Starting /dee2/code/volunteer_pipeline.sh SRR7166126 current disk space = 3110879723520 free memory = 1571371616 SRR7166126 SRAfilesize 1aeec8d28cf5e0634579e8a486b2b738 SRR7166126.sra SRR7166126.sra file validated SRR7166126 is paired end SRR7166126 is conventional basespace SRR7166126 read1 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR7166126_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 44 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 29.79375 33.0 31.0 33.0 18.0 34.0 2 32.05425 33.0 31.0 34.0 29.0 34.0 3 32.28 33.0 33.0 34.0 29.0 34.0 4 32.2345 33.0 32.0 33.0 31.0 34.0 5 32.23475 33.0 32.0 33.0 31.0 34.0 6 36.66525 38.0 37.0 38.0 34.0 38.0 7 37.363 38.0 38.0 38.0 37.0 38.0 8 37.42275 38.0 38.0 38.0 37.0 38.0 9 37.63025 38.0 38.0 38.0 38.0 38.0 10-14 37.623599999999996 38.0 38.0 38.0 38.0 38.0 15-19 37.584950000000006 38.0 38.0 38.0 38.0 38.0 20-24 37.569599999999994 38.0 38.0 38.0 38.0 38.0 25-29 37.5698 38.0 38.0 38.0 38.0 38.0 30-34 37.54425 38.0 38.0 38.0 37.8 38.0 35-39 37.505250000000004 38.0 38.0 38.0 37.8 38.0 40-44 37.495450000000005 38.0 38.0 38.0 37.4 38.0 45-49 37.4714 38.0 38.0 38.0 37.4 38.0 50-54 37.42895 38.0 38.0 38.0 37.0 38.0 55-59 37.085300000000004 38.0 38.0 38.0 37.0 38.0 60-64 37.26010000000001 38.0 38.0 38.0 37.0 38.0 65-69 37.30075000000001 38.0 38.0 38.0 37.0 38.0 70-74 37.23095 38.0 38.0 38.0 36.6 38.0 75-79 37.20925 38.0 38.0 38.0 36.4 38.0 80-84 37.09765 38.0 38.0 38.0 36.0 38.0 85-89 36.96815 38.0 38.0 38.0 35.6 38.0 90-94 36.864200000000004 38.0 38.0 38.0 35.4 38.0 95-99 36.82105 38.0 38.0 38.0 35.2 38.0 100-104 36.731899999999996 38.0 38.0 38.0 34.8 38.0 105-109 36.56419999999999 38.0 38.0 38.0 34.0 38.0 110-114 36.6243 38.0 38.0 38.0 34.2 38.0 115-119 36.33995 38.0 37.6 38.0 33.8 38.0 120-124 36.1687 38.0 37.6 38.0 33.6 38.0 125-129 36.01905 38.0 37.0 38.0 33.0 38.0 130-134 35.87755 38.0 37.0 38.0 32.6 38.0 135-139 35.725449999999995 38.0 36.2 38.0 31.4 38.0 140-144 35.36345 38.0 36.0 38.0 30.4 38.0 145-149 35.07115 38.0 36.0 38.0 30.2 38.0 150-151 31.74125 36.5 32.0 38.0 15.0 38.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 9 1.0 10 0.0 11 1.0 12 0.0 13 0.0 14 0.0 15 0.0 16 0.0 17 1.0 18 0.0 19 2.0 20 3.0 21 0.0 22 6.0 23 5.0 24 3.0 25 8.0 26 14.0 27 8.0 28 24.0 29 24.0 30 36.0 31 47.0 32 57.0 33 61.0 34 126.0 35 242.0 36 653.0 37 2678.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 42.333333333333336 16.743589743589745 10.076923076923077 30.846153846153847 2 22.3 22.825 36.575 18.3 3 17.7 31.525 27.575 23.200000000000003 4 22.625 36.625 22.85 17.9 5 21.7685370741483 34.79458917835671 23.972945891783567 19.46392785571142 6 15.775 37.25 25.374999999999996 21.6 7 13.450000000000001 21.099999999999998 44.1 21.349999999999998 8 18.775 20.674999999999997 29.475 31.075000000000003 9 18.875 22.5 29.975 28.65 10-14 20.669999999999998 29.26 26.650000000000002 23.419999999999998 15-19 20.165 28.12 28.18 23.535 20-24 20.62 28.945 27.644999999999996 22.79 25-29 20.205000000000002 28.79 28.134999999999998 22.869999999999997 30-34 21.044999999999998 28.189999999999998 27.54 23.225 35-39 20.79 28.46 27.884999999999998 22.865 40-44 20.455000000000002 29.270000000000003 27.415 22.86 45-49 21.154999999999998 28.249999999999996 27.589999999999996 23.005 50-54 20.395 28.439999999999998 27.560000000000002 23.605 55-59 20.35478506274253 28.81116766617951 27.78309731391423 23.050949957163734 60-64 20.80164131305044 28.08246597277822 27.712169735788635 23.403722978382707 65-69 20.895 28.51 27.77 22.825 70-74 21.08 27.49 28.255000000000003 23.175 75-79 20.424999999999997 28.405 28.005000000000003 23.165 80-84 20.424999999999997 28.08 28.32 23.175 85-89 21.005 28.29 28.044999999999998 22.66 90-94 20.39 29.099999999999998 27.584999999999997 22.925 95-99 20.9 28.08 27.955000000000002 23.064999999999998 100-104 21.328128909573138 27.848671370665066 27.823650102587198 22.999549617174598 105-109 21.447882246920997 28.381896465405028 27.64093321317713 22.529288074496844 110-114 21.385 28.1 27.575 22.939999999999998 115-119 21.435000000000002 28.345 27.48 22.74 120-124 21.605 28.365000000000002 26.71 23.32 125-129 21.4 28.725 26.495 23.380000000000003 130-134 21.465 28.83 26.669999999999998 23.035 135-139 21.05 28.904999999999998 26.195 23.849999999999998 140-144 20.849999999999998 28.785 26.384999999999998 23.98 145-149 21.95 28.720000000000002 26.064999999999998 23.265 150-151 22.290439794511965 27.690765568224535 26.58814684876582 23.430647788497684 >>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 0.0 10 0.0 11 0.0 12 0.0 13 0.0 14 0.5 15 0.5 16 0.0 17 0.0 18 0.0 19 1.0 20 1.5 21 2.0 22 2.0 23 2.0 24 3.0 25 3.5 26 6.0 27 8.5 28 9.0 29 14.0 30 21.5 31 26.5 32 42.0 33 57.0 34 61.5 35 79.0 36 109.5 37 127.5 38 155.0 39 175.0 40 187.5 41 211.5 42 242.0 43 249.5 44 259.5 45 267.5 46 251.5 47 248.0 48 221.0 49 175.5 50 139.5 51 112.5 52 104.0 53 88.5 54 62.0 55 54.0 56 45.5 57 33.0 58 29.0 59 23.0 60 16.0 61 16.5 62 15.0 63 13.0 64 8.0 65 5.5 66 4.5 67 3.5 68 2.5 69 1.0 70 0.5 71 1.0 72 0.5 73 0.0 74 0.0 75 0.0 76 0.0 77 0.0 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 2.5 2 0.0 3 0.0 4 0.0 5 0.2 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 0.7849999999999999 60-64 0.08 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 0.08499999999999999 105-109 0.13 110-114 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 0.2375 >>END_MODULE >>Sequence Length Distribution pass #Length Count 151 4000.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 99.55000000000001 #Duplication Level Percentage of deduplicated Percentage of total 1 99.57307885484681 99.125 2 0.4018081366147665 0.8 3 0.025113008538422906 0.075 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 0.025 0.0 0.0 0.0 0.0 70-71 0.025 0.0 0.0 0.0 0.0 72-73 0.037500000000000006 0.0 0.0 0.0 0.0 74-75 0.05 0.0 0.0 0.0 0.0 76-77 0.0625 0.0 0.0 0.0 0.0 78-79 0.1 0.0 0.0 0.0 0.0 80-81 0.125 0.0 0.0 0.0 0.0 82-83 0.2 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 0.275 0.0 0.0 0.0 0.0 90-91 0.375 0.0 0.0 0.0 0.0 92-93 0.4625 0.0 0.0 0.0 0.0 94-95 0.55 0.0 0.0 0.0 0.0 96-97 0.6875 0.0 0.0 0.0 0.0 98-99 0.8 0.0 0.0 0.0 0.0 100-101 0.95 0.0 0.0 0.0 0.0 102-103 1.2625 0.0 0.0 0.0 0.0 104-105 1.5375 0.0 0.0 0.0 0.0 106-107 1.6375 0.0 0.0 0.0 0.0 108-109 1.8624999999999998 0.0 0.0 0.0 0.0 110-111 2.2125 0.0 0.0 0.0 0.0 112-113 2.6125 0.0 0.0 0.0 0.0 114-115 2.9375 0.0 0.0 0.0 0.0 116-117 3.3875 0.0 0.0 0.0 0.0 118-119 3.6875 0.0 0.0 0.0 0.0 120-121 4.0375 0.0 0.0 0.0 0.0 122-123 4.525 0.0 0.0 0.0 0.0 124-125 5.2625 0.0 0.0 0.0 0.0 126-127 5.887499999999999 0.0 0.0 0.0 0.0 128-129 6.5875 0.0 0.0 0.0 0.0 130-131 7.175000000000001 0.0 0.0 0.0 0.0 132-133 7.625 0.0 0.0 0.0 0.0 134-135 8.3625 0.0 0.0 0.0 0.0 136-137 8.8875 0.0 0.0 0.0 0.0 138-139 9.475 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position AAAGTAC 10 0.0066489475 146.29114 5 TGAACTC 35 0.0031950038 62.696205 145 CACACGT 35 0.0036135698 20.6375 135-139 ACGTCTG 35 0.0036135698 20.6375 140-144 GTCTGAA 35 0.0036135698 20.6375 140-144 GCACACG 35 0.0036135698 20.6375 135-139 CGTCTGA 35 0.0036135698 20.6375 140-144 >>END_MODULE SRR7166126 read2 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR7166126_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 32.976 33.0 33.0 34.0 32.0 34.0 2 33.0235 33.0 33.0 34.0 32.0 34.0 3 33.078 34.0 33.0 34.0 32.0 34.0 4 33.11925 34.0 33.0 34.0 32.0 34.0 5 33.1315 34.0 33.0 34.0 33.0 34.0 6 37.308 38.0 38.0 38.0 37.0 38.0 7 37.39375 38.0 38.0 38.0 37.0 38.0 8 37.328 38.0 38.0 38.0 37.0 38.0 9 37.306 38.0 38.0 38.0 37.0 38.0 10-14 37.2657 38.0 38.0 38.0 37.0 38.0 15-19 37.283249999999995 38.0 38.0 38.0 37.0 38.0 20-24 37.2164 38.0 38.0 38.0 36.8 38.0 25-29 37.167199999999994 38.0 38.0 38.0 36.6 38.0 30-34 37.134249999999994 38.0 38.0 38.0 36.4 38.0 35-39 37.13245 38.0 38.0 38.0 36.4 38.0 40-44 37.02985 38.0 38.0 38.0 36.0 38.0 45-49 36.9565 38.0 38.0 38.0 36.0 38.0 50-54 36.810950000000005 38.0 38.0 38.0 35.0 38.0 55-59 36.769600000000004 38.0 38.0 38.0 35.2 38.0 60-64 36.6622 38.0 38.0 38.0 34.8 38.0 65-69 36.66405 38.0 38.0 38.0 35.0 38.0 70-74 36.442750000000004 38.0 38.0 38.0 34.0 38.0 75-79 36.3427 38.0 38.0 38.0 34.0 38.0 80-84 36.299 38.0 37.8 38.0 33.8 38.0 85-89 36.17905 38.0 37.6 38.0 33.6 38.0 90-94 36.03705 38.0 37.0 38.0 33.2 38.0 95-99 35.80445 38.0 37.0 38.0 31.6 38.0 100-104 35.76315 38.0 37.0 38.0 31.0 38.0 105-109 35.390299999999996 38.0 36.2 38.0 29.0 38.0 110-114 35.17960000000001 38.0 36.0 38.0 28.6 38.0 115-119 34.8738 38.0 35.8 38.0 27.4 38.0 120-124 34.6179 38.0 35.0 38.0 26.4 38.0 125-129 34.285450000000004 38.0 34.8 38.0 24.2 38.0 130-134 33.781099999999995 38.0 34.0 38.0 22.6 38.0 135-139 33.373900000000006 38.0 34.0 38.0 19.8 38.0 140-144 32.393 37.4 33.0 38.0 14.2 38.0 145-149 31.270100000000003 36.8 31.0 38.0 10.8 38.0 150-151 26.260624999999997 33.5 16.5 37.0 2.0 38.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 2 1.0 3 1.0 4 0.0 5 1.0 6 0.0 7 0.0 8 2.0 9 2.0 10 1.0 11 2.0 12 5.0 13 2.0 14 1.0 15 4.0 16 4.0 17 7.0 18 8.0 19 3.0 20 9.0 21 8.0 22 15.0 23 17.0 24 15.0 25 17.0 26 22.0 27 24.0 28 29.0 29 48.0 30 37.0 31 71.0 32 92.0 33 149.0 34 242.0 35 430.0 36 924.0 37 1807.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 41.175 16.175 13.525 29.125 2 23.425 23.474999999999998 35.875 17.224999999999998 3 20.5 25.025 32.074999999999996 22.400000000000002 4 22.725 36.1 21.45 19.725 5 21.9 37.125 22.8 18.175 6 16.775000000000002 38.574999999999996 24.2 20.45 7 17.75 15.075 47.65 19.525000000000002 8 20.775 20.424999999999997 27.575 31.225 9 21.525 24.349999999999998 28.425 25.7 10-14 23.145 28.189999999999998 27.12 21.545 15-19 22.8 27.779999999999998 27.79 21.63 20-24 22.68 27.944999999999997 28.199999999999996 21.175 25-29 22.795 28.89 26.88 21.435000000000002 30-34 22.395 27.74 27.925 21.94 35-39 22.595000000000002 28.384999999999998 28.21 20.810000000000002 40-44 22.99 28.825 27.365000000000002 20.82 45-49 22.84 28.155 28.249999999999996 20.755000000000003 50-54 22.67 27.32 28.660000000000004 21.349999999999998 55-59 22.98 27.900000000000002 27.83 21.29 60-64 22.36 28.294999999999998 27.99 21.355 65-69 22.98 28.044999999999998 27.915 21.060000000000002 70-74 22.830000000000002 28.665000000000003 27.115000000000002 21.39 75-79 22.855 26.919999999999998 28.794999999999998 21.43 80-84 22.98 28.22 27.51 21.29 85-89 23.07 27.525 27.875 21.529999999999998 90-94 22.825 28.23 28.575 20.369999999999997 95-99 23.915 28.060000000000002 27.13 20.895 100-104 23.54 28.499999999999996 27.32 20.64 105-109 23.275000000000002 27.900000000000002 27.794999999999998 21.029999999999998 110-114 23.935000000000002 27.889999999999997 27.485 20.69 115-119 23.655 28.439999999999998 27.529999999999998 20.375 120-124 24.01 28.205000000000002 27.150000000000002 20.635 125-129 24.615000000000002 28.294999999999998 27.105 19.985 130-134 24.525 28.235 26.795 20.445 135-139 24.935 27.839999999999996 27.189999999999998 20.035 140-144 24.975 28.144999999999996 26.915 19.965 145-149 25.275 28.04 27.134999999999998 19.55 150-151 25.566262044800403 28.331873357527222 26.99286697534727 19.108997622325116 >>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 0.0 10 0.0 11 0.5 12 0.5 13 0.0 14 0.0 15 0.0 16 0.0 17 0.5 18 1.5 19 1.0 20 0.5 21 0.5 22 0.5 23 2.0 24 3.0 25 2.5 26 2.0 27 5.0 28 10.5 29 11.0 30 13.0 31 22.0 32 31.5 33 37.0 34 51.5 35 75.5 36 89.0 37 114.5 38 146.5 39 168.0 40 201.0 41 224.5 42 243.0 43 261.0 44 261.0 45 267.5 46 272.5 47 253.5 48 217.5 49 184.0 50 155.5 51 125.5 52 108.0 53 90.0 54 76.0 55 60.5 56 46.5 57 34.5 58 21.5 59 20.5 60 19.0 61 17.0 62 9.5 63 8.0 64 8.0 65 5.5 66 4.0 67 2.5 68 3.5 69 2.5 70 0.5 71 0.5 72 2.0 73 2.0 74 0.5 75 0.0 76 0.0 77 0.0 78 0.0 79 0.5 80 0.5 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 0.0 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 0.11249999999999999 >>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 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 0.0125 0.0 0.0 0.0 0.0 66-67 0.025 0.0 0.0 0.0 0.0 68-69 0.05 0.0 0.0 0.0 0.0 70-71 0.075 0.0 0.0 0.0 0.0 72-73 0.0875 0.0 0.0 0.0 0.0 74-75 0.1 0.0 0.0 0.0 0.0 76-77 0.1125 0.0 0.0 0.0 0.0 78-79 0.15 0.0 0.0 0.0 0.0 80-81 0.2 0.0 0.0 0.0 0.0 82-83 0.275 0.0 0.0 0.0 0.0 84-85 0.3 0.0 0.0 0.0 0.0 86-87 0.325 0.0 0.0 0.0 0.0 88-89 0.325 0.0 0.0 0.0 0.0 90-91 0.42500000000000004 0.0 0.0 0.0 0.0 92-93 0.5125 0.0 0.0 0.0 0.0 94-95 0.6125 0.0 0.0 0.0 0.0 96-97 0.7625 0.0 0.0 0.0 0.0 98-99 0.9 0.0 0.0 0.0 0.0 100-101 1.05 0.0 0.0 0.0 0.0 102-103 1.3625 0.0 0.0 0.0 0.0 104-105 1.6375000000000002 0.0 0.0 0.0 0.0 106-107 1.7375 0.0 0.0 0.0 0.0 108-109 1.9625 0.0 0.0 0.0 0.0 110-111 2.325 0.0 0.0 0.0 0.0 112-113 2.7125 0.0 0.0 0.0 0.0 114-115 2.9875 0.0 0.0 0.0 0.0 116-117 3.4000000000000004 0.0 0.0 0.0 0.0 118-119 3.7249999999999996 0.0 0.0 0.0 0.0 120-121 4.0875 0.0 0.0 0.0 0.0 122-123 4.5625 0.0 0.0 0.0 0.0 124-125 5.3 0.0 0.0 0.0 0.0 126-127 5.9375 0.0 0.0 0.0 0.0 128-129 6.6375 0.0 0.0 0.0 0.0 130-131 7.15 0.0 0.0 0.0 0.0 132-133 7.525 0.0 0.0 0.0 0.0 134-135 8.2375 0.0 0.0 0.0 0.0 136-137 8.7375 0.0 0.0 0.0 0.0 138-139 9.325 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position GAGAACT 10 0.006832588 144.9875 1 AGGGAAA 30 0.0017087716 73.4114 145 GTGTAGG 35 0.003538379 20.7125 140-144 TGTAGGG 35 0.003538379 20.7125 140-144 GCGTCGT 35 0.003538379 20.7125 135-139 CGTCGTG 35 0.003538379 20.7125 135-139 CGTGTAG 35 0.003538379 20.7125 140-144 >>END_MODULE Read 757050 spots for SRR7166126.sra Written 757050 spots for SRR7166126.sra Read 757050 spots for SRR7166126.sra Written 757050 spots for SRR7166126.sra Read 757050 spots for SRR7166126.sra Written 757050 spots for SRR7166126.sra Read 757050 spots for SRR7166126.sra Written 757050 spots for SRR7166126.sra Read 757050 spots for SRR7166126.sra Written 757050 spots for SRR7166126.sra Read 757050 spots for SRR7166126.sra Written 757050 spots for SRR7166126.sra Read 757050 spots for SRR7166126.sra Written 757050 spots for SRR7166126.sra Read 757050 spots for SRR7166126.sra Written 757050 spots for SRR7166126.sra Read 757050 spots for SRR7166126.sra Written 757050 spots for SRR7166126.sra Read 757050 spots for SRR7166126.sra Written 757050 spots for SRR7166126.sra Read 757069 spots for SRR7166126.sra Written 757069 spots for SRR7166126.sra Read 757050 spots for SRR7166126.sra Written 757050 spots for SRR7166126.sra Read 757050 spots for SRR7166126.sra Written 757050 spots for SRR7166126.sra Read 757050 spots for SRR7166126.sra Written 757050 spots for SRR7166126.sra Read 757050 spots for SRR7166126.sra Written 757050 spots for SRR7166126.sra Read 757050 spots for SRR7166126.sra Written 757050 spots for SRR7166126.sra Read 757050 spots for SRR7166126.sra Written 757050 spots for SRR7166126.sra Read 757050 spots for SRR7166126.sra Written 757050 spots for SRR7166126.sra Read 757050 spots for SRR7166126.sra Written 757050 spots for SRR7166126.sra Read 757050 spots for SRR7166126.sra Written 757050 spots for SRR7166126.sra SRR ids: ['SRR7166126.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_xv2wk4j_ SRR7166126.sra spots: 15141019 blocks: [[1, 757050], [757051, 1514100], [1514101, 2271150], [2271151, 3028200], [3028201, 3785250], [3785251, 4542300], [4542301, 5299350], [5299351, 6056400], [6056401, 6813450], [6813451, 7570500], [7570501, 8327550], [8327551, 9084600], [9084601, 9841650], [9841651, 10598700], [10598701, 11355750], [11355751, 12112800], [12112801, 12869850], [12869851, 13626900], [13626901, 14383950], [14383951, 15141019]] SRR7166126 file size 5109094 SRR7166126 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 SRR7166126 SRR7166126_1.fastq SRR7166126_2.fastq Input file: SRR7166126_1.fastq Paired file: SRR7166126_2.fastq trimmed: SRR7166126-trimmed-pair1.fastq, SRR7166126-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 Feb 14 13:54:35 2025 >> started Fri Feb 14 13:54:51 2025 >> done (16.531s) 15141019 read pairs processed; of these: 8419 ( 0.06%) short read pairs filtered out after trimming by size control 8338 ( 0.06%) empty read pairs filtered out after trimming by size control 15124262 (99.89%) read pairs available; of these: 7567456 (50.04%) trimmed read pairs available after processing 7556806 (49.96%) untrimmed read pairs available after processing Length distribution of reads after trimming: length count percentage 18 2 0.00% 19 3 0.00% 20 7 0.00% 21 5 0.00% 22 5 0.00% 23 5 0.00% 24 6 0.00% 25 6 0.00% 26 9 0.00% 27 9 0.00% 28 10 0.00% 29 5 0.00% 30 7 0.00% 31 11 0.00% 32 7 0.00% 33 7 0.00% 34 10 0.00% 35 10 0.00% 36 11 0.00% 37 13 0.00% 38 15 0.00% 39 10 0.00% 40 13 0.00% 41 8 0.00% 42 14 0.00% 43 24 0.00% 44 20 0.00% 45 28 0.00% 46 30 0.00% 47 25 0.00% 48 36 0.00% 49 43 0.00% 50 63 0.00% 51 54 0.00% 52 64 0.00% 53 68 0.00% 54 73 0.00% 55 87 0.00% 56 96 0.00% 57 108 0.00% 58 128 0.00% 59 157 0.00% 60 195 0.00% 61 210 0.00% 62 245 0.00% 63 271 0.00% 64 331 0.00% 65 319 0.00% 66 393 0.00% 67 420 0.00% 68 491 0.00% 69 591 0.00% 70 662 0.00% 71 827 0.01% 72 964 0.01% 73 1056 0.01% 74 1158 0.01% 75 1376 0.01% 76 1471 0.01% 77 1723 0.01% 78 1854 0.01% 79 2119 0.01% 80 2465 0.02% 81 2793 0.02% 82 3150 0.02% 83 3611 0.02% 84 4339 0.03% 85 4867 0.03% 86 5091 0.03% 87 5722 0.04% 88 6229 0.04% 89 6831 0.05% 90 7451 0.05% 91 7998 0.05% 92 8745 0.06% 93 9701 0.06% 94 10540 0.07% 95 11088 0.07% 96 11879 0.08% 97 12526 0.08% 98 13568 0.09% 99 14352 0.09% 100 14823 0.10% 101 15831 0.10% 102 17039 0.11% 103 18358 0.12% 104 19226 0.13% 105 20451 0.14% 106 21322 0.14% 107 21909 0.14% 108 23156 0.15% 109 23608 0.16% 110 24672 0.16% 111 26406 0.17% 112 27697 0.18% 113 29395 0.19% 114 30750 0.20% 115 32615 0.22% 116 33931 0.22% 117 34998 0.23% 118 35773 0.24% 119 36970 0.24% 120 37795 0.25% 121 39887 0.26% 122 41255 0.27% 123 43571 0.29% 124 45632 0.30% 125 47946 0.32% 126 49777 0.33% 127 50716 0.34% 128 51775 0.34% 129 54379 0.36% 130 55983 0.37% 131 58749 0.39% 132 61518 0.41% 133 65271 0.43% 134 68438 0.45% 135 71584 0.47% 136 75247 0.50% 137 78689 0.52% 138 83509 0.55% 139 87954 0.58% 140 93957 0.62% 141 101559 0.67% 142 112249 0.74% 143 124159 0.82% 144 142702 0.94% 145 167666 1.11% 146 205559 1.36% 147 270489 1.79% 148 396342 2.62% 149 746315 4.93% 150 3356920 22.20% 151 7556806 49.96% 15124262 reads passed initial QC criterion=sequence-density sequence-density=0.17 sequence-density-rank=1 fanout-score=3.00 fanout-score-rank=29 prefix-density=0.20 prefix-fanout=2.6 sequence=GCATCTCTCATTGCCTTCTC criterion=fanout-score sequence-density=0.01 sequence-density-rank=33 fanout-score=138.58 fanout-score-rank=1 prefix-density=0.14 prefix-fanout=13.4 sequence=CTCCTTCCTCTAAATGATAAGGTTCAGTGGACTTCTCGCGACGTCGCCGGCGGCGAACCGCCCACGTCGCCGCGATCCGAACACTTCACCGGACCATTCAATCGGTAGGAGCGACGGGCGGTGTGTACAAAGGGCAGGGACGTAGTCAACGCGAGCTGATGACTCGCGCTTACTAGGAATTCCTCGTTGAAGACCAACAATTGCAATGATCTATCCCCATCACGATGAAATTTCAAAGATTACCCGGGCCTGTCGGCCAAGGCTATAGACTCGTTGAATACATCAGTGTAGCGCGCGTGCGGCCCAGAACATCTAAGGGCATCACAGACCTGTTATTGCCTCAAACTTCCTTGGCCTGGAAGGCCATAGTCCCTCTAAGAAGCTGGCCGCGGAGGGTCACCTCCGCATAGCTAGTTAGCAGGCTGAGGTCTCGTTCGTTAACGGAATTAACCAGACAAATCGCTCCACCAACTAAGAACGGCCATGCACCACCACCCAT criterion=sequence-density sequence-density=0.18 sequence-density-rank=1 fanout-score=2.65 fanout-score-rank=29 prefix-density=0.20 prefix-fanout=2.4 sequence=TTTAGCCAGTACGGTGAAATCATCGATTCGAAGATTATAAA criterion=fanout-score sequence-density=0.07 sequence-density-rank=19 fanout-score=447.72 fanout-score-rank=1 prefix-density=0.88 prefix-fanout=35.6 sequence=AAGAAGAAGAAA SRR7166126 testing PE reads STAR mapping to Ensembl genome Started job on | Feb 14 13:56:22 Started mapping on | Feb 14 13:56:22 Finished on | Feb 14 14:00:41 Mapping speed, Million of reads per hour | 210.22 Number of input reads | 15124262 Average input read length | 293 UNIQUE READS: Uniquely mapped reads number | 12823847 Uniquely mapped reads % | 84.79% Average mapped length | 292.45 Number of splices: Total | 12057930 Number of splices: Annotated (sjdb) | 11794346 Number of splices: GT/AG | 11848875 Number of splices: GC/AG | 159474 Number of splices: AT/AC | 10287 Number of splices: Non-canonical | 39294 Mismatch rate per base, % | 0.36% Deletion rate per base | 0.04% Deletion average length | 2.19 Insertion rate per base | 0.02% Insertion average length | 2.19 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 396728 % of reads mapped to multiple loci | 2.62% Number of reads mapped to too many loci | 76651 % of reads mapped to too many loci | 0.51% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 11.91% % of reads unmapped: other | 0.17% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 1911369 1911369 1911369 N_multimapping 396728 396728 396728 N_noFeature 472818 12651627 583054 N_ambiguous 135611 1532 72381 UnstrandedReadsAssigned:12215418 PositiveStrandReadsAssigned:170688 NegativeStrandReadsAssigned:12168412 Dataset is classified negative stranded MeadianReadLen=151 20thPercentileLength=149 echo kmer=145 SRR7166126 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: SRR7166126-trimmed-pair1.fastq SRR7166126-trimmed-pair2.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 15,124,262 reads, 12,204,750 reads pseudoaligned [quant] estimated average fragment length: 228.488 [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,154 rounds 52401 SRR7166126.ke.tsv 34699 SRR7166126.se.tsv 87100 total ==> SRR7166126.ke.tsv <== target_id length eff_length est_counts tpm Potri.005G200100.1.v4.1 2018 1790.51 1294 62.6166 Potri.005G024800.1.v4.1 1035 807.512 243 26.0729 Potri.004G059700.1.v4.1 961 733.512 8 0.944964 Potri.007G009000.2.v4.1 1416 1188.51 0 0 Potri.003G141000.2.v4.1 2943 2715.51 504.391 16.0934 Potri.016G087400.1.v4.1 270 87.4095 761 754.325 Potri.015G069301.1.v4.1 564 340.651 0 0 Potri.010G195200.1.v4.1 1773 1545.51 364 20.4062 Potri.012G127500.1.v4.1 977 749.512 5159 596.375 ==> SRR7166126.se.tsv <== Potri.001G166300.v4.1 0 Potri.001G448400.v4.1 2 Potri.001G233950.v4.1 0 Potri.001G122700.v4.1 303 Potri.001G212900.v4.1 0 Potri.001G182400.v4.1 0 Potri.001G256600.v4.1 0 Potri.001G040500.v4.1 1 Potri.001G416900.v4.1 1 Potri.001G452600.v4.1 433 SRR7166126 completed mapping pipeline successfully