Starting /dee2/code/volunteer_pipeline.sh SRR12671410 current disk space = 3052306247680 free memory = 1457263652 SRR12671410 SRAfilesize 62b9ec098c46c1255ab608a2dd4aad16 SRR12671410.sra SRR12671410.sra file validated SRR12671410 is paired end SRR12671410 is conventional basespace SRR12671410 read1 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR12671410_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 43 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 36.6075 37.0 37.0 37.0 37.0 37.0 2 36.31025 37.0 37.0 37.0 37.0 37.0 3 36.564 37.0 37.0 37.0 37.0 37.0 4 36.599 37.0 37.0 37.0 37.0 37.0 5 36.5885 37.0 37.0 37.0 37.0 37.0 6 36.577 37.0 37.0 37.0 37.0 37.0 7 36.6045 37.0 37.0 37.0 37.0 37.0 8 36.585 37.0 37.0 37.0 37.0 37.0 9 36.621 37.0 37.0 37.0 37.0 37.0 10-14 36.615500000000004 37.0 37.0 37.0 37.0 37.0 15-19 36.601400000000005 37.0 37.0 37.0 37.0 37.0 20-24 36.5852 37.0 37.0 37.0 37.0 37.0 25-29 36.522200000000005 37.0 37.0 37.0 37.0 37.0 30-34 36.53340000000001 37.0 37.0 37.0 37.0 37.0 35-39 36.471599999999995 37.0 37.0 37.0 37.0 37.0 40-44 36.4581 37.0 37.0 37.0 37.0 37.0 45-49 36.423 37.0 37.0 37.0 37.0 37.0 50-54 36.4051 37.0 37.0 37.0 37.0 37.0 55-59 36.3732 37.0 37.0 37.0 37.0 37.0 60-64 36.3729 37.0 37.0 37.0 37.0 37.0 65-69 36.3024 37.0 37.0 37.0 37.0 37.0 70-74 36.289699999999996 37.0 37.0 37.0 37.0 37.0 75-79 36.313900000000004 37.0 37.0 37.0 37.0 37.0 80-84 36.283899999999996 37.0 37.0 37.0 37.0 37.0 85-89 36.2152 37.0 37.0 37.0 37.0 37.0 90-94 36.2342 37.0 37.0 37.0 37.0 37.0 95-99 36.199 37.0 37.0 37.0 37.0 37.0 100-104 36.1843 37.0 37.0 37.0 37.0 37.0 105-109 36.192899999999995 37.0 37.0 37.0 37.0 37.0 110-114 36.073499999999996 37.0 37.0 37.0 37.0 37.0 115-119 36.1178 37.0 37.0 37.0 37.0 37.0 120-124 36.0701 37.0 37.0 37.0 37.0 37.0 125-129 36.04279999999999 37.0 37.0 37.0 37.0 37.0 130-134 36.050799999999995 37.0 37.0 37.0 37.0 37.0 135-139 35.9869 37.0 37.0 37.0 37.0 37.0 140-144 35.937 37.0 37.0 37.0 37.0 37.0 145-149 35.940000000000005 37.0 37.0 37.0 37.0 37.0 150-151 35.845 37.0 37.0 37.0 37.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 18 2.0 19 0.0 20 2.0 21 1.0 22 1.0 23 2.0 24 2.0 25 5.0 26 6.0 27 7.0 28 8.0 29 15.0 30 22.0 31 41.0 32 45.0 33 63.0 34 104.0 35 245.0 36 2958.0 37 471.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 53.25 10.925 5.375 30.45 2 20.57272042200452 12.057272042200452 36.222054760110524 31.1479527756845 3 17.8 18.525 29.825000000000003 33.85 4 25.2 24.099999999999998 25.650000000000002 25.05 5 22.85 33.050000000000004 24.425 19.675 6 18.7 35.825 24.9 20.575 7 15.975 24.25 44.35 15.425 8 15.5 26.025 33.35 25.124999999999996 9 17.1 22.75 35.449999999999996 24.7 10-14 19.485 29.54 28.37 22.605 15-19 19.855 28.575 28.23 23.34 20-24 20.32 28.615000000000002 27.639999999999997 23.425 25-29 20.07 28.925 28.125 22.88 30-34 19.84 28.985 27.93 23.244999999999997 35-39 20.46 28.115000000000002 28.285 23.14 40-44 19.965 29.085 28.494999999999997 22.455 45-49 20.685000000000002 28.12 27.439999999999998 23.755000000000003 50-54 20.59 29.125 27.11 23.175 55-59 19.54 28.865000000000002 27.465 24.13 60-64 20.630000000000003 28.665000000000003 27.54 23.165 65-69 20.330000000000002 28.62 28.63 22.42 70-74 20.44 28.48 27.35 23.73 75-79 20.36 28.499999999999996 27.644999999999996 23.494999999999997 80-84 20.585 28.59 27.644999999999996 23.18 85-89 20.54 28.42 28.000000000000004 23.04 90-94 20.22 28.825 27.365000000000002 23.59 95-99 20.075000000000003 28.37 27.794999999999998 23.76 100-104 20.965 28.139999999999997 28.275 22.62 105-109 21.085 28.605000000000004 27.575 22.735 110-114 20.41 28.37 27.825 23.395 115-119 20.330000000000002 28.155 27.655 23.86 120-124 20.64 28.470000000000002 27.57 23.32 125-129 20.96 27.985 27.365000000000002 23.69 130-134 20.155 29.13 26.779999999999998 23.935000000000002 135-139 21.235 28.93 27.235 22.6 140-144 20.755000000000003 28.465 27.215 23.565 145-149 21.08 28.544999999999998 27.065 23.31 150-151 19.825 29.0875 27.237499999999997 23.849999999999998 >>END_MODULE >>Per sequence GC content pass #GC Content Count 0 1.0 1 1.0 2 0.5 3 0.5 4 1.0 5 0.5 6 0.0 7 0.0 8 0.0 9 0.5 10 0.5 11 3.0 12 3.5 13 0.5 14 0.0 15 0.0 16 1.0 17 2.0 18 4.0 19 3.0 20 4.0 21 4.5 22 0.5 23 4.0 24 6.5 25 7.0 26 9.5 27 10.5 28 13.5 29 15.5 30 16.5 31 23.0 32 34.0 33 51.0 34 67.0 35 74.0 36 75.0 37 97.0 38 133.5 39 159.5 40 172.5 41 191.0 42 234.5 43 262.5 44 261.5 45 254.5 46 260.0 47 251.5 48 228.5 49 212.0 50 175.0 51 136.5 52 124.0 53 108.5 54 70.5 55 52.0 56 49.5 57 33.5 58 26.5 59 29.0 60 18.0 61 4.0 62 3.5 63 5.0 64 2.0 65 2.0 66 2.0 67 0.0 68 0.0 69 0.0 70 0.0 71 0.0 72 0.0 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 0.5 99 0.5 100 0.0 >>END_MODULE >>Per base N content pass #Base N-Count 1 0.0 2 0.475 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 81.125 #Duplication Level Percentage of deduplicated Percentage of total 1 82.43451463790447 66.875 2 13.405238828967642 21.75 3 3.0816640986132513 7.5 4 0.7395993836671803 2.4 5 0.2465331278890601 1.0 6 0.061633281972265024 0.3 7 0.030816640986132512 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 CTCGTGGACACTGTATTCAGCGGCAAGGTTAAAAACAGTCCCTGCCTCTC 7 0.17500000000000002 No Hit TGAAAGTAATAGATAGCCCTGGTGCTTTGAGCTCACAGCTTTTACCGCTA 6 0.15 No Hit ATATGAGCACAGTAAATATGAAAAGACTCATTCCACCTGGGGTTGGTTGC 6 0.15 No Hit GAATGAACTCTTTCACAAATCTCAATTGAATGAGATTTTAGGAAGCTGAA 5 0.125 No Hit GCTGATTGACTACCTATAGAGTACACCTACTGTGCTCCATGAGATGATTA 5 0.125 No Hit GTCTATTCCTATCCCCAAACAGGCAAGAATGAGCCCTAATGAAATTTAAG 5 0.125 No Hit GAGAAAATCCACACAAAATAAAGCAACCTGTAACTTGAGTGACAGAGGAA 5 0.125 No Hit AGGCAACGACGAAGATATTTCTCATCGATTGTTGTTATATGCTTTGGAAT 5 0.125 No Hit GGCCCAACCTTGGGGTATCAACTGTAAGAGCAATAGCCTTGAAACCAGCC 5 0.125 No Hit GCATACTCTACTGCTGCCCCAACTCCAGCGTACTTAGTCTTATCGTATGG 5 0.125 No Hit CCACTATATGCTCTCGTCTGCATCTGTAAGATTTTAGTGAGGCCCTGAAA 5 0.125 No Hit >>END_MODULE >>Adapter Content pass #Position Illumina Universal Adapter Illumina Small RNA 3' Adapter Illumina Small RNA 5' Adapter Nextera Transposase Sequence SOLID Small RNA Adapter 1 0.0 0.0 0.0 0.0 0.0 2 0.0 0.0 0.0 0.0 0.0 3 0.0 0.0 0.0 0.0 0.0 4 0.0 0.0 0.0 0.0 0.0 5 0.0 0.0 0.0 0.0 0.0 6 0.0 0.0 0.0 0.0 0.0 7 0.0 0.0 0.0 0.0 0.0 8 0.0 0.0 0.0 0.0 0.0 9 0.0 0.0 0.0 0.0 0.0 10-11 0.0 0.0 0.0 0.0 0.0 12-13 0.0 0.0 0.0 0.0 0.0 14-15 0.0 0.0 0.0 0.0 0.0 16-17 0.0 0.0 0.0 0.0 0.0 18-19 0.0 0.0 0.0 0.0 0.0 20-21 0.0 0.0 0.0 0.0 0.0 22-23 0.0 0.0 0.0 0.0 0.0 24-25 0.0 0.0 0.0 0.0 0.0 26-27 0.0 0.0 0.0 0.0 0.0 28-29 0.0 0.0 0.0 0.0 0.0 30-31 0.0 0.0 0.0 0.0 0.0 32-33 0.0 0.0 0.0 0.0 0.0 34-35 0.0 0.0 0.0 0.0 0.0 36-37 0.0 0.0 0.0 0.0 0.0 38-39 0.0 0.0 0.0 0.0 0.0 40-41 0.0 0.0 0.0 0.0 0.0 42-43 0.0 0.0 0.0 0.0 0.0 44-45 0.0 0.0 0.0 0.0 0.0 46-47 0.0 0.0 0.0 0.0 0.0 48-49 0.0 0.0 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 0.0 0.0 0.0 0.0 0.0 60-61 0.0 0.0 0.0 0.0 0.0 62-63 0.0 0.0 0.0 0.0 0.0 64-65 0.0 0.0 0.0 0.0 0.0 66-67 0.0 0.0 0.0 0.0 0.0 68-69 0.0 0.0 0.0 0.0 0.0 70-71 0.025 0.0 0.0 0.0 0.0 72-73 0.025 0.0 0.0 0.0 0.0 74-75 0.025 0.0 0.0 0.0 0.0 76-77 0.1125 0.0 0.0 0.0 0.0 78-79 0.125 0.0 0.0 0.0 0.0 80-81 0.1375 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 0.2625 0.0 0.0 0.0 0.0 88-89 0.3125 0.0 0.0 0.0 0.0 90-91 0.325 0.0 0.0 0.0 0.0 92-93 0.35 0.0 0.0 0.0 0.0 94-95 0.3875 0.0 0.0 0.0 0.0 96-97 0.5125 0.0 0.0 0.0 0.0 98-99 0.6 0.0 0.0 0.0 0.0 100-101 0.675 0.0 0.0 0.0 0.0 102-103 0.675 0.0 0.0 0.0 0.0 104-105 0.7 0.0 0.0 0.0 0.0 106-107 0.75 0.0 0.0 0.0 0.0 108-109 0.8125 0.0 0.0 0.0 0.0 110-111 0.9125 0.0 0.0 0.0 0.0 112-113 0.975 0.0 0.0 0.0 0.0 114-115 1.1125 0.0 0.0 0.0 0.0 116-117 1.2625 0.0 0.0 0.0 0.0 118-119 1.3 0.0 0.0 0.0 0.0 120-121 1.35 0.0 0.0 0.0 0.0 122-123 1.4500000000000002 0.0 0.0 0.0 0.0 124-125 1.6 0.0 0.0 0.0 0.0 126-127 1.6875 0.0 0.0 0.0 0.0 128-129 1.8250000000000002 0.0 0.0 0.0 0.0 130-131 1.8875 0.0 0.0 0.0 0.0 132-133 2.1625 0.0 0.0 0.0 0.0 134-135 2.5 0.0 0.0 0.0 0.0 136-137 2.7375 0.0 0.0 0.0 0.0 138-139 2.8375 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position GATACTT 10 0.006830828 145.0 5 TGATACT 10 0.006830828 145.0 4 GATCTAG 10 0.006830828 145.0 5 TTGAACC 10 0.006830828 145.0 7 >>END_MODULE SRR12671410 read2 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR12671410_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 36.2325 37.0 37.0 37.0 37.0 37.0 2 35.9305 37.0 37.0 37.0 37.0 37.0 3 36.2275 37.0 37.0 37.0 37.0 37.0 4 36.213 37.0 37.0 37.0 37.0 37.0 5 36.2315 37.0 37.0 37.0 37.0 37.0 6 36.2565 37.0 37.0 37.0 37.0 37.0 7 36.1315 37.0 37.0 37.0 37.0 37.0 8 36.2 37.0 37.0 37.0 37.0 37.0 9 36.201 37.0 37.0 37.0 37.0 37.0 10-14 36.2267 37.0 37.0 37.0 37.0 37.0 15-19 36.210699999999996 37.0 37.0 37.0 37.0 37.0 20-24 36.136900000000004 37.0 37.0 37.0 37.0 37.0 25-29 36.0774 37.0 37.0 37.0 37.0 37.0 30-34 36.0984 37.0 37.0 37.0 37.0 37.0 35-39 36.0285 37.0 37.0 37.0 37.0 37.0 40-44 36.0445 37.0 37.0 37.0 37.0 37.0 45-49 36.0583 37.0 37.0 37.0 37.0 37.0 50-54 35.962199999999996 37.0 37.0 37.0 37.0 37.0 55-59 35.9127 37.0 37.0 37.0 37.0 37.0 60-64 35.936099999999996 37.0 37.0 37.0 37.0 37.0 65-69 35.970299999999995 37.0 37.0 37.0 37.0 37.0 70-74 35.926300000000005 37.0 37.0 37.0 37.0 37.0 75-79 35.898900000000005 37.0 37.0 37.0 37.0 37.0 80-84 35.81 37.0 37.0 37.0 37.0 37.0 85-89 35.8886 37.0 37.0 37.0 37.0 37.0 90-94 35.839600000000004 37.0 37.0 37.0 37.0 37.0 95-99 35.8106 37.0 37.0 37.0 37.0 37.0 100-104 35.7299 37.0 37.0 37.0 37.0 37.0 105-109 35.6711 37.0 37.0 37.0 37.0 37.0 110-114 35.6931 37.0 37.0 37.0 37.0 37.0 115-119 35.7282 37.0 37.0 37.0 37.0 37.0 120-124 35.706900000000005 37.0 37.0 37.0 37.0 37.0 125-129 35.726099999999995 37.0 37.0 37.0 37.0 37.0 130-134 35.5783 37.0 37.0 37.0 37.0 37.0 135-139 35.5264 37.0 37.0 37.0 37.0 37.0 140-144 35.5111 37.0 37.0 37.0 37.0 37.0 145-149 35.500299999999996 37.0 37.0 37.0 37.0 37.0 150-151 35.25725 37.0 37.0 37.0 31.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 12 1.0 13 4.0 14 6.0 15 2.0 16 2.0 17 3.0 18 2.0 19 2.0 20 1.0 21 5.0 22 8.0 23 7.0 24 9.0 25 5.0 26 9.0 27 11.0 28 13.0 29 16.0 30 22.0 31 39.0 32 49.0 33 104.0 34 169.0 35 493.0 36 2746.0 37 272.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 51.5 21.925 7.425 19.15 2 27.3 23.45 31.7 17.549999999999997 3 21.05 25.374999999999996 33.5 20.075000000000003 4 25.05 32.925 23.525 18.5 5 25.4 37.475 21.375 15.75 6 20.200000000000003 40.65 21.425 17.724999999999998 7 19.3 22.525000000000002 39.050000000000004 19.125 8 18.625 25.55 27.525 28.299999999999997 9 22.125 24.925 29.275000000000002 23.674999999999997 10-14 22.915 28.845 26.950000000000003 21.29 15-19 23.22 27.634999999999998 27.560000000000002 21.584999999999997 20-24 22.5 28.975 27.29 21.235 25-29 22.830000000000002 27.63 27.894999999999996 21.645 30-34 22.605 28.110000000000003 27.76 21.525 35-39 22.955000000000002 27.534999999999997 27.665 21.845 40-44 22.945 28.265 27.33 21.46 45-49 22.720000000000002 28.235 28.000000000000004 21.044999999999998 50-54 23.200000000000003 27.63 28.33 20.84 55-59 22.53 27.265 28.65 21.555 60-64 23.22 27.275 27.700000000000003 21.805 65-69 23.145 27.185 28.000000000000004 21.67 70-74 22.715 27.875 28.18 21.23 75-79 23.599999999999998 27.365000000000002 27.994999999999997 21.04 80-84 23.68 28.494999999999997 26.82 21.005 85-89 23.635 28.215 27.325 20.825 90-94 23.575 28.189999999999998 27.49 20.745 95-99 22.445 28.105000000000004 28.02 21.43 100-104 23.565 27.625 27.605 21.205 105-109 23.330000000000002 27.825 28.37 20.474999999999998 110-114 22.93 28.29 27.74 21.04 115-119 23.830000000000002 28.299999999999997 27.35 20.52 120-124 24.169999999999998 27.339999999999996 27.66 20.830000000000002 125-129 24.11 27.74 27.450000000000003 20.7 130-134 24.05 27.955000000000002 27.58 20.415 135-139 24.0 28.07 27.529999999999998 20.4 140-144 22.865 28.439999999999998 27.750000000000004 20.945 145-149 24.877463238971693 27.628288486545966 26.868060418125438 20.626187856356907 150-151 24.0375 27.6375 26.8 21.525 >>END_MODULE >>Per sequence GC content warn #GC Content Count 0 0.0 1 0.5 2 0.5 3 0.0 4 0.0 5 0.5 6 0.5 7 0.0 8 0.5 9 1.0 10 1.0 11 0.5 12 1.0 13 2.5 14 2.5 15 1.5 16 0.5 17 0.5 18 1.0 19 1.5 20 1.5 21 0.5 22 1.0 23 2.5 24 2.5 25 4.0 26 4.5 27 5.5 28 12.0 29 13.5 30 10.5 31 9.5 32 21.0 33 33.0 34 39.0 35 60.5 36 75.0 37 112.0 38 142.0 39 155.5 40 191.0 41 215.0 42 230.0 43 240.5 44 268.5 45 301.5 46 282.0 47 240.0 48 233.0 49 211.5 50 162.5 51 135.5 52 125.0 53 103.0 54 80.5 55 65.0 56 55.0 57 39.0 58 21.0 59 16.0 60 12.5 61 9.5 62 8.0 63 7.0 64 4.0 65 2.5 66 1.5 67 2.0 68 2.0 69 0.5 70 1.0 71 1.0 72 0.5 73 0.0 74 0.0 75 0.0 76 0.0 77 0.5 78 0.5 79 0.0 80 0.0 81 0.0 82 0.5 83 0.5 84 0.0 85 0.5 86 0.5 87 0.5 88 0.5 89 0.0 90 0.0 91 0.5 92 0.5 93 0.0 94 0.0 95 0.5 96 0.5 97 0.0 98 0.0 99 0.0 100 2.5 >>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 0.03 150-151 0.0 >>END_MODULE >>Sequence Length Distribution pass #Length Count 151 4000.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 81.8 #Duplication Level Percentage of deduplicated Percentage of total 1 83.74083129584352 68.5 2 12.224938875305623 20.0 3 2.8422982885085575 6.9750000000000005 4 0.7029339853300733 2.3 5 0.3361858190709046 1.375 6 0.061124694376528114 0.3 7 0.061124694376528114 0.35000000000000003 8 0.030562347188264057 0.2 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 GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG 8 0.2 No Hit AGGGAGCACTGCATAGCTTATAAGCTTGTAAGAGATGGCTTCCTCCTCTA 7 0.17500000000000002 No Hit CGCAGATCCATGAGCTCCTCAATGTATTTGATACCGATGGTGATGGGATT 7 0.17500000000000002 No Hit TCTTATAGCTACCATTGCCTTCTCTCCCTTATCCATGGCAGCTCGAGAAT 6 0.15 No Hit AGAACACATTCATACCCCAAGTCTTTTAGTTCATCCATTTAAGCTTAATC 6 0.15 No Hit GCTATAGCTAAGCACACAAATTAAGGCTTAAAGATATAGAGAGAAAGAAA 5 0.125 No Hit GGAGTACGAGGCCATCGCCAAGCAAAAGTTACCAAAGATGGTCTTTGACT 5 0.125 No Hit CATCTTCTGACCCCAAGGCATTCGATCCTGTTGAGAAGATTAAATCCGGC 5 0.125 No Hit AGAGAACACATTCATACCCCAAGTCTTTTAGTTCATCCATTTAAGCTTAA 5 0.125 No Hit GCCTACCCTGGCGGACCCTTGTTTAACCCCCTTGGATTTGGGAAAGACGA 5 0.125 No Hit GGAGCACTGCATAGCTTATAAGCTTGTAAGAGATGGCTTCCTCCTCTATG 5 0.125 No Hit TGAAAGCATACTAGTCAGCAAACAGGATTACAGTGTCCATAATTTGATAT 5 0.125 No Hit GGGAGCACTGCATAGCTTATAAGCTTGTAAGAGATGGCTTCCTCCTCTAT 5 0.125 No Hit GGAAAGACAACCCTAATTAAAATGCTTCTCCGTCTCTATGATCCTTTACA 5 0.125 No Hit CACGTGGGAAAGCTGCGTTAAAGAGGGGAATAAAGATGGCTGAAGAATTC 5 0.125 No Hit GTTGTGAAGTCATTTCCCCCCCTTCTTCGGTGTGTTCTTTACGTGTTTCT 5 0.125 No Hit >>END_MODULE >>Adapter Content pass #Position Illumina Universal Adapter Illumina Small RNA 3' Adapter Illumina Small RNA 5' Adapter Nextera Transposase Sequence SOLID Small RNA Adapter 1 0.0 0.0 0.0 0.0 0.0 2 0.0 0.0 0.0 0.0 0.0 3 0.0 0.0 0.0 0.0 0.0 4 0.0 0.0 0.0 0.0 0.0 5 0.0 0.0 0.0 0.0 0.0 6 0.0 0.0 0.0 0.0 0.0 7 0.0 0.0 0.0 0.0 0.0 8 0.0 0.0 0.0 0.0 0.0 9 0.0 0.0 0.0 0.0 0.0 10-11 0.0 0.0 0.0 0.0 0.0 12-13 0.0 0.0 0.0 0.0 0.0 14-15 0.0 0.0 0.0 0.0 0.0 16-17 0.0 0.0 0.0 0.0 0.0 18-19 0.0 0.0 0.0 0.0 0.0 20-21 0.0 0.0 0.0 0.0 0.0 22-23 0.0 0.0 0.0 0.0 0.0 24-25 0.0 0.0 0.0 0.0 0.0 26-27 0.0 0.0 0.0 0.0 0.0 28-29 0.0 0.0 0.0 0.0 0.0 30-31 0.0 0.0 0.0 0.0 0.0 32-33 0.0 0.0 0.0 0.0 0.0 34-35 0.0 0.0 0.0 0.0 0.0 36-37 0.025 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 0.025 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 0.025 0.0 0.0 0.0 0.0 66-67 0.025 0.0 0.0 0.0 0.0 68-69 0.025 0.0 0.0 0.0 0.0 70-71 0.05 0.0 0.0 0.0 0.0 72-73 0.05 0.0 0.0 0.0 0.0 74-75 0.05 0.0 0.0 0.0 0.0 76-77 0.1375 0.0 0.0 0.0 0.0 78-79 0.15 0.0 0.0 0.0 0.0 80-81 0.16249999999999998 0.0 0.0 0.0 0.0 82-83 0.225 0.0 0.0 0.0 0.0 84-85 0.275 0.0 0.0 0.0 0.0 86-87 0.2875 0.0 0.0 0.0 0.0 88-89 0.325 0.0 0.0 0.0 0.0 90-91 0.325 0.0 0.0 0.0 0.0 92-93 0.35 0.0 0.0 0.0 0.0 94-95 0.3875 0.0 0.0 0.0 0.0 96-97 0.5125 0.0 0.0 0.0 0.0 98-99 0.6 0.0 0.0 0.0 0.0 100-101 0.675 0.0 0.0 0.0 0.0 102-103 0.675 0.0 0.0 0.0 0.0 104-105 0.7 0.0 0.0 0.0 0.0 106-107 0.7625 0.0 0.0 0.0 0.0 108-109 0.8625 0.0 0.0 0.0 0.0 110-111 0.9874999999999999 0.0 0.0 0.0 0.0 112-113 1.0499999999999998 0.0 0.0 0.0 0.0 114-115 1.2000000000000002 0.0 0.0 0.0 0.0 116-117 1.3625 0.0 0.0 0.0 0.0 118-119 1.4 0.0 0.0 0.0 0.0 120-121 1.45 0.0 0.0 0.0 0.0 122-123 1.5375 0.0 0.0 0.0 0.0 124-125 1.6625 0.0 0.0 0.0 0.0 126-127 1.7374999999999998 0.0 0.0 0.0 0.0 128-129 1.875 0.0 0.0 0.0 0.0 130-131 1.9375 0.0 0.0 0.0 0.0 132-133 2.2125 0.0 0.0 0.0 0.0 134-135 2.55 0.0 0.0 0.0 0.0 136-137 2.7875 0.0 0.0 0.0 0.0 138-139 2.8875 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position ACACATC 10 0.006830828 145.0 145 ACATATA 10 0.006830828 145.0 4 TAATCAA 10 0.006830828 145.0 4 ATATATT 10 0.006830828 145.0 6 GAAGAGA 20 0.00593511 29.0 85-89 >>END_MODULE Read 1935818 spots for SRR12671410.sra Written 1935818 spots for SRR12671410.sra Read 1935818 spots for SRR12671410.sra Written 1935818 spots for SRR12671410.sra Read 1935818 spots for SRR12671410.sra Written 1935818 spots for SRR12671410.sra Read 1935824 spots for SRR12671410.sra Written 1935824 spots for SRR12671410.sra Read 1935818 spots for SRR12671410.sra Written 1935818 spots for SRR12671410.sra Read 1935818 spots for SRR12671410.sra Written 1935818 spots for SRR12671410.sra Read 1935818 spots for SRR12671410.sra Written 1935818 spots for SRR12671410.sra Read 1935818 spots for SRR12671410.sra Written 1935818 spots for SRR12671410.sra Read 1935818 spots for SRR12671410.sra Written 1935818 spots for SRR12671410.sra Read 1935818 spots for SRR12671410.sra Written 1935818 spots for SRR12671410.sra Read 1935818 spots for SRR12671410.sra Written 1935818 spots for SRR12671410.sra Read 1935818 spots for SRR12671410.sra Written 1935818 spots for SRR12671410.sra Read 1935818 spots for SRR12671410.sra Written 1935818 spots for SRR12671410.sra Read 1935818 spots for SRR12671410.sra Written 1935818 spots for SRR12671410.sra Read 1935818 spots for SRR12671410.sra Written 1935818 spots for SRR12671410.sra Read 1935818 spots for SRR12671410.sra Written 1935818 spots for SRR12671410.sra Read 1935818 spots for SRR12671410.sra Written 1935818 spots for SRR12671410.sra Read 1935818 spots for SRR12671410.sra Written 1935818 spots for SRR12671410.sra Read 1935818 spots for SRR12671410.sra Written 1935818 spots for SRR12671410.sra Read 1935818 spots for SRR12671410.sra Written 1935818 spots for SRR12671410.sra SRR ids: ['SRR12671410.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_dree_mzt SRR12671410.sra spots: 38716366 blocks: [[1, 1935818], [1935819, 3871636], [3871637, 5807454], [5807455, 7743272], [7743273, 9679090], [9679091, 11614908], [11614909, 13550726], [13550727, 15486544], [15486545, 17422362], [17422363, 19358180], [19358181, 21293998], [21293999, 23229816], [23229817, 25165634], [25165635, 27101452], [27101453, 29037270], [29037271, 30973088], [30973089, 32908906], [32908907, 34844724], [34844725, 36780542], [36780543, 38716366]] SRR12671410 file size 13135814 SRR12671410 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 SRR12671410 SRR12671410_1.fastq SRR12671410_2.fastq Input file: SRR12671410_1.fastq Paired file: SRR12671410_2.fastq trimmed: SRR12671410-trimmed-pair1.fastq, SRR12671410-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 22:28:00 2025 >> started Tue Feb 11 22:28:44 2025 >> done (44.835s) 38716366 read pairs processed; of these: 335 ( 0.00%) short read pairs filtered out after trimming by size control 12090 ( 0.03%) empty read pairs filtered out after trimming by size control 38703941 (99.97%) read pairs available; of these: 1787271 ( 4.62%) trimmed read pairs available after processing 36916670 (95.38%) untrimmed read pairs available after processing Length distribution of reads after trimming: length count percentage 18 22 0.00% 19 35 0.00% 20 38 0.00% 21 23 0.00% 22 28 0.00% 23 37 0.00% 24 68 0.00% 25 45 0.00% 26 59 0.00% 27 77 0.00% 28 62 0.00% 29 78 0.00% 30 69 0.00% 31 65 0.00% 32 70 0.00% 33 54 0.00% 34 43 0.00% 35 75 0.00% 36 62 0.00% 37 69 0.00% 38 70 0.00% 39 67 0.00% 40 51 0.00% 41 70 0.00% 42 84 0.00% 43 83 0.00% 44 64 0.00% 45 86 0.00% 46 83 0.00% 47 109 0.00% 48 116 0.00% 49 106 0.00% 50 139 0.00% 51 116 0.00% 52 123 0.00% 53 167 0.00% 54 164 0.00% 55 184 0.00% 56 175 0.00% 57 232 0.00% 58 261 0.00% 59 282 0.00% 60 298 0.00% 61 335 0.00% 62 394 0.00% 63 423 0.00% 64 464 0.00% 65 521 0.00% 66 603 0.00% 67 584 0.00% 68 638 0.00% 69 677 0.00% 70 887 0.00% 71 973 0.00% 72 1066 0.00% 73 1285 0.00% 74 1322 0.00% 75 1551 0.00% 76 1597 0.00% 77 1811 0.00% 78 1978 0.01% 79 2310 0.01% 80 2477 0.01% 81 2784 0.01% 82 3133 0.01% 83 3557 0.01% 84 3805 0.01% 85 4194 0.01% 86 4330 0.01% 87 4820 0.01% 88 5279 0.01% 89 5521 0.01% 90 5961 0.02% 91 6391 0.02% 92 7140 0.02% 93 7979 0.02% 94 8207 0.02% 95 9087 0.02% 96 9548 0.02% 97 9823 0.03% 98 10258 0.03% 99 10975 0.03% 100 11280 0.03% 101 12048 0.03% 102 12916 0.03% 103 13665 0.04% 104 14394 0.04% 105 14917 0.04% 106 15519 0.04% 107 16070 0.04% 108 16551 0.04% 109 17123 0.04% 110 18069 0.05% 111 18675 0.05% 112 19535 0.05% 113 20226 0.05% 114 21207 0.05% 115 21698 0.06% 116 22862 0.06% 117 23655 0.06% 118 24485 0.06% 119 25151 0.06% 120 25880 0.07% 121 26476 0.07% 122 27369 0.07% 123 28569 0.07% 124 29901 0.08% 125 30906 0.08% 126 32201 0.08% 127 32679 0.08% 128 33731 0.09% 129 34600 0.09% 130 35516 0.09% 131 35822 0.09% 132 37612 0.10% 133 38635 0.10% 134 39196 0.10% 135 40769 0.11% 136 41329 0.11% 137 42180 0.11% 138 44038 0.11% 139 45762 0.12% 140 45779 0.12% 141 47251 0.12% 142 48019 0.12% 143 48858 0.13% 144 51522 0.13% 145 52179 0.13% 146 53729 0.14% 147 54694 0.14% 148 56198 0.15% 149 57296 0.15% 150 59632 0.15% 151 36916670 95.38% 38703941 reads passed initial QC criterion=sequence-density sequence-density=0.66 sequence-density-rank=1 fanout-score=1.98 fanout-score-rank=33 prefix-density=0.67 prefix-fanout=2.0 sequence=CGGTAGACCCAACCTTTCTCCAACTCGAATTCCAAGCAAGGAACCCACTTCGAGCGAAGAAGGT criterion=fanout-score sequence-density=0.03 sequence-density-rank=32 fanout-score=174.94 fanout-score-rank=1 prefix-density=0.27 prefix-fanout=16.6 sequence=CTGCTGCTGCATTTATTAGAGAAGGAGATGCTGGTAATCTCCATTTCACAAGTTCATTAATCTCGATCGAAAATATGGCTCATTTAAGCATATACAAAGTACATCTGGGAAAGAAAGTTAAGAACCAAGATAGGGTCACTGATATTTGGATGATGTTCATACGGAGAGGGAGGGAGAAAGGCTGTACTCAAGCCCCCAGAGCTCAAAACTGCCTTTGACAAAATCATAATAACCACCCTTCAGTCCTAGAGTTTTGTTCACCAAGCCATCTCTCACAAACGGGTAGGTTAGCAAGTGTCCAAGGGACACGTTCACTGCCTCCTTTTCACATTGTGTACAGAGGTCTGGGAAAGGTGCATTGGCATGTTCTGCTAAAACCTTAGTCTTGGCAGGGTAGCAAACTTTGACCCAGTCTTCTATGAAATCAGTTGATGTTGTTCCATCATAAGGGAAGGACATGAGGCCCTTAATTCCACCACAGGCGCTGTGTCCAATGACCACAATGTATTCC criterion=sequence-density sequence-density=0.74 sequence-density-rank=1 fanout-score=2.06 fanout-score-rank=36 prefix-density=0.75 prefix-fanout=2.0 sequence=TGTAAGAGATGGCTTCCTC criterion=fanout-score sequence-density=0.13 sequence-density-rank=29 fanout-score=33.48 fanout-score-rank=1 prefix-density=0.38 prefix-fanout=11.5 sequence=AAAGAAAAGAAAA SRR12671410 testing PE reads STAR mapping to Ensembl genome Started job on | Feb 11 22:29:28 Started mapping on | Feb 11 22:29:29 Finished on | Feb 11 22:33:41 Mapping speed, Million of reads per hour | 552.91 Number of input reads | 38703941 Average input read length | 299 UNIQUE READS: Uniquely mapped reads number | 35142453 Uniquely mapped reads % | 90.80% Average mapped length | 297.98 Number of splices: Total | 36174143 Number of splices: Annotated (sjdb) | 35417634 Number of splices: GT/AG | 35463207 Number of splices: GC/AG | 583240 Number of splices: AT/AC | 19840 Number of splices: Non-canonical | 107856 Mismatch rate per base, % | 0.36% Deletion rate per base | 0.03% Deletion average length | 2.86 Insertion rate per base | 0.02% Insertion average length | 2.19 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 813677 % of reads mapped to multiple loci | 2.10% Number of reads mapped to too many loci | 57270 % of reads mapped to too many loci | 0.15% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 6.79% % of reads unmapped: other | 0.16% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 2747811 2747811 2747811 N_multimapping 813677 813677 813677 N_noFeature 1213495 34597961 1381431 N_ambiguous 611022 2649 233231 UnstrandedReadsAssigned:33317936 PositiveStrandReadsAssigned:541843 NegativeStrandReadsAssigned:33527791 Dataset is classified negative stranded MeadianReadLen=151 20thPercentileLength=151 echo kmer=147 SRR12671410 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: SRR12671410-trimmed-pair1.fastq SRR12671410-trimmed-pair2.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 38,703,941 reads, 33,472,145 reads pseudoaligned [quant] estimated average fragment length: 290.404 [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,124 rounds 52401 SRR12671410.ke.tsv 34699 SRR12671410.se.tsv 87100 total ==> SRR12671410.ke.tsv <== target_id length eff_length est_counts tpm Potri.005G200100.1.v4.1 2018 1728.6 1090 16.1833 Potri.005G024800.1.v4.1 1035 745.596 515 17.7271 Potri.004G059700.1.v4.1 961 671.789 5 0.191017 Potri.007G009000.2.v4.1 1416 1126.6 0 0 Potri.003G141000.2.v4.1 2943 2653.6 1949.49 18.8548 Potri.016G087400.1.v4.1 270 71.5304 1120 401.849 Potri.015G069301.1.v4.1 564 292.706 0 0 Potri.010G195200.1.v4.1 1773 1483.6 158 2.73323 Potri.012G127500.1.v4.1 977 687.694 217 8.09841 ==> SRR12671410.se.tsv <== Potri.001G166300.v4.1 1 Potri.001G448400.v4.1 614 Potri.001G233950.v4.1 0 Potri.001G122700.v4.1 473 Potri.001G212900.v4.1 8 Potri.001G182400.v4.1 0 Potri.001G256600.v4.1 0 Potri.001G040500.v4.1 1 Potri.001G416900.v4.1 1 Potri.001G452600.v4.1 2 SRR12671410 completed mapping pipeline successfully