Starting /dee2/code/volunteer_pipeline.sh SRR12917568 current disk space = 3090012315648 free memory = 1489673768 SRR12917568 SRAfilesize d6da0b0d66fce161ffa720e682156e45 SRR12917568.sra SRR12917568.sra file validated SRR12917568 is paired end SRR12917568 is conventional basespace SRR12917568 read1 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR12917568_1.fastq File type Conventional base calls Encoding Sanger / Illumina 1.9 Total Sequences 4000 Sequences flagged as poor quality 0 Sequence length 151 %GC 44 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 36.61125 37.0 37.0 37.0 37.0 37.0 2 36.456 37.0 37.0 37.0 37.0 37.0 3 36.532 37.0 37.0 37.0 37.0 37.0 4 36.618 37.0 37.0 37.0 37.0 37.0 5 36.5845 37.0 37.0 37.0 37.0 37.0 6 36.62 37.0 37.0 37.0 37.0 37.0 7 36.5095 37.0 37.0 37.0 37.0 37.0 8 36.559 37.0 37.0 37.0 37.0 37.0 9 36.641 37.0 37.0 37.0 37.0 37.0 10-14 36.6121 37.0 37.0 37.0 37.0 37.0 15-19 36.5877 37.0 37.0 37.0 37.0 37.0 20-24 36.552299999999995 37.0 37.0 37.0 37.0 37.0 25-29 36.499 37.0 37.0 37.0 37.0 37.0 30-34 36.4985 37.0 37.0 37.0 37.0 37.0 35-39 36.4575 37.0 37.0 37.0 37.0 37.0 40-44 36.4439 37.0 37.0 37.0 37.0 37.0 45-49 36.404999999999994 37.0 37.0 37.0 37.0 37.0 50-54 36.3757 37.0 37.0 37.0 37.0 37.0 55-59 36.328199999999995 37.0 37.0 37.0 37.0 37.0 60-64 36.3048 37.0 37.0 37.0 37.0 37.0 65-69 36.207899999999995 37.0 37.0 37.0 37.0 37.0 70-74 36.260099999999994 37.0 37.0 37.0 37.0 37.0 75-79 36.2782 37.0 37.0 37.0 37.0 37.0 80-84 36.2841 37.0 37.0 37.0 37.0 37.0 85-89 36.2073 37.0 37.0 37.0 37.0 37.0 90-94 36.238099999999996 37.0 37.0 37.0 37.0 37.0 95-99 36.19019999999999 37.0 37.0 37.0 37.0 37.0 100-104 36.075700000000005 37.0 37.0 37.0 37.0 37.0 105-109 36.0669 37.0 37.0 37.0 37.0 37.0 110-114 36.0532 37.0 37.0 37.0 37.0 37.0 115-119 35.9544 37.0 37.0 37.0 37.0 37.0 120-124 35.9698 37.0 37.0 37.0 37.0 37.0 125-129 35.8416 37.0 37.0 37.0 37.0 37.0 130-134 35.764700000000005 37.0 37.0 37.0 37.0 37.0 135-139 35.705 37.0 37.0 37.0 37.0 37.0 140-144 35.6185 37.0 37.0 37.0 37.0 37.0 145-149 35.502 37.0 37.0 37.0 37.0 37.0 150-151 35.261750000000006 37.0 37.0 37.0 31.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 20 2.0 21 1.0 22 1.0 23 4.0 24 0.0 25 3.0 26 3.0 27 6.0 28 19.0 29 18.0 30 25.0 31 22.0 32 46.0 33 77.0 34 136.0 35 340.0 36 3018.0 37 279.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 49.63740935233808 13.253313328332084 5.376344086021505 31.732933233308323 2 21.175 10.525 37.9 30.4 3 17.474999999999998 14.95 29.625 37.95 4 22.225 21.475 25.45 30.85 5 23.45 28.975 24.875 22.7 6 21.875 32.65 22.650000000000002 22.825 7 15.525 28.125 40.45 15.9 8 15.575 26.375 33.75 24.3 9 17.325 23.724999999999998 36.025 22.925 10-14 19.665 30.130000000000003 27.76 22.445 15-19 20.3 28.044999999999998 28.01 23.645 20-24 19.465 28.65 28.035 23.849999999999998 25-29 20.06 28.63 27.755000000000003 23.555 30-34 19.78 29.134999999999998 27.860000000000003 23.225 35-39 19.895 28.389999999999997 28.425 23.29 40-44 19.86 28.9 27.51 23.73 45-49 19.79 28.64 27.465 24.104999999999997 50-54 20.74 28.125 27.74 23.395 55-59 20.195 29.255 27.12 23.43 60-64 20.369999999999997 27.855 27.894999999999996 23.880000000000003 65-69 19.75 28.235 27.750000000000004 24.265 70-74 20.71 28.48 27.11 23.7 75-79 19.45 29.065 27.73 23.755000000000003 80-84 19.885 27.68 28.044999999999998 24.39 85-89 20.72 27.860000000000003 27.935 23.485 90-94 20.165 27.92 27.700000000000003 24.215 95-99 20.169999999999998 28.455000000000002 27.345000000000002 24.03 100-104 20.515 28.12 27.71 23.655 105-109 20.26 27.779999999999998 27.825 24.135 110-114 20.485 28.095 27.42 24.0 115-119 20.57 27.810000000000002 27.750000000000004 23.87 120-124 20.265 28.189999999999998 27.11 24.435000000000002 125-129 20.085 27.779999999999998 28.12 24.015 130-134 20.25 27.92 27.400000000000002 24.43 135-139 21.044999999999998 28.349999999999998 26.935 23.669999999999998 140-144 20.775 28.065 27.32 23.84 145-149 20.895 28.08 26.919999999999998 24.104999999999997 150-151 20.1625 28.299999999999997 26.2625 25.275 >>END_MODULE >>Per sequence GC content pass #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 0.5 9 0.5 10 0.0 11 0.0 12 0.0 13 0.0 14 0.0 15 0.5 16 0.5 17 0.0 18 1.0 19 1.0 20 0.0 21 0.5 22 1.0 23 2.5 24 4.5 25 3.5 26 3.0 27 8.5 28 11.5 29 10.0 30 16.5 31 24.0 32 29.0 33 37.0 34 57.0 35 77.5 36 95.0 37 116.0 38 126.0 39 139.5 40 162.0 41 195.5 42 245.0 43 263.5 44 278.0 45 284.0 46 265.5 47 261.5 48 245.0 49 212.0 50 174.5 51 143.0 52 108.5 53 84.5 54 71.5 55 62.5 56 44.0 57 27.0 58 24.0 59 18.0 60 14.5 61 9.0 62 5.0 63 4.0 64 5.0 65 4.5 66 4.0 67 3.0 68 4.0 69 3.0 70 1.0 71 1.5 72 0.5 73 1.0 74 1.0 75 0.5 76 0.5 77 0.5 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 0.0 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 0.025 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 90.325 #Duplication Level Percentage of deduplicated Percentage of total 1 91.11541655134238 82.3 2 7.5560476058676995 13.65 3 1.0240797121505674 2.775 4 0.19374481040686412 0.7000000000000001 5 0.02767783005812344 0.125 6 0.08303349017437033 0.44999999999999996 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 GTCCCCAACAAGTTCTCTCCATTCTCTGGATAATTGAAATCTCCAAATAC 6 0.15 No Hit GTGCGATTTTGCAGTTGCTTCTCTCGATTTCAGCAATGGGGTCTATCAAA 6 0.15 No Hit CTCCATTCTCTGGATAATTGAAATCTCCAAATACCAGTTTACCTTTCTCC 6 0.15 No Hit GCCATATTTACTGAATGACTCCCTGTCTTGACATATACAATAGAAGAACC 5 0.125 No Hit >>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 0.0 0.0 0.0 0.0 0.0 2 0.0 0.0 0.0 0.0 0.0 3 0.0 0.0 0.0 0.0 0.0 4 0.0 0.0 0.0 0.0 0.0 5 0.0 0.0 0.0 0.0 0.0 6 0.0 0.0 0.0 0.0 0.0 7 0.0 0.0 0.0 0.0 0.0 8 0.0 0.0 0.0 0.0 0.0 9 0.0 0.0 0.0 0.0 0.0 10-11 0.0 0.0 0.0 0.0 0.0 12-13 0.0 0.0 0.0 0.0 0.0 14-15 0.0 0.0 0.0 0.0 0.0 16-17 0.0 0.0 0.0 0.0 0.0 18-19 0.0 0.0 0.0 0.0 0.0 20-21 0.0 0.0 0.0 0.0 0.0 22-23 0.0 0.0 0.0 0.0 0.0 24-25 0.0 0.0 0.0 0.0 0.0 26-27 0.0 0.0 0.0 0.0 0.0 28-29 0.0 0.0 0.0 0.0 0.0 30-31 0.0 0.0 0.0 0.0 0.0 32-33 0.0 0.0 0.0 0.0 0.0 34-35 0.0 0.0 0.0 0.0 0.0 36-37 0.0 0.0 0.0 0.0 0.0 38-39 0.0 0.0 0.0 0.0 0.0 40-41 0.0 0.0 0.0 0.0 0.0 42-43 0.0 0.0 0.0 0.0 0.0 44-45 0.0 0.0 0.0 0.0 0.0 46-47 0.0 0.0 0.0 0.0 0.0 48-49 0.0 0.0 0.0 0.0 0.0 50-51 0.0 0.0 0.0 0.0 0.0 52-53 0.0125 0.0 0.0 0.0 0.0 54-55 0.025 0.0 0.0 0.0 0.0 56-57 0.025 0.0 0.0 0.0 0.0 58-59 0.025 0.0 0.0 0.0 0.0 60-61 0.025 0.0 0.0 0.0 0.0 62-63 0.025 0.0 0.0 0.0 0.0 64-65 0.025 0.0 0.0 0.0 0.0 66-67 0.025 0.0 0.0 0.0 0.0 68-69 0.025 0.0 0.0 0.0 0.0 70-71 0.05 0.0 0.0 0.0 0.0 72-73 0.075 0.0 0.0 0.0 0.0 74-75 0.0875 0.0 0.0 0.0 0.0 76-77 0.1 0.0 0.0 0.0 0.0 78-79 0.125 0.0 0.0 0.0 0.0 80-81 0.175 0.0 0.0 0.0 0.0 82-83 0.23750000000000002 0.0 0.0 0.0 0.0 84-85 0.3125 0.0 0.0 0.0 0.0 86-87 0.3625 0.0 0.0 0.0 0.0 88-89 0.42500000000000004 0.0 0.0 0.0 0.0 90-91 0.475 0.0 0.0 0.0 0.0 92-93 0.5375000000000001 0.0 0.0 0.0 0.0 94-95 0.55 0.0 0.0 0.0 0.0 96-97 0.6125 0.0 0.0 0.0 0.0 98-99 0.7 0.0 0.0 0.0 0.0 100-101 0.7875000000000001 0.0 0.0 0.0 0.0 102-103 0.9 0.0 0.0 0.0 0.0 104-105 1.0 0.0 0.0 0.0 0.0 106-107 1.15 0.0 0.0 0.0 0.0 108-109 1.2625 0.0 0.0 0.0 0.0 110-111 1.475 0.0 0.0 0.0 0.0 112-113 1.6 0.0 0.0 0.0 0.0 114-115 1.8625 0.0 0.0 0.0 0.0 116-117 2.1875 0.0 0.0 0.0 0.0 118-119 2.4625 0.0 0.0 0.0 0.0 120-121 2.7125 0.0 0.0 0.0 0.0 122-123 2.9625 0.0 0.0 0.0 0.0 124-125 3.2750000000000004 0.0 0.0 0.0 0.0 126-127 3.5375 0.0 0.0 0.0 0.0 128-129 3.8875 0.0 0.0 0.0 0.0 130-131 4.225 0.0 0.0 0.0 0.0 132-133 4.550000000000001 0.0 0.0 0.0 0.0 134-135 4.85 0.0 0.0 0.0 0.0 136-137 5.2125 0.0 0.0 0.0 0.0 138-139 5.862500000000001 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position TGTCTTG 10 0.006830828 145.0 3 CCTGTCT 10 0.006830828 145.0 1 GCGGAGG 10 0.006830828 145.0 5 CTGTCTT 10 0.006830828 145.0 2 >>END_MODULE SRR12917568 read2 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR12917568_2.fastq File type Conventional base calls Encoding Sanger / Illumina 1.9 Total Sequences 4000 Sequences flagged as poor quality 0 Sequence length 151 %GC 44 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 36.33975 37.0 37.0 37.0 37.0 37.0 2 36.261 37.0 37.0 37.0 37.0 37.0 3 36.221 37.0 37.0 37.0 37.0 37.0 4 36.2625 37.0 37.0 37.0 37.0 37.0 5 36.3095 37.0 37.0 37.0 37.0 37.0 6 36.0765 37.0 37.0 37.0 37.0 37.0 7 36.341 37.0 37.0 37.0 37.0 37.0 8 36.4035 37.0 37.0 37.0 37.0 37.0 9 36.376 37.0 37.0 37.0 37.0 37.0 10-14 36.3913 37.0 37.0 37.0 37.0 37.0 15-19 36.3371 37.0 37.0 37.0 37.0 37.0 20-24 36.2689 37.0 37.0 37.0 37.0 37.0 25-29 36.1954 37.0 37.0 37.0 37.0 37.0 30-34 36.072 37.0 37.0 37.0 37.0 37.0 35-39 36.0789 37.0 37.0 37.0 37.0 37.0 40-44 36.047900000000006 37.0 37.0 37.0 37.0 37.0 45-49 35.9543 37.0 37.0 37.0 37.0 37.0 50-54 35.958800000000004 37.0 37.0 37.0 37.0 37.0 55-59 36.011700000000005 37.0 37.0 37.0 37.0 37.0 60-64 36.008799999999994 37.0 37.0 37.0 37.0 37.0 65-69 35.8812 37.0 37.0 37.0 37.0 37.0 70-74 35.9221 37.0 37.0 37.0 37.0 37.0 75-79 35.8106 37.0 37.0 37.0 37.0 37.0 80-84 35.8434 37.0 37.0 37.0 37.0 37.0 85-89 35.783699999999996 37.0 37.0 37.0 37.0 37.0 90-94 35.783500000000004 37.0 37.0 37.0 37.0 37.0 95-99 35.7362 37.0 37.0 37.0 37.0 37.0 100-104 35.7544 37.0 37.0 37.0 37.0 37.0 105-109 35.7011 37.0 37.0 37.0 37.0 37.0 110-114 35.6135 37.0 37.0 37.0 37.0 37.0 115-119 35.6031 37.0 37.0 37.0 37.0 37.0 120-124 35.486000000000004 37.0 37.0 37.0 37.0 37.0 125-129 35.4776 37.0 37.0 37.0 37.0 37.0 130-134 35.4242 37.0 37.0 37.0 37.0 37.0 135-139 35.4625 37.0 37.0 37.0 37.0 37.0 140-144 35.2546 37.0 37.0 37.0 32.2 37.0 145-149 35.1273 37.0 37.0 37.0 27.4 37.0 150-151 34.661 37.0 37.0 37.0 25.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 13 3.0 14 1.0 15 7.0 16 3.0 17 0.0 18 4.0 19 5.0 20 1.0 21 3.0 22 4.0 23 7.0 24 4.0 25 5.0 26 5.0 27 9.0 28 18.0 29 22.0 30 22.0 31 43.0 32 56.0 33 87.0 34 162.0 35 623.0 36 2746.0 37 160.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 42.23555888972243 28.857214303575894 7.97699424856214 20.930232558139537 2 30.3 24.325 29.775000000000002 15.6 3 19.900000000000002 28.65 33.15 18.3 4 22.325 35.575 24.2 17.9 5 25.474999999999998 36.575 21.25 16.7 6 21.65 38.3 21.325 18.725 7 21.5 22.45 37.2 18.85 8 21.6 25.25 28.7 24.45 9 21.6 24.75 30.775000000000002 22.875 10-14 23.57 29.2 26.834999999999997 20.395 15-19 24.145 27.445000000000004 27.500000000000004 20.91 20-24 23.835 28.51 27.33 20.325 25-29 23.48 28.29 27.295 20.935000000000002 30-34 22.994999999999997 28.470000000000002 27.565 20.97 35-39 23.825 28.299999999999997 26.974999999999998 20.9 40-44 23.135 28.73 27.345000000000002 20.79 45-49 23.494999999999997 27.725 27.825 20.955 50-54 24.26 27.500000000000004 28.22 20.02 55-59 23.94 27.43 27.805000000000003 20.825 60-64 24.08 27.42 27.77 20.73 65-69 24.08 27.595 27.805000000000003 20.52 70-74 24.279999999999998 28.000000000000004 27.245 20.474999999999998 75-79 24.23 27.37 28.025 20.375 80-84 24.104999999999997 27.465 27.73 20.7 85-89 24.245 27.63 27.250000000000004 20.875 90-94 24.565 28.015 27.055 20.365 95-99 23.925 28.535 27.334999999999997 20.205000000000002 100-104 24.295 27.884999999999998 26.99 20.830000000000002 105-109 24.38 27.71 27.52 20.39 110-114 23.849999999999998 28.000000000000004 27.455000000000002 20.695 115-119 24.57 28.13 27.055 20.244999999999997 120-124 24.275 28.34 27.305 20.080000000000002 125-129 24.45 28.425 26.945000000000004 20.18 130-134 24.965 27.785 27.42 19.830000000000002 135-139 24.005000000000003 28.08 27.584999999999997 20.330000000000002 140-144 25.314999999999998 27.779999999999998 26.625 20.28 145-149 25.47 27.785 26.525 20.22 150-151 25.8 27.275 27.250000000000004 19.675 >>END_MODULE >>Per sequence GC content warn #GC Content Count 0 0.0 1 0.0 2 0.0 3 0.0 4 0.0 5 0.0 6 0.0 7 0.0 8 0.0 9 0.5 10 0.5 11 0.0 12 0.0 13 0.0 14 0.0 15 0.0 16 0.5 17 0.5 18 0.5 19 0.5 20 0.0 21 0.0 22 3.0 23 4.5 24 2.5 25 3.0 26 2.5 27 3.5 28 7.5 29 11.0 30 18.5 31 24.5 32 27.5 33 31.0 34 45.5 35 59.5 36 87.5 37 113.5 38 116.0 39 158.5 40 200.5 41 238.0 42 260.5 43 272.0 44 283.5 45 269.0 46 268.0 47 257.0 48 224.5 49 185.5 50 155.0 51 138.5 52 112.0 53 79.5 54 69.0 55 56.5 56 38.0 57 29.0 58 22.5 59 19.0 60 16.5 61 15.5 62 11.0 63 5.5 64 4.5 65 4.5 66 4.5 67 2.5 68 2.5 69 2.0 70 0.0 71 0.0 72 0.0 73 0.5 74 0.5 75 1.0 76 1.0 77 0.0 78 1.0 79 1.5 80 0.5 81 0.0 82 1.0 83 1.0 84 0.0 85 0.5 86 1.0 87 0.5 88 0.0 89 0.5 90 1.0 91 1.0 92 1.5 93 1.0 94 0.0 95 0.0 96 0.5 97 0.5 98 1.0 99 3.0 100 6.5 >>END_MODULE >>Per base N content pass #Base N-Count 1 0.025 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 89.725 #Duplication Level Percentage of deduplicated Percentage of total 1 91.08386737252717 81.72500000000001 2 7.550849818891056 13.55 3 0.8916132627472835 2.4 4 0.25076623014767346 0.8999999999999999 5 0.08358874338255781 0.375 6 0.08358874338255781 0.44999999999999996 7 0.02786291446085261 0.17500000000000002 8 0.0 0.0 9 0.0 0.0 >10 0.02786291446085261 0.42500000000000004 >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 GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG 17 0.42500000000000004 No Hit AGCAGTTGCATTTATCTAAAGTATTCTCACTTTACTTAACACTTGAGCTA 7 0.17500000000000002 No Hit GTTGCATTTATCTAAAGTATTGTCACTTTACTTAACACTTGAGCTGCATA 6 0.15 No Hit GGTAAACTGGTATTTGGAGATTTCAATTATCCAGAGAATGGAGAGAACCT 6 0.15 No Hit ATTTTGGTGACTGATATGGATTTGGGTTTTGAATTGAGTGATGCGATGAC 6 0.15 No Hit GTTAGATTCAGCATTCACGGAGTCATCTATTTTGGGAATGCTGGAAGCTT 5 0.125 No Hit GCTAGATACTAGTAGTAGTTGCAGACAGAGAGCTAGTGTTAGACAGGTTC 5 0.125 No Hit AGAAAAACAAAAAAGAAATGGATGCCAAAGCTCTCTTCTTCTTTGCCTTG 5 0.125 No Hit >>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 0.0 0.0 0.0 0.0 0.0 2 0.0 0.0 0.0 0.0 0.0 3 0.0 0.0 0.0 0.0 0.0 4 0.0 0.0 0.0 0.0 0.0 5 0.0 0.0 0.0 0.0 0.0 6 0.0 0.0 0.0 0.0 0.0 7 0.0 0.0 0.0 0.0 0.0 8 0.0 0.0 0.0 0.0 0.0 9 0.0 0.0 0.0 0.0 0.0 10-11 0.0 0.0 0.0 0.0 0.0 12-13 0.0 0.0 0.0 0.0 0.0 14-15 0.0 0.0 0.0 0.0 0.0 16-17 0.0 0.0 0.0 0.0 0.0 18-19 0.0 0.0 0.0 0.0 0.0 20-21 0.0 0.0 0.0 0.0 0.0 22-23 0.0 0.0 0.0 0.0 0.0 24-25 0.0 0.0 0.0 0.0 0.0 26-27 0.0 0.0 0.0 0.0 0.0 28-29 0.0 0.0 0.0 0.0 0.0 30-31 0.0 0.0 0.0 0.0 0.0 32-33 0.0 0.0 0.0 0.0 0.0 34-35 0.0 0.0 0.0 0.0 0.0 36-37 0.0 0.0 0.0 0.0 0.0 38-39 0.0 0.0 0.0 0.0 0.0 40-41 0.0 0.0 0.0 0.0 0.0 42-43 0.0 0.0 0.0 0.0 0.0 44-45 0.0 0.0 0.0 0.0 0.0 46-47 0.0 0.0 0.0 0.0 0.0 48-49 0.0 0.0 0.0 0.0 0.0 50-51 0.0 0.0 0.0 0.0 0.0 52-53 0.0125 0.0 0.0 0.0 0.0 54-55 0.025 0.0 0.0 0.0 0.0 56-57 0.025 0.0 0.0 0.0 0.0 58-59 0.025 0.0 0.0 0.0 0.0 60-61 0.025 0.0 0.0 0.0 0.0 62-63 0.025 0.0 0.0 0.0 0.0 64-65 0.025 0.0 0.0 0.0 0.0 66-67 0.025 0.0 0.0 0.0 0.0 68-69 0.025 0.0 0.0 0.0 0.0 70-71 0.05 0.0 0.0 0.0 0.0 72-73 0.075 0.0 0.0 0.0 0.0 74-75 0.0875 0.0 0.0 0.0 0.0 76-77 0.1 0.0 0.0 0.0 0.0 78-79 0.125 0.0 0.0 0.0 0.0 80-81 0.175 0.0 0.0 0.0 0.0 82-83 0.23750000000000002 0.0 0.0 0.0 0.0 84-85 0.3125 0.0 0.0 0.0 0.0 86-87 0.3625 0.0 0.0 0.0 0.0 88-89 0.42500000000000004 0.0 0.0 0.0 0.0 90-91 0.5125 0.0 0.0 0.0 0.0 92-93 0.5874999999999999 0.0 0.0 0.0 0.0 94-95 0.6 0.0 0.0 0.0 0.0 96-97 0.6625000000000001 0.0 0.0 0.0 0.0 98-99 0.75 0.0 0.0 0.0 0.0 100-101 0.8374999999999999 0.0 0.0 0.0 0.0 102-103 0.95 0.0 0.0 0.0 0.0 104-105 1.0499999999999998 0.0 0.0 0.0 0.0 106-107 1.2 0.0 0.0 0.0 0.0 108-109 1.3125 0.0 0.0 0.0 0.0 110-111 1.525 0.0 0.0 0.0 0.0 112-113 1.65 0.0 0.0 0.0 0.0 114-115 1.9375 0.0 0.0 0.0 0.0 116-117 2.2625 0.0 0.0 0.0 0.0 118-119 2.525 0.0 0.0 0.0 0.0 120-121 2.7875 0.0 0.0 0.0 0.0 122-123 3.0375 0.0 0.0 0.0 0.0 124-125 3.3499999999999996 0.0 0.0 0.0 0.0 126-127 3.6125 0.0 0.0 0.0 0.0 128-129 3.9375 0.0 0.0 0.0 0.0 130-131 4.275 0.0 0.0 0.0 0.0 132-133 4.625 0.0 0.0 0.0 0.0 134-135 4.925 0.0 0.0 0.0 0.0 136-137 5.3 0.0 0.0 0.0 0.0 138-139 5.987500000000001 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content pass >>END_MODULE Read 617729 spots for SRR12917568.sra Written 617729 spots for SRR12917568.sra Read 617729 spots for SRR12917568.sra Written 617729 spots for SRR12917568.sra Read 617729 spots for SRR12917568.sra Written 617729 spots for SRR12917568.sra Read 617729 spots for SRR12917568.sra Written 617729 spots for SRR12917568.sra Read 617729 spots for SRR12917568.sra Written 617729 spots for SRR12917568.sra Read 617729 spots for SRR12917568.sra Written 617729 spots for SRR12917568.sra Read 617729 spots for SRR12917568.sra Written 617729 spots for SRR12917568.sra Read 617729 spots for SRR12917568.sra Written 617729 spots for SRR12917568.sra Read 617729 spots for SRR12917568.sra Written 617729 spots for SRR12917568.sra Read 617729 spots for SRR12917568.sra Written 617729 spots for SRR12917568.sra Read 617729 spots for SRR12917568.sra Written 617729 spots for SRR12917568.sra Read 617729 spots for SRR12917568.sra Written 617729 spots for SRR12917568.sra Read 617729 spots for SRR12917568.sra Written 617729 spots for SRR12917568.sra Read 617729 spots for SRR12917568.sra Written 617729 spots for SRR12917568.sra Read 617729 spots for SRR12917568.sra Written 617729 spots for SRR12917568.sra Read 617729 spots for SRR12917568.sra Written 617729 spots for SRR12917568.sra Read 617729 spots for SRR12917568.sra Written 617729 spots for SRR12917568.sra Read 617740 spots for SRR12917568.sra Written 617740 spots for SRR12917568.sra Read 617729 spots for SRR12917568.sra Written 617729 spots for SRR12917568.sra Read 617729 spots for SRR12917568.sra Written 617729 spots for SRR12917568.sra SRR ids: ['SRR12917568.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_zry50yd4 SRR12917568.sra spots: 12354591 blocks: [[1, 617729], [617730, 1235458], [1235459, 1853187], [1853188, 2470916], [2470917, 3088645], [3088646, 3706374], [3706375, 4324103], [4324104, 4941832], [4941833, 5559561], [5559562, 6177290], [6177291, 6795019], [6795020, 7412748], [7412749, 8030477], [8030478, 8648206], [8648207, 9265935], [9265936, 9883664], [9883665, 10501393], [10501394, 11119122], [11119123, 11736851], [11736852, 12354591]] SRR12917568 file size 4176930 SRR12917568 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 SRR12917568 SRR12917568_1.fastq SRR12917568_2.fastq Input file: SRR12917568_1.fastq Paired file: SRR12917568_2.fastq trimmed: SRR12917568-trimmed-pair1.fastq, SRR12917568-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 Feb 13 14:17:50 2025 >> started Thu Feb 13 14:18:03 2025 >> done (13.083s) 12354591 read pairs processed; of these: 135 ( 0.00%) short read pairs filtered out after trimming by size control 5304 ( 0.04%) empty read pairs filtered out after trimming by size control 12349152 (99.96%) read pairs available; of these: 895128 ( 7.25%) trimmed read pairs available after processing 11454024 (92.75%) untrimmed read pairs available after processing Length distribution of reads after trimming: length count percentage 18 5 0.00% 19 12 0.00% 20 13 0.00% 21 11 0.00% 22 28 0.00% 23 21 0.00% 24 29 0.00% 25 17 0.00% 26 26 0.00% 27 35 0.00% 28 24 0.00% 29 31 0.00% 30 37 0.00% 31 35 0.00% 32 24 0.00% 33 34 0.00% 34 38 0.00% 35 46 0.00% 36 25 0.00% 37 34 0.00% 38 35 0.00% 39 27 0.00% 40 35 0.00% 41 29 0.00% 42 59 0.00% 43 47 0.00% 44 39 0.00% 45 40 0.00% 46 44 0.00% 47 52 0.00% 48 48 0.00% 49 67 0.00% 50 55 0.00% 51 87 0.00% 52 79 0.00% 53 101 0.00% 54 100 0.00% 55 86 0.00% 56 108 0.00% 57 122 0.00% 58 132 0.00% 59 130 0.00% 60 170 0.00% 61 223 0.00% 62 228 0.00% 63 297 0.00% 64 343 0.00% 65 360 0.00% 66 393 0.00% 67 441 0.00% 68 453 0.00% 69 582 0.00% 70 582 0.00% 71 687 0.01% 72 789 0.01% 73 1003 0.01% 74 1006 0.01% 75 1106 0.01% 76 1203 0.01% 77 1290 0.01% 78 1361 0.01% 79 1588 0.01% 80 1726 0.01% 81 1894 0.02% 82 2130 0.02% 83 2335 0.02% 84 2635 0.02% 85 2985 0.02% 86 3003 0.02% 87 3211 0.03% 88 3247 0.03% 89 3497 0.03% 90 3584 0.03% 91 4049 0.03% 92 4258 0.03% 93 4532 0.04% 94 4873 0.04% 95 5023 0.04% 96 5571 0.05% 97 5594 0.05% 98 5933 0.05% 99 6299 0.05% 100 6325 0.05% 101 6592 0.05% 102 6895 0.06% 103 7191 0.06% 104 7649 0.06% 105 8171 0.07% 106 8551 0.07% 107 8807 0.07% 108 9177 0.07% 109 9496 0.08% 110 9275 0.08% 111 9842 0.08% 112 9803 0.08% 113 10033 0.08% 114 10760 0.09% 115 11414 0.09% 116 11456 0.09% 117 12179 0.10% 118 12616 0.10% 119 12908 0.10% 120 13294 0.11% 121 13165 0.11% 122 13462 0.11% 123 13824 0.11% 124 14913 0.12% 125 15249 0.12% 126 15945 0.13% 127 16220 0.13% 128 16547 0.13% 129 16842 0.14% 130 17721 0.14% 131 17701 0.14% 132 18145 0.15% 133 18503 0.15% 134 18590 0.15% 135 19562 0.16% 136 19951 0.16% 137 20439 0.17% 138 21128 0.17% 139 21474 0.17% 140 22449 0.18% 141 22906 0.19% 142 23064 0.19% 143 23097 0.19% 144 24918 0.20% 145 24688 0.20% 146 25303 0.20% 147 25644 0.21% 148 25453 0.21% 149 25867 0.21% 150 27393 0.22% 151 11454024 92.75% 12349152 reads passed initial QC criterion=sequence-density sequence-density=1.25 sequence-density-rank=1 fanout-score=2.02 fanout-score-rank=27 prefix-density=1.25 prefix-fanout=2.0 sequence=GCTTTATTTCGAACGTAAAAATCAGAAGTAGAACTCTTCGATCCAAAGACAACTTTGGGTTTTCCGGGCAGGCATTCATCAGAATAGCATTTTCTTAACTTCATATCCTTGAGCGCTT criterion=fanout-score sequence-density=0.05 sequence-density-rank=29 fanout-score=14.59 fanout-score-rank=1 prefix-density=0.17 prefix-fanout=3.9 sequence=TTATTTATTTAAGCAAAGTACCCAGCAACGCCACACATATGAAAAACAAGTAAGAGACTGGCCATGACATGGTTGCTGCATTTTTCTTTTGCGCGAGTTGCATTATTTCACTAACAAGGCTTGGCGCAAAAACAGCGGCGGCGGAACCCTTTGCATTCACCACCGGGAAAACCTTCAGTCTTGCACACACTAGCACAGTTGTGGCCTCTTACACATGGTCCTTTAAAACTATGGCTCTGTGACAAACAAACCCTAGCCTCAGCAGGTACCATCATTTCCTGGGAAGCCAGGGCAATGAGCAGCAACAAGAAAAGACCATAGCATTTCTTCTCCATCTCTCTGTCTAACAAGAACCTGTCTAACACTAGCTCTCTGTCTGCAACTACTACTAG criterion=sequence-density sequence-density=1.25 sequence-density-rank=1 fanout-score=2.02 fanout-score-rank=35 prefix-density=1.24 prefix-fanout=2.0 sequence=AAGCGCTCAAGGATATGAAGTTAAGAAAATGCTATTCTGATGAATGCCTGCCCGGAAAACCCAAAGTTGTCTTTGGATCGAAGAGTTCTACTTCTGATTTTTACGTTCGAAATAAAGC criterion=fanout-score sequence-density=0.01 sequence-density-rank=41 fanout-score=572.89 fanout-score-rank=1 prefix-density=0.20 prefix-fanout=15.4 sequence=AAGAAGTTGCCCCAGAGAGCTTCAAAGCATGGTCAGTGACCTATAGTGAAGAAAAACAAAAAAGAAATGGATGCCAAAGCTCTCTTCTTCTTTGCCTTGTTGTCCTTCTCAGCTGTGTCGGTCAGGCCGGCATTAGCAGAAAATGAAGAAGACCCTGGTCTTGTTATGAACTTTTACAAGGATACATGCCCTCAAGCTGAGGACATTGTCAAAGAACAAGTTAGACTCCTTTACAAGAGACACAAAAACACTGCATTTTCTTGGCTAAGAAACATCTTCCATGACTGTGCTGTTCAGTCATGTGATGCTTCACTGCTGCTGGACTCAACAAGGAGGACCTTGTCCGAGAAGGAGACAGACAGGAGCTTTGGCCTCAGGAACTTTAGATACTTTGACGATATCAAAGAAGCTGTTGAAAGAGAGTGTCCTGGAGTCGTTTCCTGTGCTGATATTCTTGTCCTGTCTGCTAGAGATGGCATTGTTTCGCTAGGAGGACCTCATATCCCTCTCA SRR12917568 testing PE reads STAR mapping to Ensembl genome Started job on | Feb 13 14:18:46 Started mapping on | Feb 13 14:18:47 Finished on | Feb 13 14:20:20 Mapping speed, Million of reads per hour | 478.03 Number of input reads | 12349152 Average input read length | 298 UNIQUE READS: Uniquely mapped reads number | 11414678 Uniquely mapped reads % | 92.43% Average mapped length | 297.13 Number of splices: Total | 11065253 Number of splices: Annotated (sjdb) | 10838681 Number of splices: GT/AG | 10876051 Number of splices: GC/AG | 146253 Number of splices: AT/AC | 11906 Number of splices: Non-canonical | 31043 Mismatch rate per base, % | 0.32% Deletion rate per base | 0.03% Deletion average length | 2.92 Insertion rate per base | 0.02% Insertion average length | 2.52 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 265065 % of reads mapped to multiple loci | 2.15% Number of reads mapped to too many loci | 93170 % of reads mapped to too many loci | 0.75% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 4.42% % of reads unmapped: other | 0.24% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 669409 669409 669409 N_multimapping 265065 265065 265065 N_noFeature 419079 11285661 474095 N_ambiguous 133699 599 59433 UnstrandedReadsAssigned:10861900 PositiveStrandReadsAssigned:128418 NegativeStrandReadsAssigned:10881150 Dataset is classified negative stranded MeadianReadLen=151 20thPercentileLength=151 echo kmer=147 SRR12917568 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: SRR12917568-trimmed-pair1.fastq SRR12917568-trimmed-pair2.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 12,349,152 reads, 10,917,146 reads pseudoaligned [quant] estimated average fragment length: 271.099 [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,033 rounds 52401 SRR12917568.ke.tsv 34699 SRR12917568.se.tsv 87100 total ==> SRR12917568.ke.tsv <== target_id length eff_length est_counts tpm Potri.005G200100.1.v4.1 2018 1747.9 464 22.6086 Potri.005G024800.1.v4.1 1035 764.901 99 11.023 Potri.004G059700.1.v4.1 961 690.992 44 5.42315 Potri.007G009000.2.v4.1 1416 1145.9 0 0 Potri.003G141000.2.v4.1 2943 2672.9 304 9.6864 Potri.016G087400.1.v4.1 270 77.4411 1219.21 1340.85 Potri.015G069301.1.v4.1 564 306.722 0 0 Potri.010G195200.1.v4.1 1773 1502.9 61 3.45678 Potri.012G127500.1.v4.1 977 706.947 6432 774.874 ==> SRR12917568.se.tsv <== Potri.001G166300.v4.1 0 Potri.001G448400.v4.1 136 Potri.001G233950.v4.1 0 Potri.001G122700.v4.1 164 Potri.001G212900.v4.1 0 Potri.001G182400.v4.1 0 Potri.001G256600.v4.1 0 Potri.001G040500.v4.1 0 Potri.001G416900.v4.1 1 Potri.001G452600.v4.1 32 SRR12917568 completed mapping pipeline successfully