Starting /dee2/code/volunteer_pipeline.sh ERR9452522 current disk space = 1547767603200 free memory = 1426146976 ERR9452522 SRAfilesize 5d9fc69c5ca3f2bf40e52f0e6fb7245b ERR9452522.sra ERR9452522.sra file validated ERR9452522 is paired end ERR9452522 is conventional basespace ERR9452522 read1 length is 150 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename ERR9452522_1.fastq File type Conventional base calls Encoding Sanger / Illumina 1.9 Total Sequences 4000 Sequences flagged as poor quality 0 Sequence length 150 %GC 55 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 35.829 37.0 37.0 37.0 37.0 37.0 2 35.6075 37.0 37.0 37.0 37.0 37.0 3 36.002 37.0 37.0 37.0 37.0 37.0 4 36.075 37.0 37.0 37.0 37.0 37.0 5 35.909 37.0 37.0 37.0 37.0 37.0 6 36.0055 37.0 37.0 37.0 37.0 37.0 7 36.1065 37.0 37.0 37.0 37.0 37.0 8 36.1535 37.0 37.0 37.0 37.0 37.0 9 36.1085 37.0 37.0 37.0 37.0 37.0 10-14 36.267399999999995 37.0 37.0 37.0 37.0 37.0 15-19 36.1781 37.0 37.0 37.0 37.0 37.0 20-24 36.1767 37.0 37.0 37.0 37.0 37.0 25-29 36.075599999999994 37.0 37.0 37.0 37.0 37.0 30-34 36.0013 37.0 37.0 37.0 37.0 37.0 35-39 35.9975 37.0 37.0 37.0 37.0 37.0 40-44 35.853 37.0 37.0 37.0 37.0 37.0 45-49 35.8183 37.0 37.0 37.0 37.0 37.0 50-54 35.8872 37.0 37.0 37.0 37.0 37.0 55-59 35.87109999999999 37.0 37.0 37.0 37.0 37.0 60-64 35.9704 37.0 37.0 37.0 37.0 37.0 65-69 35.82 37.0 37.0 37.0 37.0 37.0 70-74 35.8486 37.0 37.0 37.0 37.0 37.0 75-79 35.79430000000001 37.0 37.0 37.0 37.0 37.0 80-84 35.71810000000001 37.0 37.0 37.0 37.0 37.0 85-89 35.7753 37.0 37.0 37.0 37.0 37.0 90-94 35.6948 37.0 37.0 37.0 37.0 37.0 95-99 35.678 37.0 37.0 37.0 37.0 37.0 100-104 35.590900000000005 37.0 37.0 37.0 37.0 37.0 105-109 35.622 37.0 37.0 37.0 37.0 37.0 110-114 35.5637 37.0 37.0 37.0 37.0 37.0 115-119 35.5425 37.0 37.0 37.0 37.0 37.0 120-124 35.5199 37.0 37.0 37.0 37.0 37.0 125-129 35.6176 37.0 37.0 37.0 37.0 37.0 130-134 35.492200000000004 37.0 37.0 37.0 37.0 37.0 135-139 35.3178 37.0 37.0 37.0 34.6 37.0 140-144 35.2822 37.0 37.0 37.0 34.6 37.0 145-149 35.413599999999995 37.0 37.0 37.0 34.6 37.0 150 35.501 37.0 37.0 37.0 37.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 22 2.0 23 1.0 24 6.0 25 4.0 26 8.0 27 16.0 28 35.0 29 55.0 30 67.0 31 75.0 32 109.0 33 144.0 34 195.0 35 398.0 36 2601.0 37 284.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 28.499999999999996 12.4 13.375 45.725 2 28.639319659829916 20.885442721360683 29.289644822411205 21.1855927963982 3 26.125 26.375 19.25 28.249999999999996 4 29.95 29.825000000000003 15.275 24.95 5 28.599999999999998 30.075000000000003 18.525 22.8 6 20.974999999999998 32.625 20.4 26.0 7 20.825 14.075 36.65 28.449999999999996 8 23.674999999999997 16.825000000000003 24.55 34.949999999999996 9 24.05 17.875 27.425 30.65 10-14 25.865 23.235 22.25 28.65 15-19 26.795 22.31 22.425 28.470000000000002 20-24 26.529999999999998 22.755 22.285 28.43 25-29 27.169999999999998 23.01 21.85 27.97 30-34 26.665 23.11 22.400000000000002 27.825 35-39 26.865 22.3 22.355 28.48 40-44 27.57 22.45 21.945 28.035 45-49 26.85 22.535 22.685 27.93 50-54 26.979999999999997 22.49 22.375 28.155 55-59 27.54 22.825 21.485000000000003 28.15 60-64 27.894999999999996 22.23 21.89 27.985 65-69 27.66 22.825 21.3 28.215 70-74 28.12 22.189999999999998 21.765 27.925 75-79 27.67 21.745 22.335 28.249999999999996 80-84 27.845 22.205 22.055 27.894999999999996 85-89 27.815 22.235 21.725 28.225 90-94 27.91 22.145 22.095000000000002 27.85 95-99 28.225 21.765 21.945 28.065 100-104 27.894999999999996 22.35 22.040000000000003 27.715 105-109 27.47 21.605 22.765 28.16 110-114 28.035 22.555 21.725 27.685 115-119 28.439999999999998 22.1 21.695 27.765 120-124 28.299999999999997 22.175 21.87 27.655 125-129 28.485 21.91 21.86 27.744999999999997 130-134 28.549999999999997 21.745 21.895 27.810000000000002 135-139 28.349999999999998 22.3 21.925 27.425 140-144 28.715000000000003 22.485 21.245 27.555000000000003 145-149 28.470000000000002 22.259999999999998 21.92 27.35 150 29.375 21.775 22.625 26.224999999999998 >>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 0.0 20 0.0 21 0.0 22 0.0 23 0.0 24 0.5 25 1.0 26 2.0 27 1.5 28 0.5 29 2.5 30 6.5 31 8.5 32 7.0 33 8.0 34 11.5 35 22.5 36 39.5 37 38.5 38 42.5 39 63.0 40 78.5 41 94.0 42 113.0 43 121.0 44 124.0 45 127.5 46 139.5 47 138.5 48 127.5 49 124.5 50 118.0 51 100.0 52 86.0 53 99.0 54 105.5 55 96.5 56 92.0 57 90.5 58 93.0 59 95.0 60 87.0 61 90.0 62 96.5 63 97.0 64 95.0 65 93.5 66 92.5 67 92.0 68 99.0 69 107.5 70 101.5 71 83.5 72 76.0 73 66.5 74 56.5 75 53.0 76 41.5 77 34.0 78 26.0 79 22.5 80 22.5 81 14.5 82 10.5 83 8.5 84 4.5 85 3.5 86 2.5 87 0.5 88 0.0 89 0.5 90 0.5 91 0.5 92 0.5 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 0.05 3 0.0 4 0.0 5 0.0 6 0.0 7 0.0 8 0.0 9 0.0 10-14 0.0 15-19 0.0 20-24 0.0 25-29 0.0 30-34 0.0 35-39 0.0 40-44 0.0 45-49 0.0 50-54 0.0 55-59 0.0 60-64 0.0 65-69 0.0 70-74 0.0 75-79 0.0 80-84 0.0 85-89 0.0 90-94 0.0 95-99 0.0 100-104 0.0 105-109 0.0 110-114 0.0 115-119 0.0 120-124 0.0 125-129 0.0 130-134 0.0 135-139 0.0 140-144 0.0 145-149 0.0 150 0.0 >>END_MODULE >>Sequence Length Distribution pass #Length Count 150 4000.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 93.85 #Duplication Level Percentage of deduplicated Percentage of total 1 93.97975492807672 88.2 2 5.5673947789025044 10.45 3 0.3995737879595098 1.125 4 0.02663825253063399 0.1 5 0.02663825253063399 0.125 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 warn #Sequence Count Percentage Possible Source CGGAGGAGGCGAGGGCGTCGGGCCCGCCGGAGGCCACGTCCTTGAGGTCC 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 0.025 0.0 0.0 0.0 0.0 60-61 0.025 0.0 0.0 0.0 0.0 62-63 0.025 0.0 0.0 0.0 0.0 64-65 0.025 0.0 0.0 0.0 0.0 66-67 0.025 0.0 0.0 0.0 0.0 68-69 0.025 0.0 0.0 0.0 0.0 70-71 0.025 0.0 0.0 0.0 0.0 72-73 0.025 0.0 0.0 0.0 0.0 74-75 0.025 0.0 0.0 0.0 0.0 76-77 0.025 0.0 0.0 0.0 0.0 78-79 0.037500000000000006 0.0 0.0 0.0 0.0 80-81 0.05 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 0.05 0.0 0.0 0.0 0.0 88-89 0.1 0.0 0.0 0.0 0.0 90-91 0.1 0.0 0.0 0.0 0.0 92-93 0.1 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 0.1 0.0 0.0 0.0 0.0 100-101 0.1 0.0 0.0 0.0 0.0 102-103 0.175 0.0 0.0 0.0 0.0 104-105 0.225 0.0 0.0 0.0 0.0 106-107 0.275 0.0 0.0 0.0 0.0 108-109 0.2875 0.0 0.0 0.0 0.0 110-111 0.3375 0.0 0.0 0.0 0.0 112-113 0.375 0.0 0.0 0.0 0.0 114-115 0.4625 0.0 0.0 0.0 0.0 116-117 0.4875 0.0 0.0 0.0 0.0 118-119 0.525 0.0 0.0 0.0 0.0 120-121 0.5375000000000001 0.0 0.0 0.0 0.0 122-123 0.5874999999999999 0.0 0.0 0.0 0.0 124-125 0.7125 0.0 0.0 0.0 0.0 126-127 0.775 0.0 0.0 0.0 0.0 128-129 0.8374999999999999 0.0 0.0 0.0 0.0 130-131 0.9125 0.0 0.0 0.0 0.0 132-133 0.9624999999999999 0.0 0.0 0.0 0.0 134-135 1.025 0.0 0.0 0.0 0.0 136-137 1.1375000000000002 0.0 0.0 0.0 0.0 138 1.3 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position TGATATT 10 0.006973645 144.0 2 GTGATAT 10 0.006973645 144.0 1 >>END_MODULE ERR9452522 read2 length is 150 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename ERR9452522_2.fastq File type Conventional base calls Encoding Sanger / Illumina 1.9 Total Sequences 4000 Sequences flagged as poor quality 0 Sequence length 150 %GC 55 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 35.88 37.0 37.0 37.0 37.0 37.0 2 35.7495 37.0 37.0 37.0 37.0 37.0 3 35.9435 37.0 37.0 37.0 37.0 37.0 4 35.8245 37.0 37.0 37.0 37.0 37.0 5 35.8925 37.0 37.0 37.0 37.0 37.0 6 36.01 37.0 37.0 37.0 37.0 37.0 7 35.939 37.0 37.0 37.0 37.0 37.0 8 35.868 37.0 37.0 37.0 37.0 37.0 9 35.928 37.0 37.0 37.0 37.0 37.0 10-14 36.03189999999999 37.0 37.0 37.0 37.0 37.0 15-19 35.9272 37.0 37.0 37.0 37.0 37.0 20-24 35.96730000000001 37.0 37.0 37.0 37.0 37.0 25-29 35.978300000000004 37.0 37.0 37.0 37.0 37.0 30-34 35.88100000000001 37.0 37.0 37.0 37.0 37.0 35-39 35.881600000000006 37.0 37.0 37.0 37.0 37.0 40-44 35.8778 37.0 37.0 37.0 37.0 37.0 45-49 35.828700000000005 37.0 37.0 37.0 37.0 37.0 50-54 35.718 37.0 37.0 37.0 37.0 37.0 55-59 35.788700000000006 37.0 37.0 37.0 37.0 37.0 60-64 35.679500000000004 37.0 37.0 37.0 37.0 37.0 65-69 35.7241 37.0 37.0 37.0 37.0 37.0 70-74 35.7427 37.0 37.0 37.0 37.0 37.0 75-79 35.658 37.0 37.0 37.0 37.0 37.0 80-84 35.585100000000004 37.0 37.0 37.0 37.0 37.0 85-89 35.533500000000004 37.0 37.0 37.0 37.0 37.0 90-94 35.5104 37.0 37.0 37.0 37.0 37.0 95-99 35.4222 37.0 37.0 37.0 37.0 37.0 100-104 35.494600000000005 37.0 37.0 37.0 37.0 37.0 105-109 35.480399999999996 37.0 37.0 37.0 37.0 37.0 110-114 35.4914 37.0 37.0 37.0 34.6 37.0 115-119 35.437200000000004 37.0 37.0 37.0 37.0 37.0 120-124 35.2355 37.0 37.0 37.0 32.2 37.0 125-129 35.19799999999999 37.0 37.0 37.0 34.6 37.0 130-134 35.25840000000001 37.0 37.0 37.0 29.8 37.0 135-139 35.2501 37.0 37.0 37.0 32.2 37.0 140-144 35.1957 37.0 37.0 37.0 27.4 37.0 145-149 35.0286 37.0 37.0 37.0 27.4 37.0 150 35.382 37.0 37.0 37.0 37.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 20 1.0 21 2.0 22 6.0 23 5.0 24 12.0 25 13.0 26 18.0 27 22.0 28 34.0 29 44.0 30 40.0 31 78.0 32 110.0 33 141.0 34 231.0 35 520.0 36 2526.0 37 197.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 29.45 12.575 14.374999999999998 43.6 2 29.425 21.3 27.425 21.85 3 25.35 27.05 17.349999999999998 30.25 4 31.3 27.85 15.45 25.4 5 27.875 31.05 19.05 22.025 6 20.974999999999998 31.8 20.1 27.125 7 21.65 13.65 36.35 28.349999999999998 8 23.825 17.775 25.05 33.35 9 24.224999999999998 17.125 27.250000000000004 31.4 10-14 26.325 23.035 21.584999999999997 29.054999999999996 15-19 27.275 22.43 22.28 28.015 20-24 26.540000000000003 22.855 22.495 28.110000000000003 25-29 27.150000000000002 22.715 22.415 27.72 30-34 26.58 22.89 21.87 28.660000000000004 35-39 26.915 22.825 21.83 28.43 40-44 27.24 22.259999999999998 22.14 28.360000000000003 45-49 26.96 21.95 22.31 28.78 50-54 26.545 22.720000000000002 22.564999999999998 28.17 55-59 27.305 22.08 22.415 28.199999999999996 60-64 26.979999999999997 22.015 22.345000000000002 28.660000000000004 65-69 27.474999999999998 21.985 21.959999999999997 28.58 70-74 27.534999999999997 22.35 21.505 28.610000000000003 75-79 27.810000000000002 22.05 21.51 28.63 80-84 27.675 22.18 22.16 27.985 85-89 28.285 21.92 21.875 27.92 90-94 27.46 22.18 22.259999999999998 28.1 95-99 27.855 22.375 21.715 28.055000000000003 100-104 28.060000000000002 21.834999999999997 22.045 28.060000000000002 105-109 27.450000000000003 21.67 21.884999999999998 28.994999999999997 110-114 27.48 22.28 22.23 28.01 115-119 28.315 21.625 22.009999999999998 28.050000000000004 120-124 28.165000000000003 22.195 21.55 28.09 125-129 27.839999999999996 22.16 22.275 27.725 130-134 28.075 22.005 22.13 27.79 135-139 27.700000000000003 22.655 21.884999999999998 27.76 140-144 28.27 21.62 22.3 27.810000000000002 145-149 27.950000000000003 22.365 21.51 28.175 150 27.975 22.650000000000002 22.175 27.200000000000003 >>END_MODULE >>Per sequence GC content fail #GC Content Count 0 0.0 1 0.5 2 0.5 3 0.0 4 0.5 5 0.5 6 0.0 7 0.0 8 0.0 9 0.0 10 0.5 11 0.5 12 0.5 13 0.5 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 0.5 26 0.5 27 0.5 28 3.0 29 3.5 30 2.5 31 7.0 32 11.0 33 15.0 34 18.0 35 21.0 36 31.5 37 36.5 38 42.5 39 56.5 40 73.0 41 80.0 42 92.5 43 119.5 44 124.5 45 124.0 46 144.0 47 130.5 48 112.5 49 122.0 50 118.5 51 124.0 52 118.0 53 105.0 54 105.0 55 95.0 56 82.5 57 88.5 58 97.5 59 98.5 60 91.0 61 88.0 62 96.0 63 84.5 64 91.5 65 107.0 66 110.0 67 102.5 68 97.5 69 102.0 70 95.0 71 94.5 72 77.5 73 59.5 74 61.0 75 60.0 76 47.5 77 34.0 78 25.0 79 15.5 80 12.0 81 13.5 82 9.5 83 5.0 84 4.5 85 3.0 86 2.0 87 1.0 88 0.5 89 0.0 90 0.0 91 0.0 92 0.5 93 0.5 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 0.0 >>END_MODULE >>Sequence Length Distribution pass #Length Count 150 4000.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 93.89999999999999 #Duplication Level Percentage of deduplicated Percentage of total 1 94.03620873269436 88.3 2 5.5111821086261985 10.35 3 0.3993610223642172 1.125 4 0.026624068157614485 0.1 5 0.026624068157614485 0.125 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 warn #Sequence Count Percentage Possible Source CGCGACCGCCCCTACGGCCACTGCCTCGTCGCCGGCCTCGCCAAGTACCC 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 0.025 0.0 0.0 0.0 0.0 60-61 0.025 0.0 0.0 0.0 0.0 62-63 0.025 0.0 0.0 0.0 0.0 64-65 0.025 0.0 0.0 0.0 0.0 66-67 0.025 0.0 0.0 0.0 0.0 68-69 0.025 0.0 0.0 0.0 0.0 70-71 0.025 0.0 0.0 0.0 0.0 72-73 0.025 0.0 0.0 0.0 0.0 74-75 0.025 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 0.025 0.0 0.0 0.0 0.0 84-85 0.025 0.0 0.0 0.0 0.0 86-87 0.025 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 0.075 0.0 0.0 0.0 0.0 96-97 0.075 0.0 0.0 0.0 0.0 98-99 0.075 0.0 0.0 0.0 0.0 100-101 0.1 0.0 0.0 0.0 0.0 102-103 0.175 0.0 0.0 0.0 0.0 104-105 0.225 0.0 0.0 0.0 0.0 106-107 0.275 0.0 0.0 0.0 0.0 108-109 0.2875 0.0 0.0 0.0 0.0 110-111 0.3375 0.0 0.0 0.0 0.0 112-113 0.375 0.0 0.0 0.0 0.0 114-115 0.4375 0.0 0.0 0.0 0.0 116-117 0.4625 0.0 0.0 0.0 0.0 118-119 0.5 0.0 0.0 0.0 0.0 120-121 0.5125 0.0 0.0 0.0 0.0 122-123 0.5625 0.0 0.0 0.0 0.0 124-125 0.6875 0.0 0.0 0.0 0.0 126-127 0.75 0.0 0.0 0.0 0.0 128-129 0.8125 0.0 0.0 0.0 0.0 130-131 0.8875 0.0 0.0 0.0 0.0 132-133 0.9375 0.0 0.0 0.0 0.0 134-135 1.025 0.0 0.0 0.0 0.0 136-137 1.15 0.0 0.0 0.0 0.0 138 1.3 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position TATGATG 10 0.006973645 144.0 2 >>END_MODULE Read 1108910 spots for ERR9452522.sra Written 1108910 spots for ERR9452522.sra Read 1108910 spots for ERR9452522.sra Written 1108910 spots for ERR9452522.sra Read 1108910 spots for ERR9452522.sra Written 1108910 spots for ERR9452522.sra Read 1108910 spots for ERR9452522.sra Written 1108910 spots for ERR9452522.sra Read 1108910 spots for ERR9452522.sra Written 1108910 spots for ERR9452522.sra Read 1108910 spots for ERR9452522.sra Written 1108910 spots for ERR9452522.sra Read 1108910 spots for ERR9452522.sra Written 1108910 spots for ERR9452522.sra Read 1108910 spots for ERR9452522.sra Written 1108910 spots for ERR9452522.sra Read 1108910 spots for ERR9452522.sra Written 1108910 spots for ERR9452522.sra Read 1108910 spots for ERR9452522.sra Written 1108910 spots for ERR9452522.sra Read 1108910 spots for ERR9452522.sra Written 1108910 spots for ERR9452522.sra Read 1108926 spots for ERR9452522.sra Written 1108926 spots for ERR9452522.sra Read 1108910 spots for ERR9452522.sra Written 1108910 spots for ERR9452522.sra Read 1108910 spots for ERR9452522.sra Written 1108910 spots for ERR9452522.sra Read 1108910 spots for ERR9452522.sra Written 1108910 spots for ERR9452522.sra Read 1108910 spots for ERR9452522.sra Written 1108910 spots for ERR9452522.sra Read 1108910 spots for ERR9452522.sra Written 1108910 spots for ERR9452522.sra Read 1108910 spots for ERR9452522.sra Written 1108910 spots for ERR9452522.sra Read 1108910 spots for ERR9452522.sra Written 1108910 spots for ERR9452522.sra Read 1108910 spots for ERR9452522.sra Written 1108910 spots for ERR9452522.sra SRR ids: ['ERR9452522.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_naf8w99h ERR9452522.sra spots: 22178216 blocks: [[1, 1108910], [1108911, 2217820], [2217821, 3326730], [3326731, 4435640], [4435641, 5544550], [5544551, 6653460], [6653461, 7762370], [7762371, 8871280], [8871281, 9980190], [9980191, 11089100], [11089101, 12198010], [12198011, 13306920], [13306921, 14415830], [14415831, 15524740], [15524741, 16633650], [16633651, 17742560], [17742561, 18851470], [18851471, 19960380], [19960381, 21069290], [21069291, 22178216]] ERR9452522 file size 7450452 ERR9452522 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 ERR9452522 ERR9452522_1.fastq ERR9452522_2.fastq Input file: ERR9452522_1.fastq Paired file: ERR9452522_2.fastq trimmed: ERR9452522-trimmed-pair1.fastq, ERR9452522-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 00:02:06 2024 >> started Sat Dec 7 00:02:31 2024 >> done (25.048s) 22178216 read pairs processed; of these: 369 ( 0.00%) short read pairs filtered out after trimming by size control 1083 ( 0.00%) empty read pairs filtered out after trimming by size control 22176764 (99.99%) read pairs available; of these: 600778 ( 2.71%) trimmed read pairs available after processing 21575986 (97.29%) untrimmed read pairs available after processing Length distribution of reads after trimming: length count percentage 18 17 0.00% 19 15 0.00% 20 374 0.00% 21 15 0.00% 22 15 0.00% 23 24 0.00% 24 17 0.00% 25 14 0.00% 26 25 0.00% 27 28 0.00% 28 16 0.00% 29 27 0.00% 30 85 0.00% 31 41 0.00% 32 24 0.00% 33 21 0.00% 34 27 0.00% 35 20 0.00% 36 22 0.00% 37 21 0.00% 38 22 0.00% 39 27 0.00% 40 26 0.00% 41 32 0.00% 42 19 0.00% 43 43 0.00% 44 28 0.00% 45 34 0.00% 46 49 0.00% 47 42 0.00% 48 57 0.00% 49 45 0.00% 50 91 0.00% 51 85 0.00% 52 83 0.00% 53 112 0.00% 54 89 0.00% 55 100 0.00% 56 116 0.00% 57 129 0.00% 58 156 0.00% 59 185 0.00% 60 199 0.00% 61 203 0.00% 62 250 0.00% 63 225 0.00% 64 258 0.00% 65 248 0.00% 66 273 0.00% 67 353 0.00% 68 379 0.00% 69 412 0.00% 70 417 0.00% 71 532 0.00% 72 502 0.00% 73 497 0.00% 74 523 0.00% 75 626 0.00% 76 604 0.00% 77 652 0.00% 78 683 0.00% 79 721 0.00% 80 833 0.00% 81 852 0.00% 82 968 0.00% 83 930 0.00% 84 1092 0.00% 85 1217 0.01% 86 1151 0.01% 87 1182 0.01% 88 1316 0.01% 89 1394 0.01% 90 1448 0.01% 91 1621 0.01% 92 1657 0.01% 93 1797 0.01% 94 1842 0.01% 95 1940 0.01% 96 1985 0.01% 97 2299 0.01% 98 2414 0.01% 99 2391 0.01% 100 2598 0.01% 101 2806 0.01% 102 2731 0.01% 103 3006 0.01% 104 3247 0.01% 105 3459 0.02% 106 3473 0.02% 107 3692 0.02% 108 3934 0.02% 109 4138 0.02% 110 4391 0.02% 111 4542 0.02% 112 4722 0.02% 113 5251 0.02% 114 5403 0.02% 115 5698 0.03% 116 5879 0.03% 117 6336 0.03% 118 6462 0.03% 119 6948 0.03% 120 7120 0.03% 121 7520 0.03% 122 7961 0.04% 123 8128 0.04% 124 8802 0.04% 125 9281 0.04% 126 9855 0.04% 127 10186 0.05% 128 10696 0.05% 129 11291 0.05% 130 11816 0.05% 131 12050 0.05% 132 12749 0.06% 133 13516 0.06% 134 14537 0.07% 135 14831 0.07% 136 15505 0.07% 137 16466 0.07% 138 17004 0.08% 139 17938 0.08% 140 18682 0.08% 141 19447 0.09% 142 20678 0.09% 143 21808 0.10% 144 22330 0.10% 145 23928 0.11% 146 24905 0.11% 147 26028 0.12% 148 27377 0.12% 149 28323 0.13% 150 21575986 97.29% 22176764 reads passed initial QC criterion=sequence-density sequence-density=0.21 sequence-density-rank=1 fanout-score=3.28 fanout-score-rank=26 prefix-density=0.23 prefix-fanout=3.0 sequence=GGTGTTGTCGAAGCCGATGATGCGGAC criterion=fanout-score sequence-density=0.02 sequence-density-rank=36 fanout-score=1163.01 fanout-score-rank=1 prefix-density=1.13 prefix-fanout=25.5 sequence=GCGGCGGCGAACCGCCCCCGTCGCCGCGATCCGAACACTTCACCGGACCATTCAATCGGTAGGAGCGACGGGCGGTGTGTACAAAGGGCAGGGACGTAGTCAACGCGAGCTGATGACTCGCGCTTACTAGGCATTCCTCGTTGAAGACCAACAATTGCAATGATCTATCCCCATCACGATGAAATTTCCCAAGATTACCCGGGCCTGTCGGCCAAGGCTATATACTCGTTGAATACATCAGTGTAGCGCGCGTGCGGCCCAGAACATCTAAGGGCATCACAGACCTGTTATTGCCTCAAACTTCCGTCGCCTAAACGGCGATAGTCCCTCTAAGAAGCTAGCTGCGGAGGGATGGCTCCGCATAGCTAGTTAGCAGGCTGAGGTCTCGTTCGTTAACGGAATTAACCAGACAAATCGCTCCACCAACTAAGAACGGCCATGCACCACCACCCATAGAATCAAGAAAGAGCTCTCAGTCTGTCAATCCTTGCTATGTCTGGACCTGGTAAGT criterion=sequence-density sequence-density=0.21 sequence-density-rank=1 fanout-score=3.14 fanout-score-rank=27 prefix-density=0.22 prefix-fanout=2.9 sequence=GGTGTTGTCGAAGCCGATGATGCGGAC criterion=fanout-score sequence-density=0.02 sequence-density-rank=37 fanout-score=1198.34 fanout-score-rank=1 prefix-density=1.12 prefix-fanout=25.8 sequence=GCGGCGGCGAACCGCCCCCGTCGCCGCGATCCGAACACTTCACCGGACCATTCAATCGGTAGGAGCGACGGGCGGTGTGTACAAAGGGCAGGGACGTAGTCAACGCGAGCTGATGACTCGCGCTTACTAGGCATTCCTCGTTGAAGACCAACAATTGCAATGATCTATCCCCATCACGATGAAATTTCCCAAGATTACCCGGGCCTGTCGGCCAAGGCTATATACTCGTTGAATACATCAGTGTAGCGCGCGTGCGGCCCAGAACATCTAAGGGCATCACAGACCTGTTATTGCCTCAAACTTCCGTCGCCTAAACGGCGATAGTCCCTCTAAGAAGCTAGCTGCGGAGGGATGGCTCCGCATAGCTAGTTAGCAGGCTGAGGTCTCGTTCGTTAACGGAATTAACCAGACAAATCGCTCCACCAACTAAGAACGGCCATGCACCACCACCCATAGAATCAAGAAAGAGCTCTCAGTCTGTCAATCCTTGCTATGTCTGGACCTGGTAAGT ERR9452522 testing PE reads STAR mapping to Ensembl genome Started job on | Dec 07 00:03:59 Started mapping on | Dec 07 00:04:00 Finished on | Dec 07 00:06:12 Mapping speed, Million of reads per hour | 604.82 Number of input reads | 22176764 Average input read length | 298 UNIQUE READS: Uniquely mapped reads number | 20980451 Uniquely mapped reads % | 94.61% Average mapped length | 297.81 Number of splices: Total | 19850106 Number of splices: Annotated (sjdb) | 18701413 Number of splices: GT/AG | 19561605 Number of splices: GC/AG | 258290 Number of splices: AT/AC | 9622 Number of splices: Non-canonical | 20589 Mismatch rate per base, % | 0.20% Deletion rate per base | 0.00% Deletion average length | 1.69 Insertion rate per base | 0.00% Insertion average length | 1.21 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 207361 % of reads mapped to multiple loci | 0.94% Number of reads mapped to too many loci | 58091 % of reads mapped to too many loci | 0.26% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 1.75% % of reads unmapped: other | 2.44% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 988952 988952 988952 N_multimapping 207361 207361 207361 N_noFeature 614333 10566718 10645594 N_ambiguous 492136 57521 57292 UnstrandedReadsAssigned:19873982 PositiveStrandReadsAssigned:10356212 NegativeStrandReadsAssigned:10277565 Dataset is classified unstranded MeadianReadLen=150 20thPercentileLength=150 echo kmer=145 ERR9452522 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: ERR9452522-trimmed-pair1.fastq ERR9452522-trimmed-pair2.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 22,176,764 reads, 20,671,237 reads pseudoaligned [quant] estimated average fragment length: 234.045 [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,102 rounds 52973 ERR9452522.ke.tsv 35125 ERR9452522.se.tsv 88098 total ==> ERR9452522.ke.tsv <== target_id length eff_length est_counts tpm PNS24245 936 703.281 0 0 PNS24247 1044 810.955 30.4699 2.34487 PNS24249 1928 1694.96 254.42 9.36783 PNS24246 1044 810.955 30.4699 2.34487 PNS24248 1044 810.955 30.4699 2.34487 PNS24244 1471 1237.96 35.1702 1.77303 PNS24243 293 72.0518 15 12.9925 KQK14069 1603 1369.96 12645.2 576.056 KQK14071 474 243.661 1592.77 407.954 ==> ERR9452522.se.tsv <== BRADI_1g14170v3 15844 BRADI_1g53295v3 69 BRADI_1g59795v3 428 BRADI_1g07683v3 0 BRADI_1g00485v3 48 BRADI_1g20270v3 793 BRADI_1g74790v3 532 BRADI_1g09890v3 8 BRADI_1g77505v3 397 BRADI_1g48960v3 0 ERR9452522 completed mapping pipeline successfully