Starting /dee2/code/volunteer_pipeline.sh SRR7171474 current disk space = 3087486984192 free memory = 1582514932 SRR7171474 SRAfilesize 480439c5859205c12cb2fce1134f9a61 SRR7171474.sra SRR7171474.sra file validated SRR7171474 is paired end SRR7171474 is conventional basespace SRR7171474 read1 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR7171474_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 44 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 31.2815 33.0 33.0 34.0 31.0 34.0 2 32.8085 33.0 33.0 34.0 32.0 34.0 3 32.3985 33.0 33.0 34.0 29.0 34.0 4 32.007 33.0 32.0 33.0 31.0 34.0 5 32.768 33.0 33.0 33.0 32.0 34.0 6 36.62675 38.0 37.0 38.0 34.0 38.0 7 37.1725 38.0 38.0 38.0 36.0 38.0 8 37.29675 38.0 38.0 38.0 36.0 38.0 9 37.529 38.0 38.0 38.0 37.0 38.0 10-14 37.5555 38.0 38.0 38.0 37.8 38.0 15-19 37.485 38.0 38.0 38.0 37.4 38.0 20-24 37.48395 38.0 38.0 38.0 37.0 38.0 25-29 37.4576 38.0 38.0 38.0 37.0 38.0 30-34 37.451800000000006 38.0 38.0 38.0 37.0 38.0 35-39 37.454899999999995 38.0 38.0 38.0 37.0 38.0 40-44 37.41485 38.0 38.0 38.0 37.0 38.0 45-49 37.3734 38.0 38.0 38.0 37.0 38.0 50-54 37.37015 38.0 38.0 38.0 37.0 38.0 55-59 37.2571 38.0 38.0 38.0 36.8 38.0 60-64 37.282650000000004 38.0 38.0 38.0 36.8 38.0 65-69 37.242999999999995 38.0 38.0 38.0 36.4 38.0 70-74 37.15195 38.0 38.0 38.0 36.0 38.0 75-79 37.11605 38.0 38.0 38.0 36.0 38.0 80-84 37.11395 38.0 38.0 38.0 36.0 38.0 85-89 37.0061 38.0 38.0 38.0 36.0 38.0 90-94 36.9873 38.0 38.0 38.0 35.8 38.0 95-99 36.77465 38.0 38.0 38.0 35.0 38.0 100-104 36.7068 38.0 38.0 38.0 34.6 38.0 105-109 36.66055 38.0 38.0 38.0 34.2 38.0 110-114 36.6271 38.0 38.0 38.0 34.2 38.0 115-119 36.4073 38.0 37.8 38.0 33.8 38.0 120-124 36.3609 38.0 37.8 38.0 34.0 38.0 125-129 36.25765 38.0 37.2 38.0 33.6 38.0 130-134 36.10425 38.0 36.8 38.0 33.0 38.0 135-139 35.89385 38.0 36.2 38.0 32.2 38.0 140-144 35.6967 38.0 36.0 38.0 31.8 38.0 145-149 35.40115 38.0 35.4 38.0 30.0 38.0 150-151 33.53575 36.5 31.5 38.0 22.5 38.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 21 1.0 22 3.0 23 3.0 24 5.0 25 5.0 26 9.0 27 13.0 28 16.0 29 34.0 30 31.0 31 44.0 32 46.0 33 79.0 34 151.0 35 204.0 36 624.0 37 2732.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 39.58773784355179 11.918604651162791 10.412262156448202 38.08139534883721 2 20.7 13.750000000000002 33.775 31.775 3 19.8 18.099999999999998 26.3 35.8 4 22.625 24.125 25.275 27.975 5 24.2 29.925 24.9 20.974999999999998 6 19.925 33.7 24.474999999999998 21.9 7 13.200000000000001 26.700000000000003 41.5 18.6 8 18.4 25.4 31.4 24.8 9 16.5 24.775 33.925 24.8 10-14 19.81 29.635 27.565 22.99 15-19 20.265 28.34 27.139999999999997 24.255 20-24 20.075000000000003 28.335 27.92 23.669999999999998 25-29 19.955000000000002 28.28 27.74 24.025 30-34 19.175 28.345 28.48 24.0 35-39 19.85 28.04 27.794999999999998 24.315 40-44 19.650000000000002 28.53 27.715 24.104999999999997 45-49 19.919999999999998 28.499999999999996 27.250000000000004 24.33 50-54 19.509999999999998 28.610000000000003 27.715 24.165 55-59 20.724999999999998 28.349999999999998 27.694999999999997 23.23 60-64 20.125 28.64 27.045 24.19 65-69 20.175 28.175 27.905 23.745 70-74 20.25 28.349999999999998 27.395000000000003 24.005000000000003 75-79 19.915 28.08 27.189999999999998 24.815 80-84 20.200000000000003 28.694999999999997 27.485 23.62 85-89 20.225 28.325 27.389999999999997 24.060000000000002 90-94 19.86 27.944999999999997 28.125 24.07 95-99 20.674999999999997 28.449999999999996 26.69 24.185000000000002 100-104 20.580000000000002 28.494999999999997 27.1 23.825 105-109 20.585 28.005000000000003 27.58 23.830000000000002 110-114 20.3 27.91 27.98 23.810000000000002 115-119 20.985 28.08 27.725 23.21 120-124 20.330000000000002 27.889999999999997 27.589999999999996 24.19 125-129 20.505000000000003 27.29 27.639999999999997 24.565 130-134 20.86 27.955000000000002 27.51 23.674999999999997 135-139 20.695 28.325 26.8 24.18 140-144 20.880000000000003 27.255000000000003 26.950000000000003 24.915000000000003 145-149 21.11 28.04 26.674999999999997 24.175 150-151 20.627578447305915 28.2410301287661 26.89086135766971 24.24053006625828 >>END_MODULE >>Per sequence GC content pass #GC Content Count 0 0.0 1 0.0 2 0.0 3 0.5 4 0.5 5 0.0 6 0.5 7 0.5 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 0.5 21 1.0 22 0.5 23 1.0 24 2.0 25 3.0 26 3.5 27 4.0 28 9.0 29 12.0 30 15.5 31 20.5 32 24.0 33 30.5 34 39.0 35 51.0 36 74.5 37 104.0 38 140.5 39 159.0 40 178.0 41 217.5 42 241.5 43 274.5 44 284.0 45 276.0 46 281.0 47 256.0 48 236.5 49 227.5 50 187.5 51 155.0 52 121.5 53 80.5 54 72.0 55 60.5 56 34.0 57 23.5 58 23.5 59 17.5 60 11.0 61 8.5 62 9.5 63 7.0 64 3.0 65 4.0 66 2.5 67 1.0 68 2.0 69 2.0 70 1.0 71 1.0 72 1.0 73 1.0 74 0.5 75 0.0 76 0.0 77 0.0 78 0.0 79 0.0 80 0.0 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 warn #Base N-Count 1 5.4 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 0.0125 >>END_MODULE >>Sequence Length Distribution pass #Length Count 151 4000.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 99.85000000000001 #Duplication Level Percentage of deduplicated Percentage of total 1 99.84977466199298 99.7 2 0.15022533800701052 0.3 3 0.0 0.0 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 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 0.0125 0.0 0.0 0.0 18-19 0.0 0.025 0.0 0.0 0.0 20-21 0.0 0.025 0.0 0.0 0.0 22-23 0.0 0.025 0.0 0.0 0.0 24-25 0.0 0.025 0.0 0.0 0.0 26-27 0.0 0.025 0.0 0.0 0.0 28-29 0.0 0.025 0.0 0.0 0.0 30-31 0.0 0.025 0.0 0.0 0.0 32-33 0.0 0.025 0.0 0.0 0.0 34-35 0.0 0.025 0.0 0.0 0.0 36-37 0.0 0.025 0.0 0.0 0.0 38-39 0.0 0.025 0.0 0.0 0.0 40-41 0.0 0.025 0.0 0.0 0.0 42-43 0.0 0.025 0.0 0.0 0.0 44-45 0.0 0.025 0.0 0.0 0.0 46-47 0.0 0.025 0.0 0.0 0.0 48-49 0.0 0.025 0.0 0.0 0.0 50-51 0.0 0.025 0.0 0.0 0.0 52-53 0.0 0.025 0.0 0.0 0.0 54-55 0.0 0.025 0.0 0.0 0.0 56-57 0.0 0.025 0.0 0.0 0.0 58-59 0.0 0.025 0.0 0.0 0.0 60-61 0.0 0.025 0.0 0.0 0.0 62-63 0.0 0.025 0.0 0.0 0.0 64-65 0.0 0.025 0.0 0.0 0.0 66-67 0.0 0.025 0.0 0.0 0.0 68-69 0.0 0.025 0.0 0.0 0.0 70-71 0.0 0.025 0.0 0.0 0.0 72-73 0.0 0.025 0.0 0.0 0.0 74-75 0.0125 0.025 0.0 0.0 0.0 76-77 0.037500000000000006 0.025 0.0 0.0 0.0 78-79 0.0625 0.025 0.0 0.0 0.0 80-81 0.075 0.025 0.0 0.0 0.0 82-83 0.1375 0.025 0.0 0.0 0.0 84-85 0.2625 0.025 0.0 0.0 0.0 86-87 0.3375 0.025 0.0 0.0 0.0 88-89 0.3625 0.025 0.0 0.0 0.0 90-91 0.4375 0.025 0.0 0.0 0.0 92-93 0.5 0.025 0.0 0.0 0.0 94-95 0.6125 0.025 0.0 0.0 0.0 96-97 0.75 0.025 0.0 0.0 0.0 98-99 0.8374999999999999 0.025 0.0 0.0 0.0 100-101 1.0 0.025 0.0 0.0 0.0 102-103 1.2 0.025 0.0 0.0 0.0 104-105 1.4500000000000002 0.025 0.0 0.0 0.0 106-107 1.725 0.025 0.0 0.0 0.0 108-109 2.075 0.025 0.0 0.0 0.0 110-111 2.25 0.025 0.0 0.0 0.0 112-113 2.55 0.025 0.0 0.0 0.0 114-115 2.85 0.025 0.0 0.0 0.0 116-117 3.1375 0.025 0.0 0.0 0.0 118-119 3.4 0.025 0.0 0.0 0.0 120-121 3.775 0.025 0.0 0.0 0.0 122-123 4.137499999999999 0.025 0.0 0.0 0.0 124-125 4.550000000000001 0.025 0.0 0.0 0.0 126-127 5.0375 0.025 0.0 0.0 0.0 128-129 5.6875 0.025 0.0 0.0 0.0 130-131 6.1625 0.025 0.0 0.0 0.0 132-133 6.7375 0.025 0.0 0.0 0.0 134-135 7.2375 0.025 0.0 0.0 0.0 136-137 7.9125 0.025 0.0 0.0 0.0 138-139 8.55 0.025 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position TTCTTAG 10 0.0068343505 144.975 9 >>END_MODULE SRR7171474 read2 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR7171474_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 44 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 32.999 33.0 33.0 34.0 32.0 34.0 2 33.0875 34.0 33.0 34.0 32.0 34.0 3 33.1075 34.0 33.0 34.0 32.0 34.0 4 33.09675 34.0 33.0 34.0 32.0 34.0 5 33.068 34.0 33.0 34.0 33.0 34.0 6 37.257 38.0 38.0 38.0 37.0 38.0 7 37.29625 38.0 38.0 38.0 37.0 38.0 8 37.26075 38.0 38.0 38.0 37.0 38.0 9 37.199 38.0 38.0 38.0 37.0 38.0 10-14 37.152550000000005 38.0 38.0 38.0 36.8 38.0 15-19 37.222449999999995 38.0 38.0 38.0 37.0 38.0 20-24 37.25269999999999 38.0 38.0 38.0 37.0 38.0 25-29 37.21809999999999 38.0 38.0 38.0 37.0 38.0 30-34 37.1306 38.0 38.0 38.0 36.4 38.0 35-39 37.1245 38.0 38.0 38.0 36.6 38.0 40-44 37.09285 38.0 38.0 38.0 36.0 38.0 45-49 37.0361 38.0 38.0 38.0 36.0 38.0 50-54 37.00605 38.0 38.0 38.0 36.0 38.0 55-59 36.9139 38.0 38.0 38.0 36.0 38.0 60-64 36.90955 38.0 38.0 38.0 35.8 38.0 65-69 36.8487 38.0 38.0 38.0 35.2 38.0 70-74 36.86095 38.0 38.0 38.0 35.2 38.0 75-79 36.712450000000004 38.0 38.0 38.0 34.4 38.0 80-84 36.646449999999994 38.0 38.0 38.0 34.2 38.0 85-89 36.5788 38.0 38.0 38.0 34.0 38.0 90-94 36.45145 38.0 38.0 38.0 34.0 38.0 95-99 36.426399999999994 38.0 38.0 38.0 34.0 38.0 100-104 36.25945 38.0 37.4 38.0 33.4 38.0 105-109 36.116 38.0 37.0 38.0 33.0 38.0 110-114 35.8917 38.0 37.0 38.0 31.4 38.0 115-119 35.7609 38.0 36.4 38.0 31.0 38.0 120-124 35.591049999999996 38.0 36.0 38.0 30.6 38.0 125-129 35.3812 38.0 36.0 38.0 28.6 38.0 130-134 35.05844999999999 38.0 35.0 38.0 27.6 38.0 135-139 34.71655 38.0 35.0 38.0 25.4 38.0 140-144 34.36075 38.0 34.4 38.0 23.4 38.0 145-149 34.0531 38.0 33.4 38.0 23.0 38.0 150-151 31.18675 35.5 27.0 38.0 18.0 38.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 15 2.0 16 3.0 17 2.0 18 5.0 19 3.0 20 3.0 21 5.0 22 6.0 23 3.0 24 14.0 25 15.0 26 25.0 27 22.0 28 25.0 29 29.0 30 40.0 31 56.0 32 82.0 33 119.0 34 184.0 35 331.0 36 758.0 37 2268.0 >>END_MODULE >>Per base sequence content warn #Base G A T C 1 36.775000000000006 19.1 17.025000000000002 27.1 2 25.575 26.474999999999998 29.95 18.0 3 21.775 28.000000000000004 30.0 20.225 4 24.15 34.175 22.575 19.1 5 23.799999999999997 36.125 21.75 18.325 6 20.75 37.525 24.099999999999998 17.625 7 20.4 21.349999999999998 39.324999999999996 18.925 8 22.0 24.8 28.449999999999996 24.75 9 22.125 25.0 29.925 22.95 10-14 23.49 29.285 26.424999999999997 20.8 15-19 23.549999999999997 28.24 27.515 20.695 20-24 23.305 27.860000000000003 28.005000000000003 20.830000000000002 25-29 24.12 28.050000000000004 27.29 20.54 30-34 23.330000000000002 27.96 27.855 20.855 35-39 23.735 28.134999999999998 27.22 20.91 40-44 23.580000000000002 28.165000000000003 28.17 20.085 45-49 23.735 27.839999999999996 27.08 21.345 50-54 23.345 27.905 28.28 20.47 55-59 23.76 27.76 27.71 20.77 60-64 24.345 27.839999999999996 27.235 20.580000000000002 65-69 23.9 27.79 27.63 20.68 70-74 24.52 27.965 26.889999999999997 20.625 75-79 23.474999999999998 28.044999999999998 28.065 20.415 80-84 24.18 28.475 27.565 19.78 85-89 24.14 27.47 27.465 20.925 90-94 23.94 27.894999999999996 27.77 20.395 95-99 24.195 27.794999999999998 27.71 20.3 100-104 24.295 28.055000000000003 27.474999999999998 20.175 105-109 24.325 28.060000000000002 27.52 20.095 110-114 23.91 27.944999999999997 27.66 20.485 115-119 24.585 27.625 28.17 19.62 120-124 24.665 28.15 27.169999999999998 20.015 125-129 25.130000000000003 27.26 27.775 19.835 130-134 24.709999999999997 28.42 27.139999999999997 19.73 135-139 25.465 27.68 27.18 19.675 140-144 25.174999999999997 27.889999999999997 26.805 20.13 145-149 25.740000000000002 27.955000000000002 26.47 19.835 150-151 25.4875 27.825 26.737499999999997 19.950000000000003 >>END_MODULE >>Per sequence GC content pass #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 0.0 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 1.5 23 1.5 24 0.5 25 0.5 26 2.0 27 3.0 28 3.5 29 7.0 30 8.5 31 11.0 32 15.5 33 26.5 34 35.0 35 46.0 36 75.0 37 99.5 38 123.0 39 166.5 40 207.0 41 240.5 42 261.5 43 262.5 44 284.0 45 302.5 46 305.0 47 272.5 48 228.0 49 216.0 50 186.5 51 141.5 52 115.0 53 99.0 54 68.0 55 44.0 56 32.0 57 24.5 58 22.5 59 15.0 60 10.5 61 9.5 62 6.0 63 4.5 64 5.0 65 3.0 66 2.0 67 1.0 68 0.5 69 1.0 70 1.0 71 0.5 72 1.0 73 1.0 74 0.0 75 0.0 76 0.0 77 0.0 78 0.0 79 0.0 80 0.0 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 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 99.65 #Duplication Level Percentage of deduplicated Percentage of total 1 99.67385850476668 99.325 2 0.3010536879076769 0.6 3 0.025087807325639738 0.075 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 warn #Position Illumina Universal Adapter Illumina Small RNA 3' Adapter Illumina Small RNA 5' Adapter Nextera Transposase Sequence SOLID Small RNA Adapter 1 0.0 0.0 0.0 0.0 0.0 2 0.0 0.0 0.0 0.0 0.0 3 0.0 0.0 0.0 0.0 0.0 4 0.0 0.0 0.0 0.0 0.0 5 0.0 0.0 0.0 0.0 0.0 6 0.0 0.0 0.0 0.0 0.0 7 0.0 0.0 0.0 0.0 0.0 8 0.0 0.0 0.0 0.0 0.0 9 0.0 0.0 0.0 0.0 0.0 10-11 0.0 0.0 0.0 0.0 0.0 12-13 0.0 0.0 0.0 0.0 0.0 14-15 0.0 0.0 0.0 0.0 0.0 16-17 0.0 0.0 0.0 0.0 0.0 18-19 0.0 0.0 0.0 0.0 0.0 20-21 0.0 0.0 0.0 0.0 0.0 22-23 0.0 0.0 0.0 0.0 0.0 24-25 0.0 0.0 0.0 0.0 0.0 26-27 0.0 0.0 0.0 0.0 0.0 28-29 0.0 0.0 0.0 0.0 0.0 30-31 0.0 0.0 0.0 0.0 0.0 32-33 0.0 0.0 0.0 0.0 0.0 34-35 0.0 0.0 0.0 0.0 0.0 36-37 0.0 0.0 0.0 0.0 0.0 38-39 0.0 0.0 0.0 0.0 0.0 40-41 0.0 0.0 0.0 0.0 0.0 42-43 0.0 0.0 0.0 0.0 0.0 44-45 0.0 0.0 0.0 0.0 0.0 46-47 0.0 0.0 0.0 0.0 0.0 48-49 0.0 0.0 0.0 0.0 0.0 50-51 0.0 0.0 0.0 0.0 0.0 52-53 0.0 0.0 0.0 0.0 0.0 54-55 0.0 0.0 0.0 0.0 0.0 56-57 0.0 0.0 0.0 0.0 0.0 58-59 0.0 0.0 0.0 0.0 0.0 60-61 0.0 0.0 0.0 0.0 0.0 62-63 0.0 0.0 0.0 0.0 0.0 64-65 0.0 0.0 0.0 0.0 0.0 66-67 0.0 0.0 0.0 0.0 0.0 68-69 0.0 0.0 0.0 0.0 0.0 70-71 0.0 0.0 0.0 0.0 0.0 72-73 0.0 0.0 0.0 0.0 0.0 74-75 0.0125 0.0 0.0 0.0 0.0 76-77 0.037500000000000006 0.0 0.0 0.0 0.0 78-79 0.0625 0.0 0.0 0.0 0.0 80-81 0.075 0.0 0.0 0.0 0.0 82-83 0.1375 0.0 0.0 0.0 0.0 84-85 0.2625 0.0 0.0 0.0 0.0 86-87 0.3375 0.0 0.0 0.0 0.0 88-89 0.3625 0.0 0.0 0.0 0.0 90-91 0.4375 0.0 0.0 0.0 0.0 92-93 0.475 0.0 0.0 0.0 0.0 94-95 0.5625 0.0 0.0 0.0 0.0 96-97 0.675 0.0 0.0 0.0 0.0 98-99 0.7625 0.0 0.0 0.0 0.0 100-101 0.925 0.0 0.0 0.0 0.0 102-103 1.125 0.0 0.0 0.0 0.0 104-105 1.375 0.0 0.0 0.0 0.0 106-107 1.65 0.0 0.0 0.0 0.0 108-109 2.0125 0.0 0.0 0.0 0.0 110-111 2.2 0.0 0.0 0.0 0.0 112-113 2.5 0.0 0.0 0.0 0.0 114-115 2.825 0.0 0.0 0.0 0.0 116-117 3.1625 0.0 0.0 0.0 0.0 118-119 3.45 0.0 0.0 0.0 0.0 120-121 3.825 0.0 0.0 0.0 0.0 122-123 4.1875 0.0 0.0 0.0 0.0 124-125 4.6 0.0 0.0 0.0 0.0 126-127 5.0875 0.0 0.0 0.0 0.0 128-129 5.65 0.0 0.0 0.0 0.0 130-131 6.1 0.0 0.0 0.0 0.0 132-133 6.6125 0.0 0.0 0.0 0.0 134-135 7.125 0.0 0.0 0.0 0.0 136-137 7.8125 0.0 0.0 0.0 0.0 138-139 8.4625 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position TCGAGCA 10 0.006830828 145.0 7 >>END_MODULE Read 806453 spots for SRR7171474.sra Written 806453 spots for SRR7171474.sra Read 806453 spots for SRR7171474.sra Written 806453 spots for SRR7171474.sra Read 806453 spots for SRR7171474.sra Written 806453 spots for SRR7171474.sra Read 806453 spots for SRR7171474.sra Written 806453 spots for SRR7171474.sra Read 806453 spots for SRR7171474.sra Written 806453 spots for SRR7171474.sra Read 806453 spots for SRR7171474.sra Written 806453 spots for SRR7171474.sra Read 806453 spots for SRR7171474.sra Written 806453 spots for SRR7171474.sra Read 806464 spots for SRR7171474.sra Written 806464 spots for SRR7171474.sra Read 806453 spots for SRR7171474.sra Written 806453 spots for SRR7171474.sra Read 806453 spots for SRR7171474.sra Written 806453 spots for SRR7171474.sra Read 806453 spots for SRR7171474.sra Written 806453 spots for SRR7171474.sra Read 806453 spots for SRR7171474.sra Written 806453 spots for SRR7171474.sra Read 806453 spots for SRR7171474.sra Written 806453 spots for SRR7171474.sra Read 806453 spots for SRR7171474.sra Written 806453 spots for SRR7171474.sra Read 806453 spots for SRR7171474.sra Written 806453 spots for SRR7171474.sra Read 806453 spots for SRR7171474.sra Written 806453 spots for SRR7171474.sra Read 806453 spots for SRR7171474.sra Written 806453 spots for SRR7171474.sra Read 806453 spots for SRR7171474.sra Written 806453 spots for SRR7171474.sra Read 806453 spots for SRR7171474.sra Written 806453 spots for SRR7171474.sra Read 806453 spots for SRR7171474.sra Written 806453 spots for SRR7171474.sra SRR ids: ['SRR7171474.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd__d422s3n SRR7171474.sra spots: 16129071 blocks: [[1, 806453], [806454, 1612906], [1612907, 2419359], [2419360, 3225812], [3225813, 4032265], [4032266, 4838718], [4838719, 5645171], [5645172, 6451624], [6451625, 7258077], [7258078, 8064530], [8064531, 8870983], [8870984, 9677436], [9677437, 10483889], [10483890, 11290342], [11290343, 12096795], [12096796, 12903248], [12903249, 13709701], [13709702, 14516154], [14516155, 15322607], [15322608, 16129071]] SRR7171474 file size 5443912 SRR7171474 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 SRR7171474 SRR7171474_1.fastq SRR7171474_2.fastq Input file: SRR7171474_1.fastq Paired file: SRR7171474_2.fastq trimmed: SRR7171474-trimmed-pair1.fastq, SRR7171474-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 Thu Feb 13 19:49:52 2025 >> started Thu Feb 13 19:50:09 2025 >> done (17.435s) 16129071 read pairs processed; of these: 18 ( 0.00%) short read pairs filtered out after trimming by size control 1247 ( 0.01%) empty read pairs filtered out after trimming by size control 16127806 (99.99%) read pairs available; of these: 2170942 (13.46%) trimmed read pairs available after processing 13956864 (86.54%) untrimmed read pairs available after processing Length distribution of reads after trimming: length count percentage 18 1 0.00% 19 1 0.00% 20 0 0.00% 21 1 0.00% 22 0 0.00% 23 2 0.00% 24 0 0.00% 25 0 0.00% 26 3 0.00% 27 0 0.00% 28 1 0.00% 29 0 0.00% 30 3 0.00% 31 7 0.00% 32 1 0.00% 33 3 0.00% 34 2 0.00% 35 2 0.00% 36 2 0.00% 37 3 0.00% 38 7 0.00% 39 4 0.00% 40 0 0.00% 41 5 0.00% 42 8 0.00% 43 6 0.00% 44 8 0.00% 45 7 0.00% 46 11 0.00% 47 10 0.00% 48 11 0.00% 49 10 0.00% 50 19 0.00% 51 26 0.00% 52 23 0.00% 53 23 0.00% 54 38 0.00% 55 30 0.00% 56 49 0.00% 57 56 0.00% 58 66 0.00% 59 75 0.00% 60 111 0.00% 61 124 0.00% 62 125 0.00% 63 169 0.00% 64 180 0.00% 65 175 0.00% 66 246 0.00% 67 295 0.00% 68 336 0.00% 69 347 0.00% 70 481 0.00% 71 524 0.00% 72 614 0.00% 73 745 0.00% 74 898 0.01% 75 973 0.01% 76 1069 0.01% 77 1293 0.01% 78 1457 0.01% 79 1675 0.01% 80 1877 0.01% 81 2203 0.01% 82 2503 0.02% 83 2894 0.02% 84 3221 0.02% 85 3579 0.02% 86 4116 0.03% 87 4377 0.03% 88 4721 0.03% 89 5258 0.03% 90 5791 0.04% 91 6536 0.04% 92 7242 0.04% 93 8101 0.05% 94 8827 0.05% 95 9477 0.06% 96 10220 0.06% 97 10990 0.07% 98 11541 0.07% 99 12324 0.08% 100 13347 0.08% 101 14015 0.09% 102 15203 0.09% 103 16324 0.10% 104 17345 0.11% 105 18356 0.11% 106 19321 0.12% 107 20263 0.13% 108 21079 0.13% 109 21894 0.14% 110 22644 0.14% 111 23869 0.15% 112 24976 0.15% 113 26123 0.16% 114 27649 0.17% 115 29262 0.18% 116 30227 0.19% 117 31062 0.19% 118 32131 0.20% 119 32979 0.20% 120 33490 0.21% 121 35103 0.22% 122 35990 0.22% 123 37739 0.23% 124 39313 0.24% 125 40075 0.25% 126 41750 0.26% 127 42881 0.27% 128 43299 0.27% 129 44567 0.28% 130 44693 0.28% 131 45666 0.28% 132 47422 0.29% 133 48393 0.30% 134 49541 0.31% 135 50961 0.32% 136 53089 0.33% 137 54277 0.34% 138 54734 0.34% 139 55299 0.34% 140 55954 0.35% 141 56904 0.35% 142 58126 0.36% 143 59017 0.37% 144 60621 0.38% 145 62308 0.39% 146 62543 0.39% 147 64230 0.40% 148 65247 0.40% 149 64978 0.40% 150 66504 0.41% 151 13956864 86.54% 16127806 reads passed initial QC criterion=sequence-density sequence-density=0.32 sequence-density-rank=1 fanout-score=2.94 fanout-score-rank=26 prefix-density=0.44 prefix-fanout=2.1 sequence=CACTTGCAGCCATTCTCAGCACCAAAGTTCATCTCAGA criterion=fanout-score sequence-density=0.01 sequence-density-rank=33 fanout-score=148.15 fanout-score-rank=1 prefix-density=0.15 prefix-fanout=10.5 sequence=TCCTTCCTCTAAATGATAAGGTTCAGTGGACTTCTCGCGACGTCGCCGGCGGCGAACCGCCCACGTCGCCGCGATCCGAACACTTCACCGGACCATTCAATCGGTAGGAGCGACGGGCGGTGTGTACAAAGGGCAGGGACGTAGTCAACGCGAGCTGATGACTCGCGCTTACTAGGAATTCCTCGTTGAAGACCAACAATTGCAATGATCTATCCCCATCACGATGAAATTTCAAAGATTACCCGGGCCTGTCGGCCAAGGCTATAGACTCGTTGAATACATCAGTGTAGCGCGCGTGCGGCCCAGAACATCTAAGGGCATCACAGACCTGTTATTGCCTCAAACTTCCTTGGCCTGGAAGGCCATAGTCCCTCTAAGAAGCTGGCCGCGGAGGGTCACCTCCGCATAGCTAGTTAGCAGGCTGAGGTCTCGTTCGTTAACGGAATTAACCAGACAAATCGCTCCACCAACTAAGAACGGCCATGCACCACCACCCATAGAATCAAGAAAG criterion=sequence-density sequence-density=0.37 sequence-density-rank=1 fanout-score=2.96 fanout-score-rank=29 prefix-density=0.38 prefix-fanout=2.9 sequence=ATGTACCCTGACTT criterion=fanout-score sequence-density=0.01 sequence-density-rank=33 fanout-score=83.51 fanout-score-rank=1 prefix-density=0.11 prefix-fanout=7.2 sequence=ATTTTCTTTGAGAGTGCATAGATTTGTGTTGATATAGAAAACAATGGCACTACATGGAAAGATTGAGACAACATTAGAACTCAAGTCCTCCGCAGAGAAGTTCTACAAAGTGTGGAGGAGCCAGTCCTTCCATGTTCCCAAACATGCTTCCAAGCATATCCAAGGAGTTGATATACATGCAGGTGACTGGGAGACTGCGGGCTCTATCAGGATTTGGCAGTACACAATCGGAGGGAAAGCCGGGGTCTTTAAAGAGGAGGTTTCCTTCGATGATGAGAACAAGATCATAACTCTTAATGGTTTGGAAGGAGATGTCATGAAAATTTACAAGGTCTATA SRR7171474 testing PE reads STAR mapping to Ensembl genome Started job on | Feb 13 19:50:59 Started mapping on | Feb 13 19:50:59 Finished on | Feb 13 19:52:49 Mapping speed, Million of reads per hour | 527.82 Number of input reads | 16127806 Average input read length | 295 UNIQUE READS: Uniquely mapped reads number | 14967979 Uniquely mapped reads % | 92.81% Average mapped length | 294.60 Number of splices: Total | 14578898 Number of splices: Annotated (sjdb) | 14304715 Number of splices: GT/AG | 14352791 Number of splices: GC/AG | 177949 Number of splices: AT/AC | 11190 Number of splices: Non-canonical | 36968 Mismatch rate per base, % | 0.38% Deletion rate per base | 0.03% Deletion average length | 2.54 Insertion rate per base | 0.02% Insertion average length | 2.51 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 355563 % of reads mapped to multiple loci | 2.20% Number of reads mapped to too many loci | 156003 % of reads mapped to too many loci | 0.97% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 3.84% % of reads unmapped: other | 0.18% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 804264 804264 804264 N_multimapping 355563 355563 355563 N_noFeature 360038 14835691 410457 N_ambiguous 154169 733 71876 UnstrandedReadsAssigned:14453772 PositiveStrandReadsAssigned:131555 NegativeStrandReadsAssigned:14485646 Dataset is classified negative stranded MeadianReadLen=151 20thPercentileLength=151 echo kmer=147 SRR7171474 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: 52,400 [index] number of k-mers: 62,057,036 [index] number of equivalence classes: 130,681 [quant] running in paired-end mode [quant] will process pair 1: SRR7171474-trimmed-pair1.fastq SRR7171474-trimmed-pair2.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 16,127,806 reads, 14,557,410 reads pseudoaligned [quant] estimated average fragment length: 222.605 [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,075 rounds 52401 SRR7171474.ke.tsv 34699 SRR7171474.se.tsv 87100 total ==> SRR7171474.ke.tsv <== target_id length eff_length est_counts tpm Potri.005G200100.1.v4.1 2018 1796.4 1735 62.2976 Potri.005G024800.1.v4.1 1035 813.395 1083 85.8816 Potri.004G059700.1.v4.1 961 739.406 30 2.61705 Potri.007G009000.2.v4.1 1416 1194.4 0 0 Potri.003G141000.2.v4.1 2943 2721.4 782 18.5348 Potri.016G087400.1.v4.1 270 85.4979 1148 866.084 Potri.015G069301.1.v4.1 564 344.398 0 0 Potri.010G195200.1.v4.1 1773 1551.4 214 8.89743 Potri.012G127500.1.v4.1 977 755.401 8469 723.15 ==> SRR7171474.se.tsv <== Potri.001G166300.v4.1 0 Potri.001G448400.v4.1 61 Potri.001G233950.v4.1 0 Potri.001G122700.v4.1 503 Potri.001G212900.v4.1 0 Potri.001G182400.v4.1 2 Potri.001G256600.v4.1 0 Potri.001G040500.v4.1 0 Potri.001G416900.v4.1 0 Potri.001G452600.v4.1 87 SRR7171474 completed mapping pipeline successfully