Starting /dee2/code/volunteer_pipeline.sh SRR7171858 current disk space = 3088330661888 free memory = 1489001060 SRR7171858 SRAfilesize 446bcbb6fcdb96da123eadfe7eecae6f SRR7171858.sra SRR7171858.sra file validated SRR7171858 is paired end SRR7171858 is conventional basespace SRR7171858 read1 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR7171858_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 44 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 28.96425 32.0 25.0 33.0 18.0 33.0 2 30.174 31.0 29.0 33.0 25.0 33.0 3 31.06825 32.0 32.0 33.0 27.0 34.0 4 31.57925 33.0 32.0 33.0 28.0 33.0 5 32.009 33.0 32.0 33.0 31.0 33.0 6 36.362 37.0 36.0 38.0 34.0 38.0 7 37.18775 38.0 38.0 38.0 36.0 38.0 8 37.51125 38.0 38.0 38.0 37.0 38.0 9 37.6375 38.0 38.0 38.0 38.0 38.0 10-14 37.6106 38.0 38.0 38.0 38.0 38.0 15-19 37.593 38.0 38.0 38.0 38.0 38.0 20-24 37.5559 38.0 38.0 38.0 38.0 38.0 25-29 37.56175 38.0 38.0 38.0 38.0 38.0 30-34 37.516799999999996 38.0 38.0 38.0 38.0 38.0 35-39 37.51915 38.0 38.0 38.0 37.8 38.0 40-44 37.44875 38.0 38.0 38.0 37.0 38.0 45-49 37.451899999999995 38.0 38.0 38.0 37.0 38.0 50-54 37.425250000000005 38.0 38.0 38.0 37.0 38.0 55-59 37.36795 38.0 38.0 38.0 37.0 38.0 60-64 37.3379 38.0 38.0 38.0 37.0 38.0 65-69 37.22435 38.0 38.0 38.0 36.4 38.0 70-74 37.1678 38.0 38.0 38.0 36.0 38.0 75-79 37.11985 38.0 38.0 38.0 36.0 38.0 80-84 37.029849999999996 38.0 38.0 38.0 36.0 38.0 85-89 37.074349999999995 38.0 38.0 38.0 36.0 38.0 90-94 36.95955 38.0 38.0 38.0 36.0 38.0 95-99 36.867000000000004 38.0 38.0 38.0 35.2 38.0 100-104 36.80645 38.0 38.0 38.0 35.0 38.0 105-109 36.67035 38.0 38.0 38.0 34.8 38.0 110-114 36.56034999999999 38.0 38.0 38.0 34.2 38.0 115-119 36.4101 38.0 38.0 38.0 34.0 38.0 120-124 36.323899999999995 38.0 38.0 38.0 34.0 38.0 125-129 36.1191 38.0 37.2 38.0 33.2 38.0 130-134 35.8183 38.0 36.6 38.0 32.6 38.0 135-139 35.652550000000005 38.0 36.0 38.0 31.4 38.0 140-144 35.423249999999996 38.0 36.0 38.0 31.4 38.0 145-149 34.83045 38.0 35.4 38.0 28.4 38.0 150-151 31.99375 36.5 31.5 38.0 15.0 38.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 3 1.0 4 0.0 5 0.0 6 0.0 7 1.0 8 0.0 9 0.0 10 0.0 11 0.0 12 0.0 13 1.0 14 1.0 15 0.0 16 1.0 17 2.0 18 0.0 19 2.0 20 0.0 21 4.0 22 4.0 23 9.0 24 3.0 25 8.0 26 12.0 27 11.0 28 21.0 29 22.0 30 24.0 31 37.0 32 52.0 33 66.0 34 135.0 35 232.0 36 646.0 37 2705.0 >>END_MODULE >>Per base sequence content warn #Base G A T C 1 42.75 12.6 10.65 34.0 2 21.09081811358519 17.112834625969477 36.70252689517138 25.093820365273956 3 19.975 22.2 25.55 32.275 4 23.925 30.675 22.25 23.150000000000002 5 20.875 34.425 23.45 21.25 6 19.0 35.199999999999996 26.1 19.7 7 14.649999999999999 26.35 40.150000000000006 18.85 8 17.599999999999998 26.150000000000002 30.349999999999998 25.900000000000002 9 18.975 26.1 30.95 23.974999999999998 10-14 19.825 30.485 27.185 22.505 15-19 20.215 28.825 27.865000000000002 23.095 20-24 19.99 28.98 28.01 23.02 25-29 20.035 30.165 27.534999999999997 22.264999999999997 30-34 20.13 29.470000000000002 27.295 23.105 35-39 20.625 28.48 27.38 23.515 40-44 20.45 29.185 27.950000000000003 22.415 45-49 20.415 28.64 27.169999999999998 23.775 50-54 20.215 28.52 27.46 23.805 55-59 20.075000000000003 28.875 27.644999999999996 23.405 60-64 20.78 28.1 27.650000000000002 23.47 65-69 19.865 28.605000000000004 28.04 23.49 70-74 20.43 28.48 27.665 23.425 75-79 20.385 28.625 27.575 23.415 80-84 20.715 28.155 27.6 23.53 85-89 20.29 28.910000000000004 27.625 23.175 90-94 20.36 28.375 27.605 23.66 95-99 20.8 27.915 27.21 24.075 100-104 20.51 28.804999999999996 27.560000000000002 23.125 105-109 21.23 28.835 26.83 23.105 110-114 21.385 28.705000000000002 27.49 22.42 115-119 20.415 28.82 27.395000000000003 23.369999999999997 120-124 20.549999999999997 28.494999999999997 27.48 23.474999999999998 125-129 20.815 27.875 27.395000000000003 23.915 130-134 21.21 28.52 27.229999999999997 23.04 135-139 20.835 28.105000000000004 27.279999999999998 23.78 140-144 21.705 27.279999999999998 27.639999999999997 23.375 145-149 21.455 28.105000000000004 27.27 23.169999999999998 150-151 21.6625 27.8375 27.025 23.474999999999998 >>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 0.5 15 1.0 16 0.5 17 0.0 18 0.0 19 0.5 20 0.5 21 1.0 22 1.5 23 3.0 24 4.0 25 2.5 26 2.5 27 8.0 28 13.0 29 18.0 30 24.0 31 33.0 32 48.0 33 58.5 34 66.0 35 70.5 36 83.0 37 104.0 38 138.5 39 178.0 40 195.0 41 198.5 42 227.0 43 271.0 44 270.5 45 246.0 46 250.0 47 236.0 48 216.0 49 192.0 50 161.5 51 149.0 52 128.5 53 97.0 54 67.0 55 59.5 56 47.0 57 32.0 58 24.5 59 14.0 60 10.0 61 12.5 62 9.0 63 6.0 64 5.5 65 3.5 66 3.0 67 2.5 68 1.5 69 0.5 70 0.5 71 1.0 72 1.0 73 0.5 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 0.0 2 0.075 3 0.0 4 0.0 5 0.0 6 0.0 7 0.0 8 0.0 9 0.0 10-14 0.0 15-19 0.0 20-24 0.0 25-29 0.0 30-34 0.0 35-39 0.0 40-44 0.0 45-49 0.0 50-54 0.0 55-59 0.0 60-64 0.0 65-69 0.0 70-74 0.0 75-79 0.0 80-84 0.0 85-89 0.0 90-94 0.0 95-99 0.0 100-104 0.0 105-109 0.0 110-114 0.0 115-119 0.0 120-124 0.0 125-129 0.0 130-134 0.0 135-139 0.0 140-144 0.0 145-149 0.0 150-151 0.0 >>END_MODULE >>Sequence Length Distribution pass #Length Count 151 4000.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 99.65 #Duplication Level Percentage of deduplicated Percentage of total 1 99.67385850476668 99.325 2 0.3010536879076769 0.6 3 0.025087807325639738 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 0.0125 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 0.025 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 0.037500000000000006 0.0 0.0 0.0 0.0 88-89 0.075 0.0 0.0 0.0 0.0 90-91 0.075 0.0 0.0 0.0 0.0 92-93 0.075 0.0 0.0 0.0 0.0 94-95 0.1 0.0 0.0 0.0 0.0 96-97 0.15 0.0 0.0 0.0 0.0 98-99 0.2 0.0 0.0 0.0 0.0 100-101 0.2375 0.0 0.0 0.0 0.0 102-103 0.3 0.0 0.0 0.0 0.0 104-105 0.48750000000000004 0.0 0.0 0.0 0.0 106-107 0.6375 0.0 0.0 0.0 0.0 108-109 0.7375 0.0 0.0 0.0 0.0 110-111 0.8375 0.0 0.0 0.0 0.0 112-113 0.9125000000000001 0.0 0.0 0.0 0.0 114-115 0.975 0.0 0.0 0.0 0.0 116-117 1.0625 0.0 0.0 0.0 0.0 118-119 1.15 0.0 0.0 0.0 0.0 120-121 1.3875 0.0 0.0 0.0 0.0 122-123 1.5499999999999998 0.0 0.0 0.0 0.0 124-125 1.7875 0.0 0.0 0.0 0.0 126-127 1.975 0.0 0.0 0.0 0.0 128-129 2.1625 0.0 0.0 0.0 0.0 130-131 2.4 0.0 0.0 0.0 0.0 132-133 2.6125 0.0 0.0 0.0 0.0 134-135 2.7750000000000004 0.0 0.0 0.0 0.0 136-137 3.0375 0.0 0.0 0.0 0.0 138-139 3.4375 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content pass >>END_MODULE SRR7171858 read2 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR7171858_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 33.08775 33.0 33.0 34.0 33.0 34.0 2 33.14675 34.0 33.0 34.0 33.0 34.0 3 33.2095 34.0 33.0 34.0 33.0 34.0 4 33.1245 34.0 33.0 34.0 33.0 34.0 5 33.061 34.0 33.0 34.0 33.0 34.0 6 37.23 38.0 38.0 38.0 37.0 38.0 7 37.282 38.0 38.0 38.0 37.0 38.0 8 37.2595 38.0 38.0 38.0 37.0 38.0 9 37.261 38.0 38.0 38.0 37.0 38.0 10-14 37.165150000000004 38.0 38.0 38.0 37.0 38.0 15-19 37.1297 38.0 38.0 38.0 37.0 38.0 20-24 37.12425 38.0 38.0 38.0 37.0 38.0 25-29 37.110350000000004 38.0 38.0 38.0 37.0 38.0 30-34 37.05284999999999 38.0 38.0 38.0 37.0 38.0 35-39 36.93745 38.0 38.0 38.0 36.6 38.0 40-44 36.8429 38.0 38.0 38.0 36.4 38.0 45-49 36.96335 38.0 38.0 38.0 36.6 38.0 50-54 36.870450000000005 38.0 38.0 38.0 36.0 38.0 55-59 36.8896 38.0 38.0 38.0 36.0 38.0 60-64 36.827 38.0 38.0 38.0 36.0 38.0 65-69 36.7928 38.0 38.0 38.0 36.0 38.0 70-74 36.705349999999996 38.0 38.0 38.0 35.8 38.0 75-79 36.699349999999995 38.0 38.0 38.0 35.6 38.0 80-84 36.61545 38.0 38.0 38.0 34.8 38.0 85-89 36.51945 38.0 38.0 38.0 35.0 38.0 90-94 36.375449999999994 38.0 38.0 38.0 34.2 38.0 95-99 36.3575 38.0 38.0 38.0 34.0 38.0 100-104 36.1657 38.0 38.0 38.0 33.8 38.0 105-109 36.07615 38.0 38.0 38.0 33.8 38.0 110-114 35.96575 38.0 37.8 38.0 33.2 38.0 115-119 35.8355 38.0 37.0 38.0 33.0 38.0 120-124 35.6074 38.0 37.0 38.0 31.8 38.0 125-129 35.362300000000005 38.0 36.2 38.0 31.0 38.0 130-134 35.08669999999999 38.0 36.0 38.0 29.2 38.0 135-139 34.7723 38.0 35.6 38.0 28.0 38.0 140-144 34.52475 38.0 35.2 38.0 27.2 38.0 145-149 33.896 38.0 34.6 38.0 23.8 38.0 150-151 30.43 36.5 29.0 38.0 8.0 38.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 2 7.0 3 5.0 4 1.0 5 4.0 6 0.0 7 3.0 8 1.0 9 1.0 10 0.0 11 1.0 12 3.0 13 7.0 14 1.0 15 4.0 16 7.0 17 4.0 18 3.0 19 4.0 20 3.0 21 9.0 22 9.0 23 6.0 24 9.0 25 18.0 26 21.0 27 18.0 28 25.0 29 16.0 30 37.0 31 47.0 32 59.0 33 77.0 34 143.0 35 251.0 36 603.0 37 2593.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 39.4 18.05 16.125 26.424999999999997 2 23.474999999999998 25.0 33.85 17.675 3 21.349999999999998 28.599999999999998 28.549999999999997 21.5 4 25.75 33.75 21.85 18.65 5 24.325 36.5 22.025 17.150000000000002 6 19.1 37.325 24.625 18.95 7 19.375 18.525 41.025 21.075 8 21.0 24.05 27.55 27.400000000000002 9 21.775 25.174999999999997 28.849999999999998 24.2 10-14 23.44 29.005 25.874999999999996 21.68 15-19 23.165 28.585 27.04 21.21 20-24 23.765 27.994999999999997 27.305 20.935000000000002 25-29 22.855 28.410000000000004 27.189999999999998 21.545 30-34 23.36836836836837 28.058058058058062 27.112112112112115 21.46146146146146 35-39 23.543859649122805 27.924812030075184 27.79949874686717 20.73182957393484 40-44 23.591726076915354 27.768852294407072 27.31699969876494 21.32242192991264 45-49 23.225 28.165000000000003 27.589999999999996 21.02 50-54 23.169999999999998 28.375 27.005000000000003 21.45 55-59 23.52 27.810000000000002 27.37 21.3 60-64 23.685000000000002 27.785 27.58 20.95 65-69 23.365 27.625 27.939999999999998 21.07 70-74 23.815 28.09 26.900000000000002 21.195 75-79 23.244999999999997 28.055000000000003 27.555000000000003 21.145 80-84 22.775000000000002 28.505000000000003 27.439999999999998 21.279999999999998 85-89 23.435 27.865000000000002 28.09 20.61 90-94 24.295 28.199999999999996 27.084999999999997 20.419999999999998 95-99 23.52 27.905 28.255000000000003 20.32 100-104 23.825 27.79 27.79 20.595 105-109 23.285 27.79 28.03 20.895 110-114 24.01 28.09 27.12 20.78 115-119 24.224999999999998 27.355 27.79 20.630000000000003 120-124 23.885 28.275 27.284999999999997 20.555 125-129 24.375 28.1 27.644999999999996 19.88 130-134 24.84 27.755000000000003 26.935 20.47 135-139 23.94 27.284999999999997 28.29 20.485 140-144 23.53 27.625 28.310000000000002 20.535 145-149 23.875 28.38 27.200000000000003 20.544999999999998 150-151 23.599999999999998 28.6375 27.962500000000002 19.8 >>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 0.0 16 0.0 17 0.5 18 1.5 19 1.0 20 0.5 21 0.5 22 0.5 23 1.5 24 1.5 25 1.5 26 2.0 27 4.5 28 6.0 29 7.0 30 9.5 31 12.0 32 16.0 33 20.0 34 36.0 35 51.0 36 69.0 37 98.5 38 118.0 39 148.5 40 189.0 41 228.5 42 257.0 43 269.0 44 292.0 45 301.5 46 285.0 47 265.5 48 252.5 49 231.5 50 185.0 51 146.5 52 118.5 53 88.5 54 71.5 55 53.0 56 40.0 57 32.5 58 21.5 59 15.5 60 14.0 61 12.0 62 6.0 63 4.5 64 3.5 65 2.0 66 1.5 67 0.5 68 0.5 69 1.5 70 1.0 71 0.5 72 0.5 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 0.0 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 0.1 35-39 0.25 40-44 0.41000000000000003 45-49 0.0 50-54 0.0 55-59 0.0 60-64 0.0 65-69 0.0 70-74 0.0 75-79 0.0 80-84 0.0 85-89 0.0 90-94 0.0 95-99 0.0 100-104 0.0 105-109 0.0 110-114 0.0 115-119 0.0 120-124 0.0 125-129 0.0 130-134 0.0 135-139 0.0 140-144 0.0 145-149 0.0 150-151 0.0 >>END_MODULE >>Sequence Length Distribution pass #Length Count 151 4000.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 99.7 #Duplication Level Percentage of deduplicated Percentage of total 1 99.82447342026079 99.52499999999999 2 0.15045135406218654 0.3 3 0.0 0.0 4 0.0 0.0 5 0.0 0.0 6 0.0 0.0 7 0.025075225677031094 0.17500000000000002 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 GCTGAAAGCCCTAACTTAATGGACGGGAGGTATCCCAATAGGAGGTTTCC 7 0.17500000000000002 No Hit >>END_MODULE >>Adapter Content pass #Position Illumina Universal Adapter Illumina Small RNA 3' Adapter Illumina Small RNA 5' Adapter Nextera Transposase Sequence SOLID Small RNA Adapter 1 0.0 0.0 0.0 0.0 0.0 2 0.0 0.0 0.0 0.0 0.0 3 0.0 0.0 0.0 0.0 0.0 4 0.0 0.0 0.0 0.0 0.0 5 0.0 0.0 0.0 0.0 0.0 6 0.0 0.0 0.0 0.0 0.0 7 0.0 0.0 0.0 0.0 0.0 8 0.0 0.0 0.0 0.0 0.0 9 0.0 0.0 0.0 0.0 0.0 10-11 0.0 0.0 0.0 0.0 0.0 12-13 0.0 0.0 0.0 0.0 0.0 14-15 0.0 0.0 0.0 0.0 0.0 16-17 0.0 0.0 0.0 0.0 0.0 18-19 0.0 0.0 0.0 0.0 0.0 20-21 0.0 0.0 0.0 0.0 0.0 22-23 0.0 0.0 0.0 0.0 0.0 24-25 0.0 0.0 0.0 0.0 0.0 26-27 0.0 0.0 0.0 0.0 0.0 28-29 0.0 0.0 0.0 0.0 0.0 30-31 0.0 0.0 0.0 0.0 0.0 32-33 0.0 0.0 0.0 0.0 0.0 34-35 0.0 0.0 0.0 0.0 0.0 36-37 0.0 0.0 0.0 0.0 0.0 38-39 0.0 0.0 0.0 0.0 0.0 40-41 0.0 0.0 0.0 0.0 0.0 42-43 0.0 0.0 0.0 0.0 0.0 44-45 0.0 0.0 0.0 0.0 0.0 46-47 0.0 0.0 0.0 0.0 0.0 48-49 0.0 0.0 0.0 0.0 0.0 50-51 0.0 0.0 0.0 0.0 0.0 52-53 0.0 0.0 0.0 0.0 0.0 54-55 0.0 0.0 0.0 0.0 0.0 56-57 0.0 0.0 0.0 0.0 0.0 58-59 0.0 0.0 0.0 0.0 0.0 60-61 0.0 0.0 0.0 0.0 0.0 62-63 0.0 0.0 0.0 0.0 0.0 64-65 0.0 0.0 0.0 0.0 0.0 66-67 0.0 0.0 0.0 0.0 0.0 68-69 0.0 0.0 0.0 0.0 0.0 70-71 0.0125 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 0.025 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 0.037500000000000006 0.0 0.0 0.0 0.0 88-89 0.075 0.0 0.0 0.0 0.0 90-91 0.075 0.0 0.0 0.0 0.0 92-93 0.075 0.0 0.0 0.0 0.0 94-95 0.1 0.0 0.0 0.0 0.0 96-97 0.15 0.0 0.0 0.0 0.0 98-99 0.2 0.0 0.0 0.0 0.0 100-101 0.225 0.0 0.0 0.0 0.0 102-103 0.275 0.0 0.0 0.0 0.0 104-105 0.4625 0.0 0.0 0.0 0.0 106-107 0.5875 0.0 0.0 0.0 0.0 108-109 0.6875 0.0 0.0 0.0 0.0 110-111 0.7875 0.0 0.0 0.0 0.0 112-113 0.8625 0.0 0.0 0.0 0.0 114-115 0.925 0.0 0.0 0.0 0.0 116-117 1.0125 0.0 0.0 0.0 0.0 118-119 1.1 0.0 0.0 0.0 0.0 120-121 1.3375 0.0 0.0 0.0 0.0 122-123 1.5 0.0 0.0 0.0 0.0 124-125 1.7625 0.0 0.0 0.0 0.0 126-127 1.95 0.0 0.0 0.0 0.0 128-129 2.1500000000000004 0.0 0.0 0.0 0.0 130-131 2.4 0.0 0.0 0.0 0.0 132-133 2.6125 0.0 0.0 0.0 0.0 134-135 2.7875 0.0 0.0 0.0 0.0 136-137 3.0625 0.0 0.0 0.0 0.0 138-139 3.4625 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position TGGTTTG 10 0.006830828 145.0 7 CCGGGAT 10 0.006830828 145.0 1 >>END_MODULE Read 682344 spots for SRR7171858.sra Written 682344 spots for SRR7171858.sra Read 682344 spots for SRR7171858.sra Written 682344 spots for SRR7171858.sra Read 682344 spots for SRR7171858.sra Written 682344 spots for SRR7171858.sra Read 682344 spots for SRR7171858.sra Written 682344 spots for SRR7171858.sra Read 682344 spots for SRR7171858.sra Written 682344 spots for SRR7171858.sra Read 682344 spots for SRR7171858.sra Written 682344 spots for SRR7171858.sra Read 682344 spots for SRR7171858.sra Written 682344 spots for SRR7171858.sra Read 682344 spots for SRR7171858.sra Written 682344 spots for SRR7171858.sra Read 682344 spots for SRR7171858.sra Written 682344 spots for SRR7171858.sra Read 682344 spots for SRR7171858.sra Written 682344 spots for SRR7171858.sra Read 682344 spots for SRR7171858.sra Written 682344 spots for SRR7171858.sra Read 682344 spots for SRR7171858.sra Written 682344 spots for SRR7171858.sra Read 682344 spots for SRR7171858.sra Written 682344 spots for SRR7171858.sra Read 682344 spots for SRR7171858.sra Written 682344 spots for SRR7171858.sra Read 682344 spots for SRR7171858.sra Written 682344 spots for SRR7171858.sra Read 682344 spots for SRR7171858.sra Written 682344 spots for SRR7171858.sra Read 682344 spots for SRR7171858.sra Written 682344 spots for SRR7171858.sra Read 682344 spots for SRR7171858.sra Written 682344 spots for SRR7171858.sra Read 682362 spots for SRR7171858.sra Written 682362 spots for SRR7171858.sra Read 682344 spots for SRR7171858.sra Written 682344 spots for SRR7171858.sra SRR ids: ['SRR7171858.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_0w8e37co SRR7171858.sra spots: 13646898 blocks: [[1, 682344], [682345, 1364688], [1364689, 2047032], [2047033, 2729376], [2729377, 3411720], [3411721, 4094064], [4094065, 4776408], [4776409, 5458752], [5458753, 6141096], [6141097, 6823440], [6823441, 7505784], [7505785, 8188128], [8188129, 8870472], [8870473, 9552816], [9552817, 10235160], [10235161, 10917504], [10917505, 11599848], [11599849, 12282192], [12282193, 12964536], [12964537, 13646898]] SRR7171858 file size 4602785 SRR7171858 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 SRR7171858 SRR7171858_1.fastq SRR7171858_2.fastq Input file: SRR7171858_1.fastq Paired file: SRR7171858_2.fastq trimmed: SRR7171858-trimmed-pair1.fastq, SRR7171858-trimmed-pair2.fastq Parameters used: -- 3' end adapter sequence (-x): AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC -- paired 3' end adapter sequence (-y): AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTA -- maximum error ratio allowed (-r): 0.100 -- maximum indel error ratio allowed (-d): 0.030 -- end quality threshold (-q): 10 -- minimum read length allowed after trimming (-l): 18 -- file format (-f): Sanger/Illumina 1.8+ FASTQ -- number of concurrent threads (-t): 20 Thu Feb 13 21:36:28 2025 >> started Thu Feb 13 21:36:44 2025 >> done (16.319s) 13646898 read pairs processed; of these: 20224 ( 0.15%) short read pairs filtered out after trimming by size control 16572 ( 0.12%) empty read pairs filtered out after trimming by size control 13610102 (99.73%) read pairs available; of these: 5670220 (41.66%) trimmed read pairs available after processing 7939882 (58.34%) untrimmed read pairs available after processing Length distribution of reads after trimming: length count percentage 18 2 0.00% 19 2 0.00% 20 6 0.00% 21 5 0.00% 22 6 0.00% 23 5 0.00% 24 8 0.00% 25 7 0.00% 26 8 0.00% 27 3 0.00% 28 6 0.00% 29 6 0.00% 30 8 0.00% 31 5 0.00% 32 6 0.00% 33 12 0.00% 34 6 0.00% 35 3 0.00% 36 11 0.00% 37 5 0.00% 38 7 0.00% 39 7 0.00% 40 11 0.00% 41 7 0.00% 42 9 0.00% 43 9 0.00% 44 10 0.00% 45 11 0.00% 46 15 0.00% 47 19 0.00% 48 20 0.00% 49 25 0.00% 50 24 0.00% 51 26 0.00% 52 27 0.00% 53 33 0.00% 54 53 0.00% 55 56 0.00% 56 44 0.00% 57 61 0.00% 58 68 0.00% 59 70 0.00% 60 70 0.00% 61 85 0.00% 62 102 0.00% 63 110 0.00% 64 134 0.00% 65 139 0.00% 66 133 0.00% 67 166 0.00% 68 208 0.00% 69 208 0.00% 70 227 0.00% 71 231 0.00% 72 292 0.00% 73 313 0.00% 74 370 0.00% 75 426 0.00% 76 540 0.00% 77 539 0.00% 78 612 0.00% 79 667 0.00% 80 772 0.01% 81 882 0.01% 82 1013 0.01% 83 1220 0.01% 84 2209 0.02% 85 2942 0.02% 86 3205 0.02% 87 3599 0.03% 88 3760 0.03% 89 3939 0.03% 90 3848 0.03% 91 4043 0.03% 92 4473 0.03% 93 4431 0.03% 94 4640 0.03% 95 4882 0.04% 96 5164 0.04% 97 5352 0.04% 98 5583 0.04% 99 6145 0.05% 100 6471 0.05% 101 6820 0.05% 102 7259 0.05% 103 7708 0.06% 104 8354 0.06% 105 8719 0.06% 106 9292 0.07% 107 9911 0.07% 108 10426 0.08% 109 10948 0.08% 110 11700 0.09% 111 12504 0.09% 112 13191 0.10% 113 13946 0.10% 114 14955 0.11% 115 15442 0.11% 116 16199 0.12% 117 16442 0.12% 118 17327 0.13% 119 18067 0.13% 120 18956 0.14% 121 19603 0.14% 122 20771 0.15% 123 21865 0.16% 124 23077 0.17% 125 23550 0.17% 126 24930 0.18% 127 25883 0.19% 128 26930 0.20% 129 28235 0.21% 130 29737 0.22% 131 30993 0.23% 132 32899 0.24% 133 34988 0.26% 134 36996 0.27% 135 39503 0.29% 136 41432 0.30% 137 44132 0.32% 138 47310 0.35% 139 50689 0.37% 140 54774 0.40% 141 60148 0.44% 142 67190 0.49% 143 74792 0.55% 144 87067 0.64% 145 104590 0.77% 146 131852 0.97% 147 181358 1.33% 148 283224 2.08% 149 590630 4.34% 150 3098029 22.76% 151 7939882 58.34% 13610102 reads passed initial QC criterion=sequence-density sequence-density=0.25 sequence-density-rank=1 fanout-score=3.15 fanout-score-rank=26 prefix-density=0.38 prefix-fanout=2.1 sequence=CACTTGCAGCCATTCTCAGCACC criterion=fanout-score sequence-density=0.02 sequence-density-rank=33 fanout-score=101.23 fanout-score-rank=1 prefix-density=0.18 prefix-fanout=11.8 sequence=CTCCTTCCTCTAAATGATAAGGTTCAGTGGACTTCTCGCGACGTCGCCGGCGGCGAACCGCCCACGTCGCCGCGATCCGAACACTTCACCGGACCATTCAATCGGTAGGAGCGACGGGCGGTGTGTACAAAGGGCAGGGACGTAGTCAACGCGAGCTGATGACTCGCGCTTACTAGGAATTCCTCGTTGAAGACCAACAATTGCAATGATCTATCCCCATCACGATGAAATTTCAAAGATTACCCGGGCCTGTCGGCCAAGGCTATAGACTCGTTGAATACATCAGTGTAGCGCGCGTGCGGCCCAGAACATCTAAGGGCATCACAGACCTGTTATTGCCTCAAACTTCCTTGGCCTGGAAGGCCATAGTCCCTCTAAGAAGCTGGCCGCGGAGGGTCACCTCCGCATAGCTAGTTAGCAGGCTGAGGTCTCGTTCGTTAACGGAATTAACCAGACAAATCGCTCCACCAACTAAGAACGGCCATGCACCACCACCCAT criterion=sequence-density sequence-density=0.34 sequence-density-rank=1 fanout-score=2.10 fanout-score-rank=30 prefix-density=0.35 prefix-fanout=2.1 sequence=ATGTACCCTGACTTAGGTTTCTCAGA criterion=fanout-score sequence-density=0.09 sequence-density-rank=20 fanout-score=161.12 fanout-score-rank=1 prefix-density=0.60 prefix-fanout=25.3 sequence=GAGAAGAAGGAT SRR7171858 testing PE reads STAR mapping to Ensembl genome Started job on | Feb 13 21:37:31 Started mapping on | Feb 13 21:37:31 Finished on | Feb 13 21:39:41 Mapping speed, Million of reads per hour | 376.90 Number of input reads | 13610102 Average input read length | 296 UNIQUE READS: Uniquely mapped reads number | 12474674 Uniquely mapped reads % | 91.66% Average mapped length | 296.04 Number of splices: Total | 11743359 Number of splices: Annotated (sjdb) | 11518984 Number of splices: GT/AG | 11558814 Number of splices: GC/AG | 143897 Number of splices: AT/AC | 9153 Number of splices: Non-canonical | 31495 Mismatch rate per base, % | 0.38% Deletion rate per base | 0.03% Deletion average length | 2.46 Insertion rate per base | 0.02% Insertion average length | 2.47 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 339799 % of reads mapped to multiple loci | 2.50% Number of reads mapped to too many loci | 80288 % of reads mapped to too many loci | 0.59% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 5.12% % of reads unmapped: other | 0.13% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 815017 815017 815017 N_multimapping 339799 339799 339799 N_noFeature 310437 12327121 380041 N_ambiguous 149597 1102 70915 UnstrandedReadsAssigned:12014640 PositiveStrandReadsAssigned:146451 NegativeStrandReadsAssigned:12023718 Dataset is classified negative stranded MeadianReadLen=151 20thPercentileLength=150 echo kmer=145 SRR7171858 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: SRR7171858-trimmed-pair1.fastq SRR7171858-trimmed-pair2.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 13,610,102 reads, 11,979,218 reads pseudoaligned [quant] estimated average fragment length: 241.163 [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,089 rounds 52401 SRR7171858.ke.tsv 34699 SRR7171858.se.tsv 87100 total ==> SRR7171858.ke.tsv <== target_id length eff_length est_counts tpm Potri.005G200100.1.v4.1 2018 1777.84 1087 42.1115 Potri.005G024800.1.v4.1 1035 794.837 268 23.2231 Potri.004G059700.1.v4.1 961 720.844 26 2.48425 Potri.007G009000.2.v4.1 1416 1175.84 1 0.0585755 Potri.003G141000.2.v4.1 2943 2702.84 479 12.2062 Potri.016G087400.1.v4.1 270 71.581 1325 1274.91 Potri.015G069301.1.v4.1 564 325.871 0 0 Potri.010G195200.1.v4.1 1773 1532.84 202.831 9.11384 Potri.012G127500.1.v4.1 977 736.844 3452 322.67 ==> SRR7171858.se.tsv <== Potri.001G166300.v4.1 0 Potri.001G448400.v4.1 52 Potri.001G233950.v4.1 0 Potri.001G122700.v4.1 399 Potri.001G212900.v4.1 0 Potri.001G182400.v4.1 2 Potri.001G256600.v4.1 0 Potri.001G040500.v4.1 1 Potri.001G416900.v4.1 1 Potri.001G452600.v4.1 142 SRR7171858 completed mapping pipeline successfully