Starting /dee2/code/volunteer_pipeline.sh SRR8096906 current disk space = 1507708624896 free memory = 1357386444 SRR8096906 SRAfilesize 2dce7b35db6694d10f8312e0002f47b9 SRR8096906.sra SRR8096906.sra file validated SRR8096906 is paired end SRR8096906 is conventional basespace SRR8096906 read1 length is 150 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR8096906_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 32.52325 34.0 33.0 34.0 32.0 34.0 2 33.1555 34.0 33.0 34.0 32.0 34.0 3 33.10175 34.0 33.0 34.0 32.0 34.0 4 33.29 34.0 33.0 34.0 32.0 34.0 5 33.332 34.0 33.0 34.0 33.0 34.0 6 36.94975 38.0 37.0 38.0 35.0 38.0 7 37.245 38.0 38.0 38.0 36.0 38.0 8 37.41175 38.0 38.0 38.0 37.0 38.0 9 37.40275 38.0 38.0 38.0 37.0 38.0 10-14 37.437850000000005 38.0 38.0 38.0 37.0 38.0 15-19 37.40295 38.0 38.0 38.0 37.0 38.0 20-24 37.33945 38.0 38.0 38.0 37.0 38.0 25-29 37.2705 38.0 38.0 38.0 37.0 38.0 30-34 37.322799999999994 38.0 38.0 38.0 37.0 38.0 35-39 37.25935 38.0 38.0 38.0 37.0 38.0 40-44 37.15735 38.0 38.0 38.0 36.8 38.0 45-49 37.16925 38.0 38.0 38.0 36.8 38.0 50-54 37.15345 38.0 38.0 38.0 36.6 38.0 55-59 37.02535 38.0 38.0 38.0 36.0 38.0 60-64 36.90005 38.0 38.0 38.0 35.8 38.0 65-69 36.54405 38.0 38.0 38.0 34.6 38.0 70-74 36.41665 38.0 38.0 38.0 34.4 38.0 75-79 35.94049999999999 38.0 38.0 38.0 34.0 38.0 80-84 35.9059 38.0 38.0 38.0 33.8 38.0 85-89 35.19695 38.0 37.4 38.0 29.2 38.0 90-94 35.74295000000001 38.0 37.8 38.0 33.6 38.0 95-99 35.67775 38.0 38.0 38.0 33.2 38.0 100-104 35.559000000000005 38.0 38.0 38.0 32.6 38.0 105-109 35.29165 38.0 37.8 38.0 30.6 38.0 110-114 35.10095 38.0 37.2 38.0 29.8 38.0 115-119 34.691449999999996 38.0 36.2 38.0 26.8 38.0 120-124 34.8368 38.0 37.0 38.0 29.2 38.0 125-129 34.3977 38.0 36.2 38.0 26.0 38.0 130-134 33.7795 38.0 35.4 38.0 19.6 38.0 135-139 33.590700000000005 38.0 35.4 38.0 20.6 38.0 140-144 33.150800000000004 38.0 34.6 38.0 14.0 38.0 145-149 32.0311 38.0 33.2 38.0 6.0 38.0 150 22.68475 28.0 2.0 36.0 2.0 38.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 5 2.0 6 2.0 7 3.0 8 1.0 9 1.0 10 1.0 11 1.0 12 2.0 13 1.0 14 3.0 15 2.0 16 2.0 17 14.0 18 29.0 19 43.0 20 10.0 21 9.0 22 14.0 23 19.0 24 13.0 25 8.0 26 28.0 27 34.0 28 56.0 29 48.0 30 59.0 31 49.0 32 63.0 33 103.0 34 108.0 35 217.0 36 502.0 37 2553.0 >>END_MODULE >>Per base sequence content warn #Base G A T C 1 39.90261404407996 10.738083034341363 8.380317785750897 40.97898513582778 2 22.925 18.625 35.6 22.85 3 21.2 18.8 28.775000000000002 31.225 4 26.700000000000003 25.5 19.950000000000003 27.85 5 28.299999999999997 28.9 22.875 19.925 6 23.75 31.4 23.7 21.15 7 16.425 24.5 39.35 19.725 8 20.0 25.674999999999997 29.225 25.1 9 23.425 19.425 32.25 24.9 10-14 22.985 27.134999999999998 24.19 25.69 15-19 22.900000000000002 25.185000000000002 25.590000000000003 26.325 20-24 22.855 26.19 25.3 25.655 25-29 22.715 25.61 25.575 26.1 30-34 22.445 24.695 26.135 26.724999999999998 35-39 22.955000000000002 24.67 27.105 25.27 40-44 21.88 25.205 26.68 26.235000000000003 45-49 24.310000000000002 24.8 26.224999999999998 24.665 50-54 23.175 23.805 25.275 27.744999999999997 55-59 23.395 24.115000000000002 27.250000000000004 25.240000000000002 60-64 23.785 24.610000000000003 25.945 25.66 65-69 22.15 28.060000000000002 25.06 24.73 70-74 22.97 27.83 24.435000000000002 24.765 75-79 22.99 26.235000000000003 24.855 25.919999999999998 80-84 23.830000000000002 24.67 25.82 25.679999999999996 85-89 23.025000000000002 24.959999999999997 25.15 26.865 90-94 23.935000000000002 24.595 25.505 25.965 95-99 23.275000000000002 24.85 25.779999999999998 26.095000000000002 100-104 23.815 25.369999999999997 25.39 25.424999999999997 105-109 23.35 25.16 25.66 25.83 110-114 23.69 25.480000000000004 24.97 25.86 115-119 23.875 25.069999999999997 24.834999999999997 26.22 120-124 23.945 25.005 24.94 26.11 125-129 23.57 25.955000000000002 25.080000000000002 25.395 130-134 23.95 26.334999999999997 24.115000000000002 25.6 135-139 23.580000000000002 26.495 24.015 25.91 140-144 24.535 25.419999999999998 24.145 25.900000000000002 145-149 23.7 25.44 25.105 25.755 150 23.625 24.95 25.424999999999997 26.0 >>END_MODULE >>Per sequence GC content fail #GC Content Count 0 9.0 1 7.5 2 4.0 3 1.0 4 0.0 5 0.0 6 1.0 7 2.0 8 1.0 9 0.5 10 0.5 11 0.0 12 0.5 13 0.5 14 0.0 15 0.5 16 0.5 17 0.5 18 0.5 19 0.0 20 0.0 21 0.5 22 0.5 23 0.5 24 1.0 25 1.0 26 2.0 27 2.5 28 3.0 29 4.5 30 8.0 31 9.5 32 13.5 33 22.0 34 30.5 35 35.0 36 51.5 37 73.0 38 87.5 39 101.0 40 127.0 41 156.5 42 162.0 43 177.5 44 191.5 45 194.5 46 194.5 47 183.5 48 177.0 49 159.5 50 141.5 51 140.0 52 134.5 53 112.0 54 98.0 55 101.5 56 98.5 57 102.5 58 92.0 59 76.0 60 82.0 61 93.5 62 80.5 63 61.5 64 62.5 65 62.0 66 53.0 67 45.0 68 42.0 69 35.0 70 27.0 71 18.0 72 13.5 73 11.0 74 7.5 75 5.0 76 4.0 77 2.5 78 0.5 79 0.5 80 0.5 81 0.0 82 0.5 83 0.5 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 2.45 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 93.425 #Duplication Level Percentage of deduplicated Percentage of total 1 97.80572651859781 91.375 2 1.9534385871019535 3.65 3 0.1337971635001338 0.375 4 0.02675943270002676 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 0.05351886540005352 0.675 >50 0.0 0.0 >100 0.02675943270002676 3.8249999999999997 >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 GATCGGAAGAGCACACGTCTGAACTCCAGTCACCTTGTAATCTCGTATGC 153 3.8249999999999997 TruSeq Adapter, Index 12 (100% over 50bp) TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 14 0.35000000000000003 No Hit AGATCGGAAGAGCACACGTCTGAACTCCAGTCACCTTGTAATCTCGTATG 13 0.325 TruSeq Adapter, Index 12 (100% over 49bp) >>END_MODULE >>Adapter Content warn #Position Illumina Universal Adapter Illumina Small RNA 3' Adapter Illumina Small RNA 5' Adapter Nextera Transposase Sequence SOLID Small RNA Adapter 1 0.35 0.0 0.0 0.0 0.0 2 0.35 0.0 0.0 0.0 0.0 3 0.35 0.0 0.0 0.0 0.0 4 0.35 0.0 0.0 0.0 0.0 5 0.35 0.0 0.0 0.0 0.0 6 0.35 0.0 0.0 0.0 0.0 7 0.35 0.0 0.0 0.0 0.0 8 0.35 0.0 0.0 0.0 0.0 9 0.35 0.0 0.0 0.0 0.0 10-11 0.35 0.0 0.0 0.0 0.0 12-13 0.35 0.0 0.0 0.0 0.0 14-15 0.35 0.0 0.0 0.0 0.0 16-17 0.3625 0.0 0.0 0.0 0.0 18-19 0.375 0.0 0.0 0.0 0.0 20-21 0.375 0.0 0.0 0.0 0.0 22-23 0.375 0.0 0.0 0.0 0.0 24-25 0.375 0.0 0.0 0.0 0.0 26-27 0.375 0.0 0.0 0.0 0.0 28-29 0.375 0.0 0.0 0.0 0.0 30-31 0.375 0.0 0.0 0.0 0.0 32-33 0.375 0.0 0.0 0.0 0.0 34-35 0.375 0.0 0.0 0.0 0.0 36-37 0.375 0.0 0.0 0.0 0.0 38-39 0.375 0.0 0.0 0.0 0.0 40-41 0.375 0.0 0.0 0.0 0.0 42-43 0.375 0.0 0.0 0.0 0.0 44-45 0.375 0.0 0.0 0.0 0.0 46-47 0.375 0.0 0.0 0.0 0.0 48-49 0.3875 0.0 0.0 0.0 0.0 50-51 0.4 0.0 0.0 0.0 0.0 52-53 0.4 0.0 0.0 0.0 0.0 54-55 0.4 0.0 0.0 0.0 0.0 56-57 0.4 0.0 0.0 0.0 0.0 58-59 0.425 0.0 0.0 0.0 0.0 60-61 0.425 0.0 0.0 0.0 0.0 62-63 0.4625 0.0 0.0 0.0 0.0 64-65 0.475 0.0 0.0 0.0 0.0 66-67 0.475 0.0 0.0 0.0 0.0 68-69 0.475 0.0 0.0 0.0 0.0 70-71 0.475 0.0 0.0 0.0 0.0 72-73 0.4875 0.0 0.0 0.0 0.0 74-75 0.5 0.0 0.0 0.0 0.0 76-77 0.5125 0.0 0.0 0.0 0.0 78-79 0.525 0.0 0.0 0.0 0.0 80-81 0.525 0.0 0.0 0.0 0.0 82-83 0.525 0.0 0.0 0.0 0.0 84-85 0.525 0.0 0.0 0.0 0.0 86-87 0.525 0.0 0.0 0.0 0.0 88-89 0.5375000000000001 0.0 0.0 0.0 0.0 90-91 0.6125 0.0 0.0 0.0 0.0 92-93 0.6375 0.0 0.0 0.0 0.0 94-95 0.775 0.0 0.0 0.0 0.0 96-97 0.8 0.0 0.0 0.0 0.0 98-99 0.925 0.0 0.0 0.0 0.0 100-101 1.0125 0.0 0.0 0.0 0.0 102-103 1.15 0.0 0.0 0.0 0.0 104-105 1.275 0.0 0.0 0.0 0.0 106-107 1.4875 0.0 0.0 0.0 0.0 108-109 1.6125 0.0 0.0 0.0 0.0 110-111 1.7374999999999998 0.0 0.0 0.0 0.0 112-113 1.8625 0.0 0.0 0.0 0.0 114-115 2.075 0.0 0.0 0.0 0.0 116-117 2.2875 0.0 0.0 0.0 0.0 118-119 2.625 0.0 0.0 0.0 0.0 120-121 2.7625 0.0 0.0 0.0 0.0 122-123 3.0250000000000004 0.0 0.0 0.0 0.0 124-125 3.225 0.0 0.0 0.0 0.0 126-127 3.5375 0.0 0.0 0.0 0.0 128-129 3.9375 0.0 0.0 0.0 0.0 130-131 4.2625 0.0 0.0 0.0 0.0 132-133 4.6375 0.0 0.0 0.0 0.0 134-135 5.125 0.0 0.0 0.0 0.0 136-137 5.4875 0.0 0.0 0.0 0.0 138 5.7 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position GTGCAGG 10 0.0069754543 143.9875 8 TGCAGGT 10 0.0069754543 143.9875 9 AAAAAAA 35 0.0036832115 20.569643 65-69 >>END_MODULE SRR8096906 read2 length is 150 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR8096906_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 31.3095 33.0 32.0 34.0 27.0 34.0 2 31.562 33.0 32.0 34.0 27.0 34.0 3 31.40375 33.0 33.0 34.0 27.0 34.0 4 31.46775 33.0 33.0 34.0 27.0 34.0 5 31.04175 33.0 31.0 34.0 27.0 34.0 6 35.3745 38.0 37.0 38.0 29.0 38.0 7 35.3405 38.0 37.0 38.0 29.0 38.0 8 35.39775 38.0 37.0 38.0 29.0 38.0 9 35.34975 38.0 37.0 38.0 29.0 38.0 10-14 35.1047 38.0 37.0 38.0 27.8 38.0 15-19 34.833299999999994 38.0 37.0 38.0 26.6 38.0 20-24 34.8771 38.0 36.8 38.0 26.8 38.0 25-29 34.693200000000004 38.0 36.6 38.0 25.4 38.0 30-34 34.430150000000005 38.0 36.0 38.0 23.2 38.0 35-39 34.23389999999999 38.0 36.0 38.0 21.2 38.0 40-44 34.18535 38.0 36.0 38.0 22.6 38.0 45-49 33.9211 38.0 35.4 38.0 16.0 38.0 50-54 33.773 38.0 35.0 38.0 16.0 38.0 55-59 33.636700000000005 38.0 34.6 38.0 16.0 38.0 60-64 33.59245000000001 38.0 34.6 38.0 16.0 38.0 65-69 33.03645 38.0 33.8 38.0 15.6 38.0 70-74 32.315200000000004 38.0 33.2 38.0 15.0 38.0 75-79 31.7908 38.0 31.8 38.0 14.0 38.0 80-84 31.4218 37.8 30.8 38.0 13.6 38.0 85-89 30.9112 37.0 28.8 38.0 13.0 38.0 90-94 30.4883 37.0 28.2 38.0 10.8 38.0 95-99 29.87935 36.2 26.0 38.0 2.0 38.0 100-104 29.19545 35.6 24.0 38.0 2.0 38.0 105-109 28.6995 35.2 22.2 38.0 2.0 38.0 110-114 27.842750000000002 34.8 17.4 38.0 2.0 38.0 115-119 27.064300000000003 34.0 15.0 38.0 2.0 38.0 120-124 26.223950000000002 34.0 14.4 38.0 2.0 38.0 125-129 25.143399999999996 32.8 13.6 37.8 2.0 38.0 130-134 23.87135 31.0 10.8 36.8 2.0 38.0 135-139 22.23035 28.2 2.0 36.0 2.0 38.0 140-144 20.55765 23.6 2.0 34.6 2.0 38.0 145-149 17.63535 10.6 2.0 33.6 2.0 38.0 150 11.5645 2.0 2.0 26.0 2.0 35.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 2 62.0 3 16.0 4 9.0 5 8.0 6 10.0 7 14.0 8 9.0 9 17.0 10 12.0 11 30.0 12 32.0 13 31.0 14 31.0 15 47.0 16 38.0 17 39.0 18 35.0 19 45.0 20 41.0 21 34.0 22 60.0 23 60.0 24 77.0 25 78.0 26 69.0 27 119.0 28 122.0 29 140.0 30 170.0 31 213.0 32 240.0 33 312.0 34 390.0 35 509.0 36 584.0 37 297.0 >>END_MODULE >>Per base sequence content warn #Base G A T C 1 38.923811918531555 17.098315313050037 8.800603469952225 35.17726929846618 2 26.283987915407852 26.636455186304133 28.474320241691842 18.605236656596173 3 22.80966767371601 25.201409869083584 29.103726082578046 22.885196374622357 4 26.963746223564954 29.305135951661633 17.472306143001006 26.25881168177241 5 31.149193548387093 32.73689516129033 17.741935483870968 18.371975806451612 6 25.453629032258064 34.07258064516129 18.92641129032258 21.547379032258064 7 21.415973796926178 20.71050642479214 33.131771227009324 24.741748551272362 8 22.045855379188712 26.53061224489796 23.10405643738977 28.31947593852356 9 26.915322580645164 21.62298387096774 25.95766129032258 25.50403225806452 10-14 27.13436145549844 24.795887511339583 21.716560830561434 26.353190202600548 15-19 26.971163541036496 24.485783424077432 23.5480943738657 24.994958661020366 20-24 27.53389446096467 26.30915780454614 22.453505367673 23.703442366816187 25-29 26.741901355232002 26.98876517708701 22.273162375938334 23.996171091742657 30-34 27.105157131345685 24.969782433521353 23.62006446414182 24.304995970991136 35-39 25.79930517093802 25.05916117013242 24.001812597552995 25.13972106137657 40-44 29.103726082578046 23.846928499496475 23.031218529707957 24.018126888217523 45-49 26.69487256975924 24.554245995769115 23.310164198650146 25.4407172358215 50-54 25.86041824137062 25.054169816074577 24.464600655076847 24.620811287477952 55-59 25.537918871252202 25.936004031242128 24.227765180146132 24.298311917359534 60-64 25.10456034265558 28.944318468127996 22.438901486520535 23.512219702695894 65-69 25.27721774193548 28.568548387096776 22.96875 23.18548387096774 70-74 25.52794718008165 27.23653041681367 22.60470742402097 24.630814979083716 75-79 25.29233870967742 27.253024193548388 23.150201612903228 24.304435483870968 80-84 25.96158693350809 26.813530271714477 22.750415889499422 24.474466905278017 85-89 25.267298769416985 27.1989106314303 23.16925559814404 24.364535001008676 90-94 25.71587013510788 26.88041943940311 23.144787255495057 24.258923169993952 95-99 25.28474952121762 27.361153109565567 23.132748714847292 24.22134865436952 100-104 25.70204184522309 26.45828081673809 22.934207209478195 24.905470128560626 105-109 25.599798387096772 26.95060483870968 23.286290322580644 24.163306451612904 110-114 25.53813580682563 26.98492715632404 22.89156626506024 24.58537077179009 115-119 25.16886782941829 28.05726383708035 22.542595019659238 24.231273313842124 120-124 25.36177078606363 28.13492663742248 22.714667473402912 23.788635103110977 125-129 25.27095831022836 27.84191157937188 23.03775772546252 23.84937238493724 130-134 25.850511566957312 28.405826319237942 22.07046015825815 23.673201955546595 135-139 25.22427174679972 29.07469005140611 22.2910996875315 23.409938514262677 140-144 25.483773432775653 28.492239467849224 21.986494658335012 24.03749244104011 145-149 25.5984244015756 29.133420866579137 21.70992829007171 23.55822644177356 150 23.960695389266817 33.93801965230537 20.634920634920633 21.466364323507182 >>END_MODULE >>Per sequence GC content fail #GC Content Count 0 25.0 1 13.5 2 1.5 3 0.5 4 0.0 5 0.0 6 0.0 7 0.0 8 0.0 9 0.5 10 0.5 11 0.5 12 1.0 13 0.5 14 0.5 15 1.0 16 2.0 17 1.5 18 0.0 19 0.0 20 0.0 21 0.0 22 1.0 23 1.5 24 1.5 25 2.0 26 3.0 27 3.0 28 4.0 29 7.0 30 7.5 31 8.0 32 15.0 33 25.5 34 29.5 35 33.5 36 43.0 37 54.0 38 73.0 39 98.0 40 109.0 41 114.5 42 141.0 43 150.5 44 148.5 45 167.5 46 165.0 47 158.0 48 166.0 49 158.5 50 134.5 51 128.0 52 126.0 53 120.0 54 120.5 55 114.0 56 106.0 57 106.0 58 109.0 59 106.5 60 108.5 61 108.5 62 100.0 63 88.0 64 74.0 65 73.0 66 73.0 67 56.5 68 46.5 69 48.5 70 41.5 71 27.5 72 19.5 73 15.5 74 10.5 75 6.0 76 4.5 77 2.0 78 0.5 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 0.5 93 0.5 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 0.575 2 0.7000000000000001 3 0.7000000000000001 4 0.7000000000000001 5 0.8 6 0.8 7 0.775 8 0.775 9 0.8 10-14 0.79 15-19 0.8200000000000001 20-24 0.795 25-29 0.755 30-34 0.72 35-39 0.695 40-44 0.7000000000000001 45-49 0.73 50-54 0.775 55-59 0.775 60-64 0.775 65-69 0.8 70-74 0.795 75-79 0.8 80-84 0.815 85-89 0.86 90-94 0.8200000000000001 95-99 0.79 100-104 0.8250000000000001 105-109 0.8 110-114 0.815 115-119 0.8099999999999999 120-124 0.835 125-129 0.815 130-134 0.795 135-139 0.79 140-144 0.7799999999999999 145-149 0.9900000000000001 150 0.775 >>END_MODULE >>Sequence Length Distribution pass #Length Count 150 4000.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 96.05 #Duplication Level Percentage of deduplicated Percentage of total 1 98.46434148880792 94.575 2 1.2753774076002082 2.45 3 0.15616866215512754 0.44999999999999996 4 0.026028110359187923 0.1 5 0.026028110359187923 0.125 6 0.0 0.0 7 0.0 0.0 8 0.0 0.0 9 0.0 0.0 >10 0.026028110359187923 0.575 >50 0.026028110359187923 1.725 >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 GATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCG 69 1.725 Illumina Single End PCR Primer 1 (100% over 50bp) NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN 23 0.575 No Hit AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCC 5 0.125 Illumina Single End PCR Primer 1 (100% over 50bp) >>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 0.3 0.0 0.0 0.0 0.0 2 0.3 0.0 0.0 0.0 0.0 3 0.3 0.0 0.0 0.0 0.0 4 0.3 0.0 0.0 0.0 0.0 5 0.3 0.0 0.0 0.0 0.0 6 0.3 0.0 0.0 0.0 0.0 7 0.3 0.0 0.0 0.0 0.0 8 0.3 0.0 0.0 0.0 0.0 9 0.3 0.0 0.0 0.0 0.0 10-11 0.3 0.0 0.0 0.0 0.0 12-13 0.3 0.0 0.0 0.0 0.0 14-15 0.3 0.0 0.0 0.0 0.0 16-17 0.3125 0.0 0.0 0.0 0.0 18-19 0.325 0.0 0.0 0.0 0.0 20-21 0.325 0.0 0.0 0.0 0.0 22-23 0.325 0.0 0.0 0.0 0.0 24-25 0.325 0.0 0.0 0.0 0.0 26-27 0.325 0.0 0.0 0.0 0.0 28-29 0.325 0.0 0.0 0.0 0.0 30-31 0.325 0.0 0.0 0.0 0.0 32-33 0.325 0.0 0.0 0.0 0.0 34-35 0.325 0.0 0.0 0.0 0.0 36-37 0.35 0.0 0.0 0.0 0.0 38-39 0.35 0.0 0.0 0.0 0.0 40-41 0.35 0.0 0.0 0.0 0.0 42-43 0.35 0.0 0.0 0.0 0.0 44-45 0.35 0.0 0.0 0.0 0.0 46-47 0.3625 0.0 0.0 0.0 0.0 48-49 0.3875 0.0 0.0 0.0 0.0 50-51 0.4 0.0 0.0 0.0 0.0 52-53 0.4 0.0 0.0 0.0 0.0 54-55 0.4 0.0 0.0 0.0 0.0 56-57 0.42500000000000004 0.0 0.0 0.0 0.0 58-59 0.45 0.0 0.0 0.0 0.0 60-61 0.475 0.0 0.0 0.0 0.0 62-63 0.475 0.0 0.0 0.0 0.0 64-65 0.475 0.0 0.0 0.0 0.0 66-67 0.475 0.0 0.0 0.0 0.0 68-69 0.475 0.0 0.0 0.0 0.0 70-71 0.475 0.0 0.0 0.0 0.0 72-73 0.4875 0.0 0.0 0.0 0.0 74-75 0.5 0.0 0.0 0.0 0.0 76-77 0.5 0.0 0.0 0.0 0.0 78-79 0.5 0.0 0.0 0.0 0.0 80-81 0.5 0.0 0.0 0.0 0.0 82-83 0.5 0.0 0.0 0.0 0.0 84-85 0.5 0.0 0.0 0.0 0.0 86-87 0.5 0.0 0.0 0.0 0.0 88-89 0.5 0.0 0.0 0.0 0.0 90-91 0.5375000000000001 0.0 0.0 0.0 0.0 92-93 0.5625 0.0 0.0 0.0 0.0 94-95 0.65 0.0 0.0 0.0 0.0 96-97 0.675 0.0 0.0 0.0 0.0 98-99 0.7625 0.0 0.0 0.0 0.0 100-101 0.825 0.0 0.0 0.0 0.0 102-103 0.925 0.0 0.0 0.0 0.0 104-105 1.0 0.0 0.0 0.0 0.0 106-107 1.1375 0.0 0.0 0.0 0.0 108-109 1.2374999999999998 0.0 0.0 0.0 0.0 110-111 1.3125 0.0 0.0 0.0 0.0 112-113 1.4 0.0 0.0 0.0 0.0 114-115 1.5625 0.0 0.0 0.0 0.0 116-117 1.7625 0.0 0.0 0.0 0.0 118-119 1.975 0.0 0.0 0.0 0.0 120-121 2.0625 0.0 0.0 0.0 0.0 122-123 2.2875 0.0 0.0 0.0 0.0 124-125 2.45 0.0 0.0 0.0 0.0 126-127 2.7 0.0 0.0 0.0 0.0 128-129 2.9625 0.0 0.0 0.0 0.0 130-131 3.125 0.0 0.0 0.0 0.0 132-133 3.3 0.0 0.0 0.0 0.0 134-135 3.575 0.0 0.0 0.0 0.0 136-137 3.8125 0.0 0.0 0.0 0.0 138 3.95 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position GGCGCAG 10 0.0069668675 144.0 9 GCAACTC 10 0.0069668675 144.0 3 AACTCAA 10 0.0069668675 144.0 5 AACAGGC 10 0.0069668675 144.0 3 TTTTTTT 30 0.0015018329 23.999998 125-129 >>END_MODULE Read 1852813 spots for SRR8096906.sra Written 1852813 spots for SRR8096906.sra Read 1852813 spots for SRR8096906.sra Written 1852813 spots for SRR8096906.sra Read 1852813 spots for SRR8096906.sra Written 1852813 spots for SRR8096906.sra Read 1852813 spots for SRR8096906.sra Written 1852813 spots for SRR8096906.sra Read 1852813 spots for SRR8096906.sra Written 1852813 spots for SRR8096906.sra Read 1852813 spots for SRR8096906.sra Written 1852813 spots for SRR8096906.sra Read 1852813 spots for SRR8096906.sra Written 1852813 spots for SRR8096906.sra Read 1852813 spots for SRR8096906.sra Written 1852813 spots for SRR8096906.sra Read 1852830 spots for SRR8096906.sra Written 1852830 spots for SRR8096906.sra Read 1852813 spots for SRR8096906.sra Written 1852813 spots for SRR8096906.sra Read 1852813 spots for SRR8096906.sra Written 1852813 spots for SRR8096906.sra Read 1852813 spots for SRR8096906.sra Written 1852813 spots for SRR8096906.sra Read 1852813 spots for SRR8096906.sra Written 1852813 spots for SRR8096906.sra Read 1852813 spots for SRR8096906.sra Written 1852813 spots for SRR8096906.sra Read 1852813 spots for SRR8096906.sra Written 1852813 spots for SRR8096906.sra Read 1852813 spots for SRR8096906.sra Written 1852813 spots for SRR8096906.sra Read 1852813 spots for SRR8096906.sra Written 1852813 spots for SRR8096906.sra Read 1852813 spots for SRR8096906.sra Written 1852813 spots for SRR8096906.sra Read 1852813 spots for SRR8096906.sra Written 1852813 spots for SRR8096906.sra Read 1852813 spots for SRR8096906.sra Written 1852813 spots for SRR8096906.sra SRR ids: ['SRR8096906.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_etmyt_gv SRR8096906.sra spots: 37056277 blocks: [[1, 1852813], [1852814, 3705626], [3705627, 5558439], [5558440, 7411252], [7411253, 9264065], [9264066, 11116878], [11116879, 12969691], [12969692, 14822504], [14822505, 16675317], [16675318, 18528130], [18528131, 20380943], [20380944, 22233756], [22233757, 24086569], [24086570, 25939382], [25939383, 27792195], [27792196, 29645008], [29645009, 31497821], [31497822, 33350634], [33350635, 35203447], [35203448, 37056277]] SRR8096906 file size 12463080 SRR8096906 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 SRR8096906 SRR8096906_1.fastq SRR8096906_2.fastq Input file: SRR8096906_1.fastq Paired file: SRR8096906_2.fastq trimmed: SRR8096906-trimmed-pair1.fastq, SRR8096906-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 Sun Dec 8 14:39:10 2024 >> started Sun Dec 8 14:44:00 2024 >> done (290.382s) 37056277 read pairs processed; of these: 144095 ( 0.39%) short read pairs filtered out after trimming by size control 1938282 ( 5.23%) empty read pairs filtered out after trimming by size control 34973900 (94.38%) read pairs available; of these: 19723700 (56.40%) trimmed read pairs available after processing 15250200 (43.60%) untrimmed read pairs available after processing Length distribution of reads after trimming: length count percentage 18 131 0.00% 19 181 0.00% 20 122 0.00% 21 140 0.00% 22 231 0.00% 23 209 0.00% 24 1949 0.01% 25 163 0.00% 26 206 0.00% 27 153 0.00% 28 144 0.00% 29 221 0.00% 30 695 0.00% 31 495 0.00% 32 309 0.00% 33 228 0.00% 34 757 0.00% 35 803 0.00% 36 512 0.00% 37 434 0.00% 38 356 0.00% 39 772 0.00% 40 1027 0.00% 41 867 0.00% 42 727 0.00% 43 665 0.00% 44 837 0.00% 45 1015 0.00% 46 1463 0.00% 47 1158 0.00% 48 1246 0.00% 49 1479 0.00% 50 1813 0.01% 51 2286 0.01% 52 1785 0.01% 53 2052 0.01% 54 2303 0.01% 55 2744 0.01% 56 3168 0.01% 57 2534 0.01% 58 4150 0.01% 59 3725 0.01% 60 3250 0.01% 61 11350 0.03% 62 4580 0.01% 63 1765 0.01% 64 1709 0.00% 65 1917 0.01% 66 1952 0.01% 67 2112 0.01% 68 2521 0.01% 69 3444 0.01% 70 3300 0.01% 71 2990 0.01% 72 3144 0.01% 73 3750 0.01% 74 3625 0.01% 75 3959 0.01% 76 4595 0.01% 77 5076 0.01% 78 5684 0.02% 79 6302 0.02% 80 6556 0.02% 81 7327 0.02% 82 8528 0.02% 83 10682 0.03% 84 18059 0.05% 85 19248 0.06% 86 21106 0.06% 87 22989 0.07% 88 23532 0.07% 89 23664 0.07% 90 24150 0.07% 91 24497 0.07% 92 24815 0.07% 93 26115 0.07% 94 27694 0.08% 95 29406 0.08% 96 31868 0.09% 97 35063 0.10% 98 37384 0.11% 99 38981 0.11% 100 40133 0.11% 101 42147 0.12% 102 44988 0.13% 103 48000 0.14% 104 51254 0.15% 105 53930 0.15% 106 57236 0.16% 107 60202 0.17% 108 63664 0.18% 109 64213 0.18% 110 64959 0.19% 111 67637 0.19% 112 70545 0.20% 113 74642 0.21% 114 76397 0.22% 115 81058 0.23% 116 84537 0.24% 117 88226 0.25% 118 91665 0.26% 119 95086 0.27% 120 99048 0.28% 121 104260 0.30% 122 107111 0.31% 123 113368 0.32% 124 117965 0.34% 125 124562 0.36% 126 130024 0.37% 127 136739 0.39% 128 145347 0.42% 129 152149 0.44% 130 158316 0.45% 131 165940 0.47% 132 174483 0.50% 133 181961 0.52% 134 191987 0.55% 135 201586 0.58% 136 215349 0.62% 137 230592 0.66% 138 241417 0.69% 139 260394 0.74% 140 285879 0.82% 141 310750 0.89% 142 349674 1.00% 143 396281 1.13% 144 468449 1.34% 145 573231 1.64% 146 755568 2.16% 147 1069950 3.06% 148 1991263 5.69% 149 8364594 23.92% 150 15250200 43.60% 34973900 reads passed initial QC criterion=sequence-density sequence-density=1.33 sequence-density-rank=1 fanout-score=2.06 fanout-score-rank=34 prefix-density=1.36 prefix-fanout=2.0 sequence=AACATGGAGAACATGGCGAGGCGGCCGTTCTTGATCTCCTTCACCTTGAGCTCAGCGAA criterion=fanout-score sequence-density=0.01 sequence-density-rank=39 fanout-score=18.82 fanout-score-rank=1 prefix-density=0.04 prefix-fanout=3.7 sequence=CTGTTCACCAAATGAATATACTCAATATCTTTATATATGAACAAAAACTTTTCATGCCCAGCAATTGCTTGGATGCAATGCGGTACTTAGGTACAAAGAGTGAAACATCAGAATAATTAAAGTGGCATGCTTAAAAGGTGTAAAGGCAGCTGCCGTCGTCACTCCTTGCTGTTGGGTCGTAGTTCTCGGCATTCCGGTCAGTGCAACCTTCTGGGACGGGCAAATTACCTTGTTGTGCTCCTTTACCTCCTCCTATGCAGCTAGAGATGGTGTGTGTATGAAGAGTGTTCTAACCGTAGAAGGAACCAGTCTTCATGGCATCTGAGTTAGCATCTCCCAGAGCAGCCTCGCTCATGTACTTGTCAGCAAGCTGCACACGCTTGACATTGTCCTGCTCTTGGACGAGCATGTGGCCGTACTCCAGGAGCTTCTCGATTGTCATCTTTGGCTGCTCAAAGGACACCGGTCCATCCTTCGAGTTCACCAGCTTCTTGCCGATGTTCTCTATTCC criterion=sequence-density sequence-density=0.66 sequence-density-rank=1 fanout-score=2.03 fanout-score-rank=30 prefix-density=0.66 prefix-fanout=2.0 sequence=TTCGCTGAGCTCAAGGTGAAGGAGATCAAGAACGGCCGCCTCGCCATGTTCTCCATGTT criterion=fanout-score sequence-density=0.01 sequence-density-rank=34 fanout-score=79.92 fanout-score-rank=1 prefix-density=0.08 prefix-fanout=6.7 sequence=TGCTCATCATCTTGTTTAATACCAAAGCTCTTCATATTCTCCTCCTTGATTTCATCAGCTTGAGGTTAGAGAGATTTGGAAGATGTCTTGCAGCTGTGGATCAAGCTGCAACTGTGGCTCAAACTGCACTTGCGGGAAGATGTACCCAGACCTGGCAGAGCAGGCCAGCACCACCAGCAGCACCCAGGCCCAGGTGGTGGTTCTCGGCATGGCGCCGGAGAAG SRR8096906 testing PE reads STAR mapping to Ensembl genome Started job on | Dec 08 14:48:57 Started mapping on | Dec 08 14:48:57 Finished on | Dec 08 15:43:42 Mapping speed, Million of reads per hour | 38.33 Number of input reads | 34973900 Average input read length | 289 UNIQUE READS: Uniquely mapped reads number | 32846769 Uniquely mapped reads % | 93.92% Average mapped length | 289.48 Number of splices: Total | 31981135 Number of splices: Annotated (sjdb) | 30223814 Number of splices: GT/AG | 31560176 Number of splices: GC/AG | 365141 Number of splices: AT/AC | 9080 Number of splices: Non-canonical | 46738 Mismatch rate per base, % | 0.29% Deletion rate per base | 0.01% Deletion average length | 2.02 Insertion rate per base | 0.01% Insertion average length | 1.88 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 459279 % of reads mapped to multiple loci | 1.31% Number of reads mapped to too many loci | 21352 % of reads mapped to too many loci | 0.06% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 4.28% % of reads unmapped: other | 0.43% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 1791683 1791683 1791683 N_multimapping 459279 459279 459279 N_noFeature 1117321 31778355 1354580 N_ambiguous 973116 3313 145432 UnstrandedReadsAssigned:30756332 PositiveStrandReadsAssigned:1065101 NegativeStrandReadsAssigned:31346757 Dataset is classified negative stranded MeadianReadLen=150 20thPercentileLength=149 echo kmer=145 SRR8096906 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: SRR8096906-trimmed-pair1.fastq SRR8096906-trimmed-pair2.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 34,973,900 reads, 31,395,171 reads pseudoaligned [quant] estimated average fragment length: 259.499 [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,236 rounds 52973 SRR8096906.ke.tsv 35125 SRR8096906.se.tsv 88098 total ==> SRR8096906.ke.tsv <== target_id length eff_length est_counts tpm PNS24245 936 677.873 0 0 PNS24247 1044 785.501 75.8931 4.07697 PNS24249 1928 1669.5 44.7312 1.13059 PNS24246 1044 785.501 75.8931 4.07697 PNS24248 1044 785.501 75.8931 4.07697 PNS24244 1471 1212.5 314.59 10.9483 PNS24243 293 88.0754 0 0 KQK14069 1603 1344.5 11016 345.737 KQK14071 474 230.928 175.678 32.1014 ==> SRR8096906.se.tsv <== BRADI_1g14170v3 12636 BRADI_1g53295v3 31 BRADI_1g59795v3 1228 BRADI_1g07683v3 0 BRADI_1g00485v3 5 BRADI_1g20270v3 196 BRADI_1g74790v3 113 BRADI_1g09890v3 0 BRADI_1g77505v3 507 BRADI_1g48960v3 0 SRR8096906 completed mapping pipeline successfully