Starting /dee2/code/volunteer_pipeline.sh SRR6031161 current disk space = 1523606736896 free memory = 1460927756 SRR6031161 SRAfilesize b2db16f4693caf3375e31bed53d3684e SRR6031161.sra SRR6031161.sra file validated SRR6031161 is paired end SRR6031161 is conventional basespace SRR6031161 read1 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR6031161_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 47 >>END_MODULE >>Per base sequence quality fail #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 21.4 18.0 18.0 27.0 18.0 32.0 2 30.10425 31.0 29.0 31.0 27.0 33.0 3 31.5705 33.0 31.0 33.0 29.0 33.0 4 32.3025 33.0 33.0 33.0 31.0 33.0 5 33.12925 33.0 33.0 34.0 33.0 34.0 6 37.41975 38.0 38.0 38.0 36.0 38.0 7 37.64775 38.0 38.0 38.0 38.0 38.0 8 37.71425 38.0 38.0 38.0 38.0 38.0 9 37.76225 38.0 38.0 38.0 38.0 38.0 10-14 37.712199999999996 38.0 38.0 38.0 38.0 38.0 15-19 37.69285000000001 38.0 38.0 38.0 38.0 38.0 20-24 37.6886 38.0 38.0 38.0 38.0 38.0 25-29 37.67225 38.0 38.0 38.0 38.0 38.0 30-34 37.68055 38.0 38.0 38.0 38.0 38.0 35-39 37.669650000000004 38.0 38.0 38.0 38.0 38.0 40-44 37.630900000000004 38.0 38.0 38.0 38.0 38.0 45-49 37.5385 38.0 38.0 38.0 37.8 38.0 50-54 37.52775 38.0 38.0 38.0 37.8 38.0 55-59 37.46294999999999 38.0 38.0 38.0 37.0 38.0 60-64 37.3786 38.0 38.0 38.0 37.0 38.0 65-69 37.330149999999996 38.0 38.0 38.0 36.8 38.0 70-74 37.317750000000004 38.0 38.0 38.0 36.6 38.0 75-79 37.2767 38.0 38.0 38.0 36.4 38.0 80-84 37.187200000000004 38.0 38.0 38.0 36.0 38.0 85-89 37.113150000000005 38.0 38.0 38.0 36.0 38.0 90-94 37.06345 38.0 38.0 38.0 35.8 38.0 95-99 36.94325 38.0 38.0 38.0 35.2 38.0 100-104 36.857549999999996 38.0 38.0 38.0 35.0 38.0 105-109 36.7038 38.0 38.0 38.0 34.4 38.0 110-114 36.64235 38.0 38.0 38.0 34.2 38.0 115-119 36.4303 38.0 38.0 38.0 34.0 38.0 120-124 36.313900000000004 38.0 37.4 38.0 33.6 38.0 125-129 36.071600000000004 38.0 37.0 38.0 33.0 38.0 130-134 35.704249999999995 38.0 36.0 38.0 31.4 38.0 135-139 35.5811 38.0 36.0 38.0 31.8 38.0 140-144 35.247249999999994 38.0 35.4 38.0 30.6 38.0 145-149 34.830200000000005 38.0 35.0 38.0 28.8 38.0 150-151 31.128 36.5 30.0 38.0 15.0 38.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 10 1.0 11 0.0 12 0.0 13 0.0 14 1.0 15 1.0 16 1.0 17 0.0 18 0.0 19 1.0 20 0.0 21 0.0 22 2.0 23 6.0 24 4.0 25 7.0 26 17.0 27 10.0 28 15.0 29 15.0 30 24.0 31 20.0 32 51.0 33 62.0 34 112.0 35 277.0 36 822.0 37 2551.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 47.388731669668125 11.036789297658862 9.827630563416516 31.746848469256495 2 23.7 11.1 34.35 30.85 3 20.1 14.299999999999999 28.225 37.375 4 22.275 23.200000000000003 24.425 30.099999999999998 5 25.525 25.324999999999996 24.45 24.7 6 23.05 31.125000000000004 23.45 22.375 7 16.525000000000002 26.35 38.25 18.875 8 19.75 23.5 29.95 26.8 9 18.525 22.35 32.65 26.474999999999998 10-14 22.085 26.445 27.54 23.93 15-19 21.825 25.72 27.49 24.965 20-24 21.425 26.005 27.465 25.105 25-29 21.15 26.105 26.974999999999998 25.77 30-34 21.78 26.150000000000002 26.705000000000002 25.365 35-39 21.91 26.174999999999997 26.245 25.669999999999998 40-44 21.63 26.57 26.650000000000002 25.15 45-49 21.64 25.6 26.56 26.200000000000003 50-54 20.849999999999998 25.330000000000002 27.405 26.415 55-59 21.91 25.374999999999996 26.584999999999997 26.13 60-64 21.555 25.285000000000004 27.01 26.150000000000002 65-69 21.43 25.955000000000002 27.279999999999998 25.335 70-74 21.785 25.7 26.525 25.990000000000002 75-79 22.245 25.97 26.174999999999997 25.61 80-84 21.97 25.34 26.974999999999998 25.715 85-89 22.37 25.014999999999997 26.605 26.009999999999998 90-94 21.69 26.484999999999996 26.435 25.39 95-99 21.785 25.88 26.43 25.905 100-104 22.245 26.215 26.290000000000003 25.25 105-109 22.264999999999997 25.245 27.095000000000002 25.395 110-114 22.325 26.36 25.924999999999997 25.39 115-119 22.335 26.435 26.169999999999998 25.06 120-124 22.31 25.885 26.484999999999996 25.319999999999997 125-129 22.425 25.705 25.385 26.484999999999996 130-134 22.61 25.119999999999997 26.005 26.265 135-139 22.29 26.040000000000003 26.075 25.595000000000002 140-144 22.59 25.814999999999998 26.08 25.515 145-149 22.795 25.355 26.155 25.695 150-151 23.0375 26.375 25.5 25.087500000000002 >>END_MODULE >>Per sequence GC content warn #GC Content Count 0 0.0 1 0.0 2 0.0 3 0.0 4 0.0 5 0.5 6 0.5 7 1.0 8 1.0 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 0.5 23 1.0 24 1.0 25 1.0 26 1.0 27 1.5 28 3.5 29 5.5 30 9.5 31 12.0 32 13.0 33 21.0 34 34.0 35 43.0 36 50.0 37 73.5 38 88.5 39 103.5 40 135.0 41 157.0 42 174.5 43 191.0 44 199.0 45 211.0 46 226.0 47 217.5 48 214.0 49 210.0 50 207.0 51 205.0 52 169.0 53 131.0 54 122.5 55 104.0 56 86.0 57 81.5 58 73.5 59 67.5 60 61.5 61 51.0 62 36.0 63 32.5 64 28.5 65 26.0 66 20.5 67 18.0 68 16.5 69 11.0 70 12.5 71 12.0 72 11.0 73 6.0 74 2.0 75 2.5 76 1.5 77 2.0 78 1.0 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 2.825 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 93.525 #Duplication Level Percentage of deduplicated Percentage of total 1 95.74979951884522 89.55 2 2.9403902699812883 5.5 3 0.7751937984496124 2.175 4 0.21384656508954825 0.8 5 0.16038492381716118 0.75 6 0.05346164127238706 0.3 7 0.02673082063619353 0.17500000000000002 8 0.02673082063619353 0.2 9 0.0 0.0 >10 0.05346164127238706 0.5499999999999999 >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 GTTACGACTTCTCCTTCCTCTAAATGATAAGGTTCAATGGACTTCTCGCG 11 0.27499999999999997 No Hit CCGGCAATTTCAAGCACTCTTTGACTCTCTTTTCAAAGTCCTTTTCATCT 11 0.27499999999999997 No Hit CCGCAGGCTCCACGCCTGGTGGTGCCCTTCCGTCAATTCCTTTAAGTTTC 8 0.2 No Hit GGCAATTTCAAGCACTCTTTGACTCTCTTTTCAAAGTCCTTTTCATCTTT 7 0.17500000000000002 No Hit CGGCAATTTCAAGCACTCTTTGACTCTCTTTTCAAAGTCCTTTTCATCTT 6 0.15 No Hit GTCATCAGTAGGGTAAAACTAACCTGTCTCACGACGGTCTAAACCCAGCT 6 0.15 No Hit GTTCGATTAGTCTTTCGCCCCTATACCCAAGTCAGACGAACGATTTGCAC 5 0.125 No Hit TCCGTCAATTCCTTTAAGTTTCAGCCTTGCGACCATACTCCCCCCGGAAC 5 0.125 No Hit GGCGGTGTGTACAAAGGGCAGGGACGTAGTCAACGCGAGCTGATGACTCG 5 0.125 No Hit GTACAAAGGGCAGGGACGTAGTCAACGCGAGCTGATGACTCGCGCTTACT 5 0.125 No Hit GCCACGCTTTCACGGTTCGTATTCGTACTGGAAATCAGAATCAAACGAGC 5 0.125 No Hit CCCCGACTGTCCCTATTAATCATTACTCCGATCCCGAAGGCCAACACAAT 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 0.0 0.0 0.0 0.0 0.0 72-73 0.0 0.0 0.0 0.0 0.0 74-75 0.0 0.0 0.0 0.0 0.0 76-77 0.0 0.0 0.0 0.0 0.0 78-79 0.0 0.0 0.0 0.0 0.0 80-81 0.0 0.0 0.0 0.0 0.0 82-83 0.0 0.0 0.0 0.0 0.0 84-85 0.0 0.0 0.0 0.0 0.0 86-87 0.0125 0.0 0.0 0.0 0.0 88-89 0.025 0.0 0.0 0.0 0.0 90-91 0.0625 0.0 0.0 0.0 0.0 92-93 0.1125 0.0 0.0 0.0 0.0 94-95 0.125 0.0 0.0 0.0 0.0 96-97 0.125 0.0 0.0 0.0 0.0 98-99 0.125 0.0 0.0 0.0 0.0 100-101 0.1625 0.0 0.0 0.0 0.0 102-103 0.2 0.0 0.0 0.0 0.0 104-105 0.2 0.0 0.0 0.0 0.0 106-107 0.2 0.0 0.0 0.0 0.0 108-109 0.2 0.0 0.0 0.0 0.0 110-111 0.2 0.0 0.0 0.0 0.0 112-113 0.2625 0.0 0.0 0.0 0.0 114-115 0.3125 0.0 0.0 0.0 0.0 116-117 0.325 0.0 0.0 0.0 0.0 118-119 0.325 0.0 0.0 0.0 0.0 120-121 0.325 0.0 0.0 0.0 0.0 122-123 0.3875 0.0 0.0 0.0 0.0 124-125 0.425 0.0 0.0 0.0 0.0 126-127 0.475 0.0 0.0 0.0 0.0 128-129 0.5 0.0 0.0 0.0 0.0 130-131 0.5125 0.0 0.0 0.0 0.0 132-133 0.5375000000000001 0.0 0.0 0.0 0.0 134-135 0.55 0.0 0.0 0.0 0.0 136-137 0.55 0.0 0.0 0.0 0.0 138-139 0.55 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position CCGCAGG 10 0.006577216 146.82278 1 CTCCACG 10 0.006832588 144.9875 8 CGCAGGC 10 0.006832588 144.9875 2 TCCACGC 10 0.006832588 144.9875 9 CAGGCTC 10 0.006832588 144.9875 4 >>END_MODULE SRR6031161 read2 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR6031161_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 48 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 31.368 33.0 33.0 34.0 32.0 34.0 2 31.6765 34.0 33.0 34.0 31.0 34.0 3 31.76425 34.0 33.0 34.0 32.0 34.0 4 31.7335 34.0 33.0 34.0 32.0 34.0 5 31.80025 34.0 33.0 34.0 32.0 34.0 6 35.81075 38.0 38.0 38.0 36.0 38.0 7 35.89825 38.0 38.0 38.0 36.0 38.0 8 35.87975 38.0 38.0 38.0 36.0 38.0 9 35.97275 38.0 38.0 38.0 37.0 38.0 10-14 35.8958 38.0 38.0 38.0 36.6 38.0 15-19 35.71975 38.0 38.0 38.0 36.0 38.0 20-24 35.71085 38.0 38.0 38.0 36.0 38.0 25-29 35.834 38.0 38.0 38.0 36.0 38.0 30-34 36.24835 38.0 38.0 38.0 36.8 38.0 35-39 36.438599999999994 38.0 38.0 38.0 37.0 38.0 40-44 36.46515 38.0 38.0 38.0 37.0 38.0 45-49 36.43425 38.0 38.0 38.0 37.0 38.0 50-54 36.35935 38.0 38.0 38.0 37.0 38.0 55-59 35.9607 38.0 38.0 38.0 36.2 38.0 60-64 36.1145 38.0 38.0 38.0 36.0 38.0 65-69 36.01095 38.0 38.0 38.0 35.8 38.0 70-74 35.6298 38.0 38.0 38.0 34.6 38.0 75-79 35.8698 38.0 38.0 38.0 34.8 38.0 80-84 36.173199999999994 38.0 38.0 38.0 35.6 38.0 85-89 36.131750000000004 38.0 38.0 38.0 35.4 38.0 90-94 35.94225 38.0 38.0 38.0 34.6 38.0 95-99 35.9617 38.0 38.0 38.0 34.6 38.0 100-104 35.83325 38.0 38.0 38.0 34.0 38.0 105-109 35.388799999999996 38.0 38.0 38.0 33.4 38.0 110-114 35.1019 38.0 38.0 38.0 32.0 38.0 115-119 34.9166 38.0 38.0 38.0 30.4 38.0 120-124 34.9714 38.0 38.0 38.0 30.6 38.0 125-129 35.3907 38.0 38.0 38.0 32.4 38.0 130-134 35.302350000000004 38.0 38.0 38.0 32.4 38.0 135-139 35.11385 38.0 37.6 38.0 31.2 38.0 140-144 34.767250000000004 38.0 36.8 38.0 29.6 38.0 145-149 34.31505 38.0 36.0 38.0 27.6 38.0 150-151 30.58975 35.5 29.5 38.0 14.0 38.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 2 113.0 3 1.0 4 1.0 5 0.0 6 0.0 7 0.0 8 1.0 9 1.0 10 1.0 11 2.0 12 2.0 13 2.0 14 1.0 15 8.0 16 9.0 17 9.0 18 7.0 19 10.0 20 8.0 21 4.0 22 10.0 23 12.0 24 19.0 25 10.0 26 8.0 27 17.0 28 22.0 29 18.0 30 28.0 31 30.0 32 36.0 33 44.0 34 80.0 35 138.0 36 396.0 37 2952.0 >>END_MODULE >>Per base sequence content warn #Base G A T C 1 44.02231668437832 21.174282678002125 10.30818278427205 24.495217853347505 2 29.75878342947037 27.058206607236496 24.33141059255375 18.85159937073938 3 22.27177334732424 26.652675760755507 29.905561385099684 21.169989506820567 4 27.444794952681388 31.545741324921135 20.39957939011567 20.60988433228181 5 27.27987421383648 30.81761006289308 20.88574423480084 21.0167714884696 6 24.358974358974358 34.7723704866562 20.774463631606487 20.09419152276295 7 22.280334728033473 22.672594142259413 33.94351464435147 21.10355648535565 8 25.444560669456067 23.84937238493724 22.80334728033473 27.90271966527197 9 22.561293688054253 24.02190923317684 27.047470005216486 26.369327073552423 10-14 25.45359477124183 27.299346405228757 23.534640522875815 23.712418300653596 15-19 26.007249041340547 25.765614329988967 25.024951410411305 23.20218521825918 20-24 25.53471017920017 26.79068789741973 25.067002995428027 22.607598927952075 25-29 25.647465076126196 26.986867577041806 24.663841364516298 22.7018259823157 30-34 25.224806201550386 26.11886304909561 25.700258397932817 22.956072351421188 35-39 25.526883931325177 26.76056338028169 24.987149172406703 22.72540351598643 40-44 26.032527833358987 26.012005541018933 25.59642912113283 22.35903750448925 45-49 25.171110430074574 26.45826948615793 25.14557155991419 23.225048523853307 50-54 26.030702880320376 26.415772449555885 25.327309133850186 22.226215536273553 55-59 25.939223644499947 26.105734207513787 25.460505775835156 22.49453637215111 60-64 26.262156010759362 25.34657562590523 25.439685495551416 22.951582867783983 65-69 26.563066563066563 25.682465682465683 24.946904946904947 22.807562807562807 70-74 26.153846153846157 26.703296703296704 24.599686028257455 22.543171114599687 75-79 25.572479535799395 25.89368977308051 25.18391876489483 23.34991192622526 80-84 26.03985692386306 25.753704649974452 25.329586101175266 22.876852324987226 85-89 26.19884829027162 25.760587066197825 24.644549763033176 23.396014880497376 90-94 26.352557238284636 25.20524195604508 25.557085309265208 22.885115496405078 95-99 26.407191745837167 25.824905506180407 25.13024823781796 22.63765451016447 100-104 26.061666752457917 25.876357646574355 25.613836413239305 22.44813918772842 105-109 26.096033402922757 26.487473903966595 25.495824634655534 21.920668058455114 110-114 26.266121421830764 26.0301981755269 25.30145748138828 22.402222921254065 115-119 26.523862025515832 25.494828581928914 25.374074657426366 22.60723473512889 120-124 26.090363019065034 26.012013580569338 24.889004962131107 23.008618438234528 125-129 26.054565072188257 26.373118224323072 25.114319477983866 22.4579972255048 130-134 26.04506525285481 26.19800163132137 25.382340946166394 22.374592169657422 135-139 25.836005497022445 25.69857993586807 25.41863897796101 23.04677558914847 140-144 26.379310344827587 26.33874239350913 24.817444219066935 22.46450304259635 145-149 25.841848291136056 26.70257210449489 24.774752101474807 22.680827502894246 150-151 26.615384615384613 26.5 25.346153846153847 21.53846153846154 >>END_MODULE >>Per sequence GC content fail #GC Content Count 0 70.0 1 36.0 2 2.0 3 2.0 4 1.5 5 0.5 6 1.5 7 2.5 8 1.5 9 0.5 10 1.5 11 4.5 12 5.5 13 4.0 14 3.5 15 3.0 16 4.0 17 4.5 18 2.0 19 1.5 20 2.5 21 2.0 22 1.5 23 4.0 24 5.0 25 5.5 26 5.5 27 4.0 28 8.0 29 12.0 30 8.5 31 10.0 32 17.0 33 21.5 34 31.0 35 41.0 36 55.5 37 65.5 38 70.0 39 111.0 40 147.0 41 147.5 42 154.5 43 171.0 44 186.5 45 198.0 46 192.0 47 189.5 48 194.5 49 185.0 50 176.0 51 152.0 52 131.5 53 132.5 54 123.0 55 100.0 56 78.5 57 70.0 58 66.0 59 64.5 60 59.0 61 40.5 62 35.0 63 50.0 64 52.5 65 42.0 66 44.0 67 48.0 68 44.5 69 33.5 70 22.5 71 18.5 72 16.0 73 11.5 74 7.0 75 5.5 76 3.0 77 2.0 78 3.0 79 2.0 80 1.0 81 0.5 82 0.0 83 0.0 84 0.0 85 0.0 86 0.0 87 0.0 88 0.5 89 0.5 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 warn #Base N-Count 1 5.8999999999999995 2 4.65 3 4.7 4 4.9 5 4.6 6 4.45 7 4.3999999999999995 8 4.3999999999999995 9 4.15 10-14 4.375 15-19 4.8149999999999995 20-24 4.855 25-29 4.4350000000000005 30-34 3.25 35-39 2.73 40-44 2.545 45-49 2.11 50-54 2.6149999999999998 55-59 3.91 60-64 3.34 65-69 3.4750000000000005 70-74 4.45 75-79 3.49 80-84 2.15 85-89 1.8849999999999998 90-94 1.9449999999999998 95-99 2.11 100-104 2.8649999999999998 105-109 4.2 110-114 4.63 115-119 4.765 120-124 4.275 125-129 2.685 130-134 1.92 135-139 1.765 140-144 1.4000000000000001 145-149 0.6649999999999999 150-151 2.5 >>END_MODULE >>Sequence Length Distribution pass #Length Count 151 4000.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 91.2 #Duplication Level Percentage of deduplicated Percentage of total 1 95.9703947368421 87.52499999999999 2 2.7960526315789473 5.1 3 0.5482456140350876 1.5 4 0.3289473684210526 1.2 5 0.1370614035087719 0.625 6 0.0 0.0 7 0.08223684210526315 0.525 8 0.0 0.0 9 0.0 0.0 >10 0.10964912280701754 1.6500000000000001 >50 0.027412280701754384 1.875 >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 fail #Sequence Count Percentage Possible Source NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN 75 1.875 No Hit GGCGGGACTACCCGCTGAGTTTAAGCATATAAATAAGCGGAGGAGAAGAA 24 0.6 No Hit CCTGCCAGTAGTCATATGCTTGTCTCAAAGATTAAGCCATGCATGTGCAA 19 0.475 No Hit GGAGTCTGACATGCGTGCGAGTCGACGGGTTCTGAAACCTGGGATGCGCA 13 0.325 No Hit AAGGAGTCTGACATGCGTGCGAGTCGACGGGTTCTGAAACCTGGGATGCG 10 0.25 No Hit GTGAAATACCACTACTTTTAACGTTATTTTACTTATTCCGTGGGTCGGAA 7 0.17500000000000002 No Hit GTCAGGCGGGACTACCCGCTGAGTTTAAGCATATAAATAAGCGGAGGAGA 7 0.17500000000000002 No Hit CTTACCAGGTCCAGACATAGCAAGGATTGACAGACTGAGAGCTCTTTCTT 7 0.17500000000000002 No Hit GTCTGACATGCGTGCGAGTCGACGGGTTCTGAAACCTGGGATGCGCAAGG 5 0.125 No Hit ACTTACCAGGTCCAGACATAGCAAGGATTGACAGACTGAGAGCTCTTTCT 5 0.125 No Hit GTCATATGCTTGTCTCAAAGATTAAGCCATGCATGTGCAAGTATGAACTA 5 0.125 No Hit GCTGAGTTTAAGCATATAAATAAGCGGAGGAGAAGAAACTTACAAGGATT 5 0.125 No Hit AGGAGTCTGACATGCGTGCGAGTCGACGGGTTCTGAAACCTGGGATGCGC 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 0.0 0.0 0.0 0.0 0.0 72-73 0.0 0.0 0.0 0.0 0.0 74-75 0.0 0.0 0.0 0.0 0.0 76-77 0.0 0.0 0.0 0.0 0.0 78-79 0.0 0.0 0.0 0.0 0.0 80-81 0.0 0.0 0.0 0.0 0.0 82-83 0.0 0.0 0.0 0.0 0.0 84-85 0.0 0.0 0.0 0.0 0.0 86-87 0.0125 0.0 0.0 0.0 0.0 88-89 0.025 0.0 0.0 0.0 0.0 90-91 0.0625 0.0 0.0 0.0 0.0 92-93 0.1125 0.0 0.0 0.0 0.0 94-95 0.15 0.0 0.0 0.0 0.0 96-97 0.15 0.0 0.0 0.0 0.0 98-99 0.15 0.0 0.0 0.0 0.0 100-101 0.175 0.0 0.0 0.0 0.0 102-103 0.2 0.0 0.0 0.0 0.0 104-105 0.2 0.0 0.0 0.0 0.0 106-107 0.2 0.0 0.0 0.0 0.0 108-109 0.2 0.0 0.0 0.0 0.0 110-111 0.2 0.0 0.0 0.0 0.0 112-113 0.2625 0.0 0.0 0.0 0.0 114-115 0.3125 0.0 0.0 0.0 0.0 116-117 0.35 0.0 0.0 0.0 0.0 118-119 0.35 0.0 0.0 0.0 0.0 120-121 0.35 0.0 0.0 0.0 0.0 122-123 0.3875 0.0 0.0 0.0 0.0 124-125 0.425 0.0 0.0 0.0 0.0 126-127 0.475 0.0 0.0 0.0 0.0 128-129 0.5 0.0 0.0 0.0 0.0 130-131 0.5125 0.0 0.0 0.0 0.0 132-133 0.5375000000000001 0.0 0.0 0.0 0.0 134-135 0.55 0.0 0.0 0.0 0.0 136-137 0.55 0.0 0.0 0.0 0.0 138-139 0.55 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position CGACGGG 20 0.0053304103 29.638958 20-24 CGAGTCG 20 0.005537632 29.409794 15-19 GCGAGTC 20 0.005537632 29.409794 15-19 TGCGTGC 20 0.0056792814 29.258974 10-14 GCGTGCG 20 0.0056792814 29.258974 10-14 GGATGCG 20 0.0060459636 28.888607 40-44 ACCTGGG 20 0.0060459636 28.888607 35-39 CTGAAAC 20 0.0060459636 28.888607 30-34 CGCAAGG 20 0.0060459636 28.888607 45-49 TGAAACC 20 0.0060459636 28.888607 30-34 CCTGGGA 20 0.0060459636 28.888607 35-39 CTGACGA 30 0.0014758725 24.382479 3 GTTGGAG 35 0.0036148003 20.634722 8 AGTTGGA 40 0.007823444 18.05538 120-124 >>END_MODULE Read 1186556 spots for SRR6031161.sra Written 1186556 spots for SRR6031161.sra Read 1186556 spots for SRR6031161.sra Written 1186556 spots for SRR6031161.sra Read 1186556 spots for SRR6031161.sra Written 1186556 spots for SRR6031161.sra Read 1186556 spots for SRR6031161.sra Written 1186556 spots for SRR6031161.sra Read 1186556 spots for SRR6031161.sra Written 1186556 spots for SRR6031161.sra Read 1186556 spots for SRR6031161.sra Written 1186556 spots for SRR6031161.sra Read 1186556 spots for SRR6031161.sra Written 1186556 spots for SRR6031161.sra Read 1186556 spots for SRR6031161.sra Written 1186556 spots for SRR6031161.sra Read 1186556 spots for SRR6031161.sra Written 1186556 spots for SRR6031161.sra Read 1186556 spots for SRR6031161.sra Written 1186556 spots for SRR6031161.sra Read 1186556 spots for SRR6031161.sra Written 1186556 spots for SRR6031161.sra Read 1186556 spots for SRR6031161.sra Written 1186556 spots for SRR6031161.sra Read 1186561 spots for SRR6031161.sra Written 1186561 spots for SRR6031161.sra Read 1186556 spots for SRR6031161.sra Written 1186556 spots for SRR6031161.sra Read 1186556 spots for SRR6031161.sra Written 1186556 spots for SRR6031161.sra Read 1186556 spots for SRR6031161.sra Written 1186556 spots for SRR6031161.sra Read 1186556 spots for SRR6031161.sra Written 1186556 spots for SRR6031161.sra Read 1186556 spots for SRR6031161.sra Written 1186556 spots for SRR6031161.sra Read 1186556 spots for SRR6031161.sra Written 1186556 spots for SRR6031161.sra Read 1186556 spots for SRR6031161.sra Written 1186556 spots for SRR6031161.sra SRR ids: ['SRR6031161.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_66ebiiie SRR6031161.sra spots: 23731125 blocks: [[1, 1186556], [1186557, 2373112], [2373113, 3559668], [3559669, 4746224], [4746225, 5932780], [5932781, 7119336], [7119337, 8305892], [8305893, 9492448], [9492449, 10679004], [10679005, 11865560], [11865561, 13052116], [13052117, 14238672], [14238673, 15425228], [15425229, 16611784], [16611785, 17798340], [17798341, 18984896], [18984897, 20171452], [20171453, 21358008], [21358009, 22544564], [22544565, 23731125]] SRR6031161 file size 8019999 SRR6031161 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 SRR6031161 SRR6031161_1.fastq SRR6031161_2.fastq Input file: SRR6031161_1.fastq Paired file: SRR6031161_2.fastq trimmed: SRR6031161-trimmed-pair1.fastq, SRR6031161-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 Dec 10 00:28:06 2024 >> started Tue Dec 10 00:28:37 2024 >> done (30.747s) 23731125 read pairs processed; of these: 23993 ( 0.10%) short read pairs filtered out after trimming by size control 39609 ( 0.17%) empty read pairs filtered out after trimming by size control 23667523 (99.73%) read pairs available; of these: 7853206 (33.18%) trimmed read pairs available after processing 15814317 (66.82%) untrimmed read pairs available after processing Length distribution of reads after trimming: length count percentage 18 1 0.00% 19 3 0.00% 20 3 0.00% 21 7 0.00% 22 7 0.00% 23 7 0.00% 24 6 0.00% 25 14 0.00% 26 10 0.00% 27 10 0.00% 28 8 0.00% 29 9 0.00% 30 11 0.00% 31 5 0.00% 32 9 0.00% 33 8 0.00% 34 12 0.00% 35 10 0.00% 36 6 0.00% 37 15 0.00% 38 7 0.00% 39 8 0.00% 40 16 0.00% 41 12 0.00% 42 15 0.00% 43 12 0.00% 44 22 0.00% 45 13 0.00% 46 26 0.00% 47 24 0.00% 48 31 0.00% 49 33 0.00% 50 40 0.00% 51 44 0.00% 52 36 0.00% 53 55 0.00% 54 60 0.00% 55 62 0.00% 56 57 0.00% 57 84 0.00% 58 102 0.00% 59 94 0.00% 60 88 0.00% 61 125 0.00% 62 125 0.00% 63 148 0.00% 64 125 0.00% 65 159 0.00% 66 160 0.00% 67 184 0.00% 68 193 0.00% 69 229 0.00% 70 279 0.00% 71 301 0.00% 72 353 0.00% 73 387 0.00% 74 371 0.00% 75 449 0.00% 76 477 0.00% 77 611 0.00% 78 601 0.00% 79 658 0.00% 80 784 0.00% 81 911 0.00% 82 954 0.00% 83 1120 0.00% 84 2031 0.01% 85 2570 0.01% 86 2905 0.01% 87 3140 0.01% 88 3503 0.01% 89 3113 0.01% 90 3257 0.01% 91 3006 0.01% 92 3086 0.01% 93 3223 0.01% 94 3183 0.01% 95 3454 0.01% 96 3574 0.02% 97 3576 0.02% 98 3687 0.02% 99 3932 0.02% 100 4071 0.02% 101 4261 0.02% 102 4421 0.02% 103 4536 0.02% 104 4803 0.02% 105 6170 0.03% 106 5701 0.02% 107 5534 0.02% 108 6041 0.03% 109 6017 0.03% 110 6414 0.03% 111 6787 0.03% 112 7550 0.03% 113 8178 0.03% 114 9296 0.04% 115 10363 0.04% 116 10202 0.04% 117 10053 0.04% 118 9708 0.04% 119 9563 0.04% 120 10158 0.04% 121 9955 0.04% 122 10721 0.05% 123 11369 0.05% 124 12183 0.05% 125 12721 0.05% 126 13378 0.06% 127 13877 0.06% 128 14815 0.06% 129 15821 0.07% 130 17216 0.07% 131 18042 0.08% 132 19430 0.08% 133 20743 0.09% 134 22139 0.09% 135 24253 0.10% 136 26338 0.11% 137 28741 0.12% 138 31388 0.13% 139 34654 0.15% 140 39353 0.17% 141 43945 0.19% 142 50072 0.21% 143 60571 0.26% 144 73628 0.31% 145 94872 0.40% 146 127975 0.54% 147 188729 0.80% 148 331368 1.40% 149 821925 3.47% 150 5451111 23.03% 151 15814317 66.82% 23667523 reads passed initial QC criterion=sequence-density sequence-density=1.81 sequence-density-rank=1 fanout-score=2.44 fanout-score-rank=26 prefix-density=1.87 prefix-fanout=2.4 sequence=CCCAGCTCACGTTCCCTATTGGTGGGTGAACAATCCAACACTTGGTGAATTCTGCTTCACAATGATAGGAAGAGCCGACATCGAAGGATCAAAAAGCAACGTCGCTATGAACGCTTGGCTGCCACAAGCCAGTTATCCCTGTGGTAACTTTTCTGACACCTCTAGCTTCAAACTCCGAAGATCTAAAGGATCGATAGGCCACGCTTTCACGGTTCGTATTCGTACTGGAAATCAGAATCAAACGAGCTTTTACCCTTTTGTTCCACACGAGATTTCTGTTCTCGTTGAGCTCATCTTAGGACACCTGCGTTATCTTTTAACAGATGTGCCGCCCCAGCCAAACTCCCCACCTGACAATGTCTTCCGCCCGGATCGGCCCGGTCAGACCGGGCCTTGGAGCCAAAAGGAGGGGACTTGCCCCGCTTCCGACCCACGGAATAAGTAAAATAACGTTAAAAGTAGTGGTATTTCACTTGCGCCCGTAAAGGCTCCCACTTATCCTACACCTCTC criterion=fanout-score sequence-density=0.05 sequence-density-rank=13 fanout-score=109.83 fanout-score-rank=1 prefix-density=0.27 prefix-fanout=21.6 sequence=ATCTTCTTCTTGTCGTCCGC criterion=sequence-density sequence-density=0.20 sequence-density-rank=1 fanout-score=2.56 fanout-score-rank=31 prefix-density=0.51 prefix-fanout=1.0 sequence=GAGAAACGGCTGCCACATCCAAG criterion=fanout-score sequence-density=0.01 sequence-density-rank=31 fanout-score=504.93 fanout-score-rank=1 prefix-density=0.39 prefix-fanout=17.5 sequence=GCCGCCGCCCCTCGTCCTCTGTGTTCCTTCTCCGAGTTTCAGCCATGGGTAAGGAGAAGACTCACATCAACATCGTGGTCATTGGCCATGTCGACTCTGGCAAGTCGACCACCACTGGCCACCTGATCTACAAGCTTGGAGGTATTGACAAGCGTGTGATCGAGAGGTTCGAGAAGGAGGCTGC SRR6031161 testing PE reads STAR mapping to Ensembl genome Started job on | Dec 10 00:30:09 Started mapping on | Dec 10 00:30:09 Finished on | Dec 10 00:33:02 Mapping speed, Million of reads per hour | 492.50 Number of input reads | 23667523 Average input read length | 291 UNIQUE READS: Uniquely mapped reads number | 16707165 Uniquely mapped reads % | 70.59% Average mapped length | 291.40 Number of splices: Total | 18558737 Number of splices: Annotated (sjdb) | 17649553 Number of splices: GT/AG | 18318686 Number of splices: GC/AG | 215596 Number of splices: AT/AC | 13629 Number of splices: Non-canonical | 10826 Mismatch rate per base, % | 0.10% Deletion rate per base | 0.00% Deletion average length | 1.41 Insertion rate per base | 0.00% Insertion average length | 1.11 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 185942 % of reads mapped to multiple loci | 0.79% Number of reads mapped to too many loci | 863217 % of reads mapped to too many loci | 3.65% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 4.81% % of reads unmapped: other | 20.16% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 6787617 6787617 6787617 N_multimapping 185942 185942 185942 N_noFeature 748927 16248910 871479 N_ambiguous 415224 4223 79199 UnstrandedReadsAssigned:15543014 PositiveStrandReadsAssigned:454032 NegativeStrandReadsAssigned:15756487 Dataset is classified negative stranded MeadianReadLen=151 20thPercentileLength=150 echo kmer=145 SRR6031161 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: SRR6031161-trimmed-pair1.fastq SRR6031161-trimmed-pair2.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 23,667,523 reads, 16,206,072 reads pseudoaligned [quant] estimated average fragment length: 433.129 [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,205 rounds 52973 SRR6031161.ke.tsv 35125 SRR6031161.se.tsv 88098 total ==> SRR6031161.ke.tsv <== target_id length eff_length est_counts tpm PNS24245 936 505.274 0 0 PNS24247 1044 611.871 108.222 15.7445 PNS24249 1928 1495.87 34.7687 2.06902 PNS24246 1044 611.871 108.222 15.7445 PNS24248 1044 611.871 108.222 15.7445 PNS24244 1471 1038.87 59.5638 5.10377 PNS24243 293 65.6311 0 0 KQK14069 1603 1170.87 2521.52 191.701 KQK14071 474 131.159 18.4797 12.5421 ==> SRR6031161.se.tsv <== BRADI_1g14170v3 2569 BRADI_1g53295v3 117 BRADI_1g59795v3 604 BRADI_1g07683v3 0 BRADI_1g00485v3 70 BRADI_1g20270v3 655 BRADI_1g74790v3 209 BRADI_1g09890v3 0 BRADI_1g77505v3 177 BRADI_1g48960v3 0 SRR6031161 completed mapping pipeline successfully