Starting /dee2/code/volunteer_pipeline.sh SRR13662595 current disk space = 1526743379968 free memory = 1442043444 SRR13662595 SRAfilesize ab7adf66e1910509e97249307ea34106 SRR13662595.sra SRR13662595.sra file validated SRR13662595 is paired end SRR13662595 is conventional basespace SRR13662595 read1 length is 125 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR13662595_1.fastq File type Conventional base calls Encoding Sanger / Illumina 1.9 Total Sequences 4000 Sequences flagged as poor quality 0 Sequence length 125 %GC 53 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 32.55525 33.0 33.0 34.0 32.0 34.0 2 32.2965 33.0 33.0 34.0 30.0 34.0 3 32.449 33.0 33.0 34.0 31.0 34.0 4 32.5725 33.0 33.0 34.0 31.0 34.0 5 32.4925 33.0 33.0 34.0 31.0 34.0 6 36.105 38.0 37.0 38.0 33.0 38.0 7 36.498 38.0 37.0 38.0 34.0 38.0 8 36.6905 38.0 38.0 38.0 34.0 38.0 9 36.818 38.0 38.0 38.0 35.0 38.0 10-11 36.730500000000006 38.0 38.0 38.0 34.0 38.0 12-13 36.662875 38.0 38.0 38.0 34.0 38.0 14-15 36.7665 38.0 38.0 38.0 34.5 38.0 16-17 36.642125 38.0 38.0 38.0 34.0 38.0 18-19 36.829499999999996 38.0 38.0 38.0 35.0 38.0 20-21 36.801 38.0 38.0 38.0 35.0 38.0 22-23 36.870374999999996 38.0 38.0 38.0 35.0 38.0 24-25 36.747625 38.0 38.0 38.0 34.5 38.0 26-27 36.704875 38.0 38.0 38.0 34.5 38.0 28-29 36.70825 38.0 38.0 38.0 34.5 38.0 30-31 36.683 38.0 38.0 38.0 34.5 38.0 32-33 36.56125 38.0 38.0 38.0 34.0 38.0 34-35 36.509875 38.0 38.0 38.0 34.0 38.0 36-37 36.553375 38.0 38.0 38.0 34.0 38.0 38-39 36.49825 38.0 38.0 38.0 34.0 38.0 40-41 36.489625000000004 38.0 38.0 38.0 33.5 38.0 42-43 36.58925 38.0 38.0 38.0 34.0 38.0 44-45 36.5805 38.0 38.0 38.0 34.0 38.0 46-47 36.449875000000006 38.0 38.0 38.0 33.5 38.0 48-49 36.656625000000005 38.0 38.0 38.0 34.0 38.0 50-51 36.649 38.0 38.0 38.0 34.0 38.0 52-53 36.532624999999996 38.0 38.0 38.0 34.0 38.0 54-55 36.591125000000005 38.0 38.0 38.0 34.0 38.0 56-57 36.601375000000004 38.0 38.0 38.0 34.0 38.0 58-59 36.329875 38.0 38.0 38.0 33.5 38.0 60-61 36.416 38.0 38.0 38.0 33.5 38.0 62-63 36.321625 38.0 38.0 38.0 33.0 38.0 64-65 36.21825 38.0 38.0 38.0 33.0 38.0 66-67 36.347375 38.0 38.0 38.0 33.5 38.0 68-69 36.58575 38.0 38.0 38.0 34.0 38.0 70-71 36.40025 38.0 38.0 38.0 33.5 38.0 72-73 36.317 38.0 38.0 38.0 33.5 38.0 74-75 36.191125 38.0 38.0 38.0 33.0 38.0 76-77 36.34287500000001 38.0 38.0 38.0 33.5 38.0 78-79 36.2425 38.0 38.0 38.0 33.5 38.0 80-81 36.270875000000004 38.0 38.0 38.0 33.5 38.0 82-83 36.134375 38.0 37.5 38.0 33.0 38.0 84-85 36.050375 38.0 38.0 38.0 32.5 38.0 86-87 35.804125 38.0 37.0 38.0 31.0 38.0 88-89 36.022499999999994 38.0 37.5 38.0 32.5 38.0 90-91 36.117125 38.0 38.0 38.0 33.0 38.0 92-93 35.803875000000005 38.0 37.5 38.0 32.0 38.0 94-95 35.72225 38.0 37.5 38.0 31.0 38.0 96-97 35.770125 38.0 37.0 38.0 31.5 38.0 98-99 35.346000000000004 38.0 36.5 38.0 30.0 38.0 100-101 35.586875 38.0 37.0 38.0 30.0 38.0 102-103 35.567875 38.0 37.0 38.0 30.5 38.0 104-105 35.709999999999994 38.0 37.0 38.0 31.5 38.0 106-107 35.414125 38.0 36.5 38.0 30.0 38.0 108-109 35.272875 38.0 36.5 38.0 29.0 38.0 110-111 35.111875 38.0 36.0 38.0 28.0 38.0 112-113 35.18825 38.0 36.5 38.0 29.5 38.0 114-115 35.140125 38.0 36.0 38.0 29.0 38.0 116-117 34.901625 38.0 36.0 38.0 27.0 38.0 118-119 35.135374999999996 38.0 36.0 38.0 30.0 38.0 120-121 34.663125 38.0 35.5 38.0 26.0 38.0 122-123 34.909875 38.0 36.0 38.0 29.5 38.0 124-125 34.38175 38.0 35.5 38.0 28.0 38.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 15 3.0 16 3.0 17 4.0 18 6.0 19 2.0 20 8.0 21 1.0 22 7.0 23 9.0 24 13.0 25 24.0 26 18.0 27 37.0 28 51.0 29 55.0 30 65.0 31 78.0 32 111.0 33 175.0 34 178.0 35 235.0 36 499.0 37 2418.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 41.975 11.799999999999999 10.65 35.575 2 32.574999999999996 16.675 27.925 22.825 3 27.474999999999998 23.425 19.05 30.049999999999997 4 31.324999999999996 29.125 16.75 22.8 5 31.175000000000004 28.175 19.975 20.674999999999997 6 23.95 33.175 19.475 23.400000000000002 7 22.175 16.325 36.449999999999996 25.05 8 24.2 19.525000000000002 25.45 30.825000000000003 9 24.675 19.475 27.224999999999998 28.625 10-11 27.462500000000002 27.35 19.8875 25.3 12-13 25.2875 22.075 25.1 27.537499999999998 14-15 25.2625 23.0 24.175 27.5625 16-17 25.7125 23.3875 23.65 27.250000000000004 18-19 26.8625 22.8 24.212500000000002 26.125 20-21 26.400000000000002 22.8375 22.912499999999998 27.85 22-23 26.700000000000003 23.2375 22.925 27.1375 24-25 25.624999999999996 23.724999999999998 23.9875 26.6625 26-27 26.375 23.674999999999997 22.6375 27.3125 28-29 26.3625 23.0875 22.7125 27.8375 30-31 26.55 23.0375 22.8625 27.55 32-33 26.650000000000002 23.9375 23.525 25.887500000000003 34-35 26.575 23.1 23.599999999999998 26.724999999999998 36-37 26.825 23.724999999999998 24.1625 25.2875 38-39 27.0 22.7125 23.4875 26.8 40-41 25.650000000000002 22.162499999999998 24.075 28.1125 42-43 26.987499999999997 22.412499999999998 24.087500000000002 26.5125 44-45 26.8375 23.0625 22.575 27.525 46-47 26.5125 23.549999999999997 22.275 27.6625 48-49 26.25 23.150000000000002 23.5125 27.0875 50-51 26.0375 23.6375 23.125 27.200000000000003 52-53 27.187499999999996 22.425 23.1375 27.250000000000004 54-55 26.700000000000003 22.6125 22.975 27.712500000000002 56-57 26.4625 23.025000000000002 23.1125 27.400000000000002 58-59 26.525 23.8125 23.3625 26.3 60-61 26.6625 23.674999999999997 22.55 27.1125 62-63 26.687499999999996 22.5 23.1 27.712500000000002 64-65 26.2125 23.2125 23.175 27.400000000000002 66-67 26.05 24.1375 23.0 26.8125 68-69 27.3625 22.8375 23.2375 26.5625 70-71 26.224999999999998 23.1 23.400000000000002 27.275 72-73 26.0125 22.625 23.6875 27.675 74-75 26.6625 23.2125 23.5375 26.5875 76-77 26.424999999999997 22.5625 23.575 27.437499999999996 78-79 25.887500000000003 24.1125 23.7375 26.2625 80-81 26.4125 22.6375 23.775 27.175 82-83 27.0875 22.6 22.425 27.8875 84-85 26.937499999999996 22.6375 22.7625 27.6625 86-87 26.924999999999997 23.225 23.575 26.275 88-89 26.9625 23.0875 23.325000000000003 26.625 90-91 26.650000000000002 24.087500000000002 23.3 25.9625 92-93 26.55 23.1375 22.9375 27.375 94-95 28.249999999999996 22.8375 23.325000000000003 25.587500000000002 96-97 27.525 23.25 22.8375 26.387500000000003 98-99 27.3875 22.75 23.25 26.6125 100-101 26.6125 22.900000000000002 23.5625 26.924999999999997 102-103 26.825 23.325000000000003 22.775000000000002 27.075 104-105 27.575 23.275000000000002 22.8125 26.337500000000002 106-107 27.237499999999997 22.8875 22.7 27.175 108-109 26.5375 22.95 22.625 27.8875 110-111 26.5625 23.4875 23.4625 26.487500000000004 112-113 27.787499999999998 22.4875 22.85 26.875 114-115 26.687499999999996 21.7875 24.3875 27.1375 116-117 26.6125 23.125 23.3375 26.924999999999997 118-119 27.55 22.7 22.775000000000002 26.974999999999998 120-121 26.55 23.275000000000002 23.3625 26.8125 122-123 26.974999999999998 23.125 22.85 27.05 124-125 26.275 23.4625 23.400000000000002 26.8625 >>END_MODULE >>Per sequence GC content fail #GC Content Count 0 1.0 1 1.5 2 1.5 3 1.0 4 2.0 5 1.5 6 0.0 7 0.0 8 0.0 9 0.5 10 0.5 11 0.0 12 0.5 13 0.5 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 0.0 24 1.0 25 2.0 26 1.0 27 0.5 28 1.0 29 2.0 30 5.0 31 5.0 32 11.5 33 18.0 34 15.5 35 21.0 36 31.0 37 42.5 38 56.5 39 72.0 40 88.0 41 97.5 42 105.0 43 124.0 44 143.5 45 146.5 46 143.0 47 151.5 48 152.0 49 148.5 50 139.0 51 126.0 52 127.5 53 119.5 54 111.0 55 113.0 56 97.5 57 88.5 58 96.0 59 91.5 60 90.0 61 90.5 62 88.5 63 84.5 64 78.0 65 70.5 66 71.5 67 78.5 68 80.5 69 78.0 70 78.0 71 70.5 72 55.0 73 50.5 74 48.5 75 35.0 76 30.0 77 30.0 78 20.5 79 20.0 80 18.0 81 8.0 82 6.0 83 6.5 84 3.5 85 2.0 86 1.0 87 0.5 88 0.5 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 0.0 3 0.0 4 0.0 5 0.0 6 0.0 7 0.0 8 0.0 9 0.0 10-11 0.0 12-13 0.0 14-15 0.0 16-17 0.0 18-19 0.0 20-21 0.0 22-23 0.0 24-25 0.0 26-27 0.0 28-29 0.0 30-31 0.0 32-33 0.0 34-35 0.0 36-37 0.0 38-39 0.0 40-41 0.0 42-43 0.0 44-45 0.0 46-47 0.0 48-49 0.0 50-51 0.0 52-53 0.0 54-55 0.0 56-57 0.0 58-59 0.0 60-61 0.0 62-63 0.0 64-65 0.0 66-67 0.0 68-69 0.0 70-71 0.0 72-73 0.0 74-75 0.0 76-77 0.0 78-79 0.0 80-81 0.0 82-83 0.0 84-85 0.0 86-87 0.0 88-89 0.0 90-91 0.0 92-93 0.0 94-95 0.0 96-97 0.0 98-99 0.0 100-101 0.0 102-103 0.0 104-105 0.0 106-107 0.0 108-109 0.0 110-111 0.0 112-113 0.0 114-115 0.0 116-117 0.0 118-119 0.0 120-121 0.0 122-123 0.0 124-125 0.0 >>END_MODULE >>Sequence Length Distribution pass #Length Count 125 4000.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 99.7 #Duplication Level Percentage of deduplicated Percentage of total 1 99.74924774322969 99.45 2 0.20060180541624875 0.4 3 0.05015045135406219 0.15 4 0.0 0.0 5 0.0 0.0 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 pass >>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 0.0 0.0 0.0 0.0 0.0 88-89 0.0 0.0 0.0 0.0 0.0 90-91 0.0 0.0 0.0 0.0 0.0 92-93 0.0 0.0 0.0 0.0 0.0 94-95 0.0 0.0 0.0 0.0 0.0 96-97 0.0 0.0 0.0 0.0 0.0 98-99 0.0 0.0 0.0 0.0 0.0 100-101 0.0 0.0 0.0 0.0 0.0 102-103 0.0 0.0 0.0 0.0 0.0 104-105 0.0 0.0 0.0 0.0 0.0 106-107 0.0 0.0 0.0 0.0 0.0 108-109 0.0 0.0 0.0 0.0 0.0 110-111 0.0 0.0 0.0 0.0 0.0 112-113 0.0 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content pass >>END_MODULE SRR13662595 read2 length is 125 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR13662595_2.fastq File type Conventional base calls Encoding Sanger / Illumina 1.9 Total Sequences 4000 Sequences flagged as poor quality 0 Sequence length 125 %GC 53 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 31.3925 33.0 32.0 34.0 25.0 34.0 2 31.54525 33.0 32.0 34.0 27.0 34.0 3 31.343 33.0 32.0 34.0 25.0 34.0 4 31.3175 33.0 32.0 34.0 27.0 34.0 5 31.43425 33.0 32.0 34.0 27.0 34.0 6 35.01875 38.0 36.0 38.0 27.0 38.0 7 35.28575 38.0 36.0 38.0 28.0 38.0 8 34.88675 38.0 36.0 38.0 26.0 38.0 9 35.436 38.0 37.0 38.0 29.0 38.0 10-11 35.2935 38.0 36.5 38.0 28.0 38.0 12-13 35.409625000000005 38.0 36.5 38.0 28.5 38.0 14-15 34.997125 38.0 36.0 38.0 27.0 38.0 16-17 35.390874999999994 38.0 36.5 38.0 28.0 38.0 18-19 35.190875 38.0 36.0 38.0 27.5 38.0 20-21 34.682875 38.0 36.0 38.0 25.0 38.0 22-23 35.314750000000004 38.0 36.0 38.0 28.0 38.0 24-25 35.357124999999996 38.0 36.5 38.0 27.5 38.0 26-27 34.822625 38.0 36.0 38.0 26.0 38.0 28-29 35.438 38.0 36.5 38.0 28.0 38.0 30-31 35.238375 38.0 36.5 38.0 27.5 38.0 32-33 34.913250000000005 38.0 36.0 38.0 25.0 38.0 34-35 34.911375 38.0 36.0 38.0 25.0 38.0 36-37 35.102375 38.0 36.0 38.0 27.0 38.0 38-39 34.49375 38.0 35.5 38.0 24.0 38.0 40-41 34.934125 38.0 35.5 38.0 26.0 38.0 42-43 35.190625 38.0 36.5 38.0 27.0 38.0 44-45 34.913 38.0 35.5 38.0 25.5 38.0 46-47 35.5645 38.0 36.5 38.0 28.5 38.0 48-49 35.55225 38.0 37.0 38.0 29.0 38.0 50-51 35.567499999999995 38.0 37.0 38.0 29.0 38.0 52-53 35.6525 38.0 37.0 38.0 29.0 38.0 54-55 35.56825 38.0 37.0 38.0 29.0 38.0 56-57 35.66925 38.0 37.0 38.0 29.0 38.0 58-59 35.405875 38.0 37.0 38.0 28.0 38.0 60-61 35.506 38.0 37.0 38.0 28.5 38.0 62-63 35.561875 38.0 36.5 38.0 29.5 38.0 64-65 35.26175 38.0 36.0 38.0 27.5 38.0 66-67 35.4375 38.0 36.5 38.0 28.5 38.0 68-69 35.646125 38.0 37.0 38.0 29.0 38.0 70-71 35.580749999999995 38.0 37.0 38.0 29.0 38.0 72-73 35.541875 38.0 36.5 38.0 29.5 38.0 74-75 35.073625 38.0 36.0 38.0 26.5 38.0 76-77 35.34825 38.0 36.0 38.0 28.5 38.0 78-79 35.44675 38.0 36.5 38.0 28.5 38.0 80-81 35.299125000000004 38.0 36.5 38.0 28.5 38.0 82-83 35.280375 38.0 36.5 38.0 28.0 38.0 84-85 35.505250000000004 38.0 37.0 38.0 29.0 38.0 86-87 35.158125 38.0 36.0 38.0 27.5 38.0 88-89 35.35275 38.0 36.5 38.0 28.5 38.0 90-91 34.954625 38.0 36.0 38.0 26.5 38.0 92-93 35.227625 38.0 36.0 38.0 28.0 38.0 94-95 34.99525 38.0 35.5 38.0 27.0 38.0 96-97 35.17425 38.0 36.0 38.0 28.0 38.0 98-99 34.949875 38.0 35.5 38.0 26.5 38.0 100-101 35.101749999999996 38.0 36.0 38.0 28.0 38.0 102-103 35.072125 38.0 36.0 38.0 28.0 38.0 104-105 34.853125000000006 38.0 36.0 38.0 26.5 38.0 106-107 34.747125 38.0 35.5 38.0 25.5 38.0 108-109 34.686 38.0 35.5 38.0 25.0 38.0 110-111 34.840125 38.0 36.0 38.0 27.0 38.0 112-113 34.65875 38.0 35.0 38.0 25.0 38.0 114-115 34.917249999999996 38.0 36.0 38.0 27.5 38.0 116-117 34.469875 38.0 35.5 38.0 25.0 38.0 118-119 34.515125 38.0 35.0 38.0 25.0 38.0 120-121 34.2975 38.0 35.0 38.0 24.0 38.0 122-123 34.161249999999995 38.0 35.0 38.0 23.0 38.0 124-125 33.834500000000006 38.0 35.0 38.0 23.0 38.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 11 1.0 12 4.0 13 2.0 14 4.0 15 6.0 16 7.0 17 4.0 18 8.0 19 6.0 20 17.0 21 24.0 22 27.0 23 36.0 24 40.0 25 43.0 26 57.0 27 71.0 28 77.0 29 89.0 30 97.0 31 108.0 32 111.0 33 170.0 34 189.0 35 261.0 36 477.0 37 2064.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 40.525 12.1 11.0 36.375 2 30.125 18.099999999999998 27.200000000000003 24.575 3 28.275 23.875 19.55 28.299999999999997 4 30.75 27.525 17.150000000000002 24.575 5 29.275000000000002 31.55 18.475 20.7 6 22.025 35.35 19.625 23.0 7 22.025 16.175 37.0 24.8 8 22.825 20.150000000000002 26.025 31.0 9 23.925 20.075000000000003 27.025 28.975 10-11 27.1375 28.1625 19.3875 25.3125 12-13 25.8125 21.224999999999998 25.924999999999997 27.037499999999998 14-15 25.474999999999998 23.25 25.525 25.75 16-17 26.4125 22.575 24.25 26.7625 18-19 26.724999999999998 22.6875 23.974999999999998 26.6125 20-21 26.9125 24.025 23.75 25.3125 22-23 26.275 24.2625 22.8875 26.575 24-25 26.8375 24.0375 22.900000000000002 26.224999999999998 26-27 26.5 23.025000000000002 23.65 26.825 28-29 26.5875 23.474999999999998 23.599999999999998 26.337500000000002 30-31 25.9625 23.45 23.425 27.1625 32-33 26.375 23.35 23.9375 26.337500000000002 34-35 26.0125 23.4125 23.1 27.474999999999998 36-37 26.0375 23.962500000000002 22.45 27.55 38-39 25.6 23.9375 24.05 26.4125 40-41 26.2875 23.425 24.099999999999998 26.187500000000004 42-43 27.0 22.6 23.200000000000003 27.200000000000003 44-45 26.575 23.5875 23.625 26.2125 46-47 26.650000000000002 23.5375 23.375 26.437500000000004 48-49 27.250000000000004 22.7625 23.0125 26.974999999999998 50-51 26.737499999999997 23.3 24.099999999999998 25.8625 52-53 26.125 23.275000000000002 23.95 26.650000000000002 54-55 26.9125 23.674999999999997 23.1 26.3125 56-57 26.1125 23.35 23.3375 27.200000000000003 58-59 26.5625 23.3625 22.6375 27.437499999999996 60-61 26.2875 23.1375 23.0625 27.5125 62-63 28.000000000000004 23.2875 22.5875 26.125 64-65 26.9625 22.900000000000002 23.0875 27.05 66-67 26.525 23.4875 23.0375 26.950000000000003 68-69 26.937499999999996 22.5625 23.1 27.400000000000002 70-71 27.1625 23.0125 22.425 27.400000000000002 72-73 27.275 22.0625 23.875 26.787499999999998 74-75 27.325 22.7625 23.45 26.4625 76-77 26.387500000000003 23.3625 23.525 26.724999999999998 78-79 26.950000000000003 23.175 22.5625 27.3125 80-81 27.05 22.2 23.1625 27.5875 82-83 25.7875 23.925 23.799999999999997 26.487500000000004 84-85 27.275 22.525000000000002 23.3 26.900000000000002 86-87 26.5 23.2625 22.9375 27.3 88-89 27.212500000000002 22.2 23.599999999999998 26.987499999999997 90-91 27.6875 23.2125 22.9625 26.137500000000003 92-93 26.974999999999998 22.7125 23.4125 26.900000000000002 94-95 26.8625 23.1625 23.2125 26.7625 96-97 26.937499999999996 23.8875 21.875 27.3 98-99 27.175 23.175 23.4375 26.2125 100-101 26.237500000000004 22.912499999999998 23.25 27.6 102-103 26.700000000000003 23.95 22.425 26.924999999999997 104-105 26.150000000000002 22.6875 23.875 27.287499999999998 106-107 26.8625 22.925 23.0125 27.200000000000003 108-109 26.987499999999997 22.7125 23.200000000000003 27.1 110-111 27.6 23.7375 22.8625 25.8 112-113 27.250000000000004 22.6375 22.7 27.4125 114-115 27.700000000000003 22.325 23.275000000000002 26.700000000000003 116-117 26.6125 23.075000000000003 23.575 26.737499999999997 118-119 27.037499999999998 23.724999999999998 22.6375 26.6 120-121 27.1375 23.6375 22.8625 26.3625 122-123 27.725 23.775 22.6875 25.8125 124-125 27.3875 23.5375 23.3875 25.687500000000004 >>END_MODULE >>Per sequence GC content fail #GC Content Count 0 0.0 1 0.5 2 0.5 3 0.0 4 0.0 5 0.5 6 0.5 7 0.0 8 0.5 9 0.5 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 0.0 22 0.0 23 0.0 24 1.0 25 1.5 26 1.0 27 1.5 28 1.0 29 2.5 30 5.5 31 5.5 32 7.0 33 9.5 34 16.0 35 24.0 36 34.0 37 44.5 38 54.0 39 64.0 40 84.5 41 107.0 42 116.5 43 135.5 44 134.0 45 152.0 46 170.0 47 161.5 48 157.0 49 136.5 50 130.5 51 128.0 52 120.0 53 112.5 54 106.0 55 106.5 56 109.5 57 99.5 58 95.5 59 97.5 60 97.0 61 94.0 62 89.0 63 90.5 64 84.5 65 79.0 66 81.5 67 88.0 68 85.0 69 69.0 70 52.5 71 50.0 72 57.0 73 52.0 74 40.0 75 31.0 76 28.5 77 24.0 78 17.0 79 14.5 80 11.0 81 10.5 82 8.5 83 3.0 84 1.5 85 2.0 86 1.5 87 1.0 88 0.5 89 0.5 90 0.5 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 0.0 3 0.0 4 0.0 5 0.0 6 0.0 7 0.0 8 0.0 9 0.0 10-11 0.0 12-13 0.0 14-15 0.0 16-17 0.0 18-19 0.0 20-21 0.0 22-23 0.0 24-25 0.0 26-27 0.0 28-29 0.0 30-31 0.0 32-33 0.0 34-35 0.0 36-37 0.0 38-39 0.0 40-41 0.0 42-43 0.0 44-45 0.0 46-47 0.0 48-49 0.0 50-51 0.0 52-53 0.0 54-55 0.0 56-57 0.0 58-59 0.0 60-61 0.0 62-63 0.0 64-65 0.0 66-67 0.0 68-69 0.0 70-71 0.0 72-73 0.0 74-75 0.0 76-77 0.0 78-79 0.0 80-81 0.0 82-83 0.0 84-85 0.0 86-87 0.0 88-89 0.0 90-91 0.0 92-93 0.0 94-95 0.0 96-97 0.0 98-99 0.0 100-101 0.0 102-103 0.0 104-105 0.0 106-107 0.0 108-109 0.0 110-111 0.0 112-113 0.0 114-115 0.0 116-117 0.0 118-119 0.0 120-121 0.0 122-123 0.0 124-125 0.0 >>END_MODULE >>Sequence Length Distribution pass #Length Count 125 4000.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 99.825 #Duplication Level Percentage of deduplicated Percentage of total 1 99.82469321312296 99.65 2 0.1753067868770348 0.35000000000000003 3 0.0 0.0 4 0.0 0.0 5 0.0 0.0 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 pass >>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 0.0 0.0 0.0 0.0 0.0 88-89 0.0 0.0 0.0 0.0 0.0 90-91 0.0 0.0 0.0 0.0 0.0 92-93 0.0 0.0 0.0 0.0 0.0 94-95 0.0 0.0 0.0 0.0 0.0 96-97 0.0 0.0 0.0 0.0 0.0 98-99 0.0 0.0 0.0 0.0 0.0 100-101 0.0 0.0 0.0 0.0 0.0 102-103 0.0 0.0 0.0 0.0 0.0 104-105 0.0 0.0 0.0 0.0 0.0 106-107 0.0 0.0 0.0 0.0 0.0 108-109 0.0 0.0 0.0 0.0 0.0 110-111 0.0 0.0 0.0 0.0 0.0 112-113 0.0 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content pass >>END_MODULE Read 680725 spots for SRR13662595.sra Written 680725 spots for SRR13662595.sra Read 680725 spots for SRR13662595.sra Written 680725 spots for SRR13662595.sra Read 680725 spots for SRR13662595.sra Written 680725 spots for SRR13662595.sra Read 680725 spots for SRR13662595.sra Written 680725 spots for SRR13662595.sra Read 680725 spots for SRR13662595.sra Written 680725 spots for SRR13662595.sra Read 680740 spots for SRR13662595.sra Written 680740 spots for SRR13662595.sra Read 680725 spots for SRR13662595.sra Written 680725 spots for SRR13662595.sra Read 680725 spots for SRR13662595.sra Written 680725 spots for SRR13662595.sra Read 680725 spots for SRR13662595.sra Written 680725 spots for SRR13662595.sra Read 680725 spots for SRR13662595.sra Written 680725 spots for SRR13662595.sra Read 680725 spots for SRR13662595.sra Written 680725 spots for SRR13662595.sra Read 680725 spots for SRR13662595.sra Written 680725 spots for SRR13662595.sra Read 680725 spots for SRR13662595.sra Written 680725 spots for SRR13662595.sra Read 680725 spots for SRR13662595.sra Written 680725 spots for SRR13662595.sra Read 680725 spots for SRR13662595.sra Written 680725 spots for SRR13662595.sra Read 680725 spots for SRR13662595.sra Written 680725 spots for SRR13662595.sra Read 680725 spots for SRR13662595.sra Written 680725 spots for SRR13662595.sra Read 680725 spots for SRR13662595.sra Written 680725 spots for SRR13662595.sra Read 680725 spots for SRR13662595.sra Written 680725 spots for SRR13662595.sra Read 680725 spots for SRR13662595.sra Written 680725 spots for SRR13662595.sra SRR ids: ['SRR13662595.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_bmou_gxp SRR13662595.sra spots: 13614515 blocks: [[1, 680725], [680726, 1361450], [1361451, 2042175], [2042176, 2722900], [2722901, 3403625], [3403626, 4084350], [4084351, 4765075], [4765076, 5445800], [5445801, 6126525], [6126526, 6807250], [6807251, 7487975], [7487976, 8168700], [8168701, 8849425], [8849426, 9530150], [9530151, 10210875], [10210876, 10891600], [10891601, 11572325], [11572326, 12253050], [12253051, 12933775], [12933776, 13614515]] SRR13662595 file size 3913745 SRR13662595 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 SRR13662595 SRR13662595_1.fastq SRR13662595_2.fastq Input file: SRR13662595_1.fastq Paired file: SRR13662595_2.fastq trimmed: SRR13662595-trimmed-pair1.fastq, SRR13662595-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 Dec 10 07:52:12 2024 >> started Tue Dec 10 07:52:27 2024 >> done (14.558s) 13614515 read pairs processed; of these: 1 ( 0.00%) short read pairs filtered out after trimming by size control 274 ( 0.00%) empty read pairs filtered out after trimming by size control 13614240 (100.00%) read pairs available; of these: 1838510 (13.50%) trimmed read pairs available after processing 11775730 (86.50%) untrimmed read pairs available after processing Length distribution of reads after trimming: length count percentage 22 1 0.00% 23 0 0.00% 24 0 0.00% 25 1 0.00% 26 1 0.00% 27 0 0.00% 28 0 0.00% 29 1 0.00% 30 0 0.00% 31 0 0.00% 32 0 0.00% 33 0 0.00% 34 0 0.00% 35 2 0.00% 36 0 0.00% 37 0 0.00% 38 1 0.00% 39 0 0.00% 40 1 0.00% 41 0 0.00% 42 0 0.00% 43 1 0.00% 44 1 0.00% 45 0 0.00% 46 1 0.00% 47 0 0.00% 48 2 0.00% 49 6 0.00% 50 1 0.00% 51 1 0.00% 52 2 0.00% 53 1 0.00% 54 2 0.00% 55 0 0.00% 56 3 0.00% 57 6 0.00% 58 6 0.00% 59 6 0.00% 60 12 0.00% 61 8 0.00% 62 4 0.00% 63 35 0.00% 64 62 0.00% 65 76 0.00% 66 85 0.00% 67 118 0.00% 68 129 0.00% 69 178 0.00% 70 195 0.00% 71 210 0.00% 72 240 0.00% 73 262 0.00% 74 328 0.00% 75 360 0.00% 76 401 0.00% 77 444 0.00% 78 461 0.00% 79 511 0.00% 80 584 0.00% 81 564 0.00% 82 625 0.00% 83 696 0.01% 84 781 0.01% 85 832 0.01% 86 895 0.01% 87 1007 0.01% 88 1064 0.01% 89 1179 0.01% 90 1413 0.01% 91 1536 0.01% 92 1854 0.01% 93 2185 0.02% 94 5610 0.04% 95 5892 0.04% 96 6122 0.04% 97 6302 0.05% 98 6572 0.05% 99 6924 0.05% 100 7036 0.05% 101 7555 0.06% 102 7791 0.06% 103 7973 0.06% 104 8383 0.06% 105 8899 0.07% 106 9334 0.07% 107 9899 0.07% 108 10557 0.08% 109 11281 0.08% 110 12176 0.09% 111 13287 0.10% 112 14570 0.11% 113 16271 0.12% 114 18587 0.14% 115 21079 0.15% 116 59579 0.44% 117 65876 0.48% 118 75318 0.55% 119 86496 0.64% 120 102013 0.75% 121 127636 0.94% 122 175652 1.29% 123 272411 2.00% 124 632048 4.64% 125 11775730 86.50% 13614240 reads passed initial QC criterion=sequence-density sequence-density=0.12 sequence-density-rank=1 fanout-score=260.79 fanout-score-rank=10 prefix-density=1.12 prefix-fanout=28.0 sequence=CGCCGCCGCCGC criterion=fanout-score sequence-density=0.04 sequence-density-rank=34 fanout-score=669.65 fanout-score-rank=1 prefix-density=1.01 prefix-fanout=26.8 sequence=GGCGGCGGCGAACCGCCCCCGTCGCCGCGATCCGAACACTTCACCGGACCATTCAATCGGTAGGAGCGACGGGCGGTGTGTACAAAGGGCAGGGACGTAGTCAACGCGAGCTGATGACTCGCGCTTACTAGGCATTCCTCGTTGAAGACCAACAATTGCAATGATCTATCCCCATCACGATGAAATTTCCCAAGATTACCCGGGCCTGTCGGCCAAGGCTATATACTCGTTGAATACATCAGTGTAGCGCGCGTGCGGCCCAGAACATCTAAGGGCATCACAGACCTGTTATTGCCTCAAACTTCCGTCGCCTAAACGGCGATAGTCCCTCTAAGAAGCTAGCTGCGGAGGGATGGCTCCGCATAGCTAGTTAGCAGGCTGAGGTCTCGTTCGTTAACGGAATTAACCAGACAAATCGCTCCACCAACTAAGAACGGCCATGCACCACCACCCATAGAATCAAGAAAGAGCTCTCAGTCTGTCAATCCTTGCTATGTCTGGACCTGGTAAG criterion=sequence-density sequence-density=0.12 sequence-density-rank=1 fanout-score=258.75 fanout-score-rank=9 prefix-density=1.09 prefix-fanout=27.7 sequence=CGCCGCCGCCGC criterion=fanout-score sequence-density=0.03 sequence-density-rank=36 fanout-score=1114.72 fanout-score-rank=1 prefix-density=1.13 prefix-fanout=27.4 sequence=GCGGCGGCGAACCGCCCCCGTCGCCGCGATCCGAACACTTCACCGGACCATTCAATCGGTAGGAGCGACGGGCGGTGTGTACAAAGGGCAGGGACGTAGTCAACGCGAGCTGATGACTCGCGCTTACTAGGCATTCCTCGTTGAAGACCAACAATTGCAATGATCTATCCCCATCACGATGAAATTTCCCAAGATTACCCGGGCCTGTCGGCCAAGGCTATATACTCGTTGAATACATCAGTGTAGCGCGCGTGCGGCCCAGAACATCTAAGGGCATCACAGACCTGTTATTGCCTCAAACTTCCGTCGCCTAAACGGCGATAGTCCCTCTAAGAAGCTAGCTGCGGAGGGATGGCTCCGCATAGCTAGTTAGCAGGCTGAGGTCTCGTTCGTTAACGGAATTAACCAGACAAATCGCTCCACCAACTAAGAACGGCCATGCACCACCACCCATAGAATCAAGAAAGAGCTCTCAGTCTGTCAATCCTTGCTATGTCTGGACCTGGTAAGT SRR13662595 testing PE reads STAR mapping to Ensembl genome Started job on | Dec 10 07:53:10 Started mapping on | Dec 10 07:53:10 Finished on | Dec 10 07:54:37 Mapping speed, Million of reads per hour | 563.35 Number of input reads | 13614240 Average input read length | 248 UNIQUE READS: Uniquely mapped reads number | 12076327 Uniquely mapped reads % | 88.70% Average mapped length | 246.58 Number of splices: Total | 8418408 Number of splices: Annotated (sjdb) | 7907443 Number of splices: GT/AG | 8295699 Number of splices: GC/AG | 88669 Number of splices: AT/AC | 5105 Number of splices: Non-canonical | 28935 Mismatch rate per base, % | 0.38% Deletion rate per base | 0.01% Deletion average length | 2.15 Insertion rate per base | 0.01% Insertion average length | 2.24 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 542309 % of reads mapped to multiple loci | 3.98% Number of reads mapped to too many loci | 33072 % of reads mapped to too many loci | 0.24% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 5.66% % of reads unmapped: other | 1.41% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 995659 995659 995659 N_multimapping 542309 542309 542309 N_noFeature 397380 6123192 6132515 N_ambiguous 260867 24470 24642 UnstrandedReadsAssigned:11418080 PositiveStrandReadsAssigned:5928665 NegativeStrandReadsAssigned:5919170 Dataset is classified unstranded MeadianReadLen=125 20thPercentileLength=125 echo kmer=121 SRR13662595 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: 52,972 [index] number of k-mers: 66,720,672 [index] number of equivalence classes: 111,837 [quant] running in paired-end mode [quant] will process pair 1: SRR13662595-trimmed-pair1.fastq SRR13662595-trimmed-pair2.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 13,614,240 reads, 12,161,895 reads pseudoaligned [quant] estimated average fragment length: 185.548 [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,094 rounds 52973 SRR13662595.ke.tsv 35125 SRR13662595.se.tsv 88098 total ==> SRR13662595.ke.tsv <== target_id length eff_length est_counts tpm PNS24245 936 751.63 0 0 PNS24247 1044 859.452 47.7575 5.83698 PNS24249 1928 1743.45 235.059 14.1623 PNS24246 1044 859.452 47.7575 5.83698 PNS24248 1044 859.452 47.7575 5.83698 PNS24244 1471 1286.45 47.6685 3.8923 PNS24243 293 112.998 6 5.5776 KQK14069 1603 1418.45 4396.02 325.547 KQK14071 474 290.999 483.61 174.571 ==> SRR13662595.se.tsv <== BRADI_1g14170v3 5048 BRADI_1g53295v3 64 BRADI_1g59795v3 149 BRADI_1g07683v3 0 BRADI_1g00485v3 12 BRADI_1g20270v3 274 BRADI_1g74790v3 461 BRADI_1g09890v3 1 BRADI_1g77505v3 258 BRADI_1g48960v3 1 SRR13662595 completed mapping pipeline successfully