Starting /dee2/code/volunteer_pipeline.sh SRR13292037 current disk space = 1543242334208 free memory = 1599157884 SRR13292037 SRAfilesize 1dac929e04ba8d44fed084c0f84e32e8 SRR13292037.sra SRR13292037.sra file validated SRR13292037 is paired end SRR13292037 is conventional basespace SRR13292037 read1 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR13292037_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 36.38 37.0 37.0 37.0 37.0 37.0 2 36.06775 37.0 37.0 37.0 37.0 37.0 3 36.276 37.0 37.0 37.0 37.0 37.0 4 36.5045 37.0 37.0 37.0 37.0 37.0 5 36.5255 37.0 37.0 37.0 37.0 37.0 6 36.48 37.0 37.0 37.0 37.0 37.0 7 36.4445 37.0 37.0 37.0 37.0 37.0 8 36.4085 37.0 37.0 37.0 37.0 37.0 9 36.402 37.0 37.0 37.0 37.0 37.0 10-14 36.4611 37.0 37.0 37.0 37.0 37.0 15-19 36.439 37.0 37.0 37.0 37.0 37.0 20-24 36.432 37.0 37.0 37.0 37.0 37.0 25-29 36.3852 37.0 37.0 37.0 37.0 37.0 30-34 36.3198 37.0 37.0 37.0 37.0 37.0 35-39 36.297999999999995 37.0 37.0 37.0 37.0 37.0 40-44 36.350199999999994 37.0 37.0 37.0 37.0 37.0 45-49 36.3266 37.0 37.0 37.0 37.0 37.0 50-54 36.2287 37.0 37.0 37.0 37.0 37.0 55-59 36.2365 37.0 37.0 37.0 37.0 37.0 60-64 36.224599999999995 37.0 37.0 37.0 37.0 37.0 65-69 36.226099999999995 37.0 37.0 37.0 37.0 37.0 70-74 36.2761 37.0 37.0 37.0 37.0 37.0 75-79 36.141999999999996 37.0 37.0 37.0 37.0 37.0 80-84 36.156600000000005 37.0 37.0 37.0 37.0 37.0 85-89 36.1488 37.0 37.0 37.0 37.0 37.0 90-94 36.0939 37.0 37.0 37.0 37.0 37.0 95-99 36.051199999999994 37.0 37.0 37.0 37.0 37.0 100-104 36.0433 37.0 37.0 37.0 37.0 37.0 105-109 35.9634 37.0 37.0 37.0 37.0 37.0 110-114 35.978899999999996 37.0 37.0 37.0 37.0 37.0 115-119 35.957 37.0 37.0 37.0 37.0 37.0 120-124 35.90560000000001 37.0 37.0 37.0 37.0 37.0 125-129 35.929 37.0 37.0 37.0 37.0 37.0 130-134 35.830600000000004 37.0 37.0 37.0 37.0 37.0 135-139 35.7811 37.0 37.0 37.0 37.0 37.0 140-144 35.664 37.0 37.0 37.0 37.0 37.0 145-149 35.7186 37.0 37.0 37.0 37.0 37.0 150-151 35.2205 37.0 37.0 37.0 31.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 19 1.0 20 1.0 21 0.0 22 0.0 23 2.0 24 2.0 25 5.0 26 9.0 27 13.0 28 15.0 29 25.0 30 34.0 31 57.0 32 71.0 33 94.0 34 124.0 35 315.0 36 2737.0 37 495.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 39.15 9.625 7.000000000000001 44.224999999999994 2 22.59119496855346 13.031446540880504 36.67924528301887 27.69811320754717 3 20.275000000000002 16.0 24.224999999999998 39.5 4 26.575 24.275 19.875 29.275000000000002 5 26.775 28.375 23.175 21.675 6 21.95 32.2 22.175 23.674999999999997 7 17.825 25.374999999999996 37.65 19.15 8 20.925 24.55 29.4 25.124999999999996 9 19.575 21.45 34.075 24.9 10-14 22.89 25.845000000000002 25.619999999999997 25.645 15-19 23.18 24.795 26.22 25.805 20-24 22.805 26.235000000000003 25.55 25.41 25-29 23.755000000000003 25.635 25.44 25.169999999999998 30-34 22.835 25.835 25.83 25.5 35-39 23.1 25.455 25.36 26.085 40-44 23.485 26.290000000000003 25.080000000000002 25.145 45-49 23.09 26.369999999999997 24.9 25.64 50-54 23.11 25.590000000000003 25.53 25.77 55-59 23.93 25.295 25.31 25.465 60-64 23.615 25.71 25.55 25.124999999999996 65-69 23.685000000000002 24.759999999999998 25.580000000000002 25.974999999999998 70-74 23.57 25.555 25.169999999999998 25.705 75-79 23.625 25.575 25.535000000000004 25.264999999999997 80-84 22.905 25.025 25.755 26.314999999999998 85-89 23.685000000000002 24.89 25.165 26.26 90-94 23.265 25.195 25.419999999999998 26.119999999999997 95-99 23.865 24.52 25.465 26.150000000000002 100-104 23.985 25.650000000000002 25.180000000000003 25.185000000000002 105-109 24.224999999999998 24.92 25.41 25.445 110-114 23.835 25.64 24.88 25.645 115-119 24.055 25.264999999999997 25.185000000000002 25.495 120-124 24.26 25.105 24.39 26.245 125-129 24.38 25.509999999999998 24.69 25.419999999999998 130-134 23.41 25.540000000000003 24.44 26.61 135-139 24.135 25.0 24.68 26.185000000000002 140-144 23.990000000000002 25.515 24.995 25.5 145-149 25.185000000000002 25.28 24.395 25.14 150-151 25.2625 24.7875 24.175 25.775 >>END_MODULE >>Per sequence GC content warn #GC Content Count 0 1.0 1 0.5 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 0.5 19 0.5 20 0.0 21 0.5 22 0.5 23 0.0 24 0.0 25 1.0 26 1.5 27 1.0 28 1.0 29 0.5 30 2.0 31 5.5 32 13.0 33 22.0 34 25.0 35 32.5 36 44.0 37 62.5 38 77.0 39 84.5 40 106.0 41 134.0 42 174.0 43 190.0 44 193.5 45 215.5 46 212.0 47 203.5 48 199.0 49 188.5 50 171.0 51 155.5 52 142.0 53 140.0 54 135.0 55 118.5 56 99.0 57 84.5 58 75.0 59 66.5 60 69.5 61 68.0 62 66.5 63 62.0 64 56.0 65 49.5 66 45.5 67 41.5 68 35.0 69 31.5 70 25.0 71 15.5 72 13.0 73 13.0 74 12.0 75 8.0 76 4.0 77 3.0 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 0.625 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 92.825 #Duplication Level Percentage of deduplicated Percentage of total 1 92.88984648532185 86.225 2 6.544573121465122 12.15 3 0.5117155938594129 1.425 4 0.05386479935362241 0.2 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 0.0 0.0 0.0 0.0 0.0 88-89 0.0 0.0 0.0 0.0 0.0 90-91 0.0125 0.0 0.0 0.0 0.0 92-93 0.05 0.0 0.0 0.0 0.0 94-95 0.05 0.0 0.0 0.0 0.0 96-97 0.07500000000000001 0.0 0.0 0.0 0.0 98-99 0.16249999999999998 0.0 0.0 0.0 0.0 100-101 0.2625 0.0 0.0 0.0 0.0 102-103 0.275 0.0 0.0 0.0 0.0 104-105 0.36250000000000004 0.0 0.0 0.0 0.0 106-107 0.45 0.0 0.0 0.0 0.0 108-109 0.5125 0.0 0.0 0.0 0.0 110-111 0.6 0.0 0.0 0.0 0.0 112-113 0.725 0.0 0.0 0.0 0.0 114-115 0.8625 0.0 0.0 0.0 0.0 116-117 1.0875 0.0 0.0 0.0 0.0 118-119 1.3 0.0 0.0 0.0 0.0 120-121 1.5 0.0 0.0 0.0 0.0 122-123 1.5875 0.0 0.0 0.0 0.0 124-125 1.7625000000000002 0.0 0.0 0.0 0.0 126-127 2.0 0.0 0.0 0.0 0.0 128-129 2.3 0.0 0.0 0.0 0.0 130-131 2.5250000000000004 0.0 0.0 0.0 0.0 132-133 2.825 0.0 0.0 0.0 0.0 134-135 3.125 0.0 0.0 0.0 0.0 136-137 3.4625 0.0 0.0 0.0 0.0 138-139 3.7125 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content pass >>END_MODULE SRR13292037 read2 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR13292037_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 50 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 36.056 37.0 37.0 37.0 37.0 37.0 2 36.093 37.0 37.0 37.0 37.0 37.0 3 36.119 37.0 37.0 37.0 37.0 37.0 4 36.245 37.0 37.0 37.0 37.0 37.0 5 36.257 37.0 37.0 37.0 37.0 37.0 6 36.233 37.0 37.0 37.0 37.0 37.0 7 36.1035 37.0 37.0 37.0 37.0 37.0 8 36.182 37.0 37.0 37.0 37.0 37.0 9 36.3205 37.0 37.0 37.0 37.0 37.0 10-14 36.234899999999996 37.0 37.0 37.0 37.0 37.0 15-19 36.221 37.0 37.0 37.0 37.0 37.0 20-24 36.206100000000006 37.0 37.0 37.0 37.0 37.0 25-29 36.135999999999996 37.0 37.0 37.0 37.0 37.0 30-34 36.084999999999994 37.0 37.0 37.0 37.0 37.0 35-39 36.1054 37.0 37.0 37.0 37.0 37.0 40-44 36.1302 37.0 37.0 37.0 37.0 37.0 45-49 36.0531 37.0 37.0 37.0 37.0 37.0 50-54 36.061099999999996 37.0 37.0 37.0 37.0 37.0 55-59 36.03 37.0 37.0 37.0 37.0 37.0 60-64 35.94449999999999 37.0 37.0 37.0 37.0 37.0 65-69 35.9802 37.0 37.0 37.0 37.0 37.0 70-74 35.8995 37.0 37.0 37.0 37.0 37.0 75-79 35.908500000000004 37.0 37.0 37.0 37.0 37.0 80-84 35.938 37.0 37.0 37.0 37.0 37.0 85-89 35.9116 37.0 37.0 37.0 37.0 37.0 90-94 35.777699999999996 37.0 37.0 37.0 37.0 37.0 95-99 35.831100000000006 37.0 37.0 37.0 37.0 37.0 100-104 35.7551 37.0 37.0 37.0 37.0 37.0 105-109 35.7998 37.0 37.0 37.0 37.0 37.0 110-114 35.754 37.0 37.0 37.0 37.0 37.0 115-119 35.7238 37.0 37.0 37.0 37.0 37.0 120-124 35.7631 37.0 37.0 37.0 37.0 37.0 125-129 35.607000000000006 37.0 37.0 37.0 37.0 37.0 130-134 35.679700000000004 37.0 37.0 37.0 37.0 37.0 135-139 35.6052 37.0 37.0 37.0 37.0 37.0 140-144 35.4522 37.0 37.0 37.0 37.0 37.0 145-149 35.51219999999999 37.0 37.0 37.0 37.0 37.0 150-151 34.58425 37.0 37.0 37.0 25.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 13 3.0 14 3.0 15 4.0 16 0.0 17 2.0 18 1.0 19 0.0 20 1.0 21 2.0 22 6.0 23 6.0 24 9.0 25 4.0 26 13.0 27 5.0 28 17.0 29 21.0 30 36.0 31 56.0 32 84.0 33 98.0 34 164.0 35 435.0 36 2655.0 37 375.0 >>END_MODULE >>Per base sequence content warn #Base G A T C 1 36.325 16.85 9.75 37.075 2 27.0 22.975 30.3 19.725 3 22.375 23.65 27.975 26.0 4 24.5 30.725 21.525 23.25 5 28.125 30.925000000000004 20.8 20.150000000000002 6 23.0 35.375 20.549999999999997 21.075 7 22.6 17.849999999999998 35.099999999999994 24.45 8 23.775 21.975 24.474999999999998 29.775000000000002 9 23.5 20.974999999999998 28.1 27.425 10-14 25.515 25.790000000000003 22.869999999999997 25.825 15-19 24.990000000000002 24.959999999999997 24.36 25.69 20-24 25.14 25.055 23.56 26.245 25-29 25.224999999999998 25.345000000000002 24.19 25.240000000000002 30-34 25.66 24.615000000000002 24.44 25.285000000000004 35-39 25.835 25.040000000000003 24.375 24.75 40-44 25.715 24.185000000000002 24.67 25.430000000000003 45-49 25.285000000000004 24.855 24.435000000000002 25.424999999999997 50-54 25.385 25.240000000000002 24.85 24.525 55-59 26.13 25.14 24.224999999999998 24.505 60-64 25.605 25.264999999999997 24.895 24.235 65-69 25.83 25.650000000000002 23.985 24.535 70-74 26.125 25.259999999999998 24.15 24.465 75-79 26.484999999999996 25.515 23.810000000000002 24.19 80-84 26.064999999999998 25.285000000000004 24.355 24.295 85-89 26.36 24.745 24.615000000000002 24.279999999999998 90-94 26.32 25.535000000000004 24.43 23.715 95-99 26.534999999999997 25.215 23.895 24.355 100-104 25.929999999999996 25.655 24.4 24.015 105-109 26.125 25.295 24.27 24.310000000000002 110-114 26.215 26.115 24.25 23.419999999999998 115-119 25.46 26.035000000000004 24.735 23.77 120-124 26.179999999999996 25.319999999999997 24.64 23.86 125-129 26.575 25.480000000000004 24.445 23.5 130-134 26.235000000000003 25.074999999999996 24.915000000000003 23.775 135-139 26.695 24.9 24.965 23.44 140-144 26.68 25.455 24.515 23.35 145-149 26.900000000000002 25.895000000000003 24.125 23.080000000000002 150-151 27.224999999999998 25.900000000000002 23.962500000000002 22.912499999999998 >>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 0.5 7 1.0 8 0.5 9 0.0 10 0.0 11 0.0 12 0.0 13 1.0 14 2.0 15 1.0 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 2.0 25 1.5 26 0.5 27 1.0 28 1.5 29 3.0 30 4.5 31 8.0 32 12.0 33 12.5 34 15.0 35 16.5 36 36.0 37 59.5 38 68.0 39 81.5 40 103.5 41 124.0 42 146.5 43 178.0 44 189.0 45 197.5 46 184.0 47 171.5 48 183.0 49 184.0 50 169.5 51 150.0 52 133.5 53 129.0 54 129.5 55 108.5 56 88.5 57 87.0 58 87.0 59 82.0 60 87.5 61 90.0 62 84.5 63 71.0 64 67.0 65 59.5 66 49.5 67 57.5 68 63.0 69 46.5 70 31.0 71 32.5 72 27.5 73 22.5 74 17.0 75 10.0 76 8.0 77 5.5 78 3.0 79 2.0 80 2.0 81 1.0 82 0.0 83 0.5 84 0.5 85 1.0 86 1.0 87 0.5 88 0.5 89 0.0 90 0.0 91 0.0 92 0.0 93 0.0 94 0.0 95 0.5 96 0.5 97 0.5 98 0.5 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 92.975 #Duplication Level Percentage of deduplicated Percentage of total 1 93.08954019897821 86.55000000000001 2 6.318902930895402 11.75 3 0.5377789728421619 1.5 4 0.05377789728421619 0.2 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 0.0 0.0 0.0 0.0 0.0 88-89 0.0 0.0 0.0 0.0 0.0 90-91 0.0125 0.0 0.0 0.0 0.0 92-93 0.05 0.0 0.0 0.0 0.0 94-95 0.05 0.0 0.0 0.0 0.0 96-97 0.07500000000000001 0.0 0.0 0.0 0.0 98-99 0.16249999999999998 0.0 0.0 0.0 0.0 100-101 0.2625 0.0 0.0 0.0 0.0 102-103 0.275 0.0 0.0 0.0 0.0 104-105 0.36250000000000004 0.0 0.0 0.0 0.0 106-107 0.45 0.0 0.0 0.0 0.0 108-109 0.5125 0.0 0.0 0.0 0.0 110-111 0.6 0.0 0.0 0.0 0.0 112-113 0.725 0.0 0.0 0.0 0.0 114-115 0.8625 0.0 0.0 0.0 0.0 116-117 1.0875 0.0 0.0 0.0 0.0 118-119 1.3 0.0 0.0 0.0 0.0 120-121 1.5125000000000002 0.0 0.0 0.0 0.0 122-123 1.6124999999999998 0.0 0.0 0.0 0.0 124-125 1.7875 0.0 0.0 0.0 0.0 126-127 2.025 0.0 0.0 0.0 0.0 128-129 2.3 0.0 0.0 0.0 0.0 130-131 2.5250000000000004 0.0 0.0 0.0 0.0 132-133 2.8375 0.0 0.0 0.0 0.0 134-135 3.125 0.0 0.0 0.0 0.0 136-137 3.45 0.0 0.0 0.0 0.0 138-139 3.675 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position TCGAATC 10 0.006830828 145.0 9 GAGTCTG 10 0.006830828 145.0 2 ATCGAAT 10 0.006830828 145.0 8 >>END_MODULE Read 1530746 spots for SRR13292037.sra Written 1530746 spots for SRR13292037.sra Read 1530746 spots for SRR13292037.sra Written 1530746 spots for SRR13292037.sra Read 1530756 spots for SRR13292037.sra Written 1530756 spots for SRR13292037.sra Read 1530746 spots for SRR13292037.sra Written 1530746 spots for SRR13292037.sra Read 1530746 spots for SRR13292037.sra Written 1530746 spots for SRR13292037.sra Read 1530746 spots for SRR13292037.sra Written 1530746 spots for SRR13292037.sra Read 1530746 spots for SRR13292037.sra Written 1530746 spots for SRR13292037.sra Read 1530746 spots for SRR13292037.sra Written 1530746 spots for SRR13292037.sra Read 1530746 spots for SRR13292037.sra Written 1530746 spots for SRR13292037.sra Read 1530746 spots for SRR13292037.sra Written 1530746 spots for SRR13292037.sra Read 1530746 spots for SRR13292037.sra Written 1530746 spots for SRR13292037.sra Read 1530746 spots for SRR13292037.sra Written 1530746 spots for SRR13292037.sra Read 1530746 spots for SRR13292037.sra Written 1530746 spots for SRR13292037.sra Read 1530746 spots for SRR13292037.sra Written 1530746 spots for SRR13292037.sra Read 1530746 spots for SRR13292037.sra Written 1530746 spots for SRR13292037.sra Read 1530746 spots for SRR13292037.sra Written 1530746 spots for SRR13292037.sra Read 1530746 spots for SRR13292037.sra Written 1530746 spots for SRR13292037.sra Read 1530746 spots for SRR13292037.sra Written 1530746 spots for SRR13292037.sra Read 1530746 spots for SRR13292037.sra Written 1530746 spots for SRR13292037.sra Read 1530746 spots for SRR13292037.sra Written 1530746 spots for SRR13292037.sra SRR ids: ['SRR13292037.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_q_0_t67p SRR13292037.sra spots: 30614930 blocks: [[1, 1530746], [1530747, 3061492], [3061493, 4592238], [4592239, 6122984], [6122985, 7653730], [7653731, 9184476], [9184477, 10715222], [10715223, 12245968], [12245969, 13776714], [13776715, 15307460], [15307461, 16838206], [16838207, 18368952], [18368953, 19899698], [19899699, 21430444], [21430445, 22961190], [22961191, 24491936], [24491937, 26022682], [26022683, 27553428], [27553429, 29084174], [29084175, 30614930]] SRR13292037 file size 10382592 SRR13292037 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 SRR13292037 SRR13292037_1.fastq SRR13292037_2.fastq Input file: SRR13292037_1.fastq Paired file: SRR13292037_2.fastq trimmed: SRR13292037-trimmed-pair1.fastq, SRR13292037-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 Sat Dec 7 14:03:26 2024 >> started Sat Dec 7 14:04:01 2024 >> done (34.513s) 30614930 read pairs processed; of these: 86 ( 0.00%) short read pairs filtered out after trimming by size control 995 ( 0.00%) empty read pairs filtered out after trimming by size control 30613849 (100.00%) read pairs available; of these: 2196412 ( 7.17%) trimmed read pairs available after processing 28417437 (92.83%) untrimmed read pairs available after processing Length distribution of reads after trimming: length count percentage 18 3 0.00% 19 7 0.00% 20 7 0.00% 21 10 0.00% 22 6 0.00% 23 13 0.00% 24 12 0.00% 25 16 0.00% 26 4 0.00% 27 20 0.00% 28 15 0.00% 29 22 0.00% 30 21 0.00% 31 31 0.00% 32 25 0.00% 33 18 0.00% 34 24 0.00% 35 30 0.00% 36 36 0.00% 37 34 0.00% 38 47 0.00% 39 32 0.00% 40 46 0.00% 41 55 0.00% 42 59 0.00% 43 52 0.00% 44 36 0.00% 45 44 0.00% 46 88 0.00% 47 61 0.00% 48 66 0.00% 49 66 0.00% 50 68 0.00% 51 80 0.00% 52 87 0.00% 53 113 0.00% 54 101 0.00% 55 97 0.00% 56 112 0.00% 57 154 0.00% 58 142 0.00% 59 137 0.00% 60 195 0.00% 61 173 0.00% 62 188 0.00% 63 208 0.00% 64 228 0.00% 65 248 0.00% 66 278 0.00% 67 293 0.00% 68 276 0.00% 69 344 0.00% 70 397 0.00% 71 415 0.00% 72 448 0.00% 73 559 0.00% 74 552 0.00% 75 638 0.00% 76 724 0.00% 77 739 0.00% 78 909 0.00% 79 981 0.00% 80 1036 0.00% 81 1154 0.00% 82 1289 0.00% 83 1408 0.00% 84 1554 0.01% 85 1698 0.01% 86 1917 0.01% 87 2194 0.01% 88 2354 0.01% 89 2651 0.01% 90 2807 0.01% 91 3212 0.01% 92 3678 0.01% 93 3938 0.01% 94 4460 0.01% 95 4900 0.02% 96 5380 0.02% 97 6033 0.02% 98 6509 0.02% 99 6901 0.02% 100 7929 0.03% 101 8521 0.03% 102 9199 0.03% 103 10011 0.03% 104 11040 0.04% 105 11855 0.04% 106 13014 0.04% 107 14033 0.05% 108 15089 0.05% 109 16282 0.05% 110 17202 0.06% 111 18279 0.06% 112 19855 0.06% 113 21002 0.07% 114 22384 0.07% 115 24529 0.08% 116 25995 0.08% 117 27282 0.09% 118 28455 0.09% 119 29904 0.10% 120 31194 0.10% 121 32873 0.11% 122 34660 0.11% 123 36488 0.12% 124 38488 0.13% 125 40148 0.13% 126 42228 0.14% 127 43805 0.14% 128 45101 0.15% 129 46888 0.15% 130 48618 0.16% 131 50142 0.16% 132 51870 0.17% 133 53673 0.18% 134 54816 0.18% 135 56876 0.19% 136 59978 0.20% 137 60271 0.20% 138 62226 0.20% 139 64975 0.21% 140 65617 0.21% 141 66993 0.22% 142 69898 0.23% 143 70231 0.23% 144 72367 0.24% 145 74043 0.24% 146 75320 0.25% 147 76814 0.25% 148 79903 0.26% 149 80283 0.26% 150 81802 0.27% 151 28417437 92.83% 30613849 reads passed initial QC criterion=sequence-density sequence-density=0.17 sequence-density-rank=1 fanout-score=5.44 fanout-score-rank=19 prefix-density=0.26 prefix-fanout=3.6 sequence=GATCTCGCCGAAG criterion=fanout-score sequence-density=0.02 sequence-density-rank=32 fanout-score=280.90 fanout-score-rank=1 prefix-density=0.38 prefix-fanout=16.5 sequence=GGCGGCGGCGAACCGCCCCCGTCGCCGCGATCCGAACACTTCACCGGACCATTCAATCGGTAGGAGCGACGGGCGGTGTGTACAAAGGGCAGGGACGTAGTCAACGCGAGCTGATGACTCGCGCTTACTAGGCATTCCTCGTTGAAGACCAACAATTGCAATGATCTATCCCCATCACGATGAAATTTCCCAAGATTACCCGGGCCTGTCGGCCAAGGCTATATACTCGTTGAATACATCAGTGTAGCGCGCGTGCGGCCCAGAACATCTAAGGGCATCACAGACCTGTTATTGCCTCAAACTTCCGTCGCCTAAACGGCGATAGTCCCTCTAAGAAGCTAGCTGCGGAGGGATGGCTCCGCATAGCTAGTTAGCAGGCTGAGGTCTCGTTCGTTAACGGAATTAACCAGACAAATCGCTCCACCAACTAAGAACGGCCATGCACCACCACCCATAGAATCAAGAAAGAGCTCTCAGTCTGTCAATCCTTGCTATGTCTGGACCTGGTAAG criterion=sequence-density sequence-density=0.36 sequence-density-rank=1 fanout-score=2.34 fanout-score-rank=34 prefix-density=0.39 prefix-fanout=2.2 sequence=CGGTTCCGGTTC criterion=fanout-score sequence-density=0.07 sequence-density-rank=26 fanout-score=283.99 fanout-score-rank=1 prefix-density=0.99 prefix-fanout=20.3 sequence=CCGCCGCCGCCCCTCGTCCTCTGTGTTCCTTCTCCGAGTTTCAGCCATGGGTAAGGAGAAGACTCACATCAACATCGTGGTCATTGGCCATGTCGACTCTGGCAAGTCGACCACCACTGGCCACCTGATCTACAAGCTTGGAGGTATTGACAAGCGTGTGATCGAGAGGTTCGAGAAGGAGGCTGC SRR13292037 testing PE reads STAR mapping to Ensembl genome Started job on | Dec 07 14:05:17 Started mapping on | Dec 07 14:05:17 Finished on | Dec 07 14:10:57 Mapping speed, Million of reads per hour | 324.15 Number of input reads | 30613849 Average input read length | 291 UNIQUE READS: Uniquely mapped reads number | 26511476 Uniquely mapped reads % | 86.60% Average mapped length | 289.27 Number of splices: Total | 29475504 Number of splices: Annotated (sjdb) | 27823561 Number of splices: GT/AG | 29069051 Number of splices: GC/AG | 330109 Number of splices: AT/AC | 21758 Number of splices: Non-canonical | 54586 Mismatch rate per base, % | 0.54% Deletion rate per base | 0.03% Deletion average length | 2.99 Insertion rate per base | 0.02% Insertion average length | 2.62 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 488567 % of reads mapped to multiple loci | 1.60% Number of reads mapped to too many loci | 52717 % of reads mapped to too many loci | 0.17% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 10.92% % of reads unmapped: other | 0.71% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 3613806 3613806 3613806 N_multimapping 488567 488567 488567 N_noFeature 721000 25938448 876554 N_ambiguous 547288 5011 129879 UnstrandedReadsAssigned:25243188 PositiveStrandReadsAssigned:568017 NegativeStrandReadsAssigned:25505043 Dataset is classified negative stranded MeadianReadLen=151 20thPercentileLength=151 echo kmer=147 SRR13292037 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: SRR13292037-trimmed-pair1.fastq SRR13292037-trimmed-pair2.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 30,613,849 reads, 27,888,695 reads pseudoaligned [quant] estimated average fragment length: 278.348 [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,134 rounds 52973 SRR13292037.ke.tsv 35125 SRR13292037.se.tsv 88098 total ==> SRR13292037.ke.tsv <== target_id length eff_length est_counts tpm PNS24245 936 659.366 0 0 PNS24247 1044 766.652 123.233 8.72242 PNS24249 1928 1650.65 118.03 3.88011 PNS24246 1044 766.652 123.233 8.72242 PNS24248 1044 766.652 123.233 8.72242 PNS24244 1471 1193.65 192.271 8.74064 PNS24243 293 92.655 1 0.585651 KQK14069 1603 1325.65 4897.6 200.476 KQK14071 474 226.547 101.378 24.2826 ==> SRR13292037.se.tsv <== BRADI_1g14170v3 4769 BRADI_1g53295v3 108 BRADI_1g59795v3 389 BRADI_1g07683v3 0 BRADI_1g00485v3 58 BRADI_1g20270v3 2498 BRADI_1g74790v3 30 BRADI_1g09890v3 0 BRADI_1g77505v3 185 BRADI_1g48960v3 0 SRR13292037 completed mapping pipeline successfully