Starting /dee2/code/volunteer_pipeline.sh SRR12670129 current disk space = 3057202958336 free memory = 1460939296 SRR12670129 SRAfilesize 7c9696d7611bd2170f5d044013f00111 SRR12670129.sra SRR12670129.sra file validated SRR12670129 is paired end SRR12670129 is conventional basespace SRR12670129 read1 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR12670129_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 36.652 37.0 37.0 37.0 37.0 37.0 2 36.5565 37.0 37.0 37.0 37.0 37.0 3 36.5885 37.0 37.0 37.0 37.0 37.0 4 36.713 37.0 37.0 37.0 37.0 37.0 5 36.591 37.0 37.0 37.0 37.0 37.0 6 36.6175 37.0 37.0 37.0 37.0 37.0 7 36.5545 37.0 37.0 37.0 37.0 37.0 8 36.6015 37.0 37.0 37.0 37.0 37.0 9 36.6085 37.0 37.0 37.0 37.0 37.0 10-14 36.6288 37.0 37.0 37.0 37.0 37.0 15-19 36.601699999999994 37.0 37.0 37.0 37.0 37.0 20-24 36.569 37.0 37.0 37.0 37.0 37.0 25-29 36.509 37.0 37.0 37.0 37.0 37.0 30-34 36.521699999999996 37.0 37.0 37.0 37.0 37.0 35-39 36.519099999999995 37.0 37.0 37.0 37.0 37.0 40-44 36.473699999999994 37.0 37.0 37.0 37.0 37.0 45-49 36.4437 37.0 37.0 37.0 37.0 37.0 50-54 36.4653 37.0 37.0 37.0 37.0 37.0 55-59 36.385 37.0 37.0 37.0 37.0 37.0 60-64 36.4261 37.0 37.0 37.0 37.0 37.0 65-69 36.3815 37.0 37.0 37.0 37.0 37.0 70-74 36.3674 37.0 37.0 37.0 37.0 37.0 75-79 36.317899999999995 37.0 37.0 37.0 37.0 37.0 80-84 36.4091 37.0 37.0 37.0 37.0 37.0 85-89 36.3038 37.0 37.0 37.0 37.0 37.0 90-94 36.36280000000001 37.0 37.0 37.0 37.0 37.0 95-99 36.299600000000005 37.0 37.0 37.0 37.0 37.0 100-104 36.2694 37.0 37.0 37.0 37.0 37.0 105-109 36.311 37.0 37.0 37.0 37.0 37.0 110-114 36.2134 37.0 37.0 37.0 37.0 37.0 115-119 36.181799999999996 37.0 37.0 37.0 37.0 37.0 120-124 36.107600000000005 37.0 37.0 37.0 37.0 37.0 125-129 35.9627 37.0 37.0 37.0 37.0 37.0 130-134 35.9533 37.0 37.0 37.0 37.0 37.0 135-139 35.8403 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 35.5475 37.0 37.0 37.0 37.0 37.0 150-151 35.38825 37.0 37.0 37.0 37.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 24 2.0 25 3.0 26 3.0 27 4.0 28 7.0 29 13.0 30 28.0 31 27.0 32 38.0 33 79.0 34 140.0 35 324.0 36 2951.0 37 381.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 42.6 10.2 6.9750000000000005 40.225 2 20.12012012012012 13.213213213213212 35.585585585585584 31.08108108108108 3 18.224999999999998 18.8 26.924999999999997 36.05 4 22.075 26.1 25.25 26.575 5 22.975 29.25 26.775 21.0 6 20.150000000000002 35.35 24.0 20.5 7 15.675 26.424999999999997 40.325 17.575 8 18.325 23.400000000000002 32.1 26.174999999999997 9 18.2 22.875 34.9 24.025 10-14 20.325 29.75 26.619999999999997 23.305 15-19 20.565 27.355 28.005000000000003 24.075 20-24 21.065 27.589999999999996 27.994999999999997 23.35 25-29 20.715 28.435 27.57 23.28 30-34 20.695 28.110000000000003 27.415 23.78 35-39 20.21 27.915 28.255000000000003 23.62 40-44 20.3 28.225 28.110000000000003 23.365 45-49 20.875 27.67 27.694999999999997 23.76 50-54 20.064999999999998 28.310000000000002 28.335 23.29 55-59 19.794999999999998 28.51 27.87 23.825 60-64 20.71 27.965 28.15 23.175 65-69 20.655 27.91 28.015 23.419999999999998 70-74 21.22 27.985 28.005000000000003 22.79 75-79 21.58 27.779999999999998 26.93 23.71 80-84 20.43 28.505000000000003 27.384999999999998 23.68 85-89 20.919999999999998 28.58 27.139999999999997 23.36 90-94 20.919999999999998 28.48 27.02 23.580000000000002 95-99 20.555 28.37 27.065 24.01 100-104 21.105 28.975 26.735 23.185 105-109 21.77 28.29 26.889999999999997 23.05 110-114 21.145 28.835 26.565 23.455000000000002 115-119 21.355 28.71 25.885 24.05 120-124 21.415 29.455 25.945 23.185 125-129 21.59 28.08 26.02 24.310000000000002 130-134 22.220000000000002 28.025 25.650000000000002 24.104999999999997 135-139 21.26 28.315 26.06 24.365000000000002 140-144 21.61 28.389999999999997 25.174999999999997 24.825 145-149 21.65 27.400000000000002 26.715 24.235 150-151 21.3125 28.8625 25.912499999999998 23.9125 >>END_MODULE >>Per sequence GC content pass #GC Content Count 0 0.0 1 0.0 2 0.0 3 0.0 4 0.5 5 0.5 6 0.0 7 0.0 8 0.0 9 0.0 10 0.0 11 0.0 12 0.0 13 0.5 14 0.5 15 0.0 16 0.0 17 0.0 18 0.0 19 0.0 20 0.0 21 0.5 22 1.5 23 1.0 24 1.0 25 2.0 26 4.5 27 5.0 28 9.0 29 15.5 30 17.0 31 21.0 32 24.5 33 30.5 34 43.5 35 58.0 36 76.5 37 85.0 38 122.0 39 158.0 40 185.5 41 236.0 42 251.5 43 254.5 44 270.0 45 264.5 46 258.0 47 250.0 48 220.5 49 206.0 50 174.5 51 151.5 52 133.0 53 95.5 54 84.5 55 71.0 56 49.5 57 37.0 58 31.5 59 29.0 60 26.5 61 18.5 62 7.5 63 4.0 64 3.5 65 2.5 66 1.5 67 0.5 68 0.0 69 2.0 70 2.0 71 0.0 72 0.0 73 0.0 74 0.0 75 0.0 76 0.0 77 0.0 78 0.0 79 0.0 80 0.0 81 0.0 82 0.0 83 0.0 84 0.0 85 0.0 86 0.0 87 0.0 88 0.0 89 0.0 90 0.0 91 0.0 92 0.0 93 0.0 94 0.0 95 0.0 96 0.0 97 0.0 98 0.0 99 0.0 100 0.0 >>END_MODULE >>Per base N content pass #Base N-Count 1 0.0 2 0.1 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 82.87022900763358 67.85 2 13.526717557251908 22.15 3 2.6259541984732824 6.45 4 0.6106870229007634 2.0 5 0.3053435114503817 1.25 6 0.06106870229007634 0.3 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 GTTTGAGAGATTGCTAGGGATGTCAAGCACAACATGGCCCCCAACAGCTT 6 0.15 No Hit TTTTGTATAGAATTCCCCTGTCACCATTGCCGAAACATGATCCCCTTGCT 6 0.15 No Hit GCCAAAACACGAATAACAGTTGCATATTTCTTCAACTTCTCAAGCTGTGA 5 0.125 No Hit GGTCAACAACTGAAACATTGGGTGTCGGGACACGCAGTGCGATGCCATTG 5 0.125 No Hit GCACTGTCTGAACCTCGAGAACATAAGAGAGTTGTTTCATCAGGAAGCTC 5 0.125 No Hit GGCTGTTCTGTAACGGGACAGGCTGATCCATAACTGGTTGTGAAGAACTC 5 0.125 No Hit CAACTAATATGGTGCTCTTCTTTCTCGCAGCTGATTGTTCCTTCCCATTT 5 0.125 No Hit CTAACAGTGAGATCCTCGCATCAATTTTACAAAAATAAGTAAATTGCGCA 5 0.125 No Hit GCAGATCCATCAGCTAGGAATTTGACATGCTTATTCTCAGGGTAAGTTTT 5 0.125 No Hit AGACGCTTTACGCCCAATCATTCCGGATAACGCTTGCATCCTCTGTATTA 5 0.125 No Hit CTGTCTCCAAGTCTACCTTGGGGTGAGCAGTCATGCTCATCAGCAGCTTT 5 0.125 No Hit TTGCTATTGACAACAACCAACTTTTCAGCAACATATATTGTTTCTGGATA 5 0.125 No Hit >>END_MODULE >>Adapter Content fail #Position Illumina Universal Adapter Illumina Small RNA 3' Adapter Illumina Small RNA 5' Adapter Nextera Transposase Sequence SOLID Small RNA Adapter 1 0.0 0.0 0.0 0.0 0.0 2 0.0 0.0 0.0 0.0 0.0 3 0.0 0.0 0.0 0.0 0.0 4 0.0 0.0 0.0 0.0 0.0 5 0.0 0.0 0.0 0.0 0.0 6 0.0 0.0 0.0 0.0 0.0 7 0.0 0.0 0.0 0.0 0.0 8 0.0 0.0 0.0 0.0 0.0 9 0.0 0.0 0.0 0.0 0.0 10-11 0.0 0.0 0.0 0.0 0.0 12-13 0.0 0.0 0.0 0.0 0.0 14-15 0.0 0.0 0.0 0.0 0.0 16-17 0.0 0.0 0.0 0.0 0.0 18-19 0.0 0.0 0.0 0.0 0.0 20-21 0.0 0.0 0.0 0.0 0.0 22-23 0.0 0.0 0.0 0.0 0.0 24-25 0.0 0.0 0.0 0.0 0.0 26-27 0.0 0.0 0.0 0.0 0.0 28-29 0.0 0.0 0.0 0.0 0.0 30-31 0.0 0.0 0.0 0.0 0.0 32-33 0.0 0.0 0.0 0.0 0.0 34-35 0.0 0.0 0.0 0.0 0.0 36-37 0.0 0.0 0.0 0.0 0.0 38-39 0.0 0.0 0.0 0.0 0.0 40-41 0.0 0.0 0.0 0.0 0.0 42-43 0.0 0.0 0.0 0.0 0.0 44-45 0.0 0.0 0.0 0.0 0.0 46-47 0.05 0.0 0.0 0.0 0.0 48-49 0.05 0.0 0.0 0.0 0.0 50-51 0.05 0.0 0.0 0.0 0.0 52-53 0.05 0.0 0.0 0.0 0.0 54-55 0.05 0.0 0.0 0.0 0.0 56-57 0.075 0.0 0.0 0.0 0.0 58-59 0.075 0.0 0.0 0.0 0.0 60-61 0.1 0.0 0.0 0.0 0.0 62-63 0.1 0.0 0.0 0.0 0.0 64-65 0.1375 0.0 0.0 0.0 0.0 66-67 0.15 0.0 0.0 0.0 0.0 68-69 0.2375 0.0 0.0 0.0 0.0 70-71 0.3125 0.0 0.0 0.0 0.0 72-73 0.4125 0.0 0.0 0.0 0.0 74-75 0.5 0.0 0.0 0.0 0.0 76-77 0.6875 0.0 0.0 0.0 0.0 78-79 0.8375 0.0 0.0 0.0 0.0 80-81 1.075 0.0 0.0 0.0 0.0 82-83 1.425 0.0 0.0 0.0 0.0 84-85 1.6 0.0 0.0 0.0 0.0 86-87 1.9125 0.0 0.0 0.0 0.0 88-89 2.2 0.0 0.0 0.0 0.0 90-91 2.6125 0.0 0.0 0.0 0.0 92-93 3.2125000000000004 0.0 0.0 0.0 0.0 94-95 3.55 0.0 0.0 0.0 0.0 96-97 4.275 0.0 0.0 0.0 0.0 98-99 4.8 0.0 0.0 0.0 0.0 100-101 5.6125 0.0 0.0 0.0 0.0 102-103 6.300000000000001 0.0 0.0 0.0 0.0 104-105 6.8875 0.0 0.0 0.0 0.0 106-107 7.625 0.0 0.0 0.0 0.0 108-109 8.475 0.0 0.0 0.0 0.0 110-111 9.3125 0.0 0.0 0.0 0.0 112-113 10.1875 0.0 0.0 0.0 0.0 114-115 11.2125 0.0 0.0 0.0 0.0 116-117 12.125 0.0 0.0 0.0 0.0 118-119 12.850000000000001 0.0 0.0 0.0 0.0 120-121 13.962499999999999 0.0 0.0 0.0 0.0 122-123 14.575 0.0 0.0 0.0 0.0 124-125 15.6125 0.0 0.0 0.0 0.0 126-127 16.625 0.0 0.0 0.0 0.0 128-129 17.875 0.0 0.0 0.0 0.0 130-131 18.7125 0.0 0.0 0.0 0.0 132-133 19.6625 0.0 0.0 0.0 0.0 134-135 20.8625 0.0 0.0 0.0 0.0 136-137 21.9125 0.0 0.0 0.0 0.0 138-139 22.6 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content pass >>END_MODULE SRR12670129 read2 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR12670129_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 36.3395 37.0 37.0 37.0 37.0 37.0 2 36.248 37.0 37.0 37.0 37.0 37.0 3 36.2985 37.0 37.0 37.0 37.0 37.0 4 36.3295 37.0 37.0 37.0 37.0 37.0 5 36.3415 37.0 37.0 37.0 37.0 37.0 6 36.316 37.0 37.0 37.0 37.0 37.0 7 36.3815 37.0 37.0 37.0 37.0 37.0 8 36.356 37.0 37.0 37.0 37.0 37.0 9 36.2695 37.0 37.0 37.0 37.0 37.0 10-14 36.3855 37.0 37.0 37.0 37.0 37.0 15-19 36.3751 37.0 37.0 37.0 37.0 37.0 20-24 36.305600000000005 37.0 37.0 37.0 37.0 37.0 25-29 36.265 37.0 37.0 37.0 37.0 37.0 30-34 36.2393 37.0 37.0 37.0 37.0 37.0 35-39 36.2821 37.0 37.0 37.0 37.0 37.0 40-44 36.2376 37.0 37.0 37.0 37.0 37.0 45-49 36.2379 37.0 37.0 37.0 37.0 37.0 50-54 36.1871 37.0 37.0 37.0 37.0 37.0 55-59 36.134 37.0 37.0 37.0 37.0 37.0 60-64 36.165 37.0 37.0 37.0 37.0 37.0 65-69 36.1418 37.0 37.0 37.0 37.0 37.0 70-74 36.106700000000004 37.0 37.0 37.0 37.0 37.0 75-79 36.1119 37.0 37.0 37.0 37.0 37.0 80-84 36.022800000000004 37.0 37.0 37.0 37.0 37.0 85-89 36.0199 37.0 37.0 37.0 37.0 37.0 90-94 36.0192 37.0 37.0 37.0 37.0 37.0 95-99 35.943200000000004 37.0 37.0 37.0 37.0 37.0 100-104 35.8817 37.0 37.0 37.0 37.0 37.0 105-109 35.830400000000004 37.0 37.0 37.0 37.0 37.0 110-114 35.764300000000006 37.0 37.0 37.0 37.0 37.0 115-119 35.785999999999994 37.0 37.0 37.0 37.0 37.0 120-124 35.5961 37.0 37.0 37.0 37.0 37.0 125-129 35.5772 37.0 37.0 37.0 37.0 37.0 130-134 35.3629 37.0 37.0 37.0 34.6 37.0 135-139 35.1844 37.0 37.0 37.0 29.8 37.0 140-144 34.988299999999995 37.0 37.0 37.0 25.0 37.0 145-149 34.639700000000005 37.0 37.0 37.0 25.0 37.0 150-151 34.366749999999996 37.0 37.0 37.0 25.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 12 1.0 13 2.0 14 1.0 15 2.0 16 0.0 17 0.0 18 0.0 19 1.0 20 2.0 21 5.0 22 2.0 23 3.0 24 4.0 25 9.0 26 6.0 27 11.0 28 14.0 29 16.0 30 11.0 31 43.0 32 57.0 33 103.0 34 238.0 35 600.0 36 2600.0 37 269.0 >>END_MODULE >>Per base sequence content warn #Base G A T C 1 40.2 21.775 11.25 26.775 2 26.125 26.0 31.2 16.675 3 20.125 29.7 29.825000000000003 20.349999999999998 4 22.675 36.175000000000004 22.05 19.1 5 24.075 36.199999999999996 23.075000000000003 16.650000000000002 6 22.2 37.475 22.275 18.05 7 19.25 21.325 38.574999999999996 20.849999999999998 8 21.55 26.575 27.925 23.95 9 21.625 26.224999999999998 30.075000000000003 22.075 10-14 22.400000000000002 29.609999999999996 26.955000000000002 21.035 15-19 22.68 27.839999999999996 28.315 21.165 20-24 23.189999999999998 27.925 27.77 21.115000000000002 25-29 22.770000000000003 28.73 26.66 21.84 30-34 22.6 27.91 29.175 20.315 35-39 23.215 28.43 27.169999999999998 21.185000000000002 40-44 21.92 28.53 27.51 22.040000000000003 45-49 22.89 28.1 27.229999999999997 21.78 50-54 22.355 27.975 28.125 21.545 55-59 22.925 28.139999999999997 27.875 21.060000000000002 60-64 23.41 27.51 27.939999999999998 21.14 65-69 23.005 27.36 27.939999999999998 21.695 70-74 22.88 27.98 27.415 21.725 75-79 22.884999999999998 27.694999999999997 28.13 21.29 80-84 23.98 28.444999999999997 26.740000000000002 20.835 85-89 23.544999999999998 28.37 27.38 20.705000000000002 90-94 23.29 28.825 27.105 20.78 95-99 24.169999999999998 28.21 26.515 21.105 100-104 24.205 28.24 26.465 21.09 105-109 24.565 28.185 26.56 20.69 110-114 25.715 27.365000000000002 27.115000000000002 19.805 115-119 25.985000000000003 27.950000000000003 25.97 20.095 120-124 26.69 27.145000000000003 26.400000000000002 19.765 125-129 27.295 27.794999999999998 25.145 19.765 130-134 27.27 27.985 25.505 19.24 135-139 27.705000000000002 27.99 25.650000000000002 18.655 140-144 29.465000000000003 27.060000000000002 25.345000000000002 18.13 145-149 30.025000000000002 27.24 24.75 17.985 150-151 31.324999999999996 27.224999999999998 24.075 17.375 >>END_MODULE >>Per sequence GC content pass #GC Content Count 0 1.0 1 0.5 2 0.0 3 0.0 4 0.0 5 0.0 6 0.5 7 0.5 8 0.0 9 0.0 10 0.5 11 0.5 12 0.0 13 0.0 14 0.5 15 0.5 16 0.5 17 0.5 18 1.0 19 1.5 20 0.5 21 0.5 22 2.0 23 2.5 24 1.5 25 3.0 26 5.5 27 4.0 28 4.0 29 9.0 30 14.0 31 19.0 32 30.0 33 39.0 34 51.5 35 75.5 36 95.5 37 103.5 38 128.5 39 155.5 40 185.5 41 248.5 42 263.5 43 257.5 44 255.0 45 246.5 46 245.0 47 239.0 48 228.0 49 213.0 50 187.0 51 128.5 52 94.0 53 92.5 54 85.5 55 69.0 56 53.5 57 39.5 58 30.0 59 27.0 60 21.5 61 13.0 62 9.0 63 7.5 64 3.0 65 0.0 66 0.5 67 1.0 68 1.0 69 1.0 70 1.0 71 0.5 72 0.0 73 0.0 74 0.0 75 0.0 76 0.0 77 0.0 78 0.0 79 0.0 80 0.0 81 0.0 82 0.0 83 0.0 84 0.0 85 0.0 86 0.0 87 0.0 88 0.0 89 0.0 90 0.0 91 0.0 92 0.0 93 0.0 94 0.0 95 0.0 96 0.0 97 0.0 98 0.0 99 0.0 100 0.5 >>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 0.0 150-151 0.0 >>END_MODULE >>Sequence Length Distribution pass #Length Count 151 4000.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 82.125 #Duplication Level Percentage of deduplicated Percentage of total 1 83.50076103500761 68.575 2 12.846270928462708 21.099999999999998 3 2.5875190258751903 6.375 4 0.669710806697108 2.1999999999999997 5 0.273972602739726 1.125 6 0.091324200913242 0.44999999999999996 7 0.030441400304414005 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 AGAACACATTCATACTCCAAGTCTTTTAGTTCATCCATTTAAGCTTAATC 7 0.17500000000000002 No Hit AGCTCCTATTAAGATATGTTCCTGAGAAATTTGGGTCCAAAGACACGGCA 6 0.15 No Hit GGAAGATGCCAGCAATTTCAACGAAAGTGATGGTGAACTCTTTCATGCTG 6 0.15 No Hit GTGAAGTGATGGCTTCTCGGCCTGGAATTCTCACAGACTGGCCATGGAAA 6 0.15 No Hit AGTTAGAGCGGGTTTGTTTTATGAGCATACAAGTTTTTGCATGGACCTTC 5 0.125 No Hit ATAAAGAGTAAGATATATACATAACGTCACAGGAAAATCAGAAACATCTG 5 0.125 No Hit TAAATGTCCCTTTAAATGTTCAAGCTAGCTGGTTAGTTTAATTTAATGAC 5 0.125 No Hit GGAAAAGTGAAGTCTTTCCCCAAGGATGACCCTAATAAGCCTTGCAAGCT 5 0.125 No Hit GGCTGGTCAATTTAATCCAGCTAATGGTATTGGTCTGGCAAACACTAGCT 5 0.125 No Hit GCTTACCAAGGCGATGATCAGTAGCTGGTCCGAGAGGATGATCAGCCACA 5 0.125 No Hit TCAACACCACCGTCGATTCGATATGGCTCCGATTGCTGTTGGTGATGTCT 5 0.125 No Hit TTTCAGCAAAAAAATATTCTTGGATATGGAGGTTAGTTGTCCTATCTTAT 5 0.125 No Hit ATAGTCCCAACAAGCACTGGTGCAGCCAAAGCTGTATCTCTTGTGCTGCC 5 0.125 No Hit >>END_MODULE >>Adapter Content fail #Position Illumina Universal Adapter Illumina Small RNA 3' Adapter Illumina Small RNA 5' Adapter Nextera Transposase Sequence SOLID Small RNA Adapter 1 0.0 0.0 0.0 0.0 0.0 2 0.0 0.0 0.0 0.0 0.0 3 0.0 0.0 0.0 0.0 0.0 4 0.0 0.0 0.0 0.0 0.0 5 0.0 0.0 0.0 0.0 0.0 6 0.0 0.0 0.0 0.0 0.0 7 0.0 0.0 0.0 0.0 0.0 8 0.0 0.0 0.0 0.0 0.0 9 0.0 0.0 0.0 0.0 0.0 10-11 0.0 0.0 0.0 0.0 0.0 12-13 0.0 0.0 0.0 0.0 0.0 14-15 0.0 0.0 0.0 0.0 0.0 16-17 0.0 0.0 0.0 0.0 0.0 18-19 0.0 0.0 0.0 0.0 0.0 20-21 0.0 0.0 0.0 0.0 0.0 22-23 0.0 0.0 0.0 0.0 0.0 24-25 0.0 0.0 0.0 0.0 0.0 26-27 0.0 0.0 0.0 0.0 0.0 28-29 0.0 0.0 0.0 0.0 0.0 30-31 0.0 0.0 0.0 0.0 0.0 32-33 0.0 0.0 0.0 0.0 0.0 34-35 0.0 0.0 0.0 0.0 0.0 36-37 0.0 0.0 0.0 0.0 0.0 38-39 0.0 0.0 0.0 0.0 0.0 40-41 0.0 0.0 0.0 0.0 0.0 42-43 0.0 0.0 0.0 0.0 0.0 44-45 0.0 0.0 0.0 0.0 0.0 46-47 0.05 0.0 0.0 0.0 0.0 48-49 0.05 0.0 0.0 0.0 0.0 50-51 0.05 0.0 0.0 0.0 0.0 52-53 0.05 0.0 0.0 0.0 0.0 54-55 0.05 0.0 0.0 0.0 0.0 56-57 0.075 0.0 0.0 0.0 0.0 58-59 0.075 0.0 0.0 0.0 0.0 60-61 0.1 0.0 0.0 0.0 0.0 62-63 0.1 0.0 0.0 0.0 0.0 64-65 0.1375 0.0 0.0 0.0 0.0 66-67 0.15 0.0 0.0 0.0 0.0 68-69 0.2375 0.0 0.0 0.0 0.0 70-71 0.3125 0.0 0.0 0.0 0.0 72-73 0.4125 0.0 0.0 0.0 0.0 74-75 0.5 0.0 0.0 0.0 0.0 76-77 0.6875 0.0 0.0 0.0 0.0 78-79 0.8375 0.0 0.0 0.0 0.0 80-81 1.075 0.0 0.0 0.0 0.0 82-83 1.425 0.0 0.0 0.0 0.0 84-85 1.6 0.0 0.0 0.0 0.0 86-87 1.9 0.0 0.0 0.0 0.0 88-89 2.175 0.0 0.0 0.0 0.0 90-91 2.5875 0.0 0.0 0.0 0.0 92-93 3.1875 0.0 0.0 0.0 0.0 94-95 3.5 0.0 0.0 0.0 0.0 96-97 4.2 0.0 0.0 0.0 0.0 98-99 4.75 0.0 0.0 0.0 0.0 100-101 5.5625 0.0 0.0 0.0 0.0 102-103 6.25 0.0 0.0 0.0 0.0 104-105 6.8375 0.0 0.0 0.0 0.0 106-107 7.612500000000001 0.0 0.0 0.0 0.0 108-109 8.5 0.0 0.0 0.0 0.0 110-111 9.337499999999999 0.0 0.0 0.0 0.0 112-113 10.2125 0.0 0.0 0.0 0.0 114-115 11.2375 0.0 0.0 0.0 0.0 116-117 12.15 0.0 0.0 0.0 0.0 118-119 12.8875 0.0 0.0 0.0 0.0 120-121 13.9875 0.0 0.0 0.0 0.0 122-123 14.6 0.0 0.0 0.0 0.0 124-125 15.6875 0.0 0.0 0.0 0.0 126-127 16.700000000000003 0.0 0.0 0.0 0.0 128-129 17.9625 0.0 0.0 0.0 0.0 130-131 18.799999999999997 0.0 0.0 0.0 0.0 132-133 19.7625 0.0 0.0 0.0 0.0 134-135 20.95 0.0 0.0 0.0 0.0 136-137 21.987499999999997 0.0 0.0 0.0 0.0 138-139 22.675 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content pass >>END_MODULE Read 560023 spots for SRR12670129.sra Written 560023 spots for SRR12670129.sra Read 560023 spots for SRR12670129.sra Written 560023 spots for SRR12670129.sra Read 560023 spots for SRR12670129.sra Written 560023 spots for SRR12670129.sra Read 560023 spots for SRR12670129.sra Written 560023 spots for SRR12670129.sra Read 560023 spots for SRR12670129.sra Written 560023 spots for SRR12670129.sra Read 560023 spots for SRR12670129.sra Written 560023 spots for SRR12670129.sra Read 560023 spots for SRR12670129.sra Written 560023 spots for SRR12670129.sra Read 560023 spots for SRR12670129.sra Written 560023 spots for SRR12670129.sra Read 560023 spots for SRR12670129.sra Written 560023 spots for SRR12670129.sra Read 560023 spots for SRR12670129.sra Written 560023 spots for SRR12670129.sra Read 560023 spots for SRR12670129.sra Written 560023 spots for SRR12670129.sra Read 560023 spots for SRR12670129.sra Written 560023 spots for SRR12670129.sra Read 560023 spots for SRR12670129.sra Written 560023 spots for SRR12670129.sra Read 560042 spots for SRR12670129.sra Written 560042 spots for SRR12670129.sra Read 560023 spots for SRR12670129.sra Written 560023 spots for SRR12670129.sra Read 560023 spots for SRR12670129.sra Written 560023 spots for SRR12670129.sra Read 560023 spots for SRR12670129.sra Written 560023 spots for SRR12670129.sra Read 560023 spots for SRR12670129.sra Written 560023 spots for SRR12670129.sra Read 560023 spots for SRR12670129.sra Written 560023 spots for SRR12670129.sra Read 560023 spots for SRR12670129.sra Written 560023 spots for SRR12670129.sra SRR ids: ['SRR12670129.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_mf5jbo5g SRR12670129.sra spots: 11200479 blocks: [[1, 560023], [560024, 1120046], [1120047, 1680069], [1680070, 2240092], [2240093, 2800115], [2800116, 3360138], [3360139, 3920161], [3920162, 4480184], [4480185, 5040207], [5040208, 5600230], [5600231, 6160253], [6160254, 6720276], [6720277, 7280299], [7280300, 7840322], [7840323, 8400345], [8400346, 8960368], [8960369, 9520391], [9520392, 10080414], [10080415, 10640437], [10640438, 11200479]] SRR12670129 file size 3784712 SRR12670129 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 SRR12670129 SRR12670129_1.fastq SRR12670129_2.fastq Input file: SRR12670129_1.fastq Paired file: SRR12670129_2.fastq trimmed: SRR12670129-trimmed-pair1.fastq, SRR12670129-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 00:38:52 2025 >> started Tue Feb 11 00:39:05 2025 >> done (12.564s) 11200479 read pairs processed; of these: 65 ( 0.00%) short read pairs filtered out after trimming by size control 3541 ( 0.03%) empty read pairs filtered out after trimming by size control 11196873 (99.97%) read pairs available; of these: 2853900 (25.49%) trimmed read pairs available after processing 8342973 (74.51%) untrimmed read pairs available after processing Length distribution of reads after trimming: length count percentage 18 3 0.00% 19 3 0.00% 20 6 0.00% 21 7 0.00% 22 12 0.00% 23 17 0.00% 24 15 0.00% 25 29 0.00% 26 38 0.00% 27 31 0.00% 28 40 0.00% 29 56 0.00% 30 49 0.00% 31 54 0.00% 32 45 0.00% 33 50 0.00% 34 65 0.00% 35 51 0.00% 36 95 0.00% 37 89 0.00% 38 80 0.00% 39 116 0.00% 40 171 0.00% 41 170 0.00% 42 148 0.00% 43 160 0.00% 44 155 0.00% 45 186 0.00% 46 214 0.00% 47 292 0.00% 48 289 0.00% 49 371 0.00% 50 458 0.00% 51 493 0.00% 52 485 0.00% 53 540 0.00% 54 562 0.01% 55 680 0.01% 56 681 0.01% 57 828 0.01% 58 949 0.01% 59 1144 0.01% 60 1326 0.01% 61 1508 0.01% 62 1698 0.02% 63 1800 0.02% 64 2030 0.02% 65 2105 0.02% 66 2337 0.02% 67 2589 0.02% 68 3037 0.03% 69 3345 0.03% 70 3973 0.04% 71 4528 0.04% 72 5236 0.05% 73 5795 0.05% 74 6236 0.06% 75 6639 0.06% 76 7199 0.06% 77 7820 0.07% 78 8207 0.07% 79 9578 0.09% 80 10413 0.09% 81 11632 0.10% 82 13149 0.12% 83 14486 0.13% 84 15630 0.14% 85 16813 0.15% 86 17117 0.15% 87 18158 0.16% 88 18905 0.17% 89 19966 0.18% 90 21320 0.19% 91 23274 0.21% 92 25068 0.22% 93 26715 0.24% 94 28452 0.25% 95 29404 0.26% 96 30104 0.27% 97 30542 0.27% 98 30851 0.28% 99 31622 0.28% 100 32944 0.29% 101 34010 0.30% 102 35811 0.32% 103 37466 0.33% 104 39084 0.35% 105 39861 0.36% 106 40724 0.36% 107 39886 0.36% 108 40167 0.36% 109 39878 0.36% 110 40016 0.36% 111 41501 0.37% 112 42751 0.38% 113 43700 0.39% 114 45274 0.40% 115 46396 0.41% 116 45988 0.41% 117 45571 0.41% 118 45577 0.41% 119 44919 0.40% 120 45724 0.41% 121 45574 0.41% 122 46412 0.41% 123 47452 0.42% 124 48940 0.44% 125 48782 0.44% 126 49681 0.44% 127 48933 0.44% 128 48276 0.43% 129 47750 0.43% 130 46979 0.42% 131 47051 0.42% 132 47818 0.43% 133 48936 0.44% 134 48823 0.44% 135 50596 0.45% 136 50256 0.45% 137 50234 0.45% 138 49637 0.44% 139 48907 0.44% 140 48016 0.43% 141 47423 0.42% 142 48172 0.43% 143 48042 0.43% 144 49585 0.44% 145 49501 0.44% 146 50064 0.45% 147 49270 0.44% 148 48518 0.43% 149 48049 0.43% 150 48441 0.43% 151 8342973 74.51% 11196873 reads passed initial QC criterion=sequence-density sequence-density=0.32 sequence-density-rank=1 fanout-score=2.36 fanout-score-rank=22 prefix-density=0.35 prefix-fanout=2.2 sequence=TGAGATGCCTCAGTGCATCCAAACATGGGTAG criterion=fanout-score sequence-density=0.02 sequence-density-rank=31 fanout-score=236.36 fanout-score-rank=1 prefix-density=0.28 prefix-fanout=15.2 sequence=TGAAGAAGACACAAAGATAAAGACACTCACGGACACTTTTGTTTGTTCACTCCACACCCACAAGTACAGAAGAACACAGATTATTTATCAGAAATTACATTATTAATCCACTCCCAATCCCACATCAAACATGATAGTTGATGTGCTTGCTTAATGACCGCATGTGCAGGTAGTGCAAGTGCAGCCAGTACCGCAGTTGCACTTGCCATCGTTCTCAGCTGCTGGCACCTCCATGACTACGGAGGAGACATAGTTCTTCTCAGTCTCGACGATGCCAGCAGTGTAGCTGCTTCCCTTCTTGACACACTGGGTCTTGTCAGCGCAGTCGCAG criterion=sequence-density sequence-density=0.55 sequence-density-rank=1 fanout-score=2.09 fanout-score-rank=31 prefix-density=0.55 prefix-fanout=2.1 sequence=CTGCGACTGCGCTGACAAGACCCAGTGTGTCAAGAAGGGAAGCAGCTACACTGCTGGCATCGTCGAGACTGAGAAGAACTATGTCTCCTCCGTAGTCATGGAGGTGCCAGCAGCTGAGAACGATGGCAAGTGCAACTGCGGTACTGGCTGCACTTGCACTACCTGCACATGCGGTCATTAAGCAAGCACATCAACTATCATGTTTGATGTGGGATTGGGAGTGGATTAATAATGTAATTTCTGATAAATAATCTGTGTTCTTCTGTACTTGTGGGTGTGGAGTGAACAAACAAAAGTGTCCGTGAGTGTCTTTATCTTTGTGTCTTCTTCA criterion=fanout-score sequence-density=0.14 sequence-density-rank=16 fanout-score=33.26 fanout-score-rank=1 prefix-density=0.37 prefix-fanout=12.5 sequence=AAAGAAAAGAAAA SRR12670129 testing PE reads STAR mapping to Ensembl genome Started job on | Feb 11 00:39:47 Started mapping on | Feb 11 00:39:48 Finished on | Feb 11 00:40:59 Mapping speed, Million of reads per hour | 567.73 Number of input reads | 11196873 Average input read length | 285 UNIQUE READS: Uniquely mapped reads number | 10366770 Uniquely mapped reads % | 92.59% Average mapped length | 284.17 Number of splices: Total | 9955424 Number of splices: Annotated (sjdb) | 9727268 Number of splices: GT/AG | 9756797 Number of splices: GC/AG | 160575 Number of splices: AT/AC | 6719 Number of splices: Non-canonical | 31333 Mismatch rate per base, % | 0.34% Deletion rate per base | 0.03% Deletion average length | 2.78 Insertion rate per base | 0.02% Insertion average length | 2.49 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 257846 % of reads mapped to multiple loci | 2.30% Number of reads mapped to too many loci | 119398 % of reads mapped to too many loci | 1.07% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 3.82% % of reads unmapped: other | 0.23% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 572257 572257 572257 N_multimapping 257846 257846 257846 N_noFeature 397159 10235372 449300 N_ambiguous 136183 477 56725 UnstrandedReadsAssigned:9833428 PositiveStrandReadsAssigned:130921 NegativeStrandReadsAssigned:9860745 Dataset is classified negative stranded MeadianReadLen=151 20thPercentileLength=138 echo kmer=133 SRR12670129 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: SRR12670129-trimmed-pair1.fastq SRR12670129-trimmed-pair2.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 11,196,873 reads, 9,958,147 reads pseudoaligned [quant] estimated average fragment length: 212.71 [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,093 rounds 52401 SRR12670129.ke.tsv 34699 SRR12670129.se.tsv 87100 total ==> SRR12670129.ke.tsv <== target_id length eff_length est_counts tpm Potri.005G200100.1.v4.1 2018 1806.29 409 24.2034 Potri.005G024800.1.v4.1 1035 823.29 91 11.8149 Potri.004G059700.1.v4.1 961 749.392 10 1.42637 Potri.007G009000.2.v4.1 1416 1204.29 0 0 Potri.003G141000.2.v4.1 2943 2731.29 519.835 20.3441 Potri.016G087400.1.v4.1 270 107.725 319 316.528 Potri.015G069301.1.v4.1 564 360.38 0 0 Potri.010G195200.1.v4.1 1773 1561.29 12 0.821557 Potri.012G127500.1.v4.1 977 765.362 54 7.54166 ==> SRR12670129.se.tsv <== Potri.001G166300.v4.1 0 Potri.001G448400.v4.1 107 Potri.001G233950.v4.1 0 Potri.001G122700.v4.1 151 Potri.001G212900.v4.1 1 Potri.001G182400.v4.1 2 Potri.001G256600.v4.1 0 Potri.001G040500.v4.1 9 Potri.001G416900.v4.1 0 Potri.001G452600.v4.1 2 SRR12670129 completed mapping pipeline successfully