Starting /dee2/code/volunteer_pipeline.sh SRR7814814 current disk space = 1551538421760 free memory = 1356559756 SRR7814814 SRAfilesize 7222199f1665a347d709140b4b41f7b4 SRR7814814.sra SRR7814814.sra file validated SRR7814814 is paired end SRR7814814 is conventional basespace SRR7814814 read1 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR7814814_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 50 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 36.44125 37.0 37.0 37.0 37.0 37.0 2 36.4255 37.0 37.0 37.0 37.0 37.0 3 36.529 37.0 37.0 37.0 37.0 37.0 4 36.576 37.0 37.0 37.0 37.0 37.0 5 36.48 37.0 37.0 37.0 37.0 37.0 6 36.6255 37.0 37.0 37.0 37.0 37.0 7 36.563 37.0 37.0 37.0 37.0 37.0 8 36.5475 37.0 37.0 37.0 37.0 37.0 9 36.4925 37.0 37.0 37.0 37.0 37.0 10-14 36.5327 37.0 37.0 37.0 37.0 37.0 15-19 36.528400000000005 37.0 37.0 37.0 37.0 37.0 20-24 36.494299999999996 37.0 37.0 37.0 37.0 37.0 25-29 36.4544 37.0 37.0 37.0 37.0 37.0 30-34 36.2821 37.0 37.0 37.0 37.0 37.0 35-39 36.1722 37.0 37.0 37.0 37.0 37.0 40-44 36.1989 37.0 37.0 37.0 37.0 37.0 45-49 36.2888 37.0 37.0 37.0 37.0 37.0 50-54 36.351200000000006 37.0 37.0 37.0 37.0 37.0 55-59 36.32449999999999 37.0 37.0 37.0 37.0 37.0 60-64 36.2746 37.0 37.0 37.0 37.0 37.0 65-69 36.2401 37.0 37.0 37.0 37.0 37.0 70-74 36.0785 37.0 37.0 37.0 37.0 37.0 75-79 36.108700000000006 37.0 37.0 37.0 37.0 37.0 80-84 36.0441 37.0 37.0 37.0 37.0 37.0 85-89 36.0923 37.0 37.0 37.0 37.0 37.0 90-94 35.980199999999996 37.0 37.0 37.0 37.0 37.0 95-99 35.6822 37.0 37.0 37.0 37.0 37.0 100-104 35.4079 37.0 37.0 37.0 34.6 37.0 105-109 35.538 37.0 37.0 37.0 37.0 37.0 110-114 35.721 37.0 37.0 37.0 37.0 37.0 115-119 35.5111 37.0 37.0 37.0 37.0 37.0 120-124 34.8287 37.0 37.0 37.0 25.0 37.0 125-129 34.6701 37.0 37.0 37.0 25.0 37.0 130-134 35.1599 37.0 37.0 37.0 25.0 37.0 135-139 34.9924 37.0 37.0 37.0 25.0 37.0 140-144 35.0327 37.0 37.0 37.0 27.4 37.0 145-149 34.9628 37.0 37.0 37.0 27.4 37.0 150-151 34.293 37.0 37.0 37.0 25.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 20 1.0 21 0.0 22 0.0 23 1.0 24 2.0 25 4.0 26 10.0 27 9.0 28 13.0 29 18.0 30 37.0 31 54.0 32 100.0 33 148.0 34 263.0 35 552.0 36 2626.0 37 162.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 53.81918357124968 12.17129977460556 4.633107938893063 29.37640871525169 2 25.75 13.15 31.525 29.575000000000003 3 22.975 19.125 23.225 34.675 4 26.924999999999997 24.625 20.674999999999997 27.775 5 27.1 29.675 21.975 21.25 6 21.3 33.0 23.425 22.275 7 17.825 23.075000000000003 39.15 19.950000000000003 8 20.200000000000003 22.5 30.425 26.875 9 19.2 21.375 32.9 26.525 10-14 23.345 26.43 25.014999999999997 25.21 15-19 23.445 25.369999999999997 24.695 26.490000000000002 20-24 23.294999999999998 25.064999999999998 25.590000000000003 26.05 25-29 23.125 26.029999999999998 24.965 25.88 30-34 23.47 25.455 24.755 26.32 35-39 23.705000000000002 25.795 24.785 25.715 40-44 23.93 25.255 24.505 26.31 45-49 23.45 24.765 24.92 26.865 50-54 23.919999999999998 25.235000000000003 24.515 26.33 55-59 24.51 25.285000000000004 24.39 25.814999999999998 60-64 23.395 25.0 24.86 26.745 65-69 23.87 25.040000000000003 24.695 26.395000000000003 70-74 23.96 25.2 24.490000000000002 26.35 75-79 24.075 25.124999999999996 24.595 26.205000000000002 80-84 23.7 24.779999999999998 24.610000000000003 26.91 85-89 23.79 24.224999999999998 25.11 26.875 90-94 24.145 25.130000000000003 23.68 27.045 95-99 23.625 24.985 24.68 26.71 100-104 24.665 24.91 24.235 26.19 105-109 24.44 24.645 24.33 26.584999999999997 110-114 24.85 24.535 24.295 26.32 115-119 24.38 24.51 24.425 26.685 120-124 24.59 25.145 23.54 26.724999999999998 125-129 24.765 24.875 24.19 26.169999999999998 130-134 24.565 25.35 23.93 26.155 135-139 24.625 24.595 24.654999999999998 26.125 140-144 24.785 24.675 23.805 26.735 145-149 24.51 25.56 23.169999999999998 26.76 150-151 24.15 24.975 24.0625 26.8125 >>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 0.0 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 1.0 20 1.0 21 0.5 22 0.5 23 0.0 24 0.0 25 0.5 26 0.5 27 2.0 28 3.5 29 3.5 30 7.0 31 14.0 32 19.5 33 21.5 34 28.0 35 37.0 36 50.5 37 54.5 38 65.0 39 94.0 40 125.0 41 152.0 42 160.5 43 163.0 44 166.5 45 180.5 46 189.0 47 180.5 48 176.0 49 165.0 50 153.5 51 140.5 52 132.5 53 137.0 54 132.0 55 109.5 56 86.0 57 80.0 58 80.5 59 78.5 60 77.0 61 71.0 62 63.0 63 67.5 64 66.5 65 57.0 66 52.0 67 45.5 68 43.5 69 46.5 70 42.0 71 38.5 72 28.0 73 19.0 74 19.0 75 18.5 76 15.5 77 10.5 78 8.0 79 6.5 80 5.0 81 3.5 82 3.0 83 0.5 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 0.17500000000000002 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 91.925 #Duplication Level Percentage of deduplicated Percentage of total 1 91.73239053576285 84.325 2 7.805276040250204 14.35 3 0.4079412564590699 1.125 4 0.054392167527875984 0.2 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 0.025 0.0 0.0 34-35 0.0 0.0 0.025 0.0 0.0 36-37 0.0 0.0 0.025 0.0 0.0 38-39 0.0 0.0 0.025 0.0 0.0 40-41 0.0 0.0 0.025 0.0 0.0 42-43 0.0 0.0 0.025 0.0 0.0 44-45 0.0 0.0 0.025 0.0 0.0 46-47 0.0 0.0 0.025 0.0 0.0 48-49 0.0 0.0 0.025 0.0 0.0 50-51 0.0 0.0 0.025 0.0 0.0 52-53 0.0 0.0 0.025 0.0 0.0 54-55 0.0 0.0 0.025 0.0 0.0 56-57 0.0 0.0 0.025 0.0 0.0 58-59 0.0 0.0 0.025 0.0 0.0 60-61 0.0 0.0 0.025 0.0 0.0 62-63 0.0 0.0 0.025 0.0 0.025 64-65 0.0125 0.0 0.025 0.0 0.025 66-67 0.025 0.0 0.025 0.0 0.025 68-69 0.025 0.0 0.025 0.0 0.025 70-71 0.025 0.0 0.025 0.0 0.025 72-73 0.025 0.0 0.025 0.0 0.025 74-75 0.037500000000000006 0.0 0.025 0.0 0.025 76-77 0.05 0.0 0.025 0.0 0.025 78-79 0.05 0.0 0.025 0.0 0.025 80-81 0.0625 0.0 0.025 0.0 0.025 82-83 0.1 0.0 0.025 0.0 0.025 84-85 0.1 0.0 0.025 0.0 0.025 86-87 0.15 0.0 0.025 0.0 0.025 88-89 0.225 0.0 0.025 0.0 0.025 90-91 0.2375 0.0 0.025 0.0 0.025 92-93 0.36250000000000004 0.0 0.025 0.0 0.025 94-95 0.4125 0.0 0.025 0.0 0.025 96-97 0.575 0.0 0.025 0.0 0.025 98-99 0.7375 0.0 0.025 0.0 0.025 100-101 0.875 0.0 0.025 0.0 0.025 102-103 0.9874999999999999 0.0 0.025 0.0 0.025 104-105 1.1749999999999998 0.0 0.025 0.0 0.025 106-107 1.3125 0.0 0.025 0.0 0.025 108-109 1.4875 0.0 0.025 0.0 0.025 110-111 1.6625 0.0 0.025 0.0 0.025 112-113 1.925 0.0 0.025 0.0 0.025 114-115 2.075 0.0 0.025 0.0 0.025 116-117 2.3375 0.0 0.025 0.0 0.025 118-119 2.5999999999999996 0.0 0.025 0.0 0.025 120-121 2.875 0.0 0.025 0.0 0.025 122-123 3.225 0.0 0.025 0.0 0.025 124-125 3.5875000000000004 0.0 0.025 0.0 0.025 126-127 3.9875 0.0 0.025 0.0 0.025 128-129 4.300000000000001 0.0 0.025 0.0 0.025 130-131 4.699999999999999 0.0 0.025 0.0 0.025 132-133 5.15 0.0 0.025 0.0 0.025 134-135 5.675 0.0 0.025 0.0 0.025 136-137 6.1 0.0 0.025 0.0 0.025 138-139 6.5 0.0 0.025 0.0 0.025 >>END_MODULE >>Kmer Content pass >>END_MODULE SRR7814814 read2 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR7814814_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 pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 36.057 37.0 37.0 37.0 37.0 37.0 2 35.7395 37.0 37.0 37.0 37.0 37.0 3 35.6285 37.0 37.0 37.0 37.0 37.0 4 35.599 37.0 37.0 37.0 37.0 37.0 5 35.7055 37.0 37.0 37.0 37.0 37.0 6 35.536 37.0 37.0 37.0 37.0 37.0 7 35.3145 37.0 37.0 37.0 37.0 37.0 8 35.454 37.0 37.0 37.0 37.0 37.0 9 35.8105 37.0 37.0 37.0 37.0 37.0 10-14 35.6794 37.0 37.0 37.0 37.0 37.0 15-19 35.179899999999996 37.0 37.0 37.0 29.8 37.0 20-24 35.3756 37.0 37.0 37.0 37.0 37.0 25-29 35.3201 37.0 37.0 37.0 34.6 37.0 30-34 35.0452 37.0 37.0 37.0 29.8 37.0 35-39 35.0726 37.0 37.0 37.0 29.8 37.0 40-44 34.6689 37.0 37.0 37.0 25.0 37.0 45-49 34.8526 37.0 37.0 37.0 25.0 37.0 50-54 34.1508 37.0 37.0 37.0 25.0 37.0 55-59 34.1185 37.0 37.0 37.0 25.0 37.0 60-64 34.3822 37.0 37.0 37.0 25.0 37.0 65-69 34.384499999999996 37.0 37.0 37.0 25.0 37.0 70-74 33.9328 37.0 37.0 37.0 25.0 37.0 75-79 33.80409999999999 37.0 37.0 37.0 22.2 37.0 80-84 33.7329 37.0 37.0 37.0 22.2 37.0 85-89 34.0326 37.0 37.0 37.0 22.2 37.0 90-94 33.5894 37.0 37.0 37.0 22.2 37.0 95-99 32.6407 37.0 37.0 37.0 11.0 37.0 100-104 33.098400000000005 37.0 37.0 37.0 16.6 37.0 105-109 32.6069 37.0 37.0 37.0 11.0 37.0 110-114 32.95 37.0 37.0 37.0 11.0 37.0 115-119 33.1307 37.0 37.0 37.0 19.4 37.0 120-124 32.4216 37.0 34.6 37.0 11.0 37.0 125-129 32.6389 37.0 37.0 37.0 11.0 37.0 130-134 32.1139 37.0 29.8 37.0 11.0 37.0 135-139 32.10809999999999 37.0 32.2 37.0 11.0 37.0 140-144 32.2392 37.0 32.2 37.0 11.0 37.0 145-149 31.929399999999998 37.0 29.8 37.0 11.0 37.0 150-151 31.3495 37.0 31.0 37.0 11.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 13 1.0 14 5.0 15 4.0 16 2.0 17 6.0 18 6.0 19 4.0 20 8.0 21 16.0 22 27.0 23 39.0 24 48.0 25 59.0 26 85.0 27 91.0 28 117.0 29 96.0 30 139.0 31 145.0 32 166.0 33 213.0 34 355.0 35 817.0 36 1519.0 37 32.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 47.949999999999996 19.2 7.324999999999999 25.525 2 29.25 22.8 25.224999999999998 22.725 3 23.875 24.4 26.974999999999998 24.75 4 29.525000000000002 29.4 19.375 21.7 5 27.55 32.824999999999996 18.5 21.125 6 24.55 34.050000000000004 19.55 21.85 7 23.875 17.775 32.574999999999996 25.775 8 24.275 21.425 24.925 29.375 9 25.0 21.55 26.724999999999998 26.724999999999998 10-14 26.290000000000003 25.16 22.88 25.669999999999998 15-19 26.16 24.65 23.945 25.245 20-24 25.955000000000002 25.72 22.88 25.445 25-29 25.729999999999997 25.055 23.74 25.474999999999998 30-34 26.195 25.085 23.715 25.005 35-39 25.865 25.424999999999997 23.64 25.069999999999997 40-44 26.505000000000003 25.779999999999998 23.095 24.62 45-49 26.51 25.259999999999998 24.104999999999997 24.125 50-54 26.314999999999998 25.509999999999998 23.724999999999998 24.45 55-59 26.38 25.264999999999997 23.75 24.605 60-64 26.314999999999998 24.81 24.375 24.5 65-69 26.27 25.259999999999998 24.15 24.32 70-74 26.435 25.585 23.69 24.29 75-79 25.979999999999997 25.430000000000003 24.154999999999998 24.435000000000002 80-84 25.855 26.395000000000003 23.715 24.035 85-89 26.685 25.490000000000002 23.47 24.355 90-94 26.565 26.009999999999998 23.919999999999998 23.505000000000003 95-99 25.7 27.66 23.335 23.305 100-104 27.084999999999997 27.229999999999997 22.625 23.06 105-109 26.13 27.139999999999997 23.26 23.47 110-114 26.11 26.155 24.075 23.66 115-119 26.740000000000002 25.840000000000003 23.505000000000003 23.915 120-124 25.835 27.839999999999996 23.14 23.185 125-129 25.96 26.825 23.605 23.61 130-134 25.88 27.215 23.76 23.145 135-139 26.655 27.060000000000002 23.365 22.919999999999998 140-144 26.955000000000002 27.275 23.565 22.205 145-149 27.169999999999998 27.785 22.805 22.24 150-151 27.700000000000003 27.1125 23.3875 21.8 >>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 0.5 8 1.0 9 0.5 10 0.0 11 0.0 12 0.5 13 0.5 14 0.5 15 1.0 16 2.0 17 1.5 18 0.0 19 1.5 20 2.0 21 1.5 22 1.0 23 1.5 24 3.0 25 3.0 26 5.0 27 4.5 28 3.5 29 5.0 30 9.0 31 17.5 32 20.5 33 21.5 34 24.5 35 28.5 36 37.5 37 50.5 38 78.0 39 98.5 40 111.5 41 127.0 42 143.5 43 153.5 44 164.5 45 174.0 46 170.0 47 188.0 48 168.0 49 144.5 50 143.0 51 130.0 52 125.0 53 113.0 54 105.0 55 101.0 56 100.0 57 98.5 58 96.5 59 87.5 60 75.0 61 76.5 62 83.0 63 75.0 64 64.5 65 69.5 66 64.5 67 55.5 68 59.5 69 54.0 70 44.0 71 40.5 72 35.5 73 26.0 74 21.0 75 19.5 76 17.5 77 13.0 78 7.0 79 5.0 80 4.0 81 3.0 82 2.0 83 1.5 84 1.0 85 0.5 86 0.5 87 0.0 88 0.5 89 0.5 90 0.5 91 1.0 92 0.5 93 0.0 94 0.5 95 0.5 96 1.0 97 1.5 98 1.0 99 1.5 100 2.0 >>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 92.475 #Duplication Level Percentage of deduplicated Percentage of total 1 92.5925925925926 85.625 2 6.920789402541228 12.8 3 0.3784806704514734 1.05 4 0.027034333603676672 0.1 5 0.054068667207353344 0.25 6 0.0 0.0 7 0.027034333603676672 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 GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG 7 0.17500000000000002 No Hit AGCACACACAAGCCTAGAAGCCTTCAGCTTAATCTTCTTCCTAAGCAAGT 5 0.125 No Hit GACTTCTGCTGATGGACACATCTCATGTGCTAAGGAGATGACAAAGGTCT 5 0.125 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 0.0125 0.0 0.0 0.0 0.0 76-77 0.025 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 0.05 0.0 0.0 0.0 0.0 84-85 0.05 0.0 0.0 0.0 0.0 86-87 0.1 0.0 0.0 0.0 0.0 88-89 0.175 0.0 0.0 0.0 0.0 90-91 0.1875 0.0 0.0 0.0 0.0 92-93 0.2875 0.0 0.0 0.0 0.0 94-95 0.3375 0.0 0.0 0.0 0.0 96-97 0.5 0.0 0.0 0.0 0.0 98-99 0.675 0.0 0.0 0.0 0.0 100-101 0.825 0.0 0.0 0.0 0.0 102-103 0.9 0.0 0.0 0.0 0.0 104-105 1.0499999999999998 0.0 0.0 0.0 0.0 106-107 1.1625 0.0 0.0 0.0 0.0 108-109 1.3375 0.0 0.0 0.0 0.0 110-111 1.4625 0.0 0.0 0.0 0.0 112-113 1.6875 0.0 0.0 0.0 0.0 114-115 1.85 0.0 0.0 0.0 0.0 116-117 2.0999999999999996 0.0 0.0 0.0 0.0 118-119 2.3375 0.0 0.0 0.0 0.0 120-121 2.5250000000000004 0.0 0.0 0.0 0.0 122-123 2.8 0.0 0.0 0.0 0.0 124-125 3.1 0.0 0.0 0.0 0.0 126-127 3.45 0.0 0.0 0.0 0.0 128-129 3.725 0.0 0.0 0.0 0.0 130-131 4.0625 0.0 0.0 0.0 0.0 132-133 4.4 0.0 0.0 0.0 0.0 134-135 4.800000000000001 0.0 0.0 0.0 0.0 136-137 5.199999999999999 0.0 0.0 0.0 0.0 138-139 5.575 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content pass >>END_MODULE Read 1634625 spots for SRR7814814.sra Written 1634625 spots for SRR7814814.sra Read 1634625 spots for SRR7814814.sra Written 1634625 spots for SRR7814814.sra Read 1634625 spots for SRR7814814.sra Written 1634625 spots for SRR7814814.sra Read 1634625 spots for SRR7814814.sra Written 1634625 spots for SRR7814814.sra Read 1634625 spots for SRR7814814.sra Written 1634625 spots for SRR7814814.sra Read 1634625 spots for SRR7814814.sra Written 1634625 spots for SRR7814814.sra Read 1634635 spots for SRR7814814.sra Written 1634635 spots for SRR7814814.sra Read 1634625 spots for SRR7814814.sra Written 1634625 spots for SRR7814814.sra Read 1634625 spots for SRR7814814.sra Written 1634625 spots for SRR7814814.sra Read 1634625 spots for SRR7814814.sra Written 1634625 spots for SRR7814814.sra Read 1634625 spots for SRR7814814.sra Written 1634625 spots for SRR7814814.sra Read 1634625 spots for SRR7814814.sra Written 1634625 spots for SRR7814814.sra Read 1634625 spots for SRR7814814.sra Written 1634625 spots for SRR7814814.sra Read 1634625 spots for SRR7814814.sra Written 1634625 spots for SRR7814814.sra Read 1634625 spots for SRR7814814.sra Written 1634625 spots for SRR7814814.sra Read 1634625 spots for SRR7814814.sra Written 1634625 spots for SRR7814814.sra Read 1634625 spots for SRR7814814.sra Written 1634625 spots for SRR7814814.sra Read 1634625 spots for SRR7814814.sra Written 1634625 spots for SRR7814814.sra Read 1634625 spots for SRR7814814.sra Written 1634625 spots for SRR7814814.sra Read 1634625 spots for SRR7814814.sra Written 1634625 spots for SRR7814814.sra SRR ids: ['SRR7814814.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_d3a51ybw SRR7814814.sra spots: 32692510 blocks: [[1, 1634625], [1634626, 3269250], [3269251, 4903875], [4903876, 6538500], [6538501, 8173125], [8173126, 9807750], [9807751, 11442375], [11442376, 13077000], [13077001, 14711625], [14711626, 16346250], [16346251, 17980875], [17980876, 19615500], [19615501, 21250125], [21250126, 22884750], [22884751, 24519375], [24519376, 26154000], [26154001, 27788625], [27788626, 29423250], [29423251, 31057875], [31057876, 32692510]] SRR7814814 file size 11056718 SRR7814814 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 SRR7814814 SRR7814814_1.fastq SRR7814814_2.fastq Input file: SRR7814814_1.fastq Paired file: SRR7814814_2.fastq trimmed: SRR7814814-trimmed-pair1.fastq, SRR7814814-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 11:01:53 2024 >> started Fri Dec 6 11:02:34 2024 >> done (40.964s) 32692510 read pairs processed; of these: 161 ( 0.00%) short read pairs filtered out after trimming by size control 8198 ( 0.03%) empty read pairs filtered out after trimming by size control 32684151 (99.97%) read pairs available; of these: 2836134 ( 8.68%) trimmed read pairs available after processing 29848017 (91.32%) untrimmed read pairs available after processing Length distribution of reads after trimming: length count percentage 18 19 0.00% 19 12 0.00% 20 16 0.00% 21 26 0.00% 22 29 0.00% 23 20 0.00% 24 38 0.00% 25 36 0.00% 26 38 0.00% 27 41 0.00% 28 45 0.00% 29 52 0.00% 30 64 0.00% 31 51 0.00% 32 73 0.00% 33 58 0.00% 34 59 0.00% 35 113 0.00% 36 58 0.00% 37 86 0.00% 38 110 0.00% 39 78 0.00% 40 116 0.00% 41 89 0.00% 42 114 0.00% 43 102 0.00% 44 91 0.00% 45 129 0.00% 46 133 0.00% 47 107 0.00% 48 117 0.00% 49 144 0.00% 50 151 0.00% 51 156 0.00% 52 185 0.00% 53 223 0.00% 54 185 0.00% 55 235 0.00% 56 261 0.00% 57 259 0.00% 58 288 0.00% 59 370 0.00% 60 397 0.00% 61 432 0.00% 62 465 0.00% 63 486 0.00% 64 523 0.00% 65 564 0.00% 66 637 0.00% 67 670 0.00% 68 791 0.00% 69 860 0.00% 70 997 0.00% 71 1210 0.00% 72 1252 0.00% 73 1438 0.00% 74 1594 0.00% 75 1754 0.01% 76 1966 0.01% 77 2063 0.01% 78 2349 0.01% 79 2645 0.01% 80 2984 0.01% 81 3258 0.01% 82 3776 0.01% 83 4269 0.01% 84 4773 0.01% 85 5236 0.02% 86 5722 0.02% 87 6272 0.02% 88 6900 0.02% 89 7309 0.02% 90 8168 0.02% 91 9010 0.03% 92 10060 0.03% 93 11037 0.03% 94 11902 0.04% 95 12912 0.04% 96 13595 0.04% 97 14652 0.04% 98 15242 0.05% 99 16763 0.05% 100 17597 0.05% 101 18564 0.06% 102 19875 0.06% 103 21521 0.07% 104 22307 0.07% 105 23906 0.07% 106 25251 0.08% 107 25884 0.08% 108 27276 0.08% 109 28500 0.09% 110 29407 0.09% 111 31302 0.10% 112 32683 0.10% 113 33935 0.10% 114 35513 0.11% 115 37602 0.12% 116 38586 0.12% 117 39568 0.12% 118 41018 0.13% 119 41621 0.13% 120 43340 0.13% 121 44761 0.14% 122 46508 0.14% 123 48291 0.15% 124 50269 0.15% 125 51940 0.16% 126 52787 0.16% 127 53883 0.16% 128 54727 0.17% 129 56529 0.17% 130 57240 0.18% 131 58568 0.18% 132 61193 0.19% 133 63269 0.19% 134 64662 0.20% 135 67211 0.21% 136 68180 0.21% 137 69112 0.21% 138 69626 0.21% 139 71336 0.22% 140 72265 0.22% 141 73406 0.22% 142 75916 0.23% 143 76778 0.23% 144 79437 0.24% 145 81637 0.25% 146 83775 0.26% 147 85844 0.26% 148 85696 0.26% 149 86060 0.26% 150 88462 0.27% 151 29848017 91.32% 32684151 reads passed initial QC criterion=sequence-density sequence-density=0.23 sequence-density-rank=1 fanout-score=2.23 fanout-score-rank=32 prefix-density=0.26 prefix-fanout=1.9 sequence=GCAAGACATCTTC criterion=fanout-score sequence-density=0.03 sequence-density-rank=29 fanout-score=307.83 fanout-score-rank=1 prefix-density=0.62 prefix-fanout=15.3 sequence=GGCGGCGGCGAACCGCCCCCGTCGCCGCGATCCGAACACTTCACCGGACCATTCAATCGGTAGGAGCGACGGGCGGTGTGTACAAAGGGCAGGGACGTAGTCAACGCGAGCTGATGACTCGCGCTTACTAGGCATTCCTCGTTGAAGACCAACAATTGCAATGATCTATCCCCATCACGATGAAATTTCCCAAGATTACCCGGGCCTGTCGGCCAAGGCTATATACTCGTTGAATACATCAGTGTAGCGCGCGTGCGGCCCAGAACATCTAAGGGCATCACAGACCTGTTATTGCCTCAAACTTCCGTCGCCTAAACGGCGATAGTCCCTCTAAGAAGCTAGCTGCGGAGGGATGGCTCCGCATAGCTAGTTAGCAGGCTGAGGTCTCGTTCGTTAACGGAATTAACCAGACAAATCGCTCCACCAACTAAGAACGGCCATGCACCACCACCCATAGAATCAAGAAAGAGCTCTCAGTCTGTCAATCCTTGCTATGTCTGGACCTGGTAAG criterion=sequence-density sequence-density=0.59 sequence-density-rank=1 fanout-score=2.59 fanout-score-rank=27 prefix-density=0.65 prefix-fanout=2.3 sequence=GAAGATGTCTTGC criterion=fanout-score sequence-density=0.14 sequence-density-rank=7 fanout-score=133.46 fanout-score-rank=1 prefix-density=0.89 prefix-fanout=20.4 sequence=CGCCGCCGCCGC SRR7814814 testing PE reads STAR mapping to Ensembl genome Started job on | Dec 06 11:04:15 Started mapping on | Dec 06 11:04:16 Finished on | Dec 06 11:14:47 Mapping speed, Million of reads per hour | 186.47 Number of input reads | 32684151 Average input read length | 298 UNIQUE READS: Uniquely mapped reads number | 28245955 Uniquely mapped reads % | 86.42% Average mapped length | 295.95 Number of splices: Total | 27683595 Number of splices: Annotated (sjdb) | 26043420 Number of splices: GT/AG | 27298638 Number of splices: GC/AG | 302238 Number of splices: AT/AC | 16184 Number of splices: Non-canonical | 66535 Mismatch rate per base, % | 0.47% Deletion rate per base | 0.03% Deletion average length | 3.14 Insertion rate per base | 0.03% Insertion average length | 2.67 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 410242 % of reads mapped to multiple loci | 1.26% Number of reads mapped to too many loci | 53083 % of reads mapped to too many loci | 0.16% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 10.94% % of reads unmapped: other | 1.22% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 4027954 4027954 4027954 N_multimapping 410242 410242 410242 N_noFeature 817354 27433534 1093878 N_ambiguous 624965 3914 90094 UnstrandedReadsAssigned:26803636 PositiveStrandReadsAssigned:808507 NegativeStrandReadsAssigned:27061983 Dataset is classified negative stranded MeadianReadLen=151 20thPercentileLength=151 echo kmer=147 SRR7814814 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: SRR7814814-trimmed-pair1.fastq SRR7814814-trimmed-pair2.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 32,684,151 reads, 27,772,130 reads pseudoaligned [quant] estimated average fragment length: 271.137 [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,183 rounds 52973 SRR7814814.ke.tsv 35125 SRR7814814.se.tsv 88098 total ==> SRR7814814.ke.tsv <== target_id length eff_length est_counts tpm PNS24245 936 666.531 0 0 PNS24247 1044 773.863 113.687 7.16591 PNS24249 1928 1657.86 227.457 6.69228 PNS24246 1044 773.863 113.687 7.16591 PNS24248 1044 773.863 113.687 7.16591 PNS24244 1471 1200.86 346.481 14.0738 PNS24243 293 90.8979 3 1.60987 KQK14069 1603 1332.86 12457.7 455.906 KQK14071 474 227.95 60.8767 13.0267 ==> SRR7814814.se.tsv <== BRADI_1g14170v3 12577 BRADI_1g53295v3 1162 BRADI_1g59795v3 136 BRADI_1g07683v3 0 BRADI_1g00485v3 3 BRADI_1g20270v3 1372 BRADI_1g74790v3 588 BRADI_1g09890v3 0 BRADI_1g77505v3 459 BRADI_1g48960v3 0 SRR7814814 completed mapping pipeline successfully