Starting /dee2/code/volunteer_pipeline.sh SRR7172661 current disk space = 3058187128832 free memory = 1471014428 SRR7172661 SRAfilesize b8d346d92170221c1284325f594be260 SRR7172661.sra SRR7172661.sra file validated SRR7172661 is paired end SRR7172661 is conventional basespace SRR7172661 read1 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR7172661_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 43 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 31.622 33.0 32.0 34.0 30.0 34.0 2 32.423 33.0 33.0 34.0 31.0 34.0 3 32.81875 33.0 33.0 34.0 32.0 34.0 4 32.862 33.0 33.0 34.0 32.0 34.0 5 32.82575 33.0 33.0 34.0 32.0 34.0 6 37.09925 38.0 37.0 38.0 36.0 38.0 7 37.398 38.0 38.0 38.0 37.0 38.0 8 37.38475 38.0 38.0 38.0 37.0 38.0 9 37.52625 38.0 38.0 38.0 38.0 38.0 10-14 37.547250000000005 38.0 38.0 38.0 38.0 38.0 15-19 37.48665 38.0 38.0 38.0 38.0 38.0 20-24 37.47345 38.0 38.0 38.0 38.0 38.0 25-29 37.475049999999996 38.0 38.0 38.0 38.0 38.0 30-34 37.48960000000001 38.0 38.0 38.0 38.0 38.0 35-39 37.40315 38.0 38.0 38.0 37.8 38.0 40-44 37.4032 38.0 38.0 38.0 37.6 38.0 45-49 37.2371 38.0 38.0 38.0 37.0 38.0 50-54 37.268150000000006 38.0 38.0 38.0 37.0 38.0 55-59 37.215650000000004 38.0 38.0 38.0 37.0 38.0 60-64 37.15115 38.0 38.0 38.0 37.0 38.0 65-69 37.17144999999999 38.0 38.0 38.0 36.8 38.0 70-74 37.16265 38.0 38.0 38.0 36.6 38.0 75-79 36.97235 38.0 38.0 38.0 36.0 38.0 80-84 36.94414999999999 38.0 38.0 38.0 36.0 38.0 85-89 36.6984 38.0 38.0 38.0 35.0 38.0 90-94 36.71895 38.0 38.0 38.0 35.0 38.0 95-99 36.74235 38.0 38.0 38.0 35.2 38.0 100-104 36.6322 38.0 38.0 38.0 34.4 38.0 105-109 36.37735 38.0 38.0 38.0 34.0 38.0 110-114 36.17385 38.0 38.0 38.0 33.6 38.0 115-119 36.18345 38.0 38.0 38.0 33.6 38.0 120-124 35.95315 38.0 37.4 38.0 32.6 38.0 125-129 35.8251 38.0 37.0 38.0 32.6 38.0 130-134 35.259699999999995 38.0 36.0 38.0 28.8 38.0 135-139 35.1521 38.0 36.0 38.0 28.0 38.0 140-144 35.06150000000001 38.0 35.6 38.0 28.8 38.0 145-149 34.69855 38.0 35.2 38.0 28.2 38.0 150-151 30.65875 35.5 29.0 38.0 15.0 38.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 6 2.0 7 1.0 8 0.0 9 1.0 10 1.0 11 1.0 12 2.0 13 0.0 14 1.0 15 1.0 16 0.0 17 2.0 18 2.0 19 2.0 20 2.0 21 2.0 22 0.0 23 8.0 24 7.0 25 13.0 26 20.0 27 16.0 28 21.0 29 34.0 30 41.0 31 46.0 32 69.0 33 93.0 34 115.0 35 238.0 36 600.0 37 2659.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 33.51199591628382 13.195507912200103 15.160796324655438 38.13169984686064 2 20.06554071086463 17.292664481976306 37.963196370052934 24.678598437106125 3 20.775 22.400000000000002 26.200000000000003 30.625000000000004 4 24.275 29.099999999999998 23.05 23.575 5 22.3 33.1 25.724999999999998 18.875 6 16.825000000000003 35.6 26.6 20.974999999999998 7 13.8 23.474999999999998 43.35 19.375 8 17.625 23.474999999999998 32.6 26.3 9 16.725 24.825 34.225 24.224999999999998 10-14 19.475 29.849999999999998 28.105000000000004 22.57 15-19 19.66 29.075 28.515 22.75 20-24 19.825 28.705000000000002 27.97 23.5 25-29 19.715 29.185 27.935 23.165 30-34 19.21 28.59 27.839999999999996 24.36 35-39 19.89 28.999999999999996 27.73 23.380000000000003 40-44 19.43 29.299999999999997 27.61 23.66 45-49 20.27 28.435 27.785 23.51 50-54 19.84 28.499999999999996 28.025 23.635 55-59 19.645000000000003 29.01 27.755000000000003 23.59 60-64 20.21 28.599999999999998 27.54 23.65 65-69 19.78 28.585 28.215 23.419999999999998 70-74 20.275000000000002 27.794999999999998 28.444999999999997 23.485 75-79 20.044999999999998 28.360000000000003 28.084999999999997 23.51 80-84 19.564999999999998 27.67 28.804999999999996 23.96 85-89 20.405 28.985 27.055 23.555 90-94 20.165 28.335 27.439999999999998 24.060000000000002 95-99 20.015 28.405 27.794999999999998 23.785 100-104 20.275000000000002 28.165000000000003 28.01 23.549999999999997 105-109 19.985 28.065 27.99 23.96 110-114 20.649129825965193 27.81056211242248 28.09561912382477 23.444688937787557 115-119 20.225 28.34 28.499999999999996 22.935 120-124 20.455000000000002 28.044999999999998 27.52 23.98 125-129 20.465 27.855 27.93 23.75 130-134 20.7 28.49 27.87 22.939999999999998 135-139 20.715 28.875 26.724999999999998 23.685000000000002 140-144 21.02 28.52 27.08 23.380000000000003 145-149 21.035 28.285 27.07 23.61 150-151 20.95 28.5625 26.087500000000002 24.4 >>END_MODULE >>Per sequence GC content pass #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 1.0 10 1.5 11 0.5 12 0.0 13 0.0 14 0.5 15 0.5 16 0.5 17 0.5 18 0.5 19 1.0 20 1.0 21 1.5 22 1.5 23 1.0 24 1.5 25 4.0 26 5.0 27 6.0 28 10.5 29 19.5 30 24.5 31 36.0 32 44.5 33 48.5 34 65.5 35 73.5 36 93.0 37 120.0 38 141.0 39 164.0 40 197.0 41 229.0 42 239.5 43 256.5 44 283.0 45 284.0 46 258.5 47 238.5 48 220.5 49 196.0 50 163.0 51 132.0 52 109.5 53 79.0 54 58.0 55 50.0 56 38.0 57 23.0 58 15.5 59 15.0 60 12.0 61 9.5 62 6.0 63 3.5 64 3.0 65 2.0 66 2.0 67 1.5 68 1.0 69 1.0 70 0.5 71 0.5 72 1.0 73 0.5 74 0.0 75 0.5 76 1.0 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 pass #Base N-Count 1 2.0500000000000003 2 0.8250000000000001 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 0.02 115-119 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 99.52499999999999 #Duplication Level Percentage of deduplicated Percentage of total 1 99.5227329816629 99.05000000000001 2 0.4772670183371013 0.95 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 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 0.0125 0.0 0.0 0.0 54-55 0.0 0.025 0.0 0.0 0.0 56-57 0.0 0.025 0.0 0.0 0.0 58-59 0.0 0.025 0.0 0.0 0.0 60-61 0.0 0.025 0.0 0.0 0.0 62-63 0.0 0.025 0.0 0.0 0.0 64-65 0.0 0.025 0.0 0.0 0.0 66-67 0.0 0.025 0.0 0.0 0.0 68-69 0.0 0.025 0.0 0.0 0.0 70-71 0.0 0.025 0.0 0.0 0.0 72-73 0.0 0.025 0.0 0.0 0.0 74-75 0.0 0.025 0.0 0.0 0.0 76-77 0.0 0.025 0.0 0.0 0.0 78-79 0.0 0.025 0.0 0.0 0.0 80-81 0.0 0.025 0.0 0.0 0.0 82-83 0.0 0.025 0.0 0.0 0.0 84-85 0.0 0.025 0.0 0.0 0.0 86-87 0.0 0.025 0.0 0.0 0.0 88-89 0.0125 0.025 0.0 0.0 0.0 90-91 0.025 0.025 0.0 0.0 0.0 92-93 0.0625 0.025 0.0 0.0 0.0 94-95 0.1125 0.025 0.0 0.0 0.0 96-97 0.175 0.025 0.0 0.0 0.0 98-99 0.275 0.025 0.0 0.0 0.0 100-101 0.325 0.025 0.0 0.0 0.0 102-103 0.4 0.025 0.0 0.0 0.0 104-105 0.4875 0.025 0.0 0.0 0.0 106-107 0.6125 0.025 0.0 0.0 0.0 108-109 0.775 0.025 0.0 0.0 0.0 110-111 0.8625 0.025 0.0 0.0 0.0 112-113 1.0 0.025 0.0 0.0 0.0 114-115 1.2125 0.025 0.0 0.0 0.0 116-117 1.4 0.025 0.0 0.0 0.0 118-119 1.6 0.025 0.0 0.0 0.0 120-121 1.875 0.025 0.0 0.0 0.0 122-123 2.2 0.025 0.0 0.0 0.0 124-125 2.45 0.025 0.0 0.0 0.0 126-127 2.75 0.025 0.0 0.0 0.0 128-129 3.0375 0.025 0.0 0.0 0.0 130-131 3.3875 0.025 0.0 0.0 0.0 132-133 3.95 0.025 0.0 0.0 0.0 134-135 4.5625 0.025 0.0 0.0 0.0 136-137 5.1625 0.025 0.0 0.0 0.0 138-139 5.5875 0.025 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position CAGTAGG 10 0.0068343505 144.975 4 >>END_MODULE SRR7172661 read2 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR7172661_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 44 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 32.963 34.0 33.0 34.0 32.0 34.0 2 33.01175 34.0 33.0 34.0 32.0 34.0 3 33.0185 34.0 33.0 34.0 32.0 34.0 4 32.9535 34.0 33.0 34.0 32.0 34.0 5 33.0 34.0 33.0 34.0 32.0 34.0 6 37.032 38.0 38.0 38.0 37.0 38.0 7 37.118 38.0 38.0 38.0 37.0 38.0 8 37.0505 38.0 38.0 38.0 37.0 38.0 9 37.02325 38.0 38.0 38.0 37.0 38.0 10-14 36.96085000000001 38.0 38.0 38.0 36.8 38.0 15-19 37.0197 38.0 38.0 38.0 37.0 38.0 20-24 36.99605 38.0 38.0 38.0 37.0 38.0 25-29 36.6192 38.0 38.0 38.0 36.4 38.0 30-34 35.83835 38.0 38.0 38.0 34.8 38.0 35-39 36.1637 38.0 38.0 38.0 34.4 38.0 40-44 36.72935 38.0 38.0 38.0 36.0 38.0 45-49 36.805550000000004 38.0 38.0 38.0 36.0 38.0 50-54 36.80794999999999 38.0 38.0 38.0 36.4 38.0 55-59 36.6519 38.0 38.0 38.0 36.0 38.0 60-64 36.4028 38.0 38.0 38.0 34.4 38.0 65-69 36.3246 38.0 38.0 38.0 34.2 38.0 70-74 36.39925 38.0 38.0 38.0 34.8 38.0 75-79 36.407650000000004 38.0 38.0 38.0 34.8 38.0 80-84 36.2765 38.0 38.0 38.0 34.2 38.0 85-89 36.15794999999999 38.0 38.0 38.0 34.0 38.0 90-94 36.06185 38.0 38.0 38.0 33.8 38.0 95-99 36.01775 38.0 38.0 38.0 33.6 38.0 100-104 35.87735 38.0 38.0 38.0 33.2 38.0 105-109 35.7471 38.0 38.0 38.0 33.0 38.0 110-114 35.55105 38.0 37.2 38.0 31.4 38.0 115-119 35.32415 38.0 37.0 38.0 30.4 38.0 120-124 34.940000000000005 38.0 36.2 38.0 27.8 38.0 125-129 34.96470000000001 38.0 36.0 38.0 28.0 38.0 130-134 34.7098 38.0 35.8 38.0 27.0 38.0 135-139 34.0637 38.0 34.8 38.0 23.2 38.0 140-144 33.63685 38.0 33.0 38.0 21.8 38.0 145-149 32.470749999999995 38.0 33.0 38.0 10.8 38.0 150-151 27.24725 34.5 16.5 38.0 2.0 38.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 2 14.0 3 2.0 4 6.0 5 2.0 6 3.0 7 4.0 8 2.0 9 5.0 10 4.0 11 2.0 12 1.0 13 6.0 14 3.0 15 5.0 16 5.0 17 2.0 18 7.0 19 3.0 20 12.0 21 6.0 22 10.0 23 15.0 24 12.0 25 19.0 26 25.0 27 30.0 28 36.0 29 30.0 30 50.0 31 59.0 32 85.0 33 107.0 34 168.0 35 313.0 36 563.0 37 2384.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 35.875 16.6 18.875 28.65 2 22.35 24.474999999999998 36.125 17.05 3 20.375 27.875 30.675 21.075 4 24.725 35.425000000000004 22.225 17.625 5 24.65 37.4 22.900000000000002 15.049999999999999 6 18.775 37.775 23.724999999999998 19.725 7 18.65 18.7 41.9 20.75 8 21.099999999999998 23.95 28.425 26.525 9 21.9 25.25 28.799999999999997 24.05 10-14 22.945 29.435 26.474999999999998 21.145 15-19 22.805 28.415000000000003 27.88 20.9 20-24 22.439999999999998 28.485 28.189999999999998 20.885 25-29 23.490271196693215 28.29418288133885 27.563262425647743 20.65228349632019 30-34 22.830791426215992 28.684047815333884 27.31347897774114 21.171681780708987 35-39 23.355997564440838 28.937487314796023 27.242744063324537 20.463771057438603 40-44 23.77 27.935 27.625 20.669999999999998 45-49 22.875 27.96 28.189999999999998 20.974999999999998 50-54 23.465 28.32 27.779999999999998 20.435 55-59 23.385 28.02 27.860000000000003 20.735 60-64 23.799999999999997 27.16 28.125 20.915 65-69 23.23 28.475 27.794999999999998 20.5 70-74 23.880000000000003 28.63 27.375 20.115 75-79 23.76 28.21 27.405 20.625 80-84 23.27 28.299999999999997 27.905 20.525 85-89 24.175 28.07 28.215 19.54 90-94 23.69 27.639999999999997 28.23 20.44 95-99 23.915 28.134999999999998 28.095 19.855 100-104 24.060000000000002 28.305000000000003 27.279999999999998 20.355 105-109 24.34 28.410000000000004 27.325 19.925 110-114 24.04 28.51 27.365000000000002 20.085 115-119 23.97 28.835 27.18 20.015 120-124 23.810000000000002 28.03 27.845 20.315 125-129 23.97 28.59 27.839999999999996 19.6 130-134 24.4 28.49 27.08 20.03 135-139 24.935 28.26 27.089999999999996 19.715 140-144 24.555 28.64 26.85 19.955000000000002 145-149 25.509999999999998 28.244999999999997 26.735 19.509999999999998 150-151 26.1625 28.037499999999998 26.8 19.0 >>END_MODULE >>Per sequence GC content pass #GC Content Count 0 0.0 1 0.0 2 0.0 3 0.0 4 0.0 5 0.0 6 0.5 7 0.5 8 0.0 9 0.0 10 0.0 11 0.5 12 0.5 13 0.0 14 0.0 15 0.5 16 1.0 17 1.0 18 0.5 19 0.0 20 0.5 21 2.0 22 1.5 23 1.0 24 2.5 25 3.0 26 4.0 27 3.5 28 3.5 29 8.0 30 13.0 31 17.0 32 21.0 33 32.5 34 48.5 35 60.5 36 81.5 37 118.0 38 152.0 39 186.5 40 218.0 41 249.0 42 276.0 43 293.5 44 285.5 45 266.0 46 263.5 47 235.0 48 209.0 49 195.0 50 173.5 51 138.0 52 101.5 53 83.0 54 65.5 55 46.5 56 32.5 57 24.5 58 18.5 59 16.0 60 11.0 61 8.5 62 9.5 63 6.0 64 2.0 65 1.5 66 1.0 67 2.0 68 2.0 69 0.5 70 0.0 71 0.0 72 0.0 73 0.0 74 0.0 75 0.0 76 0.0 77 0.5 78 0.5 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 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 0.8099999999999999 30-34 2.96 35-39 1.46 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 99.175 #Duplication Level Percentage of deduplicated Percentage of total 1 99.3193849256365 98.5 2 0.604991177211999 1.2 3 0.025207965717166627 0.075 4 0.025207965717166627 0.1 5 0.025207965717166627 0.125 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 warn #Sequence Count Percentage Possible Source GTTTAATTTGAGACAGAAAACATGAAATCCTCCTACACTTTCTTCATTCT 5 0.125 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 0.0 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 0.0125 0.0 0.0 0.0 0.0 90-91 0.025 0.0 0.0 0.0 0.0 92-93 0.0625 0.0 0.0 0.0 0.0 94-95 0.1125 0.0 0.0 0.0 0.0 96-97 0.175 0.0 0.0 0.0 0.0 98-99 0.275 0.0 0.0 0.0 0.0 100-101 0.325 0.0 0.0 0.0 0.0 102-103 0.4 0.0 0.0 0.0 0.0 104-105 0.4625 0.0 0.0 0.0 0.0 106-107 0.5625 0.0 0.0 0.0 0.0 108-109 0.725 0.0 0.0 0.0 0.0 110-111 0.8125 0.0 0.0 0.0 0.0 112-113 0.95 0.0 0.0 0.0 0.0 114-115 1.175 0.0 0.0 0.0 0.0 116-117 1.375 0.0 0.0 0.0 0.0 118-119 1.5750000000000002 0.0 0.0 0.0 0.0 120-121 1.85 0.0 0.0 0.0 0.0 122-123 2.175 0.0 0.0 0.0 0.0 124-125 2.425 0.0 0.0 0.0 0.0 126-127 2.7249999999999996 0.0 0.0 0.0 0.0 128-129 3.0125 0.0 0.0 0.0 0.0 130-131 3.375 0.0 0.0 0.0 0.0 132-133 3.9625 0.0 0.0 0.0 0.0 134-135 4.574999999999999 0.0 0.0 0.0 0.0 136-137 5.15 0.0 0.0 0.0 0.0 138-139 5.5875 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position AACTCCA 10 0.0068555363 144.825 5 CAAATTC 10 0.0068555363 144.825 3 >>END_MODULE Read 806223 spots for SRR7172661.sra Written 806223 spots for SRR7172661.sra Read 806223 spots for SRR7172661.sra Written 806223 spots for SRR7172661.sra Read 806223 spots for SRR7172661.sra Written 806223 spots for SRR7172661.sra Read 806223 spots for SRR7172661.sra Written 806223 spots for SRR7172661.sra Read 806223 spots for SRR7172661.sra Written 806223 spots for SRR7172661.sra Read 806223 spots for SRR7172661.sra Written 806223 spots for SRR7172661.sra Read 806223 spots for SRR7172661.sra Written 806223 spots for SRR7172661.sra Read 806223 spots for SRR7172661.sra Written 806223 spots for SRR7172661.sra Read 806223 spots for SRR7172661.sra Written 806223 spots for SRR7172661.sra Read 806223 spots for SRR7172661.sra Written 806223 spots for SRR7172661.sra Read 806223 spots for SRR7172661.sra Written 806223 spots for SRR7172661.sra Read 806223 spots for SRR7172661.sra Written 806223 spots for SRR7172661.sra Read 806223 spots for SRR7172661.sra Written 806223 spots for SRR7172661.sra Read 806223 spots for SRR7172661.sra Written 806223 spots for SRR7172661.sra Read 806223 spots for SRR7172661.sra Written 806223 spots for SRR7172661.sra Read 806223 spots for SRR7172661.sra Written 806223 spots for SRR7172661.sra Read 806223 spots for SRR7172661.sra Written 806223 spots for SRR7172661.sra Read 806223 spots for SRR7172661.sra Written 806223 spots for SRR7172661.sra Read 806223 spots for SRR7172661.sra Written 806223 spots for SRR7172661.sra Read 806242 spots for SRR7172661.sra Written 806242 spots for SRR7172661.sra SRR ids: ['SRR7172661.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_phv5j56q SRR7172661.sra spots: 16124479 blocks: [[1, 806223], [806224, 1612446], [1612447, 2418669], [2418670, 3224892], [3224893, 4031115], [4031116, 4837338], [4837339, 5643561], [5643562, 6449784], [6449785, 7256007], [7256008, 8062230], [8062231, 8868453], [8868454, 9674676], [9674677, 10480899], [10480900, 11287122], [11287123, 12093345], [12093346, 12899568], [12899569, 13705791], [13705792, 14512014], [14512015, 15318237], [15318238, 16124479]] SRR7172661 file size 5442356 SRR7172661 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 SRR7172661 SRR7172661_1.fastq SRR7172661_2.fastq Input file: SRR7172661_1.fastq Paired file: SRR7172661_2.fastq trimmed: SRR7172661-trimmed-pair1.fastq, SRR7172661-trimmed-pair2.fastq Parameters used: -- 3' end adapter sequence (-x): AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC -- paired 3' end adapter sequence (-y): AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTA -- maximum error ratio allowed (-r): 0.100 -- maximum indel error ratio allowed (-d): 0.030 -- end quality threshold (-q): 10 -- minimum read length allowed after trimming (-l): 18 -- file format (-f): Sanger/Illumina 1.8+ FASTQ -- number of concurrent threads (-t): 20 Mon Feb 10 17:09:09 2025 >> started Mon Feb 10 17:09:27 2025 >> done (17.766s) 16124479 read pairs processed; of these: 35104 ( 0.22%) short read pairs filtered out after trimming by size control 23933 ( 0.15%) empty read pairs filtered out after trimming by size control 16065442 (99.63%) read pairs available; of these: 8348440 (51.97%) trimmed read pairs available after processing 7717002 (48.03%) untrimmed read pairs available after processing Length distribution of reads after trimming: length count percentage 18 4 0.00% 19 1 0.00% 20 7 0.00% 21 6 0.00% 22 6 0.00% 23 11 0.00% 24 7 0.00% 25 10 0.00% 26 12 0.00% 27 9 0.00% 28 24 0.00% 29 8 0.00% 30 10 0.00% 31 10 0.00% 32 8 0.00% 33 9 0.00% 34 7 0.00% 35 6 0.00% 36 5 0.00% 37 7 0.00% 38 7 0.00% 39 8 0.00% 40 4 0.00% 41 8 0.00% 42 10 0.00% 43 14 0.00% 44 11 0.00% 45 19 0.00% 46 17 0.00% 47 23 0.00% 48 22 0.00% 49 35 0.00% 50 31 0.00% 51 31 0.00% 52 34 0.00% 53 38 0.00% 54 47 0.00% 55 46 0.00% 56 41 0.00% 57 55 0.00% 58 53 0.00% 59 70 0.00% 60 78 0.00% 61 96 0.00% 62 82 0.00% 63 89 0.00% 64 129 0.00% 65 129 0.00% 66 121 0.00% 67 180 0.00% 68 178 0.00% 69 228 0.00% 70 234 0.00% 71 267 0.00% 72 330 0.00% 73 365 0.00% 74 411 0.00% 75 517 0.00% 76 716 0.00% 77 711 0.00% 78 726 0.00% 79 824 0.01% 80 898 0.01% 81 1114 0.01% 82 1311 0.01% 83 1784 0.01% 84 3720 0.02% 85 4837 0.03% 86 5548 0.03% 87 6347 0.04% 88 6194 0.04% 89 5793 0.04% 90 5844 0.04% 91 5965 0.04% 92 6283 0.04% 93 6379 0.04% 94 6613 0.04% 95 6959 0.04% 96 7509 0.05% 97 7965 0.05% 98 8268 0.05% 99 9058 0.06% 100 9641 0.06% 101 10407 0.06% 102 11215 0.07% 103 11982 0.07% 104 12640 0.08% 105 13659 0.09% 106 14560 0.09% 107 15534 0.10% 108 16536 0.10% 109 17644 0.11% 110 18981 0.12% 111 20235 0.13% 112 20921 0.13% 113 22947 0.14% 114 24544 0.15% 115 25940 0.16% 116 26963 0.17% 117 27812 0.17% 118 28867 0.18% 119 30218 0.19% 120 31558 0.20% 121 32944 0.21% 122 34438 0.21% 123 35971 0.22% 124 37493 0.23% 125 39130 0.24% 126 41239 0.26% 127 43010 0.27% 128 44276 0.28% 129 46476 0.29% 130 48875 0.30% 131 50835 0.32% 132 53873 0.34% 133 55840 0.35% 134 58589 0.36% 135 61258 0.38% 136 64353 0.40% 137 68224 0.42% 138 72744 0.45% 139 76145 0.47% 140 82091 0.51% 141 88067 0.55% 142 96707 0.60% 143 104971 0.65% 144 119050 0.74% 145 137579 0.86% 146 166031 1.03% 147 220451 1.37% 148 334779 2.08% 149 821768 5.12% 150 4682838 29.15% 151 7717002 48.03% 16065442 reads passed initial QC criterion=sequence-density sequence-density=0.29 sequence-density-rank=1 fanout-score=2.12 fanout-score-rank=30 prefix-density=0.31 prefix-fanout=2.0 sequence=CAGGTGCAGTTTGATCCACACTTGCA criterion=fanout-score sequence-density=0.02 sequence-density-rank=32 fanout-score=137.29 fanout-score-rank=1 prefix-density=0.18 prefix-fanout=12.3 sequence=CTCCTTCCTCTAAATGATAAGGTTCAGTGGACTTCTCGCGACGTCGCCGGCGGCGAACCGCCCACGTCGCCGCGATCCGAACACTTCACCGGACCATTCAATCGGTAGGAGCGACGGGCGGTGTGTACAAAGGGCAGGGACGTAGTCAACGCGAGCTGATGACTCGCGCTTACTAGGAATTCCTCGTTGAAGACCAACAATTGCAATGATCTATCCCCATCACGATGAAATTTCAAAGATTACCCGGGCCTGTCGGCCAAGGCTATAGACTCGTTGAATACATCAGTGTAGCGCGCGTGCGGCCCAGAACATCTAAGGGCATCACAGACCTGTTATTGCCTCAAACTTCCTTGGCCTGGAAGGCCATAGTCCCTCTAAGAAGCTGGCCGCGGAGGGTCACCTCCGCATAGCTAGTTAGCAGGCTGAGGTCTCGTTCGTTAACGGAATTAACCAGACAAATCGCTCCACCAACTAAGAACGGCCATGCACCACCACCCATAGAATCAAGAAA criterion=sequence-density sequence-density=0.37 sequence-density-rank=1 fanout-score=2.13 fanout-score-rank=29 prefix-density=0.37 prefix-fanout=2.1 sequence=ATGTACCCTGACTT criterion=fanout-score sequence-density=0.04 sequence-density-rank=28 fanout-score=73.19 fanout-score-rank=1 prefix-density=0.20 prefix-fanout=12.9 sequence=TCTTCCTCTCTATAATTTTCTAGGGTTTAGCAATGTCTGCCGAGGTTGAGTACAGGTGCTTTGTTGG SRR7172661 testing PE reads STAR mapping to Ensembl genome Started job on | Feb 10 17:10:10 Started mapping on | Feb 10 17:10:10 Finished on | Feb 10 17:12:33 Mapping speed, Million of reads per hour | 404.44 Number of input reads | 16065442 Average input read length | 295 UNIQUE READS: Uniquely mapped reads number | 14817846 Uniquely mapped reads % | 92.23% Average mapped length | 294.48 Number of splices: Total | 14800903 Number of splices: Annotated (sjdb) | 14482312 Number of splices: GT/AG | 14561496 Number of splices: GC/AG | 181181 Number of splices: AT/AC | 15697 Number of splices: Non-canonical | 42529 Mismatch rate per base, % | 0.39% Deletion rate per base | 0.03% Deletion average length | 2.66 Insertion rate per base | 0.02% Insertion average length | 2.59 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 393266 % of reads mapped to multiple loci | 2.45% Number of reads mapped to too many loci | 113322 % of reads mapped to too many loci | 0.71% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 4.45% % of reads unmapped: other | 0.17% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 887436 887436 887436 N_multimapping 393266 393266 393266 N_noFeature 412895 14682054 467016 N_ambiguous 160622 1136 78140 UnstrandedReadsAssigned:14244329 PositiveStrandReadsAssigned:134656 NegativeStrandReadsAssigned:14272690 Dataset is classified negative stranded MeadianReadLen=151 20thPercentileLength=150 echo kmer=145 SRR7172661 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: 52,400 [index] number of k-mers: 62,057,036 [index] number of equivalence classes: 130,681 [quant] running in paired-end mode [quant] will process pair 1: SRR7172661-trimmed-pair1.fastq SRR7172661-trimmed-pair2.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 16,065,442 reads, 14,205,543 reads pseudoaligned [quant] estimated average fragment length: 227.999 [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,133 rounds 52401 SRR7172661.ke.tsv 34699 SRR7172661.se.tsv 87100 total ==> SRR7172661.ke.tsv <== target_id length eff_length est_counts tpm Potri.005G200100.1.v4.1 2018 1791 1075 32.4872 Potri.005G024800.1.v4.1 1035 808.001 361 24.1821 Potri.004G059700.1.v4.1 961 734.007 41 3.02331 Potri.007G009000.2.v4.1 1416 1189 0 0 Potri.003G141000.2.v4.1 2943 2716 400.188 7.97505 Potri.016G087400.1.v4.1 270 80.3722 1184 797.343 Potri.015G069301.1.v4.1 564 339.157 0 0 Potri.010G195200.1.v4.1 1773 1546 347 12.1484 Potri.012G127500.1.v4.1 977 750.007 9923 716.106 ==> SRR7172661.se.tsv <== Potri.001G166300.v4.1 2 Potri.001G448400.v4.1 57 Potri.001G233950.v4.1 0 Potri.001G122700.v4.1 902 Potri.001G212900.v4.1 0 Potri.001G182400.v4.1 2 Potri.001G256600.v4.1 0 Potri.001G040500.v4.1 0 Potri.001G416900.v4.1 1 Potri.001G452600.v4.1 441 SRR7172661 completed mapping pipeline successfully