Starting /dee2/code/volunteer_pipeline.sh SRR6958413 current disk space = 1548555341824 free memory = 1600282040 SRR6958413 SRAfilesize 01236140da20d2a3db3154ca9cbb247a SRR6958413.sra SRR6958413.sra file validated SRR6958413 is paired end SRR6958413 is conventional basespace SRR6958413 read1 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR6958413_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 49 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 29.08575 33.0 32.0 33.0 2.0 34.0 2 31.363 33.0 31.0 33.0 27.0 34.0 3 32.033 33.0 31.0 34.0 27.0 34.0 4 32.78575 33.0 33.0 34.0 32.0 34.0 5 32.96475 33.0 33.0 34.0 32.0 34.0 6 37.0675 38.0 37.0 38.0 36.0 38.0 7 37.1915 38.0 38.0 38.0 36.0 38.0 8 37.34525 38.0 38.0 38.0 36.0 38.0 9 37.3645 38.0 38.0 38.0 37.0 38.0 10-14 37.305899999999994 38.0 38.0 38.0 36.6 38.0 15-19 37.27775 38.0 38.0 38.0 36.6 38.0 20-24 36.61845 38.0 37.8 38.0 34.2 38.0 25-29 36.7532 38.0 38.0 38.0 34.8 38.0 30-34 37.145599999999995 38.0 38.0 38.0 36.4 38.0 35-39 37.355399999999996 38.0 38.0 38.0 37.0 38.0 40-44 37.3339 38.0 38.0 38.0 37.0 38.0 45-49 37.256099999999996 38.0 38.0 38.0 36.6 38.0 50-54 36.98285 38.0 38.0 38.0 35.6 38.0 55-59 36.957100000000004 38.0 38.0 38.0 35.6 38.0 60-64 37.123000000000005 38.0 38.0 38.0 36.0 38.0 65-69 37.171 38.0 38.0 38.0 36.0 38.0 70-74 37.176300000000005 38.0 38.0 38.0 36.0 38.0 75-79 37.15625 38.0 38.0 38.0 36.0 38.0 80-84 37.043099999999995 38.0 38.0 38.0 35.8 38.0 85-89 36.545950000000005 38.0 38.0 38.0 34.0 38.0 90-94 36.013400000000004 38.0 37.4 38.0 32.2 38.0 95-99 35.136900000000004 38.0 36.0 38.0 27.0 38.0 100-104 34.8289 38.0 35.6 38.0 25.2 38.0 105-109 34.86645 38.0 35.4 38.0 25.2 38.0 110-114 35.282799999999995 38.0 36.0 38.0 28.0 38.0 115-119 35.8052 38.0 36.6 38.0 31.8 38.0 120-124 35.95635 38.0 37.0 38.0 33.0 38.0 125-129 36.0085 38.0 36.6 38.0 33.0 38.0 130-134 35.8498 38.0 36.0 38.0 32.6 38.0 135-139 35.624649999999995 38.0 36.0 38.0 31.6 38.0 140-144 34.57365 38.0 34.6 38.0 27.4 38.0 145-149 32.49034999999999 37.8 32.2 38.0 16.6 38.0 150-151 28.5075 34.5 17.5 38.0 2.0 38.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 8 1.0 9 1.0 10 0.0 11 0.0 12 0.0 13 0.0 14 0.0 15 0.0 16 4.0 17 2.0 18 3.0 19 0.0 20 6.0 21 1.0 22 1.0 23 3.0 24 13.0 25 15.0 26 20.0 27 24.0 28 32.0 29 48.0 30 61.0 31 80.0 32 100.0 33 148.0 34 201.0 35 350.0 36 716.0 37 2170.0 >>END_MODULE >>Per base sequence content warn #Base G A T C 1 43.33796940194715 9.95827538247566 9.207232267037552 37.49652294853964 2 26.150000000000002 14.099999999999998 33.7 26.05 3 22.225 19.85 24.675 33.25 4 25.1 25.95 22.225 26.724999999999998 5 25.674999999999997 30.075000000000003 24.099999999999998 20.150000000000002 6 22.5 32.1 23.974999999999998 21.425 7 18.45 21.975 39.675 19.900000000000002 8 21.075 22.45 28.975 27.500000000000004 9 20.225 21.025 32.9 25.85 10-14 23.064999999999998 26.3 25.505 25.130000000000003 15-19 23.189637927585515 24.299859971994398 26.44028805761152 26.07021404280856 20-24 23.44 25.380000000000003 25.505 25.674999999999997 25-29 23.09 25.580000000000002 25.590000000000003 25.740000000000002 30-34 22.955000000000002 25.195 25.885 25.965 35-39 22.994999999999997 24.64 26.085 26.279999999999998 40-44 23.365 25.040000000000003 26.115 25.480000000000004 45-49 23.265 24.959999999999997 26.185000000000002 25.590000000000003 50-54 23.189999999999998 25.205 26.395000000000003 25.21 55-59 23.595 25.305 25.759999999999998 25.34 60-64 23.52 24.560000000000002 25.509999999999998 26.41 65-69 23.485 24.959999999999997 25.985000000000003 25.569999999999997 70-74 23.68 24.775 25.895000000000003 25.650000000000002 75-79 23.955000000000002 24.7 25.115 26.229999999999997 80-84 23.135 24.6 26.38 25.885 85-89 23.06 24.93 26.105 25.905 90-94 24.07 25.290000000000003 24.915000000000003 25.724999999999998 95-99 23.32 24.834999999999997 26.025 25.82 100-104 23.145 25.490000000000002 25.564999999999998 25.8 105-109 23.22 24.91 25.874999999999996 25.995 110-114 23.375 24.995 26.119999999999997 25.509999999999998 115-119 23.205000000000002 24.555 26.36 25.88 120-124 23.549999999999997 24.83 25.805 25.814999999999998 125-129 23.49 25.11 25.655 25.745 130-134 24.03 25.4 24.845 25.724999999999998 135-139 23.735 25.41 25.28 25.575 140-144 24.055 24.89 25.324999999999996 25.729999999999997 145-149 23.84 25.09 24.985 26.085 150-151 23.425 25.2 25.112499999999997 26.2625 >>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 0.0 16 0.5 17 0.5 18 0.0 19 0.0 20 0.0 21 0.0 22 0.0 23 0.0 24 1.0 25 1.0 26 0.0 27 1.5 28 4.0 29 4.0 30 5.5 31 8.5 32 10.5 33 17.5 34 24.5 35 35.5 36 46.0 37 57.5 38 81.0 39 103.0 40 124.0 41 143.5 42 168.0 43 192.5 44 198.5 45 205.0 46 203.5 47 197.0 48 201.5 49 184.5 50 161.0 51 138.0 52 136.5 53 130.0 54 105.0 55 104.0 56 111.5 57 100.0 58 80.0 59 75.5 60 76.0 61 80.0 62 67.0 63 59.0 64 63.0 65 60.5 66 46.5 67 35.5 68 33.5 69 28.0 70 26.5 71 21.0 72 14.5 73 10.5 74 6.5 75 3.5 76 1.5 77 1.5 78 2.0 79 1.5 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 warn #Base N-Count 1 10.125 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 0.02 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 99.1 #Duplication Level Percentage of deduplicated Percentage of total 1 99.11705348133198 98.225 2 0.8577194752774974 1.7000000000000002 3 0.025227043390514632 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 0.025 0.0 0.0 0.0 0.0 64-65 0.05 0.0 0.0 0.0 0.0 66-67 0.05 0.0 0.0 0.0 0.0 68-69 0.05 0.0 0.0 0.0 0.0 70-71 0.05 0.0 0.0 0.0 0.0 72-73 0.0625 0.0 0.0 0.0 0.0 74-75 0.1 0.0 0.0 0.0 0.0 76-77 0.1375 0.0 0.0 0.0 0.0 78-79 0.15 0.0 0.0 0.0 0.0 80-81 0.16249999999999998 0.0 0.0 0.0 0.0 82-83 0.225 0.0 0.0 0.0 0.0 84-85 0.275 0.0 0.0 0.0 0.0 86-87 0.3 0.0 0.0 0.0 0.0 88-89 0.35 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 0.475 0.0 0.0 0.0 0.0 96-97 0.5125 0.0 0.0 0.0 0.0 98-99 0.6125 0.0 0.0 0.0 0.0 100-101 0.7625 0.0 0.0 0.0 0.0 102-103 0.875 0.0 0.0 0.0 0.0 104-105 0.9875 0.0 0.0 0.0 0.0 106-107 1.025 0.0 0.0 0.0 0.0 108-109 1.15 0.0 0.0 0.0 0.0 110-111 1.225 0.0 0.0 0.0 0.0 112-113 1.3625 0.0 0.0 0.0 0.0 114-115 1.55 0.0 0.0 0.0 0.0 116-117 1.6875 0.0 0.0 0.0 0.0 118-119 2.0 0.0 0.0 0.0 0.0 120-121 2.1500000000000004 0.0 0.0 0.0 0.0 122-123 2.4124999999999996 0.0 0.0 0.0 0.0 124-125 2.8375 0.0 0.0 0.0 0.0 126-127 3.1125 0.0 0.0 0.0 0.0 128-129 3.375 0.0 0.0 0.0 0.0 130-131 3.7125000000000004 0.0 0.0 0.0 0.0 132-133 4.112500000000001 0.0 0.0 0.0 0.0 134-135 4.512499999999999 0.0 0.0 0.0 0.0 136-137 4.7 0.0 0.0 0.0 0.0 138-139 5.0875 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position CTTCAGT 10 0.004973884 161.00002 1 CGAGAAT 10 0.004973884 161.00002 1 TTCAGTA 10 0.0068449317 144.90001 2 >>END_MODULE SRR6958413 read2 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR6958413_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 49 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 32.75225 33.0 33.0 34.0 32.0 34.0 2 32.8765 33.0 33.0 34.0 32.0 34.0 3 32.8695 34.0 33.0 34.0 32.0 34.0 4 32.84025 34.0 33.0 34.0 32.0 34.0 5 32.89625 34.0 33.0 34.0 32.0 34.0 6 37.02025 38.0 38.0 38.0 36.0 38.0 7 36.92325 38.0 38.0 38.0 36.0 38.0 8 36.72325 38.0 38.0 38.0 35.0 38.0 9 36.66475 38.0 38.0 38.0 35.0 38.0 10-14 36.4984 38.0 38.0 38.0 34.2 38.0 15-19 36.346900000000005 38.0 38.0 38.0 33.6 38.0 20-24 36.5231 38.0 38.0 38.0 34.2 38.0 25-29 36.70795 38.0 38.0 38.0 35.0 38.0 30-34 36.954249999999995 38.0 38.0 38.0 36.0 38.0 35-39 37.01305 38.0 38.0 38.0 36.2 38.0 40-44 36.966950000000004 38.0 38.0 38.0 36.0 38.0 45-49 36.731049999999996 38.0 38.0 38.0 35.4 38.0 50-54 36.4246 38.0 38.0 38.0 34.0 38.0 55-59 36.3163 38.0 38.0 38.0 33.6 38.0 60-64 36.64665 38.0 38.0 38.0 34.6 38.0 65-69 36.15775000000001 38.0 38.0 38.0 33.2 38.0 70-74 36.02315 38.0 38.0 38.0 32.8 38.0 75-79 35.8074 38.0 37.2 38.0 31.2 38.0 80-84 35.4919 38.0 37.2 38.0 29.4 38.0 85-89 35.358200000000004 38.0 36.8 38.0 28.4 38.0 90-94 35.89815 38.0 37.4 38.0 32.4 38.0 95-99 36.10465000000001 38.0 38.0 38.0 33.6 38.0 100-104 36.0995 38.0 38.0 38.0 33.4 38.0 105-109 35.97154999999999 38.0 37.6 38.0 32.8 38.0 110-114 35.4807 38.0 36.6 38.0 31.0 38.0 115-119 35.201049999999995 38.0 36.0 38.0 29.2 38.0 120-124 33.60255 37.8 33.4 38.0 21.2 38.0 125-129 33.2244 38.0 32.8 38.0 19.0 38.0 130-134 27.619349999999997 30.4 18.0 36.4 13.2 38.0 135-139 33.1948 37.8 32.6 38.0 20.2 38.0 140-144 33.47370000000001 38.0 33.0 38.0 21.4 38.0 145-149 32.7083 38.0 33.0 38.0 12.8 38.0 150-151 27.572125 34.5 17.5 38.0 2.0 38.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 2 9.0 3 2.0 4 2.0 5 2.0 6 1.0 7 3.0 8 0.0 9 3.0 10 1.0 11 2.0 12 3.0 13 0.0 14 2.0 15 2.0 16 5.0 17 9.0 18 6.0 19 6.0 20 8.0 21 9.0 22 13.0 23 21.0 24 26.0 25 29.0 26 24.0 27 44.0 28 47.0 29 53.0 30 67.0 31 101.0 32 106.0 33 159.0 34 258.0 35 352.0 36 863.0 37 1762.0 >>END_MODULE >>Per base sequence content warn #Base G A T C 1 37.25 18.75 11.75 32.25 2 30.975 22.85 27.6 18.575 3 21.875 27.1 27.200000000000003 23.825 4 23.674999999999997 32.425 20.4 23.5 5 26.375 33.775 18.85 21.0 6 24.025 35.425000000000004 19.6 20.95 7 22.15 19.400000000000002 35.199999999999996 23.25 8 23.0 24.25 22.1 30.65 9 23.45 21.75 28.925 25.874999999999996 10-14 25.509999999999998 26.784999999999997 22.975 24.73 15-19 25.224999999999998 25.575 24.665 24.535 20-24 26.045 25.619999999999997 24.69 23.645 25-29 25.369999999999997 25.66 24.255 24.715 30-34 25.7 25.455 24.77 24.075 35-39 24.959999999999997 26.06 24.4 24.58 40-44 26.150000000000002 25.965 24.224999999999998 23.66 45-49 26.325 25.480000000000004 24.48 23.715 50-54 26.055 26.22 23.87 23.855 55-59 25.64 25.665 24.62 24.075 60-64 26.1 25.540000000000003 24.47 23.89 65-69 25.845000000000002 25.124999999999996 24.84 24.19 70-74 25.66 25.8 24.14 24.4 75-79 25.645 25.495 24.535 24.325 80-84 26.235000000000003 25.674999999999997 24.025 24.065 85-89 25.6 25.290000000000003 24.610000000000003 24.5 90-94 25.55 25.619999999999997 25.385 23.445 95-99 25.655 25.83 24.51 24.005000000000003 100-104 25.965 25.7 25.035 23.3 105-109 26.075 25.405 24.560000000000002 23.96 110-114 26.05 25.83 24.435000000000002 23.685000000000002 115-119 25.86 26.700000000000003 24.22 23.22 120-124 26.41 25.96 24.36 23.27 125-129 26.515 26.31 23.65 23.525 130-134 26.855 25.740000000000002 24.245 23.16 135-139 26.405 26.35 24.315 22.93 140-144 27.055 26.02 24.104999999999997 22.82 145-149 26.88 25.86 24.365000000000002 22.895 150-151 27.275 26.35 23.8375 22.537499999999998 >>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 0.0 16 0.0 17 0.0 18 0.0 19 0.0 20 0.5 21 0.5 22 0.0 23 0.5 24 1.0 25 1.0 26 2.5 27 4.5 28 4.5 29 3.5 30 6.5 31 9.0 32 10.0 33 14.5 34 19.5 35 30.0 36 40.5 37 52.5 38 73.0 39 92.0 40 109.0 41 135.5 42 158.0 43 169.5 44 188.0 45 196.5 46 190.5 47 182.5 48 187.0 49 189.0 50 164.0 51 143.0 52 147.0 53 142.0 54 123.5 55 116.5 56 106.5 57 105.0 58 96.5 59 86.0 60 85.5 61 79.0 62 72.5 63 64.0 64 62.5 65 54.5 66 49.0 67 45.0 68 41.0 69 39.0 70 27.5 71 24.0 72 18.5 73 9.5 74 6.5 75 5.0 76 4.0 77 4.0 78 4.0 79 2.0 80 0.5 81 0.5 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 98.7 #Duplication Level Percentage of deduplicated Percentage of total 1 99.0628166160081 97.775 2 0.6585612968591692 1.3 3 0.22796352583586624 0.675 4 0.025329280648429587 0.1 5 0.0 0.0 6 0.025329280648429587 0.15 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 CTTGATCATCTGAAAAATCTTAATCCAGATCAGACCAAGCAGAGCAGAGA 6 0.15 No Hit >>END_MODULE >>Adapter Content pass #Position Illumina Universal Adapter Illumina Small RNA 3' Adapter Illumina Small RNA 5' Adapter Nextera Transposase Sequence SOLID Small RNA Adapter 1 0.0 0.0 0.0 0.0 0.0 2 0.0 0.0 0.0 0.0 0.0 3 0.0 0.0 0.0 0.0 0.0 4 0.0 0.0 0.0 0.0 0.0 5 0.0 0.0 0.0 0.0 0.0 6 0.0 0.0 0.0 0.0 0.0 7 0.0 0.0 0.0 0.0 0.0 8 0.0 0.0 0.0 0.0 0.0 9 0.0 0.0 0.0 0.0 0.0 10-11 0.0 0.0 0.0 0.0 0.0 12-13 0.0 0.0 0.0 0.0 0.0 14-15 0.0 0.0 0.0 0.0 0.0 16-17 0.0 0.0 0.0 0.0 0.0 18-19 0.0 0.0 0.0 0.0 0.0 20-21 0.0 0.0 0.0 0.0 0.0 22-23 0.0 0.0 0.0 0.0 0.0 24-25 0.0 0.0 0.0 0.0 0.0 26-27 0.0 0.0 0.0 0.0 0.0 28-29 0.0 0.0 0.0 0.0 0.0 30-31 0.0 0.0 0.0 0.0 0.0 32-33 0.0 0.0 0.0 0.0 0.0 34-35 0.0 0.0 0.0 0.0 0.0 36-37 0.0 0.0 0.0 0.0 0.0 38-39 0.0 0.0 0.0 0.0 0.0 40-41 0.0 0.0 0.0 0.0 0.0 42-43 0.0 0.0 0.0 0.0 0.0 44-45 0.0 0.0 0.0 0.0 0.0 46-47 0.0 0.0 0.0 0.0 0.0 48-49 0.0 0.0 0.0 0.0 0.0 50-51 0.0 0.0 0.0 0.0 0.0 52-53 0.0 0.0 0.0 0.0 0.0 54-55 0.0 0.0 0.0 0.0 0.0 56-57 0.0 0.0 0.0 0.0 0.0 58-59 0.0 0.0 0.0 0.0 0.0 60-61 0.0 0.0 0.0 0.0 0.0 62-63 0.025 0.0 0.0 0.0 0.0 64-65 0.05 0.0 0.0 0.0 0.0 66-67 0.05 0.0 0.0 0.0 0.0 68-69 0.05 0.0 0.0 0.0 0.0 70-71 0.05 0.0 0.0 0.0 0.0 72-73 0.0625 0.0 0.0 0.0 0.0 74-75 0.1 0.0 0.0 0.0 0.0 76-77 0.1375 0.0 0.0 0.0 0.0 78-79 0.15 0.0 0.0 0.0 0.0 80-81 0.16249999999999998 0.0 0.0 0.0 0.0 82-83 0.225 0.0 0.0 0.0 0.0 84-85 0.275 0.0 0.0 0.0 0.0 86-87 0.3 0.0 0.0 0.0 0.0 88-89 0.35 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 0.475 0.0 0.0 0.0 0.0 96-97 0.5125 0.0 0.0 0.0 0.0 98-99 0.6375 0.0 0.0 0.0 0.0 100-101 0.8 0.0 0.0 0.0 0.0 102-103 0.95 0.0 0.0 0.0 0.0 104-105 1.1 0.0 0.0 0.0 0.0 106-107 1.15 0.0 0.0 0.0 0.0 108-109 1.275 0.0 0.0 0.0 0.0 110-111 1.35 0.0 0.0 0.0 0.0 112-113 1.4625 0.0 0.0 0.0 0.0 114-115 1.625 0.0 0.0 0.0 0.0 116-117 1.7625000000000002 0.0 0.0 0.0 0.0 118-119 2.05 0.0 0.0 0.0 0.0 120-121 2.1875 0.0 0.0 0.0 0.0 122-123 2.3375 0.0 0.0 0.0 0.0 124-125 2.5250000000000004 0.0 0.0 0.0 0.0 126-127 2.725 0.0 0.0 0.0 0.0 128-129 2.9375 0.0 0.0 0.0 0.0 130-131 3.225 0.0 0.0 0.0 0.0 132-133 3.6125 0.0 0.0 0.0 0.0 134-135 4.0375 0.0 0.0 0.0 0.0 136-137 4.2375 0.0 0.0 0.0 0.0 138-139 4.625 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position AATTACA 10 0.006830828 145.0 4 TACTGAT 10 0.006830828 145.0 9 ACAAGGG 10 0.006830828 145.0 6 ACAGCTG 10 0.006830828 145.0 8 >>END_MODULE Read 1252190 spots for SRR6958413.sra Written 1252190 spots for SRR6958413.sra Read 1252190 spots for SRR6958413.sra Written 1252190 spots for SRR6958413.sra Read 1252190 spots for SRR6958413.sra Written 1252190 spots for SRR6958413.sra Read 1252190 spots for SRR6958413.sra Written 1252190 spots for SRR6958413.sra Read 1252190 spots for SRR6958413.sra Written 1252190 spots for SRR6958413.sra Read 1252190 spots for SRR6958413.sra Written 1252190 spots for SRR6958413.sra Read 1252190 spots for SRR6958413.sra Written 1252190 spots for SRR6958413.sra Read 1252190 spots for SRR6958413.sra Written 1252190 spots for SRR6958413.sra Read 1252190 spots for SRR6958413.sra Written 1252190 spots for SRR6958413.sra Read 1252190 spots for SRR6958413.sra Written 1252190 spots for SRR6958413.sra Read 1252190 spots for SRR6958413.sra Written 1252190 spots for SRR6958413.sra Read 1252190 spots for SRR6958413.sra Written 1252190 spots for SRR6958413.sra Read 1252201 spots for SRR6958413.sra Written 1252201 spots for SRR6958413.sra Read 1252190 spots for SRR6958413.sra Written 1252190 spots for SRR6958413.sra Read 1252190 spots for SRR6958413.sra Written 1252190 spots for SRR6958413.sra Read 1252190 spots for SRR6958413.sra Written 1252190 spots for SRR6958413.sra Read 1252190 spots for SRR6958413.sra Written 1252190 spots for SRR6958413.sra Read 1252190 spots for SRR6958413.sra Written 1252190 spots for SRR6958413.sra Read 1252190 spots for SRR6958413.sra Written 1252190 spots for SRR6958413.sra Read 1252190 spots for SRR6958413.sra Written 1252190 spots for SRR6958413.sra SRR ids: ['SRR6958413.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_d8rc3mbt SRR6958413.sra spots: 25043811 blocks: [[1, 1252190], [1252191, 2504380], [2504381, 3756570], [3756571, 5008760], [5008761, 6260950], [6260951, 7513140], [7513141, 8765330], [8765331, 10017520], [10017521, 11269710], [11269711, 12521900], [12521901, 13774090], [13774091, 15026280], [15026281, 16278470], [16278471, 17530660], [17530661, 18782850], [18782851, 20035040], [20035041, 21287230], [21287231, 22539420], [22539421, 23791610], [23791611, 25043811]] SRR6958413 file size 8464825 SRR6958413 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 SRR6958413 SRR6958413_1.fastq SRR6958413_2.fastq Input file: SRR6958413_1.fastq Paired file: SRR6958413_2.fastq trimmed: SRR6958413-trimmed-pair1.fastq, SRR6958413-trimmed-pair2.fastq Parameters used: -- 3' end adapter sequence (-x): AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC -- paired 3' end adapter sequence (-y): AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTA -- maximum error ratio allowed (-r): 0.100 -- maximum indel error ratio allowed (-d): 0.030 -- end quality threshold (-q): 10 -- minimum read length allowed after trimming (-l): 18 -- file format (-f): Sanger/Illumina 1.8+ FASTQ -- number of concurrent threads (-t): 20 Fri Dec 6 22:32:30 2024 >> started Fri Dec 6 22:32:59 2024 >> done (29.182s) 25043811 read pairs processed; of these: 22088 ( 0.09%) short read pairs filtered out after trimming by size control 19957 ( 0.08%) empty read pairs filtered out after trimming by size control 25001766 (99.83%) read pairs available; of these: 9622680 (38.49%) trimmed read pairs available after processing 15379086 (61.51%) untrimmed read pairs available after processing Length distribution of reads after trimming: length count percentage 18 3 0.00% 19 2 0.00% 20 2 0.00% 21 8 0.00% 22 2 0.00% 23 5 0.00% 24 7 0.00% 25 10 0.00% 26 8 0.00% 27 8 0.00% 28 12 0.00% 29 7 0.00% 30 12 0.00% 31 10 0.00% 32 14 0.00% 33 12 0.00% 34 11 0.00% 35 11 0.00% 36 13 0.00% 37 25 0.00% 38 17 0.00% 39 19 0.00% 40 29 0.00% 41 32 0.00% 42 23 0.00% 43 28 0.00% 44 42 0.00% 45 39 0.00% 46 45 0.00% 47 50 0.00% 48 65 0.00% 49 57 0.00% 50 72 0.00% 51 94 0.00% 52 90 0.00% 53 115 0.00% 54 103 0.00% 55 118 0.00% 56 143 0.00% 57 133 0.00% 58 167 0.00% 59 222 0.00% 60 228 0.00% 61 297 0.00% 62 298 0.00% 63 372 0.00% 64 398 0.00% 65 406 0.00% 66 488 0.00% 67 533 0.00% 68 552 0.00% 69 767 0.00% 70 862 0.00% 71 988 0.00% 72 1176 0.00% 73 1310 0.01% 74 1434 0.01% 75 1583 0.01% 76 1744 0.01% 77 1914 0.01% 78 2063 0.01% 79 2364 0.01% 80 2751 0.01% 81 3193 0.01% 82 3556 0.01% 83 4218 0.02% 84 5381 0.02% 85 6191 0.02% 86 6492 0.03% 87 6774 0.03% 88 6987 0.03% 89 7476 0.03% 90 7974 0.03% 91 8900 0.04% 92 9348 0.04% 93 10385 0.04% 94 10960 0.04% 95 11553 0.05% 96 12338 0.05% 97 12589 0.05% 98 12945 0.05% 99 13719 0.05% 100 14511 0.06% 101 15870 0.06% 102 17135 0.07% 103 18049 0.07% 104 19266 0.08% 105 20065 0.08% 106 21024 0.08% 107 21602 0.09% 108 22181 0.09% 109 23433 0.09% 110 24390 0.10% 111 25464 0.10% 112 27233 0.11% 113 28816 0.12% 114 30692 0.12% 115 32267 0.13% 116 33364 0.13% 117 34107 0.14% 118 35052 0.14% 119 35835 0.14% 120 37609 0.15% 121 38696 0.15% 122 41043 0.16% 123 42915 0.17% 124 45745 0.18% 125 47732 0.19% 126 49509 0.20% 127 51016 0.20% 128 52641 0.21% 129 54334 0.22% 130 56124 0.22% 131 58068 0.23% 132 61727 0.25% 133 65453 0.26% 134 69578 0.28% 135 73465 0.29% 136 76868 0.31% 137 81142 0.32% 138 84809 0.34% 139 90440 0.36% 140 96414 0.39% 141 104703 0.42% 142 116844 0.47% 143 130068 0.52% 144 150065 0.60% 145 177541 0.71% 146 219411 0.88% 147 296248 1.18% 148 442563 1.77% 149 847736 3.39% 150 5176425 20.70% 151 15379086 61.51% 25001766 reads passed initial QC criterion=sequence-density sequence-density=0.83 sequence-density-rank=1 fanout-score=2.89 fanout-score-rank=26 prefix-density=0.87 prefix-fanout=2.7 sequence=GGTGTTGTCGAAGCCGATGATGCGGACATAGGCGTCCGG criterion=fanout-score sequence-density=0.03 sequence-density-rank=32 fanout-score=171.52 fanout-score-rank=1 prefix-density=0.46 prefix-fanout=9.9 sequence=GGCGGCGGCGAACCGCCCCCGTCGCCGCGATCCGAACACTTCACCGGACCATTCAATCGGTAGGAGCGACGGGCGGTGTGTACAAAGGGCAGGGACGTAGTCAACGCGAGCTGATGACTCGCGCTTACTAGGCATTCCTCGTTGAAGACCAACAATTGCAATGATCTATCCCCATCACGATGAAATTTCCCAAGATTACCCGGGCCTGTCGGCCAAGGCTATATACTCGTTGAATACATCAGTGTAGCGCGCGTGCGGCCCAGAACATCTAAGGGCATCACAGACCTGTTATTGCCTCAAACTTCCGTCGCCTAAACGGCGATAGTCCCTCTAAGAAGCTAGCTGCGGAGGGATGGCTCCGCATAGCTAGTTAGCAGGCTGAGGTCTCGTTCGTTAACGGAATTAACCAGACAAATCGCTCCACCAACTAAGAACGGCCATGCACCACCACCCATAGAATCAAGAAAGAGCTCTCAGTCTGTCAATCCTTGCTATGTCTGGACCTGGTAAG criterion=sequence-density sequence-density=0.52 sequence-density-rank=1 fanout-score=3.66 fanout-score-rank=15 prefix-density=0.58 prefix-fanout=3.3 sequence=GAGTTCAGCAAGGTCGGCTT criterion=fanout-score sequence-density=0.03 sequence-density-rank=29 fanout-score=35.26 fanout-score-rank=1 prefix-density=0.18 prefix-fanout=5.9 sequence=GCAGCAGCCATTACTTGATCATCTGAAAAATCTTAATCCAGATCAGACCAAGCAGAGCAGAGATGTCTGCTACCTTCTCGTCCACCGTCGGAGCTCCGGCTTCTACGCCAACCAGCTTCCTTGGGAAGAAGCTCAAGAAGCAGGTGACCTCGGCCGTGAACTACCATGGCAAGAGCACCAAGGCCAACAGATTCACAGTCATGGCCAAGGAGGTGGACGAGTCAAAGCAGACTGACCAGGACAGGTGGAAGGGCCTCGCCTACGATATCTCCGACGACCAGCAGGACATCACCAGGGGGAAGGGTATCGTCGACTCGCTCTTCCAGGCGCCCATGGGCGACGGTACCCACGTGGCCGTCCTCAGCTCCCAAGAGTACATCAGCCAGGGCCTAAGGAAGTACGACTTCGACAACA SRR6958413 testing PE reads STAR mapping to Ensembl genome Started job on | Dec 06 22:33:42 Started mapping on | Dec 06 22:33:42 Finished on | Dec 06 22:36:19 Mapping speed, Million of reads per hour | 573.29 Number of input reads | 25001766 Average input read length | 296 UNIQUE READS: Uniquely mapped reads number | 24040495 Uniquely mapped reads % | 96.16% Average mapped length | 295.95 Number of splices: Total | 27642192 Number of splices: Annotated (sjdb) | 26042297 Number of splices: GT/AG | 27282923 Number of splices: GC/AG | 327239 Number of splices: AT/AC | 10382 Number of splices: Non-canonical | 21648 Mismatch rate per base, % | 0.13% Deletion rate per base | 0.00% Deletion average length | 1.44 Insertion rate per base | 0.00% Insertion average length | 1.42 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 207271 % of reads mapped to multiple loci | 0.83% Number of reads mapped to too many loci | 41609 % of reads mapped to too many loci | 0.17% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 1.83% % of reads unmapped: other | 1.01% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 768123 768123 768123 N_multimapping 207271 207271 207271 N_noFeature 862513 23353476 1055570 N_ambiguous 584465 3174 92442 UnstrandedReadsAssigned:22593517 PositiveStrandReadsAssigned:683845 NegativeStrandReadsAssigned:22892483 Dataset is classified negative stranded MeadianReadLen=151 20thPercentileLength=150 echo kmer=145 SRR6958413 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: SRR6958413-trimmed-pair1.fastq SRR6958413-trimmed-pair2.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 25,001,766 reads, 22,940,373 reads pseudoaligned [quant] estimated average fragment length: 262.543 [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,210 rounds 52973 SRR6958413.ke.tsv 35125 SRR6958413.se.tsv 88098 total ==> SRR6958413.ke.tsv <== target_id length eff_length est_counts tpm PNS24245 936 675.005 0 0 PNS24247 1044 782.457 73.0942 6.16953 PNS24249 1928 1666.46 69.1501 2.74049 PNS24246 1044 782.457 73.0942 6.16953 PNS24248 1044 782.457 73.0942 6.16953 PNS24244 1471 1209.46 54.5673 2.97969 PNS24243 293 87.3086 0 0 KQK14069 1603 1341.46 6680.8 328.913 KQK14071 474 228.212 141.164 40.8521 ==> SRR6958413.se.tsv <== BRADI_1g14170v3 7720 BRADI_1g53295v3 262 BRADI_1g59795v3 214 BRADI_1g07683v3 0 BRADI_1g00485v3 6 BRADI_1g20270v3 282 BRADI_1g74790v3 103 BRADI_1g09890v3 0 BRADI_1g77505v3 240 BRADI_1g48960v3 0 SRR6958413 completed mapping pipeline successfully