Starting /dee2/code/volunteer_pipeline.sh SRR28623276 current disk space = 3050301022208 free memory = 1509814476 SRR28623276 SRAfilesize 3e9110cc5eb500b25c862763dd8251f8 SRR28623276.sra SRR28623276.sra file validated SRR28623276 is paired end SRR28623276 is conventional basespace SRR28623276 read1 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR28623276_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 43 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 36.384 37.0 37.0 37.0 37.0 37.0 2 36.403 37.0 37.0 37.0 37.0 37.0 3 36.507 37.0 37.0 37.0 37.0 37.0 4 36.666 37.0 37.0 37.0 37.0 37.0 5 36.633 37.0 37.0 37.0 37.0 37.0 6 36.566 37.0 37.0 37.0 37.0 37.0 7 36.562 37.0 37.0 37.0 37.0 37.0 8 36.459 37.0 37.0 37.0 37.0 37.0 9 36.502 37.0 37.0 37.0 37.0 37.0 10-14 36.5348 37.0 37.0 37.0 37.0 37.0 15-19 36.5219 37.0 37.0 37.0 37.0 37.0 20-24 36.479 37.0 37.0 37.0 37.0 37.0 25-29 36.4498 37.0 37.0 37.0 37.0 37.0 30-34 36.4272 37.0 37.0 37.0 37.0 37.0 35-39 36.369299999999996 37.0 37.0 37.0 37.0 37.0 40-44 36.311400000000006 37.0 37.0 37.0 37.0 37.0 45-49 36.2909 37.0 37.0 37.0 37.0 37.0 50-54 36.2279 37.0 37.0 37.0 37.0 37.0 55-59 36.231700000000004 37.0 37.0 37.0 37.0 37.0 60-64 36.2753 37.0 37.0 37.0 37.0 37.0 65-69 36.237899999999996 37.0 37.0 37.0 37.0 37.0 70-74 36.1354 37.0 37.0 37.0 37.0 37.0 75-79 36.1077 37.0 37.0 37.0 37.0 37.0 80-84 36.0693 37.0 37.0 37.0 37.0 37.0 85-89 36.0834 37.0 37.0 37.0 37.0 37.0 90-94 36.0844 37.0 37.0 37.0 37.0 37.0 95-99 35.8692 37.0 37.0 37.0 37.0 37.0 100-104 35.9471 37.0 37.0 37.0 37.0 37.0 105-109 35.912699999999994 37.0 37.0 37.0 37.0 37.0 110-114 35.8887 37.0 37.0 37.0 37.0 37.0 115-119 35.858999999999995 37.0 37.0 37.0 37.0 37.0 120-124 35.6147 37.0 37.0 37.0 37.0 37.0 125-129 35.5203 37.0 37.0 37.0 37.0 37.0 130-134 35.5958 37.0 37.0 37.0 37.0 37.0 135-139 35.38699999999999 37.0 37.0 37.0 34.6 37.0 140-144 35.0424 37.0 37.0 37.0 25.0 37.0 145-149 34.9782 37.0 37.0 37.0 27.4 37.0 150-151 34.71675 37.0 37.0 37.0 25.0 37.0 >>END_MODULE >>Per tile sequence quality pass #Tile Base Mean 1101 1 0.0 1101 2 0.0 1101 3 0.0 1101 4 0.0 1101 5 0.0 1101 6 0.0 1101 7 0.0 1101 8 0.0 1101 9 0.0 1101 10-14 0.0 1101 15-19 0.0 1101 20-24 0.0 1101 25-29 0.0 1101 30-34 0.0 1101 35-39 0.0 1101 40-44 0.0 1101 45-49 0.0 1101 50-54 0.0 1101 55-59 0.0 1101 60-64 0.0 1101 65-69 0.0 1101 70-74 0.0 1101 75-79 0.0 1101 80-84 0.0 1101 85-89 0.0 1101 90-94 0.0 1101 95-99 0.0 1101 100-104 0.0 1101 105-109 0.0 1101 110-114 0.0 1101 115-119 0.0 1101 120-124 0.0 1101 125-129 0.0 1101 130-134 0.0 1101 135-139 0.0 1101 140-144 0.0 1101 145-149 0.0 1101 150-151 0.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 18 1.0 19 1.0 20 0.0 21 1.0 22 0.0 23 3.0 24 2.0 25 3.0 26 9.0 27 11.0 28 18.0 29 14.0 30 40.0 31 43.0 32 67.0 33 106.0 34 176.0 35 444.0 36 2828.0 37 233.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 41.14400401404917 15.730055193176115 8.429503261414952 34.696437531359756 2 18.875 13.950000000000001 36.15 31.025000000000002 3 17.299999999999997 18.825 30.925000000000004 32.95 4 22.175 27.500000000000004 25.224999999999998 25.1 5 23.65 30.925000000000004 24.224999999999998 21.2 6 19.475 35.925000000000004 23.674999999999997 20.925 7 16.25 27.55 40.275 15.925 8 18.025 27.125 32.65 22.2 9 17.875 22.650000000000002 35.025 24.45 10-14 19.794999999999998 30.42 27.495000000000005 22.29 15-19 19.235 28.804999999999996 28.625 23.335 20-24 19.685 29.459999999999997 27.584999999999997 23.27 25-29 19.295 29.095 27.955000000000002 23.655 30-34 19.505 28.904999999999998 27.845 23.745 35-39 19.39 28.689999999999998 28.125 23.794999999999998 40-44 19.785 28.99 28.000000000000004 23.225 45-49 19.345000000000002 29.435 28.060000000000002 23.16 50-54 20.169999999999998 28.775000000000002 27.52 23.535 55-59 19.935 29.335 27.365000000000002 23.365 60-64 19.650000000000002 28.64 28.42 23.29 65-69 19.695 28.444999999999997 28.139999999999997 23.72 70-74 19.794999999999998 29.075 27.77 23.36 75-79 20.36 29.459999999999997 27.075 23.105 80-84 20.19 28.525 27.994999999999997 23.29 85-89 19.605 29.354999999999997 28.1 22.939999999999998 90-94 20.02 28.494999999999997 27.855 23.630000000000003 95-99 19.875 28.875 27.474999999999998 23.775 100-104 20.150000000000002 29.459999999999997 27.16 23.23 105-109 20.775 28.605000000000004 26.96 23.66 110-114 20.830000000000002 28.835 27.139999999999997 23.195 115-119 20.215 28.28 26.935 24.57 120-124 20.555 28.82 26.279999999999998 24.345 125-129 20.435 28.485 27.18 23.9 130-134 21.2 28.285 26.784999999999997 23.73 135-139 21.09 28.585 26.14 24.185000000000002 140-144 21.675 27.915 26.640000000000004 23.77 145-149 21.235 28.139999999999997 26.63 23.995 150-151 21.2875 27.787499999999998 26.3 24.625 >>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 0.5 7 0.5 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 0.5 19 0.0 20 0.5 21 1.0 22 1.5 23 2.5 24 4.5 25 6.5 26 8.0 27 9.0 28 12.0 29 16.5 30 24.0 31 31.5 32 44.0 33 53.5 34 67.0 35 89.5 36 97.0 37 128.0 38 168.5 39 179.0 40 192.5 41 221.0 42 232.5 43 232.5 44 268.0 45 289.5 46 261.0 47 239.5 48 213.5 49 187.0 50 155.0 51 120.5 52 105.0 53 76.0 54 63.5 55 55.5 56 37.0 57 23.5 58 15.5 59 16.0 60 15.0 61 12.5 62 6.5 63 2.0 64 1.5 65 1.0 66 1.0 67 2.0 68 2.5 69 1.5 70 1.5 71 2.0 72 0.5 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 0.35000000000000003 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 86.3 #Duplication Level Percentage of deduplicated Percentage of total 1 87.05098493626883 75.125 2 10.573580533024334 18.25 3 1.94090382387022 5.025 4 0.3186558516801854 1.0999999999999999 5 0.11587485515643105 0.5 6 0.0 0.0 7 0.0 0.0 8 0.0 0.0 9 0.0 0.0 >10 0.0 0.0 >50 0.0 0.0 >100 0.0 0.0 >500 0.0 0.0 >1k 0.0 0.0 >5k 0.0 0.0 >10k+ 0.0 0.0 >>END_MODULE >>Overrepresented sequences warn #Sequence Count Percentage Possible Source AATGAAATCCATACGAGCACCCAGGGCTCCATTTCCCTTTCGCCTTGTAG 5 0.125 No Hit GGATAGTCTGGAGGAAAATGAATTGTGACTAGAAAGACTCCTCCTGCATA 5 0.125 No Hit CCTCAAGTCATCATAGATTACTCTGGCTCTGTCACTATACGGTCCACTCT 5 0.125 No Hit GTGCCTCTCAATCTTCAGGGTAAGTTGACGGAGACGGGATTCAACCCATC 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 0.0 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 0.025 0.0 0.0 0.0 0.0 64-65 0.025 0.0 0.0 0.0 0.0 66-67 0.05 0.0 0.0 0.0 0.0 68-69 0.07500000000000001 0.0 0.0 0.0 0.0 70-71 0.1125 0.0 0.0 0.0 0.0 72-73 0.25 0.0 0.0 0.0 0.0 74-75 0.4125 0.0 0.0 0.0 0.0 76-77 0.45 0.0 0.0 0.0 0.0 78-79 0.575 0.0 0.0 0.0 0.0 80-81 0.6875 0.0 0.0 0.0 0.0 82-83 0.8 0.0 0.0 0.0 0.0 84-85 0.95 0.0 0.0 0.0 0.0 86-87 1.2 0.0 0.0 0.0 0.0 88-89 1.4874999999999998 0.0 0.0 0.0 0.0 90-91 1.8375 0.0 0.0 0.0 0.0 92-93 2.2625 0.0 0.0 0.0 0.0 94-95 2.5875 0.0 0.0 0.0 0.0 96-97 2.9625 0.0 0.0 0.0 0.0 98-99 3.5375 0.0 0.0 0.0 0.0 100-101 3.975 0.0 0.0 0.0 0.0 102-103 4.475 0.0 0.0 0.0 0.0 104-105 4.9375 0.0 0.0 0.0 0.0 106-107 5.3125 0.0 0.0 0.0 0.0 108-109 5.8125 0.0 0.0 0.0 0.0 110-111 6.3125 0.0 0.0 0.0 0.0 112-113 6.7875 0.0 0.0 0.0 0.0 114-115 7.225 0.0 0.0 0.0 0.0 116-117 7.737500000000001 0.0 0.0 0.0 0.0 118-119 8.287500000000001 0.0 0.0 0.0 0.0 120-121 8.850000000000001 0.0 0.0 0.0 0.0 122-123 9.475000000000001 0.0 0.0 0.0 0.0 124-125 10.100000000000001 0.0 0.0 0.0 0.0 126-127 10.8375 0.0 0.0 0.0 0.0 128-129 11.525 0.0 0.0 0.0 0.0 130-131 12.5625 0.0 0.0 0.0 0.0 132-133 13.412500000000001 0.0 0.0 0.0 0.0 134-135 14.2 0.0 0.0 0.0 0.0 136-137 14.75 0.0 0.0 0.0 0.0 138-139 15.3625 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position CAAGTGC 10 0.006830828 145.0 9 >>END_MODULE SRR28623276 read2 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR28623276_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 43 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 35.9175 37.0 37.0 37.0 37.0 37.0 2 36.066 37.0 37.0 37.0 37.0 37.0 3 36.014 37.0 37.0 37.0 37.0 37.0 4 36.133 37.0 37.0 37.0 37.0 37.0 5 36.2635 37.0 37.0 37.0 37.0 37.0 6 36.154 37.0 37.0 37.0 37.0 37.0 7 36.182 37.0 37.0 37.0 37.0 37.0 8 36.0815 37.0 37.0 37.0 37.0 37.0 9 36.0785 37.0 37.0 37.0 37.0 37.0 10-14 36.0315 37.0 37.0 37.0 37.0 37.0 15-19 35.99640000000001 37.0 37.0 37.0 37.0 37.0 20-24 35.9687 37.0 37.0 37.0 37.0 37.0 25-29 35.9217 37.0 37.0 37.0 37.0 37.0 30-34 35.831100000000006 37.0 37.0 37.0 37.0 37.0 35-39 35.8291 37.0 37.0 37.0 37.0 37.0 40-44 35.7522 37.0 37.0 37.0 37.0 37.0 45-49 35.707499999999996 37.0 37.0 37.0 37.0 37.0 50-54 35.676500000000004 37.0 37.0 37.0 37.0 37.0 55-59 35.552299999999995 37.0 37.0 37.0 37.0 37.0 60-64 35.5702 37.0 37.0 37.0 37.0 37.0 65-69 35.6205 37.0 37.0 37.0 37.0 37.0 70-74 35.6062 37.0 37.0 37.0 37.0 37.0 75-79 35.6201 37.0 37.0 37.0 37.0 37.0 80-84 35.4889 37.0 37.0 37.0 37.0 37.0 85-89 35.4405 37.0 37.0 37.0 37.0 37.0 90-94 35.4846 37.0 37.0 37.0 37.0 37.0 95-99 35.4222 37.0 37.0 37.0 37.0 37.0 100-104 35.341 37.0 37.0 37.0 37.0 37.0 105-109 35.2024 37.0 37.0 37.0 32.2 37.0 110-114 35.2759 37.0 37.0 37.0 37.0 37.0 115-119 35.2361 37.0 37.0 37.0 32.2 37.0 120-124 35.220299999999995 37.0 37.0 37.0 32.2 37.0 125-129 34.839800000000004 37.0 37.0 37.0 25.0 37.0 130-134 35.0601 37.0 37.0 37.0 25.0 37.0 135-139 34.9203 37.0 37.0 37.0 25.0 37.0 140-144 34.9222 37.0 37.0 37.0 25.0 37.0 145-149 34.7673 37.0 37.0 37.0 25.0 37.0 150-151 34.569 37.0 37.0 37.0 25.0 37.0 >>END_MODULE >>Per tile sequence quality pass #Tile Base Mean 1101 1 0.0 1101 2 0.0 1101 3 0.0 1101 4 0.0 1101 5 0.0 1101 6 0.0 1101 7 0.0 1101 8 0.0 1101 9 0.0 1101 10-14 0.0 1101 15-19 0.0 1101 20-24 0.0 1101 25-29 0.0 1101 30-34 0.0 1101 35-39 0.0 1101 40-44 0.0 1101 45-49 0.0 1101 50-54 0.0 1101 55-59 0.0 1101 60-64 0.0 1101 65-69 0.0 1101 70-74 0.0 1101 75-79 0.0 1101 80-84 0.0 1101 85-89 0.0 1101 90-94 0.0 1101 95-99 0.0 1101 100-104 0.0 1101 105-109 0.0 1101 110-114 0.0 1101 115-119 0.0 1101 120-124 0.0 1101 125-129 0.0 1101 130-134 0.0 1101 135-139 0.0 1101 140-144 0.0 1101 145-149 0.0 1101 150-151 0.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 12 2.0 13 6.0 14 10.0 15 10.0 16 5.0 17 2.0 18 6.0 19 7.0 20 7.0 21 10.0 22 13.0 23 11.0 24 11.0 25 13.0 26 9.0 27 11.0 28 12.0 29 23.0 30 16.0 31 46.0 32 65.0 33 129.0 34 218.0 35 647.0 36 2437.0 37 274.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 44.0 23.45 11.675 20.875 2 29.45 23.75 30.175 16.625 3 22.2 27.900000000000002 31.175000000000004 18.725 4 24.55 33.6 24.65 17.2 5 26.8 35.125 22.0 16.075 6 21.725 40.075 21.925 16.275000000000002 7 20.875 21.975 38.275 18.875 8 21.975 24.75 28.825 24.45 9 24.675 25.35 28.575 21.4 10-14 23.97 29.82 25.985000000000003 20.225 15-19 23.54 28.74 28.17 19.55 20-24 23.68 28.64 27.815 19.865 25-29 23.735 28.49 27.334999999999997 20.44 30-34 23.474999999999998 28.84 27.715 19.97 35-39 23.79 28.37 28.1 19.74 40-44 23.255 28.43 28.03 20.285 45-49 23.735 28.694999999999997 27.965 19.605 50-54 23.82 28.310000000000002 28.125 19.744999999999997 55-59 23.915 28.26 27.744999999999997 20.080000000000002 60-64 23.485 28.060000000000002 28.435 20.02 65-69 23.705000000000002 28.62 27.96 19.715 70-74 23.695 28.205000000000002 28.345 19.755 75-79 23.595 28.555000000000003 28.54 19.31 80-84 24.07 28.255000000000003 28.09 19.585 85-89 24.335 28.645 27.765 19.255 90-94 23.669999999999998 28.62 28.084999999999997 19.625 95-99 24.169999999999998 28.860000000000003 27.700000000000003 19.27 100-104 24.385 28.43 27.834999999999997 19.35 105-109 24.529999999999998 28.025 27.675 19.77 110-114 25.245 28.599999999999998 26.939999999999998 19.215 115-119 25.195 28.415000000000003 27.16 19.23 120-124 25.135 28.465 27.61 18.790000000000003 125-129 25.735000000000003 28.335 27.24 18.69 130-134 25.5 28.199999999999996 27.310000000000002 18.990000000000002 135-139 25.72 28.54 27.060000000000002 18.68 140-144 26.095000000000002 27.634999999999998 27.284999999999997 18.985 145-149 26.915 27.625 26.685 18.775 150-151 26.2125 27.500000000000004 27.800000000000004 18.4875 >>END_MODULE >>Per sequence GC content warn #GC Content Count 0 0.0 1 0.0 2 0.0 3 0.5 4 0.5 5 0.0 6 0.5 7 1.0 8 0.5 9 0.0 10 0.0 11 1.5 12 1.5 13 0.5 14 0.5 15 0.5 16 2.0 17 2.0 18 1.0 19 1.5 20 2.0 21 3.5 22 3.0 23 2.0 24 3.0 25 4.0 26 6.0 27 9.5 28 13.0 29 19.0 30 27.5 31 32.5 32 36.0 33 45.5 34 63.5 35 78.5 36 91.0 37 127.5 38 164.0 39 170.0 40 184.0 41 226.5 42 256.5 43 276.5 44 271.5 45 260.0 46 268.0 47 237.0 48 205.5 49 185.5 50 144.5 51 121.5 52 110.0 53 81.5 54 58.0 55 40.5 56 26.0 57 22.5 58 22.0 59 14.5 60 7.0 61 8.5 62 8.0 63 3.5 64 1.5 65 1.5 66 1.5 67 1.0 68 0.5 69 0.5 70 1.0 71 2.0 72 2.0 73 0.5 74 1.0 75 1.0 76 1.0 77 2.0 78 1.0 79 0.0 80 0.5 81 1.5 82 1.0 83 1.0 84 2.5 85 1.5 86 0.0 87 0.5 88 0.5 89 0.0 90 0.5 91 2.0 92 2.0 93 0.5 94 1.0 95 1.0 96 0.5 97 0.5 98 0.5 99 1.0 100 5.0 >>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 86.85000000000001 #Duplication Level Percentage of deduplicated Percentage of total 1 87.99654576856649 76.425 2 9.873344847438112 17.150000000000002 3 1.6119746689694874 4.2 4 0.40299366724237184 1.4000000000000001 5 0.08635578583765112 0.375 6 0.0 0.0 7 0.0 0.0 8 0.0 0.0 9 0.0 0.0 >10 0.02878526194588371 0.44999999999999996 >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 GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG 18 0.44999999999999996 No Hit CGAGAGCTTGTTCGTGATGTACTAGGAAGGCCAGTATCAAGACTTGTTCC 5 0.125 No Hit GAGTGGTTTTCCTGGGTCAATTTTTTTCATTCAAAGAAGCAAAAATGGCA 5 0.125 No Hit GGCAGAATGGGACACCCTTTTTGAGCCATTTTCATTCTTTGAAGCATATA 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 0.0 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 0.025 0.0 0.0 0.0 0.0 64-65 0.025 0.0 0.0 0.0 0.0 66-67 0.05 0.0 0.0 0.0 0.0 68-69 0.07500000000000001 0.0 0.0 0.0 0.0 70-71 0.1125 0.0 0.0 0.0 0.0 72-73 0.25 0.0 0.0 0.0 0.0 74-75 0.4125 0.0 0.0 0.0 0.0 76-77 0.45 0.0 0.0 0.0 0.0 78-79 0.575 0.0 0.0 0.0 0.0 80-81 0.6875 0.0 0.0 0.0 0.0 82-83 0.8 0.0 0.0 0.025 0.0 84-85 0.95 0.0 0.0 0.025 0.0 86-87 1.2 0.0 0.0 0.025 0.0 88-89 1.4874999999999998 0.0 0.0 0.025 0.0 90-91 1.8375 0.0 0.0 0.025 0.0 92-93 2.2625 0.0 0.0 0.025 0.0 94-95 2.575 0.0 0.0 0.025 0.0 96-97 2.9625 0.0 0.0 0.025 0.0 98-99 3.5375 0.0 0.0 0.025 0.0 100-101 3.9625 0.0 0.0 0.025 0.0 102-103 4.449999999999999 0.0 0.0 0.025 0.0 104-105 4.875 0.0 0.0 0.025 0.0 106-107 5.2375 0.0 0.0 0.025 0.0 108-109 5.7375 0.0 0.0 0.025 0.0 110-111 6.275 0.0 0.0 0.025 0.0 112-113 6.762499999999999 0.0 0.0 0.025 0.0 114-115 7.199999999999999 0.0 0.0 0.025 0.0 116-117 7.7125 0.0 0.0 0.025 0.0 118-119 8.2375 0.0 0.0 0.025 0.0 120-121 8.8 0.0 0.0 0.025 0.0 122-123 9.399999999999999 0.0 0.0 0.025 0.0 124-125 10.0 0.0 0.0 0.025 0.0 126-127 10.7375 0.0 0.0 0.025 0.0 128-129 11.425 0.0 0.0 0.025 0.0 130-131 12.4625 0.0 0.0 0.025 0.0 132-133 13.3125 0.0 0.0 0.025 0.0 134-135 14.125 0.0 0.0 0.025 0.0 136-137 14.712499999999999 0.0 0.0 0.025 0.0 138-139 15.3875 0.0 0.0 0.025 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position TTCCCAG 10 0.006830828 145.0 9 >>END_MODULE Read 1284521 spots for SRR28623276.sra Written 1284521 spots for SRR28623276.sra Read 1284521 spots for SRR28623276.sra Written 1284521 spots for SRR28623276.sra Read 1284521 spots for SRR28623276.sra Written 1284521 spots for SRR28623276.sra Read 1284521 spots for SRR28623276.sra Written 1284521 spots for SRR28623276.sra Read 1284521 spots for SRR28623276.sra Written 1284521 spots for SRR28623276.sra Read 1284521 spots for SRR28623276.sra Written 1284521 spots for SRR28623276.sra Read 1284521 spots for SRR28623276.sra Written 1284521 spots for SRR28623276.sra Read 1284525 spots for SRR28623276.sra Written 1284525 spots for SRR28623276.sra Read 1284521 spots for SRR28623276.sra Written 1284521 spots for SRR28623276.sra Read 1284521 spots for SRR28623276.sra Written 1284521 spots for SRR28623276.sra Read 1284521 spots for SRR28623276.sra Written 1284521 spots for SRR28623276.sra Read 1284521 spots for SRR28623276.sra Written 1284521 spots for SRR28623276.sra Read 1284521 spots for SRR28623276.sra Written 1284521 spots for SRR28623276.sra Read 1284521 spots for SRR28623276.sra Written 1284521 spots for SRR28623276.sra Read 1284521 spots for SRR28623276.sra Written 1284521 spots for SRR28623276.sra Read 1284521 spots for SRR28623276.sra Written 1284521 spots for SRR28623276.sra Read 1284521 spots for SRR28623276.sra Written 1284521 spots for SRR28623276.sra Read 1284521 spots for SRR28623276.sra Written 1284521 spots for SRR28623276.sra Read 1284521 spots for SRR28623276.sra Written 1284521 spots for SRR28623276.sra Read 1284521 spots for SRR28623276.sra Written 1284521 spots for SRR28623276.sra SRR ids: ['SRR28623276.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_op_4r98u SRR28623276.sra spots: 25690424 blocks: [[1, 1284521], [1284522, 2569042], [2569043, 3853563], [3853564, 5138084], [5138085, 6422605], [6422606, 7707126], [7707127, 8991647], [8991648, 10276168], [10276169, 11560689], [11560690, 12845210], [12845211, 14129731], [14129732, 15414252], [15414253, 16698773], [16698774, 17983294], [17983295, 19267815], [19267816, 20552336], [20552337, 21836857], [21836858, 23121378], [23121379, 24405899], [24405900, 25690424]] SRR28623276 file size 9484189 SRR28623276 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 SRR28623276 SRR28623276_1.fastq SRR28623276_2.fastq Input file: SRR28623276_1.fastq Paired file: SRR28623276_2.fastq trimmed: SRR28623276-trimmed-pair1.fastq, SRR28623276-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 13:54:11 2025 >> started Tue Feb 11 13:54:41 2025 >> done (29.144s) 25690424 read pairs processed; of these: 29 ( 0.00%) short read pairs filtered out after trimming by size control 34629 ( 0.13%) empty read pairs filtered out after trimming by size control 25655766 (99.87%) read pairs available; of these: 5017293 (19.56%) trimmed read pairs available after processing 20638473 (80.44%) untrimmed read pairs available after processing Length distribution of reads after trimming: length count percentage 18 4 0.00% 19 4 0.00% 20 1 0.00% 21 5 0.00% 22 5 0.00% 23 6 0.00% 24 6 0.00% 25 3 0.00% 26 12 0.00% 27 16 0.00% 28 12 0.00% 29 14 0.00% 30 18 0.00% 31 16 0.00% 32 20 0.00% 33 28 0.00% 34 31 0.00% 35 32 0.00% 36 27 0.00% 37 51 0.00% 38 47 0.00% 39 74 0.00% 40 90 0.00% 41 99 0.00% 42 109 0.00% 43 128 0.00% 44 140 0.00% 45 157 0.00% 46 180 0.00% 47 217 0.00% 48 290 0.00% 49 333 0.00% 50 448 0.00% 51 451 0.00% 52 522 0.00% 53 619 0.00% 54 675 0.00% 55 854 0.00% 56 876 0.00% 57 1051 0.00% 58 1195 0.00% 59 1527 0.01% 60 1780 0.01% 61 2190 0.01% 62 2471 0.01% 63 2900 0.01% 64 3182 0.01% 65 3528 0.01% 66 4043 0.02% 67 4477 0.02% 68 5208 0.02% 69 5761 0.02% 70 6701 0.03% 71 7840 0.03% 72 8997 0.04% 73 10190 0.04% 74 11052 0.04% 75 12282 0.05% 76 13362 0.05% 77 14087 0.05% 78 15510 0.06% 79 16807 0.07% 80 17993 0.07% 81 19921 0.08% 82 21841 0.09% 83 23570 0.09% 84 25422 0.10% 85 27332 0.11% 86 28061 0.11% 87 29563 0.12% 88 30801 0.12% 89 32008 0.12% 90 33590 0.13% 91 35516 0.14% 92 37630 0.15% 93 39807 0.16% 94 41437 0.16% 95 43768 0.17% 96 45506 0.18% 97 46660 0.18% 98 47178 0.18% 99 48803 0.19% 100 50571 0.20% 101 51757 0.20% 102 53057 0.21% 103 55788 0.22% 104 57422 0.22% 105 59687 0.23% 106 61754 0.24% 107 62415 0.24% 108 63435 0.25% 109 64492 0.25% 110 65076 0.25% 111 67129 0.26% 112 68240 0.27% 113 68765 0.27% 114 71374 0.28% 115 73792 0.29% 116 75084 0.29% 117 76480 0.30% 118 78188 0.30% 119 78840 0.31% 120 78977 0.31% 121 79937 0.31% 122 80320 0.31% 123 81927 0.32% 124 84130 0.33% 125 84639 0.33% 126 86569 0.34% 127 87666 0.34% 128 88229 0.34% 129 88820 0.35% 130 90416 0.35% 131 90135 0.35% 132 90978 0.35% 133 92171 0.36% 134 92352 0.36% 135 93592 0.36% 136 94096 0.37% 137 95069 0.37% 138 97109 0.38% 139 97949 0.38% 140 97438 0.38% 141 97955 0.38% 142 98810 0.39% 143 98332 0.38% 144 100552 0.39% 145 100022 0.39% 146 99781 0.39% 147 101229 0.39% 148 102116 0.40% 149 101365 0.40% 150 102098 0.40% 151 20638473 80.44% 25655766 reads passed initial QC criterion=sequence-density sequence-density=0.22 sequence-density-rank=1 fanout-score=15.59 fanout-score-rank=13 prefix-density=0.16 prefix-fanout=15.6 sequence=GGATCGGAAGAGCACACGTCTGAACTCCAGTCACGTTCAACCATCTCGTATGCCGTCTTCTGCTTGAAA criterion=fanout-score sequence-density=0.01 sequence-density-rank=39 fanout-score=235.02 fanout-score-rank=1 prefix-density=0.16 prefix-fanout=15.1 sequence=CTCCTTCCTCTAAATGATAAGGTTCAGTGGACTTCTCGCGACGTCGCCGGCGGCGAACCGCCCACGTCGCCGCGATCCGAACACTTCACCGGACCATTCAATCGGTAGGAGCGACGGGCGGTGTGTACAAAGGGCAGGGACGTAGTCAACGCGAGCTGATGACTCGCGCTTACTAGGAATTCCTCGTTGAAGACCAACAATTGCAATGATCTATCCCCATCACGATGAAATTTCAAAGATTACCCGGGCCTGTCGGCCAAGGCTATAGACTCGTTGAATACATCAGTGTAGCGCGCGTGCGGCCCAGAACATCTAAGGGCATCACAGACCTGTTATTGCCTCAAACTTCCTTGGCCTGGAAGGCCATAGTCCCTCTAAGAAGCTGGCCGCGGAGGGTCACCTCCGCATAGCTAGTTAGCAGGCTGAGGTCTCGTTCGTTAACGGAATTAACC criterion=sequence-density sequence-density=0.18 sequence-density-rank=1 fanout-score=2.98 fanout-score-rank=30 prefix-density=0.20 prefix-fanout=2.6 sequence=GGGATGGAGAAGCTGGTTTCAGAGGTTGATCTTGTCAAGTCCTTTGAATGGGGGCA criterion=fanout-score sequence-density=0.08 sequence-density-rank=15 fanout-score=355.95 fanout-score-rank=1 prefix-density=0.90 prefix-fanout=31.1 sequence=AAGAAGAAGAAA SRR28623276 testing PE reads STAR mapping to Ensembl genome Started job on | Feb 11 13:56:22 Started mapping on | Feb 11 13:56:22 Finished on | Feb 11 13:59:16 Mapping speed, Million of reads per hour | 530.81 Number of input reads | 25655766 Average input read length | 290 UNIQUE READS: Uniquely mapped reads number | 23657978 Uniquely mapped reads % | 92.21% Average mapped length | 288.47 Number of splices: Total | 20650666 Number of splices: Annotated (sjdb) | 20105069 Number of splices: GT/AG | 20270560 Number of splices: GC/AG | 293613 Number of splices: AT/AC | 22963 Number of splices: Non-canonical | 63530 Mismatch rate per base, % | 0.42% Deletion rate per base | 0.04% Deletion average length | 3.04 Insertion rate per base | 0.03% Insertion average length | 2.36 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 599570 % of reads mapped to multiple loci | 2.34% Number of reads mapped to too many loci | 177636 % of reads mapped to too many loci | 0.69% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 4.43% % of reads unmapped: other | 0.33% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 1398218 1398218 1398218 N_multimapping 599570 599570 599570 N_noFeature 1191391 23352747 1349599 N_ambiguous 283880 2110 135478 UnstrandedReadsAssigned:22182707 PositiveStrandReadsAssigned:303121 NegativeStrandReadsAssigned:22172901 Dataset is classified negative stranded MeadianReadLen=151 20thPercentileLength=150 echo kmer=145 SRR28623276 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: SRR28623276-trimmed-pair1.fastq SRR28623276-trimmed-pair2.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 25,655,766 reads, 22,573,176 reads pseudoaligned [quant] estimated average fragment length: 219.67 [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,159 rounds 52401 SRR28623276.ke.tsv 34699 SRR28623276.se.tsv 87100 total ==> SRR28623276.ke.tsv <== target_id length eff_length est_counts tpm Potri.005G200100.1.v4.1 2018 1799.33 953 23.4941 Potri.005G024800.1.v4.1 1035 816.33 757 41.1346 Potri.004G059700.1.v4.1 961 742.344 330 19.719 Potri.007G009000.2.v4.1 1416 1197.33 0 0 Potri.003G141000.2.v4.1 2943 2724.33 660.107 10.7481 Potri.016G087400.1.v4.1 270 100.713 1655.77 729.276 Potri.015G069301.1.v4.1 564 350.333 0 0 Potri.010G195200.1.v4.1 1773 1554.33 35 0.998854 Potri.012G127500.1.v4.1 977 758.338 11896 695.85 ==> SRR28623276.se.tsv <== Potri.001G166300.v4.1 0 Potri.001G448400.v4.1 1699 Potri.001G233950.v4.1 0 Potri.001G122700.v4.1 560 Potri.001G212900.v4.1 1 Potri.001G182400.v4.1 1 Potri.001G256600.v4.1 0 Potri.001G040500.v4.1 0 Potri.001G416900.v4.1 29 Potri.001G452600.v4.1 3 SRR28623276 completed mapping pipeline successfully