Starting /dee2/code/volunteer_pipeline.sh SRR28623255 current disk space = 3050786410496 free memory = 1578431256 SRR28623255 SRAfilesize e891e297609fd2a80e6226da26843680 SRR28623255.sra SRR28623255.sra file validated SRR28623255 is paired end SRR28623255 is conventional basespace SRR28623255 read1 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR28623255_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 35.71625 37.0 37.0 37.0 37.0 37.0 2 36.3145 37.0 37.0 37.0 37.0 37.0 3 36.386 37.0 37.0 37.0 37.0 37.0 4 36.5245 37.0 37.0 37.0 37.0 37.0 5 36.648 37.0 37.0 37.0 37.0 37.0 6 36.5975 37.0 37.0 37.0 37.0 37.0 7 36.4935 37.0 37.0 37.0 37.0 37.0 8 36.6035 37.0 37.0 37.0 37.0 37.0 9 36.558 37.0 37.0 37.0 37.0 37.0 10-14 36.5998 37.0 37.0 37.0 37.0 37.0 15-19 36.554 37.0 37.0 37.0 37.0 37.0 20-24 36.5699 37.0 37.0 37.0 37.0 37.0 25-29 36.4856 37.0 37.0 37.0 37.0 37.0 30-34 36.419799999999995 37.0 37.0 37.0 37.0 37.0 35-39 36.3329 37.0 37.0 37.0 37.0 37.0 40-44 36.335899999999995 37.0 37.0 37.0 37.0 37.0 45-49 36.2954 37.0 37.0 37.0 37.0 37.0 50-54 36.1816 37.0 37.0 37.0 37.0 37.0 55-59 36.18920000000001 37.0 37.0 37.0 37.0 37.0 60-64 36.184 37.0 37.0 37.0 37.0 37.0 65-69 36.087999999999994 37.0 37.0 37.0 37.0 37.0 70-74 36.112 37.0 37.0 37.0 37.0 37.0 75-79 36.0339 37.0 37.0 37.0 37.0 37.0 80-84 36.0176 37.0 37.0 37.0 37.0 37.0 85-89 35.956 37.0 37.0 37.0 37.0 37.0 90-94 35.9463 37.0 37.0 37.0 37.0 37.0 95-99 35.8125 37.0 37.0 37.0 37.0 37.0 100-104 35.7735 37.0 37.0 37.0 37.0 37.0 105-109 35.7428 37.0 37.0 37.0 37.0 37.0 110-114 35.626599999999996 37.0 37.0 37.0 37.0 37.0 115-119 35.648199999999996 37.0 37.0 37.0 37.0 37.0 120-124 35.5989 37.0 37.0 37.0 37.0 37.0 125-129 35.4732 37.0 37.0 37.0 37.0 37.0 130-134 35.197900000000004 37.0 37.0 37.0 27.4 37.0 135-139 35.0689 37.0 37.0 37.0 25.0 37.0 140-144 34.898 37.0 37.0 37.0 25.0 37.0 145-149 34.818200000000004 37.0 37.0 37.0 25.0 37.0 150-151 34.03125 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 19 1.0 20 0.0 21 2.0 22 3.0 23 3.0 24 5.0 25 5.0 26 11.0 27 10.0 28 28.0 29 29.0 30 25.0 31 53.0 32 63.0 33 112.0 34 177.0 35 454.0 36 2867.0 37 152.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 42.29516411926835 14.006514657980457 7.767476822851416 35.930844399899776 2 18.15 14.875 37.625 29.349999999999998 3 17.575 20.625 28.499999999999996 33.300000000000004 4 21.8 27.35 24.8 26.05 5 23.200000000000003 34.725 23.175 18.9 6 20.4 37.05 22.95 19.6 7 14.85 28.999999999999996 39.4 16.75 8 16.525000000000002 27.750000000000004 31.275 24.45 9 17.875 24.425 33.300000000000004 24.4 10-14 19.32 30.17 27.584999999999997 22.925 15-19 19.575 28.735 28.044999999999998 23.645 20-24 19.455 28.939999999999998 27.744999999999997 23.86 25-29 19.675 29.34 27.375 23.61 30-34 19.355 29.09 27.805000000000003 23.75 35-39 19.035 29.044999999999998 28.12 23.799999999999997 40-44 19.125 29.86 27.325 23.69 45-49 19.5 28.904999999999998 27.615000000000002 23.98 50-54 19.63 29.365000000000002 27.43 23.575 55-59 19.075 28.875 28.015 24.035 60-64 19.744999999999997 28.605000000000004 28.055000000000003 23.595 65-69 19.525000000000002 28.435 28.33 23.71 70-74 19.759999999999998 28.92 27.615000000000002 23.705000000000002 75-79 19.525000000000002 29.025000000000002 27.37 24.08 80-84 19.759999999999998 29.465000000000003 27.284999999999997 23.49 85-89 20.16 28.52 28.139999999999997 23.18 90-94 20.07 28.665000000000003 27.750000000000004 23.515 95-99 20.369999999999997 29.95 26.534999999999997 23.145 100-104 20.62 29.29 26.68 23.41 105-109 20.78 28.884999999999998 26.735 23.599999999999998 110-114 20.794999999999998 28.694999999999997 27.08 23.43 115-119 20.794999999999998 28.854999999999997 26.86 23.49 120-124 20.78 28.985 26.715 23.52 125-129 21.005 28.74 26.939999999999998 23.315 130-134 20.715 28.165000000000003 26.619999999999997 24.5 135-139 20.66 28.465 26.36 24.515 140-144 21.32 27.905 26.68 24.095 145-149 21.029999999999998 27.800000000000004 26.61 24.560000000000002 150-151 21.3875 27.1625 27.3375 24.1125 >>END_MODULE >>Per sequence GC content pass #GC Content Count 0 3.0 1 1.5 2 0.0 3 0.0 4 1.5 5 2.0 6 0.5 7 0.0 8 0.5 9 0.5 10 0.0 11 0.5 12 0.5 13 0.0 14 0.0 15 0.5 16 1.0 17 0.5 18 1.0 19 1.0 20 1.0 21 1.0 22 1.5 23 3.0 24 5.0 25 6.0 26 5.5 27 5.5 28 10.0 29 17.5 30 24.5 31 40.5 32 43.0 33 39.5 34 59.0 35 79.0 36 100.0 37 123.0 38 136.5 39 159.0 40 204.5 41 227.5 42 239.5 43 267.0 44 273.0 45 258.0 46 248.5 47 235.5 48 208.5 49 192.0 50 169.0 51 142.0 52 113.5 53 86.0 54 69.0 55 51.0 56 35.0 57 25.5 58 23.5 59 17.5 60 10.0 61 6.0 62 7.0 63 7.0 64 2.5 65 1.0 66 3.5 67 3.5 68 0.5 69 0.0 70 0.0 71 0.0 72 0.0 73 0.0 74 0.0 75 0.0 76 0.0 77 0.0 78 0.0 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 0.22499999999999998 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 97.875 #Duplication Level Percentage of deduplicated Percentage of total 1 97.87994891443167 95.8 2 2.0689655172413794 4.05 3 0.05108556832694764 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 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 0.025 0.0 0.0 0.0 0.0 40-41 0.025 0.0 0.0 0.0 0.0 42-43 0.025 0.0 0.0 0.0 0.0 44-45 0.025 0.0 0.0 0.0 0.0 46-47 0.037500000000000006 0.0 0.0 0.0 0.0 48-49 0.05 0.0 0.0 0.0 0.0 50-51 0.05 0.0 0.0 0.0 0.0 52-53 0.05 0.0 0.0 0.0 0.0 54-55 0.0625 0.0 0.0 0.0 0.0 56-57 0.075 0.0 0.0 0.0 0.0 58-59 0.075 0.0 0.0 0.0 0.0 60-61 0.075 0.0 0.0 0.0 0.0 62-63 0.075 0.0 0.0 0.0 0.0 64-65 0.075 0.0 0.0 0.0 0.0 66-67 0.0875 0.0 0.0 0.0 0.0 68-69 0.1375 0.0 0.0 0.0 0.0 70-71 0.16249999999999998 0.0 0.0 0.0 0.0 72-73 0.2 0.0 0.0 0.0 0.0 74-75 0.25 0.0 0.0 0.0 0.0 76-77 0.32499999999999996 0.0 0.0 0.0 0.0 78-79 0.4125 0.0 0.0 0.0 0.0 80-81 0.4875 0.0 0.0 0.0 0.0 82-83 0.7 0.0 0.0 0.0 0.0 84-85 0.9125 0.0 0.0 0.0 0.0 86-87 1.125 0.0 0.0 0.0 0.0 88-89 1.4 0.0 0.0 0.0 0.0 90-91 1.6375000000000002 0.0 0.0 0.0 0.0 92-93 1.9874999999999998 0.0 0.0 0.0 0.0 94-95 2.325 0.0 0.0 0.0 0.0 96-97 2.6875 0.0 0.0 0.0 0.0 98-99 3.1375 0.0 0.0 0.0 0.0 100-101 3.5250000000000004 0.0 0.0 0.0 0.0 102-103 3.9875000000000003 0.0 0.0 0.0 0.0 104-105 4.699999999999999 0.0 0.0 0.0 0.0 106-107 5.375 0.0 0.0 0.0 0.0 108-109 6.025 0.0 0.0 0.0 0.0 110-111 6.6375 0.0 0.0 0.0 0.0 112-113 7.2375 0.0 0.0 0.0 0.0 114-115 8.0375 0.0 0.0 0.0 0.0 116-117 8.75 0.0 0.0 0.0 0.0 118-119 9.6 0.0 0.0 0.0 0.0 120-121 10.325 0.0 0.0 0.0 0.0 122-123 10.9625 0.0 0.0 0.0 0.0 124-125 11.575 0.0 0.0 0.0 0.0 126-127 12.475 0.0 0.0 0.0 0.0 128-129 13.1375 0.0 0.0 0.0 0.0 130-131 13.875 0.0 0.0 0.0 0.0 132-133 14.6875 0.0 0.0 0.0 0.0 134-135 15.475 0.0 0.0 0.0 0.0 136-137 16.0625 0.0 0.0 0.0 0.0 138-139 16.925 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position GCTCTGT 10 0.006830828 145.0 1 ACAACCT 10 0.006830828 145.0 3 >>END_MODULE SRR28623255 read2 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR28623255_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 36.16025 37.0 37.0 37.0 37.0 37.0 2 36.3745 37.0 37.0 37.0 37.0 37.0 3 36.358 37.0 37.0 37.0 37.0 37.0 4 36.2605 37.0 37.0 37.0 37.0 37.0 5 36.239 37.0 37.0 37.0 37.0 37.0 6 36.2305 37.0 37.0 37.0 37.0 37.0 7 36.3265 37.0 37.0 37.0 37.0 37.0 8 36.2105 37.0 37.0 37.0 37.0 37.0 9 36.305 37.0 37.0 37.0 37.0 37.0 10-14 36.2375 37.0 37.0 37.0 37.0 37.0 15-19 36.1412 37.0 37.0 37.0 37.0 37.0 20-24 36.0915 37.0 37.0 37.0 37.0 37.0 25-29 36.006299999999996 37.0 37.0 37.0 37.0 37.0 30-34 35.9392 37.0 37.0 37.0 37.0 37.0 35-39 35.8735 37.0 37.0 37.0 37.0 37.0 40-44 35.87 37.0 37.0 37.0 37.0 37.0 45-49 35.828199999999995 37.0 37.0 37.0 37.0 37.0 50-54 35.7604 37.0 37.0 37.0 37.0 37.0 55-59 35.746 37.0 37.0 37.0 37.0 37.0 60-64 35.681999999999995 37.0 37.0 37.0 37.0 37.0 65-69 35.606700000000004 37.0 37.0 37.0 37.0 37.0 70-74 35.5193 37.0 37.0 37.0 37.0 37.0 75-79 35.55550000000001 37.0 37.0 37.0 37.0 37.0 80-84 35.5365 37.0 37.0 37.0 37.0 37.0 85-89 35.3823 37.0 37.0 37.0 37.0 37.0 90-94 35.408300000000004 37.0 37.0 37.0 37.0 37.0 95-99 35.416199999999996 37.0 37.0 37.0 37.0 37.0 100-104 35.2347 37.0 37.0 37.0 34.6 37.0 105-109 35.2578 37.0 37.0 37.0 34.6 37.0 110-114 35.1807 37.0 37.0 37.0 29.8 37.0 115-119 35.0373 37.0 37.0 37.0 27.4 37.0 120-124 34.9154 37.0 37.0 37.0 25.0 37.0 125-129 34.9523 37.0 37.0 37.0 25.0 37.0 130-134 34.8577 37.0 37.0 37.0 25.0 37.0 135-139 34.7442 37.0 37.0 37.0 25.0 37.0 140-144 34.722699999999996 37.0 37.0 37.0 25.0 37.0 145-149 34.410000000000004 37.0 37.0 37.0 25.0 37.0 150-151 33.951 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 13 5.0 14 12.0 15 10.0 16 6.0 17 11.0 18 5.0 19 4.0 20 6.0 21 7.0 22 8.0 23 14.0 24 9.0 25 14.0 26 10.0 27 15.0 28 23.0 29 17.0 30 26.0 31 48.0 32 58.0 33 113.0 34 221.0 35 612.0 36 2532.0 37 214.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 46.161540385096274 22.95573893473368 9.402350587646911 21.48037009252313 2 28.775000000000002 25.525 29.4 16.3 3 23.325000000000003 27.725 30.825000000000003 18.125 4 26.85 33.85 21.875 17.424999999999997 5 26.625 36.125 21.099999999999998 16.150000000000002 6 21.175 38.45 23.599999999999998 16.775000000000002 7 21.5 20.825 38.75 18.925 8 21.425 24.325 29.099999999999998 25.15 9 24.0 24.9 28.499999999999996 22.6 10-14 24.87 29.62 25.69 19.82 15-19 24.725 28.134999999999998 26.935 20.205000000000002 20-24 24.365000000000002 28.860000000000003 26.82 19.955000000000002 25-29 24.445 28.775000000000002 26.979999999999997 19.8 30-34 24.195 28.725 27.005000000000003 20.075000000000003 35-39 23.9 28.925 27.41 19.765 40-44 23.845 28.765 27.195000000000004 20.195 45-49 23.945 28.235 27.944999999999997 19.875 50-54 23.995 28.015 27.985 20.005 55-59 24.3 28.74 27.860000000000003 19.1 60-64 23.705000000000002 28.199999999999996 28.205000000000002 19.89 65-69 23.84 28.439999999999998 27.58 20.14 70-74 23.97 27.755000000000003 28.360000000000003 19.915 75-79 24.305 28.235 28.235 19.225 80-84 24.240000000000002 27.785 28.315 19.66 85-89 23.925 28.13 28.07 19.875 90-94 23.335 28.18 28.54 19.945 95-99 24.310000000000002 27.575 28.035 20.080000000000002 100-104 24.349999999999998 28.965000000000003 27.639999999999997 19.045 105-109 24.315 28.110000000000003 28.360000000000003 19.215 110-114 25.080000000000002 28.694999999999997 27.015 19.21 115-119 25.240000000000002 29.025000000000002 27.08 18.655 120-124 25.590000000000003 28.439999999999998 27.169999999999998 18.8 125-129 26.33 28.155 27.12 18.395 130-134 26.57 28.29 27.065 18.075 135-139 26.0 28.389999999999997 27.325 18.285 140-144 26.695 27.93 27.139999999999997 18.235 145-149 26.979999999999997 27.46 27.88 17.68 150-151 27.400000000000002 26.05 28.999999999999996 17.549999999999997 >>END_MODULE >>Per sequence GC content warn #GC Content Count 0 0.0 1 0.0 2 0.0 3 0.5 4 0.5 5 0.0 6 0.5 7 0.5 8 1.0 9 1.5 10 1.0 11 1.5 12 1.5 13 2.0 14 3.0 15 2.0 16 1.5 17 1.5 18 2.0 19 2.5 20 4.0 21 4.5 22 2.5 23 2.5 24 3.0 25 1.5 26 4.0 27 6.5 28 7.0 29 11.0 30 17.0 31 23.0 32 30.0 33 35.0 34 44.0 35 69.5 36 91.0 37 110.0 38 138.5 39 168.0 40 216.0 41 235.5 42 237.0 43 262.0 44 273.5 45 264.5 46 246.0 47 240.0 48 231.0 49 206.0 50 172.0 51 147.0 52 115.0 53 76.5 54 62.0 55 47.0 56 32.5 57 26.5 58 21.0 59 16.0 60 11.0 61 6.0 62 5.5 63 5.0 64 2.5 65 3.5 66 2.5 67 1.5 68 1.5 69 1.5 70 1.0 71 0.0 72 0.5 73 1.0 74 0.5 75 1.0 76 2.0 77 1.0 78 0.5 79 1.0 80 0.5 81 0.0 82 0.0 83 1.0 84 2.0 85 1.0 86 0.0 87 0.5 88 0.5 89 0.5 90 1.0 91 1.5 92 2.0 93 1.5 94 1.0 95 0.5 96 0.5 97 1.5 98 1.5 99 0.5 100 5.5 >>END_MODULE >>Per base N content pass #Base N-Count 1 0.025 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 97.35000000000001 #Duplication Level Percentage of deduplicated Percentage of total 1 97.86851566512583 95.275 2 2.0287621982537236 3.95 3 0.07704160246533129 0.22499999999999998 4 0.0 0.0 5 0.0 0.0 6 0.0 0.0 7 0.0 0.0 8 0.0 0.0 9 0.0 0.0 >10 0.025680534155110426 0.5499999999999999 >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 GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG 22 0.5499999999999999 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 0.025 0.0 0.0 0.0 0.0 40-41 0.025 0.0 0.0 0.0 0.0 42-43 0.025 0.0 0.0 0.0 0.0 44-45 0.025 0.0 0.0 0.0 0.0 46-47 0.037500000000000006 0.0 0.0 0.0 0.0 48-49 0.05 0.0 0.0 0.0 0.0 50-51 0.05 0.0 0.0 0.0 0.0 52-53 0.05 0.0 0.0 0.0 0.0 54-55 0.0625 0.0 0.0 0.0 0.0 56-57 0.075 0.0 0.0 0.0 0.0 58-59 0.075 0.0 0.0 0.0 0.0 60-61 0.075 0.0 0.0 0.0 0.0 62-63 0.075 0.0 0.0 0.0 0.0 64-65 0.075 0.0 0.0 0.0 0.0 66-67 0.0875 0.0 0.0 0.0 0.0 68-69 0.1375 0.0 0.0 0.0 0.0 70-71 0.1875 0.0 0.0 0.0 0.0 72-73 0.225 0.0 0.0 0.0 0.0 74-75 0.275 0.0 0.0 0.0 0.0 76-77 0.3375 0.0 0.0 0.0 0.0 78-79 0.4125 0.0 0.0 0.0 0.0 80-81 0.4875 0.0 0.0 0.0 0.0 82-83 0.7 0.0 0.0 0.0 0.0 84-85 0.9125 0.0 0.0 0.0 0.0 86-87 1.15 0.0 0.0 0.0 0.0 88-89 1.4625 0.0 0.0 0.0 0.0 90-91 1.725 0.0 0.0 0.0 0.0 92-93 2.0875 0.0 0.0 0.0 0.0 94-95 2.425 0.0 0.0 0.0 0.0 96-97 2.8 0.0 0.0 0.0 0.0 98-99 3.2874999999999996 0.0 0.0 0.0 0.0 100-101 3.675 0.0 0.0 0.0 0.0 102-103 4.1625 0.0 0.0 0.0 0.0 104-105 4.875 0.0 0.0 0.0 0.0 106-107 5.525 0.0 0.0 0.0 0.0 108-109 6.15 0.0 0.0 0.0 0.0 110-111 6.75 0.0 0.0 0.0 0.0 112-113 7.3625 0.0 0.0 0.0 0.0 114-115 8.1375 0.0 0.0 0.0 0.0 116-117 8.8625 0.0 0.0 0.0 0.0 118-119 9.7 0.0 0.0 0.0 0.0 120-121 10.5 0.0 0.0 0.0 0.0 122-123 11.1375 0.0 0.0 0.0 0.0 124-125 11.7625 0.0 0.0 0.0 0.0 126-127 12.75 0.0 0.0 0.0 0.0 128-129 13.4375 0.0 0.0 0.0 0.0 130-131 14.1875 0.0 0.0 0.0 0.0 132-133 15.0 0.0 0.0 0.0 0.0 134-135 15.837499999999999 0.0 0.0 0.0 0.0 136-137 16.4375 0.0 0.0 0.0 0.0 138-139 17.275 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position TACAAAA 10 0.006830828 145.0 5 >>END_MODULE Read 1651430 spots for SRR28623255.sra Written 1651430 spots for SRR28623255.sra Read 1651430 spots for SRR28623255.sra Written 1651430 spots for SRR28623255.sra Read 1651430 spots for SRR28623255.sra Written 1651430 spots for SRR28623255.sra Read 1651430 spots for SRR28623255.sra Written 1651430 spots for SRR28623255.sra Read 1651430 spots for SRR28623255.sra Written 1651430 spots for SRR28623255.sra Read 1651430 spots for SRR28623255.sra Written 1651430 spots for SRR28623255.sra Read 1651430 spots for SRR28623255.sra Written 1651430 spots for SRR28623255.sra Read 1651430 spots for SRR28623255.sra Written 1651430 spots for SRR28623255.sra Read 1651430 spots for SRR28623255.sra Written 1651430 spots for SRR28623255.sra Read 1651430 spots for SRR28623255.sra Written 1651430 spots for SRR28623255.sra Read 1651430 spots for SRR28623255.sra Written 1651430 spots for SRR28623255.sra Read 1651430 spots for SRR28623255.sra Written 1651430 spots for SRR28623255.sra Read 1651430 spots for SRR28623255.sra Written 1651430 spots for SRR28623255.sra Read 1651430 spots for SRR28623255.sra Written 1651430 spots for SRR28623255.sra Read 1651430 spots for SRR28623255.sra Written 1651430 spots for SRR28623255.sra Read 1651430 spots for SRR28623255.sra Written 1651430 spots for SRR28623255.sra Read 1651430 spots for SRR28623255.sra Written 1651430 spots for SRR28623255.sra Read 1651430 spots for SRR28623255.sra Written 1651430 spots for SRR28623255.sra Read 1651430 spots for SRR28623255.sra Written 1651430 spots for SRR28623255.sra Read 1651441 spots for SRR28623255.sra Written 1651441 spots for SRR28623255.sra SRR ids: ['SRR28623255.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_ksqw4w0t SRR28623255.sra spots: 33028611 blocks: [[1, 1651430], [1651431, 3302860], [3302861, 4954290], [4954291, 6605720], [6605721, 8257150], [8257151, 9908580], [9908581, 11560010], [11560011, 13211440], [13211441, 14862870], [14862871, 16514300], [16514301, 18165730], [18165731, 19817160], [19817161, 21468590], [21468591, 23120020], [23120021, 24771450], [24771451, 26422880], [26422881, 28074310], [28074311, 29725740], [29725741, 31377170], [31377171, 33028611]] SRR28623255 file size 12196305 SRR28623255 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 SRR28623255 SRR28623255_1.fastq SRR28623255_2.fastq Input file: SRR28623255_1.fastq Paired file: SRR28623255_2.fastq trimmed: SRR28623255-trimmed-pair1.fastq, SRR28623255-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 12:35:43 2025 >> started Tue Feb 11 12:36:25 2025 >> done (41.457s) 33028611 read pairs processed; of these: 54 ( 0.00%) short read pairs filtered out after trimming by size control 73117 ( 0.22%) empty read pairs filtered out after trimming by size control 32955440 (99.78%) read pairs available; of these: 7623060 (23.13%) trimmed read pairs available after processing 25332380 (76.87%) untrimmed read pairs available after processing Length distribution of reads after trimming: length count percentage 18 6 0.00% 19 9 0.00% 20 7 0.00% 21 3 0.00% 22 5 0.00% 23 10 0.00% 24 9 0.00% 25 11 0.00% 26 14 0.00% 27 11 0.00% 28 11 0.00% 29 12 0.00% 30 18 0.00% 31 13 0.00% 32 12 0.00% 33 31 0.00% 34 23 0.00% 35 34 0.00% 36 36 0.00% 37 38 0.00% 38 63 0.00% 39 65 0.00% 40 60 0.00% 41 100 0.00% 42 102 0.00% 43 123 0.00% 44 154 0.00% 45 171 0.00% 46 204 0.00% 47 224 0.00% 48 291 0.00% 49 358 0.00% 50 469 0.00% 51 538 0.00% 52 598 0.00% 53 665 0.00% 54 765 0.00% 55 872 0.00% 56 951 0.00% 57 1165 0.00% 58 1414 0.00% 59 1671 0.01% 60 1924 0.01% 61 2183 0.01% 62 2687 0.01% 63 3093 0.01% 64 3447 0.01% 65 4008 0.01% 66 4280 0.01% 67 5088 0.02% 68 5610 0.02% 69 6810 0.02% 70 7810 0.02% 71 8573 0.03% 72 10032 0.03% 73 11555 0.04% 74 12924 0.04% 75 14298 0.04% 76 15732 0.05% 77 16993 0.05% 78 19160 0.06% 79 21211 0.06% 80 23194 0.07% 81 25921 0.08% 82 28848 0.09% 83 31549 0.10% 84 34941 0.11% 85 37476 0.11% 86 39720 0.12% 87 42637 0.13% 88 45107 0.14% 89 47470 0.14% 90 50438 0.15% 91 53824 0.16% 92 57122 0.17% 93 60962 0.18% 94 64160 0.19% 95 68313 0.21% 96 70667 0.21% 97 73610 0.22% 98 75273 0.23% 99 78133 0.24% 100 80186 0.24% 101 82438 0.25% 102 87016 0.26% 103 89889 0.27% 104 92459 0.28% 105 94995 0.29% 106 98094 0.30% 107 100332 0.30% 108 102330 0.31% 109 104725 0.32% 110 104698 0.32% 111 108351 0.33% 112 110027 0.33% 113 111963 0.34% 114 114071 0.35% 115 117042 0.36% 116 118409 0.36% 117 121089 0.37% 118 123232 0.37% 119 123649 0.38% 120 125728 0.38% 121 126625 0.38% 122 127394 0.39% 123 129410 0.39% 124 131973 0.40% 125 132498 0.40% 126 134581 0.41% 127 135583 0.41% 128 136329 0.41% 129 136919 0.42% 130 138676 0.42% 131 138166 0.42% 132 138719 0.42% 133 141382 0.43% 134 139934 0.42% 135 142528 0.43% 136 142694 0.43% 137 143114 0.43% 138 144209 0.44% 139 145383 0.44% 140 143631 0.44% 141 144660 0.44% 142 145817 0.44% 143 144757 0.44% 144 147768 0.45% 145 146519 0.44% 146 145379 0.44% 147 147022 0.45% 148 147263 0.45% 149 146712 0.45% 150 148573 0.45% 151 25332380 76.87% 32955440 reads passed initial QC criterion=sequence-density sequence-density=0.33 sequence-density-rank=1 fanout-score=21.68 fanout-score-rank=6 prefix-density=0.30 prefix-fanout=21.7 sequence=GGATCGGAAGAGCACACGTCTGAACTCCAGTCACTGTGGTACATCTCGTATGCCGTCTTCTGCTTGAAAAT criterion=fanout-score sequence-density=0.01 sequence-density-rank=34 fanout-score=163.17 fanout-score-rank=1 prefix-density=0.15 prefix-fanout=15.7 sequence=CTCCTTCCTCTAAATGATAAGGTTCAGTGGACTTCTCGCGACGTCGCCGGCGGCGAACCGCCCACGTCGCCGCGATCCGAACACTTCACCGGACCATTCAATCGGTAGGAGCGACGGGCGGTGTGTACAAAGGGCAGGGACGTAGTCAACGCGAGCTGATGACTCGCGCTTACTAGGAATTCCTCGTTGAAGACCAACAATTGCAATGATCTATCCCCATCACGATGAAATTTCAAAGATTACCCGGGCCTGTCGGCCAAGGCTATAGACTCGTTGAATACATCAGTGTAGCGCGCGTGCGGCCCAGAACATCTAAGGGCATCACAGACCTGTTATTGCCTCAAACTTCCTTGGCCTGGAAGGCCATAGTCCCTCTAAGAAGCTGGCCGCGGAGGGTCACCTCCGCATAGCTAGTTAGCAGGCTGAGGTCTCGTTCGTTAACGGAATTAAC criterion=sequence-density sequence-density=0.20 sequence-density-rank=1 fanout-score=12.38 fanout-score-rank=13 prefix-density=0.14 prefix-fanout=12.4 sequence=GAGAGAGAGAGTTAAGACAATGGCCTCGAAGAAATCTGCAATCGTATTACCTGGTTCAAAGGTGTTGAAGCACATAGTTTTTGTACGGTTTAATGATGGGATCACTGATGAACAAATTGAGAA criterion=fanout-score sequence-density=0.07 sequence-density-rank=23 fanout-score=375.55 fanout-score-rank=1 prefix-density=0.88 prefix-fanout=30.2 sequence=GAAGAAGAAGAAA SRR28623255 testing PE reads STAR mapping to Ensembl genome Started job on | Feb 11 12:37:10 Started mapping on | Feb 11 12:37:10 Finished on | Feb 11 12:40:47 Mapping speed, Million of reads per hour | 546.73 Number of input reads | 32955440 Average input read length | 288 UNIQUE READS: Uniquely mapped reads number | 30478038 Uniquely mapped reads % | 92.48% Average mapped length | 286.24 Number of splices: Total | 27387250 Number of splices: Annotated (sjdb) | 26791267 Number of splices: GT/AG | 26934449 Number of splices: GC/AG | 346960 Number of splices: AT/AC | 24830 Number of splices: Non-canonical | 81011 Mismatch rate per base, % | 0.41% Deletion rate per base | 0.03% Deletion average length | 2.94 Insertion rate per base | 0.03% Insertion average length | 2.39 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 889274 % of reads mapped to multiple loci | 2.70% Number of reads mapped to too many loci | 134415 % of reads mapped to too many loci | 0.41% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 4.02% % of reads unmapped: other | 0.39% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 1588128 1588128 1588128 N_multimapping 889274 889274 889274 N_noFeature 1161330 30093120 1361890 N_ambiguous 348929 2075 163167 UnstrandedReadsAssigned:28967779 PositiveStrandReadsAssigned:382843 NegativeStrandReadsAssigned:28952981 Dataset is classified negative stranded MeadianReadLen=151 20thPercentileLength=143 echo kmer=139 SRR28623255 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: SRR28623255-trimmed-pair1.fastq SRR28623255-trimmed-pair2.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 32,955,440 reads, 29,497,341 reads pseudoaligned [quant] estimated average fragment length: 212.355 [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,105 rounds 52401 SRR28623255.ke.tsv 34699 SRR28623255.se.tsv 87100 total ==> SRR28623255.ke.tsv <== target_id length eff_length est_counts tpm Potri.005G200100.1.v4.1 2018 1806.64 1191 22.5128 Potri.005G024800.1.v4.1 1035 823.645 1125 46.6447 Potri.004G059700.1.v4.1 961 749.724 66 3.0063 Potri.007G009000.2.v4.1 1416 1204.64 0 0 Potri.003G141000.2.v4.1 2943 2731.64 1017.77 12.7238 Potri.016G087400.1.v4.1 270 104.661 2405.58 784.917 Potri.015G069301.1.v4.1 564 359.178 0 0 Potri.010G195200.1.v4.1 1773 1561.64 134 2.9303 Potri.012G127500.1.v4.1 977 765.685 9194 410.057 ==> SRR28623255.se.tsv <== Potri.001G166300.v4.1 0 Potri.001G448400.v4.1 1235 Potri.001G233950.v4.1 0 Potri.001G122700.v4.1 592 Potri.001G212900.v4.1 10 Potri.001G182400.v4.1 2 Potri.001G256600.v4.1 0 Potri.001G040500.v4.1 1 Potri.001G416900.v4.1 1 Potri.001G452600.v4.1 3 SRR28623255 completed mapping pipeline successfully