Starting /dee2/code/volunteer_pipeline.sh SRR12949791 current disk space = 1543863930880 free memory = 1605780188 SRR12949791 SRAfilesize eb2568e312e2f4d3be237c00aec9e801 SRR12949791.sra SRR12949791.sra file validated SRR12949791 is paired end SRR12949791 is conventional basespace SRR12949791 read1 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR12949791_1.fastq File type Conventional base calls Encoding Sanger / Illumina 1.9 Total Sequences 4000 Sequences flagged as poor quality 0 Sequence length 151 %GC 49 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 36.497 37.0 37.0 37.0 37.0 37.0 2 35.98425 37.0 37.0 37.0 37.0 37.0 3 36.5855 37.0 37.0 37.0 37.0 37.0 4 36.647 37.0 37.0 37.0 37.0 37.0 5 36.573 37.0 37.0 37.0 37.0 37.0 6 36.6215 37.0 37.0 37.0 37.0 37.0 7 36.5685 37.0 37.0 37.0 37.0 37.0 8 36.6695 37.0 37.0 37.0 37.0 37.0 9 36.666 37.0 37.0 37.0 37.0 37.0 10-14 36.634699999999995 37.0 37.0 37.0 37.0 37.0 15-19 36.6169 37.0 37.0 37.0 37.0 37.0 20-24 36.616299999999995 37.0 37.0 37.0 37.0 37.0 25-29 36.62349999999999 37.0 37.0 37.0 37.0 37.0 30-34 36.57320000000001 37.0 37.0 37.0 37.0 37.0 35-39 36.5818 37.0 37.0 37.0 37.0 37.0 40-44 36.5144 37.0 37.0 37.0 37.0 37.0 45-49 36.5257 37.0 37.0 37.0 37.0 37.0 50-54 36.4415 37.0 37.0 37.0 37.0 37.0 55-59 36.5109 37.0 37.0 37.0 37.0 37.0 60-64 36.4425 37.0 37.0 37.0 37.0 37.0 65-69 36.4653 37.0 37.0 37.0 37.0 37.0 70-74 36.4309 37.0 37.0 37.0 37.0 37.0 75-79 36.444 37.0 37.0 37.0 37.0 37.0 80-84 36.375 37.0 37.0 37.0 37.0 37.0 85-89 36.3369 37.0 37.0 37.0 37.0 37.0 90-94 36.3382 37.0 37.0 37.0 37.0 37.0 95-99 36.320899999999995 37.0 37.0 37.0 37.0 37.0 100-104 36.302 37.0 37.0 37.0 37.0 37.0 105-109 36.1931 37.0 37.0 37.0 37.0 37.0 110-114 36.2171 37.0 37.0 37.0 37.0 37.0 115-119 36.1939 37.0 37.0 37.0 37.0 37.0 120-124 36.1838 37.0 37.0 37.0 37.0 37.0 125-129 36.0911 37.0 37.0 37.0 37.0 37.0 130-134 36.027300000000004 37.0 37.0 37.0 37.0 37.0 135-139 36.0617 37.0 37.0 37.0 37.0 37.0 140-144 35.9234 37.0 37.0 37.0 37.0 37.0 145-149 35.9299 37.0 37.0 37.0 37.0 37.0 150-151 35.817 37.0 37.0 37.0 37.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 20 1.0 21 1.0 22 2.0 23 0.0 24 4.0 25 4.0 26 1.0 27 9.0 28 8.0 29 10.0 30 20.0 31 28.0 32 39.0 33 69.0 34 111.0 35 256.0 36 2814.0 37 623.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 52.949999999999996 9.3 5.675 32.074999999999996 2 23.65155735629273 9.951886553557863 32.008103317295515 34.38845277285389 3 21.725 16.225 24.099999999999998 37.95 4 27.750000000000004 20.7 20.825 30.725 5 28.425 27.400000000000002 22.15 22.025 6 24.175 30.8 21.175 23.849999999999998 7 19.650000000000002 25.4 37.025000000000006 17.925 8 20.225 24.425 29.95 25.4 9 20.625 21.5 32.15 25.724999999999998 10-14 23.145 26.26 25.874999999999996 24.72 15-19 23.31 25.445 25.624999999999996 25.619999999999997 20-24 23.395 25.405 25.665 25.535000000000004 25-29 23.715 25.85 25.395 25.040000000000003 30-34 23.265 25.645 24.93 26.16 35-39 23.22 25.145 25.69 25.945 40-44 23.305 25.314999999999998 24.84 26.540000000000003 45-49 23.3 25.21 25.480000000000004 26.009999999999998 50-54 23.724999999999998 24.990000000000002 25.45 25.835 55-59 23.265 25.124999999999996 25.665 25.945 60-64 23.355 25.1 25.259999999999998 26.284999999999997 65-69 23.075000000000003 25.180000000000003 25.435000000000002 26.31 70-74 23.685000000000002 25.255 25.1 25.96 75-79 23.485 25.495 25.2 25.82 80-84 23.919999999999998 24.84 24.865000000000002 26.375 85-89 23.669999999999998 25.669999999999998 24.68 25.979999999999997 90-94 23.669999999999998 25.36 24.47 26.5 95-99 24.145 25.124999999999996 24.709999999999997 26.02 100-104 23.895 25.46 25.03 25.615 105-109 23.59 25.259999999999998 24.89 26.26 110-114 23.235 25.395 25.195 26.174999999999997 115-119 23.94 24.325 25.27 26.465 120-124 23.925 25.430000000000003 24.529999999999998 26.115 125-129 24.035 25.055 24.42 26.490000000000002 130-134 24.25 25.415 24.529999999999998 25.805 135-139 24.474999999999998 25.655 24.055 25.814999999999998 140-144 24.560000000000002 25.86 24.14 25.44 145-149 24.39 25.355 24.54 25.715 150-151 24.7875 25.9875 24.087500000000002 25.137500000000003 >>END_MODULE >>Per sequence GC content fail #GC Content Count 0 0.0 1 0.0 2 0.5 3 0.5 4 0.0 5 0.5 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 1.0 22 1.0 23 0.0 24 0.5 25 0.5 26 2.0 27 2.5 28 1.5 29 2.5 30 5.5 31 10.5 32 9.5 33 12.5 34 22.0 35 31.0 36 38.5 37 51.0 38 76.5 39 97.0 40 110.5 41 133.0 42 161.5 43 175.5 44 193.0 45 199.5 46 195.5 47 213.5 48 197.0 49 184.0 50 175.5 51 155.0 52 148.0 53 134.5 54 122.0 55 106.5 56 94.0 57 79.0 58 69.0 59 75.5 60 68.5 61 63.0 62 65.0 63 58.5 64 57.0 65 60.0 66 54.0 67 50.0 68 49.0 69 44.0 70 36.5 71 25.0 72 20.5 73 14.0 74 12.0 75 11.0 76 10.0 77 7.0 78 2.5 79 2.0 80 1.0 81 0.0 82 0.0 83 0.0 84 0.0 85 0.0 86 0.0 87 0.0 88 0.0 89 0.0 90 0.0 91 0.0 92 0.0 93 0.0 94 0.0 95 0.0 96 0.0 97 0.0 98 0.0 99 0.0 100 0.0 >>END_MODULE >>Per base N content pass #Base N-Count 1 0.0 2 1.275 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 92.15 #Duplication Level Percentage of deduplicated Percentage of total 1 92.29517091698318 85.05 2 6.972327726532828 12.85 3 0.6511123168746609 1.7999999999999998 4 0.08138903960933261 0.3 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 0.0 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 0.025 0.0 0.0 0.0 0.0 68-69 0.05 0.0 0.0 0.0 0.0 70-71 0.05 0.0 0.0 0.0 0.0 72-73 0.05 0.0 0.0 0.0 0.0 74-75 0.05 0.0 0.0 0.0 0.0 76-77 0.1 0.0 0.0 0.0 0.0 78-79 0.1625 0.0 0.0 0.0 0.0 80-81 0.225 0.0 0.0 0.0 0.0 82-83 0.25 0.0 0.0 0.0 0.0 84-85 0.2625 0.0 0.0 0.0 0.0 86-87 0.2875 0.0 0.0 0.0 0.0 88-89 0.4 0.0 0.0 0.0 0.0 90-91 0.475 0.0 0.0 0.0 0.0 92-93 0.525 0.0 0.0 0.0 0.0 94-95 0.5874999999999999 0.0 0.0 0.0 0.0 96-97 0.7375 0.0 0.0 0.0 0.0 98-99 0.8875 0.0 0.0 0.0 0.0 100-101 1.0 0.0 0.0 0.0 0.0 102-103 1.0625 0.0 0.0 0.0 0.0 104-105 1.15 0.0 0.0 0.0 0.0 106-107 1.375 0.0 0.0 0.0 0.0 108-109 1.5625 0.0 0.0 0.0 0.0 110-111 1.6375 0.0 0.0 0.0 0.0 112-113 1.775 0.0 0.0 0.0 0.0 114-115 1.9500000000000002 0.0 0.0 0.0 0.0 116-117 2.1125 0.0 0.0 0.0 0.0 118-119 2.2375 0.0 0.0 0.0 0.0 120-121 2.4 0.0 0.0 0.0 0.0 122-123 2.625 0.0 0.0 0.0 0.0 124-125 2.8 0.0 0.0 0.0 0.0 126-127 2.975 0.0 0.0 0.0 0.0 128-129 3.2 0.0 0.0 0.0 0.0 130-131 3.5875 0.0 0.0 0.0 0.0 132-133 3.8625 0.0 0.0 0.0 0.0 134-135 4.1875 0.0 0.0 0.0 0.0 136-137 4.525 0.0 0.0 0.0 0.0 138-139 5.1125 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content pass >>END_MODULE SRR12949791 read2 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR12949791_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 51 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 36.186 37.0 37.0 37.0 37.0 37.0 2 36.1525 37.0 37.0 37.0 37.0 37.0 3 36.122 37.0 37.0 37.0 37.0 37.0 4 36.2065 37.0 37.0 37.0 37.0 37.0 5 36.145 37.0 37.0 37.0 37.0 37.0 6 36.082 37.0 37.0 37.0 37.0 37.0 7 36.061 37.0 37.0 37.0 37.0 37.0 8 36.149 37.0 37.0 37.0 37.0 37.0 9 36.326 37.0 37.0 37.0 37.0 37.0 10-14 36.2607 37.0 37.0 37.0 37.0 37.0 15-19 36.229499999999994 37.0 37.0 37.0 37.0 37.0 20-24 36.1995 37.0 37.0 37.0 37.0 37.0 25-29 36.150600000000004 37.0 37.0 37.0 37.0 37.0 30-34 36.1052 37.0 37.0 37.0 37.0 37.0 35-39 36.14 37.0 37.0 37.0 37.0 37.0 40-44 36.09589999999999 37.0 37.0 37.0 37.0 37.0 45-49 36.13009999999999 37.0 37.0 37.0 37.0 37.0 50-54 36.0672 37.0 37.0 37.0 37.0 37.0 55-59 36.0062 37.0 37.0 37.0 37.0 37.0 60-64 35.985400000000006 37.0 37.0 37.0 37.0 37.0 65-69 35.9825 37.0 37.0 37.0 37.0 37.0 70-74 35.9339 37.0 37.0 37.0 37.0 37.0 75-79 35.9002 37.0 37.0 37.0 37.0 37.0 80-84 35.919799999999995 37.0 37.0 37.0 37.0 37.0 85-89 35.9418 37.0 37.0 37.0 37.0 37.0 90-94 35.8348 37.0 37.0 37.0 37.0 37.0 95-99 35.7322 37.0 37.0 37.0 37.0 37.0 100-104 35.7673 37.0 37.0 37.0 37.0 37.0 105-109 35.8009 37.0 37.0 37.0 37.0 37.0 110-114 35.759 37.0 37.0 37.0 37.0 37.0 115-119 35.7074 37.0 37.0 37.0 37.0 37.0 120-124 35.543099999999995 37.0 37.0 37.0 37.0 37.0 125-129 35.6486 37.0 37.0 37.0 37.0 37.0 130-134 35.4923 37.0 37.0 37.0 37.0 37.0 135-139 35.4422 37.0 37.0 37.0 37.0 37.0 140-144 35.453700000000005 37.0 37.0 37.0 37.0 37.0 145-149 35.421299999999995 37.0 37.0 37.0 37.0 37.0 150-151 35.06975 37.0 37.0 37.0 25.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 13 2.0 14 2.0 15 0.0 16 0.0 17 1.0 18 1.0 19 2.0 20 0.0 21 1.0 22 8.0 23 7.0 24 4.0 25 7.0 26 8.0 27 14.0 28 16.0 29 21.0 30 25.0 31 39.0 32 62.0 33 126.0 34 208.0 35 568.0 36 2590.0 37 288.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 46.325 19.3 8.325000000000001 26.05 2 30.975 21.625 25.25 22.15 3 24.474999999999998 23.525 29.15 22.85 4 28.625 28.075 19.35 23.95 5 28.449999999999996 32.0 19.900000000000002 19.650000000000002 6 23.05 35.15 18.775 23.025000000000002 7 23.875 18.675 33.25 24.2 8 23.549999999999997 24.325 24.375 27.750000000000004 9 25.474999999999998 21.825 24.25 28.449999999999996 10-14 25.715 25.745 23.415 25.124999999999996 15-19 25.94 24.104999999999997 24.709999999999997 25.245 20-24 26.009999999999998 24.915000000000003 23.87 25.205 25-29 25.665 24.905 23.565 25.865 30-34 26.46 24.709999999999997 24.03 24.8 35-39 26.045 25.130000000000003 24.02 24.805 40-44 26.419999999999998 24.255 24.41 24.915000000000003 45-49 25.955000000000002 24.154999999999998 24.37 25.52 50-54 26.950000000000003 24.310000000000002 24.3 24.44 55-59 26.355 25.025 23.985 24.635 60-64 26.305 24.715 24.37 24.610000000000003 65-69 27.250000000000004 25.06 23.61 24.08 70-74 26.525 24.95 23.794999999999998 24.73 75-79 26.515 24.925 24.47 24.09 80-84 27.1 24.38 24.245 24.275 85-89 26.55 24.5 24.42 24.529999999999998 90-94 26.555 24.5 24.385 24.560000000000002 95-99 26.36 25.019999999999996 24.25 24.37 100-104 27.384999999999998 23.89 24.51 24.215 105-109 26.150000000000002 24.82 24.779999999999998 24.25 110-114 26.715 25.765 23.485 24.035 115-119 27.465 25.124999999999996 24.154999999999998 23.255 120-124 27.02 25.1 24.25 23.630000000000003 125-129 27.229999999999997 25.085 24.125 23.56 130-134 28.09 25.045 23.555 23.31 135-139 26.875 25.285000000000004 24.205 23.635 140-144 27.73 25.345000000000002 23.715 23.21 145-149 28.044999999999998 24.915000000000003 23.52 23.52 150-151 28.3625 25.4 24.087500000000002 22.15 >>END_MODULE >>Per sequence GC content fail #GC Content Count 0 0.0 1 0.0 2 0.0 3 0.0 4 0.0 5 0.0 6 0.0 7 0.0 8 0.0 9 0.0 10 0.5 11 0.5 12 0.0 13 0.5 14 0.5 15 0.0 16 1.5 17 1.5 18 0.5 19 0.5 20 0.0 21 0.0 22 0.0 23 0.0 24 0.0 25 0.0 26 1.0 27 2.0 28 2.5 29 3.0 30 4.0 31 7.0 32 8.5 33 11.0 34 16.5 35 26.0 36 32.0 37 43.0 38 67.5 39 82.0 40 97.0 41 112.5 42 129.0 43 156.0 44 182.0 45 200.0 46 184.5 47 172.0 48 171.5 49 167.5 50 174.5 51 158.0 52 132.5 53 127.0 54 128.0 55 119.0 56 101.0 57 87.0 58 82.0 59 87.0 60 90.5 61 83.0 62 76.0 63 81.5 64 80.5 65 63.5 66 65.5 67 66.0 68 51.5 69 50.5 70 44.0 71 41.0 72 39.0 73 27.0 74 20.0 75 14.0 76 7.5 77 4.0 78 3.5 79 4.5 80 3.0 81 0.0 82 0.0 83 0.0 84 0.0 85 0.0 86 0.0 87 0.5 88 0.5 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 0.5 100 1.5 >>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 92.25 #Duplication Level Percentage of deduplicated Percentage of total 1 92.54742547425474 85.375 2 6.612466124661247 12.2 3 0.7317073170731708 2.025 4 0.10840108401084012 0.4 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 0.0 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 0.025 0.0 0.0 0.0 0.0 68-69 0.05 0.0 0.0 0.0 0.0 70-71 0.05 0.0 0.0 0.0 0.0 72-73 0.05 0.0 0.0 0.0 0.0 74-75 0.05 0.0 0.0 0.0 0.0 76-77 0.1 0.0 0.0 0.0 0.0 78-79 0.1625 0.0 0.0 0.0 0.0 80-81 0.225 0.0 0.0 0.0 0.0 82-83 0.25 0.0 0.0 0.0 0.0 84-85 0.2625 0.0 0.0 0.0 0.0 86-87 0.2875 0.0 0.0 0.0 0.0 88-89 0.4 0.0 0.0 0.0 0.0 90-91 0.475 0.0 0.0 0.0 0.0 92-93 0.525 0.0 0.0 0.0 0.0 94-95 0.5874999999999999 0.0 0.0 0.0 0.0 96-97 0.7375 0.0 0.0 0.0 0.0 98-99 0.8875 0.0 0.0 0.0 0.0 100-101 1.0 0.0 0.0 0.0 0.0 102-103 1.0625 0.0 0.0 0.0 0.0 104-105 1.15 0.0 0.0 0.0 0.0 106-107 1.35 0.0 0.0 0.0 0.0 108-109 1.5375 0.0 0.0 0.0 0.0 110-111 1.6125 0.0 0.0 0.0 0.0 112-113 1.75 0.0 0.0 0.0 0.0 114-115 1.9249999999999998 0.0 0.0 0.0 0.0 116-117 2.0875 0.0 0.0 0.0 0.0 118-119 2.2125 0.0 0.0 0.0 0.0 120-121 2.3875 0.0 0.0 0.0 0.0 122-123 2.6500000000000004 0.0 0.0 0.0 0.0 124-125 2.825 0.0 0.0 0.0 0.0 126-127 3.0125 0.0 0.0 0.0 0.0 128-129 3.25 0.0 0.0 0.0 0.0 130-131 3.6375 0.0 0.0 0.0 0.0 132-133 3.9125 0.0 0.0 0.0 0.0 134-135 4.2375 0.0 0.0 0.0 0.0 136-137 4.575 0.0 0.0 0.0 0.0 138-139 5.15 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position TAGAACT 10 0.006830828 145.0 1 AGAACTT 10 0.006830828 145.0 2 TCCCCCT 10 0.006830828 145.0 8 AGAGAGA 40 0.0076550315 18.125 20-24 >>END_MODULE Read 1761399 spots for SRR12949791.sra Written 1761399 spots for SRR12949791.sra Read 1761399 spots for SRR12949791.sra Written 1761399 spots for SRR12949791.sra Read 1761399 spots for SRR12949791.sra Written 1761399 spots for SRR12949791.sra Read 1761399 spots for SRR12949791.sra Written 1761399 spots for SRR12949791.sra Read 1761399 spots for SRR12949791.sra Written 1761399 spots for SRR12949791.sra Read 1761399 spots for SRR12949791.sra Written 1761399 spots for SRR12949791.sra Read 1761399 spots for SRR12949791.sra Written 1761399 spots for SRR12949791.sra Read 1761399 spots for SRR12949791.sra Written 1761399 spots for SRR12949791.sra Read 1761399 spots for SRR12949791.sra Written 1761399 spots for SRR12949791.sra Read 1761399 spots for SRR12949791.sra Written 1761399 spots for SRR12949791.sra Read 1761399 spots for SRR12949791.sra Written 1761399 spots for SRR12949791.sra Read 1761399 spots for SRR12949791.sra Written 1761399 spots for SRR12949791.sra Read 1761399 spots for SRR12949791.sra Written 1761399 spots for SRR12949791.sra Read 1761399 spots for SRR12949791.sra Written 1761399 spots for SRR12949791.sra Read 1761399 spots for SRR12949791.sra Written 1761399 spots for SRR12949791.sra Read 1761399 spots for SRR12949791.sra Written 1761399 spots for SRR12949791.sra Read 1761399 spots for SRR12949791.sra Written 1761399 spots for SRR12949791.sra Read 1761399 spots for SRR12949791.sra Written 1761399 spots for SRR12949791.sra Read 1761399 spots for SRR12949791.sra Written 1761399 spots for SRR12949791.sra Read 1761410 spots for SRR12949791.sra Written 1761410 spots for SRR12949791.sra SRR ids: ['SRR12949791.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_m8ryqrmn SRR12949791.sra spots: 35227991 blocks: [[1, 1761399], [1761400, 3522798], [3522799, 5284197], [5284198, 7045596], [7045597, 8806995], [8806996, 10568394], [10568395, 12329793], [12329794, 14091192], [14091193, 15852591], [15852592, 17613990], [17613991, 19375389], [19375390, 21136788], [21136789, 22898187], [22898188, 24659586], [24659587, 26420985], [26420986, 28182384], [28182385, 29943783], [29943784, 31705182], [31705183, 33466581], [33466582, 35227991]] SRR12949791 file size 11950312 SRR12949791 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 SRR12949791 SRR12949791_1.fastq SRR12949791_2.fastq Input file: SRR12949791_1.fastq Paired file: SRR12949791_2.fastq trimmed: SRR12949791-trimmed-pair1.fastq, SRR12949791-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 10:15:08 2024 >> started Sat Dec 7 10:15:58 2024 >> done (50.106s) 35227991 read pairs processed; of these: 214 ( 0.00%) short read pairs filtered out after trimming by size control 10773 ( 0.03%) empty read pairs filtered out after trimming by size control 35217004 (99.97%) read pairs available; of these: 2853244 ( 8.10%) trimmed read pairs available after processing 32363760 (91.90%) untrimmed read pairs available after processing Length distribution of reads after trimming: length count percentage 18 23 0.00% 19 18 0.00% 20 21 0.00% 21 16 0.00% 22 21 0.00% 23 22 0.00% 24 28 0.00% 25 31 0.00% 26 37 0.00% 27 28 0.00% 28 40 0.00% 29 42 0.00% 30 54 0.00% 31 56 0.00% 32 43 0.00% 33 50 0.00% 34 56 0.00% 35 60 0.00% 36 63 0.00% 37 58 0.00% 38 66 0.00% 39 78 0.00% 40 80 0.00% 41 75 0.00% 42 94 0.00% 43 91 0.00% 44 91 0.00% 45 96 0.00% 46 89 0.00% 47 117 0.00% 48 147 0.00% 49 178 0.00% 50 195 0.00% 51 239 0.00% 52 276 0.00% 53 271 0.00% 54 280 0.00% 55 314 0.00% 56 390 0.00% 57 420 0.00% 58 508 0.00% 59 538 0.00% 60 662 0.00% 61 740 0.00% 62 823 0.00% 63 907 0.00% 64 1043 0.00% 65 1200 0.00% 66 1292 0.00% 67 1496 0.00% 68 1634 0.00% 69 1846 0.01% 70 2057 0.01% 71 2403 0.01% 72 2566 0.01% 73 3029 0.01% 74 3333 0.01% 75 3652 0.01% 76 4044 0.01% 77 4372 0.01% 78 4660 0.01% 79 5123 0.01% 80 5657 0.02% 81 6082 0.02% 82 6809 0.02% 83 7168 0.02% 84 7738 0.02% 85 8558 0.02% 86 8961 0.03% 87 9533 0.03% 88 10140 0.03% 89 10625 0.03% 90 11162 0.03% 91 11800 0.03% 92 12235 0.03% 93 13130 0.04% 94 14030 0.04% 95 14775 0.04% 96 15617 0.04% 97 16162 0.05% 98 16892 0.05% 99 17777 0.05% 100 18613 0.05% 101 19084 0.05% 102 20121 0.06% 103 21259 0.06% 104 22014 0.06% 105 23027 0.07% 106 24033 0.07% 107 25170 0.07% 108 25775 0.07% 109 27283 0.08% 110 27989 0.08% 111 29314 0.08% 112 30375 0.09% 113 31619 0.09% 114 32547 0.09% 115 34071 0.10% 116 35308 0.10% 117 36667 0.10% 118 38484 0.11% 119 39765 0.11% 120 40804 0.12% 121 42199 0.12% 122 43058 0.12% 123 45015 0.13% 124 46537 0.13% 125 47838 0.14% 126 49817 0.14% 127 50893 0.14% 128 52788 0.15% 129 55088 0.16% 130 56676 0.16% 131 57495 0.16% 132 59590 0.17% 133 61191 0.17% 134 62151 0.18% 135 63682 0.18% 136 65654 0.19% 137 67056 0.19% 138 69369 0.20% 139 71646 0.20% 140 72767 0.21% 141 75570 0.21% 142 77277 0.22% 143 78102 0.22% 144 80778 0.23% 145 82307 0.23% 146 83994 0.24% 147 85846 0.24% 148 87656 0.25% 149 89113 0.25% 150 91636 0.26% 151 32363760 91.90% 35217004 reads passed initial QC criterion=sequence-density sequence-density=0.15 sequence-density-rank=1 fanout-score=4.95 fanout-score-rank=29 prefix-density=0.20 prefix-fanout=3.9 sequence=GTGATGGTCTTGCC criterion=fanout-score sequence-density=0.04 sequence-density-rank=29 fanout-score=228.27 fanout-score-rank=1 prefix-density=0.50 prefix-fanout=17.5 sequence=GGCGGCGGCGAACCGCCCCCGTCGCCGCGATCCGAACACTTCACCGGACCATTCAATCGGTAGGAGCGACGGGCGGTGTGTACAAAGGGCAGGGACGTAGTCAACGCGAGCTGATGACTCGCGCTTACTAGGCATTCCTCGTTGAAGACCAACAATTGCAATGATCTATCCCCATCACGATGAAATTTCCCAAGATTACCCGGGCCTGTCGGCCAAGGCTATATACTCGTTGAATACATCAGTGTAGCGCGCGTGCGGCCCAGAACATCTAAGGGCATCACAGACCTGTTATTGCCTCAAACTTCCGTCGCCTAAACGGCGATAGTCCCTCTAAGAAGCTAGCTGCGGAGGGATGGCTCCGCATAGCTAGTTAGCAGGCTGAGGTCTCGTTCGTTAACGGAATTAACCAGACAAATCGCTCCACCAACTAAGAACGGCCATGCACCACCACCCATAGAATCAAGAAAGAGCTCTCAGTCTGTCAATCCTTGCTATGTCTGGACCTGGTAAG criterion=sequence-density sequence-density=0.42 sequence-density-rank=1 fanout-score=2.30 fanout-score-rank=36 prefix-density=0.44 prefix-fanout=2.2 sequence=CGGTTCCGGTTC criterion=fanout-score sequence-density=0.08 sequence-density-rank=29 fanout-score=283.87 fanout-score-rank=1 prefix-density=1.07 prefix-fanout=20.2 sequence=CCGCCGCCGCCCCTCGTCCTCTGTGTTCCTTCTCCGAGTTTCAGCCATGGGTAAGGAGAAGACTCACATCAACATCGTGGTCATTGGCCATGTCGACTCTGGCAAGTCGACCACCACTGGCCACCTGATCTACAAGCTTGGAGGTATTGACAAGCGTGTGATCGAGAGGTTCGAGAAGGAGGCTGC SRR12949791 testing PE reads STAR mapping to Ensembl genome Started job on | Dec 07 10:16:48 Started mapping on | Dec 07 10:16:48 Finished on | Dec 07 10:19:28 Mapping speed, Million of reads per hour | 792.38 Number of input reads | 35217004 Average input read length | 298 UNIQUE READS: Uniquely mapped reads number | 33472846 Uniquely mapped reads % | 95.05% Average mapped length | 297.15 Number of splices: Total | 35966889 Number of splices: Annotated (sjdb) | 33726472 Number of splices: GT/AG | 35484571 Number of splices: GC/AG | 419645 Number of splices: AT/AC | 25963 Number of splices: Non-canonical | 36710 Mismatch rate per base, % | 0.15% Deletion rate per base | 0.00% Deletion average length | 1.58 Insertion rate per base | 0.00% Insertion average length | 1.30 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 403586 % of reads mapped to multiple loci | 1.15% Number of reads mapped to too many loci | 88142 % of reads mapped to too many loci | 0.25% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 2.42% % of reads unmapped: other | 1.14% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 1340572 1340572 1340572 N_multimapping 403586 403586 403586 N_noFeature 1036387 32704269 1281119 N_ambiguous 607525 4568 85388 UnstrandedReadsAssigned:31828934 PositiveStrandReadsAssigned:764009 NegativeStrandReadsAssigned:32106339 Dataset is classified negative stranded MeadianReadLen=151 20thPercentileLength=151 echo kmer=147 SRR12949791 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: SRR12949791-trimmed-pair1.fastq SRR12949791-trimmed-pair2.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 35,217,004 reads, 32,629,726 reads pseudoaligned [quant] estimated average fragment length: 291.075 [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,083 rounds 52973 SRR12949791.ke.tsv 35125 SRR12949791.se.tsv 88098 total ==> SRR12949791.ke.tsv <== target_id length eff_length est_counts tpm PNS24245 936 646.768 0 0 PNS24247 1044 753.925 110.627 6.61279 PNS24249 1928 1637.92 198.287 5.4557 PNS24246 1044 753.925 110.627 6.61279 PNS24248 1044 753.925 110.627 6.61279 PNS24244 1471 1180.92 194.831 7.43507 PNS24243 293 90.4329 1 0.498338 KQK14069 1603 1312.92 8479.11 291.045 KQK14071 474 220.281 110.664 22.64 ==> SRR12949791.se.tsv <== BRADI_1g14170v3 9345 BRADI_1g53295v3 118 BRADI_1g59795v3 584 BRADI_1g07683v3 0 BRADI_1g00485v3 84 BRADI_1g20270v3 2247 BRADI_1g74790v3 62 BRADI_1g09890v3 0 BRADI_1g77505v3 184 BRADI_1g48960v3 1 SRR12949791 completed mapping pipeline successfully