Starting /dee2/code/volunteer_pipeline.sh SRR28623278 current disk space = 3050334724096 free memory = 1445560476 SRR28623278 SRAfilesize 9f4b75155ff8f8b9f7f92be6b96f2c91 SRR28623278.sra SRR28623278.sra file validated SRR28623278 is paired end SRR28623278 is conventional basespace SRR28623278 read1 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR28623278_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 43 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 36.34575 37.0 37.0 37.0 37.0 37.0 2 36.5495 37.0 37.0 37.0 37.0 37.0 3 36.569 37.0 37.0 37.0 37.0 37.0 4 36.586 37.0 37.0 37.0 37.0 37.0 5 36.6505 37.0 37.0 37.0 37.0 37.0 6 36.631 37.0 37.0 37.0 37.0 37.0 7 36.621 37.0 37.0 37.0 37.0 37.0 8 36.3915 37.0 37.0 37.0 37.0 37.0 9 36.596 37.0 37.0 37.0 37.0 37.0 10-14 36.575900000000004 37.0 37.0 37.0 37.0 37.0 15-19 36.5398 37.0 37.0 37.0 37.0 37.0 20-24 36.502300000000005 37.0 37.0 37.0 37.0 37.0 25-29 36.4322 37.0 37.0 37.0 37.0 37.0 30-34 36.428900000000006 37.0 37.0 37.0 37.0 37.0 35-39 36.3829 37.0 37.0 37.0 37.0 37.0 40-44 36.338699999999996 37.0 37.0 37.0 37.0 37.0 45-49 36.3316 37.0 37.0 37.0 37.0 37.0 50-54 36.2517 37.0 37.0 37.0 37.0 37.0 55-59 36.2742 37.0 37.0 37.0 37.0 37.0 60-64 36.2722 37.0 37.0 37.0 37.0 37.0 65-69 36.2251 37.0 37.0 37.0 37.0 37.0 70-74 36.18 37.0 37.0 37.0 37.0 37.0 75-79 36.1004 37.0 37.0 37.0 37.0 37.0 80-84 36.006299999999996 37.0 37.0 37.0 37.0 37.0 85-89 36.0577 37.0 37.0 37.0 37.0 37.0 90-94 35.9918 37.0 37.0 37.0 37.0 37.0 95-99 35.8937 37.0 37.0 37.0 37.0 37.0 100-104 35.9283 37.0 37.0 37.0 37.0 37.0 105-109 35.9585 37.0 37.0 37.0 37.0 37.0 110-114 35.793499999999995 37.0 37.0 37.0 37.0 37.0 115-119 35.8597 37.0 37.0 37.0 37.0 37.0 120-124 35.6822 37.0 37.0 37.0 37.0 37.0 125-129 35.6022 37.0 37.0 37.0 37.0 37.0 130-134 35.811400000000006 37.0 37.0 37.0 37.0 37.0 135-139 35.643299999999996 37.0 37.0 37.0 37.0 37.0 140-144 35.4293 37.0 37.0 37.0 37.0 37.0 145-149 35.4353 37.0 37.0 37.0 37.0 37.0 150-151 35.1255 37.0 37.0 37.0 31.0 37.0 >>END_MODULE >>Per tile sequence quality pass #Tile Base Mean 1101 1 0.0 1101 2 0.0 1101 3 0.0 1101 4 0.0 1101 5 0.0 1101 6 0.0 1101 7 0.0 1101 8 0.0 1101 9 0.0 1101 10-14 0.0 1101 15-19 0.0 1101 20-24 0.0 1101 25-29 0.0 1101 30-34 0.0 1101 35-39 0.0 1101 40-44 0.0 1101 45-49 0.0 1101 50-54 0.0 1101 55-59 0.0 1101 60-64 0.0 1101 65-69 0.0 1101 70-74 0.0 1101 75-79 0.0 1101 80-84 0.0 1101 85-89 0.0 1101 90-94 0.0 1101 95-99 0.0 1101 100-104 0.0 1101 105-109 0.0 1101 110-114 0.0 1101 115-119 0.0 1101 120-124 0.0 1101 125-129 0.0 1101 130-134 0.0 1101 135-139 0.0 1101 140-144 0.0 1101 145-149 0.0 1101 150-151 0.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 21 2.0 22 5.0 23 4.0 24 4.0 25 3.0 26 6.0 27 7.0 28 14.0 29 24.0 30 37.0 31 40.0 32 55.0 33 85.0 34 137.0 35 421.0 36 2890.0 37 266.0 >>END_MODULE >>Per base sequence content warn #Base G A T C 1 31.93572683906603 12.503138337936228 11.197589756464977 44.363545066532765 2 19.175 16.6 34.25 29.975 3 18.85 18.55 26.424999999999997 36.175000000000004 4 21.8 25.275 24.525 28.4 5 22.825 33.775 24.525 18.875 6 21.0 34.2 24.775 20.025000000000002 7 15.575 27.85 39.875 16.7 8 17.224999999999998 27.250000000000004 31.175000000000004 24.349999999999998 9 17.7 24.05 34.150000000000006 24.099999999999998 10-14 18.970000000000002 30.875000000000004 27.615000000000002 22.54 15-19 19.27 28.42 28.71 23.599999999999998 20-24 19.61 29.160000000000004 27.500000000000004 23.73 25-29 19.695 28.64 27.655 24.01 30-34 19.72 27.900000000000002 28.505000000000003 23.875 35-39 19.81 28.27 28.18 23.74 40-44 19.375 29.085 28.16 23.380000000000003 45-49 20.349999999999998 28.285 27.525 23.84 50-54 19.650000000000002 29.425 27.534999999999997 23.39 55-59 19.23 28.665000000000003 28.01 24.095 60-64 20.225 28.799999999999997 27.43 23.544999999999998 65-69 20.560000000000002 28.499999999999996 27.439999999999998 23.5 70-74 19.655 28.59 27.51 24.245 75-79 19.89 28.59 28.599999999999998 22.919999999999998 80-84 20.119999999999997 28.84 27.555000000000003 23.485 85-89 19.73 28.345 27.860000000000003 24.065 90-94 20.29 28.660000000000004 27.700000000000003 23.35 95-99 20.315 29.78 26.58 23.325000000000003 100-104 20.335 28.93 27.485 23.25 105-109 20.880000000000003 28.449999999999996 27.52 23.150000000000002 110-114 20.685000000000002 28.57 27.445000000000004 23.3 115-119 20.44 28.645 27.455000000000002 23.46 120-124 21.15 28.499999999999996 27.07 23.28 125-129 20.849999999999998 28.98 26.590000000000003 23.580000000000002 130-134 20.84 28.78 27.045 23.335 135-139 21.0 28.74 26.745 23.515 140-144 20.66 28.73 25.855 24.755 145-149 20.655 28.475 26.889999999999997 23.98 150-151 19.900000000000002 29.362500000000004 27.525 23.2125 >>END_MODULE >>Per sequence GC content pass #GC Content Count 0 0.0 1 0.5 2 0.5 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 0.5 18 1.0 19 1.5 20 1.0 21 0.5 22 1.0 23 2.0 24 4.0 25 8.0 26 8.0 27 5.5 28 7.5 29 9.5 30 22.5 31 32.5 32 38.5 33 46.5 34 52.0 35 81.0 36 104.5 37 121.0 38 150.0 39 165.5 40 183.5 41 215.0 42 253.5 43 273.5 44 257.5 45 261.0 46 262.0 47 235.0 48 222.5 49 205.0 50 165.5 51 134.5 52 105.5 53 85.5 54 69.0 55 44.0 56 33.5 57 29.0 58 23.5 59 15.5 60 11.5 61 12.0 62 10.0 63 8.0 64 7.0 65 2.5 66 0.0 67 0.5 68 1.0 69 2.0 70 2.5 71 1.0 72 0.0 73 0.5 74 0.5 75 0.0 76 0.0 77 0.5 78 0.5 79 0.0 80 0.0 81 0.0 82 0.0 83 0.0 84 0.0 85 0.0 86 0.0 87 0.0 88 0.0 89 0.0 90 0.0 91 0.0 92 0.0 93 0.0 94 0.0 95 0.0 96 0.0 97 0.0 98 0.0 99 0.0 100 0.0 >>END_MODULE >>Per base N content pass #Base N-Count 1 0.42500000000000004 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 85.475 #Duplication Level Percentage of deduplicated Percentage of total 1 85.6098274349225 73.175 2 12.255045334893245 20.95 3 1.7548990933021351 4.5 4 0.2924831822170225 1.0 5 0.08774495466510676 0.375 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 CAGTGGATAAGACCTGCATTCCTTAATCTTATTCTCAATTGCTGAATTCC 5 0.125 No Hit CACACATTTATGTTGAAAAAACTTGAAAGTATAATAAACAAAAGATGAAC 5 0.125 No Hit GGCTTTTACTTATAAAAAACAATCTTTATAGTTATTGTGAAAGGTGTAGC 5 0.125 No Hit >>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 0.025 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 0.037500000000000006 0.0 0.0 0.0 0.0 82-83 0.0875 0.0 0.0 0.0 0.0 84-85 0.1375 0.0 0.0 0.0 0.0 86-87 0.175 0.0 0.0 0.0 0.0 88-89 0.2375 0.0 0.0 0.0 0.0 90-91 0.3375 0.0 0.0 0.0 0.0 92-93 0.45 0.0 0.0 0.0 0.0 94-95 0.5375 0.0 0.0 0.0 0.0 96-97 0.8374999999999999 0.0 0.0 0.0 0.0 98-99 1.1125 0.0 0.0 0.0 0.0 100-101 1.2875 0.0 0.0 0.0 0.0 102-103 1.6 0.0 0.0 0.0 0.0 104-105 1.9249999999999998 0.0 0.0 0.0 0.0 106-107 2.3 0.0 0.0 0.0 0.0 108-109 2.6500000000000004 0.0 0.0 0.0 0.0 110-111 2.9000000000000004 0.0 0.0 0.0 0.0 112-113 3.2 0.0 0.0 0.0 0.0 114-115 3.825 0.0 0.0 0.0 0.0 116-117 4.3125 0.0 0.0 0.0 0.0 118-119 4.875 0.0 0.0 0.0 0.0 120-121 5.262499999999999 0.0 0.0 0.0 0.0 122-123 5.625 0.0 0.0 0.0 0.0 124-125 6.0 0.0 0.0 0.0 0.0 126-127 6.7125 0.0 0.0 0.0 0.0 128-129 7.35 0.0 0.0 0.0 0.0 130-131 7.95 0.0 0.0 0.0 0.0 132-133 8.6375 0.0 0.0 0.0 0.0 134-135 9.175 0.0 0.0 0.0 0.0 136-137 9.7125 0.0 0.0 0.0 0.0 138-139 10.425 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content pass >>END_MODULE SRR28623278 read2 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR28623278_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 44 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 36.089 37.0 37.0 37.0 37.0 37.0 2 36.3725 37.0 37.0 37.0 37.0 37.0 3 36.1275 37.0 37.0 37.0 37.0 37.0 4 36.133 37.0 37.0 37.0 37.0 37.0 5 36.2665 37.0 37.0 37.0 37.0 37.0 6 36.254 37.0 37.0 37.0 37.0 37.0 7 36.242 37.0 37.0 37.0 37.0 37.0 8 36.1695 37.0 37.0 37.0 37.0 37.0 9 36.1315 37.0 37.0 37.0 37.0 37.0 10-14 36.1761 37.0 37.0 37.0 37.0 37.0 15-19 36.1179 37.0 37.0 37.0 37.0 37.0 20-24 36.1023 37.0 37.0 37.0 37.0 37.0 25-29 36.0726 37.0 37.0 37.0 37.0 37.0 30-34 35.9707 37.0 37.0 37.0 37.0 37.0 35-39 35.9454 37.0 37.0 37.0 37.0 37.0 40-44 35.9433 37.0 37.0 37.0 37.0 37.0 45-49 35.9423 37.0 37.0 37.0 37.0 37.0 50-54 35.9439 37.0 37.0 37.0 37.0 37.0 55-59 35.819900000000004 37.0 37.0 37.0 37.0 37.0 60-64 35.769800000000004 37.0 37.0 37.0 37.0 37.0 65-69 35.929300000000005 37.0 37.0 37.0 37.0 37.0 70-74 35.8547 37.0 37.0 37.0 37.0 37.0 75-79 35.861900000000006 37.0 37.0 37.0 37.0 37.0 80-84 35.757799999999996 37.0 37.0 37.0 37.0 37.0 85-89 35.7785 37.0 37.0 37.0 37.0 37.0 90-94 35.68339999999999 37.0 37.0 37.0 37.0 37.0 95-99 35.6657 37.0 37.0 37.0 37.0 37.0 100-104 35.613800000000005 37.0 37.0 37.0 37.0 37.0 105-109 35.526799999999994 37.0 37.0 37.0 37.0 37.0 110-114 35.599900000000005 37.0 37.0 37.0 37.0 37.0 115-119 35.524699999999996 37.0 37.0 37.0 37.0 37.0 120-124 35.5403 37.0 37.0 37.0 37.0 37.0 125-129 34.9839 37.0 37.0 37.0 29.8 37.0 130-134 35.3976 37.0 37.0 37.0 37.0 37.0 135-139 35.224999999999994 37.0 37.0 37.0 29.8 37.0 140-144 35.2157 37.0 37.0 37.0 29.8 37.0 145-149 35.170700000000004 37.0 37.0 37.0 29.8 37.0 150-151 34.85125 37.0 37.0 37.0 25.0 37.0 >>END_MODULE >>Per tile sequence quality pass #Tile Base Mean 1101 1 0.0 1101 2 0.0 1101 3 0.0 1101 4 0.0 1101 5 0.0 1101 6 0.0 1101 7 0.0 1101 8 0.0 1101 9 0.0 1101 10-14 0.0 1101 15-19 0.0 1101 20-24 0.0 1101 25-29 0.0 1101 30-34 0.0 1101 35-39 0.0 1101 40-44 0.0 1101 45-49 0.0 1101 50-54 0.0 1101 55-59 0.0 1101 60-64 0.0 1101 65-69 0.0 1101 70-74 0.0 1101 75-79 0.0 1101 80-84 0.0 1101 85-89 0.0 1101 90-94 0.0 1101 95-99 0.0 1101 100-104 0.0 1101 105-109 0.0 1101 110-114 0.0 1101 115-119 0.0 1101 120-124 0.0 1101 125-129 0.0 1101 130-134 0.0 1101 135-139 0.0 1101 140-144 0.0 1101 145-149 0.0 1101 150-151 0.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 12 1.0 13 3.0 14 8.0 15 14.0 16 2.0 17 2.0 18 4.0 19 1.0 20 3.0 21 3.0 22 6.0 23 13.0 24 7.0 25 10.0 26 15.0 27 15.0 28 12.0 29 14.0 30 15.0 31 27.0 32 52.0 33 99.0 34 218.0 35 570.0 36 2630.0 37 256.0 >>END_MODULE >>Per base sequence content warn #Base G A T C 1 34.55 21.05 15.35 29.049999999999997 2 26.924999999999997 26.8 29.9 16.375 3 21.975 27.450000000000003 32.15 18.425 4 24.0 31.0 25.3 19.7 5 26.6 34.725 22.75 15.925 6 20.825 37.05 24.099999999999998 18.025 7 21.45 20.5 39.275 18.775 8 21.375 24.224999999999998 28.299999999999997 26.1 9 22.625 25.3 29.425 22.650000000000002 10-14 23.995 28.975 25.95 21.08 15-19 23.415 28.46 27.63 20.495 20-24 23.605 28.615000000000002 27.68 20.1 25-29 22.505 28.455000000000002 28.415000000000003 20.625 30-34 23.135 27.815 28.005000000000003 21.044999999999998 35-39 23.325000000000003 28.194999999999997 28.065 20.415 40-44 23.405 28.65 27.805000000000003 20.14 45-49 23.3 27.46 28.53 20.71 50-54 22.82 28.435 28.065 20.68 55-59 23.369999999999997 27.735 28.425 20.47 60-64 23.044999999999998 28.53 28.185 20.24 65-69 23.5 28.415000000000003 27.529999999999998 20.555 70-74 23.1 28.71 27.575 20.615 75-79 23.09 28.060000000000002 28.235 20.615 80-84 23.125 28.485 28.325 20.064999999999998 85-89 23.825 28.005000000000003 27.57 20.599999999999998 90-94 22.875 29.04 27.49 20.595 95-99 23.615 28.64 27.58 20.165 100-104 23.53 28.625 27.375 20.47 105-109 24.245 28.7 26.965 20.09 110-114 24.005000000000003 28.51 27.46 20.025000000000002 115-119 24.515 28.215 27.235 20.035 120-124 24.64 27.96 28.035 19.365 125-129 24.625 29.265 27.575 18.535 130-134 25.255 28.675 27.05 19.02 135-139 25.685000000000002 28.315 26.424999999999997 19.575 140-144 24.92 29.21 26.88 18.990000000000002 145-149 26.369999999999997 28.275 26.805 18.55 150-151 26.0375 28.299999999999997 27.762500000000003 17.9 >>END_MODULE >>Per sequence GC content pass #GC Content Count 0 0.0 1 0.0 2 0.0 3 0.5 4 1.0 5 0.5 6 0.5 7 0.5 8 1.0 9 2.0 10 1.0 11 0.5 12 1.0 13 1.0 14 1.5 15 1.5 16 0.5 17 2.0 18 3.0 19 1.0 20 1.5 21 3.0 22 1.5 23 0.5 24 1.5 25 3.5 26 4.0 27 5.5 28 11.0 29 19.0 30 19.5 31 18.5 32 32.0 33 48.0 34 63.0 35 82.5 36 102.5 37 116.5 38 132.0 39 168.0 40 188.5 41 209.0 42 241.5 43 246.0 44 243.5 45 265.0 46 267.5 47 239.0 48 220.5 49 205.0 50 180.5 51 139.5 52 101.0 53 87.0 54 79.0 55 54.0 56 39.0 57 31.0 58 22.0 59 18.0 60 14.0 61 11.5 62 9.5 63 14.0 64 10.0 65 1.0 66 1.0 67 1.0 68 0.5 69 0.5 70 2.0 71 2.0 72 0.0 73 0.0 74 0.5 75 1.0 76 0.5 77 0.0 78 0.0 79 1.0 80 1.0 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 0.0 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 85.82499999999999 #Duplication Level Percentage of deduplicated Percentage of total 1 86.36760850568017 74.125 2 11.44771337023012 19.650000000000002 3 1.6603553743081854 4.275 4 0.37867754150888433 1.3 5 0.11651616661811826 0.5 6 0.029129041654529564 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 GAGCTTGAGTGCATTCTTCTAAGTAAAAGAAATCCCTTAATTTCATCACA 6 0.15 No Hit GGGAGTTAATCGAGCCTACGCTTCGCGAACTCGATGGGAAGATGAGGGAA 5 0.125 No Hit GCATTGGTTCGTTTAGTGCAGAGAGCTAACATGAGCAAGAGAACAATTGG 5 0.125 No Hit TGAGCTTGAGTGCATTCTTCTAAGTAAAAGAAATCCCTTAATTTCATCAC 5 0.125 No Hit AGTTCTTGTTGACCATGCATTGGCAAATGGAGAGAATGAGAAGAACACAA 5 0.125 No Hit >>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 0.025 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 0.037500000000000006 0.0 0.0 0.0 0.0 82-83 0.0875 0.0 0.0 0.0 0.0 84-85 0.1375 0.0 0.0 0.0 0.0 86-87 0.2 0.0 0.0 0.0 0.0 88-89 0.2625 0.0 0.0 0.0 0.0 90-91 0.36250000000000004 0.0 0.0 0.0 0.0 92-93 0.4875 0.0 0.0 0.0 0.0 94-95 0.5875 0.0 0.0 0.0 0.0 96-97 0.8875 0.0 0.0 0.0 0.0 98-99 1.1875 0.0 0.0 0.0 0.0 100-101 1.3875000000000002 0.0 0.0 0.0 0.0 102-103 1.7 0.0 0.0 0.0 0.0 104-105 2.025 0.0 0.0 0.0 0.0 106-107 2.425 0.0 0.0 0.0 0.0 108-109 2.7750000000000004 0.0 0.0 0.0 0.0 110-111 3.05 0.0 0.0 0.0 0.0 112-113 3.375 0.0 0.0 0.0 0.0 114-115 4.025 0.0 0.0 0.0 0.0 116-117 4.5125 0.0 0.0 0.0 0.0 118-119 5.1 0.0 0.0 0.0 0.0 120-121 5.525 0.0 0.0 0.0 0.0 122-123 5.95 0.0 0.0 0.0 0.0 124-125 6.375 0.0 0.0 0.0 0.0 126-127 7.075 0.0 0.0 0.0 0.0 128-129 7.7 0.0 0.0 0.0 0.0 130-131 8.325 0.0 0.0 0.0 0.0 132-133 9.025 0.0 0.0 0.0 0.0 134-135 9.5375 0.0 0.0 0.0 0.0 136-137 10.1875 0.0 0.0 0.0 0.0 138-139 10.8875 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content pass >>END_MODULE Read 1814738 spots for SRR28623278.sra Written 1814738 spots for SRR28623278.sra Read 1814738 spots for SRR28623278.sra Written 1814738 spots for SRR28623278.sra Read 1814738 spots for SRR28623278.sra Written 1814738 spots for SRR28623278.sra Read 1814738 spots for SRR28623278.sra Written 1814738 spots for SRR28623278.sra Read 1814738 spots for SRR28623278.sra Written 1814738 spots for SRR28623278.sra Read 1814738 spots for SRR28623278.sra Written 1814738 spots for SRR28623278.sra Read 1814738 spots for SRR28623278.sra Written 1814738 spots for SRR28623278.sra Read 1814738 spots for SRR28623278.sra Written 1814738 spots for SRR28623278.sra Read 1814738 spots for SRR28623278.sra Written 1814738 spots for SRR28623278.sra Read 1814738 spots for SRR28623278.sra Written 1814738 spots for SRR28623278.sra Read 1814738 spots for SRR28623278.sra Written 1814738 spots for SRR28623278.sra Read 1814738 spots for SRR28623278.sra Written 1814738 spots for SRR28623278.sra Read 1814738 spots for SRR28623278.sra Written 1814738 spots for SRR28623278.sra Read 1814738 spots for SRR28623278.sra Written 1814738 spots for SRR28623278.sra Read 1814744 spots for SRR28623278.sra Written 1814744 spots for SRR28623278.sra Read 1814738 spots for SRR28623278.sra Written 1814738 spots for SRR28623278.sra Read 1814738 spots for SRR28623278.sra Written 1814738 spots for SRR28623278.sra Read 1814738 spots for SRR28623278.sra Written 1814738 spots for SRR28623278.sra Read 1814738 spots for SRR28623278.sra Written 1814738 spots for SRR28623278.sra Read 1814738 spots for SRR28623278.sra Written 1814738 spots for SRR28623278.sra SRR ids: ['SRR28623278.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_7d12ctd6 SRR28623278.sra spots: 36294766 blocks: [[1, 1814738], [1814739, 3629476], [3629477, 5444214], [5444215, 7258952], [7258953, 9073690], [9073691, 10888428], [10888429, 12703166], [12703167, 14517904], [14517905, 16332642], [16332643, 18147380], [18147381, 19962118], [19962119, 21776856], [21776857, 23591594], [23591595, 25406332], [25406333, 27221070], [27221071, 29035808], [29035809, 30850546], [30850547, 32665284], [32665285, 34480022], [34480023, 36294766]] SRR28623278 file size 13403520 SRR28623278 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 SRR28623278 SRR28623278_1.fastq SRR28623278_2.fastq Input file: SRR28623278_1.fastq Paired file: SRR28623278_2.fastq trimmed: SRR28623278-trimmed-pair1.fastq, SRR28623278-trimmed-pair2.fastq Parameters used: -- 3' end adapter sequence (-x): AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC -- paired 3' end adapter sequence (-y): AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTA -- maximum error ratio allowed (-r): 0.100 -- maximum indel error ratio allowed (-d): 0.030 -- end quality threshold (-q): 10 -- minimum read length allowed after trimming (-l): 18 -- file format (-f): Sanger/Illumina 1.8+ FASTQ -- number of concurrent threads (-t): 20 Tue Feb 11 13:28:12 2025 >> started Tue Feb 11 13:29:05 2025 >> done (52.397s) 36294766 read pairs processed; of these: 24 ( 0.00%) short read pairs filtered out after trimming by size control 19047 ( 0.05%) empty read pairs filtered out after trimming by size control 36275695 (99.95%) read pairs available; of these: 5461226 (15.05%) trimmed read pairs available after processing 30814469 (84.95%) untrimmed read pairs available after processing Length distribution of reads after trimming: length count percentage 18 3 0.00% 19 0 0.00% 20 2 0.00% 21 6 0.00% 22 4 0.00% 23 5 0.00% 24 3 0.00% 25 5 0.00% 26 4 0.00% 27 9 0.00% 28 7 0.00% 29 6 0.00% 30 17 0.00% 31 17 0.00% 32 11 0.00% 33 15 0.00% 34 17 0.00% 35 22 0.00% 36 14 0.00% 37 22 0.00% 38 16 0.00% 39 25 0.00% 40 37 0.00% 41 51 0.00% 42 51 0.00% 43 45 0.00% 44 69 0.00% 45 54 0.00% 46 68 0.00% 47 91 0.00% 48 101 0.00% 49 132 0.00% 50 135 0.00% 51 183 0.00% 52 172 0.00% 53 226 0.00% 54 230 0.00% 55 228 0.00% 56 289 0.00% 57 339 0.00% 58 384 0.00% 59 425 0.00% 60 545 0.00% 61 653 0.00% 62 717 0.00% 63 854 0.00% 64 928 0.00% 65 1060 0.00% 66 1306 0.00% 67 1403 0.00% 68 1636 0.00% 69 1930 0.01% 70 2216 0.01% 71 2478 0.01% 72 2799 0.01% 73 3462 0.01% 74 3842 0.01% 75 4393 0.01% 76 4929 0.01% 77 5320 0.01% 78 6041 0.02% 79 6890 0.02% 80 7702 0.02% 81 8885 0.02% 82 9951 0.03% 83 11009 0.03% 84 12573 0.03% 85 14005 0.04% 86 15328 0.04% 87 16539 0.05% 88 17821 0.05% 89 19720 0.05% 90 21289 0.06% 91 23353 0.06% 92 25072 0.07% 93 27336 0.08% 94 29681 0.08% 95 32189 0.09% 96 34230 0.09% 97 36321 0.10% 98 38522 0.11% 99 40476 0.11% 100 42857 0.12% 101 44759 0.12% 102 47296 0.13% 103 50154 0.14% 104 52864 0.15% 105 55814 0.15% 106 59101 0.16% 107 60333 0.17% 108 62782 0.17% 109 65084 0.18% 110 66441 0.18% 111 69098 0.19% 112 71416 0.20% 113 73449 0.20% 114 75619 0.21% 115 79552 0.22% 116 81874 0.23% 117 84645 0.23% 118 86485 0.24% 119 87574 0.24% 120 90238 0.25% 121 91885 0.25% 122 93934 0.26% 123 95433 0.26% 124 99428 0.27% 125 100372 0.28% 126 103588 0.29% 127 105612 0.29% 128 107182 0.30% 129 108441 0.30% 130 110930 0.31% 131 111815 0.31% 132 113352 0.31% 133 115748 0.32% 134 116768 0.32% 135 118385 0.33% 136 120098 0.33% 137 123112 0.34% 138 125143 0.34% 139 125747 0.35% 140 127661 0.35% 141 128587 0.35% 142 130235 0.36% 143 130258 0.36% 144 132599 0.37% 145 133584 0.37% 146 133593 0.37% 147 135126 0.37% 148 138089 0.38% 149 138530 0.38% 150 139612 0.38% 151 30814469 84.95% 36275695 reads passed initial QC criterion=sequence-density sequence-density=0.15 sequence-density-rank=1 fanout-score=12.20 fanout-score-rank=10 prefix-density=0.11 prefix-fanout=12.2 sequence=GGATCGGAAGAGCACACGTCTGAACTCCAGTCACTGGATCACATCTCGTATGCCGTCTTCTGCTTG criterion=fanout-score sequence-density=0.02 sequence-density-rank=37 fanout-score=167.02 fanout-score-rank=1 prefix-density=0.18 prefix-fanout=15.1 sequence=CTCCTTCCTCTAAATGATAAGGTTCAGTGGACTTCTCGCGACGTCGCCGGCGGCGAACCGCCCACGTCGCCGCGATCCGAACACTTCACCGGACCATTCAATCGGTAGGAGCGACGGGCGGTGTGTACAAAGGGCAGGGACGTAGTCAACGCGAGCTGATGACTCGCGCTTACTAGGAATTCCTCGTTGAAGACCAACAATTGCAATGATCTATCCCCATCACGATGAAATTTCAAAGATTACCCGGGCCTGTCGGCCAAGGCTATAGACTCGTTGAATACATCAGTGTAGCGCGCGTGCGGCCCAGAACATCTAAGGGCATCACAGACCTGTTATTGCCTCAAACTTCCTTGGCCTGGAAGGCCATAGTCCCTCTAAGAAGCTGGCCGCGGAGGGTCACCTCCGCATAGCTAGTTAGCAGGCTGAGGTCTCGTTCGTTAACGGAATTAAC criterion=sequence-density sequence-density=0.13 sequence-density-rank=1 fanout-score=10.95 fanout-score-rank=17 prefix-density=0.22 prefix-fanout=6.7 sequence=GAAGGCAATGAGA criterion=fanout-score sequence-density=0.08 sequence-density-rank=21 fanout-score=305.96 fanout-score-rank=1 prefix-density=1.00 prefix-fanout=23.7 sequence=AAGAAGAAGAAA SRR28623278 testing PE reads STAR mapping to Ensembl genome Started job on | Feb 11 13:29:47 Started mapping on | Feb 11 13:29:47 Finished on | Feb 11 13:33:25 Mapping speed, Million of reads per hour | 599.05 Number of input reads | 36275695 Average input read length | 294 UNIQUE READS: Uniquely mapped reads number | 33944799 Uniquely mapped reads % | 93.57% Average mapped length | 292.85 Number of splices: Total | 31230995 Number of splices: Annotated (sjdb) | 30499077 Number of splices: GT/AG | 30693476 Number of splices: GC/AG | 416676 Number of splices: AT/AC | 33068 Number of splices: Non-canonical | 87775 Mismatch rate per base, % | 0.41% Deletion rate per base | 0.03% Deletion average length | 3.02 Insertion rate per base | 0.03% Insertion average length | 2.39 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 863487 % of reads mapped to multiple loci | 2.38% Number of reads mapped to too many loci | 283915 % of reads mapped to too many loci | 0.78% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 2.98% % of reads unmapped: other | 0.28% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 1467409 1467409 1467409 N_multimapping 863487 863487 863487 N_noFeature 1478852 33526436 1675002 N_ambiguous 444752 3039 220359 UnstrandedReadsAssigned:32021195 PositiveStrandReadsAssigned:415324 NegativeStrandReadsAssigned:32049438 Dataset is classified negative stranded MeadianReadLen=151 20thPercentileLength=151 echo kmer=147 SRR28623278 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: 52,400 [index] number of k-mers: 62,057,036 [index] number of equivalence classes: 130,681 [quant] running in paired-end mode [quant] will process pair 1: SRR28623278-trimmed-pair1.fastq SRR28623278-trimmed-pair2.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 36,275,695 reads, 32,587,827 reads pseudoaligned [quant] estimated average fragment length: 230.265 [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,184 rounds 52401 SRR28623278.ke.tsv 34699 SRR28623278.se.tsv 87100 total ==> SRR28623278.ke.tsv <== target_id length eff_length est_counts tpm Potri.005G200100.1.v4.1 2018 1788.74 1223 20.071 Potri.005G024800.1.v4.1 1035 805.735 874 31.8425 Potri.004G059700.1.v4.1 961 731.77 142 5.69642 Potri.007G009000.2.v4.1 1416 1186.74 0 0 Potri.003G141000.2.v4.1 2943 2713.74 1010 10.9255 Potri.016G087400.1.v4.1 270 91.8522 2587.84 827.059 Potri.015G069301.1.v4.1 564 340.632 0 0 Potri.010G195200.1.v4.1 1773 1543.74 91 1.73044 Potri.012G127500.1.v4.1 977 747.74 15813 620.8 ==> SRR28623278.se.tsv <== Potri.001G166300.v4.1 0 Potri.001G448400.v4.1 1047 Potri.001G233950.v4.1 4 Potri.001G122700.v4.1 572 Potri.001G212900.v4.1 3 Potri.001G182400.v4.1 4 Potri.001G256600.v4.1 0 Potri.001G040500.v4.1 0 Potri.001G416900.v4.1 4 Potri.001G452600.v4.1 11 SRR28623278 completed mapping pipeline successfully