Starting /dee2/code/volunteer_pipeline.sh SRR12670161 current disk space = 3055656812544 free memory = 1054708148 SRR12670161 SRAfilesize f91026917b12b420df0d39792b1e0402 SRR12670161.sra SRR12670161.sra file validated SRR12670161 is paired end SRR12670161 is conventional basespace SRR12670161 read1 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR12670161_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 45 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 36.581 37.0 37.0 37.0 37.0 37.0 2 36.46775 37.0 37.0 37.0 37.0 37.0 3 36.6035 37.0 37.0 37.0 37.0 37.0 4 36.6155 37.0 37.0 37.0 37.0 37.0 5 36.674 37.0 37.0 37.0 37.0 37.0 6 36.559 37.0 37.0 37.0 37.0 37.0 7 36.5215 37.0 37.0 37.0 37.0 37.0 8 36.6345 37.0 37.0 37.0 37.0 37.0 9 36.5655 37.0 37.0 37.0 37.0 37.0 10-14 36.5914 37.0 37.0 37.0 37.0 37.0 15-19 36.5651 37.0 37.0 37.0 37.0 37.0 20-24 36.510400000000004 37.0 37.0 37.0 37.0 37.0 25-29 36.5189 37.0 37.0 37.0 37.0 37.0 30-34 36.481899999999996 37.0 37.0 37.0 37.0 37.0 35-39 36.4757 37.0 37.0 37.0 37.0 37.0 40-44 36.4637 37.0 37.0 37.0 37.0 37.0 45-49 36.416900000000005 37.0 37.0 37.0 37.0 37.0 50-54 36.382400000000004 37.0 37.0 37.0 37.0 37.0 55-59 36.4138 37.0 37.0 37.0 37.0 37.0 60-64 36.3774 37.0 37.0 37.0 37.0 37.0 65-69 36.313300000000005 37.0 37.0 37.0 37.0 37.0 70-74 36.3392 37.0 37.0 37.0 37.0 37.0 75-79 36.3451 37.0 37.0 37.0 37.0 37.0 80-84 36.32 37.0 37.0 37.0 37.0 37.0 85-89 36.2838 37.0 37.0 37.0 37.0 37.0 90-94 36.29260000000001 37.0 37.0 37.0 37.0 37.0 95-99 36.2233 37.0 37.0 37.0 37.0 37.0 100-104 36.1985 37.0 37.0 37.0 37.0 37.0 105-109 36.162 37.0 37.0 37.0 37.0 37.0 110-114 36.1546 37.0 37.0 37.0 37.0 37.0 115-119 36.166399999999996 37.0 37.0 37.0 37.0 37.0 120-124 36.06679999999999 37.0 37.0 37.0 37.0 37.0 125-129 35.927 37.0 37.0 37.0 37.0 37.0 130-134 35.9693 37.0 37.0 37.0 37.0 37.0 135-139 35.82379999999999 37.0 37.0 37.0 37.0 37.0 140-144 35.6244 37.0 37.0 37.0 37.0 37.0 145-149 35.5214 37.0 37.0 37.0 37.0 37.0 150-151 35.147499999999994 37.0 37.0 37.0 31.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 22 1.0 23 0.0 24 2.0 25 3.0 26 2.0 27 6.0 28 17.0 29 15.0 30 26.0 31 32.0 32 54.0 33 73.0 34 115.0 35 342.0 36 2922.0 37 390.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 39.675 11.35 5.875 43.1 2 18.623279098873592 11.339173967459324 38.1226533166458 31.914893617021278 3 17.125 16.400000000000002 27.224999999999998 39.25 4 21.275 23.549999999999997 25.025 30.15 5 22.975 30.375000000000004 25.424999999999997 21.224999999999998 6 21.525 33.6 23.775 21.099999999999998 7 15.575 25.900000000000002 42.05 16.475 8 17.849999999999998 24.875 32.625 24.65 9 17.875 23.799999999999997 35.25 23.075000000000003 10-14 19.2 29.659999999999997 27.815 23.325000000000003 15-19 20.405 27.955000000000002 27.705000000000002 23.935000000000002 20-24 20.630000000000003 28.144999999999996 27.395000000000003 23.830000000000002 25-29 19.994999999999997 27.655 28.78 23.57 30-34 19.994999999999997 28.09 27.395000000000003 24.52 35-39 20.0 27.860000000000003 27.98 24.16 40-44 19.785 28.73 27.865000000000002 23.62 45-49 20.96 27.815 27.744999999999997 23.48 50-54 20.19 28.18 28.32 23.31 55-59 20.77 27.595 28.110000000000003 23.525 60-64 20.544999999999998 27.589999999999996 27.894999999999996 23.97 65-69 21.125 27.92 27.445000000000004 23.51 70-74 20.41 28.225 27.894999999999996 23.47 75-79 21.425 27.445000000000004 27.51 23.62 80-84 21.015 28.189999999999998 27.305 23.49 85-89 20.575 28.375 27.24 23.810000000000002 90-94 20.78 28.939999999999998 26.840000000000003 23.44 95-99 21.295 27.755000000000003 27.48 23.47 100-104 21.205 28.16 26.965 23.669999999999998 105-109 21.495 28.144999999999996 26.86 23.5 110-114 21.295 28.115000000000002 26.66 23.93 115-119 21.815 28.825 25.814999999999998 23.544999999999998 120-124 21.385 27.725 26.815 24.075 125-129 21.015 27.975 26.245 24.765 130-134 20.380000000000003 28.194999999999997 25.85 25.575 135-139 20.84 27.665 26.015 25.480000000000004 140-144 21.349999999999998 27.355 26.58 24.715 145-149 21.029999999999998 27.155 26.43 25.385 150-151 20.549999999999997 26.1625 26.5875 26.700000000000003 >>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 0.5 18 1.0 19 0.5 20 0.5 21 0.5 22 1.0 23 1.5 24 2.0 25 1.5 26 0.5 27 3.5 28 4.5 29 4.5 30 8.0 31 12.5 32 23.0 33 40.5 34 50.5 35 65.0 36 89.0 37 108.0 38 124.5 39 156.5 40 195.5 41 205.5 42 231.5 43 245.0 44 247.5 45 256.5 46 262.0 47 272.5 48 260.0 49 223.5 50 185.5 51 145.5 52 108.0 53 103.0 54 91.5 55 68.0 56 62.0 57 50.5 58 28.0 59 19.0 60 11.0 61 6.0 62 7.5 63 5.0 64 1.5 65 3.0 66 3.5 67 1.5 68 0.0 69 0.0 70 0.5 71 0.5 72 0.0 73 0.0 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 0.125 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 78.95 #Duplication Level Percentage of deduplicated Percentage of total 1 80.30398986700443 63.4 2 14.946168461051299 23.599999999999998 3 3.4198860037998733 8.1 4 0.8233058898036731 2.6 5 0.2849905003166561 1.125 6 0.09499683343888536 0.44999999999999996 7 0.09499683343888536 0.525 8 0.031665611146295125 0.2 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 GACCAAATAAAAGAATTTGTGCTGCCAACTGCCAGAGACTACAATCTGGT 8 0.2 No Hit CTTTGATCTACCACTATCCCTGTCATAAACCACTTTAGCATCCATCACCT 7 0.17500000000000002 No Hit AGGGTGACCAACAACGTGGTTAGGAGGGTAAGGTGCCCGATCACGAAGAG 7 0.17500000000000002 No Hit CCACAAGTACAGAAGAACACAGATTATTTATCAGAAATTACATTATTAAT 7 0.17500000000000002 No Hit CTCCAACAATCCCTCCTATTACACTGATTGCAATAATTGCTTTAGAAGGT 6 0.15 No Hit CCCTCAATGTTTTTCTTAAAATGTTCTTTGTTTTCGTCATCGAGTTTCTC 6 0.15 No Hit CCTGTCTAGAAACAATCAAGCATGCATGCGAATTATAAGGGTACTTTTCA 6 0.15 No Hit GGATAATAGTATTTGCAACATAATATTTTGATAGGGTCCCAAATCAGTCT 5 0.125 No Hit GGGCTTACTACTTAGATGCTTTCAGCAGTTATCCGCTCCGCACTTGGCTA 5 0.125 No Hit GAGCACACAAGCCAGATACCAAGGGCATCACAGTTTTCTCAGGATCTCTC 5 0.125 No Hit CCGCTTGTTATTTGCACTTTAGGAAAACGAGTTTTTGATTTACACTGCTT 5 0.125 No Hit AGCAGATGAGAGATGGGATCCAGATTCCGACATGGATGTTGATGAAGAAC 5 0.125 No Hit CCTTGATTAACTTGTACCTTTCCATATTTCTTGTGGAACAAAAAAGAGCT 5 0.125 No Hit CTGGTGTCCTCACCAGTCGGGGTCCAACTGGCACCTTCGTTTTTGGACGA 5 0.125 No Hit CCACACCAGAGGCCACAGACATGGCCAATACATAACAATGAAGAAGACAC 5 0.125 No Hit GGATCGAATGCCTTGGGGTCAGAAGATGAGGCGGTTTGTAATTCAGCTGT 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 0.0125 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 0.037500000000000006 0.0 0.0 0.0 0.0 48-49 0.0875 0.0 0.0 0.0 0.0 50-51 0.1 0.0 0.0 0.0 0.0 52-53 0.125 0.0 0.0 0.0 0.0 54-55 0.16249999999999998 0.0 0.0 0.0 0.0 56-57 0.175 0.0 0.0 0.0 0.0 58-59 0.175 0.0 0.0 0.0 0.0 60-61 0.2 0.0 0.0 0.0 0.0 62-63 0.225 0.0 0.0 0.0 0.0 64-65 0.2625 0.0 0.0 0.0 0.0 66-67 0.2875 0.0 0.0 0.0 0.0 68-69 0.32499999999999996 0.0 0.0 0.0 0.0 70-71 0.38749999999999996 0.0 0.0 0.0 0.0 72-73 0.4375 0.0 0.0 0.0 0.0 74-75 0.525 0.0 0.0 0.0 0.0 76-77 0.6625 0.0 0.0 0.0 0.0 78-79 0.8625 0.0 0.0 0.0 0.0 80-81 1.0375 0.0 0.0 0.0 0.0 82-83 1.15 0.0 0.0 0.0 0.0 84-85 1.65 0.0 0.0 0.0 0.0 86-87 2.0625 0.0 0.0 0.0 0.0 88-89 2.3375 0.0 0.0 0.0 0.0 90-91 2.7375 0.0 0.0 0.0 0.0 92-93 3.375 0.0 0.0 0.0 0.0 94-95 3.8375000000000004 0.0 0.0 0.0 0.0 96-97 4.425 0.0 0.0 0.0 0.0 98-99 5.1625 0.0 0.0 0.0 0.0 100-101 5.7375 0.0 0.0 0.0 0.0 102-103 6.5 0.0 0.0 0.0 0.0 104-105 7.3375 0.0 0.0 0.0 0.0 106-107 8.1 0.0 0.0 0.0 0.0 108-109 8.725 0.0 0.0 0.0 0.0 110-111 9.4125 0.0 0.0 0.0 0.0 112-113 10.275 0.0 0.0 0.0 0.0 114-115 10.9 0.0 0.0 0.0 0.0 116-117 11.649999999999999 0.0 0.0 0.0 0.0 118-119 12.962499999999999 0.0 0.0 0.0 0.0 120-121 13.95 0.0 0.0 0.0 0.0 122-123 14.8625 0.0 0.0 0.0 0.0 124-125 15.8125 0.0 0.0 0.0 0.0 126-127 16.7125 0.0 0.0 0.0 0.0 128-129 17.45 0.0 0.0 0.0 0.0 130-131 18.5 0.0 0.0 0.0 0.0 132-133 19.475 0.0 0.0 0.0 0.0 134-135 20.375 0.0 0.0 0.0 0.0 136-137 21.125 0.0 0.0 0.0 0.0 138-139 22.025 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content pass >>END_MODULE SRR12670161 read2 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR12670161_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 45 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 36.2905 37.0 37.0 37.0 37.0 37.0 2 36.1945 37.0 37.0 37.0 37.0 37.0 3 36.2335 37.0 37.0 37.0 37.0 37.0 4 36.252 37.0 37.0 37.0 37.0 37.0 5 36.2935 37.0 37.0 37.0 37.0 37.0 6 36.2065 37.0 37.0 37.0 37.0 37.0 7 36.2805 37.0 37.0 37.0 37.0 37.0 8 36.3675 37.0 37.0 37.0 37.0 37.0 9 36.2665 37.0 37.0 37.0 37.0 37.0 10-14 36.3599 37.0 37.0 37.0 37.0 37.0 15-19 36.3175 37.0 37.0 37.0 37.0 37.0 20-24 36.282399999999996 37.0 37.0 37.0 37.0 37.0 25-29 36.2918 37.0 37.0 37.0 37.0 37.0 30-34 36.220299999999995 37.0 37.0 37.0 37.0 37.0 35-39 36.1515 37.0 37.0 37.0 37.0 37.0 40-44 36.177499999999995 37.0 37.0 37.0 37.0 37.0 45-49 36.1899 37.0 37.0 37.0 37.0 37.0 50-54 36.1275 37.0 37.0 37.0 37.0 37.0 55-59 36.144800000000004 37.0 37.0 37.0 37.0 37.0 60-64 36.1001 37.0 37.0 37.0 37.0 37.0 65-69 36.1211 37.0 37.0 37.0 37.0 37.0 70-74 36.089 37.0 37.0 37.0 37.0 37.0 75-79 36.074400000000004 37.0 37.0 37.0 37.0 37.0 80-84 36.063100000000006 37.0 37.0 37.0 37.0 37.0 85-89 35.9544 37.0 37.0 37.0 37.0 37.0 90-94 35.957100000000004 37.0 37.0 37.0 37.0 37.0 95-99 35.882799999999996 37.0 37.0 37.0 37.0 37.0 100-104 35.8753 37.0 37.0 37.0 37.0 37.0 105-109 35.7543 37.0 37.0 37.0 37.0 37.0 110-114 35.834999999999994 37.0 37.0 37.0 37.0 37.0 115-119 35.759100000000004 37.0 37.0 37.0 37.0 37.0 120-124 35.6376 37.0 37.0 37.0 37.0 37.0 125-129 35.564499999999995 37.0 37.0 37.0 37.0 37.0 130-134 35.2919 37.0 37.0 37.0 34.6 37.0 135-139 35.092499999999994 37.0 37.0 37.0 27.4 37.0 140-144 34.869600000000005 37.0 37.0 37.0 25.0 37.0 145-149 34.4984 37.0 37.0 37.0 25.0 37.0 150-151 34.113749999999996 37.0 37.0 37.0 25.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 13 5.0 14 2.0 15 0.0 16 0.0 17 1.0 18 2.0 19 3.0 20 1.0 21 1.0 22 5.0 23 4.0 24 4.0 25 10.0 26 8.0 27 9.0 28 18.0 29 13.0 30 32.0 31 52.0 32 68.0 33 110.0 34 227.0 35 488.0 36 2618.0 37 319.0 >>END_MODULE >>Per base sequence content warn #Base G A T C 1 36.175000000000004 25.174999999999997 9.0 29.65 2 27.05 27.0 30.4 15.55 3 20.1 27.825 31.075000000000003 21.0 4 23.9 35.0 21.875 19.225 5 25.35 37.525 20.599999999999998 16.525000000000002 6 19.725 38.975 24.0 17.299999999999997 7 20.424999999999997 23.325000000000003 37.4 18.85 8 19.825 26.1 29.25 24.825 9 21.2 23.875 31.724999999999998 23.200000000000003 10-14 23.455000000000002 29.165000000000003 26.284999999999997 21.095 15-19 22.685 28.845 27.245 21.224999999999998 20-24 22.830000000000002 28.939999999999998 27.72 20.51 25-29 23.555 27.985 27.474999999999998 20.985 30-34 22.79 28.410000000000004 27.825 20.974999999999998 35-39 23.205000000000002 28.249999999999996 27.169999999999998 21.375 40-44 23.24 28.26 27.639999999999997 20.86 45-49 22.355 28.26 28.050000000000004 21.335 50-54 22.99 28.08 27.565 21.365000000000002 55-59 23.465 28.535 27.155 20.845 60-64 22.895 28.025 28.48 20.599999999999998 65-69 23.615 28.07 27.015 21.3 70-74 23.64 28.255000000000003 26.615 21.490000000000002 75-79 23.335 27.465 27.400000000000002 21.8 80-84 23.315 28.42 26.435 21.83 85-89 23.93 28.410000000000004 27.37 20.29 90-94 24.365000000000002 28.1 26.685 20.849999999999998 95-99 24.14 28.110000000000003 26.565 21.185000000000002 100-104 24.805 28.244999999999997 26.43 20.52 105-109 25.165 28.410000000000004 26.674999999999997 19.75 110-114 25.679999999999996 28.08 25.85 20.39 115-119 25.974999999999998 28.689999999999998 26.295 19.040000000000003 120-124 25.835 28.689999999999998 25.124999999999996 20.349999999999998 125-129 26.495 27.47 26.5 19.535 130-134 26.615 27.589999999999996 26.305 19.49 135-139 27.27 26.255 26.55 19.925 140-144 27.98 26.795 26.55 18.675 145-149 28.62 26.91 25.735000000000003 18.735 150-151 29.599999999999998 26.437500000000004 25.174999999999997 18.787499999999998 >>END_MODULE >>Per sequence GC content warn #GC Content Count 0 0.0 1 0.0 2 0.0 3 1.0 4 1.5 5 0.5 6 0.0 7 0.5 8 0.5 9 0.0 10 0.0 11 0.0 12 1.0 13 1.5 14 2.0 15 1.5 16 0.5 17 0.5 18 0.0 19 0.5 20 1.5 21 1.0 22 0.0 23 0.5 24 1.0 25 1.5 26 2.0 27 3.5 28 6.0 29 9.0 30 12.0 31 13.0 32 19.5 33 35.0 34 37.5 35 54.0 36 86.0 37 114.0 38 133.0 39 158.0 40 200.0 41 223.5 42 257.5 43 293.0 44 300.5 45 278.5 46 264.5 47 228.0 48 203.0 49 194.0 50 166.5 51 149.0 52 121.0 53 93.0 54 61.0 55 52.0 56 67.0 57 56.0 58 23.0 59 14.5 60 18.5 61 10.5 62 3.5 63 4.5 64 3.5 65 1.5 66 0.0 67 0.5 68 0.5 69 0.5 70 0.5 71 0.5 72 0.5 73 0.0 74 0.5 75 0.5 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 0.5 85 0.5 86 0.0 87 0.0 88 0.0 89 0.0 90 0.0 91 0.0 92 0.5 93 0.5 94 0.0 95 0.0 96 0.5 97 0.5 98 0.5 99 0.5 100 2.5 >>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 78.75 #Duplication Level Percentage of deduplicated Percentage of total 1 80.7936507936508 63.625 2 14.444444444444443 22.75 3 3.3333333333333335 7.875 4 0.7301587301587302 2.3 5 0.3492063492063492 1.375 6 0.12698412698412698 0.6 7 0.09523809523809523 0.525 8 0.031746031746031744 0.2 9 0.06349206349206349 0.44999999999999996 >10 0.031746031746031744 0.3 >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 AGAGAACACATTCATACTCCAAGTCTTTTAGTTCATCCATTTAAGCTTAA 12 0.3 No Hit AGAACACATTCATACTCCAAGTCTTTTAGTTCATCCATTTAAGCTTAATC 9 0.22499999999999998 No Hit ATTCATACTCCAAGTCTTTTAGTTCATCCATTTAAGCTTAATCAATCAAT 9 0.22499999999999998 No Hit GTCCATTGAAGGGAATTATTTCTCTACCCTTTTGTGCTCTAACTCAAATT 8 0.2 No Hit GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG 7 0.17500000000000002 No Hit AGTTGAAGCAGCTTCTCAACAGTTCAATGGCTATGAACTTGATGGGAGGC 7 0.17500000000000002 No Hit ACTCATCCGCCGTGTCGGTGCGGGTCGGAGACGACTCGCAGGTGGCCTTC 7 0.17500000000000002 No Hit GGAGCAACCTGCTTTTGACAAGAAGCAGTTTGTTACTTATATGAAGAGAT 6 0.15 No Hit CTTTAATCTTAGCAAACTGCCCCAAGATTTTTTTTTAATACCTCTTGTCT 6 0.15 No Hit GCCAGCAGCTGAGAACGATGGCAAGTGCAACTGCGGTACTGGCTGCACTT 6 0.15 No Hit AACACATTCATACTCCAAGTCTTTTAGTTCATCCATTTAAGCTTAATCAA 6 0.15 No Hit CAGGAGGCGAGCTGAGAACTTCAAAATGTCACTACCTAATCCGGTGATTG 5 0.125 No Hit AGTACACATTGCATTAACTAAATAACCCGTATTCAGAGATGAAACCATTC 5 0.125 No Hit AGCTGTGGCTCTATCAATGAATAAGGCCAGGAAGCTCGTTCATCCTAAAC 5 0.125 No Hit CACATTCATACTCCAAGTCTTTTAGTTCATCCATTTAAGCTTAATCAATC 5 0.125 No Hit GTTATTTATATGGGTAGCATATACTTTACGCGAGGAATTGTTACAATTAC 5 0.125 No Hit CCTTGAGTTTGTGGATTTGTCCTCGAATCTTATGACCGGACACATGCCGA 5 0.125 No Hit CAGAAACCAGCCTGTTTTCGCAGCCCCTGCTCCTATTCTCTATCCACCTC 5 0.125 No Hit GGACCTACGGGCCAAGGGACAGTCTCAGGTAGACAGTTTCTATGGGGCGT 5 0.125 No Hit AACCAATCAGCCTACTTGAAAAATCACCTCTGCTGAATCTGAAGAATGTA 5 0.125 No Hit TTTTGGAATAACTGCCAGAGTTTTCGATACTCTGAAATCTTGTGAGATAT 5 0.125 No Hit GGCAGCACTTCCTTGATGCAAGTGTTGCATACAAGCGAGCAGTGCTCAAT 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 0.0125 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 0.037500000000000006 0.0 0.0 0.0 0.0 48-49 0.0875 0.0 0.0 0.0 0.0 50-51 0.1 0.0 0.0 0.0 0.0 52-53 0.125 0.0 0.0 0.0 0.0 54-55 0.16249999999999998 0.0 0.0 0.0 0.0 56-57 0.175 0.0 0.0 0.0 0.0 58-59 0.175 0.0 0.0 0.0 0.0 60-61 0.2 0.0 0.0 0.0 0.0 62-63 0.225 0.0 0.0 0.0 0.0 64-65 0.2625 0.0 0.0 0.0 0.0 66-67 0.2875 0.0 0.0 0.0 0.0 68-69 0.3375 0.0 0.0 0.0 0.0 70-71 0.4125 0.0 0.0 0.0 0.0 72-73 0.4625 0.0 0.0 0.0 0.0 74-75 0.55 0.0 0.0 0.0 0.0 76-77 0.6875 0.0 0.0 0.0 0.0 78-79 0.8875 0.0 0.0 0.0 0.0 80-81 1.0625 0.0 0.0 0.0 0.0 82-83 1.2 0.0 0.0 0.0 0.0 84-85 1.7 0.0 0.0 0.0 0.0 86-87 2.1125 0.0 0.0 0.0 0.0 88-89 2.3875 0.0 0.0 0.0 0.0 90-91 2.7875 0.0 0.0 0.0 0.0 92-93 3.425 0.0 0.0 0.0 0.0 94-95 3.8875 0.0 0.0 0.0 0.0 96-97 4.45 0.0 0.0 0.0 0.0 98-99 5.1875 0.0 0.0 0.0 0.0 100-101 5.7875 0.0 0.0 0.0 0.0 102-103 6.6125 0.0 0.0 0.0 0.0 104-105 7.475 0.0 0.0 0.0 0.0 106-107 8.2375 0.0 0.0 0.0 0.0 108-109 8.8625 0.0 0.0 0.0 0.0 110-111 9.5875 0.0 0.0 0.0 0.0 112-113 10.4875 0.0 0.0 0.0 0.0 114-115 11.125 0.0 0.0 0.0 0.0 116-117 11.8875 0.0 0.0 0.0 0.0 118-119 13.212499999999999 0.0 0.0 0.0 0.0 120-121 14.2 0.0 0.0 0.0 0.0 122-123 15.1125 0.0 0.0 0.0 0.0 124-125 16.049999999999997 0.0 0.0 0.0 0.0 126-127 16.887500000000003 0.0 0.0 0.0 0.0 128-129 17.625 0.0 0.0 0.0 0.0 130-131 18.675 0.0 0.0 0.0 0.0 132-133 19.65 0.0 0.0 0.0 0.0 134-135 20.5875 0.0 0.0 0.0 0.0 136-137 21.375 0.0 0.0 0.0 0.0 138-139 22.275 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content pass >>END_MODULE Read 595657 spots for SRR12670161.sra Written 595657 spots for SRR12670161.sra Read 595657 spots for SRR12670161.sra Written 595657 spots for SRR12670161.sra Read 595657 spots for SRR12670161.sra Written 595657 spots for SRR12670161.sra Read 595657 spots for SRR12670161.sra Written 595657 spots for SRR12670161.sra Read 595657 spots for SRR12670161.sra Written 595657 spots for SRR12670161.sra Read 595657 spots for SRR12670161.sra Written 595657 spots for SRR12670161.sra Read 595657 spots for SRR12670161.sra Written 595657 spots for SRR12670161.sra Read 595657 spots for SRR12670161.sra Written 595657 spots for SRR12670161.sra Read 595657 spots for SRR12670161.sra Written 595657 spots for SRR12670161.sra Read 595657 spots for SRR12670161.sra Written 595657 spots for SRR12670161.sra Read 595657 spots for SRR12670161.sra Written 595657 spots for SRR12670161.sra Read 595657 spots for SRR12670161.sra Written 595657 spots for SRR12670161.sra Read 595657 spots for SRR12670161.sra Written 595657 spots for SRR12670161.sra Read 595672 spots for SRR12670161.sra Written 595672 spots for SRR12670161.sra Read 595657 spots for SRR12670161.sra Written 595657 spots for SRR12670161.sra Read 595657 spots for SRR12670161.sra Written 595657 spots for SRR12670161.sra Read 595657 spots for SRR12670161.sra Written 595657 spots for SRR12670161.sra Read 595657 spots for SRR12670161.sra Written 595657 spots for SRR12670161.sra Read 595657 spots for SRR12670161.sra Written 595657 spots for SRR12670161.sra Read 595657 spots for SRR12670161.sra Written 595657 spots for SRR12670161.sra SRR ids: ['SRR12670161.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_fw1l5jsq SRR12670161.sra spots: 11913155 blocks: [[1, 595657], [595658, 1191314], [1191315, 1786971], [1786972, 2382628], [2382629, 2978285], [2978286, 3573942], [3573943, 4169599], [4169600, 4765256], [4765257, 5360913], [5360914, 5956570], [5956571, 6552227], [6552228, 7147884], [7147885, 7743541], [7743542, 8339198], [8339199, 8934855], [8934856, 9530512], [9530513, 10126169], [10126170, 10721826], [10721827, 11317483], [11317484, 11913155]] SRR12670161 file size 4026910 SRR12670161 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 SRR12670161 SRR12670161_1.fastq SRR12670161_2.fastq Input file: SRR12670161_1.fastq Paired file: SRR12670161_2.fastq trimmed: SRR12670161-trimmed-pair1.fastq, SRR12670161-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 Tue Feb 11 07:35:59 2025 >> started Tue Feb 11 07:36:13 2025 >> done (14.499s) 11913155 read pairs processed; of these: 71 ( 0.00%) short read pairs filtered out after trimming by size control 5322 ( 0.04%) empty read pairs filtered out after trimming by size control 11907762 (99.95%) read pairs available; of these: 3172789 (26.64%) trimmed read pairs available after processing 8734973 (73.36%) untrimmed read pairs available after processing Length distribution of reads after trimming: length count percentage 18 4 0.00% 19 6 0.00% 20 4 0.00% 21 12 0.00% 22 23 0.00% 23 29 0.00% 24 20 0.00% 25 27 0.00% 26 49 0.00% 27 47 0.00% 28 49 0.00% 29 44 0.00% 30 73 0.00% 31 54 0.00% 32 91 0.00% 33 88 0.00% 34 99 0.00% 35 85 0.00% 36 126 0.00% 37 139 0.00% 38 132 0.00% 39 169 0.00% 40 130 0.00% 41 152 0.00% 42 183 0.00% 43 184 0.00% 44 195 0.00% 45 211 0.00% 46 236 0.00% 47 313 0.00% 48 305 0.00% 49 410 0.00% 50 464 0.00% 51 525 0.00% 52 552 0.00% 53 596 0.01% 54 607 0.01% 55 664 0.01% 56 740 0.01% 57 901 0.01% 58 985 0.01% 59 1183 0.01% 60 1373 0.01% 61 1632 0.01% 62 1758 0.01% 63 2060 0.02% 64 2204 0.02% 65 2340 0.02% 66 2491 0.02% 67 2883 0.02% 68 3145 0.03% 69 3720 0.03% 70 4252 0.04% 71 4846 0.04% 72 5551 0.05% 73 6263 0.05% 74 6786 0.06% 75 7487 0.06% 76 8018 0.07% 77 8517 0.07% 78 9427 0.08% 79 10424 0.09% 80 11447 0.10% 81 12701 0.11% 82 14149 0.12% 83 15604 0.13% 84 17344 0.15% 85 18368 0.15% 86 19541 0.16% 87 20702 0.17% 88 21976 0.18% 89 22369 0.19% 90 24261 0.20% 91 25754 0.22% 92 26927 0.23% 93 29023 0.24% 94 30870 0.26% 95 32460 0.27% 96 34352 0.29% 97 35580 0.30% 98 35999 0.30% 99 36524 0.31% 100 37979 0.32% 101 38277 0.32% 102 39746 0.33% 103 41008 0.34% 104 42689 0.36% 105 43919 0.37% 106 44791 0.38% 107 45204 0.38% 108 46389 0.39% 109 45975 0.39% 110 46066 0.39% 111 46573 0.39% 112 47847 0.40% 113 47966 0.40% 114 49335 0.41% 115 50156 0.42% 116 51266 0.43% 117 51918 0.44% 118 52466 0.44% 119 51916 0.44% 120 52677 0.44% 121 52352 0.44% 122 52939 0.44% 123 52660 0.44% 124 53132 0.45% 125 53158 0.45% 126 54487 0.46% 127 53991 0.45% 128 53795 0.45% 129 53249 0.45% 130 54002 0.45% 131 52689 0.44% 132 52711 0.44% 133 52839 0.44% 134 52854 0.44% 135 53321 0.45% 136 53253 0.45% 137 53336 0.45% 138 54081 0.45% 139 54798 0.46% 140 53946 0.45% 141 54443 0.46% 142 53661 0.45% 143 53466 0.45% 144 53719 0.45% 145 53895 0.45% 146 53501 0.45% 147 53428 0.45% 148 55091 0.46% 149 52698 0.44% 150 55097 0.46% 151 8734973 73.36% 11907762 reads passed initial QC criterion=sequence-density sequence-density=0.80 sequence-density-rank=1 fanout-score=2.00 fanout-score-rank=35 prefix-density=0.76 prefix-fanout=2.0 sequence=GTCTCGACGATGCCAGCAGTGTAGCTGCTTCCCTTCTTGACACACTGGGTCTTGTCAGCGCAGTCGCAGGTGTCGCAGGTGCTAGACATGATGATTGATTGATTAAGCTTAAATGGATGAACTAAAAGACTTGGAGTATGAATGTGTTCTCTGTGTAG criterion=fanout-score sequence-density=0.13 sequence-density-rank=14 fanout-score=26.92 fanout-score-rank=1 prefix-density=0.34 prefix-fanout=10.1 sequence=TTCTTTCCAATGCT criterion=sequence-density sequence-density=0.50 sequence-density-rank=1 fanout-score=2.93 fanout-score-rank=23 prefix-density=0.57 prefix-fanout=2.6 sequence=GAGAAGAACTATGTCTCCTCCGTAGTCATGGAGGTGCCAGCAGCTGAGAACGATGGCAAGTGCAACTGCGGTACTGGCTGCACTTGCACTACCTGCACATGCGGTCATTAAGCAAGCACATCAACTATCATGTTTGATGTGGGATTGGGAGTGGATTAATAATGTAATTTCTGATAAATAATCTGTGTTCTTCTGTACTTGTGGGTGTGGAGTGAACAAACAAAAGTGTCCGTGAGTGTCTTTATCTTTGTGTCTTCTTCATTGTTATGTATTGGCCATGTCTGTGGCCTCTGGTGTGGT criterion=fanout-score sequence-density=0.10 sequence-density-rank=28 fanout-score=42.99 fanout-score-rank=1 prefix-density=0.32 prefix-fanout=13.4 sequence=AAAGAAAAGAAAA SRR12670161 testing PE reads STAR mapping to Ensembl genome Started job on | Feb 11 07:36:55 Started mapping on | Feb 11 07:36:56 Finished on | Feb 11 07:38:22 Mapping speed, Million of reads per hour | 498.46 Number of input reads | 11907762 Average input read length | 284 UNIQUE READS: Uniquely mapped reads number | 11227747 Uniquely mapped reads % | 94.29% Average mapped length | 283.65 Number of splices: Total | 10974395 Number of splices: Annotated (sjdb) | 10716029 Number of splices: GT/AG | 10752712 Number of splices: GC/AG | 172389 Number of splices: AT/AC | 6245 Number of splices: Non-canonical | 43049 Mismatch rate per base, % | 0.35% Deletion rate per base | 0.03% Deletion average length | 2.88 Insertion rate per base | 0.02% Insertion average length | 2.42 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 273226 % of reads mapped to multiple loci | 2.29% Number of reads mapped to too many loci | 21701 % of reads mapped to too many loci | 0.18% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 3.14% % of reads unmapped: other | 0.10% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 406789 406789 406789 N_multimapping 273226 273226 273226 N_noFeature 375919 11030661 455428 N_ambiguous 185233 656 67282 UnstrandedReadsAssigned:10666595 PositiveStrandReadsAssigned:196430 NegativeStrandReadsAssigned:10705037 Dataset is classified negative stranded MeadianReadLen=151 20thPercentileLength=136 echo kmer=131 SRR12670161 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: SRR12670161-trimmed-pair1.fastq SRR12670161-trimmed-pair2.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 11,907,762 reads, 10,672,933 reads pseudoaligned [quant] estimated average fragment length: 210.499 [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,121 rounds 52401 SRR12670161.ke.tsv 34699 SRR12670161.se.tsv 87100 total ==> SRR12670161.ke.tsv <== target_id length eff_length est_counts tpm Potri.005G200100.1.v4.1 2018 1808.5 601 28.4085 Potri.005G024800.1.v4.1 1035 825.501 115 11.9089 Potri.004G059700.1.v4.1 961 751.593 1 0.113739 Potri.007G009000.2.v4.1 1416 1206.5 0 0 Potri.003G141000.2.v4.1 2943 2733.5 835.056 26.1149 Potri.016G087400.1.v4.1 270 109.094 514 402.769 Potri.015G069301.1.v4.1 564 362.921 0 0 Potri.010G195200.1.v4.1 1773 1563.5 134 7.32653 Potri.012G127500.1.v4.1 977 767.537 58 6.45982 ==> SRR12670161.se.tsv <== Potri.001G166300.v4.1 0 Potri.001G448400.v4.1 55 Potri.001G233950.v4.1 0 Potri.001G122700.v4.1 134 Potri.001G212900.v4.1 12 Potri.001G182400.v4.1 1 Potri.001G256600.v4.1 0 Potri.001G040500.v4.1 4 Potri.001G416900.v4.1 0 Potri.001G452600.v4.1 11 SRR12670161 completed mapping pipeline successfully