Starting /dee2/code/volunteer_pipeline.sh SRR6958468 current disk space = 1547632402432 free memory = 1595279040 SRR6958468 SRAfilesize fb6f089d5cc9a1be419d17f03c17576b SRR6958468.sra SRR6958468.sra file validated SRR6958468 is paired end SRR6958468 is conventional basespace SRR6958468 read1 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR6958468_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 49 >>END_MODULE >>Per base sequence quality fail #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 27.701 32.0 27.0 33.0 18.0 33.0 2 30.31075 31.0 29.0 33.0 27.0 33.0 3 30.9025 33.0 29.0 33.0 27.0 34.0 4 31.978 33.0 32.0 33.0 31.0 34.0 5 32.1905 33.0 32.0 33.0 31.0 34.0 6 36.57025 38.0 37.0 38.0 34.0 38.0 7 36.5825 38.0 37.0 38.0 34.0 38.0 8 36.4515 38.0 37.0 38.0 34.0 38.0 9 36.8395 38.0 38.0 38.0 34.0 38.0 10-14 37.07465 38.0 38.0 38.0 35.8 38.0 15-19 37.17215 38.0 38.0 38.0 36.0 38.0 20-24 37.101 38.0 38.0 38.0 36.0 38.0 25-29 36.912850000000006 38.0 38.0 38.0 35.2 38.0 30-34 36.82355 38.0 38.0 38.0 34.8 38.0 35-39 36.57430000000001 38.0 38.0 38.0 34.2 38.0 40-44 36.56155 38.0 38.0 38.0 34.2 38.0 45-49 36.48035 38.0 38.0 38.0 33.8 38.0 50-54 35.88195 38.0 36.6 38.0 31.0 38.0 55-59 35.936899999999994 38.0 37.0 38.0 31.4 38.0 60-64 36.49615 38.0 37.8 38.0 33.8 38.0 65-69 36.4354 38.0 37.6 38.0 33.6 38.0 70-74 36.23015 38.0 37.2 38.0 33.0 38.0 75-79 35.5932 38.0 36.2 38.0 30.0 38.0 80-84 35.4647 38.0 35.8 38.0 29.2 38.0 85-89 35.83215 38.0 36.8 38.0 31.4 38.0 90-94 35.757250000000006 38.0 36.2 38.0 31.0 38.0 95-99 35.0065 38.0 35.4 38.0 27.8 38.0 100-104 34.1746 38.0 34.2 38.0 23.4 38.0 105-109 33.8448 38.0 34.0 38.0 22.6 38.0 110-114 33.85875 38.0 34.0 38.0 20.8 38.0 115-119 33.724149999999995 38.0 34.0 38.0 22.2 38.0 120-124 33.26649999999999 37.6 32.4 38.0 20.4 38.0 125-129 32.69745 37.4 31.2 38.0 16.2 38.0 130-134 31.7089 36.2 30.6 38.0 14.2 38.0 135-139 30.565350000000002 35.6 27.6 38.0 12.8 38.0 140-144 29.037599999999998 34.0 24.4 38.0 7.8 38.0 145-149 26.465249999999997 33.0 14.8 38.0 2.0 38.0 150-151 19.653750000000002 16.5 2.0 35.5 2.0 38.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 12 2.0 13 0.0 14 1.0 15 0.0 16 2.0 17 4.0 18 5.0 19 7.0 20 7.0 21 6.0 22 13.0 23 23.0 24 24.0 25 48.0 26 44.0 27 65.0 28 84.0 29 109.0 30 108.0 31 188.0 32 205.0 33 263.0 34 417.0 35 582.0 36 969.0 37 824.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 46.24341558081508 10.701413917382867 7.2359301358469645 35.81924036595508 2 23.7 11.625 32.574999999999996 32.1 3 19.7 17.875 25.775 36.65 4 25.35 23.025000000000002 22.975 28.65 5 25.7 27.400000000000002 23.849999999999998 23.05 6 24.85 30.475 23.200000000000003 21.475 7 18.475 23.724999999999998 37.95 19.85 8 19.400000000000002 25.424999999999997 28.275 26.900000000000002 9 18.8 22.675 32.125 26.400000000000002 10-14 22.835 26.07 25.965 25.130000000000003 15-19 22.975 25.39 25.66 25.974999999999998 20-24 23.135 25.285000000000004 25.619999999999997 25.96 25-29 23.04 25.19 26.125 25.645 30-34 23.11 25.515 25.319999999999997 26.055 35-39 23.335 25.69 24.59 26.384999999999998 40-44 22.985 25.224999999999998 25.72 26.07 45-49 23.544999999999998 25.22 25.185000000000002 26.05 50-54 22.8 25.31 25.75 26.14 55-59 23.195 25.009999999999998 25.47 26.325 60-64 23.599999999999998 25.1 25.264999999999997 26.035000000000004 65-69 23.3 25.16 25.264999999999997 26.275 70-74 23.78 24.815 25.755 25.650000000000002 75-79 23.755000000000003 24.585 25.82 25.840000000000003 80-84 23.445 24.735 25.369999999999997 26.450000000000003 85-89 23.724999999999998 24.945 25.14 26.19 90-94 23.585 25.21 25.115 26.090000000000003 95-99 23.47 25.105 25.025 26.400000000000002 100-104 23.835 25.275 25.255 25.635 105-109 23.575 24.725 25.7 26.0 110-114 23.799999999999997 25.14 24.925 26.135 115-119 24.08 25.6 24.310000000000002 26.009999999999998 120-124 23.91 25.34 24.38 26.369999999999997 125-129 23.69 25.855 24.09 26.365 130-134 24.099999999999998 26.179999999999996 23.785 25.935000000000002 135-139 23.474999999999998 26.215 23.73 26.58 140-144 24.295 26.0 23.78 25.924999999999997 145-149 23.365 25.855 23.695 27.084999999999997 150-151 23.9125 25.775 23.4875 26.825 >>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 0.0 25 0.0 26 0.5 27 1.0 28 1.5 29 4.5 30 9.5 31 10.0 32 15.0 33 27.0 34 35.0 35 43.5 36 54.0 37 65.5 38 81.0 39 91.5 40 103.5 41 148.0 42 169.5 43 173.0 44 200.0 45 207.5 46 211.5 47 200.0 48 181.0 49 163.5 50 157.5 51 167.0 52 150.0 53 121.5 54 104.0 55 101.5 56 92.0 57 77.5 58 70.5 59 62.0 60 61.5 61 67.5 62 67.5 63 53.5 64 44.5 65 49.5 66 47.5 67 43.0 68 39.5 69 37.5 70 37.5 71 33.0 72 28.5 73 22.5 74 15.5 75 17.5 76 15.0 77 8.0 78 4.5 79 2.0 80 2.5 81 1.5 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 warn #Base N-Count 1 9.825000000000001 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 99.625 #Duplication Level Percentage of deduplicated Percentage of total 1 99.67377666248431 99.3 2 0.27603513174404015 0.5499999999999999 3 0.05018820577164366 0.15 4 0.0 0.0 5 0.0 0.0 6 0.0 0.0 7 0.0 0.0 8 0.0 0.0 9 0.0 0.0 >10 0.0 0.0 >50 0.0 0.0 >100 0.0 0.0 >500 0.0 0.0 >1k 0.0 0.0 >5k 0.0 0.0 >10k+ 0.0 0.0 >>END_MODULE >>Overrepresented sequences pass >>END_MODULE >>Adapter Content fail #Position Illumina Universal Adapter Illumina Small RNA 3' Adapter Illumina Small RNA 5' Adapter Nextera Transposase Sequence SOLID Small RNA Adapter 1 0.0 0.0 0.0 0.0 0.0 2 0.0 0.0 0.0 0.0 0.0 3 0.0 0.0 0.0 0.0 0.0 4 0.0 0.0 0.0 0.0 0.0 5 0.0 0.0 0.0 0.0 0.0 6 0.0 0.0 0.0 0.0 0.0 7 0.0 0.0 0.0 0.0 0.0 8 0.0 0.0 0.0 0.0 0.0 9 0.0 0.0 0.0 0.0 0.0 10-11 0.0 0.0 0.0 0.0 0.0 12-13 0.0 0.0 0.0 0.0 0.0 14-15 0.0 0.0 0.0 0.0 0.0 16-17 0.0 0.0 0.0 0.0 0.0 18-19 0.0 0.0 0.0 0.0 0.0 20-21 0.0 0.0 0.0 0.0 0.0 22-23 0.0 0.0 0.0 0.0 0.0 24-25 0.0 0.0 0.0 0.0 0.0 26-27 0.0 0.0 0.0 0.0 0.0 28-29 0.0 0.0 0.0 0.0 0.0 30-31 0.0 0.0 0.0 0.0 0.0 32-33 0.0 0.0 0.0 0.0 0.0 34-35 0.0 0.0 0.0 0.0 0.0 36-37 0.0 0.0 0.0 0.0 0.0 38-39 0.0 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 0.07500000000000001 0.0 0.0 0.0 0.0 80-81 0.1125 0.0 0.0 0.0 0.0 82-83 0.175 0.0 0.0 0.0 0.0 84-85 0.2375 0.0 0.0 0.0 0.0 86-87 0.30000000000000004 0.0 0.0 0.0 0.0 88-89 0.42500000000000004 0.0 0.0 0.0 0.0 90-91 0.5375000000000001 0.0 0.0 0.0 0.0 92-93 0.575 0.0 0.0 0.0 0.0 94-95 0.8 0.0 0.0 0.0 0.0 96-97 1.0 0.0 0.0 0.0 0.0 98-99 1.1625 0.0 0.0 0.0 0.0 100-101 1.2875 0.0 0.0 0.0 0.0 102-103 1.5875 0.0 0.0 0.0 0.0 104-105 1.9625 0.0 0.0 0.0 0.0 106-107 2.3125 0.0 0.0 0.0 0.0 108-109 2.7249999999999996 0.0 0.0 0.0 0.0 110-111 3.1624999999999996 0.0 0.0 0.0 0.0 112-113 3.6875 0.0 0.0 0.0 0.0 114-115 4.2375 0.0 0.0 0.0 0.0 116-117 4.75 0.0 0.0 0.0 0.0 118-119 5.425000000000001 0.0 0.0 0.0 0.0 120-121 6.1375 0.0 0.0 0.0 0.0 122-123 7.0 0.0 0.0 0.0 0.0 124-125 8.0375 0.0 0.0 0.0 0.0 126-127 8.9375 0.0 0.0 0.0 0.0 128-129 9.825 0.0 0.0 0.0 0.0 130-131 10.649999999999999 0.0 0.0 0.0 0.0 132-133 11.425 0.0 0.0 0.0 0.0 134-135 12.175 0.0 0.0 0.0 0.0 136-137 12.925 0.0 0.0 0.0 0.0 138-139 13.9875 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position GGGGGGA 10 0.004973884 161.00002 1 GTCCCTC 10 0.0068449317 144.90001 8 GGGGGAA 10 0.0068449317 144.90001 2 >>END_MODULE SRR6958468 read2 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR6958468_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 50 >>END_MODULE >>Per base sequence quality fail #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 32.23 33.0 33.0 34.0 31.0 34.0 2 31.99425 33.0 33.0 34.0 30.0 34.0 3 32.085 33.0 33.0 34.0 30.0 34.0 4 31.9875 33.0 33.0 34.0 31.0 34.0 5 31.988 33.0 33.0 34.0 31.0 34.0 6 35.777 38.0 38.0 38.0 31.0 38.0 7 35.682 38.0 37.0 38.0 30.0 38.0 8 35.69925 38.0 37.0 38.0 31.0 38.0 9 35.633 38.0 37.0 38.0 30.0 38.0 10-14 35.549099999999996 38.0 37.2 38.0 29.8 38.0 15-19 35.958749999999995 38.0 37.8 38.0 32.0 38.0 20-24 36.28105 38.0 38.0 38.0 34.4 38.0 25-29 36.2328 38.0 38.0 38.0 34.0 38.0 30-34 36.282849999999996 38.0 38.0 38.0 34.0 38.0 35-39 36.003699999999995 38.0 38.0 38.0 33.2 38.0 40-44 35.761900000000004 38.0 38.0 38.0 31.8 38.0 45-49 35.8361 38.0 38.0 38.0 32.6 38.0 50-54 35.864850000000004 38.0 38.0 38.0 33.0 38.0 55-59 35.74055 38.0 37.8 38.0 31.8 38.0 60-64 35.4964 38.0 37.0 38.0 30.2 38.0 65-69 35.15245 38.0 36.8 38.0 28.4 38.0 70-74 34.8892 38.0 36.0 38.0 27.6 38.0 75-79 35.1097 38.0 36.4 38.0 28.8 38.0 80-84 35.0318 38.0 36.0 38.0 28.6 38.0 85-89 34.91865 38.0 36.0 38.0 28.2 38.0 90-94 34.3623 38.0 34.8 38.0 25.2 38.0 95-99 33.72985 38.0 34.2 38.0 19.8 38.0 100-104 32.9607 37.8 32.6 38.0 16.2 38.0 105-109 32.75255 38.0 31.8 38.0 15.0 38.0 110-114 32.42625 38.0 31.2 38.0 15.0 38.0 115-119 31.76975 37.2 30.2 38.0 13.8 38.0 120-124 30.94795 36.8 28.2 38.0 12.4 38.0 125-129 30.032 35.8 27.0 38.0 11.2 38.0 130-134 28.697950000000002 34.0 22.4 38.0 5.6 38.0 135-139 28.040750000000003 33.0 20.6 38.0 2.0 38.0 140-144 27.2245 33.0 19.4 38.0 2.0 38.0 145-149 24.6869 33.0 6.4 38.0 2.0 38.0 150-151 17.756125 16.5 2.0 34.0 2.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 2 40.0 3 11.0 4 7.0 5 4.0 6 2.0 7 5.0 8 2.0 9 0.0 10 1.0 11 3.0 12 5.0 13 10.0 14 10.0 15 6.0 16 12.0 17 10.0 18 18.0 19 11.0 20 19.0 21 28.0 22 25.0 23 39.0 24 36.0 25 39.0 26 58.0 27 52.0 28 108.0 29 101.0 30 127.0 31 143.0 32 209.0 33 270.0 34 352.0 35 570.0 36 891.0 37 776.0 >>END_MODULE >>Per base sequence content warn #Base G A T C 1 41.325 20.325 11.0 27.35 2 28.95 23.25 26.724999999999998 21.075 3 23.05 26.450000000000003 27.05 23.45 4 26.200000000000003 30.675 20.95 22.175 5 28.275 31.5 20.45 19.775000000000002 6 24.6 33.550000000000004 20.424999999999997 21.425 7 22.575 21.05 34.325 22.05 8 24.775 23.375 23.075000000000003 28.775000000000002 9 24.25 23.3 26.174999999999997 26.275 10-14 26.484999999999996 25.669999999999998 23.285 24.560000000000002 15-19 25.8 24.759999999999998 24.34 25.1 20-24 26.55 25.14 24.03 24.279999999999998 25-29 27.034999999999997 25.430000000000003 23.845 23.69 30-34 26.005 25.590000000000003 24.48 23.925 35-39 26.665 24.685000000000002 24.73 23.919999999999998 40-44 25.929999999999996 24.6 24.795 24.675 45-49 26.565 24.695 24.965 23.775 50-54 26.11 25.255 24.59 24.044999999999998 55-59 26.275 24.88 24.5 24.345 60-64 26.6 24.57 25.14 23.69 65-69 26.290000000000003 25.005 25.025 23.68 70-74 26.314999999999998 25.005 24.605 24.075 75-79 26.505000000000003 24.66 24.795 24.04 80-84 26.125 25.155 25.224999999999998 23.494999999999997 85-89 26.645000000000003 25.395 24.365000000000002 23.595 90-94 26.705000000000002 24.9 24.92 23.474999999999998 95-99 26.27 25.3 24.925 23.505000000000003 100-104 26.979999999999997 24.945 24.36 23.715 105-109 26.91 25.629999999999995 24.279999999999998 23.18 110-114 27.165 25.82 24.07 22.945 115-119 26.505000000000003 25.34 24.529999999999998 23.625 120-124 27.744999999999997 25.45 24.349999999999998 22.455 125-129 27.615000000000002 25.905 23.990000000000002 22.49 130-134 28.16 25.955000000000002 23.91 21.975 135-139 28.799999999999997 25.979999999999997 23.665 21.555 140-144 28.715000000000003 25.540000000000003 24.04 21.705 145-149 29.25 25.895000000000003 23.9 20.955 150-151 29.912499999999998 26.0625 23.2625 20.7625 >>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 0.5 17 0.5 18 0.0 19 0.0 20 0.0 21 0.5 22 1.0 23 1.0 24 1.0 25 0.5 26 0.0 27 1.5 28 4.0 29 5.5 30 7.5 31 10.0 32 11.5 33 15.5 34 20.0 35 26.0 36 42.0 37 53.0 38 64.0 39 90.5 40 115.5 41 129.5 42 146.5 43 177.5 44 193.5 45 207.0 46 221.0 47 201.5 48 184.0 49 170.0 50 157.0 51 147.5 52 127.0 53 109.0 54 101.5 55 95.5 56 92.5 57 88.5 58 78.5 59 79.5 60 69.0 61 62.5 62 76.5 63 75.5 64 66.5 65 54.0 66 51.0 67 55.0 68 52.0 69 55.5 70 54.0 71 40.5 72 26.5 73 20.5 74 16.0 75 13.5 76 12.0 77 8.0 78 5.0 79 3.0 80 2.0 81 1.0 82 0.5 83 1.0 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 0.0 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 99.75 #Duplication Level Percentage of deduplicated Percentage of total 1 99.74937343358395 99.5 2 0.2506265664160401 0.5 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 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 0.0 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 0.07500000000000001 0.0 0.0 0.0 0.0 80-81 0.1125 0.0 0.0 0.0 0.0 82-83 0.175 0.0 0.0 0.0 0.0 84-85 0.2375 0.0 0.0 0.0 0.0 86-87 0.32499999999999996 0.0 0.0 0.0 0.0 88-89 0.4625 0.0 0.0 0.0 0.0 90-91 0.5874999999999999 0.0 0.0 0.0 0.0 92-93 0.65 0.0 0.0 0.0 0.0 94-95 0.9 0.0 0.0 0.0 0.0 96-97 1.1 0.0 0.0 0.0 0.0 98-99 1.2625000000000002 0.0 0.0 0.0 0.0 100-101 1.375 0.0 0.0 0.0 0.0 102-103 1.6625 0.0 0.0 0.0 0.0 104-105 2.05 0.0 0.0 0.0 0.0 106-107 2.3875 0.0 0.0 0.0 0.0 108-109 2.75 0.0 0.0 0.0 0.0 110-111 3.175 0.0 0.0 0.0 0.0 112-113 3.65 0.0 0.0 0.0 0.0 114-115 4.2 0.0 0.0 0.0 0.0 116-117 4.675000000000001 0.0 0.0 0.0 0.0 118-119 5.3375 0.0 0.0 0.0 0.0 120-121 6.0375 0.0 0.0 0.0 0.0 122-123 6.8625 0.0 0.0 0.0 0.0 124-125 7.825 0.0 0.0 0.0 0.0 126-127 8.7125 0.0 0.0 0.0 0.0 128-129 9.55 0.0 0.0 0.0 0.0 130-131 10.4125 0.0 0.0 0.0 0.0 132-133 11.2125 0.0 0.0 0.0 0.0 134-135 11.975 0.0 0.0 0.0 0.0 136-137 12.7625 0.0 0.0 0.0 0.0 138-139 13.8625 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content pass >>END_MODULE Read 1261523 spots for SRR6958468.sra Written 1261523 spots for SRR6958468.sra Read 1261523 spots for SRR6958468.sra Written 1261523 spots for SRR6958468.sra Read 1261523 spots for SRR6958468.sra Written 1261523 spots for SRR6958468.sra Read 1261523 spots for SRR6958468.sra Written 1261523 spots for SRR6958468.sra Read 1261533 spots for SRR6958468.sra Written 1261533 spots for SRR6958468.sra Read 1261523 spots for SRR6958468.sra Written 1261523 spots for SRR6958468.sra Read 1261523 spots for SRR6958468.sra Written 1261523 spots for SRR6958468.sra Read 1261523 spots for SRR6958468.sra Written 1261523 spots for SRR6958468.sra Read 1261523 spots for SRR6958468.sra Written 1261523 spots for SRR6958468.sra Read 1261523 spots for SRR6958468.sra Written 1261523 spots for SRR6958468.sra Read 1261523 spots for SRR6958468.sra Written 1261523 spots for SRR6958468.sra Read 1261523 spots for SRR6958468.sra Written 1261523 spots for SRR6958468.sra Read 1261523 spots for SRR6958468.sra Written 1261523 spots for SRR6958468.sra Read 1261523 spots for SRR6958468.sra Written 1261523 spots for SRR6958468.sra Read 1261523 spots for SRR6958468.sra Written 1261523 spots for SRR6958468.sra Read 1261523 spots for SRR6958468.sra Written 1261523 spots for SRR6958468.sra Read 1261523 spots for SRR6958468.sra Written 1261523 spots for SRR6958468.sra Read 1261523 spots for SRR6958468.sra Written 1261523 spots for SRR6958468.sra Read 1261523 spots for SRR6958468.sra Written 1261523 spots for SRR6958468.sra Read 1261523 spots for SRR6958468.sra Written 1261523 spots for SRR6958468.sra SRR ids: ['SRR6958468.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_6kxyb4rf SRR6958468.sra spots: 25230470 blocks: [[1, 1261523], [1261524, 2523046], [2523047, 3784569], [3784570, 5046092], [5046093, 6307615], [6307616, 7569138], [7569139, 8830661], [8830662, 10092184], [10092185, 11353707], [11353708, 12615230], [12615231, 13876753], [13876754, 15138276], [15138277, 16399799], [16399800, 17661322], [17661323, 18922845], [18922846, 20184368], [20184369, 21445891], [21445892, 22707414], [22707415, 23968937], [23968938, 25230470]] SRR6958468 file size 8528078 SRR6958468 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 SRR6958468 SRR6958468_1.fastq SRR6958468_2.fastq Input file: SRR6958468_1.fastq Paired file: SRR6958468_2.fastq trimmed: SRR6958468-trimmed-pair1.fastq, SRR6958468-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 Fri Dec 6 23:54:21 2024 >> started Fri Dec 6 23:54:47 2024 >> done (26.302s) 25230470 read pairs processed; of these: 71457 ( 0.28%) short read pairs filtered out after trimming by size control 74983 ( 0.30%) empty read pairs filtered out after trimming by size control 25084030 (99.42%) read pairs available; of these: 15615540 (62.25%) trimmed read pairs available after processing 9468490 (37.75%) untrimmed read pairs available after processing Length distribution of reads after trimming: length count percentage 18 3 0.00% 19 2 0.00% 20 4 0.00% 21 10 0.00% 22 7 0.00% 23 8 0.00% 24 10 0.00% 25 8 0.00% 26 6 0.00% 27 10 0.00% 28 10 0.00% 29 11 0.00% 30 14 0.00% 31 6 0.00% 32 17 0.00% 33 16 0.00% 34 14 0.00% 35 21 0.00% 36 22 0.00% 37 30 0.00% 38 26 0.00% 39 39 0.00% 40 30 0.00% 41 37 0.00% 42 52 0.00% 43 50 0.00% 44 55 0.00% 45 68 0.00% 46 61 0.00% 47 83 0.00% 48 83 0.00% 49 97 0.00% 50 100 0.00% 51 142 0.00% 52 160 0.00% 53 195 0.00% 54 206 0.00% 55 200 0.00% 56 221 0.00% 57 314 0.00% 58 355 0.00% 59 368 0.00% 60 454 0.00% 61 519 0.00% 62 607 0.00% 63 699 0.00% 64 765 0.00% 65 921 0.00% 66 972 0.00% 67 1171 0.00% 68 1254 0.00% 69 1457 0.01% 70 1696 0.01% 71 1944 0.01% 72 2327 0.01% 73 2715 0.01% 74 3048 0.01% 75 3521 0.01% 76 3861 0.02% 77 4268 0.02% 78 4766 0.02% 79 5565 0.02% 80 6422 0.03% 81 7300 0.03% 82 8556 0.03% 83 10067 0.04% 84 13497 0.05% 85 15867 0.06% 86 16571 0.07% 87 17699 0.07% 88 18714 0.07% 89 19925 0.08% 90 21653 0.09% 91 23771 0.09% 92 26178 0.10% 93 28611 0.11% 94 31385 0.13% 95 33872 0.14% 96 36048 0.14% 97 38066 0.15% 98 40360 0.16% 99 42938 0.17% 100 45691 0.18% 101 48507 0.19% 102 52194 0.21% 103 56123 0.22% 104 60375 0.24% 105 63275 0.25% 106 66861 0.27% 107 68677 0.27% 108 70652 0.28% 109 74179 0.30% 110 76763 0.31% 111 80388 0.32% 112 84890 0.34% 113 89280 0.36% 114 93385 0.37% 115 97903 0.39% 116 101017 0.40% 117 102686 0.41% 118 106807 0.43% 119 107200 0.43% 120 110862 0.44% 121 114560 0.46% 122 119184 0.48% 123 123987 0.49% 124 129503 0.52% 125 134150 0.53% 126 137109 0.55% 127 141299 0.56% 128 143436 0.57% 129 145930 0.58% 130 149488 0.60% 131 152771 0.61% 132 158650 0.63% 133 165721 0.66% 134 172220 0.69% 135 179967 0.72% 136 187687 0.75% 137 194179 0.77% 138 200488 0.80% 139 208374 0.83% 140 218322 0.87% 141 231621 0.92% 142 249971 1.00% 143 273984 1.09% 144 307232 1.22% 145 353157 1.41% 146 420351 1.68% 147 539378 2.15% 148 785584 3.13% 149 1473153 5.87% 150 5643168 22.50% 151 9468490 37.75% 25084030 reads passed initial QC criterion=sequence-density sequence-density=0.38 sequence-density-rank=1 fanout-score=2.94 fanout-score-rank=29 prefix-density=0.45 prefix-fanout=2.5 sequence=GAGCTGGAGCTG criterion=fanout-score sequence-density=0.03 sequence-density-rank=32 fanout-score=406.19 fanout-score-rank=1 prefix-density=0.63 prefix-fanout=16.3 sequence=GGCGGCGGCGAACCGCCCCCGTCGCCGCGATCCGAACACTTCACCGGACCATTCAATCGGTAGGAGCGACGGGCGGTGTGTACAAAGGGCAGGGACGTAGTCAACGCGAGCTGATGACTCGCGCTTACTAGGCATTCCTCGTTGAAGACCAACAATTGCAATGATCTATCCCCATCACGATGAAATTTCCCAAGATTACCCGGGCCTGTCGGCCAAGGCTATATACTCGTTGAATACATCAGTGTAGCGCGCGTGCGGCCCAGAACATCTAAGGGCATCACAGACCTGTTATTGCCTCAAACTTCCGTCGCCTAAACGGCGATAGTCCCTCTAAGAAGCTAGCTGCGGAGGGATGGCTCCGCATAGCTAGTTAGCAGGCTGAGGTCTCGTTCGTTAACGGAATTAACCAGACAAATCGCTCCACCAACTAAGAACGGCCATGCACCACCACCCATAGAATCAAGAAAGAGCTCTCAGTCTGTCAATCCTTGCTATGTCTGGACCTGGTAAG criterion=sequence-density sequence-density=0.25 sequence-density-rank=1 fanout-score=22.52 fanout-score-rank=7 prefix-density=0.99 prefix-fanout=5.6 sequence=AAGGAGAAGCTGCCTGGCCAGCACTGAGC criterion=fanout-score sequence-density=0.09 sequence-density-rank=28 fanout-score=185.99 fanout-score-rank=1 prefix-density=0.66 prefix-fanout=24.7 sequence=CGCCGCCGCCGG SRR6958468 testing PE reads STAR mapping to Ensembl genome Started job on | Dec 06 23:55:27 Started mapping on | Dec 06 23:55:27 Finished on | Dec 06 23:57:31 Mapping speed, Million of reads per hour | 728.25 Number of input reads | 25084030 Average input read length | 287 UNIQUE READS: Uniquely mapped reads number | 24120181 Uniquely mapped reads % | 96.16% Average mapped length | 286.81 Number of splices: Total | 20342156 Number of splices: Annotated (sjdb) | 18689250 Number of splices: GT/AG | 20061502 Number of splices: GC/AG | 219003 Number of splices: AT/AC | 11135 Number of splices: Non-canonical | 50516 Mismatch rate per base, % | 0.26% Deletion rate per base | 0.02% Deletion average length | 2.47 Insertion rate per base | 0.01% Insertion average length | 2.25 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 210726 % of reads mapped to multiple loci | 0.84% Number of reads mapped to too many loci | 39529 % of reads mapped to too many loci | 0.16% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 2.09% % of reads unmapped: other | 0.76% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 792254 792254 792254 N_multimapping 210726 210726 210726 N_noFeature 1278153 23266601 1666117 N_ambiguous 560979 4632 96670 UnstrandedReadsAssigned:22281049 PositiveStrandReadsAssigned:848948 NegativeStrandReadsAssigned:22357394 Dataset is classified negative stranded MeadianReadLen=150 20thPercentileLength=138 echo kmer=133 SRR6958468 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: SRR6958468-trimmed-pair1.fastq SRR6958468-trimmed-pair2.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 25,084,030 reads, 22,397,372 reads pseudoaligned [quant] estimated average fragment length: 213.384 [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,153 rounds 52973 SRR6958468.ke.tsv 35125 SRR6958468.se.tsv 88098 total ==> SRR6958468.ke.tsv <== target_id length eff_length est_counts tpm PNS24245 936 723.93 372.817 33.9845 PNS24247 1044 831.616 39.2916 3.11788 PNS24249 1928 1715.62 564.653 21.7192 PNS24246 1044 831.616 39.2916 3.11788 PNS24248 1044 831.616 39.2916 3.11788 PNS24244 1471 1258.62 172.655 9.05248 PNS24243 293 111.721 2 1.18135 KQK14069 1603 1390.62 360.296 17.0976 KQK14071 474 269.088 8.68243 2.12926 ==> SRR6958468.se.tsv <== BRADI_1g14170v3 393 BRADI_1g53295v3 1848 BRADI_1g59795v3 274 BRADI_1g07683v3 0 BRADI_1g00485v3 53 BRADI_1g20270v3 613 BRADI_1g74790v3 1854 BRADI_1g09890v3 0 BRADI_1g77505v3 278 BRADI_1g48960v3 1 SRR6958468 completed mapping pipeline successfully