Starting /dee2/code/volunteer_pipeline.sh SRR12671327 current disk space = 2823791390720 free memory = 1576389992 SRR12671327 SRAfilesize a8db569597a2a8b8ad2c3e69822117c4 SRR12671327.sra SRR12671327.sra file validated SRR12671327 is paired end SRR12671327 is conventional basespace SRR12671327 read1 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR12671327_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 36.6505 37.0 37.0 37.0 37.0 37.0 2 36.5515 37.0 37.0 37.0 37.0 37.0 3 36.6075 37.0 37.0 37.0 37.0 37.0 4 36.7015 37.0 37.0 37.0 37.0 37.0 5 36.7165 37.0 37.0 37.0 37.0 37.0 6 36.65 37.0 37.0 37.0 37.0 37.0 7 36.647 37.0 37.0 37.0 37.0 37.0 8 36.546 37.0 37.0 37.0 37.0 37.0 9 36.643 37.0 37.0 37.0 37.0 37.0 10-14 36.6725 37.0 37.0 37.0 37.0 37.0 15-19 36.6226 37.0 37.0 37.0 37.0 37.0 20-24 36.5869 37.0 37.0 37.0 37.0 37.0 25-29 36.5544 37.0 37.0 37.0 37.0 37.0 30-34 36.4989 37.0 37.0 37.0 37.0 37.0 35-39 36.4972 37.0 37.0 37.0 37.0 37.0 40-44 36.4753 37.0 37.0 37.0 37.0 37.0 45-49 36.432399999999994 37.0 37.0 37.0 37.0 37.0 50-54 36.4076 37.0 37.0 37.0 37.0 37.0 55-59 36.3613 37.0 37.0 37.0 37.0 37.0 60-64 36.379000000000005 37.0 37.0 37.0 37.0 37.0 65-69 36.309799999999996 37.0 37.0 37.0 37.0 37.0 70-74 36.306900000000006 37.0 37.0 37.0 37.0 37.0 75-79 36.2981 37.0 37.0 37.0 37.0 37.0 80-84 36.3035 37.0 37.0 37.0 37.0 37.0 85-89 36.252300000000005 37.0 37.0 37.0 37.0 37.0 90-94 36.2625 37.0 37.0 37.0 37.0 37.0 95-99 36.242000000000004 37.0 37.0 37.0 37.0 37.0 100-104 36.2332 37.0 37.0 37.0 37.0 37.0 105-109 36.16760000000001 37.0 37.0 37.0 37.0 37.0 110-114 36.181 37.0 37.0 37.0 37.0 37.0 115-119 36.09589999999999 37.0 37.0 37.0 37.0 37.0 120-124 36.09160000000001 37.0 37.0 37.0 37.0 37.0 125-129 36.0676 37.0 37.0 37.0 37.0 37.0 130-134 36.0462 37.0 37.0 37.0 37.0 37.0 135-139 36.0145 37.0 37.0 37.0 37.0 37.0 140-144 35.894099999999995 37.0 37.0 37.0 37.0 37.0 145-149 35.86659999999999 37.0 37.0 37.0 37.0 37.0 150-151 35.701499999999996 37.0 37.0 37.0 37.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 17 1.0 18 0.0 19 2.0 20 4.0 21 0.0 22 1.0 23 0.0 24 5.0 25 5.0 26 3.0 27 6.0 28 10.0 29 19.0 30 27.0 31 22.0 32 36.0 33 63.0 34 111.0 35 266.0 36 2924.0 37 495.0 >>END_MODULE >>Per base sequence content warn #Base G A T C 1 39.175 12.65 8.05 40.125 2 21.51803607214429 14.253507014028056 33.39178356713427 30.836673346693388 3 18.825 17.525 25.924999999999997 37.724999999999994 4 22.85 24.075 21.75 31.324999999999996 5 24.4 32.25 22.575 20.775 6 20.25 34.300000000000004 24.099999999999998 21.349999999999998 7 14.825 29.625 39.0 16.55 8 15.525 26.025 34.599999999999994 23.849999999999998 9 15.875 24.925 35.375 23.825 10-14 19.195 32.269999999999996 26.545 21.990000000000002 15-19 19.405 30.14 27.08 23.375 20-24 19.505 29.49 27.169999999999998 23.835 25-29 19.555 29.775000000000002 27.255000000000003 23.415 30-34 19.79 29.630000000000003 27.310000000000002 23.27 35-39 19.285 30.415 26.51 23.79 40-44 20.57 29.79 26.634999999999998 23.005 45-49 19.86 29.675 26.755000000000003 23.71 50-54 20.51 28.875 26.66 23.955000000000002 55-59 20.064999999999998 29.34 26.889999999999997 23.705000000000002 60-64 20.405 28.53 26.889999999999997 24.175 65-69 20.21 29.275000000000002 26.295 24.22 70-74 19.905 29.494999999999997 26.945000000000004 23.655 75-79 20.05 29.57 26.445 23.935000000000002 80-84 20.915 29.315 25.995 23.775 85-89 21.22 28.98 26.345000000000002 23.455000000000002 90-94 21.275 29.035 26.825 22.865 95-99 20.32 28.845 26.99 23.845 100-104 21.425 28.449999999999996 26.375 23.75 105-109 21.12 28.365000000000002 26.33 24.185000000000002 110-114 20.885 28.675 26.38 24.060000000000002 115-119 21.89 27.88 26.71 23.52 120-124 21.51 28.46 25.72 24.310000000000002 125-129 21.715 28.52 25.759999999999998 24.005000000000003 130-134 21.975 28.015 25.455 24.555 135-139 21.955 28.025 25.435000000000002 24.585 140-144 21.695 27.51 26.405 24.39 145-149 22.405 27.83 25.4 24.365000000000002 150-151 22.400000000000002 28.0625 25.6125 23.925 >>END_MODULE >>Per sequence GC content pass #GC Content Count 0 0.0 1 0.0 2 1.0 3 1.0 4 0.0 5 0.0 6 0.0 7 0.0 8 0.5 9 0.5 10 0.5 11 0.5 12 1.0 13 1.0 14 1.0 15 1.0 16 0.0 17 0.0 18 0.0 19 0.5 20 0.5 21 0.0 22 1.5 23 2.0 24 3.0 25 4.0 26 4.5 27 9.0 28 15.5 29 29.0 30 40.5 31 49.5 32 55.0 33 62.0 34 88.5 35 98.0 36 113.0 37 136.5 38 150.5 39 154.5 40 152.5 41 170.0 42 187.0 43 202.5 44 227.5 45 221.5 46 212.0 47 199.0 48 201.0 49 197.5 50 149.5 51 129.0 52 111.0 53 98.0 54 97.0 55 85.5 56 81.5 57 65.0 58 38.5 59 30.5 60 26.5 61 25.5 62 20.0 63 10.5 64 8.5 65 9.0 66 4.5 67 3.5 68 4.5 69 2.0 70 0.0 71 0.0 72 1.0 73 2.0 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 83.375 #Duplication Level Percentage of deduplicated Percentage of total 1 84.13793103448276 70.15 2 12.983508245877061 21.65 3 2.218890554722639 5.55 4 0.5097451274362819 1.7000000000000002 5 0.0 0.0 6 0.05997001499250374 0.3 7 0.02998500749625187 0.17500000000000002 8 0.0 0.0 9 0.02998500749625187 0.22499999999999998 >10 0.02998500749625187 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 GATCGGAAGAGCACACGTCTGAACTCCAGTCACGATTGCTCATCTCGTAT 10 0.25 TruSeq Adapter, Index 21 (97% over 37bp) CCAAGAATTGCTTCATATCGTAGTTGCTCTTCCCACTGAAGCATTGTCCT 9 0.22499999999999998 No Hit CAACGATCTTTTTGCCAGAGCCCAGGTACAATTTGAACAAAGCAACCCTA 7 0.17500000000000002 No Hit GTGGCTAGTTCTTTTCTGCTCGACTTGAAGAGAAGATATCTATAGACAAA 6 0.15 No Hit TAGCAGATGAATGCATCGATGTTACAAAGCCATGCCTAAGTTGTTATAAT 6 0.15 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 0.0 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 0.025 0.0 0.0 0.0 0.0 54-55 0.05 0.0 0.0 0.0 0.0 56-57 0.05 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 0.05 0.0 0.0 0.0 0.0 64-65 0.0625 0.0 0.0 0.0 0.0 66-67 0.0875 0.0 0.0 0.0 0.0 68-69 0.1 0.0 0.0 0.0 0.0 70-71 0.16249999999999998 0.0 0.0 0.0 0.0 72-73 0.21250000000000002 0.0 0.0 0.0 0.0 74-75 0.30000000000000004 0.0 0.0 0.0 0.0 76-77 0.375 0.0 0.0 0.0 0.0 78-79 0.475 0.0 0.0 0.0 0.0 80-81 0.6499999999999999 0.0 0.0 0.0 0.0 82-83 0.875 0.0 0.0 0.0 0.0 84-85 1.075 0.0 0.0 0.0 0.0 86-87 1.2125 0.0 0.0 0.0 0.0 88-89 1.325 0.0 0.0 0.0 0.0 90-91 1.4125 0.0 0.0 0.0 0.0 92-93 1.6125 0.0 0.0 0.0 0.0 94-95 1.7875 0.0 0.0 0.0 0.0 96-97 1.9500000000000002 0.0 0.0 0.0 0.0 98-99 2.125 0.0 0.0 0.0 0.0 100-101 2.375 0.0 0.0 0.0 0.0 102-103 2.5374999999999996 0.0 0.0 0.0 0.0 104-105 2.7249999999999996 0.0 0.0 0.0 0.0 106-107 3.2375 0.0 0.0 0.0 0.0 108-109 3.65 0.0 0.0 0.0 0.0 110-111 4.2 0.0 0.0 0.0 0.0 112-113 4.7 0.0 0.0 0.0 0.0 114-115 5.1375 0.0 0.0 0.0 0.0 116-117 5.5125 0.0 0.0 0.0 0.0 118-119 6.025 0.0 0.0 0.0 0.0 120-121 6.5 0.0 0.0 0.0 0.0 122-123 7.025 0.0 0.0 0.0 0.0 124-125 7.5125 0.0 0.0 0.0 0.0 126-127 8.1625 0.0 0.0 0.0 0.0 128-129 9.037500000000001 0.0 0.0 0.0 0.0 130-131 9.6875 0.0 0.0 0.0 0.0 132-133 10.25 0.0 0.0 0.0 0.0 134-135 11.0125 0.0 0.0 0.0 0.0 136-137 11.7375 0.0 0.0 0.0 0.0 138-139 12.4625 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content pass >>END_MODULE SRR12671327 read2 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR12671327_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 36.47 37.0 37.0 37.0 37.0 37.0 2 36.188 37.0 37.0 37.0 37.0 37.0 3 36.4505 37.0 37.0 37.0 37.0 37.0 4 36.4335 37.0 37.0 37.0 37.0 37.0 5 36.495 37.0 37.0 37.0 37.0 37.0 6 36.5185 37.0 37.0 37.0 37.0 37.0 7 36.521 37.0 37.0 37.0 37.0 37.0 8 36.4505 37.0 37.0 37.0 37.0 37.0 9 36.4865 37.0 37.0 37.0 37.0 37.0 10-14 36.477199999999996 37.0 37.0 37.0 37.0 37.0 15-19 36.4571 37.0 37.0 37.0 37.0 37.0 20-24 36.375299999999996 37.0 37.0 37.0 37.0 37.0 25-29 36.356700000000004 37.0 37.0 37.0 37.0 37.0 30-34 36.346199999999996 37.0 37.0 37.0 37.0 37.0 35-39 36.2907 37.0 37.0 37.0 37.0 37.0 40-44 36.2693 37.0 37.0 37.0 37.0 37.0 45-49 36.306 37.0 37.0 37.0 37.0 37.0 50-54 36.2545 37.0 37.0 37.0 37.0 37.0 55-59 36.3137 37.0 37.0 37.0 37.0 37.0 60-64 36.2204 37.0 37.0 37.0 37.0 37.0 65-69 36.2276 37.0 37.0 37.0 37.0 37.0 70-74 36.1951 37.0 37.0 37.0 37.0 37.0 75-79 36.205799999999996 37.0 37.0 37.0 37.0 37.0 80-84 36.1819 37.0 37.0 37.0 37.0 37.0 85-89 36.245099999999994 37.0 37.0 37.0 37.0 37.0 90-94 36.2277 37.0 37.0 37.0 37.0 37.0 95-99 36.1964 37.0 37.0 37.0 37.0 37.0 100-104 36.1691 37.0 37.0 37.0 37.0 37.0 105-109 36.0457 37.0 37.0 37.0 37.0 37.0 110-114 36.0691 37.0 37.0 37.0 37.0 37.0 115-119 36.0704 37.0 37.0 37.0 37.0 37.0 120-124 35.9298 37.0 37.0 37.0 37.0 37.0 125-129 35.8899 37.0 37.0 37.0 37.0 37.0 130-134 35.78340000000001 37.0 37.0 37.0 37.0 37.0 135-139 35.6515 37.0 37.0 37.0 37.0 37.0 140-144 35.6451 37.0 37.0 37.0 37.0 37.0 145-149 35.402 37.0 37.0 37.0 34.6 37.0 150-151 35.113749999999996 37.0 37.0 37.0 31.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 13 3.0 14 3.0 15 0.0 16 2.0 17 2.0 18 0.0 19 0.0 20 2.0 21 1.0 22 5.0 23 6.0 24 4.0 25 9.0 26 6.0 27 14.0 28 5.0 29 16.0 30 17.0 31 26.0 32 46.0 33 73.0 34 124.0 35 338.0 36 2875.0 37 423.0 >>END_MODULE >>Per base sequence content warn #Base G A T C 1 38.725 22.6 10.5 28.175 2 27.650000000000002 25.4 31.6 15.35 3 22.825 26.650000000000002 31.15 19.375 4 25.674999999999997 32.800000000000004 22.825 18.7 5 28.025 35.475 20.200000000000003 16.3 6 20.375 38.05 22.7 18.875 7 21.325 22.5 36.875 19.3 8 22.8 24.625 29.275000000000002 23.3 9 23.175 23.849999999999998 28.199999999999996 24.775 10-14 25.05 28.494999999999997 25.56 20.895 15-19 23.95 27.58 27.275 21.195 20-24 24.545 27.425 26.85 21.18 25-29 24.705 27.400000000000002 26.55 21.345 30-34 24.055 27.644999999999996 27.115000000000002 21.185000000000002 35-39 24.2 27.425 26.91 21.465 40-44 23.630000000000003 27.060000000000002 27.47 21.84 45-49 24.22 27.295 26.875 21.61 50-54 24.86 27.139999999999997 27.689999999999998 20.31 55-59 24.565 26.93 28.060000000000002 20.445 60-64 23.87 27.125 27.85 21.154999999999998 65-69 24.515 26.669999999999998 27.575 21.240000000000002 70-74 23.84 27.685 27.634999999999998 20.84 75-79 23.735 27.065 27.915 21.285 80-84 24.675 26.314999999999998 28.035 20.974999999999998 85-89 24.865000000000002 27.515 26.865 20.755000000000003 90-94 24.16 26.575 27.794999999999998 21.47 95-99 24.33 27.62 27.365000000000002 20.685000000000002 100-104 24.415 26.765 27.805000000000003 21.015 105-109 23.855 27.700000000000003 28.055000000000003 20.39 110-114 25.025 27.034999999999997 27.169999999999998 20.77 115-119 25.025 28.235 26.955000000000002 19.785 120-124 25.324999999999996 26.61 27.62 20.445 125-129 25.235000000000003 27.62 26.924999999999997 20.22 130-134 25.965 26.96 26.86 20.215 135-139 27.0 26.865 26.634999999999998 19.5 140-144 26.995 26.44 27.42 19.145 145-149 27.070414082816562 27.500500100020002 26.87037407481496 18.558711742348468 150-151 27.975 26.6125 26.674999999999997 18.7375 >>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 0.0 10 0.5 11 1.0 12 1.5 13 1.5 14 0.5 15 0.0 16 0.5 17 2.0 18 3.5 19 2.0 20 1.0 21 1.0 22 1.5 23 2.5 24 3.0 25 4.0 26 4.5 27 7.0 28 6.5 29 5.5 30 11.5 31 19.5 32 24.0 33 36.5 34 50.0 35 62.5 36 74.5 37 90.5 38 119.5 39 139.5 40 163.5 41 193.0 42 215.0 43 227.5 44 219.5 45 220.0 46 241.5 47 262.5 48 252.5 49 207.5 50 177.0 51 158.5 52 138.5 53 116.0 54 104.0 55 91.0 56 68.5 57 54.5 58 40.0 59 31.5 60 24.0 61 20.5 62 24.5 63 18.5 64 8.5 65 4.0 66 2.5 67 7.5 68 5.5 69 1.0 70 1.0 71 0.0 72 0.5 73 3.5 74 3.0 75 0.5 76 0.5 77 1.0 78 1.0 79 0.0 80 0.5 81 0.5 82 0.0 83 0.0 84 0.0 85 0.5 86 1.0 87 0.5 88 0.5 89 1.0 90 1.0 91 1.0 92 2.0 93 1.5 94 0.5 95 0.5 96 0.5 97 0.5 98 0.0 99 0.0 100 0.5 >>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 0.02 150-151 0.0 >>END_MODULE >>Sequence Length Distribution pass #Length Count 151 4000.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 83.72500000000001 #Duplication Level Percentage of deduplicated Percentage of total 1 84.56255598686175 70.8 2 12.481337712750076 20.9 3 2.2693341295909226 5.7 4 0.5076142131979695 1.7000000000000002 5 0.08957897879964169 0.375 6 0.059719319199761124 0.3 7 0.0 0.0 8 0.0 0.0 9 0.029859659599880562 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 GGGCAAGCCAGTTGATTCTATTGCATCTAGGCCAAACATAGACACTGTTG 9 0.22499999999999998 No Hit AGAAACTGAAGAAACAGAGGATAGGAAGCAAGAGAACCACACATAGAAAA 6 0.15 No Hit GAGTGAACAAGTGGCGCCCAGATCTCGAGGAAGAATACGAAGATAAAGAG 6 0.15 No Hit AGAGAACACATTCATACTCCAAGTCTTTTAGTTCATCCATTTAAGCTTAA 5 0.125 No Hit AGAACACATTCATACTCCAAGTCTTTTAGTTCATCCATTTAAGCTTAATC 5 0.125 No Hit ATAGCCTGTCCCAGTGATTGTCCAGAAACATAAACACTTCCTCCTCCTTG 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 0.0 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 0.025 0.0 0.0 0.0 0.0 54-55 0.05 0.0 0.0 0.0 0.0 56-57 0.05 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 0.05 0.0 0.0 0.0 0.0 64-65 0.0625 0.0 0.0 0.0 0.0 66-67 0.0875 0.0 0.0 0.0 0.0 68-69 0.1 0.0 0.0 0.0 0.0 70-71 0.16249999999999998 0.0 0.0 0.0 0.0 72-73 0.21250000000000002 0.0 0.0 0.0 0.0 74-75 0.30000000000000004 0.0 0.0 0.0 0.0 76-77 0.375 0.0 0.0 0.0 0.0 78-79 0.5 0.0 0.0 0.0 0.0 80-81 0.675 0.0 0.0 0.0 0.0 82-83 0.9 0.0 0.0 0.0 0.0 84-85 1.1 0.0 0.0 0.0 0.0 86-87 1.2375 0.0 0.0 0.0 0.0 88-89 1.35 0.0 0.0 0.0 0.0 90-91 1.4375 0.0 0.0 0.0 0.0 92-93 1.6625 0.0 0.0 0.0 0.0 94-95 1.8375 0.0 0.0 0.0 0.0 96-97 2.0 0.0 0.0 0.0 0.0 98-99 2.175 0.0 0.0 0.0 0.0 100-101 2.45 0.0 0.0 0.0 0.0 102-103 2.6125 0.0 0.0 0.0 0.0 104-105 2.825 0.0 0.0 0.0 0.0 106-107 3.2874999999999996 0.0 0.0 0.0 0.0 108-109 3.7 0.0 0.0 0.0 0.0 110-111 4.237500000000001 0.0 0.0 0.0 0.0 112-113 4.725 0.0 0.0 0.0 0.0 114-115 5.1625 0.0 0.0 0.0 0.0 116-117 5.5375 0.0 0.0 0.0 0.0 118-119 6.0375 0.0 0.0 0.0 0.0 120-121 6.5 0.0 0.0 0.0 0.0 122-123 7.0375 0.0 0.0 0.0 0.0 124-125 7.550000000000001 0.0 0.0 0.0 0.0 126-127 8.2125 0.0 0.0 0.0 0.0 128-129 9.1375 0.0 0.0 0.0 0.0 130-131 9.8125 0.0 0.0 0.0 0.0 132-133 10.375 0.0 0.0 0.0 0.0 134-135 11.1375 0.0 0.0 0.0 0.0 136-137 11.875 0.0 0.0 0.0 0.0 138-139 12.625 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content pass >>END_MODULE Read 648022 spots for SRR12671327.sra Written 648022 spots for SRR12671327.sra Read 648022 spots for SRR12671327.sra Written 648022 spots for SRR12671327.sra Read 648022 spots for SRR12671327.sra Written 648022 spots for SRR12671327.sra Read 648022 spots for SRR12671327.sra Written 648022 spots for SRR12671327.sra Read 648022 spots for SRR12671327.sra Written 648022 spots for SRR12671327.sra Read 648022 spots for SRR12671327.sra Written 648022 spots for SRR12671327.sra Read 648022 spots for SRR12671327.sra Written 648022 spots for SRR12671327.sra Read 648022 spots for SRR12671327.sra Written 648022 spots for SRR12671327.sra Read 648022 spots for SRR12671327.sra Written 648022 spots for SRR12671327.sra Read 648022 spots for SRR12671327.sra Written 648022 spots for SRR12671327.sra Read 648022 spots for SRR12671327.sra Written 648022 spots for SRR12671327.sra Read 648022 spots for SRR12671327.sra Written 648022 spots for SRR12671327.sra Read 648022 spots for SRR12671327.sra Written 648022 spots for SRR12671327.sra Read 648022 spots for SRR12671327.sra Written 648022 spots for SRR12671327.sra Read 648022 spots for SRR12671327.sra Written 648022 spots for SRR12671327.sra Read 648022 spots for SRR12671327.sra Written 648022 spots for SRR12671327.sra Read 648022 spots for SRR12671327.sra Written 648022 spots for SRR12671327.sra Read 648039 spots for SRR12671327.sra Written 648039 spots for SRR12671327.sra Read 648022 spots for SRR12671327.sra Written 648022 spots for SRR12671327.sra Read 648022 spots for SRR12671327.sra Written 648022 spots for SRR12671327.sra SRR ids: ['SRR12671327.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_gaoxfrvc SRR12671327.sra spots: 12960457 blocks: [[1, 648022], [648023, 1296044], [1296045, 1944066], [1944067, 2592088], [2592089, 3240110], [3240111, 3888132], [3888133, 4536154], [4536155, 5184176], [5184177, 5832198], [5832199, 6480220], [6480221, 7128242], [7128243, 7776264], [7776265, 8424286], [8424287, 9072308], [9072309, 9720330], [9720331, 10368352], [10368353, 11016374], [11016375, 11664396], [11664397, 12312418], [12312419, 12960457]] SRR12671327 file size 4382829 SRR12671327 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 SRR12671327 SRR12671327_1.fastq SRR12671327_2.fastq Input file: SRR12671327_1.fastq Paired file: SRR12671327_2.fastq trimmed: SRR12671327-trimmed-pair1.fastq, SRR12671327-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 Apr 10 13:02:40 2025 >> started Thu Apr 10 13:02:54 2025 >> done (14.148s) 12960457 read pairs processed; of these: 65 ( 0.00%) short read pairs filtered out after trimming by size control 39234 ( 0.30%) empty read pairs filtered out after trimming by size control 12921158 (99.70%) read pairs available; of these: 2196895 (17.00%) trimmed read pairs available after processing 10724263 (83.00%) untrimmed read pairs available after processing Length distribution of reads after trimming: length count percentage 18 4 0.00% 19 5 0.00% 20 8 0.00% 21 1 0.00% 22 8 0.00% 23 4 0.00% 24 11 0.00% 25 7 0.00% 26 8 0.00% 27 5 0.00% 28 12 0.00% 29 13 0.00% 30 16 0.00% 31 18 0.00% 32 17 0.00% 33 20 0.00% 34 23 0.00% 35 19 0.00% 36 19 0.00% 37 31 0.00% 38 36 0.00% 39 33 0.00% 40 42 0.00% 41 33 0.00% 42 50 0.00% 43 48 0.00% 44 42 0.00% 45 64 0.00% 46 80 0.00% 47 75 0.00% 48 104 0.00% 49 127 0.00% 50 149 0.00% 51 192 0.00% 52 192 0.00% 53 238 0.00% 54 262 0.00% 55 279 0.00% 56 279 0.00% 57 395 0.00% 58 483 0.00% 59 577 0.00% 60 660 0.01% 61 846 0.01% 62 932 0.01% 63 1053 0.01% 64 1200 0.01% 65 1290 0.01% 66 1526 0.01% 67 1628 0.01% 68 1854 0.01% 69 2074 0.02% 70 2467 0.02% 71 2693 0.02% 72 3177 0.02% 73 3488 0.03% 74 3805 0.03% 75 4393 0.03% 76 4857 0.04% 77 5056 0.04% 78 5524 0.04% 79 5922 0.05% 80 6280 0.05% 81 7084 0.05% 82 7552 0.06% 83 8339 0.06% 84 9404 0.07% 85 9687 0.07% 86 10554 0.08% 87 10985 0.09% 88 11496 0.09% 89 11960 0.09% 90 12461 0.10% 91 13302 0.10% 92 13608 0.11% 93 14905 0.12% 94 15555 0.12% 95 16334 0.13% 96 16998 0.13% 97 17796 0.14% 98 18102 0.14% 99 18725 0.14% 100 19184 0.15% 101 19653 0.15% 102 20348 0.16% 103 21165 0.16% 104 22125 0.17% 105 22808 0.18% 106 23995 0.19% 107 24768 0.19% 108 24912 0.19% 109 25935 0.20% 110 25625 0.20% 111 26702 0.21% 112 27862 0.22% 113 27249 0.21% 114 28651 0.22% 115 29636 0.23% 116 30937 0.24% 117 31653 0.24% 118 32491 0.25% 119 33161 0.26% 120 33919 0.26% 121 33830 0.26% 122 34404 0.27% 123 35219 0.27% 124 35875 0.28% 125 36654 0.28% 126 38136 0.30% 127 38766 0.30% 128 39868 0.31% 129 40536 0.31% 130 40956 0.32% 131 41607 0.32% 132 42117 0.33% 133 42960 0.33% 134 42626 0.33% 135 44374 0.34% 136 45072 0.35% 137 45403 0.35% 138 47127 0.36% 139 48009 0.37% 140 48633 0.38% 141 48941 0.38% 142 49133 0.38% 143 49713 0.38% 144 49998 0.39% 145 49939 0.39% 146 51188 0.40% 147 51529 0.40% 148 53141 0.41% 149 53947 0.42% 150 54814 0.42% 151 10724263 83.00% 12921158 reads passed initial QC criterion=sequence-density sequence-density=0.56 sequence-density-rank=1 fanout-score=2.02 fanout-score-rank=34 prefix-density=0.57 prefix-fanout=2.0 sequence=ATACGGATAAAGG criterion=fanout-score sequence-density=0.05 sequence-density-rank=29 fanout-score=57.54 fanout-score-rank=1 prefix-density=0.29 prefix-fanout=10.1 sequence=TGCTGCTGCTGCATTTATTAGAGAAGGAGATGCTGGTAATCTCCATTTCACAAGTTCATTAATCTCGATCGAAAATATGGCTCATTTAAGCATATACAAAGTACATCTGGGAAAGAAAGTTAAGAACCAAGATAGGGTCACTGATATTTGGATGATGTTCATACGGAGAGGGAGGGAGAAAGGCTGTACTCAAGCCCCCAGAGCTCAAAACTGCCTTTGACAAAATCATAATAACCACCCTTCAGTCCTAGAGTTTTGTTCACCAAGCCATCTCTCACAAACGGGTAGGTTAGCAAGTGTCCAAGGGACACGTTCACTGCCTCCTTTTCACATTGTGTACAGAGGTCTGGGAAAGGTGCATTGGCATGTTCTGCTAAAACCTTAGTCTTGGCAGGGTAGCAAACTTTGACCCAGTCTTCTATGAAATCAGTTGATGTTGTTCCATCATAAGGGAAGGACATGAGGCCCTTAATTCCACCACAGGCGCTGTGTCCAATGACCACAATGTATT criterion=sequence-density sequence-density=0.53 sequence-density-rank=1 fanout-score=2.58 fanout-score-rank=19 prefix-density=0.55 prefix-fanout=2.5 sequence=AGGTTGGCTATGTTCTCAATGTTCGGATTCTTTGTCCAGGCCATTGTGACCGGAAAGGGACCACTGGAGAACCTGGCTGACCACCTTTCTGACCCAGTAAACAACAACGCCTGGGCATATGCCACAAACTTCGTTCCCGGAAAGTGAGCAACAAAAGAGTTTTTTCTGTGCTGGGACTATTGGCTTGTAATGT criterion=fanout-score sequence-density=0.01 sequence-density-rank=31 fanout-score=31.75 fanout-score-rank=1 prefix-density=0.26 prefix-fanout=1.0 sequence=GCTACACAGAGAACACATTCATACTCCAAGTCTTTTAGTTCATCCATTTAAGCTTAATCAATCAATCATCATGTCTAGCACCTGCGACACCTGCGACTGCGCTGACAAGACCCAGTGTGTCAAGAAGGGAAGCAGCTACACTGCTGGCATCGTCGAGACTGAGAAGAACTATGTCTCCTCCGTAGTCATGGAGGTGCCAGCAGCTGAGAACGATGGCAAGTGCAACTGCGGTACTGGCTGCACTTGCACTACCTGCACATGCGGTCATTAAGCAAGCACATCAACTATCATGTTTGATGTGGGATTGGGAGTGGATTAATAATGTAATTTCTGATAAATAATCTGTGTTCTTCTGTACTTGTGGGTGTGGAGTGAACAAACAAAAGTGTCCGTGAGTGTCTTTATCTTTGTGTCTTCTTCATT SRR12671327 testing PE reads STAR mapping to Ensembl genome Started job on | Apr 10 13:03:34 Started mapping on | Apr 10 13:03:34 Finished on | Apr 10 13:05:00 Mapping speed, Million of reads per hour | 540.89 Number of input reads | 12921158 Average input read length | 292 UNIQUE READS: Uniquely mapped reads number | 11754396 Uniquely mapped reads % | 90.97% Average mapped length | 291.26 Number of splices: Total | 8970294 Number of splices: Annotated (sjdb) | 8779965 Number of splices: GT/AG | 8761672 Number of splices: GC/AG | 171177 Number of splices: AT/AC | 7245 Number of splices: Non-canonical | 30200 Mismatch rate per base, % | 0.36% Deletion rate per base | 0.03% Deletion average length | 2.73 Insertion rate per base | 0.03% Insertion average length | 2.32 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 388559 % of reads mapped to multiple loci | 3.01% Number of reads mapped to too many loci | 404704 % of reads mapped to too many loci | 3.13% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 2.42% % of reads unmapped: other | 0.47% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 778203 778203 778203 N_multimapping 388559 388559 388559 N_noFeature 511902 11473057 595639 N_ambiguous 287355 1389 88982 UnstrandedReadsAssigned:10955139 PositiveStrandReadsAssigned:279950 NegativeStrandReadsAssigned:11069775 Dataset is classified negative stranded MeadianReadLen=151 20thPercentileLength=151 echo kmer=147 SRR12671327 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: SRR12671327-trimmed-pair1.fastq SRR12671327-trimmed-pair2.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 12,921,158 reads, 11,427,757 reads pseudoaligned [quant] estimated average fragment length: 220.182 [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,272 rounds 52401 SRR12671327.ke.tsv 34699 SRR12671327.se.tsv 87100 total ==> SRR12671327.ke.tsv <== target_id length eff_length est_counts tpm Potri.005G200100.1.v4.1 2018 1798.82 190 7.01034 Potri.005G024800.1.v4.1 1035 815.818 270 21.9656 Potri.004G059700.1.v4.1 961 741.858 11 0.984112 Potri.007G009000.2.v4.1 1416 1196.82 0 0 Potri.003G141000.2.v4.1 2943 2723.82 363.389 8.85455 Potri.016G087400.1.v4.1 270 91.7799 432.434 312.712 Potri.015G069301.1.v4.1 564 348.757 0 0 Potri.010G195200.1.v4.1 1773 1553.82 40 1.70857 Potri.012G127500.1.v4.1 977 757.848 163 14.2751 ==> SRR12671327.se.tsv <== Potri.001G166300.v4.1 0 Potri.001G448400.v4.1 332 Potri.001G233950.v4.1 0 Potri.001G122700.v4.1 400 Potri.001G212900.v4.1 372 Potri.001G182400.v4.1 0 Potri.001G256600.v4.1 0 Potri.001G040500.v4.1 1 Potri.001G416900.v4.1 0 Potri.001G452600.v4.1 2 SRR12671327 completed mapping pipeline successfully