Starting /dee2/code/volunteer_pipeline.sh SRR12670101 current disk space = 3057568366592 free memory = 1118506032 SRR12670101 SRAfilesize 15a7eae78c146cf84a69980db79b9033 SRR12670101.sra SRR12670101.sra file validated SRR12670101 is paired end SRR12670101 is conventional basespace SRR12670101 read1 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR12670101_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 36.6395 37.0 37.0 37.0 37.0 37.0 2 36.46325 37.0 37.0 37.0 37.0 37.0 3 36.654 37.0 37.0 37.0 37.0 37.0 4 36.6995 37.0 37.0 37.0 37.0 37.0 5 36.676 37.0 37.0 37.0 37.0 37.0 6 36.5955 37.0 37.0 37.0 37.0 37.0 7 36.567 37.0 37.0 37.0 37.0 37.0 8 36.628 37.0 37.0 37.0 37.0 37.0 9 36.598 37.0 37.0 37.0 37.0 37.0 10-14 36.6344 37.0 37.0 37.0 37.0 37.0 15-19 36.6443 37.0 37.0 37.0 37.0 37.0 20-24 36.5687 37.0 37.0 37.0 37.0 37.0 25-29 36.500600000000006 37.0 37.0 37.0 37.0 37.0 30-34 36.5182 37.0 37.0 37.0 37.0 37.0 35-39 36.556999999999995 37.0 37.0 37.0 37.0 37.0 40-44 36.4916 37.0 37.0 37.0 37.0 37.0 45-49 36.499900000000004 37.0 37.0 37.0 37.0 37.0 50-54 36.437400000000004 37.0 37.0 37.0 37.0 37.0 55-59 36.4457 37.0 37.0 37.0 37.0 37.0 60-64 36.446 37.0 37.0 37.0 37.0 37.0 65-69 36.3654 37.0 37.0 37.0 37.0 37.0 70-74 36.361399999999996 37.0 37.0 37.0 37.0 37.0 75-79 36.3885 37.0 37.0 37.0 37.0 37.0 80-84 36.3013 37.0 37.0 37.0 37.0 37.0 85-89 36.328799999999994 37.0 37.0 37.0 37.0 37.0 90-94 36.355399999999996 37.0 37.0 37.0 37.0 37.0 95-99 36.238600000000005 37.0 37.0 37.0 37.0 37.0 100-104 36.3203 37.0 37.0 37.0 37.0 37.0 105-109 36.3229 37.0 37.0 37.0 37.0 37.0 110-114 36.2018 37.0 37.0 37.0 37.0 37.0 115-119 36.1876 37.0 37.0 37.0 37.0 37.0 120-124 36.0781 37.0 37.0 37.0 37.0 37.0 125-129 36.048199999999994 37.0 37.0 37.0 37.0 37.0 130-134 36.0416 37.0 37.0 37.0 37.0 37.0 135-139 35.950900000000004 37.0 37.0 37.0 37.0 37.0 140-144 35.7981 37.0 37.0 37.0 37.0 37.0 145-149 35.7468 37.0 37.0 37.0 37.0 37.0 150-151 35.72725 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 1.0 25 3.0 26 4.0 27 3.0 28 14.0 29 10.0 30 26.0 31 35.0 32 49.0 33 55.0 34 96.0 35 292.0 36 2965.0 37 445.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 39.6 10.9 5.625 43.875 2 19.86970684039088 12.47807567025808 36.25657729892258 31.395640190428466 3 16.925 15.5 26.375 41.199999999999996 4 21.425 24.125 24.2 30.25 5 22.075 30.425 25.4 22.1 6 21.85 32.275 23.925 21.95 7 14.774999999999999 26.0 42.025 17.2 8 17.375 25.924999999999997 32.75 23.95 9 17.974999999999998 23.799999999999997 34.150000000000006 24.075 10-14 20.24 28.849999999999998 27.939999999999998 22.97 15-19 20.595 27.415 27.375 24.615000000000002 20-24 21.0 28.134999999999998 27.915 22.95 25-29 19.725 28.215 27.96 24.099999999999998 30-34 19.74 27.950000000000003 28.265 24.044999999999998 35-39 20.044999999999998 28.01 27.785 24.16 40-44 20.75 28.625 27.815 22.81 45-49 20.5 27.725 27.195000000000004 24.58 50-54 20.395 28.705000000000002 26.85 24.05 55-59 20.5 27.925 27.095000000000002 24.48 60-64 21.11 27.27 27.875 23.745 65-69 20.93 27.87 27.589999999999996 23.61 70-74 20.630000000000003 28.360000000000003 27.224999999999998 23.785 75-79 21.52 28.199999999999996 26.69 23.59 80-84 20.96 27.965 27.195000000000004 23.880000000000003 85-89 20.72 28.675 27.189999999999998 23.415 90-94 20.875 28.59 26.75 23.785 95-99 21.495 27.500000000000004 26.995 24.01 100-104 21.14 28.035 26.705000000000002 24.12 105-109 21.925 27.85 26.86 23.365 110-114 21.305 28.194999999999997 26.884999999999998 23.615 115-119 21.745 28.575 26.05 23.630000000000003 120-124 21.905 27.150000000000002 26.584999999999997 24.36 125-129 22.54 28.389999999999997 25.615 23.455000000000002 130-134 22.08 28.675 25.009999999999998 24.235 135-139 22.040000000000003 28.660000000000004 25.11 24.19 140-144 22.465 27.875 25.55 24.11 145-149 22.545 27.994999999999997 25.335 24.125 150-151 22.55 26.8375 26.25 24.3625 >>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 0.5 15 0.5 16 0.0 17 0.0 18 0.5 19 1.0 20 0.5 21 0.0 22 0.0 23 1.0 24 2.0 25 2.5 26 2.5 27 2.5 28 5.0 29 7.5 30 10.0 31 12.5 32 16.0 33 28.5 34 45.0 35 53.0 36 74.5 37 96.5 38 114.0 39 144.0 40 176.5 41 209.0 42 239.0 43 270.5 44 271.5 45 259.0 46 248.0 47 258.0 48 254.0 49 223.5 50 206.5 51 170.5 52 129.0 53 94.5 54 83.0 55 70.0 56 54.5 57 46.5 58 37.0 59 28.5 60 17.5 61 13.0 62 6.5 63 2.5 64 1.5 65 2.0 66 3.0 67 1.0 68 1.5 69 2.0 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 0.22499999999999998 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 77.67500000000001 #Duplication Level Percentage of deduplicated Percentage of total 1 79.6266495011265 61.85000000000001 2 14.773093015770842 22.95 3 3.926617315738655 9.15 4 0.9011908593498551 2.8000000000000003 5 0.5471515931766977 2.125 6 0.16092693916961698 0.75 7 0.0321853878339234 0.17500000000000002 8 0.0321853878339234 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 GGCTAATGCAAGTGCTCCCAAAGTATCCATGATCATATTGACCCAGAGAA 8 0.2 No Hit CCTGGGTCCAGTCATTCTGATTACCCTCCTTCCATATTATGACTCGGCCA 7 0.17500000000000002 No Hit CAGGAACCAAAGGATTGATCTTGTTGGAATCACCGCCAAGTTGAGCCATA 6 0.15 No Hit GTTGTTTGTGATTGGAACATGATCCAAGAATCCTAAGTTGATTTGGTGTA 6 0.15 No Hit GCCAACTCCACGGCTTTTACCTGCTCTCCTAACTTTGAGAAATTAGCAGA 6 0.15 No Hit CCAGCACAGAAAAAACTCTTTTGTTGCTCACTTTCCGGGAACGAAGTTTG 6 0.15 No Hit GAGCATCTTATTGATTACATTTAACTAGACATAGTTTTTCTTTTCCCTGC 6 0.15 No Hit CCTTTGTTTACCTTGGCAAAAATGGTATTCTTCACCGAAGAAGAAGATGG 5 0.125 No Hit GTCCTCCAATTCAAACGCCCATGTTGCAGCCAAGCTTCATGGAGGCCAGC 5 0.125 No Hit CGCAAGTGCAACATATAGAGGTTTGCTAACAACAATTTTTCCATTCATCT 5 0.125 No Hit GGCGGGGGACGCTGTGGTGGTGGAGGCGGGTTTGGAGAGGGAGTTGGAGA 5 0.125 No Hit CTTGGATAGGTTTAGCTTTTCTCACAATGTCGGCAAAATGCTTTGTATAC 5 0.125 No Hit CGGCACCTTCCTTCCTCCAGTCAACGGAATCCGGCAAAGAGTCTCCAACA 5 0.125 No Hit GCCAGAATCAAAGATCAGATTCATTGTCATACATTAGCACATACATCCAA 5 0.125 No Hit GCCACATTGAGAAGCATGGAAACCACTGAACCTCTGGTGAATCGGATGGA 5 0.125 No Hit GGCACATGCAATATCAAAAGATAATTTTGATACCCAAGTTCTTATGAGCA 5 0.125 No Hit GTCTGGATGATTTGAGAGGTGAAGCAGATCTAGTTTTAGACCTTGACCTC 5 0.125 No Hit GCGACACCTGCGACTGCGCTGACAAGACCCAGTGTGTCAAGAAGGGAAGC 5 0.125 No Hit GGTAATATTGCTTCTGTATGAGAGATTCTCAACCTGGGGTTTGTGGTGGA 5 0.125 No Hit CTCAGGTACTTGTCAGCCAATTGGACTCTCTTCACATTCTCTTGCTCCTG 5 0.125 No Hit GCCTTCTCCTCCACAACAAGGATATCGTTCAATCAGAAATCAAAGCACTT 5 0.125 No Hit GTCTGTTCTCATCCTGGCACCAGTTCTCAAAGTACTTGAAAATGGGGTAA 5 0.125 No Hit GGCAGCTGCGCAAAAGCTTCTGGCACTGTCCCTGTCAATTCATTGTTTGA 5 0.125 No Hit GCCTCCTCTTGTGTTGTTTCGTCATCAGCTGTTTGCCCATCAACAGAAAG 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 0.0125 0.0 0.0 0.0 0.0 46-47 0.025 0.0 0.0 0.0 0.0 48-49 0.025 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 0.1 0.0 0.0 0.0 0.0 56-57 0.1 0.0 0.0 0.0 0.0 58-59 0.1 0.0 0.0 0.0 0.0 60-61 0.1375 0.0 0.0 0.0 0.0 62-63 0.15 0.0 0.0 0.0 0.0 64-65 0.21250000000000002 0.0 0.0 0.0 0.0 66-67 0.3125 0.0 0.0 0.0 0.0 68-69 0.42500000000000004 0.0 0.0 0.0 0.0 70-71 0.5375 0.0 0.0 0.0 0.0 72-73 0.6375 0.0 0.0 0.0 0.0 74-75 0.75 0.0 0.0 0.0 0.0 76-77 0.9625 0.0 0.0 0.0 0.0 78-79 1.075 0.0 0.0 0.0 0.0 80-81 1.2000000000000002 0.0 0.0 0.0 0.0 82-83 1.4875 0.0 0.0 0.0 0.0 84-85 1.7875 0.0 0.0 0.0 0.0 86-87 1.9874999999999998 0.0 0.0 0.0 0.0 88-89 2.3 0.0 0.0 0.0 0.0 90-91 2.675 0.0 0.0 0.0 0.0 92-93 2.975 0.0 0.0 0.0 0.0 94-95 3.425 0.0 0.0 0.0 0.0 96-97 4.3 0.0 0.0 0.0 0.0 98-99 4.8375 0.0 0.0 0.0 0.0 100-101 5.6875 0.0 0.0 0.0 0.0 102-103 6.425000000000001 0.0 0.0 0.0 0.0 104-105 7.15 0.0 0.0 0.0 0.0 106-107 7.95 0.0 0.0 0.0 0.0 108-109 9.0 0.0 0.0 0.0 0.0 110-111 9.7625 0.0 0.0 0.0 0.0 112-113 10.4625 0.0 0.0 0.0 0.0 114-115 11.3375 0.0 0.0 0.0 0.0 116-117 12.2 0.0 0.0 0.0 0.0 118-119 13.225 0.0 0.0 0.0 0.0 120-121 14.287500000000001 0.0 0.0 0.0 0.0 122-123 15.1375 0.0 0.0 0.0 0.0 124-125 16.1875 0.0 0.0 0.0 0.0 126-127 17.15 0.0 0.0 0.0 0.0 128-129 18.15 0.0 0.0 0.0 0.0 130-131 19.0 0.0 0.0 0.0 0.0 132-133 19.8375 0.0 0.0 0.0 0.0 134-135 20.925 0.0 0.0 0.0 0.0 136-137 21.85 0.0 0.0 0.0 0.0 138-139 22.6 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content pass >>END_MODULE SRR12670101 read2 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR12670101_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 36.288 37.0 37.0 37.0 37.0 37.0 2 36.13 37.0 37.0 37.0 37.0 37.0 3 36.2155 37.0 37.0 37.0 37.0 37.0 4 36.3055 37.0 37.0 37.0 37.0 37.0 5 36.287 37.0 37.0 37.0 37.0 37.0 6 36.3295 37.0 37.0 37.0 37.0 37.0 7 36.2705 37.0 37.0 37.0 37.0 37.0 8 36.4195 37.0 37.0 37.0 37.0 37.0 9 36.278 37.0 37.0 37.0 37.0 37.0 10-14 36.355000000000004 37.0 37.0 37.0 37.0 37.0 15-19 36.3278 37.0 37.0 37.0 37.0 37.0 20-24 36.2805 37.0 37.0 37.0 37.0 37.0 25-29 36.280300000000004 37.0 37.0 37.0 37.0 37.0 30-34 36.2421 37.0 37.0 37.0 37.0 37.0 35-39 36.198 37.0 37.0 37.0 37.0 37.0 40-44 36.1959 37.0 37.0 37.0 37.0 37.0 45-49 36.2188 37.0 37.0 37.0 37.0 37.0 50-54 36.130300000000005 37.0 37.0 37.0 37.0 37.0 55-59 36.128 37.0 37.0 37.0 37.0 37.0 60-64 36.1641 37.0 37.0 37.0 37.0 37.0 65-69 36.070100000000004 37.0 37.0 37.0 37.0 37.0 70-74 36.1031 37.0 37.0 37.0 37.0 37.0 75-79 35.9733 37.0 37.0 37.0 37.0 37.0 80-84 36.0712 37.0 37.0 37.0 37.0 37.0 85-89 35.9107 37.0 37.0 37.0 37.0 37.0 90-94 35.956199999999995 37.0 37.0 37.0 37.0 37.0 95-99 35.8856 37.0 37.0 37.0 37.0 37.0 100-104 35.832100000000004 37.0 37.0 37.0 37.0 37.0 105-109 35.815200000000004 37.0 37.0 37.0 37.0 37.0 110-114 35.771300000000004 37.0 37.0 37.0 37.0 37.0 115-119 35.635299999999994 37.0 37.0 37.0 37.0 37.0 120-124 35.455600000000004 37.0 37.0 37.0 37.0 37.0 125-129 35.3664 37.0 37.0 37.0 37.0 37.0 130-134 35.20049999999999 37.0 37.0 37.0 32.2 37.0 135-139 34.9808 37.0 37.0 37.0 25.0 37.0 140-144 34.6526 37.0 37.0 37.0 25.0 37.0 145-149 34.416700000000006 37.0 37.0 37.0 25.0 37.0 150-151 34.00025 37.0 37.0 37.0 25.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 13 1.0 14 1.0 15 1.0 16 2.0 17 1.0 18 0.0 19 0.0 20 3.0 21 3.0 22 1.0 23 5.0 24 4.0 25 7.0 26 12.0 27 9.0 28 15.0 29 22.0 30 26.0 31 54.0 32 67.0 33 118.0 34 249.0 35 573.0 36 2553.0 37 273.0 >>END_MODULE >>Per base sequence content warn #Base G A T C 1 36.7 23.400000000000002 9.775 30.125 2 25.924999999999997 26.474999999999998 31.374999999999996 16.225 3 21.4 27.275 31.4 19.925 4 22.875 33.025 24.025 20.075000000000003 5 26.474999999999998 37.4 19.725 16.400000000000002 6 22.025 37.65 23.9 16.425 7 21.175 21.3 37.075 20.45 8 21.4 25.825 28.000000000000004 24.775 9 20.974999999999998 25.55 30.625000000000004 22.85 10-14 23.380000000000003 28.89 26.265 21.465 15-19 23.549999999999997 27.6 27.855 20.995 20-24 22.725 29.005 27.195000000000004 21.075 25-29 23.945 28.68 26.76 20.615 30-34 23.185 28.625 26.790000000000003 21.4 35-39 24.14 27.310000000000002 27.060000000000002 21.490000000000002 40-44 23.205000000000002 28.01 27.915 20.87 45-49 23.175 27.57 27.884999999999998 21.37 50-54 22.865 28.18 27.67 21.285 55-59 23.615 27.900000000000002 27.24 21.245 60-64 23.64 28.884999999999998 26.495 20.979999999999997 65-69 23.45 28.21 27.644999999999996 20.695 70-74 23.685000000000002 27.66 27.665 20.990000000000002 75-79 23.549999999999997 27.950000000000003 27.49 21.01 80-84 24.13 28.134999999999998 27.284999999999997 20.45 85-89 24.265 28.095 27.075 20.565 90-94 24.145 28.485 26.384999999999998 20.985 95-99 24.09 28.535 26.765 20.61 100-104 24.5 28.595 25.919999999999998 20.985 105-109 25.119999999999997 28.09 26.505000000000003 20.285 110-114 26.05 28.389999999999997 25.635 19.925 115-119 26.985 27.515 25.759999999999998 19.74 120-124 26.99 27.79 25.69 19.53 125-129 27.310000000000002 28.16 25.665 18.865000000000002 130-134 28.74 27.615000000000002 25.130000000000003 18.515 135-139 29.485 27.365000000000002 25.374999999999996 17.775 140-144 30.490000000000002 26.555 25.115 17.84 145-149 31.46 26.685 25.045 16.81 150-151 32.25 25.8625 25.687500000000004 16.2 >>END_MODULE >>Per sequence GC content warn #GC Content Count 0 1.0 1 0.5 2 0.0 3 0.0 4 0.5 5 1.0 6 1.0 7 1.5 8 1.0 9 1.0 10 1.0 11 0.5 12 0.5 13 0.0 14 0.0 15 0.0 16 0.5 17 0.5 18 0.0 19 0.0 20 0.5 21 1.5 22 1.5 23 1.0 24 1.0 25 2.0 26 4.5 27 7.0 28 7.0 29 5.5 30 10.0 31 16.5 32 20.0 33 28.0 34 38.0 35 53.0 36 74.5 37 94.0 38 122.0 39 153.5 40 198.0 41 229.5 42 254.0 43 281.0 44 274.5 45 255.0 46 257.5 47 264.5 48 251.0 49 217.5 50 175.5 51 132.5 52 109.0 53 100.5 54 79.0 55 64.0 56 48.0 57 36.0 58 32.5 59 26.5 60 17.5 61 11.0 62 6.5 63 5.5 64 4.0 65 0.5 66 0.5 67 1.0 68 1.0 69 1.0 70 1.0 71 0.5 72 0.0 73 1.0 74 1.0 75 0.0 76 0.0 77 0.0 78 0.0 79 0.0 80 0.5 81 0.5 82 0.5 83 0.5 84 0.0 85 0.0 86 0.0 87 0.0 88 0.0 89 0.5 90 0.5 91 0.0 92 0.0 93 0.5 94 0.5 95 0.0 96 0.0 97 0.0 98 0.5 99 1.0 100 3.0 >>END_MODULE >>Per base N content pass #Base N-Count 1 0.0 2 0.0 3 0.0 4 0.0 5 0.0 6 0.0 7 0.0 8 0.0 9 0.0 10-14 0.0 15-19 0.0 20-24 0.0 25-29 0.0 30-34 0.0 35-39 0.0 40-44 0.0 45-49 0.0 50-54 0.0 55-59 0.0 60-64 0.0 65-69 0.0 70-74 0.0 75-79 0.0 80-84 0.0 85-89 0.0 90-94 0.0 95-99 0.0 100-104 0.0 105-109 0.0 110-114 0.0 115-119 0.0 120-124 0.0 125-129 0.0 130-134 0.0 135-139 0.0 140-144 0.0 145-149 0.0 150-151 0.0 >>END_MODULE >>Sequence Length Distribution pass #Length Count 151 4000.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 77.825 #Duplication Level Percentage of deduplicated Percentage of total 1 79.89078059749438 62.175000000000004 2 14.584002569868293 22.7 3 3.8226790876967556 8.924999999999999 4 0.9637006103437198 3.0 5 0.4818503051718599 1.875 6 0.128493414712496 0.6 7 0.09637006103437198 0.525 8 0.032123353678124 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 TGATGCTCCAGCACTTCATGAAGCAGACATTGGACTTGCAATGGGCATCG 8 0.2 No Hit CCAACGGCTGGAGGGACAGGAACATCGGTTGATAATGCAAGAACTTATAA 7 0.17500000000000002 No Hit ACTGCCTCATCGGATCATTCAATCAAAATAATTGGGGTTAACAACAATAC 7 0.17500000000000002 No Hit AGAGAACACATTCATACTCCAAGTCTTTTAGTTCATCCATTTAAGCTTAA 7 0.17500000000000002 No Hit GTTCCTAGTTCCTCTTGCTATATTGGGTGTGGCCTTTGGAATCCGCCTCT 6 0.15 No Hit GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG 6 0.15 No Hit CGCTACTTTTACCAGGAGAAAGGTTCATACTGTAGTGAAGGCCACATCTC 6 0.15 No Hit GCTATTCGTAATTGTGATAACTTCCAAGTAACAAAGGGTGATGTTGAGAA 6 0.15 No Hit GTACGAGGAGTGGCTTGTAAAGCATGGAAAGAACTACAACGCTCTAGGAG 5 0.125 No Hit CATGTTTGCCATCAACTACTACGTGGACTGGTTTGCAGTGCAACGATGAT 5 0.125 No Hit GTTCAAGGAAGCTGCTGATAAGATGCAAGGGCCTTTGAGACAGATTTTTG 5 0.125 No Hit ATCTCATCAGCCATCACAAATAATTCTGATCCATTTTTGCGTCTGTCACG 5 0.125 No Hit CTTACTGGGATGATTGGTTGCGATTGAAGGAGAATCATAAAGGTCGACAG 5 0.125 No Hit ATTAAAGCAGCGATTTGAGCAGAGTATGAAGGAAGCAGCTGACAAATTTC 5 0.125 No Hit AAGAAATTGACGGTGATAAAGATGGCAAGATAAGCAAAGATGAACTCTCC 5 0.125 No Hit CATGGGCTACCTGCTTCATTCAGGCTGCTTGGCGTCGGCACAAGAAGAGA 5 0.125 No Hit TGGAGGAATAAAAAACATTATGGTATTGGAACGTGGCTTCAATGGCTGGG 5 0.125 No Hit TGACAGCATTGGAAAGAAACTTGTGAACTCAAGGGAAGGACCCCCAACTT 5 0.125 No Hit GTTGTTTCCTTATCCTTGTCGAAATGGCTTCCATTTCTCTCCCTAAACAC 5 0.125 No Hit TATGAAACCAGAGAAGAGGAGGTAGTAGTATATGCTTAGTCCTAACACAT 5 0.125 No Hit GTCAGAACAAGGTGTTGTTGCTGCTGATGATGCCCGGTGTTCTGAAATCG 5 0.125 No Hit CTCCACCACACCCATCCGCAAACCCTCCTCCATATACCCATTACCCATTT 5 0.125 No Hit AGAACACATTCATACTCCAAGTCTTTTAGTTCATCCATTTAAGCTTAATC 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 0.0125 0.0 0.0 0.0 0.0 46-47 0.025 0.0 0.0 0.0 0.0 48-49 0.025 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 0.1 0.0 0.0 0.0 0.0 56-57 0.1 0.0 0.0 0.0 0.0 58-59 0.1 0.0 0.0 0.0 0.0 60-61 0.1375 0.0 0.0 0.0 0.0 62-63 0.15 0.0 0.0 0.0 0.0 64-65 0.21250000000000002 0.0 0.0 0.0 0.0 66-67 0.3125 0.0 0.0 0.0 0.0 68-69 0.42500000000000004 0.0 0.0 0.0 0.0 70-71 0.5375 0.0 0.0 0.0 0.0 72-73 0.6375 0.0 0.0 0.0 0.0 74-75 0.7375 0.0 0.0 0.0 0.0 76-77 0.9375 0.0 0.0 0.0 0.0 78-79 1.05 0.0 0.0 0.0 0.0 80-81 1.1749999999999998 0.0 0.0 0.0 0.0 82-83 1.4625 0.0 0.0 0.0 0.0 84-85 1.75 0.0 0.0 0.0 0.0 86-87 1.9375 0.0 0.0 0.0 0.0 88-89 2.25 0.0 0.0 0.0 0.0 90-91 2.625 0.0 0.0 0.0 0.0 92-93 2.9124999999999996 0.0 0.0 0.0 0.0 94-95 3.3875 0.0 0.0 0.0 0.0 96-97 4.25 0.0 0.0 0.0 0.0 98-99 4.7375 0.0 0.0 0.0 0.0 100-101 5.6 0.0 0.0 0.0 0.0 102-103 6.35 0.0 0.0 0.0 0.0 104-105 7.050000000000001 0.0 0.0 0.0 0.0 106-107 7.8500000000000005 0.0 0.0 0.0 0.0 108-109 8.925 0.0 0.0 0.0 0.0 110-111 9.712499999999999 0.0 0.0 0.0 0.0 112-113 10.4625 0.0 0.0 0.0 0.0 114-115 11.3625 0.0 0.0 0.0 0.0 116-117 12.225 0.0 0.0 0.0 0.0 118-119 13.2375 0.0 0.0 0.0 0.0 120-121 14.3125 0.0 0.0 0.0 0.0 122-123 15.212499999999999 0.0 0.0 0.0 0.0 124-125 16.2375 0.0 0.0 0.0 0.0 126-127 17.2875 0.0 0.0 0.0 0.0 128-129 18.2875 0.0 0.0 0.0 0.0 130-131 19.1625 0.0 0.0 0.0 0.0 132-133 19.987499999999997 0.0 0.0 0.0 0.0 134-135 21.1 0.0 0.0 0.0 0.0 136-137 22.0 0.0 0.0 0.0 0.0 138-139 22.825000000000003 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position GGGAAAT 10 0.006830828 145.0 1 >>END_MODULE Read 754779 spots for SRR12670101.sra Written 754779 spots for SRR12670101.sra Read 754779 spots for SRR12670101.sra Written 754779 spots for SRR12670101.sra Read 754779 spots for SRR12670101.sra Written 754779 spots for SRR12670101.sra Read 754779 spots for SRR12670101.sra Written 754779 spots for SRR12670101.sra Read 754779 spots for SRR12670101.sra Written 754779 spots for SRR12670101.sra Read 754779 spots for SRR12670101.sra Written 754779 spots for SRR12670101.sra Read 754779 spots for SRR12670101.sra Written 754779 spots for SRR12670101.sra Read 754779 spots for SRR12670101.sra Written 754779 spots for SRR12670101.sra Read 754779 spots for SRR12670101.sra Written 754779 spots for SRR12670101.sra Read 754779 spots for SRR12670101.sra Written 754779 spots for SRR12670101.sra Read 754789 spots for SRR12670101.sra Written 754789 spots for SRR12670101.sra Read 754779 spots for SRR12670101.sra Written 754779 spots for SRR12670101.sra Read 754779 spots for SRR12670101.sra Written 754779 spots for SRR12670101.sra Read 754779 spots for SRR12670101.sra Written 754779 spots for SRR12670101.sra Read 754779 spots for SRR12670101.sra Written 754779 spots for SRR12670101.sra Read 754779 spots for SRR12670101.sra Written 754779 spots for SRR12670101.sra Read 754779 spots for SRR12670101.sra Written 754779 spots for SRR12670101.sra Read 754779 spots for SRR12670101.sra Written 754779 spots for SRR12670101.sra Read 754779 spots for SRR12670101.sra Written 754779 spots for SRR12670101.sra Read 754779 spots for SRR12670101.sra Written 754779 spots for SRR12670101.sra SRR ids: ['SRR12670101.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_lzbvja1y SRR12670101.sra spots: 15095590 blocks: [[1, 754779], [754780, 1509558], [1509559, 2264337], [2264338, 3019116], [3019117, 3773895], [3773896, 4528674], [4528675, 5283453], [5283454, 6038232], [6038233, 6793011], [6793012, 7547790], [7547791, 8302569], [8302570, 9057348], [9057349, 9812127], [9812128, 10566906], [10566907, 11321685], [11321686, 12076464], [12076465, 12831243], [12831244, 13586022], [13586023, 14340801], [14340802, 15095590]] SRR12670101 file size 5108441 SRR12670101 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 SRR12670101 SRR12670101_1.fastq SRR12670101_2.fastq Input file: SRR12670101_1.fastq Paired file: SRR12670101_2.fastq trimmed: SRR12670101-trimmed-pair1.fastq, SRR12670101-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 Mon Feb 10 22:56:33 2025 >> started Mon Feb 10 22:56:49 2025 >> done (16.422s) 15095590 read pairs processed; of these: 76 ( 0.00%) short read pairs filtered out after trimming by size control 6810 ( 0.05%) empty read pairs filtered out after trimming by size control 15088704 (99.95%) read pairs available; of these: 3922809 (26.00%) trimmed read pairs available after processing 11165895 (74.00%) untrimmed read pairs available after processing Length distribution of reads after trimming: length count percentage 18 5 0.00% 19 2 0.00% 20 3 0.00% 21 10 0.00% 22 16 0.00% 23 14 0.00% 24 16 0.00% 25 19 0.00% 26 21 0.00% 27 30 0.00% 28 34 0.00% 29 41 0.00% 30 40 0.00% 31 46 0.00% 32 53 0.00% 33 53 0.00% 34 81 0.00% 35 76 0.00% 36 84 0.00% 37 99 0.00% 38 87 0.00% 39 134 0.00% 40 145 0.00% 41 144 0.00% 42 211 0.00% 43 154 0.00% 44 178 0.00% 45 233 0.00% 46 221 0.00% 47 253 0.00% 48 306 0.00% 49 468 0.00% 50 475 0.00% 51 556 0.00% 52 626 0.00% 53 642 0.00% 54 666 0.00% 55 693 0.00% 56 780 0.01% 57 936 0.01% 58 1091 0.01% 59 1275 0.01% 60 1490 0.01% 61 1739 0.01% 62 1950 0.01% 63 2159 0.01% 64 2406 0.02% 65 2608 0.02% 66 2790 0.02% 67 3046 0.02% 68 3367 0.02% 69 3886 0.03% 70 4541 0.03% 71 5195 0.03% 72 6257 0.04% 73 6792 0.05% 74 7441 0.05% 75 8022 0.05% 76 8745 0.06% 77 9572 0.06% 78 10302 0.07% 79 11290 0.07% 80 12334 0.08% 81 13958 0.09% 82 15673 0.10% 83 17489 0.12% 84 19193 0.13% 85 20631 0.14% 86 21876 0.14% 87 22632 0.15% 88 24373 0.16% 89 25151 0.17% 90 27414 0.18% 91 29098 0.19% 92 31114 0.21% 93 33796 0.22% 94 35866 0.24% 95 38173 0.25% 96 39836 0.26% 97 41035 0.27% 98 40944 0.27% 99 42573 0.28% 100 44009 0.29% 101 45189 0.30% 102 46902 0.31% 103 49442 0.33% 104 51218 0.34% 105 52670 0.35% 106 54389 0.36% 107 54844 0.36% 108 55435 0.37% 109 55820 0.37% 110 55824 0.37% 111 56789 0.38% 112 59008 0.39% 113 59180 0.39% 114 60796 0.40% 115 62759 0.42% 116 63695 0.42% 117 64537 0.43% 118 64536 0.43% 119 63640 0.42% 120 64570 0.43% 121 65130 0.43% 122 65958 0.44% 123 66365 0.44% 124 67018 0.44% 125 67614 0.45% 126 68648 0.45% 127 68998 0.46% 128 68786 0.46% 129 68235 0.45% 130 68747 0.46% 131 67958 0.45% 132 68230 0.45% 133 68747 0.46% 134 68524 0.45% 135 69459 0.46% 136 69881 0.46% 137 69639 0.46% 138 69990 0.46% 139 71090 0.47% 140 70036 0.46% 141 69718 0.46% 142 70126 0.46% 143 69292 0.46% 144 69889 0.46% 145 70091 0.46% 146 70912 0.47% 147 70338 0.47% 148 70564 0.47% 149 69723 0.46% 150 70077 0.46% 151 11165895 74.00% 15088704 reads passed initial QC criterion=sequence-density sequence-density=0.36 sequence-density-rank=1 fanout-score=1.97 fanout-score-rank=24 prefix-density=0.36 prefix-fanout=2.0 sequence=CGGTAGACCCAACCTTTCTCCAACTCGAATTCCAAGCAAGGAACCCACTT criterion=fanout-score sequence-density=0.03 sequence-density-rank=26 fanout-score=17.88 fanout-score-rank=1 prefix-density=0.11 prefix-fanout=5.0 sequence=AATGAAGAAGACACAAAGATAAAGACACTCACGGACACTTTTGTTTGTTCACTCCACACCCACAAGTACAGAAGAACACAGATTATTTATCAGAAATTACATTATTAATCCACTCCCAATCCCACATCAAACATGATAGTTGATGTGCTTGCTTAATGACCGCATGTGCAGGTAGTGCAAGTGCAGCCAGTACCGCAGTTGCACTTGCCATCGTTCTCAGCTGCTGGCACCTCCATGACTACGGAGGAGACATAGTTCTTCTCAGTCTCGACGATGCCAGCAGTGTAGCTGCTTCCCTTCTTGACACACTGGGTCTTGTCAGCGCAGTCGCAGTTGTCGCAGGTGCTAGACATGATGATTGATTGATTAAGCTTAAATGGATGAACTAAAAGACTTGGAGTATGAATGTGTTCTCTGTG criterion=sequence-density sequence-density=0.45 sequence-density-rank=1 fanout-score=2.08 fanout-score-rank=29 prefix-density=0.46 prefix-fanout=2.1 sequence=TGTAAGAGATGGCTTCCTC criterion=fanout-score sequence-density=0.01 sequence-density-rank=34 fanout-score=36.59 fanout-score-rank=1 prefix-density=0.13 prefix-fanout=1.9 sequence=GGAACTCAAACGCATAGCTTCCTACAAATACCCCAGCTAGCCAATACTCTCCACCACTAAACCCAAAGCTCAAAAAAAATCTTAACTGCACCCGCTCATCCAGCAATGGCAGCAGCAACAATGGCCCTCTCCTCCCCTTCGCTAGCCGGAAAGGCGGTGAAGCTCAACCCCTCCTCCTCTGAGATCATGGGCAATGGCCGTGTCTCCATGAGGAAAACCACCAAGCCTGTTCCCTCCGGGAGCCCATGGTACGGACCAGACCGTGTTAAATACTTGGGCCCGTTCTCTGGTGAGCCCCCATCCTACTTGACTGGTGAGTTCCCTGGTGACTACGGCTGGGACACTGCTGG SRR12670101 testing PE reads STAR mapping to Ensembl genome Started job on | Feb 10 22:57:32 Started mapping on | Feb 10 22:57:33 Finished on | Feb 10 22:59:03 Mapping speed, Million of reads per hour | 603.55 Number of input reads | 15088704 Average input read length | 285 UNIQUE READS: Uniquely mapped reads number | 14205791 Uniquely mapped reads % | 94.15% Average mapped length | 284.61 Number of splices: Total | 13920629 Number of splices: Annotated (sjdb) | 13623448 Number of splices: GT/AG | 13643409 Number of splices: GC/AG | 221387 Number of splices: AT/AC | 9016 Number of splices: Non-canonical | 46817 Mismatch rate per base, % | 0.35% Deletion rate per base | 0.03% Deletion average length | 2.89 Insertion rate per base | 0.02% Insertion average length | 2.50 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 340069 % of reads mapped to multiple loci | 2.25% Number of reads mapped to too many loci | 128352 % of reads mapped to too many loci | 0.85% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 2.59% % of reads unmapped: other | 0.16% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 542844 542844 542844 N_multimapping 340069 340069 340069 N_noFeature 466462 13973236 555910 N_ambiguous 228251 888 84688 UnstrandedReadsAssigned:13511078 PositiveStrandReadsAssigned:231667 NegativeStrandReadsAssigned:13565193 Dataset is classified negative stranded MeadianReadLen=151 20thPercentileLength=137 echo kmer=133 SRR12670101 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: SRR12670101-trimmed-pair1.fastq SRR12670101-trimmed-pair2.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 15,088,704 reads, 13,613,009 reads pseudoaligned [quant] estimated average fragment length: 209.534 [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,099 rounds 52401 SRR12670101.ke.tsv 34699 SRR12670101.se.tsv 87100 total ==> SRR12670101.ke.tsv <== target_id length eff_length est_counts tpm Potri.005G200100.1.v4.1 2018 1809.47 601 22.8048 Potri.005G024800.1.v4.1 1035 826.466 258 21.4337 Potri.004G059700.1.v4.1 961 752.545 4 0.364947 Potri.007G009000.2.v4.1 1416 1207.47 0 0 Potri.003G141000.2.v4.1 2943 2734.47 761 19.108 Potri.016G087400.1.v4.1 270 108.038 727 462.019 Potri.015G069301.1.v4.1 564 362.765 0 0 Potri.010G195200.1.v4.1 1773 1564.47 88 3.86206 Potri.012G127500.1.v4.1 977 768.509 135 12.0611 ==> SRR12670101.se.tsv <== Potri.001G166300.v4.1 0 Potri.001G448400.v4.1 241 Potri.001G233950.v4.1 0 Potri.001G122700.v4.1 237 Potri.001G212900.v4.1 2 Potri.001G182400.v4.1 0 Potri.001G256600.v4.1 0 Potri.001G040500.v4.1 10 Potri.001G416900.v4.1 0 Potri.001G452600.v4.1 6 SRR12670101 completed mapping pipeline successfully