Starting /dee2/code/volunteer_pipeline.sh SRR6958261 current disk space = 1550270636032 free memory = 1603424912 SRR6958261 SRAfilesize 645f0e8f0eb7750c0e7b1b664f29e0ad SRR6958261.sra SRR6958261.sra file validated SRR6958261 is paired end SRR6958261 is conventional basespace SRR6958261 read1 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR6958261_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 fail #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 21.03975 18.0 18.0 30.0 2.0 32.0 2 29.40075 30.0 27.0 33.0 27.0 33.0 3 31.296 33.0 30.0 33.0 27.0 33.0 4 31.9755 33.0 31.0 33.0 30.0 33.0 5 32.592 33.0 33.0 33.0 31.0 34.0 6 36.82025 38.0 37.0 38.0 35.0 38.0 7 37.437 38.0 38.0 38.0 37.0 38.0 8 37.4645 38.0 38.0 38.0 37.0 38.0 9 37.51825 38.0 38.0 38.0 38.0 38.0 10-14 37.356 38.0 38.0 38.0 37.0 38.0 15-19 37.448899999999995 38.0 38.0 38.0 37.2 38.0 20-24 37.4298 38.0 38.0 38.0 37.8 38.0 25-29 37.038599999999995 38.0 38.0 38.0 36.0 38.0 30-34 37.3335 38.0 38.0 38.0 37.0 38.0 35-39 36.98125 38.0 38.0 38.0 35.6 38.0 40-44 37.443799999999996 38.0 38.0 38.0 37.6 38.0 45-49 37.2385 38.0 38.0 38.0 36.8 38.0 50-54 37.106399999999994 38.0 38.0 38.0 36.2 38.0 55-59 37.07315 38.0 38.0 38.0 36.2 38.0 60-64 37.25115 38.0 38.0 38.0 36.6 38.0 65-69 37.298 38.0 38.0 38.0 37.0 38.0 70-74 37.186949999999996 38.0 38.0 38.0 36.0 38.0 75-79 37.11895 38.0 38.0 38.0 36.0 38.0 80-84 37.0097 38.0 38.0 38.0 35.8 38.0 85-89 36.43985 38.0 38.0 38.0 34.0 38.0 90-94 35.60385 38.0 36.6 38.0 29.6 38.0 95-99 33.8401 37.4 31.8 38.0 23.6 38.0 100-104 35.450599999999994 38.0 36.2 38.0 28.8 38.0 105-109 35.40325 38.0 36.2 38.0 29.4 38.0 110-114 35.18005 38.0 36.0 38.0 28.0 38.0 115-119 35.46275 38.0 36.0 38.0 30.6 38.0 120-124 35.44035 38.0 36.2 38.0 29.6 38.0 125-129 35.0837 38.0 36.0 38.0 29.2 38.0 130-134 34.8536 38.0 35.8 38.0 27.4 38.0 135-139 34.04345 38.0 33.6 38.0 24.4 38.0 140-144 32.64855 38.0 32.2 38.0 16.0 38.0 145-149 31.636950000000002 38.0 32.0 38.0 10.0 38.0 150-151 25.870125 33.0 17.0 37.0 2.0 38.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 15 1.0 16 2.0 17 4.0 18 1.0 19 2.0 20 4.0 21 6.0 22 3.0 23 15.0 24 18.0 25 21.0 26 20.0 27 28.0 28 41.0 29 46.0 30 79.0 31 76.0 32 113.0 33 146.0 34 255.0 35 416.0 36 926.0 37 1777.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 39.35349940688019 10.172004744958482 8.98576512455516 41.48873072360617 2 22.525000000000002 12.775 36.075 28.625 3 22.725 16.125 24.95 36.199999999999996 4 27.224999999999998 24.15 20.349999999999998 28.275 5 25.924999999999997 28.125 24.2 21.75 6 20.825 31.15 25.924999999999997 22.1 7 17.404351087771943 22.380595148787197 40.160040010002504 20.05501375343836 8 19.775000000000002 23.275000000000002 30.25 26.700000000000003 9 19.325 21.55 32.6 26.525 10-14 22.645 26.484999999999996 26.035000000000004 24.834999999999997 15-19 22.965 24.990000000000002 26.515 25.53 20-24 22.400000000000002 25.369999999999997 26.625 25.605 25-29 22.919999999999998 25.540000000000003 25.759999999999998 25.779999999999998 30-34 22.93 25.245 26.14 25.685000000000002 35-39 23.34 25.025 26.255 25.380000000000003 40-44 22.884999999999998 25.474999999999998 25.835 25.805 45-49 23.21 25.324999999999996 26.005 25.46 50-54 23.1 24.72 26.009999999999998 26.169999999999998 55-59 22.91 25.990000000000002 25.924999999999997 25.174999999999997 60-64 23.419999999999998 25.014999999999997 25.735000000000003 25.83 65-69 23.585 25.405 25.89 25.119999999999997 70-74 23.494999999999997 24.93 26.08 25.495 75-79 23.72 25.174999999999997 25.790000000000003 25.314999999999998 80-84 23.549999999999997 25.045 25.785000000000004 25.619999999999997 85-89 23.525 25.085 26.105 25.285000000000004 90-94 23.830000000000002 24.955 25.569999999999997 25.645 95-99 23.01 25.355 25.779999999999998 25.855 100-104 23.925 25.22 25.185000000000002 25.669999999999998 105-109 23.355 25.790000000000003 25.979999999999997 24.875 110-114 23.825 25.319999999999997 24.955 25.900000000000002 115-119 23.905 25.019999999999996 25.759999999999998 25.314999999999998 120-124 23.435 25.295 25.629999999999995 25.64 125-129 23.62 25.245 26.06 25.074999999999996 130-134 23.82 25.779999999999998 24.82 25.580000000000002 135-139 24.27 24.925 25.405 25.4 140-144 24.095 25.185000000000002 25.3 25.419999999999998 145-149 23.5 25.580000000000002 25.35 25.569999999999997 150-151 23.3 24.95 26.437500000000004 25.3125 >>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 0.0 21 0.0 22 0.0 23 0.5 24 1.0 25 1.0 26 2.0 27 2.5 28 2.0 29 4.5 30 8.0 31 9.5 32 12.0 33 19.0 34 27.5 35 35.5 36 44.5 37 58.5 38 83.0 39 109.0 40 125.0 41 146.5 42 179.0 43 194.0 44 196.0 45 219.5 46 231.5 47 213.5 48 198.5 49 184.0 50 170.5 51 150.0 52 125.0 53 119.0 54 111.5 55 98.0 56 88.5 57 81.0 58 83.0 59 79.0 60 68.5 61 64.5 62 56.0 63 56.0 64 59.0 65 47.0 66 39.5 67 36.5 68 31.5 69 28.0 70 26.5 71 20.0 72 14.5 73 10.5 74 7.5 75 8.5 76 5.0 77 2.5 78 2.0 79 1.0 80 1.0 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 warn #Base N-Count 1 15.7 2 0.0 3 0.0 4 0.0 5 0.0 6 0.0 7 0.025 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 99.7 #Duplication Level Percentage of deduplicated Percentage of total 1 99.69909729187563 99.4 2 0.3009027081243731 0.6 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 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 0.0 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 0.025 0.0 0.0 0.0 0.0 88-89 0.025 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 0.0875 0.0 0.0 0.0 0.0 96-97 0.1125 0.0 0.0 0.0 0.0 98-99 0.1875 0.0 0.0 0.0 0.0 100-101 0.2375 0.0 0.0 0.0 0.0 102-103 0.325 0.0 0.0 0.0 0.0 104-105 0.45 0.0 0.0 0.0 0.0 106-107 0.525 0.0 0.0 0.0 0.0 108-109 0.55 0.0 0.0 0.0 0.0 110-111 0.6125 0.0 0.0 0.0 0.0 112-113 0.75 0.0 0.0 0.0 0.0 114-115 0.9875 0.0 0.0 0.0 0.0 116-117 1.15 0.0 0.0 0.0 0.0 118-119 1.225 0.0 0.0 0.0 0.0 120-121 1.4 0.0 0.0 0.0 0.0 122-123 1.5875 0.0 0.0 0.0 0.0 124-125 1.8125 0.0 0.0 0.0 0.0 126-127 2.125 0.0 0.0 0.0 0.0 128-129 2.35 0.0 0.0 0.0 0.0 130-131 2.5 0.0 0.0 0.0 0.0 132-133 2.7 0.0 0.0 0.0 0.0 134-135 2.9875 0.0 0.0 0.0 0.0 136-137 3.1625 0.0 0.0 0.0 0.0 138-139 3.3375 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position TCGGAGG 10 0.0068484643 144.875 145 GTATATT 10 0.0068484643 144.875 2 GCATAGG 10 0.0068484643 144.875 5 >>END_MODULE SRR6958261 read2 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR6958261_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 32.83275 33.0 33.0 34.0 32.0 34.0 2 33.069 34.0 33.0 34.0 32.0 34.0 3 32.98325 34.0 33.0 34.0 32.0 34.0 4 32.8775 34.0 33.0 34.0 32.0 34.0 5 32.761 34.0 33.0 34.0 32.0 34.0 6 37.092 38.0 38.0 38.0 36.0 38.0 7 37.0445 38.0 38.0 38.0 36.0 38.0 8 36.69075 38.0 38.0 38.0 35.0 38.0 9 36.866 38.0 38.0 38.0 36.0 38.0 10-14 36.72285 38.0 38.0 38.0 35.2 38.0 15-19 36.76345 38.0 38.0 38.0 35.4 38.0 20-24 36.799350000000004 38.0 38.0 38.0 35.4 38.0 25-29 37.02165 38.0 38.0 38.0 36.4 38.0 30-34 37.1405 38.0 38.0 38.0 37.0 38.0 35-39 37.2231 38.0 38.0 38.0 37.0 38.0 40-44 35.0356 37.8 34.8 38.0 28.2 38.0 45-49 35.1783 37.8 35.4 38.0 29.0 38.0 50-54 34.3831 37.8 33.2 38.0 25.8 38.0 55-59 34.881099999999996 37.8 34.4 38.0 28.0 38.0 60-64 36.31585 38.0 37.8 38.0 33.2 38.0 65-69 36.03325 38.0 37.6 38.0 32.4 38.0 70-74 35.85090000000001 38.0 37.2 38.0 30.8 38.0 75-79 35.9185 38.0 37.6 38.0 31.8 38.0 80-84 35.8558 38.0 37.4 38.0 31.6 38.0 85-89 35.5845 38.0 37.0 38.0 29.8 38.0 90-94 35.54005 38.0 37.0 38.0 30.2 38.0 95-99 35.79825 38.0 37.2 38.0 32.0 38.0 100-104 34.107800000000005 37.8 33.2 38.0 25.2 38.0 105-109 35.58795 38.0 37.0 38.0 30.8 38.0 110-114 35.2123 38.0 36.6 38.0 30.2 38.0 115-119 34.330799999999996 38.0 35.8 38.0 24.2 38.0 120-124 29.697400000000005 32.8 25.4 38.0 15.0 38.0 125-129 28.015499999999996 32.0 19.2 38.0 12.2 38.0 130-134 29.10915 34.2 22.2 38.0 12.0 38.0 135-139 31.877400000000005 37.6 31.6 38.0 13.0 38.0 140-144 30.462800000000005 36.8 28.6 38.0 9.2 38.0 145-149 28.57495 35.8 23.2 38.0 2.0 38.0 150-151 22.713250000000002 28.0 11.5 35.5 2.0 38.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 2 6.0 3 2.0 4 0.0 5 0.0 6 1.0 7 0.0 8 2.0 9 4.0 10 0.0 11 1.0 12 3.0 13 6.0 14 4.0 15 2.0 16 7.0 17 8.0 18 11.0 19 14.0 20 21.0 21 20.0 22 27.0 23 18.0 24 39.0 25 32.0 26 51.0 27 53.0 28 59.0 29 76.0 30 83.0 31 132.0 32 161.0 33 247.0 34 345.0 35 620.0 36 1172.0 37 773.0 >>END_MODULE >>Per base sequence content warn #Base G A T C 1 35.75 19.25 9.975000000000001 35.025 2 27.900000000000002 24.775 28.025 19.3 3 22.475 25.825 27.3 24.4 4 24.9 32.65 20.724999999999998 21.725 5 26.575 32.95 20.724999999999998 19.75 6 22.6 35.175 20.674999999999997 21.55 7 22.625 19.425 33.6 24.349999999999998 8 23.95 23.925 23.625 28.499999999999996 9 23.549999999999997 21.75 28.349999999999998 26.35 10-14 25.97 26.384999999999998 23.18 24.465 15-19 25.295 25.295 25.27 24.14 20-24 25.4 26.355 24.37 23.875 25-29 25.405 26.229999999999997 24.19 24.175 30-34 25.53 26.47 24.075 23.925 35-39 25.71 26.07 23.86 24.36 40-44 25.759999999999998 25.91 24.41 23.919999999999998 45-49 25.255 26.064999999999998 24.8 23.880000000000003 50-54 25.419999999999998 25.729999999999997 24.98 23.87 55-59 26.655 25.27 24.0 24.075 60-64 25.485000000000003 25.324999999999996 24.740000000000002 24.45 65-69 25.674999999999997 25.485000000000003 24.355 24.485 70-74 26.395000000000003 24.82 24.9 23.885 75-79 25.46 25.119999999999997 25.195 24.224999999999998 80-84 26.105 25.124999999999996 24.69 24.08 85-89 25.44 25.56 24.41 24.59 90-94 25.785000000000004 24.92 25.424999999999997 23.87 95-99 25.795 25.235000000000003 25.035 23.935000000000002 100-104 26.009999999999998 25.585 24.485 23.919999999999998 105-109 25.665 25.455 25.105 23.775 110-114 25.16 26.35 24.445 24.044999999999998 115-119 25.785000000000004 25.985000000000003 24.19 24.04 120-124 26.11 25.724999999999998 25.245 22.919999999999998 125-129 26.127612761276126 26.117611761176118 24.402440244024405 23.352335233523352 130-134 25.585 26.555 24.51 23.35 135-139 25.82 25.869999999999997 24.89 23.419999999999998 140-144 26.47 26.19 24.025 23.315 145-149 26.595000000000002 25.91 24.455 23.04 150-151 27.175 25.662499999999998 24.5 22.662499999999998 >>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 0.0 21 0.5 22 0.5 23 0.0 24 0.0 25 0.0 26 1.0 27 2.5 28 4.5 29 6.5 30 8.0 31 8.5 32 10.0 33 17.0 34 26.0 35 32.5 36 39.0 37 52.5 38 71.0 39 94.5 40 118.0 41 140.5 42 164.0 43 168.5 44 168.5 45 190.0 46 213.5 47 202.5 48 190.0 49 176.5 50 164.5 51 159.5 52 136.5 53 124.0 54 118.5 55 104.0 56 94.5 57 98.0 58 87.0 59 83.0 60 91.0 61 82.5 62 74.0 63 70.0 64 62.5 65 52.5 66 47.0 67 44.5 68 37.0 69 35.0 70 28.5 71 25.5 72 22.5 73 14.0 74 12.0 75 10.5 76 8.5 77 4.0 78 2.0 79 0.5 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 0.0 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 0.01 130-134 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 99.725 #Duplication Level Percentage of deduplicated Percentage of total 1 99.79944848332916 99.52499999999999 2 0.12534469791927802 0.25 3 0.0752068187515668 0.22499999999999998 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 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 0.0 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 0.025 0.0 0.0 0.0 0.0 88-89 0.025 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 0.0875 0.0 0.0 0.0 0.0 96-97 0.1375 0.0 0.0 0.0 0.0 98-99 0.21250000000000002 0.0 0.0 0.0 0.0 100-101 0.2625 0.0 0.0 0.0 0.0 102-103 0.35 0.0 0.0 0.0 0.0 104-105 0.475 0.0 0.0 0.0 0.0 106-107 0.55 0.0 0.0 0.0 0.0 108-109 0.575 0.0 0.0 0.0 0.0 110-111 0.6375 0.0 0.0 0.0 0.0 112-113 0.7625 0.0 0.0 0.0 0.0 114-115 0.8999999999999999 0.0 0.0 0.0 0.0 116-117 1.0125 0.0 0.0 0.0 0.0 118-119 1.0625 0.0 0.0 0.0 0.0 120-121 1.1375000000000002 0.0 0.0 0.0 0.0 122-123 1.2375 0.0 0.0 0.0 0.0 124-125 1.4 0.0 0.0 0.0 0.0 126-127 1.7125 0.0 0.0 0.0 0.0 128-129 1.8375 0.0 0.0 0.0 0.0 130-131 1.975 0.0 0.0 0.0 0.0 132-133 2.175 0.0 0.0 0.0 0.0 134-135 2.4625000000000004 0.0 0.0 0.0 0.0 136-137 2.6375 0.0 0.0 0.0 0.0 138-139 2.7875 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content pass >>END_MODULE Read 1292623 spots for SRR6958261.sra Written 1292623 spots for SRR6958261.sra Read 1292623 spots for SRR6958261.sra Written 1292623 spots for SRR6958261.sra Read 1292623 spots for SRR6958261.sra Written 1292623 spots for SRR6958261.sra Read 1292623 spots for SRR6958261.sra Written 1292623 spots for SRR6958261.sra Read 1292623 spots for SRR6958261.sra Written 1292623 spots for SRR6958261.sra Read 1292623 spots for SRR6958261.sra Written 1292623 spots for SRR6958261.sra Read 1292623 spots for SRR6958261.sra Written 1292623 spots for SRR6958261.sra Read 1292623 spots for SRR6958261.sra Written 1292623 spots for SRR6958261.sra Read 1292623 spots for SRR6958261.sra Written 1292623 spots for SRR6958261.sra Read 1292623 spots for SRR6958261.sra Written 1292623 spots for SRR6958261.sra Read 1292623 spots for SRR6958261.sra Written 1292623 spots for SRR6958261.sra Read 1292623 spots for SRR6958261.sra Written 1292623 spots for SRR6958261.sra Read 1292626 spots for SRR6958261.sra Written 1292626 spots for SRR6958261.sra Read 1292623 spots for SRR6958261.sra Written 1292623 spots for SRR6958261.sra Read 1292623 spots for SRR6958261.sra Written 1292623 spots for SRR6958261.sra Read 1292623 spots for SRR6958261.sra Written 1292623 spots for SRR6958261.sra Read 1292623 spots for SRR6958261.sra Written 1292623 spots for SRR6958261.sra Read 1292623 spots for SRR6958261.sra Written 1292623 spots for SRR6958261.sra Read 1292623 spots for SRR6958261.sra Written 1292623 spots for SRR6958261.sra Read 1292623 spots for SRR6958261.sra Written 1292623 spots for SRR6958261.sra SRR ids: ['SRR6958261.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_34cgqh_l SRR6958261.sra spots: 25852463 blocks: [[1, 1292623], [1292624, 2585246], [2585247, 3877869], [3877870, 5170492], [5170493, 6463115], [6463116, 7755738], [7755739, 9048361], [9048362, 10340984], [10340985, 11633607], [11633608, 12926230], [12926231, 14218853], [14218854, 15511476], [15511477, 16804099], [16804100, 18096722], [18096723, 19389345], [19389346, 20681968], [20681969, 21974591], [21974592, 23267214], [23267215, 24559837], [24559838, 25852463]] SRR6958261 file size 8738851 SRR6958261 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 SRR6958261 SRR6958261_1.fastq SRR6958261_2.fastq Input file: SRR6958261_1.fastq Paired file: SRR6958261_2.fastq trimmed: SRR6958261-trimmed-pair1.fastq, SRR6958261-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 17:59:23 2024 >> started Fri Dec 6 18:00:01 2024 >> done (38.184s) 25852463 read pairs processed; of these: 22399 ( 0.09%) short read pairs filtered out after trimming by size control 29090 ( 0.11%) empty read pairs filtered out after trimming by size control 25800974 (99.80%) read pairs available; of these: 11654564 (45.17%) trimmed read pairs available after processing 14146410 (54.83%) untrimmed read pairs available after processing Length distribution of reads after trimming: length count percentage 18 5 0.00% 19 4 0.00% 20 3 0.00% 21 6 0.00% 22 6 0.00% 23 4 0.00% 24 9 0.00% 25 8 0.00% 26 9 0.00% 27 9 0.00% 28 6 0.00% 29 11 0.00% 30 14 0.00% 31 9 0.00% 32 11 0.00% 33 13 0.00% 34 7 0.00% 35 13 0.00% 36 12 0.00% 37 18 0.00% 38 23 0.00% 39 18 0.00% 40 21 0.00% 41 13 0.00% 42 26 0.00% 43 26 0.00% 44 20 0.00% 45 34 0.00% 46 39 0.00% 47 37 0.00% 48 39 0.00% 49 41 0.00% 50 41 0.00% 51 56 0.00% 52 70 0.00% 53 89 0.00% 54 80 0.00% 55 91 0.00% 56 92 0.00% 57 117 0.00% 58 129 0.00% 59 153 0.00% 60 150 0.00% 61 183 0.00% 62 226 0.00% 63 265 0.00% 64 317 0.00% 65 329 0.00% 66 352 0.00% 67 375 0.00% 68 410 0.00% 69 526 0.00% 70 596 0.00% 71 685 0.00% 72 754 0.00% 73 849 0.00% 74 970 0.00% 75 1107 0.00% 76 1219 0.00% 77 1321 0.01% 78 1510 0.01% 79 1680 0.01% 80 1870 0.01% 81 2092 0.01% 82 2476 0.01% 83 2790 0.01% 84 3998 0.02% 85 4838 0.02% 86 4906 0.02% 87 5198 0.02% 88 5452 0.02% 89 5574 0.02% 90 5892 0.02% 91 6417 0.02% 92 6917 0.03% 93 7472 0.03% 94 8204 0.03% 95 8527 0.03% 96 8997 0.03% 97 9664 0.04% 98 10039 0.04% 99 10736 0.04% 100 11519 0.04% 101 12197 0.05% 102 12995 0.05% 103 13979 0.05% 104 14909 0.06% 105 15924 0.06% 106 16712 0.06% 107 17154 0.07% 108 18069 0.07% 109 18923 0.07% 110 19758 0.08% 111 20667 0.08% 112 21940 0.09% 113 23298 0.09% 114 25071 0.10% 115 26444 0.10% 116 27400 0.11% 117 28650 0.11% 118 29714 0.12% 119 30850 0.12% 120 32326 0.13% 121 33624 0.13% 122 35529 0.14% 123 37802 0.15% 124 39962 0.15% 125 42236 0.16% 126 45339 0.18% 127 46908 0.18% 128 48820 0.19% 129 50969 0.20% 130 53994 0.21% 131 56662 0.22% 132 61060 0.24% 133 64954 0.25% 134 69013 0.27% 135 73723 0.29% 136 78735 0.31% 137 83714 0.32% 138 89286 0.35% 139 95468 0.37% 140 102838 0.40% 141 113122 0.44% 142 126865 0.49% 143 143957 0.56% 144 166877 0.65% 145 201252 0.78% 146 251839 0.98% 147 350842 1.36% 148 540921 2.10% 149 1114272 4.32% 150 6858167 26.58% 151 14146410 54.83% 25800974 reads passed initial QC criterion=sequence-density sequence-density=0.81 sequence-density-rank=1 fanout-score=2.85 fanout-score-rank=25 prefix-density=0.85 prefix-fanout=2.7 sequence=GGTGTTGTCGAAGCCGATGATGCGGACATAGGCGTCCGG criterion=fanout-score sequence-density=0.02 sequence-density-rank=30 fanout-score=205.06 fanout-score-rank=1 prefix-density=0.46 prefix-fanout=9.4 sequence=GGCGGCGGCGAACCGCCCCCGTCGCCGCGATCCGAACACTTCACCGGACCATTCAATCGGTAGGAGCGACGGGCGGTGTGTACAAAGGGCAGGGACGTAGTCAACGCGAGCTGATGACTCGCGCTTACTAGGCATTCCTCGTTGAAGACCAACAATTGCAATGATCTATCCCCATCACGATGAAATTTCCCAAGATTACCCGGGCCTGTCGGCCAAGGCTATATACTCGTTGAATACATCAGTGTAGCGCGCGTGCGGCCCAGAACATCTAAGGGCATCACAGACCTGTTATTGCCTCAAACTTCCGTCGCCTAAACGGCGATAGTCCCTCTAAGAAGCTAGCTGCGGAGGGATGGCTCCGCATAGCTAGTTAGCAGGCTGAGGTCTCGTTCGTTAACGGAATTAACCAGACAAATCGCTCCACCAACTAAGAACGGCCATGCACCACCACCCATAGAATCAAGAAAGAGCTCTCAGTCTGTCAATCCTTGCTATGTCTGGACCTGGTAAG criterion=sequence-density sequence-density=0.52 sequence-density-rank=1 fanout-score=3.79 fanout-score-rank=15 prefix-density=0.59 prefix-fanout=3.4 sequence=GAGTTCAGCAAGGTCGGCTT criterion=fanout-score sequence-density=0.03 sequence-density-rank=28 fanout-score=28.59 fanout-score-rank=1 prefix-density=0.15 prefix-fanout=5.8 sequence=GCAGCAGCCATTACTTGATCATCTGAAAAATCTTAATCCAGATCAGACCAAGCAGAGCAGAGATGTCTGCTACCTTCTCGTCCACCGTCGGAGCTCCGGCTTCTACGCCAACCAGCTTCCTTGGGAAGAAGCTCAAGAAGCAGGTGACCTCGGCCGTGAACTACCATGGCAAGAGCACCAAGGCCAACAGATTCACAGTCATGGCCAAGGAGGTGGACGAGTCAAAGCAGACTGACCAGGACAGGTGGAAGGGCCTCGCCTACGATATCTCCGACGACCAGCAGGACATCACCAGGGGGAAGGGTATCGTCGACTCGCTCTTCCAGGCGCCCATGGGCGACGGTACCCACGTGGCCGTCCTCAGCTCCCAAGAGTACATCAGCCAGGGCCTAAGGAAGTACGACTTCGACAACA SRR6958261 testing PE reads STAR mapping to Ensembl genome Started job on | Dec 06 18:00:43 Started mapping on | Dec 06 18:00:43 Finished on | Dec 06 18:02:51 Mapping speed, Million of reads per hour | 725.65 Number of input reads | 25800974 Average input read length | 297 UNIQUE READS: Uniquely mapped reads number | 25026642 Uniquely mapped reads % | 97.00% Average mapped length | 296.61 Number of splices: Total | 28939765 Number of splices: Annotated (sjdb) | 27316253 Number of splices: GT/AG | 28565644 Number of splices: GC/AG | 339902 Number of splices: AT/AC | 11189 Number of splices: Non-canonical | 23030 Mismatch rate per base, % | 0.09% Deletion rate per base | 0.00% Deletion average length | 1.41 Insertion rate per base | 0.00% Insertion average length | 1.38 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 181656 % of reads mapped to multiple loci | 0.70% Number of reads mapped to too many loci | 34937 % of reads mapped to too many loci | 0.14% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 1.39% % of reads unmapped: other | 0.77% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 606795 606795 606795 N_multimapping 181656 181656 181656 N_noFeature 913005 24318661 1095403 N_ambiguous 615627 3058 91401 UnstrandedReadsAssigned:23498010 PositiveStrandReadsAssigned:704923 NegativeStrandReadsAssigned:23839838 Dataset is classified negative stranded MeadianReadLen=151 20thPercentileLength=149 echo kmer=145 SRR6958261 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: SRR6958261-trimmed-pair1.fastq SRR6958261-trimmed-pair2.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 25,800,974 reads, 23,863,654 reads pseudoaligned [quant] estimated average fragment length: 270.55 [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,208 rounds 52973 SRR6958261.ke.tsv 35125 SRR6958261.se.tsv 88098 total ==> SRR6958261.ke.tsv <== target_id length eff_length est_counts tpm PNS24245 936 666.977 0 0 PNS24247 1044 774.45 78.8492 6.48643 PNS24249 1928 1658.45 22.6808 0.871279 PNS24246 1044 774.45 78.8492 6.48643 PNS24248 1044 774.45 78.8492 6.48643 PNS24244 1471 1201.45 53.7715 2.85133 PNS24243 293 82.9811 0 0 KQK14069 1603 1333.45 4014.29 191.793 KQK14071 474 221.604 65.4768 18.824 ==> SRR6958261.se.tsv <== BRADI_1g14170v3 4634 BRADI_1g53295v3 336 BRADI_1g59795v3 300 BRADI_1g07683v3 0 BRADI_1g00485v3 6 BRADI_1g20270v3 453 BRADI_1g74790v3 122 BRADI_1g09890v3 0 BRADI_1g77505v3 253 BRADI_1g48960v3 0 SRR6958261 completed mapping pipeline successfully