Starting /dee2/code/volunteer_pipeline.sh SRR5579212 current disk space = 1522757976064 free memory = 1597796484 SRR5579212 SRAfilesize 4a656bae930c889c2bd43c4527ab4734 SRR5579212.sra SRR5579212.sra file validated SRR5579212 is paired end SRR5579212 is conventional basespace SRR5579212 read1 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR5579212_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 29.03975 34.0 33.0 34.0 2.0 34.0 2 32.56775 34.0 33.0 34.0 28.0 34.0 3 32.88425 34.0 33.0 34.0 31.0 34.0 4 33.2415 34.0 33.0 34.0 32.0 34.0 5 33.2015 34.0 33.0 34.0 33.0 34.0 6 37.08225 38.0 37.0 38.0 36.0 38.0 7 37.42425 38.0 38.0 38.0 37.0 38.0 8 37.50475 38.0 38.0 38.0 37.0 38.0 9 37.508 38.0 38.0 38.0 38.0 38.0 10-14 37.54715 38.0 38.0 38.0 38.0 38.0 15-19 37.5261 38.0 38.0 38.0 38.0 38.0 20-24 37.516749999999995 38.0 38.0 38.0 38.0 38.0 25-29 37.51405 38.0 38.0 38.0 38.0 38.0 30-34 37.47695 38.0 38.0 38.0 37.8 38.0 35-39 37.4201 38.0 38.0 38.0 37.4 38.0 40-44 37.308099999999996 38.0 38.0 38.0 37.0 38.0 45-49 37.2467 38.0 38.0 38.0 36.6 38.0 50-54 37.1868 38.0 38.0 38.0 36.4 38.0 55-59 37.11385 38.0 38.0 38.0 36.2 38.0 60-64 37.0958 38.0 38.0 38.0 36.0 38.0 65-69 37.02915 38.0 38.0 38.0 36.0 38.0 70-74 36.94265 38.0 38.0 38.0 35.8 38.0 75-79 36.967349999999996 38.0 38.0 38.0 36.0 38.0 80-84 36.88615 38.0 38.0 38.0 35.4 38.0 85-89 36.7581 38.0 38.0 38.0 35.0 38.0 90-94 36.6739 38.0 38.0 38.0 34.8 38.0 95-99 36.52290000000001 38.0 38.0 38.0 34.4 38.0 100-104 36.39835 38.0 38.0 38.0 34.0 38.0 105-109 36.29970000000001 38.0 38.0 38.0 34.0 38.0 110-114 36.26180000000001 38.0 38.0 38.0 33.8 38.0 115-119 36.06085 38.0 37.8 38.0 33.4 38.0 120-124 35.9707 38.0 37.6 38.0 33.0 38.0 125-129 35.791850000000004 38.0 37.6 38.0 32.6 38.0 130-134 35.634550000000004 38.0 36.6 38.0 32.2 38.0 135-139 35.33885 38.0 36.0 38.0 31.0 38.0 140-144 35.1151 38.0 36.0 38.0 29.8 38.0 145-149 34.46835 38.0 35.4 38.0 27.6 38.0 150-151 31.3295 36.5 31.5 38.0 13.0 38.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 4 1.0 5 0.0 6 0.0 7 0.0 8 0.0 9 0.0 10 2.0 11 1.0 12 1.0 13 4.0 14 1.0 15 1.0 16 2.0 17 4.0 18 6.0 19 0.0 20 6.0 21 7.0 22 8.0 23 4.0 24 10.0 25 10.0 26 14.0 27 22.0 28 26.0 29 31.0 30 34.0 31 47.0 32 56.0 33 71.0 34 134.0 35 205.0 36 543.0 37 2749.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 43.05595824876776 11.539576688895332 11.742534067845753 33.66193099449116 2 24.425 19.725 32.275 23.575 3 23.125 24.925 21.5 30.45 4 28.625 32.324999999999996 18.275 20.775 5 26.450000000000003 33.75 19.55 20.25 6 21.375 35.175 21.099999999999998 22.35 7 16.625 19.925 40.45 23.0 8 21.45 20.65 26.05 31.85 9 21.75 20.75 29.575000000000003 27.925 10-14 23.095 26.200000000000003 24.3 26.405 15-19 23.605 25.555 24.5 26.340000000000003 20-24 23.46 25.369999999999997 24.85 26.32 25-29 23.465 25.525 24.84 26.169999999999998 30-34 23.575 26.07 24.13 26.224999999999998 35-39 23.945 25.215 24.845 25.995 40-44 23.74 24.805 25.235000000000003 26.22 45-49 24.075 25.285000000000004 24.365000000000002 26.275 50-54 23.810000000000002 25.615 24.29 26.284999999999997 55-59 23.915 25.185000000000002 24.01 26.889999999999997 60-64 24.240000000000002 25.155 24.68 25.924999999999997 65-69 23.59 25.255 24.485 26.669999999999998 70-74 24.435000000000002 24.875 24.665 26.025 75-79 24.7 24.765 24.275 26.26 80-84 24.57 24.805 24.285 26.340000000000003 85-89 24.01 25.290000000000003 24.51 26.19 90-94 24.325 24.745 24.26 26.669999999999998 95-99 24.75 24.775 23.830000000000002 26.645000000000003 100-104 24.404999999999998 25.130000000000003 24.279999999999998 26.185000000000002 105-109 25.22 24.95 23.86 25.97 110-114 24.735 25.145 23.71 26.41 115-119 24.709999999999997 24.295 24.060000000000002 26.935 120-124 24.855 24.709999999999997 24.04 26.395000000000003 125-129 24.865000000000002 24.925 23.82 26.39 130-134 25.16 25.005 23.395 26.44 135-139 24.925 24.73 24.03 26.314999999999998 140-144 25.005 25.064999999999998 23.51 26.419999999999998 145-149 24.75 25.185000000000002 23.315 26.75 150-151 24.85 24.15 24.3 26.700000000000003 >>END_MODULE >>Per sequence GC content fail #GC Content Count 0 0.0 1 0.0 2 0.0 3 0.0 4 0.0 5 0.0 6 0.0 7 0.0 8 0.0 9 0.0 10 0.0 11 0.0 12 0.0 13 0.0 14 0.0 15 0.5 16 0.5 17 0.0 18 0.0 19 0.0 20 0.0 21 0.0 22 0.0 23 0.0 24 0.0 25 0.0 26 1.5 27 2.0 28 1.5 29 4.5 30 7.0 31 9.0 32 13.0 33 21.5 34 26.5 35 31.5 36 45.5 37 65.5 38 94.0 39 109.0 40 117.0 41 131.0 42 143.5 43 170.5 44 188.0 45 174.0 46 169.5 47 185.0 48 173.5 49 152.0 50 157.0 51 154.5 52 133.0 53 123.0 54 126.0 55 110.5 56 96.0 57 90.0 58 84.5 59 89.5 60 82.0 61 68.0 62 70.5 63 72.5 64 59.5 65 60.0 66 56.5 67 49.0 68 53.5 69 41.5 70 35.5 71 35.5 72 29.0 73 26.5 74 20.5 75 13.5 76 7.5 77 2.5 78 4.5 79 5.5 80 3.5 81 2.0 82 0.0 83 0.0 84 0.0 85 0.0 86 0.0 87 0.0 88 0.0 89 0.0 90 0.0 91 0.0 92 0.0 93 0.0 94 0.0 95 0.0 96 0.0 97 0.0 98 0.0 99 0.0 100 0.0 >>END_MODULE >>Per base N content warn #Base N-Count 1 13.775 2 0.0 3 0.0 4 0.0 5 0.0 6 0.0 7 0.0 8 0.0 9 0.0 10-14 0.0 15-19 0.0 20-24 0.0 25-29 0.0 30-34 0.0 35-39 0.0 40-44 0.0 45-49 0.0 50-54 0.0 55-59 0.0 60-64 0.0 65-69 0.0 70-74 0.0 75-79 0.0 80-84 0.0 85-89 0.0 90-94 0.0 95-99 0.0 100-104 0.0 105-109 0.0 110-114 0.0 115-119 0.0 120-124 0.0 125-129 0.0 130-134 0.0 135-139 0.0 140-144 0.0 145-149 0.0 150-151 0.0 >>END_MODULE >>Sequence Length Distribution pass #Length Count 151 4000.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 99.5 #Duplication Level Percentage of deduplicated Percentage of total 1 99.52261306532664 99.02499999999999 2 0.4522613065326633 0.8999999999999999 3 0.02512562814070352 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 fail #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 0.037500000000000006 0.0 0.0 0.0 0.0 74-75 0.0625 0.0 0.0 0.0 0.0 76-77 0.075 0.0 0.0 0.0 0.0 78-79 0.075 0.0 0.0 0.0 0.0 80-81 0.1875 0.0 0.0 0.0 0.0 82-83 0.30000000000000004 0.0 0.0 0.0 0.0 84-85 0.4 0.0 0.0 0.0 0.0 86-87 0.575 0.0 0.0 0.0 0.0 88-89 0.7749999999999999 0.0 0.0 0.0 0.0 90-91 0.9 0.0 0.0 0.0 0.0 92-93 1.0625 0.0 0.0 0.0 0.0 94-95 1.3 0.0 0.0 0.0 0.0 96-97 1.6125 0.0 0.0 0.0 0.0 98-99 1.9249999999999998 0.0 0.0 0.0 0.0 100-101 2.3375 0.0 0.0 0.0 0.0 102-103 2.7874999999999996 0.0 0.0 0.0 0.0 104-105 3.2375 0.0 0.0 0.0 0.0 106-107 3.6375 0.0 0.0 0.0 0.0 108-109 4.0125 0.0 0.0 0.0 0.0 110-111 4.4375 0.0 0.0 0.0 0.0 112-113 4.949999999999999 0.0 0.0 0.0 0.0 114-115 5.425000000000001 0.0 0.0 0.0 0.0 116-117 5.824999999999999 0.0 0.0 0.0 0.0 118-119 6.362500000000001 0.0 0.0 0.0 0.0 120-121 7.0375 0.0 0.0 0.0 0.0 122-123 7.6125 0.0 0.0 0.0 0.0 124-125 8.25 0.0 0.0 0.0 0.0 126-127 9.0125 0.0 0.0 0.0 0.0 128-129 9.8 0.0 0.0 0.0 0.0 130-131 10.5 0.0 0.0 0.0 0.0 132-133 11.225000000000001 0.0 0.0 0.0 0.0 134-135 11.8875 0.0 0.0 0.0 0.0 136-137 12.5375 0.0 0.0 0.0 0.0 138-139 13.2375 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position GCTCGTT 10 0.0068484643 144.875 5 >>END_MODULE SRR5579212 read2 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR5579212_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 32.6875 33.0 33.0 34.0 32.0 34.0 2 32.8175 34.0 33.0 34.0 32.0 34.0 3 32.82125 34.0 33.0 34.0 32.0 34.0 4 32.812 34.0 33.0 34.0 32.0 34.0 5 32.806 34.0 33.0 34.0 32.0 34.0 6 36.94925 38.0 38.0 38.0 37.0 38.0 7 36.9815 38.0 38.0 38.0 37.0 38.0 8 36.8865 38.0 38.0 38.0 37.0 38.0 9 36.9295 38.0 38.0 38.0 36.0 38.0 10-14 36.92334999999999 38.0 38.0 38.0 36.6 38.0 15-19 36.8582 38.0 38.0 38.0 36.2 38.0 20-24 36.816900000000004 38.0 38.0 38.0 36.4 38.0 25-29 36.83344999999999 38.0 38.0 38.0 36.2 38.0 30-34 36.8395 38.0 38.0 38.0 36.2 38.0 35-39 36.7829 38.0 38.0 38.0 36.4 38.0 40-44 36.78 38.0 38.0 38.0 36.2 38.0 45-49 36.75945 38.0 38.0 38.0 36.0 38.0 50-54 36.705600000000004 38.0 38.0 38.0 36.0 38.0 55-59 36.69715000000001 38.0 38.0 38.0 36.0 38.0 60-64 36.6722 38.0 38.0 38.0 36.0 38.0 65-69 36.563900000000004 38.0 38.0 38.0 35.6 38.0 70-74 36.462900000000005 38.0 38.0 38.0 35.0 38.0 75-79 36.46685 38.0 38.0 38.0 35.0 38.0 80-84 36.5247 38.0 38.0 38.0 35.0 38.0 85-89 36.4412 38.0 38.0 38.0 35.0 38.0 90-94 36.36495 38.0 38.0 38.0 34.8 38.0 95-99 36.22975 38.0 38.0 38.0 34.4 38.0 100-104 36.12545 38.0 38.0 38.0 34.2 38.0 105-109 35.952 38.0 38.0 38.0 33.6 38.0 110-114 35.8263 38.0 38.0 38.0 33.2 38.0 115-119 35.7546 38.0 38.0 38.0 33.0 38.0 120-124 35.498549999999994 38.0 37.8 38.0 31.4 38.0 125-129 35.26265 38.0 37.0 38.0 31.0 38.0 130-134 35.0025 38.0 36.0 38.0 30.0 38.0 135-139 34.5199 38.0 35.6 38.0 26.2 38.0 140-144 34.136399999999995 38.0 35.2 38.0 24.0 38.0 145-149 33.335249999999995 38.0 34.6 38.0 15.2 38.0 150-151 29.4175 35.5 27.0 38.0 2.0 38.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 2 20.0 3 8.0 4 4.0 5 2.0 6 4.0 7 1.0 8 3.0 9 1.0 10 3.0 11 3.0 12 0.0 13 1.0 14 6.0 15 3.0 16 6.0 17 2.0 18 5.0 19 4.0 20 11.0 21 10.0 22 8.0 23 17.0 24 16.0 25 17.0 26 25.0 27 28.0 28 19.0 29 25.0 30 41.0 31 46.0 32 53.0 33 80.0 34 131.0 35 226.0 36 424.0 37 2747.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 41.65 13.375 12.475 32.5 2 28.425 22.0 27.950000000000003 21.625 3 24.725 22.55 25.5 27.224999999999998 4 29.799999999999997 31.05 16.875 22.275 5 28.625 32.15 18.875 20.349999999999998 6 21.7 33.575 18.95 25.775 7 21.0 15.024999999999999 36.525 27.450000000000003 8 24.224999999999998 20.5 22.825 32.45 9 24.3 20.4 25.5 29.799999999999997 10-14 26.095000000000002 24.54 23.235 26.13 15-19 25.865 23.45 24.0 26.685 20-24 26.07 23.985 24.104999999999997 25.840000000000003 25-29 26.41 24.51 23.345 25.735000000000003 30-34 25.974999999999998 24.005000000000003 23.7 26.32 35-39 26.295 24.315 23.474999999999998 25.915 40-44 26.845000000000002 23.98 23.455000000000002 25.72 45-49 27.075 23.72 23.75 25.455 50-54 26.265 24.490000000000002 23.565 25.679999999999996 55-59 26.735 25.06 23.115 25.09 60-64 26.565 24.035 24.01 25.39 65-69 26.965 24.445 23.974999999999998 24.615000000000002 70-74 26.43 24.505 23.71 25.355 75-79 26.724999999999998 23.86 24.08 25.335 80-84 26.565 24.57 24.185000000000002 24.68 85-89 27.235 24.16 24.035 24.57 90-94 26.724999999999998 24.415 24.044999999999998 24.815 95-99 26.715 24.64 24.065 24.58 100-104 27.315 24.43 23.69 24.565 105-109 26.91 23.98 24.695 24.415 110-114 27.82 24.84 23.62 23.72 115-119 27.284999999999997 24.83 24.22 23.665 120-124 28.09 24.73 23.73 23.45 125-129 27.6 25.39 23.365 23.645 130-134 28.82 25.1 23.105 22.975 135-139 27.96 24.97 23.76 23.31 140-144 28.689999999999998 24.915000000000003 23.46 22.935 145-149 28.895 24.92 23.465 22.720000000000002 150-151 28.775000000000002 25.474999999999998 23.2625 22.4875 >>END_MODULE >>Per sequence GC content fail #GC Content Count 0 0.0 1 0.0 2 0.5 3 0.5 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 0.5 25 0.5 26 0.5 27 0.5 28 0.5 29 1.5 30 4.5 31 6.5 32 6.0 33 9.0 34 13.0 35 16.5 36 28.5 37 40.5 38 58.0 39 77.0 40 89.0 41 110.5 42 138.5 43 152.0 44 148.0 45 155.5 46 160.5 47 185.0 48 180.0 49 153.5 50 162.5 51 152.5 52 143.5 53 134.5 54 123.0 55 114.5 56 100.5 57 99.0 58 97.0 59 100.5 60 102.5 61 89.0 62 88.5 63 91.0 64 87.0 65 78.5 66 71.0 67 64.5 68 68.5 69 62.5 70 44.0 71 39.0 72 36.0 73 31.5 74 29.5 75 23.5 76 9.5 77 6.5 78 6.5 79 3.0 80 2.0 81 1.0 82 0.5 83 0.0 84 0.0 85 0.0 86 0.0 87 0.0 88 0.0 89 0.0 90 0.0 91 0.0 92 0.0 93 0.0 94 0.0 95 0.0 96 0.0 97 0.0 98 0.0 99 0.0 100 0.0 >>END_MODULE >>Per base N content pass #Base N-Count 1 0.0 2 0.0 3 0.0 4 0.0 5 0.0 6 0.0 7 0.0 8 0.0 9 0.0 10-14 0.0 15-19 0.0 20-24 0.0 25-29 0.0 30-34 0.0 35-39 0.0 40-44 0.0 45-49 0.0 50-54 0.0 55-59 0.0 60-64 0.0 65-69 0.0 70-74 0.0 75-79 0.0 80-84 0.0 85-89 0.0 90-94 0.0 95-99 0.0 100-104 0.0 105-109 0.0 110-114 0.0 115-119 0.0 120-124 0.0 125-129 0.0 130-134 0.0 135-139 0.0 140-144 0.0 145-149 0.0 150-151 0.0 >>END_MODULE >>Sequence Length Distribution pass #Length Count 151 4000.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 99.125 #Duplication Level Percentage of deduplicated Percentage of total 1 99.19293820933164 98.32499999999999 2 0.7566204287515763 1.5 3 0.025220680958385876 0.075 4 0.025220680958385876 0.1 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 fail #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 0.037500000000000006 0.0 0.0 0.0 0.0 74-75 0.0625 0.0 0.0 0.0 0.0 76-77 0.075 0.0 0.0 0.0 0.0 78-79 0.075 0.0 0.0 0.0 0.0 80-81 0.2 0.0 0.0 0.0 0.0 82-83 0.30000000000000004 0.0 0.0 0.0 0.0 84-85 0.4 0.0 0.0 0.0 0.0 86-87 0.575 0.0 0.0 0.0 0.0 88-89 0.7749999999999999 0.0 0.0 0.0 0.0 90-91 0.925 0.0 0.0 0.0 0.0 92-93 1.0875 0.0 0.0 0.0 0.0 94-95 1.3375 0.0 0.0 0.0 0.0 96-97 1.625 0.0 0.0 0.0 0.0 98-99 1.9249999999999998 0.0 0.0 0.0 0.0 100-101 2.3625 0.0 0.0 0.0 0.0 102-103 2.8375 0.0 0.0 0.0 0.0 104-105 3.3 0.0 0.0 0.0 0.0 106-107 3.6875 0.0 0.0 0.0 0.0 108-109 4.0625 0.0 0.0 0.0 0.0 110-111 4.475 0.0 0.0 0.0 0.0 112-113 4.975 0.0 0.0 0.0 0.0 114-115 5.425000000000001 0.0 0.0 0.0 0.0 116-117 5.824999999999999 0.0 0.0 0.0 0.0 118-119 6.3375 0.0 0.0 0.0 0.0 120-121 7.012499999999999 0.0 0.0 0.0 0.0 122-123 7.6 0.0 0.0 0.0 0.0 124-125 8.25 0.0 0.0 0.0 0.0 126-127 9.0375 0.0 0.0 0.0 0.0 128-129 9.8125 0.0 0.0 0.0 0.0 130-131 10.55 0.0 0.0 0.0 0.0 132-133 11.325 0.0 0.0 0.0 0.0 134-135 12.0125 0.0 0.0 0.0 0.0 136-137 12.7 0.0 0.0 0.0 0.0 138-139 13.4625 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position AAAAAAA 35 0.0035366106 20.714287 135-139 >>END_MODULE Read 1228888 spots for SRR5579212.sra Written 1228888 spots for SRR5579212.sra Read 1228888 spots for SRR5579212.sra Written 1228888 spots for SRR5579212.sra Read 1228888 spots for SRR5579212.sra Written 1228888 spots for SRR5579212.sra Read 1228888 spots for SRR5579212.sra Written 1228888 spots for SRR5579212.sra Read 1228888 spots for SRR5579212.sra Written 1228888 spots for SRR5579212.sra Read 1228888 spots for SRR5579212.sra Written 1228888 spots for SRR5579212.sra Read 1228888 spots for SRR5579212.sra Written 1228888 spots for SRR5579212.sra Read 1228888 spots for SRR5579212.sra Written 1228888 spots for SRR5579212.sra Read 1228888 spots for SRR5579212.sra Written 1228888 spots for SRR5579212.sra Read 1228888 spots for SRR5579212.sra Written 1228888 spots for SRR5579212.sra Read 1228891 spots for SRR5579212.sra Written 1228891 spots for SRR5579212.sra Read 1228888 spots for SRR5579212.sra Written 1228888 spots for SRR5579212.sra Read 1228888 spots for SRR5579212.sra Written 1228888 spots for SRR5579212.sra Read 1228888 spots for SRR5579212.sra Written 1228888 spots for SRR5579212.sra Read 1228888 spots for SRR5579212.sra Written 1228888 spots for SRR5579212.sra Read 1228888 spots for SRR5579212.sra Written 1228888 spots for SRR5579212.sra Read 1228888 spots for SRR5579212.sra Written 1228888 spots for SRR5579212.sra Read 1228888 spots for SRR5579212.sra Written 1228888 spots for SRR5579212.sra Read 1228888 spots for SRR5579212.sra Written 1228888 spots for SRR5579212.sra Read 1228888 spots for SRR5579212.sra Written 1228888 spots for SRR5579212.sra SRR ids: ['SRR5579212.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_g15crp8e SRR5579212.sra spots: 24577763 blocks: [[1, 1228888], [1228889, 2457776], [2457777, 3686664], [3686665, 4915552], [4915553, 6144440], [6144441, 7373328], [7373329, 8602216], [8602217, 9831104], [9831105, 11059992], [11059993, 12288880], [12288881, 13517768], [13517769, 14746656], [14746657, 15975544], [15975545, 17204432], [17204433, 18433320], [18433321, 19662208], [19662209, 20891096], [20891097, 22119984], [22119985, 23348872], [23348873, 24577763]] SRR5579212 file size 8306897 SRR5579212 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 SRR5579212 SRR5579212_1.fastq SRR5579212_2.fastq Input file: SRR5579212_1.fastq Paired file: SRR5579212_2.fastq trimmed: SRR5579212-trimmed-pair1.fastq, SRR5579212-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 Dec 9 22:24:45 2024 >> started Mon Dec 9 22:25:14 2024 >> done (28.307s) 24577763 read pairs processed; of these: 53109 ( 0.22%) short read pairs filtered out after trimming by size control 78954 ( 0.32%) empty read pairs filtered out after trimming by size control 24445700 (99.46%) read pairs available; of these: 10881837 (44.51%) trimmed read pairs available after processing 13563863 (55.49%) untrimmed read pairs available after processing Length distribution of reads after trimming: length count percentage 18 9 0.00% 19 6 0.00% 20 13 0.00% 21 12 0.00% 22 14 0.00% 23 17 0.00% 24 10 0.00% 25 17 0.00% 26 15 0.00% 27 23 0.00% 28 17 0.00% 29 32 0.00% 30 25 0.00% 31 25 0.00% 32 17 0.00% 33 17 0.00% 34 28 0.00% 35 37 0.00% 36 38 0.00% 37 48 0.00% 38 60 0.00% 39 56 0.00% 40 78 0.00% 41 72 0.00% 42 89 0.00% 43 101 0.00% 44 100 0.00% 45 131 0.00% 46 149 0.00% 47 166 0.00% 48 204 0.00% 49 243 0.00% 50 266 0.00% 51 328 0.00% 52 328 0.00% 53 344 0.00% 54 434 0.00% 55 449 0.00% 56 547 0.00% 57 618 0.00% 58 757 0.00% 59 868 0.00% 60 988 0.00% 61 1126 0.00% 62 1293 0.01% 63 1393 0.01% 64 1554 0.01% 65 1711 0.01% 66 1983 0.01% 67 2449 0.01% 68 2710 0.01% 69 3119 0.01% 70 3858 0.02% 71 4050 0.02% 72 4453 0.02% 73 5112 0.02% 74 5529 0.02% 75 6022 0.02% 76 6944 0.03% 77 7661 0.03% 78 8694 0.04% 79 9903 0.04% 80 10759 0.04% 81 12173 0.05% 82 13667 0.06% 83 15394 0.06% 84 18685 0.08% 85 20415 0.08% 86 21761 0.09% 87 22741 0.09% 88 24107 0.10% 89 25773 0.11% 90 27648 0.11% 91 29534 0.12% 92 32184 0.13% 93 33857 0.14% 94 35568 0.15% 95 37404 0.15% 96 38262 0.16% 97 40041 0.16% 98 41315 0.17% 99 43340 0.18% 100 46068 0.19% 101 47974 0.20% 102 50917 0.21% 103 52945 0.22% 104 55442 0.23% 105 56881 0.23% 106 58828 0.24% 107 59517 0.24% 108 61355 0.25% 109 63260 0.26% 110 65342 0.27% 111 68221 0.28% 112 70485 0.29% 113 73100 0.30% 114 75618 0.31% 115 77742 0.32% 116 79003 0.32% 117 80236 0.33% 118 80627 0.33% 119 82688 0.34% 120 85885 0.35% 121 87245 0.36% 122 90184 0.37% 123 92965 0.38% 124 97236 0.40% 125 98126 0.40% 126 100648 0.41% 127 101229 0.41% 128 101789 0.42% 129 103761 0.42% 130 105633 0.43% 131 108037 0.44% 132 112531 0.46% 133 115980 0.47% 134 118811 0.49% 135 122914 0.50% 136 126001 0.52% 137 128030 0.52% 138 131501 0.54% 139 135051 0.55% 140 139838 0.57% 141 146915 0.60% 142 155415 0.64% 143 166012 0.68% 144 180845 0.74% 145 201144 0.82% 146 230955 0.94% 147 285454 1.17% 148 396364 1.62% 149 715385 2.93% 150 4161716 17.02% 151 13563863 55.49% 24445700 reads passed initial QC criterion=sequence-density sequence-density=0.42 sequence-density-rank=1 fanout-score=2.05 fanout-score-rank=28 prefix-density=0.43 prefix-fanout=2.0 sequence=TAGGCGTCCGGGTACTCCTTCTTGACCTCCTCCAGCTCCTT criterion=fanout-score sequence-density=0.06 sequence-density-rank=29 fanout-score=118.27 fanout-score-rank=1 prefix-density=0.49 prefix-fanout=14.3 sequence=GGCGGCGGCGAACCGCCCCCGTCGCCGCGATCCGAACACTTCACCGGACCATTCAATCGGTAGGAGCGACGGGCGGTGTGTACAAAGGGCAGGGACGTAGTCAACGCGAGCTGATGACTCGCGCTTACTAGGCATTCCTCGTTGAAGACCAACAATTGCAATGATCTATCCCCATCACGATGAAATTTCCCAAGATTACCCGGGCCTGTCGGCCAAGGCTATATACTCGTTGAATACATCAGTGTAGCGCGCGTGCGGCCCAGAACATCTAAGGGCATCACAGACCTGTTATTGCCTCAAACTTCCGTCGCCTAAACGGCGATAGTCCCTCTAAGAAGCTAGCTGCGGAGGGATGGCTCCGCATAGCTAGTTAGCAGGCTGAGGTCTCGTTCGTTAACGGAATTAACCAGACAAATCGCTCCACCAACTAAGAACGGCCATGCACCACCACCCATAGAATCAAGAAAGAGCTCTCAGTCTGTCAATCCTTGCTATGTCTGGACCTGGTAAG criterion=sequence-density sequence-density=0.46 sequence-density-rank=1 fanout-score=4.17 fanout-score-rank=10 prefix-density=0.53 prefix-fanout=3.6 sequence=GAGTTCAGCAAGGTCGGCTT criterion=fanout-score sequence-density=0.05 sequence-density-rank=28 fanout-score=47.76 fanout-score-rank=1 prefix-density=0.33 prefix-fanout=7.4 sequence=GAGGTCATCCACTGCCGCTGGGCTATGCTTGGTGCCCTCGGCTGCGTCTTCCCCGAGCTGCT SRR5579212 testing PE reads STAR mapping to Ensembl genome Started job on | Dec 09 22:26:05 Started mapping on | Dec 09 22:26:05 Finished on | Dec 09 22:30:08 Mapping speed, Million of reads per hour | 362.16 Number of input reads | 24445700 Average input read length | 289 UNIQUE READS: Uniquely mapped reads number | 22499141 Uniquely mapped reads % | 92.04% Average mapped length | 289.22 Number of splices: Total | 22071774 Number of splices: Annotated (sjdb) | 20793250 Number of splices: GT/AG | 21797248 Number of splices: GC/AG | 249137 Number of splices: AT/AC | 12742 Number of splices: Non-canonical | 12647 Mismatch rate per base, % | 0.10% Deletion rate per base | 0.00% Deletion average length | 1.36 Insertion rate per base | 0.00% Insertion average length | 1.10 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 338039 % of reads mapped to multiple loci | 1.38% Number of reads mapped to too many loci | 95480 % of reads mapped to too many loci | 0.39% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 4.07% % of reads unmapped: other | 2.12% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 1637119 1637119 1637119 N_multimapping 338039 338039 338039 N_noFeature 635713 21861452 833281 N_ambiguous 505737 3371 64950 UnstrandedReadsAssigned:21357691 PositiveStrandReadsAssigned:634318 NegativeStrandReadsAssigned:21600910 Dataset is classified negative stranded MeadianReadLen=151 20thPercentileLength=146 echo kmer=141 SRR5579212 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: SRR5579212-trimmed-pair1.fastq SRR5579212-trimmed-pair2.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 24,445,700 reads, 21,776,141 reads pseudoaligned [quant] estimated average fragment length: 240.729 [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,184 rounds 52973 SRR5579212.ke.tsv 35125 SRR5579212.se.tsv 88098 total ==> SRR5579212.ke.tsv <== target_id length eff_length est_counts tpm PNS24245 936 696.663 41.7021 3.69606 PNS24247 1044 804.271 41.7815 3.20765 PNS24249 1928 1688.27 104.584 3.82498 PNS24246 1044 804.271 41.7815 3.20765 PNS24248 1044 804.271 41.7815 3.20765 PNS24244 1471 1231.27 165.369 8.29286 PNS24243 293 107.723 0 0 KQK14069 1603 1363.27 1913.46 86.6647 KQK14071 474 252.194 60.8573 14.8998 ==> SRR5579212.se.tsv <== BRADI_1g14170v3 2064 BRADI_1g53295v3 35 BRADI_1g59795v3 412 BRADI_1g07683v3 0 BRADI_1g00485v3 27 BRADI_1g20270v3 5093 BRADI_1g74790v3 92 BRADI_1g09890v3 40 BRADI_1g77505v3 427 BRADI_1g48960v3 5 SRR5579212 completed mapping pipeline successfully