Starting /dee2/code/volunteer_pipeline.sh SRR7168999 current disk space = 3059038167040 free memory = 1417563884 SRR7168999 SRAfilesize 3b253de6ec380af8041939a53e15df93 SRR7168999.sra SRR7168999.sra file validated SRR7168999 is paired end SRR7168999 is conventional basespace SRR7168999 read1 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR7168999_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 32.89875 34.0 33.0 34.0 32.0 34.0 2 33.05775 34.0 33.0 34.0 32.0 34.0 3 33.0885 34.0 33.0 34.0 32.0 34.0 4 32.958 34.0 33.0 34.0 32.0 34.0 5 32.77725 34.0 33.0 34.0 32.0 34.0 6 36.6375 38.0 37.0 38.0 34.0 38.0 7 37.0745 38.0 38.0 38.0 36.0 38.0 8 37.22475 38.0 38.0 38.0 36.0 38.0 9 37.28 38.0 38.0 38.0 37.0 38.0 10-14 37.31745 38.0 38.0 38.0 37.0 38.0 15-19 37.21419999999999 38.0 38.0 38.0 36.4 38.0 20-24 37.162850000000006 38.0 38.0 38.0 36.0 38.0 25-29 36.9528 38.0 38.0 38.0 35.6 38.0 30-34 36.9411 38.0 38.0 38.0 35.6 38.0 35-39 36.829499999999996 38.0 38.0 38.0 34.8 38.0 40-44 36.517399999999995 38.0 38.0 38.0 34.2 38.0 45-49 36.69205 38.0 38.0 38.0 34.4 38.0 50-54 36.6297 38.0 38.0 38.0 34.0 38.0 55-59 36.317099999999996 38.0 37.8 38.0 33.6 38.0 60-64 36.46295 38.0 37.8 38.0 34.0 38.0 65-69 36.444500000000005 38.0 37.8 38.0 33.8 38.0 70-74 36.36725 38.0 37.2 38.0 33.8 38.0 75-79 36.075 38.0 37.0 38.0 32.6 38.0 80-84 36.0284 38.0 37.0 38.0 32.6 38.0 85-89 35.59185 38.0 36.6 38.0 30.0 38.0 90-94 35.3291 38.0 36.0 38.0 29.0 38.0 95-99 35.50965 38.0 36.0 38.0 29.4 38.0 100-104 34.8844 38.0 35.4 38.0 26.6 38.0 105-109 35.293 38.0 36.0 38.0 28.8 38.0 110-114 34.819 38.0 35.2 38.0 26.2 38.0 115-119 34.4795 38.0 34.6 38.0 25.0 38.0 120-124 34.42659999999999 38.0 34.6 38.0 25.0 38.0 125-129 33.464749999999995 37.8 33.8 38.0 18.2 38.0 130-134 33.254 38.0 33.6 38.0 18.6 38.0 135-139 32.74345 37.2 32.0 38.0 17.2 38.0 140-144 32.694050000000004 37.8 32.2 38.0 14.6 38.0 145-149 30.99555 36.2 31.0 38.0 10.8 38.0 150-151 26.326500000000003 33.5 16.5 37.0 2.0 38.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 8 1.0 9 0.0 10 0.0 11 0.0 12 0.0 13 0.0 14 0.0 15 0.0 16 3.0 17 3.0 18 5.0 19 2.0 20 6.0 21 14.0 22 13.0 23 12.0 24 14.0 25 26.0 26 32.0 27 45.0 28 58.0 29 65.0 30 83.0 31 113.0 32 145.0 33 187.0 34 304.0 35 430.0 36 901.0 37 1538.0 >>END_MODULE >>Per base sequence content warn #Base G A T C 1 40.0 11.575000000000001 9.225 39.2 2 21.95 16.075 34.8 27.175 3 19.025 21.325 26.424999999999997 33.225 4 22.025 29.275000000000002 22.325 26.375 5 22.241813602015114 33.75314861460957 23.425692695214106 20.579345088161208 6 19.650000000000002 35.375 24.875 20.1 7 14.025000000000002 27.175 40.275 18.525 8 16.85 26.025 30.7 26.424999999999997 9 17.575 26.650000000000002 33.300000000000004 22.475 10-14 19.475 30.445 26.634999999999998 23.445 15-19 19.64 29.285 27.395000000000003 23.68 20-24 19.6 29.625 26.889999999999997 23.885 25-29 19.16 29.720000000000002 27.450000000000003 23.669999999999998 30-34 19.28 28.88 27.779999999999998 24.060000000000002 35-39 19.665 28.985 27.51 23.84 40-44 19.869999999999997 29.015 27.450000000000003 23.665 45-49 19.585 29.48 27.12 23.815 50-54 19.645000000000003 29.15 27.084999999999997 24.12 55-59 20.089040068030613 29.198139162623182 26.181781801810818 24.53103896753539 60-64 20.105 29.23 27.250000000000004 23.415 65-69 19.825 28.415000000000003 27.169999999999998 24.59 70-74 20.59 28.285 27.33 23.794999999999998 75-79 20.007004202521514 28.86231739043426 26.77106263758255 24.359615769461676 80-84 20.23511755877939 28.709354677338673 27.298649324662332 23.75687843921961 85-89 20.18532431755572 27.738542449286253 27.67843726521412 24.397695967943903 90-94 19.778281683043588 28.47568657092467 27.362055933484502 24.38397581254724 95-99 20.150000000000002 28.28 27.029999999999998 24.54 100-104 20.119999999999997 28.605000000000004 27.395000000000003 23.880000000000003 105-109 20.298791798265402 28.214769138216273 27.071740111294933 24.414698952223393 110-114 19.38 28.22 27.985 24.415 115-119 20.375 28.285 27.565 23.775 120-124 20.244999999999997 28.325 27.735 23.695 125-129 20.419999999999998 28.310000000000002 26.845000000000002 24.425 130-134 20.350087521880468 28.33208302075519 27.35183795948987 23.96599149787447 135-139 20.76 28.645 26.945000000000004 23.65 140-144 20.294999999999998 28.15 27.42 24.135 145-149 20.902217741935484 28.281250000000004 27.34375 23.472782258064516 150-151 20.45795795795796 28.39089089089089 27.464964964964967 23.686186186186188 >>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 0.5 17 1.0 18 0.5 19 0.5 20 0.5 21 0.5 22 1.5 23 2.0 24 2.5 25 2.0 26 3.0 27 7.0 28 11.0 29 13.0 30 17.0 31 26.0 32 39.0 33 51.5 34 57.0 35 70.0 36 88.5 37 100.5 38 124.5 39 158.5 40 189.5 41 212.5 42 252.5 43 264.5 44 253.5 45 273.0 46 267.5 47 244.5 48 225.0 49 211.0 50 191.5 51 143.5 52 108.5 53 86.0 54 66.5 55 54.5 56 42.5 57 33.5 58 26.5 59 18.5 60 12.5 61 13.5 62 10.5 63 7.0 64 4.0 65 2.5 66 2.0 67 1.0 68 1.5 69 2.0 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 0.0 2 0.0 3 0.0 4 0.0 5 0.75 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 0.045 60-64 0.0 65-69 0.0 70-74 0.0 75-79 0.06 80-84 0.05 85-89 0.17500000000000002 90-94 0.775 95-99 0.0 100-104 0.0 105-109 0.265 110-114 0.0 115-119 0.0 120-124 0.0 125-129 0.0 130-134 0.025 135-139 0.0 140-144 0.0 145-149 0.8 150-151 0.1 >>END_MODULE >>Sequence Length Distribution pass #Length Count 151 4000.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 99.52499999999999 #Duplication Level Percentage of deduplicated Percentage of total 1 99.57297161517207 99.1 2 0.37678975131876413 0.75 3 0.050238633509168545 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 0.0 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 0.0125 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 0.025 0.0 0.0 0.0 0.0 74-75 0.025 0.0 0.0 0.0 0.0 76-77 0.025 0.0 0.0 0.0 0.0 78-79 0.025 0.0 0.0 0.0 0.0 80-81 0.025 0.0 0.0 0.0 0.0 82-83 0.025 0.0 0.0 0.0 0.0 84-85 0.025 0.0 0.0 0.0 0.0 86-87 0.025 0.0 0.0 0.0 0.0 88-89 0.025 0.0 0.0 0.0 0.0 90-91 0.037500000000000006 0.0 0.0 0.0 0.0 92-93 0.05 0.0 0.0 0.0 0.0 94-95 0.0625 0.0 0.0 0.0 0.0 96-97 0.075 0.0 0.0 0.0 0.0 98-99 0.1125 0.0 0.0 0.0 0.0 100-101 0.125 0.0 0.0 0.0 0.0 102-103 0.1375 0.0 0.0 0.0 0.0 104-105 0.2 0.0 0.0 0.0 0.0 106-107 0.2 0.0 0.0 0.0 0.0 108-109 0.2 0.0 0.0 0.0 0.0 110-111 0.2 0.0 0.0 0.0 0.0 112-113 0.225 0.0 0.0 0.0 0.0 114-115 0.3 0.0 0.0 0.0 0.0 116-117 0.3375 0.0 0.0 0.0 0.0 118-119 0.45 0.0 0.0 0.0 0.0 120-121 0.5375000000000001 0.0 0.0 0.0 0.0 122-123 0.6 0.0 0.0 0.0 0.0 124-125 0.675 0.0 0.0 0.0 0.0 126-127 0.825 0.0 0.0 0.0 0.0 128-129 0.9624999999999999 0.0 0.0 0.0 0.0 130-131 1.0625 0.0 0.0 0.0 0.0 132-133 1.1124999999999998 0.0 0.0 0.0 0.0 134-135 1.2374999999999998 0.0 0.0 0.0 0.0 136-137 1.35 0.0 0.0 0.0 0.0 138-139 1.4875 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position GTGCTGC 10 0.006830828 145.0 1 >>END_MODULE SRR7168999 read2 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR7168999_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 32.389 33.0 33.0 34.0 32.0 34.0 2 32.506 33.0 33.0 34.0 32.0 34.0 3 32.4765 34.0 33.0 34.0 32.0 34.0 4 32.218 34.0 33.0 34.0 32.0 34.0 5 32.413 34.0 33.0 34.0 32.0 34.0 6 36.394 38.0 38.0 38.0 34.0 38.0 7 36.38375 38.0 38.0 38.0 35.0 38.0 8 36.005 38.0 38.0 38.0 34.0 38.0 9 36.147 38.0 38.0 38.0 34.0 38.0 10-14 36.22595 38.0 38.0 38.0 34.0 38.0 15-19 36.073449999999994 38.0 38.0 38.0 33.6 38.0 20-24 36.414500000000004 38.0 38.0 38.0 35.0 38.0 25-29 36.32084999999999 38.0 38.0 38.0 34.6 38.0 30-34 36.20445 38.0 38.0 38.0 34.6 38.0 35-39 36.21315 38.0 38.0 38.0 34.4 38.0 40-44 36.3538 38.0 38.0 38.0 34.8 38.0 45-49 36.228449999999995 38.0 38.0 38.0 34.4 38.0 50-54 35.9705 38.0 38.0 38.0 33.4 38.0 55-59 35.341649999999994 38.0 38.0 38.0 29.6 38.0 60-64 35.3589 38.0 38.0 38.0 29.6 38.0 65-69 35.39725 38.0 38.0 38.0 30.0 38.0 70-74 35.719800000000006 38.0 38.0 38.0 31.8 38.0 75-79 35.556400000000004 38.0 37.8 38.0 29.8 38.0 80-84 35.5902 38.0 38.0 38.0 31.4 38.0 85-89 35.5259 38.0 37.2 38.0 30.6 38.0 90-94 35.680600000000005 38.0 38.0 38.0 31.8 38.0 95-99 35.34615 38.0 37.2 38.0 29.6 38.0 100-104 35.184000000000005 38.0 37.0 38.0 28.8 38.0 105-109 34.755250000000004 38.0 36.6 38.0 26.6 38.0 110-114 34.59335 38.0 36.8 38.0 25.2 38.0 115-119 34.51875 38.0 36.0 38.0 25.0 38.0 120-124 34.56375 38.0 36.0 38.0 25.6 38.0 125-129 34.2288 38.0 35.0 38.0 22.8 38.0 130-134 34.1477 38.0 35.0 38.0 23.0 38.0 135-139 33.8563 38.0 34.8 38.0 21.0 38.0 140-144 32.967600000000004 38.0 33.8 38.0 15.4 38.0 145-149 31.622400000000006 38.0 31.8 38.0 8.6 38.0 150-151 27.586624999999998 34.5 16.5 38.0 2.0 38.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 2 43.0 3 8.0 4 3.0 5 2.0 6 4.0 7 2.0 8 5.0 9 2.0 10 3.0 11 1.0 12 4.0 13 5.0 14 2.0 15 1.0 16 6.0 17 7.0 18 5.0 19 13.0 20 4.0 21 10.0 22 21.0 23 26.0 24 25.0 25 29.0 26 34.0 27 38.0 28 55.0 29 55.0 30 65.0 31 74.0 32 83.0 33 123.0 34 181.0 35 244.0 36 567.0 37 2250.0 >>END_MODULE >>Per base sequence content warn #Base G A T C 1 37.594553706505295 20.499243570347957 14.42259203227433 27.483610690872418 2 28.31703034863306 25.482819162277405 29.79683972911964 16.4033107599699 3 20.242608036391204 27.268132423553197 31.0841546626232 21.4051048774324 4 23.403714067667263 33.27397608750954 23.454591706944797 19.867718137878402 5 23.659147869674186 35.68922305764411 22.957393483709275 17.694235588972433 6 21.067134268537075 37.85070140280561 22.695390781563127 18.386773547094187 7 20.246789221858474 21.581465625786954 37.87459078317804 20.29715436917653 8 21.74465920651068 25.38148524923703 27.594099694811803 25.279755849440487 9 21.7544744139148 25.308797580035293 29.241240231913284 23.695487774136627 10-14 23.68713391234094 28.564936376489598 25.97960008079176 21.7683296303777 15-19 23.861621840652383 27.594590487767817 27.331205997062252 21.21258167451755 20-24 23.67546333601934 27.719580983078163 27.628928283642225 20.976027397260275 25-29 23.382485705687632 28.498344869094193 27.520312970207645 20.598856455010534 30-34 22.926313670223475 28.38232333400443 27.43607811556271 21.255284880209384 35-39 22.591060437897287 28.796286953889616 27.439208959741702 21.173443648471395 40-44 23.432708260017094 27.499874315016843 27.519983912322154 21.54743351264391 45-49 23.60978550258703 27.733962927613405 27.37730446576581 21.278947104033758 50-54 23.898040400987355 27.525061709737546 27.666112538411163 20.910785350863936 55-59 23.658275034468673 27.151100444262884 28.56559260583159 20.62503191543686 60-64 23.58418171586433 27.67176548831023 28.121962449480737 20.622090346344706 65-69 23.8809792072109 27.619584144217967 28.218785209464304 20.28065143910683 70-74 23.784275109831842 27.55138110387315 27.803868100792812 20.860475685502198 75-79 23.830002529724258 27.447508221603844 28.454338477105996 20.2681507715659 80-84 23.868709415584416 27.4604301948052 28.079342532467532 20.591517857142858 85-89 23.88134489151676 27.73462945332465 28.135491306308563 20.24853434885003 90-94 23.325982357658383 27.56114675220529 28.643744987971132 20.469125902165196 95-99 24.292108836694666 27.68696876728864 27.77246894331841 20.248453452698286 100-104 24.216739821401546 27.39014176883104 27.899702335906362 20.493416073861056 105-109 24.637166345275553 27.169390033492334 27.78849081498021 20.404952806251902 110-114 24.070950263252058 27.80248428155191 27.756479067627666 20.37008638756837 115-119 23.851203501094094 27.55076077553305 27.962953539260088 20.63508218411277 120-124 24.339234665730476 26.932143036260598 28.160890716685895 20.567731581323034 125-129 24.622257918779177 27.669293710155113 27.262687616083532 20.445760754982178 130-134 23.921450454522624 28.024709959318972 27.964441765858066 20.089397820300338 135-139 23.98655428456753 27.332931968693558 28.62733293196869 20.05318081477022 140-144 24.322830292979546 27.52902155887231 27.94110256796824 20.20704558017991 145-149 24.434480326464808 27.684014308025596 27.53791122978488 20.34359413572472 150-151 23.992972769481742 27.795206424896474 28.32224871376584 19.889572091855943 >>END_MODULE >>Per sequence GC content warn #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 1.0 9 1.0 10 1.0 11 2.0 12 3.0 13 4.0 14 2.5 15 2.0 16 2.5 17 3.5 18 3.0 19 1.0 20 1.0 21 1.0 22 3.0 23 3.0 24 2.5 25 4.0 26 4.5 27 5.5 28 6.0 29 10.5 30 19.5 31 20.0 32 25.5 33 35.0 34 44.0 35 62.5 36 71.5 37 90.0 38 128.5 39 153.5 40 183.0 41 230.0 42 260.0 43 273.5 44 289.0 45 278.5 46 264.5 47 248.0 48 226.5 49 208.0 50 176.5 51 145.5 52 120.0 53 97.0 54 69.0 55 45.5 56 41.0 57 37.0 58 25.5 59 17.0 60 8.5 61 8.0 62 9.0 63 8.0 64 4.0 65 3.0 66 3.0 67 1.5 68 0.5 69 0.5 70 0.5 71 0.0 72 0.5 73 0.5 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 0.8500000000000001 2 0.325 3 1.075 4 1.725 5 0.25 6 0.2 7 0.7250000000000001 8 1.7000000000000002 9 0.8250000000000001 10-14 0.98 15-19 1.2850000000000001 20-24 0.72 25-29 0.31 30-34 0.66 35-39 0.89 40-44 0.545 45-49 0.46499999999999997 50-54 0.745 55-59 2.085 60-64 2.265 65-69 2.37 70-74 0.985 75-79 1.175 80-84 1.44 85-89 0.215 90-94 0.24 95-99 0.585 100-104 0.895 105-109 1.47 110-114 2.185 115-119 1.745 120-124 0.305 125-129 0.395 130-134 0.445 135-139 0.33999999999999997 140-144 0.505 145-149 0.755 150-151 0.3875 >>END_MODULE >>Sequence Length Distribution pass #Length Count 151 4000.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 99.575 #Duplication Level Percentage of deduplicated Percentage of total 1 99.57318604067285 99.15 2 0.42681395932714034 0.8500000000000001 3 0.0 0.0 4 0.0 0.0 5 0.0 0.0 6 0.0 0.0 7 0.0 0.0 8 0.0 0.0 9 0.0 0.0 >10 0.0 0.0 >50 0.0 0.0 >100 0.0 0.0 >500 0.0 0.0 >1k 0.0 0.0 >5k 0.0 0.0 >10k+ 0.0 0.0 >>END_MODULE >>Overrepresented sequences pass >>END_MODULE >>Adapter Content pass #Position Illumina Universal Adapter Illumina Small RNA 3' Adapter Illumina Small RNA 5' Adapter Nextera Transposase Sequence SOLID Small RNA Adapter 1 0.0 0.0 0.0 0.0 0.0 2 0.0 0.0 0.0 0.0 0.0 3 0.0 0.0 0.0 0.0 0.0 4 0.0 0.0 0.0 0.0 0.0 5 0.0 0.0 0.0 0.0 0.0 6 0.0 0.0 0.0 0.0 0.0 7 0.0 0.0 0.0 0.0 0.0 8 0.0 0.0 0.0 0.0 0.0 9 0.0 0.0 0.0 0.0 0.0 10-11 0.0 0.0 0.0 0.0 0.0 12-13 0.0 0.0 0.0 0.0 0.0 14-15 0.0 0.0 0.0 0.0 0.0 16-17 0.0 0.0 0.0 0.0 0.0 18-19 0.0 0.0 0.0 0.0 0.0 20-21 0.0 0.0 0.0 0.0 0.0 22-23 0.0 0.0 0.0 0.0 0.0 24-25 0.0 0.0 0.0 0.0 0.0 26-27 0.0 0.0 0.0 0.0 0.0 28-29 0.0 0.0 0.0 0.0 0.0 30-31 0.0 0.0 0.0 0.0 0.0 32-33 0.0 0.0 0.0 0.0 0.0 34-35 0.0 0.0 0.0 0.0 0.0 36-37 0.0 0.0 0.0 0.0 0.0 38-39 0.0 0.0 0.0 0.0 0.0 40-41 0.0 0.0 0.0 0.0 0.0 42-43 0.0 0.0 0.0 0.0 0.0 44-45 0.0 0.0 0.0 0.0 0.0 46-47 0.0 0.0 0.0 0.0 0.0 48-49 0.0 0.0 0.0 0.0 0.0 50-51 0.0 0.0 0.0 0.0 0.0 52-53 0.0 0.0 0.0 0.0 0.0 54-55 0.0 0.0 0.0 0.0 0.0 56-57 0.0 0.0 0.0 0.0 0.0 58-59 0.0 0.0 0.0 0.0 0.0 60-61 0.0 0.0 0.0 0.0 0.0 62-63 0.0 0.0 0.0 0.0 0.0 64-65 0.0 0.0 0.0 0.0 0.0 66-67 0.0125 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 0.025 0.0 0.0 0.0 0.0 74-75 0.025 0.0 0.0 0.0 0.0 76-77 0.025 0.0 0.0 0.0 0.0 78-79 0.025 0.0 0.0 0.0 0.0 80-81 0.025 0.0 0.0 0.0 0.0 82-83 0.025 0.0 0.0 0.0 0.0 84-85 0.025 0.0 0.0 0.0 0.0 86-87 0.025 0.0 0.0 0.0 0.0 88-89 0.025 0.0 0.0 0.0 0.0 90-91 0.037500000000000006 0.0 0.0 0.0 0.0 92-93 0.05 0.0 0.0 0.0 0.0 94-95 0.0625 0.0 0.0 0.0 0.0 96-97 0.075 0.0 0.0 0.0 0.0 98-99 0.1125 0.0 0.0 0.0 0.0 100-101 0.125 0.0 0.0 0.0 0.0 102-103 0.1375 0.0 0.0 0.0 0.0 104-105 0.2 0.0 0.0 0.0 0.0 106-107 0.2 0.0 0.0 0.0 0.0 108-109 0.2 0.0 0.0 0.0 0.0 110-111 0.2 0.0 0.0 0.0 0.0 112-113 0.225 0.0 0.0 0.0 0.0 114-115 0.3 0.0 0.0 0.0 0.0 116-117 0.3375 0.0 0.0 0.0 0.0 118-119 0.45 0.0 0.0 0.0 0.0 120-121 0.5125 0.0 0.0 0.0 0.0 122-123 0.575 0.0 0.0 0.0 0.0 124-125 0.65 0.0 0.0 0.0 0.0 126-127 0.7875 0.0 0.0 0.0 0.0 128-129 0.9125000000000001 0.0 0.0 0.0 0.0 130-131 0.9875 0.0 0.0 0.0 0.0 132-133 1.0499999999999998 0.0 0.0 0.0 0.0 134-135 1.175 0.0 0.0 0.0 0.0 136-137 1.3 0.0 0.0 0.0 0.0 138-139 1.4375 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content pass >>END_MODULE Read 849655 spots for SRR7168999.sra Written 849655 spots for SRR7168999.sra Read 849655 spots for SRR7168999.sra Written 849655 spots for SRR7168999.sra Read 849655 spots for SRR7168999.sra Written 849655 spots for SRR7168999.sra Read 849655 spots for SRR7168999.sra Written 849655 spots for SRR7168999.sra Read 849655 spots for SRR7168999.sra Written 849655 spots for SRR7168999.sra Read 849655 spots for SRR7168999.sra Written 849655 spots for SRR7168999.sra Read 849655 spots for SRR7168999.sra Written 849655 spots for SRR7168999.sra Read 849655 spots for SRR7168999.sra Written 849655 spots for SRR7168999.sra Read 849655 spots for SRR7168999.sra Written 849655 spots for SRR7168999.sra Read 849655 spots for SRR7168999.sra Written 849655 spots for SRR7168999.sra Read 849656 spots for SRR7168999.sra Written 849656 spots for SRR7168999.sra Read 849655 spots for SRR7168999.sra Written 849655 spots for SRR7168999.sra Read 849655 spots for SRR7168999.sra Written 849655 spots for SRR7168999.sra Read 849655 spots for SRR7168999.sra Written 849655 spots for SRR7168999.sra Read 849655 spots for SRR7168999.sra Written 849655 spots for SRR7168999.sra Read 849655 spots for SRR7168999.sra Written 849655 spots for SRR7168999.sra Read 849655 spots for SRR7168999.sra Written 849655 spots for SRR7168999.sra Read 849655 spots for SRR7168999.sra Written 849655 spots for SRR7168999.sra Read 849655 spots for SRR7168999.sra Written 849655 spots for SRR7168999.sra Read 849655 spots for SRR7168999.sra Written 849655 spots for SRR7168999.sra SRR ids: ['SRR7168999.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_lyl0el_a SRR7168999.sra spots: 16993101 blocks: [[1, 849655], [849656, 1699310], [1699311, 2548965], [2548966, 3398620], [3398621, 4248275], [4248276, 5097930], [5097931, 5947585], [5947586, 6797240], [6797241, 7646895], [7646896, 8496550], [8496551, 9346205], [9346206, 10195860], [10195861, 11045515], [11045516, 11895170], [11895171, 12744825], [12744826, 13594480], [13594481, 14444135], [14444136, 15293790], [15293791, 16143445], [16143446, 16993101]] SRR7168999 file size 5736703 SRR7168999 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 SRR7168999 SRR7168999_1.fastq SRR7168999_2.fastq Input file: SRR7168999_1.fastq Paired file: SRR7168999_2.fastq trimmed: SRR7168999-trimmed-pair1.fastq, SRR7168999-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 Mon Feb 10 14:50:09 2025 >> started Mon Feb 10 14:50:30 2025 >> done (21.098s) 16993101 read pairs processed; of these: 24783 ( 0.15%) short read pairs filtered out after trimming by size control 32084 ( 0.19%) empty read pairs filtered out after trimming by size control 16936234 (99.67%) read pairs available; of these: 7815106 (46.14%) trimmed read pairs available after processing 9121128 (53.86%) untrimmed read pairs available after processing Length distribution of reads after trimming: length count percentage 18 2 0.00% 19 2 0.00% 20 3 0.00% 21 6 0.00% 22 4 0.00% 23 3 0.00% 24 4 0.00% 25 3 0.00% 26 6 0.00% 27 10 0.00% 28 2 0.00% 29 6 0.00% 30 8 0.00% 31 3 0.00% 32 7 0.00% 33 1 0.00% 34 7 0.00% 35 6 0.00% 36 7 0.00% 37 15 0.00% 38 13 0.00% 39 8 0.00% 40 15 0.00% 41 12 0.00% 42 16 0.00% 43 11 0.00% 44 15 0.00% 45 18 0.00% 46 24 0.00% 47 24 0.00% 48 24 0.00% 49 25 0.00% 50 34 0.00% 51 22 0.00% 52 35 0.00% 53 32 0.00% 54 35 0.00% 55 35 0.00% 56 55 0.00% 57 51 0.00% 58 62 0.00% 59 56 0.00% 60 73 0.00% 61 94 0.00% 62 96 0.00% 63 99 0.00% 64 126 0.00% 65 140 0.00% 66 153 0.00% 67 178 0.00% 68 209 0.00% 69 225 0.00% 70 246 0.00% 71 320 0.00% 72 310 0.00% 73 394 0.00% 74 416 0.00% 75 538 0.00% 76 528 0.00% 77 587 0.00% 78 657 0.00% 79 717 0.00% 80 817 0.00% 81 932 0.01% 82 1186 0.01% 83 1359 0.01% 84 2438 0.01% 85 2756 0.02% 86 2953 0.02% 87 3121 0.02% 88 3163 0.02% 89 3204 0.02% 90 3568 0.02% 91 3575 0.02% 92 3974 0.02% 93 4115 0.02% 94 4260 0.03% 95 4617 0.03% 96 4891 0.03% 97 5273 0.03% 98 5425 0.03% 99 5744 0.03% 100 5939 0.04% 101 6350 0.04% 102 6555 0.04% 103 7364 0.04% 104 7550 0.04% 105 8102 0.05% 106 8728 0.05% 107 9178 0.05% 108 9660 0.06% 109 10512 0.06% 110 10926 0.06% 111 11207 0.07% 112 11875 0.07% 113 12760 0.08% 114 13517 0.08% 115 14277 0.08% 116 14982 0.09% 117 16051 0.09% 118 16494 0.10% 119 17548 0.10% 120 18400 0.11% 121 19393 0.11% 122 20426 0.12% 123 21490 0.13% 124 23078 0.14% 125 24284 0.14% 126 26425 0.16% 127 27997 0.17% 128 29863 0.18% 129 31723 0.19% 130 34008 0.20% 131 36597 0.22% 132 39098 0.23% 133 42340 0.25% 134 45814 0.27% 135 50085 0.30% 136 54752 0.32% 137 58947 0.35% 138 65084 0.38% 139 72194 0.43% 140 80191 0.47% 141 89641 0.53% 142 102267 0.60% 143 119567 0.71% 144 142984 0.84% 145 176760 1.04% 146 226993 1.34% 147 311959 1.84% 148 475041 2.80% 149 903401 5.33% 150 4150525 24.51% 151 9121128 53.86% 16936234 reads passed initial QC criterion=sequence-density sequence-density=0.13 sequence-density-rank=1 fanout-score=1.94 fanout-score-rank=44 prefix-density=0.13 prefix-fanout=1.9 sequence=TCTGACCTGGGCTGGCAA criterion=fanout-score sequence-density=0.02 sequence-density-rank=44 fanout-score=135.26 fanout-score-rank=1 prefix-density=0.25 prefix-fanout=9.1 sequence=CTCCTTCCTCTAAATGATAAGGTTCAGTGGACTTCTCGCGACGTCGCCGGCGGCGAACCGCCCACGTCGCCGCGATCCGAACACTTCACCGGACCATTCAATCGGTAGGAGCGACGGGCGGTGTGTACAAAGGGCAGGGACGTAGTCAACGCGAGCTGATGACTCGCGCTTACTAGGAATTCCTCGTTGAAGACCAACAATTGCAATGATCTATCCCCATCACGATGAAATTTCAAAGATTACCCGGGCCTGTCGGCCAAGGCTATAGACTCGTTGAATACATCAGTGTAGCGCGCGTGCGGCCCAGAACATCTAAGGGCATCACAGACCTGTTATTGCCTCAAACTTCCTTGGCCTGGAAGGCCATAGTCCCTCTAAGAAGCTGGCCGCGGAGGGTCACCTCCGCATAGCTAGTTAGCAGGCTGAGGTCTCGTTCGTTAACGGAATTAACCAGACAAATCGCTCCACCAACTAAGAACGGCCATGCACCAC criterion=sequence-density sequence-density=0.22 sequence-density-rank=1 fanout-score=2.38 fanout-score-rank=40 prefix-density=0.23 prefix-fanout=2.2 sequence=TTGTGATTTTGATC criterion=fanout-score sequence-density=0.08 sequence-density-rank=28 fanout-score=258.87 fanout-score-rank=1 prefix-density=0.81 prefix-fanout=26.7 sequence=GAAGAAGAAGAAA SRR7168999 testing PE reads STAR mapping to Ensembl genome Started job on | Feb 10 14:51:18 Started mapping on | Feb 10 14:51:19 Finished on | Feb 10 14:53:14 Mapping speed, Million of reads per hour | 530.18 Number of input reads | 16936234 Average input read length | 297 UNIQUE READS: Uniquely mapped reads number | 15870788 Uniquely mapped reads % | 93.71% Average mapped length | 296.37 Number of splices: Total | 15319792 Number of splices: Annotated (sjdb) | 15077697 Number of splices: GT/AG | 15094333 Number of splices: GC/AG | 181142 Number of splices: AT/AC | 11696 Number of splices: Non-canonical | 32621 Mismatch rate per base, % | 0.37% Deletion rate per base | 0.03% Deletion average length | 2.59 Insertion rate per base | 0.02% Insertion average length | 2.29 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 307809 % of reads mapped to multiple loci | 1.82% Number of reads mapped to too many loci | 154099 % of reads mapped to too many loci | 0.91% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 3.38% % of reads unmapped: other | 0.18% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 781095 781095 781095 N_multimapping 307809 307809 307809 N_noFeature 327914 15701411 406562 N_ambiguous 156570 947 65188 UnstrandedReadsAssigned:15386304 PositiveStrandReadsAssigned:168430 NegativeStrandReadsAssigned:15399038 Dataset is classified negative stranded MeadianReadLen=151 20thPercentileLength=150 echo kmer=145 SRR7168999 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: SRR7168999-trimmed-pair1.fastq SRR7168999-trimmed-pair2.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 16,936,234 reads, 15,371,197 reads pseudoaligned [quant] estimated average fragment length: 267.194 [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,069 rounds 52401 SRR7168999.ke.tsv 34699 SRR7168999.se.tsv 87100 total ==> SRR7168999.ke.tsv <== target_id length eff_length est_counts tpm Potri.005G200100.1.v4.1 2018 1751.81 275 9.06708 Potri.005G024800.1.v4.1 1035 768.806 46 3.45591 Potri.004G059700.1.v4.1 961 694.857 2 0.166248 Potri.007G009000.2.v4.1 1416 1149.81 0 0 Potri.003G141000.2.v4.1 2943 2676.81 264.028 5.69709 Potri.016G087400.1.v4.1 270 64.9919 1417 1259.31 Potri.015G069301.1.v4.1 564 304.282 0 0 Potri.010G195200.1.v4.1 1773 1506.81 15 0.574983 Potri.012G127500.1.v4.1 977 710.825 7964 647.126 ==> SRR7168999.se.tsv <== Potri.001G166300.v4.1 0 Potri.001G448400.v4.1 795 Potri.001G233950.v4.1 1 Potri.001G122700.v4.1 211 Potri.001G212900.v4.1 1 Potri.001G182400.v4.1 7 Potri.001G256600.v4.1 0 Potri.001G040500.v4.1 0 Potri.001G416900.v4.1 0 Potri.001G452600.v4.1 0 SRR7168999 completed mapping pipeline successfully