Starting /dee2/code/volunteer_pipeline.sh SRR7814828 current disk space = 1551497519104 free memory = 1605434624 SRR7814828 SRAfilesize 807aed17fc804ba9cc64170a73610802 SRR7814828.sra SRR7814828.sra file validated SRR7814828 is paired end SRR7814828 is conventional basespace SRR7814828 read1 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR7814828_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 36.2215 37.0 37.0 37.0 37.0 37.0 2 36.3515 37.0 37.0 37.0 37.0 37.0 3 36.3315 37.0 37.0 37.0 37.0 37.0 4 36.531 37.0 37.0 37.0 37.0 37.0 5 36.5595 37.0 37.0 37.0 37.0 37.0 6 36.519 37.0 37.0 37.0 37.0 37.0 7 36.432 37.0 37.0 37.0 37.0 37.0 8 36.45 37.0 37.0 37.0 37.0 37.0 9 36.457 37.0 37.0 37.0 37.0 37.0 10-14 36.477 37.0 37.0 37.0 37.0 37.0 15-19 36.511399999999995 37.0 37.0 37.0 37.0 37.0 20-24 36.4678 37.0 37.0 37.0 37.0 37.0 25-29 36.4486 37.0 37.0 37.0 37.0 37.0 30-34 36.3882 37.0 37.0 37.0 37.0 37.0 35-39 36.333600000000004 37.0 37.0 37.0 37.0 37.0 40-44 36.298500000000004 37.0 37.0 37.0 37.0 37.0 45-49 36.335300000000004 37.0 37.0 37.0 37.0 37.0 50-54 36.289100000000005 37.0 37.0 37.0 37.0 37.0 55-59 36.2438 37.0 37.0 37.0 37.0 37.0 60-64 36.1495 37.0 37.0 37.0 37.0 37.0 65-69 36.183 37.0 37.0 37.0 37.0 37.0 70-74 36.1179 37.0 37.0 37.0 37.0 37.0 75-79 36.0806 37.0 37.0 37.0 37.0 37.0 80-84 36.134 37.0 37.0 37.0 37.0 37.0 85-89 36.0661 37.0 37.0 37.0 37.0 37.0 90-94 35.9816 37.0 37.0 37.0 37.0 37.0 95-99 35.914 37.0 37.0 37.0 37.0 37.0 100-104 35.889300000000006 37.0 37.0 37.0 37.0 37.0 105-109 35.925599999999996 37.0 37.0 37.0 37.0 37.0 110-114 35.82 37.0 37.0 37.0 37.0 37.0 115-119 35.708600000000004 37.0 37.0 37.0 37.0 37.0 120-124 35.6844 37.0 37.0 37.0 37.0 37.0 125-129 35.6103 37.0 37.0 37.0 37.0 37.0 130-134 35.5172 37.0 37.0 37.0 37.0 37.0 135-139 35.448499999999996 37.0 37.0 37.0 37.0 37.0 140-144 35.3641 37.0 37.0 37.0 34.6 37.0 145-149 35.1431 37.0 37.0 37.0 29.8 37.0 150-151 34.384249999999994 37.0 37.0 37.0 25.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 20 2.0 21 0.0 22 0.0 23 3.0 24 4.0 25 4.0 26 7.0 27 8.0 28 13.0 29 24.0 30 33.0 31 50.0 32 74.0 33 116.0 34 184.0 35 431.0 36 2789.0 37 258.0 >>END_MODULE >>Per base sequence content warn #Base G A T C 1 48.24561403508772 11.027568922305765 6.390977443609022 34.335839598997495 2 25.18759379689845 14.307153576788394 32.666333166583286 27.838919459729865 3 21.975 18.475 24.05 35.5 4 26.775 25.324999999999996 20.25 27.650000000000002 5 27.575 29.7 21.55 21.175 6 23.125 31.0 22.775000000000002 23.1 7 17.775 24.275 38.775 19.175 8 19.675 21.675 30.25 28.4 9 20.549999999999997 21.224999999999998 31.474999999999998 26.75 10-14 24.044999999999998 26.825 24.48 24.65 15-19 23.305 25.365 25.15 26.179999999999996 20-24 22.97 25.635 25.119999999999997 26.275 25-29 23.885 25.490000000000002 24.515 26.11 30-34 23.715 25.665 24.395 26.224999999999998 35-39 23.419999999999998 25.305 24.87 26.405 40-44 24.135 25.929999999999996 24.575 25.36 45-49 24.310000000000002 25.25 24.759999999999998 25.679999999999996 50-54 23.815 25.040000000000003 24.94 26.205000000000002 55-59 23.990000000000002 25.21 24.86 25.94 60-64 24.044999999999998 25.205 24.41 26.340000000000003 65-69 23.925 25.155 25.135 25.785000000000004 70-74 24.41 25.55 24.279999999999998 25.759999999999998 75-79 23.945 25.06 24.395 26.6 80-84 24.37 24.75 24.815 26.064999999999998 85-89 24.38 25.295 23.724999999999998 26.6 90-94 23.995 24.779999999999998 24.735 26.490000000000002 95-99 23.845 24.725 25.03 26.400000000000002 100-104 24.785 25.430000000000003 23.674999999999997 26.11 105-109 24.585 24.665 24.245 26.505000000000003 110-114 24.395 24.665 24.43 26.51 115-119 24.67 25.27 23.815 26.245 120-124 24.755 25.124999999999996 23.765 26.355 125-129 24.779999999999998 25.22 23.815 26.185000000000002 130-134 24.65 25.430000000000003 23.69 26.229999999999997 135-139 24.985 24.495 24.255 26.265 140-144 24.565 25.115 24.505 25.814999999999998 145-149 24.945 25.15 23.72 26.185000000000002 150-151 24.925 24.3625 23.599999999999998 27.1125 >>END_MODULE >>Per sequence GC content fail #GC Content Count 0 0.0 1 0.5 2 0.5 3 0.0 4 0.0 5 0.0 6 0.0 7 0.0 8 0.0 9 0.0 10 0.0 11 0.0 12 0.0 13 0.0 14 0.0 15 0.0 16 0.0 17 0.0 18 0.0 19 0.0 20 0.0 21 0.0 22 0.5 23 0.5 24 0.0 25 0.0 26 0.5 27 2.0 28 2.0 29 4.5 30 10.5 31 13.0 32 17.0 33 17.5 34 19.0 35 33.0 36 43.5 37 57.5 38 70.0 39 85.0 40 107.0 41 129.0 42 161.0 43 172.5 44 172.5 45 188.5 46 197.0 47 197.0 48 180.5 49 179.5 50 175.0 51 159.5 52 153.5 53 128.5 54 113.5 55 109.0 56 95.5 57 86.5 58 78.0 59 68.0 60 72.5 61 67.0 62 64.0 63 64.0 64 62.5 65 64.0 66 59.0 67 48.0 68 44.0 69 43.5 70 29.0 71 23.0 72 28.5 73 27.5 74 20.5 75 14.0 76 12.5 77 10.5 78 8.0 79 5.0 80 1.0 81 0.5 82 1.0 83 1.0 84 0.0 85 0.0 86 0.5 87 0.5 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 0.25 2 0.05 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 94.85 #Duplication Level Percentage of deduplicated Percentage of total 1 94.8866631523458 90.0 2 4.797047970479705 9.1 3 0.316288877174486 0.8999999999999999 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 warn #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 0.025 0.0 0.0 0.0 0.0 76-77 0.0625 0.0 0.0 0.0 0.0 78-79 0.1125 0.0 0.0 0.0 0.0 80-81 0.1375 0.0 0.0 0.0 0.0 82-83 0.1875 0.0 0.0 0.0 0.0 84-85 0.225 0.0 0.0 0.0 0.0 86-87 0.2625 0.0 0.0 0.0 0.0 88-89 0.32499999999999996 0.0 0.0 0.0 0.0 90-91 0.3625 0.0 0.0 0.0 0.0 92-93 0.4125 0.0 0.0 0.0 0.0 94-95 0.48750000000000004 0.0 0.0 0.0 0.0 96-97 0.675 0.0 0.0 0.0 0.0 98-99 0.8 0.0 0.0 0.0 0.0 100-101 1.025 0.0 0.0 0.0 0.0 102-103 1.2625000000000002 0.0 0.0 0.0 0.0 104-105 1.4 0.0 0.0 0.0 0.0 106-107 1.625 0.0 0.0 0.0 0.0 108-109 1.875 0.0 0.0 0.0 0.0 110-111 2.175 0.0 0.0 0.0 0.0 112-113 2.4375 0.0 0.0 0.0 0.0 114-115 2.7125 0.0 0.0 0.0 0.0 116-117 2.7875 0.0 0.0 0.0 0.0 118-119 3.2125000000000004 0.0 0.0 0.0 0.0 120-121 3.6875 0.0 0.0 0.0 0.0 122-123 4.125 0.0 0.0 0.0 0.0 124-125 4.6125 0.0 0.0 0.0 0.0 126-127 5.0125 0.0 0.0 0.0 0.0 128-129 5.225 0.0 0.0 0.0 0.0 130-131 5.55 0.0 0.0 0.0 0.0 132-133 6.0 0.0 0.0 0.0 0.0 134-135 6.4125 0.0 0.0 0.0 0.0 136-137 6.8375 0.0 0.0 0.0 0.0 138-139 7.262499999999999 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position CGGAAGA 40 0.005621335 54.375 145 >>END_MODULE SRR7814828 read2 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR7814828_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 36.303 37.0 37.0 37.0 37.0 37.0 2 35.912 37.0 37.0 37.0 37.0 37.0 3 36.0675 37.0 37.0 37.0 37.0 37.0 4 36.1285 37.0 37.0 37.0 37.0 37.0 5 36.234 37.0 37.0 37.0 37.0 37.0 6 36.074 37.0 37.0 37.0 37.0 37.0 7 36.0445 37.0 37.0 37.0 37.0 37.0 8 36.2255 37.0 37.0 37.0 37.0 37.0 9 36.137 37.0 37.0 37.0 37.0 37.0 10-14 36.119600000000005 37.0 37.0 37.0 37.0 37.0 15-19 36.115199999999994 37.0 37.0 37.0 37.0 37.0 20-24 36.028 37.0 37.0 37.0 37.0 37.0 25-29 35.9274 37.0 37.0 37.0 37.0 37.0 30-34 35.9169 37.0 37.0 37.0 37.0 37.0 35-39 35.8235 37.0 37.0 37.0 37.0 37.0 40-44 35.8092 37.0 37.0 37.0 37.0 37.0 45-49 35.78009999999999 37.0 37.0 37.0 37.0 37.0 50-54 35.783 37.0 37.0 37.0 37.0 37.0 55-59 35.7041 37.0 37.0 37.0 37.0 37.0 60-64 35.5855 37.0 37.0 37.0 37.0 37.0 65-69 35.6315 37.0 37.0 37.0 37.0 37.0 70-74 35.54690000000001 37.0 37.0 37.0 37.0 37.0 75-79 35.5544 37.0 37.0 37.0 37.0 37.0 80-84 35.460800000000006 37.0 37.0 37.0 37.0 37.0 85-89 35.43140000000001 37.0 37.0 37.0 37.0 37.0 90-94 35.3559 37.0 37.0 37.0 37.0 37.0 95-99 35.357600000000005 37.0 37.0 37.0 37.0 37.0 100-104 35.2845 37.0 37.0 37.0 34.6 37.0 105-109 35.260200000000005 37.0 37.0 37.0 32.2 37.0 110-114 35.010000000000005 37.0 37.0 37.0 25.0 37.0 115-119 35.063900000000004 37.0 37.0 37.0 25.0 37.0 120-124 34.9851 37.0 37.0 37.0 25.0 37.0 125-129 34.902699999999996 37.0 37.0 37.0 25.0 37.0 130-134 34.8052 37.0 37.0 37.0 25.0 37.0 135-139 34.505700000000004 37.0 37.0 37.0 25.0 37.0 140-144 34.4277 37.0 37.0 37.0 25.0 37.0 145-149 34.2992 37.0 37.0 37.0 25.0 37.0 150-151 33.668499999999995 37.0 37.0 37.0 18.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 12 1.0 13 8.0 14 5.0 15 4.0 16 4.0 17 3.0 18 6.0 19 1.0 20 3.0 21 10.0 22 8.0 23 7.0 24 7.0 25 9.0 26 9.0 27 14.0 28 20.0 29 25.0 30 39.0 31 56.0 32 77.0 33 149.0 34 313.0 35 778.0 36 2340.0 37 104.0 >>END_MODULE >>Per base sequence content warn #Base G A T C 1 43.2 18.675 7.9750000000000005 30.15 2 31.1 22.225 26.075 20.599999999999998 3 23.575 24.2 27.575 24.65 4 27.474999999999998 30.4 19.45 22.675 5 28.875 33.0 18.025 20.1 6 23.1 36.525 18.625 21.75 7 23.799999999999997 19.275000000000002 32.7 24.224999999999998 8 23.974999999999998 23.549999999999997 22.775000000000002 29.7 9 24.55 22.650000000000002 26.5 26.3 10-14 27.075 24.995 22.545 25.385 15-19 26.14 24.48 23.485 25.895000000000003 20-24 26.095000000000002 24.745 23.455000000000002 25.705 25-29 27.38 24.67 22.875 25.074999999999996 30-34 25.869999999999997 24.705 24.14 25.285000000000004 35-39 26.035000000000004 24.9 24.015 25.05 40-44 27.245 24.46 22.93 25.365 45-49 26.795 24.52 23.46 25.224999999999998 50-54 26.384999999999998 24.945 23.345 25.324999999999996 55-59 26.985 24.895 23.16 24.959999999999997 60-64 26.565 24.654999999999998 24.16 24.62 65-69 27.250000000000004 24.490000000000002 23.775 24.485 70-74 26.875 24.610000000000003 23.494999999999997 25.019999999999996 75-79 26.229999999999997 24.34 24.27 25.16 80-84 27.3 25.564999999999998 23.515 23.62 85-89 27.35 24.855 22.91 24.884999999999998 90-94 27.345000000000002 24.92 23.77 23.965 95-99 26.825 25.019999999999996 23.93 24.224999999999998 100-104 27.089999999999996 24.385 23.865 24.66 105-109 27.544999999999998 24.54 23.735 24.18 110-114 27.55 25.395 22.95 24.104999999999997 115-119 27.544999999999998 25.314999999999998 22.919999999999998 24.22 120-124 28.025 25.47 22.865 23.64 125-129 27.834999999999997 24.985 23.56 23.62 130-134 28.13 25.374999999999996 22.965 23.53 135-139 27.83 25.495 23.255 23.419999999999998 140-144 28.455000000000002 25.430000000000003 23.580000000000002 22.535 145-149 28.494999999999997 25.605 22.93 22.97 150-151 28.8625 24.0625 23.5625 23.5125 >>END_MODULE >>Per sequence GC content fail #GC Content Count 0 2.0 1 1.0 2 0.0 3 0.0 4 0.0 5 0.0 6 0.0 7 0.5 8 0.5 9 0.5 10 0.5 11 1.0 12 1.0 13 0.5 14 0.5 15 0.5 16 0.5 17 0.0 18 0.0 19 0.5 20 0.5 21 0.0 22 0.5 23 0.5 24 1.0 25 1.0 26 0.0 27 1.0 28 4.0 29 7.0 30 7.5 31 11.0 32 12.5 33 11.0 34 16.0 35 23.0 36 31.5 37 40.0 38 50.0 39 67.5 40 92.0 41 125.0 42 144.5 43 154.0 44 165.5 45 185.0 46 185.0 47 164.0 48 165.5 49 157.5 50 144.5 51 143.0 52 130.0 53 125.0 54 136.5 55 127.0 56 108.5 57 89.5 58 87.0 59 94.0 60 77.0 61 75.0 62 79.5 63 81.0 64 79.5 65 74.0 66 69.0 67 69.5 68 68.5 69 55.5 70 47.0 71 43.5 72 37.5 73 30.5 74 25.0 75 18.0 76 14.0 77 7.5 78 2.5 79 3.0 80 4.5 81 2.5 82 0.5 83 2.0 84 3.0 85 1.5 86 1.0 87 1.0 88 0.0 89 0.5 90 0.5 91 0.0 92 0.5 93 1.0 94 0.5 95 0.0 96 0.0 97 0.0 98 0.5 99 1.5 100 3.0 >>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 94.625 #Duplication Level Percentage of deduplicated Percentage of total 1 94.9009247027741 89.8 2 4.7556142668428 9.0 3 0.26420079260237783 0.75 4 0.02642007926023778 0.1 5 0.0 0.0 6 0.0 0.0 7 0.05284015852047556 0.35000000000000003 8 0.0 0.0 9 0.0 0.0 >10 0.0 0.0 >50 0.0 0.0 >100 0.0 0.0 >500 0.0 0.0 >1k 0.0 0.0 >5k 0.0 0.0 >10k+ 0.0 0.0 >>END_MODULE >>Overrepresented sequences warn #Sequence Count Percentage Possible Source GCTCATCATCCGTTTTAATACCAAAGCTCTTCATATTCTCCTCCTTGATT 7 0.17500000000000002 No Hit GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG 7 0.17500000000000002 No Hit >>END_MODULE >>Adapter Content warn #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 0.025 0.0 0.0 0.0 0.0 76-77 0.0625 0.0 0.0 0.0 0.0 78-79 0.1125 0.0 0.0 0.0 0.0 80-81 0.1375 0.0 0.0 0.0 0.0 82-83 0.1875 0.0 0.0 0.0 0.0 84-85 0.2 0.0 0.0 0.0 0.0 86-87 0.2375 0.0 0.0 0.0 0.0 88-89 0.30000000000000004 0.0 0.0 0.0 0.0 90-91 0.3375 0.0 0.0 0.0 0.0 92-93 0.38749999999999996 0.0 0.0 0.0 0.0 94-95 0.4625 0.0 0.0 0.0 0.0 96-97 0.6499999999999999 0.0 0.0 0.0 0.0 98-99 0.75 0.0 0.0 0.0 0.0 100-101 0.975 0.0 0.0 0.0 0.0 102-103 1.2374999999999998 0.0 0.0 0.0 0.0 104-105 1.35 0.0 0.0 0.0 0.0 106-107 1.55 0.0 0.0 0.0 0.0 108-109 1.7999999999999998 0.0 0.0 0.0 0.0 110-111 2.0999999999999996 0.0 0.0 0.0 0.0 112-113 2.3625 0.0 0.0 0.0 0.0 114-115 2.6500000000000004 0.0 0.0 0.0 0.0 116-117 2.7625 0.0 0.0 0.0 0.0 118-119 3.1875 0.0 0.0 0.0 0.0 120-121 3.675 0.0 0.0 0.0 0.0 122-123 4.125 0.0 0.0 0.0 0.0 124-125 4.6125 0.0 0.0 0.0 0.0 126-127 5.0125 0.0 0.0 0.0 0.0 128-129 5.199999999999999 0.0 0.0 0.0 0.0 130-131 5.55 0.0 0.0 0.0 0.0 132-133 6.0125 0.0 0.0 0.0 0.0 134-135 6.4375 0.0 0.0 0.0 0.0 136-137 6.862500000000001 0.0 0.0 0.0 0.0 138-139 7.3125 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content pass >>END_MODULE Read 1799093 spots for SRR7814828.sra Written 1799093 spots for SRR7814828.sra Read 1799093 spots for SRR7814828.sra Written 1799093 spots for SRR7814828.sra Read 1799093 spots for SRR7814828.sra Written 1799093 spots for SRR7814828.sra Read 1799093 spots for SRR7814828.sra Written 1799093 spots for SRR7814828.sra Read 1799093 spots for SRR7814828.sra Written 1799093 spots for SRR7814828.sra Read 1799099 spots for SRR7814828.sra Written 1799099 spots for SRR7814828.sra Read 1799093 spots for SRR7814828.sra Written 1799093 spots for SRR7814828.sra Read 1799093 spots for SRR7814828.sra Written 1799093 spots for SRR7814828.sra Read 1799093 spots for SRR7814828.sra Written 1799093 spots for SRR7814828.sra Read 1799093 spots for SRR7814828.sra Written 1799093 spots for SRR7814828.sra Read 1799093 spots for SRR7814828.sra Written 1799093 spots for SRR7814828.sra Read 1799093 spots for SRR7814828.sra Written 1799093 spots for SRR7814828.sra Read 1799093 spots for SRR7814828.sra Written 1799093 spots for SRR7814828.sra Read 1799093 spots for SRR7814828.sra Written 1799093 spots for SRR7814828.sra Read 1799093 spots for SRR7814828.sra Written 1799093 spots for SRR7814828.sra Read 1799093 spots for SRR7814828.sra Written 1799093 spots for SRR7814828.sra Read 1799093 spots for SRR7814828.sra Written 1799093 spots for SRR7814828.sra Read 1799093 spots for SRR7814828.sra Written 1799093 spots for SRR7814828.sra Read 1799093 spots for SRR7814828.sra Written 1799093 spots for SRR7814828.sra Read 1799093 spots for SRR7814828.sra Written 1799093 spots for SRR7814828.sra SRR ids: ['SRR7814828.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_uw_d0rb3 SRR7814828.sra spots: 35981866 blocks: [[1, 1799093], [1799094, 3598186], [3598187, 5397279], [5397280, 7196372], [7196373, 8995465], [8995466, 10794558], [10794559, 12593651], [12593652, 14392744], [14392745, 16191837], [16191838, 17990930], [17990931, 19790023], [19790024, 21589116], [21589117, 23388209], [23388210, 25187302], [25187303, 26986395], [26986396, 28785488], [28785489, 30584581], [30584582, 32383674], [32383675, 34182767], [34182768, 35981866]] SRR7814828 file size 12171373 SRR7814828 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 SRR7814828 SRR7814828_1.fastq SRR7814828_2.fastq Input file: SRR7814828_1.fastq Paired file: SRR7814828_2.fastq trimmed: SRR7814828-trimmed-pair1.fastq, SRR7814828-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 11:33:49 2024 >> started Fri Dec 6 11:34:28 2024 >> done (38.893s) 35981866 read pairs processed; of these: 210 ( 0.00%) short read pairs filtered out after trimming by size control 9585 ( 0.03%) empty read pairs filtered out after trimming by size control 35972071 (99.97%) read pairs available; of these: 3701845 (10.29%) trimmed read pairs available after processing 32270226 (89.71%) untrimmed read pairs available after processing Length distribution of reads after trimming: length count percentage 18 13 0.00% 19 10 0.00% 20 16 0.00% 21 15 0.00% 22 28 0.00% 23 31 0.00% 24 26 0.00% 25 29 0.00% 26 45 0.00% 27 39 0.00% 28 47 0.00% 29 57 0.00% 30 56 0.00% 31 68 0.00% 32 86 0.00% 33 60 0.00% 34 68 0.00% 35 69 0.00% 36 81 0.00% 37 99 0.00% 38 91 0.00% 39 81 0.00% 40 96 0.00% 41 103 0.00% 42 124 0.00% 43 94 0.00% 44 103 0.00% 45 114 0.00% 46 119 0.00% 47 125 0.00% 48 161 0.00% 49 199 0.00% 50 168 0.00% 51 238 0.00% 52 228 0.00% 53 274 0.00% 54 257 0.00% 55 291 0.00% 56 315 0.00% 57 363 0.00% 58 374 0.00% 59 483 0.00% 60 518 0.00% 61 612 0.00% 62 641 0.00% 63 734 0.00% 64 784 0.00% 65 884 0.00% 66 926 0.00% 67 1032 0.00% 68 1255 0.00% 69 1269 0.00% 70 1528 0.00% 71 1604 0.00% 72 2021 0.01% 73 2213 0.01% 74 2504 0.01% 75 2758 0.01% 76 3080 0.01% 77 3357 0.01% 78 3682 0.01% 79 4306 0.01% 80 4719 0.01% 81 5399 0.02% 82 6101 0.02% 83 6806 0.02% 84 7448 0.02% 85 8500 0.02% 86 9127 0.03% 87 9801 0.03% 88 10493 0.03% 89 11603 0.03% 90 12686 0.04% 91 13753 0.04% 92 15418 0.04% 93 16654 0.05% 94 18196 0.05% 95 19453 0.05% 96 20851 0.06% 97 22080 0.06% 98 23188 0.06% 99 25111 0.07% 100 26128 0.07% 101 27262 0.08% 102 29335 0.08% 103 31164 0.09% 104 32864 0.09% 105 34523 0.10% 106 36394 0.10% 107 37619 0.10% 108 38870 0.11% 109 40416 0.11% 110 41771 0.12% 111 43150 0.12% 112 45417 0.13% 113 47359 0.13% 114 49486 0.14% 115 50695 0.14% 116 52741 0.15% 117 54227 0.15% 118 55504 0.15% 119 56645 0.16% 120 57832 0.16% 121 59704 0.17% 122 61900 0.17% 123 63991 0.18% 124 66492 0.18% 125 67560 0.19% 126 68730 0.19% 127 70966 0.20% 128 71242 0.20% 129 73081 0.20% 130 74455 0.21% 131 75478 0.21% 132 77955 0.22% 133 80316 0.22% 134 81403 0.23% 135 83236 0.23% 136 84660 0.24% 137 85612 0.24% 138 86823 0.24% 139 89274 0.25% 140 89460 0.25% 141 91111 0.25% 142 94635 0.26% 143 94178 0.26% 144 97857 0.27% 145 99629 0.28% 146 99941 0.28% 147 101828 0.28% 148 103182 0.29% 149 102803 0.29% 150 106502 0.30% 151 32270226 89.71% 35972071 reads passed initial QC criterion=sequence-density sequence-density=0.15 sequence-density-rank=1 fanout-score=3.63 fanout-score-rank=30 prefix-density=0.18 prefix-fanout=3.1 sequence=GTGATGGTCTTGCC criterion=fanout-score sequence-density=0.03 sequence-density-rank=27 fanout-score=308.06 fanout-score-rank=1 prefix-density=0.54 prefix-fanout=19.8 sequence=GGCGGCGGCGAACCGCCCCCGTCGCCGCGATCCGAACACTTCACCGGACCATTCAATCGGTAGGAGCGACGGGCGGTGTGTACAAAGGGCAGGGACGTAGTCAACGCGAGCTGATGACTCGCGCTTACTAGGCATTCCTCGTTGAAGACCAACAATTGCAATGATCTATCCCCATCACGATGAAATTTCCCAAGATTACCCGGGCCTGTCGGCCAAGGCTATATACTCGTTGAATACATCAGTGTAGCGCGCGTGCGGCCCAGAACATCTAAGGGCATCACAGACCTGTTATTGCCTCAAACTTCCGTCGCCTAAACGGCGATAGTCCCTCTAAGAAGCTAGCTGCGGAGGGATGGCTCCGCATAGCTAGTTAGCAGGCTGAGGTCTCGTTCGTTAACGGAATTAACCAGACAAATCGCTCCACCAACTAAGAACGGCCATGCACCACCACCCATAGAATCAAGAAAGAGCTCTCAGTCTGTCAATCCTTGCTATGTCTGGACCTGGTAAG criterion=sequence-density sequence-density=0.28 sequence-density-rank=1 fanout-score=2.43 fanout-score-rank=36 prefix-density=0.31 prefix-fanout=2.3 sequence=CGGTTCCGGTTC criterion=fanout-score sequence-density=0.05 sequence-density-rank=32 fanout-score=444.47 fanout-score-rank=1 prefix-density=1.08 prefix-fanout=20.8 sequence=CGCCGCCGCCCCTCGTCCTCTGTGTTCCTTCTCCGAGTTTCAGCCATGGGTAAGGAGAAGACTCACATCAACATCGTGGTCATTGGCCATGTCGACTCTGGCAAGTCGACCACCACTGGCCACCTGATCTACAAGCTTGGAGGTATTGACAAGCGTGTGATCGAGAGGTTCGAGAAGGAGGCTGC SRR7814828 testing PE reads STAR mapping to Ensembl genome Started job on | Dec 06 11:35:18 Started mapping on | Dec 06 11:35:19 Finished on | Dec 06 11:41:54 Mapping speed, Million of reads per hour | 327.85 Number of input reads | 35972071 Average input read length | 297 UNIQUE READS: Uniquely mapped reads number | 32890809 Uniquely mapped reads % | 91.43% Average mapped length | 295.51 Number of splices: Total | 33283243 Number of splices: Annotated (sjdb) | 31299717 Number of splices: GT/AG | 32827730 Number of splices: GC/AG | 362965 Number of splices: AT/AC | 24813 Number of splices: Non-canonical | 67735 Mismatch rate per base, % | 0.43% Deletion rate per base | 0.03% Deletion average length | 3.12 Insertion rate per base | 0.02% Insertion average length | 2.61 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 537519 % of reads mapped to multiple loci | 1.49% Number of reads mapped to too many loci | 60328 % of reads mapped to too many loci | 0.17% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 5.90% % of reads unmapped: other | 1.01% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 2543743 2543743 2543743 N_multimapping 537519 537519 537519 N_noFeature 802041 31997354 1105780 N_ambiguous 671517 4188 81829 UnstrandedReadsAssigned:31417251 PositiveStrandReadsAssigned:889267 NegativeStrandReadsAssigned:31703200 Dataset is classified negative stranded MeadianReadLen=151 20thPercentileLength=151 echo kmer=147 SRR7814828 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: SRR7814828-trimmed-pair1.fastq SRR7814828-trimmed-pair2.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 35,972,071 reads, 32,166,543 reads pseudoaligned [quant] estimated average fragment length: 266.512 [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,206 rounds 52973 SRR7814828.ke.tsv 35125 SRR7814828.se.tsv 88098 total ==> SRR7814828.ke.tsv <== target_id length eff_length est_counts tpm PNS24245 936 670.951 57.2873 3.61376 PNS24247 1044 778.488 105.834 5.75394 PNS24249 1928 1662.49 337.953 8.60378 PNS24246 1044 778.488 105.834 5.75394 PNS24248 1044 778.488 105.834 5.75394 PNS24244 1471 1205.49 195.258 6.85548 PNS24243 293 93.2272 0 0 KQK14069 1603 1337.49 8598.35 272.093 KQK14071 474 231.509 43.7847 8.00473 ==> SRR7814828.se.tsv <== BRADI_1g14170v3 8779 BRADI_1g53295v3 1174 BRADI_1g59795v3 174 BRADI_1g07683v3 0 BRADI_1g00485v3 84 BRADI_1g20270v3 2347 BRADI_1g74790v3 87 BRADI_1g09890v3 0 BRADI_1g77505v3 383 BRADI_1g48960v3 1 SRR7814828 completed mapping pipeline successfully