Starting /dee2/code/volunteer_pipeline.sh SRR8096892 current disk space = 1542848917504 free memory = 1594728808 SRR8096892 SRAfilesize cb461a653d040eb6327ab1a6c368863b SRR8096892.sra SRR8096892.sra file validated SRR8096892 is paired end SRR8096892 is conventional basespace SRR8096892 read1 length is 150 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR8096892_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 49 >>END_MODULE >>Per base sequence quality fail #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 32.28425 34.0 33.0 34.0 32.0 34.0 2 33.13575 34.0 33.0 34.0 32.0 34.0 3 33.24925 34.0 33.0 34.0 32.0 34.0 4 33.2835 34.0 33.0 34.0 32.0 34.0 5 33.2685 34.0 33.0 34.0 33.0 34.0 6 36.94825 38.0 37.0 38.0 36.0 38.0 7 37.21725 38.0 38.0 38.0 36.0 38.0 8 37.36275 38.0 38.0 38.0 37.0 38.0 9 37.3535 38.0 38.0 38.0 37.0 38.0 10-14 37.316700000000004 38.0 38.0 38.0 37.0 38.0 15-19 37.36145 38.0 38.0 38.0 37.0 38.0 20-24 37.37050000000001 38.0 38.0 38.0 37.0 38.0 25-29 37.35555000000001 38.0 38.0 38.0 37.0 38.0 30-34 37.313 38.0 38.0 38.0 37.0 38.0 35-39 37.17765 38.0 38.0 38.0 36.8 38.0 40-44 37.11625 38.0 38.0 38.0 36.4 38.0 45-49 37.06595 38.0 38.0 38.0 36.0 38.0 50-54 37.02185 38.0 38.0 38.0 36.0 38.0 55-59 36.866699999999994 38.0 38.0 38.0 36.0 38.0 60-64 36.9029 38.0 38.0 38.0 35.8 38.0 65-69 36.75235 38.0 38.0 38.0 35.4 38.0 70-74 36.62465 38.0 38.0 38.0 35.0 38.0 75-79 36.32940000000001 38.0 38.0 38.0 34.8 38.0 80-84 36.265 38.0 38.0 38.0 34.0 38.0 85-89 36.245900000000006 38.0 38.0 38.0 34.0 38.0 90-94 36.04880000000001 38.0 38.0 38.0 33.4 38.0 95-99 35.9887 38.0 38.0 38.0 33.8 38.0 100-104 35.840500000000006 38.0 38.0 38.0 33.0 38.0 105-109 35.674899999999994 38.0 38.0 38.0 32.4 38.0 110-114 35.654700000000005 38.0 37.8 38.0 32.6 38.0 115-119 35.3795 38.0 37.2 38.0 31.2 38.0 120-124 35.15945 38.0 36.6 38.0 29.8 38.0 125-129 35.06425 38.0 36.2 38.0 30.0 38.0 130-134 34.7828 38.0 35.8 38.0 28.0 38.0 135-139 32.46275 37.2 28.2 38.0 21.4 38.0 140-144 32.51375 37.0 30.4 38.0 21.8 38.0 145-149 31.251950000000004 36.6 30.4 38.0 8.6 38.0 150 20.35425 24.0 2.0 34.0 2.0 38.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 5 1.0 6 0.0 7 1.0 8 3.0 9 0.0 10 1.0 11 2.0 12 3.0 13 5.0 14 1.0 15 2.0 16 4.0 17 9.0 18 14.0 19 30.0 20 5.0 21 10.0 22 14.0 23 9.0 24 11.0 25 13.0 26 20.0 27 28.0 28 32.0 29 46.0 30 46.0 31 55.0 32 72.0 33 115.0 34 177.0 35 256.0 36 717.0 37 2298.0 >>END_MODULE >>Per base sequence content warn #Base G A T C 1 42.87561417119214 12.878200155159039 8.223429014740109 36.02275665890872 2 23.325000000000003 17.549999999999997 36.3 22.825 3 22.15 21.825 26.924999999999997 29.099999999999998 4 26.75 27.175 21.825 24.25 5 26.75 31.45 22.825 18.975 6 22.2 32.05 24.3 21.45 7 17.974999999999998 23.175 39.574999999999996 19.275000000000002 8 19.6 22.8 30.475 27.125 9 21.2 20.45 32.625 25.724999999999998 10-14 23.095 26.44 24.365000000000002 26.1 15-19 23.145 25.235000000000003 25.785000000000004 25.835 20-24 22.8 25.115 26.884999999999998 25.2 25-29 23.215 24.855 25.71 26.22 30-34 23.34 25.575 25.16 25.924999999999997 35-39 23.125 24.735 26.669999999999998 25.47 40-44 22.869999999999997 25.53 25.590000000000003 26.009999999999998 45-49 23.474999999999998 24.57 26.465 25.490000000000002 50-54 23.265 24.8 25.635 26.3 55-59 22.830000000000002 24.990000000000002 26.245 25.935000000000002 60-64 23.96 25.28 25.655 25.105 65-69 22.88 26.810000000000002 25.019999999999996 25.290000000000003 70-74 23.21 26.135 24.975 25.679999999999996 75-79 23.064999999999998 25.505 25.35 26.08 80-84 23.365 25.27 25.040000000000003 26.325 85-89 23.39 25.825 24.83 25.955000000000002 90-94 23.86 25.369999999999997 24.85 25.919999999999998 95-99 23.625 25.4 25.474999999999998 25.5 100-104 23.835 25.72 25.324999999999996 25.119999999999997 105-109 22.98 25.685000000000002 24.9 26.435 110-114 23.565 25.505 25.224999999999998 25.705 115-119 24.6 25.169999999999998 24.759999999999998 25.47 120-124 23.64 25.785000000000004 25.025 25.55 125-129 23.715 25.840000000000003 24.88 25.564999999999998 130-134 23.485 25.705 24.995 25.814999999999998 135-139 24.915000000000003 24.795 24.91 25.380000000000003 140-144 23.165 25.715 24.959999999999997 26.16 145-149 24.075 24.825 24.87 26.229999999999997 150 21.875 27.275 22.85 28.000000000000004 >>END_MODULE >>Per sequence GC content fail #GC Content Count 0 12.0 1 7.0 2 2.0 3 2.0 4 2.0 5 1.0 6 0.0 7 1.0 8 1.5 9 0.5 10 0.5 11 1.5 12 1.0 13 0.0 14 0.0 15 0.0 16 0.0 17 0.5 18 0.5 19 0.0 20 0.0 21 0.0 22 0.0 23 0.0 24 0.5 25 1.5 26 2.5 27 3.0 28 4.0 29 6.0 30 8.5 31 15.0 32 20.5 33 25.0 34 31.5 35 38.5 36 47.0 37 58.5 38 83.5 39 101.5 40 118.5 41 146.0 42 174.0 43 187.0 44 195.5 45 192.5 46 194.5 47 199.5 48 179.0 49 163.0 50 144.0 51 132.0 52 123.0 53 108.0 54 96.0 55 88.0 56 93.0 57 98.0 58 88.0 59 82.0 60 87.5 61 81.5 62 71.0 63 70.0 64 65.0 65 65.0 66 58.5 67 44.0 68 41.0 69 37.5 70 25.0 71 18.5 72 17.0 73 13.0 74 10.5 75 8.0 76 5.0 77 2.5 78 1.5 79 1.0 80 0.5 81 0.0 82 0.0 83 0.0 84 0.0 85 0.5 86 0.5 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 3.325 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 96.65 #Duplication Level Percentage of deduplicated Percentage of total 1 98.70667356440765 95.39999999999999 2 1.0087946197620279 1.95 3 0.12933264355923435 0.375 4 0.0775995861355406 0.3 5 0.0 0.0 6 0.0 0.0 7 0.02586652871184687 0.17500000000000002 8 0.0 0.0 9 0.0 0.0 >10 0.02586652871184687 0.35000000000000003 >50 0.02586652871184687 1.4500000000000002 >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 GATCGGAAGAGCACACGTCTGAACTCCAGTCACACTGATATCTCGTATGC 58 1.4500000000000002 TruSeq Adapter, Index 25 (100% over 50bp) TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 14 0.35000000000000003 No Hit AGATCGGAAGAGCACACGTCTGAACTCCAGTCACACTGATATCTCGTATG 7 0.17500000000000002 TruSeq Adapter, Index 25 (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 0.175 0.0 0.0 0.0 0.0 2 0.175 0.0 0.0 0.0 0.0 3 0.175 0.0 0.0 0.0 0.0 4 0.175 0.0 0.0 0.0 0.0 5 0.175 0.0 0.0 0.0 0.0 6 0.175 0.0 0.0 0.0 0.0 7 0.175 0.0 0.0 0.0 0.0 8 0.175 0.0 0.0 0.0 0.0 9 0.175 0.0 0.0 0.0 0.0 10-11 0.175 0.0 0.0 0.0 0.0 12-13 0.175 0.0 0.0 0.0 0.0 14-15 0.1875 0.0 0.0 0.0 0.0 16-17 0.21250000000000002 0.0 0.0 0.0 0.0 18-19 0.225 0.0 0.0 0.0 0.0 20-21 0.225 0.0 0.0 0.0 0.0 22-23 0.225 0.0 0.0 0.0 0.0 24-25 0.225 0.0 0.0 0.0 0.0 26-27 0.225 0.0 0.0 0.0 0.0 28-29 0.225 0.0 0.0 0.0 0.0 30-31 0.225 0.0 0.0 0.0 0.0 32-33 0.225 0.0 0.0 0.0 0.0 34-35 0.225 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 0.225 0.0 0.0 0.0 0.0 42-43 0.225 0.0 0.0 0.0 0.0 44-45 0.225 0.0 0.0 0.0 0.0 46-47 0.225 0.0 0.0 0.0 0.0 48-49 0.225 0.0 0.0 0.0 0.0 50-51 0.225 0.0 0.0 0.0 0.0 52-53 0.225 0.0 0.0 0.0 0.0 54-55 0.225 0.0 0.0 0.0 0.0 56-57 0.225 0.0 0.0 0.0 0.0 58-59 0.225 0.0 0.0 0.0 0.0 60-61 0.225 0.0 0.0 0.0 0.0 62-63 0.2625 0.0 0.0 0.0 0.0 64-65 0.275 0.0 0.0 0.0 0.0 66-67 0.275 0.0 0.0 0.0 0.0 68-69 0.275 0.0 0.0 0.0 0.0 70-71 0.275 0.0 0.0 0.0 0.0 72-73 0.275 0.0 0.0 0.0 0.0 74-75 0.275 0.0 0.0 0.0 0.0 76-77 0.275 0.0 0.0 0.0 0.0 78-79 0.275 0.0 0.0 0.0 0.0 80-81 0.3125 0.0 0.0 0.0 0.0 82-83 0.325 0.0 0.0 0.0 0.0 84-85 0.35 0.0 0.0 0.0 0.0 86-87 0.35 0.0 0.0 0.0 0.0 88-89 0.3625 0.0 0.0 0.0 0.0 90-91 0.3875 0.0 0.0 0.0 0.0 92-93 0.45 0.0 0.0 0.0 0.0 94-95 0.4625 0.0 0.0 0.0 0.0 96-97 0.5125 0.0 0.0 0.0 0.0 98-99 0.5874999999999999 0.0 0.0 0.0 0.0 100-101 0.625 0.0 0.0 0.0 0.0 102-103 0.7124999999999999 0.0 0.0 0.0 0.0 104-105 0.7875000000000001 0.0 0.0 0.0 0.0 106-107 0.8125 0.0 0.0 0.0 0.0 108-109 0.9125 0.0 0.0 0.0 0.0 110-111 1.0375 0.0 0.0 0.0 0.0 112-113 1.2125 0.0 0.0 0.0 0.0 114-115 1.3250000000000002 0.0 0.0 0.0 0.0 116-117 1.45 0.0 0.0 0.0 0.0 118-119 1.55 0.0 0.0 0.0 0.0 120-121 1.7875 0.0 0.0 0.0 0.0 122-123 2.0125 0.0 0.0 0.0 0.0 124-125 2.1875 0.0 0.0 0.0 0.0 126-127 2.4749999999999996 0.0 0.0 0.0 0.0 128-129 2.675 0.0 0.0 0.0 0.0 130-131 2.95 0.0 0.0 0.0 0.0 132-133 3.0625 0.0 0.0 0.0 0.0 134-135 3.2375 0.0 0.0 0.0 0.0 136-137 3.4375 0.0 0.0 0.0 0.0 138 3.6 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content pass >>END_MODULE SRR8096892 read2 length is 150 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR8096892_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 50 >>END_MODULE >>Per base sequence quality fail #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 31.768 33.0 33.0 34.0 28.0 34.0 2 31.88725 33.0 33.0 34.0 30.0 34.0 3 31.75975 33.0 33.0 34.0 29.0 34.0 4 31.54625 33.0 33.0 34.0 28.0 34.0 5 31.667 33.0 33.0 34.0 28.0 34.0 6 35.67225 38.0 38.0 38.0 31.0 38.0 7 35.749 38.0 38.0 38.0 31.0 38.0 8 35.8135 38.0 38.0 38.0 31.0 38.0 9 35.751 38.0 38.0 38.0 31.0 38.0 10-14 35.73315 38.0 38.0 38.0 31.0 38.0 15-19 35.50790000000001 38.0 38.0 38.0 29.0 38.0 20-24 35.55515 38.0 37.8 38.0 29.0 38.0 25-29 35.422900000000006 38.0 37.4 38.0 29.0 38.0 30-34 35.194 38.0 37.0 38.0 28.0 38.0 35-39 35.11285 38.0 37.0 38.0 28.0 38.0 40-44 35.07355 38.0 37.0 38.0 27.8 38.0 45-49 34.9399 38.0 36.6 38.0 27.4 38.0 50-54 34.738 38.0 36.4 38.0 26.0 38.0 55-59 34.585449999999994 38.0 36.0 38.0 25.4 38.0 60-64 34.55915 38.0 36.0 38.0 26.2 38.0 65-69 34.254099999999994 38.0 35.8 38.0 23.2 38.0 70-74 33.8233 38.0 35.0 38.0 16.0 38.0 75-79 33.5234 38.0 34.6 38.0 15.4 38.0 80-84 33.3085 38.0 34.0 38.0 15.2 38.0 85-89 32.74495 38.0 33.8 38.0 15.0 38.0 90-94 32.604949999999995 38.0 33.4 38.0 15.0 38.0 95-99 32.06505 37.6 32.2 38.0 14.8 38.0 100-104 31.517449999999997 37.2 30.6 38.0 13.8 38.0 105-109 31.03945 37.0 29.0 38.0 13.0 38.0 110-114 30.492250000000002 36.4 27.4 38.0 13.0 38.0 115-119 29.9289 35.8 25.4 38.0 10.8 38.0 120-124 29.19955 35.0 23.4 38.0 2.0 38.0 125-129 28.447450000000003 35.0 21.8 38.0 2.0 38.0 130-134 27.491499999999995 34.0 16.2 38.0 2.0 38.0 135-139 26.203449999999997 33.0 13.4 38.0 2.0 38.0 140-144 24.7726 32.4 11.0 38.0 2.0 38.0 145-149 22.035149999999998 30.4 2.0 37.2 2.0 38.0 150 15.7655 2.0 2.0 33.0 2.0 38.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 2 53.0 3 4.0 4 4.0 5 6.0 6 13.0 7 7.0 8 8.0 9 7.0 10 10.0 11 14.0 12 12.0 13 13.0 14 22.0 15 24.0 16 33.0 17 33.0 18 23.0 19 26.0 20 26.0 21 38.0 22 31.0 23 39.0 24 40.0 25 64.0 26 71.0 27 79.0 28 92.0 29 107.0 30 129.0 31 157.0 32 208.0 33 273.0 34 369.0 35 578.0 36 784.0 37 603.0 >>END_MODULE >>Per base sequence content warn #Base G A T C 1 40.44154540893126 19.668840943301554 8.554942298043152 31.334671349724037 2 26.772646984607622 24.299772899318697 31.011859702245776 17.915720413827906 3 22.98560242485476 24.04647638292498 28.542561252841626 24.42535993937863 4 25.99797877716018 30.267812026275898 18.418393127842343 25.315816068721574 5 29.181404749873675 32.61748357756443 18.494188984335523 19.706922688226378 6 24.59718026183283 33.76132930513595 19.184290030211482 22.457200402819737 7 22.697533970810266 17.86612984398591 35.32964267740312 24.106693507800706 8 22.910372608257802 23.741188318227593 24.043303121852972 29.305135951661633 9 25.937106918238996 20.77987421383648 27.069182389937108 26.213836477987424 10-14 26.25962651633362 25.237831580007047 22.82679820808376 25.675743695575576 15-19 26.285311445692127 24.074726824109977 24.40203434211189 25.237927388086007 20-24 26.817724068479354 25.317220543806645 23.6404833836858 24.224572004028197 25-29 25.83178134595057 26.007952886696533 23.677455076257107 24.48281069109579 30-34 26.27818035426731 25.397544283413847 24.280394524959743 24.0438808373591 35-39 25.9072834348417 24.789852519253035 24.32677304072079 24.97609100518448 40-44 27.48314380597766 24.942135453356144 23.36721344470162 24.20750729596458 45-49 26.131159092052947 24.570939654738538 23.61970909456943 25.678192158639085 50-54 26.00946531064344 25.027691068371766 23.71362400563891 25.249219615345886 55-59 25.732407127755963 25.465619651666167 23.779321453740057 25.02265176683781 60-64 26.078421502994914 26.642170433381988 23.466049227361957 23.813358836261138 65-69 26.174057482257005 26.279760406704582 23.61705340514421 23.929128705894197 70-74 25.690983235160854 25.464431354780242 23.964154458037555 24.880430952021346 75-79 25.686965274282837 25.158530447911424 24.09159536990438 25.06290890790136 80-84 25.77366275851658 25.40633019674936 24.369747899159663 24.450259145574396 85-89 25.951278437688746 25.98651097241796 24.00845580833501 24.053754781558283 90-94 25.996376811594203 25.654186795491142 23.72685185185185 24.622584541062803 95-99 25.653027329004985 25.658060294931808 24.102873823544215 24.586038552519 100-104 27.102098324359687 25.12957278719871 23.680370351733508 24.087958536708097 105-109 26.062893081761008 25.403773584905657 24.07044025157233 24.462893081761006 110-114 26.013683469161887 25.450246503672403 23.84545728946574 24.69061273769997 115-119 25.501937301866857 25.72334322950737 24.28923665274493 24.485482815880843 120-124 25.7786947114175 25.79379057012026 24.364715946258745 24.062798772203493 125-129 26.668344237544034 26.280825364871667 22.868646200301963 24.182184197282336 130-134 25.752239106370133 26.094394686525106 24.212538995672737 23.940827211432023 135-139 26.691483475023897 26.193470496503846 23.26575783490115 23.849288193571105 140-144 26.212517609176896 26.700543368887097 23.51076675387402 23.576172268061985 145-149 26.226614895870103 26.655236750542084 23.634713327618375 23.48343502596944 150 26.113207547169807 26.69182389937107 23.345911949685537 23.849056603773587 >>END_MODULE >>Per sequence GC content fail #GC Content Count 0 17.0 1 12.0 2 3.5 3 1.0 4 1.0 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 0.5 18 0.5 19 0.5 20 0.5 21 0.5 22 0.5 23 0.0 24 0.0 25 1.0 26 2.5 27 2.5 28 3.0 29 5.5 30 7.0 31 13.0 32 15.5 33 13.5 34 18.5 35 26.0 36 41.5 37 58.5 38 72.5 39 87.0 40 105.0 41 132.5 42 144.0 43 160.5 44 166.0 45 152.5 46 169.5 47 180.5 48 164.0 49 151.0 50 144.0 51 148.0 52 138.0 53 115.5 54 115.0 55 113.5 56 104.0 57 94.5 58 95.5 59 113.5 60 115.5 61 94.5 62 85.5 63 79.5 64 77.0 65 74.5 66 66.0 67 62.0 68 55.5 69 53.5 70 43.0 71 27.5 72 20.5 73 16.5 74 11.5 75 5.5 76 4.0 77 2.5 78 1.5 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 pass #Base N-Count 1 0.35000000000000003 2 0.9249999999999999 3 1.0250000000000001 4 1.05 5 1.05 6 0.7000000000000001 7 0.65 8 0.7000000000000001 9 0.625 10-14 0.6649999999999999 15-19 0.705 20-24 0.7000000000000001 25-29 0.6649999999999999 30-34 0.64 35-39 0.6649999999999999 40-44 0.63 45-49 0.655 50-54 0.69 55-59 0.67 60-64 0.6649999999999999 65-69 0.6649999999999999 70-74 0.685 75-79 0.65 80-84 0.635 85-89 0.66 90-94 0.64 95-99 0.655 100-104 0.635 105-109 0.625 110-114 0.61 115-119 0.635 120-124 0.635 125-129 0.65 130-134 0.63 135-139 0.605 140-144 0.62 145-149 0.845 150 0.625 >>END_MODULE >>Sequence Length Distribution pass #Length Count 150 4000.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 97.0 #Duplication Level Percentage of deduplicated Percentage of total 1 98.58247422680412 95.625 2 1.134020618556701 2.1999999999999997 3 0.12886597938144329 0.375 4 0.07731958762886598 0.3 5 0.0 0.0 6 0.025773195876288662 0.15 7 0.0 0.0 8 0.0 0.0 9 0.0 0.0 >10 0.051546391752577324 1.35 >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 40 1.0 Illumina Single End PCR Primer 1 (100% over 50bp) NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN 14 0.35000000000000003 No Hit GNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN 6 0.15 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 0.2 0.0 0.0 0.0 0.0 2 0.2 0.0 0.0 0.0 0.0 3 0.2 0.0 0.0 0.0 0.0 4 0.2 0.0 0.0 0.0 0.0 5 0.2 0.0 0.0 0.0 0.0 6 0.2 0.0 0.0 0.0 0.0 7 0.2 0.0 0.0 0.0 0.0 8 0.2 0.0 0.0 0.0 0.0 9 0.2 0.0 0.0 0.0 0.0 10-11 0.2 0.0 0.0 0.0 0.0 12-13 0.2 0.0 0.0 0.0 0.0 14-15 0.21250000000000002 0.0 0.0 0.0 0.0 16-17 0.2375 0.0 0.0 0.0 0.0 18-19 0.25 0.0 0.0 0.0 0.0 20-21 0.25 0.0 0.0 0.0 0.0 22-23 0.25 0.0 0.0 0.0 0.0 24-25 0.25 0.0 0.0 0.0 0.0 26-27 0.25 0.0 0.0 0.0 0.0 28-29 0.25 0.0 0.0 0.0 0.0 30-31 0.25 0.0 0.0 0.0 0.0 32-33 0.25 0.0 0.0 0.0 0.0 34-35 0.25 0.0 0.0 0.0 0.0 36-37 0.25 0.0 0.0 0.0 0.0 38-39 0.25 0.0 0.0 0.0 0.0 40-41 0.25 0.0 0.0 0.0 0.0 42-43 0.25 0.0 0.0 0.0 0.0 44-45 0.25 0.0 0.0 0.0 0.0 46-47 0.25 0.0 0.0 0.0 0.0 48-49 0.25 0.0 0.0 0.0 0.0 50-51 0.25 0.0 0.0 0.0 0.0 52-53 0.25 0.0 0.0 0.0 0.0 54-55 0.25 0.0 0.0 0.0 0.0 56-57 0.25 0.0 0.0 0.0 0.0 58-59 0.25 0.0 0.0 0.0 0.0 60-61 0.25 0.0 0.0 0.0 0.0 62-63 0.25 0.0 0.0 0.0 0.0 64-65 0.25 0.0 0.0 0.0 0.0 66-67 0.25 0.0 0.0 0.0 0.0 68-69 0.25 0.0 0.0 0.0 0.0 70-71 0.25 0.0 0.0 0.0 0.0 72-73 0.25 0.0 0.0 0.0 0.0 74-75 0.25 0.0 0.0 0.0 0.0 76-77 0.25 0.0 0.0 0.0 0.0 78-79 0.25 0.0 0.0 0.0 0.0 80-81 0.2875 0.0 0.0 0.0 0.0 82-83 0.3 0.0 0.0 0.0 0.0 84-85 0.325 0.0 0.0 0.0 0.0 86-87 0.325 0.0 0.0 0.0 0.0 88-89 0.325 0.0 0.0 0.0 0.0 90-91 0.3375 0.0 0.0 0.0 0.0 92-93 0.4 0.0 0.0 0.0 0.0 94-95 0.4125 0.0 0.0 0.0 0.0 96-97 0.4375 0.0 0.0 0.0 0.0 98-99 0.4625 0.0 0.0 0.0 0.0 100-101 0.5 0.0 0.0 0.0 0.0 102-103 0.5125 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 0.675 0.0 0.0 0.0 0.0 110-111 0.7875000000000001 0.0 0.0 0.0 0.0 112-113 0.9375 0.0 0.0 0.0 0.0 114-115 1.0125 0.0 0.0 0.0 0.0 116-117 1.1 0.0 0.0 0.0 0.0 118-119 1.15 0.0 0.0 0.0 0.0 120-121 1.25 0.0 0.0 0.0 0.0 122-123 1.4249999999999998 0.0 0.0 0.0 0.0 124-125 1.525 0.0 0.0 0.0 0.0 126-127 1.6625 0.0 0.0 0.0 0.0 128-129 1.8125 0.0 0.0 0.0 0.0 130-131 1.9625 0.0 0.0 0.0 0.0 132-133 2.0 0.0 0.0 0.0 0.0 134-135 2.1125 0.0 0.0 0.0 0.0 136-137 2.3 0.0 0.0 0.0 0.0 138 2.45 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position TGACCGA 10 0.006973645 144.0 4 TATTGCA 10 0.006973645 144.0 7 TAACATG 10 0.006973645 144.0 3 >>END_MODULE Read 1718678 spots for SRR8096892.sra Written 1718678 spots for SRR8096892.sra Read 1718678 spots for SRR8096892.sra Written 1718678 spots for SRR8096892.sra Read 1718678 spots for SRR8096892.sra Written 1718678 spots for SRR8096892.sra Read 1718678 spots for SRR8096892.sra Written 1718678 spots for SRR8096892.sra Read 1718678 spots for SRR8096892.sra Written 1718678 spots for SRR8096892.sra Read 1718678 spots for SRR8096892.sra Written 1718678 spots for SRR8096892.sra Read 1718678 spots for SRR8096892.sra Written 1718678 spots for SRR8096892.sra Read 1718678 spots for SRR8096892.sra Written 1718678 spots for SRR8096892.sra Read 1718678 spots for SRR8096892.sra Written 1718678 spots for SRR8096892.sra Read 1718687 spots for SRR8096892.sra Written 1718687 spots for SRR8096892.sra Read 1718678 spots for SRR8096892.sra Written 1718678 spots for SRR8096892.sra Read 1718678 spots for SRR8096892.sra Written 1718678 spots for SRR8096892.sra Read 1718678 spots for SRR8096892.sra Written 1718678 spots for SRR8096892.sra Read 1718678 spots for SRR8096892.sra Written 1718678 spots for SRR8096892.sra Read 1718678 spots for SRR8096892.sra Written 1718678 spots for SRR8096892.sra Read 1718678 spots for SRR8096892.sra Written 1718678 spots for SRR8096892.sra Read 1718678 spots for SRR8096892.sra Written 1718678 spots for SRR8096892.sra Read 1718678 spots for SRR8096892.sra Written 1718678 spots for SRR8096892.sra Read 1718678 spots for SRR8096892.sra Written 1718678 spots for SRR8096892.sra Read 1718678 spots for SRR8096892.sra Written 1718678 spots for SRR8096892.sra SRR ids: ['SRR8096892.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_opgqyxff SRR8096892.sra spots: 34373569 blocks: [[1, 1718678], [1718679, 3437356], [3437357, 5156034], [5156035, 6874712], [6874713, 8593390], [8593391, 10312068], [10312069, 12030746], [12030747, 13749424], [13749425, 15468102], [15468103, 17186780], [17186781, 18905458], [18905459, 20624136], [20624137, 22342814], [22342815, 24061492], [24061493, 25780170], [25780171, 27498848], [27498849, 29217526], [29217527, 30936204], [30936205, 32654882], [32654883, 34373569]] SRR8096892 file size 11559238 SRR8096892 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 SRR8096892 SRR8096892_1.fastq SRR8096892_2.fastq Input file: SRR8096892_1.fastq Paired file: SRR8096892_2.fastq trimmed: SRR8096892-trimmed-pair1.fastq, SRR8096892-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 14:47:35 2024 >> started Sat Dec 7 14:48:11 2024 >> done (36.225s) 34373569 read pairs processed; of these: 112036 ( 0.33%) short read pairs filtered out after trimming by size control 1015998 ( 2.96%) empty read pairs filtered out after trimming by size control 33245535 (96.72%) read pairs available; of these: 17321395 (52.10%) trimmed read pairs available after processing 15924140 (47.90%) untrimmed read pairs available after processing Length distribution of reads after trimming: length count percentage 18 77 0.00% 19 114 0.00% 20 74 0.00% 21 77 0.00% 22 84 0.00% 23 69 0.00% 24 106 0.00% 25 101 0.00% 26 134 0.00% 27 114 0.00% 28 118 0.00% 29 148 0.00% 30 185 0.00% 31 141 0.00% 32 215 0.00% 33 130 0.00% 34 270 0.00% 35 264 0.00% 36 196 0.00% 37 265 0.00% 38 232 0.00% 39 348 0.00% 40 560 0.00% 41 483 0.00% 42 443 0.00% 43 438 0.00% 44 483 0.00% 45 655 0.00% 46 1022 0.00% 47 913 0.00% 48 823 0.00% 49 929 0.00% 50 931 0.00% 51 957 0.00% 52 781 0.00% 53 905 0.00% 54 1022 0.00% 55 1199 0.00% 56 1323 0.00% 57 1191 0.00% 58 1840 0.01% 59 2758 0.01% 60 1970 0.01% 61 8740 0.03% 62 3184 0.01% 63 1331 0.00% 64 1339 0.00% 65 1538 0.00% 66 1585 0.00% 67 1760 0.01% 68 2057 0.01% 69 2668 0.01% 70 2871 0.01% 71 2494 0.01% 72 2516 0.01% 73 3011 0.01% 74 3035 0.01% 75 3244 0.01% 76 3511 0.01% 77 4077 0.01% 78 4351 0.01% 79 4844 0.01% 80 5353 0.02% 81 6047 0.02% 82 7117 0.02% 83 9080 0.03% 84 15559 0.05% 85 16881 0.05% 86 18564 0.06% 87 20006 0.06% 88 20351 0.06% 89 20426 0.06% 90 20516 0.06% 91 20529 0.06% 92 20682 0.06% 93 21156 0.06% 94 22238 0.07% 95 23441 0.07% 96 25571 0.08% 97 27537 0.08% 98 29790 0.09% 99 31485 0.09% 100 31413 0.09% 101 33634 0.10% 102 35394 0.11% 103 37428 0.11% 104 39969 0.12% 105 41609 0.13% 106 45192 0.14% 107 47571 0.14% 108 49430 0.15% 109 48827 0.15% 110 49510 0.15% 111 51325 0.15% 112 53412 0.16% 113 54336 0.16% 114 56939 0.17% 115 59016 0.18% 116 61827 0.19% 117 64112 0.19% 118 66925 0.20% 119 70455 0.21% 120 73437 0.22% 121 76664 0.23% 122 80482 0.24% 123 84286 0.25% 124 87985 0.26% 125 91137 0.27% 126 96404 0.29% 127 101065 0.30% 128 105447 0.32% 129 112019 0.34% 130 116443 0.35% 131 121970 0.37% 132 131024 0.39% 133 138273 0.42% 134 148135 0.45% 135 157468 0.47% 136 168989 0.51% 137 183351 0.55% 138 195468 0.59% 139 212402 0.64% 140 233732 0.70% 141 260350 0.78% 142 290906 0.88% 143 334779 1.01% 144 400524 1.20% 145 496271 1.49% 146 658337 1.98% 147 948433 2.85% 148 1812231 5.45% 149 7939486 23.88% 150 15924140 47.90% 33245535 reads passed initial QC criterion=sequence-density sequence-density=1.11 sequence-density-rank=1 fanout-score=2.03 fanout-score-rank=33 prefix-density=1.12 prefix-fanout=2.0 sequence=AACATGGAGAACATGGCGAGGCGGCCGTTCTTGATCTCCTTCACCTTGAGCTCAGCGAA criterion=fanout-score sequence-density=0.10 sequence-density-rank=32 fanout-score=12.49 fanout-score-rank=1 prefix-density=0.49 prefix-fanout=2.6 sequence=GCCGGGAACGATTCCCTGCTCGACAAGGATGTCAACAATCTTCTTGCCATCAACAGTCGATTGGTAGAGGGTCTCCTCGAAGAGGATAGCACCAGAGATGTAATTTCCCAGGCCTGGTGGAGTGACAAGGAGGGTACGGTAAGCCTGGCGGTTAGCCTCAGTGTTCTCAAGGCCAATCGAGTCAAGTCTCTTTCCACAGGTAGCATTGGACTCATCCATGGCTAGGATGCCCCTTCCTGGTGATGCGATGGTTTTCGCGGTCTTGACAAGTTCATCAGCGTATGCGCTGGCACGGACAACCATGGAGACGGTCATCTGCTTGGGAGTGGCAGCCTGGCGGGTGGTGCCCCATTCGGACTTCTTGGGAAGGAAAGACGATTTGAGGATAGTAGCCGAGGCCATTGTTTCTGGCTCCAAAGGCAAGAGGATCAGGTGCTACCCTCTTCTTTGACACAAGCTTGCAAT criterion=sequence-density sequence-density=0.78 sequence-density-rank=1 fanout-score=3.08 fanout-score-rank=12 prefix-density=0.88 prefix-fanout=2.7 sequence=GAGTTCAGCAAGGTCGG criterion=fanout-score sequence-density=0.02 sequence-density-rank=25 fanout-score=57.62 fanout-score-rank=1 prefix-density=0.13 prefix-fanout=9.1 sequence=GCAGCAGCCATTACTTGATCATCTGAAAAATCTTAATCCAGATCAGACCAAGCAGAGCAGAGATGTCTGCTACCTTCTCGTCCACCGTCGGAGCTCCGGCTTCTACGCCAACCAGCTTCCTTGGGAAGAAGCTCAAGAAGCAGGTGACCTCGGCCGTGAACTACCATGGCAAGAGCACCAAGGCCAACAGATTCACAGTCATGGCCAAGGAGGTGGACGAGTCAAAGCAGACTGACCAGGACAGGTGGAAGGGCCTCGCCTACGATATCTCCGACGACCAGCAGGACATCACCAGGGGGAAGGGTATCGTCGACTCGCTCTTCCAGGCGCCCATGGGCGACGGTACCCACGTGGCCGTCCTCAGCTCCCAAGAGTACATCAGCCAGGGCCTAAGGAAGTACGACTTCGACAACA SRR8096892 testing PE reads STAR mapping to Ensembl genome Started job on | Dec 07 14:48:57 Started mapping on | Dec 07 14:48:57 Finished on | Dec 07 14:52:15 Mapping speed, Million of reads per hour | 604.46 Number of input reads | 33245535 Average input read length | 291 UNIQUE READS: Uniquely mapped reads number | 32141683 Uniquely mapped reads % | 96.68% Average mapped length | 291.20 Number of splices: Total | 33367981 Number of splices: Annotated (sjdb) | 31550201 Number of splices: GT/AG | 32926599 Number of splices: GC/AG | 384592 Number of splices: AT/AC | 10563 Number of splices: Non-canonical | 46227 Mismatch rate per base, % | 0.28% Deletion rate per base | 0.01% Deletion average length | 2.09 Insertion rate per base | 0.01% Insertion average length | 1.91 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 356294 % of reads mapped to multiple loci | 1.07% Number of reads mapped to too many loci | 6848 % of reads mapped to too many loci | 0.02% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 2.09% % of reads unmapped: other | 0.13% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 885544 885544 885544 N_multimapping 356294 356294 356294 N_noFeature 1127976 31130028 1399803 N_ambiguous 870691 3863 133194 UnstrandedReadsAssigned:30143016 PositiveStrandReadsAssigned:1007792 NegativeStrandReadsAssigned:30608686 Dataset is classified negative stranded MeadianReadLen=150 20thPercentileLength=149 echo kmer=145 SRR8096892 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: SRR8096892-trimmed-pair1.fastq SRR8096892-trimmed-pair2.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 33,245,535 reads, 30,643,811 reads pseudoaligned [quant] estimated average fragment length: 279.752 [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,175 rounds 52973 SRR8096892.ke.tsv 35125 SRR8096892.se.tsv 88098 total ==> SRR8096892.ke.tsv <== target_id length eff_length est_counts tpm PNS24245 936 657.772 0 0 PNS24247 1044 765.248 92.05 5.36194 PNS24249 1928 1649.25 52.9388 1.43083 PNS24246 1044 765.248 92.05 5.36194 PNS24248 1044 765.248 92.05 5.36194 PNS24244 1471 1192.25 220.911 8.25945 PNS24243 293 82.1838 0 0 KQK14069 1603 1324.25 8591.4 289.198 KQK14071 474 216.752 134.535 27.6677 ==> SRR8096892.se.tsv <== BRADI_1g14170v3 10042 BRADI_1g53295v3 72 BRADI_1g59795v3 1383 BRADI_1g07683v3 0 BRADI_1g00485v3 3 BRADI_1g20270v3 360 BRADI_1g74790v3 111 BRADI_1g09890v3 0 BRADI_1g77505v3 473 BRADI_1g48960v3 0 SRR8096892 completed mapping pipeline successfully