Starting /dee2/code/volunteer_pipeline.sh SRR7171453 current disk space = 3087841984512 free memory = 1449860588 SRR7171453 SRAfilesize 88705865ab99d751566fd67f7ae6fb41 SRR7171453.sra SRR7171453.sra file validated SRR7171453 is paired end SRR7171453 is conventional basespace SRR7171453 read1 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR7171453_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 44 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 31.7385 33.0 33.0 34.0 32.0 34.0 2 32.0935 33.0 32.0 33.0 30.0 34.0 3 32.911 33.0 33.0 34.0 32.0 34.0 4 32.5505 33.0 33.0 34.0 31.0 34.0 5 32.89625 33.0 33.0 34.0 32.0 34.0 6 37.01225 38.0 37.0 38.0 35.0 38.0 7 37.45175 38.0 38.0 38.0 37.0 38.0 8 37.5735 38.0 38.0 38.0 37.0 38.0 9 37.54075 38.0 38.0 38.0 37.0 38.0 10-14 37.6447 38.0 38.0 38.0 38.0 38.0 15-19 37.63295000000001 38.0 38.0 38.0 38.0 38.0 20-24 37.6233 38.0 38.0 38.0 38.0 38.0 25-29 37.64755 38.0 38.0 38.0 38.0 38.0 30-34 37.56420000000001 38.0 38.0 38.0 38.0 38.0 35-39 37.5752 38.0 38.0 38.0 38.0 38.0 40-44 37.57835 38.0 38.0 38.0 38.0 38.0 45-49 37.55055 38.0 38.0 38.0 38.0 38.0 50-54 37.4824 38.0 38.0 38.0 37.4 38.0 55-59 37.4528 38.0 38.0 38.0 37.0 38.0 60-64 37.44355 38.0 38.0 38.0 37.0 38.0 65-69 37.440999999999995 38.0 38.0 38.0 37.0 38.0 70-74 37.36255 38.0 38.0 38.0 37.0 38.0 75-79 37.29595 38.0 38.0 38.0 37.0 38.0 80-84 37.266149999999996 38.0 38.0 38.0 36.8 38.0 85-89 37.24105 38.0 38.0 38.0 36.4 38.0 90-94 37.179500000000004 38.0 38.0 38.0 36.0 38.0 95-99 37.02825 38.0 38.0 38.0 36.0 38.0 100-104 36.94375 38.0 38.0 38.0 35.6 38.0 105-109 36.8387 38.0 38.0 38.0 35.0 38.0 110-114 36.777499999999996 38.0 38.0 38.0 35.0 38.0 115-119 36.69805 38.0 38.0 38.0 34.6 38.0 120-124 36.580000000000005 38.0 38.0 38.0 34.0 38.0 125-129 36.39104999999999 38.0 38.0 38.0 34.0 38.0 130-134 36.3106 38.0 37.8 38.0 33.8 38.0 135-139 36.099000000000004 38.0 36.8 38.0 33.0 38.0 140-144 35.89155 38.0 36.2 38.0 32.4 38.0 145-149 35.671 38.0 36.0 38.0 31.0 38.0 150-151 33.09575 35.5 32.0 38.0 22.0 38.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 21 1.0 22 1.0 23 4.0 24 2.0 25 6.0 26 2.0 27 11.0 28 17.0 29 22.0 30 21.0 31 45.0 32 44.0 33 61.0 34 122.0 35 179.0 36 481.0 37 2981.0 >>END_MODULE >>Per base sequence content warn #Base G A T C 1 41.39098723625944 12.477207606147434 8.075019536337589 38.056785621255536 2 22.7 14.424999999999999 33.1 29.775000000000002 3 19.45 19.75 25.575 35.225 4 22.05 29.15 21.975 26.825 5 22.35 32.975 24.325 20.349999999999998 6 19.950000000000003 35.125 24.55 20.375 7 14.85 25.525 40.425 19.2 8 19.325 26.1 29.9 24.675 9 16.825000000000003 24.3 34.625 24.25 10-14 19.759999999999998 29.92 26.35 23.97 15-19 19.869999999999997 28.96 27.765 23.405 20-24 19.895 28.33 27.935 23.84 25-29 19.435 29.494999999999997 27.139999999999997 23.93 30-34 20.43 28.294999999999998 27.35 23.925 35-39 20.745 28.04 27.439999999999998 23.775 40-44 20.39 28.249999999999996 27.305 24.055 45-49 19.985 28.105000000000004 27.744999999999997 24.165 50-54 20.46 28.310000000000002 27.3 23.93 55-59 20.424999999999997 28.43 27.105 24.04 60-64 19.885 28.34 27.389999999999997 24.385 65-69 19.869999999999997 28.205000000000002 27.61 24.315 70-74 20.64 28.32 27.165 23.875 75-79 20.7 27.92 27.395000000000003 23.985 80-84 20.73 28.035 27.49 23.745 85-89 20.655 27.815 27.405 24.125 90-94 20.89 28.055000000000003 26.945000000000004 24.11 95-99 20.935000000000002 27.515 27.455000000000002 24.095 100-104 21.05605280264013 28.781439071953596 26.756337816890845 23.406170308515424 105-109 20.890445222611305 27.793896948474238 27.788894447223612 23.526763381690845 110-114 21.010252563140785 28.312078019504877 27.176794198549636 23.5008752188047 115-119 21.05605280264013 27.701385069253465 27.76638831941597 23.476173808690433 120-124 20.94 27.529999999999998 27.49 24.04 125-129 21.245 27.26 27.26 24.235 130-134 21.16 27.500000000000004 27.395000000000003 23.945 135-139 20.745 28.199999999999996 26.855 24.2 140-144 21.185000000000002 27.605 27.389999999999997 23.82 145-149 20.935000000000002 27.400000000000002 27.150000000000002 24.515 150-151 22.0875 26.7125 26.637499999999996 24.5625 >>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 0.5 16 0.5 17 0.0 18 0.0 19 0.0 20 0.5 21 0.5 22 0.0 23 0.0 24 2.0 25 2.0 26 1.0 27 3.0 28 4.5 29 11.5 30 16.5 31 20.0 32 25.5 33 30.0 34 37.0 35 41.0 36 65.0 37 101.0 38 131.5 39 146.5 40 158.0 41 214.0 42 262.5 43 271.0 44 265.5 45 280.0 46 286.0 47 276.0 48 254.0 49 210.5 50 185.5 51 162.5 52 130.5 53 102.0 54 81.0 55 60.0 56 45.0 57 33.0 58 21.5 59 14.5 60 12.0 61 10.5 62 8.5 63 6.5 64 3.5 65 2.0 66 1.5 67 1.0 68 0.5 69 0.5 70 0.5 71 0.0 72 0.0 73 0.0 74 0.0 75 0.0 76 0.0 77 0.0 78 0.0 79 0.0 80 0.0 81 0.0 82 0.0 83 0.0 84 0.0 85 0.0 86 0.0 87 0.0 88 0.0 89 0.0 90 0.0 91 0.0 92 0.0 93 0.0 94 0.0 95 0.0 96 0.0 97 0.0 98 0.0 99 0.0 100 0.0 >>END_MODULE >>Per base N content pass #Base N-Count 1 4.025 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 0.005 105-109 0.05 110-114 0.025 115-119 0.005 120-124 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 99.675 #Duplication Level Percentage of deduplicated Percentage of total 1 99.67394030599448 99.35000000000001 2 0.32605969400551793 0.65 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 warn #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 0.025 0.0 0.0 0.0 0.0 70-71 0.0625 0.0 0.0 0.0 0.0 72-73 0.075 0.0 0.0 0.0 0.0 74-75 0.075 0.0 0.0 0.0 0.0 76-77 0.075 0.0 0.0 0.0 0.0 78-79 0.0875 0.0 0.0 0.0 0.0 80-81 0.1 0.0 0.0 0.0 0.0 82-83 0.1 0.0 0.0 0.0 0.0 84-85 0.1375 0.0 0.0 0.0 0.0 86-87 0.15 0.0 0.0 0.0 0.0 88-89 0.15 0.0 0.0 0.0 0.0 90-91 0.225 0.0 0.0 0.0 0.0 92-93 0.25 0.0 0.0 0.0 0.0 94-95 0.2625 0.0 0.0 0.0 0.0 96-97 0.375 0.0 0.0 0.0 0.0 98-99 0.4875 0.0 0.0 0.0 0.0 100-101 0.5874999999999999 0.0 0.0 0.0 0.0 102-103 0.625 0.0 0.0 0.0 0.0 104-105 0.7375 0.0 0.0 0.0 0.0 106-107 0.975 0.0 0.0 0.0 0.0 108-109 1.125 0.0 0.0 0.0 0.0 110-111 1.2875 0.0 0.0 0.0 0.0 112-113 1.4625 0.0 0.0 0.0 0.0 114-115 1.6625 0.0 0.0 0.0 0.0 116-117 1.9375 0.0 0.0 0.0 0.0 118-119 2.1125 0.0 0.0 0.0 0.0 120-121 2.2875 0.0 0.0 0.0 0.0 122-123 2.4749999999999996 0.0 0.0 0.0 0.0 124-125 2.7249999999999996 0.0 0.0 0.0 0.0 126-127 3.05 0.0 0.0 0.0 0.0 128-129 3.4 0.0 0.0 0.0 0.0 130-131 3.775 0.0 0.0 0.0 0.0 132-133 4.125 0.0 0.0 0.0 0.0 134-135 4.4625 0.0 0.0 0.0 0.0 136-137 4.800000000000001 0.0 0.0 0.0 0.0 138-139 5.262499999999999 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position CCAATCC 10 0.0063298983 148.6923 1 ATTCATA 10 0.0068343505 144.975 6 >>END_MODULE SRR7171453 read2 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR7171453_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 44 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 33.0965 33.0 33.0 34.0 33.0 34.0 2 33.1815 34.0 33.0 34.0 33.0 34.0 3 33.1735 34.0 33.0 34.0 33.0 34.0 4 33.16525 34.0 33.0 34.0 33.0 34.0 5 33.20625 34.0 33.0 34.0 33.0 34.0 6 37.39825 38.0 38.0 38.0 38.0 38.0 7 37.368 38.0 38.0 38.0 38.0 38.0 8 37.3215 38.0 38.0 38.0 37.0 38.0 9 37.30575 38.0 38.0 38.0 37.0 38.0 10-14 37.36835 38.0 38.0 38.0 37.4 38.0 15-19 37.34965 38.0 38.0 38.0 37.4 38.0 20-24 37.30475 38.0 38.0 38.0 37.0 38.0 25-29 37.29355 38.0 38.0 38.0 37.2 38.0 30-34 37.3163 38.0 38.0 38.0 37.0 38.0 35-39 37.26725 38.0 38.0 38.0 37.0 38.0 40-44 37.2746 38.0 38.0 38.0 37.0 38.0 45-49 37.227549999999994 38.0 38.0 38.0 37.0 38.0 50-54 37.192949999999996 38.0 38.0 38.0 37.0 38.0 55-59 37.1632 38.0 38.0 38.0 37.0 38.0 60-64 37.1105 38.0 38.0 38.0 36.8 38.0 65-69 37.1051 38.0 38.0 38.0 36.4 38.0 70-74 37.04975 38.0 38.0 38.0 36.2 38.0 75-79 37.0071 38.0 38.0 38.0 36.0 38.0 80-84 36.92855 38.0 38.0 38.0 36.0 38.0 85-89 36.880250000000004 38.0 38.0 38.0 36.0 38.0 90-94 36.7524 38.0 38.0 38.0 35.4 38.0 95-99 36.72045 38.0 38.0 38.0 35.0 38.0 100-104 36.5669 38.0 38.0 38.0 34.0 38.0 105-109 36.51225 38.0 38.0 38.0 34.0 38.0 110-114 36.463449999999995 38.0 38.0 38.0 34.0 38.0 115-119 36.243550000000006 38.0 38.0 38.0 33.8 38.0 120-124 36.103249999999996 38.0 37.6 38.0 33.4 38.0 125-129 36.03175 38.0 37.0 38.0 32.8 38.0 130-134 35.85295 38.0 36.4 38.0 32.4 38.0 135-139 35.592349999999996 38.0 36.0 38.0 31.0 38.0 140-144 35.247400000000006 38.0 35.4 38.0 29.2 38.0 145-149 34.6827 38.0 33.6 38.0 26.2 38.0 150-151 31.881999999999998 35.5 28.0 38.0 18.5 38.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 15 4.0 16 4.0 17 2.0 18 6.0 19 6.0 20 7.0 21 5.0 22 5.0 23 8.0 24 7.0 25 11.0 26 11.0 27 18.0 28 23.0 29 22.0 30 32.0 31 47.0 32 48.0 33 95.0 34 123.0 35 189.0 36 545.0 37 2782.0 >>END_MODULE >>Per base sequence content warn #Base G A T C 1 36.525 21.375 15.299999999999999 26.8 2 26.450000000000003 27.6 28.749999999999996 17.2 3 20.474999999999998 30.15 29.075 20.3 4 22.85 34.949999999999996 22.825 19.375 5 24.15 36.175000000000004 22.1 17.575 6 21.15 37.7 23.05 18.099999999999998 7 20.4 20.0 39.725 19.875 8 22.3 24.775 26.200000000000003 26.724999999999998 9 20.65 24.6 29.925 24.825 10-14 23.595 29.2 25.580000000000002 21.625 15-19 23.369999999999997 28.485 26.895000000000003 21.25 20-24 23.13 28.194999999999997 27.224999999999998 21.45 25-29 23.555 27.62 27.26 21.565 30-34 23.65 28.395 26.924999999999997 21.029999999999998 35-39 23.064999999999998 28.384999999999998 27.384999999999998 21.165 40-44 23.26 28.46 27.339999999999996 20.94 45-49 23.685000000000002 27.975 27.68 20.66 50-54 23.31 27.189999999999998 27.705000000000002 21.795 55-59 23.605 27.439999999999998 27.785 21.17 60-64 24.085 27.339999999999996 27.88 20.695 65-69 23.525 28.384999999999998 27.169999999999998 20.919999999999998 70-74 23.905 28.000000000000004 27.315 20.78 75-79 23.849999999999998 28.355000000000004 27.005000000000003 20.79 80-84 24.060000000000002 28.015 27.125 20.8 85-89 24.175 27.74 27.450000000000003 20.635 90-94 23.895 27.395000000000003 27.625 21.085 95-99 23.77 28.27 27.134999999999998 20.825 100-104 24.36 27.595 27.169999999999998 20.875 105-109 23.98 27.200000000000003 28.165000000000003 20.655 110-114 24.215 27.725 26.924999999999997 21.135 115-119 24.279999999999998 27.435 27.515 20.77 120-124 24.51 27.425 27.800000000000004 20.265 125-129 24.365000000000002 27.825 27.395000000000003 20.415 130-134 24.285 27.85 27.195000000000004 20.669999999999998 135-139 24.875 27.33 27.389999999999997 20.405 140-144 24.335 28.105000000000004 26.515 21.044999999999998 145-149 25.169999999999998 27.91 27.1 19.82 150-151 24.837500000000002 27.0 27.5875 20.575 >>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 0.0 21 0.5 22 1.0 23 1.0 24 1.0 25 0.5 26 0.5 27 1.0 28 2.5 29 6.5 30 10.5 31 10.0 32 16.5 33 27.0 34 31.5 35 43.0 36 56.0 37 79.0 38 124.0 39 169.5 40 205.5 41 223.5 42 241.5 43 276.5 44 298.5 45 305.0 46 298.5 47 277.5 48 237.0 49 192.5 50 180.5 51 162.0 52 123.0 53 100.5 54 83.5 55 56.5 56 37.0 57 29.5 58 24.0 59 16.0 60 10.0 61 12.0 62 9.0 63 2.5 64 5.5 65 5.0 66 1.0 67 2.0 68 1.0 69 0.5 70 0.5 71 0.5 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 0.0 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 99.7 #Duplication Level Percentage of deduplicated Percentage of total 1 99.69909729187563 99.4 2 0.3009027081243731 0.6 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 warn #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 0.025 0.0 0.0 0.0 0.0 70-71 0.0625 0.0 0.0 0.0 0.0 72-73 0.075 0.0 0.0 0.0 0.0 74-75 0.075 0.0 0.0 0.0 0.0 76-77 0.075 0.0 0.0 0.0 0.0 78-79 0.0875 0.0 0.0 0.0 0.0 80-81 0.1 0.0 0.0 0.0 0.0 82-83 0.1 0.0 0.0 0.0 0.0 84-85 0.1375 0.0 0.0 0.0 0.0 86-87 0.15 0.0 0.0 0.0 0.0 88-89 0.15 0.0 0.0 0.0 0.0 90-91 0.225 0.0 0.0 0.0 0.0 92-93 0.275 0.0 0.0 0.0 0.0 94-95 0.2875 0.0 0.0 0.0 0.0 96-97 0.4 0.0 0.0 0.0 0.0 98-99 0.5125 0.0 0.0 0.0 0.0 100-101 0.6125 0.0 0.0 0.0 0.0 102-103 0.65 0.0 0.0 0.0 0.0 104-105 0.7625 0.0 0.0 0.0 0.0 106-107 1.0 0.0 0.0 0.0 0.0 108-109 1.15 0.0 0.0 0.0 0.0 110-111 1.3125 0.0 0.0 0.0 0.0 112-113 1.4874999999999998 0.0 0.0 0.0 0.0 114-115 1.6875 0.0 0.0 0.0 0.0 116-117 1.9875 0.0 0.0 0.0 0.0 118-119 2.1875 0.0 0.0 0.0 0.0 120-121 2.3625 0.0 0.0 0.0 0.0 122-123 2.55 0.0 0.0 0.0 0.0 124-125 2.7875 0.0 0.0 0.0 0.0 126-127 3.075 0.0 0.0 0.0 0.0 128-129 3.4125 0.0 0.0 0.0 0.0 130-131 3.7625 0.0 0.0 0.0 0.0 132-133 4.1 0.0 0.0 0.0 0.0 134-135 4.4375 0.0 0.0 0.0 0.0 136-137 4.800000000000001 0.0 0.0 0.0 0.0 138-139 5.262499999999999 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content pass >>END_MODULE Read 701943 spots for SRR7171453.sra Written 701943 spots for SRR7171453.sra Read 701943 spots for SRR7171453.sra Written 701943 spots for SRR7171453.sra Read 701943 spots for SRR7171453.sra Written 701943 spots for SRR7171453.sra Read 701943 spots for SRR7171453.sra Written 701943 spots for SRR7171453.sra Read 701943 spots for SRR7171453.sra Written 701943 spots for SRR7171453.sra Read 701943 spots for SRR7171453.sra Written 701943 spots for SRR7171453.sra Read 701943 spots for SRR7171453.sra Written 701943 spots for SRR7171453.sra Read 701943 spots for SRR7171453.sra Written 701943 spots for SRR7171453.sra Read 701943 spots for SRR7171453.sra Written 701943 spots for SRR7171453.sra Read 701943 spots for SRR7171453.sra Written 701943 spots for SRR7171453.sra Read 701943 spots for SRR7171453.sra Written 701943 spots for SRR7171453.sra Read 701943 spots for SRR7171453.sra Written 701943 spots for SRR7171453.sra Read 701943 spots for SRR7171453.sra Written 701943 spots for SRR7171453.sra Read 701943 spots for SRR7171453.sra Written 701943 spots for SRR7171453.sra Read 701943 spots for SRR7171453.sra Written 701943 spots for SRR7171453.sra Read 701943 spots for SRR7171453.sra Written 701943 spots for SRR7171453.sra Read 701943 spots for SRR7171453.sra Written 701943 spots for SRR7171453.sra Read 701943 spots for SRR7171453.sra Written 701943 spots for SRR7171453.sra Read 701943 spots for SRR7171453.sra Written 701943 spots for SRR7171453.sra Read 701946 spots for SRR7171453.sra Written 701946 spots for SRR7171453.sra SRR ids: ['SRR7171453.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_1o85xyqw SRR7171453.sra spots: 14038863 blocks: [[1, 701943], [701944, 1403886], [1403887, 2105829], [2105830, 2807772], [2807773, 3509715], [3509716, 4211658], [4211659, 4913601], [4913602, 5615544], [5615545, 6317487], [6317488, 7019430], [7019431, 7721373], [7721374, 8423316], [8423317, 9125259], [9125260, 9827202], [9827203, 10529145], [10529146, 11231088], [11231089, 11933031], [11933032, 12634974], [12634975, 13336917], [13336918, 14038863]] SRR7171453 file size 4735609 SRR7171453 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 SRR7171453 SRR7171453_1.fastq SRR7171453_2.fastq Input file: SRR7171453_1.fastq Paired file: SRR7171453_2.fastq trimmed: SRR7171453-trimmed-pair1.fastq, SRR7171453-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 Thu Feb 13 18:38:53 2025 >> started Thu Feb 13 18:39:08 2025 >> done (14.613s) 14038863 read pairs processed; of these: 27 ( 0.00%) short read pairs filtered out after trimming by size control 667 ( 0.00%) empty read pairs filtered out after trimming by size control 14038169 (100.00%) read pairs available; of these: 1340820 ( 9.55%) trimmed read pairs available after processing 12697349 (90.45%) untrimmed read pairs available after processing Length distribution of reads after trimming: length count percentage 18 1 0.00% 19 2 0.00% 20 2 0.00% 21 2 0.00% 22 3 0.00% 23 4 0.00% 24 1 0.00% 25 4 0.00% 26 2 0.00% 27 0 0.00% 28 4 0.00% 29 2 0.00% 30 3 0.00% 31 2 0.00% 32 1 0.00% 33 0 0.00% 34 0 0.00% 35 6 0.00% 36 1 0.00% 37 1 0.00% 38 1 0.00% 39 3 0.00% 40 2 0.00% 41 6 0.00% 42 1 0.00% 43 5 0.00% 44 1 0.00% 45 6 0.00% 46 6 0.00% 47 8 0.00% 48 9 0.00% 49 8 0.00% 50 8 0.00% 51 17 0.00% 52 24 0.00% 53 16 0.00% 54 22 0.00% 55 26 0.00% 56 36 0.00% 57 33 0.00% 58 33 0.00% 59 32 0.00% 60 51 0.00% 61 54 0.00% 62 67 0.00% 63 85 0.00% 64 100 0.00% 65 92 0.00% 66 110 0.00% 67 118 0.00% 68 148 0.00% 69 176 0.00% 70 190 0.00% 71 245 0.00% 72 276 0.00% 73 353 0.00% 74 349 0.00% 75 433 0.00% 76 483 0.00% 77 528 0.00% 78 598 0.00% 79 682 0.00% 80 795 0.01% 81 913 0.01% 82 1036 0.01% 83 1200 0.01% 84 1429 0.01% 85 1556 0.01% 86 1737 0.01% 87 1932 0.01% 88 2047 0.01% 89 2264 0.02% 90 2559 0.02% 91 2902 0.02% 92 3185 0.02% 93 3734 0.03% 94 4223 0.03% 95 4337 0.03% 96 4745 0.03% 97 5119 0.04% 98 5423 0.04% 99 5872 0.04% 100 6276 0.04% 101 6973 0.05% 102 7462 0.05% 103 8186 0.06% 104 8688 0.06% 105 9437 0.07% 106 10023 0.07% 107 10479 0.07% 108 10851 0.08% 109 11385 0.08% 110 12041 0.09% 111 12810 0.09% 112 13274 0.09% 113 14488 0.10% 114 15566 0.11% 115 16313 0.12% 116 17033 0.12% 117 17451 0.12% 118 17758 0.13% 119 18395 0.13% 120 19403 0.14% 121 20359 0.15% 122 21041 0.15% 123 22617 0.16% 124 23502 0.17% 125 24421 0.17% 126 25388 0.18% 127 25740 0.18% 128 26315 0.19% 129 27064 0.19% 130 27901 0.20% 131 28472 0.20% 132 30130 0.21% 133 31043 0.22% 134 32181 0.23% 135 33901 0.24% 136 35310 0.25% 137 35219 0.25% 138 36293 0.26% 139 36751 0.26% 140 37343 0.27% 141 38193 0.27% 142 39302 0.28% 143 40469 0.29% 144 42504 0.30% 145 43503 0.31% 146 43888 0.31% 147 45405 0.32% 148 46054 0.33% 149 46144 0.33% 150 47585 0.34% 151 12697349 90.45% 14038169 reads passed initial QC criterion=sequence-density sequence-density=0.17 sequence-density-rank=1 fanout-score=2.39 fanout-score-rank=37 prefix-density=0.18 prefix-fanout=2.3 sequence=GATGTTAGCTTTGATGGCAGTGCAAAGGCAAACAGCAGCCTCGAGATCAAGAAGGCCTTGAATGA criterion=fanout-score sequence-density=0.02 sequence-density-rank=39 fanout-score=114.47 fanout-score-rank=1 prefix-density=0.16 prefix-fanout=11.6 sequence=CTCCTTCCTCTAAATGATAAGGTTCAGTGGACTTCTCGCGACGTCGCCGGCGGCGAACCGCCCACGTCGCCGCGATCCGAACACTTCACCGGACCATTCAATCGGTAGGAGCGACGGGCGGTGTGTACAAAGGGCAGGGACGTAGTCAACGCGAGCTGATGACTCGCGCTTACTAGGAATTCCTCGTTGAAGACCAACAATTGCAATGATCTATCCCCATCACGATGAAATTTCAAAGATTACCCGGGCCTGTCGGCCAAGGCTATAGACTCGTTGAATACATCAGTGTAGCGCGCGTGCGGCCCAGAACATCTAAGGGCATCACAGACCTGTTATTGCCTCAAACTTCCTTGGCCTGGAAGGCCATAGTCCCTCTAAGAAGCTGGCCGCGGAGGGTCACCTCCGCATAGCTAGTTAGCAGGCTGAGGTCTCGTTCGTTAACGGAATTAACCAGACAAATCGCTCCACCAACTAAGAACGGCCATGCACCACCACCCAT criterion=sequence-density sequence-density=0.23 sequence-density-rank=1 fanout-score=6.31 fanout-score-rank=18 prefix-density=0.36 prefix-fanout=4.0 sequence=CTGCAAATGTGG criterion=fanout-score sequence-density=0.03 sequence-density-rank=28 fanout-score=42.00 fanout-score-rank=1 prefix-density=0.17 prefix-fanout=7.8 sequence=AATGGTGGTGCCAATATGGTCGCTCATGGTTACACCAAAGGTGATGGCCTTGGTGCTGAGA SRR7171453 testing PE reads STAR mapping to Ensembl genome Started job on | Feb 13 18:39:54 Started mapping on | Feb 13 18:39:55 Finished on | Feb 13 18:41:19 Mapping speed, Million of reads per hour | 601.64 Number of input reads | 14038169 Average input read length | 298 UNIQUE READS: Uniquely mapped reads number | 13070532 Uniquely mapped reads % | 93.11% Average mapped length | 296.85 Number of splices: Total | 13084852 Number of splices: Annotated (sjdb) | 12894019 Number of splices: GT/AG | 12884713 Number of splices: GC/AG | 158597 Number of splices: AT/AC | 8910 Number of splices: Non-canonical | 32632 Mismatch rate per base, % | 0.36% Deletion rate per base | 0.03% Deletion average length | 2.58 Insertion rate per base | 0.02% Insertion average length | 2.66 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 370581 % of reads mapped to multiple loci | 2.64% Number of reads mapped to too many loci | 159694 % of reads mapped to too many loci | 1.14% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 2.94% % of reads unmapped: other | 0.18% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 597056 597056 597056 N_multimapping 370581 370581 370581 N_noFeature 230243 12976718 266606 N_ambiguous 114652 697 56701 UnstrandedReadsAssigned:12725637 PositiveStrandReadsAssigned:93117 NegativeStrandReadsAssigned:12747225 Dataset is classified negative stranded MeadianReadLen=151 20thPercentileLength=151 echo kmer=147 SRR7171453 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: SRR7171453-trimmed-pair1.fastq SRR7171453-trimmed-pair2.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 14,038,169 reads, 12,790,821 reads pseudoaligned [quant] estimated average fragment length: 233.548 [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,065 rounds 52401 SRR7171453.ke.tsv 34699 SRR7171453.se.tsv 87100 total ==> SRR7171453.ke.tsv <== target_id length eff_length est_counts tpm Potri.005G200100.1.v4.1 2018 1785.45 642 26.3398 Potri.005G024800.1.v4.1 1035 802.452 152 13.8756 Potri.004G059700.1.v4.1 961 728.458 47 4.72628 Potri.007G009000.2.v4.1 1416 1183.45 0 0 Potri.003G141000.2.v4.1 2943 2710.45 396 10.7024 Potri.016G087400.1.v4.1 270 79.6917 1094 1005.61 Potri.015G069301.1.v4.1 564 334.438 0 0 Potri.010G195200.1.v4.1 1773 1540.45 129 6.13434 Potri.012G127500.1.v4.1 977 744.458 1446 142.283 ==> SRR7171453.se.tsv <== Potri.001G166300.v4.1 7 Potri.001G448400.v4.1 24 Potri.001G233950.v4.1 0 Potri.001G122700.v4.1 257 Potri.001G212900.v4.1 1 Potri.001G182400.v4.1 0 Potri.001G256600.v4.1 0 Potri.001G040500.v4.1 0 Potri.001G416900.v4.1 2 Potri.001G452600.v4.1 54 SRR7171453 completed mapping pipeline successfully