Starting /dee2/code/volunteer_pipeline.sh SRR1797573 current disk space = 1525826666496 free memory = 1576361340 SRR1797573 SRAfilesize 89922849620d117eb72e0055f70c2e55 SRR1797573.sra SRR1797573.sra file validated SRR1797573 is paired end SRR1797573 is conventional basespace SRR1797573 read1 length is 150 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR1797573_1.fastq File type Conventional base calls Encoding Sanger / Illumina 1.9 Total Sequences 4000 Sequences flagged as poor quality 0 Sequence length 150 %GC 55 >>END_MODULE >>Per base sequence quality fail #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 31.937 34.0 34.0 34.0 31.0 34.0 2 32.7775 34.0 34.0 34.0 31.0 34.0 3 33.32225 34.0 34.0 34.0 31.0 34.0 4 36.71775 37.0 37.0 37.0 35.0 37.0 5 36.701 37.0 37.0 37.0 35.0 37.0 6 36.7545 37.0 37.0 37.0 37.0 37.0 7 36.6815 37.0 37.0 37.0 37.0 37.0 8 36.71 37.0 37.0 37.0 37.0 37.0 9 38.67425 39.0 39.0 39.0 38.0 39.0 10-14 38.9296 39.4 39.2 39.4 38.0 39.4 15-19 40.185050000000004 41.0 40.0 41.0 38.4 41.0 20-24 40.1119 41.0 40.0 41.0 38.0 41.0 25-29 39.6925 41.0 39.8 41.0 37.2 41.0 30-34 39.47275 41.0 39.8 41.0 35.8 41.0 35-39 39.1006 41.0 39.0 41.0 35.0 41.0 40-44 38.699850000000005 40.6 37.4 41.0 35.0 41.0 45-49 38.0 40.0 35.6 41.0 34.2 41.0 50-54 37.333000000000006 39.2 35.0 41.0 33.0 41.0 55-59 36.602 37.8 35.0 41.0 32.6 41.0 60-64 35.9285 36.4 35.0 40.0 31.4 41.0 65-69 35.3236 35.2 35.0 39.0 32.0 41.0 70-74 34.71315 35.0 35.0 37.2 31.8 39.4 75-79 33.650549999999996 35.0 33.8 35.8 29.8 37.4 80-84 33.4317 35.0 34.0 35.0 30.4 36.4 85-89 33.0929 35.0 34.0 35.0 30.2 35.6 90-94 32.77825 35.0 34.0 35.0 29.2 35.0 95-99 32.3152 35.0 33.4 35.0 27.4 35.0 100-104 31.69905 35.0 33.0 35.0 25.0 35.0 105-109 31.45825 35.0 32.8 35.0 24.2 35.0 110-114 30.954349999999998 35.0 32.0 35.0 21.4 35.0 115-119 30.34375 34.0 31.0 35.0 18.8 35.0 120-124 29.4591 34.0 29.4 35.0 11.2 35.0 125-129 28.9581 34.0 29.0 35.0 4.6 35.0 130-134 27.90025 33.2 26.6 35.0 2.0 35.0 135-139 26.851300000000002 33.0 24.4 35.0 2.0 35.0 140-144 26.0733 32.8 23.4 35.0 2.0 35.0 145-149 24.214550000000003 31.8 9.8 34.2 2.0 35.0 150 17.3405 20.0 2.0 29.0 2.0 33.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 4 1.0 5 0.0 6 0.0 7 3.0 8 9.0 9 5.0 10 6.0 11 6.0 12 7.0 13 10.0 14 8.0 15 9.0 16 9.0 17 17.0 18 12.0 19 14.0 20 20.0 21 23.0 22 33.0 23 33.0 24 37.0 25 42.0 26 39.0 27 49.0 28 77.0 29 101.0 30 96.0 31 125.0 32 185.0 33 279.0 34 411.0 35 619.0 36 988.0 37 723.0 38 4.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 32.131578947368425 11.368421052631579 13.5 43.0 2 29.9 10.424999999999999 23.275000000000002 36.4 3 23.525 11.899999999999999 15.950000000000001 48.625 4 29.625 15.1 16.2 39.074999999999996 5 30.4 21.45 20.724999999999998 27.425 6 32.375 22.875 18.725 26.025 7 21.425 27.55 30.5 20.525 8 23.775 22.175 28.675 25.374999999999996 9 23.1 19.1 28.9 28.9 10-14 25.18751875187519 24.61246124612461 24.117411741174116 26.082608260826085 15-19 25.685000000000002 22.96 23.52 27.834999999999997 20-24 25.656282814140706 23.286164308215408 23.651182559127957 27.406370318515926 25-29 25.215 23.599999999999998 22.8 28.384999999999998 30-34 25.275 23.355 23.169999999999998 28.199999999999996 35-39 25.595000000000002 23.155 22.655 28.595 40-44 25.595000000000002 22.865 22.955000000000002 28.585 45-49 26.125 22.42 22.91 28.544999999999998 50-54 26.105 22.564999999999998 22.919999999999998 28.410000000000004 55-59 25.874999999999996 22.27 23.075000000000003 28.78 60-64 26.840000000000003 22.64 22.634999999999998 27.884999999999998 65-69 26.205000000000002 22.745 22.45 28.599999999999998 70-74 26.71 22.015 22.685 28.59 75-79 26.165 22.505 22.57 28.76 80-84 26.76 22.09 22.49 28.660000000000004 85-89 26.63 22.515 21.89 28.965000000000003 90-94 26.090000000000003 22.17 22.115000000000002 29.625 95-99 26.875 22.175 22.225 28.725 100-104 27.200000000000003 21.865000000000002 22.53 28.405 105-109 26.445 22.35 22.264999999999997 28.939999999999998 110-114 26.96 21.52 22.814999999999998 28.705000000000002 115-119 27.62 21.235 22.045 29.099999999999998 120-124 27.169999999999998 21.834999999999997 22.295 28.7 125-129 27.145000000000003 21.34 22.46 29.054999999999996 130-134 27.32 22.39 21.86 28.43 135-139 27.63 21.365000000000002 22.285 28.720000000000002 140-144 27.57 21.6 21.790000000000003 29.04 145-149 28.43 21.07 21.235 29.265 150 30.15 20.349999999999998 18.675 30.825000000000003 >>END_MODULE >>Per sequence GC content fail #GC Content Count 0 1.0 1 1.0 2 1.0 3 0.5 4 0.0 5 0.5 6 0.5 7 0.0 8 0.0 9 0.0 10 0.0 11 0.0 12 0.0 13 0.0 14 0.0 15 0.0 16 0.0 17 0.0 18 0.0 19 0.0 20 0.0 21 0.0 22 0.0 23 0.0 24 0.0 25 0.0 26 0.0 27 0.0 28 0.5 29 2.0 30 2.5 31 3.0 32 6.0 33 6.5 34 10.0 35 18.5 36 27.0 37 36.0 38 44.5 39 63.0 40 83.5 41 92.0 42 102.5 43 127.0 44 138.0 45 139.0 46 154.5 47 162.5 48 150.5 49 151.0 50 153.5 51 132.5 52 120.5 53 113.5 54 100.0 55 84.0 56 80.0 57 90.0 58 94.5 59 81.5 60 69.0 61 75.5 62 83.5 63 82.0 64 83.5 65 90.5 66 88.0 67 81.0 68 80.0 69 85.0 70 81.0 71 68.0 72 70.5 73 70.5 74 56.5 75 47.5 76 42.0 77 39.0 78 31.0 79 22.0 80 21.5 81 19.5 82 12.5 83 7.5 84 5.5 85 3.5 86 3.0 87 3.0 88 1.0 89 0.0 90 0.5 91 1.0 92 1.0 93 0.5 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 5.0 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 0.01 15-19 0.0 20-24 0.005 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 0.0 >>END_MODULE >>Sequence Length Distribution pass #Length Count 150 4000.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 99.6 #Duplication Level Percentage of deduplicated Percentage of total 1 99.62349397590361 99.225 2 0.3514056224899598 0.7000000000000001 3 0.0251004016064257 0.075 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 0.0 0.0 0.0 0.0 0.0 82-83 0.0 0.0 0.0 0.0 0.0 84-85 0.0 0.0 0.0 0.0 0.0 86-87 0.0 0.0 0.0 0.0 0.0 88-89 0.0 0.0 0.0 0.0 0.0 90-91 0.0 0.0 0.0 0.0 0.0 92-93 0.0 0.0 0.0 0.0 0.0 94-95 0.0 0.0 0.0 0.0 0.0 96-97 0.0 0.0 0.0 0.0 0.0 98-99 0.0 0.0 0.0 0.0 0.0 100-101 0.0 0.0 0.0 0.0 0.0 102-103 0.0 0.0 0.0 0.0 0.0 104-105 0.0 0.0 0.0 0.0 0.0 106-107 0.0 0.0 0.0 0.0 0.0 108-109 0.0125 0.0 0.0 0.0 0.0 110-111 0.05 0.0 0.0 0.0 0.0 112-113 0.0625 0.0 0.0 0.0 0.0 114-115 0.0875 0.0 0.0 0.0 0.0 116-117 0.15 0.0 0.0 0.0 0.0 118-119 0.25 0.0 0.0 0.0 0.0 120-121 0.32499999999999996 0.0 0.0 0.0 0.0 122-123 0.375 0.0 0.0 0.0 0.0 124-125 0.4 0.0 0.0 0.0 0.0 126-127 0.4 0.0 0.0 0.0 0.0 128-129 0.5249999999999999 0.0 0.0 0.0 0.0 130-131 0.6625 0.0 0.0 0.0 0.0 132-133 0.9375 0.0 0.0 0.0 0.0 134-135 1.3 0.0 0.0 0.0 0.0 136-137 1.6875 0.0 0.0 0.0 0.0 138 1.95 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position GCCTCCA 10 0.0064622764 147.66667 1 >>END_MODULE SRR1797573 read2 length is 150 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR1797573_2.fastq File type Conventional base calls Encoding Sanger / Illumina 1.9 Total Sequences 4000 Sequences flagged as poor quality 0 Sequence length 150 %GC 56 >>END_MODULE >>Per base sequence quality fail #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 33.06525 34.0 33.0 34.0 31.0 34.0 2 33.21825 34.0 33.0 34.0 31.0 34.0 3 33.216 34.0 34.0 34.0 31.0 34.0 4 36.5505 37.0 37.0 37.0 35.0 37.0 5 36.6485 37.0 37.0 37.0 37.0 37.0 6 36.58175 37.0 37.0 37.0 35.0 37.0 7 36.5145 37.0 37.0 37.0 35.0 37.0 8 36.55875 37.0 37.0 37.0 35.0 37.0 9 38.5375 39.0 39.0 39.0 38.0 39.0 10-14 38.807 39.4 39.2 39.4 38.0 39.4 15-19 39.811 41.0 40.0 41.0 38.2 41.0 20-24 39.71275 41.0 40.0 41.0 37.8 41.0 25-29 39.33565 41.0 39.8 41.0 36.2 41.0 30-34 38.814350000000005 40.6 38.6 41.0 35.0 41.0 35-39 38.70055 41.0 38.0 41.0 35.0 41.0 40-44 38.033449999999995 40.0 36.0 41.0 34.4 41.0 45-49 37.3857 39.4 35.0 41.0 33.2 41.0 50-54 36.34495 37.6 34.8 40.2 32.0 40.8 55-59 36.01715 36.6 35.0 40.2 32.0 41.0 60-64 35.7075 35.2 35.0 39.6 32.8 41.0 65-69 34.9919 35.0 35.0 38.2 32.0 40.6 70-74 34.32005 35.0 35.0 36.4 31.2 39.0 75-79 33.53915 35.0 34.4 35.4 30.2 37.0 80-84 32.92020000000001 35.0 33.8 35.0 29.2 36.0 85-89 32.58155 35.0 33.8 35.0 29.0 35.2 90-94 32.17999999999999 35.0 33.2 35.0 27.4 35.0 95-99 31.85175 35.0 33.0 35.0 26.0 35.0 100-104 31.46595 35.0 33.0 35.0 24.2 35.0 105-109 31.018150000000002 35.0 32.2 35.0 22.0 35.0 110-114 30.2069 34.2 31.0 35.0 18.2 35.0 115-119 29.645500000000006 34.0 30.0 35.0 13.0 35.0 120-124 29.00865 34.0 29.0 35.0 5.2 35.0 125-129 28.4407 33.6 27.8 35.0 2.0 35.0 130-134 27.90855 33.8 27.4 35.0 2.0 35.0 135-139 26.597299999999997 33.0 24.0 35.0 2.0 35.0 140-144 25.477349999999998 32.0 21.0 34.6 2.0 35.0 145-149 23.472800000000003 31.2 4.6 34.0 2.0 35.0 150 17.31475 20.0 2.0 30.0 2.0 33.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 2 6.0 3 3.0 4 3.0 5 5.0 6 6.0 7 3.0 8 6.0 9 3.0 10 6.0 11 7.0 12 12.0 13 6.0 14 12.0 15 11.0 16 19.0 17 14.0 18 14.0 19 23.0 20 22.0 21 30.0 22 29.0 23 39.0 24 34.0 25 35.0 26 51.0 27 60.0 28 66.0 29 94.0 30 123.0 31 139.0 32 185.0 33 268.0 34 429.0 35 710.0 36 992.0 37 531.0 38 4.0 >>END_MODULE >>Per base sequence content warn #Base G A T C 1 30.0 18.0 10.725 41.275 2 35.033758439609905 22.9057264316079 18.529632408102024 23.53088272068017 3 25.1 26.025 20.625 28.249999999999996 4 29.15 24.425 19.75 26.674999999999997 5 31.85 26.424999999999997 19.0 22.725 6 26.35 31.45 17.175 25.025 7 25.4 17.775 29.5 27.325 8 27.575 21.275 20.625 30.525000000000002 9 25.775 20.925 23.375 29.925 10-14 28.96 24.19 20.200000000000003 26.650000000000002 15-19 28.025 23.025000000000002 20.95 28.000000000000004 20-24 28.17 23.515 20.294999999999998 28.02 25-29 28.694999999999997 22.725 21.18 27.400000000000002 30-34 28.925 22.939999999999998 20.945 27.189999999999998 35-39 28.71 22.634999999999998 21.12 27.534999999999997 40-44 29.049999999999997 22.09 21.445 27.415 45-49 28.42 23.145 21.584999999999997 26.85 50-54 29.01 22.855 21.395 26.740000000000002 55-59 29.205 22.314999999999998 21.025 27.455000000000002 60-64 29.065 22.54 21.775 26.619999999999997 65-69 28.735 22.275 22.155 26.834999999999997 70-74 29.134999999999998 21.990000000000002 21.959999999999997 26.915 75-79 29.095 22.035 21.685 27.185 80-84 29.275000000000002 22.34 21.665 26.72 85-89 29.29 22.040000000000003 21.545 27.125 90-94 28.28 22.495 22.1 27.125 95-99 29.5 22.195 21.955 26.35 100-104 29.28 22.54 21.39 26.790000000000003 105-109 28.575 22.075 22.650000000000002 26.700000000000003 110-114 29.42 22.545 21.525 26.51 115-119 29.99 22.15 21.455 26.405 120-124 28.694999999999997 22.585 21.83 26.889999999999997 125-129 29.494999999999997 22.75 21.54 26.215 130-134 29.64 22.7 21.035 26.625 135-139 29.455 22.605 21.59 26.35 140-144 29.759999999999998 22.759999999999998 21.04 26.44 145-149 30.195 22.61 21.095 26.1 150 31.8 21.9 17.549999999999997 28.749999999999996 >>END_MODULE >>Per sequence GC content fail #GC Content Count 0 1.0 1 1.0 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 0.0 16 0.0 17 0.0 18 0.0 19 0.5 20 0.5 21 0.0 22 0.0 23 0.0 24 0.0 25 0.5 26 1.0 27 1.0 28 0.5 29 1.0 30 4.0 31 4.0 32 1.5 33 5.5 34 13.0 35 16.5 36 21.5 37 31.0 38 39.5 39 50.5 40 64.5 41 75.5 42 88.5 43 109.5 44 125.0 45 128.5 46 131.0 47 135.0 48 141.5 49 133.0 50 126.5 51 122.5 52 110.0 53 106.5 54 105.0 55 98.5 56 102.5 57 104.5 58 102.5 59 102.0 60 99.5 61 93.5 62 85.0 63 95.5 64 93.5 65 90.0 66 97.5 67 93.0 68 87.0 69 89.0 70 87.0 71 88.5 72 85.5 73 66.0 74 58.5 75 55.5 76 45.5 77 40.0 78 37.5 79 26.0 80 20.0 81 15.5 82 9.0 83 10.0 84 6.5 85 4.5 86 3.5 87 2.5 88 4.0 89 2.5 90 0.5 91 0.5 92 0.0 93 0.0 94 0.0 95 0.0 96 0.0 97 0.0 98 0.5 99 0.5 100 0.0 >>END_MODULE >>Per base N content pass #Base N-Count 1 0.0 2 0.025 3 0.0 4 0.0 5 0.0 6 0.0 7 0.0 8 0.0 9 0.0 10-14 0.0 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 0.0 >>END_MODULE >>Sequence Length Distribution pass #Length Count 150 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 0.0 0.0 0.0 0.0 0.0 82-83 0.0 0.0 0.0 0.0 0.0 84-85 0.0 0.0 0.0 0.0 0.0 86-87 0.0 0.0 0.0 0.0 0.0 88-89 0.0 0.0 0.0 0.0 0.0 90-91 0.0 0.0 0.0 0.0 0.0 92-93 0.0 0.0 0.0 0.0 0.0 94-95 0.0 0.0 0.0 0.0 0.0 96-97 0.0 0.0 0.0 0.0 0.0 98-99 0.0 0.0 0.0 0.0 0.0 100-101 0.0 0.0 0.0 0.0 0.0 102-103 0.0 0.0 0.0 0.0 0.0 104-105 0.0 0.0 0.0 0.0 0.0 106-107 0.0 0.0 0.0 0.0 0.0 108-109 0.0125 0.0 0.0 0.0 0.0 110-111 0.05 0.0 0.0 0.0 0.0 112-113 0.0625 0.0 0.0 0.0 0.0 114-115 0.0875 0.0 0.0 0.0 0.0 116-117 0.15 0.0 0.0 0.0 0.0 118-119 0.25 0.0 0.0 0.0 0.0 120-121 0.32499999999999996 0.0 0.0 0.0 0.0 122-123 0.375 0.0 0.0 0.0 0.0 124-125 0.4 0.0 0.0 0.0 0.0 126-127 0.4 0.0 0.0 0.0 0.0 128-129 0.5375 0.0 0.0 0.0 0.0 130-131 0.7375 0.0 0.0 0.0 0.0 132-133 0.9875 0.0 0.0 0.0 0.0 134-135 1.3625 0.0 0.0 0.0 0.0 136-137 1.7125 0.0 0.0 0.0 0.0 138 1.975 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position AAAAAAA 50 5.915723E-5 20.16 60-64 >>END_MODULE Read 1317816 spots for SRR1797573.sra Written 1317816 spots for SRR1797573.sra Read 1317816 spots for SRR1797573.sra Written 1317816 spots for SRR1797573.sra Read 1317816 spots for SRR1797573.sra Written 1317816 spots for SRR1797573.sra Read 1317816 spots for SRR1797573.sra Written 1317816 spots for SRR1797573.sra Read 1317816 spots for SRR1797573.sra Written 1317816 spots for SRR1797573.sra Read 1317816 spots for SRR1797573.sra Written 1317816 spots for SRR1797573.sra Read 1317816 spots for SRR1797573.sra Written 1317816 spots for SRR1797573.sra Read 1317816 spots for SRR1797573.sra Written 1317816 spots for SRR1797573.sra Read 1317816 spots for SRR1797573.sra Written 1317816 spots for SRR1797573.sra Read 1317816 spots for SRR1797573.sra Written 1317816 spots for SRR1797573.sra Read 1317816 spots for SRR1797573.sra Written 1317816 spots for SRR1797573.sra Read 1317816 spots for SRR1797573.sra Written 1317816 spots for SRR1797573.sra Read 1317816 spots for SRR1797573.sra Written 1317816 spots for SRR1797573.sra Read 1317816 spots for SRR1797573.sra Written 1317816 spots for SRR1797573.sra Read 1317816 spots for SRR1797573.sra Written 1317816 spots for SRR1797573.sra Read 1317835 spots for SRR1797573.sra Written 1317835 spots for SRR1797573.sra Read 1317816 spots for SRR1797573.sra Written 1317816 spots for SRR1797573.sra Read 1317816 spots for SRR1797573.sra Written 1317816 spots for SRR1797573.sra Read 1317816 spots for SRR1797573.sra Written 1317816 spots for SRR1797573.sra Read 1317816 spots for SRR1797573.sra Written 1317816 spots for SRR1797573.sra SRR ids: ['SRR1797573.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_arqr1jch SRR1797573.sra spots: 26356339 blocks: [[1, 1317816], [1317817, 2635632], [2635633, 3953448], [3953449, 5271264], [5271265, 6589080], [6589081, 7906896], [7906897, 9224712], [9224713, 10542528], [10542529, 11860344], [11860345, 13178160], [13178161, 14495976], [14495977, 15813792], [15813793, 17131608], [17131609, 18449424], [18449425, 19767240], [19767241, 21085056], [21085057, 22402872], [22402873, 23720688], [23720689, 25038504], [25038505, 26356339]] SRR1797573 file size 8858120 SRR1797573 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 SRR1797573 SRR1797573_1.fastq SRR1797573_2.fastq Input file: SRR1797573_1.fastq Paired file: SRR1797573_2.fastq trimmed: SRR1797573-trimmed-pair1.fastq, SRR1797573-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 Mon Dec 9 12:51:14 2024 >> started Mon Dec 9 12:52:19 2024 >> done (65.192s) 26356339 read pairs processed; of these: 57158 ( 0.22%) short read pairs filtered out after trimming by size control 40334 ( 0.15%) empty read pairs filtered out after trimming by size control 26258847 (99.63%) read pairs available; of these: 19143824 (72.90%) trimmed read pairs available after processing 7115023 (27.10%) untrimmed read pairs available after processing Length distribution of reads after trimming: length count percentage 18 11 0.00% 19 46 0.00% 20 64 0.00% 21 115 0.00% 22 153 0.00% 23 226 0.00% 24 289 0.00% 25 380 0.00% 26 448 0.00% 27 610 0.00% 28 709 0.00% 29 788 0.00% 30 896 0.00% 31 1065 0.00% 32 1206 0.00% 33 1376 0.01% 34 1455 0.01% 35 1677 0.01% 36 1792 0.01% 37 1891 0.01% 38 2057 0.01% 39 2243 0.01% 40 2395 0.01% 41 2554 0.01% 42 2770 0.01% 43 2851 0.01% 44 2929 0.01% 45 3235 0.01% 46 3331 0.01% 47 3578 0.01% 48 3753 0.01% 49 3942 0.02% 50 4104 0.02% 51 4449 0.02% 52 4484 0.02% 53 4735 0.02% 54 5118 0.02% 55 5225 0.02% 56 5586 0.02% 57 5943 0.02% 58 6151 0.02% 59 6349 0.02% 60 6838 0.03% 61 7062 0.03% 62 7480 0.03% 63 7878 0.03% 64 8310 0.03% 65 8856 0.03% 66 9257 0.04% 67 9501 0.04% 68 10312 0.04% 69 10631 0.04% 70 11077 0.04% 71 11852 0.05% 72 12258 0.05% 73 13023 0.05% 74 13786 0.05% 75 14551 0.06% 76 15672 0.06% 77 16738 0.06% 78 17526 0.07% 79 18531 0.07% 80 19676 0.07% 81 20978 0.08% 82 22394 0.09% 83 24735 0.09% 84 29644 0.11% 85 31309 0.12% 86 32364 0.12% 87 34670 0.13% 88 35983 0.14% 89 38026 0.14% 90 39305 0.15% 91 41423 0.16% 92 43130 0.16% 93 44358 0.17% 94 46078 0.18% 95 48511 0.18% 96 50531 0.19% 97 51409 0.20% 98 54143 0.21% 99 56486 0.22% 100 57450 0.22% 101 60055 0.23% 102 62155 0.24% 103 64967 0.25% 104 67984 0.26% 105 72173 0.27% 106 75691 0.29% 107 81089 0.31% 108 86324 0.33% 109 90014 0.34% 110 95270 0.36% 111 100330 0.38% 112 105122 0.40% 113 109096 0.42% 114 116776 0.44% 115 124498 0.47% 116 132287 0.50% 117 138047 0.53% 118 144747 0.55% 119 151655 0.58% 120 159683 0.61% 121 171061 0.65% 122 180993 0.69% 123 188664 0.72% 124 196241 0.75% 125 206188 0.79% 126 222683 0.85% 127 231517 0.88% 128 244590 0.93% 129 258515 0.98% 130 277556 1.06% 131 292435 1.11% 132 310731 1.18% 133 332341 1.27% 134 339676 1.29% 135 356570 1.36% 136 374077 1.42% 137 395485 1.51% 138 415942 1.58% 139 444634 1.69% 140 474775 1.81% 141 509394 1.94% 142 549382 2.09% 143 592927 2.26% 144 657230 2.50% 145 752007 2.86% 146 892320 3.40% 147 1125244 4.29% 148 1564050 5.96% 149 3391912 12.92% 150 7115023 27.10% 26258847 reads passed initial QC criterion=sequence-density sequence-density=0.32 sequence-density-rank=1 fanout-score=3.43 fanout-score-rank=32 prefix-density=0.34 prefix-fanout=3.2 sequence=TGCCGCACTTGCAGGATGACCCGCAGTTGCAGTTTCCTCCGCAGCAAGACATCTTCGGTCGAGTGCTCGAACTTGCTTAGGAAGAAGATTAAGCTGAAGGCTTCTAGGCTTGTGTGTGC criterion=fanout-score sequence-density=0.05 sequence-density-rank=32 fanout-score=471.76 fanout-score-rank=1 prefix-density=1.06 prefix-fanout=20.4 sequence=GGCGGCGGCGAACCGCCCCCGTCGCCGCGATCCGAACACTTCACCGGACCATTCAATCGGTAGGAGCGACGGGCGGTGTGTACAAAGGGCAGGGACGTAGTCAACGCGAGCTGATGACTCGCGCTTACTAGGCATTCCTCGTTGAAGACCAACAATTGCAATGATCTATCCCCATCACGATGAAATTTCCCAAGATTACCCGGGCCTGTCGGCCAAGGCTATATACTCGTTGAATACATCAGTGTAGCGCGCGTGCGGCCCAGAACATCTAAGGGCATCACAGACCTGTTATTGCCTCAAACTTCCGTCGCCTAAACGGCGATAGTCCCTCTAAGAAGCTAGCTGCGGAGGGATGGCTCCGCATAGCTAGTTAGCAGGCTGAGGTCTCGTTCGTTAACGGAATTAACCAGACAAATCGCTCCACCAACTAAGAACGGCCATGCACCACCACCCATAGAATCAAGAAAGAGCTCTCAGTCTGTCAATCCTTGCTATGTCTGGACCTGGTAAG criterion=sequence-density sequence-density=0.28 sequence-density-rank=1 fanout-score=4.96 fanout-score-rank=24 prefix-density=0.65 prefix-fanout=2.1 sequence=CAAGTGCGGCAGCGGCTGCAACGGCTGCAACATGTACCCTGAAGCCGAGGTCCAGACCTCCAGCCTCCTCGTCGTCGCCACCGCCGCCCACAAGGCGAGCTCCGGCGGGATGGAGATGGCCGCGGAGAACGGCGGCTGCGGCTGCAGCACCTGCAAGTGC criterion=fanout-score sequence-density=0.12 sequence-density-rank=22 fanout-score=288.70 fanout-score-rank=1 prefix-density=1.55 prefix-fanout=22.6 sequence=CGGCGGCGGCAG SRR1797573 testing PE reads STAR mapping to Ensembl genome Started job on | Dec 09 12:55:09 Started mapping on | Dec 09 12:55:15 Finished on | Dec 09 12:58:01 Mapping speed, Million of reads per hour | 569.47 Number of input reads | 26258847 Average input read length | 278 UNIQUE READS: Uniquely mapped reads number | 25041254 Uniquely mapped reads % | 95.36% Average mapped length | 277.43 Number of splices: Total | 18768322 Number of splices: Annotated (sjdb) | 17757040 Number of splices: GT/AG | 18511735 Number of splices: GC/AG | 214672 Number of splices: AT/AC | 11104 Number of splices: Non-canonical | 30811 Mismatch rate per base, % | 0.28% Deletion rate per base | 0.02% Deletion average length | 2.45 Insertion rate per base | 0.01% Insertion average length | 2.28 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 354623 % of reads mapped to multiple loci | 1.35% Number of reads mapped to too many loci | 79808 % of reads mapped to too many loci | 0.30% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 0.85% % of reads unmapped: other | 2.13% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 890434 890434 890434 N_multimapping 354623 354623 354623 N_noFeature 527783 24181135 1011755 N_ambiguous 435701 3203 62593 UnstrandedReadsAssigned:24077770 PositiveStrandReadsAssigned:856916 NegativeStrandReadsAssigned:23966906 Dataset is classified negative stranded MeadianReadLen=150 20thPercentileLength=142 echo kmer=137 SRR1797573 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: SRR1797573-trimmed-pair1.fastq SRR1797573-trimmed-pair2.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 26,258,847 reads, 24,148,987 reads pseudoaligned [quant] estimated average fragment length: 209.882 [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,155 rounds 52973 SRR1797573.ke.tsv 35125 SRR1797573.se.tsv 88098 total ==> SRR1797573.ke.tsv <== target_id length eff_length est_counts tpm PNS24245 936 727.382 0 0 PNS24247 1044 835.118 56.0307 3.85066 PNS24249 1928 1719.12 561.378 18.7416 PNS24246 1044 835.118 56.0307 3.85066 PNS24248 1044 835.118 56.0307 3.85066 PNS24244 1471 1262.12 52.5303 2.38873 PNS24243 293 93.4092 1 0.614423 KQK14069 1603 1394.12 6745.12 277.682 KQK14071 474 266.648 272.352 58.6204 ==> SRR1797573.se.tsv <== BRADI_1g14170v3 7128 BRADI_1g53295v3 238 BRADI_1g59795v3 247 BRADI_1g07683v3 0 BRADI_1g00485v3 4 BRADI_1g20270v3 612 BRADI_1g74790v3 726 BRADI_1g09890v3 0 BRADI_1g77505v3 150 BRADI_1g48960v3 0 SRR1797573 completed mapping pipeline successfully