Starting /dee2/code/volunteer_pipeline.sh SRR6958207 current disk space = 1550478942208 free memory = 1383286272 SRR6958207 SRAfilesize f9f0db41e9c8c21f32f597b3d2442f94 SRR6958207.sra SRR6958207.sra file validated SRR6958207 is paired end SRR6958207 is conventional basespace SRR6958207 read1 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR6958207_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 49 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 27.9965 32.0 18.0 33.0 18.0 34.0 2 31.97125 33.0 31.0 34.0 29.0 34.0 3 32.7965 33.0 33.0 34.0 31.0 34.0 4 32.70025 33.0 33.0 34.0 31.0 34.0 5 32.86675 33.0 33.0 34.0 32.0 34.0 6 36.49575 38.0 37.0 38.0 34.0 38.0 7 36.84175 38.0 37.0 38.0 35.0 38.0 8 37.27975 38.0 38.0 38.0 36.0 38.0 9 37.50025 38.0 38.0 38.0 37.0 38.0 10-14 37.55815 38.0 38.0 38.0 38.0 38.0 15-19 37.5741 38.0 38.0 38.0 38.0 38.0 20-24 37.5468 38.0 38.0 38.0 37.8 38.0 25-29 37.4989 38.0 38.0 38.0 38.0 38.0 30-34 37.5028 38.0 38.0 38.0 37.8 38.0 35-39 37.49075 38.0 38.0 38.0 37.4 38.0 40-44 37.495850000000004 38.0 38.0 38.0 37.4 38.0 45-49 37.4397 38.0 38.0 38.0 37.0 38.0 50-54 37.45275 38.0 38.0 38.0 37.0 38.0 55-59 37.0029 38.0 38.0 38.0 36.4 38.0 60-64 36.4306 38.0 38.0 38.0 35.6 38.0 65-69 37.20705 38.0 38.0 38.0 36.2 38.0 70-74 37.33785 38.0 38.0 38.0 37.0 38.0 75-79 37.236599999999996 38.0 38.0 38.0 36.6 38.0 80-84 37.11105 38.0 38.0 38.0 35.8 38.0 85-89 37.0266 38.0 38.0 38.0 35.8 38.0 90-94 36.971199999999996 38.0 38.0 38.0 35.6 38.0 95-99 36.875 38.0 38.0 38.0 35.0 38.0 100-104 36.71565 38.0 38.0 38.0 34.6 38.0 105-109 36.54655 38.0 38.0 38.0 34.0 38.0 110-114 36.45005 38.0 38.0 38.0 33.8 38.0 115-119 36.296949999999995 38.0 37.8 38.0 33.8 38.0 120-124 36.04445 38.0 37.2 38.0 32.4 38.0 125-129 35.9405 38.0 37.0 38.0 31.8 38.0 130-134 35.67 38.0 36.4 38.0 31.4 38.0 135-139 34.96275000000001 38.0 36.0 38.0 29.2 38.0 140-144 34.33985 38.0 34.6 38.0 26.4 38.0 145-149 34.081 38.0 34.6 38.0 25.8 38.0 150-151 28.634999999999998 34.5 17.5 38.0 7.0 38.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 5 1.0 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 2.0 16 3.0 17 1.0 18 1.0 19 0.0 20 2.0 21 3.0 22 5.0 23 6.0 24 11.0 25 5.0 26 7.0 27 18.0 28 22.0 29 33.0 30 28.0 31 48.0 32 68.0 33 89.0 34 153.0 35 297.0 36 713.0 37 2484.0 >>END_MODULE >>Per base sequence content warn #Base G A T C 1 40.0 11.35 9.75 38.9 2 22.900000000000002 13.4 32.824999999999996 30.875000000000004 3 21.325 17.474999999999998 25.074999999999996 36.125 4 25.174999999999997 24.525 23.375 26.924999999999997 5 26.900000000000002 27.950000000000003 23.05 22.1 6 22.925 30.425 23.549999999999997 23.1 7 17.8 25.4 37.9 18.9 8 21.8 23.1 28.325 26.775 9 19.525000000000002 22.7 32.800000000000004 24.975 10-14 22.624049619847938 26.925770308123248 25.42016806722689 25.03001200480192 15-19 23.1 24.88 26.39 25.629999999999995 20-24 22.755 26.029999999999998 25.83 25.385 25-29 22.814999999999998 25.86 25.805 25.52 30-34 22.455 25.840000000000003 25.405 26.3 35-39 23.105 25.124999999999996 25.5 26.27 40-44 22.97 25.25 25.795 25.985000000000003 45-49 23.255 25.735000000000003 25.46 25.55 50-54 23.155 25.374999999999996 25.4 26.07 55-59 23.757630795620805 25.372080117047574 24.791887392159833 26.078401695171788 60-64 22.872911237160814 25.187797025908328 25.709029587613063 26.230262149317802 65-69 23.705000000000002 24.435000000000002 25.865 25.995 70-74 22.875 25.61 25.779999999999998 25.735000000000003 75-79 23.669999999999998 24.775 25.605 25.95 80-84 23.669999999999998 25.27 24.759999999999998 26.3 85-89 23.400000000000002 25.405 25.305 25.89 90-94 23.580000000000002 25.259999999999998 25.14 26.02 95-99 23.865 25.1 25.119999999999997 25.915 100-104 23.77 25.3 25.34 25.590000000000003 105-109 23.635 24.435000000000002 25.569999999999997 26.36 110-114 23.68 25.22 25.124999999999996 25.974999999999998 115-119 24.0 24.654999999999998 25.395 25.95 120-124 23.955000000000002 25.11 25.205 25.729999999999997 125-129 23.165 25.165 25.255 26.415 130-134 24.275 24.67 24.855 26.200000000000003 135-139 23.935000000000002 24.834999999999997 25.44 25.790000000000003 140-144 23.544999999999998 25.669999999999998 24.545 26.240000000000002 145-149 24.19 25.25 24.48 26.08 150-151 23.8375 24.9125 25.362499999999997 25.887500000000003 >>END_MODULE >>Per sequence GC content fail #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 0.5 23 0.0 24 0.0 25 0.0 26 0.5 27 1.5 28 1.5 29 3.5 30 7.0 31 9.0 32 13.0 33 20.5 34 25.0 35 33.5 36 46.5 37 52.0 38 71.5 39 105.5 40 131.5 41 156.5 42 186.5 43 200.0 44 201.0 45 210.5 46 196.5 47 187.5 48 196.5 49 185.5 50 162.5 51 142.0 52 136.5 53 126.5 54 114.0 55 108.5 56 104.0 57 90.0 58 73.0 59 69.5 60 69.5 61 61.5 62 52.5 63 53.0 64 57.0 65 54.0 66 49.0 67 42.0 68 29.5 69 25.5 70 29.5 71 27.0 72 20.5 73 17.0 74 13.0 75 11.5 76 7.5 77 4.0 78 2.5 79 1.0 80 2.0 81 1.0 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 0.04 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 0.895 60-64 2.155 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 99.625 #Duplication Level Percentage of deduplicated Percentage of total 1 99.64868255959848 99.275 2 0.32622333751568383 0.65 3 0.02509410288582183 0.075 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 0.0125 0.0 0.0 0.0 0.0 74-75 0.05 0.0 0.0 0.0 0.0 76-77 0.0625 0.0 0.0 0.0 0.0 78-79 0.075 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 0.125 0.0 0.0 0.0 0.0 86-87 0.1375 0.0 0.0 0.0 0.0 88-89 0.15 0.0 0.0 0.0 0.0 90-91 0.15 0.0 0.0 0.0 0.0 92-93 0.15 0.0 0.0 0.0 0.0 94-95 0.2 0.0 0.0 0.0 0.0 96-97 0.2375 0.0 0.0 0.0 0.0 98-99 0.25 0.0 0.0 0.0 0.0 100-101 0.2625 0.0 0.0 0.0 0.0 102-103 0.275 0.0 0.0 0.0 0.0 104-105 0.3125 0.0 0.0 0.0 0.0 106-107 0.4625 0.0 0.0 0.0 0.0 108-109 0.5375000000000001 0.0 0.0 0.0 0.0 110-111 0.5874999999999999 0.0 0.0 0.0 0.0 112-113 0.65 0.0 0.0 0.0 0.0 114-115 0.7 0.0 0.0 0.0 0.0 116-117 0.7875 0.0 0.0 0.0 0.0 118-119 0.9375 0.0 0.0 0.0 0.0 120-121 1.0875 0.0 0.0 0.0 0.0 122-123 1.2999999999999998 0.0 0.0 0.0 0.0 124-125 1.375 0.0 0.0 0.0 0.0 126-127 1.5125000000000002 0.0 0.0 0.0 0.0 128-129 1.8 0.0 0.0 0.0 0.0 130-131 2.0375 0.0 0.0 0.0 0.0 132-133 2.2375 0.0 0.0 0.0 0.0 134-135 2.4875 0.0 0.0 0.0 0.0 136-137 2.7375 0.0 0.0 0.0 0.0 138-139 3.075 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position TTTTTTT 20 0.0059980154 28.937498 65-69 >>END_MODULE SRR6958207 read2 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR6958207_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 50 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 33.0265 33.0 33.0 34.0 32.0 34.0 2 33.07925 34.0 33.0 34.0 32.0 34.0 3 33.1455 34.0 33.0 34.0 33.0 34.0 4 33.1485 34.0 33.0 34.0 33.0 34.0 5 33.1265 34.0 33.0 34.0 33.0 34.0 6 37.26275 38.0 38.0 38.0 37.0 38.0 7 37.25225 38.0 38.0 38.0 37.0 38.0 8 37.19675 38.0 38.0 38.0 37.0 38.0 9 37.27625 38.0 38.0 38.0 37.0 38.0 10-14 37.283100000000005 38.0 38.0 38.0 37.0 38.0 15-19 37.2472 38.0 38.0 38.0 37.0 38.0 20-24 37.18175 38.0 38.0 38.0 37.0 38.0 25-29 37.1685 38.0 38.0 38.0 37.0 38.0 30-34 37.150400000000005 38.0 38.0 38.0 37.0 38.0 35-39 37.13175 38.0 38.0 38.0 37.0 38.0 40-44 37.1177 38.0 38.0 38.0 36.6 38.0 45-49 37.11030000000001 38.0 38.0 38.0 36.8 38.0 50-54 37.024150000000006 38.0 38.0 38.0 36.2 38.0 55-59 37.01755000000001 38.0 38.0 38.0 36.0 38.0 60-64 36.9076 38.0 38.0 38.0 36.0 38.0 65-69 36.950300000000006 38.0 38.0 38.0 36.0 38.0 70-74 36.8896 38.0 38.0 38.0 35.8 38.0 75-79 36.892700000000005 38.0 38.0 38.0 36.0 38.0 80-84 36.81224999999999 38.0 38.0 38.0 35.4 38.0 85-89 36.709250000000004 38.0 38.0 38.0 35.0 38.0 90-94 36.5884 38.0 38.0 38.0 35.0 38.0 95-99 36.4735 38.0 38.0 38.0 34.2 38.0 100-104 36.32655 38.0 38.0 38.0 34.0 38.0 105-109 36.257600000000004 38.0 38.0 38.0 34.0 38.0 110-114 35.98795 38.0 38.0 38.0 33.2 38.0 115-119 35.82305 38.0 37.4 38.0 32.6 38.0 120-124 35.881099999999996 38.0 37.8 38.0 33.0 38.0 125-129 35.803349999999995 38.0 37.6 38.0 33.0 38.0 130-134 35.5683 38.0 36.4 38.0 31.8 38.0 135-139 35.19645 38.0 36.0 38.0 30.2 38.0 140-144 34.948150000000005 38.0 36.0 38.0 30.6 38.0 145-149 34.30754999999999 38.0 35.2 38.0 27.4 38.0 150-151 30.149250000000002 35.5 27.5 38.0 12.5 38.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 2 6.0 3 6.0 4 1.0 5 0.0 6 1.0 7 0.0 8 1.0 9 0.0 10 2.0 11 0.0 12 3.0 13 2.0 14 2.0 15 2.0 16 4.0 17 4.0 18 3.0 19 3.0 20 6.0 21 5.0 22 7.0 23 6.0 24 12.0 25 10.0 26 13.0 27 13.0 28 19.0 29 27.0 30 41.0 31 55.0 32 73.0 33 97.0 34 125.0 35 194.0 36 525.0 37 2732.0 >>END_MODULE >>Per base sequence content warn #Base G A T C 1 36.975 17.7 12.025 33.300000000000004 2 28.832208052013 23.055763940985248 27.031757939484873 21.080270067516878 3 23.1615807903952 25.812906453226613 27.788894447223612 23.23661830915458 4 26.556639159789945 30.257564391097773 20.630157539384847 22.55563890972743 5 29.25 30.65 19.85 20.25 6 24.236354531797698 33.700550826239365 20.40560841261893 21.657486229344016 7 21.392785571142284 19.31362725450902 34.66933867735471 24.62424849699399 8 24.161241862794192 23.209814722083124 23.83575363044567 28.793189784677015 9 23.38507761642464 23.360040060090135 27.891837756634953 25.363044566850274 10-14 25.7337473705299 25.969147550836425 22.46318741861164 25.83391766002204 15-19 25.57743373916529 25.432135878551033 23.838869682849843 25.15156069943384 20-24 25.953204068340096 25.191642867879153 23.873941580239492 24.98121148354126 25-29 26.064735945485516 25.57871530213448 23.118548952800882 25.237999799579114 30-34 25.82164328657315 25.150300601202403 24.263527054108216 24.76452905811623 35-39 26.66700065126998 24.592956264716197 24.22724312409198 24.512799959921846 40-44 26.108078329243252 24.540491811488955 24.6656984023639 24.68573145690389 45-49 25.89384076114171 24.96745117676515 24.73710565848773 24.40160240360541 50-54 26.05559729526672 24.993739043325817 24.207362885048838 24.74330077635863 55-59 26.039058587881826 25.24787180771157 24.231347020530798 24.481722583875815 60-64 26.208485698542304 24.906076241045934 24.375093923758953 24.510344136652805 65-69 26.264396594892336 25.14271407110666 24.13119679519279 24.461692538808215 70-74 26.522435897435898 25.135216346153843 24.103565705128204 24.23878205128205 75-79 26.05778378649041 25.331731009964447 24.059886835912074 24.550598367633068 80-84 26.724094756347977 24.6707066659989 24.565533129663947 24.03966544798918 85-89 25.87881822734101 24.68202303455183 24.631947921882823 24.807210816224337 90-94 26.282565130260522 25.22044088176353 24.36372745490982 24.133266533066134 95-99 26.415756239350507 25.017540342788415 24.48130700611406 24.085396411747016 100-104 25.883414365194728 24.565184702521176 25.25186707433211 24.29953385795198 105-109 26.35297654840649 24.67428342353177 24.478853477650834 24.493886550410902 110-114 26.398356054530876 24.84963913392141 24.724338412189255 24.02766639935846 115-119 26.726771850738796 25.609817180065114 24.052091159529176 23.611319809666917 120-124 26.24749498997996 25.37074148296593 24.819639278557116 23.562124248496993 125-129 26.104377441650804 25.4382450165281 24.36141440448763 24.095963137333467 130-134 26.741798146756825 25.384422739794644 24.00701227147508 23.86676684197345 135-139 27.138421474358974 25.510817307692307 24.343950320512818 23.006810897435898 140-144 26.026642628205128 25.565905448717945 24.534254807692307 23.873197115384613 145-149 26.786877034810917 25.018782870022537 24.573002754820937 23.621337340345605 150-151 26.827741612418627 26.627441161742617 23.760640961442164 22.784176264396592 >>END_MODULE >>Per sequence GC content fail #GC Content Count 0 1.0 1 1.0 2 2.0 3 1.5 4 0.5 5 0.5 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 0.5 17 0.5 18 0.0 19 0.0 20 0.0 21 0.0 22 0.0 23 0.0 24 0.0 25 0.5 26 1.5 27 2.0 28 2.0 29 1.5 30 3.5 31 5.5 32 10.5 33 17.0 34 18.0 35 21.5 36 32.0 37 44.0 38 61.0 39 85.0 40 107.5 41 135.5 42 157.0 43 168.5 44 187.5 45 199.0 46 192.0 47 187.0 48 191.0 49 173.5 50 155.0 51 143.5 52 129.0 53 122.5 54 103.5 55 99.0 56 103.5 57 89.5 58 83.0 59 88.5 60 92.0 61 86.5 62 84.0 63 77.0 64 66.5 65 60.5 66 61.0 67 62.0 68 58.0 69 55.0 70 43.5 71 39.0 72 27.5 73 12.5 74 12.5 75 12.0 76 7.5 77 4.0 78 3.0 79 2.0 80 2.0 81 2.0 82 1.0 83 0.5 84 0.5 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 0.025 3 0.05 4 0.025 5 0.0 6 0.15 7 0.2 8 0.15 9 0.15 10-14 0.16999999999999998 15-19 0.20500000000000002 20-24 0.20500000000000002 25-29 0.21 30-34 0.2 35-39 0.19499999999999998 40-44 0.165 45-49 0.15 50-54 0.17500000000000002 55-59 0.15 60-64 0.185 65-69 0.15 70-74 0.16 75-79 0.145 80-84 0.165 85-89 0.15 90-94 0.2 95-99 0.22999999999999998 100-104 0.245 105-109 0.22 110-114 0.24 115-119 0.17500000000000002 120-124 0.2 125-129 0.16999999999999998 130-134 0.17500000000000002 135-139 0.16 140-144 0.16 145-149 0.17500000000000002 150-151 0.15 >>END_MODULE >>Sequence Length Distribution pass #Length Count 151 4000.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 99.6 #Duplication Level Percentage of deduplicated Percentage of total 1 99.64859437751004 99.25 2 0.30120481927710846 0.6 3 0.0502008032128514 0.15 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 0.0125 0.0 0.0 0.0 0.0 54-55 0.025 0.0 0.0 0.0 0.0 56-57 0.025 0.0 0.0 0.0 0.0 58-59 0.025 0.0 0.0 0.0 0.0 60-61 0.025 0.0 0.0 0.0 0.0 62-63 0.025 0.0 0.0 0.0 0.0 64-65 0.025 0.0 0.0 0.0 0.0 66-67 0.025 0.0 0.0 0.0 0.0 68-69 0.025 0.0 0.0 0.0 0.0 70-71 0.025 0.0 0.0 0.0 0.0 72-73 0.037500000000000006 0.0 0.0 0.0 0.0 74-75 0.075 0.0 0.0 0.0 0.0 76-77 0.0875 0.0 0.0 0.0 0.0 78-79 0.1 0.0 0.0 0.0 0.0 80-81 0.125 0.0 0.0 0.0 0.0 82-83 0.125 0.0 0.0 0.0 0.0 84-85 0.15 0.0 0.0 0.0 0.0 86-87 0.16249999999999998 0.0 0.0 0.0 0.0 88-89 0.175 0.0 0.0 0.0 0.0 90-91 0.175 0.0 0.0 0.0 0.0 92-93 0.175 0.0 0.0 0.0 0.0 94-95 0.225 0.0 0.0 0.0 0.0 96-97 0.2625 0.0 0.0 0.0 0.0 98-99 0.275 0.0 0.0 0.0 0.0 100-101 0.2875 0.0 0.0 0.0 0.0 102-103 0.3 0.0 0.0 0.0 0.0 104-105 0.3375 0.0 0.0 0.0 0.0 106-107 0.4875 0.0 0.0 0.0 0.0 108-109 0.5625 0.0 0.0 0.0 0.0 110-111 0.6125 0.0 0.0 0.0 0.0 112-113 0.675 0.0 0.0 0.0 0.0 114-115 0.725 0.0 0.0 0.0 0.0 116-117 0.8375 0.0 0.0 0.0 0.0 118-119 1.0 0.0 0.0 0.0 0.0 120-121 1.1625 0.0 0.0 0.0 0.0 122-123 1.375 0.0 0.0 0.0 0.0 124-125 1.45 0.0 0.0 0.0 0.0 126-127 1.5875 0.0 0.0 0.0 0.0 128-129 1.875 0.0 0.0 0.0 0.0 130-131 2.1125 0.0 0.0 0.0 0.0 132-133 2.3125 0.0 0.0 0.0 0.0 134-135 2.5625 0.0 0.0 0.0 0.0 136-137 2.8125 0.0 0.0 0.0 0.0 138-139 3.1500000000000004 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position TGTTATT 10 0.006830828 145.0 1 ACCCCTT 10 0.006830828 145.0 145 GTTATTC 10 0.006830828 145.0 2 TTTTTTT 35 0.0035366106 20.714287 115-119 >>END_MODULE Read 1179579 spots for SRR6958207.sra Written 1179579 spots for SRR6958207.sra Read 1179579 spots for SRR6958207.sra Written 1179579 spots for SRR6958207.sra Read 1179579 spots for SRR6958207.sra Written 1179579 spots for SRR6958207.sra Read 1179579 spots for SRR6958207.sra Written 1179579 spots for SRR6958207.sra Read 1179579 spots for SRR6958207.sra Written 1179579 spots for SRR6958207.sra Read 1179579 spots for SRR6958207.sra Written 1179579 spots for SRR6958207.sra Read 1179579 spots for SRR6958207.sra Written 1179579 spots for SRR6958207.sra Read 1179579 spots for SRR6958207.sra Written 1179579 spots for SRR6958207.sra Read 1179586 spots for SRR6958207.sra Written 1179586 spots for SRR6958207.sra Read 1179579 spots for SRR6958207.sra Written 1179579 spots for SRR6958207.sra Read 1179579 spots for SRR6958207.sra Written 1179579 spots for SRR6958207.sra Read 1179579 spots for SRR6958207.sra Written 1179579 spots for SRR6958207.sra Read 1179579 spots for SRR6958207.sra Written 1179579 spots for SRR6958207.sra Read 1179579 spots for SRR6958207.sra Written 1179579 spots for SRR6958207.sra Read 1179579 spots for SRR6958207.sra Written 1179579 spots for SRR6958207.sra Read 1179579 spots for SRR6958207.sra Written 1179579 spots for SRR6958207.sra Read 1179579 spots for SRR6958207.sra Written 1179579 spots for SRR6958207.sra Read 1179579 spots for SRR6958207.sra Written 1179579 spots for SRR6958207.sra Read 1179579 spots for SRR6958207.sra Written 1179579 spots for SRR6958207.sra Read 1179579 spots for SRR6958207.sra Written 1179579 spots for SRR6958207.sra SRR ids: ['SRR6958207.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_j049w4dy SRR6958207.sra spots: 23591587 blocks: [[1, 1179579], [1179580, 2359158], [2359159, 3538737], [3538738, 4718316], [4718317, 5897895], [5897896, 7077474], [7077475, 8257053], [8257054, 9436632], [9436633, 10616211], [10616212, 11795790], [11795791, 12975369], [12975370, 14154948], [14154949, 15334527], [15334528, 16514106], [16514107, 17693685], [17693686, 18873264], [18873265, 20052843], [20052844, 21232422], [21232423, 22412001], [22412002, 23591587]] SRR6958207 file size 7972714 SRR6958207 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 SRR6958207 SRR6958207_1.fastq SRR6958207_2.fastq Input file: SRR6958207_1.fastq Paired file: SRR6958207_2.fastq trimmed: SRR6958207-trimmed-pair1.fastq, SRR6958207-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 Fri Dec 6 16:10:13 2024 >> started Fri Dec 6 16:10:43 2024 >> done (29.699s) 23591587 read pairs processed; of these: 32357 ( 0.14%) short read pairs filtered out after trimming by size control 33412 ( 0.14%) empty read pairs filtered out after trimming by size control 23525818 (99.72%) read pairs available; of these: 8656114 (36.79%) trimmed read pairs available after processing 14869704 (63.21%) untrimmed read pairs available after processing Length distribution of reads after trimming: length count percentage 18 2 0.00% 19 2 0.00% 20 2 0.00% 21 3 0.00% 22 3 0.00% 23 3 0.00% 24 6 0.00% 25 4 0.00% 26 9 0.00% 27 3 0.00% 28 3 0.00% 29 2 0.00% 30 6 0.00% 31 6 0.00% 32 6 0.00% 33 5 0.00% 34 4 0.00% 35 4 0.00% 36 5 0.00% 37 4 0.00% 38 5 0.00% 39 7 0.00% 40 9 0.00% 41 5 0.00% 42 13 0.00% 43 12 0.00% 44 9 0.00% 45 9 0.00% 46 17 0.00% 47 20 0.00% 48 10 0.00% 49 24 0.00% 50 27 0.00% 51 23 0.00% 52 26 0.00% 53 37 0.00% 54 37 0.00% 55 41 0.00% 56 35 0.00% 57 57 0.00% 58 57 0.00% 59 45 0.00% 60 78 0.00% 61 84 0.00% 62 79 0.00% 63 90 0.00% 64 108 0.00% 65 117 0.00% 66 137 0.00% 67 147 0.00% 68 162 0.00% 69 173 0.00% 70 226 0.00% 71 223 0.00% 72 269 0.00% 73 344 0.00% 74 338 0.00% 75 423 0.00% 76 471 0.00% 77 542 0.00% 78 607 0.00% 79 663 0.00% 80 725 0.00% 81 916 0.00% 82 1038 0.00% 83 1171 0.00% 84 2081 0.01% 85 2503 0.01% 86 2573 0.01% 87 2739 0.01% 88 2949 0.01% 89 2997 0.01% 90 3136 0.01% 91 3454 0.01% 92 3753 0.02% 93 3997 0.02% 94 4167 0.02% 95 4603 0.02% 96 4801 0.02% 97 5102 0.02% 98 5449 0.02% 99 6004 0.03% 100 6216 0.03% 101 6889 0.03% 102 7441 0.03% 103 7855 0.03% 104 8597 0.04% 105 9158 0.04% 106 9592 0.04% 107 10284 0.04% 108 10906 0.05% 109 11807 0.05% 110 12402 0.05% 111 13068 0.06% 112 13992 0.06% 113 14949 0.06% 114 15860 0.07% 115 16895 0.07% 116 17894 0.08% 117 18866 0.08% 118 19864 0.08% 119 20738 0.09% 120 21614 0.09% 121 22654 0.10% 122 24021 0.10% 123 25449 0.11% 124 26569 0.11% 125 28440 0.12% 126 29929 0.13% 127 31117 0.13% 128 32411 0.14% 129 34141 0.15% 130 35637 0.15% 131 37324 0.16% 132 40103 0.17% 133 42304 0.18% 134 45169 0.19% 135 48135 0.20% 136 51117 0.22% 137 53944 0.23% 138 57562 0.24% 139 61683 0.26% 140 66507 0.28% 141 72306 0.31% 142 80357 0.34% 143 90171 0.38% 144 103505 0.44% 145 125077 0.53% 146 157586 0.67% 147 231135 0.98% 148 319401 1.36% 149 706520 3.00% 150 5630907 23.94% 151 14869704 63.21% 23525818 reads passed initial QC criterion=sequence-density sequence-density=0.28 sequence-density-rank=1 fanout-score=2.91 fanout-score-rank=27 prefix-density=0.33 prefix-fanout=2.5 sequence=AGCACCTGCGTGGCGTCGGTGCACCCGAACATGGGCAGCTTCCACATTGTCCAGTACCT criterion=fanout-score sequence-density=0.03 sequence-density-rank=42 fanout-score=190.29 fanout-score-rank=1 prefix-density=0.47 prefix-fanout=13.7 sequence=GGCGGCGGCGAACCGCCCCCGTCGCCGCGATCCGAACACTTCACCGGACCATTCAATCGGTAGGAGCGACGGGCGGTGTGTACAAAGGGCAGGGACGTAGTCAACGCGAGCTGATGACTCGCGCTTACTAGGCATTCCTCGTTGAAGACCAACAATTGCAATGATCTATCCCCATCACGATGAAATTTCCCAAGATTACCCGGGCCTGTCGGCCAAGGCTATATACTCGTTGAATACATCAGTGTAGCGCGCGTGCGGCCCAGAACATCTAAGGGCATCACAGACCTGTTATTGCCTCAAACTTCCGTCGCCTAAACGGCGATAGTCCCTCTAAGAAGCTAGCTGCGGAGGGATGGCTCCGCATAGCTAGTTAGCAGGCTGAGGTCTCGTTCGTTAACGGAATTAACCAGACAAATCGCTCCACCAACTAAGAACGGCCATGCACCACCACCCATAGAATCAAGAAAGAGCTCTCAGTCTGTCAATCCTTGCTATGTCTGGACCTGGTAAG criterion=sequence-density sequence-density=0.36 sequence-density-rank=1 fanout-score=4.16 fanout-score-rank=22 prefix-density=0.42 prefix-fanout=3.6 sequence=GAGTTCAGCAAGGTCGGCTT criterion=fanout-score sequence-density=0.10 sequence-density-rank=22 fanout-score=162.23 fanout-score-rank=1 prefix-density=0.75 prefix-fanout=21.8 sequence=CGCCGCCGCCGC SRR6958207 testing PE reads STAR mapping to Ensembl genome Started job on | Dec 06 16:11:37 Started mapping on | Dec 06 16:11:38 Finished on | Dec 06 16:13:02 Mapping speed, Million of reads per hour | 1008.25 Number of input reads | 23525818 Average input read length | 298 UNIQUE READS: Uniquely mapped reads number | 22719418 Uniquely mapped reads % | 96.57% Average mapped length | 298.15 Number of splices: Total | 25074572 Number of splices: Annotated (sjdb) | 23607340 Number of splices: GT/AG | 24755171 Number of splices: GC/AG | 283132 Number of splices: AT/AC | 13142 Number of splices: Non-canonical | 23127 Mismatch rate per base, % | 0.07% Deletion rate per base | 0.00% Deletion average length | 1.39 Insertion rate per base | 0.00% Insertion average length | 1.10 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 212645 % of reads mapped to multiple loci | 0.90% Number of reads mapped to too many loci | 35406 % of reads mapped to too many loci | 0.15% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 1.32% % of reads unmapped: other | 1.05% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 605795 605795 605795 N_multimapping 212645 212645 212645 N_noFeature 852669 22100625 1052853 N_ambiguous 501579 3310 84314 UnstrandedReadsAssigned:21365170 PositiveStrandReadsAssigned:615483 NegativeStrandReadsAssigned:21582251 Dataset is classified negative stranded MeadianReadLen=151 20thPercentileLength=150 echo kmer=145 SRR6958207 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: SRR6958207-trimmed-pair1.fastq SRR6958207-trimmed-pair2.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 23,525,818 reads, 21,649,805 reads pseudoaligned [quant] estimated average fragment length: 271.271 [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,181 rounds 52973 SRR6958207.ke.tsv 35125 SRR6958207.se.tsv 88098 total ==> SRR6958207.ke.tsv <== target_id length eff_length est_counts tpm PNS24245 936 666.294 73.3967 7.35833 PNS24247 1044 773.729 74.3438 6.41836 PNS24249 1928 1657.73 115.329 4.64722 PNS24246 1044 773.729 74.3438 6.41836 PNS24248 1044 773.729 74.3438 6.41836 PNS24244 1471 1200.73 92.2432 5.13166 PNS24243 293 79.7487 1 0.837616 KQK14069 1603 1332.73 2823.1 141.499 KQK14071 474 219.553 40.4705 12.3131 ==> SRR6958207.se.tsv <== BRADI_1g14170v3 3148 BRADI_1g53295v3 385 BRADI_1g59795v3 209 BRADI_1g07683v3 0 BRADI_1g00485v3 17 BRADI_1g20270v3 1612 BRADI_1g74790v3 716 BRADI_1g09890v3 5 BRADI_1g77505v3 302 BRADI_1g48960v3 1 SRR6958207 completed mapping pipeline successfully