Starting /dee2/code/volunteer_pipeline.sh SRR6958298 current disk space = 1550061568000 free memory = 1324462068 SRR6958298 SRAfilesize 22c873db2e1a05402b4a18f27ed44fe3 SRR6958298.sra SRR6958298.sra file validated SRR6958298 is paired end SRR6958298 is conventional basespace SRR6958298 read1 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR6958298_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 pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 25.32175 25.0 18.0 33.0 18.0 33.0 2 29.64375 30.0 27.0 33.0 25.0 33.0 3 31.53125 33.0 31.0 33.0 29.0 33.0 4 31.54325 33.0 31.0 33.0 29.0 33.0 5 32.00775 33.0 31.0 33.0 30.0 34.0 6 34.979 37.0 34.0 38.0 29.0 38.0 7 35.65275 37.0 35.0 38.0 31.0 38.0 8 36.29525 38.0 36.0 38.0 33.0 38.0 9 37.0075 38.0 38.0 38.0 35.0 38.0 10-14 37.2999 38.0 38.0 38.0 36.6 38.0 15-19 37.51825 38.0 38.0 38.0 37.2 38.0 20-24 37.52034999999999 38.0 38.0 38.0 37.6 38.0 25-29 37.533849999999994 38.0 38.0 38.0 37.6 38.0 30-34 37.5274 38.0 38.0 38.0 37.6 38.0 35-39 37.46065 38.0 38.0 38.0 37.2 38.0 40-44 37.411 38.0 38.0 38.0 37.0 38.0 45-49 37.41895 38.0 38.0 38.0 37.0 38.0 50-54 37.309000000000005 38.0 38.0 38.0 37.0 38.0 55-59 36.6901 38.0 38.0 38.0 36.0 38.0 60-64 36.43535000000001 38.0 38.0 38.0 35.4 38.0 65-69 36.887899999999995 38.0 38.0 38.0 35.8 38.0 70-74 37.14745 38.0 38.0 38.0 36.0 38.0 75-79 37.13 38.0 38.0 38.0 36.0 38.0 80-84 37.005599999999994 38.0 38.0 38.0 35.8 38.0 85-89 36.961 38.0 38.0 38.0 35.4 38.0 90-94 36.825450000000004 38.0 38.0 38.0 35.0 38.0 95-99 36.659749999999995 38.0 38.0 38.0 34.2 38.0 100-104 36.5553 38.0 38.0 38.0 34.0 38.0 105-109 36.4989 38.0 38.0 38.0 34.0 38.0 110-114 36.30165 38.0 37.8 38.0 33.6 38.0 115-119 36.201350000000005 38.0 37.6 38.0 33.2 38.0 120-124 35.7592 38.0 36.4 38.0 31.4 38.0 125-129 35.31905 38.0 36.0 38.0 31.0 38.0 130-134 35.2602 38.0 36.0 38.0 28.8 38.0 135-139 34.3608 38.0 34.2 38.0 25.8 38.0 140-144 34.04705 38.0 33.6 38.0 25.0 38.0 145-149 33.3926 38.0 33.0 38.0 21.6 38.0 150-151 28.21575 34.0 17.5 37.0 2.0 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 0.0 8 0.0 9 0.0 10 1.0 11 2.0 12 0.0 13 0.0 14 0.0 15 0.0 16 1.0 17 1.0 18 0.0 19 2.0 20 3.0 21 1.0 22 3.0 23 5.0 24 12.0 25 12.0 26 18.0 27 21.0 28 25.0 29 30.0 30 47.0 31 47.0 32 81.0 33 117.0 34 219.0 35 343.0 36 856.0 37 2152.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 45.45 8.275 9.775 36.5 2 25.906476619154787 10.05251312828207 34.08352088022005 29.957489372343087 3 21.45 17.1 25.5 35.949999999999996 4 24.575 24.325 22.85 28.249999999999996 5 25.4 26.575 25.025 23.0 6 24.075 30.55 23.549999999999997 21.825 7 19.2 22.975 38.45 19.375 8 21.075 22.45 29.925 26.55 9 20.674999999999997 22.650000000000002 32.675 24.0 10-14 22.96878126876126 26.540924554732843 25.980588353011807 24.509705823494095 15-19 22.705000000000002 25.205 26.919999999999998 25.169999999999998 20-24 23.49 25.369999999999997 26.02 25.119999999999997 25-29 23.119999999999997 25.665 25.795 25.419999999999998 30-34 23.16 25.495 26.009999999999998 25.335 35-39 23.71 25.155 25.629999999999995 25.505 40-44 23.25 24.825 25.81 26.115 45-49 23.585 24.959999999999997 25.629999999999995 25.825 50-54 23.775 25.245 25.564999999999998 25.415 55-59 23.558375634517766 25.45685279187817 25.58883248730964 25.395939086294415 60-64 23.41794780121559 24.587568312988406 25.711221206394608 26.283262679401396 65-69 22.867031148116567 25.24953603852134 26.347996187992173 25.53543662536992 70-74 23.715 24.845 25.624999999999996 25.814999999999998 75-79 23.535 25.53 25.324999999999996 25.61 80-84 23.064999999999998 25.41 25.755 25.77 85-89 23.169999999999998 25.35 25.6 25.88 90-94 23.44 24.785 25.874999999999996 25.900000000000002 95-99 23.43 25.124999999999996 26.02 25.424999999999997 100-104 23.395 24.759999999999998 25.900000000000002 25.945 105-109 23.43 24.490000000000002 25.605 26.474999999999998 110-114 23.465 25.34 25.635 25.56 115-119 23.845 25.145 25.61 25.4 120-124 23.535 24.990000000000002 25.665 25.81 125-129 24.115000000000002 23.96 25.669999999999998 26.255 130-134 23.849999999999998 25.03 25.290000000000003 25.83 135-139 23.66 24.92 24.98 26.44 140-144 23.72 24.865000000000002 25.66 25.755 145-149 24.11 24.985 24.9 26.005 150-151 24.6875 23.9125 24.6625 26.737499999999997 >>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 0.0 24 0.0 25 0.5 26 1.0 27 2.0 28 4.0 29 4.0 30 5.5 31 10.0 32 11.0 33 17.5 34 28.5 35 36.0 36 44.5 37 57.0 38 78.0 39 95.0 40 127.5 41 152.5 42 163.0 43 188.5 44 210.0 45 209.0 46 210.5 47 208.5 48 194.5 49 182.0 50 160.5 51 158.5 52 150.5 53 129.5 54 113.5 55 99.5 56 95.5 57 86.0 58 79.0 59 86.5 60 78.0 61 63.5 62 52.0 63 47.0 64 55.5 65 56.0 66 47.0 67 41.0 68 35.5 69 27.0 70 18.0 71 13.0 72 19.5 73 19.5 74 13.5 75 8.5 76 2.5 77 1.0 78 1.5 79 1.0 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 0.0 2 0.025 3 0.0 4 0.0 5 0.0 6 0.0 7 0.0 8 0.0 9 0.0 10-14 0.06 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 1.5 60-64 2.105 65-69 0.315 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 99.3 #Duplication Level Percentage of deduplicated Percentage of total 1 99.34541792547836 98.65 2 0.6042296072507553 1.2 3 0.050352467270896276 0.15 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 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 0.025 0.0 0.0 0.0 0.0 68-69 0.025 0.0 0.0 0.0 0.0 70-71 0.025 0.0 0.0 0.0 0.0 72-73 0.025 0.0 0.0 0.0 0.0 74-75 0.025 0.0 0.0 0.0 0.0 76-77 0.025 0.0 0.0 0.0 0.0 78-79 0.025 0.0 0.0 0.0 0.0 80-81 0.07500000000000001 0.0 0.0 0.0 0.0 82-83 0.1125 0.0 0.0 0.0 0.0 84-85 0.125 0.0 0.0 0.0 0.0 86-87 0.16249999999999998 0.0 0.0 0.0 0.0 88-89 0.1875 0.0 0.0 0.0 0.0 90-91 0.275 0.0 0.0 0.0 0.0 92-93 0.3125 0.0 0.0 0.0 0.0 94-95 0.3875 0.0 0.0 0.0 0.0 96-97 0.4625 0.0 0.0 0.0 0.0 98-99 0.525 0.0 0.0 0.0 0.0 100-101 0.525 0.0 0.0 0.0 0.0 102-103 0.575 0.0 0.0 0.0 0.0 104-105 0.6625000000000001 0.0 0.0 0.0 0.0 106-107 0.7124999999999999 0.0 0.0 0.0 0.0 108-109 0.7625 0.0 0.0 0.0 0.0 110-111 0.8625 0.0 0.0 0.0 0.0 112-113 0.9375 0.0 0.0 0.0 0.0 114-115 1.0375 0.0 0.0 0.0 0.0 116-117 1.2125 0.0 0.0 0.0 0.0 118-119 1.2999999999999998 0.0 0.0 0.0 0.0 120-121 1.425 0.0 0.0 0.0 0.0 122-123 1.5375 0.0 0.0 0.0 0.0 124-125 1.65 0.0 0.0 0.0 0.0 126-127 1.85 0.0 0.0 0.0 0.0 128-129 2.0250000000000004 0.0 0.0 0.0 0.0 130-131 2.175 0.0 0.0 0.0 0.0 132-133 2.4375 0.0 0.0 0.0 0.0 134-135 2.7249999999999996 0.0 0.0 0.0 0.0 136-137 2.9375 0.0 0.0 0.0 0.0 138-139 3.175 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position GGTACAT 10 0.0068555363 144.825 5 >>END_MODULE SRR6958298 read2 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR6958298_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 50 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 32.96025 33.0 33.0 34.0 32.0 34.0 2 33.05775 33.0 33.0 34.0 32.0 34.0 3 33.04425 34.0 33.0 34.0 33.0 34.0 4 33.11275 34.0 33.0 34.0 33.0 34.0 5 33.0975 34.0 33.0 34.0 33.0 34.0 6 37.31525 38.0 38.0 38.0 37.0 38.0 7 37.2655 38.0 38.0 38.0 37.0 38.0 8 37.205 38.0 38.0 38.0 37.0 38.0 9 37.23075 38.0 38.0 38.0 37.0 38.0 10-14 37.2245 38.0 38.0 38.0 37.0 38.0 15-19 37.198750000000004 38.0 38.0 38.0 37.0 38.0 20-24 37.123400000000004 38.0 38.0 38.0 37.0 38.0 25-29 37.151799999999994 38.0 38.0 38.0 37.0 38.0 30-34 37.09815 38.0 38.0 38.0 36.6 38.0 35-39 37.09325 38.0 38.0 38.0 36.4 38.0 40-44 37.10945 38.0 38.0 38.0 36.6 38.0 45-49 37.07655 38.0 38.0 38.0 36.2 38.0 50-54 36.94505 38.0 38.0 38.0 36.0 38.0 55-59 36.91785 38.0 38.0 38.0 35.8 38.0 60-64 36.78075 38.0 38.0 38.0 35.2 38.0 65-69 36.79975 38.0 38.0 38.0 35.6 38.0 70-74 36.8544 38.0 38.0 38.0 35.4 38.0 75-79 36.78835 38.0 38.0 38.0 35.2 38.0 80-84 36.755250000000004 38.0 38.0 38.0 35.0 38.0 85-89 36.6517 38.0 38.0 38.0 34.8 38.0 90-94 36.6283 38.0 38.0 38.0 35.0 38.0 95-99 36.481550000000006 38.0 38.0 38.0 34.4 38.0 100-104 36.39534999999999 38.0 38.0 38.0 34.0 38.0 105-109 36.128249999999994 38.0 37.8 38.0 33.6 38.0 110-114 35.89295 38.0 37.4 38.0 32.6 38.0 115-119 35.7222 38.0 36.8 38.0 31.8 38.0 120-124 35.628949999999996 38.0 36.6 38.0 31.2 38.0 125-129 35.5632 38.0 36.2 38.0 31.4 38.0 130-134 35.4874 38.0 36.0 38.0 31.2 38.0 135-139 35.076649999999994 38.0 35.6 38.0 29.8 38.0 140-144 34.74175 38.0 35.4 38.0 28.4 38.0 145-149 34.14765 38.0 34.4 38.0 26.6 38.0 150-151 29.725125 35.5 27.0 38.0 7.5 38.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 2 9.0 3 2.0 4 1.0 5 0.0 6 1.0 7 3.0 8 1.0 9 0.0 10 2.0 11 1.0 12 0.0 13 3.0 14 0.0 15 1.0 16 3.0 17 3.0 18 1.0 19 4.0 20 2.0 21 3.0 22 7.0 23 11.0 24 11.0 25 13.0 26 13.0 27 24.0 28 26.0 29 33.0 30 38.0 31 57.0 32 74.0 33 95.0 34 141.0 35 234.0 36 578.0 37 2605.0 >>END_MODULE >>Per base sequence content warn #Base G A T C 1 37.574999999999996 17.9 13.275 31.25 2 29.549999999999997 22.325 27.474999999999998 20.65 3 24.15 24.825 27.425 23.599999999999998 4 26.825 29.925 20.05 23.200000000000003 5 26.125 32.2 19.950000000000003 21.725 6 24.2 34.775 19.8 21.224999999999998 7 23.825 19.325 35.099999999999994 21.75 8 23.400000000000002 22.6 24.275 29.725 9 24.15 21.925 27.575 26.35 10-14 25.650000000000002 25.395 23.355 25.6 15-19 25.4 25.55 24.529999999999998 24.52 20-24 25.509999999999998 25.674999999999997 23.985 24.83 25-29 25.515 25.55 24.38 24.555 30-34 25.785000000000004 25.224999999999998 24.44 24.55 35-39 25.945 25.605 23.73 24.72 40-44 25.95 24.51 24.34 25.2 45-49 25.96 25.39 23.810000000000002 24.84 50-54 25.66 25.259999999999998 24.654999999999998 24.425 55-59 25.6 25.019999999999996 24.725 24.654999999999998 60-64 26.695 25.275 24.085 23.945 65-69 25.319999999999997 25.535000000000004 24.645 24.5 70-74 26.369999999999997 25.14 23.87 24.62 75-79 26.279999999999998 25.119999999999997 24.13 24.47 80-84 26.229999999999997 25.745 24.39 23.635 85-89 26.224999999999998 25.064999999999998 24.3 24.41 90-94 26.174999999999997 25.335 24.43 24.060000000000002 95-99 25.655 25.845000000000002 24.67 23.830000000000002 100-104 26.005 25.569999999999997 24.34 24.085 105-109 26.450000000000003 25.145 24.735 23.669999999999998 110-114 26.125 25.81 24.565 23.5 115-119 26.009999999999998 24.705 25.290000000000003 23.995 120-124 26.169999999999998 25.97 24.46 23.400000000000002 125-129 26.02 25.490000000000002 24.38 24.11 130-134 26.715 24.93 24.58 23.775 135-139 26.22 25.955000000000002 24.3 23.525 140-144 26.090000000000003 26.27 24.145 23.494999999999997 145-149 26.38 25.505 24.875 23.24 150-151 27.5875 26.4625 23.400000000000002 22.55 >>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 0.5 16 0.5 17 0.0 18 0.0 19 0.0 20 0.0 21 0.0 22 0.0 23 1.0 24 1.0 25 0.5 26 1.0 27 0.5 28 1.0 29 3.0 30 6.5 31 8.0 32 8.0 33 13.0 34 16.5 35 24.0 36 36.0 37 48.5 38 71.0 39 94.5 40 109.0 41 126.0 42 154.5 43 179.5 44 179.5 45 177.0 46 197.0 47 203.5 48 187.5 49 177.0 50 162.5 51 136.5 52 128.5 53 135.5 54 124.5 55 116.0 56 115.5 57 106.5 58 89.5 59 84.0 60 78.0 61 70.5 62 71.5 63 70.0 64 68.5 65 55.5 66 50.5 67 56.5 68 53.0 69 44.0 70 38.0 71 36.5 72 30.5 73 16.0 74 11.5 75 10.0 76 4.5 77 2.0 78 2.0 79 2.5 80 2.0 81 1.0 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 0.5 97 0.5 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 98.625 #Duplication Level Percentage of deduplicated Percentage of total 1 98.88466413181241 97.52499999999999 2 0.9125475285171103 1.7999999999999998 3 0.1520912547528517 0.44999999999999996 4 0.025348542458808618 0.1 5 0.025348542458808618 0.125 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 warn #Sequence Count Percentage Possible Source CTGCAATTGCAAGCTTGTGTCAAAGAAGAGGGTAGCACCTGATCCTCTTG 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 0.025 0.0 0.0 0.0 0.0 68-69 0.025 0.0 0.0 0.0 0.0 70-71 0.025 0.0 0.0 0.0 0.0 72-73 0.025 0.0 0.0 0.0 0.0 74-75 0.025 0.0 0.0 0.0 0.0 76-77 0.025 0.0 0.0 0.0 0.0 78-79 0.025 0.0 0.0 0.0 0.0 80-81 0.07500000000000001 0.0 0.0 0.0 0.0 82-83 0.1125 0.0 0.0 0.0 0.0 84-85 0.125 0.0 0.0 0.0 0.0 86-87 0.16249999999999998 0.0 0.0 0.0 0.0 88-89 0.1875 0.0 0.0 0.0 0.0 90-91 0.275 0.0 0.0 0.0 0.0 92-93 0.3125 0.0 0.0 0.0 0.0 94-95 0.3875 0.0 0.0 0.0 0.0 96-97 0.4625 0.0 0.0 0.0 0.0 98-99 0.525 0.0 0.0 0.0 0.0 100-101 0.525 0.0 0.0 0.0 0.0 102-103 0.575 0.0 0.0 0.0 0.0 104-105 0.6625000000000001 0.0 0.0 0.0 0.0 106-107 0.7124999999999999 0.0 0.0 0.0 0.0 108-109 0.7625 0.0 0.0 0.0 0.0 110-111 0.8625 0.0 0.0 0.0 0.0 112-113 0.9375 0.0 0.0 0.0 0.0 114-115 1.025 0.0 0.0 0.0 0.0 116-117 1.1875 0.0 0.0 0.0 0.0 118-119 1.275 0.0 0.0 0.0 0.0 120-121 1.4375 0.0 0.0 0.0 0.0 122-123 1.5750000000000002 0.0 0.0 0.0 0.0 124-125 1.7000000000000002 0.0 0.0 0.0 0.0 126-127 1.9 0.0 0.0 0.0 0.0 128-129 2.075 0.0 0.0 0.0 0.0 130-131 2.2249999999999996 0.0 0.0 0.0 0.0 132-133 2.4625 0.0 0.0 0.0 0.0 134-135 2.75 0.0 0.0 0.0 0.0 136-137 2.9625 0.0 0.0 0.0 0.0 138-139 3.2 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position CATCCAG 10 0.006830828 145.0 5 >>END_MODULE Read 1403457 spots for SRR6958298.sra Written 1403457 spots for SRR6958298.sra Read 1403457 spots for SRR6958298.sra Written 1403457 spots for SRR6958298.sra Read 1403457 spots for SRR6958298.sra Written 1403457 spots for SRR6958298.sra Read 1403457 spots for SRR6958298.sra Written 1403457 spots for SRR6958298.sra Read 1403457 spots for SRR6958298.sra Written 1403457 spots for SRR6958298.sra Read 1403457 spots for SRR6958298.sra Written 1403457 spots for SRR6958298.sra Read 1403457 spots for SRR6958298.sra Written 1403457 spots for SRR6958298.sra Read 1403457 spots for SRR6958298.sra Written 1403457 spots for SRR6958298.sra Read 1403457 spots for SRR6958298.sra Written 1403457 spots for SRR6958298.sra Read 1403457 spots for SRR6958298.sra Written 1403457 spots for SRR6958298.sra Read 1403457 spots for SRR6958298.sra Written 1403457 spots for SRR6958298.sra Read 1403457 spots for SRR6958298.sra Written 1403457 spots for SRR6958298.sra Read 1403457 spots for SRR6958298.sra Written 1403457 spots for SRR6958298.sra Read 1403457 spots for SRR6958298.sra Written 1403457 spots for SRR6958298.sra Read 1403457 spots for SRR6958298.sra Written 1403457 spots for SRR6958298.sra Read 1403457 spots for SRR6958298.sra Written 1403457 spots for SRR6958298.sra Read 1403457 spots for SRR6958298.sra Written 1403457 spots for SRR6958298.sra Read 1403457 spots for SRR6958298.sra Written 1403457 spots for SRR6958298.sra Read 1403457 spots for SRR6958298.sra Written 1403457 spots for SRR6958298.sra Read 1403457 spots for SRR6958298.sra Written 1403457 spots for SRR6958298.sra SRR ids: ['SRR6958298.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_9lymv0f9 SRR6958298.sra spots: 28069140 blocks: [[1, 1403457], [1403458, 2806914], [2806915, 4210371], [4210372, 5613828], [5613829, 7017285], [7017286, 8420742], [8420743, 9824199], [9824200, 11227656], [11227657, 12631113], [12631114, 14034570], [14034571, 15438027], [15438028, 16841484], [16841485, 18244941], [18244942, 19648398], [19648399, 21051855], [21051856, 22455312], [22455313, 23858769], [23858770, 25262226], [25262227, 26665683], [26665684, 28069140]] SRR6958298 file size 9490010 SRR6958298 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 SRR6958298 SRR6958298_1.fastq SRR6958298_2.fastq Input file: SRR6958298_1.fastq Paired file: SRR6958298_2.fastq trimmed: SRR6958298-trimmed-pair1.fastq, SRR6958298-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 19:09:18 2024 >> started Fri Dec 6 19:10:18 2024 >> done (59.698s) 28069140 read pairs processed; of these: 31141 ( 0.11%) short read pairs filtered out after trimming by size control 35120 ( 0.13%) empty read pairs filtered out after trimming by size control 28002879 (99.76%) read pairs available; of these: 10558739 (37.71%) trimmed read pairs available after processing 17444140 (62.29%) untrimmed read pairs available after processing Length distribution of reads after trimming: length count percentage 18 3 0.00% 19 4 0.00% 20 6 0.00% 21 0 0.00% 22 6 0.00% 23 6 0.00% 24 6 0.00% 25 8 0.00% 26 7 0.00% 27 7 0.00% 28 6 0.00% 29 8 0.00% 30 4 0.00% 31 7 0.00% 32 9 0.00% 33 6 0.00% 34 9 0.00% 35 12 0.00% 36 15 0.00% 37 16 0.00% 38 9 0.00% 39 11 0.00% 40 25 0.00% 41 19 0.00% 42 13 0.00% 43 24 0.00% 44 25 0.00% 45 37 0.00% 46 29 0.00% 47 46 0.00% 48 56 0.00% 49 59 0.00% 50 54 0.00% 51 85 0.00% 52 104 0.00% 53 91 0.00% 54 76 0.00% 55 93 0.00% 56 109 0.00% 57 139 0.00% 58 130 0.00% 59 167 0.00% 60 195 0.00% 61 217 0.00% 62 258 0.00% 63 299 0.00% 64 318 0.00% 65 342 0.00% 66 386 0.00% 67 409 0.00% 68 414 0.00% 69 518 0.00% 70 575 0.00% 71 689 0.00% 72 805 0.00% 73 896 0.00% 74 981 0.00% 75 1126 0.00% 76 1274 0.00% 77 1469 0.01% 78 1450 0.01% 79 1785 0.01% 80 1895 0.01% 81 2179 0.01% 82 2495 0.01% 83 2953 0.01% 84 4028 0.01% 85 4901 0.02% 86 5026 0.02% 87 5329 0.02% 88 5542 0.02% 89 5985 0.02% 90 6266 0.02% 91 6573 0.02% 92 7052 0.03% 93 7487 0.03% 94 7875 0.03% 95 8351 0.03% 96 8676 0.03% 97 9344 0.03% 98 9610 0.03% 99 10095 0.04% 100 10561 0.04% 101 11269 0.04% 102 11988 0.04% 103 12826 0.05% 104 13429 0.05% 105 14087 0.05% 106 14723 0.05% 107 15737 0.06% 108 16060 0.06% 109 17088 0.06% 110 17780 0.06% 111 18598 0.07% 112 19566 0.07% 113 20762 0.07% 114 22006 0.08% 115 23209 0.08% 116 24371 0.09% 117 25159 0.09% 118 26249 0.09% 119 26980 0.10% 120 28266 0.10% 121 29647 0.11% 122 31334 0.11% 123 33257 0.12% 124 34308 0.12% 125 35950 0.13% 126 37493 0.13% 127 38841 0.14% 128 40350 0.14% 129 41837 0.15% 130 44010 0.16% 131 45720 0.16% 132 48939 0.17% 133 52178 0.19% 134 54968 0.20% 135 59067 0.21% 136 62384 0.22% 137 66298 0.24% 138 70082 0.25% 139 76534 0.27% 140 81812 0.29% 141 89537 0.32% 142 99751 0.36% 143 112780 0.40% 144 130113 0.46% 145 156346 0.56% 146 198159 0.71% 147 285307 1.02% 148 433865 1.55% 149 908573 3.24% 150 6630971 23.68% 151 17444140 62.29% 28002879 reads passed initial QC criterion=sequence-density sequence-density=0.68 sequence-density-rank=1 fanout-score=3.23 fanout-score-rank=18 prefix-density=0.72 prefix-fanout=3.0 sequence=GGTGTTGTCGAAGCCGATGATGCGGAC criterion=fanout-score sequence-density=0.03 sequence-density-rank=31 fanout-score=178.62 fanout-score-rank=1 prefix-density=0.52 prefix-fanout=8.6 sequence=GGCGGCGGCGAACCGCCCCCGTCGCCGCGATCCGAACACTTCACCGGACCATTCAATCGGTAGGAGCGACGGGCGGTGTGTACAAAGGGCAGGGACGTAGTCAACGCGAGCTGATGACTCGCGCTTACTAGGCATTCCTCGTTGAAGACCAACAATTGCAATGATCTATCCCCATCACGATGAAATTTCCCAAGATTACCCGGGCCTGTCGGCCAAGGCTATATACTCGTTGAATACATCAGTGTAGCGCGCGTGCGGCCCAGAACATCTAAGGGCATCACAGACCTGTTATTGCCTCAAACTTCCGTCGCCTAAACGGCGATAGTCCCTCTAAGAAGCTAGCTGCGGAGGGATGGCTCCGCATAGCTAGTTAGCAGGCTGAGGTCTCGTTCGTTAACGGAATTAACCAGACAAATCGCTCCACCAACTAAGAACGGCCATGCACCACCACCCATAGAATCAAGAAAGAGCTCTCAGTCTGTCAATCCTTGCTATGTCTGGACCTGGTAAG criterion=sequence-density sequence-density=0.43 sequence-density-rank=1 fanout-score=2.99 fanout-score-rank=24 prefix-density=0.51 prefix-fanout=2.6 sequence=CTTCGACAACACC criterion=fanout-score sequence-density=0.01 sequence-density-rank=31 fanout-score=193.97 fanout-score-rank=1 prefix-density=0.17 prefix-fanout=7.2 sequence=AAGAAGCACACACAAGCCTAGAAGCCTTCAGCTTAATCTTCTTCCTAAGCAAGTTCGAGCACTCGACCGAAGATGTCTT SRR6958298 testing PE reads STAR mapping to Ensembl genome Started job on | Dec 06 19:12:05 Started mapping on | Dec 06 19:12:05 Finished on | Dec 06 19:14:55 Mapping speed, Million of reads per hour | 593.00 Number of input reads | 28002879 Average input read length | 298 UNIQUE READS: Uniquely mapped reads number | 26719209 Uniquely mapped reads % | 95.42% Average mapped length | 297.10 Number of splices: Total | 31215226 Number of splices: Annotated (sjdb) | 29379288 Number of splices: GT/AG | 30772123 Number of splices: GC/AG | 369003 Number of splices: AT/AC | 12783 Number of splices: Non-canonical | 61317 Mismatch rate per base, % | 0.31% Deletion rate per base | 0.02% Deletion average length | 3.02 Insertion rate per base | 0.02% Insertion average length | 2.77 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 350251 % of reads mapped to multiple loci | 1.25% Number of reads mapped to too many loci | 36018 % of reads mapped to too many loci | 0.13% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 2.40% % of reads unmapped: other | 0.81% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 949837 949837 949837 N_multimapping 350251 350251 350251 N_noFeature 987370 25995359 1167480 N_ambiguous 649072 3465 106825 UnstrandedReadsAssigned:25082767 PositiveStrandReadsAssigned:720385 NegativeStrandReadsAssigned:25444904 Dataset is classified negative stranded MeadianReadLen=151 20thPercentileLength=150 echo kmer=145 SRR6958298 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: SRR6958298-trimmed-pair1.fastq SRR6958298-trimmed-pair2.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 28,002,879 reads, 25,413,566 reads pseudoaligned [quant] estimated average fragment length: 273.853 [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,187 rounds 52973 SRR6958298.ke.tsv 35125 SRR6958298.se.tsv 88098 total ==> SRR6958298.ke.tsv <== target_id length eff_length est_counts tpm PNS24245 936 663.617 0 0 PNS24247 1044 771.147 81.1754 6.01742 PNS24249 1928 1655.15 68.1082 2.35226 PNS24246 1044 771.147 81.1754 6.01742 PNS24248 1044 771.147 81.1754 6.01742 PNS24244 1471 1198.15 37.3655 1.78272 PNS24243 293 79.6528 0 0 KQK14069 1603 1330.15 2880.35 123.785 KQK14071 474 217.62 49.3106 12.9528 ==> SRR6958298.se.tsv <== BRADI_1g14170v3 3288 BRADI_1g53295v3 2018 BRADI_1g59795v3 153 BRADI_1g07683v3 0 BRADI_1g00485v3 0 BRADI_1g20270v3 617 BRADI_1g74790v3 197 BRADI_1g09890v3 0 BRADI_1g77505v3 386 BRADI_1g48960v3 0 SRR6958298 completed mapping pipeline successfully