Starting /dee2/code/volunteer_pipeline.sh SRR8096900 current disk space = 1515503468544 free memory = 1607680036 SRR8096900 SRAfilesize 133b26d628d14c9a21a1a638010402a4 SRR8096900.sra SRR8096900.sra file validated SRR8096900 is paired end SRR8096900 is conventional basespace SRR8096900 read1 length is 150 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR8096900_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 48 >>END_MODULE >>Per base sequence quality fail #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 32.2085 34.0 33.0 34.0 32.0 34.0 2 33.018 34.0 33.0 34.0 32.0 34.0 3 32.97375 34.0 33.0 34.0 32.0 34.0 4 33.17225 34.0 33.0 34.0 32.0 34.0 5 33.2885 34.0 33.0 34.0 33.0 34.0 6 36.79675 38.0 37.0 38.0 35.0 38.0 7 37.24275 38.0 38.0 38.0 36.0 38.0 8 37.3025 38.0 38.0 38.0 37.0 38.0 9 37.26475 38.0 38.0 38.0 37.0 38.0 10-14 37.399 38.0 38.0 38.0 37.0 38.0 15-19 37.375 38.0 38.0 38.0 37.0 38.0 20-24 37.3463 38.0 38.0 38.0 37.0 38.0 25-29 37.23855 38.0 38.0 38.0 37.0 38.0 30-34 37.2214 38.0 38.0 38.0 37.0 38.0 35-39 37.19985 38.0 38.0 38.0 37.0 38.0 40-44 36.893899999999995 38.0 38.0 38.0 35.8 38.0 45-49 36.99465 38.0 38.0 38.0 36.0 38.0 50-54 36.954899999999995 38.0 38.0 38.0 36.0 38.0 55-59 36.821400000000004 38.0 38.0 38.0 35.8 38.0 60-64 36.68615 38.0 38.0 38.0 35.2 38.0 65-69 36.38085 38.0 38.0 38.0 34.0 38.0 70-74 36.11475 38.0 38.0 38.0 33.6 38.0 75-79 35.59780000000001 38.0 38.0 38.0 32.8 38.0 80-84 35.51705 38.0 38.0 38.0 33.2 38.0 85-89 34.89425 38.0 36.8 38.0 27.8 38.0 90-94 35.30225 38.0 37.8 38.0 30.8 38.0 95-99 35.2414 38.0 38.0 38.0 31.0 38.0 100-104 35.16065 38.0 37.8 38.0 30.6 38.0 105-109 34.876 38.0 37.0 38.0 28.2 38.0 110-114 34.68575 38.0 37.0 38.0 27.2 38.0 115-119 34.3547 38.0 36.0 38.0 24.0 38.0 120-124 34.32575 38.0 36.0 38.0 24.6 38.0 125-129 33.87134999999999 38.0 36.0 38.0 21.0 38.0 130-134 33.0683 38.0 33.8 38.0 15.6 38.0 135-139 32.97315 38.0 33.4 38.0 13.0 38.0 140-144 32.53855 38.0 33.0 38.0 11.6 38.0 145-149 31.294149999999995 38.0 32.2 38.0 2.0 38.0 150 22.105 28.0 2.0 36.0 2.0 38.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 6 2.0 7 2.0 8 4.0 9 1.0 10 7.0 11 2.0 12 4.0 13 3.0 14 4.0 15 5.0 16 8.0 17 15.0 18 32.0 19 60.0 20 5.0 21 9.0 22 10.0 23 15.0 24 21.0 25 22.0 26 25.0 27 42.0 28 46.0 29 61.0 30 50.0 31 54.0 32 68.0 33 94.0 34 153.0 35 226.0 36 571.0 37 2379.0 >>END_MODULE >>Per base sequence content warn #Base G A T C 1 47.22293980883492 12.787393438388014 7.336605528287264 32.6530612244898 2 22.45 19.1 35.0 23.45 3 21.925 19.900000000000002 29.075 29.099999999999998 4 26.875 25.35 21.075 26.700000000000003 5 29.049999999999997 29.45 23.799999999999997 17.7 6 21.675 32.0 23.25 23.075000000000003 7 17.575 25.174999999999997 38.35 18.9 8 19.55 23.175 29.75 27.525 9 23.7 20.325 30.95 25.025 10-14 22.93 26.924999999999997 24.465 25.679999999999996 15-19 23.150000000000002 24.535 26.115 26.200000000000003 20-24 22.675 25.44 26.490000000000002 25.395 25-29 23.07 25.275 25.845000000000002 25.81 30-34 21.654999999999998 25.619999999999997 26.200000000000003 26.525 35-39 23.24 26.32 25.455 24.985 40-44 21.915000000000003 25.16 26.86 26.064999999999998 45-49 23.849999999999998 25.05 26.590000000000003 24.51 50-54 23.135 24.4 26.11 26.355 55-59 23.630000000000003 23.28 28.139999999999997 24.95 60-64 23.200000000000003 25.264999999999997 25.835 25.7 65-69 21.575 28.444999999999997 25.369999999999997 24.610000000000003 70-74 22.835 27.295 25.424999999999997 24.445 75-79 22.695 27.6 24.474999999999998 25.230000000000004 80-84 22.735 25.995 25.685000000000002 25.585 85-89 23.615 25.314999999999998 25.419999999999998 25.650000000000002 90-94 23.285 25.135 25.474999999999998 26.105 95-99 23.25 24.67 26.445 25.635 100-104 22.975 26.455000000000002 25.28 25.290000000000003 105-109 23.61 26.16 25.21 25.019999999999996 110-114 22.71 25.845000000000002 25.900000000000002 25.545 115-119 23.565 25.21 25.795 25.430000000000003 120-124 23.51 25.85 25.41 25.230000000000004 125-129 23.485 26.419999999999998 25.195 24.9 130-134 23.35 26.919999999999998 24.555 25.174999999999997 135-139 23.425 26.71 24.8 25.064999999999998 140-144 23.61 26.005 24.959999999999997 25.424999999999997 145-149 24.145 26.200000000000003 24.425 25.230000000000004 150 24.15 25.35 26.6 23.9 >>END_MODULE >>Per sequence GC content fail #GC Content Count 0 16.0 1 10.0 2 2.0 3 2.0 4 2.5 5 1.0 6 2.0 7 2.0 8 1.5 9 1.5 10 1.0 11 2.0 12 1.5 13 1.0 14 1.0 15 0.5 16 0.5 17 1.0 18 1.0 19 0.0 20 0.0 21 0.5 22 1.0 23 0.5 24 0.5 25 1.0 26 2.0 27 5.5 28 5.0 29 5.0 30 8.0 31 14.0 32 22.5 33 25.0 34 31.5 35 40.5 36 53.5 37 68.5 38 91.5 39 110.0 40 128.5 41 158.5 42 173.5 43 169.5 44 175.0 45 200.0 46 194.0 47 185.0 48 176.5 49 169.0 50 155.5 51 126.0 52 130.5 53 130.0 54 99.0 55 83.0 56 89.0 57 89.5 58 84.5 59 84.5 60 77.0 61 71.0 62 65.0 63 62.5 64 66.0 65 60.0 66 53.5 67 44.5 68 36.5 69 33.0 70 31.0 71 23.5 72 15.0 73 8.5 74 6.0 75 6.5 76 4.5 77 2.5 78 2.5 79 1.5 80 0.5 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 3.225 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 93.475 #Duplication Level Percentage of deduplicated Percentage of total 1 98.36854774003744 91.95 2 1.3105108317732013 2.45 3 0.18721583311045736 0.525 4 0.02674511901577962 0.1 5 0.0 0.0 6 0.0 0.0 7 0.0 0.0 8 0.0 0.0 9 0.02674511901577962 0.22499999999999998 >10 0.05349023803155924 0.975 >50 0.0 0.0 >100 0.02674511901577962 3.775 >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 GATCGGAAGAGCACACGTCTGAACTCCAGTCACAGTCAAATCTCGTATGC 151 3.775 TruSeq Adapter, Index 13 (98% over 50bp) TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 22 0.5499999999999999 No Hit ATCGGAAGAGCACACGTCTGAACTCCAGTCACAGTCAAATCTCGTATGCC 17 0.42500000000000004 TruSeq Adapter, Index 13 (98% over 50bp) AGATCGGAAGAGCACACGTCTGAACTCCAGTCACAGTCAAATCTCGTATG 9 0.22499999999999998 TruSeq Adapter, Index 13 (97% 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 0.225 0.0 0.0 0.0 0.0 2 0.225 0.0 0.0 0.0 0.0 3 0.225 0.0 0.0 0.0 0.0 4 0.225 0.0 0.0 0.0 0.0 5 0.225 0.0 0.0 0.0 0.0 6 0.225 0.0 0.0 0.0 0.0 7 0.225 0.0 0.0 0.0 0.0 8 0.225 0.0 0.0 0.0 0.0 9 0.225 0.0 0.0 0.0 0.0 10-11 0.2375 0.0 0.0 0.0 0.0 12-13 0.25 0.0 0.0 0.0 0.0 14-15 0.25 0.0 0.0 0.0 0.0 16-17 0.25 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 0.275 0.0 0.0 0.0 0.0 38-39 0.3 0.0 0.0 0.0 0.0 40-41 0.3 0.0 0.0 0.0 0.0 42-43 0.3 0.0 0.0 0.0 0.0 44-45 0.3 0.0 0.0 0.0 0.0 46-47 0.3 0.0 0.0 0.0 0.0 48-49 0.3 0.0 0.0 0.0 0.0 50-51 0.325 0.0 0.0 0.0 0.0 52-53 0.325 0.0 0.0 0.0 0.0 54-55 0.325 0.0 0.0 0.0 0.0 56-57 0.325 0.0 0.0 0.0 0.0 58-59 0.325 0.0 0.0 0.0 0.0 60-61 0.3375 0.0 0.0 0.0 0.0 62-63 0.3625 0.0 0.0 0.0 0.0 64-65 0.375 0.0 0.0 0.0 0.0 66-67 0.375 0.0 0.0 0.0 0.0 68-69 0.375 0.0 0.0 0.0 0.0 70-71 0.375 0.0 0.0 0.0 0.0 72-73 0.375 0.0 0.0 0.0 0.0 74-75 0.375 0.0 0.0 0.0 0.0 76-77 0.3875 0.0 0.0 0.0 0.0 78-79 0.4 0.0 0.0 0.0 0.0 80-81 0.4 0.0 0.0 0.0 0.0 82-83 0.425 0.0 0.0 0.0 0.0 84-85 0.45 0.0 0.0 0.0 0.0 86-87 0.45 0.0 0.0 0.0 0.0 88-89 0.45 0.0 0.0 0.0 0.0 90-91 0.4625 0.0 0.0 0.0 0.0 92-93 0.475 0.0 0.0 0.0 0.0 94-95 0.475 0.0 0.0 0.0 0.0 96-97 0.5125 0.0 0.0 0.0 0.0 98-99 0.5375000000000001 0.0 0.0 0.0 0.0 100-101 0.6 0.0 0.0 0.0 0.0 102-103 0.6 0.0 0.0 0.0 0.0 104-105 0.625 0.0 0.0 0.0 0.0 106-107 0.775 0.0 0.0 0.0 0.0 108-109 0.8375 0.0 0.0 0.0 0.0 110-111 0.975 0.0 0.0 0.0 0.0 112-113 1.0125 0.0 0.0 0.0 0.0 114-115 1.0750000000000002 0.0 0.0 0.0 0.0 116-117 1.2 0.0 0.0 0.0 0.0 118-119 1.2625 0.0 0.0 0.0 0.0 120-121 1.4375 0.0 0.0 0.0 0.0 122-123 1.525 0.0 0.0 0.0 0.0 124-125 1.8375 0.0 0.0 0.0 0.0 126-127 1.9625 0.0 0.0 0.0 0.0 128-129 2.0999999999999996 0.0 0.0 0.0 0.0 130-131 2.3875 0.0 0.0 0.0 0.0 132-133 2.625 0.0 0.0 0.0 0.0 134-135 2.9000000000000004 0.0 0.0 0.0 0.0 136-137 3.05 0.0 0.0 0.0 0.0 138 3.225 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position CTGGAAT 10 0.0064622764 147.66667 1 GATACTC 10 0.0069772652 143.975 5 GAAGAGC 25 5.9093345E-6 115.18 6 GATCGGA 30 1.28541105E-5 98.44444 1 GAGCACA 35 3.143894E-5 82.27143 9 AGAGCAC 35 3.143894E-5 82.27143 8 ATCGGAA 35 3.143894E-5 82.27143 2 GGAAGAG 35 3.143894E-5 82.27143 5 AAGAGCA 40 6.096386E-5 71.9875 7 TCGGAAG 40 6.096386E-5 71.9875 3 CGGAAGA 40 6.096386E-5 71.9875 4 AAATCTC 30 0.0015047102 23.995832 35-39 AAAAAAA 275 3.2339303E-6 7.8531823 65-69 >>END_MODULE SRR8096900 read2 length is 150 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR8096900_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 49 >>END_MODULE >>Per base sequence quality fail #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 30.81825 33.0 32.0 33.0 25.0 34.0 2 31.09375 33.0 32.0 34.0 25.0 34.0 3 30.92075 33.0 31.0 34.0 25.0 34.0 4 31.0205 33.0 32.0 34.0 25.0 34.0 5 30.7845 33.0 31.0 34.0 25.0 34.0 6 34.89825 38.0 36.0 38.0 28.0 38.0 7 34.86 38.0 37.0 38.0 27.0 38.0 8 34.85525 38.0 37.0 38.0 27.0 38.0 9 34.756 38.0 37.0 38.0 26.0 38.0 10-14 34.59045 38.0 36.4 38.0 24.4 38.0 15-19 34.29325 38.0 36.0 38.0 21.6 38.0 20-24 34.160999999999994 38.0 35.8 38.0 20.8 38.0 25-29 34.03725 38.0 35.8 38.0 16.0 38.0 30-34 33.692750000000004 38.0 34.8 38.0 16.0 38.0 35-39 33.49875 38.0 34.2 38.0 16.0 38.0 40-44 33.3803 38.0 34.2 38.0 16.0 38.0 45-49 33.14945 38.0 34.0 38.0 16.0 38.0 50-54 32.8917 38.0 34.0 38.0 16.0 38.0 55-59 32.6186 38.0 33.0 38.0 16.0 38.0 60-64 32.5126 38.0 32.8 38.0 15.8 38.0 65-69 31.98565 38.0 31.2 38.0 14.8 38.0 70-74 31.140050000000002 37.0 29.0 38.0 13.8 38.0 75-79 30.6829 37.0 28.0 38.0 13.0 38.0 80-84 30.206599999999998 37.0 26.8 38.0 8.6 38.0 85-89 29.66805 36.2 25.2 38.0 2.0 38.0 90-94 29.19875 35.8 24.0 38.0 2.0 38.0 95-99 28.61945 35.2 21.8 38.0 2.0 38.0 100-104 27.886599999999998 34.6 16.2 38.0 2.0 38.0 105-109 27.429449999999996 34.2 15.0 38.0 2.0 38.0 110-114 26.639400000000002 34.0 15.0 38.0 2.0 38.0 115-119 25.8219 34.0 14.4 38.0 2.0 38.0 120-124 24.8578 31.8 14.0 37.4 2.0 38.0 125-129 23.9607 30.6 13.0 36.6 2.0 38.0 130-134 22.6783 27.4 4.2 36.0 2.0 38.0 135-139 21.0443 24.4 2.0 35.0 2.0 38.0 140-144 19.151149999999998 21.8 2.0 33.8 2.0 38.0 145-149 16.246050000000004 8.6 2.0 32.8 2.0 38.0 150 10.82025 2.0 2.0 24.0 2.0 34.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 2 86.0 3 24.0 4 15.0 5 11.0 6 13.0 7 19.0 8 16.0 9 17.0 10 21.0 11 22.0 12 36.0 13 27.0 14 35.0 15 41.0 16 57.0 17 48.0 18 45.0 19 41.0 20 52.0 21 47.0 22 56.0 23 63.0 24 79.0 25 99.0 26 108.0 27 127.0 28 139.0 29 162.0 30 193.0 31 193.0 32 243.0 33 352.0 34 394.0 35 450.0 36 476.0 37 193.0 >>END_MODULE >>Per base sequence content warn #Base G A T C 1 43.49246231155779 20.502512562814072 8.768844221105528 27.236180904522612 2 25.84213172448467 26.31975867269985 28.95927601809955 18.878833584715938 3 22.510060362173036 23.038229376257547 32.04225352112676 22.409456740442657 4 26.213836477987424 31.42138364779874 17.81132075471698 24.553459119496857 5 29.869149471565176 33.442375440362355 17.31253145445395 19.37594363361852 6 25.52227535867103 33.29977347092877 20.161087339541908 21.01686383085829 7 21.892299949672875 21.565173628585807 33.99597382989431 22.546552591847004 8 20.961248112732765 26.220432813286358 24.106693507800706 28.71162556618017 9 27.30246602918973 21.238047307498743 24.484146955208857 26.97533970810267 10-14 26.462003019627577 25.732259687971816 22.10367388022144 25.702063412179164 15-19 26.82104203372766 24.57588723886232 23.90133400453058 24.701736722879435 20-24 26.793174611164243 26.340162077817485 23.526450898474856 23.340212412543412 25-29 26.154775083023047 27.070544429908423 22.788567978263057 23.986112508805473 30-34 26.716290298244733 25.217522506663986 24.483226877231807 23.582960317859477 35-39 25.933004727894577 25.243939241525 24.19776682426315 24.625289206317273 40-44 27.91691812512573 24.612753973043652 23.461074230537115 24.0092536712935 45-49 25.97735849056604 24.68930817610063 23.68301886792453 25.650314465408808 50-54 25.585023400936034 25.06164762719541 24.32187610085049 25.031452871018068 55-59 24.67290660225443 26.358695652173914 24.335748792270532 24.63264895330113 60-64 24.604932058379468 28.983392048314045 22.56668344237544 23.844992450931052 65-69 24.782280392650392 28.195318399194562 23.357664233576642 23.664736974578403 70-74 25.12332628611698 27.48917748917749 23.341387294875666 24.04610892982986 75-79 25.638056883966776 27.218726403221748 23.36773219229801 23.775484520513466 80-84 25.210168638308584 26.86131386861314 23.53888749056129 24.38963000251699 85-89 24.898061917946137 27.8882456581928 22.496853762899573 24.71683866096149 90-94 25.73370249181978 27.133148754090108 23.21671281147747 23.916435942612637 95-99 25.70465069458426 26.927722971612646 23.50010066438494 23.86752566941816 100-104 25.729963753523965 27.210028191703582 23.086991542488924 23.97301651228353 105-109 25.26050843191543 26.876415806695192 23.292222501887743 24.570853259501636 110-114 24.797382330732447 27.178454568336267 23.186508935313366 24.83765416561792 115-119 24.287727776099867 27.98248263364542 22.832980972515855 24.89680861773885 120-124 23.876164107727156 28.517493078278378 23.151271079788575 24.45507173420589 125-129 24.443773280982583 28.601630927212323 22.77760998691231 24.17698580489278 130-134 24.497911108874014 28.640459052700457 22.690894448079728 24.170735390345797 135-139 24.270183209180594 28.966176766659956 23.062210589893294 23.701429434266156 140-144 24.85153497735279 28.570709612481128 22.184197282335177 24.3935581278309 145-149 24.088732039324427 29.35215528106882 22.248550541971262 24.310562137635493 150 23.729240060392552 33.8701560140916 20.03019627579265 22.3704076497232 >>END_MODULE >>Per sequence GC content fail #GC Content Count 0 20.0 1 11.0 2 1.0 3 0.0 4 0.5 5 0.5 6 0.5 7 1.0 8 1.0 9 2.5 10 2.0 11 0.0 12 0.0 13 0.0 14 1.0 15 1.0 16 0.0 17 0.0 18 0.5 19 0.5 20 0.0 21 2.0 22 2.5 23 1.5 24 3.0 25 3.0 26 3.0 27 4.0 28 7.5 29 10.0 30 13.0 31 21.5 32 21.0 33 18.0 34 25.5 35 32.5 36 44.0 37 60.5 38 73.0 39 91.0 40 118.0 41 130.0 42 137.0 43 158.0 44 174.0 45 182.0 46 175.0 47 162.5 48 155.0 49 162.0 50 156.5 51 130.5 52 124.0 53 111.5 54 106.0 55 107.0 56 90.0 57 94.5 58 100.0 59 101.5 60 100.0 61 93.5 62 92.0 63 77.5 64 69.5 65 68.0 66 65.0 67 59.0 68 57.5 69 54.0 70 40.5 71 25.5 72 14.5 73 13.5 74 12.5 75 6.0 76 1.5 77 1.0 78 0.5 79 1.5 80 2.0 81 0.5 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 0.5 2 0.5499999999999999 3 0.6 4 0.625 5 0.65 6 0.675 7 0.65 8 0.65 9 0.65 10-14 0.65 15-19 0.675 20-24 0.6649999999999999 25-29 0.63 30-34 0.585 35-39 0.59 40-44 0.58 45-49 0.625 50-54 0.645 55-59 0.64 60-64 0.65 65-69 0.675 70-74 0.67 75-79 0.675 80-84 0.675 85-89 0.675 90-94 0.675 95-99 0.66 100-104 0.6799999999999999 105-109 0.675 110-114 0.675 115-119 0.67 120-124 0.675 125-129 0.67 130-134 0.6649999999999999 135-139 0.66 140-144 0.65 145-149 0.8250000000000001 150 0.65 >>END_MODULE >>Sequence Length Distribution pass #Length Count 150 4000.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 96.39999999999999 #Duplication Level Percentage of deduplicated Percentage of total 1 98.59958506224066 95.05 2 1.1151452282157677 2.15 3 0.18153526970954356 0.525 4 0.025933609958506226 0.1 5 0.0 0.0 6 0.0 0.0 7 0.025933609958506226 0.17500000000000002 8 0.0 0.0 9 0.0 0.0 >10 0.025933609958506226 0.5 >50 0.025933609958506226 1.5 >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 60 1.5 Illumina Single End PCR Primer 1 (100% over 50bp) NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN 20 0.5 No Hit AAGCAGAAGACGGCATACGAGATTTGACTGTGACTGGAGTTCAGACGTGT 7 0.17500000000000002 TruSeq Adapter, Index 13 (98% 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 0.2 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 0.21250000000000002 0.0 0.0 0.0 0.0 12-13 0.225 0.0 0.0 0.0 0.0 14-15 0.225 0.0 0.0 0.0 0.0 16-17 0.225 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 0.25 0.0 0.0 0.0 0.0 52-53 0.25 0.0 0.0 0.0 0.0 54-55 0.275 0.0 0.0 0.0 0.0 56-57 0.275 0.0 0.0 0.0 0.0 58-59 0.275 0.0 0.0 0.0 0.0 60-61 0.2875 0.0 0.0 0.0 0.0 62-63 0.4 0.0 0.0 0.0 0.0 64-65 0.425 0.0 0.0 0.0 0.0 66-67 0.425 0.0 0.0 0.0 0.0 68-69 0.425 0.0 0.0 0.0 0.0 70-71 0.425 0.0 0.0 0.0 0.0 72-73 0.425 0.0 0.0 0.0 0.0 74-75 0.425 0.0 0.0 0.0 0.0 76-77 0.425 0.0 0.0 0.0 0.0 78-79 0.425 0.0 0.0 0.0 0.0 80-81 0.425 0.0 0.0 0.0 0.0 82-83 0.425 0.0 0.0 0.0 0.0 84-85 0.45 0.0 0.0 0.0 0.0 86-87 0.45 0.0 0.0 0.0 0.0 88-89 0.45 0.0 0.0 0.0 0.0 90-91 0.45 0.0 0.0 0.0 0.0 92-93 0.45 0.0 0.0 0.0 0.0 94-95 0.45 0.0 0.0 0.0 0.0 96-97 0.4875 0.0 0.0 0.0 0.0 98-99 0.5125 0.0 0.0 0.0 0.0 100-101 0.525 0.0 0.0 0.0 0.0 102-103 0.525 0.0 0.0 0.0 0.0 104-105 0.525 0.0 0.0 0.0 0.0 106-107 0.575 0.0 0.0 0.0 0.0 108-109 0.625 0.0 0.0 0.0 0.0 110-111 0.725 0.0 0.0 0.0 0.0 112-113 0.7625 0.0 0.0 0.0 0.0 114-115 0.7875000000000001 0.0 0.0 0.0 0.0 116-117 0.8375 0.0 0.0 0.0 0.0 118-119 0.8875 0.0 0.0 0.0 0.0 120-121 1.0125 0.0 0.0 0.0 0.0 122-123 1.05 0.0 0.0 0.0 0.0 124-125 1.225 0.0 0.0 0.0 0.0 126-127 1.3125 0.0 0.0 0.0 0.0 128-129 1.3875000000000002 0.0 0.0 0.0 0.0 130-131 1.6125 0.0 0.0 0.0 0.0 132-133 1.7625 0.0 0.0 0.0 0.0 134-135 1.9625 0.0 0.0 0.0 0.0 136-137 2.025 0.0 0.0 0.0 0.0 138 2.075 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content fail #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position AAGAGCG 25 5.8536134E-6 115.36202 7 TCGGAAG 25 5.8536134E-6 115.36202 3 CGGAAGA 25 5.8536134E-6 115.36202 4 GATCGGA 30 1.4487059E-5 96.135025 1 GAGCGTC 25 8.897792E-4 86.521515 9 AGAGCGT 25 8.897792E-4 86.521515 8 ATCGGAA 35 3.1143303E-5 82.40144 2 GGAAGAG 35 3.1143303E-5 82.40144 5 GAAGAGC 40 6.0391365E-5 72.101265 6 CATTAAA 20 0.0060953954 28.840506 50-54 TCATTAA 20 0.0060953954 28.840506 50-54 ATCTCGG 20 0.0064836787 28.480001 35-39 AAAAAAA 380 5.991664E-6 6.4511657 60-64 >>END_MODULE Read 2740650 spots for SRR8096900.sra Written 2740650 spots for SRR8096900.sra Read 2740650 spots for SRR8096900.sra Written 2740650 spots for SRR8096900.sra Read 2740650 spots for SRR8096900.sra Written 2740650 spots for SRR8096900.sra Read 2740650 spots for SRR8096900.sra Written 2740650 spots for SRR8096900.sra Read 2740650 spots for SRR8096900.sra Written 2740650 spots for SRR8096900.sra Read 2740650 spots for SRR8096900.sra Written 2740650 spots for SRR8096900.sra Read 2740650 spots for SRR8096900.sra Written 2740650 spots for SRR8096900.sra Read 2740650 spots for SRR8096900.sra Written 2740650 spots for SRR8096900.sra Read 2740659 spots for SRR8096900.sra Written 2740659 spots for SRR8096900.sra Read 2740650 spots for SRR8096900.sra Written 2740650 spots for SRR8096900.sra Read 2740650 spots for SRR8096900.sra Written 2740650 spots for SRR8096900.sra Read 2740650 spots for SRR8096900.sra Written 2740650 spots for SRR8096900.sra Read 2740650 spots for SRR8096900.sra Written 2740650 spots for SRR8096900.sra Read 2740650 spots for SRR8096900.sra Written 2740650 spots for SRR8096900.sra Read 2740650 spots for SRR8096900.sra Written 2740650 spots for SRR8096900.sra Read 2740650 spots for SRR8096900.sra Written 2740650 spots for SRR8096900.sra Read 2740650 spots for SRR8096900.sra Written 2740650 spots for SRR8096900.sra Read 2740650 spots for SRR8096900.sra Written 2740650 spots for SRR8096900.sra Read 2740650 spots for SRR8096900.sra Written 2740650 spots for SRR8096900.sra Read 2740650 spots for SRR8096900.sra Written 2740650 spots for SRR8096900.sra SRR ids: ['SRR8096900.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_u65xg5zm SRR8096900.sra spots: 54813009 blocks: [[1, 2740650], [2740651, 5481300], [5481301, 8221950], [8221951, 10962600], [10962601, 13703250], [13703251, 16443900], [16443901, 19184550], [19184551, 21925200], [21925201, 24665850], [24665851, 27406500], [27406501, 30147150], [30147151, 32887800], [32887801, 35628450], [35628451, 38369100], [38369101, 41109750], [41109751, 43850400], [43850401, 46591050], [46591051, 49331700], [49331701, 52072350], [52072351, 54813009]] SRR8096900 file size 18445573 SRR8096900 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 SRR8096900 SRR8096900_1.fastq SRR8096900_2.fastq Input file: SRR8096900_1.fastq Paired file: SRR8096900_2.fastq trimmed: SRR8096900-trimmed-pair1.fastq, SRR8096900-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 Thu Dec 12 02:55:03 2024 >> started Thu Dec 12 02:56:13 2024 >> done (70.249s) 54813009 read pairs processed; of these: 297094 ( 0.54%) short read pairs filtered out after trimming by size control 3177202 ( 5.80%) empty read pairs filtered out after trimming by size control 51338713 (93.66%) read pairs available; of these: 29464236 (57.39%) trimmed read pairs available after processing 21874477 (42.61%) untrimmed read pairs available after processing Length distribution of reads after trimming: length count percentage 18 140 0.00% 19 227 0.00% 20 132 0.00% 21 267 0.00% 22 204 0.00% 23 199 0.00% 24 403 0.00% 25 281 0.00% 26 270 0.00% 27 235 0.00% 28 232 0.00% 29 303 0.00% 30 459 0.00% 31 317 0.00% 32 548 0.00% 33 280 0.00% 34 446 0.00% 35 578 0.00% 36 428 0.00% 37 512 0.00% 38 496 0.00% 39 692 0.00% 40 910 0.00% 41 1099 0.00% 42 1060 0.00% 43 1330 0.00% 44 1680 0.00% 45 3053 0.01% 46 3698 0.01% 47 3588 0.01% 48 3760 0.01% 49 3893 0.01% 50 3944 0.01% 51 3900 0.01% 52 3646 0.01% 53 4351 0.01% 54 4934 0.01% 55 5580 0.01% 56 8807 0.02% 57 5404 0.01% 58 10889 0.02% 59 14546 0.03% 60 9311 0.02% 61 47014 0.09% 62 14092 0.03% 63 3908 0.01% 64 3609 0.01% 65 4145 0.01% 66 4244 0.01% 67 4815 0.01% 68 5610 0.01% 69 7969 0.02% 70 8211 0.02% 71 7110 0.01% 72 6502 0.01% 73 7032 0.01% 74 5960 0.01% 75 6443 0.01% 76 6873 0.01% 77 7448 0.01% 78 8299 0.02% 79 9190 0.02% 80 9829 0.02% 81 10910 0.02% 82 12712 0.02% 83 17061 0.03% 84 30911 0.06% 85 32615 0.06% 86 36879 0.07% 87 38713 0.08% 88 39228 0.08% 89 38612 0.08% 90 37968 0.07% 91 37609 0.07% 92 37720 0.07% 93 38039 0.07% 94 40146 0.08% 95 41795 0.08% 96 44915 0.09% 97 49375 0.10% 98 52476 0.10% 99 54773 0.11% 100 55896 0.11% 101 59033 0.11% 102 62421 0.12% 103 66132 0.13% 104 69991 0.14% 105 74611 0.15% 106 77797 0.15% 107 81090 0.16% 108 84176 0.16% 109 83730 0.16% 110 85162 0.17% 111 87774 0.17% 112 90207 0.18% 113 93238 0.18% 114 96342 0.19% 115 100427 0.20% 116 105192 0.20% 117 109871 0.21% 118 114000 0.22% 119 119219 0.23% 120 124710 0.24% 121 130773 0.25% 122 135744 0.26% 123 144456 0.28% 124 150336 0.29% 125 159621 0.31% 126 168849 0.33% 127 177392 0.35% 128 192000 0.37% 129 200956 0.39% 130 211304 0.41% 131 224585 0.44% 132 238780 0.47% 133 250716 0.49% 134 266072 0.52% 135 281977 0.55% 136 305215 0.59% 137 329904 0.64% 138 350863 0.68% 139 380689 0.74% 140 421824 0.82% 141 462492 0.90% 142 527936 1.03% 143 603933 1.18% 144 726218 1.41% 145 896036 1.75% 146 1195039 2.33% 147 1700479 3.31% 148 3164440 6.16% 149 12646796 24.63% 150 21874477 42.61% 51338713 reads passed initial QC criterion=sequence-density sequence-density=1.08 sequence-density-rank=1 fanout-score=2.01 fanout-score-rank=38 prefix-density=1.10 prefix-fanout=2.0 sequence=AACATGGAGAACATGGCGAGGCGGCCGTTCTTGATCTCCTTCACCTTGAGCTCAGCGAA criterion=fanout-score sequence-density=0.09 sequence-density-rank=35 fanout-score=37.40 fanout-score-rank=1 prefix-density=0.34 prefix-fanout=9.4 sequence=GGCGGCGGCGGCCTCGCCGTCGCTGGTGTACTTCCCCAGCTGCGCCAGGGAGTTTGCCTTGGCGCGCAGCAGCAGTGCCTCCTGGGCCGCCGCCACGTTCTCCGGCCGTCCTCCCCACGTCTTCAGGCACGTGTTCTGCAGCGCCCTCGCGTATGAGAAGGACACGTGCCACGGGTTCGGCGACTGGTTCATCGCGTTCAGGTTCAGCGTTGCCTCCACCTCTGACTGCCCGCCCGACAGGAACATGATGCCGGGGACGGAAGGAGGGATCCTCCTCTGGAGGAGCTTGAGGG criterion=sequence-density sequence-density=0.48 sequence-density-rank=1 fanout-score=2.14 fanout-score-rank=33 prefix-density=0.49 prefix-fanout=2.1 sequence=TTCGCTGAGCTCAAGGTGAAGGAGATCAAGAACGGCCGCCTCGCCATGTTCTCCATGTT criterion=fanout-score sequence-density=0.01 sequence-density-rank=36 fanout-score=43.22 fanout-score-rank=1 prefix-density=0.07 prefix-fanout=4.8 sequence=AGGAAAGGCTGCAATTGCAAGCTTGTGTCAAAGAAGAGGGTAGCACCTGATCCTCTTGCCTTTGGAGCCAGAAACAATGGCCTCGGCTACTATCCTCAAATCGTCTTTCCTTCCCAAGAAGTCCGAATGGGGCACCACCCGCCAGGCTGCCACTCCCAAGCAGATGACCGTCTCCATGGTTGTCCGTGCCAGCGCATACGCTGATGAACTTGTCAAGACCGCGAAAACCATCGCATCACCAGGAAGGGGCATCCTAGCCATGGATGAGTCCAATGCTACCTGTGGAAAGAGACTTGACTCGATTGGCCTTGAGAACACTGAGGCTAACCGCCAGGCTTACCGTACCCTCCTTGTCACTCCACCAGGCCTGGGAAATTACATCTCTGGTGCTATCCTCTTCGAGGAGACCCTCTACCAATCGACTGTTGATGGCAAGAAGATTGTTGACATCCTTGTCGAGCAGGGAATCGTTCCCGGCATCAAGGTTGACAAGGGTCTTGTGCCACTCGTT SRR8096900 testing PE reads STAR mapping to Ensembl genome Started job on | Dec 12 02:56:58 Started mapping on | Dec 12 02:56:58 Finished on | Dec 12 03:02:39 Mapping speed, Million of reads per hour | 541.99 Number of input reads | 51338713 Average input read length | 289 UNIQUE READS: Uniquely mapped reads number | 49338257 Uniquely mapped reads % | 96.10% Average mapped length | 290.15 Number of splices: Total | 51052574 Number of splices: Annotated (sjdb) | 48235143 Number of splices: GT/AG | 50379452 Number of splices: GC/AG | 589047 Number of splices: AT/AC | 15456 Number of splices: Non-canonical | 68619 Mismatch rate per base, % | 0.30% Deletion rate per base | 0.01% Deletion average length | 2.09 Insertion rate per base | 0.01% Insertion average length | 1.90 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 654000 % of reads mapped to multiple loci | 1.27% Number of reads mapped to too many loci | 19376 % of reads mapped to too many loci | 0.04% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 2.32% % of reads unmapped: other | 0.26% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 1652504 1652504 1652504 N_multimapping 654000 654000 654000 N_noFeature 1846313 47804577 2222666 N_ambiguous 1373177 6099 219744 UnstrandedReadsAssigned:46118767 PositiveStrandReadsAssigned:1527581 NegativeStrandReadsAssigned:46895847 Dataset is classified negative stranded MeadianReadLen=150 20thPercentileLength=149 echo kmer=145 SRR8096900 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: SRR8096900-trimmed-pair1.fastq SRR8096900-trimmed-pair2.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 51,338,713 reads, 46,986,883 reads pseudoaligned [quant] estimated average fragment length: 284.243 [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,202 rounds 52973 SRR8096900.ke.tsv 35125 SRR8096900.se.tsv 88098 total ==> SRR8096900.ke.tsv <== target_id length eff_length est_counts tpm PNS24245 936 653.495 0 0 PNS24247 1044 760.757 131.035 5.02707 PNS24249 1928 1644.76 90.1294 1.59933 PNS24246 1044 760.757 131.035 5.02707 PNS24248 1044 760.757 131.035 5.02707 PNS24244 1471 1187.76 327.766 8.05396 PNS24243 293 78.8944 0 0 KQK14069 1603 1319.76 12832.7 283.79 KQK14071 474 213.274 183.738 25.144 ==> SRR8096900.se.tsv <== BRADI_1g14170v3 14834 BRADI_1g53295v3 45 BRADI_1g59795v3 1978 BRADI_1g07683v3 0 BRADI_1g00485v3 1 BRADI_1g20270v3 371 BRADI_1g74790v3 131 BRADI_1g09890v3 0 BRADI_1g77505v3 618 BRADI_1g48960v3 0 SRR8096900 completed mapping pipeline successfully