Starting /dee2/code/volunteer_pipeline.sh ERR9452515 current disk space = 1547791536128 free memory = 1599934448 ERR9452515 SRAfilesize 1eb8d48f7ae81a3a2f3db70550e5d77e ERR9452515.sra ERR9452515.sra file validated ERR9452515 is paired end ERR9452515 is conventional basespace ERR9452515 read1 length is 150 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename ERR9452515_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 36.365 37.0 37.0 37.0 37.0 37.0 2 36.4325 37.0 37.0 37.0 37.0 37.0 3 36.67 37.0 37.0 37.0 37.0 37.0 4 36.6985 37.0 37.0 37.0 37.0 37.0 5 36.678 37.0 37.0 37.0 37.0 37.0 6 36.627 37.0 37.0 37.0 37.0 37.0 7 36.6575 37.0 37.0 37.0 37.0 37.0 8 36.7155 37.0 37.0 37.0 37.0 37.0 9 36.7135 37.0 37.0 37.0 37.0 37.0 10-14 36.7135 37.0 37.0 37.0 37.0 37.0 15-19 36.6917 37.0 37.0 37.0 37.0 37.0 20-24 36.656 37.0 37.0 37.0 37.0 37.0 25-29 36.6292 37.0 37.0 37.0 37.0 37.0 30-34 36.6247 37.0 37.0 37.0 37.0 37.0 35-39 36.574999999999996 37.0 37.0 37.0 37.0 37.0 40-44 36.5456 37.0 37.0 37.0 37.0 37.0 45-49 36.52890000000001 37.0 37.0 37.0 37.0 37.0 50-54 36.541599999999995 37.0 37.0 37.0 37.0 37.0 55-59 36.4683 37.0 37.0 37.0 37.0 37.0 60-64 36.4716 37.0 37.0 37.0 37.0 37.0 65-69 36.3836 37.0 37.0 37.0 37.0 37.0 70-74 36.412600000000005 37.0 37.0 37.0 37.0 37.0 75-79 36.41850000000001 37.0 37.0 37.0 37.0 37.0 80-84 36.4114 37.0 37.0 37.0 37.0 37.0 85-89 36.3865 37.0 37.0 37.0 37.0 37.0 90-94 36.3657 37.0 37.0 37.0 37.0 37.0 95-99 36.3554 37.0 37.0 37.0 37.0 37.0 100-104 36.288599999999995 37.0 37.0 37.0 37.0 37.0 105-109 36.3351 37.0 37.0 37.0 37.0 37.0 110-114 36.2984 37.0 37.0 37.0 37.0 37.0 115-119 36.2382 37.0 37.0 37.0 37.0 37.0 120-124 36.2331 37.0 37.0 37.0 37.0 37.0 125-129 36.185500000000005 37.0 37.0 37.0 37.0 37.0 130-134 36.23819999999999 37.0 37.0 37.0 37.0 37.0 135-139 36.134 37.0 37.0 37.0 37.0 37.0 140-144 36.1468 37.0 37.0 37.0 37.0 37.0 145-149 36.1747 37.0 37.0 37.0 37.0 37.0 150 36.113 37.0 37.0 37.0 37.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 20 1.0 21 1.0 22 3.0 23 1.0 24 3.0 25 4.0 26 13.0 27 10.0 28 5.0 29 19.0 30 19.0 31 23.0 32 28.0 33 51.0 34 64.0 35 175.0 36 2748.0 37 832.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 29.06860290435653 13.044566850275412 15.12268402603906 42.76414621932899 2 28.125 21.525 29.15 21.2 3 27.224999999999998 25.05 19.3 28.425 4 30.25 29.425 15.25 25.074999999999996 5 28.000000000000004 28.925 19.325 23.75 6 21.25 31.724999999999998 20.65 26.375 7 19.900000000000002 12.725 38.574999999999996 28.799999999999997 8 23.849999999999998 17.575 23.925 34.65 9 22.875 18.15 26.35 32.625 10-14 26.474999999999998 23.225 21.935 28.365000000000002 15-19 26.455000000000002 22.545 22.525000000000002 28.475 20-24 27.245 22.43 21.865000000000002 28.46 25-29 27.11271127112711 22.737273727372738 22.142214221422144 28.007800780078007 30-34 27.384999999999998 22.634999999999998 22.07 27.91 35-39 27.07 22.31 22.75 27.87 40-44 27.435 22.134999999999998 22.495 27.935 45-49 27.07 22.025 21.995 28.910000000000004 50-54 27.465 21.925 22.63 27.98 55-59 27.810000000000002 22.31 21.57 28.310000000000002 60-64 26.740000000000002 22.355 22.205 28.7 65-69 27.715 22.259999999999998 21.47 28.555000000000003 70-74 27.48 22.115000000000002 21.805 28.599999999999998 75-79 27.495000000000005 22.49 21.495 28.52 80-84 27.27 22.025 22.264999999999997 28.439999999999998 85-89 27.655 22.275 21.84 28.23 90-94 27.765 21.95 22.085 28.199999999999996 95-99 27.750000000000004 22.485 21.755 28.01 100-104 27.839999999999996 22.770000000000003 21.545 27.845 105-109 28.48 21.945 21.93 27.644999999999996 110-114 27.975 21.790000000000003 22.08 28.155 115-119 27.74 21.675 22.03 28.555000000000003 120-124 28.075 22.35 21.959999999999997 27.615000000000002 125-129 27.97 21.855 21.87 28.305000000000003 130-134 28.139999999999997 22.245 21.72 27.894999999999996 135-139 27.485 22.415 21.795 28.305000000000003 140-144 28.595 21.94 21.875 27.589999999999996 145-149 28.38 22.1 21.12 28.4 150 28.1 21.8 22.775000000000002 27.325 >>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 0.0 23 0.0 24 0.5 25 1.0 26 0.5 27 0.0 28 0.5 29 2.5 30 2.5 31 5.5 32 11.5 33 13.0 34 17.0 35 23.5 36 30.5 37 38.5 38 51.0 39 67.0 40 72.0 41 83.5 42 96.5 43 108.5 44 125.0 45 127.5 46 129.0 47 137.0 48 131.5 49 122.5 50 130.0 51 127.5 52 108.0 53 101.0 54 105.5 55 96.0 56 87.5 57 99.0 58 94.0 59 84.0 60 92.0 61 82.0 62 92.0 63 105.0 64 94.5 65 91.0 66 96.5 67 98.5 68 87.5 69 93.0 70 86.0 71 72.5 72 73.0 73 67.0 74 60.5 75 54.5 76 49.5 77 41.5 78 34.0 79 26.5 80 17.0 81 15.0 82 12.5 83 8.0 84 6.0 85 5.0 86 4.0 87 2.0 88 1.5 89 0.5 90 0.5 91 0.5 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 0.15 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 0.01 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 91.7 #Duplication Level Percentage of deduplicated Percentage of total 1 92.23009814612868 84.575 2 6.652126499454744 12.2 3 0.9541984732824428 2.625 4 0.16357688113413305 0.6 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 0.025 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 0.025 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 0.05 0.0 0.0 0.0 0.0 60-61 0.05 0.0 0.0 0.0 0.0 62-63 0.05 0.0 0.0 0.0 0.0 64-65 0.05 0.0 0.0 0.0 0.0 66-67 0.0625 0.0 0.0 0.0 0.0 68-69 0.075 0.0 0.0 0.0 0.0 70-71 0.075 0.0 0.0 0.0 0.0 72-73 0.075 0.0 0.0 0.0 0.0 74-75 0.075 0.0 0.0 0.0 0.0 76-77 0.075 0.0 0.0 0.0 0.0 78-79 0.075 0.0 0.0 0.0 0.0 80-81 0.075 0.0 0.0 0.0 0.0 82-83 0.075 0.0 0.0 0.0 0.0 84-85 0.075 0.0 0.0 0.0 0.0 86-87 0.075 0.0 0.0 0.0 0.0 88-89 0.1125 0.0 0.0 0.0 0.0 90-91 0.15 0.0 0.0 0.0 0.0 92-93 0.1875 0.0 0.0 0.0 0.0 94-95 0.2 0.0 0.0 0.0 0.0 96-97 0.2 0.0 0.0 0.0 0.0 98-99 0.2 0.0 0.0 0.0 0.0 100-101 0.2 0.0 0.0 0.0 0.0 102-103 0.21250000000000002 0.0 0.0 0.0 0.0 104-105 0.225 0.0 0.0 0.0 0.0 106-107 0.225 0.0 0.0 0.0 0.0 108-109 0.225 0.0 0.0 0.0 0.0 110-111 0.275 0.0 0.0 0.0 0.0 112-113 0.3375 0.0 0.0 0.0 0.0 114-115 0.375 0.0 0.0 0.0 0.0 116-117 0.4 0.0 0.0 0.0 0.0 118-119 0.4 0.0 0.0 0.0 0.0 120-121 0.5874999999999999 0.0 0.0 0.0 0.0 122-123 0.675 0.0 0.0 0.0 0.0 124-125 0.7625 0.0 0.0 0.0 0.0 126-127 0.825 0.0 0.0 0.0 0.0 128-129 0.9125000000000001 0.0 0.0 0.0 0.0 130-131 1.05 0.0 0.0 0.0 0.0 132-133 1.25 0.0 0.0 0.0 0.0 134-135 1.4375 0.0 0.0 0.0 0.0 136-137 1.4875 0.0 0.0 0.0 0.0 138 1.575 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position GCGCGCT 10 0.006973645 144.0 8 >>END_MODULE ERR9452515 read2 length is 150 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename ERR9452515_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 35.7955 37.0 37.0 37.0 37.0 37.0 2 36.807 37.0 37.0 37.0 37.0 37.0 3 36.7395 37.0 37.0 37.0 37.0 37.0 4 36.708 37.0 37.0 37.0 37.0 37.0 5 36.7485 37.0 37.0 37.0 37.0 37.0 6 36.7145 37.0 37.0 37.0 37.0 37.0 7 36.707 37.0 37.0 37.0 37.0 37.0 8 36.6925 37.0 37.0 37.0 37.0 37.0 9 36.727 37.0 37.0 37.0 37.0 37.0 10-14 36.658300000000004 37.0 37.0 37.0 37.0 37.0 15-19 36.6698 37.0 37.0 37.0 37.0 37.0 20-24 36.590799999999994 37.0 37.0 37.0 37.0 37.0 25-29 36.4623 37.0 37.0 37.0 37.0 37.0 30-34 36.4543 37.0 37.0 37.0 37.0 37.0 35-39 36.4211 37.0 37.0 37.0 37.0 37.0 40-44 36.4092 37.0 37.0 37.0 37.0 37.0 45-49 36.395799999999994 37.0 37.0 37.0 37.0 37.0 50-54 36.3623 37.0 37.0 37.0 37.0 37.0 55-59 36.3718 37.0 37.0 37.0 37.0 37.0 60-64 36.4418 37.0 37.0 37.0 37.0 37.0 65-69 36.354 37.0 37.0 37.0 37.0 37.0 70-74 36.2484 37.0 37.0 37.0 37.0 37.0 75-79 36.241499999999995 37.0 37.0 37.0 37.0 37.0 80-84 36.4085 37.0 37.0 37.0 37.0 37.0 85-89 36.3095 37.0 37.0 37.0 37.0 37.0 90-94 36.3519 37.0 37.0 37.0 37.0 37.0 95-99 36.3509 37.0 37.0 37.0 37.0 37.0 100-104 36.35529999999999 37.0 37.0 37.0 37.0 37.0 105-109 36.318 37.0 37.0 37.0 37.0 37.0 110-114 36.326 37.0 37.0 37.0 37.0 37.0 115-119 36.267700000000005 37.0 37.0 37.0 37.0 37.0 120-124 36.231700000000004 37.0 37.0 37.0 37.0 37.0 125-129 36.298700000000004 37.0 37.0 37.0 37.0 37.0 130-134 36.2047 37.0 37.0 37.0 37.0 37.0 135-139 36.1947 37.0 37.0 37.0 37.0 37.0 140-144 36.174600000000005 37.0 37.0 37.0 37.0 37.0 145-149 36.194100000000006 37.0 37.0 37.0 37.0 37.0 150 36.272 37.0 37.0 37.0 37.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 20 1.0 21 0.0 22 1.0 23 4.0 24 5.0 25 4.0 26 6.0 27 4.0 28 9.0 29 7.0 30 12.0 31 12.0 32 10.0 33 38.0 34 69.0 35 274.0 36 3209.0 37 335.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 28.00616649537513 13.489208633093524 15.853031860226105 42.65159301130524 2 26.825 21.025 28.675 23.474999999999998 3 28.425 24.8 18.8 27.975 4 30.95 28.749999999999996 15.4 24.9 5 28.599999999999998 29.4 17.9 24.099999999999998 6 23.200000000000003 31.45 18.775 26.575 7 21.025 13.5 36.925000000000004 28.549999999999997 8 22.35 18.75 24.95 33.95 9 24.5 18.85 26.75 29.9 10-14 26.965 23.115 22.25 27.67 15-19 26.895000000000003 22.13 22.67 28.305000000000003 20-24 26.87 22.96 22.485 27.685 25-29 26.255 22.645 22.830000000000002 28.27 30-34 27.735 22.655 22.435 27.175 35-39 27.055 22.575 22.115000000000002 28.255000000000003 40-44 27.185 22.46 22.259999999999998 28.095 45-49 27.439999999999998 22.07 22.305 28.185 50-54 27.575 22.36 21.88 28.185 55-59 27.644999999999996 21.82 22.05 28.485 60-64 27.439999999999998 22.06 22.295 28.205000000000002 65-69 27.66 22.615 21.855 27.87 70-74 27.884999999999998 22.1 21.515 28.499999999999996 75-79 27.544999999999998 22.055 21.97 28.43 80-84 28.01 21.959999999999997 21.915000000000003 28.115000000000002 85-89 28.389999999999997 22.58 21.15 27.88 90-94 27.525 22.245 21.73 28.499999999999996 95-99 27.779999999999998 22.415 21.86 27.944999999999997 100-104 28.549999999999997 21.65 22.0 27.800000000000004 105-109 27.805000000000003 22.25 21.98 27.965 110-114 28.625 21.515 22.13 27.73 115-119 28.09 21.695 22.145 28.07 120-124 27.950000000000003 21.72 22.31 28.02 125-129 28.24 21.86 22.02 27.88 130-134 28.705000000000002 21.87 22.27 27.155 135-139 28.185 21.725 22.509999999999998 27.58 140-144 28.689999999999998 21.990000000000002 22.095000000000002 27.224999999999998 145-149 29.15 22.29 21.790000000000003 26.77 150 27.875 21.925 22.625 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 0.0 13 0.0 14 0.0 15 0.0 16 0.5 17 0.5 18 0.0 19 0.5 20 1.0 21 0.5 22 0.0 23 0.0 24 0.0 25 0.0 26 1.0 27 1.0 28 1.0 29 1.5 30 3.0 31 7.5 32 12.0 33 13.0 34 16.0 35 21.0 36 26.5 37 38.0 38 53.0 39 66.0 40 74.5 41 82.0 42 91.0 43 108.0 44 118.0 45 129.5 46 150.0 47 136.5 48 115.5 49 117.5 50 122.5 51 114.5 52 99.5 53 107.5 54 109.5 55 101.0 56 98.5 57 91.0 58 92.5 59 92.5 60 89.5 61 109.5 62 119.0 63 101.5 64 94.0 65 92.0 66 89.5 67 96.5 68 90.0 69 87.0 70 95.5 71 85.5 72 77.0 73 68.5 74 50.0 75 42.5 76 38.5 77 34.0 78 35.5 79 25.0 80 14.5 81 14.0 82 11.0 83 8.0 84 7.0 85 4.0 86 2.0 87 2.0 88 1.0 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 2.7 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 92.025 #Duplication Level Percentage of deduplicated Percentage of total 1 92.42053789731052 85.05 2 6.628633523499048 12.2 3 0.8149959250203749 2.25 4 0.1358326541700625 0.5 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 0.025 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 0.025 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 0.05 0.0 0.0 0.0 0.0 60-61 0.05 0.0 0.0 0.0 0.0 62-63 0.05 0.0 0.0 0.0 0.0 64-65 0.05 0.0 0.0 0.0 0.0 66-67 0.07500000000000001 0.0 0.0 0.0 0.0 68-69 0.1 0.0 0.0 0.0 0.0 70-71 0.1 0.0 0.0 0.0 0.0 72-73 0.1 0.0 0.0 0.0 0.0 74-75 0.1 0.0 0.0 0.0 0.0 76-77 0.1 0.0 0.0 0.0 0.0 78-79 0.1 0.0 0.0 0.0 0.0 80-81 0.1 0.0 0.0 0.0 0.0 82-83 0.1 0.0 0.0 0.0 0.0 84-85 0.1 0.0 0.0 0.0 0.0 86-87 0.1 0.0 0.0 0.0 0.0 88-89 0.1375 0.0 0.0 0.0 0.0 90-91 0.175 0.0 0.0 0.0 0.0 92-93 0.21250000000000002 0.0 0.0 0.0 0.0 94-95 0.225 0.0 0.0 0.0 0.0 96-97 0.225 0.0 0.0 0.0 0.0 98-99 0.225 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 0.25 0.0 0.0 0.0 0.0 106-107 0.25 0.0 0.0 0.0 0.0 108-109 0.25 0.0 0.0 0.0 0.0 110-111 0.30000000000000004 0.0 0.0 0.0 0.0 112-113 0.3625 0.0 0.0 0.0 0.0 114-115 0.4 0.0 0.0 0.0 0.0 116-117 0.425 0.0 0.0 0.0 0.0 118-119 0.425 0.0 0.0 0.0 0.0 120-121 0.6125 0.0 0.0 0.0 0.0 122-123 0.7124999999999999 0.0 0.0 0.0 0.0 124-125 0.8125 0.0 0.0 0.0 0.0 126-127 0.875 0.0 0.0 0.0 0.0 128-129 0.9624999999999999 0.0 0.0 0.0 0.0 130-131 1.1 0.0 0.0 0.0 0.0 132-133 1.3 0.0 0.0 0.0 0.0 134-135 1.4874999999999998 0.0 0.0 0.0 0.0 136-137 1.5375 0.0 0.0 0.0 0.0 138 1.6 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position CTTGGGT 10 0.0064622764 147.66667 1 >>END_MODULE Read 1606448 spots for ERR9452515.sra Written 1606448 spots for ERR9452515.sra Read 1606448 spots for ERR9452515.sra Written 1606448 spots for ERR9452515.sra Read 1606448 spots for ERR9452515.sra Written 1606448 spots for ERR9452515.sra Read 1606448 spots for ERR9452515.sra Written 1606448 spots for ERR9452515.sra Read 1606448 spots for ERR9452515.sra Written 1606448 spots for ERR9452515.sra Read 1606448 spots for ERR9452515.sra Written 1606448 spots for ERR9452515.sra Read 1606448 spots for ERR9452515.sra Written 1606448 spots for ERR9452515.sra Read 1606448 spots for ERR9452515.sra Written 1606448 spots for ERR9452515.sra Read 1606448 spots for ERR9452515.sra Written 1606448 spots for ERR9452515.sra Read 1606448 spots for ERR9452515.sra Written 1606448 spots for ERR9452515.sra Read 1606448 spots for ERR9452515.sra Written 1606448 spots for ERR9452515.sra Read 1606448 spots for ERR9452515.sra Written 1606448 spots for ERR9452515.sra Read 1606448 spots for ERR9452515.sra Written 1606448 spots for ERR9452515.sra Read 1606448 spots for ERR9452515.sra Written 1606448 spots for ERR9452515.sra Read 1606448 spots for ERR9452515.sra Written 1606448 spots for ERR9452515.sra Read 1606448 spots for ERR9452515.sra Written 1606448 spots for ERR9452515.sra Read 1606448 spots for ERR9452515.sra Written 1606448 spots for ERR9452515.sra Read 1606448 spots for ERR9452515.sra Written 1606448 spots for ERR9452515.sra Read 1606448 spots for ERR9452515.sra Written 1606448 spots for ERR9452515.sra Read 1606448 spots for ERR9452515.sra Written 1606448 spots for ERR9452515.sra SRR ids: ['ERR9452515.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_sp9d4xtn ERR9452515.sra spots: 32128960 blocks: [[1, 1606448], [1606449, 3212896], [3212897, 4819344], [4819345, 6425792], [6425793, 8032240], [8032241, 9638688], [9638689, 11245136], [11245137, 12851584], [12851585, 14458032], [14458033, 16064480], [16064481, 17670928], [17670929, 19277376], [19277377, 20883824], [20883825, 22490272], [22490273, 24096720], [24096721, 25703168], [25703169, 27309616], [27309617, 28916064], [28916065, 30522512], [30522513, 32128960]] ERR9452515 file size 10802998 ERR9452515 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 ERR9452515 ERR9452515_1.fastq ERR9452515_2.fastq Input file: ERR9452515_1.fastq Paired file: ERR9452515_2.fastq trimmed: ERR9452515-trimmed-pair1.fastq, ERR9452515-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 23:08:16 2024 >> started Fri Dec 6 23:08:50 2024 >> done (33.663s) 32128960 read pairs processed; of these: 321 ( 0.00%) short read pairs filtered out after trimming by size control 1602 ( 0.00%) empty read pairs filtered out after trimming by size control 32127037 (99.99%) read pairs available; of these: 863406 ( 2.69%) trimmed read pairs available after processing 31263631 (97.31%) untrimmed read pairs available after processing Length distribution of reads after trimming: length count percentage 18 27 0.00% 19 34 0.00% 20 2324 0.01% 21 53 0.00% 22 43 0.00% 23 33 0.00% 24 38 0.00% 25 46 0.00% 26 43 0.00% 27 55 0.00% 28 43 0.00% 29 77 0.00% 30 107 0.00% 31 102 0.00% 32 75 0.00% 33 62 0.00% 34 57 0.00% 35 87 0.00% 36 64 0.00% 37 73 0.00% 38 80 0.00% 39 65 0.00% 40 84 0.00% 41 75 0.00% 42 85 0.00% 43 67 0.00% 44 88 0.00% 45 85 0.00% 46 96 0.00% 47 106 0.00% 48 115 0.00% 49 121 0.00% 50 148 0.00% 51 162 0.00% 52 184 0.00% 53 205 0.00% 54 193 0.00% 55 209 0.00% 56 217 0.00% 57 271 0.00% 58 275 0.00% 59 324 0.00% 60 319 0.00% 61 393 0.00% 62 453 0.00% 63 441 0.00% 64 491 0.00% 65 487 0.00% 66 504 0.00% 67 531 0.00% 68 612 0.00% 69 659 0.00% 70 735 0.00% 71 769 0.00% 72 813 0.00% 73 878 0.00% 74 911 0.00% 75 1062 0.00% 76 1092 0.00% 77 1101 0.00% 78 1176 0.00% 79 1304 0.00% 80 1438 0.00% 81 1307 0.00% 82 1549 0.00% 83 1582 0.00% 84 1601 0.00% 85 1799 0.01% 86 1808 0.01% 87 2031 0.01% 88 1936 0.01% 89 2181 0.01% 90 2244 0.01% 91 2389 0.01% 92 2597 0.01% 93 2701 0.01% 94 2877 0.01% 95 3066 0.01% 96 3069 0.01% 97 3238 0.01% 98 3407 0.01% 99 3844 0.01% 100 3818 0.01% 101 4364 0.01% 102 4392 0.01% 103 4586 0.01% 104 5042 0.02% 105 5128 0.02% 106 5406 0.02% 107 5643 0.02% 108 5949 0.02% 109 5999 0.02% 110 6482 0.02% 111 6590 0.02% 112 6987 0.02% 113 7541 0.02% 114 7886 0.02% 115 8314 0.03% 116 8702 0.03% 117 8693 0.03% 118 9535 0.03% 119 9971 0.03% 120 10304 0.03% 121 11052 0.03% 122 11505 0.04% 123 12217 0.04% 124 12452 0.04% 125 13695 0.04% 126 14289 0.04% 127 14555 0.05% 128 15355 0.05% 129 15756 0.05% 130 16804 0.05% 131 17156 0.05% 132 18109 0.06% 133 19751 0.06% 134 19959 0.06% 135 20992 0.07% 136 22559 0.07% 137 23758 0.07% 138 24102 0.08% 139 25559 0.08% 140 26517 0.08% 141 27199 0.08% 142 28932 0.09% 143 29838 0.09% 144 30851 0.10% 145 32846 0.10% 146 34485 0.11% 147 35999 0.11% 148 37851 0.12% 149 39838 0.12% 150 31263631 97.31% 32127037 reads passed initial QC criterion=sequence-density sequence-density=0.32 sequence-density-rank=1 fanout-score=2.93 fanout-score-rank=23 prefix-density=0.34 prefix-fanout=2.8 sequence=GGTGTTGTCGAAGCCGATGATGCGGAC criterion=fanout-score sequence-density=0.03 sequence-density-rank=34 fanout-score=774.82 fanout-score-rank=1 prefix-density=1.03 prefix-fanout=22.0 sequence=GCGGCGGCGAACCGCCCCCGTCGCCGCGATCCGAACACTTCACCGGACCATTCAATCGGTAGGAGCGACGGGCGGTGTGTACAAAGGGCAGGGACGTAGTCAACGCGAGCTGATGACTCGCGCTTACTAGGCATTCCTCGTTGAAGACCAACAATTGCAATGATCTATCCCCATCACGATGAAATTTCCCAAGATTACCCGGGCCTGTCGGCCAAGGCTATATACTCGTTGAATACATCAGTGTAGCGCGCGTGCGGCCCAGAACATCTAAGGGCATCACAGACCTGTTATTGCCTCAAACTTCCGTCGCCTAAACGGCGATAGTCCCTCTAAGAAGCTAGCTGCGGAGGGATGGCTCCGCATAGCTAGTTAGCAGGCTGAGGTCTCGTTCGTTAACGGAATTAACCAGACAAATCGCTCCACCAACTAAGAACGGCCATGCACCACCACCCATAGAATCAAGAAAGAGCTCTCAGTCTGTCAATCCTTGCTATGTCTGGACCTGGTAAGT criterion=sequence-density sequence-density=0.33 sequence-density-rank=1 fanout-score=2.90 fanout-score-rank=22 prefix-density=0.34 prefix-fanout=2.8 sequence=GGTGTTGTCGAAGCCGATGATGCGGAC criterion=fanout-score sequence-density=0.14 sequence-density-rank=21 fanout-score=138.67 fanout-score-rank=1 prefix-density=1.06 prefix-fanout=17.7 sequence=GCCGCCGCCGCC ERR9452515 testing PE reads STAR mapping to Ensembl genome Started job on | Dec 06 23:12:13 Started mapping on | Dec 06 23:12:13 Finished on | Dec 06 23:14:29 Mapping speed, Million of reads per hour | 850.42 Number of input reads | 32127037 Average input read length | 298 UNIQUE READS: Uniquely mapped reads number | 30612602 Uniquely mapped reads % | 95.29% Average mapped length | 298.13 Number of splices: Total | 30016971 Number of splices: Annotated (sjdb) | 28301395 Number of splices: GT/AG | 29594108 Number of splices: GC/AG | 379300 Number of splices: AT/AC | 12940 Number of splices: Non-canonical | 30623 Mismatch rate per base, % | 0.11% Deletion rate per base | 0.00% Deletion average length | 1.68 Insertion rate per base | 0.00% Insertion average length | 1.23 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 312252 % of reads mapped to multiple loci | 0.97% Number of reads mapped to too many loci | 101593 % of reads mapped to too many loci | 0.32% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 0.77% % of reads unmapped: other | 2.66% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 1202183 1202183 1202183 N_multimapping 312252 312252 312252 N_noFeature 964955 15421467 15603525 N_ambiguous 729217 91657 91837 UnstrandedReadsAssigned:28918430 PositiveStrandReadsAssigned:15099478 NegativeStrandReadsAssigned:14917240 Dataset is classified unstranded MeadianReadLen=150 20thPercentileLength=150 echo kmer=145 ERR9452515 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: ERR9452515-trimmed-pair1.fastq ERR9452515-trimmed-pair2.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 32,127,037 reads, 29,998,417 reads pseudoaligned [quant] estimated average fragment length: 237.653 [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,244 rounds 52973 ERR9452515.ke.tsv 35125 ERR9452515.se.tsv 88098 total ==> ERR9452515.ke.tsv <== target_id length eff_length est_counts tpm PNS24245 936 699.699 0 0 PNS24247 1044 807.347 21.9554 1.15488 PNS24249 1928 1691.35 444.782 11.1679 PNS24246 1044 807.347 21.9554 1.15488 PNS24248 1044 807.347 21.9554 1.15488 PNS24244 1471 1234.35 21.3522 0.734621 PNS24243 293 69.5054 41 25.0509 KQK14069 1603 1366.35 17224.6 535.361 KQK14071 474 239.677 1375.49 243.72 ==> ERR9452515.se.tsv <== BRADI_1g14170v3 20319 BRADI_1g53295v3 122 BRADI_1g59795v3 731 BRADI_1g07683v3 0 BRADI_1g00485v3 55 BRADI_1g20270v3 1070 BRADI_1g74790v3 566 BRADI_1g09890v3 3 BRADI_1g77505v3 532 BRADI_1g48960v3 0 ERR9452515 completed mapping pipeline successfully