Starting /dee2/code/volunteer_pipeline.sh SRR12951303 current disk space = 1543248392192 free memory = 1596169604 SRR12951303 SRAfilesize b179fcf9924203428fbb19f8a76d0033 SRR12951303.sra SRR12951303.sra file validated SRR12951303 is paired end SRR12951303 is conventional basespace SRR12951303 read1 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR12951303_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 50 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 36.605 37.0 37.0 37.0 37.0 37.0 2 36.2565 37.0 37.0 37.0 37.0 37.0 3 36.527 37.0 37.0 37.0 37.0 37.0 4 36.5095 37.0 37.0 37.0 37.0 37.0 5 36.585 37.0 37.0 37.0 37.0 37.0 6 36.653 37.0 37.0 37.0 37.0 37.0 7 36.505 37.0 37.0 37.0 37.0 37.0 8 36.516 37.0 37.0 37.0 37.0 37.0 9 36.5135 37.0 37.0 37.0 37.0 37.0 10-14 36.5412 37.0 37.0 37.0 37.0 37.0 15-19 36.54880000000001 37.0 37.0 37.0 37.0 37.0 20-24 36.4915 37.0 37.0 37.0 37.0 37.0 25-29 36.464600000000004 37.0 37.0 37.0 37.0 37.0 30-34 36.443200000000004 37.0 37.0 37.0 37.0 37.0 35-39 36.441900000000004 37.0 37.0 37.0 37.0 37.0 40-44 36.4012 37.0 37.0 37.0 37.0 37.0 45-49 36.3722 37.0 37.0 37.0 37.0 37.0 50-54 36.374399999999994 37.0 37.0 37.0 37.0 37.0 55-59 36.2897 37.0 37.0 37.0 37.0 37.0 60-64 36.2818 37.0 37.0 37.0 37.0 37.0 65-69 36.2598 37.0 37.0 37.0 37.0 37.0 70-74 36.2139 37.0 37.0 37.0 37.0 37.0 75-79 36.2752 37.0 37.0 37.0 37.0 37.0 80-84 36.254599999999996 37.0 37.0 37.0 37.0 37.0 85-89 36.2567 37.0 37.0 37.0 37.0 37.0 90-94 36.2439 37.0 37.0 37.0 37.0 37.0 95-99 36.186499999999995 37.0 37.0 37.0 37.0 37.0 100-104 36.1923 37.0 37.0 37.0 37.0 37.0 105-109 36.162099999999995 37.0 37.0 37.0 37.0 37.0 110-114 36.139100000000006 37.0 37.0 37.0 37.0 37.0 115-119 36.150600000000004 37.0 37.0 37.0 37.0 37.0 120-124 36.0764 37.0 37.0 37.0 37.0 37.0 125-129 36.0051 37.0 37.0 37.0 37.0 37.0 130-134 35.99249999999999 37.0 37.0 37.0 37.0 37.0 135-139 35.918600000000005 37.0 37.0 37.0 37.0 37.0 140-144 35.77289999999999 37.0 37.0 37.0 37.0 37.0 145-149 35.7205 37.0 37.0 37.0 37.0 37.0 150-151 35.556 37.0 37.0 37.0 37.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 20 1.0 21 1.0 22 3.0 23 0.0 24 4.0 25 6.0 26 5.0 27 4.0 28 18.0 29 17.0 30 26.0 31 38.0 32 55.0 33 56.0 34 137.0 35 301.0 36 2862.0 37 466.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 47.275 11.625 4.275 36.825 2 21.460843373493976 11.320281124497992 34.06124497991968 33.157630522088354 3 19.475 14.499999999999998 27.650000000000002 38.375 4 26.025 20.974999999999998 21.8 31.2 5 25.624999999999996 29.975 22.375 22.025 6 26.375 29.599999999999998 20.25 23.775 7 18.725 25.124999999999996 36.6 19.55 8 19.625 24.175 28.4 27.800000000000004 9 20.225 21.8 31.65 26.325 10-14 23.599999999999998 26.655 24.104999999999997 25.64 15-19 23.625 24.85 24.68 26.845000000000002 20-24 24.025 25.014999999999997 24.715 26.245 25-29 24.015 25.435000000000002 24.615000000000002 25.935000000000002 30-34 23.515 25.580000000000002 24.959999999999997 25.945 35-39 24.14 24.759999999999998 24.72 26.38 40-44 23.345 25.66 24.81 26.185000000000002 45-49 23.599999999999998 24.9 24.465 27.034999999999997 50-54 23.535 24.905 25.09 26.47 55-59 24.84 24.57 24.685000000000002 25.905 60-64 23.825 24.495 25.069999999999997 26.61 65-69 23.674999999999997 25.27 24.625 26.43 70-74 24.895 24.865000000000002 24.385 25.855 75-79 24.385 25.53 24.25 25.835 80-84 24.93 24.77 24.365000000000002 25.935000000000002 85-89 25.385 24.455 23.875 26.284999999999997 90-94 24.745 24.205 24.67 26.38 95-99 25.285000000000004 24.675 23.474999999999998 26.565 100-104 25.21 25.165 23.75 25.874999999999996 105-109 25.205 25.2 23.285 26.31 110-114 24.825 24.9 23.43 26.845000000000002 115-119 25.045 24.87 23.165 26.919999999999998 120-124 24.875 25.314999999999998 23.68 26.13 125-129 25.185000000000002 25.25 23.22 26.345000000000002 130-134 24.295 24.895 23.955000000000002 26.855 135-139 24.12 25.05 23.695 27.134999999999998 140-144 25.19 24.68 23.635 26.495 145-149 25.509999999999998 24.965 24.015 25.509999999999998 150-151 25.0125 24.075 23.8125 27.1 >>END_MODULE >>Per sequence GC content fail #GC Content Count 0 0.0 1 0.5 2 0.5 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 0.5 14 0.5 15 0.0 16 0.0 17 0.0 18 0.0 19 0.0 20 0.0 21 0.0 22 0.0 23 0.0 24 0.0 25 0.0 26 0.5 27 2.0 28 2.5 29 2.0 30 4.5 31 12.5 32 16.5 33 20.0 34 23.0 35 27.0 36 42.5 37 63.5 38 73.5 39 86.0 40 106.5 41 115.5 42 140.5 43 175.5 44 184.0 45 179.0 46 191.0 47 188.0 48 173.5 49 163.0 50 154.0 51 157.5 52 136.5 53 117.0 54 124.0 55 112.5 56 89.5 57 90.5 58 87.5 59 83.5 60 84.0 61 70.0 62 59.5 63 53.5 64 57.5 65 70.0 66 81.0 67 68.5 68 49.0 69 46.5 70 39.0 71 41.5 72 39.5 73 23.0 74 14.5 75 16.0 76 16.5 77 8.5 78 4.0 79 4.0 80 2.5 81 0.5 82 0.5 83 1.5 84 1.5 85 0.5 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 0.4 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 0.0 150-151 0.0 >>END_MODULE >>Sequence Length Distribution pass #Length Count 151 4000.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 81.8 #Duplication Level Percentage of deduplicated Percentage of total 1 82.94621026894865 67.85 2 12.95843520782396 21.2 3 3.4229828850855744 8.4 4 0.4278728606356968 1.4000000000000001 5 0.18337408312958436 0.75 6 0.030562347188264057 0.15 7 0.0 0.0 8 0.0 0.0 9 0.0 0.0 >10 0.030562347188264057 0.25 >50 0.0 0.0 >100 0.0 0.0 >500 0.0 0.0 >1k 0.0 0.0 >5k 0.0 0.0 >10k+ 0.0 0.0 >>END_MODULE >>Overrepresented sequences warn #Sequence Count Percentage Possible Source GATCGGAAGAGCACACGTCTGAACTCCAGTCACTCGGTTACATCTCGTAT 10 0.25 TruSeq Adapter, Index 10 (97% over 36bp) GGGGAAACGAGAACAATGTGGATGCGAGAGAGAGGAGGGAAAGGAGAAGG 6 0.15 No Hit GCCTGCATTCCGGGCATTCGTAGAAGACAGTCTGCCCTTCATCCGCTGCC 5 0.125 No Hit CCCATGCGCGGCCGTCGGCGTCAGTGGCCGAGCCGGACTCGCCGCAGTTC 5 0.125 No Hit GTATGTTCAGTCCAATTGCAGGTTAAAGAAACTGCAGATGAATTGACCTG 5 0.125 No Hit CCTCTGTTTACAGTTCATCAAACATCATTTTAGACCCTGGTACTATAAGA 5 0.125 No Hit CAACGGTTCAATATAATTTACCAGATGAGGTAGTTGACCGTGAGTAAATA 5 0.125 No Hit TTTTTTTTTTTTAAACTGATGAACATCCCATCTCTTCATTTTAACCTTAA 5 0.125 No Hit >>END_MODULE >>Adapter Content fail #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 0.0125 0.0 0.0 0.0 0.0 48-49 0.025 0.0 0.0 0.0 0.0 50-51 0.025 0.0 0.0 0.0 0.0 52-53 0.025 0.0 0.0 0.0 0.0 54-55 0.025 0.0 0.0 0.0 0.0 56-57 0.037500000000000006 0.0 0.0 0.0 0.0 58-59 0.05 0.0 0.0 0.0 0.0 60-61 0.05 0.0 0.0 0.0 0.0 62-63 0.0625 0.0 0.0 0.0 0.0 64-65 0.125 0.0 0.0 0.0 0.0 66-67 0.15 0.0 0.0 0.0 0.0 68-69 0.2 0.0 0.0 0.0 0.0 70-71 0.2375 0.0 0.0 0.0 0.0 72-73 0.30000000000000004 0.0 0.0 0.0 0.0 74-75 0.3625 0.0 0.0 0.0 0.0 76-77 0.5 0.0 0.0 0.0 0.0 78-79 0.625 0.0 0.0 0.0 0.0 80-81 0.9125 0.0 0.0 0.0 0.0 82-83 1.0625 0.0 0.0 0.0 0.0 84-85 1.3250000000000002 0.0 0.0 0.0 0.0 86-87 1.575 0.0 0.0 0.0 0.0 88-89 1.8375 0.0 0.0 0.0 0.0 90-91 2.1125 0.0 0.0 0.0 0.0 92-93 2.625 0.0 0.0 0.0 0.0 94-95 3.0625 0.0 0.0 0.0 0.0 96-97 3.4875 0.0 0.0 0.0 0.0 98-99 4.1 0.0 0.0 0.0 0.0 100-101 4.574999999999999 0.0 0.0 0.0 0.0 102-103 5.1125 0.0 0.0 0.0 0.0 104-105 5.85 0.0 0.0 0.0 0.0 106-107 6.612500000000001 0.0 0.0 0.0 0.0 108-109 7.1625 0.0 0.0 0.0 0.0 110-111 7.7625 0.0 0.0 0.0 0.0 112-113 8.375 0.0 0.0 0.0 0.0 114-115 9.0625 0.0 0.0 0.0 0.0 116-117 9.537500000000001 0.0 0.0 0.0 0.0 118-119 10.212499999999999 0.0 0.0 0.0 0.0 120-121 11.225 0.0 0.0 0.0 0.0 122-123 12.225000000000001 0.0 0.0 0.0 0.0 124-125 13.2125 0.0 0.0 0.0 0.0 126-127 14.0875 0.0 0.0 0.0 0.0 128-129 14.95 0.0 0.0 0.0 0.0 130-131 15.775 0.0 0.0 0.0 0.0 132-133 16.737499999999997 0.0 0.0 0.0 0.0 134-135 17.6625 0.0 0.0 0.0 0.0 136-137 18.775 0.0 0.0 0.0 0.0 138-139 19.85 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position CCAAAGC 10 0.006830828 145.0 3 CCCAAAG 10 0.006830828 145.0 2 >>END_MODULE SRR12951303 read2 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR12951303_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 51 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 36.2585 37.0 37.0 37.0 37.0 37.0 2 36.1585 37.0 37.0 37.0 37.0 37.0 3 36.213 37.0 37.0 37.0 37.0 37.0 4 36.16 37.0 37.0 37.0 37.0 37.0 5 36.336 37.0 37.0 37.0 37.0 37.0 6 36.3345 37.0 37.0 37.0 37.0 37.0 7 36.21 37.0 37.0 37.0 37.0 37.0 8 36.265 37.0 37.0 37.0 37.0 37.0 9 36.2805 37.0 37.0 37.0 37.0 37.0 10-14 36.2726 37.0 37.0 37.0 37.0 37.0 15-19 36.226 37.0 37.0 37.0 37.0 37.0 20-24 36.1674 37.0 37.0 37.0 37.0 37.0 25-29 36.189299999999996 37.0 37.0 37.0 37.0 37.0 30-34 36.1626 37.0 37.0 37.0 37.0 37.0 35-39 36.0622 37.0 37.0 37.0 37.0 37.0 40-44 36.1083 37.0 37.0 37.0 37.0 37.0 45-49 36.110499999999995 37.0 37.0 37.0 37.0 37.0 50-54 36.0895 37.0 37.0 37.0 37.0 37.0 55-59 36.0516 37.0 37.0 37.0 37.0 37.0 60-64 36.0454 37.0 37.0 37.0 37.0 37.0 65-69 36.0107 37.0 37.0 37.0 37.0 37.0 70-74 35.984899999999996 37.0 37.0 37.0 37.0 37.0 75-79 35.9362 37.0 37.0 37.0 37.0 37.0 80-84 35.95309999999999 37.0 37.0 37.0 37.0 37.0 85-89 35.8602 37.0 37.0 37.0 37.0 37.0 90-94 35.9928 37.0 37.0 37.0 37.0 37.0 95-99 35.90650000000001 37.0 37.0 37.0 37.0 37.0 100-104 35.9082 37.0 37.0 37.0 37.0 37.0 105-109 35.738600000000005 37.0 37.0 37.0 37.0 37.0 110-114 35.7423 37.0 37.0 37.0 37.0 37.0 115-119 35.7669 37.0 37.0 37.0 37.0 37.0 120-124 35.648799999999994 37.0 37.0 37.0 37.0 37.0 125-129 35.4885 37.0 37.0 37.0 37.0 37.0 130-134 35.3505 37.0 37.0 37.0 34.6 37.0 135-139 35.263999999999996 37.0 37.0 37.0 34.6 37.0 140-144 34.9682 37.0 37.0 37.0 25.0 37.0 145-149 34.7699 37.0 37.0 37.0 25.0 37.0 150-151 34.414249999999996 37.0 37.0 37.0 25.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 13 4.0 14 5.0 15 3.0 16 2.0 17 0.0 18 3.0 19 4.0 20 1.0 21 4.0 22 10.0 23 11.0 24 6.0 25 7.0 26 14.0 27 9.0 28 14.0 29 11.0 30 23.0 31 46.0 32 58.0 33 103.0 34 181.0 35 516.0 36 2593.0 37 372.0 >>END_MODULE >>Per base sequence content warn #Base G A T C 1 42.05 22.1 7.049999999999999 28.799999999999997 2 30.425 23.325000000000003 26.650000000000002 19.6 3 22.400000000000002 24.6 30.525000000000002 22.475 4 25.6 30.85 19.975 23.575 5 27.800000000000004 33.1 18.7 20.4 6 24.45 34.875 19.650000000000002 21.025 7 23.724999999999998 19.275000000000002 33.324999999999996 23.674999999999997 8 24.5 23.05 24.375 28.075 9 25.0 20.424999999999997 27.875 26.700000000000003 10-14 26.105 24.685000000000002 23.03 26.179999999999996 15-19 25.629999999999995 24.16 24.395 25.814999999999998 20-24 26.905 24.285 24.065 24.745 25-29 26.484999999999996 24.725 23.615 25.174999999999997 30-34 26.384999999999998 24.415 23.255 25.945 35-39 26.125 24.605 24.09 25.180000000000003 40-44 26.51 24.64 23.755000000000003 25.095 45-49 26.26 24.765 23.54 25.435000000000002 50-54 26.915 24.41 24.315 24.36 55-59 26.83 23.925 24.08 25.165 60-64 26.845000000000002 24.610000000000003 24.13 24.415 65-69 26.69 24.884999999999998 24.325 24.099999999999998 70-74 26.950000000000003 24.46 23.565 25.025 75-79 26.845000000000002 23.72 24.97 24.465 80-84 26.515 24.3 24.205 24.98 85-89 27.169999999999998 24.14 24.725 23.965 90-94 27.384999999999998 25.135 22.925 24.555 95-99 27.99 24.44 23.515 24.055 100-104 28.1 24.385 23.745 23.77 105-109 27.6 25.264999999999997 23.74 23.395 110-114 28.23 24.84 23.515 23.415 115-119 28.975 25.355 22.755 22.915 120-124 29.32 24.265 23.36 23.055 125-129 29.13 24.515 23.810000000000002 22.545 130-134 30.255 24.685000000000002 23.150000000000002 21.91 135-139 30.09 24.099999999999998 23.794999999999998 22.015 140-144 30.964999999999996 24.240000000000002 23.71 21.085 145-149 31.145 24.445 23.365 21.044999999999998 150-151 32.237500000000004 23.375 24.3875 20.0 >>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 0.5 6 0.5 7 0.0 8 0.0 9 0.0 10 0.0 11 0.0 12 0.5 13 0.5 14 0.5 15 1.0 16 0.5 17 0.5 18 0.5 19 0.0 20 0.5 21 0.5 22 0.0 23 1.0 24 2.5 25 2.5 26 1.0 27 3.0 28 4.0 29 2.5 30 2.0 31 6.0 32 10.5 33 15.0 34 21.5 35 28.0 36 32.0 37 51.5 38 87.5 39 95.0 40 101.0 41 109.0 42 120.0 43 148.5 44 163.0 45 169.0 46 180.0 47 175.5 48 166.0 49 166.0 50 150.5 51 140.0 52 144.0 53 129.0 54 106.5 55 109.5 56 92.5 57 79.0 58 97.5 59 99.5 60 98.5 61 83.0 62 71.5 63 78.0 64 69.5 65 67.0 66 68.0 67 67.5 68 63.5 69 50.5 70 42.5 71 45.0 72 43.0 73 31.0 74 25.5 75 20.5 76 13.5 77 9.5 78 7.0 79 3.5 80 2.0 81 2.0 82 2.0 83 2.0 84 0.5 85 0.0 86 0.0 87 0.0 88 0.5 89 0.5 90 0.0 91 1.0 92 1.0 93 0.5 94 1.0 95 1.5 96 1.5 97 1.0 98 1.5 99 2.0 100 2.5 >>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 0.0 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 0.0 150-151 0.0 >>END_MODULE >>Sequence Length Distribution pass #Length Count 151 4000.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 82.05 #Duplication Level Percentage of deduplicated Percentage of total 1 83.2114564290067 68.27499999999999 2 12.583790371724557 20.65 3 3.5648994515539303 8.774999999999999 4 0.42656916514320536 1.4000000000000001 5 0.18281535648994515 0.75 6 0.030469226081657527 0.15 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 warn #Sequence Count Percentage Possible Source CACGCAGTACTTTTCCCCGGTCTACAAAGACCTCACTCTCCTCCCCCCCG 6 0.15 No Hit CAACTGGCGTACACTCTTCCTAGTCCCATGGCCATCTCGACTCTACTCCG 5 0.125 No Hit CAGTACCCCTGGGGCTCTGGCTGCTGTTGTTCCGACAAACATTAATGCAA 5 0.125 No Hit GCGACGGGGCGGTGAAGCCGGCGGCGGCGGCGCGGGAGCGAGCGGGCATG 5 0.125 No Hit GGTTCATGTCCCAGGTGTTACGCTGTAAGCCGTGTCTGACTGAGGGTTAT 5 0.125 No Hit GATATGCAGAAGATTTGTCGCCGTAGCAGCTAAAAACCATTCGTTGTTGG 5 0.125 No Hit AGAATCTCGCGTTAATGTTGGAGACTCTTGGTGAATTGGCTATTGCTAAT 5 0.125 No Hit >>END_MODULE >>Adapter Content fail #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 0.0125 0.0 0.0 0.0 0.0 48-49 0.025 0.0 0.0 0.0 0.0 50-51 0.025 0.0 0.0 0.0 0.0 52-53 0.025 0.0 0.0 0.0 0.0 54-55 0.025 0.0 0.0 0.0 0.0 56-57 0.037500000000000006 0.0 0.0 0.0 0.0 58-59 0.05 0.0 0.0 0.0 0.0 60-61 0.05 0.0 0.0 0.0 0.0 62-63 0.0625 0.0 0.0 0.0 0.0 64-65 0.125 0.0 0.0 0.0 0.0 66-67 0.15 0.0 0.0 0.0 0.0 68-69 0.2 0.0 0.0 0.0 0.0 70-71 0.2375 0.0 0.0 0.0 0.0 72-73 0.30000000000000004 0.0 0.0 0.0 0.0 74-75 0.3625 0.0 0.0 0.0 0.0 76-77 0.5 0.0 0.0 0.0 0.0 78-79 0.625 0.0 0.0 0.0 0.0 80-81 0.8999999999999999 0.0 0.0 0.0 0.0 82-83 1.0375 0.0 0.0 0.0 0.0 84-85 1.2999999999999998 0.0 0.0 0.0 0.0 86-87 1.55 0.0 0.0 0.0 0.0 88-89 1.8125 0.0 0.0 0.0 0.0 90-91 2.0875 0.0 0.0 0.0 0.0 92-93 2.5999999999999996 0.0 0.0 0.0 0.0 94-95 3.025 0.0 0.0 0.0 0.0 96-97 3.4625000000000004 0.0 0.0 0.0 0.0 98-99 4.075 0.0 0.0 0.0 0.0 100-101 4.550000000000001 0.0 0.0 0.0 0.0 102-103 5.0875 0.0 0.0 0.0 0.0 104-105 5.825 0.0 0.0 0.0 0.0 106-107 6.5625 0.0 0.0 0.0 0.0 108-109 7.1 0.0 0.0 0.0 0.0 110-111 7.6625 0.0 0.0 0.0 0.0 112-113 8.275 0.0 0.0 0.0 0.0 114-115 8.9625 0.0 0.0 0.0 0.0 116-117 9.4375 0.0 0.0 0.0 0.0 118-119 10.1125 0.0 0.0 0.0 0.0 120-121 11.1125 0.0 0.0 0.0 0.0 122-123 12.125 0.0 0.0 0.0 0.0 124-125 13.1125 0.0 0.0 0.0 0.0 126-127 14.0 0.0 0.0 0.0 0.0 128-129 14.875 0.0 0.0 0.0 0.0 130-131 15.7125 0.0 0.0 0.0 0.0 132-133 16.65 0.0 0.0 0.0 0.0 134-135 17.5625 0.0 0.0 0.0 0.0 136-137 18.7 0.0 0.0 0.0 0.0 138-139 19.775 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content pass >>END_MODULE Read 1505543 spots for SRR12951303.sra Written 1505543 spots for SRR12951303.sra Read 1505543 spots for SRR12951303.sra Written 1505543 spots for SRR12951303.sra Read 1505543 spots for SRR12951303.sra Written 1505543 spots for SRR12951303.sra Read 1505543 spots for SRR12951303.sra Written 1505543 spots for SRR12951303.sra Read 1505543 spots for SRR12951303.sra Written 1505543 spots for SRR12951303.sra Read 1505543 spots for SRR12951303.sra Written 1505543 spots for SRR12951303.sra Read 1505543 spots for SRR12951303.sra Written 1505543 spots for SRR12951303.sra Read 1505543 spots for SRR12951303.sra Written 1505543 spots for SRR12951303.sra Read 1505543 spots for SRR12951303.sra Written 1505543 spots for SRR12951303.sra Read 1505543 spots for SRR12951303.sra Written 1505543 spots for SRR12951303.sra Read 1505543 spots for SRR12951303.sra Written 1505543 spots for SRR12951303.sra Read 1505543 spots for SRR12951303.sra Written 1505543 spots for SRR12951303.sra Read 1505543 spots for SRR12951303.sra Written 1505543 spots for SRR12951303.sra Read 1505543 spots for SRR12951303.sra Written 1505543 spots for SRR12951303.sra Read 1505543 spots for SRR12951303.sra Written 1505543 spots for SRR12951303.sra Read 1505546 spots for SRR12951303.sra Written 1505546 spots for SRR12951303.sra Read 1505543 spots for SRR12951303.sra Written 1505543 spots for SRR12951303.sra Read 1505543 spots for SRR12951303.sra Written 1505543 spots for SRR12951303.sra Read 1505543 spots for SRR12951303.sra Written 1505543 spots for SRR12951303.sra Read 1505543 spots for SRR12951303.sra Written 1505543 spots for SRR12951303.sra SRR ids: ['SRR12951303.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_no70suiv SRR12951303.sra spots: 30110863 blocks: [[1, 1505543], [1505544, 3011086], [3011087, 4516629], [4516630, 6022172], [6022173, 7527715], [7527716, 9033258], [9033259, 10538801], [10538802, 12044344], [12044345, 13549887], [13549888, 15055430], [15055431, 16560973], [16560974, 18066516], [18066517, 19572059], [19572060, 21077602], [21077603, 22583145], [22583146, 24088688], [24088689, 25594231], [25594232, 27099774], [27099775, 28605317], [28605318, 30110863]] SRR12951303 file size 10211288 SRR12951303 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 SRR12951303 SRR12951303_1.fastq SRR12951303_2.fastq Input file: SRR12951303_1.fastq Paired file: SRR12951303_2.fastq trimmed: SRR12951303-trimmed-pair1.fastq, SRR12951303-trimmed-pair2.fastq Parameters used: -- 3' end adapter sequence (-x): AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC -- paired 3' end adapter sequence (-y): AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTA -- maximum error ratio allowed (-r): 0.100 -- maximum indel error ratio allowed (-d): 0.030 -- end quality threshold (-q): 10 -- minimum read length allowed after trimming (-l): 18 -- file format (-f): Sanger/Illumina 1.8+ FASTQ -- number of concurrent threads (-t): 20 Sat Dec 7 11:09:11 2024 >> started Sat Dec 7 11:09:59 2024 >> done (47.756s) 30110863 read pairs processed; of these: 394 ( 0.00%) short read pairs filtered out after trimming by size control 58361 ( 0.19%) empty read pairs filtered out after trimming by size control 30052108 (99.80%) read pairs available; of these: 7141530 (23.76%) trimmed read pairs available after processing 22910578 (76.24%) untrimmed read pairs available after processing Length distribution of reads after trimming: length count percentage 18 32 0.00% 19 39 0.00% 20 46 0.00% 21 70 0.00% 22 72 0.00% 23 93 0.00% 24 121 0.00% 25 141 0.00% 26 158 0.00% 27 151 0.00% 28 204 0.00% 29 147 0.00% 30 200 0.00% 31 192 0.00% 32 203 0.00% 33 178 0.00% 34 228 0.00% 35 238 0.00% 36 226 0.00% 37 277 0.00% 38 230 0.00% 39 288 0.00% 40 271 0.00% 41 328 0.00% 42 336 0.00% 43 340 0.00% 44 385 0.00% 45 405 0.00% 46 431 0.00% 47 545 0.00% 48 575 0.00% 49 650 0.00% 50 821 0.00% 51 807 0.00% 52 943 0.00% 53 1049 0.00% 54 1110 0.00% 55 1221 0.00% 56 1410 0.00% 57 1598 0.01% 58 1824 0.01% 59 2262 0.01% 60 2559 0.01% 61 2961 0.01% 62 3293 0.01% 63 3701 0.01% 64 4187 0.01% 65 4256 0.01% 66 4806 0.02% 67 5430 0.02% 68 6205 0.02% 69 7099 0.02% 70 8304 0.03% 71 9236 0.03% 72 10683 0.04% 73 11847 0.04% 74 13226 0.04% 75 14702 0.05% 76 15683 0.05% 77 16696 0.06% 78 18404 0.06% 79 20361 0.07% 80 22935 0.08% 81 25607 0.09% 82 28177 0.09% 83 30906 0.10% 84 33594 0.11% 85 35951 0.12% 86 38056 0.13% 87 40581 0.14% 88 42422 0.14% 89 45078 0.15% 90 47199 0.16% 91 50657 0.17% 92 54078 0.18% 93 58514 0.19% 94 62116 0.21% 95 63646 0.21% 96 66827 0.22% 97 68416 0.23% 98 70692 0.24% 99 72789 0.24% 100 74615 0.25% 101 76661 0.26% 102 80274 0.27% 103 84277 0.28% 104 86050 0.29% 105 89465 0.30% 106 91707 0.31% 107 93679 0.31% 108 94301 0.31% 109 96183 0.32% 110 97291 0.32% 111 99813 0.33% 112 103040 0.34% 113 105078 0.35% 114 107972 0.36% 115 109195 0.36% 116 110866 0.37% 117 112499 0.37% 118 113342 0.38% 119 113706 0.38% 120 114943 0.38% 121 116520 0.39% 122 117353 0.39% 123 120266 0.40% 124 122950 0.41% 125 124108 0.41% 126 125415 0.42% 127 125710 0.42% 128 125944 0.42% 129 127635 0.42% 130 127066 0.42% 131 126751 0.42% 132 128775 0.43% 133 131247 0.44% 134 132284 0.44% 135 134355 0.45% 136 135179 0.45% 137 134650 0.45% 138 134268 0.45% 139 134415 0.45% 140 132778 0.44% 141 133991 0.45% 142 136913 0.46% 143 134867 0.45% 144 136997 0.46% 145 138554 0.46% 146 136866 0.46% 147 137422 0.46% 148 137997 0.46% 149 134897 0.45% 150 137675 0.46% 151 22910578 76.24% 30052108 reads passed initial QC criterion=sequence-density sequence-density=0.21 sequence-density-rank=1 fanout-score=3.53 fanout-score-rank=34 prefix-density=0.25 prefix-fanout=3.0 sequence=GTGATGGTCTTGCC criterion=fanout-score sequence-density=0.03 sequence-density-rank=34 fanout-score=519.62 fanout-score-rank=1 prefix-density=0.73 prefix-fanout=18.8 sequence=GGCGGCGGCGAACCGCCCCCGTCGCCGCGATCCGAACACTTCACCGGACCATTCAATCGGTAGGAGCGACGGGCGGTGTGTACAAAGGGCAGGGACGTAGTCAACGCGAGCTGATGACTCGCGCTTACTAGGCATTCCTCGTTGAAGACCAACAATTGCAATGATCTATCCCCATCACGATGAAATTTCCCAAGATTACCCGGGCCTGTCGGCCAAGGCTATATACTCGTTGAATACATCAGTGTAGCGCGCGTGCGGCCCAGAACATCTAAGGGCATCACAGACCTGTTATTGCCTCAAACTTCCGTCGCCTAAACGGCGATAGTCCCTCTAAGAAGCTAGCTGCGGAGGGATGGCTCCGCATAGCTAGTTAGCAGGCTGAGGTCTCGTTCGTTAACGGAATTAACCAGACAAATCGCTCCACCAACTAAGAACGGCCATGCACCACCACCCATAGAATCAAGAAAGAGCTCTCAGTCTGTCAATCCTTGCTATGTCTGGACCTGGTAAG criterion=sequence-density sequence-density=0.51 sequence-density-rank=1 fanout-score=2.08 fanout-score-rank=33 prefix-density=0.52 prefix-fanout=2.1 sequence=CGGTTCCGGTTC criterion=fanout-score sequence-density=0.12 sequence-density-rank=16 fanout-score=198.43 fanout-score-rank=1 prefix-density=1.00 prefix-fanout=23.7 sequence=CGCCGCCGCCGC SRR12951303 testing PE reads STAR mapping to Ensembl genome Started job on | Dec 07 11:10:45 Started mapping on | Dec 07 11:10:45 Finished on | Dec 07 11:13:50 Mapping speed, Million of reads per hour | 584.80 Number of input reads | 30052108 Average input read length | 287 UNIQUE READS: Uniquely mapped reads number | 28687089 Uniquely mapped reads % | 95.46% Average mapped length | 286.56 Number of splices: Total | 25884114 Number of splices: Annotated (sjdb) | 24171194 Number of splices: GT/AG | 25530288 Number of splices: GC/AG | 290580 Number of splices: AT/AC | 16466 Number of splices: Non-canonical | 46780 Mismatch rate per base, % | 0.22% Deletion rate per base | 0.01% Deletion average length | 2.50 Insertion rate per base | 0.01% Insertion average length | 2.34 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 309847 % of reads mapped to multiple loci | 1.03% Number of reads mapped to too many loci | 42912 % of reads mapped to too many loci | 0.14% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 2.72% % of reads unmapped: other | 0.65% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 1055172 1055172 1055172 N_multimapping 309847 309847 309847 N_noFeature 1126406 27942773 1378646 N_ambiguous 575293 3348 83388 UnstrandedReadsAssigned:26985390 PositiveStrandReadsAssigned:740968 NegativeStrandReadsAssigned:27225055 Dataset is classified negative stranded MeadianReadLen=151 20thPercentileLength=141 echo kmer=137 SRR12951303 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: SRR12951303-trimmed-pair1.fastq SRR12951303-trimmed-pair2.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 30,052,108 reads, 27,582,427 reads pseudoaligned [quant] estimated average fragment length: 226.783 [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,177 rounds 52973 SRR12951303.ke.tsv 35125 SRR12951303.se.tsv 88098 total ==> SRR12951303.ke.tsv <== target_id length eff_length est_counts tpm PNS24245 936 710.756 0 0 PNS24247 1044 818.217 173.539 11.4748 PNS24249 1928 1702.22 462.722 14.707 PNS24246 1044 818.217 173.539 11.4748 PNS24248 1044 818.217 173.539 11.4748 PNS24244 1471 1245.22 242.661 10.5432 PNS24243 293 118.916 0 0 KQK14069 1603 1377.22 18560.1 729.115 KQK14071 474 267.443 664.169 134.358 ==> SRR12951303.se.tsv <== BRADI_1g14170v3 21317 BRADI_1g53295v3 164 BRADI_1g59795v3 518 BRADI_1g07683v3 0 BRADI_1g00485v3 40 BRADI_1g20270v3 1351 BRADI_1g74790v3 2265 BRADI_1g09890v3 0 BRADI_1g77505v3 264 BRADI_1g48960v3 0 SRR12951303 completed mapping pipeline successfully