Starting /dee2/code/volunteer_pipeline.sh ERR9452523 current disk space = 1547769323520 free memory = 1410164332 ERR9452523 SRAfilesize a8a154692c81d0f6a7fea2bc6ccbc714 ERR9452523.sra ERR9452523.sra file validated ERR9452523 is paired end ERR9452523 is conventional basespace ERR9452523 read1 length is 150 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename ERR9452523_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 35.83075 37.0 37.0 37.0 37.0 37.0 2 35.6735 37.0 37.0 37.0 37.0 37.0 3 36.154 37.0 37.0 37.0 37.0 37.0 4 36.2265 37.0 37.0 37.0 37.0 37.0 5 36.124 37.0 37.0 37.0 37.0 37.0 6 36.2095 37.0 37.0 37.0 37.0 37.0 7 36.078 37.0 37.0 37.0 37.0 37.0 8 36.1705 37.0 37.0 37.0 37.0 37.0 9 36.26 37.0 37.0 37.0 37.0 37.0 10-14 36.269400000000005 37.0 37.0 37.0 37.0 37.0 15-19 36.2587 37.0 37.0 37.0 37.0 37.0 20-24 36.2185 37.0 37.0 37.0 37.0 37.0 25-29 36.1745 37.0 37.0 37.0 37.0 37.0 30-34 36.0949 37.0 37.0 37.0 37.0 37.0 35-39 36.1414 37.0 37.0 37.0 37.0 37.0 40-44 35.942499999999995 37.0 37.0 37.0 37.0 37.0 45-49 35.9446 37.0 37.0 37.0 37.0 37.0 50-54 35.995 37.0 37.0 37.0 37.0 37.0 55-59 35.9054 37.0 37.0 37.0 37.0 37.0 60-64 36.0398 37.0 37.0 37.0 37.0 37.0 65-69 35.938100000000006 37.0 37.0 37.0 37.0 37.0 70-74 35.911199999999994 37.0 37.0 37.0 37.0 37.0 75-79 35.8455 37.0 37.0 37.0 37.0 37.0 80-84 35.843399999999995 37.0 37.0 37.0 37.0 37.0 85-89 35.9227 37.0 37.0 37.0 37.0 37.0 90-94 35.812200000000004 37.0 37.0 37.0 37.0 37.0 95-99 35.7995 37.0 37.0 37.0 37.0 37.0 100-104 35.7312 37.0 37.0 37.0 37.0 37.0 105-109 35.6488 37.0 37.0 37.0 37.0 37.0 110-114 35.6297 37.0 37.0 37.0 37.0 37.0 115-119 35.609700000000004 37.0 37.0 37.0 37.0 37.0 120-124 35.6221 37.0 37.0 37.0 37.0 37.0 125-129 35.6023 37.0 37.0 37.0 37.0 37.0 130-134 35.516999999999996 37.0 37.0 37.0 37.0 37.0 135-139 35.4409 37.0 37.0 37.0 37.0 37.0 140-144 35.2624 37.0 37.0 37.0 32.2 37.0 145-149 35.468999999999994 37.0 37.0 37.0 37.0 37.0 150 35.5325 37.0 37.0 37.0 37.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 21 1.0 22 0.0 23 2.0 24 6.0 25 7.0 26 12.0 27 16.0 28 27.0 29 34.0 30 56.0 31 76.0 32 86.0 33 125.0 34 224.0 35 364.0 36 2648.0 37 316.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 29.08227056764191 12.80320080020005 15.303825956489122 42.810702675668914 2 28.214107053526767 20.785392696348172 29.314657328664335 21.68584292146073 3 27.1 25.15 19.3 28.449999999999996 4 29.775000000000002 29.4 16.025 24.8 5 28.599999999999998 29.75 19.975 21.675 6 21.349999999999998 31.974999999999998 20.349999999999998 26.325 7 21.4 14.475 37.025000000000006 27.1 8 24.175 17.599999999999998 24.675 33.550000000000004 9 24.15 17.95 27.1 30.8 10-14 26.479999999999997 23.105 22.225 28.189999999999998 15-19 26.8 22.2 22.57 28.43 20-24 26.805 23.28 22.085 27.83 25-29 27.405 23.735 21.69 27.169999999999998 30-34 27.450000000000003 22.830000000000002 22.48 27.24 35-39 26.845000000000002 22.775000000000002 22.045 28.335 40-44 27.22 22.97 21.985 27.825 45-49 26.8 22.56 22.845 27.794999999999998 50-54 27.555000000000003 22.2 22.415 27.83 55-59 27.38 22.88 21.990000000000002 27.750000000000004 60-64 27.245 22.12 22.775000000000002 27.860000000000003 65-69 26.979999999999997 22.575 22.64 27.805000000000003 70-74 27.279999999999998 22.08 22.475 28.165000000000003 75-79 27.16 22.905 21.205 28.73 80-84 27.83 21.84 22.325 28.005000000000003 85-89 27.650000000000002 22.58 22.13 27.639999999999997 90-94 28.410000000000004 21.775 21.985 27.83 95-99 27.92 22.395 22.245 27.439999999999998 100-104 28.265 22.03 21.945 27.76 105-109 27.860000000000003 22.495 22.12 27.525 110-114 28.225 22.475 21.925 27.375 115-119 27.644999999999996 22.67 22.34 27.345000000000002 120-124 27.85 21.805 22.165000000000003 28.18 125-129 27.800000000000004 22.415 21.905 27.88 130-134 27.715 22.515 21.959999999999997 27.810000000000002 135-139 28.455000000000002 22.735 21.515 27.295 140-144 27.715 22.005 22.55 27.73 145-149 28.355000000000004 21.57 22.115000000000002 27.96 150 26.775 22.125 22.575 28.525 >>END_MODULE >>Per sequence GC content fail #GC Content Count 0 2.0 1 1.0 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 1.0 24 1.0 25 0.0 26 0.0 27 0.5 28 3.0 29 6.0 30 7.0 31 8.5 32 12.0 33 15.0 34 19.5 35 23.5 36 29.5 37 41.5 38 49.5 39 62.5 40 70.5 41 80.5 42 108.5 43 112.5 44 114.0 45 124.0 46 140.5 47 152.5 48 142.5 49 136.0 50 125.5 51 117.0 52 117.0 53 116.0 54 106.0 55 91.5 56 87.5 57 90.0 58 98.0 59 96.5 60 75.5 61 77.0 62 83.0 63 84.0 64 85.5 65 79.5 66 96.0 67 105.0 68 81.5 69 83.0 70 93.5 71 88.0 72 80.5 73 70.0 74 63.0 75 49.0 76 40.5 77 34.0 78 29.0 79 27.0 80 21.5 81 15.5 82 10.5 83 7.5 84 5.5 85 3.0 86 0.5 87 1.0 88 1.0 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 0.025 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 93.95 #Duplication Level Percentage of deduplicated Percentage of total 1 93.85311335816924 88.175 2 5.8807876530069185 11.05 3 0.2394890899414582 0.675 4 0.026609898882384245 0.1 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 0.025 0.0 0.0 0.0 0.0 26-27 0.025 0.0 0.0 0.0 0.0 28-29 0.025 0.0 0.0 0.0 0.0 30-31 0.025 0.0 0.0 0.0 0.0 32-33 0.025 0.0 0.0 0.0 0.0 34-35 0.025 0.0 0.0 0.0 0.0 36-37 0.025 0.0 0.0 0.0 0.0 38-39 0.025 0.0 0.0 0.0 0.0 40-41 0.025 0.0 0.0 0.0 0.0 42-43 0.025 0.0 0.0 0.0 0.0 44-45 0.025 0.0 0.0 0.0 0.0 46-47 0.025 0.0 0.0 0.0 0.0 48-49 0.025 0.0 0.0 0.0 0.0 50-51 0.025 0.0 0.0 0.0 0.0 52-53 0.025 0.0 0.0 0.0 0.0 54-55 0.025 0.0 0.0 0.0 0.0 56-57 0.025 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 0.05 0.0 0.0 0.0 0.0 68-69 0.05 0.0 0.0 0.0 0.0 70-71 0.075 0.0 0.0 0.0 0.0 72-73 0.1 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 0.1 0.0 0.0 0.0 0.0 80-81 0.1 0.0 0.0 0.0 0.0 82-83 0.1 0.0 0.0 0.0 0.0 84-85 0.1 0.0 0.0 0.0 0.0 86-87 0.1 0.0 0.0 0.0 0.0 88-89 0.1 0.0 0.0 0.0 0.0 90-91 0.1125 0.0 0.0 0.0 0.0 92-93 0.125 0.0 0.0 0.0 0.0 94-95 0.125 0.0 0.0 0.0 0.0 96-97 0.175 0.0 0.0 0.0 0.0 98-99 0.2375 0.0 0.0 0.0 0.0 100-101 0.2875 0.0 0.0 0.0 0.0 102-103 0.3625 0.0 0.0 0.0 0.0 104-105 0.375 0.0 0.0 0.0 0.0 106-107 0.375 0.0 0.0 0.0 0.0 108-109 0.375 0.0 0.0 0.0 0.0 110-111 0.4625 0.0 0.0 0.0 0.0125 112-113 0.5375000000000001 0.0 0.0 0.0 0.025 114-115 0.55 0.0 0.0 0.0 0.025 116-117 0.5625 0.0 0.0 0.0 0.025 118-119 0.575 0.0 0.0 0.0 0.025 120-121 0.6125 0.0 0.0 0.0 0.025 122-123 0.65 0.0 0.0 0.0 0.025 124-125 0.7 0.0 0.0 0.0 0.025 126-127 0.775 0.0 0.0 0.0 0.025 128-129 0.85 0.0 0.0 0.0 0.025 130-131 0.9874999999999999 0.0 0.0 0.0 0.025 132-133 1.0375 0.0 0.0 0.0 0.025 134-135 1.1 0.0 0.0 0.0 0.025 136-137 1.2000000000000002 0.0 0.0 0.0 0.025 138 1.275 0.0 0.0 0.0 0.025 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position ATCTTCC 10 0.006973645 144.0 8 TAAAATA 10 0.006973645 144.0 4 GGCAAGT 10 0.006973645 144.0 1 ATCTGCC 10 0.006973645 144.0 6 >>END_MODULE ERR9452523 read2 length is 150 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename ERR9452523_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 35.858 37.0 37.0 37.0 37.0 37.0 2 35.7855 37.0 37.0 37.0 37.0 37.0 3 36.042 37.0 37.0 37.0 37.0 37.0 4 35.9575 37.0 37.0 37.0 37.0 37.0 5 35.9805 37.0 37.0 37.0 37.0 37.0 6 36.0265 37.0 37.0 37.0 37.0 37.0 7 36.0245 37.0 37.0 37.0 37.0 37.0 8 35.9845 37.0 37.0 37.0 37.0 37.0 9 36.1005 37.0 37.0 37.0 37.0 37.0 10-14 36.1494 37.0 37.0 37.0 37.0 37.0 15-19 36.029700000000005 37.0 37.0 37.0 37.0 37.0 20-24 35.9732 37.0 37.0 37.0 37.0 37.0 25-29 36.0647 37.0 37.0 37.0 37.0 37.0 30-34 36.0458 37.0 37.0 37.0 37.0 37.0 35-39 36.048899999999996 37.0 37.0 37.0 37.0 37.0 40-44 36.020799999999994 37.0 37.0 37.0 37.0 37.0 45-49 35.981 37.0 37.0 37.0 37.0 37.0 50-54 35.9285 37.0 37.0 37.0 37.0 37.0 55-59 35.9533 37.0 37.0 37.0 37.0 37.0 60-64 35.9067 37.0 37.0 37.0 37.0 37.0 65-69 35.9094 37.0 37.0 37.0 37.0 37.0 70-74 35.866200000000006 37.0 37.0 37.0 37.0 37.0 75-79 35.744600000000005 37.0 37.0 37.0 37.0 37.0 80-84 35.721000000000004 37.0 37.0 37.0 37.0 37.0 85-89 35.6666 37.0 37.0 37.0 37.0 37.0 90-94 35.6651 37.0 37.0 37.0 37.0 37.0 95-99 35.5995 37.0 37.0 37.0 37.0 37.0 100-104 35.605599999999995 37.0 37.0 37.0 37.0 37.0 105-109 35.6411 37.0 37.0 37.0 37.0 37.0 110-114 35.6014 37.0 37.0 37.0 37.0 37.0 115-119 35.5099 37.0 37.0 37.0 37.0 37.0 120-124 35.467 37.0 37.0 37.0 37.0 37.0 125-129 35.3645 37.0 37.0 37.0 34.6 37.0 130-134 35.3351 37.0 37.0 37.0 32.2 37.0 135-139 35.4117 37.0 37.0 37.0 34.6 37.0 140-144 35.2738 37.0 37.0 37.0 32.2 37.0 145-149 35.05800000000001 37.0 37.0 37.0 25.0 37.0 150 35.4535 37.0 37.0 37.0 37.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 16 1.0 17 1.0 18 0.0 19 1.0 20 2.0 21 0.0 22 3.0 23 8.0 24 10.0 25 11.0 26 14.0 27 17.0 28 21.0 29 36.0 30 44.0 31 52.0 32 91.0 33 134.0 34 189.0 35 531.0 36 2600.0 37 234.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 31.075000000000003 12.575 14.799999999999999 41.55 2 27.85 20.175 27.500000000000004 24.474999999999998 3 27.375 24.675 19.575 28.375 4 31.125000000000004 29.325000000000003 14.85 24.7 5 28.375 30.099999999999998 18.75 22.775000000000002 6 22.625 32.4 19.85 25.124999999999996 7 21.4 14.575 36.575 27.450000000000003 8 23.125 18.475 25.624999999999996 32.775 9 24.575 17.375 27.025 31.025000000000002 10-14 25.974999999999998 23.630000000000003 22.545 27.85 15-19 26.119999999999997 22.955000000000002 22.869999999999997 28.055000000000003 20-24 26.369999999999997 22.900000000000002 22.81 27.92 25-29 27.345000000000002 23.07 22.0 27.584999999999997 30-34 27.185 22.925 22.23 27.66 35-39 26.97 22.415 22.220000000000002 28.395 40-44 26.484999999999996 23.0 22.16 28.355000000000004 45-49 27.025 22.15 22.08 28.744999999999997 50-54 26.445 22.7 22.27 28.585 55-59 27.400000000000002 22.6 22.275 27.725 60-64 27.305 22.695 21.884999999999998 28.115000000000002 65-69 27.32 22.23 22.255 28.194999999999997 70-74 28.32 21.915000000000003 22.055 27.71 75-79 27.47 22.785 21.395 28.349999999999998 80-84 27.650000000000002 22.78 21.759999999999998 27.810000000000002 85-89 28.084999999999997 22.12 21.605 28.189999999999998 90-94 27.92 22.205 22.009999999999998 27.865000000000002 95-99 27.755000000000003 21.86 22.32 28.065 100-104 27.435 22.46 21.735 28.37 105-109 28.134999999999998 21.935 22.165000000000003 27.765 110-114 28.139999999999997 22.314999999999998 21.795 27.750000000000004 115-119 27.525 21.42 22.56 28.494999999999997 120-124 27.905 22.21 22.355 27.529999999999998 125-129 27.450000000000003 22.285 22.314999999999998 27.950000000000003 130-134 27.91 22.56 21.88 27.650000000000002 135-139 28.125 22.225 22.155 27.495000000000005 140-144 28.105000000000004 22.475 22.355 27.065 145-149 27.865000000000002 22.84 21.765 27.529999999999998 150 27.35 21.85 24.025 26.775 >>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 0.5 20 0.5 21 0.5 22 0.5 23 0.0 24 0.5 25 2.5 26 2.5 27 1.5 28 2.5 29 3.0 30 4.0 31 6.0 32 10.5 33 16.0 34 19.5 35 21.0 36 24.0 37 35.5 38 55.0 39 69.5 40 82.0 41 88.5 42 89.5 43 102.0 44 115.0 45 130.5 46 136.5 47 140.0 48 150.5 49 147.0 50 124.0 51 107.0 52 112.0 53 103.5 54 98.0 55 102.0 56 91.0 57 85.0 58 87.0 59 96.5 60 106.0 61 88.5 62 81.5 63 91.5 64 88.0 65 90.5 66 86.0 67 85.5 68 100.0 69 91.5 70 80.5 71 77.5 72 76.5 73 68.5 74 60.0 75 62.5 76 53.0 77 38.5 78 33.0 79 24.0 80 11.5 81 11.0 82 11.5 83 7.5 84 4.0 85 3.0 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 0.0 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 94.125 #Duplication Level Percentage of deduplicated Percentage of total 1 94.05046480743692 88.52499999999999 2 5.657370517928287 10.65 3 0.2921646746347942 0.8250000000000001 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 0.025 0.0 0.0 0.0 0.0 26-27 0.025 0.0 0.0 0.0 0.0 28-29 0.025 0.0 0.0 0.0 0.0 30-31 0.025 0.0 0.0 0.0 0.0 32-33 0.025 0.0 0.0 0.0 0.0 34-35 0.025 0.0 0.0 0.0 0.0 36-37 0.025 0.0 0.0 0.0 0.0 38-39 0.025 0.0 0.0 0.0 0.0 40-41 0.025 0.0 0.0 0.0 0.0 42-43 0.025 0.0 0.0 0.0 0.0 44-45 0.025 0.0 0.0 0.0 0.0 46-47 0.025 0.0 0.0 0.0 0.0 48-49 0.025 0.0 0.0 0.0 0.0 50-51 0.025 0.0 0.0 0.0 0.0 52-53 0.025 0.0 0.0 0.0 0.0 54-55 0.025 0.0 0.0 0.0 0.0 56-57 0.025 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 0.05 0.0 0.0 0.0 0.0 68-69 0.05 0.0 0.0 0.0 0.0 70-71 0.075 0.0 0.0 0.0 0.0 72-73 0.1 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 0.1 0.0 0.0 0.0 0.0 80-81 0.1 0.0 0.0 0.0 0.0 82-83 0.1 0.0 0.0 0.0 0.0 84-85 0.1 0.0 0.0 0.0 0.0 86-87 0.1 0.0 0.0 0.0 0.0 88-89 0.1 0.0 0.0 0.0 0.0 90-91 0.1125 0.0 0.0 0.0 0.0 92-93 0.125 0.0 0.0 0.0 0.0 94-95 0.125 0.0 0.0 0.0 0.0 96-97 0.175 0.0 0.0 0.0 0.0 98-99 0.2375 0.0 0.0 0.0 0.0 100-101 0.2875 0.0 0.0 0.0 0.0 102-103 0.3625 0.0 0.0 0.0 0.0 104-105 0.375 0.0 0.0 0.0 0.0 106-107 0.375 0.0 0.0 0.0 0.0 108-109 0.375 0.0 0.0 0.0 0.0 110-111 0.4625 0.0 0.0 0.0 0.0 112-113 0.5375000000000001 0.0 0.0 0.0 0.0 114-115 0.55 0.0 0.0 0.0 0.0 116-117 0.5625 0.0 0.0 0.0 0.0 118-119 0.575 0.0 0.0 0.0 0.0 120-121 0.6125 0.0 0.0 0.0 0.0 122-123 0.65 0.0 0.0 0.0 0.0 124-125 0.7 0.0 0.0 0.0 0.0 126-127 0.75 0.0 0.0 0.0 0.0 128-129 0.825 0.0 0.0 0.0 0.0 130-131 0.9625 0.0 0.0 0.0 0.0 132-133 1.0125 0.0 0.0 0.0 0.0 134-135 1.0750000000000002 0.0 0.0 0.0 0.0 136-137 1.1749999999999998 0.0 0.0 0.0 0.0 138 1.25 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position TATGGTC 10 0.006973645 144.0 7 >>END_MODULE Read 1222511 spots for ERR9452523.sra Written 1222511 spots for ERR9452523.sra Read 1222511 spots for ERR9452523.sra Written 1222511 spots for ERR9452523.sra Read 1222511 spots for ERR9452523.sra Written 1222511 spots for ERR9452523.sra Read 1222511 spots for ERR9452523.sra Written 1222511 spots for ERR9452523.sra Read 1222511 spots for ERR9452523.sra Written 1222511 spots for ERR9452523.sra Read 1222511 spots for ERR9452523.sra Written 1222511 spots for ERR9452523.sra Read 1222511 spots for ERR9452523.sra Written 1222511 spots for ERR9452523.sra Read 1222511 spots for ERR9452523.sra Written 1222511 spots for ERR9452523.sra Read 1222511 spots for ERR9452523.sra Written 1222511 spots for ERR9452523.sra Read 1222511 spots for ERR9452523.sra Written 1222511 spots for ERR9452523.sra Read 1222516 spots for ERR9452523.sra Written 1222516 spots for ERR9452523.sra Read 1222511 spots for ERR9452523.sra Written 1222511 spots for ERR9452523.sra Read 1222511 spots for ERR9452523.sra Written 1222511 spots for ERR9452523.sra Read 1222511 spots for ERR9452523.sra Written 1222511 spots for ERR9452523.sra Read 1222511 spots for ERR9452523.sra Written 1222511 spots for ERR9452523.sra Read 1222511 spots for ERR9452523.sra Written 1222511 spots for ERR9452523.sra Read 1222511 spots for ERR9452523.sra Written 1222511 spots for ERR9452523.sra Read 1222511 spots for ERR9452523.sra Written 1222511 spots for ERR9452523.sra Read 1222511 spots for ERR9452523.sra Written 1222511 spots for ERR9452523.sra Read 1222511 spots for ERR9452523.sra Written 1222511 spots for ERR9452523.sra SRR ids: ['ERR9452523.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_8ts1ycph ERR9452523.sra spots: 24450225 blocks: [[1, 1222511], [1222512, 2445022], [2445023, 3667533], [3667534, 4890044], [4890045, 6112555], [6112556, 7335066], [7335067, 8557577], [8557578, 9780088], [9780089, 11002599], [11002600, 12225110], [12225111, 13447621], [13447622, 14670132], [14670133, 15892643], [15892644, 17115154], [17115155, 18337665], [18337666, 19560176], [19560177, 20782687], [20782688, 22005198], [22005199, 23227709], [23227710, 24450225]] ERR9452523 file size 8215924 ERR9452523 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 ERR9452523 ERR9452523_1.fastq ERR9452523_2.fastq Input file: ERR9452523_1.fastq Paired file: ERR9452523_2.fastq trimmed: ERR9452523-trimmed-pair1.fastq, ERR9452523-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 00:03:22 2024 >> started Sat Dec 7 00:04:02 2024 >> done (39.891s) 24450225 read pairs processed; of these: 441 ( 0.00%) short read pairs filtered out after trimming by size control 1014 ( 0.00%) empty read pairs filtered out after trimming by size control 24448770 (99.99%) read pairs available; of these: 723426 ( 2.96%) trimmed read pairs available after processing 23725344 (97.04%) untrimmed read pairs available after processing Length distribution of reads after trimming: length count percentage 18 26 0.00% 19 28 0.00% 20 226 0.00% 21 23 0.00% 22 15 0.00% 23 18 0.00% 24 37 0.00% 25 33 0.00% 26 27 0.00% 27 31 0.00% 28 31 0.00% 29 53 0.00% 30 116 0.00% 31 59 0.00% 32 29 0.00% 33 32 0.00% 34 33 0.00% 35 25 0.00% 36 29 0.00% 37 23 0.00% 38 28 0.00% 39 33 0.00% 40 31 0.00% 41 45 0.00% 42 44 0.00% 43 50 0.00% 44 39 0.00% 45 46 0.00% 46 69 0.00% 47 50 0.00% 48 71 0.00% 49 83 0.00% 50 101 0.00% 51 94 0.00% 52 103 0.00% 53 133 0.00% 54 155 0.00% 55 126 0.00% 56 187 0.00% 57 203 0.00% 58 201 0.00% 59 233 0.00% 60 287 0.00% 61 283 0.00% 62 324 0.00% 63 334 0.00% 64 354 0.00% 65 432 0.00% 66 441 0.00% 67 526 0.00% 68 506 0.00% 69 581 0.00% 70 647 0.00% 71 620 0.00% 72 827 0.00% 73 854 0.00% 74 735 0.00% 75 912 0.00% 76 948 0.00% 77 1007 0.00% 78 1109 0.00% 79 1148 0.00% 80 1187 0.00% 81 1237 0.01% 82 1396 0.01% 83 1478 0.01% 84 1593 0.01% 85 1724 0.01% 86 1735 0.01% 87 1829 0.01% 88 1831 0.01% 89 1971 0.01% 90 2078 0.01% 91 2202 0.01% 92 2396 0.01% 93 2492 0.01% 94 2652 0.01% 95 2868 0.01% 96 2850 0.01% 97 3019 0.01% 98 3041 0.01% 99 3235 0.01% 100 3423 0.01% 101 3661 0.01% 102 3781 0.02% 103 4004 0.02% 104 4137 0.02% 105 4490 0.02% 106 4665 0.02% 107 4784 0.02% 108 4894 0.02% 109 5244 0.02% 110 5468 0.02% 111 5764 0.02% 112 6155 0.03% 113 6351 0.03% 114 6692 0.03% 115 7043 0.03% 116 7304 0.03% 117 7785 0.03% 118 7863 0.03% 119 8450 0.03% 120 9097 0.04% 121 9373 0.04% 122 9635 0.04% 123 9959 0.04% 124 10523 0.04% 125 11230 0.05% 126 11820 0.05% 127 12246 0.05% 128 12793 0.05% 129 13194 0.05% 130 13779 0.06% 131 14400 0.06% 132 15224 0.06% 133 16125 0.07% 134 17019 0.07% 135 17624 0.07% 136 19025 0.08% 137 19364 0.08% 138 20041 0.08% 139 21061 0.09% 140 21701 0.09% 141 22848 0.09% 142 23582 0.10% 143 25019 0.10% 144 25822 0.11% 145 27355 0.11% 146 28553 0.12% 147 29685 0.12% 148 31905 0.13% 149 32758 0.13% 150 23725344 97.04% 24448770 reads passed initial QC criterion=sequence-density sequence-density=0.23 sequence-density-rank=1 fanout-score=3.22 fanout-score-rank=25 prefix-density=0.25 prefix-fanout=3.0 sequence=GGTGTTGTCGAAGCCGATGATGCGGAC criterion=fanout-score sequence-density=0.03 sequence-density-rank=34 fanout-score=1027.85 fanout-score-rank=1 prefix-density=1.11 prefix-fanout=24.0 sequence=GCGGCGGCGAACCGCCCCCGTCGCCGCGATCCGAACACTTCACCGGACCATTCAATCGGTAGGAGCGACGGGCGGTGTGTACAAAGGGCAGGGACGTAGTCAACGCGAGCTGATGACTCGCGCTTACTAGGCATTCCTCGTTGAAGACCAACAATTGCAATGATCTATCCCCATCACGATGAAATTTCCCAAGATTACCCGGGCCTGTCGGCCAAGGCTATATACTCGTTGAATACATCAGTGTAGCGCGCGTGCGGCCCAGAACATCTAAGGGCATCACAGACCTGTTATTGCCTCAAACTTCCGTCGCCTAAACGGCGATAGTCCCTCTAAGAAGCTAGCTGCGGAGGGATGGCTCCGCATAGCTAGTTAGCAGGCTGAGGTCTCGTTCGTTAACGGAATTAACCAGACAAATCGCTCCACCAACTAAGAACGGCCATGCACCACCACCCATAGAATCAAGAAAGAGCTCTCAGTCTGTCAATCCTTGCTATGTCTGGACCTGGTAAGT criterion=sequence-density sequence-density=0.23 sequence-density-rank=1 fanout-score=3.20 fanout-score-rank=23 prefix-density=0.24 prefix-fanout=3.0 sequence=GGTGTTGTCGAAGCCGATGATGCGGAC criterion=fanout-score sequence-density=0.11 sequence-density-rank=21 fanout-score=174.67 fanout-score-rank=1 prefix-density=1.04 prefix-fanout=18.6 sequence=CCGCCGCCGCCG ERR9452523 testing PE reads STAR mapping to Ensembl genome Started job on | Dec 07 00:05:07 Started mapping on | Dec 07 00:05:07 Finished on | Dec 07 00:08:16 Mapping speed, Million of reads per hour | 465.69 Number of input reads | 24448770 Average input read length | 298 UNIQUE READS: Uniquely mapped reads number | 23076243 Uniquely mapped reads % | 94.39% Average mapped length | 297.72 Number of splices: Total | 21752952 Number of splices: Annotated (sjdb) | 20482082 Number of splices: GT/AG | 21438886 Number of splices: GC/AG | 280745 Number of splices: AT/AC | 10792 Number of splices: Non-canonical | 22529 Mismatch rate per base, % | 0.18% Deletion rate per base | 0.00% Deletion average length | 1.70 Insertion rate per base | 0.00% Insertion average length | 1.21 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 234265 % of reads mapped to multiple loci | 0.96% Number of reads mapped to too many loci | 69118 % of reads mapped to too many loci | 0.28% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 1.75% % of reads unmapped: other | 2.63% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 1138262 1138262 1138262 N_multimapping 234265 234265 234265 N_noFeature 720448 11644706 11718705 N_ambiguous 557948 65670 65592 UnstrandedReadsAssigned:21797847 PositiveStrandReadsAssigned:11365867 NegativeStrandReadsAssigned:11291946 Dataset is classified unstranded MeadianReadLen=150 20thPercentileLength=150 echo kmer=145 ERR9452523 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: ERR9452523-trimmed-pair1.fastq ERR9452523-trimmed-pair2.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 24,448,770 reads, 22,679,922 reads pseudoaligned [quant] estimated average fragment length: 233.614 [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,236 rounds 52973 ERR9452523.ke.tsv 35125 ERR9452523.se.tsv 88098 total ==> ERR9452523.ke.tsv <== target_id length eff_length est_counts tpm PNS24245 936 703.703 0 0 PNS24247 1044 811.386 61.7899 4.28566 PNS24249 1928 1695.39 255.84 8.49235 PNS24246 1044 811.386 61.7899 4.28566 PNS24248 1044 811.386 61.7899 4.28566 PNS24244 1471 1238.39 54.7903 2.48986 PNS24243 293 72.0481 27 21.0896 KQK14069 1603 1370.39 14700.3 603.687 KQK14071 474 243.615 1833.23 423.488 ==> ERR9452523.se.tsv <== BRADI_1g14170v3 18843 BRADI_1g53295v3 104 BRADI_1g59795v3 543 BRADI_1g07683v3 0 BRADI_1g00485v3 62 BRADI_1g20270v3 848 BRADI_1g74790v3 611 BRADI_1g09890v3 1 BRADI_1g77505v3 496 BRADI_1g48960v3 0 ERR9452523 completed mapping pipeline successfully