Starting /dee2/code/volunteer_pipeline.sh SRR12670166 current disk space = 3055885352960 free memory = 1147623668 SRR12670166 SRAfilesize 340b657cc9f44377b086ac4aab1acff0 SRR12670166.sra SRR12670166.sra file validated SRR12670166 is paired end SRR12670166 is conventional basespace SRR12670166 read1 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR12670166_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 45 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 36.5445 37.0 37.0 37.0 37.0 37.0 2 36.318 37.0 37.0 37.0 37.0 37.0 3 36.6065 37.0 37.0 37.0 37.0 37.0 4 36.6485 37.0 37.0 37.0 37.0 37.0 5 36.628 37.0 37.0 37.0 37.0 37.0 6 36.6435 37.0 37.0 37.0 37.0 37.0 7 36.5575 37.0 37.0 37.0 37.0 37.0 8 36.621 37.0 37.0 37.0 37.0 37.0 9 36.6155 37.0 37.0 37.0 37.0 37.0 10-14 36.589299999999994 37.0 37.0 37.0 37.0 37.0 15-19 36.53060000000001 37.0 37.0 37.0 37.0 37.0 20-24 36.5268 37.0 37.0 37.0 37.0 37.0 25-29 36.486399999999996 37.0 37.0 37.0 37.0 37.0 30-34 36.513999999999996 37.0 37.0 37.0 37.0 37.0 35-39 36.46580000000001 37.0 37.0 37.0 37.0 37.0 40-44 36.4576 37.0 37.0 37.0 37.0 37.0 45-49 36.4439 37.0 37.0 37.0 37.0 37.0 50-54 36.420399999999994 37.0 37.0 37.0 37.0 37.0 55-59 36.3867 37.0 37.0 37.0 37.0 37.0 60-64 36.3785 37.0 37.0 37.0 37.0 37.0 65-69 36.4047 37.0 37.0 37.0 37.0 37.0 70-74 36.3291 37.0 37.0 37.0 37.0 37.0 75-79 36.35170000000001 37.0 37.0 37.0 37.0 37.0 80-84 36.277699999999996 37.0 37.0 37.0 37.0 37.0 85-89 36.301500000000004 37.0 37.0 37.0 37.0 37.0 90-94 36.2959 37.0 37.0 37.0 37.0 37.0 95-99 36.277300000000004 37.0 37.0 37.0 37.0 37.0 100-104 36.256800000000005 37.0 37.0 37.0 37.0 37.0 105-109 36.2172 37.0 37.0 37.0 37.0 37.0 110-114 36.0945 37.0 37.0 37.0 37.0 37.0 115-119 36.1325 37.0 37.0 37.0 37.0 37.0 120-124 36.045100000000005 37.0 37.0 37.0 37.0 37.0 125-129 35.9024 37.0 37.0 37.0 37.0 37.0 130-134 35.801 37.0 37.0 37.0 37.0 37.0 135-139 35.634699999999995 37.0 37.0 37.0 37.0 37.0 140-144 35.2898 37.0 37.0 37.0 37.0 37.0 145-149 35.1502 37.0 37.0 37.0 32.2 37.0 150-151 34.78075 37.0 37.0 37.0 25.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 21 1.0 22 1.0 23 0.0 24 0.0 25 2.0 26 3.0 27 9.0 28 12.0 29 18.0 30 18.0 31 44.0 32 48.0 33 97.0 34 149.0 35 338.0 36 2877.0 37 383.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 42.1 11.125 6.35 40.425 2 19.539078156312627 12.700400801603207 36.87374749498998 30.886773547094187 3 18.825 15.775 27.650000000000002 37.75 4 23.7 24.725 23.65 27.925 5 24.4 30.275000000000002 25.1 20.225 6 20.8 33.900000000000006 25.025 20.275000000000002 7 15.475 25.825 41.949999999999996 16.75 8 17.7 25.275 31.95 25.074999999999996 9 17.849999999999998 24.525 34.425 23.200000000000003 10-14 20.435 29.825000000000003 27.245 22.495 15-19 20.16 28.15 28.12 23.57 20-24 20.24 27.52 28.384999999999998 23.855 25-29 20.380000000000003 28.4 27.785 23.435 30-34 20.055 29.049999999999997 27.065 23.830000000000002 35-39 20.525 27.97 27.32 24.185000000000002 40-44 20.580000000000002 28.38 27.29 23.75 45-49 20.26 28.744999999999997 27.589999999999996 23.405 50-54 20.330000000000002 28.854999999999997 27.389999999999997 23.425 55-59 20.505000000000003 28.525 27.155 23.815 60-64 20.595 28.76 27.224999999999998 23.419999999999998 65-69 20.424999999999997 28.625 27.315 23.635 70-74 21.475 28.025 26.68 23.82 75-79 20.145 27.88 27.765 24.21 80-84 21.099999999999998 27.389999999999997 27.834999999999997 23.674999999999997 85-89 21.015 27.905 27.55 23.53 90-94 21.8 28.26 26.955000000000002 22.985 95-99 21.33 28.249999999999996 26.8 23.62 100-104 21.88 28.59 26.665 22.865 105-109 21.404999999999998 28.605000000000004 26.33 23.66 110-114 21.455 28.744999999999997 26.14 23.66 115-119 21.895 28.395 25.740000000000002 23.97 120-124 21.57 29.175 25.419999999999998 23.835 125-129 21.665 28.12 25.305 24.91 130-134 21.165 28.435 25.695 24.705 135-139 21.375 28.13 25.759999999999998 24.735 140-144 22.040000000000003 27.750000000000004 25.624999999999996 24.585 145-149 22.32 27.825 25.55 24.305 150-151 22.237499999999997 28.6125 24.887500000000003 24.2625 >>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 0.5 7 0.5 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 0.5 24 0.5 25 0.0 26 0.5 27 4.5 28 8.0 29 12.5 30 20.5 31 25.0 32 27.0 33 31.0 34 38.5 35 71.5 36 89.5 37 89.5 38 109.5 39 148.0 40 165.5 41 185.5 42 229.0 43 261.5 44 302.0 45 271.5 46 238.0 47 266.0 48 262.0 49 217.5 50 186.0 51 163.0 52 139.5 53 106.5 54 77.0 55 63.0 56 46.0 57 36.5 58 28.0 59 24.5 60 20.5 61 13.0 62 4.0 63 2.5 64 3.5 65 1.5 66 0.5 67 4.0 68 3.5 69 0.0 70 0.0 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 0.2 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 81.10000000000001 #Duplication Level Percentage of deduplicated Percentage of total 1 81.3501849568434 65.975 2 14.76572133168927 23.95 3 3.390875462392109 8.25 4 0.33908754623921084 1.0999999999999999 5 0.06165228113440197 0.25 6 0.06165228113440197 0.3 7 0.030826140567200986 0.17500000000000002 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 CCTGTTTATTGTGCGTCTATTTGGCCTGGCAAACTTGGGAAGGGCAGACA 7 0.17500000000000002 No Hit CTTGCTTAATGACCGCATGTGCAGGTAGTGCAAGTGCAGCCAGTACCGCA 6 0.15 No Hit GGAAGAACTGAACTTCCCCATCTTCACTTGCACCAAACTGGAAGAGCACC 6 0.15 No Hit GTGGAGGAAGGAGAAGAGAGGGATTGAGCAAAAGAAACGGAAGAGGGAAT 5 0.125 No Hit GCTTCTGTAGCTTTTGGTACTTGTACCAGTTGAATAAGCCGACACCAACC 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 0.05 0.0 0.0 0.0 0.0 48-49 0.05 0.0 0.0 0.0 0.0 50-51 0.15 0.0 0.0 0.0 0.0 52-53 0.16249999999999998 0.0 0.0 0.0 0.0 54-55 0.175 0.0 0.0 0.0 0.0 56-57 0.175 0.0 0.0 0.0 0.0 58-59 0.225 0.0 0.0 0.0 0.0 60-61 0.225 0.0 0.0 0.0 0.0 62-63 0.2875 0.0 0.0 0.0 0.0 64-65 0.35 0.0 0.0 0.0 0.0 66-67 0.4125 0.0 0.0 0.0 0.0 68-69 0.44999999999999996 0.0 0.0 0.0 0.0 70-71 0.575 0.0 0.0 0.0 0.0 72-73 0.7875 0.0 0.0 0.0 0.0 74-75 0.925 0.0 0.0 0.0 0.0 76-77 1.0125 0.0 0.0 0.0 0.0 78-79 1.2125 0.0 0.0 0.0 0.0 80-81 1.4625 0.0 0.0 0.0 0.0 82-83 1.775 0.0 0.0 0.0 0.0 84-85 2.175 0.0 0.0 0.0 0.0 86-87 2.575 0.0 0.0 0.0 0.0 88-89 2.9625 0.0 0.0 0.0 0.0 90-91 3.45 0.0 0.0 0.0 0.0 92-93 4.074999999999999 0.0 0.0 0.0 0.0 94-95 4.675 0.0 0.0 0.0 0.0 96-97 5.4625 0.0 0.0 0.0 0.0 98-99 6.1875 0.0 0.0 0.0 0.0 100-101 7.1 0.0 0.0 0.0 0.0 102-103 7.699999999999999 0.0 0.0 0.0 0.0 104-105 8.3875 0.0 0.0 0.0 0.0 106-107 9.2875 0.0 0.0 0.0 0.0 108-109 10.175 0.0 0.0 0.0 0.0 110-111 11.0 0.0 0.0 0.0 0.0 112-113 11.8375 0.0 0.0 0.0 0.0 114-115 12.825 0.0 0.0 0.0 0.0 116-117 13.675 0.0 0.0 0.0 0.0 118-119 14.3625 0.0 0.0 0.0 0.0 120-121 14.9375 0.0 0.0 0.0 0.0 122-123 16.15 0.0 0.0 0.0 0.0 124-125 17.2 0.0 0.0 0.0 0.0 126-127 18.0375 0.0 0.0 0.0 0.0 128-129 19.125 0.0 0.0 0.0 0.0 130-131 20.1625 0.0 0.0 0.0 0.0 132-133 21.325000000000003 0.0 0.0 0.0 0.0 134-135 22.25 0.0 0.0 0.0 0.0 136-137 23.075 0.0 0.0 0.0 0.0 138-139 23.9875 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position ACTTGCT 10 0.006830828 145.0 6 TCGGTTC 10 0.006830828 145.0 2 TTACATG 10 0.006830828 145.0 2 ATCGGTT 10 0.006830828 145.0 1 TGTAACA 10 0.006830828 145.0 3 >>END_MODULE SRR12670166 read2 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR12670166_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 45 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 36.2805 37.0 37.0 37.0 37.0 37.0 2 36.24 37.0 37.0 37.0 37.0 37.0 3 36.256 37.0 37.0 37.0 37.0 37.0 4 36.2225 37.0 37.0 37.0 37.0 37.0 5 36.3045 37.0 37.0 37.0 37.0 37.0 6 36.225 37.0 37.0 37.0 37.0 37.0 7 36.3935 37.0 37.0 37.0 37.0 37.0 8 36.3185 37.0 37.0 37.0 37.0 37.0 9 36.1875 37.0 37.0 37.0 37.0 37.0 10-14 36.2997 37.0 37.0 37.0 37.0 37.0 15-19 36.280199999999994 37.0 37.0 37.0 37.0 37.0 20-24 36.1908 37.0 37.0 37.0 37.0 37.0 25-29 36.1801 37.0 37.0 37.0 37.0 37.0 30-34 36.1991 37.0 37.0 37.0 37.0 37.0 35-39 36.1361 37.0 37.0 37.0 37.0 37.0 40-44 36.0783 37.0 37.0 37.0 37.0 37.0 45-49 36.1283 37.0 37.0 37.0 37.0 37.0 50-54 36.0564 37.0 37.0 37.0 37.0 37.0 55-59 36.020500000000006 37.0 37.0 37.0 37.0 37.0 60-64 36.0298 37.0 37.0 37.0 37.0 37.0 65-69 36.014900000000004 37.0 37.0 37.0 37.0 37.0 70-74 35.948800000000006 37.0 37.0 37.0 37.0 37.0 75-79 35.9908 37.0 37.0 37.0 37.0 37.0 80-84 35.8933 37.0 37.0 37.0 37.0 37.0 85-89 35.904 37.0 37.0 37.0 37.0 37.0 90-94 35.849199999999996 37.0 37.0 37.0 37.0 37.0 95-99 35.7441 37.0 37.0 37.0 37.0 37.0 100-104 35.6962 37.0 37.0 37.0 37.0 37.0 105-109 35.673199999999994 37.0 37.0 37.0 37.0 37.0 110-114 35.525 37.0 37.0 37.0 37.0 37.0 115-119 35.4088 37.0 37.0 37.0 37.0 37.0 120-124 35.203399999999995 37.0 37.0 37.0 29.8 37.0 125-129 35.067600000000006 37.0 37.0 37.0 27.4 37.0 130-134 34.7636 37.0 37.0 37.0 27.4 37.0 135-139 34.528999999999996 37.0 37.0 37.0 25.0 37.0 140-144 34.185199999999995 37.0 37.0 37.0 25.0 37.0 145-149 33.89 37.0 37.0 37.0 25.0 37.0 150-151 33.69475 37.0 37.0 37.0 25.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 12 1.0 13 3.0 14 4.0 15 4.0 16 2.0 17 1.0 18 2.0 19 1.0 20 4.0 21 5.0 22 6.0 23 6.0 24 9.0 25 8.0 26 3.0 27 12.0 28 13.0 29 21.0 30 36.0 31 59.0 32 83.0 33 179.0 34 252.0 35 522.0 36 2498.0 37 266.0 >>END_MODULE >>Per base sequence content warn #Base G A T C 1 42.05 22.35 9.375 26.224999999999998 2 27.05 26.200000000000003 30.049999999999997 16.7 3 20.175 28.15 32.9 18.775 4 23.875 35.175 22.6 18.35 5 24.775 35.6 22.1 17.525 6 20.4 39.45 23.625 16.525000000000002 7 20.4 20.9 38.224999999999994 20.474999999999998 8 21.0 27.1 28.175 23.724999999999998 9 21.175 24.575 30.575000000000003 23.674999999999997 10-14 23.46 29.39 26.26 20.89 15-19 22.355 28.165000000000003 28.439999999999998 21.04 20-24 23.05 28.48 27.165 21.305 25-29 23.525 27.034999999999997 27.794999999999998 21.645 30-34 22.955000000000002 27.74 28.075 21.23 35-39 22.99 28.035 27.575 21.4 40-44 23.265 27.675 27.83 21.23 45-49 23.095 27.82 28.16 20.925 50-54 23.44 28.105000000000004 27.860000000000003 20.595 55-59 23.28 27.245 28.294999999999998 21.18 60-64 23.395 27.089999999999996 28.4 21.115000000000002 65-69 23.605 28.02 27.785 20.59 70-74 23.65 27.48 27.189999999999998 21.68 75-79 23.025000000000002 28.1 27.405 21.47 80-84 23.56 27.615000000000002 27.04 21.785 85-89 24.295 27.76 27.3 20.645 90-94 24.785 28.244999999999997 26.240000000000002 20.73 95-99 24.42 28.665000000000003 26.5 20.415 100-104 24.805 28.105000000000004 26.965 20.125 105-109 25.419999999999998 27.750000000000004 26.82 20.01 110-114 25.919999999999998 28.689999999999998 25.624999999999996 19.765 115-119 26.035000000000004 28.09 25.874999999999996 20.0 120-124 26.369999999999997 28.42 26.16 19.05 125-129 27.505000000000003 27.215 26.5 18.78 130-134 28.975 27.474999999999998 25.305 18.245 135-139 28.994999999999997 28.294999999999998 24.39 18.32 140-144 30.014999999999997 26.505000000000003 25.585 17.895 145-149 31.11 26.415 24.805 17.669999999999998 150-151 33.137499999999996 25.224999999999998 24.05 17.5875 >>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 0.5 6 0.5 7 1.0 8 1.0 9 0.0 10 0.5 11 0.5 12 1.0 13 1.0 14 0.5 15 0.5 16 1.0 17 2.0 18 1.0 19 0.5 20 0.5 21 0.5 22 0.5 23 0.0 24 1.5 25 5.0 26 5.5 27 6.0 28 8.5 29 9.0 30 14.5 31 22.5 32 22.0 33 26.5 34 45.5 35 63.0 36 70.0 37 95.5 38 137.5 39 168.0 40 184.5 41 202.0 42 235.0 43 258.0 44 284.5 45 263.5 46 237.0 47 252.0 48 237.0 49 231.0 50 204.0 51 157.0 52 130.0 53 97.0 54 73.5 55 57.5 56 41.0 57 35.5 58 26.0 59 20.5 60 19.0 61 10.0 62 4.5 63 4.0 64 3.0 65 0.5 66 0.5 67 0.5 68 1.0 69 1.0 70 0.0 71 0.0 72 0.5 73 0.5 74 0.5 75 0.5 76 0.0 77 0.0 78 0.5 79 0.5 80 0.0 81 0.5 82 0.5 83 0.0 84 0.0 85 0.0 86 0.0 87 0.5 88 0.5 89 0.0 90 0.5 91 1.0 92 1.0 93 1.0 94 0.5 95 0.0 96 0.0 97 0.5 98 0.5 99 0.0 100 3.0 >>END_MODULE >>Per base N content pass #Base N-Count 1 0.0 2 0.0 3 0.0 4 0.0 5 0.0 6 0.0 7 0.0 8 0.0 9 0.0 10-14 0.0 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 81.3 #Duplication Level Percentage of deduplicated Percentage of total 1 81.94956949569494 66.625 2 14.114391143911439 22.95 3 3.4440344403444034 8.4 4 0.3075030750307503 1.0 5 0.03075030750307503 0.125 6 0.06150061500615006 0.3 7 0.03075030750307503 0.17500000000000002 8 0.03075030750307503 0.2 9 0.03075030750307503 0.22499999999999998 >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 AGAACACATTCATACTCCAAGTCTTTTAGTTCATCCATTTAAGCTTAATC 9 0.22499999999999998 No Hit GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG 8 0.2 No Hit AAACAAGATATTGAGAAATGGATAGCGAGGCAGTGAGACGGAGAATGAAC 7 0.17500000000000002 No Hit AGAGAACACATTCATACTCCAAGTCTTTTAGTTCATCCATTTAAGCTTAA 6 0.15 No Hit CAGTATTGTCTCTGAGAAGAAGGGTGTGGGTGTGTTTGAGTATGACAAGG 6 0.15 No Hit TTCTTCTTCTTCCCATGCTCTTCTTCAGTCCCCATTTTAACATGACTAAA 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 0.05 0.0 0.0 0.0 0.0 48-49 0.05 0.0 0.0 0.0 0.0 50-51 0.15 0.0 0.0 0.0 0.0 52-53 0.16249999999999998 0.0 0.0 0.0 0.0 54-55 0.175 0.0 0.0 0.0 0.0 56-57 0.175 0.0 0.0 0.0 0.0 58-59 0.225 0.0 0.0 0.0 0.0 60-61 0.225 0.0 0.0 0.0 0.0 62-63 0.275 0.0 0.0 0.0 0.0 64-65 0.32499999999999996 0.0 0.0 0.0 0.0 66-67 0.3875 0.0 0.0 0.0 0.0 68-69 0.42500000000000004 0.0 0.0 0.0 0.0 70-71 0.55 0.0 0.0 0.0 0.0 72-73 0.7625 0.0 0.0 0.0 0.0 74-75 0.9 0.0 0.0 0.0 0.0 76-77 0.9874999999999999 0.0 0.0 0.0 0.0 78-79 1.1875 0.0 0.0 0.0 0.0 80-81 1.4625 0.0 0.0 0.0 0.0 82-83 1.775 0.0 0.0 0.0 0.0 84-85 2.175 0.0 0.0 0.0 0.0 86-87 2.575 0.0 0.0 0.0 0.0 88-89 2.9625 0.0 0.0 0.0 0.0 90-91 3.45 0.0 0.0 0.0 0.0 92-93 4.05 0.0 0.0 0.0 0.0 94-95 4.675 0.0 0.0 0.0 0.0 96-97 5.4625 0.0 0.0 0.0 0.0 98-99 6.2125 0.0 0.0 0.0 0.0 100-101 7.125 0.0 0.0 0.0 0.0 102-103 7.7125 0.0 0.0 0.0 0.0 104-105 8.3875 0.0 0.0 0.0 0.0 106-107 9.2625 0.0 0.0 0.0 0.0 108-109 10.149999999999999 0.0 0.0 0.0 0.0 110-111 10.925 0.0 0.0 0.0 0.0 112-113 11.7375 0.0 0.0 0.0 0.0 114-115 12.75 0.0 0.0 0.0 0.0 116-117 13.6375 0.0 0.0 0.0 0.0 118-119 14.337499999999999 0.0 0.0 0.0 0.0 120-121 14.912500000000001 0.0 0.0 0.0 0.0 122-123 16.137500000000003 0.0 0.0 0.0 0.0 124-125 17.2125 0.0 0.0 0.0 0.0 126-127 17.987499999999997 0.0 0.0 0.0 0.0 128-129 19.0875 0.0 0.0 0.0 0.0 130-131 20.1375 0.0 0.0 0.0 0.0 132-133 21.2875 0.0 0.0 0.0 0.0 134-135 22.225 0.0 0.0 0.0 0.0 136-137 23.05 0.0 0.0 0.0 0.0 138-139 23.9625 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position GGTTGCA 10 0.006830828 145.0 1 >>END_MODULE Read 650201 spots for SRR12670166.sra Written 650201 spots for SRR12670166.sra Read 650201 spots for SRR12670166.sra Written 650201 spots for SRR12670166.sra Read 650201 spots for SRR12670166.sra Written 650201 spots for SRR12670166.sra Read 650201 spots for SRR12670166.sra Written 650201 spots for SRR12670166.sra Read 650201 spots for SRR12670166.sra Written 650201 spots for SRR12670166.sra Read 650201 spots for SRR12670166.sra Written 650201 spots for SRR12670166.sra Read 650201 spots for SRR12670166.sra Written 650201 spots for SRR12670166.sra Read 650201 spots for SRR12670166.sra Written 650201 spots for SRR12670166.sra Read 650201 spots for SRR12670166.sra Written 650201 spots for SRR12670166.sra Read 650201 spots for SRR12670166.sra Written 650201 spots for SRR12670166.sra Read 650201 spots for SRR12670166.sra Written 650201 spots for SRR12670166.sra Read 650201 spots for SRR12670166.sra Written 650201 spots for SRR12670166.sra Read 650201 spots for SRR12670166.sra Written 650201 spots for SRR12670166.sra Read 650201 spots for SRR12670166.sra Written 650201 spots for SRR12670166.sra Read 650201 spots for SRR12670166.sra Written 650201 spots for SRR12670166.sra Read 650201 spots for SRR12670166.sra Written 650201 spots for SRR12670166.sra Read 650201 spots for SRR12670166.sra Written 650201 spots for SRR12670166.sra Read 650206 spots for SRR12670166.sra Written 650206 spots for SRR12670166.sra Read 650201 spots for SRR12670166.sra Written 650201 spots for SRR12670166.sra Read 650201 spots for SRR12670166.sra Written 650201 spots for SRR12670166.sra SRR ids: ['SRR12670166.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_iqit3xas SRR12670166.sra spots: 13004025 blocks: [[1, 650201], [650202, 1300402], [1300403, 1950603], [1950604, 2600804], [2600805, 3251005], [3251006, 3901206], [3901207, 4551407], [4551408, 5201608], [5201609, 5851809], [5851810, 6502010], [6502011, 7152211], [7152212, 7802412], [7802413, 8452613], [8452614, 9102814], [9102815, 9753015], [9753016, 10403216], [10403217, 11053417], [11053418, 11703618], [11703619, 12353819], [12353820, 13004025]] SRR12670166 file size 4397636 SRR12670166 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 SRR12670166 SRR12670166_1.fastq SRR12670166_2.fastq Input file: SRR12670166_1.fastq Paired file: SRR12670166_2.fastq trimmed: SRR12670166-trimmed-pair1.fastq, SRR12670166-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 Tue Feb 11 07:55:56 2025 >> started Tue Feb 11 07:56:17 2025 >> done (20.604s) 13004025 read pairs processed; of these: 67 ( 0.00%) short read pairs filtered out after trimming by size control 10188 ( 0.08%) empty read pairs filtered out after trimming by size control 12993770 (99.92%) read pairs available; of these: 3793046 (29.19%) trimmed read pairs available after processing 9200724 (70.81%) untrimmed read pairs available after processing Length distribution of reads after trimming: length count percentage 18 4 0.00% 19 4 0.00% 20 8 0.00% 21 17 0.00% 22 8 0.00% 23 16 0.00% 24 19 0.00% 25 28 0.00% 26 22 0.00% 27 38 0.00% 28 42 0.00% 29 51 0.00% 30 56 0.00% 31 52 0.00% 32 73 0.00% 33 73 0.00% 34 93 0.00% 35 117 0.00% 36 113 0.00% 37 145 0.00% 38 161 0.00% 39 157 0.00% 40 194 0.00% 41 223 0.00% 42 253 0.00% 43 275 0.00% 44 227 0.00% 45 279 0.00% 46 281 0.00% 47 358 0.00% 48 473 0.00% 49 597 0.00% 50 644 0.00% 51 753 0.01% 52 722 0.01% 53 822 0.01% 54 879 0.01% 55 967 0.01% 56 1104 0.01% 57 1310 0.01% 58 1503 0.01% 59 1772 0.01% 60 2009 0.02% 61 2383 0.02% 62 2681 0.02% 63 2894 0.02% 64 3124 0.02% 65 3351 0.03% 66 3665 0.03% 67 4124 0.03% 68 4691 0.04% 69 5226 0.04% 70 6207 0.05% 71 6942 0.05% 72 7832 0.06% 73 8802 0.07% 74 9599 0.07% 75 10423 0.08% 76 11271 0.09% 77 12085 0.09% 78 12828 0.10% 79 14545 0.11% 80 15884 0.12% 81 17703 0.14% 82 19825 0.15% 83 21502 0.17% 84 23547 0.18% 85 24826 0.19% 86 26236 0.20% 87 27080 0.21% 88 27741 0.21% 89 29474 0.23% 90 31596 0.24% 91 33789 0.26% 92 35720 0.27% 93 38343 0.30% 94 40544 0.31% 95 42446 0.33% 96 43665 0.34% 97 44215 0.34% 98 45101 0.35% 99 45880 0.35% 100 47697 0.37% 101 48295 0.37% 102 50482 0.39% 103 52445 0.40% 104 53360 0.41% 105 54662 0.42% 106 55708 0.43% 107 55646 0.43% 108 55457 0.43% 109 55632 0.43% 110 55635 0.43% 111 56513 0.43% 112 57381 0.44% 113 57395 0.44% 114 59365 0.46% 115 60772 0.47% 116 60828 0.47% 117 61477 0.47% 118 61708 0.47% 119 59836 0.46% 120 60718 0.47% 121 60473 0.47% 122 61235 0.47% 123 61776 0.48% 124 62353 0.48% 125 62039 0.48% 126 63268 0.49% 127 62965 0.48% 128 62131 0.48% 129 62153 0.48% 130 61333 0.47% 131 60365 0.46% 132 60617 0.47% 133 61640 0.47% 134 61789 0.48% 135 61381 0.47% 136 61643 0.47% 137 61401 0.47% 138 60704 0.47% 139 61374 0.47% 140 60060 0.46% 141 59931 0.46% 142 59536 0.46% 143 59787 0.46% 144 59882 0.46% 145 60494 0.47% 146 60016 0.46% 147 59461 0.46% 148 59885 0.46% 149 58729 0.45% 150 58881 0.45% 151 9200724 70.81% 12993770 reads passed initial QC criterion=sequence-density sequence-density=0.55 sequence-density-rank=1 fanout-score=1.95 fanout-score-rank=28 prefix-density=0.56 prefix-fanout=1.9 sequence=CGGTAGACCCAACCTTTCTCCAACTCGAATTCCAAGCAAGGAACCCACTTCGAGCGAAGAAGGTA criterion=fanout-score sequence-density=0.02 sequence-density-rank=30 fanout-score=164.21 fanout-score-rank=1 prefix-density=0.27 prefix-fanout=13.6 sequence=TGAAGAAGACACAAAGATAAAGACACTCACGGACACTTTTGTTTGTTCACTCCACACCCACAAGTACAGAAGAACACAGATTATTTATCAGAAATTACATTATTAATCCACTCCCAATCCCACATCAAACATGATAGTTGATGTGCTTGCTTAATGACCGCATGTGCAGGTAGTGCAAGTGCAGCCAGTACCGCAGTTGCACTTGCCATCGTTCTCAGCTGCTGGCACCTCCATGACTACGGAGGAGACATAGTTCTTCTCAGTCTCGACGATGCCAGCAGTGTAGCTGCTTCCCTTCTTGACACACTGGGTCTTGTCAGCGCAGTCGCAGGTGTCGCAGGTGCTAGACATGATGATTGATTGATTAAGCTTAAATGGATGAACTAAAAGACTTGGAGTATGAATGTGTTCTCTGTG criterion=sequence-density sequence-density=0.76 sequence-density-rank=1 fanout-score=2.05 fanout-score-rank=27 prefix-density=0.77 prefix-fanout=2.0 sequence=TGTAAGAGATGGCTTCCTC criterion=fanout-score sequence-density=0.01 sequence-density-rank=32 fanout-score=55.30 fanout-score-rank=1 prefix-density=0.13 prefix-fanout=2.7 sequence=AGGAACTCAAACGCATAGCTTCCTACAAATACCCCAGCTAGCCAATACTCTCAACCACTAAACCCAAAGCTCAAAAAAAATCTTAACTGCACCCGCTCATCCAGCAATGGCAGCAGCAACAATGGCCCTCTCGTCCCCTTCGCTAGCCGGAAAGGCGGTGAAGCTCAACCCCTCCTCCTCTGAGATCATGGGCAATGGCCGTGTCTCCATGAGGAAAACCACCAAGCCTGTTCCCTCCGGGAGCCCATGGTACGGACCAGACCGTGTTAAATACTTGGGCCCGTTCTCTGGTGAGCCCCCATCCTACTTGACTGGTGAGTTCCCTGGTGACTACGGCTGGGACACTGCTGGCCTCTCTGCTGACCCAGAGACCTTTGCCAAGAACCGTGAGCTTGAAGTCATCCATTCCAGGTGGGCCATGCTTGGAGCTCTTGGATGCGTCTTCCCCGAGCTCTTGTCCCGCAACGGTGTCAAGTTCGGCGAGGCTGTATGGTTCAAGGCTGGAGCCCAG SRR12670166 testing PE reads STAR mapping to Ensembl genome Started job on | Feb 11 07:57:00 Started mapping on | Feb 11 07:57:01 Finished on | Feb 11 07:58:28 Mapping speed, Million of reads per hour | 537.67 Number of input reads | 12993770 Average input read length | 282 UNIQUE READS: Uniquely mapped reads number | 12158652 Uniquely mapped reads % | 93.57% Average mapped length | 281.08 Number of splices: Total | 11602618 Number of splices: Annotated (sjdb) | 11358462 Number of splices: GT/AG | 11357830 Number of splices: GC/AG | 201377 Number of splices: AT/AC | 7777 Number of splices: Non-canonical | 35634 Mismatch rate per base, % | 0.35% Deletion rate per base | 0.03% Deletion average length | 2.97 Insertion rate per base | 0.02% Insertion average length | 2.35 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 276061 % of reads mapped to multiple loci | 2.12% Number of reads mapped to too many loci | 88510 % of reads mapped to too many loci | 0.68% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 3.46% % of reads unmapped: other | 0.16% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 559057 559057 559057 N_multimapping 276061 276061 276061 N_noFeature 444464 11992596 515436 N_ambiguous 159234 535 63883 UnstrandedReadsAssigned:11554954 PositiveStrandReadsAssigned:165521 NegativeStrandReadsAssigned:11579333 Dataset is classified negative stranded MeadianReadLen=151 20thPercentileLength=131 echo kmer=127 SRR12670166 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: SRR12670166-trimmed-pair1.fastq SRR12670166-trimmed-pair2.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 12,993,770 reads, 11,682,997 reads pseudoaligned [quant] estimated average fragment length: 206.255 [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,131 rounds 52401 SRR12670166.ke.tsv 34699 SRR12670166.se.tsv 87100 total ==> SRR12670166.ke.tsv <== target_id length eff_length est_counts tpm Potri.005G200100.1.v4.1 2018 1812.74 309 15.29 Potri.005G024800.1.v4.1 1035 829.745 103 11.1347 Potri.004G059700.1.v4.1 961 755.84 16 1.89879 Potri.007G009000.2.v4.1 1416 1210.74 0 0 Potri.003G141000.2.v4.1 2943 2737.74 567.3 18.5869 Potri.016G087400.1.v4.1 270 113.306 530 419.574 Potri.015G069301.1.v4.1 564 368.496 0 0 Potri.010G195200.1.v4.1 1773 1567.74 13 0.743798 Potri.012G127500.1.v4.1 977 771.786 41 4.76512 ==> SRR12670166.se.tsv <== Potri.001G166300.v4.1 0 Potri.001G448400.v4.1 107 Potri.001G233950.v4.1 0 Potri.001G122700.v4.1 150 Potri.001G212900.v4.1 0 Potri.001G182400.v4.1 0 Potri.001G256600.v4.1 0 Potri.001G040500.v4.1 0 Potri.001G416900.v4.1 0 Potri.001G452600.v4.1 17 SRR12670166 completed mapping pipeline successfully