Starting /dee2/code/volunteer_pipeline.sh SRR12667009 current disk space = 1540796989440 free memory = 1602356212 SRR12667009 SRAfilesize a28f61d2cba2bf34fdf6523a3f9c99df SRR12667009.sra SRR12667009.sra file validated SRR12667009 is paired end SRR12667009 is conventional basespace SRR12667009 read1 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR12667009_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 pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 36.4755 37.0 37.0 37.0 37.0 37.0 2 36.4015 37.0 37.0 37.0 37.0 37.0 3 36.512 37.0 37.0 37.0 37.0 37.0 4 36.4525 37.0 37.0 37.0 37.0 37.0 5 36.5785 37.0 37.0 37.0 37.0 37.0 6 36.5995 37.0 37.0 37.0 37.0 37.0 7 36.494 37.0 37.0 37.0 37.0 37.0 8 36.5985 37.0 37.0 37.0 37.0 37.0 9 36.603 37.0 37.0 37.0 37.0 37.0 10-14 36.5735 37.0 37.0 37.0 37.0 37.0 15-19 36.582100000000004 37.0 37.0 37.0 37.0 37.0 20-24 36.5453 37.0 37.0 37.0 37.0 37.0 25-29 36.5144 37.0 37.0 37.0 37.0 37.0 30-34 36.4779 37.0 37.0 37.0 37.0 37.0 35-39 36.4717 37.0 37.0 37.0 37.0 37.0 40-44 36.425 37.0 37.0 37.0 37.0 37.0 45-49 36.4086 37.0 37.0 37.0 37.0 37.0 50-54 36.3607 37.0 37.0 37.0 37.0 37.0 55-59 36.4025 37.0 37.0 37.0 37.0 37.0 60-64 36.40169999999999 37.0 37.0 37.0 37.0 37.0 65-69 36.3231 37.0 37.0 37.0 37.0 37.0 70-74 36.333000000000006 37.0 37.0 37.0 37.0 37.0 75-79 36.301700000000004 37.0 37.0 37.0 37.0 37.0 80-84 36.21320000000001 37.0 37.0 37.0 37.0 37.0 85-89 36.2635 37.0 37.0 37.0 37.0 37.0 90-94 36.2798 37.0 37.0 37.0 37.0 37.0 95-99 36.173500000000004 37.0 37.0 37.0 37.0 37.0 100-104 36.1738 37.0 37.0 37.0 37.0 37.0 105-109 36.224900000000005 37.0 37.0 37.0 37.0 37.0 110-114 36.0952 37.0 37.0 37.0 37.0 37.0 115-119 36.0791 37.0 37.0 37.0 37.0 37.0 120-124 36.0336 37.0 37.0 37.0 37.0 37.0 125-129 36.077099999999994 37.0 37.0 37.0 37.0 37.0 130-134 36.0438 37.0 37.0 37.0 37.0 37.0 135-139 35.99210000000001 37.0 37.0 37.0 37.0 37.0 140-144 35.827 37.0 37.0 37.0 37.0 37.0 145-149 35.8051 37.0 37.0 37.0 37.0 37.0 150-151 35.65575 37.0 37.0 37.0 37.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 22 1.0 23 2.0 24 0.0 25 4.0 26 8.0 27 7.0 28 8.0 29 18.0 30 25.0 31 32.0 32 37.0 33 87.0 34 158.0 35 272.0 36 2822.0 37 519.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 43.824999999999996 13.25 8.425 34.5 2 22.233350025037556 17.45117676514772 34.55182774161242 25.763645468202302 3 21.05 22.675 25.75 30.525000000000002 4 24.375 31.25 20.775 23.599999999999998 5 24.25 34.4 22.35 19.0 6 20.45 35.05 21.45 23.05 7 17.349999999999998 21.275 41.575 19.8 8 20.125 21.475 29.725 28.675 9 19.325 21.325 31.225 28.125 10-14 22.675 27.3 24.825 25.2 15-19 22.145 26.565 25.69 25.6 20-24 22.065 26.41 25.874999999999996 25.650000000000002 25-29 22.795 26.229999999999997 25.965 25.009999999999998 30-34 22.205 25.985000000000003 26.115 25.695 35-39 22.575 25.83 26.169999999999998 25.424999999999997 40-44 22.845 26.68 25.45 25.025 45-49 22.17 26.900000000000002 25.345000000000002 25.585 50-54 22.31 26.515 25.805 25.369999999999997 55-59 22.264999999999997 26.695 25.655 25.385 60-64 22.355 26.05 25.569999999999997 26.025 65-69 23.150000000000002 26.19 25.735000000000003 24.925 70-74 22.705000000000002 26.32 25.480000000000004 25.495 75-79 23.435 26.25 25.715 24.6 80-84 22.439999999999998 26.43 25.52 25.61 85-89 22.795 26.445 25.19 25.569999999999997 90-94 23.075000000000003 26.055 24.985 25.885 95-99 23.09 25.7 25.745 25.465 100-104 22.475 26.015 25.645 25.865 105-109 23.235 25.88 25.814999999999998 25.069999999999997 110-114 23.07 26.615 25.069999999999997 25.245 115-119 22.95 25.965 25.924999999999997 25.16 120-124 22.91 26.325 25.235000000000003 25.53 125-129 22.57 25.790000000000003 26.05 25.590000000000003 130-134 23.515 26.655 24.715 25.115 135-139 23.5 25.5 25.335 25.665 140-144 23.810000000000002 25.990000000000002 25.259999999999998 24.94 145-149 23.035 26.355 25.06 25.55 150-151 23.7875 25.525 24.712500000000002 25.974999999999998 >>END_MODULE >>Per sequence GC content warn #GC Content Count 0 0.0 1 0.0 2 0.5 3 0.5 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 1.0 24 2.5 25 2.0 26 0.5 27 0.5 28 2.0 29 5.5 30 8.5 31 10.5 32 14.0 33 18.0 34 25.0 35 41.5 36 55.0 37 72.5 38 88.0 39 102.5 40 127.0 41 170.0 42 194.5 43 184.5 44 192.5 45 217.0 46 216.5 47 201.0 48 205.5 49 197.0 50 179.0 51 170.5 52 161.0 53 140.0 54 120.0 55 105.0 56 80.5 57 79.0 58 85.0 59 72.0 60 63.0 61 52.0 62 43.0 63 47.0 64 47.0 65 40.5 66 33.5 67 22.0 68 24.5 69 24.0 70 13.0 71 12.5 72 11.5 73 7.5 74 5.0 75 2.5 76 1.0 77 1.0 78 0.5 79 0.0 80 0.0 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 0.15 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 91.64999999999999 #Duplication Level Percentage of deduplicated Percentage of total 1 91.62575013638843 83.975 2 7.6923076923076925 14.099999999999998 3 0.6273867975995636 1.725 4 0.05455537370430987 0.2 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 0.0125 0.0 0.0 0.0 0.0 78-79 0.025 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 0.025 0.0 0.0 0.0 0.0 86-87 0.05 0.0 0.0 0.0 0.0 88-89 0.075 0.0 0.0 0.0 0.0 90-91 0.1 0.0 0.0 0.0 0.0 92-93 0.125 0.0 0.0 0.0 0.0 94-95 0.15 0.0 0.0 0.0 0.0 96-97 0.2625 0.0 0.0 0.0 0.0 98-99 0.3 0.0 0.0 0.0 0.0 100-101 0.4 0.0 0.0 0.0 0.0 102-103 0.5125 0.0 0.0 0.0 0.0 104-105 0.625 0.0 0.0 0.0 0.0 106-107 0.8125 0.0 0.0 0.0 0.0 108-109 1.0125 0.0 0.0 0.0 0.0 110-111 1.1375000000000002 0.0 0.0 0.0 0.0 112-113 1.3125 0.0 0.0 0.0 0.0 114-115 1.4875 0.0 0.0 0.0 0.0 116-117 1.65 0.0 0.0 0.0 0.0 118-119 1.8875000000000002 0.0 0.0 0.0 0.0 120-121 2.1875 0.0 0.0 0.0 0.0 122-123 2.4875 0.0 0.0 0.0 0.0 124-125 2.8375000000000004 0.0 0.0 0.0 0.0 126-127 3.175 0.0 0.0 0.0 0.0 128-129 3.4124999999999996 0.0 0.0 0.0 0.0 130-131 3.7249999999999996 0.0 0.0 0.0 0.0 132-133 4.025 0.0 0.0 0.0 0.0 134-135 4.3125 0.0 0.0 0.0 0.0 136-137 4.6125 0.0 0.0 0.0 0.0 138-139 4.925000000000001 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content pass >>END_MODULE SRR12667009 read2 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR12667009_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 pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 36.0305 37.0 37.0 37.0 37.0 37.0 2 36.027 37.0 37.0 37.0 37.0 37.0 3 36.14 37.0 37.0 37.0 37.0 37.0 4 36.3175 37.0 37.0 37.0 37.0 37.0 5 36.3005 37.0 37.0 37.0 37.0 37.0 6 36.246 37.0 37.0 37.0 37.0 37.0 7 36.233 37.0 37.0 37.0 37.0 37.0 8 36.4015 37.0 37.0 37.0 37.0 37.0 9 36.265 37.0 37.0 37.0 37.0 37.0 10-14 36.312599999999996 37.0 37.0 37.0 37.0 37.0 15-19 36.2787 37.0 37.0 37.0 37.0 37.0 20-24 36.2188 37.0 37.0 37.0 37.0 37.0 25-29 36.2192 37.0 37.0 37.0 37.0 37.0 30-34 36.1954 37.0 37.0 37.0 37.0 37.0 35-39 36.2105 37.0 37.0 37.0 37.0 37.0 40-44 36.1677 37.0 37.0 37.0 37.0 37.0 45-49 36.1255 37.0 37.0 37.0 37.0 37.0 50-54 36.1437 37.0 37.0 37.0 37.0 37.0 55-59 36.1122 37.0 37.0 37.0 37.0 37.0 60-64 36.0626 37.0 37.0 37.0 37.0 37.0 65-69 36.0424 37.0 37.0 37.0 37.0 37.0 70-74 35.998200000000004 37.0 37.0 37.0 37.0 37.0 75-79 36.033500000000004 37.0 37.0 37.0 37.0 37.0 80-84 36.0225 37.0 37.0 37.0 37.0 37.0 85-89 35.9533 37.0 37.0 37.0 37.0 37.0 90-94 35.9068 37.0 37.0 37.0 37.0 37.0 95-99 35.9906 37.0 37.0 37.0 37.0 37.0 100-104 35.9423 37.0 37.0 37.0 37.0 37.0 105-109 35.8601 37.0 37.0 37.0 37.0 37.0 110-114 35.868100000000005 37.0 37.0 37.0 37.0 37.0 115-119 35.8638 37.0 37.0 37.0 37.0 37.0 120-124 35.8729 37.0 37.0 37.0 37.0 37.0 125-129 35.8922 37.0 37.0 37.0 37.0 37.0 130-134 35.777 37.0 37.0 37.0 37.0 37.0 135-139 35.70399999999999 37.0 37.0 37.0 37.0 37.0 140-144 35.610699999999994 37.0 37.0 37.0 37.0 37.0 145-149 35.5674 37.0 37.0 37.0 37.0 37.0 150-151 35.2 37.0 37.0 37.0 31.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 12 1.0 13 6.0 14 9.0 15 0.0 16 3.0 17 0.0 18 0.0 19 2.0 20 3.0 21 5.0 22 8.0 23 3.0 24 3.0 25 4.0 26 7.0 27 7.0 28 14.0 29 16.0 30 24.0 31 37.0 32 44.0 33 81.0 34 141.0 35 465.0 36 2645.0 37 472.0 >>END_MODULE >>Per base sequence content warn #Base G A T C 1 46.25 15.925 10.75 27.075 2 29.299999999999997 20.7 28.7 21.3 3 23.275000000000002 24.075 28.65 24.0 4 26.825 30.875000000000004 20.175 22.125 5 26.724999999999998 34.949999999999996 18.85 19.475 6 22.025 36.199999999999996 19.950000000000003 21.825 7 21.975 16.225 35.65 26.150000000000002 8 24.099999999999998 20.825 24.275 30.8 9 24.2 21.65 26.6 27.55 10-14 25.900000000000002 25.305 23.7 25.095 15-19 25.385 25.1 25.16 24.355 20-24 25.715 25.845000000000002 24.865000000000002 23.575 25-29 25.385 25.779999999999998 24.915000000000003 23.919999999999998 30-34 25.324999999999996 25.590000000000003 25.03 24.055 35-39 26.179999999999996 25.040000000000003 24.94 23.84 40-44 25.72 25.25 24.95 24.08 45-49 25.165 25.645 25.64 23.549999999999997 50-54 25.465 25.874999999999996 25.035 23.625 55-59 25.515 26.145000000000003 24.545 23.794999999999998 60-64 25.759999999999998 25.365 25.124999999999996 23.75 65-69 25.979999999999997 25.81 25.415 22.795 70-74 25.924999999999997 25.595000000000002 25.19 23.29 75-79 25.745 25.22 25.525 23.51 80-84 25.655 25.91 25.424999999999997 23.01 85-89 26.295 25.515 25.009999999999998 23.18 90-94 25.905 26.169999999999998 24.635 23.29 95-99 25.56 26.405 25.180000000000003 22.855 100-104 26.395000000000003 25.39 24.695 23.52 105-109 25.395 25.979999999999997 25.779999999999998 22.845 110-114 26.265 25.75 25.095 22.89 115-119 25.905 25.929999999999996 25.335 22.830000000000002 120-124 25.94 26.44 24.959999999999997 22.66 125-129 25.91 26.545 25.09 22.455 130-134 26.63 26.240000000000002 25.05 22.08 135-139 26.229999999999997 25.8 25.385 22.585 140-144 26.375 25.44 25.485000000000003 22.7 145-149 26.790000000000003 25.5 25.205 22.505 150-151 26.5375 25.75 25.624999999999996 22.0875 >>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 0.5 9 0.5 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 0.5 20 1.0 21 0.5 22 0.5 23 1.0 24 1.0 25 2.5 26 2.5 27 1.5 28 4.0 29 4.0 30 5.0 31 9.0 32 13.0 33 15.5 34 22.0 35 36.0 36 42.5 37 50.5 38 75.0 39 99.0 40 114.5 41 137.0 42 156.0 43 183.5 44 205.0 45 193.0 46 193.5 47 201.0 48 186.5 49 172.0 50 167.5 51 167.5 52 141.0 53 128.5 54 123.5 55 103.0 56 105.0 57 99.5 58 89.0 59 83.5 60 77.0 61 72.0 62 69.0 63 65.0 64 57.5 65 53.5 66 55.0 67 52.0 68 38.0 69 27.0 70 24.0 71 16.5 72 14.5 73 13.5 74 8.5 75 5.5 76 2.0 77 0.0 78 0.5 79 0.5 80 0.0 81 0.0 82 0.0 83 1.0 84 1.0 85 0.0 86 0.5 87 0.5 88 0.0 89 0.0 90 0.5 91 0.5 92 0.0 93 0.0 94 1.0 95 1.0 96 0.0 97 0.0 98 0.5 99 0.5 100 1.5 >>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 91.35 #Duplication Level Percentage of deduplicated Percentage of total 1 91.51614668856048 83.6 2 7.717569786535304 14.099999999999998 3 0.6568144499178982 1.7999999999999998 4 0.05473453749315819 0.2 5 0.0 0.0 6 0.05473453749315819 0.3 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 GTTGGCTTCTCCTCCCCCTCACTAGTCCTCGGTTCCGGTTCCGGTTCGTT 6 0.15 No Hit GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG 6 0.15 No Hit >>END_MODULE >>Adapter Content warn #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 0.0125 0.0 0.0 0.0 0.0 78-79 0.025 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 0.025 0.0 0.0 0.0 0.0 86-87 0.05 0.0 0.0 0.0 0.0 88-89 0.075 0.0 0.0 0.0 0.0 90-91 0.11249999999999999 0.0 0.0 0.0 0.0 92-93 0.15 0.0 0.0 0.0 0.0 94-95 0.175 0.0 0.0 0.0 0.0 96-97 0.2875 0.0 0.0 0.0 0.0 98-99 0.325 0.0 0.0 0.0 0.0 100-101 0.42500000000000004 0.0 0.0 0.0 0.0 102-103 0.5375000000000001 0.0 0.0 0.0 0.0 104-105 0.6625 0.0 0.0 0.0 0.0 106-107 0.8625 0.0 0.0 0.0 0.0 108-109 1.0625 0.0 0.0 0.0 0.0 110-111 1.1875 0.0 0.0 0.0 0.0 112-113 1.3625 0.0 0.0 0.0 0.0 114-115 1.5375 0.0 0.0 0.0 0.0 116-117 1.7 0.0 0.0 0.0 0.0 118-119 1.9375 0.0 0.0 0.0 0.0 120-121 2.2625 0.0 0.0 0.0 0.0 122-123 2.575 0.0 0.0 0.0 0.0 124-125 2.9375 0.0 0.0 0.0 0.0 126-127 3.2750000000000004 0.0 0.0 0.0 0.0 128-129 3.5125 0.0 0.0 0.0 0.0 130-131 3.8499999999999996 0.0 0.0 0.0 0.0 132-133 4.1875 0.0 0.0 0.0 0.0 134-135 4.5375 0.0 0.0 0.0 0.0 136-137 4.8375 0.0 0.0 0.0 0.0 138-139 5.137499999999999 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position CCATGAT 10 0.006830828 145.0 145 >>END_MODULE Read 1584286 spots for SRR12667009.sra Written 1584286 spots for SRR12667009.sra Read 1584286 spots for SRR12667009.sra Written 1584286 spots for SRR12667009.sra Read 1584286 spots for SRR12667009.sra Written 1584286 spots for SRR12667009.sra Read 1584286 spots for SRR12667009.sra Written 1584286 spots for SRR12667009.sra Read 1584286 spots for SRR12667009.sra Written 1584286 spots for SRR12667009.sra Read 1584286 spots for SRR12667009.sra Written 1584286 spots for SRR12667009.sra Read 1584286 spots for SRR12667009.sra Written 1584286 spots for SRR12667009.sra Read 1584286 spots for SRR12667009.sra Written 1584286 spots for SRR12667009.sra Read 1584286 spots for SRR12667009.sra Written 1584286 spots for SRR12667009.sra Read 1584286 spots for SRR12667009.sra Written 1584286 spots for SRR12667009.sra Read 1584286 spots for SRR12667009.sra Written 1584286 spots for SRR12667009.sra Read 1584286 spots for SRR12667009.sra Written 1584286 spots for SRR12667009.sra Read 1584286 spots for SRR12667009.sra Written 1584286 spots for SRR12667009.sra Read 1584286 spots for SRR12667009.sra Written 1584286 spots for SRR12667009.sra Read 1584286 spots for SRR12667009.sra Written 1584286 spots for SRR12667009.sra Read 1584286 spots for SRR12667009.sra Written 1584286 spots for SRR12667009.sra Read 1584286 spots for SRR12667009.sra Written 1584286 spots for SRR12667009.sra Read 1584286 spots for SRR12667009.sra Written 1584286 spots for SRR12667009.sra Read 1584286 spots for SRR12667009.sra Written 1584286 spots for SRR12667009.sra Read 1584288 spots for SRR12667009.sra Written 1584288 spots for SRR12667009.sra SRR ids: ['SRR12667009.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_7bj3vhha SRR12667009.sra spots: 31685722 blocks: [[1, 1584286], [1584287, 3168572], [3168573, 4752858], [4752859, 6337144], [6337145, 7921430], [7921431, 9505716], [9505717, 11090002], [11090003, 12674288], [12674289, 14258574], [14258575, 15842860], [15842861, 17427146], [17427147, 19011432], [19011433, 20595718], [20595719, 22180004], [22180005, 23764290], [23764291, 25348576], [25348577, 26932862], [26932863, 28517148], [28517149, 30101434], [30101435, 31685722]] SRR12667009 file size 10746494 SRR12667009 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 SRR12667009 SRR12667009_1.fastq SRR12667009_2.fastq Input file: SRR12667009_1.fastq Paired file: SRR12667009_2.fastq trimmed: SRR12667009-trimmed-pair1.fastq, SRR12667009-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 Sat Dec 7 18:14:47 2024 >> started Sat Dec 7 18:15:43 2024 >> done (55.784s) 31685722 read pairs processed; of these: 65 ( 0.00%) short read pairs filtered out after trimming by size control 7200 ( 0.02%) empty read pairs filtered out after trimming by size control 31678457 (99.98%) read pairs available; of these: 2641774 ( 8.34%) trimmed read pairs available after processing 29036683 (91.66%) untrimmed read pairs available after processing Length distribution of reads after trimming: length count percentage 18 8 0.00% 19 6 0.00% 20 13 0.00% 21 19 0.00% 22 25 0.00% 23 29 0.00% 24 10 0.00% 25 27 0.00% 26 26 0.00% 27 26 0.00% 28 26 0.00% 29 38 0.00% 30 42 0.00% 31 31 0.00% 32 67 0.00% 33 44 0.00% 34 50 0.00% 35 53 0.00% 36 43 0.00% 37 45 0.00% 38 62 0.00% 39 39 0.00% 40 56 0.00% 41 58 0.00% 42 61 0.00% 43 68 0.00% 44 67 0.00% 45 66 0.00% 46 76 0.00% 47 64 0.00% 48 87 0.00% 49 103 0.00% 50 102 0.00% 51 79 0.00% 52 123 0.00% 53 117 0.00% 54 104 0.00% 55 121 0.00% 56 133 0.00% 57 167 0.00% 58 139 0.00% 59 195 0.00% 60 204 0.00% 61 219 0.00% 62 231 0.00% 63 250 0.00% 64 270 0.00% 65 315 0.00% 66 383 0.00% 67 384 0.00% 68 448 0.00% 69 506 0.00% 70 551 0.00% 71 673 0.00% 72 846 0.00% 73 903 0.00% 74 972 0.00% 75 1080 0.00% 76 1173 0.00% 77 1360 0.00% 78 1459 0.00% 79 1866 0.01% 80 2108 0.01% 81 2452 0.01% 82 2769 0.01% 83 3135 0.01% 84 3587 0.01% 85 3782 0.01% 86 4219 0.01% 87 4503 0.01% 88 5199 0.02% 89 5571 0.02% 90 6332 0.02% 91 7123 0.02% 92 7939 0.03% 93 8878 0.03% 94 9609 0.03% 95 10694 0.03% 96 11431 0.04% 97 11973 0.04% 98 12791 0.04% 99 13776 0.04% 100 14778 0.05% 101 15889 0.05% 102 17227 0.05% 103 18930 0.06% 104 19924 0.06% 105 21151 0.07% 106 22235 0.07% 107 23267 0.07% 108 24202 0.08% 109 25238 0.08% 110 26333 0.08% 111 28073 0.09% 112 29695 0.09% 113 31562 0.10% 114 33175 0.10% 115 34551 0.11% 116 35617 0.11% 117 36342 0.11% 118 37436 0.12% 119 38136 0.12% 120 40315 0.13% 121 41777 0.13% 122 42838 0.14% 123 45923 0.14% 124 48011 0.15% 125 49344 0.16% 126 51020 0.16% 127 51512 0.16% 128 51973 0.16% 129 53668 0.17% 130 54298 0.17% 131 55035 0.17% 132 58231 0.18% 133 60090 0.19% 134 61780 0.20% 135 64669 0.20% 136 66053 0.21% 137 66734 0.21% 138 67750 0.21% 139 68316 0.22% 140 68491 0.22% 141 70133 0.22% 142 72651 0.23% 143 74034 0.23% 144 77677 0.25% 145 79594 0.25% 146 81077 0.26% 147 81791 0.26% 148 82590 0.26% 149 82117 0.26% 150 83842 0.26% 151 29036683 91.66% 31678457 reads passed initial QC criterion=sequence-density sequence-density=0.17 sequence-density-rank=1 fanout-score=4.75 fanout-score-rank=23 prefix-density=0.21 prefix-fanout=3.9 sequence=GTGATGGTCTTGCC criterion=fanout-score sequence-density=0.03 sequence-density-rank=31 fanout-score=166.02 fanout-score-rank=1 prefix-density=0.31 prefix-fanout=15.0 sequence=GGCGGCGGCGAACCGCCCCCGTCGCCGCGATCCGAACACTTCACCGGACCATTCAATCGGTAGGAGCGACGGGCGGTGTGTACAAAGGGCAGGGACGTAGTCAACGCGAGCTGATGACTCGCGCTTACTAGGCATTCCTCGTTGAAGACCAACAATTGCAATGATCTATCCCCATCACGATGAAATTTCCCAAGATTACCCGGGCCTGTCGGCCAAGGCTATATACTCGTTGAATACATCAGTGTAGCGCGCGTGCGGCCCAGAACATCTAAGGGCATCACAGACCTGTTATTGCCTCAAACTTCCGTCGCCTAAACGGCGATAGTCCCTCTAAGAAGCTAGCTGCGGAGGGATGGCTCCGCATAGCTAGTTAGCAGGCTGAGGTCTCGTTCGTTAACGGAATTAACCAGACAAATCGCTCCACCAACTAAGAACGGCCATGCACCACCACCCATAGAATCAAGAAAGAGCTCTCAGTCTGTCAATCCTTGCTATGTCTGGACCTGGTAAG criterion=sequence-density sequence-density=0.31 sequence-density-rank=1 fanout-score=2.43 fanout-score-rank=32 prefix-density=0.33 prefix-fanout=2.3 sequence=CGGTTCCGGTTC criterion=fanout-score sequence-density=0.02 sequence-density-rank=33 fanout-score=508.47 fanout-score-rank=1 prefix-density=0.69 prefix-fanout=17.2 sequence=GCCGCCGCCCCTCGTCCTCTGTGTTCCTTCTCCGAGTTTCAGCCATGGGTAAGGAGAAGACTCACATCAACATCGTGGTCATTGGCCATGTCGACTCTGGCAAGTCGACCACCACTGGCCACCTGATCTACAAGCTTGGAGGTATTGACAAGCGTGTGATCGAGAGGTTCGAGAAGGAGGCTGCTGAGATGAACAAGAGGTCATTCAAGTACGCGTGGGTGCTTGACAAGCTGAAGGCTGAGCGTGAGAGAGGTATCACCATCGATATTGCCTTGTGGAAGTTCGAGACCACCAAGTACTACTGCACCGTCATTGATGCCCCTGGACACCGTGACTTCATCAAGAACATGATTACCGGTACCTCCCAGGCTGACTGTGCCGTGCTTATCATTGACTCCACGACTGGAGGTTTTGAGGCTGGTATCTCCAAGGATGGCCAGACCCGTGAGCATGCCCTCCTTGCTTTCACTCTTGGAGTGAAGCAGATGATCTGCTGCTGCAACAAGATGGA SRR12667009 testing PE reads STAR mapping to Ensembl genome Started job on | Dec 07 18:16:35 Started mapping on | Dec 07 18:16:35 Finished on | Dec 07 18:19:53 Mapping speed, Million of reads per hour | 575.97 Number of input reads | 31678457 Average input read length | 298 UNIQUE READS: Uniquely mapped reads number | 30030797 Uniquely mapped reads % | 94.80% Average mapped length | 297.18 Number of splices: Total | 33446083 Number of splices: Annotated (sjdb) | 31392230 Number of splices: GT/AG | 32961416 Number of splices: GC/AG | 375580 Number of splices: AT/AC | 23923 Number of splices: Non-canonical | 85164 Mismatch rate per base, % | 0.30% Deletion rate per base | 0.02% Deletion average length | 2.54 Insertion rate per base | 0.02% Insertion average length | 2.19 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 447035 % of reads mapped to multiple loci | 1.41% Number of reads mapped to too many loci | 31872 % of reads mapped to too many loci | 0.10% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 3.07% % of reads unmapped: other | 0.62% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 1200625 1200625 1200625 N_multimapping 447035 447035 447035 N_noFeature 1087196 29300349 1304849 N_ambiguous 616452 4724 104470 UnstrandedReadsAssigned:28327149 PositiveStrandReadsAssigned:725724 NegativeStrandReadsAssigned:28621478 Dataset is classified negative stranded MeadianReadLen=151 20thPercentileLength=151 echo kmer=147 SRR12667009 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: SRR12667009-trimmed-pair1.fastq SRR12667009-trimmed-pair2.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 31,678,457 reads, 28,970,834 reads pseudoaligned [quant] estimated average fragment length: 285.012 [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,272 rounds 52973 SRR12667009.ke.tsv 35125 SRR12667009.se.tsv 88098 total ==> SRR12667009.ke.tsv <== target_id length eff_length est_counts tpm PNS24245 936 652.788 0 0 PNS24247 1044 759.988 143.707 10.2479 PNS24249 1928 1643.99 98.7745 3.25619 PNS24246 1044 759.988 143.707 10.2479 PNS24248 1044 759.988 143.707 10.2479 PNS24244 1471 1186.99 324.105 14.798 PNS24243 293 90.1046 1 0.601474 KQK14069 1603 1318.99 3526.93 144.917 KQK14071 474 224.446 67.2797 16.2456 ==> SRR12667009.se.tsv <== BRADI_1g14170v3 3940 BRADI_1g53295v3 293 BRADI_1g59795v3 915 BRADI_1g07683v3 0 BRADI_1g00485v3 130 BRADI_1g20270v3 2450 BRADI_1g74790v3 82 BRADI_1g09890v3 0 BRADI_1g77505v3 195 BRADI_1g48960v3 0 SRR12667009 completed mapping pipeline successfully