Starting /dee2/code/volunteer_pipeline.sh ERR9452514 current disk space = 1547613331456 free memory = 1430510188 ERR9452514 SRAfilesize 30bb889400f0edbf3cb48627ea1b070d ERR9452514.sra ERR9452514.sra file validated ERR9452514 is paired end ERR9452514 is conventional basespace ERR9452514 read1 length is 150 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename ERR9452514_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 35.588 37.0 37.0 37.0 37.0 37.0 2 35.6715 37.0 37.0 37.0 37.0 37.0 3 36.084 37.0 37.0 37.0 37.0 37.0 4 35.9685 37.0 37.0 37.0 37.0 37.0 5 36.0605 37.0 37.0 37.0 37.0 37.0 6 36.1005 37.0 37.0 37.0 37.0 37.0 7 35.9195 37.0 37.0 37.0 37.0 37.0 8 36.072 37.0 37.0 37.0 37.0 37.0 9 36.232 37.0 37.0 37.0 37.0 37.0 10-14 36.1983 37.0 37.0 37.0 37.0 37.0 15-19 36.155499999999996 37.0 37.0 37.0 37.0 37.0 20-24 36.1036 37.0 37.0 37.0 37.0 37.0 25-29 36.0372 37.0 37.0 37.0 37.0 37.0 30-34 35.9511 37.0 37.0 37.0 37.0 37.0 35-39 35.9658 37.0 37.0 37.0 37.0 37.0 40-44 35.8517 37.0 37.0 37.0 37.0 37.0 45-49 35.7806 37.0 37.0 37.0 37.0 37.0 50-54 35.881899999999995 37.0 37.0 37.0 37.0 37.0 55-59 35.8063 37.0 37.0 37.0 37.0 37.0 60-64 35.9375 37.0 37.0 37.0 37.0 37.0 65-69 35.8326 37.0 37.0 37.0 37.0 37.0 70-74 35.8519 37.0 37.0 37.0 37.0 37.0 75-79 35.787400000000005 37.0 37.0 37.0 37.0 37.0 80-84 35.7745 37.0 37.0 37.0 37.0 37.0 85-89 35.7799 37.0 37.0 37.0 37.0 37.0 90-94 35.7779 37.0 37.0 37.0 37.0 37.0 95-99 35.6877 37.0 37.0 37.0 37.0 37.0 100-104 35.6885 37.0 37.0 37.0 37.0 37.0 105-109 35.563300000000005 37.0 37.0 37.0 37.0 37.0 110-114 35.59590000000001 37.0 37.0 37.0 37.0 37.0 115-119 35.504999999999995 37.0 37.0 37.0 37.0 37.0 120-124 35.54449999999999 37.0 37.0 37.0 37.0 37.0 125-129 35.5858 37.0 37.0 37.0 37.0 37.0 130-134 35.4813 37.0 37.0 37.0 37.0 37.0 135-139 35.317400000000006 37.0 37.0 37.0 34.6 37.0 140-144 35.2996 37.0 37.0 37.0 34.6 37.0 145-149 35.4031 37.0 37.0 37.0 34.6 37.0 150 35.4935 37.0 37.0 37.0 37.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 22 1.0 23 3.0 24 5.0 25 10.0 26 16.0 27 27.0 28 20.0 29 43.0 30 53.0 31 93.0 32 127.0 33 139.0 34 185.0 35 357.0 36 2634.0 37 287.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 28.217325988983475 13.26990485728593 15.923885828743115 42.58888332498748 2 28.225 21.525 28.15 22.1 3 27.0 25.25 19.3 28.449999999999996 4 30.275000000000002 28.999999999999996 16.05 24.675 5 30.099999999999998 29.45 17.65 22.8 6 21.15 32.300000000000004 20.075000000000003 26.474999999999998 7 22.35 12.85 37.675 27.125 8 24.474999999999998 17.175 24.275 34.075 9 24.45 17.25 27.500000000000004 30.8 10-14 26.215 23.18 22.235 28.37 15-19 27.134999999999998 22.52 22.465 27.88 20-24 27.169999999999998 22.98 22.08 27.77 25-29 27.095000000000002 22.535 22.52 27.85 30-34 27.189999999999998 22.220000000000002 22.34 28.249999999999996 35-39 26.919999999999998 22.615 22.25 28.215 40-44 27.36 22.415 22.065 28.16 45-49 27.49 22.314999999999998 22.205 27.99 50-54 27.560000000000002 22.770000000000003 22.405 27.265 55-59 27.325 22.52 21.97 28.185 60-64 26.71 22.015 22.695 28.58 65-69 27.99 22.2 21.6 28.21 70-74 27.565 22.245 21.745 28.444999999999997 75-79 27.61 21.935 22.185 28.27 80-84 27.905 22.435 21.935 27.725 85-89 27.465 22.24 22.02 28.275 90-94 27.595 22.175 21.404999999999998 28.825 95-99 27.855 22.225 22.009999999999998 27.91 100-104 27.295 22.29 22.439999999999998 27.975 105-109 27.67 22.02 22.59 27.72 110-114 28.415000000000003 22.634999999999998 21.78 27.169999999999998 115-119 27.634999999999998 22.305 22.005 28.055000000000003 120-124 27.810000000000002 22.225 22.11 27.855 125-129 28.34 21.805 22.18 27.675 130-134 28.970000000000002 22.03 21.560000000000002 27.439999999999998 135-139 28.09 22.495 21.62 27.794999999999998 140-144 28.199999999999996 22.365 21.43 28.005000000000003 145-149 27.93 22.27 21.78 28.02 150 27.325 22.45 22.7 27.525 >>END_MODULE >>Per sequence GC content fail #GC Content Count 0 1.0 1 1.5 2 1.5 3 0.5 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 0.5 20 0.5 21 0.0 22 0.0 23 0.0 24 0.0 25 0.0 26 1.0 27 2.0 28 2.0 29 2.5 30 3.5 31 4.5 32 6.0 33 10.0 34 17.5 35 29.5 36 34.5 37 39.0 38 50.5 39 55.5 40 67.5 41 82.0 42 103.0 43 117.0 44 119.5 45 128.0 46 126.0 47 134.0 48 132.5 49 123.0 50 129.5 51 123.5 52 114.0 53 110.0 54 105.0 55 95.0 56 91.5 57 89.0 58 86.0 59 94.0 60 95.0 61 90.0 62 91.5 63 91.5 64 92.0 65 98.0 66 90.0 67 90.0 68 99.0 69 95.5 70 87.0 71 90.5 72 83.0 73 65.0 74 62.0 75 55.0 76 43.0 77 37.5 78 34.5 79 24.5 80 15.0 81 12.5 82 10.5 83 5.0 84 2.5 85 2.5 86 2.5 87 1.0 88 0.0 89 0.5 90 0.5 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 0.15 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 94.025 #Duplication Level Percentage of deduplicated Percentage of total 1 94.07072587077904 88.44999999999999 2 5.557032704068067 10.45 3 0.3190640787024727 0.8999999999999999 4 0.05317734645041213 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 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 0.05 0.0 0.0 0.0 0.0 76-77 0.05 0.0 0.0 0.0 0.0 78-79 0.075 0.0 0.0 0.0 0.0 80-81 0.075 0.0 0.0 0.0 0.0 82-83 0.075 0.0 0.0 0.0 0.0 84-85 0.075 0.0 0.0 0.0 0.0 86-87 0.1 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 0.1125 0.0 0.0 0.0 0.0 98-99 0.125 0.0 0.0 0.0 0.0 100-101 0.125 0.0 0.0 0.0 0.0 102-103 0.125 0.0 0.0 0.0 0.0 104-105 0.125 0.0 0.0 0.0 0.0 106-107 0.125 0.0 0.0 0.0 0.0 108-109 0.1375 0.0 0.0 0.0 0.0 110-111 0.15 0.0 0.0 0.0 0.0 112-113 0.2125 0.0 0.0 0.0 0.0 114-115 0.275 0.0 0.0 0.0 0.0 116-117 0.3375 0.0 0.0 0.0 0.0 118-119 0.375 0.0 0.0 0.0 0.0 120-121 0.4125 0.0 0.0 0.0 0.0 122-123 0.48750000000000004 0.0 0.0 0.0 0.0 124-125 0.525 0.0 0.0 0.0 0.0 126-127 0.5874999999999999 0.0 0.0 0.0 0.0 128-129 0.7375 0.0 0.0 0.0 0.0 130-131 0.85 0.0 0.0 0.0 0.0 132-133 0.8875 0.0 0.0 0.0 0.0 134-135 1.05 0.0 0.0 0.0 0.0 136-137 1.15 0.0 0.0 0.0 0.0 138 1.175 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position TAAAAGA 10 0.006973645 144.0 1 CGATGCA 10 0.006973645 144.0 4 >>END_MODULE ERR9452514 read2 length is 150 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename ERR9452514_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 35.7465 37.0 37.0 37.0 37.0 37.0 2 35.7755 37.0 37.0 37.0 37.0 37.0 3 35.893 37.0 37.0 37.0 37.0 37.0 4 35.889 37.0 37.0 37.0 37.0 37.0 5 35.827 37.0 37.0 37.0 37.0 37.0 6 35.8285 37.0 37.0 37.0 37.0 37.0 7 35.79 37.0 37.0 37.0 37.0 37.0 8 35.656 37.0 37.0 37.0 37.0 37.0 9 35.9075 37.0 37.0 37.0 37.0 37.0 10-14 35.9536 37.0 37.0 37.0 37.0 37.0 15-19 35.843399999999995 37.0 37.0 37.0 37.0 37.0 20-24 35.819 37.0 37.0 37.0 37.0 37.0 25-29 35.8411 37.0 37.0 37.0 37.0 37.0 30-34 35.8067 37.0 37.0 37.0 37.0 37.0 35-39 35.868700000000004 37.0 37.0 37.0 37.0 37.0 40-44 35.8165 37.0 37.0 37.0 37.0 37.0 45-49 35.7078 37.0 37.0 37.0 37.0 37.0 50-54 35.6914 37.0 37.0 37.0 37.0 37.0 55-59 35.700599999999994 37.0 37.0 37.0 37.0 37.0 60-64 35.672399999999996 37.0 37.0 37.0 37.0 37.0 65-69 35.6413 37.0 37.0 37.0 37.0 37.0 70-74 35.6077 37.0 37.0 37.0 37.0 37.0 75-79 35.5612 37.0 37.0 37.0 37.0 37.0 80-84 35.5714 37.0 37.0 37.0 37.0 37.0 85-89 35.3849 37.0 37.0 37.0 32.2 37.0 90-94 35.408300000000004 37.0 37.0 37.0 34.6 37.0 95-99 35.3691 37.0 37.0 37.0 34.6 37.0 100-104 35.3029 37.0 37.0 37.0 34.6 37.0 105-109 35.3822 37.0 37.0 37.0 34.6 37.0 110-114 35.314499999999995 37.0 37.0 37.0 32.2 37.0 115-119 35.275400000000005 37.0 37.0 37.0 34.6 37.0 120-124 35.1235 37.0 37.0 37.0 25.0 37.0 125-129 35.007400000000004 37.0 37.0 37.0 25.0 37.0 130-134 35.0634 37.0 37.0 37.0 25.0 37.0 135-139 35.1354 37.0 37.0 37.0 27.4 37.0 140-144 35.0231 37.0 37.0 37.0 27.4 37.0 145-149 34.8306 37.0 37.0 37.0 25.0 37.0 150 35.093 37.0 37.0 37.0 25.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 18 1.0 19 1.0 20 1.0 21 1.0 22 4.0 23 4.0 24 17.0 25 17.0 26 15.0 27 25.0 28 47.0 29 51.0 30 64.0 31 88.0 32 98.0 33 151.0 34 199.0 35 558.0 36 2508.0 37 150.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 26.924999999999997 14.2 16.175 42.699999999999996 2 28.9 22.2 28.000000000000004 20.9 3 26.400000000000002 26.525 18.325 28.749999999999996 4 30.4 28.525 14.6 26.474999999999998 5 29.975 29.4 17.424999999999997 23.200000000000003 6 22.900000000000002 30.65 19.275000000000002 27.175 7 22.875 14.2 36.05 26.875 8 22.3 18.224999999999998 23.974999999999998 35.5 9 24.3 18.25 27.0 30.45 10-14 25.8 23.565 22.115000000000002 28.52 15-19 26.235000000000003 22.52 22.919999999999998 28.325 20-24 26.63 23.405 22.16 27.805000000000003 25-29 26.915 22.985 22.005 28.095 30-34 26.540000000000003 23.07 22.29 28.1 35-39 26.284999999999997 23.355 21.91 28.449999999999996 40-44 26.645000000000003 22.335 22.865 28.155 45-49 26.845000000000002 22.075 22.314999999999998 28.765 50-54 27.435 22.97 21.875 27.72 55-59 27.32 22.855 22.05 27.775 60-64 27.425 21.675 22.259999999999998 28.64 65-69 26.93 22.63 22.17 28.27 70-74 27.384999999999998 22.865 21.84 27.91 75-79 27.189999999999998 22.509999999999998 21.92 28.38 80-84 27.725 22.05 22.3 27.925 85-89 27.66 22.485 21.385 28.470000000000002 90-94 26.974999999999998 22.43 21.955 28.64 95-99 27.615000000000002 21.83 22.25 28.305000000000003 100-104 27.595 22.175 22.485 27.744999999999997 105-109 27.705000000000002 21.965 22.11 28.22 110-114 28.095 22.445 21.565 27.894999999999996 115-119 27.595 22.16 21.560000000000002 28.685 120-124 27.584999999999997 21.98 22.215 28.22 125-129 28.470000000000002 21.395 21.945 28.189999999999998 130-134 28.18 22.435 22.175 27.21 135-139 28.27 22.415 21.875 27.439999999999998 140-144 28.325 22.23 21.645 27.800000000000004 145-149 28.615000000000002 22.425 21.915000000000003 27.045 150 29.125 21.3 21.675 27.900000000000002 >>END_MODULE >>Per sequence GC content fail #GC Content Count 0 0.0 1 0.0 2 0.0 3 0.5 4 1.0 5 1.0 6 0.5 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 0.5 26 2.0 27 3.5 28 3.5 29 4.0 30 5.0 31 5.0 32 6.0 33 8.0 34 14.5 35 21.0 36 27.0 37 40.0 38 48.5 39 67.0 40 79.5 41 83.5 42 101.5 43 117.5 44 138.0 45 144.5 46 136.5 47 127.0 48 119.5 49 113.0 50 117.0 51 124.0 52 118.0 53 111.5 54 100.5 55 92.0 56 92.5 57 104.5 58 105.0 59 87.0 60 87.5 61 89.0 62 94.0 63 104.5 64 94.0 65 89.0 66 90.5 67 93.0 68 93.0 69 90.5 70 86.5 71 86.5 72 77.0 73 58.5 74 59.0 75 50.5 76 37.5 77 39.5 78 32.5 79 19.5 80 15.5 81 13.0 82 9.0 83 5.0 84 2.5 85 4.0 86 4.5 87 2.0 88 1.0 89 0.5 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 0.0 >>END_MODULE >>Sequence Length Distribution pass #Length Count 150 4000.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 93.95 #Duplication Level Percentage of deduplicated Percentage of total 1 94.01277275146354 88.325 2 5.5880787653006925 10.5 3 0.3459286854709952 0.975 4 0.05321979776476849 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 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 0.0125 0.0 0.0 0.0 0.0 58-59 0.05 0.0 0.0 0.0 0.0 60-61 0.05 0.0 0.0 0.0 0.0 62-63 0.05 0.0 0.0 0.0 0.0 64-65 0.05 0.0 0.0 0.0 0.0 66-67 0.075 0.0 0.0 0.0 0.0 68-69 0.075 0.0 0.0 0.0 0.0 70-71 0.075 0.0 0.0 0.0 0.0 72-73 0.075 0.0 0.0 0.0 0.0 74-75 0.1 0.0 0.0 0.0 0.0 76-77 0.1 0.0 0.0 0.0 0.0 78-79 0.125 0.0 0.0 0.0 0.0 80-81 0.125 0.0 0.0 0.0 0.0 82-83 0.125 0.0 0.0 0.0 0.0 84-85 0.125 0.0 0.0 0.0 0.0 86-87 0.15 0.0 0.0 0.0 0.0 88-89 0.15 0.0 0.0 0.0 0.0 90-91 0.175 0.0 0.0 0.0 0.0 92-93 0.175 0.0 0.0 0.0 0.0 94-95 0.175 0.0 0.0 0.0 0.0 96-97 0.1875 0.0 0.0 0.0 0.0 98-99 0.2 0.0 0.0 0.0 0.0 100-101 0.2 0.0 0.0 0.0 0.0 102-103 0.2 0.0 0.0 0.0 0.0 104-105 0.2 0.0 0.0 0.0 0.0 106-107 0.2 0.0 0.0 0.0 0.0 108-109 0.21250000000000002 0.0 0.0 0.0 0.0 110-111 0.225 0.0 0.0 0.0 0.0 112-113 0.2875 0.0 0.0 0.0 0.0 114-115 0.35 0.0 0.0 0.0 0.0 116-117 0.42500000000000004 0.0 0.0 0.0 0.0 118-119 0.475 0.0 0.0 0.0 0.0 120-121 0.5125 0.0 0.0 0.0 0.0 122-123 0.5875 0.0 0.0 0.0 0.0 124-125 0.625 0.0 0.0 0.0 0.0 126-127 0.6875 0.0 0.0 0.0 0.0 128-129 0.8375 0.0 0.0 0.0 0.0 130-131 0.95 0.0 0.0 0.0 0.0 132-133 0.9875 0.0 0.0 0.0 0.0 134-135 1.15 0.0 0.0 0.0 0.0 136-137 1.25 0.0 0.0 0.0 0.0 138 1.275 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position GGGGGGG 40 0.007966741 18.0 140-144 >>END_MODULE Read 1507114 spots for ERR9452514.sra Written 1507114 spots for ERR9452514.sra Read 1507114 spots for ERR9452514.sra Written 1507114 spots for ERR9452514.sra Read 1507114 spots for ERR9452514.sra Written 1507114 spots for ERR9452514.sra Read 1507114 spots for ERR9452514.sra Written 1507114 spots for ERR9452514.sra Read 1507114 spots for ERR9452514.sra Written 1507114 spots for ERR9452514.sra Read 1507114 spots for ERR9452514.sra Written 1507114 spots for ERR9452514.sra Read 1507114 spots for ERR9452514.sra Written 1507114 spots for ERR9452514.sra Read 1507114 spots for ERR9452514.sra Written 1507114 spots for ERR9452514.sra Read 1507114 spots for ERR9452514.sra Written 1507114 spots for ERR9452514.sra Read 1507114 spots for ERR9452514.sra Written 1507114 spots for ERR9452514.sra Read 1507114 spots for ERR9452514.sra Written 1507114 spots for ERR9452514.sra Read 1507114 spots for ERR9452514.sra Written 1507114 spots for ERR9452514.sra Read 1507114 spots for ERR9452514.sra Written 1507114 spots for ERR9452514.sra Read 1507114 spots for ERR9452514.sra Written 1507114 spots for ERR9452514.sra Read 1507123 spots for ERR9452514.sra Written 1507123 spots for ERR9452514.sra Read 1507114 spots for ERR9452514.sra Written 1507114 spots for ERR9452514.sra Read 1507114 spots for ERR9452514.sra Written 1507114 spots for ERR9452514.sra Read 1507114 spots for ERR9452514.sra Written 1507114 spots for ERR9452514.sra Read 1507114 spots for ERR9452514.sra Written 1507114 spots for ERR9452514.sra Read 1507114 spots for ERR9452514.sra Written 1507114 spots for ERR9452514.sra SRR ids: ['ERR9452514.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_m8f85g08 ERR9452514.sra spots: 30142289 blocks: [[1, 1507114], [1507115, 3014228], [3014229, 4521342], [4521343, 6028456], [6028457, 7535570], [7535571, 9042684], [9042685, 10549798], [10549799, 12056912], [12056913, 13564026], [13564027, 15071140], [15071141, 16578254], [16578255, 18085368], [18085369, 19592482], [19592483, 21099596], [21099597, 22606710], [22606711, 24113824], [24113825, 25620938], [25620939, 27128052], [27128053, 28635166], [28635167, 30142289]] ERR9452514 file size 10133660 ERR9452514 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 ERR9452514 ERR9452514_1.fastq ERR9452514_2.fastq Input file: ERR9452514_1.fastq Paired file: ERR9452514_2.fastq trimmed: ERR9452514-trimmed-pair1.fastq, ERR9452514-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 00:02:51 2024 >> started Sat Dec 7 00:05:41 2024 >> done (170.133s) 30142289 read pairs processed; of these: 235 ( 0.00%) short read pairs filtered out after trimming by size control 752 ( 0.00%) empty read pairs filtered out after trimming by size control 30141302 (100.00%) read pairs available; of these: 569582 ( 1.89%) trimmed read pairs available after processing 29571720 (98.11%) untrimmed read pairs available after processing Length distribution of reads after trimming: length count percentage 18 50 0.00% 19 22 0.00% 20 2261 0.01% 21 25 0.00% 22 35 0.00% 23 23 0.00% 24 63 0.00% 25 22 0.00% 26 79 0.00% 27 26 0.00% 28 188 0.00% 29 41 0.00% 30 171 0.00% 31 48 0.00% 32 63 0.00% 33 28 0.00% 34 41 0.00% 35 43 0.00% 36 70 0.00% 37 18 0.00% 38 132 0.00% 39 43 0.00% 40 71 0.00% 41 47 0.00% 42 72 0.00% 43 55 0.00% 44 64 0.00% 45 59 0.00% 46 97 0.00% 47 68 0.00% 48 162 0.00% 49 84 0.00% 50 137 0.00% 51 108 0.00% 52 160 0.00% 53 145 0.00% 54 178 0.00% 55 191 0.00% 56 195 0.00% 57 190 0.00% 58 309 0.00% 59 228 0.00% 60 328 0.00% 61 294 0.00% 62 343 0.00% 63 366 0.00% 64 375 0.00% 65 432 0.00% 66 425 0.00% 67 467 0.00% 68 562 0.00% 69 576 0.00% 70 635 0.00% 71 733 0.00% 72 691 0.00% 73 734 0.00% 74 776 0.00% 75 817 0.00% 76 887 0.00% 77 966 0.00% 78 1024 0.00% 79 1046 0.00% 80 1117 0.00% 81 1132 0.00% 82 1221 0.00% 83 1346 0.00% 84 1293 0.00% 85 1416 0.00% 86 1560 0.01% 87 1465 0.00% 88 1703 0.01% 89 1723 0.01% 90 1903 0.01% 91 1985 0.01% 92 2087 0.01% 93 2041 0.01% 94 2241 0.01% 95 2348 0.01% 96 2425 0.01% 97 2435 0.01% 98 2587 0.01% 99 2587 0.01% 100 2964 0.01% 101 3011 0.01% 102 3108 0.01% 103 3289 0.01% 104 3394 0.01% 105 3515 0.01% 106 3758 0.01% 107 3842 0.01% 108 4027 0.01% 109 4137 0.01% 110 4446 0.01% 111 4475 0.01% 112 4786 0.02% 113 5120 0.02% 114 5277 0.02% 115 5527 0.02% 116 5802 0.02% 117 6137 0.02% 118 6228 0.02% 119 6480 0.02% 120 6971 0.02% 121 7129 0.02% 122 7518 0.02% 123 7421 0.02% 124 8376 0.03% 125 8676 0.03% 126 9152 0.03% 127 9596 0.03% 128 9905 0.03% 129 10396 0.03% 130 10590 0.04% 131 11175 0.04% 132 11617 0.04% 133 12466 0.04% 134 13034 0.04% 135 13794 0.05% 136 14355 0.05% 137 14585 0.05% 138 15070 0.05% 139 15841 0.05% 140 17143 0.06% 141 17495 0.06% 142 18276 0.06% 143 18788 0.06% 144 19810 0.07% 145 20704 0.07% 146 22200 0.07% 147 22794 0.08% 148 24187 0.08% 149 25991 0.09% 150 29571720 98.11% 30141302 reads passed initial QC criterion=sequence-density sequence-density=0.31 sequence-density-rank=1 fanout-score=2.90 fanout-score-rank=26 prefix-density=0.33 prefix-fanout=2.8 sequence=GGTGTTGTCGAAGCCGATGATGCGGAC criterion=fanout-score sequence-density=0.03 sequence-density-rank=36 fanout-score=688.44 fanout-score-rank=1 prefix-density=1.08 prefix-fanout=21.6 sequence=GCGGCGGCGAACCGCCCCCGTCGCCGCGATCCGAACACTTCACCGGACCATTCAATCGGTAGGAGCGACGGGCGGTGTGTACAAAGGGCAGGGACGTAGTCAACGCGAGCTGATGACTCGCGCTTACTAGGCATTCCTCGTTGAAGACCAACAATTGCAATGATCTATCCCCATCACGATGAAATTTCCCAAGATTACCCGGGCCTGTCGGCCAAGGCTATATACTCGTTGAATACATCAGTGTAGCGCGCGTGCGGCCCAGAACATCTAAGGGCATCACAGACCTGTTATTGCCTCAAACTTCCGTCGCCTAAACGGCGATAGTCCCTCTAAGAAGCTAGCTGCGGAGGGATGGCTCCGCATAGCTAGTTAGCAGGCTGAGGTCTCGTTCGTTAACGGAATTAACCAGACAAATCGCTCCACCAACTAAGAACGGCCATGCACCACCACCCATAGAATCAAGAAAGAGCTCTCAGTCTGTCAATCCTTGCTATGTCTGGACCTGGTAAGT criterion=sequence-density sequence-density=0.33 sequence-density-rank=1 fanout-score=2.71 fanout-score-rank=26 prefix-density=0.34 prefix-fanout=2.6 sequence=GGTGTTGTCGAAGCCGATGATGCGGAC criterion=fanout-score sequence-density=0.03 sequence-density-rank=39 fanout-score=801.26 fanout-score-rank=1 prefix-density=1.06 prefix-fanout=22.3 sequence=GCGGCGGCGAACCGCCCCCGTCGCCGCGATCCGAACACTTCACCGGACCATTCAATCGGTAGGAGCGACGGGCGGTGTGTACAAAGGGCAGGGACGTAGTCAACGCGAGCTGATGACTCGCGCTTACTAGGCATTCCTCGTTGAAGACCAACAATTGCAATGATCTATCCCCATCACGATGAAATTTCCCAAGATTACCCGGGCCTGTCGGCCAAGGCTATATACTCGTTGAATACATCAGTGTAGCGCGCGTGCGGCCCAGAACATCTAAGGGCATCACAGACCTGTTATTGCCTCAAACTTCCGTCGCCTAAACGGCGATAGTCCCTCTAAGAAGCTAGCTGCGGAGGGATGGCTCCGCATAGCTAGTTAGCAGGCTGAGGTCTCGTTCGTTAACGGAATTAACCAGACAAATCGCTCCACCAACTAAGAACGGCCATGCACCACCACCCATAGAATCAAGAAAGAGCTCTCAGTCTGTCAATCCTTGCTATGTCTGGACCTGGTAAGT ERR9452514 testing PE reads STAR mapping to Ensembl genome Started job on | Dec 07 00:06:56 Started mapping on | Dec 07 00:06:56 Finished on | Dec 07 00:15:59 Mapping speed, Million of reads per hour | 199.83 Number of input reads | 30141302 Average input read length | 299 UNIQUE READS: Uniquely mapped reads number | 28288863 Uniquely mapped reads % | 93.85% Average mapped length | 298.06 Number of splices: Total | 27265801 Number of splices: Annotated (sjdb) | 25739413 Number of splices: GT/AG | 26884176 Number of splices: GC/AG | 343924 Number of splices: AT/AC | 11367 Number of splices: Non-canonical | 26334 Mismatch rate per base, % | 0.20% Deletion rate per base | 0.00% Deletion average length | 1.68 Insertion rate per base | 0.00% Insertion average length | 1.22 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 312561 % of reads mapped to multiple loci | 1.04% Number of reads mapped to too many loci | 99752 % of reads mapped to too many loci | 0.33% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 1.42% % of reads unmapped: other | 3.36% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 1539878 1539878 1539878 N_multimapping 312561 312561 312561 N_noFeature 882583 14279379 14381313 N_ambiguous 677252 85828 86100 UnstrandedReadsAssigned:26729028 PositiveStrandReadsAssigned:13923656 NegativeStrandReadsAssigned:13821450 Dataset is classified unstranded MeadianReadLen=150 20thPercentileLength=150 echo kmer=145 ERR9452514 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: ERR9452514-trimmed-pair1.fastq ERR9452514-trimmed-pair2.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 30,141,302 reads, 27,860,365 reads pseudoaligned [quant] estimated average fragment length: 245.341 [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,125 rounds 52973 ERR9452514.ke.tsv 35125 ERR9452514.se.tsv 88098 total ==> ERR9452514.ke.tsv <== target_id length eff_length est_counts tpm PNS24245 936 691.947 0 0 PNS24247 1044 799.659 27.9827 1.55271 PNS24249 1928 1683.66 287.943 7.5885 PNS24246 1044 799.659 27.9827 1.55271 PNS24248 1044 799.659 27.9827 1.55271 PNS24244 1471 1226.66 68.1093 2.4637 PNS24243 293 63.7623 41 28.5315 KQK14069 1603 1358.66 22810.1 744.941 KQK14071 474 232.159 1995.09 381.312 ==> ERR9452514.se.tsv <== BRADI_1g14170v3 26616 BRADI_1g53295v3 104 BRADI_1g59795v3 642 BRADI_1g07683v3 0 BRADI_1g00485v3 67 BRADI_1g20270v3 1068 BRADI_1g74790v3 415 BRADI_1g09890v3 9 BRADI_1g77505v3 522 BRADI_1g48960v3 0 ERR9452514 completed mapping pipeline successfully