Starting /dee2/code/volunteer_pipeline.sh SRR12671398 current disk space = 3052571504640 free memory = 1478014108 SRR12671398 SRAfilesize 938e1f98f4fee1bc29f22bf21c2d70de SRR12671398.sra SRR12671398.sra file validated SRR12671398 is paired end SRR12671398 is conventional basespace SRR12671398 read1 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR12671398_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 36.6445 37.0 37.0 37.0 37.0 37.0 2 36.395 37.0 37.0 37.0 37.0 37.0 3 36.5465 37.0 37.0 37.0 37.0 37.0 4 36.6895 37.0 37.0 37.0 37.0 37.0 5 36.646 37.0 37.0 37.0 37.0 37.0 6 36.555 37.0 37.0 37.0 37.0 37.0 7 36.5465 37.0 37.0 37.0 37.0 37.0 8 36.5945 37.0 37.0 37.0 37.0 37.0 9 36.653 37.0 37.0 37.0 37.0 37.0 10-14 36.5912 37.0 37.0 37.0 37.0 37.0 15-19 36.5799 37.0 37.0 37.0 37.0 37.0 20-24 36.5872 37.0 37.0 37.0 37.0 37.0 25-29 36.5419 37.0 37.0 37.0 37.0 37.0 30-34 36.5224 37.0 37.0 37.0 37.0 37.0 35-39 36.4833 37.0 37.0 37.0 37.0 37.0 40-44 36.4712 37.0 37.0 37.0 37.0 37.0 45-49 36.444 37.0 37.0 37.0 37.0 37.0 50-54 36.4363 37.0 37.0 37.0 37.0 37.0 55-59 36.4137 37.0 37.0 37.0 37.0 37.0 60-64 36.333000000000006 37.0 37.0 37.0 37.0 37.0 65-69 36.3411 37.0 37.0 37.0 37.0 37.0 70-74 36.3435 37.0 37.0 37.0 37.0 37.0 75-79 36.355399999999996 37.0 37.0 37.0 37.0 37.0 80-84 36.31949999999999 37.0 37.0 37.0 37.0 37.0 85-89 36.309400000000004 37.0 37.0 37.0 37.0 37.0 90-94 36.2975 37.0 37.0 37.0 37.0 37.0 95-99 36.2146 37.0 37.0 37.0 37.0 37.0 100-104 36.1649 37.0 37.0 37.0 37.0 37.0 105-109 36.221799999999995 37.0 37.0 37.0 37.0 37.0 110-114 36.1464 37.0 37.0 37.0 37.0 37.0 115-119 36.1696 37.0 37.0 37.0 37.0 37.0 120-124 36.1251 37.0 37.0 37.0 37.0 37.0 125-129 36.078500000000005 37.0 37.0 37.0 37.0 37.0 130-134 36.0843 37.0 37.0 37.0 37.0 37.0 135-139 36.0226 37.0 37.0 37.0 37.0 37.0 140-144 35.9465 37.0 37.0 37.0 37.0 37.0 145-149 35.974000000000004 37.0 37.0 37.0 37.0 37.0 150-151 35.855000000000004 37.0 37.0 37.0 37.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 23 2.0 24 3.0 25 3.0 26 5.0 27 3.0 28 6.0 29 16.0 30 25.0 31 38.0 32 41.0 33 79.0 34 105.0 35 260.0 36 2961.0 37 453.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 50.575 10.424999999999999 5.55 33.45 2 19.76452905811623 11.623246492985972 36.77354709418837 31.83867735470942 3 18.325 18.475 26.950000000000003 36.25 4 23.425 23.425 23.974999999999998 29.175 5 24.15 30.325000000000003 23.45 22.075 6 19.975 33.275 23.599999999999998 23.150000000000002 7 15.45 25.55 43.375 15.625 8 14.075 26.775 34.699999999999996 24.45 9 17.925 24.25 34.175 23.65 10-14 19.735 29.459999999999997 27.845 22.96 15-19 20.4 27.805000000000003 27.705000000000002 24.09 20-24 19.3 28.384999999999998 27.694999999999997 24.62 25-29 20.544999999999998 28.175 27.365000000000002 23.915 30-34 19.885 28.095 28.07 23.95 35-39 20.39 28.449999999999996 26.919999999999998 24.240000000000002 40-44 19.705000000000002 28.37 27.97 23.955000000000002 45-49 20.65 28.475 26.640000000000004 24.235 50-54 20.085 27.93 27.779999999999998 24.205 55-59 20.285 28.139999999999997 27.589999999999996 23.985 60-64 19.875 27.955000000000002 27.765 24.404999999999998 65-69 20.495 28.365000000000002 27.24 23.9 70-74 20.200000000000003 27.775 27.825 24.2 75-79 20.965 27.61 27.515 23.91 80-84 19.72 28.050000000000004 28.125 24.104999999999997 85-89 20.89 27.634999999999998 27.62 23.855 90-94 20.785 27.015 27.500000000000004 24.7 95-99 19.6 27.750000000000004 27.185 25.465 100-104 20.02 28.355000000000004 27.165 24.46 105-109 20.9 28.555000000000003 26.57 23.974999999999998 110-114 20.87 27.555000000000003 27.76 23.815 115-119 20.985 27.47 27.33 24.215 120-124 20.82 27.505000000000003 27.26 24.415 125-129 21.085 27.625 26.88 24.41 130-134 20.45 28.38 27.415 23.755000000000003 135-139 20.52 28.175 26.740000000000002 24.565 140-144 21.025 27.450000000000003 27.11 24.415 145-149 20.835 27.315 27.560000000000002 24.29 150-151 20.775 27.875 26.525 24.825 >>END_MODULE >>Per sequence GC content pass #GC Content Count 0 0.0 1 0.0 2 0.0 3 0.5 4 1.5 5 1.0 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 0.0 16 0.0 17 0.5 18 0.5 19 0.5 20 0.5 21 0.5 22 1.0 23 2.5 24 4.0 25 4.0 26 6.0 27 5.5 28 8.5 29 18.5 30 27.5 31 31.0 32 32.5 33 41.5 34 52.0 35 63.5 36 81.5 37 101.0 38 112.5 39 125.5 40 166.5 41 202.5 42 217.5 43 226.5 44 239.0 45 260.0 46 255.0 47 239.5 48 236.5 49 216.5 50 174.5 51 157.0 52 136.0 53 109.5 54 95.0 55 67.0 56 56.5 57 53.5 58 41.5 59 33.5 60 27.5 61 18.0 62 13.0 63 10.0 64 5.0 65 6.0 66 5.0 67 2.0 68 1.0 69 0.5 70 0.5 71 0.5 72 0.5 73 1.0 74 1.0 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 81.875 #Duplication Level Percentage of deduplicated Percentage of total 1 82.41221374045801 67.475 2 14.106870229007635 23.1 3 2.717557251908397 6.675000000000001 4 0.5190839694656488 1.7000000000000002 5 0.2137404580152672 0.8750000000000001 6 0.0 0.0 7 0.03053435114503817 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 GTTGATCATAATTCCTGATGCTTGAGGGAACTGAGTGGCAAAATCAAGAA 7 0.17500000000000002 No Hit GTTCGATTAGTCTTTCGCCCCTATACCCAAGTCAGACGAACGATTTGCAC 5 0.125 No Hit GCATTATATGAGTTACTTTCATTCATTGATCCTGAATCATCTGCAGTATT 5 0.125 No Hit CCATCATCAAACAGAATGGCGAGAGAATTATATTGGAAAAAAAAGGAAAA 5 0.125 No Hit GCTGAAGGTTTATCTGTACAAAGGGGGAAAGCTGTTTCATGGAAAACCTG 5 0.125 No Hit CTCATCATAAGGTGAATGCTTCAGTAGAATAAGACGCCAGATACCAACCC 5 0.125 No Hit GTGCTTGCTTAATGACCGCATGTGCAGGTAGTGCAAGTGCAGCCAGTACC 5 0.125 No Hit CACCGCCTCACGGTACCTTTGCCTGATAAGCTTTGCGGGTTCACCAGCGT 5 0.125 No Hit >>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 0.0 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 0.025 0.0 0.0 0.0 50-51 0.0 0.05 0.0 0.0 0.0 52-53 0.0 0.05 0.0 0.0 0.0 54-55 0.0 0.05 0.0 0.0 0.0 56-57 0.0 0.05 0.0 0.0 0.0 58-59 0.0 0.05 0.0 0.0 0.0 60-61 0.0 0.05 0.0 0.0 0.0 62-63 0.0 0.05 0.0 0.0 0.0 64-65 0.0 0.05 0.0 0.0 0.0 66-67 0.0 0.05 0.0 0.0 0.0 68-69 0.0 0.05 0.0 0.0 0.0 70-71 0.0 0.05 0.0 0.0 0.0 72-73 0.0125 0.05 0.0 0.0 0.0 74-75 0.025 0.05 0.0 0.0 0.0 76-77 0.037500000000000006 0.05 0.0 0.0 0.0 78-79 0.05 0.05 0.0 0.0 0.0 80-81 0.05 0.05 0.0 0.0 0.0 82-83 0.125 0.05 0.0 0.0 0.0 84-85 0.125 0.05 0.0 0.0 0.0 86-87 0.15 0.05 0.0 0.0 0.0 88-89 0.16249999999999998 0.05 0.0 0.0 0.0 90-91 0.175 0.05 0.0 0.0 0.0 92-93 0.225 0.05 0.0 0.0 0.0 94-95 0.32499999999999996 0.05 0.0 0.0 0.0 96-97 0.3875 0.05 0.0 0.0 0.0 98-99 0.5125 0.05 0.0 0.0 0.0 100-101 0.7 0.05 0.0 0.0 0.0 102-103 0.8 0.05 0.0 0.0 0.0 104-105 0.85 0.05 0.0 0.0 0.0 106-107 0.9875 0.05 0.0 0.0 0.0 108-109 1.1625 0.05 0.0 0.0 0.0 110-111 1.2125 0.05 0.0 0.0 0.0 112-113 1.35 0.05 0.0 0.0 0.0 114-115 1.6 0.05 0.0 0.0 0.0 116-117 1.8375 0.05 0.0 0.0 0.0 118-119 2.0 0.05 0.0 0.0 0.0 120-121 2.0875 0.05 0.0 0.0 0.0 122-123 2.3125 0.05 0.0 0.0 0.0 124-125 2.5875000000000004 0.05 0.0 0.0 0.0 126-127 2.8 0.05 0.0 0.0 0.0 128-129 2.9749999999999996 0.05 0.0 0.0 0.0 130-131 3.1875 0.05 0.0 0.0 0.0 132-133 3.375 0.05 0.0 0.0 0.0 134-135 3.6875 0.05 0.0 0.0 0.0 136-137 4.0625 0.05 0.0 0.0 0.0 138-139 4.3375 0.05 0.0 0.0 0.0 >>END_MODULE >>Kmer Content pass >>END_MODULE SRR12671398 read2 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR12671398_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 36.23 37.0 37.0 37.0 37.0 37.0 2 35.9935 37.0 37.0 37.0 37.0 37.0 3 36.2205 37.0 37.0 37.0 37.0 37.0 4 36.173 37.0 37.0 37.0 37.0 37.0 5 36.299 37.0 37.0 37.0 37.0 37.0 6 36.185 37.0 37.0 37.0 37.0 37.0 7 36.2215 37.0 37.0 37.0 37.0 37.0 8 36.2125 37.0 37.0 37.0 37.0 37.0 9 36.251 37.0 37.0 37.0 37.0 37.0 10-14 36.2748 37.0 37.0 37.0 37.0 37.0 15-19 36.2128 37.0 37.0 37.0 37.0 37.0 20-24 36.160000000000004 37.0 37.0 37.0 37.0 37.0 25-29 36.106700000000004 37.0 37.0 37.0 37.0 37.0 30-34 36.074299999999994 37.0 37.0 37.0 37.0 37.0 35-39 36.0559 37.0 37.0 37.0 37.0 37.0 40-44 36.0262 37.0 37.0 37.0 37.0 37.0 45-49 36.0101 37.0 37.0 37.0 37.0 37.0 50-54 35.9467 37.0 37.0 37.0 37.0 37.0 55-59 35.929500000000004 37.0 37.0 37.0 37.0 37.0 60-64 35.9474 37.0 37.0 37.0 37.0 37.0 65-69 35.907 37.0 37.0 37.0 37.0 37.0 70-74 35.87230000000001 37.0 37.0 37.0 37.0 37.0 75-79 35.867599999999996 37.0 37.0 37.0 37.0 37.0 80-84 35.8033 37.0 37.0 37.0 37.0 37.0 85-89 35.895 37.0 37.0 37.0 37.0 37.0 90-94 35.813900000000004 37.0 37.0 37.0 37.0 37.0 95-99 35.804899999999996 37.0 37.0 37.0 37.0 37.0 100-104 35.7082 37.0 37.0 37.0 37.0 37.0 105-109 35.698699999999995 37.0 37.0 37.0 37.0 37.0 110-114 35.6936 37.0 37.0 37.0 37.0 37.0 115-119 35.7224 37.0 37.0 37.0 37.0 37.0 120-124 35.65089999999999 37.0 37.0 37.0 37.0 37.0 125-129 35.6773 37.0 37.0 37.0 37.0 37.0 130-134 35.569399999999995 37.0 37.0 37.0 37.0 37.0 135-139 35.5427 37.0 37.0 37.0 37.0 37.0 140-144 35.523399999999995 37.0 37.0 37.0 37.0 37.0 145-149 35.4504 37.0 37.0 37.0 37.0 37.0 150-151 35.32225 37.0 37.0 37.0 31.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 12 1.0 13 5.0 14 5.0 15 9.0 16 5.0 17 2.0 18 3.0 19 2.0 20 4.0 21 6.0 22 5.0 23 6.0 24 8.0 25 5.0 26 6.0 27 6.0 28 18.0 29 15.0 30 22.0 31 29.0 32 48.0 33 99.0 34 143.0 35 484.0 36 2746.0 37 318.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 44.925 24.7 8.924999999999999 21.45 2 28.599999999999998 24.3 31.3 15.8 3 21.25 26.55 33.900000000000006 18.3 4 24.9 33.7 22.75 18.65 5 27.85 35.175 20.724999999999998 16.25 6 21.425 39.475 20.4 18.7 7 19.75 23.7 37.7 18.85 8 20.150000000000002 25.474999999999998 28.299999999999997 26.075 9 22.225 25.074999999999996 29.275000000000002 23.425 10-14 24.42 29.25 25.56 20.77 15-19 23.974999999999998 28.33 26.924999999999997 20.77 20-24 23.49 27.655 27.73 21.125 25-29 23.71 28.035 27.939999999999998 20.315 30-34 23.145 28.060000000000002 27.555000000000003 21.240000000000002 35-39 24.25 27.279999999999998 27.169999999999998 21.3 40-44 23.76 28.555000000000003 26.44 21.245 45-49 23.515 27.834999999999997 27.744999999999997 20.905 50-54 24.63 27.715 27.21 20.445 55-59 24.15 27.49 27.685 20.674999999999997 60-64 24.015 27.295 27.634999999999998 21.055 65-69 24.635 27.47 27.284999999999997 20.61 70-74 24.505 27.155 26.935 21.404999999999998 75-79 24.515 27.215 27.034999999999997 21.235 80-84 24.595 27.79 26.795 20.82 85-89 24.43 28.205000000000002 26.525 20.84 90-94 24.060000000000002 27.889999999999997 27.49 20.560000000000002 95-99 24.035 28.050000000000004 26.005 21.91 100-104 24.65 27.495000000000005 27.465 20.39 105-109 24.215 27.810000000000002 27.195000000000004 20.78 110-114 24.15 27.779999999999998 27.169999999999998 20.9 115-119 25.165 28.444999999999997 26.56 19.830000000000002 120-124 25.145 28.050000000000004 26.1 20.705000000000002 125-129 25.040000000000003 28.110000000000003 26.540000000000003 20.31 130-134 24.255 28.065 27.115000000000002 20.565 135-139 25.345000000000002 27.665 27.305 19.685 140-144 24.985 28.000000000000004 27.13 19.885 145-149 25.782578257825783 27.467746774677465 26.68266826682668 20.067006700670067 150-151 26.375 28.262500000000003 25.5 19.8625 >>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 1.0 11 0.5 12 0.0 13 0.5 14 0.5 15 0.0 16 0.5 17 1.0 18 1.5 19 2.0 20 1.0 21 2.0 22 2.5 23 3.5 24 4.5 25 3.5 26 6.0 27 7.5 28 10.0 29 10.0 30 17.0 31 19.5 32 21.0 33 29.0 34 29.0 35 45.0 36 74.5 37 112.5 38 148.5 39 172.5 40 182.5 41 191.5 42 236.5 43 262.5 44 268.0 45 262.5 46 241.5 47 224.5 48 207.0 49 196.5 50 170.0 51 139.5 52 123.5 53 103.5 54 84.0 55 81.0 56 62.0 57 44.0 58 38.5 59 31.5 60 23.0 61 16.5 62 13.0 63 10.0 64 8.0 65 4.5 66 5.0 67 3.0 68 1.0 69 1.0 70 1.0 71 1.0 72 2.5 73 2.5 74 1.5 75 1.5 76 0.5 77 0.5 78 0.5 79 0.0 80 0.0 81 0.0 82 0.5 83 1.5 84 1.5 85 1.5 86 1.0 87 0.0 88 0.0 89 0.0 90 0.0 91 0.0 92 0.0 93 1.0 94 2.5 95 2.0 96 1.5 97 1.0 98 0.5 99 2.0 100 5.5 >>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 0.01 150-151 0.0 >>END_MODULE >>Sequence Length Distribution pass #Length Count 151 4000.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 81.5 #Duplication Level Percentage of deduplicated Percentage of total 1 82.66871165644172 67.375 2 13.895705521472394 22.650000000000002 3 2.607361963190184 6.375 4 0.4601226993865031 1.5 5 0.15337423312883436 0.625 6 0.09202453987730061 0.44999999999999996 7 0.030674846625766874 0.17500000000000002 8 0.0 0.0 9 0.030674846625766874 0.22499999999999998 >10 0.06134969325153375 0.625 >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 15 0.375 No Hit ATTCATACTCCAAGTCTTTTAGTTCATCCATTTAAGCTTAATCAATCAAT 10 0.25 No Hit AGAGAACACATTCATACTCCAAGTCTTTTAGTTCATCCATTTAAGCTTAA 9 0.22499999999999998 No Hit CAGAGAACACATTCATACTCCAAGTCTTTTAGTTCATCCATTTAAGCTTA 7 0.17500000000000002 No Hit ACCACATGTTCATGAAGAGCTCCTCAACATATCCAAAAGGTATAAAATTC 6 0.15 No Hit AGAACACATTCATACTCCAAGTCTTTTAGTTCATCCATTTAAGCTTAATC 6 0.15 No Hit TTTTTTTTTCCCAGACAGTGTTTATATGTACGATCAGATCCATCTCAATG 6 0.15 No Hit GTTATGGAGGATAAGCCCGTGAAAGACGGATCTCAGTCATCCCCATTATT 5 0.125 No Hit AGAAGAAAGAAAAGAGCGGGGACAAGAAGAAGTAGAAGAAGCATGACAGC 5 0.125 No Hit ATATACTATGTGTAATCATTCGGACGTTACCGTCCATTTGACCCCAGGTG 5 0.125 No Hit GGCGGGACTACCCGCTGAGTTTAAGCATATCAATAAGCGGAGGAAAAGAA 5 0.125 No Hit CTGTCAACACAGCACCGCTGGCTTTGAATGGCTCTGGCGCTGGATCCACA 5 0.125 No Hit >>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 0.0 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 0.025 0.0 0.0 10-11 0.0 0.0 0.025 0.0 0.0 12-13 0.0 0.0 0.025 0.0 0.0 14-15 0.0 0.0 0.025 0.0 0.0 16-17 0.0 0.0 0.025 0.0 0.0 18-19 0.0 0.0 0.025 0.0 0.0 20-21 0.0 0.0 0.025 0.0 0.0 22-23 0.0 0.0 0.025 0.0 0.0 24-25 0.0 0.0 0.025 0.0 0.0 26-27 0.0 0.0 0.025 0.0 0.0 28-29 0.0 0.0 0.025 0.0 0.0 30-31 0.0 0.0 0.025 0.0 0.0 32-33 0.0 0.0 0.025 0.0 0.0 34-35 0.0 0.0 0.025 0.0 0.0 36-37 0.0 0.0 0.025 0.0 0.0 38-39 0.0 0.0 0.025 0.0 0.0 40-41 0.0 0.0 0.025 0.0 0.0 42-43 0.0 0.0 0.025 0.0 0.0 44-45 0.0 0.0 0.025 0.0 0.0 46-47 0.0 0.0 0.025 0.0 0.0 48-49 0.0 0.0 0.025 0.0 0.0 50-51 0.0 0.0 0.025 0.0 0.0 52-53 0.0 0.0 0.025 0.0 0.0 54-55 0.0 0.0 0.025 0.0 0.0 56-57 0.0 0.0 0.025 0.0 0.0 58-59 0.0 0.0 0.025 0.0 0.0 60-61 0.0 0.0 0.025 0.0 0.0 62-63 0.0 0.0 0.025 0.0 0.0 64-65 0.0 0.0 0.025 0.0 0.0 66-67 0.0 0.0 0.025 0.0 0.0 68-69 0.0 0.0 0.025 0.0 0.0 70-71 0.0 0.0 0.025 0.0 0.0 72-73 0.0125 0.0 0.025 0.0 0.0 74-75 0.025 0.0 0.025 0.0 0.0 76-77 0.037500000000000006 0.0 0.025 0.0 0.0 78-79 0.05 0.0 0.025 0.0 0.0 80-81 0.05 0.0 0.025 0.0 0.0 82-83 0.125 0.0 0.025 0.0 0.0 84-85 0.125 0.0 0.025 0.0 0.0 86-87 0.15 0.0 0.025 0.0 0.0 88-89 0.16249999999999998 0.0 0.025 0.0 0.0 90-91 0.175 0.0 0.025 0.0 0.0 92-93 0.225 0.0 0.025 0.0 0.0 94-95 0.32499999999999996 0.0 0.025 0.0 0.0 96-97 0.3875 0.0 0.025 0.0 0.0 98-99 0.5125 0.0 0.025 0.0 0.0 100-101 0.7 0.0 0.025 0.0 0.0 102-103 0.8 0.0 0.025 0.0 0.0 104-105 0.85 0.0 0.025 0.0 0.0 106-107 0.9875 0.0 0.025 0.0 0.0 108-109 1.1749999999999998 0.0 0.025 0.0 0.0 110-111 1.2375 0.0 0.025 0.0 0.0 112-113 1.35 0.0 0.025 0.0 0.0 114-115 1.6 0.0 0.025 0.0 0.0 116-117 1.8375 0.0 0.025 0.0 0.0 118-119 2.0 0.0 0.025 0.0 0.0 120-121 2.0875 0.0 0.025 0.0 0.0 122-123 2.3125 0.0 0.025 0.0 0.0 124-125 2.5875000000000004 0.0 0.025 0.0 0.0 126-127 2.8 0.0 0.025 0.0 0.0 128-129 2.9625 0.0 0.025 0.0 0.0 130-131 3.1625 0.0 0.025 0.0 0.0 132-133 3.4000000000000004 0.0 0.025 0.0 0.0 134-135 3.7625 0.0 0.025 0.0 0.0 136-137 4.1375 0.0 0.025 0.0 0.0 138-139 4.425 0.0 0.025 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position GTGTTCC 10 0.006830828 145.0 2 CTGAGCC 10 0.006830828 145.0 8 CCTGAGC 10 0.006830828 145.0 7 TGAGCCA 10 0.006830828 145.0 9 >>END_MODULE Read 934064 spots for SRR12671398.sra Written 934064 spots for SRR12671398.sra Read 934064 spots for SRR12671398.sra Written 934064 spots for SRR12671398.sra Read 934064 spots for SRR12671398.sra Written 934064 spots for SRR12671398.sra Read 934064 spots for SRR12671398.sra Written 934064 spots for SRR12671398.sra Read 934064 spots for SRR12671398.sra Written 934064 spots for SRR12671398.sra Read 934064 spots for SRR12671398.sra Written 934064 spots for SRR12671398.sra Read 934064 spots for SRR12671398.sra Written 934064 spots for SRR12671398.sra Read 934064 spots for SRR12671398.sra Written 934064 spots for SRR12671398.sra Read 934064 spots for SRR12671398.sra Written 934064 spots for SRR12671398.sra Read 934064 spots for SRR12671398.sra Written 934064 spots for SRR12671398.sra Read 934064 spots for SRR12671398.sra Written 934064 spots for SRR12671398.sra Read 934064 spots for SRR12671398.sra Written 934064 spots for SRR12671398.sra Read 934064 spots for SRR12671398.sra Written 934064 spots for SRR12671398.sra Read 934064 spots for SRR12671398.sra Written 934064 spots for SRR12671398.sra Read 934064 spots for SRR12671398.sra Written 934064 spots for SRR12671398.sra Read 934064 spots for SRR12671398.sra Written 934064 spots for SRR12671398.sra Read 934064 spots for SRR12671398.sra Written 934064 spots for SRR12671398.sra Read 934064 spots for SRR12671398.sra Written 934064 spots for SRR12671398.sra Read 934081 spots for SRR12671398.sra Written 934081 spots for SRR12671398.sra Read 934064 spots for SRR12671398.sra Written 934064 spots for SRR12671398.sra SRR ids: ['SRR12671398.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_9_hcosgc SRR12671398.sra spots: 18681297 blocks: [[1, 934064], [934065, 1868128], [1868129, 2802192], [2802193, 3736256], [3736257, 4670320], [4670321, 5604384], [5604385, 6538448], [6538449, 7472512], [7472513, 8406576], [8406577, 9340640], [9340641, 10274704], [10274705, 11208768], [11208769, 12142832], [12142833, 13076896], [13076897, 14010960], [14010961, 14945024], [14945025, 15879088], [15879089, 16813152], [16813153, 17747216], [17747217, 18681297]] SRR12671398 file size 6327021 SRR12671398 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 SRR12671398 SRR12671398_1.fastq SRR12671398_2.fastq Input file: SRR12671398_1.fastq Paired file: SRR12671398_2.fastq trimmed: SRR12671398-trimmed-pair1.fastq, SRR12671398-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 21:47:43 2025 >> started Tue Feb 11 21:48:03 2025 >> done (19.825s) 18681297 read pairs processed; of these: 84 ( 0.00%) short read pairs filtered out after trimming by size control 11220 ( 0.06%) empty read pairs filtered out after trimming by size control 18669993 (99.94%) read pairs available; of these: 1213032 ( 6.50%) trimmed read pairs available after processing 17456961 (93.50%) untrimmed read pairs available after processing Length distribution of reads after trimming: length count percentage 18 10 0.00% 19 11 0.00% 20 13 0.00% 21 4 0.00% 22 18 0.00% 23 14 0.00% 24 19 0.00% 25 25 0.00% 26 29 0.00% 27 31 0.00% 28 30 0.00% 29 25 0.00% 30 32 0.00% 31 40 0.00% 32 24 0.00% 33 22 0.00% 34 32 0.00% 35 33 0.00% 36 40 0.00% 37 30 0.00% 38 20 0.00% 39 28 0.00% 40 38 0.00% 41 29 0.00% 42 33 0.00% 43 48 0.00% 44 31 0.00% 45 41 0.00% 46 44 0.00% 47 53 0.00% 48 64 0.00% 49 90 0.00% 50 73 0.00% 51 92 0.00% 52 74 0.00% 53 81 0.00% 54 79 0.00% 55 115 0.00% 56 110 0.00% 57 127 0.00% 58 151 0.00% 59 190 0.00% 60 231 0.00% 61 274 0.00% 62 297 0.00% 63 327 0.00% 64 363 0.00% 65 399 0.00% 66 413 0.00% 67 485 0.00% 68 508 0.00% 69 636 0.00% 70 673 0.00% 71 837 0.00% 72 889 0.00% 73 1049 0.01% 74 1199 0.01% 75 1347 0.01% 76 1386 0.01% 77 1473 0.01% 78 1551 0.01% 79 1942 0.01% 80 2025 0.01% 81 2305 0.01% 82 2612 0.01% 83 2879 0.02% 84 3115 0.02% 85 3442 0.02% 86 3759 0.02% 87 4047 0.02% 88 4285 0.02% 89 4473 0.02% 90 4795 0.03% 91 5102 0.03% 92 5467 0.03% 93 5986 0.03% 94 6459 0.03% 95 7002 0.04% 96 7122 0.04% 97 7734 0.04% 98 7942 0.04% 99 8268 0.04% 100 8626 0.05% 101 8705 0.05% 102 9516 0.05% 103 9711 0.05% 104 10462 0.06% 105 10759 0.06% 106 11191 0.06% 107 11808 0.06% 108 12004 0.06% 109 12582 0.07% 110 12610 0.07% 111 13079 0.07% 112 13666 0.07% 113 13917 0.07% 114 14564 0.08% 115 15006 0.08% 116 16234 0.09% 117 16664 0.09% 118 17056 0.09% 119 17566 0.09% 120 18171 0.10% 121 18223 0.10% 122 19048 0.10% 123 19488 0.10% 124 20081 0.11% 125 20360 0.11% 126 21572 0.12% 127 22127 0.12% 128 23223 0.12% 129 23376 0.13% 130 23764 0.13% 131 24386 0.13% 132 25058 0.13% 133 25233 0.14% 134 25802 0.14% 135 26674 0.14% 136 27412 0.15% 137 28118 0.15% 138 28850 0.15% 139 30072 0.16% 140 30043 0.16% 141 31102 0.17% 142 31209 0.17% 143 31924 0.17% 144 32958 0.18% 145 33568 0.18% 146 34098 0.18% 147 34362 0.18% 148 36367 0.19% 149 36143 0.19% 150 37303 0.20% 151 17456961 93.50% 18669993 reads passed initial QC criterion=sequence-density sequence-density=0.52 sequence-density-rank=1 fanout-score=2.01 fanout-score-rank=31 prefix-density=0.53 prefix-fanout=2.0 sequence=TGAGATGCCTCAGTGCATCCAAACATGGGTAG criterion=fanout-score sequence-density=0.01 sequence-density-rank=38 fanout-score=307.02 fanout-score-rank=1 prefix-density=0.24 prefix-fanout=14.2 sequence=TGAAGAAGACACAAAGATAAAGACACTCACGGACACTTTTGTTTGTTCACTCCACACCCACAAGTACAGAAGAACACAGATTATTTATCAGAAATTACATTATTAATCCACTCCCAATCCCACATCAAACATGATAGTTGATGTGCTTGCTTAATGACCGCATGTGCAGGTAGTGCAAGTGCAGCCAGTACCGCAGTTGCACTTGCCATCGTTCTCAGCTGCTGGCACCTCCATGACTACGGAGGAGACATAGTTCTTCTCAGTCTCGACGATGCCAGCAGTGTAGCTGCTTCCCTTCTTGACACACTGGGTCTTGTCAGCGCAGTCGCAG criterion=sequence-density sequence-density=1.16 sequence-density-rank=1 fanout-score=2.04 fanout-score-rank=30 prefix-density=1.16 prefix-fanout=2.0 sequence=CTGCGACTGCGCTGACAAGACCCAGTGTGTCAAGAAGGGAAGCAGCTACACTGCTGGCATCGTCGAGACTGAGAAGAACTATGTCTCCTCCGTAGTCATGGAGGTGCCAGCAGCTGAGAACGATGGCAAGTGCAACTGCGGTACTGGCTGCACTTGCACTACCTGCACATGCGGTCATTAAGCAAGCACATCAACTATCATGTTTGATGTGGGATTGGGAGTGGATTAATAATGTAATTTCTGATAAATAATCTGTGTTCTTCTGTACTTGTGGGTGTGGAGTGAACAAACAAAAGTGTCCGTGAGTGTCTTTATCTTTGTGTCTTCTTCA criterion=fanout-score sequence-density=0.01 sequence-density-rank=37 fanout-score=26.64 fanout-score-rank=1 prefix-density=0.08 prefix-fanout=1.9 sequence=CCACCACTAAACCCAAAGCTCAAAAAAAATCTTAACTGCACCCGCTCATCCAGCAATGGCAGCAGCAACAATGGCCCTCTCCTCCCCTTCGCTAGCCGGAAAGGCGGTGAAGCTCAACCCCTCCTCCTCTGAGATCATGGGCAATGGCCGTGTCTCCATGAGGAAAACCACCAAGCCTGTTCCCTCCGGGAGCCCATGGTACGGACCAGACCGTGTTAAATACTTGGGCCCGTTCTCTGGTGAGCCCCCATCCTACTTGACTGGTGAGTTCCCTGGTGACTACGGCTGGGACACTGCTGGCCTCTCTGCTGACCCAGAGACCTTTGCCAAGAACCGTGAGCTTGAAGTCATCCATTCCAGGTGGGCCATGCTTGGAGCTCTTGGATGCGTCTTCCCCGAGCTCTTGTCCCGCAACGGTGTCAAGTTCGGCGAGGCTGTATGGTTCAAGGCTGGAGCCCAGATCTTCAGCGAGGGTGGACTTGACTACTTGGGCAACCCAAGCTTGATCCAC SRR12671398 testing PE reads STAR mapping to Ensembl genome Started job on | Feb 11 21:48:47 Started mapping on | Feb 11 21:48:47 Finished on | Feb 11 21:50:56 Mapping speed, Million of reads per hour | 521.02 Number of input reads | 18669993 Average input read length | 298 UNIQUE READS: Uniquely mapped reads number | 16913983 Uniquely mapped reads % | 90.59% Average mapped length | 297.37 Number of splices: Total | 16858183 Number of splices: Annotated (sjdb) | 16542408 Number of splices: GT/AG | 16521571 Number of splices: GC/AG | 285285 Number of splices: AT/AC | 9721 Number of splices: Non-canonical | 41606 Mismatch rate per base, % | 0.37% Deletion rate per base | 0.03% Deletion average length | 2.71 Insertion rate per base | 0.03% Insertion average length | 2.26 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 492884 % of reads mapped to multiple loci | 2.64% Number of reads mapped to too many loci | 338897 % of reads mapped to too many loci | 1.82% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 4.54% % of reads unmapped: other | 0.41% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 1263126 1263126 1263126 N_multimapping 492884 492884 492884 N_noFeature 792278 16562857 891940 N_ambiguous 348410 1347 96205 UnstrandedReadsAssigned:15773295 PositiveStrandReadsAssigned:349779 NegativeStrandReadsAssigned:15925838 Dataset is classified negative stranded MeadianReadLen=151 20thPercentileLength=151 echo kmer=147 SRR12671398 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: SRR12671398-trimmed-pair1.fastq SRR12671398-trimmed-pair2.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 18,669,993 reads, 16,134,435 reads pseudoaligned [quant] estimated average fragment length: 273.508 [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,064 rounds 52401 SRR12671398.ke.tsv 34699 SRR12671398.se.tsv 87100 total ==> SRR12671398.ke.tsv <== target_id length eff_length est_counts tpm Potri.005G200100.1.v4.1 2018 1745.49 559 15.036 Potri.005G024800.1.v4.1 1035 762.492 485 29.8637 Potri.004G059700.1.v4.1 961 688.605 1 0.0681816 Potri.007G009000.2.v4.1 1416 1143.49 0 0 Potri.003G141000.2.v4.1 2943 2670.49 877.455 15.4266 Potri.016G087400.1.v4.1 270 74.8915 879.916 551.627 Potri.015G069301.1.v4.1 564 303.647 0 0 Potri.010G195200.1.v4.1 1773 1500.49 117 3.66091 Potri.012G127500.1.v4.1 977 704.552 138 9.19609 ==> SRR12671398.se.tsv <== Potri.001G166300.v4.1 0 Potri.001G448400.v4.1 92 Potri.001G233950.v4.1 0 Potri.001G122700.v4.1 226 Potri.001G212900.v4.1 4 Potri.001G182400.v4.1 0 Potri.001G256600.v4.1 0 Potri.001G040500.v4.1 7 Potri.001G416900.v4.1 0 Potri.001G452600.v4.1 7 SRR12671398 completed mapping pipeline successfully