Starting /dee2/code/volunteer_pipeline.sh SRR12670138 current disk space = 3057147912192 free memory = 1465721180 SRR12670138 SRAfilesize 29b71e15dd27cb0371fcb0420991a7c1 SRR12670138.sra SRR12670138.sra file validated SRR12670138 is paired end SRR12670138 is conventional basespace SRR12670138 read1 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR12670138_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 45 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 36.594 37.0 37.0 37.0 37.0 37.0 2 36.4785 37.0 37.0 37.0 37.0 37.0 3 36.586 37.0 37.0 37.0 37.0 37.0 4 36.6425 37.0 37.0 37.0 37.0 37.0 5 36.634 37.0 37.0 37.0 37.0 37.0 6 36.687 37.0 37.0 37.0 37.0 37.0 7 36.593 37.0 37.0 37.0 37.0 37.0 8 36.6115 37.0 37.0 37.0 37.0 37.0 9 36.6695 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 36.5698 37.0 37.0 37.0 37.0 37.0 20-24 36.5514 37.0 37.0 37.0 37.0 37.0 25-29 36.5416 37.0 37.0 37.0 37.0 37.0 30-34 36.507 37.0 37.0 37.0 37.0 37.0 35-39 36.53750000000001 37.0 37.0 37.0 37.0 37.0 40-44 36.5011 37.0 37.0 37.0 37.0 37.0 45-49 36.4858 37.0 37.0 37.0 37.0 37.0 50-54 36.4649 37.0 37.0 37.0 37.0 37.0 55-59 36.4028 37.0 37.0 37.0 37.0 37.0 60-64 36.4078 37.0 37.0 37.0 37.0 37.0 65-69 36.3602 37.0 37.0 37.0 37.0 37.0 70-74 36.3337 37.0 37.0 37.0 37.0 37.0 75-79 36.306 37.0 37.0 37.0 37.0 37.0 80-84 36.3224 37.0 37.0 37.0 37.0 37.0 85-89 36.297700000000006 37.0 37.0 37.0 37.0 37.0 90-94 36.3134 37.0 37.0 37.0 37.0 37.0 95-99 36.2476 37.0 37.0 37.0 37.0 37.0 100-104 36.20100000000001 37.0 37.0 37.0 37.0 37.0 105-109 36.2907 37.0 37.0 37.0 37.0 37.0 110-114 36.196 37.0 37.0 37.0 37.0 37.0 115-119 36.178599999999996 37.0 37.0 37.0 37.0 37.0 120-124 36.1101 37.0 37.0 37.0 37.0 37.0 125-129 36.0735 37.0 37.0 37.0 37.0 37.0 130-134 35.992000000000004 37.0 37.0 37.0 37.0 37.0 135-139 35.906 37.0 37.0 37.0 37.0 37.0 140-144 35.783 37.0 37.0 37.0 37.0 37.0 145-149 35.706 37.0 37.0 37.0 37.0 37.0 150-151 35.456500000000005 37.0 37.0 37.0 37.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 19 1.0 20 1.0 21 0.0 22 0.0 23 0.0 24 1.0 25 0.0 26 1.0 27 4.0 28 11.0 29 17.0 30 19.0 31 36.0 32 54.0 33 63.0 34 132.0 35 278.0 36 2975.0 37 407.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 34.5 11.35 7.95 46.2 2 19.409704852426213 12.556278139069535 37.843921960980495 30.190095047523762 3 17.599999999999998 16.150000000000002 27.474999999999998 38.775 4 20.25 26.325 23.150000000000002 30.275000000000002 5 23.375 30.625000000000004 23.599999999999998 22.400000000000002 6 21.7 32.475 25.15 20.674999999999997 7 16.400000000000002 25.924999999999997 39.95 17.724999999999998 8 18.075 26.200000000000003 30.475 25.25 9 17.525 24.224999999999998 34.150000000000006 24.099999999999998 10-14 19.98 29.330000000000002 26.985 23.705000000000002 15-19 20.035 28.065 27.365000000000002 24.535 20-24 19.895 28.725 27.950000000000003 23.43 25-29 20.445 28.115000000000002 27.58 23.86 30-34 20.115 27.544999999999998 28.13 24.21 35-39 20.005 27.925 27.894999999999996 24.175 40-44 20.380000000000003 27.975 27.735 23.91 45-49 20.44 28.125 27.3 24.135 50-54 21.125 27.515 28.389999999999997 22.97 55-59 20.685000000000002 28.055000000000003 27.47 23.79 60-64 20.79 27.925 27.615000000000002 23.669999999999998 65-69 20.325 27.750000000000004 27.845 24.08 70-74 20.990000000000002 27.750000000000004 27.834999999999997 23.425 75-79 20.995 28.285 26.87 23.849999999999998 80-84 20.535 27.76 28.425 23.28 85-89 20.47 27.529999999999998 28.075 23.925 90-94 20.335 28.110000000000003 27.534999999999997 24.02 95-99 21.23 27.985 27.439999999999998 23.345 100-104 21.735 27.71 26.695 23.86 105-109 21.325 27.915 27.155 23.605 110-114 21.215 28.24 27.045 23.5 115-119 21.59 27.71 26.52 24.18 120-124 22.2 27.894999999999996 25.840000000000003 24.065 125-129 22.165000000000003 27.54 26.41 23.885 130-134 21.93 27.88 26.775 23.415 135-139 21.990000000000002 26.83 26.155 25.025 140-144 22.134999999999998 26.405 27.435 24.025 145-149 22.105 26.419999999999998 27.025 24.45 150-151 22.425 25.1 27.05 25.424999999999997 >>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 0.0 16 0.0 17 0.0 18 0.0 19 0.0 20 0.0 21 1.0 22 1.0 23 0.0 24 0.0 25 0.0 26 0.0 27 3.5 28 7.5 29 10.5 30 9.5 31 13.5 32 26.5 33 30.0 34 40.0 35 52.0 36 79.0 37 92.0 38 105.5 39 142.5 40 192.0 41 244.5 42 269.0 43 281.0 44 262.0 45 253.0 46 257.5 47 264.0 48 243.0 49 205.5 50 185.5 51 154.0 52 117.0 53 98.5 54 90.5 55 66.0 56 54.0 57 44.5 58 31.0 59 21.5 60 10.0 61 9.5 62 11.5 63 6.0 64 3.0 65 4.5 66 3.0 67 0.5 68 0.5 69 1.5 70 1.0 71 0.5 72 0.5 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 0.05 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 80.55 #Duplication Level Percentage of deduplicated Percentage of total 1 81.99875853507137 66.05 2 13.531967721911856 21.8 3 3.2588454376163876 7.875 4 0.8690254500310366 2.8000000000000003 5 0.2482929857231533 1.0 6 0.06207324643078833 0.3 7 0.031036623215394164 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 GTCATCAAAACCCAAGCCATTAGTGATTCTGAAATATTCAGCACCGCCAA 7 0.17500000000000002 No Hit ACTTGTTGTAGGTGCCTTAGTGGTAGGGGCAGTTGGTGCAGTTGAACCAT 6 0.15 No Hit CTTGCTTTCACTCTCAGTGGGTTCAATCATAAGTGTTCCAGGAACTGGCC 6 0.15 No Hit GACCTCTCCATTGGGGAACACCCTGTAAAACTGGTACTTGATCTTGTACT 5 0.125 No Hit CACCGCTGTAGAATGCAATAACAATATTTGCTGATGCACCATCAGAGGCC 5 0.125 No Hit CTCTGGGAGCTCGGCAGGATTTTCTTTTATTTCGGGATTTACATCTTCTT 5 0.125 No Hit ATGGATATACTTAGGATTGACAAATTCACACGAGAAGTTTTTGGCAACAA 5 0.125 No Hit GGACGACAAGCAGCTAACACGACTTGAGACTTGATACTTGATACTAGAGA 5 0.125 No Hit CTTGATGCAAAGGTCGCAAAAGACATGCAACATTTCTTTAGTCCAAGCAG 5 0.125 No Hit GATCGGAAGAGCACACGTCTGAACTCCAGTCACTTGTGTGCATCTCGTAT 5 0.125 TruSeq Adapter, Index 15 (97% over 37bp) CCAAGGGAGAGCATCTATCAGTAGCCTCGATAATATAAGGAATTAAGCAT 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 0.05 0.0 22-23 0.0 0.0 0.0 0.05 0.0 24-25 0.0 0.0 0.0 0.05 0.0 26-27 0.0 0.0 0.0 0.05 0.0 28-29 0.0 0.0 0.0 0.05 0.0 30-31 0.0 0.0 0.0 0.05 0.0 32-33 0.0 0.0 0.0 0.05 0.0 34-35 0.0 0.0 0.0 0.05 0.0 36-37 0.0 0.0 0.0 0.05 0.0 38-39 0.0 0.0 0.0 0.05 0.0 40-41 0.0 0.0 0.0 0.05 0.0 42-43 0.0 0.0 0.0 0.05 0.0 44-45 0.0 0.0 0.0 0.05 0.0 46-47 0.0 0.0 0.0 0.05 0.0 48-49 0.0 0.0 0.0 0.05 0.0 50-51 0.0 0.0 0.0 0.05 0.0 52-53 0.0 0.0 0.0 0.05 0.0 54-55 0.0 0.0 0.0 0.05 0.0 56-57 0.0 0.0 0.0 0.05 0.0 58-59 0.0125 0.0 0.0 0.05 0.0 60-61 0.025 0.0 0.0 0.05 0.0 62-63 0.025 0.0 0.0 0.05 0.0 64-65 0.1 0.0 0.0 0.05 0.0 66-67 0.125 0.0 0.0 0.05 0.0 68-69 0.1375 0.0 0.0 0.05 0.0 70-71 0.2125 0.0 0.0 0.05 0.0 72-73 0.325 0.0 0.0 0.05 0.0 74-75 0.3625 0.0 0.0 0.05 0.0 76-77 0.4375 0.0 0.0 0.05 0.0 78-79 0.6 0.0 0.0 0.05 0.0 80-81 0.7875 0.0 0.0 0.05 0.0 82-83 1.025 0.0 0.0 0.05 0.0 84-85 1.2374999999999998 0.0 0.0 0.05 0.0 86-87 1.4 0.0 0.0 0.05 0.0 88-89 1.75 0.0 0.0 0.05 0.0 90-91 2.1625 0.0 0.0 0.05 0.0 92-93 2.45 0.0 0.0 0.05 0.0 94-95 3.075 0.0 0.0 0.05 0.0 96-97 3.7125000000000004 0.0 0.0 0.05 0.0 98-99 4.4375 0.0 0.0 0.05 0.0 100-101 5.025 0.0 0.0 0.05 0.0 102-103 5.8125 0.0 0.0 0.05 0.0 104-105 6.525 0.0 0.0 0.05 0.0 106-107 7.387499999999999 0.0 0.0 0.05 0.0 108-109 8.0875 0.0 0.0 0.05 0.0 110-111 8.8875 0.0 0.0 0.05 0.0 112-113 9.75 0.0 0.0 0.05 0.0 114-115 10.45 0.0 0.0 0.05 0.0 116-117 11.35 0.0 0.0 0.05 0.0 118-119 12.25 0.0 0.0 0.05 0.0 120-121 13.275 0.0 0.0 0.05 0.0 122-123 14.45 0.0 0.0 0.05 0.0 124-125 15.175 0.0 0.0 0.05 0.0 126-127 16.1875 0.0 0.0 0.05 0.0 128-129 17.0125 0.0 0.0 0.05 0.0 130-131 17.675 0.0 0.0 0.05 0.0 132-133 18.7125 0.0 0.0 0.05 0.0 134-135 19.675 0.0 0.0 0.05 0.0 136-137 20.6875 0.0 0.0 0.05 0.0 138-139 21.450000000000003 0.0 0.0 0.05 0.0 >>END_MODULE >>Kmer Content pass >>END_MODULE SRR12670138 read2 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR12670138_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 36.292 37.0 37.0 37.0 37.0 37.0 2 36.0925 37.0 37.0 37.0 37.0 37.0 3 36.204 37.0 37.0 37.0 37.0 37.0 4 36.173 37.0 37.0 37.0 37.0 37.0 5 36.312 37.0 37.0 37.0 37.0 37.0 6 36.184 37.0 37.0 37.0 37.0 37.0 7 36.239 37.0 37.0 37.0 37.0 37.0 8 36.3 37.0 37.0 37.0 37.0 37.0 9 36.313 37.0 37.0 37.0 37.0 37.0 10-14 36.3431 37.0 37.0 37.0 37.0 37.0 15-19 36.3536 37.0 37.0 37.0 37.0 37.0 20-24 36.2873 37.0 37.0 37.0 37.0 37.0 25-29 36.226 37.0 37.0 37.0 37.0 37.0 30-34 36.2615 37.0 37.0 37.0 37.0 37.0 35-39 36.1941 37.0 37.0 37.0 37.0 37.0 40-44 36.23049999999999 37.0 37.0 37.0 37.0 37.0 45-49 36.2116 37.0 37.0 37.0 37.0 37.0 50-54 36.1211 37.0 37.0 37.0 37.0 37.0 55-59 36.0972 37.0 37.0 37.0 37.0 37.0 60-64 36.1367 37.0 37.0 37.0 37.0 37.0 65-69 36.091899999999995 37.0 37.0 37.0 37.0 37.0 70-74 36.1019 37.0 37.0 37.0 37.0 37.0 75-79 36.045100000000005 37.0 37.0 37.0 37.0 37.0 80-84 35.978100000000005 37.0 37.0 37.0 37.0 37.0 85-89 35.9808 37.0 37.0 37.0 37.0 37.0 90-94 35.9955 37.0 37.0 37.0 37.0 37.0 95-99 35.9391 37.0 37.0 37.0 37.0 37.0 100-104 35.933899999999994 37.0 37.0 37.0 37.0 37.0 105-109 35.849900000000005 37.0 37.0 37.0 37.0 37.0 110-114 35.751099999999994 37.0 37.0 37.0 37.0 37.0 115-119 35.818 37.0 37.0 37.0 37.0 37.0 120-124 35.6434 37.0 37.0 37.0 37.0 37.0 125-129 35.5443 37.0 37.0 37.0 37.0 37.0 130-134 35.268600000000006 37.0 37.0 37.0 32.2 37.0 135-139 35.1418 37.0 37.0 37.0 25.0 37.0 140-144 34.9387 37.0 37.0 37.0 25.0 37.0 145-149 34.6117 37.0 37.0 37.0 25.0 37.0 150-151 34.203125 37.0 37.0 37.0 25.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 13 1.0 14 0.0 15 1.0 16 0.0 17 0.0 18 2.0 19 1.0 20 3.0 21 1.0 22 4.0 23 2.0 24 7.0 25 3.0 26 8.0 27 8.0 28 16.0 29 20.0 30 31.0 31 48.0 32 65.0 33 97.0 34 245.0 35 596.0 36 2593.0 37 248.0 >>END_MODULE >>Per base sequence content warn #Base G A T C 1 33.925 22.025 13.025 31.025000000000002 2 27.375 27.075 30.475 15.075 3 20.674999999999997 28.025 32.125 19.175 4 23.599999999999998 34.675 23.974999999999998 17.75 5 25.15 37.675 21.875 15.299999999999999 6 20.7 40.475 22.825 16.0 7 21.45 21.3 36.775000000000006 20.474999999999998 8 21.9 25.724999999999998 27.150000000000002 25.224999999999998 9 23.375 25.224999999999998 29.049999999999997 22.35 10-14 23.82 28.884999999999998 25.895000000000003 21.4 15-19 22.895 28.985 26.69 21.43 20-24 22.99 28.315 27.265 21.43 25-29 22.935 28.73 27.175 21.16 30-34 22.99 29.28 26.845000000000002 20.885 35-39 23.115 28.63 27.155 21.099999999999998 40-44 23.189999999999998 28.499999999999996 27.01 21.3 45-49 23.155 28.54 27.224999999999998 21.08 50-54 23.830000000000002 27.63 27.485 21.055 55-59 23.36 27.200000000000003 27.87 21.57 60-64 23.46 27.575 27.35 21.615000000000002 65-69 22.650000000000002 27.565 27.965 21.82 70-74 23.7 28.23 26.82 21.25 75-79 22.919999999999998 28.18 27.755000000000003 21.145 80-84 23.835 28.38 26.384999999999998 21.4 85-89 24.04 28.27 26.91 20.78 90-94 24.474999999999998 27.639999999999997 26.919999999999998 20.965 95-99 24.46 28.485 26.669999999999998 20.385 100-104 25.324999999999996 27.88 26.240000000000002 20.555 105-109 24.845 28.720000000000002 26.029999999999998 20.405 110-114 25.615 28.235 26.784999999999997 19.365 115-119 25.96 28.395 26.484999999999996 19.16 120-124 26.525 27.534999999999997 25.924999999999997 20.015 125-129 26.46 28.265 25.759999999999998 19.515 130-134 27.985 27.485 26.025 18.505 135-139 27.455000000000002 27.185 26.85 18.509999999999998 140-144 28.744999999999997 25.624999999999996 26.965 18.665000000000003 145-149 29.247924792479246 26.347634763476346 27.04770477047705 17.356735673567357 150-151 29.59119889986248 25.153144143017876 26.915864483060382 18.33979247405926 >>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 0.5 7 1.0 8 0.5 9 0.0 10 0.0 11 0.5 12 1.5 13 1.5 14 0.5 15 0.0 16 0.0 17 0.0 18 0.0 19 0.0 20 0.0 21 1.0 22 1.5 23 0.5 24 0.0 25 0.5 26 2.0 27 2.5 28 2.0 29 7.0 30 11.5 31 10.5 32 13.0 33 25.5 34 33.5 35 44.5 36 75.0 37 98.0 38 139.0 39 168.0 40 195.0 41 236.0 42 253.0 43 289.0 44 285.0 45 266.5 46 269.5 47 260.5 48 248.5 49 209.0 50 169.0 51 134.5 52 111.0 53 95.0 54 75.5 55 65.0 56 49.0 57 44.5 58 35.5 59 18.0 60 11.0 61 7.0 62 9.5 63 7.5 64 2.0 65 1.0 66 1.5 67 1.0 68 0.0 69 0.0 70 0.5 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 0.5 84 0.5 85 0.0 86 0.0 87 0.0 88 0.0 89 0.5 90 0.5 91 0.5 92 0.5 93 0.5 94 0.5 95 0.0 96 0.0 97 0.5 98 1.0 99 1.0 100 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 0.01 150-151 0.0125 >>END_MODULE >>Sequence Length Distribution pass #Length Count 151 4000.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 80.925 #Duplication Level Percentage of deduplicated Percentage of total 1 82.39110287303059 66.675 2 13.191226444238493 21.349999999999998 3 3.3673154155081866 8.175 4 0.7414272474513438 2.4 5 0.18535681186283595 0.75 6 0.06178560395427865 0.3 7 0.06178560395427865 0.35000000000000003 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 CAGAGAACACATTCATACTCCAAGTCTTTTAGTTCATCCATTTAAGCTTA 7 0.17500000000000002 No Hit CTTGACTGGAGAAGTCCCTGGAGACTATGGTTACGATCCTTTTGGTCTCA 7 0.17500000000000002 No Hit GGCAAAGCGATTGGAGAATTACTATCCCATTCTTTTCCGTGGTGTCAACG 6 0.15 No Hit TGAAAGGCAGTATTTTTGACATCGAAGTTAAACCTGAAGACACGGTTGCT 6 0.15 No Hit GTGCCGGAGCATTTCCCAGGTTCCTTTACCATCAGTTCAGCCTCCGATAT 5 0.125 No Hit TCTTCACCCCCACGACCCTCTCCACCCTAAAATCAAGCAACCAAACCATT 5 0.125 No Hit TTTGCAACAGCAGCAACCTCAATTTTCAGATCCACCGACACTGCTGAGAG 5 0.125 No Hit TGGTTATATGGCTACCACGAATGGTATGCCAGTATCTCCAAATGGCTTCC 5 0.125 No Hit TGATCTCTTGGAGTCTGCACTCAAAACATACCAGAACTATTTTCATCTGA 5 0.125 No Hit AAATGATCTTCGCAAGGATGACGTGGAGAGTCTTAGATGTGCACTTGTTT 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 0.0 0.0 0.0 0.0 0.0 54-55 0.0 0.0 0.0 0.0 0.0 56-57 0.0 0.0 0.0 0.0 0.0 58-59 0.0125 0.0 0.0 0.0 0.0 60-61 0.025 0.0 0.0 0.0 0.0 62-63 0.025 0.0 0.0 0.0 0.0 64-65 0.1 0.0 0.0 0.0 0.0 66-67 0.125 0.0 0.0 0.0 0.0 68-69 0.1375 0.0 0.0 0.0 0.0 70-71 0.2125 0.0 0.0 0.0 0.0 72-73 0.325 0.0 0.0 0.0 0.0 74-75 0.3625 0.0 0.0 0.0 0.0 76-77 0.4375 0.0 0.0 0.0 0.0 78-79 0.6 0.0 0.0 0.0 0.0 80-81 0.7875 0.0 0.0 0.0 0.0 82-83 1.025 0.0 0.0 0.0 0.0 84-85 1.2374999999999998 0.0 0.0 0.0 0.0 86-87 1.4 0.0 0.0 0.0 0.0 88-89 1.75 0.0 0.0 0.0 0.0 90-91 2.1625 0.0 0.0 0.0 0.0 92-93 2.475 0.0 0.0 0.0 0.0 94-95 3.0999999999999996 0.0 0.0 0.0 0.0 96-97 3.7375 0.0 0.0 0.0 0.0 98-99 4.4625 0.0 0.0 0.0 0.0 100-101 5.0625 0.0 0.0 0.0 0.0 102-103 5.875 0.0 0.0 0.0 0.0 104-105 6.575 0.0 0.0 0.0 0.0 106-107 7.4125 0.0 0.0 0.0 0.0 108-109 8.1125 0.0 0.0 0.0 0.0 110-111 8.9125 0.0 0.0 0.0 0.0 112-113 9.775 0.0 0.0 0.0 0.0 114-115 10.4625 0.0 0.0 0.0 0.0 116-117 11.375 0.0 0.0 0.0 0.0 118-119 12.287500000000001 0.0 0.0 0.0 0.0 120-121 13.337499999999999 0.0 0.0 0.0 0.0 122-123 14.525 0.0 0.0 0.0 0.0 124-125 15.2625 0.0 0.0 0.0 0.0 126-127 16.325 0.0 0.0 0.0 0.0 128-129 17.2 0.0 0.0 0.0 0.0 130-131 17.875 0.0 0.0 0.0 0.0 132-133 18.8625 0.0 0.0 0.0 0.0 134-135 19.8375 0.0 0.0 0.0 0.0 136-137 20.8125 0.0 0.0 0.0 0.0 138-139 21.5875 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content pass >>END_MODULE Read 471820 spots for SRR12670138.sra Written 471820 spots for SRR12670138.sra Read 471820 spots for SRR12670138.sra Written 471820 spots for SRR12670138.sra Read 471820 spots for SRR12670138.sra Written 471820 spots for SRR12670138.sra Read 471820 spots for SRR12670138.sra Written 471820 spots for SRR12670138.sra Read 471820 spots for SRR12670138.sra Written 471820 spots for SRR12670138.sra Read 471820 spots for SRR12670138.sra Written 471820 spots for SRR12670138.sra Read 471820 spots for SRR12670138.sra Written 471820 spots for SRR12670138.sra Read 471820 spots for SRR12670138.sra Written 471820 spots for SRR12670138.sra Read 471820 spots for SRR12670138.sra Written 471820 spots for SRR12670138.sra Read 471820 spots for SRR12670138.sra Written 471820 spots for SRR12670138.sra Read 471820 spots for SRR12670138.sra Written 471820 spots for SRR12670138.sra Read 471820 spots for SRR12670138.sra Written 471820 spots for SRR12670138.sra Read 471820 spots for SRR12670138.sra Written 471820 spots for SRR12670138.sra Read 471820 spots for SRR12670138.sra Written 471820 spots for SRR12670138.sra Read 471820 spots for SRR12670138.sra Written 471820 spots for SRR12670138.sra Read 471820 spots for SRR12670138.sra Written 471820 spots for SRR12670138.sra Read 471820 spots for SRR12670138.sra Written 471820 spots for SRR12670138.sra Read 471831 spots for SRR12670138.sra Written 471831 spots for SRR12670138.sra Read 471820 spots for SRR12670138.sra Written 471820 spots for SRR12670138.sra Read 471820 spots for SRR12670138.sra Written 471820 spots for SRR12670138.sra SRR ids: ['SRR12670138.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_d7a47cai SRR12670138.sra spots: 9436411 blocks: [[1, 471820], [471821, 943640], [943641, 1415460], [1415461, 1887280], [1887281, 2359100], [2359101, 2830920], [2830921, 3302740], [3302741, 3774560], [3774561, 4246380], [4246381, 4718200], [4718201, 5190020], [5190021, 5661840], [5661841, 6133660], [6133661, 6605480], [6605481, 7077300], [7077301, 7549120], [7549121, 8020940], [8020941, 8492760], [8492761, 8964580], [8964581, 9436411]] SRR12670138 file size 3186305 SRR12670138 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 SRR12670138 SRR12670138_1.fastq SRR12670138_2.fastq Input file: SRR12670138_1.fastq Paired file: SRR12670138_2.fastq trimmed: SRR12670138-trimmed-pair1.fastq, SRR12670138-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 01:10:25 2025 >> started Tue Feb 11 01:10:37 2025 >> done (11.542s) 9436411 read pairs processed; of these: 18 ( 0.00%) short read pairs filtered out after trimming by size control 5425 ( 0.06%) empty read pairs filtered out after trimming by size control 9430968 (99.94%) read pairs available; of these: 2530595 (26.83%) trimmed read pairs available after processing 6900373 (73.17%) untrimmed read pairs available after processing Length distribution of reads after trimming: length count percentage 18 1 0.00% 19 0 0.00% 20 4 0.00% 21 0 0.00% 22 4 0.00% 23 9 0.00% 24 6 0.00% 25 7 0.00% 26 7 0.00% 27 5 0.00% 28 24 0.00% 29 19 0.00% 30 18 0.00% 31 31 0.00% 32 37 0.00% 33 39 0.00% 34 43 0.00% 35 49 0.00% 36 41 0.00% 37 59 0.00% 38 70 0.00% 39 87 0.00% 40 76 0.00% 41 109 0.00% 42 87 0.00% 43 97 0.00% 44 109 0.00% 45 115 0.00% 46 150 0.00% 47 194 0.00% 48 212 0.00% 49 242 0.00% 50 268 0.00% 51 292 0.00% 52 372 0.00% 53 412 0.00% 54 431 0.00% 55 465 0.00% 56 498 0.01% 57 589 0.01% 58 775 0.01% 59 858 0.01% 60 1080 0.01% 61 1193 0.01% 62 1303 0.01% 63 1515 0.02% 64 1675 0.02% 65 1905 0.02% 66 2010 0.02% 67 2247 0.02% 68 2449 0.03% 69 2821 0.03% 70 3274 0.03% 71 3717 0.04% 72 4255 0.05% 73 4819 0.05% 74 5220 0.06% 75 5725 0.06% 76 6393 0.07% 77 6810 0.07% 78 7216 0.08% 79 7914 0.08% 80 8887 0.09% 81 9772 0.10% 82 11069 0.12% 83 12196 0.13% 84 13258 0.14% 85 14733 0.16% 86 15147 0.16% 87 15877 0.17% 88 17049 0.18% 89 17564 0.19% 90 19137 0.20% 91 20112 0.21% 92 21420 0.23% 93 23398 0.25% 94 24489 0.26% 95 26203 0.28% 96 27151 0.29% 97 27818 0.29% 98 28431 0.30% 99 28676 0.30% 100 29911 0.32% 101 30406 0.32% 102 31623 0.34% 103 33156 0.35% 104 33715 0.36% 105 34994 0.37% 106 35987 0.38% 107 36439 0.39% 108 36680 0.39% 109 37233 0.39% 110 36731 0.39% 111 37145 0.39% 112 37659 0.40% 113 38624 0.41% 114 39520 0.42% 115 40380 0.43% 116 41181 0.44% 117 41360 0.44% 118 41656 0.44% 119 41341 0.44% 120 41383 0.44% 121 41196 0.44% 122 41898 0.44% 123 41723 0.44% 124 42278 0.45% 125 43357 0.46% 126 43418 0.46% 127 43852 0.46% 128 43403 0.46% 129 43500 0.46% 130 43218 0.46% 131 42991 0.46% 132 42318 0.45% 133 42781 0.45% 134 42759 0.45% 135 43296 0.46% 136 43676 0.46% 137 43582 0.46% 138 43362 0.46% 139 43767 0.46% 140 43275 0.46% 141 43565 0.46% 142 43302 0.46% 143 42494 0.45% 144 42950 0.46% 145 42889 0.45% 146 43409 0.46% 147 43008 0.46% 148 43066 0.46% 149 43046 0.46% 150 43253 0.46% 151 6900373 73.17% 9430968 reads passed initial QC criterion=sequence-density sequence-density=0.44 sequence-density-rank=1 fanout-score=2.24 fanout-score-rank=32 prefix-density=0.46 prefix-fanout=2.1 sequence=TGAGATGCCTCAGTGCATCCAAACATGGGTAGCTTCCACATAGTCCAGTAGCGTCCATCATAGTACCCTGGTGAGCTGTGGTGCTCACGGTAGACCCAACCTTTCTCCAACTCGAATTCCAAGCAAGGAACCCACTTCGAGCGAAGAAGGTAATCAATTTCCTTGGCCAATTCCTCCTCTGTGAGATCTGGAAGGTAAGAAAGAGTCTCGAACTTCTTCAATCCAGTTGGTGGCCACACCTGCATGCATTGAACTCGTCCACCATTGCTTGCAATGGAAGTAATGTCATTAGCCTTTCTGGTACTGACTGGGAAAGCTGCGGCAGACTTGAGACCATTGAATGGTGCCACCAT criterion=fanout-score sequence-density=0.03 sequence-density-rank=35 fanout-score=125.78 fanout-score-rank=1 prefix-density=0.28 prefix-fanout=11.8 sequence=TGAAGAAGACACAAAGATAAAGACACTCACGGACACTTTTGTTTGTTCACTCCACACCCACAAGTACAGAAGAACACAGATTATTTATCAGAAATTACATTATTAATCCACTCCCAATCCCACATCAAACATGATAGTTGATGTGCTTGCTTAATGACCGCATGTGCAGGTAGTGCAAGTGCAGCCAGTACCGCAGTTGCACTTGCCATCGTTCTCAGCTGCTGGCACCTCCATGACTACGGAGGAGACATAGTTCTTCTCAGTCTCGACGATGCCAGCAGTGTAGCTGCTTCCCTTCTTGACACACTGGGTCTTGTCAGCGCAGTCGCAGGTGTCGCAGGTGCTAGACATGATGATTGATTGATTAAGCTTAAATGGATGAACTAAAAGACTTGGAGTATGAATGTGTTCTCTGTGTA criterion=sequence-density sequence-density=0.80 sequence-density-rank=1 fanout-score=1.98 fanout-score-rank=33 prefix-density=0.81 prefix-fanout=2.0 sequence=AACCGCACCCCGGCACA criterion=fanout-score sequence-density=0.09 sequence-density-rank=32 fanout-score=16.11 fanout-score-rank=1 prefix-density=0.22 prefix-fanout=7.0 sequence=AGAGAATGGCCACCA SRR12670138 testing PE reads STAR mapping to Ensembl genome Started job on | Feb 11 01:11:19 Started mapping on | Feb 11 01:11:19 Finished on | Feb 11 01:12:25 Mapping speed, Million of reads per hour | 514.42 Number of input reads | 9430968 Average input read length | 284 UNIQUE READS: Uniquely mapped reads number | 8928658 Uniquely mapped reads % | 94.67% Average mapped length | 283.76 Number of splices: Total | 8712151 Number of splices: Annotated (sjdb) | 8539464 Number of splices: GT/AG | 8539154 Number of splices: GC/AG | 143751 Number of splices: AT/AC | 5210 Number of splices: Non-canonical | 24036 Mismatch rate per base, % | 0.35% Deletion rate per base | 0.02% Deletion average length | 2.90 Insertion rate per base | 0.02% Insertion average length | 2.42 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 203551 % of reads mapped to multiple loci | 2.16% Number of reads mapped to too many loci | 19310 % of reads mapped to too many loci | 0.20% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 2.89% % of reads unmapped: other | 0.08% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 298759 298759 298759 N_multimapping 203551 203551 203551 N_noFeature 235146 8799722 285312 N_ambiguous 131639 504 52582 UnstrandedReadsAssigned:8561873 PositiveStrandReadsAssigned:128432 NegativeStrandReadsAssigned:8590764 Dataset is classified negative stranded MeadianReadLen=151 20thPercentileLength=135 echo kmer=131 SRR12670138 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: SRR12670138-trimmed-pair1.fastq SRR12670138-trimmed-pair2.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 9,430,968 reads, 8,579,100 reads pseudoaligned [quant] estimated average fragment length: 210.809 [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,021 rounds 52401 SRR12670138.ke.tsv 34699 SRR12670138.se.tsv 87100 total ==> SRR12670138.ke.tsv <== target_id length eff_length est_counts tpm Potri.005G200100.1.v4.1 2018 1808.19 317 19.926 Potri.005G024800.1.v4.1 1035 825.191 108 14.8756 Potri.004G059700.1.v4.1 961 751.24 6 0.907775 Potri.007G009000.2.v4.1 1416 1206.19 0 0 Potri.003G141000.2.v4.1 2943 2733.19 494 20.543 Potri.016G087400.1.v4.1 270 108.973 445 464.14 Potri.015G069301.1.v4.1 564 362.109 0 0 Potri.010G195200.1.v4.1 1773 1563.19 23 1.67233 Potri.012G127500.1.v4.1 977 767.216 24 3.55549 ==> SRR12670138.se.tsv <== Potri.001G166300.v4.1 0 Potri.001G448400.v4.1 101 Potri.001G233950.v4.1 0 Potri.001G122700.v4.1 122 Potri.001G212900.v4.1 1 Potri.001G182400.v4.1 0 Potri.001G256600.v4.1 0 Potri.001G040500.v4.1 0 Potri.001G416900.v4.1 0 Potri.001G452600.v4.1 3 SRR12670138 completed mapping pipeline successfully