Starting /dee2/code/volunteer_pipeline.sh SRR12670177 current disk space = 3055709331456 free memory = 1484345736 SRR12670177 SRAfilesize ba4450d89905dcd514978d2d9fb6597f SRR12670177.sra SRR12670177.sra file validated SRR12670177 is paired end SRR12670177 is conventional basespace SRR12670177 read1 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR12670177_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 36.647 37.0 37.0 37.0 37.0 37.0 2 36.43025 37.0 37.0 37.0 37.0 37.0 3 36.63 37.0 37.0 37.0 37.0 37.0 4 36.607 37.0 37.0 37.0 37.0 37.0 5 36.6595 37.0 37.0 37.0 37.0 37.0 6 36.627 37.0 37.0 37.0 37.0 37.0 7 36.5105 37.0 37.0 37.0 37.0 37.0 8 36.5615 37.0 37.0 37.0 37.0 37.0 9 36.555 37.0 37.0 37.0 37.0 37.0 10-14 36.6287 37.0 37.0 37.0 37.0 37.0 15-19 36.598400000000005 37.0 37.0 37.0 37.0 37.0 20-24 36.5595 37.0 37.0 37.0 37.0 37.0 25-29 36.5342 37.0 37.0 37.0 37.0 37.0 30-34 36.501999999999995 37.0 37.0 37.0 37.0 37.0 35-39 36.45700000000001 37.0 37.0 37.0 37.0 37.0 40-44 36.402499999999996 37.0 37.0 37.0 37.0 37.0 45-49 36.4304 37.0 37.0 37.0 37.0 37.0 50-54 36.396699999999996 37.0 37.0 37.0 37.0 37.0 55-59 36.3975 37.0 37.0 37.0 37.0 37.0 60-64 36.412099999999995 37.0 37.0 37.0 37.0 37.0 65-69 36.342699999999994 37.0 37.0 37.0 37.0 37.0 70-74 36.297399999999996 37.0 37.0 37.0 37.0 37.0 75-79 36.2858 37.0 37.0 37.0 37.0 37.0 80-84 36.2844 37.0 37.0 37.0 37.0 37.0 85-89 36.2275 37.0 37.0 37.0 37.0 37.0 90-94 36.263 37.0 37.0 37.0 37.0 37.0 95-99 36.17979999999999 37.0 37.0 37.0 37.0 37.0 100-104 36.2373 37.0 37.0 37.0 37.0 37.0 105-109 36.256299999999996 37.0 37.0 37.0 37.0 37.0 110-114 36.1404 37.0 37.0 37.0 37.0 37.0 115-119 36.1436 37.0 37.0 37.0 37.0 37.0 120-124 36.0935 37.0 37.0 37.0 37.0 37.0 125-129 36.0337 37.0 37.0 37.0 37.0 37.0 130-134 35.968500000000006 37.0 37.0 37.0 37.0 37.0 135-139 35.8711 37.0 37.0 37.0 37.0 37.0 140-144 35.6884 37.0 37.0 37.0 37.0 37.0 145-149 35.704 37.0 37.0 37.0 37.0 37.0 150-151 35.4925 37.0 37.0 37.0 37.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 23 1.0 24 1.0 25 3.0 26 5.0 27 8.0 28 10.0 29 19.0 30 31.0 31 34.0 32 51.0 33 67.0 34 119.0 35 291.0 36 2930.0 37 430.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 38.95 10.775 4.95 45.324999999999996 2 18.407212622088657 11.419984973703983 39.7946406210869 30.37816178312046 3 18.3 15.125 26.5 40.075 4 21.25 24.224999999999998 24.099999999999998 30.425 5 21.975 29.95 26.200000000000003 21.875 6 20.375 34.025 22.675 22.925 7 14.499999999999998 26.85 40.325 18.325 8 19.5 24.099999999999998 32.0 24.4 9 17.95 21.55 37.625 22.875 10-14 20.085 29.060000000000002 27.884999999999998 22.97 15-19 19.245 27.16 28.715000000000003 24.88 20-24 20.52 28.115000000000002 27.48 23.885 25-29 20.13 28.17 27.88 23.82 30-34 20.119999999999997 28.249999999999996 28.035 23.595 35-39 20.385 27.794999999999998 28.08 23.74 40-44 20.48 27.810000000000002 27.42 24.29 45-49 20.455000000000002 27.72 27.91 23.915 50-54 20.555 27.675 27.61 24.16 55-59 20.285 28.33 28.155 23.23 60-64 20.485 27.944999999999997 27.96 23.61 65-69 20.935000000000002 27.169999999999998 28.335 23.56 70-74 21.16 27.939999999999998 27.915 22.985 75-79 20.445 28.185 27.785 23.585 80-84 20.4 27.675 27.71 24.215 85-89 21.335 27.965 26.8 23.9 90-94 20.615 28.505000000000003 27.48 23.400000000000002 95-99 20.895 28.37 27.11 23.625 100-104 21.884999999999998 29.32 25.69 23.105 105-109 21.47 27.965 26.665 23.9 110-114 21.69 28.560000000000002 25.83 23.919999999999998 115-119 21.645 28.985 25.77 23.599999999999998 120-124 21.775 28.544999999999998 25.905 23.775 125-129 21.959999999999997 28.26 25.595000000000002 24.185000000000002 130-134 21.45 28.26 26.200000000000003 24.09 135-139 21.475 27.98 25.965 24.58 140-144 21.455 28.035 25.96 24.55 145-149 22.005 27.26 25.655 25.080000000000002 150-151 20.849999999999998 27.450000000000003 27.237499999999997 24.462500000000002 >>END_MODULE >>Per sequence GC content pass #GC Content Count 0 0.0 1 1.0 2 1.0 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 0.5 22 0.5 23 0.5 24 1.0 25 2.0 26 2.5 27 2.0 28 5.0 29 6.0 30 9.5 31 16.0 32 23.5 33 32.0 34 43.5 35 54.0 36 74.0 37 103.5 38 121.5 39 156.0 40 175.0 41 195.5 42 228.5 43 245.0 44 268.5 45 297.0 46 297.0 47 265.0 48 247.0 49 233.0 50 197.0 51 158.5 52 125.5 53 89.0 54 71.5 55 71.5 56 56.0 57 39.5 58 29.0 59 20.0 60 13.0 61 4.0 62 2.5 63 2.5 64 4.5 65 5.0 66 2.0 67 1.0 68 1.0 69 0.0 70 0.0 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 0.17500000000000002 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 78.8 #Duplication Level Percentage of deduplicated Percentage of total 1 80.17131979695431 63.175000000000004 2 14.530456852791879 22.900000000000002 3 3.8705583756345177 9.15 4 1.1421319796954315 3.5999999999999996 5 0.2220812182741117 0.8750000000000001 6 0.06345177664974619 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 GTCAGCTGCTTCTCGGACTGTTGTTATGTTCTGAGAGTTCTCCTCTTCTA 6 0.15 No Hit GCAAGGACGAGGTTGATGGGGATGTTCTTGCCAAAGTAGTTCAATGTGTT 6 0.15 No Hit CCATAATGGACCTTTTAGACTTGAGTCCCGAAACACTGCATCCATAGCGG 5 0.125 No Hit GCACGTCCTTCTGCTTTGAAGGGATATTGAGGTTCTCCTTATAAGTCCCG 5 0.125 No Hit TTCATTTCGCAGCATCTCTAATCACTTTCAATAATGCTGCTGCTGTCATG 5 0.125 No Hit AGCAAAATTACGAATTATTAAGAGATGTCCTGCACCCATTGTACTTTCAG 5 0.125 No Hit ACAGTATCTTGCATACTCCGGCCCAACCATTAGTATGGCTTGACAGAAAG 5 0.125 No Hit CCCTTTTTTTGCTGTTCTTAGCTGGTTCTGCATGCTTATCCAACTGCTCA 5 0.125 No Hit GGTCAGTTGCATTGCTGAAGCACTGTCGCGACTGAGCAAACCACTTTTCT 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 0.0 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 0.0125 0.0 0.0 0.0 0.0 50-51 0.025 0.0 0.0 0.0 0.0 52-53 0.025 0.0 0.0 0.0 0.0 54-55 0.037500000000000006 0.0 0.0 0.0 0.0 56-57 0.0625 0.0 0.0 0.0 0.0 58-59 0.075 0.0 0.0 0.0 0.0 60-61 0.0875 0.0 0.0 0.0 0.0 62-63 0.16249999999999998 0.0 0.0 0.0 0.0 64-65 0.2 0.0 0.0 0.0 0.0 66-67 0.225 0.0 0.0 0.0 0.0 68-69 0.25 0.0 0.0 0.0 0.0 70-71 0.32499999999999996 0.0 0.0 0.0 0.0 72-73 0.375 0.0 0.0 0.0 0.0 74-75 0.575 0.0 0.0 0.0 0.0 76-77 0.8 0.0 0.0 0.0 0.0 78-79 0.9375 0.0 0.0 0.0 0.0 80-81 1.0499999999999998 0.0 0.0 0.0 0.0 82-83 1.3875000000000002 0.0 0.0 0.0 0.0 84-85 1.775 0.0 0.0 0.0 0.0 86-87 1.9625 0.0 0.0 0.0 0.0 88-89 2.45 0.0 0.0 0.0 0.0 90-91 2.9125 0.0 0.0 0.0 0.0 92-93 3.325 0.0 0.0 0.0 0.0 94-95 4.1625 0.0 0.0 0.0 0.0 96-97 4.8375 0.0 0.0 0.0 0.0 98-99 5.525 0.0 0.0 0.0 0.0 100-101 6.1375 0.0 0.0 0.0 0.0 102-103 6.85 0.0 0.0 0.0 0.0 104-105 7.75 0.0 0.0 0.0 0.0 106-107 8.425 0.0 0.0 0.0 0.0 108-109 9.4875 0.0 0.0 0.0 0.0 110-111 10.375 0.0 0.0 0.0 0.0 112-113 11.4375 0.0 0.0 0.0 0.0 114-115 12.4625 0.0 0.0 0.0 0.0 116-117 13.287500000000001 0.0 0.0 0.0 0.0 118-119 14.0125 0.0 0.0 0.0 0.0 120-121 15.125 0.0 0.0 0.0 0.0 122-123 15.85 0.0 0.0 0.0 0.0 124-125 16.5625 0.0 0.0 0.0 0.0 126-127 17.3875 0.0 0.0 0.0 0.0 128-129 18.6125 0.0 0.0 0.0 0.0 130-131 19.7375 0.0 0.0 0.0 0.0 132-133 20.8125 0.0 0.0 0.0 0.0 134-135 21.924999999999997 0.0 0.0 0.0 0.0 136-137 23.1375 0.0 0.0 0.0 0.0 138-139 23.8625 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content pass >>END_MODULE SRR12670177 read2 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR12670177_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 36.2835 37.0 37.0 37.0 37.0 37.0 2 36.234 37.0 37.0 37.0 37.0 37.0 3 36.2505 37.0 37.0 37.0 37.0 37.0 4 36.2305 37.0 37.0 37.0 37.0 37.0 5 36.308 37.0 37.0 37.0 37.0 37.0 6 36.279 37.0 37.0 37.0 37.0 37.0 7 36.3685 37.0 37.0 37.0 37.0 37.0 8 36.3935 37.0 37.0 37.0 37.0 37.0 9 36.3265 37.0 37.0 37.0 37.0 37.0 10-14 36.3471 37.0 37.0 37.0 37.0 37.0 15-19 36.3564 37.0 37.0 37.0 37.0 37.0 20-24 36.3117 37.0 37.0 37.0 37.0 37.0 25-29 36.294599999999996 37.0 37.0 37.0 37.0 37.0 30-34 36.2572 37.0 37.0 37.0 37.0 37.0 35-39 36.2013 37.0 37.0 37.0 37.0 37.0 40-44 36.1514 37.0 37.0 37.0 37.0 37.0 45-49 36.18920000000001 37.0 37.0 37.0 37.0 37.0 50-54 36.135600000000004 37.0 37.0 37.0 37.0 37.0 55-59 36.114 37.0 37.0 37.0 37.0 37.0 60-64 36.1913 37.0 37.0 37.0 37.0 37.0 65-69 36.086499999999994 37.0 37.0 37.0 37.0 37.0 70-74 36.055400000000006 37.0 37.0 37.0 37.0 37.0 75-79 36.078199999999995 37.0 37.0 37.0 37.0 37.0 80-84 36.025400000000005 37.0 37.0 37.0 37.0 37.0 85-89 35.978 37.0 37.0 37.0 37.0 37.0 90-94 35.9828 37.0 37.0 37.0 37.0 37.0 95-99 35.928700000000006 37.0 37.0 37.0 37.0 37.0 100-104 35.8201 37.0 37.0 37.0 37.0 37.0 105-109 35.8289 37.0 37.0 37.0 37.0 37.0 110-114 35.76539999999999 37.0 37.0 37.0 37.0 37.0 115-119 35.7648 37.0 37.0 37.0 37.0 37.0 120-124 35.5716 37.0 37.0 37.0 37.0 37.0 125-129 35.4934 37.0 37.0 37.0 37.0 37.0 130-134 35.2321 37.0 37.0 37.0 32.2 37.0 135-139 35.021699999999996 37.0 37.0 37.0 27.4 37.0 140-144 34.732299999999995 37.0 37.0 37.0 25.0 37.0 145-149 34.3946 37.0 37.0 37.0 25.0 37.0 150-151 34.0535 37.0 37.0 37.0 25.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 13 3.0 14 3.0 15 2.0 16 2.0 17 0.0 18 1.0 19 0.0 20 1.0 21 3.0 22 3.0 23 5.0 24 6.0 25 7.0 26 10.0 27 10.0 28 13.0 29 18.0 30 28.0 31 48.0 32 75.0 33 102.0 34 230.0 35 539.0 36 2571.0 37 320.0 >>END_MODULE >>Per base sequence content warn #Base G A T C 1 37.425000000000004 24.349999999999998 10.325 27.900000000000002 2 25.8 27.150000000000002 30.5 16.55 3 19.55 28.675 31.825 19.950000000000003 4 22.775000000000002 34.975 22.775000000000002 19.475 5 23.400000000000002 37.724999999999994 21.5 17.375 6 21.85 37.425000000000004 22.475 18.25 7 18.95 22.25 37.525 21.275 8 20.375 25.15 29.225 25.25 9 22.075 23.525 31.4 23.0 10-14 23.095 28.96 26.490000000000002 21.455 15-19 22.725 29.15 27.18 20.945 20-24 22.865 28.185 28.025 20.925 25-29 22.86 28.405 27.38 21.355 30-34 22.535 28.110000000000003 27.834999999999997 21.52 35-39 22.48 28.515 28.34 20.665 40-44 23.315 27.725 28.275 20.685000000000002 45-49 23.355 28.24 27.634999999999998 20.77 50-54 23.02 28.03 27.500000000000004 21.45 55-59 23.205000000000002 27.685 28.050000000000004 21.060000000000002 60-64 23.685000000000002 27.810000000000002 27.445000000000004 21.060000000000002 65-69 23.135 27.900000000000002 27.965 21.0 70-74 23.3 28.59 26.83 21.279999999999998 75-79 23.71 27.675 27.655 20.96 80-84 24.03 28.01 26.875 21.085 85-89 23.965 27.950000000000003 27.200000000000003 20.885 90-94 24.005000000000003 28.07 27.36 20.565 95-99 24.465 27.985 26.305 21.245 100-104 24.565 27.750000000000004 27.075 20.61 105-109 25.965 27.474999999999998 26.655 19.905 110-114 25.405 28.17 26.47 19.955000000000002 115-119 26.179999999999996 28.494999999999997 25.974999999999998 19.35 120-124 26.825 28.16 26.44 18.575 125-129 27.775 27.685 25.790000000000003 18.75 130-134 27.71 27.884999999999998 25.305 19.1 135-139 28.535 27.485 25.71 18.27 140-144 29.49 26.76 25.779999999999998 17.97 145-149 29.95 27.04 25.055 17.955 150-151 30.7375 27.1375 24.887500000000003 17.2375 >>END_MODULE >>Per sequence GC content pass #GC Content Count 0 0.0 1 0.0 2 0.0 3 0.0 4 0.5 5 1.0 6 0.5 7 0.0 8 0.0 9 0.0 10 0.0 11 0.5 12 0.5 13 0.0 14 0.5 15 0.5 16 0.0 17 0.5 18 0.5 19 0.0 20 0.0 21 1.5 22 3.5 23 2.0 24 2.0 25 3.5 26 4.0 27 4.5 28 4.5 29 4.5 30 7.0 31 13.5 32 27.5 33 37.0 34 41.5 35 56.5 36 85.5 37 113.0 38 126.5 39 162.0 40 199.5 41 215.0 42 242.0 43 269.0 44 279.0 45 276.0 46 265.0 47 232.5 48 223.5 49 231.0 50 200.0 51 156.5 52 120.5 53 92.0 54 71.5 55 63.0 56 45.0 57 26.5 58 20.0 59 20.0 60 17.0 61 7.5 62 5.0 63 4.5 64 2.0 65 1.5 66 1.5 67 1.0 68 1.0 69 0.5 70 1.0 71 1.5 72 1.0 73 0.5 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 0.5 99 0.5 100 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 0.0 150-151 0.0 >>END_MODULE >>Sequence Length Distribution pass #Length Count 151 4000.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 78.325 #Duplication Level Percentage of deduplicated Percentage of total 1 79.66804979253112 62.4 2 14.842004468560486 23.25 3 4.053622725821896 9.525 4 1.117140121289499 3.5000000000000004 5 0.22342802425789976 0.8750000000000001 6 0.0957548675390999 0.44999999999999996 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 TGCTGACTCTCTTGACACAGTGGAGATAGTAATGGCATTGGAAGAAGAAT 6 0.15 No Hit TCCTTTTGGTCTCAGCAAGAAGCCAGACGACTTCGAAAAATATCAGGCAT 6 0.15 No Hit AGAGAACACATTCATACTCCAAGTCTTTTAGTTCATCCATTTAAGCTTAA 6 0.15 No Hit GAGATAGAAGCCCATGCAGTAGTGGCAAGGGATGGGAGTGGGACCCATAC 5 0.125 No Hit CAGAGAACACATTCATACTCCAAGTCTTTTAGTTCATCCATTTAAGCTTA 5 0.125 No Hit CTCCCATGCTAGGTGATTCAAGTGTGCTAGCAAGCTCTAGTGATGTTGCG 5 0.125 No Hit AGAAGAGGGAAAATACTCATTAGAATCCCAATTTAGCCTCGATCACCATG 5 0.125 No Hit GAACATCAAGAATGTTAGCTCTGAATACAGTTATGAAGGAGAATTTGAAA 5 0.125 No Hit CTTCAACTTTGAAATACTTCATGCTCGCTGGGCTATGCTTGCTGCTCTCG 5 0.125 No Hit GAAGAGGATGCACAGAATTTCTCTAACTCAACAGAAGTGTTTGGTGGAAT 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 0.0 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 0.0125 0.0 0.0 0.0 0.0 50-51 0.025 0.0 0.0 0.0 0.0 52-53 0.025 0.0 0.0 0.0 0.0 54-55 0.037500000000000006 0.0 0.0 0.0 0.0 56-57 0.0625 0.0 0.0 0.0 0.0 58-59 0.075 0.0 0.0 0.0 0.0 60-61 0.0875 0.0 0.0 0.0 0.0 62-63 0.16249999999999998 0.0 0.0 0.0 0.0 64-65 0.2 0.0 0.0 0.0 0.0 66-67 0.225 0.0 0.0 0.0 0.0 68-69 0.25 0.0 0.0 0.0 0.0 70-71 0.32499999999999996 0.0 0.0 0.0 0.0 72-73 0.375 0.0 0.0 0.0 0.0 74-75 0.575 0.0 0.0 0.0 0.0 76-77 0.8 0.0 0.0 0.0 0.0 78-79 0.9375 0.0 0.0 0.0 0.0 80-81 1.0499999999999998 0.0 0.0 0.0 0.0 82-83 1.3875000000000002 0.0 0.0 0.0 0.0 84-85 1.775 0.0 0.0 0.0 0.0 86-87 1.9625 0.0 0.0 0.0 0.0 88-89 2.425 0.0 0.0 0.0 0.0 90-91 2.8875 0.0 0.0 0.0 0.0 92-93 3.275 0.0 0.0 0.0 0.0 94-95 4.0875 0.0 0.0 0.0 0.0 96-97 4.7625 0.0 0.0 0.0 0.0 98-99 5.425000000000001 0.0 0.0 0.0 0.0 100-101 6.0375 0.0 0.0 0.0 0.0 102-103 6.75 0.0 0.0 0.0 0.0 104-105 7.6625 0.0 0.0 0.0 0.0 106-107 8.350000000000001 0.0 0.0 0.0 0.0 108-109 9.4375 0.0 0.0 0.0 0.0 110-111 10.325 0.0 0.0 0.0 0.0 112-113 11.375 0.0 0.0 0.0 0.0 114-115 12.399999999999999 0.0 0.0 0.0 0.0 116-117 13.2375 0.0 0.0 0.0 0.0 118-119 13.975000000000001 0.0 0.0 0.0 0.0 120-121 15.1 0.0 0.0 0.0 0.0 122-123 15.837499999999999 0.0 0.0 0.0 0.0 124-125 16.5625 0.0 0.0 0.0 0.0 126-127 17.4 0.0 0.0 0.0 0.0 128-129 18.625 0.0 0.0 0.0 0.0 130-131 19.7375 0.0 0.0 0.0 0.0 132-133 20.7875 0.0 0.0 0.0 0.0 134-135 21.875 0.0 0.0 0.0 0.0 136-137 23.0875 0.0 0.0 0.0 0.0 138-139 23.8125 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position TTTTACA 10 0.006830828 145.0 2 CAAAGCT 10 0.006830828 145.0 4 TTTACAT 10 0.006830828 145.0 3 >>END_MODULE Read 814825 spots for SRR12670177.sra Written 814825 spots for SRR12670177.sra Read 814825 spots for SRR12670177.sra Written 814825 spots for SRR12670177.sra Read 814825 spots for SRR12670177.sra Written 814825 spots for SRR12670177.sra Read 814825 spots for SRR12670177.sra Written 814825 spots for SRR12670177.sra Read 814825 spots for SRR12670177.sra Written 814825 spots for SRR12670177.sra Read 814825 spots for SRR12670177.sra Written 814825 spots for SRR12670177.sra Read 814842 spots for SRR12670177.sra Written 814842 spots for SRR12670177.sra Read 814825 spots for SRR12670177.sra Written 814825 spots for SRR12670177.sra Read 814825 spots for SRR12670177.sra Written 814825 spots for SRR12670177.sra Read 814825 spots for SRR12670177.sra Written 814825 spots for SRR12670177.sra Read 814825 spots for SRR12670177.sra Written 814825 spots for SRR12670177.sra Read 814825 spots for SRR12670177.sra Written 814825 spots for SRR12670177.sra Read 814825 spots for SRR12670177.sra Written 814825 spots for SRR12670177.sra Read 814825 spots for SRR12670177.sra Written 814825 spots for SRR12670177.sra Read 814825 spots for SRR12670177.sra Written 814825 spots for SRR12670177.sra Read 814825 spots for SRR12670177.sra Written 814825 spots for SRR12670177.sra Read 814825 spots for SRR12670177.sra Written 814825 spots for SRR12670177.sra Read 814825 spots for SRR12670177.sra Written 814825 spots for SRR12670177.sra Read 814825 spots for SRR12670177.sra Written 814825 spots for SRR12670177.sra Read 814825 spots for SRR12670177.sra Written 814825 spots for SRR12670177.sra SRR ids: ['SRR12670177.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_maivlf7m SRR12670177.sra spots: 16296517 blocks: [[1, 814825], [814826, 1629650], [1629651, 2444475], [2444476, 3259300], [3259301, 4074125], [4074126, 4888950], [4888951, 5703775], [5703776, 6518600], [6518601, 7333425], [7333426, 8148250], [8148251, 8963075], [8963076, 9777900], [9777901, 10592725], [10592726, 11407550], [11407551, 12222375], [12222376, 13037200], [13037201, 13852025], [13852026, 14666850], [14666851, 15481675], [15481676, 16296517]] SRR12670177 file size 5516569 SRR12670177 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 SRR12670177 SRR12670177_1.fastq SRR12670177_2.fastq Input file: SRR12670177_1.fastq Paired file: SRR12670177_2.fastq trimmed: SRR12670177-trimmed-pair1.fastq, SRR12670177-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 08:46:44 2025 >> started Tue Feb 11 08:47:11 2025 >> done (27.175s) 16296517 read pairs processed; of these: 79 ( 0.00%) short read pairs filtered out after trimming by size control 10007 ( 0.06%) empty read pairs filtered out after trimming by size control 16286431 (99.94%) read pairs available; of these: 4726043 (29.02%) trimmed read pairs available after processing 11560388 (70.98%) untrimmed read pairs available after processing Length distribution of reads after trimming: length count percentage 18 4 0.00% 19 3 0.00% 20 5 0.00% 21 15 0.00% 22 17 0.00% 23 22 0.00% 24 25 0.00% 25 36 0.00% 26 41 0.00% 27 31 0.00% 28 48 0.00% 29 52 0.00% 30 76 0.00% 31 52 0.00% 32 57 0.00% 33 80 0.00% 34 69 0.00% 35 120 0.00% 36 112 0.00% 37 154 0.00% 38 179 0.00% 39 139 0.00% 40 175 0.00% 41 183 0.00% 42 237 0.00% 43 248 0.00% 44 260 0.00% 45 244 0.00% 46 288 0.00% 47 342 0.00% 48 459 0.00% 49 519 0.00% 50 586 0.00% 51 734 0.00% 52 780 0.00% 53 879 0.01% 54 947 0.01% 55 999 0.01% 56 1094 0.01% 57 1300 0.01% 58 1552 0.01% 59 1885 0.01% 60 2348 0.01% 61 2639 0.02% 62 3075 0.02% 63 3277 0.02% 64 3520 0.02% 65 3803 0.02% 66 4197 0.03% 67 4667 0.03% 68 5122 0.03% 69 6044 0.04% 70 7120 0.04% 71 7959 0.05% 72 8906 0.05% 73 10493 0.06% 74 11476 0.07% 75 12351 0.08% 76 13341 0.08% 77 14056 0.09% 78 15256 0.09% 79 17067 0.10% 80 18910 0.12% 81 20888 0.13% 82 23341 0.14% 83 25098 0.15% 84 27388 0.17% 85 29928 0.18% 86 31021 0.19% 87 32400 0.20% 88 34211 0.21% 89 35653 0.22% 90 38414 0.24% 91 40216 0.25% 92 42581 0.26% 93 45718 0.28% 94 48325 0.30% 95 50885 0.31% 96 52621 0.32% 97 53467 0.33% 98 53719 0.33% 99 55984 0.34% 100 57364 0.35% 101 57994 0.36% 102 60343 0.37% 103 62559 0.38% 104 64076 0.39% 105 65733 0.40% 106 67788 0.42% 107 68195 0.42% 108 68753 0.42% 109 69511 0.43% 110 68465 0.42% 111 69654 0.43% 112 70703 0.43% 113 70520 0.43% 114 73342 0.45% 115 73989 0.45% 116 75775 0.47% 117 76529 0.47% 118 77729 0.48% 119 76300 0.47% 120 76168 0.47% 121 75820 0.47% 122 76740 0.47% 123 77243 0.47% 124 77385 0.48% 125 77756 0.48% 126 80091 0.49% 127 79337 0.49% 128 79088 0.49% 129 78553 0.48% 130 79247 0.49% 131 77167 0.47% 132 77677 0.48% 133 77949 0.48% 134 77737 0.48% 135 78220 0.48% 136 79214 0.49% 137 78660 0.48% 138 78548 0.48% 139 79572 0.49% 140 79430 0.49% 141 78403 0.48% 142 78761 0.48% 143 77869 0.48% 144 77676 0.48% 145 77832 0.48% 146 77727 0.48% 147 77158 0.47% 148 77651 0.48% 149 76502 0.47% 150 77007 0.47% 151 11560388 70.98% 16286431 reads passed initial QC criterion=sequence-density sequence-density=0.39 sequence-density-rank=1 fanout-score=2.35 fanout-score-rank=23 prefix-density=0.41 prefix-fanout=2.2 sequence=TTCCACATAGTCCAGTAGCGTCCATCATAGTACCCTGGTGAGCTGTGGTGCTCACGGTAGACCCAACCTTTCTCCAACTCGAATTCCAAGCAAGGAACCCACTTCGAGCGAAGAAGGTAATCAATTTCCTTGGCCAATTCCTCCTCTGTGAGATCTGGAAGGTAAGAAAGAGTCTCGAACTTCTTCAATCCAGTTGGTGGCCACACCTGCATGCATTGAACTCGTCCACCATTGCTTGCAATGGAAGTAATGTCATTAGCCTTTCTGGTACTGACTGGGAAAGCTGCGGCAGACTTGAGACCATTGAATGGTGCCACCATGTTGGCTTGTGCCGGGGTGCGGTTGACGGTGGCAACGGCTGCCGATGAGATCATAGAGGAGGAAGCCAT criterion=fanout-score sequence-density=0.05 sequence-density-rank=27 fanout-score=15.55 fanout-score-rank=1 prefix-density=0.23 prefix-fanout=3.6 sequence=ACACCCACAAGCCTAGAAAAGGAATTAGAATTTGTAAGTGCAGCTTCCATCATCACTCCTTGCAGTTGGATCAAAGTTTGCTGCATTTGGATCAGTACAGCCTTCAGCGACAGGCACCTTTACTTGCTGTGCCGCTTGGCC criterion=sequence-density sequence-density=0.61 sequence-density-rank=1 fanout-score=2.20 fanout-score-rank=23 prefix-density=0.62 prefix-fanout=2.1 sequence=TGTAAGAGATGGCTTCCTC criterion=fanout-score sequence-density=0.13 sequence-density-rank=22 fanout-score=38.81 fanout-score-rank=1 prefix-density=0.40 prefix-fanout=13.1 sequence=AAAGAAAAGAAAA SRR12670177 testing PE reads STAR mapping to Ensembl genome Started job on | Feb 11 08:48:02 Started mapping on | Feb 11 08:48:02 Finished on | Feb 11 08:50:32 Mapping speed, Million of reads per hour | 390.87 Number of input reads | 16286431 Average input read length | 283 UNIQUE READS: Uniquely mapped reads number | 15470194 Uniquely mapped reads % | 94.99% Average mapped length | 281.77 Number of splices: Total | 14958853 Number of splices: Annotated (sjdb) | 14648219 Number of splices: GT/AG | 14648419 Number of splices: GC/AG | 257983 Number of splices: AT/AC | 9422 Number of splices: Non-canonical | 43029 Mismatch rate per base, % | 0.34% Deletion rate per base | 0.03% Deletion average length | 2.85 Insertion rate per base | 0.02% Insertion average length | 2.39 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 382339 % of reads mapped to multiple loci | 2.35% Number of reads mapped to too many loci | 31512 % of reads mapped to too many loci | 0.19% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 2.39% % of reads unmapped: other | 0.08% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 433898 433898 433898 N_multimapping 382339 382339 382339 N_noFeature 495883 15282614 581615 N_ambiguous 188191 754 85940 UnstrandedReadsAssigned:14786120 PositiveStrandReadsAssigned:186826 NegativeStrandReadsAssigned:14802639 Dataset is classified negative stranded MeadianReadLen=151 20thPercentileLength=131 echo kmer=127 SRR12670177 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: SRR12670177-trimmed-pair1.fastq SRR12670177-trimmed-pair2.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 16,286,431 reads, 14,880,620 reads pseudoaligned [quant] estimated average fragment length: 200.044 [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,168 rounds 52401 SRR12670177.ke.tsv 34699 SRR12670177.se.tsv 87100 total ==> SRR12670177.ke.tsv <== target_id length eff_length est_counts tpm Potri.005G200100.1.v4.1 2018 1818.96 578 23.6055 Potri.005G024800.1.v4.1 1035 835.956 177 15.7289 Potri.004G059700.1.v4.1 961 762.011 4 0.389947 Potri.007G009000.2.v4.1 1416 1216.96 0 0 Potri.003G141000.2.v4.1 2943 2743.96 956.708 25.9006 Potri.016G087400.1.v4.1 270 111.448 829 552.574 Potri.015G069301.1.v4.1 564 371.022 0 0 Potri.010G195200.1.v4.1 1773 1573.96 38 1.79349 Potri.012G127500.1.v4.1 977 777.971 81 7.73444 ==> SRR12670177.se.tsv <== Potri.001G166300.v4.1 0 Potri.001G448400.v4.1 347 Potri.001G233950.v4.1 0 Potri.001G122700.v4.1 235 Potri.001G212900.v4.1 2 Potri.001G182400.v4.1 3 Potri.001G256600.v4.1 0 Potri.001G040500.v4.1 5 Potri.001G416900.v4.1 0 Potri.001G452600.v4.1 3 SRR12670177 completed mapping pipeline successfully