Starting /dee2/code/volunteer_pipeline.sh SRR7169775 current disk space = 3049920872448 free memory = 1460087260 SRR7169775 SRAfilesize 221f390bb9cf55201e0e06a0af5ccd88 SRR7169775.sra SRR7169775.sra file validated SRR7169775 is paired end SRR7169775 is conventional basespace SRR7169775 read1 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR7169775_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 fail #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 19.998 18.0 18.0 18.0 18.0 32.0 2 25.66 27.0 25.0 27.0 18.0 32.0 3 25.86025 27.0 25.0 29.0 18.0 31.0 4 28.15775 29.0 27.0 31.0 15.0 33.0 5 30.31725 32.0 31.0 33.0 25.0 33.0 6 35.1565 37.0 34.0 38.0 30.0 38.0 7 36.49375 38.0 37.0 38.0 34.0 38.0 8 36.73625 38.0 37.0 38.0 34.0 38.0 9 37.06475 38.0 38.0 38.0 36.0 38.0 10-14 37.316449999999996 38.0 38.0 38.0 36.8 38.0 15-19 37.3918 38.0 38.0 38.0 37.0 38.0 20-24 37.4173 38.0 38.0 38.0 37.2 38.0 25-29 37.45915 38.0 38.0 38.0 37.4 38.0 30-34 37.431799999999996 38.0 38.0 38.0 37.2 38.0 35-39 37.31034999999999 38.0 38.0 38.0 37.0 38.0 40-44 37.1097 38.0 38.0 38.0 36.6 38.0 45-49 37.2986 38.0 38.0 38.0 37.0 38.0 50-54 37.2373 38.0 38.0 38.0 36.8 38.0 55-59 36.959050000000005 38.0 38.0 38.0 35.8 38.0 60-64 36.795249999999996 38.0 38.0 38.0 35.0 38.0 65-69 36.838100000000004 38.0 38.0 38.0 35.6 38.0 70-74 36.9035 38.0 38.0 38.0 36.0 38.0 75-79 36.25895 38.0 38.0 38.0 34.6 38.0 80-84 36.040800000000004 38.0 38.0 38.0 34.0 38.0 85-89 35.84395 38.0 38.0 38.0 33.6 38.0 90-94 35.79344999999999 38.0 38.0 38.0 33.2 38.0 95-99 35.857350000000004 38.0 38.0 38.0 33.8 38.0 100-104 35.71925 38.0 38.0 38.0 33.2 38.0 105-109 35.39540000000001 38.0 37.8 38.0 32.2 38.0 110-114 35.1246 38.0 37.2 38.0 30.2 38.0 115-119 35.0668 38.0 37.0 38.0 29.2 38.0 120-124 35.01875 38.0 36.6 38.0 29.6 38.0 125-129 34.948350000000005 38.0 36.6 38.0 29.6 38.0 130-134 34.602700000000006 38.0 36.0 38.0 27.8 38.0 135-139 34.1694 38.0 35.4 38.0 24.2 38.0 140-144 33.56705 38.0 35.0 38.0 20.2 38.0 145-149 33.4284 38.0 35.0 38.0 17.0 38.0 150-151 29.960625 36.5 29.0 38.0 2.0 38.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 2 3.0 3 1.0 4 0.0 5 0.0 6 0.0 7 1.0 8 0.0 9 0.0 10 0.0 11 2.0 12 1.0 13 1.0 14 2.0 15 1.0 16 8.0 17 10.0 18 34.0 19 43.0 20 6.0 21 13.0 22 8.0 23 8.0 24 4.0 25 8.0 26 15.0 27 23.0 28 25.0 29 35.0 30 49.0 31 51.0 32 77.0 33 101.0 34 176.0 35 333.0 36 811.0 37 2150.0 >>END_MODULE >>Per base sequence content warn #Base G A T C 1 34.06813627254509 19.789579158316634 10.070140280561123 36.07214428857716 2 23.25 17.625 29.675 29.45 3 20.95 16.75 26.325 35.975 4 21.875 24.0 20.8 33.324999999999996 5 25.8 28.025 23.25 22.925 6 23.849999999999998 31.25 23.400000000000002 21.5 7 14.975 31.724999999999998 37.075 16.225 8 17.525 31.624999999999996 29.225 21.625 9 20.474999999999998 25.525 32.324999999999996 21.675 10-14 19.125 30.725 26.265 23.885 15-19 19.335 29.455 27.584999999999997 23.625 20-24 19.49 30.325000000000003 26.905 23.28 25-29 19.38 29.849999999999998 26.645000000000003 24.125 30-34 18.765 30.19 26.6 24.445 35-39 20.185 29.78 26.07 23.965 40-44 19.345000000000002 29.885 27.125 23.645 45-49 19.34 29.575000000000003 27.685 23.400000000000002 50-54 20.115 28.444999999999997 26.995 24.445 55-59 19.259999999999998 28.4 28.58 23.76 60-64 20.09 28.16 28.360000000000003 23.39 65-69 19.72 30.365 25.96 23.955000000000002 70-74 19.435 31.569999999999997 26.235000000000003 22.759999999999998 75-79 19.465 30.17 26.345000000000002 24.02 80-84 20.085 29.205 26.41 24.3 85-89 19.650000000000002 29.494999999999997 26.76 24.095 90-94 20.380000000000003 29.330000000000002 26.21 24.08 95-99 20.21 29.304999999999996 26.775 23.71 100-104 20.84 28.975 26.534999999999997 23.65 105-109 20.445872665193814 28.675436834705764 26.59168507732476 24.287005422775657 110-114 20.302755984711325 28.82719774693221 27.097163548581776 23.772882719774692 115-119 20.665 29.325000000000003 25.869999999999997 24.14 120-124 19.98 29.770000000000003 25.919999999999998 24.33 125-129 20.61 28.865000000000002 26.400000000000002 24.125 130-134 20.615 30.165 25.16 24.060000000000002 135-139 20.29 30.085 25.2 24.425 140-144 21.23 29.244999999999997 24.560000000000002 24.965 145-149 20.87 28.79 25.36 24.98 150-151 21.082906089783666 29.473552582218332 24.434162811054144 25.009378516943855 >>END_MODULE >>Per sequence GC content pass #GC Content Count 0 0.0 1 0.5 2 0.5 3 0.0 4 0.5 5 0.5 6 0.0 7 0.0 8 0.0 9 0.0 10 0.5 11 0.5 12 0.0 13 0.0 14 0.0 15 0.5 16 1.0 17 0.5 18 0.0 19 0.0 20 0.5 21 0.5 22 2.5 23 2.5 24 3.0 25 7.0 26 10.5 27 13.0 28 12.5 29 19.0 30 27.0 31 32.5 32 44.0 33 54.0 34 62.0 35 76.0 36 97.5 37 112.0 38 142.0 39 166.0 40 168.0 41 184.5 42 206.0 43 234.0 44 247.0 45 245.5 46 255.0 47 255.0 48 231.0 49 193.0 50 171.5 51 151.5 52 132.5 53 113.0 54 89.0 55 66.5 56 42.5 57 34.0 58 25.5 59 22.5 60 16.5 61 8.0 62 5.5 63 1.5 64 1.5 65 2.5 66 3.0 67 2.5 68 0.5 69 1.0 70 1.0 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 0.2 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 0.42 110-114 0.58 115-119 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 0.0375 >>END_MODULE >>Sequence Length Distribution pass #Length Count 151 4000.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 96.125 #Duplication Level Percentage of deduplicated Percentage of total 1 99.08972691807543 95.25 2 0.7802340702210664 1.5 3 0.0 0.0 4 0.0 0.0 5 0.07802340702210664 0.375 6 0.0 0.0 7 0.02600780234070221 0.17500000000000002 8 0.0 0.0 9 0.0 0.0 >10 0.0 0.0 >50 0.0 0.0 >100 0.02600780234070221 2.7 >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 GATCGGAAGAGCACACGTCTGAACTCCAGTCACTCCGGAGAATCTCGTAT 108 2.7 TruSeq Adapter, Index 6 (97% over 36bp) AATCGGAAGAGCACACGTCTGAACTCCAGTCACTCCGGAGAATCTCGTAT 7 0.17500000000000002 TruSeq Adapter, Index 3 (97% over 34bp) AGATCGGAAGAGCACACGTCTGAACTCCAGTCACTCCGGAGAATCTCGTA 5 0.125 TruSeq Adapter, Index 6 (97% over 36bp) ATCGGAAGAGCACACGTCTGAACTCCAGTCACTCCGGAGAATCTCGTATG 5 0.125 TruSeq Adapter, Index 6 (97% over 35bp) CGGAAGAGCACACGTCTGAACTCCAGTCACTCCGGAGAATCTCGTATGCC 5 0.125 TruSeq Adapter, Index 6 (96% over 33bp) >>END_MODULE >>Adapter Content fail #Position Illumina Universal Adapter Illumina Small RNA 3' Adapter Illumina Small RNA 5' Adapter Nextera Transposase Sequence SOLID Small RNA Adapter 1 0.125 0.0 0.0 0.0 0.0 2 0.125 0.0 0.0 0.0 0.0 3 0.125 0.0 0.0 0.0 0.0 4 0.125 0.0 0.0 0.0 0.0 5 0.125 0.0 0.0 0.0 0.0 6 0.125 0.0 0.0 0.0 0.0 7 0.125 0.0 0.0 0.0 0.0 8 0.15 0.0 0.0 0.0 0.0 9 0.15 0.0 0.0 0.0 0.0 10-11 0.15 0.0 0.0 0.0 0.0 12-13 0.175 0.0 0.0 0.0 0.0 14-15 0.175 0.0 0.0 0.0 0.0 16-17 0.175 0.0 0.0 0.0 0.0 18-19 0.175 0.0 0.0 0.0 0.0 20-21 0.175 0.0 0.0 0.0 0.0 22-23 0.175 0.0 0.0 0.0 0.0 24-25 0.175 0.0 0.0 0.0 0.0 26-27 0.175 0.0 0.0 0.0 0.0 28-29 0.175 0.0 0.0 0.0 0.0 30-31 0.175 0.0 0.0 0.0 0.0 32-33 0.1875 0.0 0.0 0.0 0.0 34-35 0.2 0.0 0.0 0.0 0.0 36-37 0.225 0.0 0.0 0.0 0.0 38-39 0.225 0.0 0.0 0.0 0.0 40-41 0.2875 0.0 0.0 0.0 0.0 42-43 0.3 0.0 0.0 0.0 0.0 44-45 0.3 0.0 0.0 0.0 0.0 46-47 0.3 0.0 0.0 0.0 0.0 48-49 0.3375 0.0 0.0 0.0 0.0 50-51 0.3625 0.0 0.0 0.0 0.0 52-53 0.375 0.0 0.0 0.0 0.0 54-55 0.4 0.0 0.0 0.0 0.0 56-57 0.425 0.0 0.0 0.0 0.0 58-59 0.425 0.0 0.0 0.0 0.0 60-61 0.4625 0.0 0.0 0.0 0.0 62-63 0.625 0.0 0.0 0.0 0.0 64-65 0.65 0.0 0.0 0.0 0.0 66-67 0.65 0.0 0.0 0.0 0.0 68-69 0.65 0.0 0.0 0.0 0.0 70-71 0.65 0.0 0.0 0.0 0.0 72-73 0.6875 0.0 0.0 0.0 0.0 74-75 0.725 0.0 0.0 0.0 0.0 76-77 0.775 0.0 0.0 0.0 0.0 78-79 0.8125 0.0 0.0 0.0 0.0 80-81 0.8625 0.0 0.0 0.0 0.0 82-83 0.975 0.0 0.0 0.0 0.0 84-85 1.1 0.0 0.0 0.0 0.0 86-87 1.3125 0.0 0.0 0.0 0.0 88-89 1.625 0.0 0.0 0.0 0.0 90-91 1.8375 0.0 0.0 0.0 0.0 92-93 2.25 0.0 0.0 0.0 0.0 94-95 2.7125000000000004 0.0 0.0 0.0 0.0 96-97 3.1 0.0 0.0 0.0 0.0 98-99 3.5125 0.0 0.0 0.0 0.0 100-101 3.8625 0.0 0.0 0.0 0.0 102-103 4.175 0.0 0.0 0.0 0.0 104-105 4.4125 0.0 0.0 0.0 0.0 106-107 4.7375 0.0 0.0 0.0 0.0 108-109 5.2875 0.0 0.0 0.0 0.0 110-111 5.95 0.0 0.0 0.0 0.0 112-113 6.65 0.0 0.0 0.0 0.0 114-115 7.3125 0.0 0.0 0.0 0.0 116-117 7.775 0.0 0.0 0.0 0.0 118-119 8.4375 0.0 0.0 0.0 0.0 120-121 9.0 0.0 0.0 0.0 0.0 122-123 9.774999999999999 0.0 0.0 0.0 0.0 124-125 10.5875 0.0 0.0 0.0 0.0 126-127 11.45 0.0 0.0 0.0 0.0 128-129 12.35 0.0 0.0 0.0 0.0 130-131 13.337499999999999 0.0 0.0 0.0 0.0 132-133 14.225 0.0 0.0 0.0 0.0 134-135 15.0 0.0 0.0 0.0 0.0 136-137 15.799999999999999 0.0 0.0 0.0 0.0 138-139 16.700000000000003 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position GATGTAG 10 0.006864391 144.7625 9 GATTGAA 10 0.006864391 144.7625 7 TGATGTA 10 0.006864391 144.7625 8 >>END_MODULE SRR7169775 read2 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR7169775_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 32.37125 33.0 33.0 34.0 31.0 34.0 2 32.45225 33.0 33.0 34.0 31.0 34.0 3 32.50425 34.0 33.0 34.0 31.0 34.0 4 32.545 34.0 33.0 34.0 32.0 34.0 5 32.4075 34.0 33.0 34.0 32.0 34.0 6 36.527 38.0 38.0 38.0 35.0 38.0 7 36.58275 38.0 38.0 38.0 35.0 38.0 8 36.52425 38.0 38.0 38.0 35.0 38.0 9 36.494 38.0 38.0 38.0 35.0 38.0 10-14 36.4683 38.0 38.0 38.0 35.0 38.0 15-19 36.400349999999996 38.0 38.0 38.0 34.4 38.0 20-24 36.362449999999995 38.0 38.0 38.0 34.6 38.0 25-29 36.34734999999999 38.0 38.0 38.0 34.4 38.0 30-34 36.07245 38.0 37.8 38.0 32.6 38.0 35-39 35.94695 38.0 38.0 38.0 32.4 38.0 40-44 36.008 38.0 37.8 38.0 32.8 38.0 45-49 35.970600000000005 38.0 38.0 38.0 33.2 38.0 50-54 35.5149 38.0 37.6 38.0 29.8 38.0 55-59 35.37015 38.0 37.4 38.0 28.0 38.0 60-64 35.758799999999994 38.0 37.8 38.0 31.4 38.0 65-69 36.05075 38.0 38.0 38.0 34.0 38.0 70-74 35.64125 38.0 38.0 38.0 31.6 38.0 75-79 34.693799999999996 38.0 37.2 38.0 27.6 38.0 80-84 34.5415 38.0 37.0 38.0 26.6 38.0 85-89 34.831149999999994 38.0 37.6 38.0 28.2 38.0 90-94 34.86685 38.0 37.6 38.0 28.6 38.0 95-99 34.58135 38.0 37.0 38.0 26.8 38.0 100-104 34.12135000000001 38.0 36.6 38.0 20.4 38.0 105-109 33.241 38.0 35.6 38.0 14.6 38.0 110-114 31.624350000000003 38.0 32.8 38.0 4.2 38.0 115-119 31.614749999999997 38.0 34.0 38.0 2.0 38.0 120-124 31.637549999999997 38.0 33.8 38.0 2.0 38.0 125-129 31.953899999999997 38.0 34.0 38.0 4.2 38.0 130-134 32.4391 38.0 34.0 38.0 13.6 38.0 135-139 32.13075 38.0 33.6 38.0 13.4 38.0 140-144 31.26635 37.6 31.2 38.0 6.4 38.0 145-149 30.950200000000002 38.0 31.0 38.0 2.0 38.0 150-151 26.468375 34.0 16.5 38.0 2.0 38.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 2 28.0 3 10.0 4 3.0 5 4.0 6 4.0 7 7.0 8 3.0 9 4.0 10 2.0 11 4.0 12 8.0 13 8.0 14 14.0 15 13.0 16 20.0 17 13.0 18 14.0 19 30.0 20 50.0 21 17.0 22 31.0 23 21.0 24 24.0 25 28.0 26 36.0 27 37.0 28 60.0 29 74.0 30 74.0 31 77.0 32 113.0 33 140.0 34 185.0 35 302.0 36 645.0 37 1897.0 >>END_MODULE >>Per base sequence content warn #Base G A T C 1 33.675 17.625 21.825 26.875 2 26.025 26.174999999999997 28.375 19.425 3 23.724999999999998 25.95 31.525 18.8 4 24.125 30.725 23.65 21.5 5 27.781945486371594 32.18304576144036 22.9057264316079 17.129282320580145 6 24.8 35.525 22.475 17.2 7 19.675 24.8 37.2 18.325 8 20.625 27.825 27.400000000000002 24.15 9 24.65 25.85 28.050000000000004 21.45 10-14 25.055 28.82 24.93 21.195 15-19 24.971248562428123 26.986349317465873 27.321366068303416 20.721036051802592 20-24 25.495099019803963 28.040608121624327 26.23524704940988 20.229045809161832 25-29 24.847484748474848 29.222922292229224 26.162616261626166 19.766976697669765 30-34 24.026006501625407 26.806701675418854 28.882220555138783 20.285071267816953 35-39 24.883732559883985 27.014052107816173 26.508976346451966 21.593238985847876 40-44 24.996249812490625 27.04635231761588 27.67138356917846 20.286014300715035 45-49 24.301075268817204 28.902225556389098 26.30657664416104 20.49012253063266 50-54 24.23954372623574 26.906143686211724 27.761656994196514 21.092655593356014 55-59 25.046280082053336 26.802421574023118 27.262720768499527 20.888577575424026 60-64 24.18362754413162 27.71915787368105 27.274091113667048 20.823123468520276 65-69 23.621181059052955 27.376368818440923 28.70143507175359 20.30101505075254 70-74 23.350637568670933 29.766644826369635 27.186129731364346 19.69658787359508 75-79 23.14590527238056 29.552131113745293 27.701901767767872 19.60006184610627 80-84 23.483779971791254 28.994559742091475 27.50352609308886 20.018134193028413 85-89 24.177088544272134 28.07903951975988 27.748874437218607 19.994997498749374 90-94 24.52480992396959 27.435974389755902 28.501400560224088 19.537815126050422 95-99 24.73994798959792 27.370474094818963 27.860572114422883 20.02900580116023 100-104 24.5606128886886 27.574983726403286 27.584998247458813 20.279405137449302 105-109 24.887179487179488 27.38974358974359 28.06153846153846 19.66153846153846 110-114 25.564665432425283 27.45305474742132 27.738693467336685 19.243586352816717 115-119 25.263667671114938 27.819629789065864 27.636676711149377 19.28002582866982 120-124 24.842450881745485 27.898109410580947 27.649208282582215 19.61023142509135 125-129 25.269210663878727 27.37584945112389 27.501306847882905 19.85363303711448 130-134 25.56058320764203 27.747611865258925 27.621920563097035 19.06988436400201 135-139 26.033905085762864 28.114217132569884 26.82402360354053 19.02785417812672 140-144 26.005402160864342 27.696078431372552 27.110844337735095 19.187675070028014 145-149 26.431894352458606 27.05217347806513 26.912110449702364 19.603821719773897 150-151 26.458802905083896 27.28524918607563 26.897069872276486 19.358878036563986 >>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 0.0 22 0.5 23 1.0 24 1.5 25 2.5 26 3.5 27 3.0 28 4.0 29 6.5 30 10.0 31 16.5 32 25.0 33 33.5 34 37.0 35 43.0 36 66.0 37 96.0 38 118.0 39 141.0 40 169.5 41 208.5 42 251.5 43 288.0 44 290.0 45 295.5 46 288.5 47 264.0 48 257.5 49 212.0 50 174.5 51 153.5 52 124.0 53 108.5 54 85.0 55 57.5 56 43.0 57 33.5 58 23.0 59 16.5 60 12.5 61 6.5 62 5.5 63 5.5 64 4.0 65 4.0 66 3.0 67 1.0 68 0.5 69 1.5 70 1.5 71 0.0 72 0.0 73 0.0 74 0.5 75 0.5 76 0.0 77 0.0 78 0.5 79 0.5 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 warn #Base N-Count 1 0.0 2 0.0 3 0.0 4 0.0 5 0.025 6 0.0 7 0.0 8 0.0 9 0.0 10-14 0.0 15-19 0.005 20-24 0.02 25-29 0.01 30-34 0.025 35-39 0.015 40-44 0.005 45-49 0.025 50-54 0.06 55-59 0.065 60-64 0.015 65-69 0.005 70-74 0.795 75-79 2.9850000000000003 80-84 0.74 85-89 0.05 90-94 0.04 95-99 0.02 100-104 0.145 105-109 2.5 110-114 5.475 115-119 7.08 120-124 5.585 125-129 4.35 130-134 0.5499999999999999 135-139 0.015 140-144 0.04 145-149 0.045 150-151 0.17500000000000002 >>END_MODULE >>Sequence Length Distribution pass #Length Count 151 4000.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 97.3 #Duplication Level Percentage of deduplicated Percentage of total 1 99.20349434737923 96.525 2 0.7451181911613566 1.4500000000000002 3 0.0 0.0 4 0.025693730729701953 0.1 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 0.025693730729701953 1.925 >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 fail #Sequence Count Percentage Possible Source GATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTCTTCGCCTGTGTAGATCT 77 1.925 Illumina Single End PCR Primer 1 (96% over 32bp) >>END_MODULE >>Adapter Content fail #Position Illumina Universal Adapter Illumina Small RNA 3' Adapter Illumina Small RNA 5' Adapter Nextera Transposase Sequence SOLID Small RNA Adapter 1 0.125 0.0 0.0 0.0 0.0 2 0.125 0.0 0.0 0.0 0.0 3 0.125 0.0 0.0 0.0 0.0 4 0.125 0.0 0.0 0.0 0.0 5 0.125 0.0 0.0 0.0 0.0 6 0.125 0.0 0.0 0.0 0.0 7 0.125 0.0 0.0 0.0 0.0 8 0.125 0.0 0.0 0.0 0.0 9 0.125 0.0 0.0 0.0 0.0 10-11 0.125 0.0 0.0 0.0 0.0 12-13 0.125 0.0 0.0 0.0 0.0 14-15 0.125 0.0 0.0 0.0 0.0 16-17 0.125 0.0 0.0 0.0 0.0 18-19 0.125 0.0 0.0 0.0 0.0 20-21 0.125 0.0 0.0 0.0 0.0 22-23 0.125 0.0 0.0 0.0 0.0 24-25 0.125 0.0 0.0 0.0 0.0 26-27 0.125 0.0 0.0 0.0125 0.0 28-29 0.125 0.0 0.0 0.025 0.0 30-31 0.125 0.0 0.0 0.025 0.0 32-33 0.1375 0.0 0.0 0.025 0.0 34-35 0.15 0.0 0.0 0.025 0.0 36-37 0.175 0.0 0.0 0.025 0.0 38-39 0.175 0.0 0.0 0.025 0.0 40-41 0.225 0.0 0.0 0.025 0.0 42-43 0.225 0.0 0.0 0.025 0.0 44-45 0.225 0.0 0.0 0.025 0.0 46-47 0.225 0.0 0.0 0.025 0.0 48-49 0.225 0.0 0.0 0.025 0.0 50-51 0.2375 0.0 0.0 0.025 0.0 52-53 0.25 0.0 0.0 0.025 0.0 54-55 0.2625 0.0 0.0 0.025 0.0 56-57 0.275 0.0 0.0 0.025 0.0 58-59 0.275 0.0 0.0 0.025 0.0 60-61 0.30000000000000004 0.0 0.0 0.025 0.0 62-63 0.325 0.0 0.0 0.025 0.0 64-65 0.35 0.0 0.0 0.025 0.0 66-67 0.35 0.0 0.0 0.025 0.0 68-69 0.35 0.0 0.0 0.025 0.0 70-71 0.35 0.0 0.0 0.025 0.0 72-73 0.3875 0.0 0.0 0.025 0.0 74-75 0.425 0.0 0.0 0.025 0.0 76-77 0.475 0.0 0.0 0.025 0.0 78-79 0.5125 0.0 0.0 0.025 0.0 80-81 0.5375000000000001 0.0 0.0 0.025 0.0 82-83 0.6499999999999999 0.0 0.0 0.025 0.0 84-85 0.7749999999999999 0.0 0.0 0.025 0.0 86-87 0.9625 0.0 0.0 0.025 0.0 88-89 1.2625000000000002 0.0 0.0 0.025 0.0 90-91 1.5125 0.0 0.0 0.025 0.0 92-93 1.9500000000000002 0.0 0.0 0.025 0.0 94-95 2.3875 0.0 0.0 0.025 0.0 96-97 2.7375 0.0 0.0 0.025 0.0 98-99 3.125 0.0 0.0 0.025 0.0 100-101 3.45 0.0 0.0 0.025 0.0 102-103 3.7249999999999996 0.0 0.0 0.025 0.0 104-105 3.9625000000000004 0.0 0.0 0.025 0.0 106-107 4.2625 0.0 0.0 0.025 0.0 108-109 4.7625 0.0 0.0 0.025 0.0 110-111 5.324999999999999 0.0 0.0 0.025 0.0 112-113 5.95 0.0 0.0 0.025 0.0 114-115 6.55 0.0 0.0 0.025 0.0 116-117 7.025 0.0 0.0 0.025 0.0 118-119 7.6625 0.0 0.0 0.025 0.0 120-121 8.1375 0.0 0.0 0.025 0.0 122-123 8.875 0.0 0.0 0.025 0.0 124-125 9.587499999999999 0.0 0.0 0.025 0.0 126-127 10.3125 0.0 0.0 0.025 0.0 128-129 11.125 0.0 0.0 0.025 0.0 130-131 12.1 0.0 0.0 0.025 0.0 132-133 12.975 0.0 0.0 0.025 0.0 134-135 13.6875 0.0 0.0 0.025 0.0 136-137 14.475 0.0 0.0 0.025 0.0 138-139 15.35 0.0 0.0 0.025 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position AGAGCGG 10 0.0071578217 142.75 145 >>END_MODULE Read 631043 spots for SRR7169775.sra Written 631043 spots for SRR7169775.sra Read 631043 spots for SRR7169775.sra Written 631043 spots for SRR7169775.sra Read 631043 spots for SRR7169775.sra Written 631043 spots for SRR7169775.sra Read 631043 spots for SRR7169775.sra Written 631043 spots for SRR7169775.sra Read 631043 spots for SRR7169775.sra Written 631043 spots for SRR7169775.sra Read 631043 spots for SRR7169775.sra Written 631043 spots for SRR7169775.sra Read 631043 spots for SRR7169775.sra Written 631043 spots for SRR7169775.sra Read 631043 spots for SRR7169775.sra Written 631043 spots for SRR7169775.sra Read 631043 spots for SRR7169775.sra Written 631043 spots for SRR7169775.sra Read 631043 spots for SRR7169775.sra Written 631043 spots for SRR7169775.sra Read 631043 spots for SRR7169775.sra Written 631043 spots for SRR7169775.sra Read 631043 spots for SRR7169775.sra Written 631043 spots for SRR7169775.sra Read 631043 spots for SRR7169775.sra Written 631043 spots for SRR7169775.sra Read 631043 spots for SRR7169775.sra Written 631043 spots for SRR7169775.sra Read 631043 spots for SRR7169775.sra Written 631043 spots for SRR7169775.sra Read 631043 spots for SRR7169775.sra Written 631043 spots for SRR7169775.sra Read 631061 spots for SRR7169775.sra Written 631061 spots for SRR7169775.sra Read 631043 spots for SRR7169775.sra Written 631043 spots for SRR7169775.sra Read 631043 spots for SRR7169775.sra Written 631043 spots for SRR7169775.sra Read 631043 spots for SRR7169775.sra Written 631043 spots for SRR7169775.sra SRR ids: ['SRR7169775.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_eu15tbki SRR7169775.sra spots: 12620878 blocks: [[1, 631043], [631044, 1262086], [1262087, 1893129], [1893130, 2524172], [2524173, 3155215], [3155216, 3786258], [3786259, 4417301], [4417302, 5048344], [5048345, 5679387], [5679388, 6310430], [6310431, 6941473], [6941474, 7572516], [7572517, 8203559], [8203560, 8834602], [8834603, 9465645], [9465646, 10096688], [10096689, 10727731], [10727732, 11358774], [11358775, 11989817], [11989818, 12620878]] SRR7169775 file size 4255101 SRR7169775 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 SRR7169775 SRR7169775_1.fastq SRR7169775_2.fastq Input file: SRR7169775_1.fastq Paired file: SRR7169775_2.fastq trimmed: SRR7169775-trimmed-pair1.fastq, SRR7169775-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 14:42:00 2025 >> started Tue Feb 11 14:42:19 2025 >> done (19.566s) 12620878 read pairs processed; of these: 55180 ( 0.44%) short read pairs filtered out after trimming by size control 566497 ( 4.49%) empty read pairs filtered out after trimming by size control 11999201 (95.07%) read pairs available; of these: 6413718 (53.45%) trimmed read pairs available after processing 5585483 (46.55%) untrimmed read pairs available after processing Length distribution of reads after trimming: length count percentage 18 119 0.00% 19 78 0.00% 20 103 0.00% 21 153 0.00% 22 76 0.00% 23 87 0.00% 24 86 0.00% 25 105 0.00% 26 114 0.00% 27 141 0.00% 28 140 0.00% 29 238 0.00% 30 727 0.01% 31 280 0.00% 32 420 0.00% 33 225 0.00% 34 238 0.00% 35 544 0.00% 36 701 0.01% 37 1805 0.02% 38 1068 0.01% 39 2415 0.02% 40 507 0.00% 41 479 0.00% 42 337 0.00% 43 422 0.00% 44 421 0.00% 45 541 0.00% 46 744 0.01% 47 714 0.01% 48 778 0.01% 49 770 0.01% 50 833 0.01% 51 1294 0.01% 52 1419 0.01% 53 1850 0.02% 54 1525 0.01% 55 1486 0.01% 56 1458 0.01% 57 1913 0.02% 58 2719 0.02% 59 3223 0.03% 60 4636 0.04% 61 2605 0.02% 62 1861 0.02% 63 2351 0.02% 64 1571 0.01% 65 1596 0.01% 66 1675 0.01% 67 1760 0.01% 68 1908 0.02% 69 2059 0.02% 70 2254 0.02% 71 2807 0.02% 72 3759 0.03% 73 4130 0.03% 74 5288 0.04% 75 7426 0.06% 76 15904 0.13% 77 13272 0.11% 78 6755 0.06% 79 6006 0.05% 80 6343 0.05% 81 6939 0.06% 82 7699 0.06% 83 8524 0.07% 84 10370 0.09% 85 12081 0.10% 86 12960 0.11% 87 13861 0.12% 88 15140 0.13% 89 15748 0.13% 90 16774 0.14% 91 17050 0.14% 92 17922 0.15% 93 19185 0.16% 94 20765 0.17% 95 22628 0.19% 96 23930 0.20% 97 25469 0.21% 98 26164 0.22% 99 26685 0.22% 100 28236 0.24% 101 28679 0.24% 102 30340 0.25% 103 31292 0.26% 104 33375 0.28% 105 34978 0.29% 106 36519 0.30% 107 37540 0.31% 108 38430 0.32% 109 39544 0.33% 110 40962 0.34% 111 41481 0.35% 112 42562 0.35% 113 43981 0.37% 114 45203 0.38% 115 47651 0.40% 116 48491 0.40% 117 49912 0.42% 118 50196 0.42% 119 50705 0.42% 120 52137 0.43% 121 52311 0.44% 122 53449 0.45% 123 54639 0.46% 124 55939 0.47% 125 56677 0.47% 126 58861 0.49% 127 61158 0.51% 128 62802 0.52% 129 62696 0.52% 130 63604 0.53% 131 64669 0.54% 132 65781 0.55% 133 66553 0.55% 134 67712 0.56% 135 69481 0.58% 136 71438 0.60% 137 74814 0.62% 138 77645 0.65% 139 81097 0.68% 140 84396 0.70% 141 87972 0.73% 142 92398 0.77% 143 98181 0.82% 144 106894 0.89% 145 119476 1.00% 146 139519 1.16% 147 175682 1.46% 148 245657 2.05% 149 447091 3.73% 150 2293756 19.12% 151 5585483 46.55% 11999201 reads passed initial QC criterion=sequence-density sequence-density=0.17 sequence-density-rank=1 fanout-score=5.41 fanout-score-rank=17 prefix-density=0.05 prefix-fanout=5.4 sequence=GATCGGAAGAGCACACGTCTGAACTCCAGTCACTCCGGAGAATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAATTAAC criterion=fanout-score sequence-density=0.03 sequence-density-rank=42 fanout-score=197.93 fanout-score-rank=1 prefix-density=0.34 prefix-fanout=19.1 sequence=AAAAACAAAAAGAAGATCAAAGCCTTTCTTGTCCAATCACTATCGTGAAATGACACCATTATTCTGGACCCGGAACCCGACTCAAACCAACCCATGTTTCCTTGATTTCTCCAGCTCCATTTACTCGATAGTCAAAGGAACAGAATCAGCCAATTTGCGATATTTGAGTGCATAGAACATTTCCAGATAGCGACGGCTCTCACGATGATCAAGGTTGGAAACATGCTTCCAGAAGCCATAAACTCCTGTGAGAGTCAGGAGCCTTTGAGAGTAAATTTTCCAGGTATACTTCTCTTGGATTCGCTGCAGGCCTCCCTGGGAGATTTTGTCCCAGTAACTGGGATCAGCCTTGCACTTCTCAAAGAAGTCAACAAGGAGTTCAGCAGCCTGTACTCCATGGTAAGGATCAATATGGAATCCGGATTTTCCATGCACAATGATCTCAGCA criterion=sequence-density sequence-density=0.32 sequence-density-rank=1 fanout-score=4.33 fanout-score-rank=30 prefix-density=0.46 prefix-fanout=3.0 sequence=GCTGACGAGTGGCGGACGGGTGAGTAATGTCTGGGAAACTGCCTGATGGAGGGGGATAACTACTGGAAACGGTAGCTAATACCGCATAACGTCGCAAGACCAAAGAGGGGGACCTTCGGGCCTCTTGCCATCGGATGTGCCCAGATGGGATTAGCTAGTAGGTGGGGTAACGGCTCACCTAGGCGACGATCCCTAGCTGGTCTGAGAGGATGACCAGCCACACTGGAACTGAGACACGGTCCAGACTCCTACGGGAGGCAGCAGTGGGGAATATTGCACAATGGGCGCAAGCCTGATGCAGCCATGCCGCGTGTATGAAGAAGGCCTTCGGGTTGTAAAGTACTTTCAGCGGGGAGGAAGGGAGTAAAGTTAATACCTTTGCTCATTGACGTTACCCGCAGAAGAAGCACCGGCTAACTCCGTGCCAGCAGCCGCGGTAATACGGAGGGTGCAAGCGTTAATCGGAATTACTGGGCGTAAAGCGCACGCAGGCGGTTTGTTAAGTCAGATG criterion=fanout-score sequence-density=0.02 sequence-density-rank=42 fanout-score=133.96 fanout-score-rank=1 prefix-density=0.24 prefix-fanout=13.1 sequence=GAGGAGAAGGAACACGAGGATACTAGTGTTCCTGTCGAGGTAGTCCATACAGAGACACCCCATGAACCAGAGGATAAGAAGGGTTTCCTTGACAAAATCAAGGAGAAATTGCCAGGACATAAGAAAGCTGACGAGGTCCCTCCTCCAGCTCCTGAACATGTTTCCCCTGAAGCTGCAGTTTCCCATGAAGGAGAT SRR7169775 testing PE reads STAR mapping to Ensembl genome Started job on | Feb 11 14:43:06 Started mapping on | Feb 11 14:43:07 Finished on | Feb 11 14:44:30 Mapping speed, Million of reads per hour | 520.45 Number of input reads | 11999201 Average input read length | 285 UNIQUE READS: Uniquely mapped reads number | 11158408 Uniquely mapped reads % | 92.99% Average mapped length | 286.81 Number of splices: Total | 8784320 Number of splices: Annotated (sjdb) | 8612886 Number of splices: GT/AG | 8646394 Number of splices: GC/AG | 105153 Number of splices: AT/AC | 8529 Number of splices: Non-canonical | 24244 Mismatch rate per base, % | 0.38% Deletion rate per base | 0.03% Deletion average length | 2.64 Insertion rate per base | 0.02% Insertion average length | 2.30 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 214046 % of reads mapped to multiple loci | 1.78% Number of reads mapped to too many loci | 24581 % of reads mapped to too many loci | 0.20% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 4.93% % of reads unmapped: other | 0.09% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 646632 646632 646632 N_multimapping 214046 214046 214046 N_noFeature 294256 11001690 364102 N_ambiguous 132021 633 44778 UnstrandedReadsAssigned:10732131 PositiveStrandReadsAssigned:156085 NegativeStrandReadsAssigned:10749528 Dataset is classified negative stranded MeadianReadLen=151 20thPercentileLength=140 echo kmer=135 SRR7169775 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: SRR7169775-trimmed-pair1.fastq SRR7169775-trimmed-pair2.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 11,999,201 reads, 10,754,195 reads pseudoaligned [quant] estimated average fragment length: 198.368 [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,091 rounds 52401 SRR7169775.ke.tsv 34699 SRR7169775.se.tsv 87100 total ==> SRR7169775.ke.tsv <== target_id length eff_length est_counts tpm Potri.005G200100.1.v4.1 2018 1820.63 250 12.1596 Potri.005G024800.1.v4.1 1035 837.632 34 3.59441 Potri.004G059700.1.v4.1 961 763.636 1 0.115962 Potri.007G009000.2.v4.1 1416 1218.63 0 0 Potri.003G141000.2.v4.1 2943 2745.63 160 5.16036 Potri.016G087400.1.v4.1 270 97.3448 1429 1299.93 Potri.015G069301.1.v4.1 564 367.633 0 0 Potri.010G195200.1.v4.1 1773 1575.63 36 2.02325 Potri.012G127500.1.v4.1 977 779.636 3886 441.38 ==> SRR7169775.se.tsv <== Potri.001G166300.v4.1 0 Potri.001G448400.v4.1 905 Potri.001G233950.v4.1 3 Potri.001G122700.v4.1 285 Potri.001G212900.v4.1 0 Potri.001G182400.v4.1 3 Potri.001G256600.v4.1 0 Potri.001G040500.v4.1 4 Potri.001G416900.v4.1 0 Potri.001G452600.v4.1 0 SRR7169775 completed mapping pipeline successfully