Starting /dee2/code/volunteer_pipeline.sh SRR8846518 current disk space = 1515383459840 free memory = 1604481540 SRR8846518 SRAfilesize dffe6aaf774d26cac5b384c35e50d185 SRR8846518.sra SRR8846518.sra file validated SRR8846518 is paired end SRR8846518 is conventional basespace SRR8846518 read1 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR8846518_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 fail #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 29.4015 33.0 30.0 33.0 18.0 34.0 2 31.4125 33.0 32.0 33.0 27.0 34.0 3 30.66225 33.0 30.0 33.0 27.0 33.0 4 31.6305 33.0 31.0 33.0 29.0 34.0 5 32.33375 33.0 33.0 33.0 31.0 34.0 6 36.8415 38.0 37.0 38.0 34.0 38.0 7 37.257 38.0 38.0 38.0 36.0 38.0 8 37.30175 38.0 38.0 38.0 36.0 38.0 9 37.42775 38.0 38.0 38.0 37.0 38.0 10-14 37.27355 38.0 38.0 38.0 36.4 38.0 15-19 37.10075 38.0 38.0 38.0 35.8 38.0 20-24 37.06795 38.0 38.0 38.0 35.8 38.0 25-29 37.250299999999996 38.0 38.0 38.0 36.4 38.0 30-34 37.129149999999996 38.0 38.0 38.0 36.0 38.0 35-39 36.9382 38.0 38.0 38.0 35.6 38.0 40-44 36.656600000000005 38.0 38.0 38.0 34.6 38.0 45-49 36.51800000000001 38.0 38.0 38.0 33.6 38.0 50-54 36.730149999999995 38.0 38.0 38.0 34.6 38.0 55-59 36.57555 38.0 38.0 38.0 34.0 38.0 60-64 36.2687 38.0 37.0 38.0 33.0 38.0 65-69 36.075149999999994 38.0 37.0 38.0 32.0 38.0 70-74 35.8301 38.0 36.6 38.0 30.4 38.0 75-79 35.9559 38.0 36.8 38.0 31.6 38.0 80-84 35.9048 38.0 36.6 38.0 31.6 38.0 85-89 35.665000000000006 38.0 36.2 38.0 30.6 38.0 90-94 34.9532 38.0 35.0 38.0 28.0 38.0 95-99 34.595749999999995 38.0 34.6 38.0 26.0 38.0 100-104 35.07895 38.0 35.0 38.0 28.6 38.0 105-109 34.623000000000005 38.0 34.6 38.0 26.6 38.0 110-114 33.007549999999995 37.0 32.0 38.0 16.6 38.0 115-119 32.4566 36.2 31.0 38.0 15.0 38.0 120-124 32.78515 36.8 31.8 38.0 15.0 38.0 125-129 32.502449999999996 36.6 32.0 38.0 15.0 38.0 130-134 31.150149999999996 35.2 28.2 38.0 14.4 38.0 135-139 29.86345 34.6 24.8 38.0 13.6 38.0 140-144 28.68655 34.0 22.2 38.0 13.0 38.0 145-149 27.293650000000003 33.8 18.2 38.0 2.0 38.0 150-151 22.281750000000002 28.5 2.0 35.5 2.0 38.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 7 1.0 8 0.0 9 0.0 10 0.0 11 0.0 12 1.0 13 0.0 14 1.0 15 1.0 16 2.0 17 3.0 18 5.0 19 5.0 20 5.0 21 8.0 22 10.0 23 9.0 24 19.0 25 29.0 26 39.0 27 45.0 28 58.0 29 87.0 30 127.0 31 158.0 32 256.0 33 342.0 34 458.0 35 761.0 36 1048.0 37 522.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 35.87210813621004 15.050688848453339 10.163763971926176 38.91343904341045 2 23.25 21.5 37.075 18.175 3 18.55 29.175 25.124999999999996 27.150000000000002 4 24.85 34.2 20.200000000000003 20.75 5 23.655913978494624 35.23380845211303 21.605401350337583 19.504876219054765 6 19.125 33.45 24.05 23.375 7 16.1 19.475 41.199999999999996 23.225 8 19.1 20.175 29.7 31.025000000000002 9 18.275 19.7 31.275 30.75 10-14 22.994999999999997 25.5 24.625 26.88 15-19 22.595000000000002 26.0 25.86 25.545 20-24 22.465 26.355 26.005 25.174999999999997 25-29 22.145 26.265 26.08 25.509999999999998 30-34 22.07 26.765 26.305 24.86 35-39 22.74 26.290000000000003 25.840000000000003 25.130000000000003 40-44 22.29 26.729999999999997 25.674999999999997 25.305 45-49 22.41 26.090000000000003 25.874999999999996 25.624999999999996 50-54 22.165000000000003 25.86 26.334999999999997 25.64 55-59 22.15 26.6 26.075 25.174999999999997 60-64 22.945 26.450000000000003 25.685000000000002 24.92 65-69 22.689999999999998 25.564999999999998 26.145000000000003 25.6 70-74 22.845 25.97 25.86 25.324999999999996 75-79 22.655 25.485000000000003 26.334999999999997 25.525 80-84 23.044999999999998 25.25 26.505000000000003 25.2 85-89 22.965 25.45 25.985000000000003 25.6 90-94 23.11 25.61 25.735000000000003 25.545 95-99 22.75 25.965 25.705 25.580000000000002 100-104 22.85 26.064999999999998 26.045 25.040000000000003 105-109 23.150000000000002 25.64 25.665 25.545 110-114 23.43 25.96 25.555 25.055 115-119 23.380000000000003 25.535000000000004 25.990000000000002 25.095 120-124 23.855 25.755 25.715 24.675 125-129 23.955000000000002 25.06 25.724999999999998 25.259999999999998 130-134 23.755000000000003 25.195 25.729999999999997 25.319999999999997 135-139 23.5 25.619999999999997 25.679999999999996 25.2 140-144 23.425 25.635 25.86 25.080000000000002 145-149 23.605 25.69 25.264999999999997 25.44 150-151 23.724999999999998 26.2625 24.9125 25.1 >>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 0.0 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 0.5 25 2.0 26 2.5 27 1.5 28 2.5 29 5.5 30 9.0 31 13.0 32 23.0 33 29.5 34 31.0 35 38.0 36 54.0 37 72.5 38 95.5 39 125.0 40 147.5 41 168.5 42 184.0 43 199.0 44 216.5 45 219.5 46 209.0 47 215.5 48 209.5 49 179.0 50 163.0 51 153.0 52 130.5 53 110.0 54 98.5 55 96.5 56 87.0 57 69.0 58 74.5 59 70.5 60 58.0 61 51.0 62 45.5 63 45.0 64 42.5 65 36.0 66 32.5 67 32.0 68 33.5 69 32.0 70 22.0 71 16.0 72 11.0 73 9.0 74 10.5 75 7.5 76 5.0 77 2.5 78 0.5 79 0.0 80 0.0 81 0.0 82 0.0 83 0.0 84 0.5 85 0.5 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 3.8249999999999997 2 0.0 3 0.0 4 0.0 5 0.025 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 99.725 #Duplication Level Percentage of deduplicated Percentage of total 1 99.72424166457759 99.45 2 0.2757583354224116 0.5499999999999999 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 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 0.025 0.0 0.0 0.0 0.0 82-83 0.025 0.0 0.0 0.0 0.0 84-85 0.037500000000000006 0.0 0.0 0.0 0.0 86-87 0.05 0.0 0.0 0.0 0.0 88-89 0.1 0.0 0.0 0.0 0.0 90-91 0.1125 0.0 0.0 0.0 0.0 92-93 0.1375 0.0 0.0 0.0 0.0 94-95 0.15 0.0 0.0 0.0 0.0 96-97 0.175 0.0 0.0 0.0 0.0 98-99 0.225 0.0 0.0 0.0 0.0 100-101 0.30000000000000004 0.0 0.0 0.0 0.0 102-103 0.3875 0.0 0.0 0.0 0.0 104-105 0.4 0.0 0.0 0.0 0.0 106-107 0.4625 0.0 0.0 0.0 0.0 108-109 0.5375000000000001 0.0 0.0 0.0 0.0 110-111 0.6125 0.0 0.0 0.0 0.0 112-113 0.75 0.0 0.0 0.0 0.0 114-115 0.8125 0.0 0.0 0.0 0.0 116-117 0.875 0.0 0.0 0.0 0.0 118-119 0.9375 0.0 0.0 0.0 0.0 120-121 1.0125 0.0 0.0 0.0 0.0 122-123 1.1 0.0 0.0 0.0 0.0 124-125 1.225 0.0 0.0 0.0 0.0 126-127 1.4625 0.0 0.0 0.0 0.0 128-129 1.7 0.0 0.0 0.0 0.0 130-131 1.7875 0.0 0.0 0.0 0.0 132-133 2.0125 0.0 0.0 0.0 0.0 134-135 2.2750000000000004 0.0 0.0 0.0 0.0 136-137 2.55 0.0 0.0 0.0 0.0 138-139 2.9625 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position GATGAGC 10 0.006832588 144.9875 5 TCACTCC 10 0.006832588 144.9875 3 GACCAGC 10 0.006832588 144.9875 6 CTTCTCT 10 0.006832588 144.9875 6 >>END_MODULE SRR8846518 read2 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR8846518_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 32.7715 33.0 33.0 34.0 32.0 34.0 2 32.785 33.0 33.0 34.0 32.0 34.0 3 32.703 33.0 33.0 34.0 32.0 34.0 4 32.81325 33.0 33.0 34.0 32.0 34.0 5 32.70075 33.0 33.0 34.0 32.0 34.0 6 36.96175 38.0 38.0 38.0 36.0 38.0 7 36.96725 38.0 38.0 38.0 36.0 38.0 8 37.0045 38.0 38.0 38.0 36.0 38.0 9 36.95225 38.0 38.0 38.0 36.0 38.0 10-14 36.959050000000005 38.0 38.0 38.0 36.0 38.0 15-19 36.9507 38.0 38.0 38.0 35.8 38.0 20-24 36.98375 38.0 38.0 38.0 36.0 38.0 25-29 36.78065 38.0 38.0 38.0 35.2 38.0 30-34 36.692150000000005 38.0 38.0 38.0 34.6 38.0 35-39 36.780750000000005 38.0 38.0 38.0 35.0 38.0 40-44 36.699650000000005 38.0 38.0 38.0 34.6 38.0 45-49 36.564800000000005 38.0 38.0 38.0 33.8 38.0 50-54 36.3349 38.0 38.0 38.0 33.6 38.0 55-59 36.1635 38.0 37.4 38.0 32.8 38.0 60-64 36.26665 38.0 37.8 38.0 33.2 38.0 65-69 36.46575 38.0 38.0 38.0 34.0 38.0 70-74 36.182249999999996 38.0 37.2 38.0 32.8 38.0 75-79 35.75605 38.0 37.0 38.0 30.0 38.0 80-84 35.893950000000004 38.0 37.0 38.0 31.6 38.0 85-89 35.7516 38.0 37.0 38.0 31.4 38.0 90-94 35.380849999999995 38.0 36.2 38.0 29.6 38.0 95-99 34.84160000000001 38.0 35.2 38.0 27.0 38.0 100-104 34.6479 38.0 35.0 38.0 26.4 38.0 105-109 34.59335 38.0 34.8 38.0 26.2 38.0 110-114 34.241699999999994 38.0 34.2 38.0 24.2 38.0 115-119 33.55745 38.0 33.8 38.0 20.2 38.0 120-124 32.92645 37.4 32.6 38.0 15.0 38.0 125-129 32.7395 37.0 32.8 38.0 15.0 38.0 130-134 32.09505 36.0 31.0 38.0 14.2 38.0 135-139 30.955750000000002 35.4 29.4 38.0 13.2 38.0 140-144 29.3239 33.2 24.8 38.0 10.8 38.0 145-149 27.61685 33.0 20.0 38.0 2.0 38.0 150-151 20.8445 26.5 2.0 35.5 2.0 38.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 2 5.0 3 2.0 4 1.0 5 0.0 6 0.0 7 0.0 8 1.0 9 1.0 10 0.0 11 0.0 12 1.0 13 3.0 14 3.0 15 3.0 16 8.0 17 5.0 18 7.0 19 9.0 20 8.0 21 11.0 22 14.0 23 10.0 24 34.0 25 30.0 26 36.0 27 46.0 28 59.0 29 71.0 30 104.0 31 147.0 32 182.0 33 229.0 34 380.0 35 548.0 36 1074.0 37 968.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 38.800000000000004 13.450000000000001 12.6 35.15 2 29.425 19.0 32.2 19.375 3 22.475 23.125 29.075 25.324999999999996 4 26.55 32.025 18.525 22.900000000000002 5 26.025 34.300000000000004 20.125 19.55 6 20.45 34.1 21.7 23.75 7 20.25 15.425 39.0 25.324999999999996 8 23.075000000000003 20.625 24.825 31.474999999999998 9 22.225 21.675 27.650000000000002 28.449999999999996 10-14 26.195 23.79 23.435 26.58 15-19 25.16 24.955 25.180000000000003 24.705 20-24 24.490000000000002 25.669999999999998 25.2 24.64 25-29 25.145 25.605 25.285000000000004 23.965 30-34 25.695 25.174999999999997 25.130000000000003 24.0 35-39 25.165 25.365 25.230000000000004 24.240000000000002 40-44 25.424999999999997 25.374999999999996 24.779999999999998 24.42 45-49 25.564999999999998 25.040000000000003 25.45 23.945 50-54 26.009999999999998 25.069999999999997 24.845 24.075 55-59 25.215 26.155 24.145 24.485 60-64 25.535000000000004 25.314999999999998 25.09 24.060000000000002 65-69 25.035 25.580000000000002 25.28 24.104999999999997 70-74 25.575 25.724999999999998 24.654999999999998 24.044999999999998 75-79 25.25 25.419999999999998 25.245 24.085 80-84 26.205000000000002 25.185000000000002 24.68 23.93 85-89 25.44 25.955000000000002 25.355 23.25 90-94 26.115 25.355 24.759999999999998 23.77 95-99 25.53 26.009999999999998 24.79 23.669999999999998 100-104 26.284999999999997 24.945 24.955 23.815 105-109 25.929999999999996 25.515 25.040000000000003 23.515 110-114 25.740000000000002 26.314999999999998 24.91 23.035 115-119 26.22 25.465 25.11 23.205000000000002 120-124 25.805 25.655 25.290000000000003 23.25 125-129 25.66 25.430000000000003 25.669999999999998 23.24 130-134 25.295 25.795 25.85 23.06 135-139 25.290000000000003 25.95 25.53 23.23 140-144 26.13 25.564999999999998 25.7 22.605 145-149 25.845000000000002 25.81 25.619999999999997 22.725 150-151 26.387500000000003 26.125 25.8625 21.625 >>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 0.5 11 0.5 12 0.0 13 0.5 14 0.5 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 1.0 26 1.5 27 1.0 28 1.5 29 2.5 30 5.0 31 10.5 32 14.0 33 18.5 34 27.0 35 34.0 36 42.0 37 59.5 38 75.5 39 91.0 40 116.5 41 124.5 42 149.5 43 175.5 44 192.0 45 208.0 46 217.0 47 219.5 48 197.5 49 168.5 50 155.5 51 152.0 52 129.0 53 112.5 54 108.0 55 95.5 56 88.0 57 84.0 58 88.5 59 87.0 60 76.0 61 74.5 62 69.0 63 76.0 64 67.5 65 56.5 66 56.0 67 54.5 68 48.0 69 39.5 70 40.5 71 31.5 72 19.0 73 10.5 74 7.0 75 7.0 76 6.5 77 2.5 78 0.5 79 1.0 80 0.5 81 0.0 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 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 99.5 #Duplication Level Percentage of deduplicated Percentage of total 1 99.59798994974875 99.1 2 0.37688442211055273 0.75 3 0.0 0.0 4 0.0 0.0 5 0.0 0.0 6 0.02512562814070352 0.15 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 CTCTTGTTAGCTATCTACGTACGTGTACGATGGCTCCCACAGTGATGTCG 6 0.15 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 0.025 0.0 0.0 0.0 0.0 82-83 0.025 0.0 0.0 0.0 0.0 84-85 0.037500000000000006 0.0 0.0 0.0 0.0 86-87 0.05 0.0 0.0 0.0 0.0 88-89 0.1 0.0 0.0 0.0 0.0 90-91 0.1125 0.0 0.0 0.0 0.0 92-93 0.1375 0.0 0.0 0.0 0.0 94-95 0.15 0.0 0.0 0.0 0.0 96-97 0.175 0.0 0.0 0.0 0.0 98-99 0.225 0.0 0.0 0.0 0.0 100-101 0.30000000000000004 0.0 0.0 0.0 0.0 102-103 0.3875 0.0 0.0 0.0 0.0 104-105 0.4 0.0 0.0 0.0 0.0 106-107 0.4625 0.0 0.0 0.0 0.0 108-109 0.5375000000000001 0.0 0.0 0.0 0.0 110-111 0.6 0.0 0.0 0.0 0.0 112-113 0.7250000000000001 0.0 0.0 0.0 0.0 114-115 0.7875000000000001 0.0 0.0 0.0 0.0 116-117 0.85 0.0 0.0 0.0 0.0 118-119 0.9125000000000001 0.0 0.0 0.0 0.0 120-121 0.9875 0.0 0.0 0.0 0.0 122-123 1.075 0.0 0.0 0.0 0.0 124-125 1.225 0.0 0.0 0.0 0.0 126-127 1.4625 0.0 0.0 0.0 0.0 128-129 1.7374999999999998 0.0 0.0 0.0 0.0 130-131 1.8375 0.0 0.0 0.0 0.0 132-133 2.0625 0.0 0.0 0.0 0.0 134-135 2.325 0.0 0.0 0.0 0.0 136-137 2.55 0.0 0.0 0.0 0.0 138-139 2.95 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position CTGAGCG 10 0.006830828 145.0 1 >>END_MODULE Read 1004220 spots for SRR8846518.sra Written 1004220 spots for SRR8846518.sra Read 1004220 spots for SRR8846518.sra Written 1004220 spots for SRR8846518.sra Read 1004220 spots for SRR8846518.sra Written 1004220 spots for SRR8846518.sra Read 1004220 spots for SRR8846518.sra Written 1004220 spots for SRR8846518.sra Read 1004220 spots for SRR8846518.sra Written 1004220 spots for SRR8846518.sra Read 1004220 spots for SRR8846518.sra Written 1004220 spots for SRR8846518.sra Read 1004220 spots for SRR8846518.sra Written 1004220 spots for SRR8846518.sra Read 1004220 spots for SRR8846518.sra Written 1004220 spots for SRR8846518.sra Read 1004220 spots for SRR8846518.sra Written 1004220 spots for SRR8846518.sra Read 1004220 spots for SRR8846518.sra Written 1004220 spots for SRR8846518.sra Read 1004220 spots for SRR8846518.sra Written 1004220 spots for SRR8846518.sra Read 1004220 spots for SRR8846518.sra Read 1004220 spots for SRR8846518.sra Written 1004220 spots for SRR8846518.sra Written 1004220 spots for SRR8846518.sra Read 1004220 spots for SRR8846518.sra Written 1004220 spots for SRR8846518.sra Read 1004220 spots for SRR8846518.sra Written 1004220 spots for SRR8846518.sra Read 1004220 spots for SRR8846518.sra Written 1004220 spots for SRR8846518.sra Read 1004220 spots for SRR8846518.sra Written 1004220 spots for SRR8846518.sra Read 1004237 spots for SRR8846518.sra Written 1004237 spots for SRR8846518.sra Read 1004220 spots for SRR8846518.sra Written 1004220 spots for SRR8846518.sra Read 1004220 spots for SRR8846518.sra Written 1004220 spots for SRR8846518.sra SRR ids: ['SRR8846518.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_rs_pb6mv SRR8846518.sra spots: 20084417 blocks: [[1, 1004220], [1004221, 2008440], [2008441, 3012660], [3012661, 4016880], [4016881, 5021100], [5021101, 6025320], [6025321, 7029540], [7029541, 8033760], [8033761, 9037980], [9037981, 10042200], [10042201, 11046420], [11046421, 12050640], [12050641, 13054860], [13054861, 14059080], [14059081, 15063300], [15063301, 16067520], [16067521, 17071740], [17071741, 18075960], [18075961, 19080180], [19080181, 20084417]] SRR8846518 file size 6784249 SRR8846518 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 SRR8846518 SRR8846518_1.fastq SRR8846518_2.fastq Input file: SRR8846518_1.fastq Paired file: SRR8846518_2.fastq trimmed: SRR8846518-trimmed-pair1.fastq, SRR8846518-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 Thu Dec 12 02:58:08 2024 >> started Thu Dec 12 02:58:31 2024 >> done (23.149s) 20084417 read pairs processed; of these: 13189 ( 0.07%) short read pairs filtered out after trimming by size control 9384 ( 0.05%) empty read pairs filtered out after trimming by size control 20061844 (99.89%) read pairs available; of these: 11530767 (57.48%) trimmed read pairs available after processing 8531077 (42.52%) untrimmed read pairs available after processing Length distribution of reads after trimming: length count percentage 18 3 0.00% 19 9 0.00% 20 1 0.00% 21 7 0.00% 22 7 0.00% 23 8 0.00% 24 7 0.00% 25 6 0.00% 26 7 0.00% 27 18 0.00% 28 6 0.00% 29 14 0.00% 30 9 0.00% 31 12 0.00% 32 16 0.00% 33 15 0.00% 34 16 0.00% 35 12 0.00% 36 10 0.00% 37 12 0.00% 38 15 0.00% 39 16 0.00% 40 7 0.00% 41 14 0.00% 42 25 0.00% 43 21 0.00% 44 25 0.00% 45 24 0.00% 46 26 0.00% 47 20 0.00% 48 39 0.00% 49 43 0.00% 50 44 0.00% 51 51 0.00% 52 50 0.00% 53 63 0.00% 54 55 0.00% 55 54 0.00% 56 62 0.00% 57 76 0.00% 58 76 0.00% 59 99 0.00% 60 101 0.00% 61 123 0.00% 62 123 0.00% 63 164 0.00% 64 147 0.00% 65 181 0.00% 66 192 0.00% 67 224 0.00% 68 243 0.00% 69 280 0.00% 70 305 0.00% 71 338 0.00% 72 414 0.00% 73 446 0.00% 74 470 0.00% 75 557 0.00% 76 624 0.00% 77 656 0.00% 78 761 0.00% 79 823 0.00% 80 997 0.00% 81 1073 0.01% 82 1253 0.01% 83 1450 0.01% 84 2057 0.01% 85 2421 0.01% 86 2453 0.01% 87 2687 0.01% 88 2811 0.01% 89 3051 0.02% 90 3078 0.02% 91 3558 0.02% 92 3717 0.02% 93 4003 0.02% 94 4398 0.02% 95 4778 0.02% 96 5104 0.03% 97 5712 0.03% 98 5877 0.03% 99 6406 0.03% 100 6815 0.03% 101 7384 0.04% 102 7913 0.04% 103 8566 0.04% 104 9098 0.05% 105 9859 0.05% 106 10944 0.05% 107 11432 0.06% 108 12235 0.06% 109 13206 0.07% 110 13747 0.07% 111 14712 0.07% 112 15840 0.08% 113 16755 0.08% 114 18019 0.09% 115 19332 0.10% 116 20351 0.10% 117 21689 0.11% 118 23204 0.12% 119 24903 0.12% 120 26083 0.13% 121 27801 0.14% 122 29313 0.15% 123 31191 0.16% 124 33438 0.17% 125 35671 0.18% 126 38030 0.19% 127 41065 0.20% 128 43492 0.22% 129 46819 0.23% 130 50331 0.25% 131 54052 0.27% 132 58876 0.29% 133 63629 0.32% 134 68828 0.34% 135 75413 0.38% 136 83010 0.41% 137 91733 0.46% 138 101858 0.51% 139 114678 0.57% 140 128578 0.64% 141 145886 0.73% 142 169628 0.85% 143 199725 1.00% 144 240089 1.20% 145 300092 1.50% 146 392354 1.96% 147 553321 2.76% 148 803449 4.00% 149 1521344 7.58% 150 5599830 27.91% 151 8531077 42.52% 20061844 reads passed initial QC criterion=sequence-density sequence-density=0.27 sequence-density-rank=1 fanout-score=2.11 fanout-score-rank=39 prefix-density=0.27 prefix-fanout=2.1 sequence=AACATGGAGAACATGGCGAGGCGGCCGTTCTTGATCTCCTTCACCTTGAGCTCAGCGAA criterion=fanout-score sequence-density=0.03 sequence-density-rank=37 fanout-score=98.21 fanout-score-rank=1 prefix-density=0.29 prefix-fanout=10.5 sequence=GGCGGCGGCGAACCGCCCCCGTCGCCGCGATCCGAACACTTCACCGGACCATTCAATCGGTAGGAGCGACGGGCGGTGTGTACAAAGGGCAGGGACGTAGTCAACGCGAGCTGATGACTCGCGCTTACTAGGCATTCCTCGTTGAAGACCAACAATTGCAATGATCTATCCCCATCACGATGAAATTTCCCAAGATTACCCGGGCCTGTCGGCCAAGGCTATATACTCGTTGAATACATCAGTGTAGCGCGCGTGCGGCCCAGAACATCTAAGGGCATCACAGACCTGTTATTGCCTCAAACTTCCGTCGCCTAAACGGCGATAGTCCCTCTAAGAAGCTAGCTGCGGAGGGATGGCTCCGCATAGCTAGTTAGCAGGCTGAGGTCTCGTTCGTTAACGGAATTAACCAGACAAATCGCTCCACCAACTAAGAACGGCCATGCACCACCACCCATAGAATCAAGAAAGAGCTCTCAGTCTGTCAATCCTTGCTATGTCTGGACCTGGTAAG criterion=sequence-density sequence-density=0.35 sequence-density-rank=1 fanout-score=2.33 fanout-score-rank=34 prefix-density=0.36 prefix-fanout=2.3 sequence=CGGTTCCGGTTC criterion=fanout-score sequence-density=0.02 sequence-density-rank=35 fanout-score=700.33 fanout-score-rank=1 prefix-density=0.68 prefix-fanout=20.6 sequence=GCCGCCGCCCCTCGTCCTCTGTGTTCCTTCTCCGAGTTTCAGCCATGGGTAAGGAGAAGACTCACATCAACATCGTGGTCATTGGCCATGTCGACTCTGGCAAGTCGACCACCACTGGCCACCTGATCTACAAGCTTGGAGGTATTGACAAGCGTGTGATCGAGAGGTTCGAGAAGGAGGCTGC SRR8846518 testing PE reads STAR mapping to Ensembl genome Started job on | Dec 12 02:59:10 Started mapping on | Dec 12 02:59:10 Finished on | Dec 12 03:01:13 Mapping speed, Million of reads per hour | 587.18 Number of input reads | 20061844 Average input read length | 296 UNIQUE READS: Uniquely mapped reads number | 19488997 Uniquely mapped reads % | 97.14% Average mapped length | 295.85 Number of splices: Total | 22478201 Number of splices: Annotated (sjdb) | 21210695 Number of splices: GT/AG | 22191425 Number of splices: GC/AG | 258167 Number of splices: AT/AC | 11845 Number of splices: Non-canonical | 16764 Mismatch rate per base, % | 0.15% Deletion rate per base | 0.00% Deletion average length | 1.39 Insertion rate per base | 0.00% Insertion average length | 1.15 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 174415 % of reads mapped to multiple loci | 0.87% Number of reads mapped to too many loci | 21273 % of reads mapped to too many loci | 0.11% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 1.30% % of reads unmapped: other | 0.58% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 407212 407212 407212 N_multimapping 174415 174415 174415 N_noFeature 722338 18969903 884036 N_ambiguous 413847 2645 57178 UnstrandedReadsAssigned:18352812 PositiveStrandReadsAssigned:516449 NegativeStrandReadsAssigned:18547783 Dataset is classified negative stranded MeadianReadLen=151 20thPercentileLength=147 echo kmer=143 SRR8846518 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: SRR8846518-trimmed-pair1.fastq SRR8846518-trimmed-pair2.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 20,061,844 reads, 18,600,493 reads pseudoaligned [quant] estimated average fragment length: 276.885 [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,153 rounds 52973 SRR8846518.ke.tsv 35125 SRR8846518.se.tsv 88098 total ==> SRR8846518.ke.tsv <== target_id length eff_length est_counts tpm PNS24245 936 660.426 23.9109 2.80477 PNS24247 1044 768.115 53.9778 5.44397 PNS24249 1928 1652.11 45.7117 2.14345 PNS24246 1044 768.115 53.9778 5.44397 PNS24248 1044 768.115 53.9778 5.44397 PNS24244 1471 1195.11 73.4439 4.76072 PNS24243 293 79.6627 0 0 KQK14069 1603 1327.11 1602.93 93.5693 KQK14071 474 217.202 15.1529 5.40452 ==> SRR8846518.se.tsv <== BRADI_1g14170v3 1732 BRADI_1g53295v3 68 BRADI_1g59795v3 278 BRADI_1g07683v3 0 BRADI_1g00485v3 34 BRADI_1g20270v3 2656 BRADI_1g74790v3 123 BRADI_1g09890v3 1 BRADI_1g77505v3 252 BRADI_1g48960v3 0 SRR8846518 completed mapping pipeline successfully