Starting /dee2/code/volunteer_pipeline.sh SRR12671375 current disk space = 3052994764800 free memory = 1395403980 SRR12671375 SRAfilesize 9e7c2639a3cd07e17b05dca1dae8acd1 SRR12671375.sra SRR12671375.sra file validated SRR12671375 is paired end SRR12671375 is conventional basespace SRR12671375 read1 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR12671375_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 36.6275 37.0 37.0 37.0 37.0 37.0 2 36.41725 37.0 37.0 37.0 37.0 37.0 3 36.576 37.0 37.0 37.0 37.0 37.0 4 36.6635 37.0 37.0 37.0 37.0 37.0 5 36.563 37.0 37.0 37.0 37.0 37.0 6 36.618 37.0 37.0 37.0 37.0 37.0 7 36.4885 37.0 37.0 37.0 37.0 37.0 8 36.601 37.0 37.0 37.0 37.0 37.0 9 36.6795 37.0 37.0 37.0 37.0 37.0 10-14 36.5847 37.0 37.0 37.0 37.0 37.0 15-19 36.597 37.0 37.0 37.0 37.0 37.0 20-24 36.6005 37.0 37.0 37.0 37.0 37.0 25-29 36.5689 37.0 37.0 37.0 37.0 37.0 30-34 36.5226 37.0 37.0 37.0 37.0 37.0 35-39 36.5229 37.0 37.0 37.0 37.0 37.0 40-44 36.5262 37.0 37.0 37.0 37.0 37.0 45-49 36.450599999999994 37.0 37.0 37.0 37.0 37.0 50-54 36.4762 37.0 37.0 37.0 37.0 37.0 55-59 36.4754 37.0 37.0 37.0 37.0 37.0 60-64 36.4227 37.0 37.0 37.0 37.0 37.0 65-69 36.3868 37.0 37.0 37.0 37.0 37.0 70-74 36.3718 37.0 37.0 37.0 37.0 37.0 75-79 36.3699 37.0 37.0 37.0 37.0 37.0 80-84 36.3437 37.0 37.0 37.0 37.0 37.0 85-89 36.248400000000004 37.0 37.0 37.0 37.0 37.0 90-94 36.1971 37.0 37.0 37.0 37.0 37.0 95-99 36.22539999999999 37.0 37.0 37.0 37.0 37.0 100-104 36.2017 37.0 37.0 37.0 37.0 37.0 105-109 36.2315 37.0 37.0 37.0 37.0 37.0 110-114 36.1784 37.0 37.0 37.0 37.0 37.0 115-119 36.137 37.0 37.0 37.0 37.0 37.0 120-124 36.134299999999996 37.0 37.0 37.0 37.0 37.0 125-129 36.121 37.0 37.0 37.0 37.0 37.0 130-134 36.0713 37.0 37.0 37.0 37.0 37.0 135-139 36.052499999999995 37.0 37.0 37.0 37.0 37.0 140-144 35.9831 37.0 37.0 37.0 37.0 37.0 145-149 35.9919 37.0 37.0 37.0 37.0 37.0 150-151 35.889250000000004 37.0 37.0 37.0 37.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 21 1.0 22 0.0 23 1.0 24 0.0 25 3.0 26 4.0 27 12.0 28 9.0 29 12.0 30 17.0 31 24.0 32 44.0 33 68.0 34 101.0 35 305.0 36 2978.0 37 421.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 38.4 10.45 6.65 44.5 2 17.02127659574468 12.315394242803505 40.65081351689612 30.01251564455569 3 17.2 17.224999999999998 27.05 38.525 4 22.125 25.575 22.6 29.7 5 24.224999999999998 33.25 24.349999999999998 18.175 6 18.575 32.875 25.624999999999996 22.925 7 14.274999999999999 25.0 44.2 16.525000000000002 8 16.150000000000002 24.825 34.949999999999996 24.075 9 15.975 21.925 36.425000000000004 25.674999999999997 10-14 19.625 30.19 27.765 22.42 15-19 19.295 28.18 28.660000000000004 23.865 20-24 19.8 27.98 28.425 23.794999999999998 25-29 19.005 29.015 27.794999999999998 24.185000000000002 30-34 19.625 28.134999999999998 27.495000000000005 24.745 35-39 19.225 28.26 28.294999999999998 24.22 40-44 20.03 28.275 27.744999999999997 23.95 45-49 19.939999999999998 28.27 28.125 23.665 50-54 19.89 29.25 27.165 23.695 55-59 19.52 28.12 28.01 24.349999999999998 60-64 18.985 29.110000000000003 27.689999999999998 24.215 65-69 19.71 28.449999999999996 28.22 23.62 70-74 19.935 28.67 27.439999999999998 23.955000000000002 75-79 19.935 28.335 27.935 23.794999999999998 80-84 19.59 28.615000000000002 27.91 23.885 85-89 19.765 28.499999999999996 28.12 23.615 90-94 19.725 28.655 27.400000000000002 24.22 95-99 20.68 27.975 28.115000000000002 23.23 100-104 20.119999999999997 29.39 26.915 23.575 105-109 20.32 28.215 27.54 23.925 110-114 20.155 27.765 28.565 23.515 115-119 20.02 27.555000000000003 28.82 23.605 120-124 20.715 27.165 28.62 23.5 125-129 20.695 27.35 28.025 23.93 130-134 20.09 28.22 27.79 23.9 135-139 20.51 28.48 27.034999999999997 23.974999999999998 140-144 20.915 28.199999999999996 27.650000000000002 23.235 145-149 20.64 28.71 26.68 23.97 150-151 20.2625 28.1375 27.125 24.474999999999998 >>END_MODULE >>Per sequence GC content warn #GC Content Count 0 0.0 1 0.5 2 0.5 3 0.0 4 0.0 5 0.0 6 0.0 7 0.0 8 0.0 9 0.5 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 2.0 21 3.5 22 4.0 23 3.0 24 0.5 25 3.5 26 11.0 27 13.5 28 13.5 29 14.0 30 23.0 31 32.0 32 30.0 33 39.5 34 56.0 35 63.0 36 82.0 37 106.0 38 130.0 39 163.0 40 181.5 41 201.0 42 237.5 43 257.0 44 249.0 45 275.0 46 286.5 47 262.5 48 238.0 49 202.5 50 179.0 51 152.0 52 121.0 53 88.5 54 68.5 55 57.5 56 39.0 57 30.0 58 25.0 59 13.5 60 11.0 61 10.5 62 6.0 63 4.5 64 3.0 65 2.0 66 0.5 67 0.0 68 0.5 69 1.0 70 0.5 71 0.0 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 82.6 #Duplication Level Percentage of deduplicated Percentage of total 1 83.20217917675545 68.72500000000001 2 13.58958837772397 22.45 3 2.4213075060532687 6.0 4 0.6053268765133172 2.0 5 0.12106537530266344 0.5 6 0.03026634382566586 0.15 7 0.03026634382566586 0.17500000000000002 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 CTCATGTTTTTATTTTTTTAAAATACACTTGCGATAGCTAAACAAGAATA 7 0.17500000000000002 No Hit TAGCGTTCTATGCAAATGGATGGTGGCAGATTGTTCACAGTGAACACTGA 6 0.15 No Hit GGTAGACACCATCCTTGGGATGCAAGTACTGAACCTCTCCATTGGGGAAC 5 0.125 No Hit GCCATCCGTAGATTATAGTGTGGTATCCTCGATGAAACATGATGGGGTAT 5 0.125 No Hit GGTTGCTTCAACCTCGGATTGCCCACCAGACAAAAACATGATTCCAGGGA 5 0.125 No Hit TGCTATCATATCTGTATCCCTTGAGATTATTATCCCAATCAGTCAGCGAA 5 0.125 No Hit >>END_MODULE >>Adapter Content pass #Position Illumina Universal Adapter Illumina Small RNA 3' Adapter Illumina Small RNA 5' Adapter Nextera Transposase Sequence SOLID Small RNA Adapter 1 0.0 0.0 0.0 0.0 0.0 2 0.0 0.0 0.0 0.0 0.0 3 0.0 0.0 0.0 0.0 0.0 4 0.0 0.0 0.0 0.0 0.0 5 0.0 0.0 0.0 0.0 0.0 6 0.0 0.0 0.0 0.0 0.0 7 0.0 0.0 0.0 0.0 0.0 8 0.0 0.0 0.0 0.0 0.0 9 0.0 0.0 0.0 0.0 0.0 10-11 0.0 0.0 0.0 0.0 0.0 12-13 0.0 0.0 0.0 0.0 0.0 14-15 0.0 0.0 0.0 0.0 0.0 16-17 0.0 0.0 0.0 0.0 0.0 18-19 0.0 0.0 0.0 0.0 0.0 20-21 0.0 0.0 0.0 0.0 0.0 22-23 0.0 0.0 0.0 0.0 0.0 24-25 0.0 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 0.0 0.0 0.0 0.0 0.0 76-77 0.0 0.0 0.0 0.0 0.0 78-79 0.0 0.0 0.0 0.0 0.0 80-81 0.0 0.0 0.0 0.0 0.0 82-83 0.0 0.0 0.0 0.0 0.0 84-85 0.0 0.0 0.0 0.0 0.0 86-87 0.0125 0.0 0.0 0.0 0.0 88-89 0.075 0.0 0.0 0.0 0.0 90-91 0.0875 0.0 0.0 0.0 0.0 92-93 0.1 0.0 0.0 0.0 0.0 94-95 0.1375 0.0 0.0 0.0 0.0 96-97 0.15 0.0 0.0 0.0 0.0 98-99 0.175 0.0 0.0 0.0 0.0 100-101 0.2375 0.0 0.0 0.0 0.0 102-103 0.3375 0.0 0.0 0.0 0.0 104-105 0.4125 0.0 0.0 0.0 0.0 106-107 0.4625 0.0 0.0 0.0 0.0 108-109 0.5875 0.0 0.0 0.0 0.0 110-111 0.7 0.0 0.0 0.0 0.0 112-113 0.7375 0.0 0.0 0.0 0.0 114-115 0.8125 0.0 0.0 0.0 0.0 116-117 0.9 0.0 0.0 0.0 0.0 118-119 0.9624999999999999 0.0 0.0 0.0 0.0 120-121 1.05 0.0 0.0 0.0 0.0 122-123 1.125 0.0 0.0 0.0 0.0 124-125 1.275 0.0 0.0 0.0 0.0 126-127 1.35 0.0 0.0 0.0 0.0 128-129 1.4500000000000002 0.0 0.0 0.0 0.0 130-131 1.6875 0.0 0.0 0.0 0.0 132-133 1.85 0.0 0.0 0.0 0.0 134-135 2.0625 0.0 0.0 0.0 0.0 136-137 2.2875 0.0 0.0 0.0 0.0 138-139 2.45 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content pass >>END_MODULE SRR12671375 read2 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR12671375_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 36.2735 37.0 37.0 37.0 37.0 37.0 2 35.9945 37.0 37.0 37.0 37.0 37.0 3 36.147 37.0 37.0 37.0 37.0 37.0 4 36.238 37.0 37.0 37.0 37.0 37.0 5 36.25 37.0 37.0 37.0 37.0 37.0 6 36.0715 37.0 37.0 37.0 37.0 37.0 7 36.1925 37.0 37.0 37.0 37.0 37.0 8 36.2555 37.0 37.0 37.0 37.0 37.0 9 36.268 37.0 37.0 37.0 37.0 37.0 10-14 36.2434 37.0 37.0 37.0 37.0 37.0 15-19 36.2387 37.0 37.0 37.0 37.0 37.0 20-24 36.199 37.0 37.0 37.0 37.0 37.0 25-29 36.1502 37.0 37.0 37.0 37.0 37.0 30-34 36.0861 37.0 37.0 37.0 37.0 37.0 35-39 36.1343 37.0 37.0 37.0 37.0 37.0 40-44 36.0937 37.0 37.0 37.0 37.0 37.0 45-49 36.0971 37.0 37.0 37.0 37.0 37.0 50-54 36.0291 37.0 37.0 37.0 37.0 37.0 55-59 36.0085 37.0 37.0 37.0 37.0 37.0 60-64 35.921 37.0 37.0 37.0 37.0 37.0 65-69 35.931200000000004 37.0 37.0 37.0 37.0 37.0 70-74 35.9189 37.0 37.0 37.0 37.0 37.0 75-79 35.9068 37.0 37.0 37.0 37.0 37.0 80-84 35.843900000000005 37.0 37.0 37.0 37.0 37.0 85-89 35.8947 37.0 37.0 37.0 37.0 37.0 90-94 35.8493 37.0 37.0 37.0 37.0 37.0 95-99 35.79600000000001 37.0 37.0 37.0 37.0 37.0 100-104 35.791700000000006 37.0 37.0 37.0 37.0 37.0 105-109 35.6873 37.0 37.0 37.0 37.0 37.0 110-114 35.6673 37.0 37.0 37.0 37.0 37.0 115-119 35.774 37.0 37.0 37.0 37.0 37.0 120-124 35.675000000000004 37.0 37.0 37.0 37.0 37.0 125-129 35.6971 37.0 37.0 37.0 37.0 37.0 130-134 35.5902 37.0 37.0 37.0 37.0 37.0 135-139 35.5394 37.0 37.0 37.0 37.0 37.0 140-144 35.5373 37.0 37.0 37.0 37.0 37.0 145-149 35.4452 37.0 37.0 37.0 37.0 37.0 150-151 35.125249999999994 37.0 37.0 37.0 31.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 13 2.0 14 4.0 15 2.0 16 0.0 17 0.0 18 2.0 19 1.0 20 1.0 21 2.0 22 1.0 23 1.0 24 4.0 25 4.0 26 7.0 27 14.0 28 14.0 29 19.0 30 30.0 31 40.0 32 73.0 33 100.0 34 198.0 35 616.0 36 2641.0 37 224.0 >>END_MODULE >>Per base sequence content warn #Base G A T C 1 36.825 20.925 11.700000000000001 30.55 2 23.75 27.325 33.85 15.075 3 19.425 28.825 32.574999999999996 19.175 4 23.674999999999997 33.925 22.225 20.175 5 24.45 37.1 22.025 16.425 6 17.9 41.099999999999994 23.425 17.575 7 20.05 21.5 38.975 19.475 8 19.425 24.9 30.025000000000002 25.650000000000002 9 20.9 24.3 31.474999999999998 23.325000000000003 10-14 22.11 29.720000000000002 26.895000000000003 21.275 15-19 22.63 27.229999999999997 28.265 21.875 20-24 22.3 28.78 28.02 20.9 25-29 21.895 28.505000000000003 27.939999999999998 21.66 30-34 21.92 28.444999999999997 28.23 21.404999999999998 35-39 22.005 28.03 28.57 21.395 40-44 21.765 28.439999999999998 27.994999999999997 21.8 45-49 21.945 28.415000000000003 27.965 21.675 50-54 22.689999999999998 27.82 27.815 21.675 55-59 22.16 28.155 28.360000000000003 21.325 60-64 22.31 27.365000000000002 28.4 21.925 65-69 22.535 27.810000000000002 28.189999999999998 21.465 70-74 23.06 28.535 26.86 21.545 75-79 22.785 27.750000000000004 27.57 21.895 80-84 22.765 28.305000000000003 27.35 21.58 85-89 22.91 28.095 27.189999999999998 21.805 90-94 22.85 28.175 27.145000000000003 21.83 95-99 23.06 28.125 27.705000000000002 21.11 100-104 23.1 27.694999999999997 27.92 21.285 105-109 22.645 27.884999999999998 28.285 21.185000000000002 110-114 23.305 28.21 27.084999999999997 21.4 115-119 23.549999999999997 27.98 28.1 20.369999999999997 120-124 24.3 28.060000000000002 27.42 20.22 125-129 22.775000000000002 28.365000000000002 27.810000000000002 21.05 130-134 23.724999999999998 28.23 27.544999999999998 20.5 135-139 23.97 27.76 28.050000000000004 20.22 140-144 23.9 27.85 28.04 20.21 145-149 24.127412741274128 27.727772777277725 27.16271627162716 20.982098209820983 150-151 24.525 27.5625 28.65 19.2625 >>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 0.5 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 0.5 16 1.0 17 0.5 18 0.0 19 0.0 20 0.0 21 0.5 22 0.5 23 0.5 24 1.0 25 1.5 26 4.0 27 10.5 28 11.0 29 10.5 30 18.0 31 24.5 32 28.0 33 39.0 34 56.5 35 79.5 36 101.0 37 109.5 38 142.0 39 172.5 40 185.0 41 225.5 42 254.5 43 277.0 44 288.5 45 266.0 46 251.0 47 239.5 48 220.0 49 208.5 50 174.5 51 127.5 52 96.0 53 76.5 54 79.5 55 65.0 56 35.5 57 26.0 58 22.5 59 20.0 60 15.0 61 5.5 62 3.5 63 6.5 64 5.5 65 1.0 66 1.0 67 2.0 68 1.0 69 0.5 70 0.5 71 0.0 72 0.0 73 0.5 74 0.5 75 0.5 76 0.5 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 0.5 86 0.5 87 0.0 88 0.0 89 0.0 90 0.0 91 0.0 92 0.0 93 0.5 94 1.0 95 0.5 96 0.0 97 0.0 98 0.0 99 0.0 100 0.5 >>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 0.01 150-151 0.0 >>END_MODULE >>Sequence Length Distribution pass #Length Count 151 4000.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 82.69999999999999 #Duplication Level Percentage of deduplicated Percentage of total 1 83.61547762998791 69.15 2 12.968561064087062 21.45 3 2.5090689238210397 6.225 4 0.7557436517533254 2.5 5 0.09068923821039904 0.375 6 0.06045949214026602 0.3 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 GGAAAAAACAGCTACAAAAGAGGCTCCAGTGGGATTTACTCCACCGGAGT 6 0.15 No Hit AACAGCAGTAGCAGCATCAGCTTCATTGTGTTCATCAACGCAAATCAATG 6 0.15 No Hit CTCTGCATTTGCTAGCTAGAAGTCACTCTACCCTTCGCATTACTTCCTCA 5 0.125 No Hit GTGCAAGGTAAAAGAAGGAGCGTGCAGCGACCTCGTCAACTACCTGCGGC 5 0.125 No Hit ATTCATACTCCAAGTCTTTTAGTTCATCCATTTAAGCTTAATCAATCAAT 5 0.125 No Hit >>END_MODULE >>Adapter Content pass #Position Illumina Universal Adapter Illumina Small RNA 3' Adapter Illumina Small RNA 5' Adapter Nextera Transposase Sequence SOLID Small RNA Adapter 1 0.0 0.0 0.0 0.0 0.0 2 0.0 0.0 0.0 0.0 0.0 3 0.0 0.0 0.0 0.0 0.0 4 0.0 0.0 0.0 0.0 0.0 5 0.0 0.0 0.0 0.0 0.0 6 0.0 0.0 0.0 0.0 0.0 7 0.0 0.0 0.0 0.0 0.0 8 0.0 0.0 0.0 0.0 0.0 9 0.0 0.0 0.0 0.0 0.0 10-11 0.0 0.0 0.0 0.0 0.0 12-13 0.0 0.0 0.0 0.0 0.0 14-15 0.0 0.0 0.0 0.0 0.0 16-17 0.0 0.0 0.0 0.0 0.0 18-19 0.0 0.0 0.0 0.0 0.0 20-21 0.0 0.0 0.0 0.0 0.0 22-23 0.0 0.0 0.0 0.0 0.0 24-25 0.0 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 0.0 0.0 0.0 0.0 0.0 76-77 0.0 0.0 0.0 0.0 0.0 78-79 0.0 0.0 0.0 0.0 0.0 80-81 0.0 0.0 0.0 0.0 0.0 82-83 0.0 0.0 0.0 0.0 0.0 84-85 0.0 0.0 0.0 0.0 0.0 86-87 0.0125 0.0 0.0 0.0 0.0 88-89 0.075 0.0 0.0 0.0 0.0 90-91 0.0875 0.0 0.0 0.0 0.0 92-93 0.1 0.0 0.0 0.0 0.0 94-95 0.1375 0.0 0.0 0.0 0.0 96-97 0.15 0.0 0.0 0.0 0.0 98-99 0.175 0.0 0.0 0.0 0.0 100-101 0.2375 0.0 0.0 0.0 0.0 102-103 0.3375 0.0 0.0 0.0 0.0 104-105 0.4125 0.0 0.0 0.0 0.0 106-107 0.4625 0.0 0.0 0.0 0.0 108-109 0.5875 0.0 0.0 0.0 0.0 110-111 0.7 0.0 0.0 0.0 0.0 112-113 0.7375 0.0 0.0 0.0 0.0 114-115 0.8125 0.0 0.0 0.0 0.0 116-117 0.9 0.0 0.0 0.0 0.0 118-119 0.9624999999999999 0.0 0.0 0.0 0.0 120-121 1.05 0.0 0.0 0.0 0.0 122-123 1.1125 0.0 0.0 0.0 0.0 124-125 1.25 0.0 0.0 0.0 0.0 126-127 1.325 0.0 0.0 0.0 0.0 128-129 1.4249999999999998 0.0 0.0 0.0 0.0 130-131 1.6625 0.0 0.0 0.0 0.0 132-133 1.825 0.0 0.0 0.0 0.0 134-135 2.0625 0.0 0.0 0.0 0.0 136-137 2.2875 0.0 0.0 0.0 0.0 138-139 2.4625 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position TTTTTTT 25 4.977651E-4 29.0 70-74 >>END_MODULE Read 856157 spots for SRR12671375.sra Written 856157 spots for SRR12671375.sra Read 856157 spots for SRR12671375.sra Written 856157 spots for SRR12671375.sra Read 856157 spots for SRR12671375.sra Written 856157 spots for SRR12671375.sra Read 856157 spots for SRR12671375.sra Written 856157 spots for SRR12671375.sra Read 856157 spots for SRR12671375.sra Written 856157 spots for SRR12671375.sra Read 856157 spots for SRR12671375.sra Written 856157 spots for SRR12671375.sra Read 856157 spots for SRR12671375.sra Written 856157 spots for SRR12671375.sra Read 856157 spots for SRR12671375.sra Written 856157 spots for SRR12671375.sra Read 856157 spots for SRR12671375.sra Written 856157 spots for SRR12671375.sra Read 856157 spots for SRR12671375.sra Written 856157 spots for SRR12671375.sra Read 856157 spots for SRR12671375.sra Written 856157 spots for SRR12671375.sra Read 856157 spots for SRR12671375.sra Written 856157 spots for SRR12671375.sra Read 856157 spots for SRR12671375.sra Written 856157 spots for SRR12671375.sra Read 856157 spots for SRR12671375.sra Written 856157 spots for SRR12671375.sra Read 856157 spots for SRR12671375.sra Written 856157 spots for SRR12671375.sra Read 856157 spots for SRR12671375.sra Written 856157 spots for SRR12671375.sra Read 856157 spots for SRR12671375.sra Written 856157 spots for SRR12671375.sra Read 856158 spots for SRR12671375.sra Written 856158 spots for SRR12671375.sra Read 856157 spots for SRR12671375.sra Written 856157 spots for SRR12671375.sra Read 856157 spots for SRR12671375.sra Written 856157 spots for SRR12671375.sra SRR ids: ['SRR12671375.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_iyde78gd SRR12671375.sra spots: 17123141 blocks: [[1, 856157], [856158, 1712314], [1712315, 2568471], [2568472, 3424628], [3424629, 4280785], [4280786, 5136942], [5136943, 5993099], [5993100, 6849256], [6849257, 7705413], [7705414, 8561570], [8561571, 9417727], [9417728, 10273884], [10273885, 11130041], [11130042, 11986198], [11986199, 12842355], [12842356, 13698512], [13698513, 14554669], [14554670, 15410826], [15410827, 16266983], [16266984, 17123141]] SRR12671375 file size 5797492 SRR12671375 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 SRR12671375 SRR12671375_1.fastq SRR12671375_2.fastq Input file: SRR12671375_1.fastq Paired file: SRR12671375_2.fastq trimmed: SRR12671375-trimmed-pair1.fastq, SRR12671375-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 20:28:40 2025 >> started Tue Feb 11 20:28:58 2025 >> done (18.351s) 17123141 read pairs processed; of these: 109 ( 0.00%) short read pairs filtered out after trimming by size control 2132 ( 0.01%) empty read pairs filtered out after trimming by size control 17120900 (99.99%) read pairs available; of these: 543429 ( 3.17%) trimmed read pairs available after processing 16577471 (96.83%) untrimmed read pairs available after processing Length distribution of reads after trimming: length count percentage 18 8 0.00% 19 10 0.00% 20 7 0.00% 21 5 0.00% 22 11 0.00% 23 15 0.00% 24 15 0.00% 25 7 0.00% 26 10 0.00% 27 13 0.00% 28 8 0.00% 29 13 0.00% 30 18 0.00% 31 16 0.00% 32 12 0.00% 33 12 0.00% 34 13 0.00% 35 13 0.00% 36 16 0.00% 37 15 0.00% 38 17 0.00% 39 12 0.00% 40 25 0.00% 41 20 0.00% 42 22 0.00% 43 15 0.00% 44 20 0.00% 45 23 0.00% 46 39 0.00% 47 33 0.00% 48 34 0.00% 49 36 0.00% 50 48 0.00% 51 68 0.00% 52 62 0.00% 53 64 0.00% 54 53 0.00% 55 77 0.00% 56 97 0.00% 57 86 0.00% 58 105 0.00% 59 115 0.00% 60 139 0.00% 61 166 0.00% 62 187 0.00% 63 152 0.00% 64 216 0.00% 65 241 0.00% 66 319 0.00% 67 288 0.00% 68 366 0.00% 69 364 0.00% 70 448 0.00% 71 471 0.00% 72 518 0.00% 73 550 0.00% 74 645 0.00% 75 755 0.00% 76 766 0.00% 77 767 0.00% 78 927 0.01% 79 1094 0.01% 80 1217 0.01% 81 1268 0.01% 82 1459 0.01% 83 1520 0.01% 84 1693 0.01% 85 1910 0.01% 86 1985 0.01% 87 2174 0.01% 88 2309 0.01% 89 2284 0.01% 90 2588 0.02% 91 2671 0.02% 92 2764 0.02% 93 3083 0.02% 94 3202 0.02% 95 3540 0.02% 96 3521 0.02% 97 3956 0.02% 98 4007 0.02% 99 4116 0.02% 100 4323 0.03% 101 4412 0.03% 102 4700 0.03% 103 4861 0.03% 104 5014 0.03% 105 5176 0.03% 106 5477 0.03% 107 5612 0.03% 108 5773 0.03% 109 5946 0.03% 110 5950 0.03% 111 6397 0.04% 112 6311 0.04% 113 6442 0.04% 114 7078 0.04% 115 7016 0.04% 116 7350 0.04% 117 7562 0.04% 118 7948 0.05% 119 7973 0.05% 120 8170 0.05% 121 8324 0.05% 122 8430 0.05% 123 8655 0.05% 124 8911 0.05% 125 9225 0.05% 126 9490 0.06% 127 9717 0.06% 128 9937 0.06% 129 10256 0.06% 130 10452 0.06% 131 10265 0.06% 132 10696 0.06% 133 10831 0.06% 134 10897 0.06% 135 11412 0.07% 136 11780 0.07% 137 11811 0.07% 138 12238 0.07% 139 12811 0.07% 140 12795 0.07% 141 13101 0.08% 142 13187 0.08% 143 13624 0.08% 144 14086 0.08% 145 13926 0.08% 146 14359 0.08% 147 14316 0.08% 148 15354 0.09% 149 15193 0.09% 150 15905 0.09% 151 16577471 96.83% 17120900 reads passed initial QC criterion=sequence-density sequence-density=0.62 sequence-density-rank=1 fanout-score=1.97 fanout-score-rank=24 prefix-density=0.62 prefix-fanout=2.0 sequence=CGGTAGACCCAACCTTTCTCCAACTCGAATTCCAAGCAAGGAACCCACTT criterion=fanout-score sequence-density=0.01 sequence-density-rank=28 fanout-score=58.49 fanout-score-rank=1 prefix-density=0.07 prefix-fanout=7.4 sequence=CAAGCTTCCGATTAAAGATACATAATTCCATGGAATGGAACCAACAAAGCAGCAGGAAATACAAGACACTTACAGATTACTAGCCATCAAATGAGATCCTGTAGAAAGGATTTGAGGAGGCCATGGCTAGCTAACTGTACTTTAATTTACAGCAAATACTATATTAGACAAACATGGAGTGACCAGACTTCTTCTTTTTATTTATTATAGTTCCATAAAACTGCTTGGTTGGAGCCATGCGGCGACGTTTTCTCATTTGCAGGAGCATGGATCACAGGTGCAGTTTGATCCACATTTGCAGCCATTCTCAGCACCAAAGTTCATCTCAGAGCTCTCGTAGAACATCCTAACTGGAGCTACACCAGCAATGATTGTCTGACTTGTGGTGGTCTCGGAGAAACTCAAGTCTGGGTACATGCTGCATCCATTGCAGCCACTGCCGCACTTGC criterion=sequence-density sequence-density=0.99 sequence-density-rank=1 fanout-score=2.01 fanout-score-rank=32 prefix-density=0.98 prefix-fanout=2.0 sequence=CCAAGTCTTTTAGTTCATCCATTTAAGCTTAATCAATCAATCATCATGTCTAGCACCTGCGACACCTGCGACTGCGCTGACAAGACCCAGTGTGTCAAGAAGGGAAGCAGCTACACTGCTGGCATCGTCGAGACTGAGAAGAACTATGTCTCCTCCGTAGTCATGGAGGTGCCAGCAGCTGAGAACGATGGCAAGTGCAACTGCGGTACTGGCTGCACTTGCACTACCTGCACATGCGGTCATTAAGCAAGCACATCAACTATCATGTTTGATGTGGGATTGGGAGTGGATTAATAATGTAATTTCTGATAAATAATCTGTGTTCTTCTGTACTTGTGGGTGTGGAGTGAACAAACAAAAGTGTCCGTGAGTGTCTTTAT criterion=fanout-score sequence-density=0.01 sequence-density-rank=32 fanout-score=22.15 fanout-score-rank=1 prefix-density=0.08 prefix-fanout=2.2 sequence=CCACCACTAAACCCAAAGCTCAAAAAAAATCTTAACTGCACCCGCTCATCCAGCAATGGCAGCAGCAACAATGGCCCTCTCCTCCCCTTCGCTAGCCGGAAAGGCGGTGAAGCTCAACCCCTCCTCCTCTGAGATCATGGGCAATGGCCGTGTCTCCATGAGGAAAACCACCAAGCCTGTTCCCTCCGGGAGCCCATGGTACGGACCAGACCGTGTTAAATACTTGGGCCCGTTCTCTGGTGAGCCCCCATCCTACTTGACTGGTGAGTTCCCTGGTGACTACGGCTGGGACACTGCTGG SRR12671375 testing PE reads STAR mapping to Ensembl genome Started job on | Feb 11 20:29:39 Started mapping on | Feb 11 20:29:39 Finished on | Feb 11 20:31:39 Mapping speed, Million of reads per hour | 513.63 Number of input reads | 17120900 Average input read length | 300 UNIQUE READS: Uniquely mapped reads number | 16060941 Uniquely mapped reads % | 93.81% Average mapped length | 298.85 Number of splices: Total | 16315586 Number of splices: Annotated (sjdb) | 16018332 Number of splices: GT/AG | 15997161 Number of splices: GC/AG | 264933 Number of splices: AT/AC | 9101 Number of splices: Non-canonical | 44391 Mismatch rate per base, % | 0.38% Deletion rate per base | 0.03% Deletion average length | 2.88 Insertion rate per base | 0.02% Insertion average length | 2.23 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 382885 % of reads mapped to multiple loci | 2.24% Number of reads mapped to too many loci | 59188 % of reads mapped to too many loci | 0.35% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 3.50% % of reads unmapped: other | 0.11% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 677074 677074 677074 N_multimapping 382885 382885 382885 N_noFeature 547265 15791851 610277 N_ambiguous 318889 922 112259 UnstrandedReadsAssigned:15194787 PositiveStrandReadsAssigned:268168 NegativeStrandReadsAssigned:15338405 Dataset is classified negative stranded MeadianReadLen=151 20thPercentileLength=151 echo kmer=147 SRR12671375 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: SRR12671375-trimmed-pair1.fastq SRR12671375-trimmed-pair2.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 17,120,900 reads, 15,209,862 reads pseudoaligned [quant] estimated average fragment length: 330.514 [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,097 rounds 52401 SRR12671375.ke.tsv 34699 SRR12671375.se.tsv 87100 total ==> SRR12671375.ke.tsv <== target_id length eff_length est_counts tpm Potri.005G200100.1.v4.1 2018 1688.49 764 25.7832 Potri.005G024800.1.v4.1 1035 705.486 316 25.5235 Potri.004G059700.1.v4.1 961 631.933 6 0.54103 Potri.007G009000.2.v4.1 1416 1086.49 0 0 Potri.003G141000.2.v4.1 2943 2613.49 716 15.6111 Potri.016G087400.1.v4.1 270 67.1937 898 761.534 Potri.015G069301.1.v4.1 564 261.173 0 0 Potri.010G195200.1.v4.1 1773 1443.49 53 2.09221 Potri.012G127500.1.v4.1 977 647.737 113 9.94081 ==> SRR12671375.se.tsv <== Potri.001G166300.v4.1 0 Potri.001G448400.v4.1 165 Potri.001G233950.v4.1 0 Potri.001G122700.v4.1 150 Potri.001G212900.v4.1 9 Potri.001G182400.v4.1 0 Potri.001G256600.v4.1 0 Potri.001G040500.v4.1 12 Potri.001G416900.v4.1 0 Potri.001G452600.v4.1 0 SRR12671375 completed mapping pipeline successfully