Starting /dee2/code/volunteer_pipeline.sh SRR12951309 current disk space = 1543092080640 free memory = 1602795480 SRR12951309 SRAfilesize c30c18cd8ccb2c65e0856edc5294273d SRR12951309.sra SRR12951309.sra file validated SRR12951309 is paired end SRR12951309 is conventional basespace SRR12951309 read1 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR12951309_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 51 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 36.4645 37.0 37.0 37.0 37.0 37.0 2 36.17 37.0 37.0 37.0 37.0 37.0 3 36.406 37.0 37.0 37.0 37.0 37.0 4 36.613 37.0 37.0 37.0 37.0 37.0 5 36.531 37.0 37.0 37.0 37.0 37.0 6 36.545 37.0 37.0 37.0 37.0 37.0 7 36.506 37.0 37.0 37.0 37.0 37.0 8 36.5505 37.0 37.0 37.0 37.0 37.0 9 36.548 37.0 37.0 37.0 37.0 37.0 10-14 36.56850000000001 37.0 37.0 37.0 37.0 37.0 15-19 36.5306 37.0 37.0 37.0 37.0 37.0 20-24 36.5067 37.0 37.0 37.0 37.0 37.0 25-29 36.475199999999994 37.0 37.0 37.0 37.0 37.0 30-34 36.458499999999994 37.0 37.0 37.0 37.0 37.0 35-39 36.4412 37.0 37.0 37.0 37.0 37.0 40-44 36.37820000000001 37.0 37.0 37.0 37.0 37.0 45-49 36.34160000000001 37.0 37.0 37.0 37.0 37.0 50-54 36.3395 37.0 37.0 37.0 37.0 37.0 55-59 36.3001 37.0 37.0 37.0 37.0 37.0 60-64 36.3136 37.0 37.0 37.0 37.0 37.0 65-69 36.274100000000004 37.0 37.0 37.0 37.0 37.0 70-74 36.263099999999994 37.0 37.0 37.0 37.0 37.0 75-79 36.2927 37.0 37.0 37.0 37.0 37.0 80-84 36.2697 37.0 37.0 37.0 37.0 37.0 85-89 36.199400000000004 37.0 37.0 37.0 37.0 37.0 90-94 36.2172 37.0 37.0 37.0 37.0 37.0 95-99 36.200700000000005 37.0 37.0 37.0 37.0 37.0 100-104 36.1503 37.0 37.0 37.0 37.0 37.0 105-109 36.170100000000005 37.0 37.0 37.0 37.0 37.0 110-114 36.0769 37.0 37.0 37.0 37.0 37.0 115-119 36.1321 37.0 37.0 37.0 37.0 37.0 120-124 36.034800000000004 37.0 37.0 37.0 37.0 37.0 125-129 35.948899999999995 37.0 37.0 37.0 37.0 37.0 130-134 36.0073 37.0 37.0 37.0 37.0 37.0 135-139 35.9411 37.0 37.0 37.0 37.0 37.0 140-144 35.8584 37.0 37.0 37.0 37.0 37.0 145-149 35.8241 37.0 37.0 37.0 37.0 37.0 150-151 35.686 37.0 37.0 37.0 37.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 21 1.0 22 2.0 23 0.0 24 5.0 25 2.0 26 7.0 27 7.0 28 16.0 29 12.0 30 24.0 31 41.0 32 54.0 33 69.0 34 130.0 35 318.0 36 2836.0 37 476.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 50.74999999999999 10.75 5.2749999999999995 33.225 2 21.987951807228914 10.818273092369477 32.95682730923695 34.23694779116466 3 20.125 15.475 26.825 37.574999999999996 4 26.05 20.974999999999998 21.025 31.95 5 27.500000000000004 26.5 21.5 24.5 6 26.224999999999998 28.875 21.525 23.375 7 19.15 26.575 36.4 17.875 8 20.875 23.150000000000002 29.675 26.3 9 21.525 20.45 31.974999999999998 26.05 10-14 23.330000000000002 25.75 24.990000000000002 25.929999999999996 15-19 23.945 24.875 24.89 26.290000000000003 20-24 23.375 25.61 25.224999999999998 25.790000000000003 25-29 23.575 24.75 25.230000000000004 26.445 30-34 23.955000000000002 25.09 24.505 26.450000000000003 35-39 24.065 25.480000000000004 24.87 25.585 40-44 24.07 24.92 25.05 25.96 45-49 24.044999999999998 25.21 24.175 26.57 50-54 24.365000000000002 24.66 24.355 26.619999999999997 55-59 24.75 24.95 24.060000000000002 26.240000000000002 60-64 24.715 24.759999999999998 24.205 26.32 65-69 24.745 25.03 24.08 26.145000000000003 70-74 24.91 24.695 24.59 25.805 75-79 24.72 24.415 23.935000000000002 26.93 80-84 24.615000000000002 24.855 23.71 26.82 85-89 25.119999999999997 25.245 24.15 25.485000000000003 90-94 24.529999999999998 24.805 24.240000000000002 26.424999999999997 95-99 25.035 23.849999999999998 24.245 26.87 100-104 25.080000000000002 24.29 24.065 26.565 105-109 25.14 24.865000000000002 23.544999999999998 26.450000000000003 110-114 25.095 25.41 23.369999999999997 26.125 115-119 25.224999999999998 24.965 23.39 26.419999999999998 120-124 24.81 24.605 23.665 26.919999999999998 125-129 25.419999999999998 24.605 24.05 25.924999999999997 130-134 24.154999999999998 24.93 23.865 27.05 135-139 25.259999999999998 23.87 24.415 26.455000000000002 140-144 25.36 24.09 23.43 27.12 145-149 24.945 25.47 23.580000000000002 26.005 150-151 24.9375 23.8875 24.2375 26.937499999999996 >>END_MODULE >>Per sequence GC content fail #GC Content Count 0 0.0 1 0.0 2 0.5 3 0.5 4 0.0 5 0.0 6 0.5 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 0.0 18 0.0 19 0.0 20 0.0 21 0.0 22 0.0 23 0.0 24 0.5 25 0.5 26 1.0 27 3.5 28 3.5 29 3.0 30 6.0 31 10.5 32 15.0 33 18.0 34 24.5 35 35.5 36 47.0 37 61.5 38 81.0 39 100.5 40 117.0 41 135.0 42 144.0 43 155.5 44 172.5 45 166.5 46 176.5 47 198.0 48 192.0 49 158.0 50 149.5 51 144.0 52 117.5 53 115.5 54 109.0 55 94.0 56 87.5 57 89.0 58 79.5 59 67.5 60 63.0 61 54.0 62 64.5 63 74.0 64 71.5 65 72.5 66 70.0 67 66.5 68 56.5 69 45.5 70 43.5 71 43.5 72 39.0 73 37.5 74 33.0 75 24.0 76 15.0 77 13.0 78 13.0 79 8.5 80 3.0 81 0.5 82 1.0 83 3.5 84 2.5 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 0.4 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 79.60000000000001 #Duplication Level Percentage of deduplicated Percentage of total 1 81.12437185929649 64.575 2 14.133165829145728 22.5 3 3.5175879396984926 8.4 4 0.8165829145728644 2.6 5 0.2198492462311558 0.8750000000000001 6 0.09422110552763818 0.44999999999999996 7 0.031407035175879394 0.17500000000000002 8 0.031407035175879394 0.2 9 0.031407035175879394 0.22499999999999998 >10 0.0 0.0 >50 0.0 0.0 >100 0.0 0.0 >500 0.0 0.0 >1k 0.0 0.0 >5k 0.0 0.0 >10k+ 0.0 0.0 >>END_MODULE >>Overrepresented sequences warn #Sequence Count Percentage Possible Source TGGCGGACGCGAGCCGGTCGAGCTTGCGGAAGAGCCTGGTGTCTGCGGCG 9 0.22499999999999998 No Hit GTGGATTCCTTCTGGATATTGTAATCAGCAAGGGTGCGGCCATCCTCAAG 8 0.2 No Hit GATCGGAAGAGCACACGTCTGAACTCCAGTCACGCTACGTTATCTCGTAT 7 0.17500000000000002 TruSeq Adapter, Index 6 (97% over 37bp) GCCGCAAAGTAATGGGTGCAGCACCTCGTCGTCTTCACGCGACGCCTTAG 6 0.15 No Hit GGGGGATGCCCTCCTTGTCCTGGATCTTTGCCTTCACATTGTCGATCGTG 6 0.15 No Hit GCTTCGTTGACGGTGATGTTGCGGCCATCCAGGTCCTTGCCGTTCATGCC 6 0.15 No Hit GTCTGTAGGGTATCTAGTATACAGTCCTGTCATTTGACACCTGTTAGCAC 5 0.125 No Hit GCCGACCTATCGATTCTTTAGCTACAGCGTGCGCTGCTGCGCTCGCCATG 5 0.125 No Hit GCATTCCTCTGTCCCACAAATTTCCGTGCAACGCCAAAGATTAGAGCCTT 5 0.125 No Hit GATCGGAAGAGCACACGTCTGAACTCCAGTCACGCTACGTTATCGCGTAT 5 0.125 TruSeq Adapter, Index 6 (97% over 37bp) AGCCATTCTTGGTCTCCGCAATATCGTGCTGACAGTCTGTTCTTCCGATA 5 0.125 No Hit GCAACACTTTTTGAGATGGCACCAAGGAGAAATGCTGAGAAAGCAGAAAG 5 0.125 No Hit CTGCCCAACTAGCTGGTTATCACTGAGGTCCAGCTTCTGGAGGAAGGACA 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 0.025 0.0 0.0 0.0 0.0 20-21 0.025 0.0 0.0 0.0 0.0 22-23 0.025 0.0 0.0 0.0 0.0 24-25 0.025 0.0 0.0 0.0 0.0 26-27 0.025 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 0.1 0.0 0.0 0.0 0.0 56-57 0.1 0.0 0.0 0.0 0.0 58-59 0.1 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 0.1 0.0 0.0 0.0 0.0 66-67 0.1 0.0 0.0 0.0 0.0 68-69 0.1 0.0 0.0 0.0 0.0 70-71 0.1 0.0 0.0 0.0 0.0 72-73 0.1 0.0 0.0 0.0 0.0 74-75 0.1 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 0.125 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 0.325 0.0 0.0 0.0 0.0 88-89 0.3625 0.0 0.0 0.0 0.0 90-91 0.475 0.0 0.0 0.0 0.0 92-93 0.6625 0.0 0.0 0.0 0.0 94-95 0.775 0.0 0.0 0.0 0.0 96-97 0.8999999999999999 0.0 0.0 0.0 0.0 98-99 1.0625 0.0 0.0 0.0 0.0 100-101 1.2625000000000002 0.0 0.0 0.0 0.0 102-103 1.5499999999999998 0.0 0.0 0.0 0.0 104-105 1.8875 0.0 0.0 0.0 0.0 106-107 2.3875 0.0 0.0 0.0 0.0 108-109 2.7625 0.0 0.0 0.0 0.0 110-111 3.175 0.0 0.0 0.0 0.0 112-113 3.3625 0.0 0.0 0.0 0.0 114-115 3.7375 0.0 0.0 0.0 0.0 116-117 4.125 0.0 0.0 0.0 0.0 118-119 4.65 0.0 0.0 0.0 0.0 120-121 5.1875 0.0 0.0 0.0 0.0 122-123 5.425000000000001 0.0 0.0 0.0 0.0 124-125 5.8625 0.0 0.0 0.0 0.0 126-127 6.300000000000001 0.0 0.0 0.0 0.0 128-129 6.75 0.0 0.0 0.0 0.0 130-131 7.225 0.0 0.0 0.0 0.0 132-133 7.65 0.0 0.0 0.0 0.0 134-135 8.4375 0.0 0.0 0.0 0.0 136-137 9.075 0.0 0.0 0.0 0.0 138-139 9.925 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position GGTGGAT 10 0.006830828 145.0 2 >>END_MODULE SRR12951309 read2 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR12951309_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 52 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 36.2525 37.0 37.0 37.0 37.0 37.0 2 36.12 37.0 37.0 37.0 37.0 37.0 3 36.1495 37.0 37.0 37.0 37.0 37.0 4 36.194 37.0 37.0 37.0 37.0 37.0 5 36.2395 37.0 37.0 37.0 37.0 37.0 6 36.1025 37.0 37.0 37.0 37.0 37.0 7 36.112 37.0 37.0 37.0 37.0 37.0 8 36.2355 37.0 37.0 37.0 37.0 37.0 9 36.102 37.0 37.0 37.0 37.0 37.0 10-14 36.1422 37.0 37.0 37.0 37.0 37.0 15-19 36.1565 37.0 37.0 37.0 37.0 37.0 20-24 36.0775 37.0 37.0 37.0 37.0 37.0 25-29 36.073600000000006 37.0 37.0 37.0 37.0 37.0 30-34 35.9377 37.0 37.0 37.0 37.0 37.0 35-39 35.8904 37.0 37.0 37.0 37.0 37.0 40-44 35.9344 37.0 37.0 37.0 37.0 37.0 45-49 35.922000000000004 37.0 37.0 37.0 37.0 37.0 50-54 35.892999999999994 37.0 37.0 37.0 37.0 37.0 55-59 35.8344 37.0 37.0 37.0 37.0 37.0 60-64 35.828199999999995 37.0 37.0 37.0 37.0 37.0 65-69 35.830999999999996 37.0 37.0 37.0 37.0 37.0 70-74 35.7384 37.0 37.0 37.0 37.0 37.0 75-79 35.783699999999996 37.0 37.0 37.0 37.0 37.0 80-84 35.7051 37.0 37.0 37.0 37.0 37.0 85-89 35.7004 37.0 37.0 37.0 37.0 37.0 90-94 35.7167 37.0 37.0 37.0 37.0 37.0 95-99 35.6305 37.0 37.0 37.0 37.0 37.0 100-104 35.616499999999995 37.0 37.0 37.0 37.0 37.0 105-109 35.55120000000001 37.0 37.0 37.0 37.0 37.0 110-114 35.5124 37.0 37.0 37.0 37.0 37.0 115-119 35.6473 37.0 37.0 37.0 37.0 37.0 120-124 35.5192 37.0 37.0 37.0 37.0 37.0 125-129 35.479 37.0 37.0 37.0 37.0 37.0 130-134 35.4183 37.0 37.0 37.0 34.6 37.0 135-139 35.4324 37.0 37.0 37.0 37.0 37.0 140-144 35.394600000000004 37.0 37.0 37.0 37.0 37.0 145-149 35.2369 37.0 37.0 37.0 32.2 37.0 150-151 34.77425 37.0 37.0 37.0 25.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 13 6.0 14 5.0 15 4.0 16 9.0 17 2.0 18 4.0 19 3.0 20 3.0 21 5.0 22 9.0 23 7.0 24 6.0 25 12.0 26 6.0 27 24.0 28 19.0 29 24.0 30 28.0 31 37.0 32 65.0 33 82.0 34 175.0 35 497.0 36 2642.0 37 326.0 >>END_MODULE >>Per base sequence content warn #Base G A T C 1 46.375 19.875 6.65 27.1 2 28.425 22.075 26.775 22.725 3 24.25 24.4 28.95 22.400000000000002 4 28.975 28.825 19.6 22.6 5 27.700000000000003 32.25 19.3 20.75 6 24.7 33.475 18.224999999999998 23.599999999999998 7 24.275 20.8 31.775 23.150000000000002 8 24.05 22.125 23.45 30.375000000000004 9 25.174999999999997 21.175 26.474999999999998 27.175 10-14 26.424999999999997 24.625 23.825 25.124999999999996 15-19 26.455000000000002 25.009999999999998 23.16 25.374999999999996 20-24 27.11 25.085 22.39 25.415 25-29 26.51 23.645 23.52 26.325 30-34 26.875 24.46 23.494999999999997 25.169999999999998 35-39 27.18 25.09 23.325000000000003 24.404999999999998 40-44 26.595000000000002 24.42 23.385 25.6 45-49 26.66 24.22 23.380000000000003 25.740000000000002 50-54 26.279999999999998 24.990000000000002 23.89 24.84 55-59 27.115000000000002 24.055 23.055 25.775 60-64 26.479999999999997 24.41 23.91 25.2 65-69 27.279999999999998 23.885 23.87 24.965 70-74 27.465 23.599999999999998 23.785 25.15 75-79 26.705000000000002 24.68 24.03 24.585 80-84 27.005000000000003 24.610000000000003 23.494999999999997 24.89 85-89 26.99 24.495 23.055 25.46 90-94 27.405 24.605 22.919999999999998 25.069999999999997 95-99 26.810000000000002 24.455 24.11 24.625 100-104 27.205000000000002 24.575 23.36 24.86 105-109 27.310000000000002 24.595 24.115000000000002 23.98 110-114 27.925 24.115000000000002 23.435 24.525 115-119 28.349999999999998 24.07 23.169999999999998 24.41 120-124 28.075 24.36 23.425 24.14 125-129 28.925 24.615000000000002 23.115 23.345 130-134 28.335 24.795 23.205000000000002 23.665 135-139 28.994999999999997 24.8 23.830000000000002 22.375 140-144 28.79 24.654999999999998 22.835 23.72 145-149 29.805 24.7 22.28 23.215 150-151 30.475 24.2625 23.3875 21.875 >>END_MODULE >>Per sequence GC content fail #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 0.5 9 0.5 10 0.5 11 1.0 12 0.5 13 0.0 14 0.0 15 0.5 16 0.5 17 0.5 18 0.5 19 0.0 20 1.5 21 2.0 22 0.5 23 0.0 24 1.0 25 1.5 26 0.5 27 1.5 28 4.5 29 5.0 30 9.0 31 11.0 32 11.5 33 14.0 34 19.5 35 34.5 36 45.5 37 52.5 38 58.5 39 85.0 40 123.5 41 125.5 42 125.0 43 147.0 44 155.0 45 169.0 46 183.0 47 177.5 48 164.0 49 154.5 50 140.0 51 124.5 52 111.0 53 111.0 54 114.0 55 86.5 56 88.0 57 101.5 58 97.5 59 90.0 60 72.5 61 66.5 62 75.5 63 76.0 64 70.5 65 70.0 66 73.5 67 69.0 68 53.0 69 47.5 70 46.0 71 44.0 72 50.0 73 47.0 74 33.5 75 30.5 76 29.0 77 19.0 78 12.0 79 9.5 80 7.0 81 3.5 82 2.5 83 2.5 84 3.0 85 2.0 86 0.5 87 1.0 88 2.5 89 3.0 90 2.0 91 1.0 92 1.5 93 3.0 94 1.5 95 0.0 96 1.0 97 1.5 98 1.5 99 2.0 100 6.0 >>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 80.325 #Duplication Level Percentage of deduplicated Percentage of total 1 81.97945845004668 65.85 2 13.507625272331156 21.7 3 3.3924680983504514 8.175 4 0.8092125739184562 2.6 5 0.18674136321195145 0.75 6 0.06224712107065049 0.3 7 0.0 0.0 8 0.0 0.0 9 0.031123560535325244 0.22499999999999998 >10 0.031123560535325244 0.4 >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 16 0.4 No Hit AGAAGCTCGACGCGCTCAACCGCGTCGCCGCCGTCGCCTCCCGCCTCGGC 9 0.22499999999999998 No Hit AGGGAATTCCACCGGACCAGCAGCGCCTAATCTTTGCTGGCAAACAGCTT 6 0.15 No Hit GTCAACAACAACACGACGTTGACGTACACCATGGTGGATGGAGCTAGACG 6 0.15 No Hit CCTTCCCATCCCATGCACTGCATCCCCCCTCTTCTAACAGGATGGTGAGC 5 0.125 No Hit CCTGATTCCGATCGAAAAGTCCCCGCAAGAGCAAGCGACCGATCTCGTGA 5 0.125 No Hit AATTAGGGCTGAAAGCCCTAACTTAATGGACGGGAGGTATCCCAATAGGA 5 0.125 No Hit CTAATATAGTCTTACCAAAAAAGGAAGCAAAGTTGCAGCAAAATAGCCAT 5 0.125 No Hit CTTTAAATGAAGCCATGGAAGGAGAGAAGACTGGCCACCACCATCTTCCA 5 0.125 No Hit GCAACTCTTGCTGAAGGTACATGGCTTGAGGCATTCGATGGCTTGGGCAT 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 0.025 0.0 0.0 0.0 0.0 20-21 0.025 0.0 0.0 0.0 0.0 22-23 0.025 0.0 0.0 0.0 0.0 24-25 0.025 0.0 0.0 0.0 0.0 26-27 0.025 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 0.1 0.0 0.0 0.0 0.0 56-57 0.1 0.0 0.0 0.0 0.0 58-59 0.1 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 0.1 0.0 0.0 0.0 0.0 66-67 0.1 0.0 0.0 0.0 0.0 68-69 0.1 0.0 0.0 0.0 0.0 70-71 0.1 0.0 0.0 0.0 0.0 72-73 0.1 0.0 0.0 0.0 0.0 74-75 0.1 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 0.125 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 0.325 0.0 0.0 0.0 0.0 88-89 0.3625 0.0 0.0 0.0 0.0 90-91 0.475 0.0 0.0 0.0 0.0 92-93 0.6625 0.0 0.0 0.0 0.0 94-95 0.775 0.0 0.0 0.0 0.0 96-97 0.8999999999999999 0.0 0.0 0.0 0.0 98-99 1.0625 0.0 0.0 0.0 0.0 100-101 1.275 0.0 0.0 0.0 0.0 102-103 1.5750000000000002 0.0 0.0 0.0 0.0 104-105 1.9125 0.0 0.0 0.0 0.0 106-107 2.425 0.0 0.0 0.0 0.0 108-109 2.85 0.0 0.0 0.0 0.0 110-111 3.2875 0.0 0.0 0.0 0.0 112-113 3.4625 0.0 0.0 0.0 0.0 114-115 3.8375000000000004 0.0 0.0 0.0 0.0 116-117 4.225 0.0 0.0 0.0 0.0 118-119 4.75 0.0 0.0 0.0 0.0 120-121 5.262499999999999 0.0 0.0 0.0 0.0 122-123 5.512499999999999 0.0 0.0 0.0 0.0 124-125 5.9875 0.0 0.0 0.0 0.0 126-127 6.45 0.0 0.0 0.0 0.0 128-129 6.9 0.0 0.0 0.0 0.0 130-131 7.387499999999999 0.0 0.0 0.0 0.0 132-133 7.824999999999999 0.0 0.0 0.0 0.0 134-135 8.6375 0.0 0.0 0.0 0.0 136-137 9.275 0.0 0.0 0.0 0.0 138-139 10.125 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position CCCCCCC 20 0.00593511 29.0 130-134 >>END_MODULE Read 1871947 spots for SRR12951309.sra Written 1871947 spots for SRR12951309.sra Read 1871947 spots for SRR12951309.sra Written 1871947 spots for SRR12951309.sra Read 1871952 spots for SRR12951309.sra Written 1871952 spots for SRR12951309.sra Read 1871947 spots for SRR12951309.sra Written 1871947 spots for SRR12951309.sra Read 1871947 spots for SRR12951309.sra Written 1871947 spots for SRR12951309.sra Read 1871947 spots for SRR12951309.sra Written 1871947 spots for SRR12951309.sra Read 1871947 spots for SRR12951309.sra Written 1871947 spots for SRR12951309.sra Read 1871947 spots for SRR12951309.sra Written 1871947 spots for SRR12951309.sra Read 1871947 spots for SRR12951309.sra Written 1871947 spots for SRR12951309.sra Read 1871947 spots for SRR12951309.sra Written 1871947 spots for SRR12951309.sra Read 1871947 spots for SRR12951309.sra Written 1871947 spots for SRR12951309.sra Read 1871947 spots for SRR12951309.sra Written 1871947 spots for SRR12951309.sra Read 1871947 spots for SRR12951309.sra Written 1871947 spots for SRR12951309.sra Read 1871947 spots for SRR12951309.sra Written 1871947 spots for SRR12951309.sra Read 1871947 spots for SRR12951309.sra Written 1871947 spots for SRR12951309.sra Read 1871947 spots for SRR12951309.sra Written 1871947 spots for SRR12951309.sra Read 1871947 spots for SRR12951309.sra Written 1871947 spots for SRR12951309.sra Read 1871947 spots for SRR12951309.sra Written 1871947 spots for SRR12951309.sra Read 1871947 spots for SRR12951309.sra Written 1871947 spots for SRR12951309.sra Read 1871947 spots for SRR12951309.sra Written 1871947 spots for SRR12951309.sra SRR ids: ['SRR12951309.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_aw18suwc SRR12951309.sra spots: 37438945 blocks: [[1, 1871947], [1871948, 3743894], [3743895, 5615841], [5615842, 7487788], [7487789, 9359735], [9359736, 11231682], [11231683, 13103629], [13103630, 14975576], [14975577, 16847523], [16847524, 18719470], [18719471, 20591417], [20591418, 22463364], [22463365, 24335311], [24335312, 26207258], [26207259, 28079205], [28079206, 29951152], [29951153, 31823099], [31823100, 33695046], [33695047, 35566993], [35566994, 37438945]] SRR12951309 file size 12701691 SRR12951309 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 SRR12951309 SRR12951309_1.fastq SRR12951309_2.fastq Input file: SRR12951309_1.fastq Paired file: SRR12951309_2.fastq trimmed: SRR12951309-trimmed-pair1.fastq, SRR12951309-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 Sat Dec 7 11:20:53 2024 >> started Sat Dec 7 11:21:43 2024 >> done (50.330s) 37438945 read pairs processed; of these: 215 ( 0.00%) short read pairs filtered out after trimming by size control 91959 ( 0.25%) empty read pairs filtered out after trimming by size control 37346771 (99.75%) read pairs available; of these: 5130876 (13.74%) trimmed read pairs available after processing 32215895 (86.26%) untrimmed read pairs available after processing Length distribution of reads after trimming: length count percentage 18 23 0.00% 19 20 0.00% 20 30 0.00% 21 23 0.00% 22 32 0.00% 23 47 0.00% 24 45 0.00% 25 57 0.00% 26 69 0.00% 27 55 0.00% 28 64 0.00% 29 79 0.00% 30 64 0.00% 31 85 0.00% 32 73 0.00% 33 67 0.00% 34 62 0.00% 35 88 0.00% 36 85 0.00% 37 91 0.00% 38 101 0.00% 39 112 0.00% 40 126 0.00% 41 107 0.00% 42 162 0.00% 43 127 0.00% 44 147 0.00% 45 165 0.00% 46 191 0.00% 47 181 0.00% 48 213 0.00% 49 258 0.00% 50 277 0.00% 51 269 0.00% 52 340 0.00% 53 342 0.00% 54 382 0.00% 55 418 0.00% 56 458 0.00% 57 545 0.00% 58 650 0.00% 59 811 0.00% 60 878 0.00% 61 1033 0.00% 62 1281 0.00% 63 1357 0.00% 64 1497 0.00% 65 1503 0.00% 66 1748 0.00% 67 2010 0.01% 68 2267 0.01% 69 2572 0.01% 70 3212 0.01% 71 3574 0.01% 72 4185 0.01% 73 4595 0.01% 74 5168 0.01% 75 5903 0.02% 76 6353 0.02% 77 7086 0.02% 78 7629 0.02% 79 8755 0.02% 80 9494 0.03% 81 11101 0.03% 82 12383 0.03% 83 13664 0.04% 84 14885 0.04% 85 15911 0.04% 86 17390 0.05% 87 18236 0.05% 88 19737 0.05% 89 20779 0.06% 90 22651 0.06% 91 24446 0.07% 92 26783 0.07% 93 28821 0.08% 94 30882 0.08% 95 33059 0.09% 96 34289 0.09% 97 36042 0.10% 98 36975 0.10% 99 38080 0.10% 100 40184 0.11% 101 42588 0.11% 102 44965 0.12% 103 47513 0.13% 104 50259 0.13% 105 52404 0.14% 106 54144 0.14% 107 55562 0.15% 108 57263 0.15% 109 58801 0.16% 110 60519 0.16% 111 62969 0.17% 112 65254 0.17% 113 67101 0.18% 114 71623 0.19% 115 73401 0.20% 116 75845 0.20% 117 77670 0.21% 118 79562 0.21% 119 79687 0.21% 120 81211 0.22% 121 83976 0.22% 122 84016 0.22% 123 88737 0.24% 124 91708 0.25% 125 92750 0.25% 126 95702 0.26% 127 97416 0.26% 128 99057 0.27% 129 99895 0.27% 130 101153 0.27% 131 101101 0.27% 132 103432 0.28% 133 106268 0.28% 134 109179 0.29% 135 111923 0.30% 136 112907 0.30% 137 114852 0.31% 138 115622 0.31% 139 116493 0.31% 140 117305 0.31% 141 118361 0.32% 142 119209 0.32% 143 119984 0.32% 144 123176 0.33% 145 125071 0.33% 146 124742 0.33% 147 126910 0.34% 148 128015 0.34% 149 127986 0.34% 150 129650 0.35% 151 32215895 86.26% 37346771 reads passed initial QC criterion=sequence-density sequence-density=0.18 sequence-density-rank=1 fanout-score=3.69 fanout-score-rank=29 prefix-density=0.24 prefix-fanout=2.8 sequence=GAACCGGAACCG criterion=fanout-score sequence-density=0.03 sequence-density-rank=30 fanout-score=444.70 fanout-score-rank=1 prefix-density=0.72 prefix-fanout=17.3 sequence=GGCGGCGGCGAACCGCCCCCGTCGCCGCGATCCGAACACTTCACCGGACCATTCAATCGGTAGGAGCGACGGGCGGTGTGTACAAAGGGCAGGGACGTAGTCAACGCGAGCTGATGACTCGCGCTTACTAGGCATTCCTCGTTGAAGACCAACAATTGCAATGATCTATCCCCATCACGATGAAATTTCCCAAGATTACCCGGGCCTGTCGGCCAAGGCTATATACTCGTTGAATACATCAGTGTAGCGCGCGTGCGGCCCAGAACATCTAAGGGCATCACAGACCTGTTATTGCCTCAAACTTCCGTCGCCTAAACGGCGATAGTCCCTCTAAGAAGCTAGCTGCGGAGGGATGGCTCCGCATAGCTAGTTAGCAGGCTGAGGTCTCGTTCGTTAACGGAATTAACCAGACAAATCGCTCCACCAACTAAGAACGGCCATGCACCACCACCCATAGAATCAAGAAAGAGCTCTCAGTCTGTCAATCCTTGCTATGTCTGGACCTGGTAAG criterion=sequence-density sequence-density=0.93 sequence-density-rank=1 fanout-score=2.02 fanout-score-rank=35 prefix-density=0.93 prefix-fanout=2.0 sequence=CGGTTCCGGTTC criterion=fanout-score sequence-density=0.11 sequence-density-rank=18 fanout-score=212.07 fanout-score-rank=1 prefix-density=0.99 prefix-fanout=23.3 sequence=CGCCGCCGCCGC SRR12951309 testing PE reads STAR mapping to Ensembl genome Started job on | Dec 07 11:22:54 Started mapping on | Dec 07 11:22:54 Finished on | Dec 07 11:27:50 Mapping speed, Million of reads per hour | 454.22 Number of input reads | 37346771 Average input read length | 294 UNIQUE READS: Uniquely mapped reads number | 35016665 Uniquely mapped reads % | 93.76% Average mapped length | 293.62 Number of splices: Total | 31821926 Number of splices: Annotated (sjdb) | 29413757 Number of splices: GT/AG | 31332548 Number of splices: GC/AG | 405168 Number of splices: AT/AC | 17626 Number of splices: Non-canonical | 66584 Mismatch rate per base, % | 0.24% Deletion rate per base | 0.01% Deletion average length | 2.25 Insertion rate per base | 0.01% Insertion average length | 2.41 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 377625 % of reads mapped to multiple loci | 1.01% Number of reads mapped to too many loci | 42359 % of reads mapped to too many loci | 0.11% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 4.48% % of reads unmapped: other | 0.63% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 1952481 1952481 1952481 N_multimapping 377625 377625 377625 N_noFeature 1631555 33953016 2005031 N_ambiguous 810277 5106 120197 UnstrandedReadsAssigned:32574833 PositiveStrandReadsAssigned:1058543 NegativeStrandReadsAssigned:32891437 Dataset is classified negative stranded MeadianReadLen=151 20thPercentileLength=151 echo kmer=147 SRR12951309 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: 52,972 [index] number of k-mers: 66,720,672 [index] number of equivalence classes: 111,837 [quant] running in paired-end mode [quant] will process pair 1: SRR12951309-trimmed-pair1.fastq SRR12951309-trimmed-pair2.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 37,346,771 reads, 33,400,223 reads pseudoaligned [quant] estimated average fragment length: 260.602 [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,210 rounds 52973 SRR12951309.ke.tsv 35125 SRR12951309.se.tsv 88098 total ==> SRR12951309.ke.tsv <== target_id length eff_length est_counts tpm PNS24245 936 676.979 0 0 PNS24247 1044 784.398 240.909 13.0209 PNS24249 1928 1668.4 510.126 12.9629 PNS24246 1044 784.398 240.909 13.0209 PNS24248 1044 784.398 240.909 13.0209 PNS24244 1471 1211.4 263.147 9.20948 PNS24243 293 103.244 2 0.821279 KQK14069 1603 1343.4 81859.3 2583.37 KQK14071 474 240.218 510.378 90.0764 ==> SRR12951309.se.tsv <== BRADI_1g14170v3 83406 BRADI_1g53295v3 367 BRADI_1g59795v3 1187 BRADI_1g07683v3 0 BRADI_1g00485v3 19 BRADI_1g20270v3 442 BRADI_1g74790v3 3431 BRADI_1g09890v3 0 BRADI_1g77505v3 358 BRADI_1g48960v3 0 SRR12951309 completed mapping pipeline successfully