Starting /dee2/code/volunteer_pipeline.sh SRR1797578 current disk space = 1525109764096 free memory = 1583544504 SRR1797578 SRAfilesize 304a9caf34d9911465c6763014ab031a SRR1797578.sra SRR1797578.sra file validated SRR1797578 is paired end SRR1797578 is conventional basespace SRR1797578 read1 length is 150 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR1797578_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 fail #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 32.52925 34.0 34.0 34.0 31.0 34.0 2 33.0965 34.0 34.0 34.0 31.0 34.0 3 33.5065 34.0 34.0 34.0 31.0 34.0 4 36.7685 37.0 37.0 37.0 37.0 37.0 5 36.76225 37.0 37.0 37.0 37.0 37.0 6 36.78925 37.0 37.0 37.0 37.0 37.0 7 36.77475 37.0 37.0 37.0 37.0 37.0 8 36.78725 37.0 37.0 37.0 37.0 37.0 9 38.65125 39.0 39.0 39.0 38.0 39.0 10-14 39.0216 39.4 39.4 39.4 38.6 39.4 15-19 40.30285000000001 41.0 40.4 41.0 39.0 41.0 20-24 40.081399999999995 41.0 40.0 41.0 38.4 41.0 25-29 39.81845 41.0 40.0 41.0 37.6 41.0 30-34 39.637600000000006 41.0 40.0 41.0 36.6 41.0 35-39 39.29235 41.0 39.2 41.0 35.0 41.0 40-44 38.74275 40.8 37.8 41.0 35.0 41.0 45-49 38.222750000000005 40.0 35.8 41.0 34.8 41.0 50-54 37.67105 39.4 35.0 41.0 33.8 41.0 55-59 36.87755 38.0 35.0 40.8 33.0 41.0 60-64 36.2847 36.4 35.0 40.0 33.0 41.0 65-69 35.76975 35.2 35.0 39.0 33.0 41.0 70-74 34.90509999999999 35.0 35.0 37.0 31.6 39.4 75-79 33.937850000000005 35.0 34.0 35.4 31.0 37.4 80-84 33.65425 35.0 34.0 35.0 30.8 36.4 85-89 32.8243 35.0 33.2 35.0 28.6 35.4 90-94 32.52175 35.0 33.0 35.0 28.2 35.0 95-99 32.17725 35.0 33.0 35.0 27.4 35.0 100-104 31.78665 35.0 32.6 35.0 25.2 35.0 105-109 31.238 34.4 31.6 35.0 24.2 35.0 110-114 30.796699999999998 34.0 31.0 35.0 22.2 35.0 115-119 29.9784 34.0 30.2 35.0 17.8 35.0 120-124 28.771449999999998 33.4 28.6 35.0 8.2 35.0 125-129 27.870600000000003 33.0 26.6 35.0 2.0 35.0 130-134 26.838 32.6 24.4 35.0 2.0 35.0 135-139 25.656349999999996 31.8 21.2 34.0 2.0 35.0 140-144 24.356299999999997 31.0 14.8 34.0 2.0 35.0 145-149 22.2668 30.6 2.0 34.0 2.0 35.0 150 14.465 16.0 2.0 27.0 2.0 32.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 5 1.0 6 0.0 7 4.0 8 5.0 9 2.0 10 5.0 11 4.0 12 3.0 13 4.0 14 4.0 15 9.0 16 8.0 17 9.0 18 20.0 19 16.0 20 17.0 21 20.0 22 24.0 23 29.0 24 50.0 25 49.0 26 57.0 27 65.0 28 89.0 29 114.0 30 141.0 31 164.0 32 231.0 33 312.0 34 380.0 35 671.0 36 977.0 37 516.0 >>END_MODULE >>Per base sequence content warn #Base G A T C 1 31.66192814680796 11.346601188937711 13.543551305246835 43.4479193590075 2 30.875000000000004 10.274999999999999 23.75 35.099999999999994 3 26.450000000000003 11.25 17.775 44.525 4 30.599999999999998 15.45 16.075 37.875 5 31.3 21.475 20.849999999999998 26.375 6 31.974999999999998 20.849999999999998 20.349999999999998 26.825 7 20.9 30.425 27.425 21.25 8 22.8 24.525 27.0 25.674999999999997 9 23.3 19.775000000000002 29.075 27.85 10-14 24.57 25.055 23.665 26.71 15-19 25.183961555789157 23.06152074886119 23.6371827601742 28.117334935175453 20-24 25.8 22.95 23.715 27.534999999999997 25-29 25.380000000000003 23.48 23.435 27.705000000000002 30-34 25.69 23.330000000000002 23.055 27.925 35-39 25.665 22.465 23.565 28.305000000000003 40-44 25.119999999999997 23.04 23.05 28.79 45-49 25.55 22.345000000000002 23.91 28.194999999999997 50-54 25.895000000000003 22.55 23.125 28.43 55-59 26.224999999999998 23.385 21.935 28.455000000000002 60-64 26.529999999999998 22.564999999999998 22.655 28.249999999999996 65-69 26.39 22.919999999999998 22.1 28.59 70-74 26.340000000000003 22.64 22.43 28.59 75-79 26.540000000000003 22.27 22.55 28.64 80-84 26.41 22.02 23.285 28.285 85-89 26.68 22.06 22.535 28.725 90-94 26.435 22.28 22.98 28.305000000000003 95-99 26.55 21.985 22.605 28.860000000000003 100-104 26.695 22.105 22.84 28.360000000000003 105-109 26.419999999999998 21.775 22.865 28.939999999999998 110-114 26.83 22.045 22.295 28.83 115-119 27.125 21.98 22.155 28.74 120-124 27.950000000000003 21.58 22.245 28.225 125-129 27.584999999999997 21.25 22.05 29.115000000000002 130-134 27.800000000000004 21.185000000000002 21.87 29.145 135-139 28.410000000000004 21.335 21.95 28.305000000000003 140-144 28.265 21.175 21.485000000000003 29.075 145-149 28.925 21.38 20.71 28.985 150 29.65 20.599999999999998 17.974999999999998 31.775 >>END_MODULE >>Per sequence GC content fail #GC Content Count 0 0.0 1 0.0 2 0.5 3 1.0 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 0.0 19 0.0 20 0.0 21 0.0 22 0.5 23 0.5 24 0.5 25 0.5 26 0.5 27 0.5 28 0.0 29 0.0 30 1.0 31 2.5 32 4.5 33 7.5 34 11.0 35 18.0 36 28.5 37 35.0 38 47.0 39 66.0 40 82.0 41 95.5 42 104.0 43 125.0 44 148.5 45 158.5 46 151.0 47 143.0 48 148.0 49 146.5 50 140.5 51 138.5 52 136.0 53 125.5 54 99.0 55 80.5 56 90.5 57 94.5 58 92.0 59 87.5 60 82.5 61 79.5 62 78.0 63 75.0 64 71.0 65 77.0 66 90.0 67 95.0 68 92.5 69 89.5 70 75.0 71 66.5 72 63.0 73 59.0 74 52.5 75 42.5 76 41.0 77 36.5 78 26.5 79 19.5 80 17.0 81 12.0 82 12.5 83 15.5 84 9.0 85 3.5 86 2.5 87 1.5 88 0.0 89 0.5 90 0.5 91 0.0 92 0.0 93 0.0 94 0.5 95 0.5 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 3.2750000000000004 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 0.11499999999999999 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 99.55000000000001 #Duplication Level Percentage of deduplicated Percentage of total 1 99.62330487192365 99.175 2 0.3264691109994977 0.65 3 0.025113008538422906 0.075 4 0.025113008538422906 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 0.0 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 0.037500000000000006 0.0 0.0 0.0 0.0 114-115 0.0875 0.0 0.0 0.0 0.0 116-117 0.1375 0.0 0.0 0.0 0.0 118-119 0.25 0.0 0.0 0.0 0.0 120-121 0.3125 0.0 0.0 0.0 0.0 122-123 0.3625 0.0 0.0 0.0 0.0 124-125 0.45 0.0 0.0 0.0 0.0 126-127 0.5625 0.0 0.0 0.0 0.0 128-129 0.6375 0.0 0.0 0.0 0.0 130-131 0.8125 0.0 0.0 0.0 0.0 132-133 1.0875 0.0 0.0 0.0 0.0 134-135 1.45 0.0 0.0 0.0 0.0 136-137 1.8875 0.0 0.0 0.0 0.0 138 2.15 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position ACAGCAG 10 0.0069899606 143.8875 8 CCGAACA 10 0.0069899606 143.8875 4 >>END_MODULE SRR1797578 read2 length is 150 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR1797578_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 fail #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 32.8295 34.0 33.0 34.0 31.0 34.0 2 33.20275 34.0 33.0 34.0 31.0 34.0 3 33.31325 34.0 34.0 34.0 31.0 34.0 4 36.48925 37.0 37.0 37.0 35.0 37.0 5 36.67725 37.0 37.0 37.0 35.0 37.0 6 36.7165 37.0 37.0 37.0 37.0 37.0 7 36.745 37.0 37.0 37.0 37.0 37.0 8 36.69175 37.0 37.0 37.0 37.0 37.0 9 38.618 39.0 39.0 39.0 38.0 39.0 10-14 38.86365 39.4 39.2 39.4 38.2 39.4 15-19 40.1085 41.0 40.0 41.0 38.4 41.0 20-24 39.93435 41.0 40.0 41.0 38.2 41.0 25-29 39.624 41.0 39.6 41.0 37.0 41.0 30-34 38.978049999999996 40.2 38.4 41.0 35.0 41.0 35-39 38.71145 40.2 38.2 41.0 35.0 41.0 40-44 38.24855 40.0 36.4 41.0 34.8 41.0 45-49 37.491699999999994 39.4 35.0 41.0 33.0 41.0 50-54 36.56605 38.2 34.8 40.2 32.4 41.0 55-59 36.1029 36.6 35.0 40.2 32.0 41.0 60-64 35.75125 35.2 35.0 39.4 32.6 41.0 65-69 35.140150000000006 35.0 35.0 38.0 32.0 40.8 70-74 34.35355 35.0 34.6 36.4 31.0 39.0 75-79 33.553650000000005 35.0 34.0 35.2 29.8 37.2 80-84 32.79535 35.0 33.2 35.0 28.2 36.2 85-89 32.37910000000001 35.0 33.0 35.0 27.6 35.2 90-94 31.7695 35.0 32.6 35.0 25.2 35.0 95-99 31.516299999999994 35.0 32.4 35.0 24.6 35.0 100-104 31.018649999999997 34.6 31.6 35.0 23.0 35.0 105-109 30.51215 34.0 31.0 35.0 21.0 35.0 110-114 29.45965 34.0 29.2 35.0 15.4 35.0 115-119 28.99105 34.0 28.6 35.0 8.6 35.0 120-124 28.488450000000007 33.4 27.8 35.0 3.6 35.0 125-129 27.126749999999998 32.8 24.8 35.0 2.0 35.0 130-134 26.24325 32.4 23.4 34.8 2.0 35.0 135-139 24.6762 31.0 18.2 34.0 2.0 35.0 140-144 23.1689 30.2 5.2 34.0 2.0 35.0 145-149 21.352349999999998 29.8 2.0 34.0 2.0 35.0 150 15.2095 18.0 2.0 29.0 2.0 33.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 2 4.0 3 1.0 4 1.0 5 1.0 6 1.0 7 3.0 8 2.0 9 8.0 10 6.0 11 12.0 12 3.0 13 10.0 14 8.0 15 11.0 16 14.0 17 21.0 18 21.0 19 29.0 20 18.0 21 28.0 22 23.0 23 41.0 24 48.0 25 44.0 26 73.0 27 88.0 28 110.0 29 111.0 30 160.0 31 150.0 32 221.0 33 357.0 34 465.0 35 640.0 36 841.0 37 425.0 38 1.0 >>END_MODULE >>Per base sequence content warn #Base G A T C 1 30.002510670348983 17.59979914637208 10.444388651770023 41.95330153150891 2 36.875 22.825 17.1 23.200000000000003 3 24.05 27.075 20.8 28.075 4 28.625 24.725 19.925 26.724999999999998 5 32.475 26.174999999999997 18.224999999999998 23.125 6 24.9 31.674999999999997 17.474999999999998 25.95 7 25.575 17.125 28.825 28.475 8 28.249999999999996 20.65 21.6 29.5 9 27.35 21.15 22.35 29.15 10-14 28.139999999999997 24.135 20.27 27.455000000000002 15-19 27.655 22.79 22.12 27.435 20-24 28.53 23.119999999999997 21.22 27.13 25-29 28.99 23.025000000000002 20.655 27.33 30-34 28.515 23.32 20.955 27.21 35-39 28.105000000000004 23.18 21.65 27.065 40-44 28.754999999999995 22.58 21.355 27.310000000000002 45-49 28.105000000000004 23.215 21.645 27.034999999999997 50-54 28.705000000000002 22.195 21.240000000000002 27.860000000000003 55-59 28.915000000000003 22.305 21.29 27.49 60-64 28.21 22.715 21.345 27.73 65-69 28.71 22.465 21.845 26.979999999999997 70-74 29.599999999999998 22.185 21.205 27.01 75-79 29.115000000000002 22.45 21.759999999999998 26.674999999999997 80-84 28.465 22.655 22.07 26.810000000000002 85-89 28.62 22.33 21.615000000000002 27.435 90-94 28.599999999999998 22.375 21.945 27.08 95-99 29.630000000000003 22.32 21.33 26.72 100-104 28.804999999999996 22.275 21.58 27.339999999999996 105-109 29.085 22.585 21.745 26.584999999999997 110-114 28.685 23.095 21.51 26.71 115-119 28.655 22.245 22.040000000000003 27.060000000000002 120-124 29.01 22.68 21.790000000000003 26.52 125-129 28.83 23.215 21.505 26.450000000000003 130-134 29.4 22.495 21.12 26.985 135-139 29.67 22.49 21.525 26.314999999999998 140-144 30.31 22.575 20.880000000000003 26.235000000000003 145-149 30.294999999999998 23.169999999999998 19.985 26.55 150 32.25 22.725 18.575 26.450000000000003 >>END_MODULE >>Per sequence GC content fail #GC Content Count 0 1.0 1 0.5 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 0.5 16 0.5 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 0.5 27 0.5 28 1.5 29 3.0 30 3.5 31 3.5 32 3.0 33 6.0 34 8.5 35 11.5 36 19.0 37 27.0 38 36.5 39 51.0 40 71.0 41 93.0 42 101.5 43 111.0 44 127.0 45 134.5 46 134.0 47 130.5 48 133.5 49 132.0 50 120.5 51 122.0 52 126.5 53 118.0 54 111.0 55 96.0 56 95.5 57 92.5 58 86.0 59 101.5 60 90.0 61 82.5 62 87.0 63 83.5 64 91.5 65 92.5 66 93.5 67 100.5 68 100.5 69 99.0 70 93.5 71 88.5 72 83.5 73 70.5 74 59.5 75 57.0 76 49.5 77 37.0 78 29.0 79 22.5 80 18.5 81 17.0 82 12.0 83 5.5 84 4.5 85 4.5 86 4.0 87 2.0 88 1.0 89 1.5 90 2.0 91 1.0 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 0.42500000000000004 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 99.65 #Duplication Level Percentage of deduplicated Percentage of total 1 99.64877069744105 99.3 2 0.35122930255895635 0.7000000000000001 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 0.0125 0.0 0.0 0.0 0.0 114-115 0.0625 0.0 0.0 0.0 0.0 116-117 0.1125 0.0 0.0 0.0 0.0 118-119 0.225 0.0 0.0 0.0 0.0 120-121 0.2875 0.0 0.0 0.0 0.0 122-123 0.3375 0.0 0.0 0.0 0.0 124-125 0.4375 0.0 0.0 0.0 0.0 126-127 0.5625 0.0 0.0 0.0 0.0 128-129 0.6375 0.0 0.0 0.0 0.0 130-131 0.8125 0.0 0.0 0.0 0.0 132-133 1.1 0.0 0.0 0.0 0.0 134-135 1.45 0.0 0.0 0.0 0.0 136-137 1.8875 0.0 0.0 0.0 0.0 138 2.175 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content pass >>END_MODULE Read 1119881 spots for SRR1797578.sra Written 1119881 spots for SRR1797578.sra Read 1119881 spots for SRR1797578.sra Written 1119881 spots for SRR1797578.sra Read 1119881 spots for SRR1797578.sra Written 1119881 spots for SRR1797578.sra Read 1119881 spots for SRR1797578.sra Written 1119881 spots for SRR1797578.sra Read 1119881 spots for SRR1797578.sra Written 1119881 spots for SRR1797578.sra Read 1119881 spots for SRR1797578.sra Written 1119881 spots for SRR1797578.sra Read 1119881 spots for SRR1797578.sra Written 1119881 spots for SRR1797578.sra Read 1119881 spots for SRR1797578.sra Written 1119881 spots for SRR1797578.sra Read 1119881 spots for SRR1797578.sra Written 1119881 spots for SRR1797578.sra Read 1119881 spots for SRR1797578.sra Written 1119881 spots for SRR1797578.sra Read 1119881 spots for SRR1797578.sra Written 1119881 spots for SRR1797578.sra Read 1119881 spots for SRR1797578.sra Written 1119881 spots for SRR1797578.sra Read 1119881 spots for SRR1797578.sra Written 1119881 spots for SRR1797578.sra Read 1119881 spots for SRR1797578.sra Written 1119881 spots for SRR1797578.sra Read 1119881 spots for SRR1797578.sra Written 1119881 spots for SRR1797578.sra Read 1119881 spots for SRR1797578.sra Written 1119881 spots for SRR1797578.sra Read 1119881 spots for SRR1797578.sra Written 1119881 spots for SRR1797578.sra Read 1119881 spots for SRR1797578.sra Written 1119881 spots for SRR1797578.sra Read 1119881 spots for SRR1797578.sra Written 1119881 spots for SRR1797578.sra Read 1119888 spots for SRR1797578.sra Written 1119888 spots for SRR1797578.sra SRR ids: ['SRR1797578.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_ozgsx_lk SRR1797578.sra spots: 22397627 blocks: [[1, 1119881], [1119882, 2239762], [2239763, 3359643], [3359644, 4479524], [4479525, 5599405], [5599406, 6719286], [6719287, 7839167], [7839168, 8959048], [8959049, 10078929], [10078930, 11198810], [11198811, 12318691], [12318692, 13438572], [13438573, 14558453], [14558454, 15678334], [15678335, 16798215], [16798216, 17918096], [17918097, 19037977], [19037978, 20157858], [20157859, 21277739], [21277740, 22397627]] SRR1797578 file size 7524375 SRR1797578 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 SRR1797578 SRR1797578_1.fastq SRR1797578_2.fastq Input file: SRR1797578_1.fastq Paired file: SRR1797578_2.fastq trimmed: SRR1797578-trimmed-pair1.fastq, SRR1797578-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 Mon Dec 9 13:22:03 2024 >> started Mon Dec 9 13:22:59 2024 >> done (56.738s) 22397627 read pairs processed; of these: 44873 ( 0.20%) short read pairs filtered out after trimming by size control 30415 ( 0.14%) empty read pairs filtered out after trimming by size control 22322339 (99.66%) read pairs available; of these: 17356580 (77.75%) trimmed read pairs available after processing 4965759 (22.25%) untrimmed read pairs available after processing Length distribution of reads after trimming: length count percentage 18 12 0.00% 19 38 0.00% 20 59 0.00% 21 99 0.00% 22 117 0.00% 23 150 0.00% 24 241 0.00% 25 273 0.00% 26 330 0.00% 27 397 0.00% 28 537 0.00% 29 587 0.00% 30 667 0.00% 31 845 0.00% 32 895 0.00% 33 936 0.00% 34 1076 0.00% 35 1162 0.01% 36 1386 0.01% 37 1354 0.01% 38 1457 0.01% 39 1628 0.01% 40 1718 0.01% 41 1781 0.01% 42 1943 0.01% 43 2075 0.01% 44 2177 0.01% 45 2237 0.01% 46 2530 0.01% 47 2552 0.01% 48 2582 0.01% 49 2683 0.01% 50 2971 0.01% 51 2957 0.01% 52 3274 0.01% 53 3234 0.01% 54 3539 0.02% 55 3683 0.02% 56 3842 0.02% 57 4047 0.02% 58 4278 0.02% 59 4361 0.02% 60 4599 0.02% 61 4994 0.02% 62 5004 0.02% 63 5432 0.02% 64 5590 0.03% 65 5978 0.03% 66 6330 0.03% 67 6516 0.03% 68 7076 0.03% 69 7403 0.03% 70 7716 0.03% 71 8112 0.04% 72 8666 0.04% 73 9301 0.04% 74 9561 0.04% 75 10331 0.05% 76 10932 0.05% 77 11622 0.05% 78 12361 0.06% 79 13077 0.06% 80 13992 0.06% 81 14845 0.07% 82 16190 0.07% 83 17745 0.08% 84 21236 0.10% 85 22039 0.10% 86 23353 0.10% 87 24794 0.11% 88 25372 0.11% 89 27256 0.12% 90 28053 0.13% 91 29173 0.13% 92 30103 0.13% 93 31415 0.14% 94 32346 0.14% 95 33701 0.15% 96 35445 0.16% 97 36112 0.16% 98 37887 0.17% 99 39379 0.18% 100 40173 0.18% 101 41547 0.19% 102 43805 0.20% 103 45651 0.20% 104 47780 0.21% 105 50975 0.23% 106 53920 0.24% 107 58046 0.26% 108 61954 0.28% 109 65506 0.29% 110 68914 0.31% 111 73527 0.33% 112 76768 0.34% 113 80027 0.36% 114 87245 0.39% 115 95022 0.43% 116 101318 0.45% 117 107393 0.48% 118 113021 0.51% 119 121733 0.55% 120 128378 0.58% 121 138394 0.62% 122 145881 0.65% 123 157227 0.70% 124 166403 0.75% 125 174965 0.78% 126 190726 0.85% 127 200074 0.90% 128 214391 0.96% 129 234925 1.05% 130 252148 1.13% 131 267670 1.20% 132 287917 1.29% 133 312619 1.40% 134 326124 1.46% 135 342153 1.53% 136 364374 1.63% 137 386284 1.73% 138 410635 1.84% 139 439044 1.97% 140 471162 2.11% 141 506552 2.27% 142 544410 2.44% 143 591991 2.65% 144 660895 2.96% 145 752166 3.37% 146 888211 3.98% 147 1110934 4.98% 148 1497015 6.71% 149 2984840 13.37% 150 4965759 22.25% 22322339 reads passed initial QC criterion=sequence-density sequence-density=0.31 sequence-density-rank=1 fanout-score=3.64 fanout-score-rank=31 prefix-density=0.33 prefix-fanout=3.4 sequence=TGCCGCACTTGCAGGATGACCCGCAGTTGCAGTTTCCTCCGCAGCAAGACATCTTCGGTCGAGTGCTCGAACTTGCTTAGGAAGAAGATTAAGCTGAAGGCTTCTAGGCTTGTGTGTGC criterion=fanout-score sequence-density=0.05 sequence-density-rank=31 fanout-score=459.00 fanout-score-rank=1 prefix-density=1.03 prefix-fanout=20.9 sequence=GGCGGCGGCGAACCGCCCCCGTCGCCGCGATCCGAACACTTCACCGGACCATTCAATCGGTAGGAGCGACGGGCGGTGTGTACAAAGGGCAGGGACGTAGTCAACGCGAGCTGATGACTCGCGCTTACTAGGCATTCCTCGTTGAAGACCAACAATTGCAATGATCTATCCCCATCACGATGAAATTTCCCAAGATTACCCGGGCCTGTCGGCCAAGGCTATATACTCGTTGAATACATCAGTGTAGCGCGCGTGCGGCCCAGAACATCTAAGGGCATCACAGACCTGTTATTGCCTCAAACTTCCGTCGCCTAAACGGCGATAGTCCCTCTAAGAAGCTAGCTGCGGAGGGATGGCTCCGCATAGCTAGTTAGCAGGCTGAGGTCTCGTTCGTTAACGGAATTAACCAGACAAATCGCTCCACCAACTAAGAACGGCCATGCACCACCACCCATAGAATCAAGAAAGAGCTCTCAGTCTGTCAATCCTTGCTATGTCTGGACCTGGTAAG criterion=sequence-density sequence-density=0.24 sequence-density-rank=1 fanout-score=5.68 fanout-score-rank=22 prefix-density=0.60 prefix-fanout=2.3 sequence=CAAGTGCGGCAGCGGCTGCAACGGCTGCAACATGTACCCTGAAGCCGAGGTCCAGACCTCCAGCCTCCTCGTCGTCGCCACCGCCGCCCACAAGGCGAGCTCCGGCGGGATGGAGATGGCCGCGGAGAACGGCGGCTGCGGCTGCAGCACCTGCAAGTGC criterion=fanout-score sequence-density=0.11 sequence-density-rank=25 fanout-score=319.61 fanout-score-rank=1 prefix-density=1.43 prefix-fanout=25.6 sequence=CGGCGGCGGCAG SRR1797578 testing PE reads STAR mapping to Ensembl genome Started job on | Dec 09 13:25:47 Started mapping on | Dec 09 13:25:48 Finished on | Dec 09 13:27:58 Mapping speed, Million of reads per hour | 618.16 Number of input reads | 22322339 Average input read length | 278 UNIQUE READS: Uniquely mapped reads number | 21187367 Uniquely mapped reads % | 94.92% Average mapped length | 278.21 Number of splices: Total | 16753099 Number of splices: Annotated (sjdb) | 15874644 Number of splices: GT/AG | 16531945 Number of splices: GC/AG | 184518 Number of splices: AT/AC | 10281 Number of splices: Non-canonical | 26355 Mismatch rate per base, % | 0.26% Deletion rate per base | 0.02% Deletion average length | 2.51 Insertion rate per base | 0.01% Insertion average length | 2.36 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 293710 % of reads mapped to multiple loci | 1.32% Number of reads mapped to too many loci | 84008 % of reads mapped to too many loci | 0.38% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 0.83% % of reads unmapped: other | 2.56% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 862163 862163 862163 N_multimapping 293710 293710 293710 N_noFeature 450781 20526172 802196 N_ambiguous 359042 2544 51717 UnstrandedReadsAssigned:20377544 PositiveStrandReadsAssigned:658651 NegativeStrandReadsAssigned:20333454 Dataset is classified negative stranded MeadianReadLen=149 20thPercentileLength=137 echo kmer=133 SRR1797578 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: SRR1797578-trimmed-pair1.fastq SRR1797578-trimmed-pair2.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 22,322,339 reads, 20,485,149 reads pseudoaligned [quant] estimated average fragment length: 208.173 [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,256 rounds 52973 SRR1797578.ke.tsv 35125 SRR1797578.se.tsv 88098 total ==> SRR1797578.ke.tsv <== target_id length eff_length est_counts tpm PNS24245 936 729.018 0 0 PNS24247 1044 836.827 29.1434 2.42256 PNS24249 1928 1720.83 425.683 17.2076 PNS24246 1044 836.827 29.1434 2.42256 PNS24248 1044 836.827 29.1434 2.42256 PNS24244 1471 1263.83 48.8864 2.69074 PNS24243 293 94.77 1 0.734007 KQK14069 1603 1395.83 7114.53 354.556 KQK14071 474 268.315 296.006 76.741 ==> SRR1797578.se.tsv <== BRADI_1g14170v3 7543 BRADI_1g53295v3 202 BRADI_1g59795v3 186 BRADI_1g07683v3 0 BRADI_1g00485v3 5 BRADI_1g20270v3 501 BRADI_1g74790v3 482 BRADI_1g09890v3 0 BRADI_1g77505v3 182 BRADI_1g48960v3 0 SRR1797578 completed mapping pipeline successfully