Starting /dee2/code/volunteer_pipeline.sh SRR5579215 current disk space = 1522832809984 free memory = 1568657404 SRR5579215 SRAfilesize 5ec5ff5241bcb98a0b0ba52186c463a7 SRR5579215.sra SRR5579215.sra file validated SRR5579215 is paired end SRR5579215 is conventional basespace SRR5579215 read1 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR5579215_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 50 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 28.36425 34.0 32.0 34.0 2.0 34.0 2 32.31875 34.0 33.0 34.0 28.0 34.0 3 32.58775 34.0 33.0 34.0 28.0 34.0 4 33.02 34.0 33.0 34.0 32.0 34.0 5 33.158 34.0 33.0 34.0 32.0 34.0 6 36.967 38.0 37.0 38.0 36.0 38.0 7 37.2025 38.0 38.0 38.0 36.0 38.0 8 37.35325 38.0 38.0 38.0 37.0 38.0 9 37.39975 38.0 38.0 38.0 37.0 38.0 10-14 37.37955 38.0 38.0 38.0 37.0 38.0 15-19 37.3628 38.0 38.0 38.0 37.0 38.0 20-24 37.3373 38.0 38.0 38.0 37.0 38.0 25-29 37.349199999999996 38.0 38.0 38.0 37.0 38.0 30-34 37.2589 38.0 38.0 38.0 37.0 38.0 35-39 37.22539999999999 38.0 38.0 38.0 36.8 38.0 40-44 37.034949999999995 38.0 38.0 38.0 36.0 38.0 45-49 37.0137 38.0 38.0 38.0 36.0 38.0 50-54 36.9554 38.0 38.0 38.0 35.8 38.0 55-59 36.91065 38.0 38.0 38.0 35.2 38.0 60-64 36.88525 38.0 38.0 38.0 35.0 38.0 65-69 36.86495 38.0 38.0 38.0 35.0 38.0 70-74 36.702600000000004 38.0 38.0 38.0 34.4 38.0 75-79 36.674699999999994 38.0 38.0 38.0 34.4 38.0 80-84 36.60895000000001 38.0 38.0 38.0 34.0 38.0 85-89 36.45555 38.0 38.0 38.0 34.0 38.0 90-94 36.3494 38.0 38.0 38.0 34.0 38.0 95-99 36.3148 38.0 38.0 38.0 33.6 38.0 100-104 36.14825 38.0 37.6 38.0 33.2 38.0 105-109 35.98055 38.0 37.2 38.0 32.6 38.0 110-114 35.7144 38.0 37.0 38.0 31.4 38.0 115-119 35.5718 38.0 36.6 38.0 30.8 38.0 120-124 35.380900000000004 38.0 36.0 38.0 30.2 38.0 125-129 34.99294999999999 38.0 35.6 38.0 27.4 38.0 130-134 34.920750000000005 38.0 35.2 38.0 27.8 38.0 135-139 34.92685 38.0 35.2 38.0 28.2 38.0 140-144 34.43495 38.0 35.0 38.0 25.6 38.0 145-149 33.76800000000001 38.0 35.0 38.0 22.4 38.0 150-151 30.38075 36.5 29.0 38.0 7.5 38.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 4 1.0 5 0.0 6 0.0 7 0.0 8 0.0 9 0.0 10 0.0 11 1.0 12 0.0 13 1.0 14 1.0 15 0.0 16 0.0 17 6.0 18 3.0 19 4.0 20 3.0 21 9.0 22 12.0 23 9.0 24 8.0 25 17.0 26 20.0 27 34.0 28 45.0 29 36.0 30 66.0 31 71.0 32 87.0 33 96.0 34 153.0 35 260.0 36 642.0 37 2415.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 44.611750811927955 13.197519929140833 10.628875110717448 31.561854148213758 2 24.85 17.95 35.125 22.075 3 21.975 24.925 24.95 28.15 4 28.9 29.7 20.025000000000002 21.375 5 25.374999999999996 33.825 20.424999999999997 20.375 6 20.925 34.225 21.9 22.95 7 17.575 19.950000000000003 41.175 21.3 8 21.175 20.325 26.55 31.95 9 21.5 19.85 30.5 28.15 10-14 23.465 26.275 24.145 26.115 15-19 23.45 24.97 25.064999999999998 26.515 20-24 23.805 25.4 25.31 25.485000000000003 25-29 23.48 25.655 24.65 26.215 30-34 23.68 25.2 25.27 25.85 35-39 23.48 24.905 25.790000000000003 25.825 40-44 23.82 25.040000000000003 24.86 26.279999999999998 45-49 24.0 25.45 24.875 25.674999999999997 50-54 24.05 24.505 24.715 26.729999999999997 55-59 23.46 24.85 25.11 26.58 60-64 24.33 25.03 24.08 26.56 65-69 24.025 24.12 25.35 26.505000000000003 70-74 23.585 25.455 24.725 26.235000000000003 75-79 24.12 25.16 24.435000000000002 26.284999999999997 80-84 24.39 24.135 25.03 26.445 85-89 24.075 24.845 25.119999999999997 25.96 90-94 24.349999999999998 24.595 24.595 26.46 95-99 24.73 24.87 24.529999999999998 25.869999999999997 100-104 25.025 24.48 24.279999999999998 26.215 105-109 24.955 25.235000000000003 24.044999999999998 25.765 110-114 24.565 24.855 24.805 25.775 115-119 24.52 24.875 24.355 26.25 120-124 25.165 24.92 23.89 26.025 125-129 24.695 25.305 24.265 25.735000000000003 130-134 25.040000000000003 25.2 23.810000000000002 25.95 135-139 24.490000000000002 25.124999999999996 24.09 26.295 140-144 24.95 25.540000000000003 23.57 25.94 145-149 24.79 24.935 23.835 26.44 150-151 25.387500000000003 25.2875 23.4625 25.8625 >>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 0.0 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 0.5 25 0.5 26 0.0 27 0.5 28 3.5 29 7.5 30 9.0 31 10.0 32 15.5 33 20.0 34 25.5 35 38.0 36 51.0 37 64.0 38 84.0 39 100.5 40 118.0 41 149.5 42 166.5 43 180.0 44 182.5 45 174.5 46 192.0 47 195.0 48 172.0 49 162.0 50 148.0 51 137.0 52 127.0 53 121.5 54 114.5 55 104.0 56 96.5 57 81.0 58 85.5 59 83.5 60 69.0 61 66.5 62 71.0 63 71.5 64 62.5 65 50.5 66 54.0 67 52.5 68 42.5 69 41.5 70 38.0 71 34.0 72 36.0 73 29.5 74 16.5 75 11.0 76 10.5 77 7.0 78 3.5 79 3.5 80 2.0 81 2.5 82 2.5 83 0.5 84 0.5 85 0.5 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 warn #Base N-Count 1 15.325 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 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 fail #Position Illumina Universal Adapter Illumina Small RNA 3' Adapter Illumina Small RNA 5' Adapter Nextera Transposase Sequence SOLID Small RNA Adapter 1 0.0 0.0 0.0 0.0 0.0 2 0.0 0.0 0.0 0.0 0.0 3 0.0 0.0 0.0 0.0 0.0 4 0.0 0.0 0.0 0.0 0.0 5 0.0 0.0 0.0 0.0 0.0 6 0.0 0.0 0.0 0.0 0.0 7 0.0 0.0 0.0 0.0 0.0 8 0.0 0.0 0.0 0.0 0.0 9 0.0 0.0 0.0 0.0 0.0 10-11 0.0 0.0 0.0 0.0 0.0 12-13 0.0 0.0 0.0 0.0 0.0 14-15 0.0 0.0 0.0 0.0 0.0 16-17 0.0 0.0 0.0 0.0 0.0 18-19 0.0 0.0 0.0 0.0 0.0 20-21 0.0 0.0 0.0 0.0 0.0 22-23 0.0 0.0 0.0 0.0 0.0 24-25 0.0 0.0 0.0 0.0 0.0 26-27 0.0 0.0 0.0 0.0 0.0 28-29 0.0 0.0 0.0 0.0 0.0 30-31 0.0 0.0 0.0 0.0 0.0 32-33 0.0 0.0 0.0 0.0 0.0 34-35 0.0 0.0 0.0 0.0 0.0 36-37 0.0 0.0 0.0 0.0 0.0 38-39 0.0 0.0 0.0 0.0 0.0 40-41 0.0 0.0 0.0 0.0 0.0 42-43 0.0 0.0 0.0 0.0 0.0 44-45 0.0 0.0 0.0 0.0 0.0 46-47 0.0 0.0 0.0 0.0 0.0 48-49 0.0 0.0 0.0 0.0 0.0 50-51 0.0 0.0 0.0 0.0 0.0 52-53 0.0 0.0 0.0 0.0 0.0 54-55 0.0 0.0 0.0 0.0 0.0 56-57 0.0 0.0 0.0 0.0 0.0 58-59 0.0 0.0 0.0 0.0 0.0 60-61 0.0 0.0 0.0 0.0 0.0 62-63 0.0 0.0 0.0 0.0 0.0 64-65 0.0 0.0 0.0 0.0 0.0 66-67 0.037500000000000006 0.0 0.0 0.0 0.0 68-69 0.05 0.0 0.0 0.0 0.0 70-71 0.075 0.0 0.0 0.0 0.0 72-73 0.075 0.0 0.0 0.0 0.0 74-75 0.11249999999999999 0.0 0.0 0.0 0.0 76-77 0.175 0.0 0.0 0.0 0.0 78-79 0.2 0.0 0.0 0.0 0.0 80-81 0.2625 0.0 0.0 0.0 0.0 82-83 0.3 0.0 0.0 0.0 0.0 84-85 0.3125 0.0 0.0 0.0 0.0 86-87 0.375 0.0 0.0 0.0 0.0 88-89 0.4375 0.0 0.0 0.0 0.0 90-91 0.625 0.0 0.0 0.0 0.0 92-93 0.8875 0.0 0.0 0.0 0.0 94-95 1.0375 0.0 0.0 0.0 0.0 96-97 1.25 0.0 0.0 0.0 0.0 98-99 1.475 0.0 0.0 0.0 0.0 100-101 1.6625 0.0 0.0 0.0 0.0 102-103 1.875 0.0 0.0 0.0 0.0 104-105 2.3375000000000004 0.0 0.0 0.0 0.0 106-107 2.625 0.0 0.0 0.0 0.0 108-109 3.0 0.0 0.0 0.0 0.0 110-111 3.3 0.0 0.0 0.0 0.0 112-113 3.5375 0.0 0.0 0.0 0.0 114-115 3.9000000000000004 0.0 0.0 0.0 0.0 116-117 4.3125 0.0 0.0 0.0 0.0 118-119 4.975 0.0 0.0 0.0 0.0 120-121 5.9125 0.0 0.0 0.0 0.0 122-123 6.4625 0.0 0.0 0.0 0.0 124-125 6.862500000000001 0.0 0.0 0.0 0.0 126-127 7.300000000000001 0.0 0.0 0.0 0.0 128-129 7.775 0.0 0.0 0.0 0.0 130-131 8.2125 0.0 0.0 0.0 0.0 132-133 8.8375 0.0 0.0 0.0 0.0 134-135 9.425 0.0 0.0 0.0 0.0 136-137 10.075 0.0 0.0 0.0 0.0 138-139 10.6 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content pass >>END_MODULE SRR5579215 read2 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR5579215_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 51 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 32.4545 33.0 33.0 34.0 31.0 34.0 2 32.602 33.0 33.0 34.0 32.0 34.0 3 32.5925 33.0 33.0 34.0 32.0 34.0 4 32.468 33.0 33.0 34.0 31.0 34.0 5 32.4525 33.0 33.0 34.0 32.0 34.0 6 36.5825 38.0 38.0 38.0 34.0 38.0 7 36.64825 38.0 38.0 38.0 35.0 38.0 8 36.674 38.0 38.0 38.0 35.0 38.0 9 36.621 38.0 38.0 38.0 35.0 38.0 10-14 36.619150000000005 38.0 38.0 38.0 34.8 38.0 15-19 36.5925 38.0 38.0 38.0 35.0 38.0 20-24 36.5487 38.0 38.0 38.0 35.0 38.0 25-29 36.2971 38.0 38.0 38.0 33.6 38.0 30-34 36.5346 38.0 38.0 38.0 35.0 38.0 35-39 36.5049 38.0 38.0 38.0 34.6 38.0 40-44 36.469100000000005 38.0 38.0 38.0 34.4 38.0 45-49 36.3648 38.0 38.0 38.0 34.2 38.0 50-54 36.42645 38.0 38.0 38.0 34.2 38.0 55-59 36.3643 38.0 38.0 38.0 34.2 38.0 60-64 36.2484 38.0 38.0 38.0 33.8 38.0 65-69 36.168 38.0 38.0 38.0 33.8 38.0 70-74 36.179500000000004 38.0 38.0 38.0 33.8 38.0 75-79 36.06275 38.0 38.0 38.0 33.4 38.0 80-84 36.06025 38.0 38.0 38.0 33.6 38.0 85-89 35.95685 38.0 38.0 38.0 33.2 38.0 90-94 35.400150000000004 38.0 37.4 38.0 29.6 38.0 95-99 35.67455 38.0 38.0 38.0 31.6 38.0 100-104 35.468050000000005 38.0 37.4 38.0 30.6 38.0 105-109 35.36685 38.0 37.2 38.0 31.0 38.0 110-114 35.32155 38.0 37.2 38.0 30.6 38.0 115-119 35.0903 38.0 36.6 38.0 29.2 38.0 120-124 34.83225 38.0 36.0 38.0 27.4 38.0 125-129 34.5464 38.0 35.8 38.0 25.4 38.0 130-134 34.167649999999995 38.0 35.2 38.0 23.2 38.0 135-139 34.022299999999994 38.0 35.0 38.0 22.6 38.0 140-144 33.639250000000004 38.0 35.0 38.0 18.6 38.0 145-149 32.67635 38.0 34.0 38.0 11.4 38.0 150-151 28.406375 36.0 18.0 38.0 2.0 38.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 2 9.0 3 6.0 4 8.0 5 1.0 6 4.0 7 5.0 8 4.0 9 3.0 10 4.0 11 4.0 12 1.0 13 3.0 14 12.0 15 10.0 16 7.0 17 4.0 18 6.0 19 6.0 20 9.0 21 18.0 22 8.0 23 20.0 24 27.0 25 20.0 26 28.0 27 32.0 28 40.0 29 47.0 30 50.0 31 74.0 32 92.0 33 111.0 34 144.0 35 236.0 36 516.0 37 2431.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 43.7 14.625 11.975 29.7 2 27.950000000000003 21.575 28.1 22.375 3 24.05 23.75 26.200000000000003 26.0 4 28.799999999999997 31.324999999999996 16.675 23.200000000000003 5 27.825 32.175 18.75 21.25 6 21.75 34.849999999999994 19.05 24.349999999999998 7 20.849999999999998 15.2 37.974999999999994 25.974999999999998 8 21.3 21.6 23.5 33.6 9 23.925 20.849999999999998 26.35 28.875 10-14 25.52 24.7 23.265 26.515 15-19 26.38 24.05 23.52 26.05 20-24 26.115 24.654999999999998 23.494999999999997 25.735000000000003 25-29 26.325 24.905 22.98 25.790000000000003 30-34 26.715 24.54 23.905 24.84 35-39 25.990000000000002 24.54 23.62 25.85 40-44 27.07 24.015 23.59 25.324999999999996 45-49 26.695 23.919999999999998 23.544999999999998 25.840000000000003 50-54 25.900000000000002 24.525 23.87 25.705 55-59 26.705000000000002 24.560000000000002 23.715 25.019999999999996 60-64 26.634999999999998 24.435000000000002 24.075 24.855 65-69 26.490000000000002 24.635 23.990000000000002 24.884999999999998 70-74 26.205000000000002 24.154999999999998 24.125 25.515 75-79 26.529999999999998 24.235 23.919999999999998 25.314999999999998 80-84 26.669999999999998 24.445 23.465 25.419999999999998 85-89 26.924999999999997 24.245 24.415 24.415 90-94 26.565 24.525 23.875 25.035 95-99 26.63 24.64 24.025 24.705 100-104 26.590000000000003 24.685000000000002 23.785 24.94 105-109 27.045 24.945 23.544999999999998 24.465 110-114 26.83 25.485000000000003 23.71 23.974999999999998 115-119 27.689999999999998 24.349999999999998 24.11 23.849999999999998 120-124 27.52 25.259999999999998 23.445 23.775 125-129 27.58 25.540000000000003 23.599999999999998 23.28 130-134 27.27 24.68 24.01 24.04 135-139 27.900000000000002 25.380000000000003 23.98 22.74 140-144 27.735 25.869999999999997 23.36 23.035 145-149 27.905 25.715 23.419999999999998 22.96 150-151 28.037499999999998 24.575 24.3875 23.0 >>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 0.0 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 0.5 24 0.5 25 0.0 26 1.5 27 2.5 28 2.0 29 1.5 30 5.5 31 6.5 32 7.5 33 13.5 34 19.5 35 28.0 36 39.5 37 54.5 38 63.0 39 76.0 40 93.5 41 115.0 42 138.5 43 153.5 44 153.0 45 161.0 46 174.0 47 171.0 48 173.0 49 162.0 50 139.0 51 136.5 52 137.0 53 114.5 54 105.5 55 113.5 56 106.5 57 93.5 58 97.0 59 99.0 60 90.0 61 85.0 62 93.5 63 96.0 64 75.5 65 64.0 66 77.5 67 78.0 68 62.0 69 62.0 70 56.0 71 50.0 72 44.0 73 29.5 74 24.0 75 20.0 76 13.5 77 8.5 78 5.0 79 2.0 80 1.0 81 2.0 82 1.5 83 0.0 84 0.5 85 0.5 86 0.0 87 0.0 88 0.0 89 0.0 90 0.0 91 0.0 92 0.0 93 0.0 94 0.0 95 0.0 96 0.0 97 0.0 98 0.0 99 0.0 100 0.0 >>END_MODULE >>Per base N content pass #Base N-Count 1 0.0 2 0.0 3 0.0 4 0.0 5 0.0 6 0.0 7 0.0 8 0.0 9 0.0 10-14 0.0 15-19 0.0 20-24 0.0 25-29 0.0 30-34 0.0 35-39 0.0 40-44 0.0 45-49 0.0 50-54 0.0 55-59 0.0 60-64 0.0 65-69 0.0 70-74 0.0 75-79 0.0 80-84 0.0 85-89 0.0 90-94 0.0 95-99 0.0 100-104 0.0 105-109 0.0 110-114 0.0 115-119 0.0 120-124 0.0 125-129 0.0 130-134 0.0 135-139 0.0 140-144 0.0 145-149 0.0 150-151 0.0 >>END_MODULE >>Sequence Length Distribution pass #Length Count 151 4000.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 99.325 #Duplication Level Percentage of deduplicated Percentage of total 1 99.42109237352128 98.75 2 0.47822803926503904 0.95 3 0.10067958721369243 0.3 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 0.0 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 0.037500000000000006 0.0 0.0 0.0 0.0 68-69 0.05 0.0 0.0 0.0 0.0 70-71 0.075 0.0 0.0 0.0 0.0 72-73 0.075 0.0 0.0 0.0 0.0 74-75 0.11249999999999999 0.0 0.0 0.0 0.0 76-77 0.175 0.0 0.0 0.0 0.0 78-79 0.2 0.0 0.0 0.0 0.0 80-81 0.2625 0.0 0.0 0.0 0.0 82-83 0.3 0.0 0.0 0.0 0.0 84-85 0.3125 0.0 0.0 0.0 0.0 86-87 0.375 0.0 0.0 0.0 0.0 88-89 0.4125 0.0 0.0 0.0 0.0 90-91 0.5625 0.0 0.0 0.0 0.0 92-93 0.8125 0.0 0.0 0.0 0.0 94-95 0.9625 0.0 0.0 0.0 0.0 96-97 1.175 0.0 0.0 0.0 0.0 98-99 1.375 0.0 0.0 0.0 0.0 100-101 1.6124999999999998 0.0 0.0 0.0 0.0 102-103 1.825 0.0 0.0 0.0 0.0 104-105 2.275 0.0 0.0 0.0 0.0 106-107 2.575 0.0 0.0 0.0 0.0 108-109 2.95 0.0 0.0 0.0 0.0 110-111 3.25 0.0 0.0 0.0 0.0 112-113 3.4875 0.0 0.0 0.0 0.0 114-115 3.8625 0.0 0.0 0.0 0.0 116-117 4.3 0.0 0.0 0.0 0.0 118-119 4.9625 0.0 0.0 0.0 0.0 120-121 5.85 0.0 0.0 0.0 0.0 122-123 6.425 0.0 0.0 0.0 0.0 124-125 6.862500000000001 0.0 0.0 0.0 0.0 126-127 7.25 0.0 0.0 0.0 0.0 128-129 7.7125 0.0 0.0 0.0 0.0 130-131 8.162500000000001 0.0 0.0 0.0 0.0 132-133 8.7625 0.0 0.0 0.0 0.0 134-135 9.375 0.0 0.0 0.0 0.0 136-137 10.0125 0.0 0.0 0.0 0.0 138-139 10.525 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position TGCGCCT 10 0.006830828 145.0 3 GCGCCTG 10 0.006830828 145.0 4 GATCATC 20 3.5877043E-4 108.75 2 >>END_MODULE Read 1603250 spots for SRR5579215.sra Written 1603250 spots for SRR5579215.sra Read 1603250 spots for SRR5579215.sra Written 1603250 spots for SRR5579215.sra Read 1603250 spots for SRR5579215.sra Written 1603250 spots for SRR5579215.sra Read 1603250 spots for SRR5579215.sra Written 1603250 spots for SRR5579215.sra Read 1603250 spots for SRR5579215.sra Written 1603250 spots for SRR5579215.sra Read 1603250 spots for SRR5579215.sra Written 1603250 spots for SRR5579215.sra Read 1603250 spots for SRR5579215.sra Written 1603250 spots for SRR5579215.sra Read 1603250 spots for SRR5579215.sra Written 1603250 spots for SRR5579215.sra Read 1603250 spots for SRR5579215.sra Written 1603250 spots for SRR5579215.sra Read 1603250 spots for SRR5579215.sra Written 1603250 spots for SRR5579215.sra Read 1603250 spots for SRR5579215.sra Written 1603250 spots for SRR5579215.sra Read 1603262 spots for SRR5579215.sra Written 1603262 spots for SRR5579215.sra Read 1603250 spots for SRR5579215.sra Written 1603250 spots for SRR5579215.sra Read 1603250 spots for SRR5579215.sra Written 1603250 spots for SRR5579215.sra Read 1603250 spots for SRR5579215.sra Written 1603250 spots for SRR5579215.sra Read 1603250 spots for SRR5579215.sra Written 1603250 spots for SRR5579215.sra Read 1603250 spots for SRR5579215.sra Written 1603250 spots for SRR5579215.sra Read 1603250 spots for SRR5579215.sra Written 1603250 spots for SRR5579215.sra Read 1603250 spots for SRR5579215.sra Written 1603250 spots for SRR5579215.sra Read 1603250 spots for SRR5579215.sra Written 1603250 spots for SRR5579215.sra SRR ids: ['SRR5579215.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_6kpnivu2 SRR5579215.sra spots: 32065012 blocks: [[1, 1603250], [1603251, 3206500], [3206501, 4809750], [4809751, 6413000], [6413001, 8016250], [8016251, 9619500], [9619501, 11222750], [11222751, 12826000], [12826001, 14429250], [14429251, 16032500], [16032501, 17635750], [17635751, 19239000], [19239001, 20842250], [20842251, 22445500], [22445501, 24048750], [24048751, 25652000], [25652001, 27255250], [27255251, 28858500], [28858501, 30461750], [30461751, 32065012]] SRR5579215 file size 10844080 SRR5579215 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 SRR5579215 SRR5579215_1.fastq SRR5579215_2.fastq Input file: SRR5579215_1.fastq Paired file: SRR5579215_2.fastq trimmed: SRR5579215-trimmed-pair1.fastq, SRR5579215-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 22:29:49 2024 >> started Mon Dec 9 22:30:26 2024 >> done (36.688s) 32065012 read pairs processed; of these: 73526 ( 0.23%) short read pairs filtered out after trimming by size control 58892 ( 0.18%) empty read pairs filtered out after trimming by size control 31932594 (99.59%) read pairs available; of these: 14661648 (45.91%) trimmed read pairs available after processing 17270946 (54.09%) untrimmed read pairs available after processing Length distribution of reads after trimming: length count percentage 18 11 0.00% 19 14 0.00% 20 21 0.00% 21 33 0.00% 22 30 0.00% 23 20 0.00% 24 28 0.00% 25 24 0.00% 26 36 0.00% 27 26 0.00% 28 33 0.00% 29 36 0.00% 30 38 0.00% 31 41 0.00% 32 33 0.00% 33 45 0.00% 34 54 0.00% 35 55 0.00% 36 52 0.00% 37 67 0.00% 38 81 0.00% 39 62 0.00% 40 72 0.00% 41 100 0.00% 42 97 0.00% 43 112 0.00% 44 143 0.00% 45 130 0.00% 46 160 0.00% 47 200 0.00% 48 239 0.00% 49 276 0.00% 50 285 0.00% 51 316 0.00% 52 360 0.00% 53 413 0.00% 54 424 0.00% 55 518 0.00% 56 548 0.00% 57 705 0.00% 58 743 0.00% 59 890 0.00% 60 970 0.00% 61 1165 0.00% 62 1386 0.00% 63 1428 0.00% 64 1653 0.01% 65 1931 0.01% 66 2128 0.01% 67 2409 0.01% 68 2761 0.01% 69 3515 0.01% 70 4176 0.01% 71 4337 0.01% 72 4889 0.02% 73 5337 0.02% 74 5868 0.02% 75 6579 0.02% 76 7449 0.02% 77 7949 0.02% 78 9084 0.03% 79 10283 0.03% 80 11574 0.04% 81 13091 0.04% 82 14957 0.05% 83 16760 0.05% 84 20794 0.07% 85 23478 0.07% 86 24205 0.08% 87 26102 0.08% 88 27570 0.09% 89 29237 0.09% 90 31134 0.10% 91 33784 0.11% 92 36059 0.11% 93 38847 0.12% 94 40925 0.13% 95 43003 0.13% 96 44454 0.14% 97 45939 0.14% 98 47260 0.15% 99 50772 0.16% 100 52915 0.17% 101 55957 0.18% 102 59791 0.19% 103 62505 0.20% 104 65089 0.20% 105 67631 0.21% 106 69285 0.22% 107 70447 0.22% 108 72947 0.23% 109 74572 0.23% 110 77883 0.24% 111 81368 0.25% 112 85216 0.27% 113 87760 0.27% 114 91272 0.29% 115 94791 0.30% 116 95709 0.30% 117 97637 0.31% 118 98815 0.31% 119 100832 0.32% 120 104361 0.33% 121 107461 0.34% 122 110994 0.35% 123 115360 0.36% 124 119486 0.37% 125 122571 0.38% 126 135260 0.42% 127 115763 0.36% 128 127949 0.40% 129 131797 0.41% 130 133784 0.42% 131 136829 0.43% 132 143344 0.45% 133 148249 0.46% 134 153357 0.48% 135 160309 0.50% 136 164231 0.51% 137 171796 0.54% 138 177821 0.56% 139 172534 0.54% 140 178982 0.56% 141 191376 0.60% 142 207038 0.65% 143 223834 0.70% 144 248139 0.78% 145 280557 0.88% 146 330703 1.04% 147 414624 1.30% 148 582719 1.82% 149 1061280 3.32% 150 5913905 18.52% 151 17270946 54.09% 31932594 reads passed initial QC criterion=sequence-density sequence-density=0.36 sequence-density-rank=1 fanout-score=3.52 fanout-score-rank=12 prefix-density=0.39 prefix-fanout=3.2 sequence=AGGCAAGGAACCCACTTGGAGCGGATCAGGTACTCGATCTGCTTCAGGAGAGACTCCACGGAGAGAGGGGGCAGGTACGAGAGGGTCTCGAACTTCTTGATGCCCTCGATCGGCCACACCTGCATGCACCTGATCCTTCCACCGTTG criterion=fanout-score sequence-density=0.06 sequence-density-rank=28 fanout-score=155.11 fanout-score-rank=1 prefix-density=0.56 prefix-fanout=16.4 sequence=GGCGGCGGCGAACCGCCCCCGTCGCCGCGATCCGAACACTTCACCGGACCATTCAATCGGTAGGAGCGACGGGCGGTGTGTACAAAGGGCAGGGACGTAGTCAACGCGAGCTGATGACTCGCGCTTACTAGGCATTCCTCGTTGAAGACCAACAATTGCAATGATCTATCCCCATCACGATGAAATTTCCCAAGATTACCCGGGCCTGTCGGCCAAGGCTATATACTCGTTGAATACATCAGTGTAGCGCGCGTGCGGCCCAGAACATCTAAGGGCATCACAGACCTGTTATTGCCTCAAACTTCCGTCGCCTAAACGGCGATAGTCCCTCTAAGAAGCTAGCTGCGGAGGGATGGCTCCGCATAGCTAGTTAGCAGGCTGAGGTCTCGTTCGTTAACGGAATTAACCAGACAAATCGCTCCACCAACTAAGAACGGCCATGCACCACCACCCATAGAATCAAGAAAGAGCTCTCAGTCTGTCAATCCTTGCTATGTCTGGACCTGGTAAG criterion=sequence-density sequence-density=0.39 sequence-density-rank=1 fanout-score=6.59 fanout-score-rank=12 prefix-density=0.56 prefix-fanout=4.5 sequence=AAGGAGCTGGAGGAGGTCAAGAAGGAGTACCCGGACGCCTA criterion=fanout-score sequence-density=0.13 sequence-density-rank=16 fanout-score=163.50 fanout-score-rank=1 prefix-density=0.97 prefix-fanout=22.1 sequence=CGCCGCCGCCGC SRR5579215 testing PE reads STAR mapping to Ensembl genome Started job on | Dec 09 22:31:14 Started mapping on | Dec 09 22:31:14 Finished on | Dec 09 22:35:05 Mapping speed, Million of reads per hour | 497.65 Number of input reads | 31932594 Average input read length | 290 UNIQUE READS: Uniquely mapped reads number | 29902862 Uniquely mapped reads % | 93.64% Average mapped length | 289.99 Number of splices: Total | 29924862 Number of splices: Annotated (sjdb) | 28148566 Number of splices: GT/AG | 29544415 Number of splices: GC/AG | 339477 Number of splices: AT/AC | 19452 Number of splices: Non-canonical | 21518 Mismatch rate per base, % | 0.12% Deletion rate per base | 0.00% Deletion average length | 1.40 Insertion rate per base | 0.00% Insertion average length | 1.11 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 390369 % of reads mapped to multiple loci | 1.22% Number of reads mapped to too many loci | 94612 % of reads mapped to too many loci | 0.30% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 2.93% % of reads unmapped: other | 1.91% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 1685683 1685683 1685683 N_multimapping 390369 390369 390369 N_noFeature 1053231 29021859 1409883 N_ambiguous 614477 5156 89148 UnstrandedReadsAssigned:28235154 PositiveStrandReadsAssigned:875847 NegativeStrandReadsAssigned:28403831 Dataset is classified negative stranded MeadianReadLen=151 20thPercentileLength=147 echo kmer=143 SRR5579215 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: SRR5579215-trimmed-pair1.fastq SRR5579215-trimmed-pair2.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 31,932,594 reads, 28,618,102 reads pseudoaligned [quant] estimated average fragment length: 250.181 [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,247 rounds 52973 SRR5579215.ke.tsv 35125 SRR5579215.se.tsv 88098 total ==> SRR5579215.ke.tsv <== target_id length eff_length est_counts tpm PNS24245 936 687.426 30.6861 2.2687 PNS24247 1044 794.819 84.3951 5.39648 PNS24249 1928 1678.82 201.767 6.10811 PNS24246 1044 794.819 84.3951 5.39648 PNS24248 1044 794.819 84.3951 5.39648 PNS24244 1471 1221.82 136.362 5.67215 PNS24243 293 104.611 0 0 KQK14069 1603 1353.82 853.249 32.0314 KQK14071 474 246.05 34.2829 7.08134 ==> SRR5579215.se.tsv <== BRADI_1g14170v3 965 BRADI_1g53295v3 74 BRADI_1g59795v3 722 BRADI_1g07683v3 0 BRADI_1g00485v3 33 BRADI_1g20270v3 6268 BRADI_1g74790v3 108 BRADI_1g09890v3 35 BRADI_1g77505v3 507 BRADI_1g48960v3 15 SRR5579215 completed mapping pipeline successfully