Starting /dee2/code/volunteer_pipeline.sh SRR6958367 current disk space = 1549156151296 free memory = 1600293552 SRR6958367 SRAfilesize 851cfd488408ee680c3703a1e62cc12c SRR6958367.sra SRR6958367.sra file validated SRR6958367 is paired end SRR6958367 is conventional basespace SRR6958367 read1 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR6958367_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 21.03 18.0 18.0 25.0 18.0 32.0 2 21.1485 18.0 18.0 25.0 18.0 29.0 3 25.8435 27.0 25.0 29.0 18.0 31.0 4 29.3095 32.0 27.0 32.0 25.0 33.0 5 30.6935 32.0 32.0 33.0 27.0 33.0 6 35.38775 37.0 35.0 38.0 31.0 38.0 7 36.11025 38.0 36.0 38.0 33.0 38.0 8 36.321 38.0 37.0 38.0 33.0 38.0 9 36.96 38.0 38.0 38.0 35.0 38.0 10-14 37.15590000000001 38.0 38.0 38.0 36.0 38.0 15-19 37.2108 38.0 38.0 38.0 36.2 38.0 20-24 37.173199999999994 38.0 38.0 38.0 36.0 38.0 25-29 36.965799999999994 38.0 38.0 38.0 35.8 38.0 30-34 36.9302 38.0 38.0 38.0 35.2 38.0 35-39 36.7448 38.0 38.0 38.0 34.8 38.0 40-44 36.68000000000001 38.0 38.0 38.0 34.6 38.0 45-49 36.72005 38.0 38.0 38.0 34.6 38.0 50-54 36.3233 38.0 37.4 38.0 33.4 38.0 55-59 36.17645 38.0 37.0 38.0 32.6 38.0 60-64 36.47775 38.0 37.8 38.0 33.8 38.0 65-69 36.431050000000006 38.0 38.0 38.0 33.8 38.0 70-74 36.34349999999999 38.0 37.8 38.0 33.6 38.0 75-79 35.82335 38.0 37.0 38.0 31.4 38.0 80-84 35.572199999999995 38.0 36.0 38.0 30.0 38.0 85-89 35.9042 38.0 37.0 38.0 31.6 38.0 90-94 35.7573 38.0 36.6 38.0 31.4 38.0 95-99 35.24485 38.0 35.6 38.0 28.4 38.0 100-104 34.60065 38.0 34.6 38.0 26.0 38.0 105-109 34.38125 38.0 34.4 38.0 24.4 38.0 110-114 34.24725 38.0 34.0 38.0 23.6 38.0 115-119 34.15335 38.0 34.0 38.0 23.4 38.0 120-124 33.41815 37.8 32.6 38.0 20.8 38.0 125-129 32.976 37.6 31.6 38.0 17.4 38.0 130-134 31.8935 36.2 30.0 38.0 14.2 38.0 135-139 30.906 35.6 28.2 38.0 13.0 38.0 140-144 29.551499999999997 34.2 26.2 38.0 9.8 38.0 145-149 27.1719 33.2 16.8 38.0 2.0 38.0 150-151 20.3575 25.5 2.0 35.5 2.0 38.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 2 1.0 3 0.0 4 0.0 5 0.0 6 0.0 7 0.0 8 0.0 9 1.0 10 1.0 11 1.0 12 1.0 13 2.0 14 0.0 15 1.0 16 4.0 17 4.0 18 0.0 19 3.0 20 4.0 21 16.0 22 13.0 23 21.0 24 18.0 25 35.0 26 47.0 27 49.0 28 85.0 29 84.0 30 120.0 31 162.0 32 212.0 33 251.0 34 394.0 35 727.0 36 1148.0 37 595.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 29.841434884325444 22.09513906940473 4.211073563815961 43.85235248245386 2 16.025 21.65 25.5 36.825 3 17.150000000000002 16.5 22.85 43.5 4 23.25 21.275 24.6 30.875000000000004 5 28.050000000000004 25.6 23.625 22.725 6 24.099999999999998 30.45 22.75 22.7 7 16.5 25.35 37.775 20.375 8 20.775 24.775 27.750000000000004 26.700000000000003 9 19.15 22.175 32.25 26.424999999999997 10-14 22.705000000000002 26.474999999999998 24.93 25.89 15-19 22.759999999999998 24.990000000000002 26.145000000000003 26.105 20-24 22.38 25.25 25.480000000000004 26.889999999999997 25-29 22.53 25.435000000000002 25.629999999999995 26.405 30-34 22.919999999999998 25.275 25.674999999999997 26.13 35-39 23.085 25.235000000000003 25.7 25.979999999999997 40-44 22.965 25.224999999999998 25.945 25.865 45-49 22.685 24.64 25.75 26.924999999999997 50-54 23.285 24.975 25.624999999999996 26.115 55-59 23.47 25.055 25.39 26.085 60-64 22.935 24.865000000000002 25.34 26.86 65-69 22.895 24.97 25.650000000000002 26.484999999999996 70-74 22.85 25.615 25.525 26.009999999999998 75-79 23.119999999999997 24.67 25.55 26.66 80-84 22.85 24.435000000000002 26.415 26.3 85-89 22.53 24.94 26.119999999999997 26.41 90-94 23.419999999999998 25.0 25.34 26.240000000000002 95-99 23.380000000000003 24.635 25.61 26.375 100-104 23.200000000000003 25.180000000000003 25.22 26.400000000000002 105-109 22.925 25.515 25.145 26.415 110-114 23.86 25.009999999999998 25.205 25.924999999999997 115-119 23.16 24.175 25.95 26.715 120-124 23.39 24.665 25.5 26.445 125-129 23.835 24.95 24.77 26.445 130-134 23.41 25.135 25.16 26.295 135-139 24.12 24.675 24.9 26.305 140-144 23.665 24.845 24.985 26.505000000000003 145-149 23.175 25.040000000000003 24.875 26.91 150-151 24.1625 23.825 25.662499999999998 26.35 >>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 0.0 25 0.0 26 0.5 27 1.0 28 1.5 29 3.0 30 4.0 31 6.0 32 10.5 33 16.0 34 24.0 35 40.5 36 57.5 37 64.5 38 80.0 39 105.5 40 120.5 41 145.0 42 167.5 43 191.5 44 200.5 45 201.0 46 206.5 47 202.0 48 200.5 49 183.0 50 176.5 51 163.5 52 127.5 53 113.0 54 109.5 55 92.5 56 83.5 57 77.5 58 70.5 59 68.0 60 68.0 61 63.5 62 66.0 63 67.0 64 55.0 65 52.5 66 49.0 67 37.5 68 35.0 69 36.0 70 29.0 71 21.5 72 19.0 73 20.0 74 18.5 75 19.5 76 13.0 77 5.5 78 5.0 79 3.0 80 1.0 81 0.5 82 0.5 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 3.8249999999999997 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 0.0 82-83 0.025 0.0 0.0 0.0 0.0 84-85 0.025 0.0 0.0 0.0 0.0 86-87 0.05 0.0 0.0 0.0 0.0 88-89 0.075 0.0 0.0 0.0 0.0 90-91 0.125 0.0 0.0 0.0 0.0 92-93 0.125 0.0 0.0 0.0 0.0 94-95 0.16249999999999998 0.0 0.0 0.0 0.0 96-97 0.175 0.0 0.0 0.0 0.0 98-99 0.175 0.0 0.0 0.0 0.0 100-101 0.175 0.0 0.0 0.0 0.0 102-103 0.175 0.0 0.0 0.0 0.0 104-105 0.21250000000000002 0.0 0.0 0.0 0.0 106-107 0.325 0.0 0.0 0.0 0.0 108-109 0.4625 0.0 0.0 0.0 0.0 110-111 0.4875 0.0 0.0 0.0 0.0 112-113 0.5375000000000001 0.0 0.0 0.0 0.0 114-115 0.575 0.0 0.0 0.0 0.0 116-117 0.8375 0.0 0.0 0.0 0.0 118-119 0.9874999999999999 0.0 0.0 0.0 0.0 120-121 1.175 0.0 0.0 0.0 0.0 122-123 1.4 0.0 0.0 0.0 0.0 124-125 1.725 0.0 0.0 0.0 0.0 126-127 1.9625 0.0 0.0 0.0 0.0 128-129 2.175 0.0 0.0 0.0 0.0 130-131 2.4875 0.0 0.0 0.0 0.0 132-133 2.8625 0.0 0.0 0.0 0.0 134-135 3.175 0.0 0.0 0.0 0.0 136-137 3.5875000000000004 0.0 0.0 0.0 0.0 138-139 3.9125 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position AGAAAAT 10 0.006836113 144.9625 9 >>END_MODULE SRR6958367 read2 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR6958367_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 32.2815 33.0 33.0 34.0 31.0 34.0 2 32.15825 33.0 33.0 34.0 31.0 34.0 3 32.32175 33.0 33.0 34.0 31.0 34.0 4 32.2625 33.0 33.0 34.0 31.0 34.0 5 32.2065 33.0 33.0 34.0 31.0 34.0 6 36.179 38.0 38.0 38.0 33.0 38.0 7 36.0275 38.0 38.0 38.0 32.0 38.0 8 36.0015 38.0 38.0 38.0 33.0 38.0 9 35.934 38.0 38.0 38.0 33.0 38.0 10-14 35.92355 38.0 38.0 38.0 31.4 38.0 15-19 36.13275 38.0 38.0 38.0 33.2 38.0 20-24 36.291000000000004 38.0 38.0 38.0 33.8 38.0 25-29 36.2678 38.0 38.0 38.0 33.8 38.0 30-34 36.28404999999999 38.0 38.0 38.0 34.0 38.0 35-39 36.14815 38.0 38.0 38.0 33.4 38.0 40-44 35.96125 38.0 38.0 38.0 32.8 38.0 45-49 35.973099999999995 38.0 37.8 38.0 33.0 38.0 50-54 35.98315 38.0 38.0 38.0 33.0 38.0 55-59 35.8617 38.0 37.6 38.0 32.6 38.0 60-64 35.73345 38.0 37.0 38.0 31.4 38.0 65-69 35.4341 38.0 37.0 38.0 29.4 38.0 70-74 35.0495 38.0 36.0 38.0 28.6 38.0 75-79 35.275400000000005 38.0 36.6 38.0 29.0 38.0 80-84 35.03959999999999 38.0 36.0 38.0 28.4 38.0 85-89 34.86354999999999 38.0 36.0 38.0 27.6 38.0 90-94 34.46805 38.0 34.8 38.0 25.6 38.0 95-99 33.95954999999999 38.0 34.4 38.0 21.6 38.0 100-104 33.34155 38.0 33.8 38.0 17.4 38.0 105-109 33.1754 38.0 33.0 38.0 17.4 38.0 110-114 32.5565 38.0 31.2 38.0 15.0 38.0 115-119 31.8832 37.2 30.4 38.0 14.2 38.0 120-124 31.235599999999998 37.0 29.0 38.0 12.8 38.0 125-129 30.40535 36.0 27.0 38.0 11.8 38.0 130-134 29.182499999999997 34.6 23.8 38.0 11.0 38.0 135-139 28.537950000000002 33.6 22.2 38.0 2.0 38.0 140-144 27.795500000000004 33.2 20.8 38.0 2.0 38.0 145-149 25.2917 33.0 8.4 38.0 2.0 38.0 150-151 18.63625 17.5 2.0 34.5 2.0 38.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 2 30.0 3 6.0 4 4.0 5 2.0 6 3.0 7 3.0 8 4.0 9 5.0 10 5.0 11 2.0 12 6.0 13 4.0 14 4.0 15 10.0 16 11.0 17 10.0 18 10.0 19 24.0 20 20.0 21 20.0 22 28.0 23 41.0 24 35.0 25 52.0 26 48.0 27 56.0 28 82.0 29 115.0 30 96.0 31 131.0 32 174.0 33 260.0 34 383.0 35 609.0 36 950.0 37 757.0 >>END_MODULE >>Per base sequence content warn #Base G A T C 1 39.65 20.1 11.15 29.099999999999998 2 28.199999999999996 24.5 25.3 22.0 3 23.200000000000003 26.974999999999998 26.674999999999997 23.150000000000002 4 26.5 31.15 20.95 21.4 5 28.825 32.25 20.0 18.925 6 24.5 36.575 19.85 19.075 7 23.925 19.775000000000002 34.075 22.225 8 24.65 23.599999999999998 24.099999999999998 27.650000000000002 9 23.549999999999997 22.650000000000002 26.700000000000003 27.1 10-14 26.05 26.495 22.770000000000003 24.685000000000002 15-19 26.5 25.480000000000004 24.45 23.57 20-24 26.284999999999997 25.040000000000003 24.6 24.075 25-29 26.400000000000002 25.36 24.055 24.185000000000002 30-34 25.905 25.15 24.785 24.16 35-39 26.755000000000003 25.205 24.015 24.025 40-44 25.965 25.335 24.46 24.240000000000002 45-49 25.575 25.935000000000002 24.3 24.19 50-54 26.32 25.855 24.0 23.825 55-59 26.355 25.405 24.505 23.735 60-64 27.060000000000002 25.245 24.495 23.200000000000003 65-69 26.810000000000002 25.224999999999998 24.67 23.294999999999998 70-74 26.83 25.180000000000003 24.635 23.355 75-79 26.179999999999996 25.275 25.009999999999998 23.535 80-84 26.795 25.240000000000002 24.84 23.125 85-89 26.945000000000004 25.145 24.529999999999998 23.380000000000003 90-94 26.669999999999998 25.39 24.705 23.235 95-99 26.790000000000003 25.53 24.395 23.285 100-104 26.595000000000002 25.474999999999998 24.115000000000002 23.815 105-109 27.034999999999997 25.540000000000003 24.215 23.21 110-114 26.995 25.66 24.560000000000002 22.785 115-119 27.139999999999997 25.69 24.19 22.98 120-124 26.69 25.814999999999998 24.465 23.03 125-129 27.139999999999997 25.014999999999997 24.83 23.015 130-134 27.42 24.98 24.555 23.044999999999998 135-139 27.08 25.235000000000003 24.935 22.75 140-144 27.13 25.685000000000002 24.175 23.01 145-149 26.815 25.56 24.57 23.055 150-151 28.775000000000002 24.587500000000002 24.125 22.5125 >>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 1.0 22 1.0 23 0.5 24 2.0 25 1.5 26 0.0 27 0.0 28 1.5 29 4.5 30 7.0 31 6.5 32 6.0 33 10.0 34 17.5 35 27.0 36 35.0 37 45.5 38 56.5 39 92.5 40 121.0 41 134.0 42 163.5 43 181.5 44 197.0 45 210.0 46 209.5 47 191.5 48 199.5 49 208.0 50 177.0 51 154.5 52 141.0 53 121.0 54 100.0 55 89.0 56 90.5 57 92.5 58 77.5 59 68.5 60 64.5 61 59.5 62 64.0 63 65.5 64 68.0 65 63.0 66 56.0 67 50.0 68 37.5 69 36.0 70 42.0 71 38.0 72 29.0 73 24.5 74 24.5 75 18.0 76 8.0 77 4.0 78 2.5 79 1.5 80 0.5 81 0.5 82 0.5 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 0.0 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 99.175 #Duplication Level Percentage of deduplicated Percentage of total 1 99.44542475422233 98.625 2 0.4285354171918326 0.8500000000000001 3 0.07562389715149988 0.22499999999999998 4 0.0 0.0 5 0.025207965717166627 0.125 6 0.0 0.0 7 0.025207965717166627 0.17500000000000002 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 warn #Sequence Count Percentage Possible Source CAGACACAGCCACGAATTTGCAGTGTACGCAGTTCTAGTAAACAAGAACC 7 0.17500000000000002 No Hit CACACAGGCAAAACACAGCTGATTCGTGTACTCGATCTCCCCAGCAAGTT 5 0.125 No Hit >>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 0.025 0.0 0.0 0.0 0.0 86-87 0.05 0.0 0.0 0.0 0.0 88-89 0.075 0.0 0.0 0.0 0.0 90-91 0.125 0.0 0.0 0.0 0.0 92-93 0.125 0.0 0.0 0.0 0.0 94-95 0.16249999999999998 0.0 0.0 0.0 0.0 96-97 0.175 0.0 0.0 0.0 0.0 98-99 0.175 0.0 0.0 0.0 0.0 100-101 0.175 0.0 0.0 0.0 0.0 102-103 0.175 0.0 0.0 0.0 0.0 104-105 0.21250000000000002 0.0 0.0 0.0 0.0 106-107 0.325 0.0 0.0 0.0 0.0 108-109 0.4625 0.0 0.0 0.0 0.0 110-111 0.4875 0.0 0.0 0.0 0.0 112-113 0.55 0.0 0.0 0.0 0.0 114-115 0.6 0.0 0.0 0.0 0.0 116-117 0.8625 0.0 0.0 0.0 0.0 118-119 1.0125 0.0 0.0 0.0 0.0 120-121 1.1875 0.0 0.0 0.0 0.0 122-123 1.4 0.0 0.0 0.0 0.0 124-125 1.7125 0.0 0.0 0.0 0.0 126-127 1.9375 0.0 0.0 0.0 0.0 128-129 2.1500000000000004 0.0 0.0 0.0 0.0 130-131 2.4625000000000004 0.0 0.0 0.0 0.0 132-133 2.85 0.0 0.0 0.0 0.0 134-135 3.1624999999999996 0.0 0.0 0.0 0.0 136-137 3.5875 0.0 0.0 0.0 0.0 138-139 3.8625 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content pass >>END_MODULE Read 767740 spots for SRR6958367.sra Written 767740 spots for SRR6958367.sra Read 767740 spots for SRR6958367.sra Written 767740 spots for SRR6958367.sra Read 767740 spots for SRR6958367.sra Written 767740 spots for SRR6958367.sra Read 767740 spots for SRR6958367.sra Written 767740 spots for SRR6958367.sra Read 767740 spots for SRR6958367.sra Written 767740 spots for SRR6958367.sra Read 767740 spots for SRR6958367.sra Written 767740 spots for SRR6958367.sra Read 767740 spots for SRR6958367.sra Written 767740 spots for SRR6958367.sra Read 767740 spots for SRR6958367.sra Written 767740 spots for SRR6958367.sra Read 767740 spots for SRR6958367.sra Written 767740 spots for SRR6958367.sra Read 767740 spots for SRR6958367.sra Written 767740 spots for SRR6958367.sra Read 767740 spots for SRR6958367.sra Written 767740 spots for SRR6958367.sra Read 767740 spots for SRR6958367.sra Written 767740 spots for SRR6958367.sra Read 767740 spots for SRR6958367.sra Written 767740 spots for SRR6958367.sra Read 767751 spots for SRR6958367.sra Written 767751 spots for SRR6958367.sra Read 767740 spots for SRR6958367.sra Written 767740 spots for SRR6958367.sra Read 767740 spots for SRR6958367.sra Written 767740 spots for SRR6958367.sra Read 767740 spots for SRR6958367.sra Written 767740 spots for SRR6958367.sra Read 767740 spots for SRR6958367.sra Written 767740 spots for SRR6958367.sra Read 767740 spots for SRR6958367.sra Written 767740 spots for SRR6958367.sra Read 767740 spots for SRR6958367.sra Written 767740 spots for SRR6958367.sra SRR ids: ['SRR6958367.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_1r230n5b SRR6958367.sra spots: 15354811 blocks: [[1, 767740], [767741, 1535480], [1535481, 2303220], [2303221, 3070960], [3070961, 3838700], [3838701, 4606440], [4606441, 5374180], [5374181, 6141920], [6141921, 6909660], [6909661, 7677400], [7677401, 8445140], [8445141, 9212880], [9212881, 9980620], [9980621, 10748360], [10748361, 11516100], [11516101, 12283840], [12283841, 13051580], [13051581, 13819320], [13819321, 14587060], [14587061, 15354811]] SRR6958367 file size 5181541 SRR6958367 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 SRR6958367 SRR6958367_1.fastq SRR6958367_2.fastq Input file: SRR6958367_1.fastq Paired file: SRR6958367_2.fastq trimmed: SRR6958367-trimmed-pair1.fastq, SRR6958367-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 21:07:57 2024 >> started Fri Dec 6 21:08:16 2024 >> done (19.231s) 15354811 read pairs processed; of these: 44510 ( 0.29%) short read pairs filtered out after trimming by size control 44565 ( 0.29%) empty read pairs filtered out after trimming by size control 15265736 (99.42%) read pairs available; of these: 8230531 (53.92%) trimmed read pairs available after processing 7035205 (46.08%) untrimmed read pairs available after processing Length distribution of reads after trimming: length count percentage 18 1 0.00% 19 3 0.00% 20 4 0.00% 21 0 0.00% 22 3 0.00% 23 4 0.00% 24 5 0.00% 25 4 0.00% 26 2 0.00% 27 5 0.00% 28 3 0.00% 29 9 0.00% 30 5 0.00% 31 5 0.00% 32 7 0.00% 33 10 0.00% 34 10 0.00% 35 9 0.00% 36 17 0.00% 37 8 0.00% 38 10 0.00% 39 10 0.00% 40 14 0.00% 41 14 0.00% 42 13 0.00% 43 28 0.00% 44 24 0.00% 45 21 0.00% 46 27 0.00% 47 29 0.00% 48 29 0.00% 49 28 0.00% 50 53 0.00% 51 51 0.00% 52 56 0.00% 53 60 0.00% 54 75 0.00% 55 82 0.00% 56 80 0.00% 57 88 0.00% 58 96 0.00% 59 116 0.00% 60 128 0.00% 61 119 0.00% 62 156 0.00% 63 186 0.00% 64 187 0.00% 65 210 0.00% 66 236 0.00% 67 274 0.00% 68 320 0.00% 69 339 0.00% 70 336 0.00% 71 386 0.00% 72 476 0.00% 73 547 0.00% 74 526 0.00% 75 594 0.00% 76 726 0.00% 77 782 0.01% 78 907 0.01% 79 1045 0.01% 80 1168 0.01% 81 1398 0.01% 82 1582 0.01% 83 1899 0.01% 84 3446 0.02% 85 4122 0.03% 86 4326 0.03% 87 4285 0.03% 88 4284 0.03% 89 4520 0.03% 90 4588 0.03% 91 4733 0.03% 92 5344 0.04% 93 5456 0.04% 94 5761 0.04% 95 6210 0.04% 96 6576 0.04% 97 7113 0.05% 98 7513 0.05% 99 7864 0.05% 100 8494 0.06% 101 8898 0.06% 102 9482 0.06% 103 10320 0.07% 104 10972 0.07% 105 11749 0.08% 106 12123 0.08% 107 13212 0.09% 108 13692 0.09% 109 14573 0.10% 110 15098 0.10% 111 16309 0.11% 112 17273 0.11% 113 18138 0.12% 114 19348 0.13% 115 20858 0.14% 116 22019 0.14% 117 22648 0.15% 118 23946 0.16% 119 25004 0.16% 120 26354 0.17% 121 27973 0.18% 122 29485 0.19% 123 31012 0.20% 124 33656 0.22% 125 35413 0.23% 126 37689 0.25% 127 39586 0.26% 128 41622 0.27% 129 44048 0.29% 130 46716 0.31% 131 49153 0.32% 132 52779 0.35% 133 56914 0.37% 134 60192 0.39% 135 64582 0.42% 136 69381 0.45% 137 74824 0.49% 138 79944 0.52% 139 86527 0.57% 140 94861 0.62% 141 104143 0.68% 142 117169 0.77% 143 133494 0.87% 144 156060 1.02% 145 187350 1.23% 146 236534 1.55% 147 320398 2.10% 148 493620 3.23% 149 989522 6.48% 150 3993588 26.16% 151 7035205 46.08% 15265736 reads passed initial QC criterion=sequence-density sequence-density=0.78 sequence-density-rank=1 fanout-score=2.35 fanout-score-rank=34 prefix-density=0.84 prefix-fanout=2.2 sequence=GAGCTGGAGCTG criterion=fanout-score sequence-density=0.02 sequence-density-rank=33 fanout-score=210.35 fanout-score-rank=1 prefix-density=0.54 prefix-fanout=9.4 sequence=GGCGGCGGCGAACCGCCCCCGTCGCCGCGATCCGAACACTTCACCGGACCATTCAATCGGTAGGAGCGACGGGCGGTGTGTACAAAGGGCAGGGACGTAGTCAACGCGAGCTGATGACTCGCGCTTACTAGGCATTCCTCGTTGAAGACCAACAATTGCAATGATCTATCCCCATCACGATGAAATTTCCCAAGATTACCCGGGCCTGTCGGCCAAGGCTATATACTCGTTGAATACATCAGTGTAGCGCGCGTGCGGCCCAGAACATCTAAGGGCATCACAGACCTGTTATTGCCTCAAACTTCCGTCGCCTAAACGGCGATAGTCCCTCTAAGAAGCTAGCTGCGGAGGGATGGCTCCGCATAGCTAGTTAGCAGGCTGAGGTCTCGTTCGTTAACGGAATTAACCAGACAAATCGCTCCACCAACTAAGAACGGCCATGCACCACCACCCATAGAATCAAGAAAGAGCTCTCAGTCTGTCAATCCTTGCTATGTCTGGACCTGGTAAG criterion=sequence-density sequence-density=0.52 sequence-density-rank=1 fanout-score=12.26 fanout-score-rank=12 prefix-density=1.64 prefix-fanout=3.9 sequence=AAGGAGAAGCTGCCTGGCCAGCACTGAGC criterion=fanout-score sequence-density=0.10 sequence-density-rank=17 fanout-score=143.07 fanout-score-rank=1 prefix-density=0.69 prefix-fanout=21.2 sequence=CAAGAAGAAGGT SRR6958367 testing PE reads STAR mapping to Ensembl genome Started job on | Dec 06 21:09:25 Started mapping on | Dec 06 21:09:26 Finished on | Dec 06 21:10:37 Mapping speed, Million of reads per hour | 774.04 Number of input reads | 15265736 Average input read length | 295 UNIQUE READS: Uniquely mapped reads number | 14658122 Uniquely mapped reads % | 96.02% Average mapped length | 294.36 Number of splices: Total | 14982642 Number of splices: Annotated (sjdb) | 14090187 Number of splices: GT/AG | 14793838 Number of splices: GC/AG | 153900 Number of splices: AT/AC | 5865 Number of splices: Non-canonical | 29039 Mismatch rate per base, % | 0.26% Deletion rate per base | 0.01% Deletion average length | 2.19 Insertion rate per base | 0.01% Insertion average length | 2.34 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 119005 % of reads mapped to multiple loci | 0.78% Number of reads mapped to too many loci | 23204 % of reads mapped to too many loci | 0.15% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 1.94% % of reads unmapped: other | 1.11% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 512830 512830 512830 N_multimapping 119005 119005 119005 N_noFeature 552755 14217840 708851 N_ambiguous 331402 2121 48329 UnstrandedReadsAssigned:13773965 PositiveStrandReadsAssigned:438161 NegativeStrandReadsAssigned:13900942 Dataset is classified negative stranded MeadianReadLen=151 20thPercentileLength=148 echo kmer=143 SRR6958367 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: SRR6958367-trimmed-pair1.fastq SRR6958367-trimmed-pair2.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 15,265,736 reads, 13,893,893 reads pseudoaligned [quant] estimated average fragment length: 242.959 [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,140 rounds 52973 SRR6958367.ke.tsv 35125 SRR6958367.se.tsv 88098 total ==> SRR6958367.ke.tsv <== target_id length eff_length est_counts tpm PNS24245 936 694.391 86.2134 12.2419 PNS24247 1044 802.041 40.8982 5.0279 PNS24249 1928 1686.04 113.686 6.64841 PNS24246 1044 802.041 40.8982 5.0279 PNS24248 1044 802.041 40.8982 5.0279 PNS24244 1471 1229.04 54.4063 4.36478 PNS24243 293 87.804 2 2.24592 KQK14069 1603 1361.04 592.29 42.9085 KQK14071 474 239.753 22.0371 9.06294 ==> SRR6958367.se.tsv <== BRADI_1g14170v3 669 BRADI_1g53295v3 221 BRADI_1g59795v3 104 BRADI_1g07683v3 0 BRADI_1g00485v3 10 BRADI_1g20270v3 530 BRADI_1g74790v3 704 BRADI_1g09890v3 0 BRADI_1g77505v3 97 BRADI_1g48960v3 0 SRR6958367 completed mapping pipeline successfully