Starting /dee2/code/volunteer_pipeline.sh SRR6958466 current disk space = 1547614453760 free memory = 1590657012 SRR6958466 SRAfilesize 5685eefb9f4dbd0882728c5337ae53f4 SRR6958466.sra SRR6958466.sra file validated SRR6958466 is paired end SRR6958466 is conventional basespace SRR6958466 read1 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR6958466_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 49 >>END_MODULE >>Per base sequence quality fail #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 20.02275 18.0 18.0 25.0 18.0 32.0 2 25.601 27.0 18.0 29.0 18.0 31.0 3 27.38 29.0 25.0 31.0 18.0 33.0 4 29.299 32.0 27.0 33.0 25.0 33.0 5 29.91425 32.0 30.0 33.0 25.0 33.0 6 35.8605 37.0 36.0 38.0 31.0 38.0 7 36.0905 38.0 36.0 38.0 33.0 38.0 8 36.42275 38.0 37.0 38.0 33.0 38.0 9 36.9145 38.0 38.0 38.0 35.0 38.0 10-14 37.198899999999995 38.0 38.0 38.0 36.2 38.0 15-19 37.234249999999996 38.0 38.0 38.0 36.6 38.0 20-24 37.2217 38.0 38.0 38.0 36.4 38.0 25-29 36.9689 38.0 38.0 38.0 35.8 38.0 30-34 36.93725 38.0 38.0 38.0 35.4 38.0 35-39 36.7274 38.0 38.0 38.0 34.4 38.0 40-44 36.712050000000005 38.0 38.0 38.0 34.6 38.0 45-49 36.7657 38.0 38.0 38.0 34.6 38.0 50-54 36.21915 38.0 37.4 38.0 32.8 38.0 55-59 36.1505 38.0 37.0 38.0 32.6 38.0 60-64 36.524699999999996 38.0 37.8 38.0 33.8 38.0 65-69 36.531150000000004 38.0 37.8 38.0 34.0 38.0 70-74 36.36370000000001 38.0 37.6 38.0 33.4 38.0 75-79 35.871950000000005 38.0 36.8 38.0 31.2 38.0 80-84 35.65235 38.0 36.4 38.0 30.2 38.0 85-89 36.02115 38.0 37.0 38.0 32.8 38.0 90-94 35.93415 38.0 36.8 38.0 31.8 38.0 95-99 35.28815 38.0 35.6 38.0 28.8 38.0 100-104 34.54545 38.0 34.6 38.0 25.2 38.0 105-109 34.29225 38.0 34.0 38.0 24.0 38.0 110-114 34.22205 38.0 34.0 38.0 23.6 38.0 115-119 34.17965 38.0 34.0 38.0 23.8 38.0 120-124 33.474199999999996 38.0 32.4 38.0 21.8 38.0 125-129 33.0548 37.4 31.6 38.0 18.6 38.0 130-134 32.00535 36.4 30.6 38.0 14.2 38.0 135-139 30.90715 35.8 28.4 38.0 13.0 38.0 140-144 29.47155 34.6 25.8 38.0 9.8 38.0 145-149 27.235699999999998 33.4 17.4 38.0 2.0 38.0 150-151 20.1645 25.5 2.0 35.5 2.0 38.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 11 1.0 12 0.0 13 0.0 14 0.0 15 1.0 16 3.0 17 1.0 18 4.0 19 4.0 20 3.0 21 8.0 22 13.0 23 27.0 24 31.0 25 28.0 26 40.0 27 51.0 28 72.0 29 108.0 30 95.0 31 157.0 32 186.0 33 317.0 34 422.0 35 668.0 36 1138.0 37 622.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 29.276754737123035 24.60635174806512 4.1099546303709635 42.006938884440885 2 19.45 12.049999999999999 27.625 40.875 3 17.7 15.174999999999999 21.425 45.7 4 22.900000000000002 25.2 21.825 30.075000000000003 5 24.05 29.9 22.075 23.974999999999998 6 24.525 31.6 22.425 21.45 7 17.05 24.375 38.824999999999996 19.75 8 19.625 23.474999999999998 29.15 27.750000000000004 9 19.75 21.75 34.25 24.25 10-14 22.830000000000002 26.795 25.5 24.875 15-19 21.63 25.615 26.669999999999998 26.085 20-24 22.400000000000002 25.974999999999998 25.94 25.685000000000002 25-29 22.705000000000002 25.95 25.490000000000002 25.855 30-34 22.869999999999997 25.805 25.81 25.515 35-39 22.795 25.869999999999997 25.814999999999998 25.52 40-44 22.785 26.06 25.255 25.900000000000002 45-49 22.650000000000002 25.924999999999997 25.81 25.615 50-54 23.09 26.06 25.545 25.305 55-59 22.91 25.72 25.669999999999998 25.7 60-64 22.41 25.845000000000002 25.490000000000002 26.255 65-69 23.16 25.105 25.83 25.905 70-74 22.695 25.900000000000002 25.45 25.955000000000002 75-79 23.26 25.740000000000002 25.255 25.745 80-84 22.900000000000002 25.785000000000004 25.869999999999997 25.445 85-89 23.39 25.415 25.215 25.979999999999997 90-94 23.09 26.08 24.83 26.0 95-99 23.13 25.955000000000002 25.145 25.77 100-104 23.895 25.055 25.415 25.635 105-109 23.525 25.715 25.285000000000004 25.474999999999998 110-114 23.86 26.340000000000003 24.325 25.474999999999998 115-119 24.2 26.334999999999997 24.44 25.025 120-124 23.65 26.005 24.665 25.679999999999996 125-129 23.575 25.569999999999997 24.535 26.32 130-134 23.61 26.224999999999998 24.555 25.61 135-139 24.255 25.935000000000002 24.615000000000002 25.195 140-144 23.724999999999998 25.995 24.895 25.385 145-149 23.465 25.44 25.295 25.8 150-151 23.025000000000002 25.2625 24.2 27.5125 >>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 0.0 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 2.0 27 3.5 28 6.5 29 7.5 30 11.5 31 15.5 32 18.5 33 27.0 34 28.0 35 35.0 36 56.0 37 82.0 38 96.5 39 112.0 40 133.5 41 143.0 42 165.0 43 191.5 44 203.0 45 209.5 46 198.5 47 201.0 48 202.0 49 173.0 50 175.5 51 168.5 52 133.0 53 107.5 54 104.5 55 91.0 56 66.0 57 62.0 58 67.0 59 64.5 60 54.5 61 56.5 62 59.0 63 61.5 64 52.0 65 37.0 66 36.0 67 41.5 68 46.5 69 41.0 70 29.5 71 25.0 72 22.5 73 18.0 74 14.5 75 10.0 76 9.5 77 8.0 78 6.0 79 4.5 80 2.0 81 0.5 82 0.0 83 0.5 84 0.5 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 warn #Base N-Count 1 6.325 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 99.825 #Duplication Level Percentage of deduplicated Percentage of total 1 99.82469321312296 99.65 2 0.1753067868770348 0.35000000000000003 3 0.0 0.0 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 fail #Position Illumina Universal Adapter Illumina Small RNA 3' Adapter Illumina Small RNA 5' Adapter Nextera Transposase Sequence SOLID Small RNA Adapter 1 0.0 0.0 0.0 0.0 0.0 2 0.0 0.0 0.0 0.0 0.0 3 0.0 0.0 0.0 0.0 0.0 4 0.0 0.0 0.0 0.0 0.0 5 0.0 0.0 0.0 0.0 0.0 6 0.0 0.0 0.0 0.0 0.0 7 0.0 0.0 0.0 0.0 0.0 8 0.0 0.0 0.0 0.0 0.0 9 0.0 0.0 0.0 0.0 0.0 10-11 0.0 0.0 0.0 0.0 0.0 12-13 0.0 0.0 0.0 0.0 0.0 14-15 0.0 0.0 0.0 0.0 0.0 16-17 0.0 0.0 0.0 0.0 0.0 18-19 0.0 0.0 0.0 0.0 0.0 20-21 0.0 0.0 0.0 0.0 0.0 22-23 0.0 0.0 0.0 0.0 0.0 24-25 0.0 0.0 0.0 0.0 0.0 26-27 0.0 0.0 0.0 0.0 0.0 28-29 0.0 0.0 0.0 0.0 0.0 30-31 0.0 0.0 0.0 0.0 0.0 32-33 0.0 0.0 0.0 0.0 0.0 34-35 0.0 0.0 0.0 0.0 0.0 36-37 0.0 0.0 0.0 0.0 0.0 38-39 0.0 0.0 0.0 0.0 0.0 40-41 0.0 0.0 0.0 0.0 0.0 42-43 0.0 0.0 0.0 0.0 0.0 44-45 0.0 0.0 0.0 0.0 0.0 46-47 0.0 0.0 0.0 0.0 0.0 48-49 0.0 0.0 0.0 0.0 0.0 50-51 0.0 0.0 0.0 0.0 0.0 52-53 0.0 0.0 0.0 0.0 0.0 54-55 0.0 0.0 0.0 0.0 0.0 56-57 0.0 0.0 0.0 0.0 0.0 58-59 0.0 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 0.025 0.0 0.0 0.0 0.0 76-77 0.025 0.0 0.0 0.0 0.0 78-79 0.037500000000000006 0.0 0.0 0.0 0.0 80-81 0.05 0.0 0.0 0.0 0.0 82-83 0.05 0.0 0.0 0.0 0.0 84-85 0.1 0.0 0.0 0.0 0.0 86-87 0.1375 0.0 0.0 0.0 0.0 88-89 0.16249999999999998 0.0 0.0 0.0 0.0 90-91 0.2875 0.0 0.0 0.0 0.0 92-93 0.3875 0.0 0.0 0.0 0.0 94-95 0.44999999999999996 0.0 0.0 0.0 0.0 96-97 0.6000000000000001 0.0 0.0 0.0 0.0 98-99 0.7875 0.0 0.0 0.0 0.0 100-101 0.9625 0.0 0.0 0.0 0.0 102-103 1.175 0.0 0.0 0.0 0.0 104-105 1.3875000000000002 0.0 0.0 0.0 0.0 106-107 1.6375000000000002 0.0 0.0 0.0 0.0 108-109 1.9875 0.0 0.0 0.0 0.0 110-111 2.375 0.0 0.0 0.0 0.0 112-113 2.7874999999999996 0.0 0.0 0.0 0.0 114-115 3.25 0.0 0.0 0.0 0.0 116-117 3.7 0.0 0.0 0.0 0.0 118-119 4.225 0.0 0.0 0.0 0.0 120-121 4.6625 0.0 0.0 0.0 0.0 122-123 5.25 0.0 0.0 0.0 0.0 124-125 5.987500000000001 0.0 0.0 0.0 0.0 126-127 6.8 0.0 0.0 0.0 0.0 128-129 7.3625 0.0 0.0 0.0 0.0 130-131 8.2 0.0 0.0 0.0 0.0 132-133 8.85 0.0 0.0 0.0 0.0 134-135 9.725000000000001 0.0 0.0 0.0 0.0 136-137 10.575 0.0 0.0 0.0 0.0 138-139 11.399999999999999 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content pass >>END_MODULE SRR6958466 read2 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR6958466_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 fail #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 32.44075 33.0 33.0 34.0 32.0 34.0 2 32.33025 33.0 33.0 34.0 31.0 34.0 3 32.39075 33.0 33.0 34.0 31.0 34.0 4 32.3215 33.0 33.0 34.0 31.0 34.0 5 32.285 33.0 33.0 34.0 31.0 34.0 6 36.18575 38.0 38.0 38.0 33.0 38.0 7 36.213 38.0 38.0 38.0 33.0 38.0 8 36.1105 38.0 38.0 38.0 33.0 38.0 9 36.19675 38.0 38.0 38.0 33.0 38.0 10-14 36.09475 38.0 38.0 38.0 32.2 38.0 15-19 36.2658 38.0 38.0 38.0 33.6 38.0 20-24 36.542249999999996 38.0 38.0 38.0 34.6 38.0 25-29 36.50505 38.0 38.0 38.0 34.2 38.0 30-34 36.4941 38.0 38.0 38.0 34.8 38.0 35-39 36.322750000000006 38.0 38.0 38.0 34.0 38.0 40-44 36.11065 38.0 38.0 38.0 33.0 38.0 45-49 36.15925 38.0 38.0 38.0 33.2 38.0 50-54 36.17875 38.0 38.0 38.0 33.2 38.0 55-59 36.045849999999994 38.0 37.6 38.0 33.0 38.0 60-64 35.85045 38.0 37.2 38.0 31.6 38.0 65-69 35.5729 38.0 37.0 38.0 30.2 38.0 70-74 35.20055 38.0 36.4 38.0 28.4 38.0 75-79 35.37705 38.0 37.0 38.0 29.4 38.0 80-84 35.25585 38.0 36.2 38.0 29.0 38.0 85-89 35.0791 38.0 36.0 38.0 28.2 38.0 90-94 34.65745 38.0 35.6 38.0 26.4 38.0 95-99 34.0206 38.0 34.4 38.0 21.6 38.0 100-104 33.41330000000001 38.0 33.8 38.0 17.8 38.0 105-109 33.12245 38.0 32.8 38.0 16.2 38.0 110-114 32.79729999999999 38.0 32.2 38.0 15.0 38.0 115-119 32.07795 37.2 30.6 38.0 14.6 38.0 120-124 31.370350000000002 37.0 29.0 38.0 13.0 38.0 125-129 30.5582 36.0 27.8 38.0 11.8 38.0 130-134 29.20645 34.6 23.6 38.0 11.0 38.0 135-139 28.563650000000003 33.8 21.8 38.0 3.8 38.0 140-144 27.70765 33.4 20.2 38.0 2.0 38.0 145-149 24.94535 33.0 8.2 38.0 2.0 38.0 150-151 17.909875 16.5 2.0 34.0 2.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 2 18.0 3 2.0 4 3.0 5 4.0 6 3.0 7 0.0 8 2.0 9 3.0 10 2.0 11 7.0 12 5.0 13 11.0 14 8.0 15 9.0 16 11.0 17 14.0 18 13.0 19 18.0 20 17.0 21 20.0 22 24.0 23 35.0 24 41.0 25 48.0 26 53.0 27 47.0 28 90.0 29 84.0 30 114.0 31 158.0 32 208.0 33 262.0 34 376.0 35 591.0 36 928.0 37 771.0 >>END_MODULE >>Per base sequence content warn #Base G A T C 1 38.65 18.9 12.9 29.549999999999997 2 28.225 24.2 27.525 20.05 3 23.3 25.224999999999998 28.4 23.075000000000003 4 26.5 30.525000000000002 20.3 22.675 5 25.85 34.1 19.2 20.849999999999998 6 22.675 36.225 20.4 20.7 7 22.975 19.950000000000003 34.75 22.325 8 23.65 23.175 24.9 28.275 9 24.075 23.325000000000003 27.450000000000003 25.15 10-14 25.56 25.94 23.599999999999998 24.9 15-19 25.85 25.335 24.779999999999998 24.035 20-24 25.324999999999996 25.715 25.035 23.925 25-29 25.435000000000002 25.080000000000002 25.14 24.345 30-34 25.39 25.669999999999998 25.124999999999996 23.815 35-39 25.395 25.580000000000002 25.3 23.724999999999998 40-44 25.64 25.374999999999996 25.34 23.645 45-49 25.590000000000003 24.995 25.405 24.01 50-54 25.919999999999998 24.69 25.53 23.86 55-59 26.545 25.39 25.06 23.005 60-64 26.005 25.430000000000003 25.155 23.41 65-69 26.22 25.624999999999996 24.84 23.315 70-74 26.115 25.064999999999998 25.095 23.724999999999998 75-79 25.569999999999997 25.53 25.415 23.485 80-84 25.935000000000002 25.145 25.605 23.315 85-89 25.83 25.53 25.330000000000002 23.31 90-94 25.845000000000002 25.64 25.369999999999997 23.145 95-99 26.085 25.924999999999997 25.135 22.855 100-104 26.035000000000004 25.324999999999996 25.924999999999997 22.715 105-109 25.515 25.735000000000003 25.590000000000003 23.16 110-114 26.195 25.825 25.2 22.78 115-119 26.66 24.645 25.465 23.23 120-124 27.495000000000005 24.88 25.215 22.41 125-129 27.47 25.905 24.715 21.91 130-134 28.03 25.385 24.775 21.81 135-139 28.225 25.71 24.77 21.295 140-144 28.285 25.61 25.174999999999997 20.93 145-149 28.83 25.119999999999997 25.14 20.91 150-151 28.9375 25.087500000000002 26.125 19.85 >>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 0.0 17 0.5 18 0.5 19 0.0 20 0.5 21 1.0 22 1.0 23 1.5 24 1.0 25 0.5 26 1.5 27 2.5 28 3.5 29 5.5 30 7.0 31 9.5 32 14.0 33 16.5 34 29.5 35 39.0 36 44.5 37 62.0 38 76.5 39 103.0 40 131.5 41 156.5 42 194.5 43 202.0 44 197.5 45 207.0 46 203.0 47 194.5 48 179.5 49 163.5 50 152.5 51 136.5 52 123.5 53 118.5 54 108.5 55 91.5 56 84.5 57 79.0 58 69.0 59 69.0 60 66.5 61 57.5 62 58.5 63 62.5 64 53.5 65 53.0 66 54.5 67 42.5 68 39.0 69 43.5 70 38.0 71 33.5 72 30.5 73 23.0 74 18.0 75 11.0 76 7.0 77 6.5 78 6.0 79 4.0 80 3.5 81 2.5 82 0.5 83 0.0 84 0.5 85 1.0 86 0.5 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 0.0 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 99.775 #Duplication Level Percentage of deduplicated Percentage of total 1 99.79954898521673 99.575 2 0.17539463793535454 0.35000000000000003 3 0.025056376847907794 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 fail #Position Illumina Universal Adapter Illumina Small RNA 3' Adapter Illumina Small RNA 5' Adapter Nextera Transposase Sequence SOLID Small RNA Adapter 1 0.0 0.0 0.0 0.0 0.0 2 0.0 0.0 0.0 0.0 0.0 3 0.0 0.0 0.0 0.0 0.0 4 0.0 0.0 0.0 0.0 0.0 5 0.0 0.0 0.0 0.0 0.0 6 0.0 0.0 0.0 0.0 0.0 7 0.0 0.0 0.0 0.0 0.0 8 0.0 0.0 0.0 0.0 0.0 9 0.0 0.0 0.0 0.0 0.0 10-11 0.0 0.0 0.0 0.0 0.0 12-13 0.0 0.0 0.0 0.0 0.0 14-15 0.0 0.0 0.0 0.0 0.0 16-17 0.0 0.0 0.0 0.0 0.0 18-19 0.0 0.0 0.0 0.0 0.0 20-21 0.0 0.0 0.0 0.0 0.0 22-23 0.0 0.0 0.0 0.0 0.0 24-25 0.0 0.0 0.0 0.0 0.0 26-27 0.0 0.0 0.0 0.0 0.0 28-29 0.0 0.0 0.0 0.0 0.0 30-31 0.0 0.0 0.0 0.0 0.0 32-33 0.0 0.0 0.0 0.0 0.0 34-35 0.0 0.0 0.0 0.0 0.0 36-37 0.0 0.0 0.0 0.0 0.0 38-39 0.0 0.0 0.0 0.0 0.0 40-41 0.0 0.0 0.0 0.0 0.0 42-43 0.0 0.0 0.0 0.0 0.0 44-45 0.0 0.0 0.0 0.0 0.0 46-47 0.0 0.0 0.0 0.0 0.0 48-49 0.0 0.0 0.0 0.0 0.0 50-51 0.0 0.0 0.0 0.0 0.0 52-53 0.0 0.0 0.0 0.0 0.0 54-55 0.0 0.0 0.0 0.0 0.0 56-57 0.0 0.0 0.0 0.0 0.0 58-59 0.0 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 0.025 0.0 0.0 0.0 0.0 76-77 0.025 0.0 0.0 0.0 0.0 78-79 0.037500000000000006 0.0 0.0 0.0 0.0 80-81 0.05 0.0 0.0 0.0 0.0 82-83 0.05 0.0 0.0 0.0 0.0 84-85 0.1 0.0 0.0 0.0 0.0 86-87 0.1375 0.0 0.0 0.0 0.0 88-89 0.15 0.0 0.0 0.0 0.0 90-91 0.2625 0.0 0.0 0.0 0.0 92-93 0.3625 0.0 0.0 0.0 0.0 94-95 0.4375 0.0 0.0 0.0 0.0 96-97 0.5875 0.0 0.0 0.0 0.0 98-99 0.7625 0.0 0.0 0.0 0.0 100-101 0.9375 0.0 0.0 0.0 0.0 102-103 1.1375 0.0 0.0 0.0 0.0 104-105 1.3375 0.0 0.0 0.0 0.0 106-107 1.5875 0.0 0.0 0.0 0.0 108-109 1.9375 0.0 0.0 0.0 0.0 110-111 2.325 0.0 0.0 0.0 0.0 112-113 2.7125000000000004 0.0 0.0 0.0 0.0 114-115 3.1625 0.0 0.0 0.0 0.0 116-117 3.6125 0.0 0.0 0.0 0.0 118-119 4.1125 0.0 0.0 0.0 0.0 120-121 4.5625 0.0 0.0 0.0 0.0 122-123 5.112500000000001 0.0 0.0 0.0 0.0 124-125 5.9125 0.0 0.0 0.0 0.0 126-127 6.7125 0.0 0.0 0.0 0.0 128-129 7.25 0.0 0.0 0.0 0.0 130-131 8.1 0.0 0.0 0.0 0.0 132-133 8.775 0.0 0.0 0.0 0.0 134-135 9.600000000000001 0.0 0.0 0.0 0.0 136-137 10.462499999999999 0.0 0.0 0.0 0.0 138-139 11.3375 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content pass >>END_MODULE Read 950373 spots for SRR6958466.sra Written 950373 spots for SRR6958466.sra Read 950373 spots for SRR6958466.sra Written 950373 spots for SRR6958466.sra Read 950373 spots for SRR6958466.sra Written 950373 spots for SRR6958466.sra Read 950373 spots for SRR6958466.sra Written 950373 spots for SRR6958466.sra Read 950373 spots for SRR6958466.sra Written 950373 spots for SRR6958466.sra Read 950377 spots for SRR6958466.sra Written 950377 spots for SRR6958466.sra Read 950373 spots for SRR6958466.sra Written 950373 spots for SRR6958466.sra Read 950373 spots for SRR6958466.sra Written 950373 spots for SRR6958466.sra Read 950373 spots for SRR6958466.sra Written 950373 spots for SRR6958466.sra Read 950373 spots for SRR6958466.sra Written 950373 spots for SRR6958466.sra Read 950373 spots for SRR6958466.sra Written 950373 spots for SRR6958466.sra Read 950373 spots for SRR6958466.sra Written 950373 spots for SRR6958466.sra Read 950373 spots for SRR6958466.sra Written 950373 spots for SRR6958466.sra Read 950373 spots for SRR6958466.sra Written 950373 spots for SRR6958466.sra Read 950373 spots for SRR6958466.sra Written 950373 spots for SRR6958466.sra Read 950373 spots for SRR6958466.sra Written 950373 spots for SRR6958466.sra Read 950373 spots for SRR6958466.sra Written 950373 spots for SRR6958466.sra Read 950373 spots for SRR6958466.sra Written 950373 spots for SRR6958466.sra Read 950373 spots for SRR6958466.sra Written 950373 spots for SRR6958466.sra Read 950373 spots for SRR6958466.sra Written 950373 spots for SRR6958466.sra SRR ids: ['SRR6958466.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_eavxv8ct SRR6958466.sra spots: 19007464 blocks: [[1, 950373], [950374, 1900746], [1900747, 2851119], [2851120, 3801492], [3801493, 4751865], [4751866, 5702238], [5702239, 6652611], [6652612, 7602984], [7602985, 8553357], [8553358, 9503730], [9503731, 10454103], [10454104, 11404476], [11404477, 12354849], [12354850, 13305222], [13305223, 14255595], [14255596, 15205968], [15205969, 16156341], [16156342, 17106714], [17106715, 18057087], [18057088, 19007464]] SRR6958466 file size 6419305 SRR6958466 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 SRR6958466 SRR6958466_1.fastq SRR6958466_2.fastq Input file: SRR6958466_1.fastq Paired file: SRR6958466_2.fastq trimmed: SRR6958466-trimmed-pair1.fastq, SRR6958466-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 23:49:47 2024 >> started Fri Dec 6 23:50:07 2024 >> done (20.220s) 19007464 read pairs processed; of these: 34565 ( 0.18%) short read pairs filtered out after trimming by size control 29145 ( 0.15%) empty read pairs filtered out after trimming by size control 18943754 (99.66%) read pairs available; of these: 11116162 (58.68%) trimmed read pairs available after processing 7827592 (41.32%) untrimmed read pairs available after processing Length distribution of reads after trimming: length count percentage 18 2 0.00% 19 4 0.00% 20 2 0.00% 21 1 0.00% 22 4 0.00% 23 1 0.00% 24 2 0.00% 25 3 0.00% 26 4 0.00% 27 3 0.00% 28 4 0.00% 29 5 0.00% 30 5 0.00% 31 7 0.00% 32 12 0.00% 33 5 0.00% 34 12 0.00% 35 6 0.00% 36 17 0.00% 37 7 0.00% 38 12 0.00% 39 13 0.00% 40 11 0.00% 41 27 0.00% 42 16 0.00% 43 30 0.00% 44 19 0.00% 45 25 0.00% 46 31 0.00% 47 32 0.00% 48 37 0.00% 49 59 0.00% 50 54 0.00% 51 59 0.00% 52 68 0.00% 53 83 0.00% 54 72 0.00% 55 96 0.00% 56 133 0.00% 57 116 0.00% 58 139 0.00% 59 173 0.00% 60 190 0.00% 61 233 0.00% 62 243 0.00% 63 292 0.00% 64 329 0.00% 65 385 0.00% 66 406 0.00% 67 525 0.00% 68 546 0.00% 69 607 0.00% 70 718 0.00% 71 855 0.00% 72 973 0.01% 73 1165 0.01% 74 1307 0.01% 75 1430 0.01% 76 1712 0.01% 77 1920 0.01% 78 2151 0.01% 79 2375 0.01% 80 2849 0.02% 81 3284 0.02% 82 3924 0.02% 83 4421 0.02% 84 6163 0.03% 85 7088 0.04% 86 7452 0.04% 87 8005 0.04% 88 8499 0.04% 89 9066 0.05% 90 10020 0.05% 91 11099 0.06% 92 12183 0.06% 93 13445 0.07% 94 14822 0.08% 95 15807 0.08% 96 17268 0.09% 97 18546 0.10% 98 19672 0.10% 99 21202 0.11% 100 22897 0.12% 101 24793 0.13% 102 26503 0.14% 103 29011 0.15% 104 31134 0.16% 105 32770 0.17% 106 34545 0.18% 107 36273 0.19% 108 37742 0.20% 109 40026 0.21% 110 41738 0.22% 111 44227 0.23% 112 46829 0.25% 113 49048 0.26% 114 52015 0.27% 115 55220 0.29% 116 57127 0.30% 117 59134 0.31% 118 60761 0.32% 119 62322 0.33% 120 64655 0.34% 121 67068 0.35% 122 70244 0.37% 123 73523 0.39% 124 76798 0.41% 125 80458 0.42% 126 82738 0.44% 127 86040 0.45% 128 87702 0.46% 129 90542 0.48% 130 92731 0.49% 131 95892 0.51% 132 100238 0.53% 133 105785 0.56% 134 109599 0.58% 135 115484 0.61% 136 121247 0.64% 137 126576 0.67% 138 130926 0.69% 139 138308 0.73% 140 145812 0.77% 141 156059 0.82% 142 171212 0.90% 143 187994 0.99% 144 211711 1.12% 145 247166 1.30% 146 299705 1.58% 147 390765 2.06% 148 584900 3.09% 149 1141613 6.03% 150 4583968 24.20% 151 7827592 41.32% 18943754 reads passed initial QC criterion=sequence-density sequence-density=0.34 sequence-density-rank=1 fanout-score=2.84 fanout-score-rank=30 prefix-density=0.40 prefix-fanout=2.5 sequence=GAGCTGGAGCTG criterion=fanout-score sequence-density=0.02 sequence-density-rank=32 fanout-score=278.72 fanout-score-rank=1 prefix-density=0.49 prefix-fanout=13.7 sequence=GGCGGCGGCGAACCGCCCCCGTCGCCGCGATCCGAACACTTCACCGGACCATTCAATCGGTAGGAGCGACGGGCGGTGTGTACAAAGGGCAGGGACGTAGTCAACGCGAGCTGATGACTCGCGCTTACTAGGCATTCCTCGTTGAAGACCAACAATTGCAATGATCTATCCCCATCACGATGAAATTTCCCAAGATTACCCGGGCCTGTCGGCCAAGGCTATATACTCGTTGAATACATCAGTGTAGCGCGCGTGCGGCCCAGAACATCTAAGGGCATCACAGACCTGTTATTGCCTCAAACTTCCGTCGCCTAAACGGCGATAGTCCCTCTAAGAAGCTAGCTGCGGAGGGATGGCTCCGCATAGCTAGTTAGCAGGCTGAGGTCTCGTTCGTTAACGGAATTAACCAGACAAATCGCTCCACCAACTAAGAACGGCCATGCACCACCACCCATAGAATCAAGAAAGAGCTCTCAGTCTGTCAATCCTTGCTATGTCTGGACCTGGTAAG criterion=sequence-density sequence-density=0.23 sequence-density-rank=1 fanout-score=24.63 fanout-score-rank=6 prefix-density=0.92 prefix-fanout=6.0 sequence=AAGGAGAAGCTGCCTGGCCAGCACTGAGC criterion=fanout-score sequence-density=0.08 sequence-density-rank=22 fanout-score=174.91 fanout-score-rank=1 prefix-density=0.56 prefix-fanout=25.3 sequence=CGCCGCCGCCGG SRR6958466 testing PE reads STAR mapping to Ensembl genome Started job on | Dec 06 23:50:56 Started mapping on | Dec 06 23:50:56 Finished on | Dec 06 23:52:17 Mapping speed, Million of reads per hour | 841.94 Number of input reads | 18943754 Average input read length | 290 UNIQUE READS: Uniquely mapped reads number | 18335186 Uniquely mapped reads % | 96.79% Average mapped length | 290.16 Number of splices: Total | 15111181 Number of splices: Annotated (sjdb) | 13816436 Number of splices: GT/AG | 14901838 Number of splices: GC/AG | 162039 Number of splices: AT/AC | 7404 Number of splices: Non-canonical | 39900 Mismatch rate per base, % | 0.25% Deletion rate per base | 0.02% Deletion average length | 2.39 Insertion rate per base | 0.01% Insertion average length | 2.28 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 146243 % of reads mapped to multiple loci | 0.77% Number of reads mapped to too many loci | 30160 % of reads mapped to too many loci | 0.16% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 1.37% % of reads unmapped: other | 0.91% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 480113 480113 480113 N_multimapping 146243 146243 146243 N_noFeature 1259726 17622514 1634532 N_ambiguous 417093 4407 79052 UnstrandedReadsAssigned:16658367 PositiveStrandReadsAssigned:708265 NegativeStrandReadsAssigned:16621602 Dataset is classified negative stranded MeadianReadLen=150 20thPercentileLength=143 echo kmer=139 SRR6958466 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: SRR6958466-trimmed-pair1.fastq SRR6958466-trimmed-pair2.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 18,943,754 reads, 16,607,957 reads pseudoaligned [quant] estimated average fragment length: 226.12 [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,145 rounds 52973 SRR6958466.ke.tsv 35125 SRR6958466.se.tsv 88098 total ==> SRR6958466.ke.tsv <== target_id length eff_length est_counts tpm PNS24245 936 711.103 248.635 32.1899 PNS24247 1044 818.88 69.3578 7.79766 PNS24249 1928 1702.88 344.03 18.5995 PNS24246 1044 818.88 69.3578 7.79766 PNS24248 1044 818.88 69.3578 7.79766 PNS24244 1471 1245.88 203.261 15.02 PNS24243 293 104.483 3 2.64342 KQK14069 1603 1377.88 208.971 13.9625 KQK14071 474 257.413 0 0 ==> SRR6958466.se.tsv <== BRADI_1g14170v3 227 BRADI_1g53295v3 764 BRADI_1g59795v3 118 BRADI_1g07683v3 0 BRADI_1g00485v3 52 BRADI_1g20270v3 656 BRADI_1g74790v3 1317 BRADI_1g09890v3 0 BRADI_1g77505v3 138 BRADI_1g48960v3 0 SRR6958466 completed mapping pipeline successfully