Starting /dee2/code/volunteer_pipeline.sh SRR12666363 current disk space = 1543056293888 free memory = 1596729024 SRR12666363 SRAfilesize 84f1b1b2e9679d1f0448e69c64dcf666 SRR12666363.sra SRR12666363.sra file validated SRR12666363 is paired end SRR12666363 is conventional basespace SRR12666363 read1 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR12666363_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 48 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 36.403 37.0 37.0 37.0 37.0 37.0 2 36.29225 37.0 37.0 37.0 37.0 37.0 3 36.363 37.0 37.0 37.0 37.0 37.0 4 36.5215 37.0 37.0 37.0 37.0 37.0 5 36.497 37.0 37.0 37.0 37.0 37.0 6 36.4595 37.0 37.0 37.0 37.0 37.0 7 36.482 37.0 37.0 37.0 37.0 37.0 8 36.473 37.0 37.0 37.0 37.0 37.0 9 36.5275 37.0 37.0 37.0 37.0 37.0 10-14 36.5125 37.0 37.0 37.0 37.0 37.0 15-19 36.5631 37.0 37.0 37.0 37.0 37.0 20-24 36.4832 37.0 37.0 37.0 37.0 37.0 25-29 36.4851 37.0 37.0 37.0 37.0 37.0 30-34 36.4057 37.0 37.0 37.0 37.0 37.0 35-39 36.3675 37.0 37.0 37.0 37.0 37.0 40-44 36.3633 37.0 37.0 37.0 37.0 37.0 45-49 36.301300000000005 37.0 37.0 37.0 37.0 37.0 50-54 36.3594 37.0 37.0 37.0 37.0 37.0 55-59 36.3281 37.0 37.0 37.0 37.0 37.0 60-64 36.317 37.0 37.0 37.0 37.0 37.0 65-69 36.273399999999995 37.0 37.0 37.0 37.0 37.0 70-74 36.2811 37.0 37.0 37.0 37.0 37.0 75-79 36.2281 37.0 37.0 37.0 37.0 37.0 80-84 36.2609 37.0 37.0 37.0 37.0 37.0 85-89 36.21169999999999 37.0 37.0 37.0 37.0 37.0 90-94 36.1971 37.0 37.0 37.0 37.0 37.0 95-99 36.0469 37.0 37.0 37.0 37.0 37.0 100-104 36.1036 37.0 37.0 37.0 37.0 37.0 105-109 36.1524 37.0 37.0 37.0 37.0 37.0 110-114 36.0923 37.0 37.0 37.0 37.0 37.0 115-119 36.0513 37.0 37.0 37.0 37.0 37.0 120-124 35.977 37.0 37.0 37.0 37.0 37.0 125-129 35.9519 37.0 37.0 37.0 37.0 37.0 130-134 35.942499999999995 37.0 37.0 37.0 37.0 37.0 135-139 35.928799999999995 37.0 37.0 37.0 37.0 37.0 140-144 35.776799999999994 37.0 37.0 37.0 37.0 37.0 145-149 35.695800000000006 37.0 37.0 37.0 37.0 37.0 150-151 35.5115 37.0 37.0 37.0 37.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 19 1.0 20 0.0 21 0.0 22 1.0 23 1.0 24 0.0 25 1.0 26 8.0 27 10.0 28 19.0 29 17.0 30 37.0 31 42.0 32 64.0 33 80.0 34 120.0 35 309.0 36 2780.0 37 510.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 46.6 13.225000000000001 7.025 33.15 2 22.641981486114584 16.837628221165872 36.90267700775582 23.617713284963724 3 19.45 23.35 26.8 30.4 4 24.95 32.45 20.275000000000002 22.325 5 24.45 34.125 21.85 19.575 6 20.474999999999998 34.5 22.95 22.075 7 16.45 22.400000000000002 41.05 20.1 8 19.55 21.9 28.000000000000004 30.55 9 19.875 20.674999999999997 32.574999999999996 26.875 10-14 23.064999999999998 27.12 24.625 25.19 15-19 22.525000000000002 26.72 25.355 25.4 20-24 22.78 26.105 26.135 24.98 25-29 22.689999999999998 26.025 25.97 25.314999999999998 30-34 23.025000000000002 25.985000000000003 25.255 25.735000000000003 35-39 23.46 25.629999999999995 25.52 25.39 40-44 23.34 25.365 25.655 25.64 45-49 23.085 25.290000000000003 26.040000000000003 25.585 50-54 22.830000000000002 26.229999999999997 25.56 25.380000000000003 55-59 22.965 26.095000000000002 25.430000000000003 25.509999999999998 60-64 23.150000000000002 26.240000000000002 25.46 25.15 65-69 22.585 25.45 26.240000000000002 25.724999999999998 70-74 23.135 25.979999999999997 25.56 25.324999999999996 75-79 23.71 25.945 25.1 25.245 80-84 23.715 25.724999999999998 24.865000000000002 25.695 85-89 23.01 26.119999999999997 25.564999999999998 25.305 90-94 23.34 26.11 24.834999999999997 25.715 95-99 22.855 25.480000000000004 25.825 25.840000000000003 100-104 24.055 25.4 25.430000000000003 25.115 105-109 23.64 25.305 25.545 25.509999999999998 110-114 24.175 25.455 24.88 25.490000000000002 115-119 23.47 26.545 24.51 25.474999999999998 120-124 23.335 26.325 24.610000000000003 25.729999999999997 125-129 23.494999999999997 25.955000000000002 25.155 25.395 130-134 23.895 26.16 24.445 25.5 135-139 24.115000000000002 26.179999999999996 24.515 25.19 140-144 23.155 25.900000000000002 25.285000000000004 25.66 145-149 24.04 25.474999999999998 24.62 25.865 150-151 23.0875 27.275 24.45 25.1875 >>END_MODULE >>Per sequence GC content warn #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 0.5 22 0.5 23 0.5 24 0.5 25 0.0 26 0.5 27 2.5 28 2.5 29 5.0 30 9.0 31 10.0 32 19.0 33 31.5 34 37.5 35 38.0 36 54.0 37 75.5 38 86.5 39 100.0 40 119.0 41 149.0 42 166.0 43 177.0 44 191.0 45 199.5 46 236.0 47 220.5 48 178.5 49 193.0 50 191.0 51 154.5 52 136.5 53 121.5 54 99.0 55 98.5 56 99.0 57 88.0 58 74.0 59 70.0 60 71.5 61 65.0 62 53.5 63 52.0 64 59.5 65 61.5 66 46.0 67 36.5 68 36.0 69 29.0 70 19.0 71 9.5 72 7.5 73 6.5 74 4.0 75 2.5 76 2.5 77 2.0 78 0.5 79 0.5 80 0.0 81 0.0 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 pass #Base N-Count 1 0.0 2 0.075 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 90.85 #Duplication Level Percentage of deduplicated Percentage of total 1 91.19427627958173 82.85 2 7.815079801871216 14.2 3 0.7154650522839846 1.95 4 0.27517886626307103 1.0 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 warn #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 0.025 0.0 0.0 0.0 64-65 0.0 0.025 0.0 0.0 0.0 66-67 0.0 0.025 0.0 0.0 0.0 68-69 0.0 0.025 0.0 0.0 0.0 70-71 0.0 0.025 0.0 0.0 0.0 72-73 0.0 0.025 0.0 0.0 0.0 74-75 0.025 0.025 0.0 0.0 0.0 76-77 0.037500000000000006 0.025 0.0 0.0 0.0 78-79 0.05 0.025 0.0 0.0 0.0 80-81 0.05 0.025 0.0 0.0 0.0 82-83 0.0875 0.025 0.0 0.0 0.0 84-85 0.1 0.025 0.0 0.0 0.0 86-87 0.1 0.025 0.0 0.0 0.0 88-89 0.15 0.025 0.0 0.0 0.0 90-91 0.21250000000000002 0.025 0.0 0.0 0.0 92-93 0.3125 0.025 0.0 0.0 0.0 94-95 0.3625 0.025 0.0 0.0 0.0 96-97 0.4375 0.025 0.0 0.0 0.0 98-99 0.525 0.025 0.0 0.0 0.0 100-101 0.65 0.025 0.0 0.0 0.0 102-103 0.7375 0.025 0.0 0.0 0.0 104-105 0.95 0.025 0.0 0.0 0.0 106-107 1.0875 0.025 0.0 0.0 0.0 108-109 1.2625 0.025 0.0 0.0 0.0 110-111 1.4500000000000002 0.025 0.0 0.0 0.0 112-113 1.6625 0.025 0.0 0.0 0.0 114-115 1.85 0.025 0.0 0.0 0.0 116-117 2.0625 0.025 0.0 0.0 0.0 118-119 2.3125 0.025 0.0 0.0 0.0 120-121 2.6500000000000004 0.025 0.0 0.0 0.0 122-123 3.0625 0.025 0.0 0.0 0.0 124-125 3.325 0.025 0.0 0.0 0.0 126-127 3.9499999999999997 0.025 0.0 0.0 0.0 128-129 4.3875 0.025 0.0 0.0 0.0 130-131 4.625 0.025 0.0 0.0 0.0 132-133 5.025 0.025 0.0 0.0 0.0 134-135 5.375 0.025 0.0 0.0 0.0 136-137 5.95 0.025 0.0 0.0 0.0 138-139 6.487500000000001 0.025 0.0 0.0 0.0 >>END_MODULE >>Kmer Content pass >>END_MODULE SRR12666363 read2 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR12666363_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 49 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 35.79 37.0 37.0 37.0 37.0 37.0 2 35.903 37.0 37.0 37.0 37.0 37.0 3 36.0625 37.0 37.0 37.0 37.0 37.0 4 36.1045 37.0 37.0 37.0 37.0 37.0 5 36.2575 37.0 37.0 37.0 37.0 37.0 6 36.092 37.0 37.0 37.0 37.0 37.0 7 36.0685 37.0 37.0 37.0 37.0 37.0 8 36.1095 37.0 37.0 37.0 37.0 37.0 9 36.162 37.0 37.0 37.0 37.0 37.0 10-14 36.148999999999994 37.0 37.0 37.0 37.0 37.0 15-19 36.15689999999999 37.0 37.0 37.0 37.0 37.0 20-24 36.1556 37.0 37.0 37.0 37.0 37.0 25-29 36.1 37.0 37.0 37.0 37.0 37.0 30-34 36.09400000000001 37.0 37.0 37.0 37.0 37.0 35-39 36.0321 37.0 37.0 37.0 37.0 37.0 40-44 36.0508 37.0 37.0 37.0 37.0 37.0 45-49 35.9919 37.0 37.0 37.0 37.0 37.0 50-54 35.947599999999994 37.0 37.0 37.0 37.0 37.0 55-59 35.9327 37.0 37.0 37.0 37.0 37.0 60-64 35.8501 37.0 37.0 37.0 37.0 37.0 65-69 35.879400000000004 37.0 37.0 37.0 37.0 37.0 70-74 35.938399999999994 37.0 37.0 37.0 37.0 37.0 75-79 35.9169 37.0 37.0 37.0 37.0 37.0 80-84 35.8859 37.0 37.0 37.0 37.0 37.0 85-89 35.849000000000004 37.0 37.0 37.0 37.0 37.0 90-94 35.829800000000006 37.0 37.0 37.0 37.0 37.0 95-99 35.7944 37.0 37.0 37.0 37.0 37.0 100-104 35.759100000000004 37.0 37.0 37.0 37.0 37.0 105-109 35.714600000000004 37.0 37.0 37.0 37.0 37.0 110-114 35.623000000000005 37.0 37.0 37.0 37.0 37.0 115-119 35.5989 37.0 37.0 37.0 37.0 37.0 120-124 35.747499999999995 37.0 37.0 37.0 37.0 37.0 125-129 35.6452 37.0 37.0 37.0 37.0 37.0 130-134 35.6271 37.0 37.0 37.0 37.0 37.0 135-139 35.4643 37.0 37.0 37.0 37.0 37.0 140-144 35.453700000000005 37.0 37.0 37.0 37.0 37.0 145-149 35.3715 37.0 37.0 37.0 37.0 37.0 150-151 34.961 37.0 37.0 37.0 31.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 14 5.0 15 2.0 16 0.0 17 1.0 18 5.0 19 2.0 20 4.0 21 0.0 22 1.0 23 7.0 24 8.0 25 7.0 26 12.0 27 12.0 28 18.0 29 29.0 30 33.0 31 60.0 32 71.0 33 94.0 34 211.0 35 477.0 36 2561.0 37 380.0 >>END_MODULE >>Per base sequence content warn #Base G A T C 1 46.975 17.95 7.675 27.400000000000002 2 26.6 21.8 31.424999999999997 20.175 3 22.675 22.95 30.25 24.125 4 27.224999999999998 31.424999999999997 19.1 22.25 5 25.8 33.074999999999996 21.0 20.125 6 21.075 35.35 20.225 23.35 7 21.175 17.0 37.0 24.825 8 20.7 20.925 24.825 33.550000000000004 9 21.725 21.15 27.250000000000004 29.875 10-14 26.25 24.98 23.59 25.180000000000003 15-19 25.5 25.230000000000004 24.265 25.005 20-24 24.865000000000002 25.83 24.43 24.875 25-29 25.21 25.21 24.995 24.585 30-34 25.424999999999997 24.805 25.224999999999998 24.545 35-39 25.035 24.89 25.569999999999997 24.505 40-44 25.28 25.255 24.404999999999998 25.06 45-49 25.564999999999998 25.435000000000002 24.87 24.13 50-54 25.424999999999997 25.674999999999997 24.7 24.2 55-59 25.53 25.28 24.81 24.38 60-64 26.0 25.21 24.875 23.915 65-69 25.19 25.855 24.975 23.98 70-74 25.445 25.705 24.89 23.96 75-79 25.385 25.185000000000002 25.52 23.91 80-84 25.245 25.745 24.63 24.38 85-89 25.66 26.02 25.025 23.294999999999998 90-94 26.150000000000002 25.485000000000003 24.845 23.52 95-99 26.085 25.465 24.975 23.474999999999998 100-104 25.72 26.015 24.41 23.855 105-109 25.91 25.31 25.095 23.685000000000002 110-114 25.755 26.640000000000004 24.33 23.275000000000002 115-119 26.155 25.36 25.255 23.23 120-124 25.979999999999997 25.790000000000003 24.84 23.39 125-129 26.55 25.515 24.845 23.09 130-134 26.865 25.615 24.695 22.825 135-139 27.48 25.945 23.805 22.770000000000003 140-144 27.134999999999998 25.86 24.435000000000002 22.57 145-149 26.99 26.055 24.88 22.075 150-151 27.6 25.4625 24.6125 22.325 >>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 0.5 7 0.5 8 0.5 9 0.5 10 0.0 11 0.5 12 1.0 13 0.5 14 0.5 15 1.0 16 0.5 17 1.0 18 1.5 19 1.0 20 1.5 21 1.0 22 0.0 23 0.5 24 0.5 25 0.0 26 0.5 27 3.0 28 3.0 29 2.5 30 4.0 31 7.0 32 12.0 33 13.5 34 24.0 35 36.5 36 35.5 37 48.5 38 74.0 39 95.5 40 126.5 41 149.5 42 157.5 43 167.5 44 190.5 45 186.5 46 195.0 47 197.0 48 176.5 49 176.5 50 164.0 51 161.0 52 150.0 53 122.5 54 115.5 55 107.0 56 82.0 57 75.5 58 86.5 59 87.5 60 82.5 61 79.5 62 69.5 63 69.0 64 71.0 65 63.0 66 62.0 67 58.5 68 45.5 69 33.0 70 29.0 71 29.0 72 20.5 73 12.5 74 6.0 75 4.0 76 3.5 77 1.0 78 1.5 79 1.5 80 0.5 81 0.5 82 0.0 83 0.0 84 0.5 85 1.0 86 0.5 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 0.5 98 1.0 99 0.5 100 2.5 >>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 90.77499999999999 #Duplication Level Percentage of deduplicated Percentage of total 1 91.5725695400716 83.125 2 7.270724318369595 13.200000000000001 3 0.8262186725419994 2.25 4 0.27540622418066646 1.0 5 0.0 0.0 6 0.02754062241806665 0.15 7 0.0 0.0 8 0.0 0.0 9 0.0 0.0 >10 0.02754062241806665 0.27499999999999997 >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 warn #Sequence Count Percentage Possible Source GTTGGCTTCTCCTCCCCCTCACTAGTCCTCGGTTCCGGTTCCGGTTCGTT 11 0.27499999999999997 No Hit GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG 6 0.15 No Hit >>END_MODULE >>Adapter Content warn #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 0.0125 0.0 0.0 0.0 0.0 78-79 0.025 0.0 0.0 0.0 0.0 80-81 0.025 0.0 0.0 0.0 0.0 82-83 0.0625 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 0.15 0.0 0.0 0.0 0.0 90-91 0.21250000000000002 0.0 0.0 0.0 0.0 92-93 0.3 0.0 0.0 0.0 0.0 94-95 0.3625 0.0 0.0 0.0 0.0 96-97 0.4375 0.0 0.0 0.0 0.0 98-99 0.525 0.0 0.0 0.0 0.0 100-101 0.65 0.0 0.0 0.0 0.0 102-103 0.7375 0.0 0.0 0.0 0.0 104-105 0.95 0.0 0.0 0.0 0.0 106-107 1.0875 0.0 0.0 0.0 0.0 108-109 1.2875 0.0 0.0 0.0 0.0 110-111 1.475 0.0 0.0 0.0 0.0 112-113 1.6875 0.0 0.0 0.0 0.0 114-115 1.8875000000000002 0.0 0.0 0.0 0.0 116-117 2.1125 0.0 0.0 0.0 0.0 118-119 2.3625 0.0 0.0 0.0 0.0 120-121 2.7 0.0 0.0 0.0 0.0 122-123 3.1125 0.0 0.0 0.0 0.0 124-125 3.375 0.0 0.0 0.0 0.0 126-127 4.0 0.0 0.0 0.0 0.0 128-129 4.4375 0.0 0.0 0.0 0.0 130-131 4.675000000000001 0.0 0.0 0.0 0.0 132-133 5.074999999999999 0.0 0.0 0.0 0.0 134-135 5.4 0.0 0.0 0.0 0.0 136-137 5.9625 0.0 0.0 0.0 0.0 138-139 6.5 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position AGCTAAA 10 0.006830828 145.0 5 CACCTAC 10 0.006830828 145.0 9 >>END_MODULE Read 1577406 spots for SRR12666363.sra Written 1577406 spots for SRR12666363.sra Read 1577406 spots for SRR12666363.sra Written 1577406 spots for SRR12666363.sra Read 1577406 spots for SRR12666363.sra Written 1577406 spots for SRR12666363.sra Read 1577406 spots for SRR12666363.sra Written 1577406 spots for SRR12666363.sra Read 1577406 spots for SRR12666363.sra Written 1577406 spots for SRR12666363.sra Read 1577406 spots for SRR12666363.sra Written 1577406 spots for SRR12666363.sra Read 1577406 spots for SRR12666363.sra Written 1577406 spots for SRR12666363.sra Read 1577406 spots for SRR12666363.sra Written 1577406 spots for SRR12666363.sra Read 1577406 spots for SRR12666363.sra Written 1577406 spots for SRR12666363.sra Read 1577406 spots for SRR12666363.sra Written 1577406 spots for SRR12666363.sra Read 1577406 spots for SRR12666363.sra Written 1577406 spots for SRR12666363.sra Read 1577406 spots for SRR12666363.sra Written 1577406 spots for SRR12666363.sra Read 1577406 spots for SRR12666363.sra Written 1577406 spots for SRR12666363.sra Read 1577406 spots for SRR12666363.sra Written 1577406 spots for SRR12666363.sra Read 1577406 spots for SRR12666363.sra Written 1577406 spots for SRR12666363.sra Read 1577406 spots for SRR12666363.sra Written 1577406 spots for SRR12666363.sra Read 1577420 spots for SRR12666363.sra Written 1577420 spots for SRR12666363.sra Read 1577406 spots for SRR12666363.sra Written 1577406 spots for SRR12666363.sra Read 1577406 spots for SRR12666363.sra Written 1577406 spots for SRR12666363.sra Read 1577406 spots for SRR12666363.sra Written 1577406 spots for SRR12666363.sra SRR ids: ['SRR12666363.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_03rrlj5k SRR12666363.sra spots: 31548134 blocks: [[1, 1577406], [1577407, 3154812], [3154813, 4732218], [4732219, 6309624], [6309625, 7887030], [7887031, 9464436], [9464437, 11041842], [11041843, 12619248], [12619249, 14196654], [14196655, 15774060], [15774061, 17351466], [17351467, 18928872], [18928873, 20506278], [20506279, 22083684], [22083685, 23661090], [23661091, 25238496], [25238497, 26815902], [26815903, 28393308], [28393309, 29970714], [29970715, 31548134]] SRR12666363 file size 10699735 SRR12666363 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 SRR12666363 SRR12666363_1.fastq SRR12666363_2.fastq Input file: SRR12666363_1.fastq Paired file: SRR12666363_2.fastq trimmed: SRR12666363-trimmed-pair1.fastq, SRR12666363-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 Sat Dec 7 13:05:58 2024 >> started Sat Dec 7 13:06:43 2024 >> done (44.929s) 31548134 read pairs processed; of these: 83 ( 0.00%) short read pairs filtered out after trimming by size control 4432 ( 0.01%) empty read pairs filtered out after trimming by size control 31543619 (99.99%) read pairs available; of these: 2797085 ( 8.87%) trimmed read pairs available after processing 28746534 (91.13%) untrimmed read pairs available after processing Length distribution of reads after trimming: length count percentage 18 10 0.00% 19 12 0.00% 20 9 0.00% 21 21 0.00% 22 21 0.00% 23 25 0.00% 24 19 0.00% 25 21 0.00% 26 29 0.00% 27 31 0.00% 28 31 0.00% 29 26 0.00% 30 33 0.00% 31 39 0.00% 32 36 0.00% 33 45 0.00% 34 36 0.00% 35 63 0.00% 36 57 0.00% 37 58 0.00% 38 53 0.00% 39 70 0.00% 40 54 0.00% 41 67 0.00% 42 87 0.00% 43 56 0.00% 44 68 0.00% 45 83 0.00% 46 96 0.00% 47 108 0.00% 48 102 0.00% 49 106 0.00% 50 117 0.00% 51 91 0.00% 52 110 0.00% 53 135 0.00% 54 140 0.00% 55 163 0.00% 56 156 0.00% 57 179 0.00% 58 163 0.00% 59 212 0.00% 60 233 0.00% 61 253 0.00% 62 292 0.00% 63 326 0.00% 64 336 0.00% 65 383 0.00% 66 439 0.00% 67 464 0.00% 68 503 0.00% 69 645 0.00% 70 726 0.00% 71 838 0.00% 72 963 0.00% 73 1152 0.00% 74 1291 0.00% 75 1449 0.00% 76 1579 0.01% 77 1746 0.01% 78 2099 0.01% 79 2277 0.01% 80 2522 0.01% 81 2956 0.01% 82 3468 0.01% 83 3896 0.01% 84 4303 0.01% 85 4872 0.02% 86 5239 0.02% 87 5769 0.02% 88 6338 0.02% 89 7025 0.02% 90 7804 0.02% 91 8699 0.03% 92 9634 0.03% 93 10550 0.03% 94 11541 0.04% 95 12432 0.04% 96 13167 0.04% 97 13914 0.04% 98 14761 0.05% 99 16091 0.05% 100 16965 0.05% 101 18080 0.06% 102 19834 0.06% 103 20772 0.07% 104 22151 0.07% 105 23715 0.08% 106 24864 0.08% 107 25711 0.08% 108 26544 0.08% 109 27845 0.09% 110 28786 0.09% 111 30425 0.10% 112 32254 0.10% 113 33617 0.11% 114 35686 0.11% 115 37334 0.12% 116 37976 0.12% 117 39306 0.12% 118 40023 0.13% 119 41463 0.13% 120 42593 0.14% 121 44282 0.14% 122 45924 0.15% 123 48022 0.15% 124 50251 0.16% 125 51009 0.16% 126 53085 0.17% 127 53575 0.17% 128 55322 0.18% 129 56582 0.18% 130 57467 0.18% 131 58386 0.19% 132 61194 0.19% 133 63210 0.20% 134 64419 0.20% 135 66601 0.21% 136 68479 0.22% 137 69170 0.22% 138 70915 0.22% 139 71271 0.23% 140 71503 0.23% 141 73307 0.23% 142 74626 0.24% 143 76279 0.24% 144 79078 0.25% 145 80539 0.26% 146 82215 0.26% 147 84568 0.27% 148 84558 0.27% 149 83074 0.26% 150 86217 0.27% 151 28746534 91.13% 31543619 reads passed initial QC criterion=sequence-density sequence-density=0.19 sequence-density-rank=1 fanout-score=4.30 fanout-score-rank=23 prefix-density=0.23 prefix-fanout=3.5 sequence=GTGATGGTCTTGCC criterion=fanout-score sequence-density=0.04 sequence-density-rank=26 fanout-score=128.61 fanout-score-rank=1 prefix-density=0.39 prefix-fanout=14.3 sequence=GGCGGCGGCGAACCGCCCCCGTCGCCGCGATCCGAACACTTCACCGGACCATTCAATCGGTAGGAGCGACGGGCGGTGTGTACAAAGGGCAGGGACGTAGTCAACGCGAGCTGATGACTCGCGCTTACTAGGCATTCCTCGTTGAAGACCAACAATTGCAATGATCTATCCCCATCACGATGAAATTTCCCAAGATTACCCGGGCCTGTCGGCCAAGGCTATATACTCGTTGAATACATCAGTGTAGCGCGCGTGCGGCCCAGAACATCTAAGGGCATCACAGACCTGTTATTGCCTCAAACTTCCGTCGCCTAAACGGCGATAGTCCCTCTAAGAAGCTAGCTGCGGAGGGATGGCTCCGCATAGCTAGTTAGCAGGCTGAGGTCTCGTTCGTTAACGGAATTAACCAGACAAATCGCTCCACCAACTAAGAACGGCCATGCACCACCACCCATAGAATCAAGAAAGAGCTCTCAGTCTGTCAATCCTTGCTATGTCTGGACCTGGTAAG criterion=sequence-density sequence-density=0.40 sequence-density-rank=1 fanout-score=2.28 fanout-score-rank=32 prefix-density=0.41 prefix-fanout=2.2 sequence=CGGTTCCGGTTC criterion=fanout-score sequence-density=0.03 sequence-density-rank=30 fanout-score=504.85 fanout-score-rank=1 prefix-density=0.81 prefix-fanout=18.8 sequence=GCCGCCGCCCCTCGTCCTCTGTGTTCCTTCTCCGAGTTTCAGCCATGGGTAAGGAGAAGACTCACATCAACATCGTGGTCATTGGCCATGTCGACTCTGGCAAGTCGACCACCACTGGCCACCTGATCTACAAGCTTGGAGGTATTGACAAGCGTGTGATCGAGAGGTTCGAGAAGGAGGCTGC SRR12666363 testing PE reads STAR mapping to Ensembl genome Started job on | Dec 07 13:08:16 Started mapping on | Dec 07 13:08:16 Finished on | Dec 07 13:12:19 Mapping speed, Million of reads per hour | 467.31 Number of input reads | 31543619 Average input read length | 289 UNIQUE READS: Uniquely mapped reads number | 27875568 Uniquely mapped reads % | 88.37% Average mapped length | 289.77 Number of splices: Total | 30690085 Number of splices: Annotated (sjdb) | 28828025 Number of splices: GT/AG | 30254558 Number of splices: GC/AG | 340926 Number of splices: AT/AC | 21476 Number of splices: Non-canonical | 73125 Mismatch rate per base, % | 0.38% Deletion rate per base | 0.02% Deletion average length | 2.84 Insertion rate per base | 0.02% Insertion average length | 2.44 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 427462 % of reads mapped to multiple loci | 1.36% Number of reads mapped to too many loci | 53232 % of reads mapped to too many loci | 0.17% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 9.44% % of reads unmapped: other | 0.66% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 3240592 3240592 3240592 N_multimapping 427462 427462 427462 N_noFeature 915658 27191623 1153211 N_ambiguous 579409 4694 133680 UnstrandedReadsAssigned:26380501 PositiveStrandReadsAssigned:679251 NegativeStrandReadsAssigned:26588677 Dataset is classified negative stranded MeadianReadLen=151 20thPercentileLength=151 echo kmer=147 SRR12666363 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: SRR12666363-trimmed-pair1.fastq SRR12666363-trimmed-pair2.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 31,543,619 reads, 28,821,322 reads pseudoaligned [quant] estimated average fragment length: 283.751 [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,268 rounds 52973 SRR12666363.ke.tsv 35125 SRR12666363.se.tsv 88098 total ==> SRR12666363.ke.tsv <== target_id length eff_length est_counts tpm PNS24245 936 654.355 0 0 PNS24247 1044 761.249 118.879 8.51931 PNS24249 1928 1645.25 117.469 3.89508 PNS24246 1044 761.249 118.879 8.51931 PNS24248 1044 761.249 118.879 8.51931 PNS24244 1471 1188.25 312.893 14.3653 PNS24243 293 98.0061 5 2.78319 KQK14069 1603 1320.25 3513.29 145.172 KQK14071 474 232.344 64.2997 15.0974 ==> SRR12666363.se.tsv <== BRADI_1g14170v3 3191 BRADI_1g53295v3 1045 BRADI_1g59795v3 168 BRADI_1g07683v3 0 BRADI_1g00485v3 128 BRADI_1g20270v3 3315 BRADI_1g74790v3 78 BRADI_1g09890v3 0 BRADI_1g77505v3 192 BRADI_1g48960v3 0 SRR12666363 completed mapping pipeline successfully