Starting /dee2/code/volunteer_pipeline.sh SRR12671386 current disk space = 3052650299392 free memory = 1493885820 SRR12671386 SRAfilesize 9d177b7c4c37c902edc1012ded272ff5 SRR12671386.sra SRR12671386.sra file validated SRR12671386 is paired end SRR12671386 is conventional basespace SRR12671386 read1 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR12671386_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 36.6185 37.0 37.0 37.0 37.0 37.0 2 36.45525 37.0 37.0 37.0 37.0 37.0 3 36.581 37.0 37.0 37.0 37.0 37.0 4 36.642 37.0 37.0 37.0 37.0 37.0 5 36.6615 37.0 37.0 37.0 37.0 37.0 6 36.665 37.0 37.0 37.0 37.0 37.0 7 36.5625 37.0 37.0 37.0 37.0 37.0 8 36.6175 37.0 37.0 37.0 37.0 37.0 9 36.6665 37.0 37.0 37.0 37.0 37.0 10-14 36.6346 37.0 37.0 37.0 37.0 37.0 15-19 36.5798 37.0 37.0 37.0 37.0 37.0 20-24 36.584199999999996 37.0 37.0 37.0 37.0 37.0 25-29 36.5792 37.0 37.0 37.0 37.0 37.0 30-34 36.5638 37.0 37.0 37.0 37.0 37.0 35-39 36.5516 37.0 37.0 37.0 37.0 37.0 40-44 36.5419 37.0 37.0 37.0 37.0 37.0 45-49 36.4482 37.0 37.0 37.0 37.0 37.0 50-54 36.4624 37.0 37.0 37.0 37.0 37.0 55-59 36.460499999999996 37.0 37.0 37.0 37.0 37.0 60-64 36.4332 37.0 37.0 37.0 37.0 37.0 65-69 36.39 37.0 37.0 37.0 37.0 37.0 70-74 36.3504 37.0 37.0 37.0 37.0 37.0 75-79 36.3677 37.0 37.0 37.0 37.0 37.0 80-84 36.3202 37.0 37.0 37.0 37.0 37.0 85-89 36.2752 37.0 37.0 37.0 37.0 37.0 90-94 36.2826 37.0 37.0 37.0 37.0 37.0 95-99 36.240300000000005 37.0 37.0 37.0 37.0 37.0 100-104 36.2512 37.0 37.0 37.0 37.0 37.0 105-109 36.238600000000005 37.0 37.0 37.0 37.0 37.0 110-114 36.1137 37.0 37.0 37.0 37.0 37.0 115-119 36.1456 37.0 37.0 37.0 37.0 37.0 120-124 36.1023 37.0 37.0 37.0 37.0 37.0 125-129 36.117399999999996 37.0 37.0 37.0 37.0 37.0 130-134 36.0439 37.0 37.0 37.0 37.0 37.0 135-139 35.9897 37.0 37.0 37.0 37.0 37.0 140-144 35.8647 37.0 37.0 37.0 37.0 37.0 145-149 35.7906 37.0 37.0 37.0 37.0 37.0 150-151 35.78425 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 0.0 20 0.0 21 1.0 22 1.0 23 0.0 24 0.0 25 1.0 26 5.0 27 8.0 28 7.0 29 17.0 30 16.0 31 32.0 32 39.0 33 68.0 34 121.0 35 273.0 36 2963.0 37 447.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 50.74999999999999 10.65 4.775 33.825 2 18.548185231539424 12.540675844806007 38.598247809762206 30.312891113892366 3 16.925 18.825 30.375000000000004 33.875 4 23.425 26.85 23.974999999999998 25.75 5 23.95 32.775 24.125 19.15 6 18.775 35.55 25.3 20.375 7 15.15 25.15 43.925 15.775 8 16.2 24.6 33.225 25.974999999999998 9 16.075 22.8 36.175000000000004 24.95 10-14 19.235 30.3 27.755000000000003 22.71 15-19 19.84 27.589999999999996 28.505000000000003 24.065 20-24 18.965 28.74 28.305000000000003 23.990000000000002 25-29 19.314999999999998 29.515 27.725 23.445 30-34 20.5 27.525 28.095 23.880000000000003 35-39 19.89 28.244999999999997 27.96 23.905 40-44 20.580000000000002 28.785 27.47 23.165 45-49 20.3 28.725 27.415 23.56 50-54 19.935 28.43 27.875 23.76 55-59 20.03 28.249999999999996 27.77 23.95 60-64 20.04 27.925 28.044999999999998 23.990000000000002 65-69 19.17 28.58 28.38 23.87 70-74 19.28 27.860000000000003 28.365000000000002 24.495 75-79 20.405 28.175 28.050000000000004 23.369999999999997 80-84 20.04 28.144999999999996 28.000000000000004 23.815 85-89 20.21 29.080000000000002 27.425 23.285 90-94 21.095 27.76 27.74 23.405 95-99 20.669999999999998 28.815 27.83 22.685 100-104 20.615 28.365000000000002 27.01 24.01 105-109 20.200000000000003 28.189999999999998 27.76 23.849999999999998 110-114 20.330000000000002 28.244999999999997 27.565 23.86 115-119 21.13 28.144999999999996 27.18 23.544999999999998 120-124 20.77 28.24 26.939999999999998 24.05 125-129 20.080000000000002 28.685 27.075 24.16 130-134 20.68 27.810000000000002 27.544999999999998 23.965 135-139 21.345 27.794999999999998 27.185 23.674999999999997 140-144 20.455000000000002 28.15 27.73 23.665 145-149 20.965 27.755000000000003 27.275 24.005000000000003 150-151 19.9375 28.249999999999996 27.712500000000002 24.099999999999998 >>END_MODULE >>Per sequence GC content pass #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 0.0 11 0.0 12 0.0 13 0.0 14 0.0 15 1.0 16 1.5 17 0.5 18 2.0 19 2.5 20 1.5 21 3.5 22 4.5 23 2.0 24 5.0 25 7.0 26 3.5 27 4.5 28 12.0 29 17.0 30 18.5 31 32.5 32 42.0 33 42.0 34 60.5 35 74.0 36 80.0 37 112.0 38 134.0 39 147.0 40 197.5 41 233.5 42 229.5 43 235.0 44 259.5 45 276.0 46 246.5 47 218.0 48 215.0 49 208.0 50 199.0 51 159.5 52 116.5 53 90.5 54 75.0 55 57.0 56 45.5 57 41.5 58 27.5 59 21.0 60 13.5 61 6.5 62 4.0 63 2.5 64 1.5 65 1.0 66 0.5 67 2.5 68 2.0 69 0.5 70 0.5 71 1.0 72 1.0 73 0.5 74 0.5 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 0.125 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 83.72500000000001 #Duplication Level Percentage of deduplicated Percentage of total 1 84.8014332636608 71.0 2 11.76470588235294 19.7 3 2.8366676619886535 7.124999999999999 4 0.41803523439832785 1.4000000000000001 5 0.1492982979994028 0.625 6 0.029859659599880562 0.15 7 0.0 0.0 8 0.0 0.0 9 0.0 0.0 >10 0.0 0.0 >50 0.0 0.0 >100 0.0 0.0 >500 0.0 0.0 >1k 0.0 0.0 >5k 0.0 0.0 >10k+ 0.0 0.0 >>END_MODULE >>Overrepresented sequences warn #Sequence Count Percentage Possible Source ATGAGATTGACATCACTTGGATAGTATCCAAACCTTTTGAGGTATTGTTT 6 0.15 No Hit GTCGGATCCTGAACCGCGTCCTTCTCATTCGGATTCTCCTCCTCTTCTCC 5 0.125 No Hit CTTGTCTATTCCAGTTGCCTTCCAGTAGCCAGAGCCTGTGGCTCTGTTGG 5 0.125 No Hit GCCTGCCCAAATCTTGGAGTATTTGTTTCTTCCTAACTGGTCTGCGAGGG 5 0.125 No Hit ATCAAATGAAAGCACAACTCCAGCAACCTCAGTAATCCTCTCCAAAATAT 5 0.125 No Hit GCTACTTTCAGCTACATGCTTCACCGCTCTGCTTGATATAGTATCGAAAT 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 0.025 0.0 0.0 0.0 0.0 30-31 0.025 0.0 0.0 0.0 0.0 32-33 0.025 0.0 0.0 0.0 0.0 34-35 0.025 0.0 0.0 0.0 0.0 36-37 0.025 0.0 0.0 0.0 0.0 38-39 0.025 0.0 0.0 0.0 0.0 40-41 0.025 0.0 0.0 0.0 0.0 42-43 0.025 0.0 0.0 0.0 0.0 44-45 0.025 0.0 0.0 0.0 0.0 46-47 0.025 0.0 0.0 0.0 0.0 48-49 0.025 0.0 0.0 0.0 0.0 50-51 0.025 0.0 0.0 0.0 0.0 52-53 0.025 0.0 0.0 0.0 0.0 54-55 0.025 0.0 0.0 0.0 0.0 56-57 0.025 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 0.075 0.0 0.0 0.0 0.0 66-67 0.075 0.0 0.0 0.0 0.0 68-69 0.075 0.0 0.0 0.0 0.0 70-71 0.075 0.0 0.0 0.0 0.0 72-73 0.0875 0.0 0.0 0.0 0.0 74-75 0.1 0.0 0.0 0.0 0.0 76-77 0.125 0.0 0.0 0.0 0.0 78-79 0.125 0.0 0.0 0.0 0.0 80-81 0.16249999999999998 0.0 0.0 0.0 0.0 82-83 0.2 0.0 0.0 0.0 0.0 84-85 0.25 0.0 0.0 0.0 0.0 86-87 0.3875 0.0 0.0 0.0 0.0 88-89 0.4375 0.0 0.0 0.0 0.0 90-91 0.5874999999999999 0.0 0.0 0.0 0.0 92-93 0.6375 0.0 0.0 0.0 0.0 94-95 0.7625 0.0 0.0 0.0 0.0 96-97 0.8625 0.0 0.0 0.0 0.0 98-99 1.0375 0.0 0.0 0.0 0.0 100-101 1.2375 0.0 0.0 0.0 0.0 102-103 1.4875 0.0 0.0 0.0 0.0 104-105 1.7125 0.0 0.0 0.0 0.0 106-107 2.125 0.0 0.0 0.0 0.0 108-109 2.4124999999999996 0.0 0.0 0.0 0.0 110-111 2.5250000000000004 0.0 0.0 0.0 0.0 112-113 2.7 0.0 0.0 0.0 0.0 114-115 2.8375 0.0 0.0 0.0 0.0 116-117 3.1125 0.0 0.0 0.0 0.0 118-119 3.4625 0.0 0.0 0.0 0.0 120-121 3.6875 0.0 0.0 0.0 0.0 122-123 3.9000000000000004 0.0 0.0 0.0 0.0 124-125 4.1625 0.0 0.0 0.0 0.0 126-127 4.5 0.0 0.0 0.0 0.0 128-129 4.9875 0.0 0.0 0.0 0.0 130-131 5.387499999999999 0.0 0.0 0.0 0.0 132-133 6.025 0.0 0.0 0.0 0.0 134-135 6.625 0.0 0.0 0.0 0.0 136-137 7.175000000000001 0.0 0.0 0.0 0.0 138-139 7.6125 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content pass >>END_MODULE SRR12671386 read2 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR12671386_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 36.2875 37.0 37.0 37.0 37.0 37.0 2 36.16 37.0 37.0 37.0 37.0 37.0 3 36.15 37.0 37.0 37.0 37.0 37.0 4 36.339 37.0 37.0 37.0 37.0 37.0 5 36.348 37.0 37.0 37.0 37.0 37.0 6 36.2705 37.0 37.0 37.0 37.0 37.0 7 36.3755 37.0 37.0 37.0 37.0 37.0 8 36.395 37.0 37.0 37.0 37.0 37.0 9 36.4015 37.0 37.0 37.0 37.0 37.0 10-14 36.310500000000005 37.0 37.0 37.0 37.0 37.0 15-19 36.28249999999999 37.0 37.0 37.0 37.0 37.0 20-24 36.2444 37.0 37.0 37.0 37.0 37.0 25-29 36.2449 37.0 37.0 37.0 37.0 37.0 30-34 36.16930000000001 37.0 37.0 37.0 37.0 37.0 35-39 36.1445 37.0 37.0 37.0 37.0 37.0 40-44 36.0915 37.0 37.0 37.0 37.0 37.0 45-49 36.1452 37.0 37.0 37.0 37.0 37.0 50-54 36.1065 37.0 37.0 37.0 37.0 37.0 55-59 36.0092 37.0 37.0 37.0 37.0 37.0 60-64 36.0539 37.0 37.0 37.0 37.0 37.0 65-69 36.037800000000004 37.0 37.0 37.0 37.0 37.0 70-74 36.0012 37.0 37.0 37.0 37.0 37.0 75-79 36.0056 37.0 37.0 37.0 37.0 37.0 80-84 35.943200000000004 37.0 37.0 37.0 37.0 37.0 85-89 35.98610000000001 37.0 37.0 37.0 37.0 37.0 90-94 35.912400000000005 37.0 37.0 37.0 37.0 37.0 95-99 35.9086 37.0 37.0 37.0 37.0 37.0 100-104 35.92229999999999 37.0 37.0 37.0 37.0 37.0 105-109 35.88779999999999 37.0 37.0 37.0 37.0 37.0 110-114 35.8219 37.0 37.0 37.0 37.0 37.0 115-119 35.8292 37.0 37.0 37.0 37.0 37.0 120-124 35.829899999999995 37.0 37.0 37.0 37.0 37.0 125-129 35.784200000000006 37.0 37.0 37.0 37.0 37.0 130-134 35.685 37.0 37.0 37.0 37.0 37.0 135-139 35.604200000000006 37.0 37.0 37.0 37.0 37.0 140-144 35.64569999999999 37.0 37.0 37.0 37.0 37.0 145-149 35.5751 37.0 37.0 37.0 37.0 37.0 150-151 35.304249999999996 37.0 37.0 37.0 31.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 12 3.0 13 4.0 14 4.0 15 4.0 16 1.0 17 0.0 18 2.0 19 0.0 20 1.0 21 0.0 22 5.0 23 2.0 24 7.0 25 3.0 26 6.0 27 10.0 28 15.0 29 16.0 30 15.0 31 22.0 32 47.0 33 104.0 34 175.0 35 506.0 36 2764.0 37 284.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 46.075 25.224999999999998 8.175 20.525 2 26.424999999999997 24.15 33.35 16.075 3 21.4 26.025 33.675 18.9 4 22.900000000000002 36.05 23.375 17.675 5 26.450000000000003 36.6 19.675 17.275 6 19.7 39.75 21.7 18.85 7 19.900000000000002 22.05 38.525 19.525000000000002 8 19.7 25.825 29.7 24.775 9 21.975 23.799999999999997 30.099999999999998 24.125 10-14 23.919999999999998 29.34 26.47 20.27 15-19 24.04 27.060000000000002 28.17 20.73 20-24 23.380000000000003 27.939999999999998 27.915 20.765 25-29 23.24 28.185 27.800000000000004 20.775 30-34 23.044999999999998 28.494999999999997 27.860000000000003 20.599999999999998 35-39 23.555 27.92 27.67 20.855 40-44 23.630000000000003 27.82 27.224999999999998 21.325 45-49 23.26 27.92 28.16 20.66 50-54 23.055 28.575 27.765 20.605 55-59 23.175 27.644999999999996 28.415000000000003 20.765 60-64 23.294999999999998 27.92 28.439999999999998 20.345 65-69 23.415 27.985 28.060000000000002 20.54 70-74 23.355 28.04 27.900000000000002 20.705000000000002 75-79 23.23 28.499999999999996 27.389999999999997 20.880000000000003 80-84 23.419999999999998 27.82 27.794999999999998 20.965 85-89 23.505000000000003 28.185 27.37 20.94 90-94 23.665 28.384999999999998 27.83 20.119999999999997 95-99 23.724999999999998 27.96 27.894999999999996 20.419999999999998 100-104 23.674999999999997 28.54 27.52 20.265 105-109 24.404999999999998 27.925 27.834999999999997 19.835 110-114 24.38 28.349999999999998 27.12 20.150000000000002 115-119 24.560000000000002 27.705000000000002 27.365000000000002 20.369999999999997 120-124 24.595 27.189999999999998 28.105000000000004 20.11 125-129 24.785 27.57 26.939999999999998 20.705000000000002 130-134 24.645 28.155 26.75 20.45 135-139 25.435000000000002 27.51 27.515 19.54 140-144 24.665 27.500000000000004 27.37 20.465 145-149 25.54010802160432 27.345469093818764 27.145429085817163 19.96899379875975 150-151 24.6125 27.5875 27.787499999999998 20.0125 >>END_MODULE >>Per sequence GC content warn #GC Content Count 0 0.0 1 0.0 2 0.0 3 0.5 4 0.5 5 0.5 6 1.0 7 0.5 8 0.0 9 0.0 10 0.0 11 0.0 12 0.0 13 0.0 14 0.0 15 0.0 16 0.0 17 1.0 18 1.5 19 1.5 20 1.5 21 1.5 22 2.0 23 3.5 24 4.0 25 5.0 26 8.0 27 6.0 28 8.0 29 8.0 30 12.0 31 29.5 32 36.0 33 41.5 34 50.0 35 55.0 36 78.0 37 110.0 38 134.0 39 157.5 40 189.0 41 229.5 42 258.0 43 267.5 44 274.0 45 282.0 46 275.0 47 251.5 48 238.5 49 196.0 50 155.5 51 132.5 52 100.0 53 82.5 54 65.5 55 53.0 56 43.0 57 32.0 58 24.0 59 19.0 60 16.5 61 11.0 62 5.5 63 7.0 64 7.0 65 3.0 66 1.5 67 3.0 68 2.0 69 0.5 70 0.5 71 0.5 72 0.5 73 1.5 74 1.5 75 0.5 76 0.0 77 1.5 78 1.5 79 0.0 80 0.0 81 0.5 82 0.5 83 0.0 84 0.5 85 1.0 86 1.0 87 0.5 88 0.0 89 0.0 90 0.0 91 0.5 92 0.5 93 0.0 94 0.5 95 0.5 96 0.0 97 0.0 98 0.0 99 0.0 100 1.5 >>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 83.55 #Duplication Level Percentage of deduplicated Percentage of total 1 84.53022142429683 70.625 2 12.17833632555356 20.349999999999998 3 2.633153800119689 6.6000000000000005 4 0.41891083183722316 1.4000000000000001 5 0.20945541591861158 0.8750000000000001 6 0.029922202274087373 0.15 7 0.0 0.0 8 0.0 0.0 9 0.0 0.0 >10 0.0 0.0 >50 0.0 0.0 >100 0.0 0.0 >500 0.0 0.0 >1k 0.0 0.0 >5k 0.0 0.0 >10k+ 0.0 0.0 >>END_MODULE >>Overrepresented sequences warn #Sequence Count Percentage Possible Source GCGAGGATTTTGAAATCCGAGCATCAGCAATATTCTTTTAGCTCCCTTCA 6 0.15 No Hit CCTGATGTTGTTGCTGAGAAGCCCTGGTATGGCCTTGAGCAAGAATACAC 5 0.125 No Hit ACCAACTGATATTATCAAGCAGATGACGAAGAGTTTTGCTCAAGTTGTCT 5 0.125 No Hit TTGTTGTCCAGTACTTGAAGAGAAAGGTGTTTGCTTGCCCCTTGCCTGCT 5 0.125 No Hit ATTCACTCAAAATTAGGGTTTTTGTTTGGTCAAAATTGAACCAAGTTACT 5 0.125 No Hit ACTCTATACTCCAAGCTGTTTTAACAAAAGAAAAAAGAAGGCAGTCAAAT 5 0.125 No Hit CTTCAAATTCTTGCTCTTTGACTCTTGCAGACAAATGGGGTGCTACCCAA 5 0.125 No Hit AGAACACATTCATACTCCAAGTCTTTTAGTTCATCCATTTAAGCTTAATC 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 0.025 0.0 0.0 0.0 0.0 30-31 0.025 0.0 0.0 0.0 0.0 32-33 0.025 0.0 0.0 0.0 0.0 34-35 0.025 0.0 0.0 0.0 0.0 36-37 0.025 0.0 0.0 0.0 0.0 38-39 0.025 0.0 0.0 0.0 0.0 40-41 0.025 0.0 0.0 0.0 0.0 42-43 0.025 0.0 0.0 0.0 0.0 44-45 0.025 0.0 0.0 0.0 0.0 46-47 0.025 0.0 0.0 0.0 0.0 48-49 0.025 0.0 0.0 0.0 0.0 50-51 0.025 0.0 0.0 0.0 0.0 52-53 0.025 0.0 0.0 0.0 0.0 54-55 0.025 0.0 0.0 0.0 0.0 56-57 0.025 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 0.075 0.0 0.0 0.0 0.0 66-67 0.075 0.0 0.0 0.0 0.0 68-69 0.075 0.0 0.0 0.0 0.0 70-71 0.075 0.0 0.0 0.0 0.0 72-73 0.0875 0.0 0.0 0.0 0.0 74-75 0.1 0.0 0.0 0.0 0.0 76-77 0.125 0.0 0.0 0.0 0.0 78-79 0.125 0.0 0.0 0.0 0.0 80-81 0.16249999999999998 0.0 0.0 0.0 0.0 82-83 0.2 0.0 0.0 0.0 0.0 84-85 0.25 0.0 0.0 0.0 0.0 86-87 0.3875 0.0 0.0 0.0 0.0 88-89 0.4375 0.0 0.0 0.0 0.0 90-91 0.5874999999999999 0.0 0.0 0.0 0.0 92-93 0.6375 0.0 0.0 0.0 0.0 94-95 0.7625 0.0 0.0 0.0 0.0 96-97 0.8625 0.0 0.0 0.0 0.0 98-99 1.05 0.0 0.0 0.0 0.0 100-101 1.2625 0.0 0.0 0.0 0.0 102-103 1.5125 0.0 0.0 0.0 0.0 104-105 1.7375 0.0 0.0 0.0 0.0 106-107 2.15 0.0 0.0 0.0 0.0 108-109 2.4375 0.0 0.0 0.0 0.0 110-111 2.55 0.0 0.0 0.0 0.0 112-113 2.725 0.0 0.0 0.0 0.0 114-115 2.8375 0.0 0.0 0.0 0.0 116-117 3.0875 0.0 0.0 0.0 0.0 118-119 3.4375 0.0 0.0 0.0 0.0 120-121 3.6625 0.0 0.0 0.0 0.0 122-123 3.875 0.0 0.0 0.0 0.0 124-125 4.137499999999999 0.0 0.0 0.0 0.0 126-127 4.475 0.0 0.0 0.0 0.0 128-129 4.975 0.0 0.0 0.0 0.0 130-131 5.387499999999999 0.0 0.0 0.0 0.0 132-133 6.0125 0.0 0.0 0.0 0.0 134-135 6.612500000000001 0.0 0.0 0.0 0.0 136-137 7.175000000000001 0.0 0.0 0.0 0.0 138-139 7.65 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content pass >>END_MODULE Read 742918 spots for SRR12671386.sra Written 742918 spots for SRR12671386.sra Read 742918 spots for SRR12671386.sra Written 742918 spots for SRR12671386.sra Read 742918 spots for SRR12671386.sra Written 742918 spots for SRR12671386.sra Read 742918 spots for SRR12671386.sra Written 742918 spots for SRR12671386.sra Read 742918 spots for SRR12671386.sra Written 742918 spots for SRR12671386.sra Read 742918 spots for SRR12671386.sra Written 742918 spots for SRR12671386.sra Read 742918 spots for SRR12671386.sra Written 742918 spots for SRR12671386.sra Read 742932 spots for SRR12671386.sra Written 742932 spots for SRR12671386.sra Read 742918 spots for SRR12671386.sra Written 742918 spots for SRR12671386.sra Read 742918 spots for SRR12671386.sra Written 742918 spots for SRR12671386.sra Read 742918 spots for SRR12671386.sra Written 742918 spots for SRR12671386.sra Read 742918 spots for SRR12671386.sra Written 742918 spots for SRR12671386.sra Read 742918 spots for SRR12671386.sra Written 742918 spots for SRR12671386.sra Read 742918 spots for SRR12671386.sra Written 742918 spots for SRR12671386.sra Read 742918 spots for SRR12671386.sra Written 742918 spots for SRR12671386.sra Read 742918 spots for SRR12671386.sra Written 742918 spots for SRR12671386.sra Read 742918 spots for SRR12671386.sra Written 742918 spots for SRR12671386.sra Read 742918 spots for SRR12671386.sra Written 742918 spots for SRR12671386.sra Read 742918 spots for SRR12671386.sra Written 742918 spots for SRR12671386.sra Read 742918 spots for SRR12671386.sra Written 742918 spots for SRR12671386.sra SRR ids: ['SRR12671386.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_0jq7_pw1 SRR12671386.sra spots: 14858374 blocks: [[1, 742918], [742919, 1485836], [1485837, 2228754], [2228755, 2971672], [2971673, 3714590], [3714591, 4457508], [4457509, 5200426], [5200427, 5943344], [5943345, 6686262], [6686263, 7429180], [7429181, 8172098], [8172099, 8915016], [8915017, 9657934], [9657935, 10400852], [10400853, 11143770], [11143771, 11886688], [11886689, 12629606], [12629607, 13372524], [13372525, 14115442], [14115443, 14858374]] SRR12671386 file size 5027825 SRR12671386 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 SRR12671386 SRR12671386_1.fastq SRR12671386_2.fastq Input file: SRR12671386_1.fastq Paired file: SRR12671386_2.fastq trimmed: SRR12671386-trimmed-pair1.fastq, SRR12671386-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 21:31:05 2025 >> started Tue Feb 11 21:31:22 2025 >> done (16.633s) 14858374 read pairs processed; of these: 62 ( 0.00%) short read pairs filtered out after trimming by size control 6225 ( 0.04%) empty read pairs filtered out after trimming by size control 14852087 (99.96%) read pairs available; of these: 1460253 ( 9.83%) trimmed read pairs available after processing 13391834 (90.17%) untrimmed read pairs available after processing Length distribution of reads after trimming: length count percentage 18 5 0.00% 19 12 0.00% 20 8 0.00% 21 9 0.00% 22 3 0.00% 23 11 0.00% 24 10 0.00% 25 16 0.00% 26 13 0.00% 27 18 0.00% 28 17 0.00% 29 14 0.00% 30 17 0.00% 31 20 0.00% 32 20 0.00% 33 18 0.00% 34 23 0.00% 35 6 0.00% 36 31 0.00% 37 28 0.00% 38 27 0.00% 39 39 0.00% 40 29 0.00% 41 37 0.00% 42 38 0.00% 43 26 0.00% 44 42 0.00% 45 39 0.00% 46 45 0.00% 47 55 0.00% 48 77 0.00% 49 84 0.00% 50 98 0.00% 51 101 0.00% 52 93 0.00% 53 145 0.00% 54 117 0.00% 55 145 0.00% 56 188 0.00% 57 225 0.00% 58 210 0.00% 59 283 0.00% 60 290 0.00% 61 408 0.00% 62 379 0.00% 63 474 0.00% 64 575 0.00% 65 567 0.00% 66 602 0.00% 67 803 0.01% 68 907 0.01% 69 905 0.01% 70 1156 0.01% 71 1372 0.01% 72 1447 0.01% 73 1685 0.01% 74 1779 0.01% 75 2068 0.01% 76 2188 0.01% 77 2397 0.02% 78 2712 0.02% 79 2963 0.02% 80 3202 0.02% 81 3549 0.02% 82 4018 0.03% 83 4252 0.03% 84 4671 0.03% 85 4967 0.03% 86 5124 0.03% 87 5750 0.04% 88 6014 0.04% 89 6169 0.04% 90 6725 0.05% 91 7076 0.05% 92 7560 0.05% 93 7994 0.05% 94 8334 0.06% 95 9180 0.06% 96 9559 0.06% 97 9867 0.07% 98 9976 0.07% 99 10869 0.07% 100 11189 0.08% 101 11539 0.08% 102 12155 0.08% 103 12599 0.08% 104 13044 0.09% 105 13681 0.09% 106 14211 0.10% 107 14569 0.10% 108 15114 0.10% 109 15692 0.11% 110 16001 0.11% 111 16922 0.11% 112 17240 0.12% 113 17486 0.12% 114 18375 0.12% 115 19208 0.13% 116 19589 0.13% 117 20543 0.14% 118 21027 0.14% 119 21492 0.14% 120 21939 0.15% 121 22762 0.15% 122 23186 0.16% 123 23419 0.16% 124 24697 0.17% 125 24921 0.17% 126 26157 0.18% 127 26645 0.18% 128 27122 0.18% 129 28379 0.19% 130 28293 0.19% 131 28787 0.19% 132 29669 0.20% 133 30216 0.20% 134 30427 0.20% 135 31614 0.21% 136 32435 0.22% 137 32708 0.22% 138 33234 0.22% 139 34361 0.23% 140 34449 0.23% 141 35083 0.24% 142 35731 0.24% 143 36260 0.24% 144 36780 0.25% 145 37764 0.25% 146 38233 0.26% 147 39200 0.26% 148 40071 0.27% 149 39971 0.27% 150 41089 0.28% 151 13391834 90.17% 14852087 reads passed initial QC criterion=sequence-density sequence-density=0.36 sequence-density-rank=1 fanout-score=2.29 fanout-score-rank=37 prefix-density=0.38 prefix-fanout=2.2 sequence=TGAGATGCCTCAGTGCATCCAAACATGGGTAG criterion=fanout-score sequence-density=0.01 sequence-density-rank=40 fanout-score=488.84 fanout-score-rank=1 prefix-density=0.26 prefix-fanout=18.1 sequence=TGAAGAAGACACAAAGATAAAGACACTCACGGACACTTTTGTTTGTTCACTCCACACCCACAAGTACAGAAGAACACAGATTATTTATCAGAAATTACATTATTAATCCACTCCCAATCCCACATCAAACATGATAGTTGATGTGCTTGCTTAATGACCGCATGTGCAGGTAGTGCAAGTGCAGCCAGTACCGCAGTTGCACTTGCCATCGTTCTCAGCTGCTGGCACCTCCATGACTACGGAGGAGACATAGTTCTTCTCAGTCTCGACGATGCCAGCAGTGTAGCTGCTTCCCTTCTTGACACACTGGGTCTTGTCAGCGCAGTCGCAGGTGTCGCAGGTGCTAGACATGATGATTGATTGATTAAGCTTAAATGGATGAACTAAAAGACTTGG criterion=sequence-density sequence-density=0.58 sequence-density-rank=1 fanout-score=2.15 fanout-score-rank=34 prefix-density=0.60 prefix-fanout=2.1 sequence=CCAAGTCTTTTAGTTCATCCATTTAAGCTTAATCAATCAATCATCATGTCTAGCACCTGCGACACCTGCGACTGCGCTGACAAGACCCAGTGTGTCAAGAAGGGAAGCAGCTACACTGCTGGCATCGTCGAGACTGAGAAGAACTATGTCTCCTCCGTAGTCATGGAGGTGCCAGCAGCTGAGAACGATGGCAAGTGCAACTGCGGTACTGGCTGCACTTGCACTACCTGCACATGCGGTCATTAAGCAAGCACATCAACTATCATGTTTGATGTGGGATTGGGAGTGGATTAATAATGTAATTTCTGATAAATAATCTGTGTTCTTCTGTACTTGTGGGTGTGGAGTGAACAAACAAAAGTGTCCGTGAGTGTCTTTATCTTTGTGTCTTCTTCA criterion=fanout-score sequence-density=0.11 sequence-density-rank=22 fanout-score=39.55 fanout-score-rank=1 prefix-density=0.33 prefix-fanout=13.3 sequence=AAAGAAAAGAAAA SRR12671386 testing PE reads STAR mapping to Ensembl genome Started job on | Feb 11 21:32:07 Started mapping on | Feb 11 21:32:07 Finished on | Feb 11 21:33:55 Mapping speed, Million of reads per hour | 495.07 Number of input reads | 14852087 Average input read length | 296 UNIQUE READS: Uniquely mapped reads number | 13607292 Uniquely mapped reads % | 91.62% Average mapped length | 295.23 Number of splices: Total | 13494776 Number of splices: Annotated (sjdb) | 13196160 Number of splices: GT/AG | 13229496 Number of splices: GC/AG | 215780 Number of splices: AT/AC | 7769 Number of splices: Non-canonical | 41731 Mismatch rate per base, % | 0.37% Deletion rate per base | 0.03% Deletion average length | 2.89 Insertion rate per base | 0.03% Insertion average length | 2.26 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 379940 % of reads mapped to multiple loci | 2.56% Number of reads mapped to too many loci | 136852 % of reads mapped to too many loci | 0.92% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 4.66% % of reads unmapped: other | 0.25% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 864855 864855 864855 N_multimapping 379940 379940 379940 N_noFeature 563914 13393634 649661 N_ambiguous 220045 1057 91593 UnstrandedReadsAssigned:12823333 PositiveStrandReadsAssigned:212601 NegativeStrandReadsAssigned:12866038 Dataset is classified negative stranded MeadianReadLen=151 20thPercentileLength=151 echo kmer=147 SRR12671386 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: SRR12671386-trimmed-pair1.fastq SRR12671386-trimmed-pair2.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 14,852,087 reads, 12,928,895 reads pseudoaligned [quant] estimated average fragment length: 264.737 [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 958 rounds 52401 SRR12671386.ke.tsv 34699 SRR12671386.se.tsv 87100 total ==> SRR12671386.ke.tsv <== target_id length eff_length est_counts tpm Potri.005G200100.1.v4.1 2018 1754.26 534 22.2307 Potri.005G024800.1.v4.1 1035 771.263 369 34.9406 Potri.004G059700.1.v4.1 961 697.466 0 0 Potri.007G009000.2.v4.1 1416 1152.26 0 0 Potri.003G141000.2.v4.1 2943 2679.26 708 19.2985 Potri.016G087400.1.v4.1 270 84.4449 561 485.172 Potri.015G069301.1.v4.1 564 316.145 0 0 Potri.010G195200.1.v4.1 1773 1509.26 172.871 8.36495 Potri.012G127500.1.v4.1 977 713.332 65 6.65469 ==> SRR12671386.se.tsv <== Potri.001G166300.v4.1 0 Potri.001G448400.v4.1 219 Potri.001G233950.v4.1 1 Potri.001G122700.v4.1 177 Potri.001G212900.v4.1 1 Potri.001G182400.v4.1 0 Potri.001G256600.v4.1 0 Potri.001G040500.v4.1 19 Potri.001G416900.v4.1 0 Potri.001G452600.v4.1 3 SRR12671386 completed mapping pipeline successfully