Starting /dee2/code/volunteer_pipeline.sh SRR6958167 current disk space = 1550505095168 free memory = 1603687148 SRR6958167 SRAfilesize 8378c1aa9eccf6048c0ce26473e4ffdc SRR6958167.sra SRR6958167.sra file validated SRR6958167 is paired end SRR6958167 is conventional basespace SRR6958167 read1 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR6958167_1.fastq File type Conventional base calls Encoding Sanger / Illumina 1.9 Total Sequences 4000 Sequences flagged as poor quality 0 Sequence length 151 %GC 49 >>END_MODULE >>Per base sequence quality fail #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 27.30175 32.0 27.0 33.0 2.0 33.0 2 29.02725 31.0 27.0 33.0 18.0 33.0 3 30.5685 33.0 29.0 33.0 27.0 33.0 4 31.754 33.0 32.0 33.0 28.0 34.0 5 31.68275 33.0 32.0 33.0 30.0 34.0 6 35.661 38.0 36.0 38.0 31.0 38.0 7 36.2845 38.0 37.0 38.0 33.0 38.0 8 36.26 38.0 37.0 38.0 33.0 38.0 9 36.569 38.0 37.0 38.0 34.0 38.0 10-14 36.83525 38.0 38.0 38.0 34.6 38.0 15-19 37.0861 38.0 38.0 38.0 36.0 38.0 20-24 37.01195 38.0 38.0 38.0 35.6 38.0 25-29 36.73115 38.0 38.0 38.0 34.8 38.0 30-34 36.66245 38.0 38.0 38.0 34.6 38.0 35-39 36.4325 38.0 38.0 38.0 33.6 38.0 40-44 36.3763 38.0 38.0 38.0 33.4 38.0 45-49 36.379450000000006 38.0 37.8 38.0 33.6 38.0 50-54 35.6659 38.0 36.4 38.0 29.8 38.0 55-59 35.6684 38.0 36.8 38.0 29.8 38.0 60-64 36.264149999999994 38.0 37.0 38.0 33.0 38.0 65-69 36.3253 38.0 37.4 38.0 33.2 38.0 70-74 36.01095 38.0 37.0 38.0 32.2 38.0 75-79 35.32605 38.0 35.8 38.0 28.6 38.0 80-84 35.231500000000004 38.0 35.8 38.0 28.2 38.0 85-89 35.612700000000004 38.0 36.2 38.0 29.8 38.0 90-94 35.545500000000004 38.0 36.0 38.0 29.8 38.0 95-99 34.76625 38.0 34.8 38.0 26.4 38.0 100-104 33.9197 38.0 34.0 38.0 21.4 38.0 105-109 33.503699999999995 37.8 33.6 38.0 16.2 38.0 110-114 33.559000000000005 38.0 33.6 38.0 19.4 38.0 115-119 33.3858 37.6 33.4 38.0 19.4 38.0 120-124 32.6631 37.2 31.8 38.0 16.2 38.0 125-129 32.18635 36.8 31.0 38.0 15.0 38.0 130-134 31.235950000000003 35.8 29.4 38.0 13.8 38.0 135-139 29.844899999999996 35.0 26.2 38.0 12.2 38.0 140-144 28.265050000000002 33.4 21.8 38.0 4.2 38.0 145-149 25.895799999999998 32.6 12.2 38.0 2.0 38.0 150-151 19.329625 16.5 2.0 35.5 2.0 38.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 4 1.0 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 3.0 15 3.0 16 5.0 17 5.0 18 7.0 19 4.0 20 15.0 21 16.0 22 21.0 23 28.0 24 36.0 25 39.0 26 49.0 27 92.0 28 89.0 29 112.0 30 120.0 31 159.0 32 225.0 33 281.0 34 422.0 35 602.0 36 992.0 37 674.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 43.897692521545736 9.36891854323047 8.034473172087852 38.69891576313595 2 22.05 11.375 35.65 30.925000000000004 3 21.725 17.4 27.200000000000003 33.675 4 27.375 23.275000000000002 22.175 27.175 5 26.450000000000003 27.650000000000002 23.925 21.975 6 22.525000000000002 31.95 24.099999999999998 21.425 7 17.375 24.224999999999998 38.125 20.275000000000002 8 20.875 23.9 30.375000000000004 24.85 9 19.8 21.55 33.6 25.05 10-14 22.634999999999998 26.400000000000002 25.935000000000002 25.03 15-19 22.875 25.545 25.900000000000002 25.679999999999996 20-24 22.81 25.490000000000002 26.495 25.205 25-29 23.185 25.585 25.36 25.869999999999997 30-34 22.255 25.490000000000002 26.584999999999997 25.669999999999998 35-39 22.78 25.195 26.56 25.465 40-44 23.189999999999998 25.615 25.619999999999997 25.575 45-49 23.330000000000002 25.45 25.685000000000002 25.535000000000004 50-54 22.91 25.735000000000003 25.91 25.445 55-59 22.86 25.21 26.005 25.924999999999997 60-64 23.305 25.509999999999998 25.785000000000004 25.4 65-69 22.915 25.22 25.540000000000003 26.325 70-74 22.61 24.965 26.25 26.174999999999997 75-79 23.16 25.650000000000002 25.180000000000003 26.009999999999998 80-84 23.494999999999997 25.27 25.380000000000003 25.855 85-89 23.39 24.995 25.75 25.865 90-94 23.189999999999998 25.380000000000003 25.365 26.064999999999998 95-99 23.36 25.19 25.380000000000003 26.07 100-104 23.325000000000003 24.67 25.97 26.035000000000004 105-109 23.18 25.165 25.66 25.995 110-114 23.335 24.709999999999997 25.95 26.005 115-119 23.28 24.575 26.155 25.990000000000002 120-124 23.72 24.740000000000002 25.740000000000002 25.8 125-129 23.39 25.055 25.595000000000002 25.96 130-134 23.845 25.019999999999996 25.005 26.13 135-139 23.82 24.560000000000002 26.02 25.6 140-144 24.115000000000002 24.545 25.455 25.885 145-149 23.93 24.4 26.1 25.569999999999997 150-151 24.325 24.0625 25.9875 25.624999999999996 >>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 0.5 21 0.5 22 0.0 23 0.0 24 0.5 25 1.0 26 0.5 27 1.0 28 4.0 29 6.0 30 6.0 31 6.5 32 8.5 33 15.5 34 20.5 35 31.0 36 49.5 37 71.0 38 92.5 39 115.0 40 135.0 41 155.0 42 177.0 43 193.0 44 202.0 45 212.0 46 225.0 47 212.0 48 192.5 49 185.0 50 166.5 51 148.5 52 134.5 53 113.0 54 97.0 55 86.0 56 85.0 57 89.0 58 84.0 59 72.5 60 66.0 61 65.0 62 55.0 63 47.0 64 52.5 65 54.5 66 44.5 67 35.5 68 29.5 69 30.5 70 30.5 71 22.5 72 21.0 73 21.5 74 14.5 75 6.5 76 2.5 77 1.0 78 1.0 79 2.0 80 2.0 81 0.5 82 0.0 83 0.0 84 0.0 85 0.0 86 0.0 87 0.0 88 0.0 89 0.0 90 0.0 91 0.0 92 0.0 93 0.0 94 0.0 95 0.0 96 0.0 97 0.0 98 0.0 99 0.0 100 0.0 >>END_MODULE >>Per base N content warn #Base N-Count 1 10.075000000000001 2 0.0 3 0.0 4 0.0 5 0.0 6 0.0 7 0.0 8 0.0 9 0.0 10-14 0.0 15-19 0.0 20-24 0.0 25-29 0.0 30-34 0.0 35-39 0.0 40-44 0.0 45-49 0.0 50-54 0.0 55-59 0.0 60-64 0.0 65-69 0.0 70-74 0.0 75-79 0.0 80-84 0.0 85-89 0.0 90-94 0.0 95-99 0.0 100-104 0.0 105-109 0.0 110-114 0.0 115-119 0.0 120-124 0.0 125-129 0.0 130-134 0.0 135-139 0.0 140-144 0.0 145-149 0.0 150-151 0.0 >>END_MODULE >>Sequence Length Distribution pass #Length Count 151 4000.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 99.575 #Duplication Level Percentage of deduplicated Percentage of total 1 99.62339944765253 99.2 2 0.3263871453678132 0.65 3 0.05021340697966357 0.15 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 0.0125 0.0 0.0 0.0 0.0 82-83 0.025 0.0 0.0 0.0 0.0 84-85 0.05 0.0 0.0 0.0 0.0 86-87 0.0625 0.0 0.0 0.0 0.0 88-89 0.075 0.0 0.0 0.0 0.0 90-91 0.075 0.0 0.0 0.0 0.0 92-93 0.075 0.0 0.0 0.0 0.0 94-95 0.1 0.0 0.0 0.0 0.0 96-97 0.1 0.0 0.0 0.0 0.0 98-99 0.1375 0.0 0.0 0.0 0.0 100-101 0.175 0.0 0.0 0.0 0.0 102-103 0.21250000000000002 0.0 0.0 0.0 0.0 104-105 0.2375 0.0 0.0 0.0 0.0 106-107 0.275 0.0 0.0 0.0 0.0 108-109 0.3125 0.0 0.0 0.0 0.0 110-111 0.375 0.0 0.0 0.0 0.0 112-113 0.3875 0.0 0.0 0.0 0.0 114-115 0.4 0.0 0.0 0.0 0.0 116-117 0.4625 0.0 0.0 0.0 0.0 118-119 0.6499999999999999 0.0 0.0 0.0 0.0 120-121 0.7375 0.0 0.0 0.0 0.0 122-123 0.7875000000000001 0.0 0.0 0.0 0.0 124-125 0.8625 0.0 0.0 0.0 0.0 126-127 0.9625 0.0 0.0 0.0 0.0 128-129 1.0750000000000002 0.0 0.0 0.0 0.0 130-131 1.2 0.0 0.0 0.0 0.0 132-133 1.35 0.0 0.0 0.0 0.0 134-135 1.5 0.0 0.0 0.0 0.0 136-137 1.65 0.0 0.0 0.0 0.0 138-139 1.825 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content pass >>END_MODULE SRR6958167 read2 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR6958167_2.fastq File type Conventional base calls Encoding Sanger / Illumina 1.9 Total Sequences 4000 Sequences flagged as poor quality 0 Sequence length 151 %GC 50 >>END_MODULE >>Per base sequence quality fail #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 32.012 33.0 32.0 34.0 28.0 34.0 2 31.80575 33.0 32.0 34.0 27.0 34.0 3 31.76525 33.0 32.0 34.0 27.0 34.0 4 31.6555 33.0 32.0 34.0 27.0 34.0 5 31.67675 33.0 32.0 34.0 28.0 34.0 6 35.4595 38.0 37.0 38.0 29.0 38.0 7 35.4455 38.0 37.0 38.0 29.0 38.0 8 35.1875 38.0 37.0 38.0 28.0 38.0 9 35.39325 38.0 37.0 38.0 29.0 38.0 10-14 35.28255 38.0 36.6 38.0 28.2 38.0 15-19 35.7646 38.0 37.6 38.0 30.6 38.0 20-24 36.090900000000005 38.0 38.0 38.0 32.6 38.0 25-29 36.0788 38.0 38.0 38.0 33.0 38.0 30-34 36.11445 38.0 38.0 38.0 33.4 38.0 35-39 35.76005 38.0 37.6 38.0 31.0 38.0 40-44 35.544200000000004 38.0 37.0 38.0 29.4 38.0 45-49 35.550850000000004 38.0 37.0 38.0 29.8 38.0 50-54 35.6957 38.0 37.0 38.0 30.8 38.0 55-59 35.5933 38.0 37.0 38.0 30.0 38.0 60-64 35.1893 38.0 36.4 38.0 28.4 38.0 65-69 34.89954999999999 38.0 35.8 38.0 27.2 38.0 70-74 34.64490000000001 38.0 35.6 38.0 25.6 38.0 75-79 34.836149999999996 38.0 36.0 38.0 26.8 38.0 80-84 34.72985 38.0 36.0 38.0 26.6 38.0 85-89 34.5985 38.0 35.6 38.0 26.2 38.0 90-94 34.084799999999994 38.0 34.6 38.0 23.6 38.0 95-99 33.40125 38.0 33.8 38.0 16.6 38.0 100-104 32.54385 37.4 31.8 38.0 15.0 38.0 105-109 32.2158 37.4 31.0 38.0 15.0 38.0 110-114 32.15655 37.2 31.0 38.0 15.0 38.0 115-119 31.48385 37.0 29.8 38.0 13.4 38.0 120-124 30.699599999999997 36.6 27.8 38.0 12.0 38.0 125-129 29.477749999999997 35.6 24.8 38.0 11.0 38.0 130-134 28.34655 33.8 21.4 38.0 2.0 38.0 135-139 27.81805 33.0 20.2 38.0 2.0 38.0 140-144 26.8607 33.0 16.2 38.0 2.0 38.0 145-149 24.333799999999997 32.2 6.2 38.0 2.0 38.0 150-151 17.602125 16.5 2.0 34.0 2.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 2 22.0 3 10.0 4 5.0 5 5.0 6 3.0 7 3.0 8 2.0 9 2.0 10 3.0 11 7.0 12 8.0 13 6.0 14 10.0 15 7.0 16 10.0 17 15.0 18 23.0 19 18.0 20 26.0 21 39.0 22 43.0 23 35.0 24 52.0 25 60.0 26 75.0 27 81.0 28 102.0 29 106.0 30 137.0 31 139.0 32 201.0 33 282.0 34 380.0 35 537.0 36 822.0 37 724.0 >>END_MODULE >>Per base sequence content warn #Base G A T C 1 39.5 18.6 13.0 28.9 2 28.749999999999996 23.599999999999998 27.150000000000002 20.5 3 23.825 25.650000000000002 28.725 21.8 4 25.95 31.05 20.599999999999998 22.400000000000002 5 26.55 32.7 19.525000000000002 21.224999999999998 6 23.05 35.85 20.825 20.275000000000002 7 22.900000000000002 18.875 34.55 23.674999999999997 8 23.75 23.275000000000002 23.075000000000003 29.9 9 24.325 22.625 28.299999999999997 24.75 10-14 26.290000000000003 26.125 23.165 24.42 15-19 25.56 25.005 24.72 24.715 20-24 25.935000000000002 25.485000000000003 24.37 24.21 25-29 25.955000000000002 25.419999999999998 24.285 24.34 30-34 25.035 25.35 24.955 24.66 35-39 25.595000000000002 25.575 24.135 24.695 40-44 25.919999999999998 24.87 24.83 24.38 45-49 25.64 25.8 24.395 24.165 50-54 25.88 25.695 24.685000000000002 23.74 55-59 26.58 25.324999999999996 23.849999999999998 24.245 60-64 26.22 25.365 24.46 23.955000000000002 65-69 25.885 25.255 24.975 23.885 70-74 26.384999999999998 24.955 24.995 23.665 75-79 25.91 25.319999999999997 24.63 24.14 80-84 26.025 25.990000000000002 24.36 23.625 85-89 26.51 25.855 24.02 23.615 90-94 26.26 24.98 24.474999999999998 24.285 95-99 26.26 24.865000000000002 24.905 23.97 100-104 25.895000000000003 25.205 25.06 23.84 105-109 26.05 24.97 25.215 23.765 110-114 26.029999999999998 25.8 24.585 23.585 115-119 26.46 25.380000000000003 24.745 23.415 120-124 26.5 24.845 25.155 23.5 125-129 25.77 25.71 24.834999999999997 23.685000000000002 130-134 26.729999999999997 25.405 24.265 23.599999999999998 135-139 26.825 25.345000000000002 25.014999999999997 22.814999999999998 140-144 26.26 25.14 25.319999999999997 23.28 145-149 26.445 25.755 24.665 23.135 150-151 26.437500000000004 26.174999999999997 24.925 22.4625 >>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 0.5 26 0.0 27 0.0 28 2.5 29 5.5 30 6.0 31 8.5 32 13.5 33 17.5 34 19.0 35 26.0 36 41.0 37 59.0 38 83.5 39 105.0 40 123.5 41 150.0 42 162.0 43 177.0 44 188.0 45 187.5 46 183.0 47 185.0 48 180.5 49 160.5 50 159.5 51 149.0 52 143.5 53 117.0 54 98.5 55 105.0 56 95.0 57 90.0 58 91.0 59 80.0 60 71.5 61 75.0 62 73.5 63 68.5 64 66.0 65 73.0 66 59.5 67 45.5 68 45.0 69 49.0 70 44.0 71 30.5 72 21.0 73 16.0 74 18.0 75 11.5 76 4.5 77 2.5 78 3.0 79 4.0 80 2.5 81 1.0 82 0.5 83 0.0 84 0.0 85 0.0 86 0.5 87 0.5 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 10-14 0.0 15-19 0.0 20-24 0.0 25-29 0.0 30-34 0.0 35-39 0.0 40-44 0.0 45-49 0.0 50-54 0.0 55-59 0.0 60-64 0.0 65-69 0.0 70-74 0.0 75-79 0.0 80-84 0.0 85-89 0.0 90-94 0.0 95-99 0.0 100-104 0.0 105-109 0.0 110-114 0.0 115-119 0.0 120-124 0.0 125-129 0.0 130-134 0.0 135-139 0.0 140-144 0.0 145-149 0.0 150-151 0.0 >>END_MODULE >>Sequence Length Distribution pass #Length Count 151 4000.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 99.5 #Duplication Level Percentage of deduplicated Percentage of total 1 99.57286432160805 99.075 2 0.35175879396984927 0.7000000000000001 3 0.07537688442211055 0.22499999999999998 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 0.0125 0.0 0.0 0.0 0.0125 82-83 0.025 0.0 0.0 0.0 0.025 84-85 0.05 0.0 0.0 0.0 0.025 86-87 0.0625 0.0 0.0 0.0 0.025 88-89 0.075 0.0 0.0 0.0 0.025 90-91 0.075 0.0 0.0 0.0 0.025 92-93 0.075 0.0 0.0 0.0 0.025 94-95 0.1 0.0 0.0 0.0 0.025 96-97 0.1 0.0 0.0 0.0 0.025 98-99 0.1375 0.0 0.0 0.0 0.025 100-101 0.175 0.0 0.0 0.0 0.025 102-103 0.21250000000000002 0.0 0.0 0.0 0.025 104-105 0.2375 0.0 0.0 0.0 0.025 106-107 0.275 0.0 0.0 0.0 0.025 108-109 0.3375 0.0 0.0 0.0 0.025 110-111 0.4 0.0 0.0 0.0 0.025 112-113 0.4125 0.0 0.0 0.0 0.025 114-115 0.425 0.0 0.0 0.0 0.025 116-117 0.5125 0.0 0.0 0.0 0.025 118-119 0.6875 0.0 0.0 0.0 0.025 120-121 0.7625 0.0 0.0 0.0 0.025 122-123 0.8125 0.0 0.0 0.0 0.025 124-125 0.8875 0.0 0.0 0.0 0.025 126-127 0.9874999999999999 0.0 0.0 0.0 0.025 128-129 1.125 0.0 0.0 0.0 0.025 130-131 1.25 0.0 0.0 0.0 0.025 132-133 1.4500000000000002 0.0 0.0 0.0 0.025 134-135 1.6125 0.0 0.0 0.0 0.025 136-137 1.7625000000000002 0.0 0.0 0.0 0.025 138-139 1.9125 0.0 0.0 0.0 0.025 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position GATCAAA 10 0.006830828 145.0 145 AAGTGGA 10 0.006830828 145.0 8 >>END_MODULE Read 1346329 spots for SRR6958167.sra Written 1346329 spots for SRR6958167.sra Read 1346325 spots for SRR6958167.sra Written 1346325 spots for SRR6958167.sra Read 1346325 spots for SRR6958167.sra Written 1346325 spots for SRR6958167.sra Read 1346325 spots for SRR6958167.sra Written 1346325 spots for SRR6958167.sra Read 1346325 spots for SRR6958167.sra Written 1346325 spots for SRR6958167.sra Read 1346325 spots for SRR6958167.sra Written 1346325 spots for SRR6958167.sra Read 1346325 spots for SRR6958167.sra Written 1346325 spots for SRR6958167.sra Read 1346325 spots for SRR6958167.sra Written 1346325 spots for SRR6958167.sra Read 1346325 spots for SRR6958167.sra Written 1346325 spots for SRR6958167.sra Read 1346325 spots for SRR6958167.sra Written 1346325 spots for SRR6958167.sra Read 1346325 spots for SRR6958167.sra Written 1346325 spots for SRR6958167.sra Read 1346325 spots for SRR6958167.sra Written 1346325 spots for SRR6958167.sra Read 1346325 spots for SRR6958167.sra Written 1346325 spots for SRR6958167.sra Read 1346325 spots for SRR6958167.sra Written 1346325 spots for SRR6958167.sra Read 1346325 spots for SRR6958167.sra Written 1346325 spots for SRR6958167.sra Read 1346325 spots for SRR6958167.sra Written 1346325 spots for SRR6958167.sra Read 1346325 spots for SRR6958167.sra Written 1346325 spots for SRR6958167.sra Read 1346325 spots for SRR6958167.sra Written 1346325 spots for SRR6958167.sra Read 1346325 spots for SRR6958167.sra Written 1346325 spots for SRR6958167.sra Read 1346325 spots for SRR6958167.sra Written 1346325 spots for SRR6958167.sra SRR ids: ['SRR6958167.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_zhhgrp8z SRR6958167.sra spots: 26926504 blocks: [[1, 1346325], [1346326, 2692650], [2692651, 4038975], [4038976, 5385300], [5385301, 6731625], [6731626, 8077950], [8077951, 9424275], [9424276, 10770600], [10770601, 12116925], [12116926, 13463250], [13463251, 14809575], [14809576, 16155900], [16155901, 17502225], [17502226, 18848550], [18848551, 20194875], [20194876, 21541200], [21541201, 22887525], [22887526, 24233850], [24233851, 25580175], [25580176, 26926504]] SRR6958167 file size 9102808 SRR6958167 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 SRR6958167 SRR6958167_1.fastq SRR6958167_2.fastq Input file: SRR6958167_1.fastq Paired file: SRR6958167_2.fastq trimmed: SRR6958167-trimmed-pair1.fastq, SRR6958167-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 14:55:27 2024 >> started Fri Dec 6 14:55:57 2024 >> done (30.241s) 26926504 read pairs processed; of these: 68269 ( 0.25%) short read pairs filtered out after trimming by size control 70243 ( 0.26%) empty read pairs filtered out after trimming by size control 26787992 (99.49%) read pairs available; of these: 14880199 (55.55%) trimmed read pairs available after processing 11907793 (44.45%) untrimmed read pairs available after processing Length distribution of reads after trimming: length count percentage 18 2 0.00% 19 3 0.00% 20 4 0.00% 21 4 0.00% 22 7 0.00% 23 6 0.00% 24 12 0.00% 25 12 0.00% 26 9 0.00% 27 6 0.00% 28 8 0.00% 29 17 0.00% 30 13 0.00% 31 13 0.00% 32 22 0.00% 33 19 0.00% 34 16 0.00% 35 21 0.00% 36 20 0.00% 37 27 0.00% 38 27 0.00% 39 41 0.00% 40 30 0.00% 41 29 0.00% 42 38 0.00% 43 28 0.00% 44 41 0.00% 45 51 0.00% 46 52 0.00% 47 73 0.00% 48 51 0.00% 49 96 0.00% 50 85 0.00% 51 113 0.00% 52 106 0.00% 53 133 0.00% 54 142 0.00% 55 151 0.00% 56 160 0.00% 57 172 0.00% 58 229 0.00% 59 236 0.00% 60 261 0.00% 61 287 0.00% 62 346 0.00% 63 332 0.00% 64 370 0.00% 65 447 0.00% 66 475 0.00% 67 535 0.00% 68 585 0.00% 69 609 0.00% 70 691 0.00% 71 822 0.00% 72 898 0.00% 73 969 0.00% 74 1111 0.00% 75 1183 0.00% 76 1395 0.01% 77 1490 0.01% 78 1737 0.01% 79 1909 0.01% 80 2061 0.01% 81 2484 0.01% 82 2788 0.01% 83 3438 0.01% 84 5848 0.02% 85 7183 0.03% 86 7129 0.03% 87 7114 0.03% 88 7219 0.03% 89 7238 0.03% 90 7421 0.03% 91 7803 0.03% 92 8233 0.03% 93 8626 0.03% 94 9037 0.03% 95 9373 0.03% 96 9809 0.04% 97 10311 0.04% 98 10932 0.04% 99 11395 0.04% 100 11981 0.04% 101 12728 0.05% 102 13563 0.05% 103 14443 0.05% 104 15013 0.06% 105 15716 0.06% 106 16774 0.06% 107 17435 0.07% 108 18450 0.07% 109 19504 0.07% 110 20535 0.08% 111 21832 0.08% 112 23000 0.09% 113 24495 0.09% 114 26097 0.10% 115 28011 0.10% 116 29343 0.11% 117 30973 0.12% 118 32667 0.12% 119 34055 0.13% 120 35971 0.13% 121 38380 0.14% 122 40658 0.15% 123 43762 0.16% 124 46713 0.17% 125 50132 0.19% 126 53122 0.20% 127 57059 0.21% 128 60254 0.22% 129 64958 0.24% 130 69971 0.26% 131 74646 0.28% 132 81749 0.31% 133 88376 0.33% 134 95250 0.36% 135 103923 0.39% 136 113903 0.43% 137 123987 0.46% 138 135123 0.50% 139 149496 0.56% 140 166050 0.62% 141 187311 0.70% 142 215497 0.80% 143 249326 0.93% 144 295147 1.10% 145 361493 1.35% 146 464471 1.73% 147 642602 2.40% 148 994374 3.71% 149 1952699 7.29% 150 7232962 27.00% 151 11907793 44.45% 26787992 reads passed initial QC criterion=sequence-density sequence-density=0.39 sequence-density-rank=1 fanout-score=5.18 fanout-score-rank=17 prefix-density=0.56 prefix-fanout=3.6 sequence=GCAGGTGCAGCTGGTGC criterion=fanout-score sequence-density=0.02 sequence-density-rank=35 fanout-score=197.89 fanout-score-rank=1 prefix-density=0.53 prefix-fanout=8.2 sequence=GGCGGCGGCGAACCGCCCCCGTCGCCGCGATCCGAACACTTCACCGGACCATTCAATCGGTAGGAGCGACGGGCGGTGTGTACAAAGGGCAGGGACGTAGTCAACGCGAGCTGATGACTCGCGCTTACTAGGCATTCCTCGTTGAAGACCAACAATTGCAATGATCTATCCCCATCACGATGAAATTTCCCAAGATTACCCGGGCCTGTCGGCCAAGGCTATATACTCGTTGAATACATCAGTGTAGCGCGCGTGCGGCCCAGAACATCTAAGGGCATCACAGACCTGTTATTGCCTCAAACTTCCGTCGCCTAAACGGCGATAGTCCCTCTAAGAAGCTAGCTGCGGAGGGATGGCTCCGCATAGCTAGTTAGCAGGCTGAGGTCTCGTTCGTTAACGGAATTAACCAGACAAATCGCTCCACCAACTAAGAACGGCCATGCACCACCACCCATAGAATCAAGAAAGAGCTCTCAGTCTGTCAATCCTTGCTATGTCTGGACCTGGTAAG criterion=sequence-density sequence-density=0.23 sequence-density-rank=1 fanout-score=5.82 fanout-score-rank=13 prefix-density=0.33 prefix-fanout=4.1 sequence=CTGCAAGTGCGGCA criterion=fanout-score sequence-density=0.01 sequence-density-rank=37 fanout-score=174.82 fanout-score-rank=1 prefix-density=0.16 prefix-fanout=7.9 sequence=AAGAAGCACACACAAGCCTAGAAGCCTTCAGCTTAATCTTCTTCCTAAGCAAGTTCGAGCACTCGACCGAAGATGTCTT SRR6958167 testing PE reads STAR mapping to Ensembl genome Started job on | Dec 06 14:56:41 Started mapping on | Dec 06 14:56:41 Finished on | Dec 06 14:59:44 Mapping speed, Million of reads per hour | 526.98 Number of input reads | 26787992 Average input read length | 295 UNIQUE READS: Uniquely mapped reads number | 25632505 Uniquely mapped reads % | 95.69% Average mapped length | 295.06 Number of splices: Total | 27824841 Number of splices: Annotated (sjdb) | 26135433 Number of splices: GT/AG | 27461389 Number of splices: GC/AG | 305487 Number of splices: AT/AC | 14095 Number of splices: Non-canonical | 43870 Mismatch rate per base, % | 0.27% Deletion rate per base | 0.01% Deletion average length | 2.45 Insertion rate per base | 0.01% Insertion average length | 2.39 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 215156 % of reads mapped to multiple loci | 0.80% Number of reads mapped to too many loci | 28764 % of reads mapped to too many loci | 0.11% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 2.62% % of reads unmapped: other | 0.78% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 981381 981381 981381 N_multimapping 215156 215156 215156 N_noFeature 984430 24915475 1212613 N_ambiguous 586820 4419 98548 UnstrandedReadsAssigned:24061255 PositiveStrandReadsAssigned:712611 NegativeStrandReadsAssigned:24321344 Dataset is classified negative stranded MeadianReadLen=151 20thPercentileLength=147 echo kmer=143 SRR6958167 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: SRR6958167-trimmed-pair1.fastq SRR6958167-trimmed-pair2.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 26,787,992 reads, 24,324,903 reads pseudoaligned [quant] estimated average fragment length: 278.196 [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,157 rounds 52973 SRR6958167.ke.tsv 35125 SRR6958167.se.tsv 88098 total ==> SRR6958167.ke.tsv <== target_id length eff_length est_counts tpm PNS24245 936 659.285 0 0 PNS24247 1044 766.804 127.807 9.85011 PNS24249 1928 1650.8 112.764 4.03687 PNS24246 1044 766.804 127.807 9.85011 PNS24248 1044 766.804 127.807 9.85011 PNS24244 1471 1193.8 123.813 6.1292 PNS24243 293 75.2442 0 0 KQK14069 1603 1325.8 1479.12 65.9316 KQK14071 474 212.616 39.8982 11.0899 ==> SRR6958167.se.tsv <== BRADI_1g14170v3 1699 BRADI_1g53295v3 507 BRADI_1g59795v3 656 BRADI_1g07683v3 0 BRADI_1g00485v3 11 BRADI_1g20270v3 754 BRADI_1g74790v3 555 BRADI_1g09890v3 1 BRADI_1g77505v3 301 BRADI_1g48960v3 0 SRR6958167 completed mapping pipeline successfully