Starting /dee2/code/volunteer_pipeline.sh SRR8474565 current disk space = 3050175856640 free memory = 1466103176 SRR8474565 SRAfilesize 9a50e3d823d23b25a05020dec63e9d25 SRR8474565.sra SRR8474565.sra file validated SRR8474565 is paired end SRR8474565 is conventional basespace SRR8474565 read1 length is 99-150 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR8474565_1.fastq File type Conventional base calls Encoding Illumina 1.3 Total Sequences 4000 Sequences flagged as poor quality 0 Sequence length 99-150 %GC 42 >>END_MODULE >>Per base sequence quality fail #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 1.0 1.0 1.0 1.0 1.0 1.0 2 1.0 1.0 1.0 1.0 1.0 1.0 3 5.8125 6.0 6.0 6.0 6.0 6.0 4 5.94625 6.0 6.0 6.0 6.0 6.0 5 5.995 6.0 6.0 6.0 6.0 6.0 6 9.9245 10.0 10.0 10.0 10.0 10.0 7 9.852 10.0 10.0 10.0 10.0 10.0 8 9.95125 10.0 10.0 10.0 10.0 10.0 9 9.8915 10.0 10.0 10.0 10.0 10.0 10-14 9.95925 10.0 10.0 10.0 10.0 10.0 15-19 9.96835 10.0 10.0 10.0 10.0 10.0 20-24 9.9644 10.0 10.0 10.0 10.0 10.0 25-29 9.961699999999999 10.0 10.0 10.0 10.0 10.0 30-34 9.92905 10.0 10.0 10.0 10.0 10.0 35-39 9.95385 10.0 10.0 10.0 10.0 10.0 40-44 9.9587 10.0 10.0 10.0 10.0 10.0 45-49 9.9277 10.0 10.0 10.0 10.0 10.0 50-54 9.938550000000001 10.0 10.0 10.0 10.0 10.0 55-59 9.9067 10.0 10.0 10.0 10.0 10.0 60-64 9.92095 10.0 10.0 10.0 10.0 10.0 65-69 9.919149999999998 10.0 10.0 10.0 10.0 10.0 70-74 9.847750000000001 10.0 10.0 10.0 10.0 10.0 75-79 9.833450000000003 10.0 10.0 10.0 10.0 10.0 80-84 9.89495 10.0 10.0 10.0 10.0 10.0 85-89 9.88495 10.0 10.0 10.0 10.0 10.0 90-94 9.90095 10.0 10.0 10.0 10.0 10.0 95-99 9.839599999999999 10.0 10.0 10.0 10.0 10.0 100-104 9.84733392184479 10.0 10.0 10.0 10.0 10.0 105-109 9.847844366656236 10.0 10.0 10.0 10.0 10.0 110-114 9.871401797860438 10.0 10.0 10.0 10.0 10.0 115-119 9.865938413715234 10.0 10.0 10.0 10.0 10.0 120-124 9.844730126559943 10.0 10.0 10.0 10.0 10.0 125-129 9.84004792631256 10.0 10.0 10.0 10.0 10.0 130-134 9.77037533206026 10.0 10.0 10.0 10.0 10.0 135-139 9.760404796437282 10.0 10.0 10.0 10.0 10.0 140-144 9.683577895784719 10.0 10.0 10.0 10.0 10.0 145-149 9.620917969963907 10.0 10.0 10.0 10.0 10.0 150 9.622300745975657 10.0 10.0 10.0 10.0 10.0 >>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 0.0 >>END_MODULE >>Per sequence quality scores fail #Quality Count 8 5.0 9 3995.0 >>END_MODULE >>Per base sequence content warn #Base G A T C 1 37.35 10.375 18.15 34.125 2 22.8 15.725 29.45 32.025 3 20.9 22.85 24.275 31.974999999999998 4 24.925 30.075000000000003 20.75 24.25 5 22.925 33.800000000000004 22.6 20.674999999999997 6 17.599999999999998 38.025 24.375 20.0 7 12.9 29.549999999999997 40.175 17.375 8 16.0 26.125 33.825 24.05 9 16.05 25.525 34.075 24.349999999999998 10-14 18.955 30.805 27.150000000000002 23.09 15-19 19.07 29.895 27.61 23.425 20-24 18.37 30.915 27.800000000000004 22.915 25-29 18.435000000000002 30.814999999999998 27.310000000000002 23.44 30-34 18.2 30.695 27.884999999999998 23.22 35-39 18.385 30.099999999999998 27.85 23.665 40-44 18.425 30.580000000000002 27.189999999999998 23.805 45-49 18.67 29.67 27.77 23.89 50-54 18.61 30.23 27.85 23.31 55-59 18.775 30.145 27.805000000000003 23.275000000000002 60-64 18.715 29.705 27.46 24.12 65-69 18.67 30.035 27.62 23.674999999999997 70-74 18.790000000000003 29.515 28.005000000000003 23.69 75-79 18.87 29.875 27.595 23.66 80-84 18.86 29.515 27.755000000000003 23.87 85-89 18.265 29.555 28.475 23.705000000000002 90-94 18.855 29.945 27.66 23.54 95-99 18.72 29.205 27.845 24.23 100-104 18.505536929797824 29.945138677232553 27.9183175861018 23.631006806867823 105-109 19.18238993710692 29.465408805031444 27.599580712788256 23.752620545073373 110-114 18.729606264955407 29.731346530345874 27.66478137916032 23.874265825538394 115-119 17.969860676713107 29.320443559852144 28.22860392379869 24.481091839636054 120-124 18.27159016099108 29.696570710395598 27.82332874498773 24.208510383625594 125-129 18.030819754957687 29.682960717443475 28.091448781103956 24.194770746494886 130-134 19.305277221108884 29.519038076152306 27.461589846359384 23.714094856379425 135-139 18.678383128295255 28.92091388400703 27.6414762741652 24.759226713532513 140-144 18.16220238095238 28.616071428571427 27.74553571428571 25.476190476190474 145-149 19.001408671153545 29.261230239474095 27.899514791047114 23.837846298325246 150 18.060463290145268 29.328621908127207 26.933647428347072 25.677267373380445 >>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 0.0 15 0.0 16 0.0 17 0.0 18 0.0 19 1.0 20 1.5 21 0.5 22 1.0 23 2.5 24 4.5 25 4.5 26 6.5 27 9.0 28 11.5 29 20.0 30 30.0 31 41.0 32 56.5 33 69.5 34 85.0 35 94.0 36 106.5 37 140.5 38 156.5 39 178.0 40 231.5 41 260.0 42 270.5 43 271.5 44 272.0 45 277.5 46 251.0 47 226.0 48 209.5 49 165.5 50 128.5 51 104.0 52 84.0 53 66.0 54 48.5 55 35.5 56 21.5 57 17.5 58 11.0 59 8.0 60 8.5 61 5.0 62 2.5 63 2.5 64 1.5 65 0.5 66 0.0 67 0.0 68 0.0 69 0.0 70 0.0 71 0.0 72 0.0 73 0.0 74 0.0 75 0.0 76 0.0 77 0.0 78 0.0 79 0.0 80 0.0 81 0.0 82 0.0 83 0.0 84 0.0 85 0.0 86 0.0 87 0.0 88 0.0 89 0.0 90 0.0 91 0.0 92 0.0 93 0.0 94 0.0 95 0.0 96 0.0 97 0.0 98 0.0 99 0.0 100 0.0 >>END_MODULE >>Per base N content pass #Base N-Count 1 0.0 2 0.0 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 warn #Length Count 98-99 23.0 100-101 37.0 102-103 46.0 104-105 50.0 106-107 50.0 108-109 58.0 110-111 60.0 112-113 57.0 114-115 67.0 116-117 63.0 118-119 82.0 120-121 69.0 122-123 60.0 124-125 69.0 126-127 74.0 128-129 71.0 130-131 77.0 132-133 54.0 134-135 70.0 136-137 30.0 138-139 76.0 140-141 68.0 142-143 70.0 144-145 72.0 146-147 0.0 148-149 0.0 150-151 2547.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 98.15 #Duplication Level Percentage of deduplicated Percentage of total 1 98.11512990320938 96.3 2 1.8848700967906264 3.6999999999999997 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 0.0 114-115 0.0 0.0 0.0 0.0 0.0 116-117 0.0 0.0 0.0 0.0 0.0 118-119 0.0 0.0 0.0 0.0 0.0 120-121 0.0 0.0 0.0 0.0 0.0 122-123 0.0 0.0 0.0 0.0 0.0 124-125 0.0 0.0 0.0 0.0 0.0 126-127 0.0 0.0 0.0 0.0 0.0 128-129 0.0 0.0 0.0 0.0 0.0 130-131 0.0 0.0 0.0 0.0 0.0 132-133 0.0 0.0 0.0 0.0 0.0 134-135 0.0 0.0 0.0 0.0 0.0 136-137 0.0 0.0 0.0 0.0 0.0 138 0.0 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position ATTAACA 10 0.008754825 133.45001 8 TATTAAC 10 0.008754825 133.45001 7 >>END_MODULE SRR8474565 read2 length is 99-150 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR8474565_2.fastq File type Conventional base calls Encoding Illumina 1.3 Total Sequences 4000 Sequences flagged as poor quality 0 Sequence length 99-150 %GC 42 >>END_MODULE >>Per base sequence quality fail #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 1.0 1.0 1.0 1.0 1.0 1.0 2 1.0 1.0 1.0 1.0 1.0 1.0 3 5.36375 6.0 6.0 6.0 1.0 6.0 4 5.8375 6.0 6.0 6.0 6.0 6.0 5 5.875 6.0 6.0 6.0 6.0 6.0 6 9.75225 10.0 10.0 10.0 10.0 10.0 7 9.618 10.0 10.0 10.0 10.0 10.0 8 9.89775 10.0 10.0 10.0 10.0 10.0 9 9.9155 10.0 10.0 10.0 10.0 10.0 10-14 9.90205 10.0 10.0 10.0 10.0 10.0 15-19 9.911950000000001 10.0 10.0 10.0 10.0 10.0 20-24 9.846699999999998 10.0 10.0 10.0 10.0 10.0 25-29 9.88205 10.0 10.0 10.0 10.0 10.0 30-34 9.918099999999999 10.0 10.0 10.0 10.0 10.0 35-39 9.913149999999998 10.0 10.0 10.0 10.0 10.0 40-44 9.935749999999999 10.0 10.0 10.0 10.0 10.0 45-49 9.908150000000001 10.0 10.0 10.0 10.0 10.0 50-54 9.8958 10.0 10.0 10.0 10.0 10.0 55-59 9.8989 10.0 10.0 10.0 10.0 10.0 60-64 9.86945 10.0 10.0 10.0 10.0 10.0 65-69 9.8672 10.0 10.0 10.0 10.0 10.0 70-74 9.872150000000001 10.0 10.0 10.0 10.0 10.0 75-79 9.8074 10.0 10.0 10.0 10.0 10.0 80-84 9.8232 10.0 10.0 10.0 10.0 10.0 85-89 9.8611 10.0 10.0 10.0 10.0 10.0 90-94 9.82055 10.0 10.0 10.0 10.0 10.0 95-99 9.829150000000002 10.0 10.0 10.0 10.0 10.0 100-104 9.769477074223126 10.0 10.0 10.0 10.0 10.0 105-109 9.740136327279293 10.0 10.0 10.0 10.0 10.0 110-114 9.708431614798403 10.0 10.0 10.0 10.0 10.0 115-119 9.563317808061626 10.0 10.0 10.0 8.4 10.0 120-124 9.530866768077345 10.0 10.0 10.0 7.6 10.0 125-129 9.567056632518113 10.0 10.0 10.0 8.4 10.0 130-134 9.553853875694738 10.0 10.0 10.0 9.2 10.0 135-139 9.395967788614676 10.0 10.0 10.0 6.8 10.0 140-144 9.266865474551881 10.0 10.0 10.0 6.0 10.0 145-149 9.18037791451219 10.0 10.0 10.0 6.0 10.0 150 9.029053788771103 10.0 10.0 10.0 6.0 10.0 >>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 0.0 >>END_MODULE >>Per sequence quality scores fail #Quality Count 8 47.0 9 3953.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 34.075 16.875 22.025 27.025 2 26.924999999999997 30.65 27.474999999999998 14.95 3 24.2 32.225 26.825 16.75 4 28.65 35.125 21.349999999999998 14.875 5 26.3 37.625 22.125 13.950000000000001 6 18.5 40.0 25.974999999999998 15.525 7 21.0 18.875 41.3 18.825 8 24.325 23.175 30.0 22.5 9 25.45 23.474999999999998 29.5 21.575 10-14 24.87 27.889999999999997 27.665 19.575 15-19 24.535 27.025 29.365000000000002 19.075 20-24 23.745 28.349999999999998 29.409999999999997 18.495 25-29 24.0 27.68 29.79 18.529999999999998 30-34 23.880000000000003 28.16 29.509999999999998 18.45 35-39 23.72 28.355000000000004 28.9 19.025 40-44 24.560000000000002 27.245 29.439999999999998 18.755 45-49 23.805 27.16 29.65 19.384999999999998 50-54 24.415 27.85 29.285 18.45 55-59 23.64 27.575 29.695 19.09 60-64 24.0 27.725 29.225 19.05 65-69 24.25 27.794999999999998 29.65 18.305 70-74 23.71 27.825 29.630000000000003 18.834999999999997 75-79 23.77 27.37 30.154999999999998 18.705 80-84 24.255 26.924999999999997 29.885 18.935 85-89 24.075 28.005000000000003 29.53 18.39 90-94 24.05 28.050000000000004 29.205 18.695 95-99 23.45 27.665 30.404999999999998 18.48 100-104 24.088184496596565 27.96911510718277 29.52351925226049 18.419181143960177 105-109 23.957023060796644 27.452830188679243 30.052410901467507 18.537735849056602 110-114 22.987818142266693 27.485316510767895 30.10115292582119 19.425712421144226 115-119 23.696332101222634 28.023883992038666 29.889110036963324 18.390673869775377 120-124 23.633969716919026 27.212879286612008 30.384822550721168 18.7683284457478 125-129 23.702159909056462 27.7567260325881 30.156624984211188 18.38448907414425 130-134 23.520374081496325 28.40347361389445 29.946559786239145 18.129592518370075 135-139 23.70474516695958 28.738137082601057 29.216168717047452 18.340949033391915 140-144 22.12053571428571 28.668154761904763 30.163690476190474 19.047619047619047 145-149 23.493504460791986 28.259508530286432 28.979496008765064 19.267491000156518 150 25.284648606203376 27.718884962701217 29.2893600314095 17.707106399685905 >>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 0.0 15 0.0 16 0.0 17 0.0 18 0.0 19 0.0 20 0.5 21 1.5 22 1.5 23 1.0 24 2.5 25 4.0 26 3.0 27 4.5 28 10.5 29 17.5 30 25.0 31 32.5 32 37.0 33 44.0 34 58.5 35 79.0 36 103.5 37 145.0 38 179.5 39 199.5 40 227.5 41 250.0 42 272.5 43 304.5 44 304.0 45 291.0 46 270.0 47 225.5 48 185.0 49 156.0 50 138.0 51 110.5 52 91.0 53 68.5 54 43.5 55 28.5 56 23.5 57 21.5 58 14.0 59 8.0 60 6.0 61 4.5 62 1.5 63 1.5 64 1.0 65 0.5 66 0.0 67 0.0 68 0.5 69 0.5 70 0.0 71 0.0 72 0.0 73 0.0 74 0.0 75 0.5 76 0.5 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 0.0 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 warn #Length Count 98-99 23.0 100-101 37.0 102-103 46.0 104-105 50.0 106-107 50.0 108-109 58.0 110-111 60.0 112-113 57.0 114-115 67.0 116-117 63.0 118-119 82.0 120-121 69.0 122-123 60.0 124-125 69.0 126-127 74.0 128-129 71.0 130-131 77.0 132-133 54.0 134-135 70.0 136-137 30.0 138-139 76.0 140-141 68.0 142-143 70.0 144-145 72.0 146-147 0.0 148-149 0.0 150-151 2547.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 98.2 #Duplication Level Percentage of deduplicated Percentage of total 1 98.16700610997964 96.39999999999999 2 1.8329938900203666 3.5999999999999996 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 0.0 114-115 0.0 0.0 0.0 0.0 0.0 116-117 0.0 0.0 0.0 0.0 0.0 118-119 0.0 0.0 0.0 0.0 0.0 120-121 0.0 0.0 0.0 0.0 0.0 122-123 0.0 0.0 0.0 0.0 0.0 124-125 0.0 0.0 0.0 0.0 0.0 126-127 0.0 0.0 0.0 0.0 0.0 128-129 0.0 0.0 0.0 0.0 0.0 130-131 0.0 0.0 0.0 0.0 0.0 132-133 0.0 0.0 0.0 0.0 0.0 134-135 0.0 0.0 0.0 0.0 0.0 136-137 0.0 0.0 0.0 0.0 0.0 138 0.0 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content pass >>END_MODULE Read 1168858 spots for SRR8474565.sra Written 1168858 spots for SRR8474565.sra Read 1168858 spots for SRR8474565.sra Written 1168858 spots for SRR8474565.sra Read 1168858 spots for SRR8474565.sra Written 1168858 spots for SRR8474565.sra Read 1168858 spots for SRR8474565.sra Written 1168858 spots for SRR8474565.sra Read 1168858 spots for SRR8474565.sra Written 1168858 spots for SRR8474565.sra Read 1168858 spots for SRR8474565.sra Written 1168858 spots for SRR8474565.sra Read 1168858 spots for SRR8474565.sra Written 1168858 spots for SRR8474565.sra Read 1168858 spots for SRR8474565.sra Written 1168858 spots for SRR8474565.sra Read 1168858 spots for SRR8474565.sra Written 1168858 spots for SRR8474565.sra Read 1168858 spots for SRR8474565.sra Written 1168858 spots for SRR8474565.sra Read 1168858 spots for SRR8474565.sra Written 1168858 spots for SRR8474565.sra Read 1168858 spots for SRR8474565.sra Written 1168858 spots for SRR8474565.sra Read 1168858 spots for SRR8474565.sra Written 1168858 spots for SRR8474565.sra Read 1168858 spots for SRR8474565.sra Written 1168858 spots for SRR8474565.sra Read 1168858 spots for SRR8474565.sra Written 1168858 spots for SRR8474565.sra Read 1168858 spots for SRR8474565.sra Written 1168858 spots for SRR8474565.sra Read 1168858 spots for SRR8474565.sra Written 1168858 spots for SRR8474565.sra Read 1168858 spots for SRR8474565.sra Written 1168858 spots for SRR8474565.sra Read 1168875 spots for SRR8474565.sra Written 1168875 spots for SRR8474565.sra Read 1168858 spots for SRR8474565.sra Written 1168858 spots for SRR8474565.sra SRR ids: ['SRR8474565.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_n9x1ky6l SRR8474565.sra spots: 23377177 blocks: [[1, 1168858], [1168859, 2337716], [2337717, 3506574], [3506575, 4675432], [4675433, 5844290], [5844291, 7013148], [7013149, 8182006], [8182007, 9350864], [9350865, 10519722], [10519723, 11688580], [11688581, 12857438], [12857439, 14026296], [14026297, 15195154], [15195155, 16364012], [16364013, 17532870], [17532871, 18701728], [18701729, 19870586], [19870587, 21039444], [21039445, 22208302], [22208303, 23377177]] SRR8474565 file size 8387321 SRR8474565 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 SRR8474565 SRR8474565_1.fastq SRR8474565_2.fastq Input file: SRR8474565_1.fastq Paired file: SRR8474565_2.fastq trimmed: SRR8474565-trimmed-pair1.fastq, SRR8474565-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 14:19:35 2025 >> started Tue Feb 11 14:20:04 2025 >> done (29.421s) 23377177 read pairs processed; of these: 2 ( 0.00%) short read pairs filtered out after trimming by size control 140 ( 0.00%) empty read pairs filtered out after trimming by size control 23377035 (100.00%) read pairs available; of these: 1568513 ( 6.71%) trimmed read pairs available after processing 21808522 (93.29%) untrimmed read pairs available after processing Length distribution of reads after trimming: length count percentage 25 1 0.00% 26 0 0.00% 27 1 0.00% 28 0 0.00% 29 3 0.00% 30 0 0.00% 31 1 0.00% 32 1 0.00% 33 1 0.00% 34 2 0.00% 35 4 0.00% 36 1 0.00% 37 0 0.00% 38 1 0.00% 39 3 0.00% 40 4 0.00% 41 5 0.00% 42 2 0.00% 43 7 0.00% 44 6 0.00% 45 3 0.00% 46 4 0.00% 47 2 0.00% 48 6 0.00% 49 6 0.00% 50 4 0.00% 51 9 0.00% 52 5 0.00% 53 2 0.00% 54 4 0.00% 55 9 0.00% 56 4 0.00% 57 10 0.00% 58 5 0.00% 59 7 0.00% 60 7 0.00% 61 17 0.00% 62 4 0.00% 63 10 0.00% 64 8 0.00% 65 10 0.00% 66 16 0.00% 67 12 0.00% 68 11 0.00% 69 13 0.00% 70 9 0.00% 71 10 0.00% 72 9 0.00% 73 17 0.00% 74 16 0.00% 75 19 0.00% 76 20 0.00% 77 11 0.00% 78 14 0.00% 79 9 0.00% 80 14 0.00% 81 17 0.00% 82 19 0.00% 83 28 0.00% 84 19 0.00% 85 32 0.00% 86 23 0.00% 87 23 0.00% 88 24 0.00% 89 32 0.00% 90 29 0.00% 91 28 0.00% 92 40 0.00% 93 55 0.00% 94 95 0.00% 95 118 0.00% 96 140 0.00% 97 111 0.00% 98 161 0.00% 99 30463 0.13% 100 31381 0.13% 101 32704 0.14% 102 33122 0.14% 103 35103 0.15% 104 36913 0.16% 105 39441 0.17% 106 41926 0.18% 107 44239 0.19% 108 47808 0.20% 109 49593 0.21% 110 51484 0.22% 111 51763 0.22% 112 52462 0.22% 113 54612 0.23% 114 56313 0.24% 115 58965 0.25% 116 60137 0.26% 117 64254 0.27% 118 68103 0.29% 119 71364 0.31% 120 73202 0.31% 121 73680 0.32% 122 74335 0.32% 123 74598 0.32% 124 76478 0.33% 125 77931 0.33% 126 80985 0.35% 127 84687 0.36% 128 87853 0.38% 129 92404 0.40% 130 95436 0.41% 131 96844 0.41% 132 97141 0.42% 133 96165 0.41% 134 97117 0.42% 135 98648 0.42% 136 98728 0.42% 137 5747 0.02% 138 104440 0.45% 139 108093 0.46% 140 111344 0.48% 141 115808 0.50% 142 119173 0.51% 143 121859 0.52% 144 126421 0.54% 145 162245 0.69% 146 117784 0.50% 147 134078 0.57% 148 215519 0.92% 149 1009553 4.32% 150 18435216 78.86% 23377035 reads passed initial QC criterion=sequence-density sequence-density=0.09 sequence-density-rank=1 fanout-score=1.93 fanout-score-rank=39 prefix-density=0.09 prefix-fanout=1.9 sequence=TTAATTTACAGCAAATACTATATTAGACAAACATGGAGTG criterion=fanout-score sequence-density=0.01 sequence-density-rank=41 fanout-score=373.45 fanout-score-rank=1 prefix-density=0.20 prefix-fanout=17.5 sequence=CTCCTTCCTCTAAATGATAAGGTTCAGTGGACTTCTCGCGACGTCGCCGGCGGCGAACCGCCCACGTCGCCGCGATCCGAACACTTCACCGGACCATTCAATCGGTAGGAGCGACGGGCGGTGTGTACAAAGGGCAGGGACGTAGTCAACGCGAGCTGATGACTCGCGCTTACTAGGAATTCCTCGTTGAAGACCAACAATTGCAATGATCTATCCCCATCACGATGAAATTTCAAAGATTACCCGGGCCTGTCGGCCAAGGCTATAGACTCGTTGAATACATCAGTGTAGCGCGCGTGCGGCCCAGAACATCTAAGGGCATCACAGACCTGTTATTGCCTCAAACTTCCTTGGCCTGGAAGGCCATAGTCCCTCTAAGAAGCTGGCCGCGGAGGGTCACCTCCGCATAGCTAGTTAGCAGGCTGAGGTCTCGTTCGTTAACGGAATTAACCAGACAAATCGCTCCACCAACTAAGAACGGCCATGCACCACCACCCATAGAATCAAGAAA criterion=sequence-density sequence-density=0.11 sequence-density-rank=1 fanout-score=1.94 fanout-score-rank=39 prefix-density=0.11 prefix-fanout=1.9 sequence=GCGGGAGCAGCTA criterion=fanout-score sequence-density=0.07 sequence-density-rank=15 fanout-score=215.97 fanout-score-rank=1 prefix-density=0.55 prefix-fanout=26.5 sequence=GAGAAGAAGGATCC SRR8474565 testing PE reads STAR mapping to Ensembl genome Started job on | Feb 11 14:20:58 Started mapping on | Feb 11 14:20:58 Finished on | Feb 11 14:26:26 Mapping speed, Million of reads per hour | 256.58 Number of input reads | 23377035 Average input read length | 293 UNIQUE READS: Uniquely mapped reads number | 19957054 Uniquely mapped reads % | 85.37% Average mapped length | 286.73 Number of splices: Total | 17840681 Number of splices: Annotated (sjdb) | 17446713 Number of splices: GT/AG | 17483078 Number of splices: GC/AG | 242740 Number of splices: AT/AC | 14104 Number of splices: Non-canonical | 100759 Mismatch rate per base, % | 1.52% Deletion rate per base | 0.09% Deletion average length | 2.92 Insertion rate per base | 0.06% Insertion average length | 2.64 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 882243 % of reads mapped to multiple loci | 3.77% Number of reads mapped to too many loci | 305715 % of reads mapped to too many loci | 1.31% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 8.54% % of reads unmapped: other | 1.01% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 2537738 2537738 2537738 N_multimapping 882243 882243 882243 N_noFeature 507596 19723506 643935 N_ambiguous 245634 1851 147314 UnstrandedReadsAssigned:19203824 PositiveStrandReadsAssigned:231697 NegativeStrandReadsAssigned:19165805 Dataset is classified negative stranded MeadianReadLen=150 20thPercentileLength=130 echo kmer=125 SRR8474565 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: SRR8474565-trimmed-pair1.fastq SRR8474565-trimmed-pair2.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 23,377,035 reads, 19,967,550 reads pseudoaligned [quant] estimated average fragment length: 170.218 [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,314 rounds 52401 SRR8474565.ke.tsv 34699 SRR8474565.se.tsv 87100 total ==> SRR8474565.ke.tsv <== target_id length eff_length est_counts tpm Potri.005G200100.1.v4.1 2018 1848.78 874 27.3967 Potri.005G024800.1.v4.1 1035 865.782 129 8.63483 Potri.004G059700.1.v4.1 961 791.782 87 6.36775 Potri.007G009000.2.v4.1 1416 1246.78 0 0 Potri.003G141000.2.v4.1 2943 2773.78 771.775 16.1247 Potri.016G087400.1.v4.1 270 105.633 1257.53 689.912 Potri.015G069301.1.v4.1 564 394.822 0 0 Potri.010G195200.1.v4.1 1773 1603.78 35 1.26472 Potri.012G127500.1.v4.1 977 807.782 11853 850.367 ==> SRR8474565.se.tsv <== Potri.001G166300.v4.1 0 Potri.001G448400.v4.1 1 Potri.001G233950.v4.1 0 Potri.001G122700.v4.1 122 Potri.001G212900.v4.1 2 Potri.001G182400.v4.1 0 Potri.001G256600.v4.1 0 Potri.001G040500.v4.1 85 Potri.001G416900.v4.1 0 Potri.001G452600.v4.1 1 SRR8474565 completed mapping pipeline successfully