Starting /dee2/code/volunteer_pipeline.sh SRR12951291 current disk space = 1543498768384 free memory = 1601566684 SRR12951291 SRAfilesize 74bab2e1c90eba05f9ed510a4bab2ad4 SRR12951291.sra SRR12951291.sra file validated SRR12951291 is paired end SRR12951291 is conventional basespace SRR12951291 read1 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR12951291_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 51 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 36.5455 37.0 37.0 37.0 37.0 37.0 2 36.17725 37.0 37.0 37.0 37.0 37.0 3 36.556 37.0 37.0 37.0 37.0 37.0 4 36.489 37.0 37.0 37.0 37.0 37.0 5 36.6585 37.0 37.0 37.0 37.0 37.0 6 36.638 37.0 37.0 37.0 37.0 37.0 7 36.4425 37.0 37.0 37.0 37.0 37.0 8 36.63 37.0 37.0 37.0 37.0 37.0 9 36.58 37.0 37.0 37.0 37.0 37.0 10-14 36.5906 37.0 37.0 37.0 37.0 37.0 15-19 36.56570000000001 37.0 37.0 37.0 37.0 37.0 20-24 36.5476 37.0 37.0 37.0 37.0 37.0 25-29 36.5478 37.0 37.0 37.0 37.0 37.0 30-34 36.5067 37.0 37.0 37.0 37.0 37.0 35-39 36.50019999999999 37.0 37.0 37.0 37.0 37.0 40-44 36.458099999999995 37.0 37.0 37.0 37.0 37.0 45-49 36.402 37.0 37.0 37.0 37.0 37.0 50-54 36.4323 37.0 37.0 37.0 37.0 37.0 55-59 36.3394 37.0 37.0 37.0 37.0 37.0 60-64 36.3095 37.0 37.0 37.0 37.0 37.0 65-69 36.3037 37.0 37.0 37.0 37.0 37.0 70-74 36.2799 37.0 37.0 37.0 37.0 37.0 75-79 36.292899999999996 37.0 37.0 37.0 37.0 37.0 80-84 36.2987 37.0 37.0 37.0 37.0 37.0 85-89 36.24849999999999 37.0 37.0 37.0 37.0 37.0 90-94 36.2431 37.0 37.0 37.0 37.0 37.0 95-99 36.185300000000005 37.0 37.0 37.0 37.0 37.0 100-104 36.22710000000001 37.0 37.0 37.0 37.0 37.0 105-109 36.250099999999996 37.0 37.0 37.0 37.0 37.0 110-114 36.1718 37.0 37.0 37.0 37.0 37.0 115-119 36.1239 37.0 37.0 37.0 37.0 37.0 120-124 36.058800000000005 37.0 37.0 37.0 37.0 37.0 125-129 36.0248 37.0 37.0 37.0 37.0 37.0 130-134 36.005 37.0 37.0 37.0 37.0 37.0 135-139 35.926500000000004 37.0 37.0 37.0 37.0 37.0 140-144 35.851299999999995 37.0 37.0 37.0 37.0 37.0 145-149 35.8106 37.0 37.0 37.0 37.0 37.0 150-151 35.61 37.0 37.0 37.0 37.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 17 1.0 18 1.0 19 1.0 20 0.0 21 1.0 22 2.0 23 1.0 24 2.0 25 2.0 26 4.0 27 6.0 28 4.0 29 12.0 30 32.0 31 34.0 32 58.0 33 71.0 34 126.0 35 301.0 36 2832.0 37 509.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 45.2 11.025 5.8500000000000005 37.925 2 21.77844762622457 11.002260738507912 32.931424265259984 34.28786737000753 3 21.65 14.799999999999999 26.650000000000002 36.9 4 26.450000000000003 19.2 22.1 32.25 5 26.75 26.375 22.875 24.0 6 25.174999999999997 29.375 21.224999999999998 24.224999999999998 7 19.875 26.8 35.6 17.724999999999998 8 21.725 24.55 27.650000000000002 26.075 9 20.625 22.95 33.375 23.05 10-14 23.53 26.515 24.310000000000002 25.645 15-19 24.185000000000002 24.77 25.679999999999996 25.365 20-24 23.085 25.5 24.67 26.745 25-29 23.985 24.395 25.055 26.565 30-34 24.245 24.654999999999998 24.355 26.745 35-39 23.515 24.555 25.509999999999998 26.419999999999998 40-44 24.355 25.03 24.735 25.88 45-49 24.51 25.405 24.565 25.52 50-54 24.195 24.79 23.95 27.065 55-59 24.46 24.349999999999998 24.755 26.435 60-64 24.46 24.97 24.41 26.16 65-69 23.7 24.834999999999997 24.975 26.490000000000002 70-74 25.064999999999998 24.555 24.035 26.345000000000002 75-79 24.37 24.505 23.849999999999998 27.275 80-84 24.505 24.45 24.445 26.6 85-89 24.785 24.435000000000002 24.75 26.029999999999998 90-94 24.545 23.895 25.124999999999996 26.435 95-99 24.8 24.51 23.865 26.825 100-104 24.959999999999997 25.290000000000003 24.165 25.585 105-109 25.135 24.135 23.71 27.02 110-114 24.635 24.185000000000002 23.474999999999998 27.705000000000002 115-119 24.9 24.759999999999998 24.035 26.305 120-124 24.9 24.654999999999998 24.13 26.314999999999998 125-129 25.2 23.87 24.044999999999998 26.884999999999998 130-134 25.424999999999997 24.62 23.885 26.07 135-139 25.395 24.43 23.39 26.784999999999997 140-144 25.2 24.81 22.939999999999998 27.05 145-149 25.124999999999996 24.705 23.265 26.905 150-151 25.0625 25.1 23.325000000000003 26.5125 >>END_MODULE >>Per sequence GC content fail #GC Content Count 0 0.0 1 0.5 2 0.5 3 0.5 4 0.5 5 0.0 6 0.0 7 0.0 8 0.5 9 1.0 10 0.5 11 0.0 12 0.0 13 0.0 14 0.0 15 0.0 16 0.0 17 0.5 18 0.5 19 0.0 20 0.0 21 0.0 22 0.5 23 0.5 24 0.5 25 1.0 26 2.5 27 2.5 28 2.5 29 3.0 30 3.5 31 5.0 32 10.0 33 14.5 34 20.5 35 35.5 36 46.5 37 58.0 38 75.0 39 99.5 40 109.5 41 119.5 42 146.0 43 164.5 44 176.0 45 193.0 46 198.0 47 182.0 48 162.0 49 155.5 50 167.5 51 150.0 52 128.0 53 123.5 54 115.0 55 96.0 56 85.5 57 88.0 58 81.0 59 81.0 60 73.5 61 61.5 62 70.0 63 67.0 64 66.5 65 70.5 66 59.5 67 56.5 68 55.5 69 53.5 70 50.5 71 39.0 72 30.0 73 32.0 74 27.5 75 21.0 76 18.0 77 12.0 78 10.0 79 7.0 80 2.5 81 2.0 82 3.5 83 2.5 84 0.5 85 0.5 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 0.475 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 83.7 #Duplication Level Percentage of deduplicated Percentage of total 1 84.88649940262843 71.05 2 11.947431302270012 20.0 3 2.2998805256869774 5.775 4 0.6869772998805257 2.3 5 0.11947431302270012 0.5 6 0.02986857825567503 0.15 7 0.0 0.0 8 0.0 0.0 9 0.02986857825567503 0.22499999999999998 >10 0.0 0.0 >50 0.0 0.0 >100 0.0 0.0 >500 0.0 0.0 >1k 0.0 0.0 >5k 0.0 0.0 >10k+ 0.0 0.0 >>END_MODULE >>Overrepresented sequences warn #Sequence Count Percentage Possible Source GATCGGAAGAGCACACGTCTGAACTCCAGTCACAGTAGTCCATCTCGTAT 9 0.22499999999999998 TruSeq Adapter, Index 22 (97% over 37bp) GTTTCAGAGTCACACCGCCAAATCTATAATGACATAAATCCATATTGCAA 6 0.15 No Hit CTGGGCCACAGATCAGCACACTCCTTTCCGATCGGTCCGGTGATGGCAGA 5 0.125 No Hit GGCCTTCCTGTTGCCACTGAGCGGACCGGCCCAAACCTCCAGACCGTTGT 5 0.125 No Hit TGGCACTCTTCATTTTTAGTGGACGCTAGTGTGTTTGCAGCTGTTGAGCA 5 0.125 No Hit GTAGCATATTCTTCAGCATATCCAGAACAGATCACTTAAGTGGTCTCTAC 5 0.125 No Hit >>END_MODULE >>Adapter Content fail #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 0.0125 0.0 0.0 0.0 0.0 38-39 0.037500000000000006 0.0 0.0 0.0 0.0 40-41 0.05 0.0 0.0 0.0 0.0 42-43 0.05 0.0 0.0 0.0 0.0 44-45 0.05 0.0 0.0 0.0 0.0 46-47 0.05 0.0 0.0 0.0 0.0 48-49 0.05 0.0 0.0 0.0 0.0 50-51 0.05 0.0 0.0 0.0 0.0 52-53 0.05 0.0 0.0 0.0 0.0 54-55 0.05 0.0 0.0 0.0 0.0 56-57 0.05 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 0.1 0.0 0.0 0.0 0.0 74-75 0.125 0.0 0.0 0.0 0.0 76-77 0.2 0.0 0.0 0.0 0.0 78-79 0.2875 0.0 0.0 0.0 0.0 80-81 0.4625 0.0 0.0 0.0 0.0 82-83 0.475 0.0 0.0 0.0 0.0 84-85 0.55 0.0 0.0 0.0 0.0 86-87 0.6875 0.0 0.0 0.0 0.0 88-89 0.9 0.0 0.0 0.0 0.0 90-91 0.925 0.0 0.0 0.0 0.0 92-93 1.0499999999999998 0.0 0.0 0.0 0.0 94-95 1.4249999999999998 0.0 0.0 0.0 0.0 96-97 1.7125 0.0 0.0 0.0 0.0 98-99 2.0375 0.0 0.0 0.0 0.0 100-101 2.3625 0.0 0.0 0.0 0.0 102-103 2.7375 0.0 0.0 0.0 0.0 104-105 3.1875 0.0 0.0 0.0 0.0 106-107 3.6375 0.0 0.0 0.0 0.0 108-109 3.9875 0.0 0.0 0.0 0.0 110-111 4.4375 0.0 0.0 0.0 0.0 112-113 4.875 0.0 0.0 0.0 0.0 114-115 5.362500000000001 0.0 0.0 0.0 0.0 116-117 5.9 0.0 0.0 0.0 0.0 118-119 6.2625 0.0 0.0 0.0 0.0 120-121 6.7875 0.0 0.0 0.0 0.0 122-123 7.4 0.0 0.0 0.0 0.0 124-125 8.1875 0.0 0.0 0.0 0.0 126-127 8.975000000000001 0.0 0.0 0.0 0.0 128-129 9.6875 0.0 0.0 0.0 0.0 130-131 10.5 0.0 0.0 0.0 0.0 132-133 11.274999999999999 0.0 0.0 0.0 0.0 134-135 11.825 0.0 0.0 0.0 0.0 136-137 12.537500000000001 0.0 0.0 0.0 0.0 138-139 13.1625 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content pass >>END_MODULE SRR12951291 read2 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR12951291_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 36.251 37.0 37.0 37.0 37.0 37.0 2 36.3715 37.0 37.0 37.0 37.0 37.0 3 36.176 37.0 37.0 37.0 37.0 37.0 4 36.211 37.0 37.0 37.0 37.0 37.0 5 36.3855 37.0 37.0 37.0 37.0 37.0 6 36.2285 37.0 37.0 37.0 37.0 37.0 7 36.266 37.0 37.0 37.0 37.0 37.0 8 36.3565 37.0 37.0 37.0 37.0 37.0 9 36.381 37.0 37.0 37.0 37.0 37.0 10-14 36.3534 37.0 37.0 37.0 37.0 37.0 15-19 36.3381 37.0 37.0 37.0 37.0 37.0 20-24 36.2164 37.0 37.0 37.0 37.0 37.0 25-29 36.215700000000005 37.0 37.0 37.0 37.0 37.0 30-34 36.194100000000006 37.0 37.0 37.0 37.0 37.0 35-39 36.1474 37.0 37.0 37.0 37.0 37.0 40-44 36.175599999999996 37.0 37.0 37.0 37.0 37.0 45-49 36.165499999999994 37.0 37.0 37.0 37.0 37.0 50-54 36.090399999999995 37.0 37.0 37.0 37.0 37.0 55-59 36.0641 37.0 37.0 37.0 37.0 37.0 60-64 36.0793 37.0 37.0 37.0 37.0 37.0 65-69 36.0775 37.0 37.0 37.0 37.0 37.0 70-74 36.0689 37.0 37.0 37.0 37.0 37.0 75-79 36.0071 37.0 37.0 37.0 37.0 37.0 80-84 35.9658 37.0 37.0 37.0 37.0 37.0 85-89 35.929199999999994 37.0 37.0 37.0 37.0 37.0 90-94 36.0236 37.0 37.0 37.0 37.0 37.0 95-99 35.9249 37.0 37.0 37.0 37.0 37.0 100-104 35.8867 37.0 37.0 37.0 37.0 37.0 105-109 35.864799999999995 37.0 37.0 37.0 37.0 37.0 110-114 35.8104 37.0 37.0 37.0 37.0 37.0 115-119 35.8428 37.0 37.0 37.0 37.0 37.0 120-124 35.7737 37.0 37.0 37.0 37.0 37.0 125-129 35.6709 37.0 37.0 37.0 37.0 37.0 130-134 35.627300000000005 37.0 37.0 37.0 37.0 37.0 135-139 35.4869 37.0 37.0 37.0 37.0 37.0 140-144 35.4014 37.0 37.0 37.0 37.0 37.0 145-149 35.1437 37.0 37.0 37.0 32.2 37.0 150-151 34.7415 37.0 37.0 37.0 25.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 12 2.0 13 2.0 14 5.0 15 2.0 16 2.0 17 2.0 18 2.0 19 1.0 20 4.0 21 9.0 22 6.0 23 4.0 24 9.0 25 11.0 26 9.0 27 6.0 28 11.0 29 16.0 30 11.0 31 26.0 32 57.0 33 81.0 34 168.0 35 456.0 36 2731.0 37 367.0 >>END_MODULE >>Per base sequence content warn #Base G A T C 1 42.6 19.6 8.25 29.549999999999997 2 27.650000000000002 23.724999999999998 25.974999999999998 22.650000000000002 3 24.075 25.7 27.0 23.225 4 27.975 30.475 19.875 21.675 5 27.750000000000004 33.15 18.575 20.525 6 24.6 34.050000000000004 19.35 22.0 7 24.4 20.3 30.575000000000003 24.725 8 23.5 22.775000000000002 23.275000000000002 30.45 9 24.375 22.15 27.175 26.3 10-14 26.85 25.485000000000003 22.105 25.56 15-19 26.179999999999996 24.834999999999997 23.125 25.86 20-24 26.495 24.41 23.200000000000003 25.895000000000003 25-29 27.229999999999997 24.16 23.25 25.36 30-34 27.065 24.865000000000002 22.98 25.09 35-39 26.41 24.305 24.285 25.0 40-44 26.845000000000002 23.78 23.880000000000003 25.495 45-49 27.01 24.995 23.335 24.66 50-54 27.065 24.3 23.49 25.145 55-59 26.76 24.44 23.995 24.805 60-64 26.545 24.815 23.53 25.11 65-69 27.235 24.785 23.355 24.625 70-74 27.07 24.125 23.82 24.985 75-79 26.735 24.42 24.135 24.709999999999997 80-84 27.169999999999998 24.4 23.965 24.465 85-89 27.265 24.18 23.880000000000003 24.675 90-94 27.115000000000002 25.165 23.43 24.29 95-99 27.644999999999996 24.905 22.695 24.755 100-104 27.805000000000003 24.595 23.59 24.01 105-109 28.285 25.39 22.66 23.665 110-114 27.750000000000004 24.395 23.830000000000002 24.025 115-119 27.93 24.779999999999998 22.925 24.365000000000002 120-124 28.205000000000002 25.615 23.28 22.900000000000002 125-129 28.065 24.94 23.135 23.86 130-134 29.385 24.975 22.825 22.814999999999998 135-139 29.404999999999998 25.759999999999998 22.645 22.189999999999998 140-144 29.5 24.990000000000002 23.085 22.425 145-149 30.445 24.3 22.939999999999998 22.314999999999998 150-151 30.55 25.575 22.6875 21.1875 >>END_MODULE >>Per sequence GC content fail #GC Content Count 0 0.0 1 0.0 2 0.0 3 0.0 4 0.5 5 0.5 6 0.0 7 0.5 8 0.5 9 0.5 10 0.5 11 0.5 12 0.5 13 0.0 14 0.0 15 0.5 16 0.5 17 0.0 18 0.0 19 0.0 20 0.5 21 0.5 22 0.0 23 0.0 24 1.0 25 2.5 26 2.5 27 1.0 28 0.0 29 2.5 30 6.5 31 7.5 32 8.0 33 8.5 34 13.0 35 23.5 36 35.0 37 48.0 38 56.5 39 77.5 40 105.5 41 119.0 42 131.0 43 152.5 44 168.0 45 177.0 46 182.0 47 184.0 48 174.5 49 156.5 50 144.5 51 135.5 52 141.0 53 133.5 54 112.5 55 94.0 56 82.5 57 93.0 58 106.0 59 103.5 60 86.0 61 80.0 62 74.5 63 65.5 64 72.5 65 72.0 66 63.5 67 69.5 68 69.5 69 55.5 70 48.0 71 42.0 72 41.0 73 38.5 74 30.0 75 19.5 76 17.0 77 16.0 78 8.0 79 5.5 80 5.5 81 4.5 82 3.0 83 2.5 84 2.0 85 0.0 86 0.5 87 0.5 88 0.0 89 0.5 90 1.5 91 1.5 92 1.0 93 0.5 94 0.5 95 1.5 96 1.0 97 0.0 98 0.5 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 83.975 #Duplication Level Percentage of deduplicated Percentage of total 1 85.17415897588569 71.525 2 11.491515331944031 19.3 3 2.5602857993450434 6.45 4 0.6251860672819292 2.1 5 0.14885382554331647 0.625 6 0.0 0.0 7 0.0 0.0 8 0.0 0.0 9 0.0 0.0 >10 0.0 0.0 >50 0.0 0.0 >100 0.0 0.0 >500 0.0 0.0 >1k 0.0 0.0 >5k 0.0 0.0 >10k+ 0.0 0.0 >>END_MODULE >>Overrepresented sequences warn #Sequence Count Percentage Possible Source CCAGACATTAGTAATACTTGACTTGGTGCAAGCCTCGCTCTTGTGATGTG 5 0.125 No Hit AACGAATTTATGGACCACGGGAATGAGTTTTAAGCTGCTTGGTTTTTACC 5 0.125 No Hit GCAGCTCCTACAGTGAAGCCTGTTACACTGGAACTTGGTGGCAAAAGTCC 5 0.125 No Hit GCCAAGGCTCCTCTTCTGATCGGGTGTGACGTGCGCACGATGAGCCAGCA 5 0.125 No Hit GTTCCGCTGGTAACAAGTTCCGCATGTCACTGGGTCTACCAGTGGCAGCC 5 0.125 No Hit >>END_MODULE >>Adapter Content fail #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 0.0125 0.0 0.0 0.0 0.0 38-39 0.037500000000000006 0.0 0.0 0.0 0.0 40-41 0.05 0.0 0.0 0.0 0.0 42-43 0.05 0.0 0.0 0.0 0.0 44-45 0.05 0.0 0.0 0.0 0.0 46-47 0.05 0.0 0.0 0.0 0.0 48-49 0.05 0.0 0.0 0.0 0.0 50-51 0.05 0.0 0.0 0.0 0.0 52-53 0.05 0.0 0.0 0.0 0.0 54-55 0.05 0.0 0.0 0.0 0.0 56-57 0.05 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 0.1 0.0 0.0 0.0 0.0 74-75 0.125 0.0 0.0 0.0 0.0 76-77 0.2 0.0 0.0 0.0 0.0 78-79 0.2875 0.0 0.0 0.0 0.0 80-81 0.4625 0.0 0.0 0.0 0.0 82-83 0.4875 0.0 0.0 0.0 0.0 84-85 0.575 0.0 0.0 0.0 0.0 86-87 0.7 0.0 0.0 0.0 0.0 88-89 0.9 0.0 0.0 0.0 0.0 90-91 0.925 0.0 0.0 0.0 0.0 92-93 1.0499999999999998 0.0 0.0 0.0 0.0 94-95 1.4125 0.0 0.0 0.0 0.0 96-97 1.6875 0.0 0.0 0.0 0.0 98-99 2.0125 0.0 0.0 0.0 0.0 100-101 2.3125 0.0 0.0 0.0 0.0 102-103 2.65 0.0 0.0 0.0 0.0 104-105 3.0875 0.0 0.0 0.0 0.0 106-107 3.5374999999999996 0.0 0.0 0.0 0.0 108-109 3.875 0.0 0.0 0.0 0.0 110-111 4.3375 0.0 0.0 0.0 0.0 112-113 4.775 0.0 0.0 0.0 0.0 114-115 5.275 0.0 0.0 0.0 0.0 116-117 5.824999999999999 0.0 0.0 0.0 0.0 118-119 6.1625 0.0 0.0 0.0 0.0 120-121 6.6625 0.0 0.0 0.0 0.0 122-123 7.25 0.0 0.0 0.0 0.0 124-125 8.0625 0.0 0.0 0.0 0.0 126-127 8.8875 0.0 0.0 0.0 0.0 128-129 9.575 0.0 0.0 0.0 0.0 130-131 10.375 0.0 0.0 0.0 0.0 132-133 11.1625 0.0 0.0 0.0 0.0 134-135 11.725 0.0 0.0 0.0 0.0 136-137 12.462499999999999 0.0 0.0 0.0 0.0 138-139 13.0875 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content pass >>END_MODULE Read 2339660 spots for SRR12951291.sra Written 2339660 spots for SRR12951291.sra Read 2339660 spots for SRR12951291.sra Written 2339660 spots for SRR12951291.sra Read 2339660 spots for SRR12951291.sra Written 2339660 spots for SRR12951291.sra Read 2339660 spots for SRR12951291.sra Written 2339660 spots for SRR12951291.sra Read 2339660 spots for SRR12951291.sra Written 2339660 spots for SRR12951291.sra Read 2339660 spots for SRR12951291.sra Written 2339660 spots for SRR12951291.sra Read 2339660 spots for SRR12951291.sra Written 2339660 spots for SRR12951291.sra Read 2339660 spots for SRR12951291.sra Written 2339660 spots for SRR12951291.sra Read 2339660 spots for SRR12951291.sra Written 2339660 spots for SRR12951291.sra Read 2339660 spots for SRR12951291.sra Written 2339660 spots for SRR12951291.sra Read 2339660 spots for SRR12951291.sra Written 2339660 spots for SRR12951291.sra Read 2339660 spots for SRR12951291.sra Written 2339660 spots for SRR12951291.sra Read 2339672 spots for SRR12951291.sra Written 2339672 spots for SRR12951291.sra Read 2339660 spots for SRR12951291.sra Written 2339660 spots for SRR12951291.sra Read 2339660 spots for SRR12951291.sra Written 2339660 spots for SRR12951291.sra Read 2339660 spots for SRR12951291.sra Written 2339660 spots for SRR12951291.sra Read 2339660 spots for SRR12951291.sra Written 2339660 spots for SRR12951291.sra Read 2339660 spots for SRR12951291.sra Written 2339660 spots for SRR12951291.sra Read 2339660 spots for SRR12951291.sra Written 2339660 spots for SRR12951291.sra Read 2339660 spots for SRR12951291.sra Written 2339660 spots for SRR12951291.sra SRR ids: ['SRR12951291.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_q3o53xvr SRR12951291.sra spots: 46793212 blocks: [[1, 2339660], [2339661, 4679320], [4679321, 7018980], [7018981, 9358640], [9358641, 11698300], [11698301, 14037960], [14037961, 16377620], [16377621, 18717280], [18717281, 21056940], [21056941, 23396600], [23396601, 25736260], [25736261, 28075920], [28075921, 30415580], [30415581, 32755240], [32755241, 35094900], [35094901, 37434560], [37434561, 39774220], [39774221, 42113880], [42113881, 44453540], [44453541, 46793212]] SRR12951291 file size 15880680 SRR12951291 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 SRR12951291 SRR12951291_1.fastq SRR12951291_2.fastq Input file: SRR12951291_1.fastq Paired file: SRR12951291_2.fastq trimmed: SRR12951291-trimmed-pair1.fastq, SRR12951291-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 10:42:54 2024 >> started Sat Dec 7 10:43:50 2024 >> done (55.965s) 46793212 read pairs processed; of these: 328 ( 0.00%) short read pairs filtered out after trimming by size control 138373 ( 0.30%) empty read pairs filtered out after trimming by size control 46654511 (99.70%) read pairs available; of these: 7935430 (17.01%) trimmed read pairs available after processing 38719081 (82.99%) untrimmed read pairs available after processing Length distribution of reads after trimming: length count percentage 18 17 0.00% 19 36 0.00% 20 32 0.00% 21 48 0.00% 22 55 0.00% 23 63 0.00% 24 87 0.00% 25 97 0.00% 26 80 0.00% 27 99 0.00% 28 142 0.00% 29 145 0.00% 30 122 0.00% 31 120 0.00% 32 125 0.00% 33 140 0.00% 34 148 0.00% 35 171 0.00% 36 158 0.00% 37 172 0.00% 38 192 0.00% 39 196 0.00% 40 216 0.00% 41 244 0.00% 42 230 0.00% 43 228 0.00% 44 253 0.00% 45 294 0.00% 46 350 0.00% 47 301 0.00% 48 387 0.00% 49 403 0.00% 50 513 0.00% 51 559 0.00% 52 653 0.00% 53 631 0.00% 54 722 0.00% 55 791 0.00% 56 826 0.00% 57 1033 0.00% 58 1122 0.00% 59 1289 0.00% 60 1588 0.00% 61 1798 0.00% 62 2130 0.00% 63 2344 0.01% 64 2541 0.01% 65 2710 0.01% 66 3088 0.01% 67 3470 0.01% 68 3922 0.01% 69 4449 0.01% 70 5386 0.01% 71 6131 0.01% 72 7059 0.02% 73 8104 0.02% 74 9055 0.02% 75 9917 0.02% 76 11085 0.02% 77 12000 0.03% 78 13224 0.03% 79 14869 0.03% 80 16582 0.04% 81 18587 0.04% 82 20920 0.04% 83 23507 0.05% 84 25585 0.05% 85 28058 0.06% 86 30750 0.07% 87 32710 0.07% 88 35176 0.08% 89 37314 0.08% 90 40662 0.09% 91 43683 0.09% 92 47321 0.10% 93 50090 0.11% 94 54685 0.12% 95 57674 0.12% 96 60557 0.13% 97 63819 0.14% 98 66079 0.14% 99 68427 0.15% 100 71027 0.15% 101 74529 0.16% 102 78311 0.17% 103 82246 0.18% 104 85400 0.18% 105 90313 0.19% 106 92916 0.20% 107 95406 0.20% 108 98163 0.21% 109 100872 0.22% 110 103126 0.22% 111 105471 0.23% 112 108616 0.23% 113 112213 0.24% 114 117523 0.25% 115 119089 0.26% 116 122484 0.26% 117 125044 0.27% 118 127130 0.27% 119 128553 0.28% 120 130058 0.28% 121 132184 0.28% 122 135435 0.29% 123 138133 0.30% 124 141231 0.30% 125 143723 0.31% 126 146388 0.31% 127 148694 0.32% 128 149129 0.32% 129 150515 0.32% 130 152163 0.33% 131 153450 0.33% 132 156380 0.34% 133 157776 0.34% 134 161692 0.35% 135 164016 0.35% 136 165075 0.35% 137 167393 0.36% 138 165916 0.36% 139 167241 0.36% 140 169452 0.36% 141 169480 0.36% 142 170746 0.37% 143 171997 0.37% 144 171846 0.37% 145 174808 0.37% 146 176270 0.38% 147 173654 0.37% 148 178061 0.38% 149 176815 0.38% 150 176731 0.38% 151 38719081 82.99% 46654511 reads passed initial QC criterion=sequence-density sequence-density=0.19 sequence-density-rank=1 fanout-score=49.46 fanout-score-rank=9 prefix-density=0.83 prefix-fanout=11.3 sequence=CGCCGCCGCCGCGGGAGGAGGACGCGATCTCCACCACCGGGTGGCCCGGGGGCACCACGAACGCTGAGCCGACGGACACCCGGGCGCGGATCCTCTCGTACCTTCCCTGCTGCTG criterion=fanout-score sequence-density=0.04 sequence-density-rank=29 fanout-score=281.60 fanout-score-rank=1 prefix-density=0.79 prefix-fanout=15.7 sequence=GGCGGCGGCGAACCGCCCCCGTCGCCGCGATCCGAACACTTCACCGGACCATTCAATCGGTAGGAGCGACGGGCGGTGTGTACAAAGGGCAGGGACGTAGTCAACGCGAGCTGATGACTCGCGCTTACTAGGCATTCCTCGTTGAAGACCAACAATTGCAATGATCTATCCCCATCACGATGAAATTTCCCAAGATTACCCGGGCCTGTCGGCCAAGGCTATATACTCGTTGAATACATCAGTGTAGCGCGCGTGCGGCCCAGAACATCTAAGGGCATCACAGACCTGTTATTGCCTCAAACTTCCGTCGCCTAAACGGCGATAGTCCCTCTAAGAAGCTAGCTGCGGAGGGATGGCTCCGCATAGCTAGTTAGCAGGCTGAGGTCTCGTTCGTTAACGGAATTAACCAGACAAATCGCTCCACCAACTAAGAACGGCCATGCACCACCACCCATAGAATCAAGAAAGAGCTCTCAGTCTGTCAATCCTTGCTATGTCTGGACCTGGTAAG criterion=sequence-density sequence-density=0.65 sequence-density-rank=1 fanout-score=2.00 fanout-score-rank=33 prefix-density=0.65 prefix-fanout=2.0 sequence=CGGTTCCGGTTC criterion=fanout-score sequence-density=0.11 sequence-density-rank=18 fanout-score=210.11 fanout-score-rank=1 prefix-density=1.06 prefix-fanout=22.0 sequence=CGCCGCCGCCGG SRR12951291 testing PE reads STAR mapping to Ensembl genome Started job on | Dec 07 10:44:30 Started mapping on | Dec 07 10:44:30 Finished on | Dec 07 10:49:27 Mapping speed, Million of reads per hour | 565.51 Number of input reads | 46654511 Average input read length | 292 UNIQUE READS: Uniquely mapped reads number | 43859849 Uniquely mapped reads % | 94.01% Average mapped length | 291.67 Number of splices: Total | 39094005 Number of splices: Annotated (sjdb) | 36216261 Number of splices: GT/AG | 38500654 Number of splices: GC/AG | 500157 Number of splices: AT/AC | 22481 Number of splices: Non-canonical | 70713 Mismatch rate per base, % | 0.22% Deletion rate per base | 0.01% Deletion average length | 2.11 Insertion rate per base | 0.01% Insertion average length | 2.46 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 504221 % of reads mapped to multiple loci | 1.08% Number of reads mapped to too many loci | 117898 % of reads mapped to too many loci | 0.25% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 2.99% % of reads unmapped: other | 1.67% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 2290441 2290441 2290441 N_multimapping 504221 504221 504221 N_noFeature 1618076 42625858 2014247 N_ambiguous 977781 5592 140637 UnstrandedReadsAssigned:41263992 PositiveStrandReadsAssigned:1228399 NegativeStrandReadsAssigned:41704965 Dataset is classified negative stranded MeadianReadLen=151 20thPercentileLength=151 echo kmer=147 SRR12951291 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: SRR12951291-trimmed-pair1.fastq SRR12951291-trimmed-pair2.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 46,654,511 reads, 42,299,939 reads pseudoaligned [quant] estimated average fragment length: 248.789 [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,270 rounds 52973 SRR12951291.ke.tsv 35125 SRR12951291.se.tsv 88098 total ==> SRR12951291.ke.tsv <== target_id length eff_length est_counts tpm PNS24245 936 688.896 0 0 PNS24247 1044 796.211 275.016 11.5965 PNS24249 1928 1680.21 667.858 13.3449 PNS24246 1044 796.211 275.016 11.5965 PNS24248 1044 796.211 275.016 11.5965 PNS24244 1471 1223.21 368.093 10.1031 PNS24243 293 108.6 8 2.47318 KQK14069 1603 1355.21 82738.4 2049.73 KQK14071 474 249.024 220.789 29.7668 ==> SRR12951291.se.tsv <== BRADI_1g14170v3 83009 BRADI_1g53295v3 522 BRADI_1g59795v3 825 BRADI_1g07683v3 0 BRADI_1g00485v3 5 BRADI_1g20270v3 1266 BRADI_1g74790v3 3379 BRADI_1g09890v3 0 BRADI_1g77505v3 534 BRADI_1g48960v3 0 SRR12951291 completed mapping pipeline successfully