Starting /dee2/code/volunteer_pipeline.sh SRR6958467 current disk space = 1547651334144 free memory = 1595069900 SRR6958467 SRAfilesize 122c224951f569b1d0ec8fc2805d10f7 SRR6958467.sra SRR6958467.sra file validated SRR6958467 is paired end SRR6958467 is conventional basespace SRR6958467 read1 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR6958467_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 47 >>END_MODULE >>Per base sequence quality fail #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 19.62825 18.0 18.0 18.0 18.0 32.0 2 24.571 27.0 18.0 29.0 18.0 31.0 3 27.50625 29.0 25.0 31.0 18.0 33.0 4 28.963 31.0 28.0 33.0 25.0 33.0 5 30.1365 31.0 29.0 33.0 27.0 33.0 6 36.359 38.0 36.0 38.0 34.0 38.0 7 36.56125 38.0 37.0 38.0 34.0 38.0 8 36.663 38.0 37.0 38.0 34.0 38.0 9 36.91625 38.0 38.0 38.0 35.0 38.0 10-14 37.15615 38.0 38.0 38.0 36.0 38.0 15-19 37.25855 38.0 38.0 38.0 36.4 38.0 20-24 37.41185 38.0 38.0 38.0 37.0 38.0 25-29 37.372550000000004 38.0 38.0 38.0 36.8 38.0 30-34 37.199 38.0 38.0 38.0 36.2 38.0 35-39 37.21215 38.0 38.0 38.0 36.4 38.0 40-44 36.98825000000001 38.0 38.0 38.0 35.8 38.0 45-49 37.20049999999999 38.0 38.0 38.0 36.2 38.0 50-54 37.18835 38.0 38.0 38.0 36.2 38.0 55-59 36.74555 38.0 38.0 38.0 34.4 38.0 60-64 36.370650000000005 38.0 37.2 38.0 33.6 38.0 65-69 36.0704 38.0 37.0 38.0 32.4 38.0 70-74 36.055099999999996 38.0 37.0 38.0 32.4 38.0 75-79 36.413399999999996 38.0 37.2 38.0 33.6 38.0 80-84 36.4763 38.0 37.6 38.0 33.8 38.0 85-89 36.01115 38.0 37.0 38.0 32.4 38.0 90-94 36.23895 38.0 37.0 38.0 33.4 38.0 95-99 35.970600000000005 38.0 36.6 38.0 32.0 38.0 100-104 35.60525 38.0 36.2 38.0 30.0 38.0 105-109 35.123599999999996 38.0 35.2 38.0 28.4 38.0 110-114 34.6002 38.0 34.6 38.0 26.0 38.0 115-119 33.8348 37.8 34.0 38.0 22.6 38.0 120-124 33.895050000000005 38.0 34.0 38.0 23.0 38.0 125-129 34.3479 38.0 34.4 38.0 24.6 38.0 130-134 34.48514999999999 38.0 34.6 38.0 26.0 38.0 135-139 34.12795 38.0 34.0 38.0 23.6 38.0 140-144 33.372699999999995 38.0 33.6 38.0 20.2 38.0 145-149 31.953650000000003 36.8 32.0 38.0 11.6 38.0 150-151 27.50025 34.5 16.5 37.0 2.0 38.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 10 1.0 11 0.0 12 1.0 13 1.0 14 1.0 15 1.0 16 1.0 17 2.0 18 1.0 19 0.0 20 1.0 21 4.0 22 3.0 23 6.0 24 13.0 25 11.0 26 19.0 27 28.0 28 40.0 29 51.0 30 85.0 31 121.0 32 162.0 33 212.0 34 309.0 35 586.0 36 1269.0 37 1071.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 23.18840579710145 23.67149758454106 5.636070853462158 47.50402576489533 2 17.8 14.424999999999999 31.35 36.425000000000004 3 18.075 16.625 22.0 43.3 4 22.05 27.650000000000002 21.175 29.125 5 22.936468234117058 31.94097048524262 23.111555777888945 22.011005502751377 6 22.7 33.324999999999996 23.175 20.8 7 15.725 23.875 41.6 18.8 8 19.275000000000002 23.95 29.925 26.85 9 18.275 23.225 33.825 24.675 10-14 21.13 27.465 26.695 24.709999999999997 15-19 21.325 26.724999999999998 26.979999999999997 24.97 20-24 22.470000000000002 26.39 26.805 24.335 25-29 22.065 26.455000000000002 26.685 24.795 30-34 22.2 26.240000000000002 26.715 24.845 35-39 21.785 26.805 26.205000000000002 25.205 40-44 21.715 26.810000000000002 26.41 25.064999999999998 45-49 21.515 26.275 26.705000000000002 25.505 50-54 22.58 26.325 26.229999999999997 24.865000000000002 55-59 21.8 26.44 26.900000000000002 24.86 60-64 22.285 26.240000000000002 26.44 25.035 65-69 22.185 26.44 26.450000000000003 24.925 70-74 21.85 25.95 27.034999999999997 25.165 75-79 22.085 26.195 26.724999999999998 24.995 80-84 22.775000000000002 26.025 26.075 25.124999999999996 85-89 21.9 26.490000000000002 26.57 25.040000000000003 90-94 22.71 25.895000000000003 26.095000000000002 25.3 95-99 22.869999999999997 25.7 26.810000000000002 24.62 100-104 22.7 25.955000000000002 26.145000000000003 25.2 105-109 22.585 26.174999999999997 25.974999999999998 25.264999999999997 110-114 22.955000000000002 26.029999999999998 25.8 25.215 115-119 22.36 25.955000000000002 26.31 25.374999999999996 120-124 22.49 25.895000000000003 26.55 25.064999999999998 125-129 22.355 26.025 26.534999999999997 25.085 130-134 22.15 25.61 26.8 25.44 135-139 22.725 25.94 26.455000000000002 24.88 140-144 22.915 26.265 26.22 24.6 145-149 22.99 25.874999999999996 25.955000000000002 25.180000000000003 150-151 23.0375 25.374999999999996 25.95 25.637500000000003 >>END_MODULE >>Per sequence GC content warn #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 1.5 27 2.0 28 3.0 29 6.5 30 7.0 31 11.5 32 18.0 33 25.0 34 34.5 35 45.5 36 55.0 37 75.0 38 103.0 39 136.5 40 160.5 41 173.0 42 203.0 43 229.5 44 230.5 45 228.0 46 221.0 47 210.0 48 221.0 49 219.0 50 192.5 51 161.5 52 127.5 53 99.0 54 82.5 55 81.0 56 74.5 57 60.0 58 57.5 59 47.0 60 38.5 61 46.0 62 45.0 63 39.0 64 35.5 65 29.0 66 23.5 67 25.0 68 29.0 69 26.5 70 22.0 71 14.5 72 4.5 73 4.5 74 6.5 75 5.0 76 3.0 77 0.5 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 warn #Base N-Count 1 6.8500000000000005 2 0.0 3 0.0 4 0.0 5 0.05 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 99.7 #Duplication Level Percentage of deduplicated Percentage of total 1 99.69909729187563 99.4 2 0.3009027081243731 0.6 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 0.0125 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 0.037500000000000006 0.0 0.0 0.0 0.0 82-83 0.0625 0.0 0.0 0.0 0.0 84-85 0.1 0.0 0.0 0.0 0.0 86-87 0.1 0.0 0.0 0.0 0.0 88-89 0.1 0.0 0.0 0.0 0.0 90-91 0.1 0.0 0.0 0.0 0.0 92-93 0.125 0.0 0.0 0.0 0.0 94-95 0.1875 0.0 0.0 0.0 0.0 96-97 0.21250000000000002 0.0 0.0 0.0 0.0 98-99 0.2875 0.0 0.0 0.0 0.0 100-101 0.35 0.0 0.0 0.0 0.0 102-103 0.475 0.0 0.0 0.0 0.0 104-105 0.575 0.0 0.0 0.0 0.0 106-107 0.6375 0.0 0.0 0.0 0.0 108-109 0.675 0.0 0.0 0.0 0.0 110-111 0.6875 0.0 0.0 0.0 0.0 112-113 0.7375 0.0 0.0 0.0 0.0 114-115 0.8500000000000001 0.0 0.0 0.0 0.0 116-117 0.975 0.0 0.0 0.0 0.0 118-119 1.0875 0.0 0.0 0.0 0.0 120-121 1.15 0.0 0.0 0.0 0.0 122-123 1.2625 0.0 0.0 0.0 0.0 124-125 1.4874999999999998 0.0 0.0 0.0 0.0 126-127 1.6875 0.0 0.0 0.0 0.0 128-129 1.9 0.0 0.0 0.0 0.0 130-131 2.15 0.0 0.0 0.0 0.0 132-133 2.375 0.0 0.0 0.0 0.0 134-135 2.7375 0.0 0.0 0.0 0.0 136-137 3.0375 0.0 0.0 0.0 0.0 138-139 3.2875 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position CATTTGC 10 0.0068396386 144.9375 9 AGCATTT 10 0.0068396386 144.9375 7 GCATTTG 10 0.0068396386 144.9375 8 >>END_MODULE SRR6958467 read2 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR6958467_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 48 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 32.9285 33.0 33.0 34.0 32.0 34.0 2 32.95775 34.0 33.0 34.0 32.0 34.0 3 32.93975 34.0 33.0 34.0 32.0 34.0 4 32.9835 34.0 33.0 34.0 32.0 34.0 5 32.964 34.0 33.0 34.0 32.0 34.0 6 37.069 38.0 38.0 38.0 37.0 38.0 7 36.83025 38.0 38.0 38.0 35.0 38.0 8 36.9755 38.0 38.0 38.0 36.0 38.0 9 36.8865 38.0 38.0 38.0 36.0 38.0 10-14 36.9262 38.0 38.0 38.0 36.0 38.0 15-19 36.93825 38.0 38.0 38.0 36.0 38.0 20-24 37.0396 38.0 38.0 38.0 36.2 38.0 25-29 36.984 38.0 38.0 38.0 36.0 38.0 30-34 36.81805 38.0 38.0 38.0 35.4 38.0 35-39 36.84695 38.0 38.0 38.0 35.6 38.0 40-44 36.7144 38.0 38.0 38.0 35.0 38.0 45-49 36.771550000000005 38.0 38.0 38.0 35.2 38.0 50-54 36.636 38.0 38.0 38.0 34.6 38.0 55-59 36.67685 38.0 38.0 38.0 35.0 38.0 60-64 36.52465 38.0 38.0 38.0 34.0 38.0 65-69 36.5737 38.0 38.0 38.0 34.6 38.0 70-74 36.5496 38.0 38.0 38.0 34.0 38.0 75-79 36.34824999999999 38.0 38.0 38.0 33.6 38.0 80-84 36.10525 38.0 37.4 38.0 32.8 38.0 85-89 36.16420000000001 38.0 38.0 38.0 33.2 38.0 90-94 36.208600000000004 38.0 38.0 38.0 34.0 38.0 95-99 36.055099999999996 38.0 37.2 38.0 33.4 38.0 100-104 35.5546 38.0 36.4 38.0 30.6 38.0 105-109 35.1308 38.0 36.0 38.0 27.8 38.0 110-114 34.6362 38.0 35.0 38.0 26.0 38.0 115-119 34.5942 38.0 35.0 38.0 25.4 38.0 120-124 34.269349999999996 38.0 34.8 38.0 24.0 38.0 125-129 33.45590000000001 38.0 33.8 38.0 18.2 38.0 130-134 32.62155 37.4 33.0 38.0 14.8 38.0 135-139 31.580849999999998 35.8 29.8 38.0 14.0 38.0 140-144 31.2024 35.6 29.8 38.0 13.8 38.0 145-149 31.057499999999997 36.4 30.8 38.0 8.8 38.0 150-151 26.16575 33.5 16.5 37.0 2.0 38.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 2 4.0 3 3.0 4 1.0 5 1.0 6 2.0 7 1.0 8 2.0 9 1.0 10 2.0 11 0.0 12 1.0 13 1.0 14 1.0 15 0.0 16 5.0 17 7.0 18 5.0 19 2.0 20 9.0 21 8.0 22 15.0 23 13.0 24 23.0 25 30.0 26 27.0 27 42.0 28 47.0 29 52.0 30 66.0 31 73.0 32 130.0 33 195.0 34 267.0 35 432.0 36 949.0 37 1583.0 >>END_MODULE >>Per base sequence content warn #Base G A T C 1 36.4 18.75 12.65 32.2 2 29.125 23.95 29.575000000000003 17.349999999999998 3 22.7 26.974999999999998 28.749999999999996 21.575 4 25.1 31.15 21.675 22.075 5 26.924999999999997 34.575 19.45 19.05 6 23.45 35.949999999999996 21.5 19.1 7 20.525 18.6 37.925 22.95 8 22.8 24.725 24.925 27.55 9 23.125 23.200000000000003 27.250000000000004 26.424999999999997 10-14 25.825 26.93 23.865 23.380000000000003 15-19 25.380000000000003 26.41 25.424999999999997 22.785 20-24 25.5 26.290000000000003 25.130000000000003 23.080000000000002 25-29 25.245 26.5 25.91 22.345000000000002 30-34 25.22 26.68 25.290000000000003 22.81 35-39 25.215 26.565 25.145 23.075000000000003 40-44 24.685000000000002 26.77 25.555 22.99 45-49 25.615 25.86 25.540000000000003 22.985 50-54 25.19 26.0 25.56 23.25 55-59 26.200000000000003 25.7 25.380000000000003 22.720000000000002 60-64 25.365 25.835 25.990000000000002 22.81 65-69 25.235000000000003 26.474999999999998 25.525 22.765 70-74 25.1 26.07 26.179999999999996 22.650000000000002 75-79 25.06 25.805 25.95 23.185 80-84 25.369999999999997 26.235000000000003 25.445 22.95 85-89 25.180000000000003 26.735 25.69 22.395 90-94 25.580000000000002 26.240000000000002 25.39 22.79 95-99 25.564999999999998 26.085 25.955000000000002 22.395 100-104 25.22 26.555 25.52 22.705000000000002 105-109 25.1 26.205000000000002 26.19 22.505 110-114 25.66 26.305 25.825 22.21 115-119 25.014999999999997 26.415 26.400000000000002 22.17 120-124 25.564999999999998 26.685 25.624999999999996 22.125 125-129 25.44 26.395000000000003 25.924999999999997 22.24 130-134 25.795 26.240000000000002 25.82 22.145 135-139 25.665 25.990000000000002 25.96 22.384999999999998 140-144 26.119999999999997 26.790000000000003 25.230000000000004 21.86 145-149 26.029999999999998 26.325 25.855 21.790000000000003 150-151 25.1875 26.2125 26.450000000000003 22.15 >>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 0.5 13 0.5 14 0.0 15 0.0 16 0.0 17 0.0 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 1.5 27 2.0 28 4.0 29 8.0 30 9.5 31 11.0 32 15.5 33 17.5 34 27.0 35 44.5 36 51.5 37 61.0 38 87.5 39 123.0 40 146.5 41 168.0 42 194.5 43 205.5 44 212.0 45 214.5 46 208.0 47 203.0 48 193.0 49 203.5 50 189.5 51 148.0 52 124.5 53 105.5 54 106.0 55 90.0 56 78.5 57 78.5 58 66.5 59 60.0 60 66.0 61 65.5 62 50.0 63 47.5 64 46.0 65 39.5 66 37.5 67 34.5 68 30.0 69 23.5 70 21.0 71 22.0 72 19.0 73 12.0 74 8.0 75 7.0 76 2.5 77 1.5 78 1.5 79 0.5 80 0.5 81 0.5 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 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 99.575 #Duplication Level Percentage of deduplicated Percentage of total 1 99.57318604067285 99.15 2 0.42681395932714034 0.8500000000000001 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 0.0125 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 0.037500000000000006 0.0 0.0 0.0 0.0 82-83 0.0625 0.0 0.0 0.0 0.0 84-85 0.1 0.0 0.0 0.0 0.0 86-87 0.1 0.0 0.0 0.0 0.0 88-89 0.1 0.0 0.0 0.0 0.0 90-91 0.1 0.0 0.0 0.0 0.0 92-93 0.15 0.0 0.0 0.0 0.0 94-95 0.21250000000000002 0.0 0.0 0.0 0.0 96-97 0.2375 0.0 0.0 0.0 0.0 98-99 0.3 0.0 0.0 0.0 0.0 100-101 0.35 0.0 0.0 0.0 0.0 102-103 0.475 0.0 0.0 0.0 0.0 104-105 0.575 0.0 0.0 0.0 0.0 106-107 0.6375 0.0 0.0 0.0 0.0 108-109 0.675 0.0 0.0 0.0 0.0 110-111 0.6875 0.0 0.0 0.0 0.0 112-113 0.7375 0.0 0.0 0.0 0.0 114-115 0.8500000000000001 0.0 0.0 0.0 0.0 116-117 0.975 0.0 0.0 0.0 0.0 118-119 1.0750000000000002 0.0 0.0 0.0 0.0 120-121 1.125 0.0 0.0 0.0 0.0 122-123 1.2375 0.0 0.0 0.0 0.0 124-125 1.4625 0.0 0.0 0.0 0.0 126-127 1.6625 0.0 0.0 0.0 0.0 128-129 1.875 0.0 0.0 0.0 0.0 130-131 2.1125 0.0 0.0 0.0 0.0 132-133 2.3375 0.0 0.0 0.0 0.0 134-135 2.7125 0.0 0.0 0.0 0.0 136-137 3.0250000000000004 0.0 0.0 0.0 0.0 138-139 3.2875 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content pass >>END_MODULE Read 876372 spots for SRR6958467.sra Written 876372 spots for SRR6958467.sra Read 876357 spots for SRR6958467.sra Written 876357 spots for SRR6958467.sra Read 876357 spots for SRR6958467.sra Written 876357 spots for SRR6958467.sra Read 876357 spots for SRR6958467.sra Written 876357 spots for SRR6958467.sra Read 876357 spots for SRR6958467.sra Written 876357 spots for SRR6958467.sra Read 876357 spots for SRR6958467.sra Written 876357 spots for SRR6958467.sra Read 876357 spots for SRR6958467.sra Written 876357 spots for SRR6958467.sra Read 876357 spots for SRR6958467.sra Written 876357 spots for SRR6958467.sra Read 876357 spots for SRR6958467.sra Written 876357 spots for SRR6958467.sra Read 876357 spots for SRR6958467.sra Written 876357 spots for SRR6958467.sra Read 876357 spots for SRR6958467.sra Written 876357 spots for SRR6958467.sra Read 876357 spots for SRR6958467.sra Written 876357 spots for SRR6958467.sra Read 876357 spots for SRR6958467.sra Written 876357 spots for SRR6958467.sra Read 876357 spots for SRR6958467.sra Written 876357 spots for SRR6958467.sra Read 876357 spots for SRR6958467.sra Written 876357 spots for SRR6958467.sra Read 876357 spots for SRR6958467.sra Written 876357 spots for SRR6958467.sra Read 876357 spots for SRR6958467.sra Written 876357 spots for SRR6958467.sra Read 876357 spots for SRR6958467.sra Written 876357 spots for SRR6958467.sra Read 876357 spots for SRR6958467.sra Written 876357 spots for SRR6958467.sra Read 876357 spots for SRR6958467.sra Written 876357 spots for SRR6958467.sra SRR ids: ['SRR6958467.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_kqqs1b3o SRR6958467.sra spots: 17527155 blocks: [[1, 876357], [876358, 1752714], [1752715, 2629071], [2629072, 3505428], [3505429, 4381785], [4381786, 5258142], [5258143, 6134499], [6134500, 7010856], [7010857, 7887213], [7887214, 8763570], [8763571, 9639927], [9639928, 10516284], [10516285, 11392641], [11392642, 12268998], [12268999, 13145355], [13145356, 14021712], [14021713, 14898069], [14898070, 15774426], [15774427, 16650783], [16650784, 17527155]] SRR6958467 file size 5917677 SRR6958467 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 SRR6958467 SRR6958467_1.fastq SRR6958467_2.fastq Input file: SRR6958467_1.fastq Paired file: SRR6958467_2.fastq trimmed: SRR6958467-trimmed-pair1.fastq, SRR6958467-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 23:49:36 2024 >> started Fri Dec 6 23:49:57 2024 >> done (20.885s) 17527155 read pairs processed; of these: 11516 ( 0.07%) short read pairs filtered out after trimming by size control 8115 ( 0.05%) empty read pairs filtered out after trimming by size control 17507524 (99.89%) read pairs available; of these: 7113104 (40.63%) trimmed read pairs available after processing 10394420 (59.37%) untrimmed read pairs available after processing Length distribution of reads after trimming: length count percentage 18 2 0.00% 19 2 0.00% 20 4 0.00% 21 2 0.00% 22 3 0.00% 23 1 0.00% 24 3 0.00% 25 5 0.00% 26 7 0.00% 27 2 0.00% 28 3 0.00% 29 5 0.00% 30 3 0.00% 31 4 0.00% 32 4 0.00% 33 4 0.00% 34 9 0.00% 35 5 0.00% 36 7 0.00% 37 3 0.00% 38 5 0.00% 39 11 0.00% 40 10 0.00% 41 8 0.00% 42 21 0.00% 43 11 0.00% 44 12 0.00% 45 12 0.00% 46 10 0.00% 47 20 0.00% 48 15 0.00% 49 18 0.00% 50 28 0.00% 51 15 0.00% 52 31 0.00% 53 34 0.00% 54 30 0.00% 55 42 0.00% 56 49 0.00% 57 54 0.00% 58 55 0.00% 59 64 0.00% 60 73 0.00% 61 74 0.00% 62 83 0.00% 63 109 0.00% 64 127 0.00% 65 127 0.00% 66 136 0.00% 67 158 0.00% 68 174 0.00% 69 202 0.00% 70 230 0.00% 71 268 0.00% 72 325 0.00% 73 344 0.00% 74 438 0.00% 75 468 0.00% 76 490 0.00% 77 558 0.00% 78 643 0.00% 79 705 0.00% 80 831 0.00% 81 964 0.01% 82 1077 0.01% 83 1302 0.01% 84 1911 0.01% 85 2217 0.01% 86 2399 0.01% 87 2482 0.01% 88 2646 0.02% 89 2779 0.02% 90 3094 0.02% 91 3270 0.02% 92 3736 0.02% 93 3940 0.02% 94 4347 0.02% 95 4865 0.03% 96 5124 0.03% 97 5336 0.03% 98 5667 0.03% 99 6096 0.03% 100 6515 0.04% 101 7171 0.04% 102 7476 0.04% 103 8313 0.05% 104 8983 0.05% 105 9603 0.05% 106 10189 0.06% 107 10760 0.06% 108 11280 0.06% 109 11824 0.07% 110 12658 0.07% 111 13448 0.08% 112 14481 0.08% 113 15245 0.09% 114 16474 0.09% 115 17697 0.10% 116 18715 0.11% 117 19737 0.11% 118 20126 0.11% 119 21268 0.12% 120 22502 0.13% 121 23324 0.13% 122 25005 0.14% 123 26225 0.15% 124 27912 0.16% 125 29962 0.17% 126 31493 0.18% 127 33327 0.19% 128 34622 0.20% 129 36393 0.21% 130 38114 0.22% 131 40798 0.23% 132 43482 0.25% 133 46850 0.27% 134 50217 0.29% 135 54142 0.31% 136 58269 0.33% 137 63398 0.36% 138 68226 0.39% 139 75313 0.43% 140 81590 0.47% 141 89115 0.51% 142 99073 0.57% 143 107445 0.61% 144 117076 0.67% 145 133590 0.76% 146 156604 0.89% 147 214941 1.23% 148 346086 1.98% 149 740546 4.23% 150 3865053 22.08% 151 10394420 59.37% 17507524 reads passed initial QC criterion=sequence-density sequence-density=0.51 sequence-density-rank=1 fanout-score=3.03 fanout-score-rank=19 prefix-density=0.54 prefix-fanout=2.8 sequence=GGTGTTGTCGAAGCCGATGATGCGGAC criterion=fanout-score sequence-density=0.02 sequence-density-rank=32 fanout-score=186.09 fanout-score-rank=1 prefix-density=0.31 prefix-fanout=9.4 sequence=GGCGGCGGCGAACCGCCCCCGTCGCCGCGATCCGAACACTTCACCGGACCATTCAATCGGTAGGAGCGACGGGCGGTGTGTACAAAGGGCAGGGACGTAGTCAACGCGAGCTGATGACTCGCGCTTACTAGGCATTCCTCGTTGAAGACCAACAATTGCAATGATCTATCCCCATCACGATGAAATTTCCCAAGATTACCCGGGCCTGTCGGCCAAGGCTATATACTCGTTGAATACATCAGTGTAGCGCGCGTGCGGCCCAGAACATCTAAGGGCATCACAGACCTGTTATTGCCTCAAACTTCCGTCGCCTAAACGGCGATAGTCCCTCTAAGAAGCTAGCTGCGGAGGGATGGCTCCGCATAGCTAGTTAGCAGGCTGAGGTCTCGTTCGTTAACGGAATTAACCAGACAAATCGCTCCACCAACTAAGAACGGCCATGCACCACCACCCATAGAATCAAGAAAGAGCTCTCAGTCTGTCAATCCTTGCTATGTCTGGACCTGGTAAG criterion=sequence-density sequence-density=0.35 sequence-density-rank=1 fanout-score=4.18 fanout-score-rank=18 prefix-density=0.40 prefix-fanout=3.6 sequence=GAGTTCAGCAAGGTCGGCTT criterion=fanout-score sequence-density=0.01 sequence-density-rank=33 fanout-score=58.63 fanout-score-rank=1 prefix-density=0.07 prefix-fanout=6.9 sequence=TGCTCATCATCTTGTTTAATACCAAAGCTCTTCATATTCTCCTCCTTGATTTCATCAGCTTGAGGTTAGAGAGATTTGGAAGATGTCTTGCAGCTGTGGATCAAGCTGCAACTGTGGCTCAAACTGCACTTGCGGGAAGATGTACCCAGACCTGGCAGAGCAGGCCAGCACCACCAGCAGCACCCAGGCCCAGGTGCTGGTTCTCGGCATGGCGCCGGAGAAG SRR6958467 testing PE reads STAR mapping to Ensembl genome Started job on | Dec 06 23:50:52 Started mapping on | Dec 06 23:50:53 Finished on | Dec 06 23:52:11 Mapping speed, Million of reads per hour | 808.04 Number of input reads | 17507524 Average input read length | 297 UNIQUE READS: Uniquely mapped reads number | 17116601 Uniquely mapped reads % | 97.77% Average mapped length | 296.77 Number of splices: Total | 20037912 Number of splices: Annotated (sjdb) | 18924567 Number of splices: GT/AG | 19778415 Number of splices: GC/AG | 234512 Number of splices: AT/AC | 10560 Number of splices: Non-canonical | 14425 Mismatch rate per base, % | 0.13% Deletion rate per base | 0.00% Deletion average length | 1.42 Insertion rate per base | 0.00% Insertion average length | 1.24 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 137853 % of reads mapped to multiple loci | 0.79% Number of reads mapped to too many loci | 17103 % of reads mapped to too many loci | 0.10% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 0.76% % of reads unmapped: other | 0.59% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 260485 260485 260485 N_multimapping 137853 137853 137853 N_noFeature 724701 16675206 849164 N_ambiguous 379992 2300 64199 UnstrandedReadsAssigned:16011908 PositiveStrandReadsAssigned:439095 NegativeStrandReadsAssigned:16203238 Dataset is classified negative stranded MeadianReadLen=151 20thPercentileLength=150 echo kmer=145 SRR6958467 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: SRR6958467-trimmed-pair1.fastq SRR6958467-trimmed-pair2.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 17,507,524 reads, 16,250,208 reads pseudoaligned [quant] estimated average fragment length: 263.546 [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,155 rounds 52973 SRR6958467.ke.tsv 35125 SRR6958467.se.tsv 88098 total ==> SRR6958467.ke.tsv <== target_id length eff_length est_counts tpm PNS24245 936 673.818 0 0 PNS24247 1044 781.454 55.1555 6.65658 PNS24249 1928 1665.45 41.3557 2.34191 PNS24246 1044 781.454 55.1555 6.65658 PNS24248 1044 781.454 55.1555 6.65658 PNS24244 1471 1208.45 23.1779 1.80889 PNS24243 293 82.9138 0 0 KQK14069 1603 1340.45 1201.42 84.5299 KQK14071 474 224.838 32.0174 13.4302 ==> SRR6958467.se.tsv <== BRADI_1g14170v3 1374 BRADI_1g53295v3 421 BRADI_1g59795v3 406 BRADI_1g07683v3 0 BRADI_1g00485v3 10 BRADI_1g20270v3 419 BRADI_1g74790v3 210 BRADI_1g09890v3 0 BRADI_1g77505v3 269 BRADI_1g48960v3 0 SRR6958467 completed mapping pipeline successfully