Starting /dee2/code/volunteer_pipeline.sh ERR9452512 current disk space = 1548336496640 free memory = 1602807196 ERR9452512 SRAfilesize 144281cae9d8133d45793872f60f1870 ERR9452512.sra ERR9452512.sra file validated ERR9452512 is paired end ERR9452512 is conventional basespace ERR9452512 read1 length is 150 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename ERR9452512_1.fastq File type Conventional base calls Encoding Sanger / Illumina 1.9 Total Sequences 4000 Sequences flagged as poor quality 0 Sequence length 150 %GC 56 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 35.657 37.0 37.0 37.0 37.0 37.0 2 35.778 37.0 37.0 37.0 37.0 37.0 3 36.0395 37.0 37.0 37.0 37.0 37.0 4 36.1285 37.0 37.0 37.0 37.0 37.0 5 36.163 37.0 37.0 37.0 37.0 37.0 6 36.2455 37.0 37.0 37.0 37.0 37.0 7 35.965 37.0 37.0 37.0 37.0 37.0 8 36.19 37.0 37.0 37.0 37.0 37.0 9 36.286 37.0 37.0 37.0 37.0 37.0 10-14 36.212900000000005 37.0 37.0 37.0 37.0 37.0 15-19 36.1771 37.0 37.0 37.0 37.0 37.0 20-24 36.1435 37.0 37.0 37.0 37.0 37.0 25-29 36.0954 37.0 37.0 37.0 37.0 37.0 30-34 36.0416 37.0 37.0 37.0 37.0 37.0 35-39 36.057599999999994 37.0 37.0 37.0 37.0 37.0 40-44 35.8485 37.0 37.0 37.0 37.0 37.0 45-49 35.8197 37.0 37.0 37.0 37.0 37.0 50-54 35.923500000000004 37.0 37.0 37.0 37.0 37.0 55-59 35.8919 37.0 37.0 37.0 37.0 37.0 60-64 35.9875 37.0 37.0 37.0 37.0 37.0 65-69 35.889799999999994 37.0 37.0 37.0 37.0 37.0 70-74 35.910199999999996 37.0 37.0 37.0 37.0 37.0 75-79 35.862 37.0 37.0 37.0 37.0 37.0 80-84 35.87180000000001 37.0 37.0 37.0 37.0 37.0 85-89 35.85889999999999 37.0 37.0 37.0 37.0 37.0 90-94 35.7992 37.0 37.0 37.0 37.0 37.0 95-99 35.7292 37.0 37.0 37.0 37.0 37.0 100-104 35.7119 37.0 37.0 37.0 37.0 37.0 105-109 35.715199999999996 37.0 37.0 37.0 37.0 37.0 110-114 35.7314 37.0 37.0 37.0 37.0 37.0 115-119 35.6111 37.0 37.0 37.0 37.0 37.0 120-124 35.5915 37.0 37.0 37.0 37.0 37.0 125-129 35.732600000000005 37.0 37.0 37.0 37.0 37.0 130-134 35.549099999999996 37.0 37.0 37.0 37.0 37.0 135-139 35.46999999999999 37.0 37.0 37.0 37.0 37.0 140-144 35.4625 37.0 37.0 37.0 34.6 37.0 145-149 35.4872 37.0 37.0 37.0 37.0 37.0 150 35.61 37.0 37.0 37.0 37.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 19 1.0 20 0.0 21 1.0 22 1.0 23 8.0 24 2.0 25 4.0 26 8.0 27 20.0 28 30.0 29 34.0 30 65.0 31 78.0 32 100.0 33 126.0 34 201.0 35 367.0 36 2619.0 37 335.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 29.629629629629626 12.512512512512513 14.23923923923924 43.61861861861862 2 27.700000000000003 20.575 29.45 22.275 3 25.374999999999996 25.900000000000002 19.775000000000002 28.95 4 31.324999999999996 27.85 15.2 25.624999999999996 5 30.65 27.725 18.475 23.150000000000002 6 21.95 31.85 20.05 26.150000000000002 7 22.375 12.425 37.325 27.875 8 23.849999999999998 16.975 23.575 35.6 9 23.375 17.7 26.150000000000002 32.775 10-14 26.424999999999997 23.41 21.855 28.310000000000002 15-19 26.8 21.765 22.645 28.79 20-24 27.584999999999997 22.21 22.43 27.775 25-29 26.665 22.71 22.325 28.299999999999997 30-34 27.11 22.57 21.805 28.515 35-39 27.35 22.825 21.645 28.18 40-44 27.339999999999996 21.93 22.185 28.544999999999998 45-49 27.27 22.055 21.895 28.78 50-54 27.310000000000002 22.59 21.81 28.29 55-59 27.97 21.91 21.495 28.625 60-64 27.785 22.365 21.38 28.470000000000002 65-69 27.925 22.220000000000002 22.09 27.765 70-74 27.944999999999997 21.665 21.9 28.49 75-79 27.689999999999998 21.935 21.465 28.910000000000004 80-84 28.02 22.12 21.62 28.24 85-89 28.185 22.18 21.745 27.889999999999997 90-94 28.465 22.025 21.060000000000002 28.449999999999996 95-99 27.985 21.65 22.175 28.189999999999998 100-104 28.244999999999997 21.535 21.740000000000002 28.48 105-109 28.32 21.665 21.745 28.27 110-114 27.82 21.92 22.03 28.23 115-119 27.83 21.73 22.275 28.165000000000003 120-124 27.98 21.959999999999997 22.13 27.93 125-129 28.82 21.990000000000002 21.325 27.865000000000002 130-134 28.549999999999997 21.605 21.51 28.335 135-139 28.065 21.72 22.255 27.96 140-144 28.4 21.740000000000002 21.404999999999998 28.455000000000002 145-149 28.375 21.51 21.905 28.21 150 27.450000000000003 22.275 22.625 27.650000000000002 >>END_MODULE >>Per sequence GC content fail #GC Content Count 0 1.0 1 1.0 2 0.5 3 0.0 4 0.0 5 0.0 6 0.0 7 0.0 8 0.0 9 0.0 10 0.0 11 0.0 12 0.0 13 0.0 14 0.0 15 0.0 16 0.0 17 0.0 18 0.0 19 0.0 20 0.0 21 0.0 22 0.0 23 0.0 24 0.0 25 0.0 26 2.0 27 3.0 28 3.0 29 4.0 30 8.5 31 9.0 32 5.0 33 6.5 34 15.5 35 21.0 36 22.0 37 31.5 38 39.5 39 60.5 40 77.0 41 81.5 42 105.5 43 118.5 44 128.5 45 123.0 46 118.5 47 127.5 48 125.0 49 128.0 50 116.5 51 107.0 52 113.0 53 110.5 54 97.5 55 82.5 56 79.0 57 88.5 58 94.0 59 100.0 60 102.0 61 90.5 62 94.5 63 102.5 64 93.0 65 90.5 66 105.0 67 105.0 68 86.5 69 86.5 70 92.0 71 88.0 72 81.0 73 80.0 74 72.0 75 59.5 76 51.5 77 41.5 78 32.5 79 25.0 80 18.5 81 14.5 82 11.5 83 9.5 84 6.5 85 1.5 86 2.0 87 1.5 88 0.0 89 0.0 90 0.5 91 0.5 92 0.0 93 0.0 94 0.0 95 0.0 96 0.0 97 0.0 98 0.0 99 0.0 100 0.0 >>END_MODULE >>Per base N content pass #Base N-Count 1 0.1 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 0.0 >>END_MODULE >>Sequence Length Distribution pass #Length Count 150 4000.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 93.30000000000001 #Duplication Level Percentage of deduplicated Percentage of total 1 93.32797427652733 87.075 2 6.216505894962487 11.600000000000001 3 0.40192926045016075 1.125 4 0.05359056806002144 0.2 5 0.0 0.0 6 0.0 0.0 7 0.0 0.0 8 0.0 0.0 9 0.0 0.0 >10 0.0 0.0 >50 0.0 0.0 >100 0.0 0.0 >500 0.0 0.0 >1k 0.0 0.0 >5k 0.0 0.0 >10k+ 0.0 0.0 >>END_MODULE >>Overrepresented sequences pass >>END_MODULE >>Adapter Content pass #Position Illumina Universal Adapter Illumina Small RNA 3' Adapter Illumina Small RNA 5' Adapter Nextera Transposase Sequence SOLID Small RNA Adapter 1 0.0 0.0 0.0 0.0 0.0 2 0.0 0.0 0.0 0.0 0.0 3 0.0 0.0 0.0 0.0 0.0 4 0.0 0.0 0.0 0.0 0.0 5 0.0 0.0 0.0 0.0 0.0 6 0.0 0.0 0.0 0.0 0.0 7 0.0 0.0 0.0 0.0 0.0 8 0.0 0.0 0.0 0.0 0.0 9 0.0 0.0 0.0 0.0 0.0 10-11 0.0 0.0 0.0 0.0 0.0 12-13 0.0 0.0 0.0 0.0 0.0 14-15 0.0 0.0 0.0 0.0 0.0 16-17 0.0 0.0 0.0 0.0 0.0 18-19 0.0 0.0 0.0 0.0 0.0 20-21 0.0 0.0 0.0 0.0 0.0 22-23 0.0 0.0 0.0 0.0 0.0 24-25 0.0 0.0 0.0 0.0 0.0 26-27 0.0 0.0 0.0 0.0 0.0 28-29 0.0 0.0 0.0 0.0 0.0 30-31 0.0 0.0 0.0 0.0 0.0 32-33 0.0 0.0 0.0 0.0 0.0 34-35 0.0 0.0 0.0 0.0 0.0 36-37 0.0 0.0 0.0 0.0 0.0 38-39 0.0 0.0 0.0 0.0 0.0 40-41 0.0 0.0 0.0 0.0 0.0 42-43 0.0 0.0 0.0 0.0 0.0 44-45 0.0 0.0 0.0 0.0 0.0 46-47 0.0 0.0 0.0 0.0 0.0 48-49 0.0 0.0 0.0 0.0 0.0 50-51 0.0 0.0 0.0 0.0 0.0 52-53 0.0 0.0 0.0 0.0 0.0 54-55 0.0 0.0 0.0 0.0 0.0 56-57 0.0 0.0 0.0 0.0 0.0 58-59 0.0 0.0 0.0 0.0 0.0 60-61 0.0 0.0 0.0 0.0 0.0 62-63 0.0 0.0 0.0 0.0 0.0 64-65 0.0 0.0 0.0 0.0 0.0 66-67 0.0 0.0 0.0 0.0 0.0 68-69 0.0 0.0 0.0 0.0 0.0 70-71 0.0 0.0 0.0 0.0 0.0 72-73 0.0 0.0 0.0 0.0 0.0 74-75 0.0 0.0 0.0 0.0 0.0 76-77 0.0 0.0 0.0 0.0 0.0 78-79 0.0 0.0 0.0 0.0 0.0 80-81 0.0 0.0 0.0 0.0 0.0 82-83 0.0 0.0 0.0 0.0 0.0 84-85 0.0 0.0 0.0 0.0 0.0 86-87 0.0 0.0 0.0 0.0 0.0 88-89 0.0 0.0 0.0 0.0 0.0 90-91 0.0 0.0 0.0 0.0 0.0 92-93 0.0 0.0 0.0 0.0 0.0 94-95 0.0 0.0 0.0 0.0 0.0 96-97 0.0 0.0 0.0 0.0 0.0 98-99 0.025 0.0 0.0 0.0 0.0 100-101 0.025 0.0 0.0 0.0 0.0 102-103 0.0625 0.0 0.0 0.0 0.0 104-105 0.125 0.0 0.0 0.0 0.0 106-107 0.2 0.0 0.0 0.0 0.0 108-109 0.225 0.0 0.0 0.0 0.0 110-111 0.2375 0.0 0.0 0.0 0.0 112-113 0.25 0.0 0.0 0.0 0.0 114-115 0.3125 0.0 0.0 0.0 0.0 116-117 0.375 0.0 0.0 0.0 0.0 118-119 0.44999999999999996 0.0 0.0 0.0 0.0 120-121 0.4875 0.0 0.0 0.0 0.0 122-123 0.5375000000000001 0.0 0.0 0.0 0.0 124-125 0.5874999999999999 0.0 0.0 0.0 0.0 126-127 0.6125 0.0 0.0 0.0 0.0 128-129 0.675 0.0 0.0 0.0 0.0 130-131 0.8 0.0 0.0 0.0 0.0 132-133 0.8625 0.0 0.0 0.0 0.0 134-135 0.925 0.0 0.0 0.0 0.0 136-137 1.0375 0.0 0.0 0.0 0.0 138 1.125 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position GATCATC 10 0.006973645 144.0 2 >>END_MODULE ERR9452512 read2 length is 150 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename ERR9452512_2.fastq File type Conventional base calls Encoding Sanger / Illumina 1.9 Total Sequences 4000 Sequences flagged as poor quality 0 Sequence length 150 %GC 56 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 35.7965 37.0 37.0 37.0 37.0 37.0 2 35.8635 37.0 37.0 37.0 37.0 37.0 3 35.919 37.0 37.0 37.0 37.0 37.0 4 35.881 37.0 37.0 37.0 37.0 37.0 5 35.9635 37.0 37.0 37.0 37.0 37.0 6 35.851 37.0 37.0 37.0 37.0 37.0 7 35.8005 37.0 37.0 37.0 37.0 37.0 8 35.699 37.0 37.0 37.0 37.0 37.0 9 35.886 37.0 37.0 37.0 37.0 37.0 10-14 35.900400000000005 37.0 37.0 37.0 37.0 37.0 15-19 35.8006 37.0 37.0 37.0 37.0 37.0 20-24 35.717 37.0 37.0 37.0 37.0 37.0 25-29 35.7843 37.0 37.0 37.0 37.0 37.0 30-34 35.70199999999999 37.0 37.0 37.0 37.0 37.0 35-39 35.7802 37.0 37.0 37.0 37.0 37.0 40-44 35.7575 37.0 37.0 37.0 37.0 37.0 45-49 35.7105 37.0 37.0 37.0 37.0 37.0 50-54 35.6828 37.0 37.0 37.0 37.0 37.0 55-59 35.6775 37.0 37.0 37.0 37.0 37.0 60-64 35.5163 37.0 37.0 37.0 37.0 37.0 65-69 35.6739 37.0 37.0 37.0 37.0 37.0 70-74 35.5814 37.0 37.0 37.0 37.0 37.0 75-79 35.5325 37.0 37.0 37.0 37.0 37.0 80-84 35.4988 37.0 37.0 37.0 37.0 37.0 85-89 35.413599999999995 37.0 37.0 37.0 34.6 37.0 90-94 35.3951 37.0 37.0 37.0 34.6 37.0 95-99 35.352000000000004 37.0 37.0 37.0 32.2 37.0 100-104 35.338 37.0 37.0 37.0 37.0 37.0 105-109 35.3445 37.0 37.0 37.0 34.6 37.0 110-114 35.3151 37.0 37.0 37.0 32.2 37.0 115-119 35.298500000000004 37.0 37.0 37.0 34.6 37.0 120-124 35.153 37.0 37.0 37.0 25.0 37.0 125-129 35.15560000000001 37.0 37.0 37.0 29.8 37.0 130-134 35.088899999999995 37.0 37.0 37.0 27.4 37.0 135-139 35.18169999999999 37.0 37.0 37.0 29.8 37.0 140-144 35.0265 37.0 37.0 37.0 25.0 37.0 145-149 34.783100000000005 37.0 37.0 37.0 25.0 37.0 150 35.235 37.0 37.0 37.0 37.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 14 1.0 15 0.0 16 1.0 17 1.0 18 0.0 19 1.0 20 3.0 21 4.0 22 6.0 23 4.0 24 10.0 25 6.0 26 24.0 27 21.0 28 37.0 29 48.0 30 54.0 31 80.0 32 112.0 33 155.0 34 229.0 35 628.0 36 2426.0 37 149.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 29.799999999999997 13.5 14.75 41.949999999999996 2 29.5 20.7 25.624999999999996 24.175 3 26.650000000000002 26.3 18.35 28.7 4 31.574999999999996 28.999999999999996 15.075 24.349999999999998 5 29.475 29.849999999999998 17.075000000000003 23.599999999999998 6 21.375 31.125000000000004 19.8 27.700000000000003 7 22.75 13.55 34.699999999999996 28.999999999999996 8 22.650000000000002 17.424999999999997 25.05 34.875 9 23.95 18.85 25.974999999999998 31.225 10-14 26.525 22.775000000000002 21.985 28.715000000000003 15-19 27.150000000000002 22.005 22.770000000000003 28.075 20-24 27.365000000000002 22.88 21.935 27.82 25-29 27.295 23.080000000000002 21.990000000000002 27.634999999999998 30-34 27.005000000000003 22.95 22.3 27.744999999999997 35-39 27.205000000000002 22.855 21.495 28.444999999999997 40-44 27.705000000000002 22.555 21.3 28.439999999999998 45-49 27.500000000000004 22.665 21.68 28.155 50-54 26.8 22.605 21.815 28.78 55-59 28.139999999999997 22.32 21.41 28.13 60-64 27.61 22.67 22.03 27.689999999999998 65-69 27.139999999999997 22.939999999999998 21.279999999999998 28.64 70-74 27.975 22.625 21.43 27.97 75-79 28.165000000000003 22.18 21.154999999999998 28.499999999999996 80-84 28.115000000000002 21.775 21.07 29.04 85-89 28.275 22.259999999999998 20.880000000000003 28.585 90-94 28.155 22.065 21.67 28.110000000000003 95-99 27.975 22.075 21.6 28.349999999999998 100-104 28.09 22.009999999999998 21.47 28.43 105-109 27.529999999999998 22.14 21.515 28.815 110-114 28.384999999999998 21.47 21.58 28.565 115-119 28.494999999999997 21.87 21.165 28.470000000000002 120-124 27.655 22.06 22.15 28.134999999999998 125-129 28.439999999999998 21.69 21.959999999999997 27.91 130-134 28.175 21.895 21.959999999999997 27.97 135-139 28.33 22.009999999999998 21.39 28.27 140-144 28.48 21.25 22.07 28.199999999999996 145-149 28.625 21.895 21.8 27.68 150 29.725 21.825 21.05 27.400000000000002 >>END_MODULE >>Per sequence GC content fail #GC Content Count 0 0.0 1 0.5 2 1.0 3 0.5 4 0.0 5 0.0 6 0.5 7 0.5 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 0.5 19 0.5 20 1.5 21 1.0 22 0.5 23 1.5 24 1.0 25 1.0 26 4.0 27 5.5 28 3.0 29 3.0 30 5.5 31 6.5 32 7.5 33 10.0 34 16.5 35 23.0 36 25.0 37 31.5 38 46.5 39 58.5 40 69.5 41 89.0 42 106.5 43 120.5 44 112.0 45 116.0 46 137.0 47 128.5 48 120.0 49 117.0 50 114.5 51 102.5 52 94.5 53 101.5 54 94.0 55 90.5 56 95.5 57 93.5 58 95.5 59 100.5 60 99.5 61 102.0 62 94.0 63 83.0 64 95.5 65 96.0 66 92.5 67 98.0 68 102.0 69 100.0 70 99.0 71 96.0 72 76.5 73 62.5 74 58.0 75 59.5 76 57.5 77 45.0 78 29.5 79 21.0 80 20.0 81 15.5 82 13.0 83 11.5 84 6.0 85 3.5 86 3.0 87 1.5 88 0.5 89 0.5 90 1.0 91 0.5 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 0.5 >>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 0.0 >>END_MODULE >>Sequence Length Distribution pass #Length Count 150 4000.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 93.875 #Duplication Level Percentage of deduplicated Percentage of total 1 93.95472703062583 88.2 2 5.619174434087883 10.549999999999999 3 0.37283621837549935 1.05 4 0.05326231691078562 0.2 5 0.0 0.0 6 0.0 0.0 7 0.0 0.0 8 0.0 0.0 9 0.0 0.0 >10 0.0 0.0 >50 0.0 0.0 >100 0.0 0.0 >500 0.0 0.0 >1k 0.0 0.0 >5k 0.0 0.0 >10k+ 0.0 0.0 >>END_MODULE >>Overrepresented sequences pass >>END_MODULE >>Adapter Content pass #Position Illumina Universal Adapter Illumina Small RNA 3' Adapter Illumina Small RNA 5' Adapter Nextera Transposase Sequence SOLID Small RNA Adapter 1 0.0 0.0 0.0 0.0 0.0 2 0.0 0.0 0.0 0.0 0.0 3 0.0 0.0 0.0 0.0 0.0 4 0.0 0.0 0.0 0.0 0.0 5 0.0 0.0 0.0 0.0 0.0 6 0.0 0.0 0.0 0.0 0.0 7 0.0 0.0 0.0 0.0 0.0 8 0.0 0.0 0.0 0.0 0.0 9 0.0 0.0 0.0 0.0 0.0 10-11 0.0 0.0 0.0 0.0 0.0 12-13 0.0 0.0 0.0 0.0 0.0 14-15 0.0 0.0 0.0 0.0 0.0 16-17 0.0 0.0 0.0 0.0 0.0 18-19 0.0 0.0 0.0 0.0 0.0 20-21 0.0 0.0 0.0 0.0 0.0 22-23 0.0 0.0 0.0 0.0 0.0 24-25 0.0 0.0 0.0 0.0 0.0 26-27 0.0 0.0 0.0 0.0 0.0 28-29 0.0 0.0 0.0 0.0 0.0 30-31 0.0 0.0 0.0 0.0 0.0 32-33 0.0 0.0 0.0 0.0 0.0 34-35 0.0 0.0 0.0 0.0 0.0 36-37 0.0 0.0 0.0 0.0 0.0 38-39 0.0 0.0 0.0 0.0 0.0 40-41 0.0 0.0 0.0 0.0 0.0 42-43 0.0 0.0 0.0 0.0 0.0 44-45 0.0 0.0 0.0 0.0 0.0 46-47 0.0 0.0 0.0 0.0 0.0 48-49 0.0 0.0 0.0 0.0 0.0 50-51 0.0 0.0 0.0 0.0 0.0 52-53 0.0 0.0 0.0 0.0 0.0 54-55 0.0 0.0 0.0 0.0 0.0 56-57 0.0 0.0 0.0 0.0 0.0 58-59 0.0 0.0 0.0 0.0 0.0 60-61 0.0 0.0 0.0 0.0 0.0 62-63 0.0 0.0 0.0 0.0 0.0 64-65 0.0 0.0 0.0 0.0 0.0 66-67 0.0 0.0 0.0 0.0 0.0 68-69 0.0 0.0 0.0 0.0 0.0 70-71 0.0 0.0 0.0 0.0 0.0 72-73 0.0 0.0 0.0 0.0 0.0 74-75 0.0 0.0 0.0 0.0 0.0 76-77 0.0 0.0 0.0 0.0 0.0 78-79 0.0 0.0 0.0 0.0 0.0 80-81 0.0 0.0 0.0 0.0 0.0 82-83 0.0 0.0 0.0 0.0 0.0 84-85 0.0 0.0 0.0 0.0 0.0 86-87 0.0 0.0 0.0 0.0 0.0 88-89 0.0 0.0 0.0 0.0 0.0 90-91 0.0 0.0 0.0 0.0 0.0 92-93 0.0 0.0 0.0 0.0 0.0 94-95 0.0 0.0 0.0 0.0 0.0 96-97 0.0 0.0 0.0 0.0 0.0 98-99 0.025 0.0 0.0 0.0 0.0 100-101 0.025 0.0 0.0 0.0 0.0 102-103 0.0625 0.0 0.0 0.0 0.0 104-105 0.125 0.0 0.0 0.0 0.0 106-107 0.1875 0.0 0.0 0.0 0.0 108-109 0.2 0.0 0.0 0.0 0.0 110-111 0.21250000000000002 0.0 0.0 0.0 0.0 112-113 0.225 0.0 0.0 0.0 0.0 114-115 0.2875 0.0 0.0 0.0 0.0 116-117 0.35 0.0 0.0 0.0 0.0 118-119 0.42500000000000004 0.0 0.0 0.0 0.0 120-121 0.4625 0.0 0.0 0.0 0.0 122-123 0.5125 0.0 0.0 0.0 0.0 124-125 0.5625 0.0 0.0 0.0 0.0 126-127 0.5874999999999999 0.0 0.0 0.0 0.0 128-129 0.65 0.0 0.0 0.0 0.0 130-131 0.775 0.0 0.0 0.0 0.0 132-133 0.85 0.0 0.0 0.0 0.0 134-135 0.9 0.0 0.0 0.0 0.0 136-137 1.0125 0.0 0.0 0.0 0.0 138 1.1 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position ACTTAAG 10 0.006973645 144.0 6 >>END_MODULE Read 1566724 spots for ERR9452512.sra Written 1566724 spots for ERR9452512.sra Read 1566724 spots for ERR9452512.sra Written 1566724 spots for ERR9452512.sra Read 1566724 spots for ERR9452512.sra Written 1566724 spots for ERR9452512.sra Read 1566724 spots for ERR9452512.sra Written 1566724 spots for ERR9452512.sra Read 1566724 spots for ERR9452512.sra Written 1566724 spots for ERR9452512.sra Read 1566724 spots for ERR9452512.sra Written 1566724 spots for ERR9452512.sra Read 1566724 spots for ERR9452512.sra Written 1566724 spots for ERR9452512.sra Read 1566724 spots for ERR9452512.sra Written 1566724 spots for ERR9452512.sra Read 1566724 spots for ERR9452512.sra Written 1566724 spots for ERR9452512.sra Read 1566724 spots for ERR9452512.sra Written 1566724 spots for ERR9452512.sra Read 1566724 spots for ERR9452512.sra Written 1566724 spots for ERR9452512.sra Read 1566724 spots for ERR9452512.sra Written 1566724 spots for ERR9452512.sra Read 1566724 spots for ERR9452512.sra Written 1566724 spots for ERR9452512.sra Read 1566724 spots for ERR9452512.sra Written 1566724 spots for ERR9452512.sra Read 1566728 spots for ERR9452512.sra Written 1566728 spots for ERR9452512.sra Read 1566724 spots for ERR9452512.sra Written 1566724 spots for ERR9452512.sra Read 1566724 spots for ERR9452512.sra Written 1566724 spots for ERR9452512.sra Read 1566724 spots for ERR9452512.sra Written 1566724 spots for ERR9452512.sra Read 1566724 spots for ERR9452512.sra Written 1566724 spots for ERR9452512.sra Read 1566724 spots for ERR9452512.sra Written 1566724 spots for ERR9452512.sra SRR ids: ['ERR9452512.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_6nv3ezzw ERR9452512.sra spots: 31334484 blocks: [[1, 1566724], [1566725, 3133448], [3133449, 4700172], [4700173, 6266896], [6266897, 7833620], [7833621, 9400344], [9400345, 10967068], [10967069, 12533792], [12533793, 14100516], [14100517, 15667240], [15667241, 17233964], [17233965, 18800688], [18800689, 20367412], [20367413, 21934136], [21934137, 23500860], [23500861, 25067584], [25067585, 26634308], [26634309, 28201032], [28201033, 29767756], [29767757, 31334484]] ERR9452512 file size 10535327 ERR9452512 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 ERR9452512 ERR9452512_1.fastq ERR9452512_2.fastq Input file: ERR9452512_1.fastq Paired file: ERR9452512_2.fastq trimmed: ERR9452512-trimmed-pair1.fastq, ERR9452512-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 22:57:11 2024 >> started Fri Dec 6 22:57:44 2024 >> done (33.556s) 31334484 read pairs processed; of these: 267 ( 0.00%) short read pairs filtered out after trimming by size control 1817 ( 0.01%) empty read pairs filtered out after trimming by size control 31332400 (99.99%) read pairs available; of these: 541681 ( 1.73%) trimmed read pairs available after processing 30790719 (98.27%) untrimmed read pairs available after processing Length distribution of reads after trimming: length count percentage 18 14 0.00% 19 41 0.00% 20 3504 0.01% 21 32 0.00% 22 17 0.00% 23 18 0.00% 24 12 0.00% 25 22 0.00% 26 15 0.00% 27 22 0.00% 28 27 0.00% 29 66 0.00% 30 117 0.00% 31 74 0.00% 32 29 0.00% 33 43 0.00% 34 34 0.00% 35 24 0.00% 36 36 0.00% 37 38 0.00% 38 31 0.00% 39 36 0.00% 40 41 0.00% 41 42 0.00% 42 51 0.00% 43 39 0.00% 44 59 0.00% 45 73 0.00% 46 64 0.00% 47 62 0.00% 48 107 0.00% 49 74 0.00% 50 91 0.00% 51 110 0.00% 52 121 0.00% 53 121 0.00% 54 155 0.00% 55 145 0.00% 56 166 0.00% 57 186 0.00% 58 213 0.00% 59 198 0.00% 60 252 0.00% 61 297 0.00% 62 296 0.00% 63 319 0.00% 64 302 0.00% 65 295 0.00% 66 389 0.00% 67 382 0.00% 68 439 0.00% 69 424 0.00% 70 445 0.00% 71 499 0.00% 72 548 0.00% 73 617 0.00% 74 624 0.00% 75 628 0.00% 76 695 0.00% 77 687 0.00% 78 871 0.00% 79 765 0.00% 80 866 0.00% 81 873 0.00% 82 934 0.00% 83 972 0.00% 84 1085 0.00% 85 1139 0.00% 86 1125 0.00% 87 1199 0.00% 88 1353 0.00% 89 1322 0.00% 90 1437 0.00% 91 1563 0.00% 92 1531 0.00% 93 1727 0.01% 94 1846 0.01% 95 1946 0.01% 96 2001 0.01% 97 2140 0.01% 98 1941 0.01% 99 2218 0.01% 100 2414 0.01% 101 2514 0.01% 102 2563 0.01% 103 2952 0.01% 104 3044 0.01% 105 3214 0.01% 106 3315 0.01% 107 3328 0.01% 108 3645 0.01% 109 3941 0.01% 110 3874 0.01% 111 4190 0.01% 112 4333 0.01% 113 4658 0.01% 114 4999 0.02% 115 5191 0.02% 116 5372 0.02% 117 5332 0.02% 118 5758 0.02% 119 6244 0.02% 120 6257 0.02% 121 6626 0.02% 122 6941 0.02% 123 7500 0.02% 124 7801 0.02% 125 8352 0.03% 126 8709 0.03% 127 9281 0.03% 128 9515 0.03% 129 9866 0.03% 130 10435 0.03% 131 10699 0.03% 132 11047 0.04% 133 11610 0.04% 134 12762 0.04% 135 13220 0.04% 136 14083 0.04% 137 14490 0.05% 138 15163 0.05% 139 15615 0.05% 140 16772 0.05% 141 16928 0.05% 142 17753 0.06% 143 19032 0.06% 144 19338 0.06% 145 21138 0.07% 146 21760 0.07% 147 23250 0.07% 148 24221 0.08% 149 25274 0.08% 150 30790719 98.27% 31332400 reads passed initial QC criterion=sequence-density sequence-density=0.32 sequence-density-rank=1 fanout-score=2.71 fanout-score-rank=26 prefix-density=0.33 prefix-fanout=2.6 sequence=GGTGTTGTCGAAGCCGATGATGCGGAC criterion=fanout-score sequence-density=0.03 sequence-density-rank=35 fanout-score=798.37 fanout-score-rank=1 prefix-density=1.11 prefix-fanout=21.3 sequence=GCGGCGGCGAACCGCCCCCGTCGCCGCGATCCGAACACTTCACCGGACCATTCAATCGGTAGGAGCGACGGGCGGTGTGTACAAAGGGCAGGGACGTAGTCAACGCGAGCTGATGACTCGCGCTTACTAGGCATTCCTCGTTGAAGACCAACAATTGCAATGATCTATCCCCATCACGATGAAATTTCCCAAGATTACCCGGGCCTGTCGGCCAAGGCTATATACTCGTTGAATACATCAGTGTAGCGCGCGTGCGGCCCAGAACATCTAAGGGCATCACAGACCTGTTATTGCCTCAAACTTCCGTCGCCTAAACGGCGATAGTCCCTCTAAGAAGCTAGCTGCGGAGGGATGGCTCCGCATAGCTAGTTAGCAGGCTGAGGTCTCGTTCGTTAACGGAATTAACCAGACAAATCGCTCCACCAACTAAGAACGGCCATGCACCACCACCCATAGAATCAAGAAAGAGCTCTCAGTCTGTCAATCCTTGCTATGTCTGGACCTGGTAAGT criterion=sequence-density sequence-density=0.30 sequence-density-rank=1 fanout-score=2.66 fanout-score-rank=27 prefix-density=0.31 prefix-fanout=2.6 sequence=GGTGTTGTCGAAGCCGATGATGCGGAC criterion=fanout-score sequence-density=0.12 sequence-density-rank=29 fanout-score=155.87 fanout-score-rank=1 prefix-density=1.07 prefix-fanout=17.9 sequence=CCGCCGCCGCCG ERR9452512 testing PE reads STAR mapping to Ensembl genome Started job on | Dec 06 23:00:43 Started mapping on | Dec 06 23:00:44 Finished on | Dec 06 23:03:26 Mapping speed, Million of reads per hour | 696.28 Number of input reads | 31332400 Average input read length | 299 UNIQUE READS: Uniquely mapped reads number | 29699081 Uniquely mapped reads % | 94.79% Average mapped length | 298.16 Number of splices: Total | 27741175 Number of splices: Annotated (sjdb) | 26157612 Number of splices: GT/AG | 27346145 Number of splices: GC/AG | 355804 Number of splices: AT/AC | 11872 Number of splices: Non-canonical | 27354 Mismatch rate per base, % | 0.20% Deletion rate per base | 0.00% Deletion average length | 1.67 Insertion rate per base | 0.00% Insertion average length | 1.23 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 307741 % of reads mapped to multiple loci | 0.98% Number of reads mapped to too many loci | 83957 % of reads mapped to too many loci | 0.27% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 1.35% % of reads unmapped: other | 2.62% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 1325578 1325578 1325578 N_multimapping 307741 307741 307741 N_noFeature 936141 14987008 15102469 N_ambiguous 720842 91039 89764 UnstrandedReadsAssigned:28042098 PositiveStrandReadsAssigned:14621034 NegativeStrandReadsAssigned:14506848 Dataset is classified unstranded MeadianReadLen=150 20thPercentileLength=150 echo kmer=145 ERR9452512 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: ERR9452512-trimmed-pair1.fastq ERR9452512-trimmed-pair2.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 31,332,400 reads, 29,196,545 reads pseudoaligned [quant] estimated average fragment length: 248.945 [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,134 rounds 52973 ERR9452512.ke.tsv 35125 ERR9452512.se.tsv 88098 total ==> ERR9452512.ke.tsv <== target_id length eff_length est_counts tpm PNS24245 936 688.444 0 0 PNS24247 1044 796.055 67.1844 3.54863 PNS24249 1928 1680.06 340.771 8.52856 PNS24246 1044 796.055 67.1844 3.54863 PNS24248 1044 796.055 67.1844 3.54863 PNS24244 1471 1223.06 23.6752 0.813922 PNS24243 293 63.7216 37 24.4147 KQK14069 1603 1355.06 21343.1 662.273 KQK14071 474 229.445 1848.76 338.795 ==> ERR9452512.se.tsv <== BRADI_1g14170v3 24589 BRADI_1g53295v3 180 BRADI_1g59795v3 685 BRADI_1g07683v3 0 BRADI_1g00485v3 57 BRADI_1g20270v3 1109 BRADI_1g74790v3 421 BRADI_1g09890v3 8 BRADI_1g77505v3 494 BRADI_1g48960v3 0 ERR9452512 completed mapping pipeline successfully