25 6.0 26 16.0 27 11.0 28 22.0 29 30.0 30 50.0 31 81.0 32 93.0 33 108.0 34 203.0 35 432.0 36 2687.0 37 252.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 29.325000000000003 13.05 15.275 42.35 2 28.114057028514257 20.485242621310658 29.114557278639317 22.28614307153577 3 26.125 25.7 19.325 28.849999999999998 4 31.05 28.549999999999997 15.425 24.975 5 29.125 28.275 19.0 23.599999999999998 6 22.35 31.125000000000004 19.375 27.150000000000002 7 22.25 13.825000000000001 36.775000000000006 27.150000000000002 8 22.900000000000002 18.275 24.625 34.2 9 24.925 18.4 27.0 29.675 10-14 26.055 23.630000000000003 21.82 28.494999999999997 15-19 27.255000000000003 22.375 22.14 28.23 20-24 27.325 22.85 21.69 28.134999999999998 25-29 27.41 22.235 22.505 27.85 30-34 27.250000000000004 22.1 22.41 28.24 35-39 27.405 22.32 22.155 28.12 40-44 26.889999999999997 22.675 22.09 28.345 45-49 26.82 22.67 22.220000000000002 28.29 50-54 27.284999999999997 22.725 21.785 28.205000000000002 55-59 27.400000000000002 22.675 21.775 28.15 60-64 27.689999999999998 22.415 21.715 28.18 65-69 27.1 22.53 21.93 28.439999999999998 70-74 27.765 21.23 22.1 28.904999999999998 75-79 27.845 21.95 22.27 27.935 80-84 27.98 21.725 21.87 28.425 85-89 28.115000000000002 22.25 21.455 28.18 90-94 27.534999999999997 22.205 22.16 28.1 95-99 28.355000000000004 21.88 21.83 27.935 100-104 28.884999999999998 21.990000000000002 21.485000000000003 27.639999999999997 105-109 28.975 21.425 21.36 28.24 110-114 27.99 22.585 21.215 28.21 115-119 28.465 21.7 21.54 28.294999999999998 120-124 28.694999999999997 22.05 21.584999999999997 27.67 125-129 28.610000000000003 21.98 21.615000000000002 27.794999999999998 130-134 28.634999999999998 21.395 21.91 28.060000000000002 135-139 27.85 22.125 21.765 28.26 140-144 28.265 22.08 21.865000000000002 27.79 145-149 28.655 21.69 21.46 28.194999999999997 150 28.225 23.025000000000002 20.8 27.950000000000003 >>END_MODULE >>Per sequence GC content fail #GC Content Count 0 0.0 1 0.5 2 0.5 3 0.0 4 0.0 5 0.0 6 0.0 7 0.0 8 0.0 9 0.0 10 0.0 11 0.0 12 0.0 13 0.0 14 0.0 15 0.0 16 0.5 17 0.5 18 0.0 19 0.5 20 0.5 21 0.0 22 0.0 23 0.0 24 0.5 25 0.5 26 1.5 27 2.0 28 1.5 29 2.0 30 2.0 31 7.0 32 10.5 33 12.5 34 14.5 35 17.5 36 26.0 37 33.0 38 37.5 39 49.5 40 72.5 41 87.0 42 103.5 43 116.5 44 123.0 45 128.0 46 131.5 47 140.5 48 134.5 49 116.5 50 117.5 51 121.0 52 115.0 53 116.0 54 107.5 55 101.0 56 105.0 57 97.0 58 86.0 59 94.0 60 91.5 61 80.0 62 90.5 63 94.0 64 90.5 65 98.5 66 92.0 67 94.0 68 97.0 69 90.0 70 97.0 71 90.0 72 80.5 73 71.0 74 59.0 75 55.0 76 45.0 77 34.5 78 30.0 79 24.0 80 15.5 81 12.0 82 11.5 83 9.0 84 5.5 85 3.5 86 2.0 87 0.5 88 0.5 89 0.5 90 0.0 91 0.0 92 0.0 93 0.0 94 0.0 95 0.5 96 0.5 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 0.05 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 0.0 >>END_MODULE >>Sequence Length Distribution pass #Length Count 150 4000.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 93.45 #Duplication Level Percentage of deduplicated Percentage of total 1 93.39218833600856 87.275 2 6.233279828785446 11.65 3 0.3477795612627073 0.975 4 0.026752273943285176 0.1 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 0.0125 0.0 0.0 0.0 0.0 30-31 0.025 0.0 0.0 0.0 0.0 32-33 0.025 0.0 0.0 0.0 0.0 34-35 0.025 0.0 0.0 0.0 0.0 36-37 0.025 0.0 0.0 0.0 0.0 38-39 0.025 0.0 0.0 0.0 0.0 40-41 0.025 0.0 0.0 0.0 0.0 42-43 0.025 0.0 0.0 0.0 0.0 44-45 0.025 0.0 0.0 0.0 0.0 46-47 0.025 0.0 0.0 0.0 0.0 48-49 0.025 0.0 0.0 0.0 0.0 50-51 0.025 0.0 0.0 0.0 0.0 52-53 0.025 0.0 0.0 0.0 0.0 54-55 0.025 0.0 0.0 0.0 0.0 56-57 0.025 0.0 0.0 0.0 0.0 58-59 0.025 0.0 0.0 0.0 0.0 60-61 0.025 0.0 0.0 0.0 0.0 62-63 0.025 0.0 0.0 0.0 0.0 64-65 0.025 0.0 0.0 0.0 0.0 66-67 0.05 0.0 0.0 0.0 0.0 68-69 0.05 0.0 0.0 0.0 0.0 70-71 0.0625 0.0 0.0 0.0 0.0 72-73 0.0875 0.0 0.0 0.0 0.0 74-75 0.125 0.0 0.0 0.0 0.0 76-77 0.125 0.0 0.0 0.0 0.0 78-79 0.125 0.0 0.0 0.0 0.0 80-81 0.125 0.0 0.0 0.0 0.0 82-83 0.125 0.0 0.0 0.0 0.0 84-85 0.125 0.0 0.0 0.0 0.0 86-87 0.125 0.0 0.0 0.0 0.0 88-89 0.125 0.0 0.0 0.0 0.0 90-91 0.125 0.0 0.0 0.0 0.0 92-93 0.1375 0.0 0.0 0.0 0.0 94-95 0.16249999999999998 0.0 0.0 0.0 0.0 96-97 0.175 0.0 0.0 0.0 0.0 98-99 0.1875 0.0 0.0 0.0 0.0 100-101 0.275 0.0 0.0 0.0 0.0 102-103 0.2875 0.0 0.0 0.0 0.0 104-105 0.3375 0.0 0.0 0.0 0.0 106-107 0.3625 0.0 0.0 0.0 0.0 108-109 0.4 0.0 0.0 0.0 0.0 110-111 0.4 0.0 0.0 0.0 0.0 112-113 0.4875 0.0 0.0 0.0 0.0 114-115 0.5 0.0 0.0 0.0 0.0 116-117 0.5125 0.0 0.0 0.0 0.0 118-119 0.55 0.0 0.0 0.0 0.0 120-121 0.575 0.0 0.0 0.0 0.0 122-123 0.6375 0.0 0.0 0.0 0.0 124-125 0.7 0.0 0.0 0.0 0.0 126-127 0.75 0.0 0.0 0.0 0.0 128-129 0.825 0.0 0.0 0.0 0.0 130-131 0.9 0.0 0.0 0.0 0.0 132-133 0.9875 0.0 0.0 0.0 0.0 134-135 1.0125 0.0 0.0 0.0 0.0 136-137 1.1625 0.0 0.0 0.0 0.0 138 1.275 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content pass >>END_MODULE ERR9452527 read2 length is 150 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename ERR9452527_2.fastq File type Conventional base calls Encoding Sanger / Illumina 1.9 Total Sequences 4000 Sequences flagged as poor quality 0 Sequence length 150 %GC 55 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 35.809 37.0 37.0 37.0 37.0 37.0 2 35.8515 37.0 37.0 37.0 37.0 37.0 3 36.021 37.0 37.0 37.0 37.0 37.0 4 35.9815 37.0 37.0 37.0 37.0 37.0 5 36.0075 37.0 37.0 37.0 37.0 37.0 6 35.6785 37.0 37.0 37.0 37.0 37.0 7 36.045 37.0 37.0 37.0 37.0 37.0 8 35.771 37.0 37.0 37.0 37.0 37.0 9 35.8255 37.0 37.0 37.0 37.0 37.0 10-14 35.8822 37.0 37.0 37.0 37.0 37.0 15-19 35.8149 37.0 37.0 37.0 37.0 37.0 20-24 35.7928 37.0 37.0 37.0 37.0 37.0 25-29 35.7308 37.0 37.0 37.0 37.0 37.0 30-34 35.7417 37.0 37.0 37.0 37.0 37.0 35-39 35.7098 37.0 37.0 37.0 37.0 37.0 40-44 35.846000000000004 37.0 37.0 37.0 37.0 37.0 45-49 35.782000000000004 37.0 37.0 37.0 37.0 37.0 50-54 35.6863 37.0 37.0 37.0 37.0 37.0 55-59 35.5887 37.0 37.0 37.0 37.0 37.0 60-64 35.6743 37.0 37.0 37.0 37.0 37.0 65-69 35.677699999999994 37.0 37.0 37.0 37.0 37.0 70-74 35.5629 37.0 37.0 37.0 37.0 37.0 75-79 35.6255 37.0 37.0 37.0 37.0 37.0 80-84 35.5492 37.0 37.0 37.0 37.0 37.0 85-89 35.5471 37.0 37.0 37.0 37.0 37.0 90-94 35.5722 37.0 37.0 37.0 37.0 37.0 95-99 35.47089999999999 37.0 37.0 37.0 37.0 37.0 100-104 35.3777 37.0 37.0 37.0 34.6 37.0 105-109 35.3729 37.0 37.0 37.0 37.0 37.0 110-114 35.0717 37.0 37.0 37.0 27.4 37.0 115-119 35.25500000000001 37.0 37.0 37.0 29.8 37.0 120-124 35.0869 37.0 37.0 37.0 27.4 37.0 125-129 35.2396 37.0 37.0 37.0 29.8 37.0 130-134 35.2056 37.0 37.0 37.0 27.4 37.0 135-139 35.0255 37.0 37.0 37.0 25.0 37.0 140-144 34.908699999999996 37.0 37.0 37.0 25.0 37.0 145-149 34.7256 37.0 37.0 37.0 25.0 37.0 150 35.016 37.0 37.0 37.0 25.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 15 1.0 16 1.0 17 2.0 18 0.0 19 1.0 20 1.0 21 2.0 22 3.0 23 5.0 24 7.0 25 14.0 26 16.0 27 26.0 28 33.0 29 40.0 30 57.0 31 61.0 32 104.0 33 142.0 34 262.0 35 713.0 36 2410.0 37 99.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 27.63881940970485 13.506753376688344 14.85742871435718 43.99699849924962 2 29.575000000000003 20.925 26.075 23.425 3 27.05 27.3 18.575 27.075 4 29.95 29.275000000000002 15.049999999999999 25.724999999999998 5 29.049999999999997 30.025000000000002 19.175 21.75 6 21.9 32.775 19.175 26.150000000000002 7 20.674999999999997 13.200000000000001 37.925 28.199999999999996 8 23.599999999999998 17.525 23.974999999999998 34.9 9 25.8 17.424999999999997 27.200000000000003 29.575000000000003 10-14 25.974999999999998 23.65 21.8 28.575 15-19 26.695 22.055 23.044999999999998 28.205000000000002 20-24 26.665 23.380000000000003 22.695 27.26 25-29 26.334999999999997 23.225 22.23 28.21 30-34 26.685 23.145 22.439999999999998 27.73 35-39 26.38 23.23 22.09 28.299999999999997 40-44 26.810000000000002 23.150000000000002 22.43 27.61 45-49 26.865 22.975 21.745 28.415000000000003 50-54 26.88 22.795 22.585 27.74 55-59 27.46 22.195 22.155 28.189999999999998 60-64 27.07 22.400000000000002 22.06 28.470000000000002 65-69 27.075 22.470000000000002 21.94 28.515 70-74 27.48 22.3 21.945 28.275 75-79 27.025 22.17 22.2 28.605000000000004 80-84 27.79 22.15 21.915000000000003 28.144999999999996 85-89 27.555000000000003 22.055 21.725 28.665000000000003 90-94 27.275 22.035 22.165000000000003 28.525 95-99 28.035 22.025 21.82 28.12 100-104 27.49 22.405 22.28 27.825 105-109 28.084999999999997 21.279999999999998 22.08 28.555000000000003 110-114 28.815 22.63 21.529999999999998 27.025 115-119 28.544999999999998 22.235 21.105 28.115000000000002 120-124 28.035 21.59 21.725 28.65 125-129 28.255000000000003 22.41 21.45 27.884999999999998 130-134 27.77 21.57 22.439999999999998 28.22 135-139 28.084999999999997 21.965 21.5 28.449999999999996 140-144 28.665000000000003 21.67 21.735 27.93 145-149 28.65 21.345 21.995 28.01 150 27.575 22.525000000000002 23.325000000000003 26.575 >>END_MODULE >>Per sequence GC content fail #GC Content Count 0 1.0 1 0.5 2 0.5 3 0.5 4 0.0 5 0.5 6 0.5 7 0.5 8 0.5 9 0.0 10 0.5 11 0.5 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 0.5 25 0.5 26 0.0 27 0.5 28 2.0 29 2.0 30 3.0 31 7.5 32 8.5 33 10.5 34 17.0 35 24.5 36 31.5 37 37.5 38 46.0 39 54.0 40 65.0 41 79.5 42 99.5 43 111.5 44 116.5 45 128.0 46 143.5 47 146.5 48 139.0 49 135.5 50 128.0 51 125.0 52 128.0 53 119.5 54 112.0 55 111.0 56 100.5 57 94.5 58 87.5 59 97.0 60 94.0 61 83.0 62 98.0 63 96.5 64 88.0 65 80.5 66 81.5 67 84.5 68 84.5 69 86.5 70 83.5 71 83.5 72 73.0 73 54.5 74 54.0 75 55.0 76 44.5 77 36.5 78 27.0 79 22.0 80 18.5 81 14.5 82 12.0 83 8.5 84 6.5 85 3.0 86 2.0 87 2.0 88 1.5 89 1.0 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 0.5 99 0.5 100 0.5 >>END_MODULE >>Per base N content pass #Base N-Count 1 0.05 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 0.0 >>END_MODULE >>Sequence Length Distribution pass #Length Count 150 4000.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 93.65 #Duplication Level Percentage of deduplicated Percentage of total 1 93.78003203416978 87.825 2 5.712760277629472 10.7 3 0.4538174052322477 1.275 4 0.05339028296849973 0.2 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 0.0125 0.0 0.0 0.0 0.0 30-31 0.025 0.0 0.0 0.0 0.0 32-33 0.025 0.0 0.0 0.0 0.0 34-35 0.025 0.0 0.0 0.0 0.0 36-37 0.025 0.0 0.0 0.0 0.0 38-39 0.025 0.0 0.0 0.0 0.0 40-41 0.025 0.0 0.0 0.0 0.0 42-43 0.025 0.0 0.0 0.0 0.0 44-45 0.025 0.0 0.0 0.0 0.0 46-47 0.025 0.0 0.0 0.0 0.0 48-49 0.025 0.0 0.0 0.0 0.0 50-51 0.025 0.0 0.0 0.0 0.0 52-53 0.025 0.0 0.0 0.0 0.0 54-55 0.025 0.0 0.0 0.0 0.0 56-57 0.025 0.0 0.0 0.0 0.0 58-59 0.025 0.0 0.0 0.0 0.0 60-61 0.025 0.0 0.0 0.0 0.0 62-63 0.025 0.0 0.0 0.0 0.0 64-65 0.025 0.0 0.0 0.0 0.0 66-67 0.05 0.0 0.0 0.0 0.0 68-69 0.05 0.0 0.0 0.0 0.0 70-71 0.0625 0.0 0.0 0.0 0.0 72-73 0.0875 0.0 0.0 0.0 0.0 74-75 0.125 0.0 0.0 0.0 0.0 76-77 0.125 0.0 0.0 0.0 0.0 78-79 0.125 0.0 0.0 0.0 0.0 80-81 0.125 0.0 0.0 0.0 0.0 82-83 0.125 0.0 0.0 0.0 0.0 84-85 0.125 0.0 0.0 0.0 0.0 86-87 0.125 0.0 0.0 0.0 0.0 88-89 0.125 0.0 0.0 0.0 0.0 90-91 0.125 0.0 0.0 0.0 0.0 92-93 0.1375 0.0 0.0 0.0 0.0 94-95 0.16249999999999998 0.0 0.0 0.0 0.0 96-97 0.175 0.0 0.0 0.0 0.0 98-99 0.1875 0.0 0.0 0.0 0.0 100-101 0.225 0.0 0.0 0.0 0.0 102-103 0.2375 0.0 0.0 0.0 0.0 104-105 0.2875 0.0 0.0 0.0 0.0 106-107 0.3125 0.0 0.0 0.0 0.0 108-109 0.35 0.0 0.0 0.0 0.0 110-111 0.35 0.0 0.0 0.0 0.0 112-113 0.425 0.0 0.0 0.0 0.0 114-115 0.425 0.0 0.0 0.0 0.0 116-117 0.425 0.0 0.0 0.0 0.0 118-119 0.45 0.0 0.0 0.0 0.0 120-121 0.475 0.0 0.0 0.0 0.0 122-123 0.5375000000000001 0.0 0.0 0.0 0.0 124-125 0.6 0.0 0.0 0.0 0.0 126-127 0.625 0.0 0.0 0.0 0.0 128-129 0.725 0.0 0.0 0.0 0.0 130-131 0.8 0.0 0.0 0.0 0.0 132-133 0.8875 0.0 0.0 0.0 0.0 134-135 0.9125000000000001 0.0 0.0 0.0 0.0 136-137 1.025 0.0 0.0 0.0 0.0 138 1.075 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position TTGCTCT 10 0.006973645 144.0 3 >>END_MODULE Read 1285275 spots for ERR9452527.sra Written 1285275 spots for ERR9452527.sra Read 1285275 spots for ERR9452527.sra Written 1285275 spots for ERR9452527.sra Read 1285275 spots for ERR9452527.sra Written 1285275 spots for ERR9452527.sra Read 1285275 spots for ERR9452527.sra Written 1285275 spots for ERR9452527.sra Read 1285275 spots for ERR9452527.sra Written 1285275 spots for ERR9452527.sra Read 1285275 spots for ERR9452527.sra Written 1285275 spots for ERR9452527.sra Read 1285275 spots for ERR9452527.sra Written 1285275 spots for ERR9452527.sra Read 1285275 spots for ERR9452527.sra Written 1285275 spots for ERR9452527.sra Read 1285275 spots for ERR9452527.sra Written 1285275 spots for ERR9452527.sra Read 1285275 spots for ERR9452527.sra Written 1285275 spots for ERR9452527.sra Read 1285275 spots for ERR9452527.sra Written 1285275 spots for ERR9452527.sra Read 1285275 spots for ERR9452527.sra Written 1285275 spots for ERR9452527.sra Read 1285275 spots for ERR9452527.sra Written 1285275 spots for ERR9452527.sra Read 1285275 spots for ERR9452527.sra Written 1285275 spots for ERR9452527.sra Read 1285275 spots for ERR9452527.sra Written 1285275 spots for ERR9452527.sra Read 1285275 spots for ERR9452527.sra Written 1285275 spots for ERR9452527.sra Read 1285275 spots for ERR9452527.sra Written 1285275 spots for ERR9452527.sra Read 1285277 spots for ERR9452527.sra Written 1285277 spots for ERR9452527.sra Read 1285275 spots for ERR9452527.sra Written 1285275 spots for ERR9452527.sra Read 1285275 spots for ERR9452527.sra Written 1285275 spots for ERR9452527.sra SRR ids: ['ERR9452527.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_ajct6dep ERR9452527.sra spots: 25705502 blocks: [[1, 1285275], [1285276, 2570550], [2570551, 3855825], [3855826, 5141100], [5141101, 6426375], [6426376, 7711650], [7711651, 8996925], [8996926, 10282200], [10282201, 11567475], [11567476, 12852750], [12852751, 14138025], [14138026, 15423300], [15423301, 16708575], [16708576, 17993850], [17993851, 19279125], [19279126, 20564400], [20564401, 21849675], [21849676, 23134950], [23134951, 24420225], [24420226, 25705502]] ERR9452527 file size 8638844 ERR9452527 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 ERR9452527 ERR9452527_1.fastq ERR9452527_2.fastq Input file: ERR9452527_1.fastq Paired file: ERR9452527_2.fastq trimmed: ERR9452527-trimmed-pair1.fastq, ERR9452527-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 Fri Dec 6 23:49:00 2024 >> started Fri Dec 6 23:49:36 2024 >> done (35.765s) 25705502 read pairs processed; of these: 280 ( 0.00%) short read pairs filtered out after trimming by size control 949 ( 0.00%) empty read pairs filtered out after trimming by size control 25704273 (100.00%) read pairs available; of these: 569144 ( 2.21%) trimmed read pairs available after processing 25135129 (97.79%) untrimmed read pairs available after processing Length distribution of reads after trimming: length count percentage 18 14 0.00% 19 22 0.00% 20 114 0.00% 21 19 0.00% 22 22 0.00% 23 17 0.00% 24 18 0.00% 25 19 0.00% 26 28 0.00% 27 35 0.00% 28 50 0.00% 29 54 0.00% 30 124 0.00% 31 61 0.00% 32 31 0.00% 33 33 0.00% 34 44 0.00% 35 41 0.00% 36 37 0.00% 37 31 0.00% 38 39 0.00% 39 43 0.00% 40 58 0.00% 41 53 0.00% 42 50 0.00% 43 72 0.00% 44 62 0.00% 45 65 0.00% 46 80 0.00% 47 74 0.00% 48 89 0.00% 49 113 0.00% 50 144 0.00% 51 147 0.00% 52 147 0.00% 53 149 0.00% 54 169 0.00% 55 177 0.00% 56 223 0.00% 57 264 0.00% 58 305 0.00% 59 331 0.00% 60 319 0.00% 61 398 0.00% 62 401 0.00% 63 405 0.00% 64 495 0.00% 65 531 0.00% 66 519 0.00% 67 632 0.00% 68 601 0.00% 69 748 0.00% 70 732 0.00% 71 750 0.00% 72 828 0.00% 73 843 0.00% 74 879 0.00% 75 940 0.00% 76 981 0.00% 77 1015 0.00% 78 1142 0.00% 79 1235 0.00% 80 1267 0.00% 81 1318 0.01% 82 1437 0.01% 83 1481 0.01% 84 1580 0.01% 85 1592 0.01% 86 1682 0.01% 87 1719 0.01% 88 1853 0.01% 89 1871 0.01% 90 2075 0.01% 91 2066 0.01% 92 2199 0.01% 93 2156 0.01% 94 2383 0.01% 95 2480 0.01% 96 2584 0.01% 97 2700 0.01% 98 2836 0.01% 99 2999 0.01% 100 3099 0.01% 101 3239 0.01% 102 3363 0.01% 103 3654 0.01% 104 3714 0.01% 105 3839 0.01% 106 3920 0.02% 107 4148 0.02% 108 4212 0.02% 109 4408 0.02% 110 4513 0.02% 111 4780 0.02% 112 5012 0.02% 113 5314 0.02% 114 5665 0.02% 115 5847 0.02% 116 6094 0.02% 117 6253 0.02% 118 6538 0.03% 119 6344 0.02% 120 6759 0.03% 121 7298 0.03% 122 7524 0.03% 123 7812 0.03% 124 8212 0.03% 125 8912 0.03% 126 9326 0.04% 127 9605 0.04% 128 10006 0.04% 129 10490 0.04% 130 10811 0.04% 131 11300 0.04% 132 11917 0.05% 133 12014 0.05% 134 12697 0.05% 135 13308 0.05% 136 13880 0.05% 137 14801 0.06% 138 15001 0.06% 139 15754 0.06% 140 16304 0.06% 141 16721 0.07% 142 17472 0.07% 143 18573 0.07% 144 19430 0.08% 145 20264 0.08% 146 21122 0.08% 147 21974 0.09% 148 23485 0.09% 149 24076 0.09% 150 25135129 97.79% 25704273 reads passed initial QC criterion=sequence-density sequence-density=0.23 sequence-density-rank=1 fanout-score=3.25 fanout-score-rank=22 prefix-density=0.26 prefix-fanout=2.9 sequence=GGTGTTGTCGAAGCCGATGATGCGGAC criterion=fanout-score sequence-density=0.06 sequence-density-rank=33 fanout-score=346.20 fanout-score-rank=1 prefix-density=1.06 prefix-fanout=20.3 sequence=GGCGGCGGCGAACCGCCCCCGTCGCCGCGATCCGAACACTTCACCGGACCATTCAATCGGTAGGAGCGACGGGCGGTGTGTACAAAGGGCAGGGACGTAGTCAACGCGAGCTGATGACTCGCGCTTACTAGGCATTCCTCGTTGAAGACCAACAATTGCAATGATCTATCCCCATCACGATGAAATTTCCCAAGATTACCCGGGCCTGTCGGCCAAGGCTATATACTCGTTGAATACATCAGTGTAGCGCGCGTGCGGCCCAGAACATCTAAGGGCATCACAGACCTGTTATTGCCTCAAACTTCCGTCGCCTAAACGGCGATAGTCCCTCTAAGAAGCTAGCTGCGGAGGGATGGCTCCGCATAGCTAGTTAGCAGGCTGAGGTCTCGTTCGTTAACGGAATTAACCAGACAAATCGCTCCACCAACTAAGAACGGCCATGCACCACCACCCATAGAATCAAGAAAGAGCTCTCAGTCTGTCAATCCTTGCTATGTCTGGACCTGGTAAG criterion=sequence-density sequence-density=0.24 sequence-density-rank=1 fanout-score=3.08 fanout-score-rank=24 prefix-density=0.26 prefix-fanout=2.8 sequence=GGTGTTGTCGAAGCCGATGATGCGGAC criterion=fanout-score sequence-density=0.04 sequence-density-rank=37 fanout-score=688.90 fanout-score-rank=1 prefix-density=1.06 prefix-fanout=24.5 sequence=GCGGCGGCGAACCGCCCCCGTCGCCGCGATCCGAACACTTCACCGGACCATTCAATCGGTAGGAGCGACGGGCGGTGTGTACAAAGGGCAGGGACGTAGTCAACGCGAGCTGATGACTCGCGCTTACTAGGCATTCCTCGTTGAAGACCAACAATTGCAATGATCTATCCCCATCACGATGAAATTTCCCAAGATTACCCGGGCCTGTCGGCCAAGGCTATATACTCGTTGAATACATCAGTGTAGCGCGCGTGCGGCCCAGAACATCTAAGGGCATCACAGACCTGTTATTGCCTCAAACTTCCGTCGCCTAAACGGCGATAGTCCCTCTAAGAAGCTAGCTGCGGAGGGATGGCTCCGCATAGCTAGTTAGCAGGCTGAGGTCTCGTTCGTTAACGGAATTAACCAGACAAATCGCTCCACCAACTAAGAACGGCCATGCACCACCACCCATAGAATCAAGAAAGAGCTCTCAGTCTGTCAATCCTTGCTATGTCTGGACCTGGTAAGT ERR9452527 testing PE reads STAR mapping to Ensembl genome Started job on | Dec 06 23:50:43 Started mapping on | Dec 06 23:50:44 Finished on | Dec 06 23:54:42 Mapping speed, Million of reads per hour | 388.80 Number of input reads | 25704273 Average input read length | 299 UNIQUE READS: Uniquely mapped reads number | 23337713 Uniquely mapped reads % | 90.79% Average mapped length | 297.32 Number of splices: Total | 21558298 Number of splices: Annotated (sjdb) | 20351661 Number of splices: GT/AG | 21220255 Number of splices: GC/AG | 273192 Number of splices: AT/AC | 9144 Number of splices: Non-canonical | 55707 Mismatch rate per base, % | 0.45% Deletion rate per base | 0.03% Deletion average length | 2.97 Insertion rate per base | 0.02% Insertion average length | 2.91 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 430789 % of reads mapped to multiple loci | 1.68% Number of reads mapped to too many loci | 93884 % of reads mapped to too many loci | 0.37% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 3.32% % of reads unmapped: other | 3.84% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 1935771 1935771 1935771 N_multimapping 430789 430789 430789 N_noFeature 838080 11814901 11926156 N_ambiguous 567228 69383 68742 UnstrandedReadsAssigned:21932405 PositiveStrandReadsAssigned:11453429 NegativeStrandReadsAssigned:11342815 Dataset is classified unstranded MeadianReadLen=150 20thPercentileLength=150 echo kmer=145 ERR9452527 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: ERR9452527-trimmed-pair1.fastq ERR9452527-trimmed-pair2.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 25,704,273 reads, 22,923,220 reads pseudoaligned [quant] estimated average fragment length: 256.395 [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,138 rounds 52973 ERR9452527.ke.tsv 35125 ERR9452527.se.tsv 88098 total ==> ERR9452527.ke.tsv <== target_id length eff_length est_counts tpm PNS24245 936 680.943 0 0 PNS24247 1044 788.605 58.6013 4.08803 PNS24249 1928 1672.61 478.499 15.7382 PNS24246 1044 788.605 58.6013 4.08803 PNS24248 1044 788.605 58.6013 4.08803 PNS24244 1471 1215.61 46.6966 2.11329 PNS24243 293 67.4867 22 17.9337 KQK14069 1603 1347.61 16511 674.025 KQK14071 474 225.579 1691.54 412.526 ==> ERR9452527.se.tsv <== BRADI_1g14170v3 20435 BRADI_1g53295v3 720 BRADI_1g59795v3 84 BRADI_1g07683v3 0 BRADI_1g00485v3 50 BRADI_1g20270v3 1034 BRADI_1g74790v3 1075 BRADI_1g09890v3 1 BRADI_1g77505v3 479 BRADI_1g48960v3 0 ERR9452527 completed mapping pipeline successfully