Starting /dee2/code/volunteer_pipeline.sh SRR8096891 current disk space = 1542893645824 free memory = 1594105448 SRR8096891 SRAfilesize 8aee31cb201e01627a839244726d996c SRR8096891.sra SRR8096891.sra file validated SRR8096891 is paired end SRR8096891 is conventional basespace SRR8096891 read1 length is 150 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR8096891_1.fastq File type Conventional base calls Encoding Sanger / Illumina 1.9 Total Sequences 4000 Sequences flagged as poor quality 0 Sequence length 150 %GC 48 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 32.15725 34.0 33.0 34.0 32.0 34.0 2 33.05975 34.0 33.0 34.0 32.0 34.0 3 33.121 34.0 33.0 34.0 32.0 34.0 4 33.18125 34.0 33.0 34.0 32.0 34.0 5 33.257 34.0 33.0 34.0 33.0 34.0 6 36.9305 38.0 37.0 38.0 36.0 38.0 7 37.2305 38.0 38.0 38.0 36.0 38.0 8 37.37925 38.0 38.0 38.0 37.0 38.0 9 37.38725 38.0 38.0 38.0 37.0 38.0 10-14 37.3657 38.0 38.0 38.0 37.0 38.0 15-19 37.2698 38.0 38.0 38.0 36.8 38.0 20-24 37.3637 38.0 38.0 38.0 37.0 38.0 25-29 37.307700000000004 38.0 38.0 38.0 37.0 38.0 30-34 37.2117 38.0 38.0 38.0 36.8 38.0 35-39 37.1486 38.0 38.0 38.0 36.8 38.0 40-44 37.021100000000004 38.0 38.0 38.0 36.2 38.0 45-49 37.03855 38.0 38.0 38.0 36.2 38.0 50-54 37.03425 38.0 38.0 38.0 36.2 38.0 55-59 37.005399999999995 38.0 38.0 38.0 36.0 38.0 60-64 36.89105 38.0 38.0 38.0 36.0 38.0 65-69 36.67094999999999 38.0 38.0 38.0 35.8 38.0 70-74 36.46730000000001 38.0 38.0 38.0 34.8 38.0 75-79 36.0519 38.0 38.0 38.0 34.2 38.0 80-84 36.0454 38.0 38.0 38.0 34.0 38.0 85-89 35.94475 38.0 38.0 38.0 33.8 38.0 90-94 35.9127 38.0 38.0 38.0 33.8 38.0 95-99 35.8444 38.0 38.0 38.0 34.0 38.0 100-104 35.71215 38.0 38.0 38.0 33.6 38.0 105-109 35.5043 38.0 38.0 38.0 32.6 38.0 110-114 35.3941 38.0 38.0 38.0 32.2 38.0 115-119 35.32325 38.0 38.0 38.0 31.8 38.0 120-124 35.2269 38.0 38.0 38.0 31.2 38.0 125-129 34.996 38.0 37.8 38.0 30.4 38.0 130-134 34.70915 38.0 36.6 38.0 28.2 38.0 135-139 34.4409 38.0 36.0 38.0 26.4 38.0 140-144 34.3027 38.0 36.0 38.0 26.0 38.0 145-149 33.4295 38.0 35.2 38.0 13.2 38.0 150 27.89375 35.0 23.0 38.0 2.0 38.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 5 1.0 6 0.0 7 1.0 8 8.0 9 3.0 10 2.0 11 2.0 12 4.0 13 3.0 14 6.0 15 6.0 16 4.0 17 5.0 18 32.0 19 35.0 20 6.0 21 6.0 22 14.0 23 8.0 24 10.0 25 14.0 26 24.0 27 17.0 28 33.0 29 42.0 30 39.0 31 45.0 32 50.0 33 90.0 34 112.0 35 180.0 36 437.0 37 2761.0 >>END_MODULE >>Per base sequence content warn #Base G A T C 1 46.661490683229815 12.965838509316772 9.109730848861282 31.262939958592135 2 23.95 18.025 34.599999999999994 23.425 3 21.575 20.424999999999997 27.875 30.125 4 26.8 26.05 21.2 25.95 5 28.349999999999998 29.425 22.6 19.625 6 23.400000000000002 32.05 23.05 21.5 7 17.349999999999998 23.225 40.0 19.425 8 18.3 24.2 29.5 28.000000000000004 9 21.975 20.8 30.575000000000003 26.650000000000002 10-14 22.884999999999998 26.915 25.174999999999997 25.025 15-19 22.465 24.755 26.314999999999998 26.465 20-24 22.375 25.979999999999997 26.840000000000003 24.805 25-29 22.445 25.945 26.224999999999998 25.385 30-34 22.63 25.319999999999997 26.279999999999998 25.77 35-39 22.245 25.86 26.395000000000003 25.5 40-44 22.015 25.27 27.224999999999998 25.490000000000002 45-49 23.705000000000002 25.305 26.235000000000003 24.755 50-54 23.035 23.915 26.52 26.529999999999998 55-59 22.85 24.08 27.865000000000002 25.205 60-64 23.25 25.105 26.75 24.895 65-69 21.83 28.235 25.385 24.55 70-74 22.78 27.700000000000003 25.380000000000003 24.14 75-79 22.79 26.384999999999998 25.119999999999997 25.705 80-84 22.875 25.645 26.0 25.480000000000004 85-89 23.22 26.235000000000003 25.324999999999996 25.22 90-94 23.13 24.95 25.96 25.96 95-99 23.14 25.6 25.525 25.735000000000003 100-104 23.13 26.05 25.974999999999998 24.845 105-109 23.085 25.474999999999998 25.77 25.669999999999998 110-114 23.07 26.8 24.93 25.2 115-119 22.945 25.509999999999998 25.990000000000002 25.555 120-124 22.86 25.81 25.335 25.995 125-129 23.72 26.105 25.240000000000002 24.935 130-134 23.169999999999998 27.075 24.79 24.965 135-139 23.72 26.400000000000002 24.38 25.5 140-144 22.81 26.174999999999997 25.15 25.865 145-149 23.494999999999997 25.61 24.915000000000003 25.979999999999997 150 22.625 24.625 25.5 27.250000000000004 >>END_MODULE >>Per sequence GC content fail #GC Content Count 0 19.0 1 12.0 2 3.5 3 3.0 4 2.5 5 3.0 6 2.5 7 1.5 8 1.5 9 1.0 10 1.5 11 0.5 12 0.0 13 0.5 14 0.5 15 0.0 16 0.0 17 0.0 18 0.0 19 0.0 20 0.0 21 0.5 22 1.0 23 1.0 24 1.0 25 0.5 26 0.5 27 3.0 28 6.5 29 10.0 30 14.5 31 15.5 32 17.5 33 22.5 34 29.0 35 38.0 36 50.5 37 67.5 38 76.0 39 98.0 40 136.0 41 160.5 42 172.5 43 180.5 44 180.0 45 187.0 46 206.0 47 207.5 48 193.5 49 172.5 50 151.5 51 145.0 52 135.0 53 114.5 54 103.0 55 97.0 56 92.5 57 88.0 58 74.0 59 78.0 60 82.5 61 77.0 62 72.5 63 63.0 64 61.0 65 58.0 66 48.0 67 38.5 68 35.5 69 29.0 70 21.0 71 14.0 72 11.0 73 8.5 74 5.0 75 3.0 76 1.0 77 0.5 78 0.5 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 3.4000000000000004 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 0.0 >>END_MODULE >>Sequence Length Distribution pass #Length Count 150 4000.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 94.69999999999999 #Duplication Level Percentage of deduplicated Percentage of total 1 98.44244984160507 93.22500000000001 2 1.2671594508975714 2.4 3 0.13199577613516367 0.375 4 0.07919746568109821 0.3 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 0.05279831045406547 0.975 >50 0.0 0.0 >100 0.026399155227032733 2.725 >500 0.0 0.0 >1k 0.0 0.0 >5k 0.0 0.0 >10k+ 0.0 0.0 >>END_MODULE >>Overrepresented sequences fail #Sequence Count Percentage Possible Source GATCGGAAGAGCACACGTCTGAACTCCAGTCACGATCAGATCTCGTATGC 109 2.725 TruSeq Adapter, Index 9 (100% over 50bp) TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 21 0.525 No Hit AGATCGGAAGAGCACACGTCTGAACTCCAGTCACGATCAGATCTCGTATG 18 0.44999999999999996 TruSeq Adapter, Index 9 (100% over 49bp) >>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 0.475 0.0 0.0 0.0 0.0 2 0.475 0.0 0.0 0.0 0.0 3 0.475 0.0 0.0 0.0 0.0 4 0.475 0.0 0.0 0.0 0.0 5 0.475 0.0 0.0 0.0 0.0 6 0.475 0.0 0.0 0.0 0.0 7 0.475 0.0 0.0 0.0 0.0 8 0.475 0.0 0.0 0.0 0.0 9 0.475 0.0 0.0 0.0 0.0 10-11 0.475 0.0 0.0 0.0 0.0 12-13 0.475 0.0 0.0 0.0 0.0 14-15 0.475 0.0 0.0 0.0 0.0 16-17 0.475 0.0 0.0 0.0 0.0 18-19 0.475 0.0 0.0 0.0 0.0 20-21 0.475 0.0 0.0 0.0 0.0 22-23 0.475 0.0 0.0 0.0 0.0 24-25 0.475 0.0 0.0 0.0 0.0 26-27 0.475 0.0 0.0 0.0 0.0 28-29 0.475 0.0 0.0 0.0 0.0 30-31 0.475 0.0 0.0 0.0 0.0 32-33 0.475 0.0 0.0 0.0 0.0 34-35 0.475 0.0 0.0 0.0 0.0 36-37 0.475 0.0 0.0 0.0 0.0 38-39 0.475 0.0 0.0 0.0 0.0 40-41 0.475 0.0 0.0 0.0 0.0 42-43 0.475 0.0 0.0 0.0 0.0 44-45 0.475 0.0 0.0 0.0 0.0 46-47 0.475 0.0 0.0 0.0 0.0 48-49 0.475 0.0 0.0 0.0 0.0 50-51 0.4875 0.0 0.0 0.0 0.0 52-53 0.5 0.0 0.0 0.0 0.0 54-55 0.5 0.0 0.0 0.0 0.0 56-57 0.5125 0.0 0.0 0.0 0.0 58-59 0.525 0.0 0.0 0.0 0.0 60-61 0.525 0.0 0.0 0.0 0.0 62-63 0.525 0.0 0.0 0.0 0.0 64-65 0.575 0.0 0.0 0.0 0.0 66-67 0.575 0.0 0.0 0.0 0.0 68-69 0.575 0.0 0.0 0.0 0.0 70-71 0.575 0.0 0.0 0.0 0.0 72-73 0.575 0.0 0.0 0.0 0.0 74-75 0.575 0.0 0.0 0.0 0.0 76-77 0.575 0.0 0.0 0.0 0.0 78-79 0.575 0.0 0.0 0.0 0.0 80-81 0.575 0.0 0.0 0.0 0.0 82-83 0.6125 0.0 0.0 0.0 0.0 84-85 0.625 0.0 0.0 0.0 0.0 86-87 0.625 0.0 0.0 0.0 0.0 88-89 0.6625000000000001 0.0 0.0 0.0 0.0 90-91 0.675 0.0 0.0 0.0 0.0 92-93 0.675 0.0 0.0 0.0 0.0 94-95 0.6875 0.0 0.0 0.0 0.0 96-97 0.75 0.0 0.0 0.0 0.0 98-99 0.8 0.0 0.0 0.0 0.0 100-101 0.825 0.0 0.0 0.0 0.0 102-103 0.925 0.0 0.0 0.0 0.0 104-105 0.975 0.0 0.0 0.0 0.0 106-107 1.0375 0.0 0.0 0.0 0.0 108-109 1.1375 0.0 0.0 0.0 0.0 110-111 1.2125 0.0 0.0 0.0 0.0 112-113 1.35 0.0 0.0 0.0 0.0 114-115 1.4249999999999998 0.0 0.0 0.0 0.0 116-117 1.525 0.0 0.0 0.0 0.0 118-119 1.725 0.0 0.0 0.0 0.0 120-121 1.9375 0.0 0.0 0.0 0.0 122-123 2.0625 0.0 0.0 0.0 0.0 124-125 2.1875 0.0 0.0 0.0 0.0 126-127 2.3375000000000004 0.0 0.0 0.0 0.0 128-129 2.4749999999999996 0.0 0.0 0.0 0.0 130-131 2.7 0.0 0.0 0.0 0.0 132-133 3.0375 0.0 0.0 0.0 0.0 134-135 3.2750000000000004 0.0 0.0 0.0 0.0 136-137 3.575 0.0 0.0 0.0 0.0 138 3.75 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position GGGTCAT 10 0.0069790767 143.96251 2 GGTCATC 10 0.0069790767 143.96251 3 AAGAGCA 50 1.8411933E-4 57.584995 7 GAAGAGC 40 0.005783394 53.98594 6 GAGCACA 45 0.009215165 47.9875 9 AGAGCAC 45 0.009215165 47.9875 8 AAAAAAA 125 4.5557195E-4 10.365301 65-69 >>END_MODULE SRR8096891 read2 length is 150 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR8096891_2.fastq File type Conventional base calls Encoding Sanger / Illumina 1.9 Total Sequences 4000 Sequences flagged as poor quality 0 Sequence length 150 %GC 49 >>END_MODULE >>Per base sequence quality fail #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 30.16475 33.0 32.0 33.0 18.0 34.0 2 30.45375 33.0 32.0 33.0 18.0 34.0 3 30.33725 33.0 31.0 33.0 18.0 34.0 4 30.25975 33.0 32.0 33.0 15.0 34.0 5 30.23525 33.0 31.0 33.0 25.0 34.0 6 33.70325 38.0 34.0 38.0 16.0 38.0 7 33.80125 38.0 35.0 38.0 16.0 38.0 8 34.09025 38.0 35.0 38.0 26.0 38.0 9 33.908 38.0 35.0 38.0 16.0 38.0 10-14 33.84259999999999 38.0 35.0 38.0 16.0 38.0 15-19 33.4944 38.0 34.4 38.0 16.0 38.0 20-24 33.30475 38.0 34.0 38.0 16.0 38.0 25-29 33.0261 38.0 33.8 38.0 16.0 38.0 30-34 32.7341 38.0 33.6 38.0 16.0 38.0 35-39 32.4836 38.0 33.0 38.0 16.0 38.0 40-44 32.426300000000005 38.0 33.0 38.0 16.0 38.0 45-49 31.9654 37.6 31.0 38.0 15.0 38.0 50-54 31.608099999999997 37.2 29.4 38.0 15.0 38.0 55-59 31.3666 37.0 29.0 38.0 15.0 38.0 60-64 31.047050000000002 37.0 28.6 38.0 14.4 38.0 65-69 30.548099999999998 36.4 27.4 38.0 14.0 38.0 70-74 30.11425 36.0 27.0 38.0 14.0 38.0 75-79 29.439600000000002 36.0 25.2 38.0 6.8 38.0 80-84 28.892049999999994 35.4 23.2 38.0 2.0 38.0 85-89 28.374599999999997 34.8 20.0 38.0 2.0 38.0 90-94 27.680449999999997 34.0 15.0 38.0 2.0 38.0 95-99 27.1899 34.0 15.0 38.0 2.0 38.0 100-104 26.27985 33.4 15.0 37.8 2.0 38.0 105-109 25.41745 31.8 14.8 37.2 2.0 38.0 110-114 24.502750000000002 31.0 13.8 37.0 2.0 38.0 115-119 23.543400000000002 28.0 13.0 36.4 2.0 38.0 120-124 22.457949999999997 26.6 6.4 35.6 2.0 38.0 125-129 20.875100000000003 23.2 2.0 35.0 2.0 38.0 130-134 19.378950000000003 19.0 2.0 34.6 2.0 38.0 135-139 17.69175 14.2 2.0 34.0 2.0 38.0 140-144 15.57005 8.8 2.0 33.6 2.0 37.0 145-149 12.9883 2.0 2.0 30.8 2.0 36.0 150 8.7805 2.0 2.0 2.0 2.0 34.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 2 124.0 3 33.0 4 20.0 5 16.0 6 27.0 7 21.0 8 14.0 9 14.0 10 18.0 11 31.0 12 36.0 13 28.0 14 28.0 15 45.0 16 43.0 17 46.0 18 48.0 19 62.0 20 64.0 21 77.0 22 91.0 23 77.0 24 102.0 25 127.0 26 132.0 27 172.0 28 198.0 29 228.0 30 206.0 31 286.0 32 305.0 33 332.0 34 367.0 35 318.0 36 222.0 37 42.0 >>END_MODULE >>Per base sequence content warn #Base G A T C 1 43.16926167754897 20.0652938221999 9.819186338523355 26.946258161727776 2 27.079646017699115 25.56257901390645 29.355246523388118 18.002528445006323 3 24.45624683864441 24.96206373292868 27.718765806777945 22.86292362164896 4 28.046617684317205 30.47884469217127 17.63364580694198 23.840891816569545 5 28.386933400860975 32.89440364649278 18.4856925804001 20.23297037224614 6 25.728770595690747 33.71356147021547 19.315589353612168 21.24207858048162 7 22.503801317790167 19.792194627470856 34.08514951849975 23.61885453623923 8 22.599442614644033 25.234355206485937 24.018241702558907 28.147960476311123 9 27.033189764378008 21.712693184697237 25.614390676463138 25.63972637446162 10-14 27.246464953626276 25.508083726116265 22.234047944858347 25.011403375399116 15-19 26.62814859865187 24.818813035325125 24.235973848259086 24.317064517763924 20-24 26.330191547582853 26.254180602006688 23.208675382588424 24.20695246782203 25-29 25.666227581315233 26.76562974972135 23.78660451920154 23.78153814976188 30-34 26.454195379002837 25.81070125658695 24.143696797730037 23.591406566680178 35-39 25.681150612782332 26.283804314797933 23.84786792261724 24.18717714980249 40-44 26.978982020764754 25.312737401873893 23.73259052924791 23.975690048113446 45-49 26.017125196331765 24.99366671733293 24.031007751937985 24.958200334397322 50-54 26.032534333350227 25.429483606141996 24.567982567273095 23.969999493234685 55-59 25.300228021281985 26.65315429440081 24.07904737775526 23.967570306561946 60-64 25.17865288125285 27.991485479701993 23.318635649485582 23.511225989559577 65-69 24.11293592862936 28.380981346309813 23.44890510948905 24.057177615571774 70-74 25.0595569973136 27.994323077702877 23.32606822444118 23.620051700542348 75-79 24.921423501977085 26.10260569806347 24.561492446517285 24.414478353442156 80-84 24.973378631915217 26.631509558338827 24.060646011865526 24.33446579788043 85-89 25.15082382762991 27.112801013941702 23.401774397972115 24.334600760456272 90-94 24.980990520606277 27.06442946215846 23.9265980635677 24.027981953667563 95-99 25.659095518150476 27.37781383086595 23.34212127357534 23.620969377408233 100-104 25.750354897586696 27.1496653822754 23.727438653417156 23.372541066720746 105-109 25.25728770595691 27.487959442332066 23.371356147021547 23.88339670468948 110-114 25.56535848291248 27.74566473988439 23.385052225940576 23.30392455126255 115-119 24.61702343512225 27.462716850968853 23.41483209901593 24.50542761489297 120-124 25.140741492113406 27.468681848151345 23.72571892275701 23.66485773697824 125-129 25.20156178692764 28.12230617108666 23.614421175396785 23.061710866588918 130-134 24.808560271819058 29.134337441046704 23.053907398955324 23.003194888178914 135-139 24.950565329817977 28.535212695837348 23.11007453227197 23.404147442072706 140-144 24.979720137903062 28.888663557087813 22.216588927195293 23.91502737781383 145-149 24.324735987002438 29.655767668562145 22.532493907392364 23.487002437043056 150 24.89226869455006 30.39290240811153 21.368821292775667 23.34600760456274 >>END_MODULE >>Per sequence GC content fail #GC Content Count 0 32.0 1 25.5 2 10.0 3 1.0 4 0.5 5 0.5 6 0.5 7 0.0 8 0.0 9 0.0 10 0.0 11 0.0 12 0.0 13 0.0 14 1.0 15 1.0 16 0.5 17 1.0 18 1.0 19 1.0 20 0.5 21 2.0 22 2.5 23 1.5 24 1.5 25 3.0 26 5.0 27 4.5 28 5.0 29 6.5 30 10.5 31 17.0 32 19.0 33 18.0 34 25.5 35 32.5 36 45.5 37 65.0 38 74.0 39 92.5 40 115.5 41 142.5 42 151.5 43 145.5 44 149.0 45 151.0 46 169.5 47 183.5 48 181.5 49 171.0 50 159.0 51 150.5 52 139.5 53 118.0 54 106.0 55 121.0 56 104.0 57 80.5 58 92.5 59 97.5 60 90.5 61 86.0 62 89.5 63 89.0 64 72.0 65 63.0 66 61.0 67 56.5 68 46.0 69 31.0 70 26.5 71 23.0 72 17.5 73 13.0 74 6.5 75 3.0 76 3.0 77 1.0 78 0.0 79 0.5 80 0.5 81 0.5 82 0.5 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 0.44999999999999996 2 1.125 3 1.15 4 1.325 5 1.275 6 1.375 7 1.35 8 1.325 9 1.325 10-14 1.345 15-19 1.345 20-24 1.3299999999999998 25-29 1.31 30-34 1.32 35-39 1.27 40-44 1.275 45-49 1.315 50-54 1.335 55-59 1.325 60-64 1.345 65-69 1.3599999999999999 70-74 1.355 75-79 1.37 80-84 1.395 85-89 1.375 90-94 1.365 95-99 1.38 100-104 1.38 105-109 1.375 110-114 1.39 115-119 1.43 120-124 1.415 125-129 1.395 130-134 1.405 135-139 1.385 140-144 1.38 145-149 1.52 150 1.375 >>END_MODULE >>Sequence Length Distribution pass #Length Count 150 4000.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 97.075 #Duplication Level Percentage of deduplicated Percentage of total 1 98.6608292557301 95.775 2 1.0816379088333763 2.1 3 0.05150656708730364 0.15 4 0.05150656708730364 0.2 5 0.02575328354365182 0.125 6 0.0 0.0 7 0.0 0.0 8 0.05150656708730364 0.4 9 0.02575328354365182 0.22499999999999998 >10 0.05150656708730364 1.0250000000000001 >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 GATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCG 23 0.575 Illumina Single End PCR Primer 1 (100% over 50bp) NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN 18 0.44999999999999996 No Hit ANNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN 9 0.22499999999999998 No Hit GNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN 8 0.2 No Hit CNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN 8 0.2 No Hit CTGCAATTGCAAGCTTGTGTCAAAGAAGAGGGTAGCACCTGATCCTCTTG 5 0.125 No Hit >>END_MODULE >>Adapter Content pass #Position Illumina Universal Adapter Illumina Small RNA 3' Adapter Illumina Small RNA 5' Adapter Nextera Transposase Sequence SOLID Small RNA Adapter 1 0.3 0.0 0.0 0.0 0.0 2 0.3 0.0 0.0 0.0 0.0 3 0.3 0.0 0.0 0.0 0.0 4 0.3 0.0 0.0 0.0 0.0 5 0.3 0.0 0.0 0.0 0.0 6 0.3 0.0 0.0 0.0 0.0 7 0.3 0.0 0.0 0.0 0.0 8 0.3 0.0 0.0 0.0 0.0 9 0.3 0.0 0.0 0.0 0.0 10-11 0.3 0.0 0.0 0.0 0.0 12-13 0.3 0.0 0.0 0.0 0.0 14-15 0.3 0.0 0.0 0.0 0.0 16-17 0.3 0.0 0.0 0.0 0.0 18-19 0.3 0.0 0.0 0.0 0.0 20-21 0.3 0.0 0.0 0.0 0.0 22-23 0.3 0.0 0.0 0.0 0.0 24-25 0.3 0.0 0.0 0.0 0.0 26-27 0.3 0.0 0.0 0.0 0.0 28-29 0.3 0.0 0.0 0.0 0.0 30-31 0.3 0.0 0.0 0.0 0.0 32-33 0.3 0.0 0.0 0.0 0.0 34-35 0.3 0.0 0.0 0.0 0.0 36-37 0.3 0.0 0.0 0.0 0.0 38-39 0.3 0.0 0.0 0.0 0.0 40-41 0.325 0.0 0.0 0.0 0.0 42-43 0.325 0.0 0.0 0.0 0.0 44-45 0.325 0.0 0.0 0.0 0.0 46-47 0.325 0.0 0.0 0.0 0.0 48-49 0.325 0.0 0.0 0.0 0.0 50-51 0.3375 0.0 0.0 0.0 0.0 52-53 0.35 0.0 0.0 0.0 0.0 54-55 0.35 0.0 0.0 0.0 0.0 56-57 0.35 0.0 0.0 0.0 0.0 58-59 0.35 0.0 0.0 0.0 0.0 60-61 0.35 0.0 0.0 0.0 0.0 62-63 0.35 0.0 0.0 0.0 0.0 64-65 0.3625 0.0 0.0 0.0 0.0 66-67 0.375 0.0 0.0 0.0 0.0 68-69 0.375 0.0 0.0 0.0 0.0 70-71 0.375 0.0 0.0 0.0 0.0 72-73 0.375 0.0 0.0 0.0 0.0 74-75 0.375 0.0 0.0 0.0 0.0 76-77 0.375 0.0 0.0 0.0 0.0 78-79 0.375 0.0 0.0 0.0 0.0 80-81 0.375 0.0 0.0 0.0 0.0 82-83 0.4 0.0 0.0 0.0 0.0 84-85 0.4 0.0 0.0 0.0 0.0 86-87 0.4 0.0 0.0 0.0 0.0 88-89 0.4375 0.0 0.0 0.0 0.0 90-91 0.45 0.0 0.0 0.0 0.0 92-93 0.45 0.0 0.0 0.0 0.0 94-95 0.45 0.0 0.0 0.0 0.0 96-97 0.475 0.0 0.0 0.0 0.0 98-99 0.4875 0.0 0.0 0.0 0.0 100-101 0.5 0.0 0.0 0.0 0.0 102-103 0.5375000000000001 0.0 0.0 0.0 0.0 104-105 0.5625 0.0 0.0 0.0 0.0 106-107 0.5874999999999999 0.0 0.0 0.0 0.0 108-109 0.65 0.0 0.0 0.0 0.0 110-111 0.675 0.0 0.0 0.0 0.0 112-113 0.7 0.0 0.0 0.0 0.0 114-115 0.725 0.0 0.0 0.0 0.0 116-117 0.75 0.0 0.0 0.0 0.0 118-119 0.8125 0.0 0.0 0.0 0.0 120-121 0.875 0.0 0.0 0.0 0.0 122-123 0.9 0.0 0.0 0.0 0.0 124-125 0.925 0.0 0.0 0.0 0.0 126-127 0.925 0.0 0.0 0.0 0.0 128-129 0.9624999999999999 0.0 0.0 0.0 0.0 130-131 0.975 0.0 0.0 0.0 0.0 132-133 1.025 0.0 0.0 0.0 0.0 134-135 1.05 0.0 0.0 0.0 0.0 136-137 1.125 0.0 0.0 0.0 0.0 138 1.175 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position GAGCGTC 15 1.202288E-4 143.1125 9 GTCATCC 10 0.007103748 143.1125 4 AAGAGCG 15 1.202288E-4 143.1125 7 GGACAAG 10 0.007103748 143.1125 1 GAAGAGC 15 1.202288E-4 143.1125 6 AGAGCGT 15 1.202288E-4 143.1125 8 GATCGGA 20 3.7797078E-4 107.33438 1 CGGAAGA 20 3.7797078E-4 107.33438 4 GGAAGAG 20 3.7797078E-4 107.33438 5 TCGGAAG 25 9.1789616E-4 85.8675 3 ATCGGAA 25 9.1789616E-4 85.8675 2 AAAAAAA 315 2.4054767E-5 6.8148813 60-64 >>END_MODULE Read 1903106 spots for SRR8096891.sra Written 1903106 spots for SRR8096891.sra Read 1903106 spots for SRR8096891.sra Written 1903106 spots for SRR8096891.sra Read 1903106 spots for SRR8096891.sra Written 1903106 spots for SRR8096891.sra Read 1903106 spots for SRR8096891.sra Written 1903106 spots for SRR8096891.sra Read 1903106 spots for SRR8096891.sra Written 1903106 spots for SRR8096891.sra Read 1903106 spots for SRR8096891.sra Written 1903106 spots for SRR8096891.sra Read 1903114 spots for SRR8096891.sra Written 1903114 spots for SRR8096891.sra Read 1903106 spots for SRR8096891.sra Written 1903106 spots for SRR8096891.sra Read 1903106 spots for SRR8096891.sra Written 1903106 spots for SRR8096891.sra Read 1903106 spots for SRR8096891.sra Written 1903106 spots for SRR8096891.sra Read 1903106 spots for SRR8096891.sra Written 1903106 spots for SRR8096891.sra Read 1903106 spots for SRR8096891.sra Written 1903106 spots for SRR8096891.sra Read 1903106 spots for SRR8096891.sra Written 1903106 spots for SRR8096891.sra Read 1903106 spots for SRR8096891.sra Written 1903106 spots for SRR8096891.sra Read 1903106 spots for SRR8096891.sra Written 1903106 spots for SRR8096891.sra Read 1903106 spots for SRR8096891.sra Written 1903106 spots for SRR8096891.sra Read 1903106 spots for SRR8096891.sra Written 1903106 spots for SRR8096891.sra Read 1903106 spots for SRR8096891.sra Written 1903106 spots for SRR8096891.sra Read 1903106 spots for SRR8096891.sra Written 1903106 spots for SRR8096891.sra Read 1903106 spots for SRR8096891.sra Written 1903106 spots for SRR8096891.sra SRR ids: ['SRR8096891.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_8t6rune5 SRR8096891.sra spots: 38062128 blocks: [[1, 1903106], [1903107, 3806212], [3806213, 5709318], [5709319, 7612424], [7612425, 9515530], [9515531, 11418636], [11418637, 13321742], [13321743, 15224848], [15224849, 17127954], [17127955, 19031060], [19031061, 20934166], [20934167, 22837272], [22837273, 24740378], [24740379, 26643484], [26643485, 28546590], [28546591, 30449696], [30449697, 32352802], [32352803, 34255908], [34255909, 36159014], [36159015, 38062128]] SRR8096891 file size 12801965 SRR8096891 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 SRR8096891 SRR8096891_1.fastq SRR8096891_2.fastq Input file: SRR8096891_1.fastq Paired file: SRR8096891_2.fastq trimmed: SRR8096891-trimmed-pair1.fastq, SRR8096891-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 Sat Dec 7 14:45:55 2024 >> started Sat Dec 7 14:46:47 2024 >> done (52.866s) 38062128 read pairs processed; of these: 217233 ( 0.57%) short read pairs filtered out after trimming by size control 1896951 ( 4.98%) empty read pairs filtered out after trimming by size control 35947944 (94.45%) read pairs available; of these: 21066494 (58.60%) trimmed read pairs available after processing 14881450 (41.40%) untrimmed read pairs available after processing Length distribution of reads after trimming: length count percentage 18 100 0.00% 19 248 0.00% 20 315 0.00% 21 148 0.00% 22 297 0.00% 23 165 0.00% 24 1614 0.00% 25 1705 0.00% 26 234 0.00% 27 182 0.00% 28 229 0.00% 29 445 0.00% 30 260 0.00% 31 266 0.00% 32 311 0.00% 33 362 0.00% 34 636 0.00% 35 1234 0.00% 36 1257 0.00% 37 1110 0.00% 38 1231 0.00% 39 2504 0.01% 40 4361 0.01% 41 6039 0.02% 42 3331 0.01% 43 2884 0.01% 44 1904 0.01% 45 2387 0.01% 46 2123 0.01% 47 2265 0.01% 48 2369 0.01% 49 3262 0.01% 50 3046 0.01% 51 3989 0.01% 52 2686 0.01% 53 2774 0.01% 54 2990 0.01% 55 3837 0.01% 56 4233 0.01% 57 3449 0.01% 58 4078 0.01% 59 4485 0.01% 60 4932 0.01% 61 9374 0.03% 62 8645 0.02% 63 2486 0.01% 64 2490 0.01% 65 2610 0.01% 66 2742 0.01% 67 3027 0.01% 68 3718 0.01% 69 6051 0.02% 70 6053 0.02% 71 4559 0.01% 72 4435 0.01% 73 4529 0.01% 74 4429 0.01% 75 4678 0.01% 76 5325 0.01% 77 5900 0.02% 78 6255 0.02% 79 7058 0.02% 80 7521 0.02% 81 8369 0.02% 82 9691 0.03% 83 12412 0.03% 84 24412 0.07% 85 25447 0.07% 86 27179 0.08% 87 29104 0.08% 88 29239 0.08% 89 29319 0.08% 90 29235 0.08% 91 29036 0.08% 92 29487 0.08% 93 29621 0.08% 94 31903 0.09% 95 33199 0.09% 96 35754 0.10% 97 37819 0.11% 98 40925 0.11% 99 43242 0.12% 100 44442 0.12% 101 47187 0.13% 102 49876 0.14% 103 52576 0.15% 104 55393 0.15% 105 57795 0.16% 106 61779 0.17% 107 63375 0.18% 108 66563 0.19% 109 68623 0.19% 110 71692 0.20% 111 74491 0.21% 112 77928 0.22% 113 80575 0.22% 114 83100 0.23% 115 87469 0.24% 116 92341 0.26% 117 96510 0.27% 118 101420 0.28% 119 108029 0.30% 120 113596 0.32% 121 119443 0.33% 122 126254 0.35% 123 133309 0.37% 124 138642 0.39% 125 146684 0.41% 126 153287 0.43% 127 162377 0.45% 128 172366 0.48% 129 180031 0.50% 130 192979 0.54% 131 205748 0.57% 132 215710 0.60% 133 228549 0.64% 134 241285 0.67% 135 260106 0.72% 136 281401 0.78% 137 301911 0.84% 138 322050 0.90% 139 347179 0.97% 140 377728 1.05% 141 416998 1.16% 142 455155 1.27% 143 513930 1.43% 144 584393 1.63% 145 713977 1.99% 146 912359 2.54% 147 1282296 3.57% 148 2208682 6.14% 149 7393350 20.57% 150 14881450 41.40% 35947944 reads passed initial QC criterion=sequence-density sequence-density=1.11 sequence-density-rank=1 fanout-score=2.05 fanout-score-rank=29 prefix-density=1.13 prefix-fanout=2.0 sequence=AACATGGAGAACATGGCGAGGCGGCCGTTCTTGATCTCCTTCACCTTGAGCTCAGCGAA criterion=fanout-score sequence-density=0.01 sequence-density-rank=33 fanout-score=11.47 fanout-score-rank=1 prefix-density=0.04 prefix-fanout=2.0 sequence=TCACCAAATGAATATACTCAATATCTTTATATATGAACAAAAACTTTTCATGCCCAGCAATTGCTTGGATGCAATGCGGTACTTAGGTACAAAGAGTGAAACATCAGAATAATTAAAGTGGCATGCTTAAAAGGTGTAAAGGCAGCTGCCGTCGTCACTCCTTGCTGTTGGGTCGTAGTTCTCGGCATTCCGGTCAGTGCAACCTTCTGGGACGGGCAAATTACCTTGTTGTGCTCCTTTACCTCCTCCTATGCAGCTAGAGATGGTGTGTGTATGAAGAGTGTTCTAACCGTAGAAGGAACCAGTCTTCATGGCATCTGAGTTAGCATCTCCCAGAGCAGCCTCGCTCATGTACTTGTCAGCAAGCTGCACACGCTTGACATTGTCCTGCTCTTGGACGAGCATGTGGCCGTACTCCAGGAGCTTCTCGATTGTCATCTTTGGCTGCTCAAAGGACACCGGTCCATCCTTCGAGTTCACCAGCTTCTTGCCGATGTTCTCTATTCCGGTT criterion=sequence-density sequence-density=0.47 sequence-density-rank=1 fanout-score=2.16 fanout-score-rank=35 prefix-density=0.49 prefix-fanout=2.1 sequence=TTCGCTGAGCTCAAGGTGAAGGAGATCAAGAACGGCCGCCTCGCCATGTTCTCCATGTT criterion=fanout-score sequence-density=0.01 sequence-density-rank=39 fanout-score=41.03 fanout-score-rank=1 prefix-density=0.06 prefix-fanout=5.0 sequence=AGGAAAGGCTGCAATTGCAAGCTTGTGTCAAAGAAGAGGGTAGCACCTGATCCTCTTGCCTTTGGAGCCAGAAACAATGGCCTCGGCTACTATCCTCAAATCGTCTTTCCTTCCCAAGAAGTCCGAATGGGGCACCACCCGCCAGGCTGCCACTCCCAAGCAGATGACCGTCTCCATGGTTGTCCGTGCCAGCGCATACGCTGATGAACTTGTCAAGACCGCGAAAACCATCGCATCACCAGGAAGGGGCATCCTAGCCATGGATGAGTCCAATGCTACCTGTGGAAAGAGACTTGACTCGATTGGCCTTGAGAACACTGAGGCTAACCGCCAGGCTTACCGTACCCTCCTTGTCACTCCACCAGGCCTGGGAAATTACATCTCTGGTGCTATCCTCTTCGAGGAGACCCTCTACCAATCGACTGTTGATGGCAAGAAGATTGTTGACATCCTTGTCGAGCAGGGAATCGTTCCCGGCATCAAGGTTGACAAGGGTCTTGTGCCACTCGTT SRR8096891 testing PE reads STAR mapping to Ensembl genome Started job on | Dec 07 14:47:43 Started mapping on | Dec 07 14:47:43 Finished on | Dec 07 14:51:14 Mapping speed, Million of reads per hour | 613.33 Number of input reads | 35947944 Average input read length | 288 UNIQUE READS: Uniquely mapped reads number | 34612005 Uniquely mapped reads % | 96.28% Average mapped length | 288.03 Number of splices: Total | 35946885 Number of splices: Annotated (sjdb) | 33946768 Number of splices: GT/AG | 35473662 Number of splices: GC/AG | 414431 Number of splices: AT/AC | 10933 Number of splices: Non-canonical | 47859 Mismatch rate per base, % | 0.36% Deletion rate per base | 0.01% Deletion average length | 1.94 Insertion rate per base | 0.01% Insertion average length | 1.89 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 463815 % of reads mapped to multiple loci | 1.29% Number of reads mapped to too many loci | 13111 % of reads mapped to too many loci | 0.04% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 2.11% % of reads unmapped: other | 0.28% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 1093135 1093135 1093135 N_multimapping 463815 463815 463815 N_noFeature 1232030 33533459 1509352 N_ambiguous 951643 4364 153753 UnstrandedReadsAssigned:32428332 PositiveStrandReadsAssigned:1074182 NegativeStrandReadsAssigned:32948900 Dataset is classified negative stranded MeadianReadLen=150 20thPercentileLength=150 echo kmer=145 SRR8096891 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: SRR8096891-trimmed-pair1.fastq SRR8096891-trimmed-pair2.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 35,947,944 reads, 33,052,989 reads pseudoaligned [quant] estimated average fragment length: 279.973 [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,174 rounds 52973 SRR8096891.ke.tsv 35125 SRR8096891.se.tsv 88098 total ==> SRR8096891.ke.tsv <== target_id length eff_length est_counts tpm PNS24245 936 657.687 0 0 PNS24247 1044 765.027 92.1612 5.00991 PNS24249 1928 1649.03 26.7124 0.673664 PNS24246 1044 765.027 92.1612 5.00991 PNS24248 1044 765.027 92.1612 5.00991 PNS24244 1471 1192.03 241.804 8.43599 PNS24243 293 81.5167 0 0 KQK14069 1603 1324.03 8849.98 277.974 KQK14071 474 217.105 131.958 25.2769 ==> SRR8096891.se.tsv <== BRADI_1g14170v3 10358 BRADI_1g53295v3 50 BRADI_1g59795v3 1389 BRADI_1g07683v3 0 BRADI_1g00485v3 0 BRADI_1g20270v3 345 BRADI_1g74790v3 115 BRADI_1g09890v3 0 BRADI_1g77505v3 431 BRADI_1g48960v3 0 SRR8096891 completed mapping pipeline successfully