Starting /dee2/code/volunteer_pipeline.sh SRR6958193 current disk space = 1550404497408 free memory = 1604367992 SRR6958193 SRAfilesize c0c4a2c412dd38c32fabf9099339e34a SRR6958193.sra SRR6958193.sra file validated SRR6958193 is paired end SRR6958193 is conventional basespace SRR6958193 read1 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR6958193_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 48 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 29.87325 33.0 32.0 33.0 18.0 33.0 2 28.95 31.0 27.0 33.0 18.0 33.0 3 31.58825 33.0 31.0 33.0 28.0 33.0 4 32.60025 33.0 33.0 33.0 32.0 34.0 5 33.04625 33.0 33.0 34.0 32.0 34.0 6 37.13225 38.0 38.0 38.0 36.0 38.0 7 37.38025 38.0 38.0 38.0 37.0 38.0 8 37.514 38.0 38.0 38.0 37.0 38.0 9 37.633 38.0 38.0 38.0 38.0 38.0 10-14 37.594350000000006 38.0 38.0 38.0 38.0 38.0 15-19 37.4735 38.0 38.0 38.0 38.0 38.0 20-24 37.61155 38.0 38.0 38.0 38.0 38.0 25-29 37.64205 38.0 38.0 38.0 38.0 38.0 30-34 37.5712 38.0 38.0 38.0 38.0 38.0 35-39 37.55365 38.0 38.0 38.0 38.0 38.0 40-44 37.5676 38.0 38.0 38.0 38.0 38.0 45-49 37.538599999999995 38.0 38.0 38.0 38.0 38.0 50-54 37.5148 38.0 38.0 38.0 38.0 38.0 55-59 37.472699999999996 38.0 38.0 38.0 37.8 38.0 60-64 37.32595 38.0 38.0 38.0 37.0 38.0 65-69 37.431400000000004 38.0 38.0 38.0 37.2 38.0 70-74 37.4033 38.0 38.0 38.0 37.6 38.0 75-79 37.346199999999996 38.0 38.0 38.0 37.0 38.0 80-84 37.361000000000004 38.0 38.0 38.0 37.0 38.0 85-89 36.174200000000006 38.0 36.8 38.0 31.0 38.0 90-94 37.1074 38.0 38.0 38.0 35.8 38.0 95-99 37.14834999999999 38.0 38.0 38.0 36.2 38.0 100-104 37.05765 38.0 38.0 38.0 36.0 38.0 105-109 36.952600000000004 38.0 38.0 38.0 35.6 38.0 110-114 36.5824 38.0 37.8 38.0 34.0 38.0 115-119 36.798 38.0 38.0 38.0 35.0 38.0 120-124 36.669650000000004 38.0 38.0 38.0 34.6 38.0 125-129 36.461850000000005 38.0 38.0 38.0 34.2 38.0 130-134 36.327 38.0 38.0 38.0 34.0 38.0 135-139 36.2016 38.0 38.0 38.0 33.4 38.0 140-144 35.568549999999995 38.0 37.0 38.0 30.2 38.0 145-149 33.89745 37.6 33.6 38.0 24.2 38.0 150-151 31.84725 35.5 32.0 38.0 16.5 38.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 2 1.0 3 0.0 4 0.0 5 0.0 6 0.0 7 1.0 8 0.0 9 1.0 10 0.0 11 0.0 12 0.0 13 0.0 14 1.0 15 1.0 16 0.0 17 0.0 18 1.0 19 0.0 20 3.0 21 0.0 22 3.0 23 2.0 24 4.0 25 5.0 26 7.0 27 12.0 28 17.0 29 25.0 30 24.0 31 33.0 32 53.0 33 69.0 34 124.0 35 211.0 36 599.0 37 2803.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 45.93517534537726 9.909670563230605 5.579171094580234 38.5759829968119 2 23.7 13.25 34.300000000000004 28.749999999999996 3 21.5 15.9 25.324999999999996 37.275000000000006 4 26.575 26.025 21.15 26.25 5 26.0 29.049999999999997 22.650000000000002 22.3 6 21.725 32.15 25.0 21.125 7 16.650000000000002 22.0 41.4 19.950000000000003 8 19.15 23.724999999999998 30.675 26.450000000000003 9 20.7 19.775000000000002 35.15 24.375 10-14 22.43 26.529999999999998 26.115 24.925 15-19 23.075000000000003 25.419999999999998 26.279999999999998 25.224999999999998 20-24 22.785 25.979999999999997 26.105 25.130000000000003 25-29 22.93 25.955000000000002 25.96 25.155 30-34 22.5 25.61 26.125 25.765 35-39 22.720000000000002 25.374999999999996 26.505000000000003 25.4 40-44 23.14 25.755 25.430000000000003 25.674999999999997 45-49 22.436731019305793 25.58267480244073 26.182854856456938 25.797739321796538 50-54 23.1 25.82 25.490000000000002 25.590000000000003 55-59 22.585 25.474999999999998 26.275 25.665 60-64 22.919999999999998 25.235000000000003 25.44 26.405 65-69 22.96114805740287 26.17130856542827 25.721286064303218 25.146257312865643 70-74 22.98 25.074999999999996 26.135 25.81 75-79 23.5 25.130000000000003 25.915 25.455 80-84 23.150000000000002 25.09 26.14 25.619999999999997 85-89 22.900000000000002 25.47 26.22 25.41 90-94 23.57 25.575 25.314999999999998 25.540000000000003 95-99 22.825 25.424999999999997 25.835 25.915 100-104 23.91 25.230000000000004 25.615 25.245 105-109 23.26 25.27 25.290000000000003 26.179999999999996 110-114 23.630000000000003 25.235000000000003 25.69 25.445 115-119 22.73 25.775 25.735000000000003 25.759999999999998 120-124 23.599999999999998 26.135 25.205 25.06 125-129 23.735 25.21 25.624999999999996 25.430000000000003 130-134 23.91 26.325 24.035 25.729999999999997 135-139 23.415 25.35 25.295 25.94 140-144 23.715 25.619999999999997 25.4 25.264999999999997 145-149 23.195 25.924999999999997 25.25 25.629999999999995 150-151 24.177199349267926 24.389938681016144 25.41609310474284 26.016768864973095 >>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 0.0 6 0.0 7 0.0 8 0.0 9 0.5 10 0.5 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 0.5 24 0.5 25 1.5 26 1.5 27 2.5 28 3.5 29 3.5 30 7.0 31 9.5 32 13.5 33 18.5 34 28.0 35 44.0 36 48.5 37 60.0 38 84.0 39 110.5 40 131.0 41 153.0 42 196.0 43 203.5 44 190.5 45 185.5 46 182.0 47 205.0 48 214.0 49 201.5 50 182.0 51 152.0 52 131.5 53 124.0 54 121.5 55 109.5 56 96.0 57 83.0 58 72.0 59 66.0 60 67.0 61 69.0 62 54.0 63 47.0 64 50.5 65 48.0 66 42.0 67 38.5 68 31.5 69 26.0 70 23.5 71 21.5 72 15.5 73 7.0 74 8.0 75 7.0 76 3.5 77 1.0 78 0.0 79 0.0 80 0.5 81 0.5 82 0.5 83 0.5 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 warn #Base N-Count 1 5.8999999999999995 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 0.03 50-54 0.0 55-59 0.0 60-64 0.0 65-69 0.005 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 0.11249999999999999 >>END_MODULE >>Sequence Length Distribution pass #Length Count 151 4000.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 99.52499999999999 #Duplication Level Percentage of deduplicated Percentage of total 1 99.54785229841748 99.075 2 0.42702838482793265 0.8500000000000001 3 0.025119316754584273 0.075 4 0.0 0.0 5 0.0 0.0 6 0.0 0.0 7 0.0 0.0 8 0.0 0.0 9 0.0 0.0 >10 0.0 0.0 >50 0.0 0.0 >100 0.0 0.0 >500 0.0 0.0 >1k 0.0 0.0 >5k 0.0 0.0 >10k+ 0.0 0.0 >>END_MODULE >>Overrepresented sequences pass >>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 0.025 0.0 0.0 0.0 0.0 5 0.025 0.0 0.0 0.0 0.0 6 0.025 0.0 0.0 0.0 0.0 7 0.025 0.0 0.0 0.0 0.0 8 0.025 0.0 0.0 0.0 0.0 9 0.025 0.0 0.0 0.0 0.0 10-11 0.025 0.0 0.0 0.0 0.0 12-13 0.025 0.0 0.0 0.0 0.0 14-15 0.025 0.0 0.0 0.0 0.0 16-17 0.025 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 0.05 0.0 0.0 0.0 0.0 48-49 0.05 0.0 0.0 0.0 0.0 50-51 0.05 0.0 0.0 0.0 0.0 52-53 0.05 0.0 0.0 0.0 0.0 54-55 0.05 0.0 0.0 0.0 0.0 56-57 0.05 0.0 0.0 0.0 0.0 58-59 0.05 0.0 0.0 0.0 0.0 60-61 0.05 0.0 0.0 0.0 0.0 62-63 0.05 0.0 0.0 0.0 0.0 64-65 0.05 0.0 0.0 0.0 0.0 66-67 0.05 0.0 0.0 0.0 0.0 68-69 0.05 0.0 0.0 0.0 0.0 70-71 0.0625 0.0 0.0 0.0 0.0 72-73 0.075 0.0 0.0 0.0 0.0 74-75 0.075 0.0 0.0 0.0 0.0 76-77 0.1 0.0 0.0 0.0 0.0 78-79 0.15 0.0 0.0 0.0 0.0 80-81 0.175 0.0 0.0 0.0 0.0 82-83 0.2 0.0 0.0 0.0 0.0 84-85 0.2375 0.0 0.0 0.0 0.0 86-87 0.35 0.0 0.0 0.0 0.0 88-89 0.4625 0.0 0.0 0.0 0.0 90-91 0.5125 0.0 0.0 0.0 0.0 92-93 0.575 0.0 0.0 0.0 0.0 94-95 0.7125 0.0 0.0 0.0 0.0 96-97 0.8625 0.0 0.0 0.0 0.0 98-99 1.025 0.0 0.0 0.0 0.0 100-101 1.2125 0.0 0.0 0.0 0.0 102-103 1.4249999999999998 0.0 0.0 0.0 0.0 104-105 1.7125 0.0 0.0 0.0 0.0 106-107 1.8250000000000002 0.0 0.0 0.0 0.0 108-109 2.0125 0.0 0.0 0.0 0.0 110-111 2.1375 0.0 0.0 0.0 0.0 112-113 2.4375 0.0 0.0 0.0 0.0 114-115 2.7125 0.0 0.0 0.0 0.0 116-117 2.9875 0.0 0.0 0.0 0.0 118-119 3.4625 0.0 0.0 0.0 0.0 120-121 3.75 0.0 0.0 0.0 0.0 122-123 4.175000000000001 0.0 0.0 0.0 0.0 124-125 4.5 0.0 0.0 0.0 0.0 126-127 4.9375 0.0 0.0 0.0 0.0 128-129 5.525 0.0 0.0 0.0 0.0 130-131 6.1375 0.0 0.0 0.0 0.0 132-133 6.7125 0.0 0.0 0.0 0.0 134-135 7.15 0.0 0.0 0.0 0.0 136-137 7.6 0.0 0.0 0.0 0.0 138-139 8.2625 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position GAAGCAG 10 0.006841402 144.925 9 >>END_MODULE SRR6958193 read2 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR6958193_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 49 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 32.612 33.0 33.0 34.0 32.0 34.0 2 33.0775 34.0 33.0 34.0 32.0 34.0 3 33.1085 34.0 33.0 34.0 32.0 34.0 4 33.174 34.0 33.0 34.0 33.0 34.0 5 32.93575 34.0 33.0 34.0 32.0 34.0 6 37.33025 38.0 38.0 38.0 37.0 38.0 7 37.3885 38.0 38.0 38.0 38.0 38.0 8 37.35 38.0 38.0 38.0 38.0 38.0 9 37.28375 38.0 38.0 38.0 38.0 38.0 10-14 37.132600000000004 38.0 38.0 38.0 37.0 38.0 15-19 37.321349999999995 38.0 38.0 38.0 37.4 38.0 20-24 37.34665 38.0 38.0 38.0 38.0 38.0 25-29 36.97525 38.0 38.0 38.0 35.8 38.0 30-34 37.35975 38.0 38.0 38.0 37.8 38.0 35-39 37.2102 38.0 38.0 38.0 37.2 38.0 40-44 36.8765 38.0 38.0 38.0 36.2 38.0 45-49 36.94695 38.0 38.0 38.0 36.4 38.0 50-54 36.873900000000006 38.0 38.0 38.0 36.0 38.0 55-59 37.21955 38.0 38.0 38.0 37.0 38.0 60-64 37.1917 38.0 38.0 38.0 37.0 38.0 65-69 36.388850000000005 38.0 38.0 38.0 33.0 38.0 70-74 36.986000000000004 38.0 38.0 38.0 36.2 38.0 75-79 37.146499999999996 38.0 38.0 38.0 37.0 38.0 80-84 37.0015 38.0 38.0 38.0 36.0 38.0 85-89 36.87235 38.0 38.0 38.0 35.8 38.0 90-94 36.6507 38.0 38.0 38.0 35.2 38.0 95-99 35.33395 38.0 36.2 38.0 27.8 38.0 100-104 36.65885 38.0 38.0 38.0 34.6 38.0 105-109 36.09955000000001 38.0 37.6 38.0 32.6 38.0 110-114 36.52815 38.0 38.0 38.0 34.8 38.0 115-119 36.45415 38.0 38.0 38.0 34.4 38.0 120-124 35.4048 38.0 36.6 38.0 28.2 38.0 125-129 35.88425 38.0 37.4 38.0 32.8 38.0 130-134 35.864599999999996 38.0 38.0 38.0 32.4 38.0 135-139 34.2497 38.0 34.2 38.0 25.2 38.0 140-144 34.866299999999995 38.0 36.2 38.0 29.8 38.0 145-149 33.61715 38.0 34.4 38.0 21.0 38.0 150-151 29.341 35.5 19.0 38.0 7.5 38.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 2 5.0 3 5.0 4 4.0 5 0.0 6 0.0 7 0.0 8 0.0 9 1.0 10 1.0 11 0.0 12 1.0 13 0.0 14 1.0 15 1.0 16 3.0 17 2.0 18 4.0 19 2.0 20 2.0 21 7.0 22 1.0 23 7.0 24 13.0 25 16.0 26 23.0 27 21.0 28 23.0 29 32.0 30 39.0 31 55.0 32 75.0 33 103.0 34 126.0 35 236.0 36 576.0 37 2615.0 >>END_MODULE >>Per base sequence content warn #Base G A T C 1 40.949999999999996 19.5 8.774999999999999 30.775000000000002 2 29.775000000000002 22.425 30.025000000000002 17.775 3 21.625 24.349999999999998 28.95 25.074999999999996 4 24.7 32.125 21.425 21.75 5 26.525 34.65 19.575 19.25 6 22.25 37.35 20.724999999999998 19.675 7 23.400000000000002 18.65 35.449999999999996 22.5 8 23.9 22.95 24.325 28.825 9 22.74774774774775 23.723723723723726 27.37737737737738 26.151151151151154 10-14 25.745 25.955000000000002 24.095 24.205 15-19 25.950190038007605 25.53510702140428 24.56991398279656 23.94478895779156 20-24 25.169999999999998 25.564999999999998 24.884999999999998 24.38 25-29 26.072607260726073 25.63256325632563 24.277427742774275 24.01740174017402 30-34 25.074999999999996 25.81 24.67 24.445 35-39 25.432629788936683 25.477643292987896 24.852455736721016 24.237271181354405 40-44 25.616280814040703 25.056252812640633 24.8012400620031 24.526226311315565 45-49 25.241262063103154 25.726286314315715 24.401220061003052 24.63123156157808 50-54 25.541385346336583 25.771442860715176 24.746186546636658 23.940985246311577 55-59 26.113056528264135 25.62281140570285 24.252126063031515 24.012006003001503 60-64 25.424999999999997 25.575 25.255 23.745 65-69 25.535000000000004 26.590000000000003 24.305 23.57 70-74 25.929999999999996 25.380000000000003 24.93 23.76 75-79 26.090218043608722 25.700140028005602 24.43988797759552 23.769753950790157 80-84 25.431357839459867 26.066516629157288 25.021255313828455 23.48087021755439 85-89 25.56 25.635 25.22 23.585 90-94 26.06521304260852 25.800160032006403 24.16983396679336 23.96479295859172 95-99 25.19 26.57 24.66 23.580000000000002 100-104 25.665 26.395000000000003 24.525 23.415 105-109 25.970194038807758 25.565113022604518 24.989997999599918 23.4746949389878 110-114 26.405281056211244 25.870174034806958 24.93498699739948 22.789557911582317 115-119 26.855 26.179999999999996 24.310000000000002 22.655 120-124 26.265 26.41 24.59 22.735 125-129 26.985 25.665 24.5 22.85 130-134 27.205000000000002 26.22 24.08 22.495 135-139 27.224999999999998 26.384999999999998 24.29 22.1 140-144 27.185 26.26 24.37 22.185 145-149 27.589999999999996 26.33 24.425 21.654999999999998 150-151 27.392120075046904 26.29143214509068 24.165103189493433 22.15134459036898 >>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 0.0 9 0.0 10 0.0 11 0.0 12 0.0 13 0.0 14 0.0 15 0.0 16 0.5 17 0.5 18 0.5 19 0.5 20 0.5 21 1.5 22 1.0 23 0.0 24 0.0 25 0.5 26 2.5 27 4.0 28 3.5 29 2.5 30 4.5 31 9.5 32 13.5 33 17.0 34 22.5 35 32.5 36 46.0 37 58.5 38 78.0 39 104.5 40 125.5 41 150.0 42 175.0 43 186.0 44 183.5 45 199.0 46 209.0 47 194.0 48 181.5 49 161.0 50 153.0 51 157.0 52 145.0 53 122.5 54 100.5 55 89.0 56 83.0 57 85.0 58 85.0 59 72.0 60 65.5 61 70.0 62 74.5 63 70.5 64 70.5 65 66.0 66 54.5 67 55.0 68 54.5 69 40.0 70 29.0 71 29.5 72 25.5 73 15.0 74 6.0 75 5.0 76 4.5 77 0.5 78 1.0 79 1.5 80 0.5 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 0.0 3 0.0 4 0.0 5 0.0 6 0.0 7 0.0 8 0.0 9 0.1 10-14 0.0 15-19 0.02 20-24 0.0 25-29 0.01 30-34 0.0 35-39 0.03 40-44 0.005 45-49 0.005 50-54 0.025 55-59 0.05 60-64 0.0 65-69 0.0 70-74 0.0 75-79 0.02 80-84 0.025 85-89 0.0 90-94 0.02 95-99 0.0 100-104 0.0 105-109 0.02 110-114 0.02 115-119 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 0.0625 >>END_MODULE >>Sequence Length Distribution pass #Length Count 151 4000.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 99.225 #Duplication Level Percentage of deduplicated Percentage of total 1 99.29453262786596 98.52499999999999 2 0.6298815822625347 1.25 3 0.07558578987150416 0.22499999999999998 4 0.0 0.0 5 0.0 0.0 6 0.0 0.0 7 0.0 0.0 8 0.0 0.0 9 0.0 0.0 >10 0.0 0.0 >50 0.0 0.0 >100 0.0 0.0 >500 0.0 0.0 >1k 0.0 0.0 >5k 0.0 0.0 >10k+ 0.0 0.0 >>END_MODULE >>Overrepresented sequences pass >>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 0.025 0.0 0.0 0.0 0.0 5 0.025 0.0 0.0 0.0 0.0 6 0.025 0.0 0.0 0.0 0.0 7 0.025 0.0 0.0 0.0 0.0 8 0.025 0.0 0.0 0.0 0.0 9 0.025 0.0 0.0 0.0 0.0 10-11 0.025 0.0 0.0 0.0 0.0 12-13 0.025 0.0 0.0 0.0 0.0 14-15 0.025 0.0 0.0 0.0 0.0 16-17 0.025 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 0.05 0.0 0.0 0.0 0.0 48-49 0.05 0.0 0.0 0.0 0.0 50-51 0.05 0.0 0.0 0.0 0.0 52-53 0.05 0.0 0.0 0.0 0.0 54-55 0.05 0.0 0.0 0.0 0.0 56-57 0.05 0.0 0.0 0.0 0.0 58-59 0.05 0.0 0.0 0.0 0.0 60-61 0.05 0.0 0.0 0.0 0.0 62-63 0.05 0.0 0.0 0.0 0.0 64-65 0.05 0.0 0.0 0.0 0.0 66-67 0.05 0.0 0.0 0.0 0.0 68-69 0.05 0.0 0.0 0.0 0.0 70-71 0.0625 0.0 0.0 0.0 0.0 72-73 0.075 0.0 0.0 0.0 0.0 74-75 0.075 0.0 0.0 0.0 0.0 76-77 0.1 0.0 0.0 0.0 0.0 78-79 0.15 0.0 0.0 0.0 0.0 80-81 0.175 0.0 0.0 0.0 0.0 82-83 0.2 0.0 0.0 0.0 0.0 84-85 0.2375 0.0 0.0 0.0 0.0 86-87 0.32499999999999996 0.0 0.0 0.0 0.0 88-89 0.4375 0.0 0.0 0.0 0.0 90-91 0.4875 0.0 0.0 0.0 0.0 92-93 0.55 0.0 0.0 0.0 0.0 94-95 0.6875 0.0 0.0 0.0 0.0 96-97 0.8375 0.0 0.0 0.0 0.0 98-99 1.0 0.0 0.0 0.0 0.0 100-101 1.1749999999999998 0.0 0.0 0.0 0.0 102-103 1.375 0.0 0.0 0.0 0.0 104-105 1.6625 0.0 0.0 0.0 0.0 106-107 1.7875 0.0 0.0 0.0 0.0 108-109 1.975 0.0 0.0 0.0 0.0 110-111 2.0875 0.0 0.0 0.0 0.0 112-113 2.375 0.0 0.0 0.0 0.0 114-115 2.6375 0.0 0.0 0.0 0.0 116-117 2.9000000000000004 0.0 0.0 0.0 0.0 118-119 3.3625 0.0 0.0 0.0 0.0 120-121 3.6500000000000004 0.0 0.0 0.0 0.0 122-123 4.025 0.0 0.0 0.0 0.0 124-125 4.35 0.0 0.0 0.0 0.0 126-127 4.8 0.0 0.0 0.0 0.0 128-129 5.4 0.0 0.0 0.0 0.0 130-131 5.9875 0.0 0.0 0.0 0.0 132-133 6.550000000000001 0.0 0.0 0.0 0.0 134-135 6.975 0.0 0.0 0.0 0.0 136-137 7.45 0.0 0.0 0.0 0.0 138-139 8.1625 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position TTCATTT 10 0.006830828 145.0 7 TGTCCCG 10 0.006830828 145.0 5 GAGTCAT 10 0.006830828 145.0 5 CTGTCCC 10 0.006830828 145.0 4 AGTCATG 10 0.006830828 145.0 6 TTTTTTT 35 0.0035366106 20.714287 90-94 >>END_MODULE Read 1178010 spots for SRR6958193.sra Written 1178010 spots for SRR6958193.sra Read 1178010 spots for SRR6958193.sra Written 1178010 spots for SRR6958193.sra Read 1178010 spots for SRR6958193.sra Written 1178010 spots for SRR6958193.sra Read 1178010 spots for SRR6958193.sra Written 1178010 spots for SRR6958193.sra Read 1178010 spots for SRR6958193.sra Written 1178010 spots for SRR6958193.sra Read 1178010 spots for SRR6958193.sra Written 1178010 spots for SRR6958193.sra Read 1178010 spots for SRR6958193.sra Written 1178010 spots for SRR6958193.sra Read 1178010 spots for SRR6958193.sra Written 1178010 spots for SRR6958193.sra Read 1178010 spots for SRR6958193.sra Written 1178010 spots for SRR6958193.sra Read 1178010 spots for SRR6958193.sra Written 1178010 spots for SRR6958193.sra Read 1178010 spots for SRR6958193.sra Written 1178010 spots for SRR6958193.sra Read 1178010 spots for SRR6958193.sra Written 1178010 spots for SRR6958193.sra Read 1178010 spots for SRR6958193.sra Written 1178010 spots for SRR6958193.sra Read 1178010 spots for SRR6958193.sra Written 1178010 spots for SRR6958193.sra Read 1178010 spots for SRR6958193.sra Written 1178010 spots for SRR6958193.sra Read 1178021 spots for SRR6958193.sra Written 1178021 spots for SRR6958193.sra Read 1178010 spots for SRR6958193.sra Written 1178010 spots for SRR6958193.sra Read 1178010 spots for SRR6958193.sra Written 1178010 spots for SRR6958193.sra Read 1178010 spots for SRR6958193.sra Written 1178010 spots for SRR6958193.sra Read 1178010 spots for SRR6958193.sra Written 1178010 spots for SRR6958193.sra SRR ids: ['SRR6958193.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_4i12w64f SRR6958193.sra spots: 23560211 blocks: [[1, 1178010], [1178011, 2356020], [2356021, 3534030], [3534031, 4712040], [4712041, 5890050], [5890051, 7068060], [7068061, 8246070], [8246071, 9424080], [9424081, 10602090], [10602091, 11780100], [11780101, 12958110], [12958111, 14136120], [14136121, 15314130], [15314131, 16492140], [16492141, 17670150], [17670151, 18848160], [18848161, 20026170], [20026171, 21204180], [21204181, 22382190], [22382191, 23560211]] SRR6958193 file size 7962082 SRR6958193 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 SRR6958193 SRR6958193_1.fastq SRR6958193_2.fastq Input file: SRR6958193_1.fastq Paired file: SRR6958193_2.fastq trimmed: SRR6958193-trimmed-pair1.fastq, SRR6958193-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 Fri Dec 6 15:43:02 2024 >> started Fri Dec 6 15:43:26 2024 >> done (23.714s) 23560211 read pairs processed; of these: 14928 ( 0.06%) short read pairs filtered out after trimming by size control 12036 ( 0.05%) empty read pairs filtered out after trimming by size control 23533247 (99.89%) read pairs available; of these: 8486054 (36.06%) trimmed read pairs available after processing 15047193 (63.94%) untrimmed read pairs available after processing Length distribution of reads after trimming: length count percentage 18 13 0.00% 19 9 0.00% 20 16 0.00% 21 5 0.00% 22 13 0.00% 23 12 0.00% 24 16 0.00% 25 6 0.00% 26 15 0.00% 27 11 0.00% 28 14 0.00% 29 15 0.00% 30 14 0.00% 31 16 0.00% 32 17 0.00% 33 29 0.00% 34 19 0.00% 35 24 0.00% 36 13 0.00% 37 17 0.00% 38 25 0.00% 39 33 0.00% 40 23 0.00% 41 37 0.00% 42 36 0.00% 43 35 0.00% 44 40 0.00% 45 49 0.00% 46 51 0.00% 47 48 0.00% 48 81 0.00% 49 72 0.00% 50 87 0.00% 51 106 0.00% 52 76 0.00% 53 116 0.00% 54 126 0.00% 55 132 0.00% 56 140 0.00% 57 172 0.00% 58 200 0.00% 59 214 0.00% 60 273 0.00% 61 314 0.00% 62 332 0.00% 63 399 0.00% 64 432 0.00% 65 480 0.00% 66 538 0.00% 67 590 0.00% 68 648 0.00% 69 728 0.00% 70 851 0.00% 71 935 0.00% 72 1162 0.00% 73 1228 0.01% 74 1380 0.01% 75 1608 0.01% 76 1735 0.01% 77 1980 0.01% 78 2191 0.01% 79 2484 0.01% 80 2783 0.01% 81 3213 0.01% 82 3736 0.02% 83 4069 0.02% 84 5228 0.02% 85 6012 0.03% 86 6486 0.03% 87 6794 0.03% 88 7502 0.03% 89 8089 0.03% 90 8709 0.04% 91 9706 0.04% 92 10334 0.04% 93 11381 0.05% 94 12141 0.05% 95 12885 0.05% 96 13826 0.06% 97 14865 0.06% 98 15425 0.07% 99 16507 0.07% 100 17834 0.08% 101 18992 0.08% 102 20538 0.09% 103 21400 0.09% 104 22747 0.10% 105 24159 0.10% 106 25447 0.11% 107 26206 0.11% 108 27830 0.12% 109 29244 0.12% 110 30093 0.13% 111 32001 0.14% 112 33493 0.14% 113 34892 0.15% 114 36555 0.16% 115 38207 0.16% 116 39608 0.17% 117 40863 0.17% 118 42308 0.18% 119 43278 0.18% 120 45106 0.19% 121 46465 0.20% 122 47850 0.20% 123 50309 0.21% 124 51799 0.22% 125 54108 0.23% 126 55615 0.24% 127 57367 0.24% 128 58788 0.25% 129 60148 0.26% 130 62126 0.26% 131 63795 0.27% 132 65960 0.28% 133 68711 0.29% 134 70966 0.30% 135 74141 0.32% 136 76689 0.33% 137 78842 0.34% 138 81571 0.35% 139 86096 0.37% 140 89222 0.38% 141 94871 0.40% 142 102587 0.44% 143 109828 0.47% 144 121635 0.52% 145 139233 0.59% 146 163553 0.69% 147 207346 0.88% 148 301541 1.28% 149 638386 2.71% 150 4453533 18.92% 151 15047193 63.94% 23533247 reads passed initial QC criterion=sequence-density sequence-density=0.56 sequence-density-rank=1 fanout-score=3.31 fanout-score-rank=19 prefix-density=0.60 prefix-fanout=3.1 sequence=GGTGTTGTCGAAGCCGATGATGCGGAC criterion=fanout-score sequence-density=0.03 sequence-density-rank=32 fanout-score=133.56 fanout-score-rank=1 prefix-density=0.39 prefix-fanout=11.3 sequence=GGCGGCGGCGAACCGCCCCCGTCGCCGCGATCCGAACACTTCACCGGACCATTCAATCGGTAGGAGCGACGGGCGGTGTGTACAAAGGGCAGGGACGTAGTCAACGCGAGCTGATGACTCGCGCTTACTAGGCATTCCTCGTTGAAGACCAACAATTGCAATGATCTATCCCCATCACGATGAAATTTCCCAAGATTACCCGGGCCTGTCGGCCAAGGCTATATACTCGTTGAATACATCAGTGTAGCGCGCGTGCGGCCCAGAACATCTAAGGGCATCACAGACCTGTTATTGCCTCAAACTTCCGTCGCCTAAACGGCGATAGTCCCTCTAAGAAGCTAGCTGCGGAGGGATGGCTCCGCATAGCTAGTTAGCAGGCTGAGGTCTCGTTCGTTAACGGAATTAACCAGACAAATCGCTCCACCAACTAAGAACGGCCATGCACCACCACCCATAGAATCAAGAAAGAGCTCTCAGTCTGTCAATCCTTGCTATGTCTGGACCTGGTAAG criterion=sequence-density sequence-density=0.36 sequence-density-rank=1 fanout-score=4.10 fanout-score-rank=12 prefix-density=0.41 prefix-fanout=3.6 sequence=GAGTTCAGCAAGGTCGGCTT criterion=fanout-score sequence-density=0.02 sequence-density-rank=32 fanout-score=111.20 fanout-score-rank=1 prefix-density=0.17 prefix-fanout=9.8 sequence=GCAGCAGCCATTACTTGATCATCTGAAAAATCTTAATCCAGATCAGACCAAGCAGAGCAGAGATGTCTGCTACCTTCTCGTCCACCGTCGGAGCTCCGGCTTCTACGCCAACCAGCTTCCTTGGGAAGAAGCTCAAGAAGCAGGTGACCTCGGCCGTGAACTACCATGGCAAGAGCACCAAGGCCAACAGATTCACAGTCATGGCCAAGGAGGTGGACGAGTCAAAGCAGACTGACCAGGACAGGTGGAAGGGCCTCGCCTACGATATCTCCGACGACCAGCAGGACATCACCAGGGGGAAGGGTATCGTCGACTCGCTCTTCCAGGCGCCCATGGGCGACGGTACCCACGTGGCCGTCCTCAGCTCCCAAGAGTACATCAGCCAGGGCCTAAGGAAGTACGACTTCGACAACA SRR6958193 testing PE reads STAR mapping to Ensembl genome Started job on | Dec 06 15:44:06 Started mapping on | Dec 06 15:44:06 Finished on | Dec 06 15:45:32 Mapping speed, Million of reads per hour | 985.11 Number of input reads | 23533247 Average input read length | 295 UNIQUE READS: Uniquely mapped reads number | 22940678 Uniquely mapped reads % | 97.48% Average mapped length | 295.34 Number of splices: Total | 25349034 Number of splices: Annotated (sjdb) | 23819655 Number of splices: GT/AG | 25018587 Number of splices: GC/AG | 293917 Number of splices: AT/AC | 13822 Number of splices: Non-canonical | 22708 Mismatch rate per base, % | 0.07% Deletion rate per base | 0.00% Deletion average length | 1.43 Insertion rate per base | 0.00% Insertion average length | 1.23 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 199550 % of reads mapped to multiple loci | 0.85% Number of reads mapped to too many loci | 39032 % of reads mapped to too many loci | 0.17% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 0.70% % of reads unmapped: other | 0.81% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 404174 404174 404174 N_multimapping 199550 199550 199550 N_noFeature 998378 22324606 1204320 N_ambiguous 488657 3571 78811 UnstrandedReadsAssigned:21453643 PositiveStrandReadsAssigned:612501 NegativeStrandReadsAssigned:21657547 Dataset is classified negative stranded MeadianReadLen=151 20thPercentileLength=150 echo kmer=145 SRR6958193 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: SRR6958193-trimmed-pair1.fastq SRR6958193-trimmed-pair2.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 23,533,247 reads, 21,734,398 reads pseudoaligned [quant] estimated average fragment length: 259.03 [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,238 rounds 52973 SRR6958193.ke.tsv 35125 SRR6958193.se.tsv 88098 total ==> SRR6958193.ke.tsv <== target_id length eff_length est_counts tpm PNS24245 936 678.562 0 0 PNS24247 1044 785.97 74.3664 6.76459 PNS24249 1928 1669.97 29.8864 1.27948 PNS24246 1044 785.97 74.3664 6.76459 PNS24248 1044 785.97 74.3664 6.76459 PNS24244 1471 1212.97 27.0144 1.59227 PNS24243 293 93.4363 0 0 KQK14069 1603 1344.97 2260.37 120.154 KQK14071 474 235.108 76.1335 23.1515 ==> SRR6958193.se.tsv <== BRADI_1g14170v3 2862 BRADI_1g53295v3 350 BRADI_1g59795v3 708 BRADI_1g07683v3 0 BRADI_1g00485v3 36 BRADI_1g20270v3 1961 BRADI_1g74790v3 185 BRADI_1g09890v3 1 BRADI_1g77505v3 291 BRADI_1g48960v3 0 SRR6958193 completed mapping pipeline successfully