Starting /dee2/code/volunteer_pipeline.sh SRR6958420 current disk space = 1548577959936 free memory = 1597860696 SRR6958420 SRAfilesize cf75426175861a8cb6b5e53bc74750fd SRR6958420.sra SRR6958420.sra file validated SRR6958420 is paired end SRR6958420 is conventional basespace SRR6958420 read1 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR6958420_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 48 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 27.3125 32.0 25.0 33.0 18.0 33.0 2 27.65925 29.0 25.0 31.0 18.0 33.0 3 31.10175 33.0 30.0 33.0 27.0 33.0 4 32.27675 33.0 32.0 33.0 32.0 33.0 5 32.83525 33.0 33.0 34.0 32.0 34.0 6 37.1155 38.0 37.0 38.0 36.0 38.0 7 37.12075 38.0 38.0 38.0 35.0 38.0 8 37.34 38.0 38.0 38.0 37.0 38.0 9 37.359 38.0 38.0 38.0 37.0 38.0 10-14 35.941050000000004 37.8 35.4 38.0 31.4 38.0 15-19 37.4646 38.0 38.0 38.0 38.0 38.0 20-24 37.5791 38.0 38.0 38.0 38.0 38.0 25-29 37.52835 38.0 38.0 38.0 37.8 38.0 30-34 37.1793 38.0 38.0 38.0 36.6 38.0 35-39 37.33575 38.0 38.0 38.0 37.0 38.0 40-44 37.3036 38.0 38.0 38.0 37.0 38.0 45-49 36.64745 38.0 37.2 38.0 32.2 38.0 50-54 37.34495 38.0 38.0 38.0 36.8 38.0 55-59 37.30505 38.0 38.0 38.0 36.8 38.0 60-64 37.33475 38.0 38.0 38.0 37.0 38.0 65-69 37.2041 38.0 38.0 38.0 36.6 38.0 70-74 37.223600000000005 38.0 38.0 38.0 36.8 38.0 75-79 37.21165 38.0 38.0 38.0 36.4 38.0 80-84 37.210300000000004 38.0 38.0 38.0 36.4 38.0 85-89 35.93795 38.0 36.0 38.0 30.0 38.0 90-94 34.82865 37.8 34.0 38.0 25.8 38.0 95-99 36.71195 38.0 37.8 38.0 34.8 38.0 100-104 36.877250000000004 38.0 38.0 38.0 35.0 38.0 105-109 36.830850000000005 38.0 38.0 38.0 34.8 38.0 110-114 36.77425 38.0 38.0 38.0 35.0 38.0 115-119 36.54600000000001 38.0 38.0 38.0 34.6 38.0 120-124 36.3123 38.0 38.0 38.0 34.0 38.0 125-129 36.1673 38.0 38.0 38.0 33.0 38.0 130-134 36.14975 38.0 37.8 38.0 33.0 38.0 135-139 35.9813 38.0 37.2 38.0 32.8 38.0 140-144 35.560249999999996 38.0 36.0 38.0 31.6 38.0 145-149 33.3597 37.6 32.0 38.0 24.2 38.0 150-151 30.927999999999997 35.5 29.0 38.0 16.5 38.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 3 1.0 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 2.0 13 0.0 14 2.0 15 2.0 16 0.0 17 0.0 18 0.0 19 0.0 20 2.0 21 0.0 22 0.0 23 4.0 24 6.0 25 12.0 26 15.0 27 8.0 28 28.0 29 27.0 30 42.0 31 42.0 32 69.0 33 99.0 34 166.0 35 289.0 36 933.0 37 2251.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 45.774647887323944 11.55451225873761 6.285863328116849 36.38497652582159 2 23.150000000000002 12.925 34.875 29.049999999999997 3 19.575 18.475 26.450000000000003 35.5 4 26.081520380095025 24.431107776944234 22.330582645661416 27.156789197299325 5 24.575 30.349999999999998 23.05 22.025 6 21.525 33.2 23.575 21.7 7 16.45 23.05 41.55 18.95 8 18.95 23.075000000000003 30.3 27.675 9 19.15 20.25 33.875 26.724999999999998 10-14 22.66 27.0 25.679999999999996 24.66 15-19 22.43 25.855 26.525 25.19 20-24 22.42 25.895000000000003 26.58 25.105 25-29 22.545 25.655 26.38 25.419999999999998 30-34 22.73 25.435000000000002 26.590000000000003 25.245 35-39 22.925 25.665 26.08 25.330000000000002 40-44 22.17 25.814999999999998 26.69 25.324999999999996 45-49 22.405 25.795 26.33 25.47 50-54 22.575 25.615 26.474999999999998 25.335 55-59 22.96 25.34 26.125 25.575 60-64 22.55 25.805 26.279999999999998 25.365 65-69 22.770000000000003 25.55 26.435 25.245 70-74 22.855 25.174999999999997 26.5 25.47 75-79 23.165 26.064999999999998 25.564999999999998 25.205 80-84 22.675 26.11 25.655 25.56 85-89 22.99 25.430000000000003 26.095000000000002 25.485000000000003 90-94 23.335 25.485000000000003 26.724999999999998 24.455 95-99 23.085 25.61 25.785000000000004 25.52 100-104 23.175 26.115 25.485000000000003 25.224999999999998 105-109 23.086154307715386 25.03625181259063 26.3963198159908 25.481274063703186 110-114 22.994999999999997 25.979999999999997 26.119999999999997 24.905 115-119 23.195 26.31 26.064999999999998 24.43 120-124 23.064999999999998 25.695 25.685000000000002 25.555 125-129 23.22 25.619999999999997 26.0 25.16 130-134 23.135 25.85 26.155 24.86 135-139 23.724999999999998 26.16 25.16 24.955 140-144 23.14 26.055 24.905 25.900000000000002 145-149 24.085 25.419999999999998 25.855 24.64 150-151 24.0 26.3 24.4875 25.2125 >>END_MODULE >>Per sequence GC content warn #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 0.5 8 0.5 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 1.0 23 1.0 24 0.5 25 2.0 26 2.5 27 3.5 28 5.0 29 5.5 30 5.5 31 13.0 32 19.0 33 28.5 34 35.0 35 39.5 36 55.5 37 71.0 38 92.0 39 111.5 40 129.0 41 160.5 42 184.5 43 184.5 44 198.5 45 213.0 46 209.5 47 203.5 48 201.5 49 193.5 50 161.5 51 156.0 52 148.5 53 121.5 54 104.5 55 94.5 56 95.5 57 86.5 58 82.5 59 78.0 60 65.0 61 57.0 62 51.0 63 46.5 64 43.5 65 38.5 66 38.5 67 33.5 68 26.0 69 23.0 70 16.5 71 15.0 72 15.0 73 11.5 74 6.5 75 2.5 76 4.0 77 4.0 78 1.5 79 1.0 80 0.5 81 0.0 82 0.0 83 0.0 84 0.0 85 0.0 86 0.0 87 0.0 88 0.0 89 0.0 90 0.0 91 0.0 92 0.0 93 0.0 94 0.0 95 0.0 96 0.0 97 0.0 98 0.0 99 0.0 100 0.0 >>END_MODULE >>Per base N content pass #Base N-Count 1 4.15 2 0.0 3 0.0 4 0.025 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 0.005 110-114 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 99.52499999999999 #Duplication Level Percentage of deduplicated Percentage of total 1 99.5227329816629 99.05000000000001 2 0.4772670183371013 0.95 3 0.0 0.0 4 0.0 0.0 5 0.0 0.0 6 0.0 0.0 7 0.0 0.0 8 0.0 0.0 9 0.0 0.0 >10 0.0 0.0 >50 0.0 0.0 >100 0.0 0.0 >500 0.0 0.0 >1k 0.0 0.0 >5k 0.0 0.0 >10k+ 0.0 0.0 >>END_MODULE >>Overrepresented sequences pass >>END_MODULE >>Adapter Content warn #Position Illumina Universal Adapter Illumina Small RNA 3' Adapter Illumina Small RNA 5' Adapter Nextera Transposase Sequence SOLID Small RNA Adapter 1 0.0 0.0 0.0 0.0 0.0 2 0.0 0.0 0.0 0.0 0.0 3 0.0 0.0 0.0 0.0 0.0 4 0.0 0.0 0.0 0.0 0.0 5 0.0 0.0 0.0 0.0 0.0 6 0.0 0.0 0.0 0.0 0.0 7 0.0 0.0 0.0 0.0 0.0 8 0.0 0.0 0.0 0.0 0.0 9 0.0 0.0 0.0 0.0 0.0 10-11 0.0 0.0 0.0 0.0 0.0 12-13 0.0 0.0 0.0 0.0 0.0 14-15 0.0 0.0 0.0 0.0 0.0 16-17 0.0 0.0 0.0 0.0 0.0 18-19 0.0 0.0 0.0 0.0 0.0 20-21 0.0 0.0 0.0 0.0 0.0 22-23 0.0 0.0 0.0 0.0 0.0 24-25 0.0 0.0 0.0 0.0 0.0 26-27 0.0 0.0 0.0 0.0 0.0 28-29 0.0 0.0 0.0 0.0 0.0 30-31 0.0 0.0 0.0 0.0 0.0 32-33 0.0 0.0 0.0 0.0 0.0 34-35 0.0 0.0 0.0 0.0 0.0 36-37 0.0 0.0 0.0 0.0 0.0 38-39 0.0 0.0 0.0 0.0 0.0 40-41 0.0 0.0 0.0 0.0 0.0 42-43 0.0 0.0 0.0 0.0 0.0 44-45 0.0 0.0 0.0 0.0 0.0 46-47 0.0 0.0 0.0 0.0 0.0 48-49 0.0 0.0 0.0 0.0 0.0 50-51 0.0 0.0 0.0 0.0 0.0 52-53 0.0 0.0 0.0 0.0 0.0 54-55 0.0 0.0 0.0 0.0 0.0 56-57 0.0 0.0 0.0 0.0 0.0 58-59 0.0 0.0 0.0 0.0 0.0 60-61 0.0 0.0 0.0 0.0 0.0 62-63 0.0 0.0 0.0 0.0 0.0 64-65 0.0 0.0 0.0 0.0 0.0 66-67 0.0 0.0 0.0 0.0 0.0 68-69 0.0125 0.0 0.0 0.0 0.0 70-71 0.025 0.0 0.0 0.0 0.0 72-73 0.025 0.0 0.0 0.0 0.0 74-75 0.025 0.0 0.0 0.0 0.0 76-77 0.0875 0.0 0.0 0.0 0.0 78-79 0.1 0.0 0.0 0.0 0.0 80-81 0.1 0.0 0.0 0.0 0.0 82-83 0.1 0.0 0.0 0.0 0.0 84-85 0.1125 0.0 0.0 0.0 0.0 86-87 0.16249999999999998 0.0 0.0 0.0 0.0 88-89 0.2 0.0 0.0 0.0 0.0 90-91 0.2875 0.0 0.0 0.0 0.0 92-93 0.3625 0.0 0.0 0.0 0.0 94-95 0.425 0.0 0.0 0.0 0.0 96-97 0.625 0.0 0.0 0.0 0.0 98-99 0.7125 0.0 0.0 0.0 0.0 100-101 0.825 0.0 0.0 0.0 0.0 102-103 0.9624999999999999 0.0 0.0 0.0 0.0 104-105 1.15 0.0 0.0 0.0 0.0 106-107 1.375 0.0 0.0 0.0 0.0 108-109 1.6625 0.0 0.0 0.0 0.0 110-111 1.8375 0.0 0.0 0.0 0.0 112-113 2.1375 0.0 0.0 0.0 0.0 114-115 2.375 0.0 0.0 0.0 0.0 116-117 2.5999999999999996 0.0 0.0 0.0 0.0 118-119 2.8625 0.0 0.0 0.0 0.0 120-121 3.1375 0.0 0.0 0.0 0.0 122-123 3.45 0.0 0.0 0.0 0.0 124-125 3.8375000000000004 0.0 0.0 0.0 0.0 126-127 4.275 0.0 0.0 0.0 0.0 128-129 4.6625 0.0 0.0 0.0 0.0 130-131 5.1375 0.0 0.0 0.0 0.0 132-133 5.55 0.0 0.0 0.0 0.0 134-135 6.125 0.0 0.0 0.0 0.0 136-137 6.6875 0.0 0.0 0.0 0.0 138-139 7.275 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content pass >>END_MODULE SRR6958420 read2 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR6958420_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 48 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 32.6335 33.0 33.0 34.0 32.0 34.0 2 32.909 33.0 33.0 34.0 32.0 34.0 3 32.986 34.0 33.0 34.0 32.0 34.0 4 32.4995 34.0 33.0 34.0 32.0 34.0 5 32.8975 34.0 33.0 34.0 32.0 34.0 6 37.128 38.0 38.0 38.0 37.0 38.0 7 37.141 38.0 38.0 38.0 37.0 38.0 8 37.11425 38.0 38.0 38.0 37.0 38.0 9 37.145 38.0 38.0 38.0 37.0 38.0 10-14 36.7727 38.0 37.8 38.0 35.2 38.0 15-19 37.056799999999996 38.0 38.0 38.0 36.4 38.0 20-24 37.1586 38.0 38.0 38.0 37.0 38.0 25-29 37.0942 38.0 38.0 38.0 36.8 38.0 30-34 37.13955 38.0 38.0 38.0 37.0 38.0 35-39 36.63465000000001 38.0 38.0 38.0 35.0 38.0 40-44 36.4675 38.0 38.0 38.0 34.2 38.0 45-49 36.78385 38.0 38.0 38.0 35.8 38.0 50-54 36.7515 38.0 38.0 38.0 35.2 38.0 55-59 36.45345 38.0 37.8 38.0 33.4 38.0 60-64 36.60880000000001 38.0 38.0 38.0 34.6 38.0 65-69 36.48975 38.0 38.0 38.0 33.6 38.0 70-74 36.351299999999995 38.0 37.8 38.0 33.4 38.0 75-79 36.78404999999999 38.0 38.0 38.0 35.6 38.0 80-84 36.71125 38.0 38.0 38.0 35.2 38.0 85-89 36.5477 38.0 38.0 38.0 34.6 38.0 90-94 34.6882 38.0 34.6 38.0 26.2 38.0 95-99 36.150549999999996 38.0 37.8 38.0 32.8 38.0 100-104 36.3414 38.0 38.0 38.0 34.0 38.0 105-109 35.54405 38.0 36.6 38.0 28.6 38.0 110-114 36.226350000000004 38.0 38.0 38.0 34.0 38.0 115-119 36.0774 38.0 37.8 38.0 33.8 38.0 120-124 35.765550000000005 38.0 36.8 38.0 32.2 38.0 125-129 35.3425 38.0 36.2 38.0 29.8 38.0 130-134 35.23385 38.0 36.0 38.0 31.0 38.0 135-139 34.85029999999999 38.0 35.8 38.0 28.2 38.0 140-144 34.46655 38.0 35.6 38.0 27.4 38.0 145-149 32.4841 37.6 32.8 38.0 14.2 38.0 150-151 27.178874999999998 33.5 17.5 37.0 2.0 38.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 2 10.0 3 1.0 4 0.0 5 2.0 6 0.0 7 0.0 8 1.0 9 4.0 10 1.0 11 1.0 12 0.0 13 2.0 14 1.0 15 2.0 16 3.0 17 3.0 18 5.0 19 3.0 20 3.0 21 8.0 22 5.0 23 13.0 24 14.0 25 21.0 26 14.0 27 31.0 28 29.0 29 49.0 30 54.0 31 63.0 32 78.0 33 133.0 34 166.0 35 296.0 36 716.0 37 2268.0 >>END_MODULE >>Per base sequence content warn #Base G A T C 1 42.199999999999996 21.05 8.4 28.349999999999998 2 29.275000000000002 24.474999999999998 28.749999999999996 17.5 3 22.25 25.474999999999998 29.125 23.150000000000002 4 25.5 33.1 20.4 21.0 5 26.974999999999998 34.825 19.75 18.45 6 23.35 35.075 20.599999999999998 20.974999999999998 7 22.525000000000002 19.75 35.875 21.85 8 21.099999999999998 24.575 25.275 29.049999999999997 9 22.925 22.75 27.500000000000004 26.825 10-14 25.72 26.135 23.525 24.62 15-19 25.590000000000003 25.27 25.385 23.755000000000003 20-24 26.27 26.005 24.709999999999997 23.015 25-29 25.755 26.005 24.81 23.43 30-34 25.71 25.755 24.915000000000003 23.62 35-39 24.825 26.075 25.290000000000003 23.810000000000002 40-44 25.515 25.91 24.84 23.735 45-49 25.009999999999998 25.91 25.245 23.835 50-54 25.025 25.69 25.235000000000003 24.05 55-59 25.81 25.259999999999998 25.285000000000004 23.645 60-64 25.324999999999996 25.735000000000003 25.665 23.275000000000002 65-69 25.45 25.89 24.755 23.905 70-74 25.605 26.41 24.805 23.18 75-79 25.75 25.424999999999997 25.540000000000003 23.285 80-84 25.35 25.835 25.235000000000003 23.580000000000002 85-89 25.19 26.590000000000003 24.985 23.235 90-94 25.21 25.81 25.445 23.535 95-99 25.785000000000004 25.740000000000002 24.695 23.78 100-104 25.97 26.064999999999998 25.22 22.745 105-109 25.900000000000002 25.995 25.124999999999996 22.98 110-114 25.7 26.474999999999998 25.05 22.775000000000002 115-119 26.21 26.325 24.86 22.605 120-124 26.115 26.555 24.97 22.36 125-129 26.38 26.22 25.174999999999997 22.225 130-134 26.290000000000003 26.384999999999998 24.945 22.38 135-139 26.395000000000003 26.229999999999997 25.305 22.07 140-144 26.810000000000002 26.31 24.84 22.040000000000003 145-149 26.740000000000002 26.695 24.745 21.82 150-151 26.5625 26.650000000000002 25.0 21.7875 >>END_MODULE >>Per sequence GC content warn #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 0.5 25 1.0 26 2.5 27 2.5 28 3.0 29 4.0 30 5.0 31 10.0 32 16.0 33 21.5 34 30.0 35 38.0 36 50.0 37 64.0 38 86.0 39 122.0 40 139.5 41 147.5 42 172.5 43 186.0 44 192.0 45 185.0 46 196.0 47 208.0 48 186.5 49 174.5 50 159.5 51 137.0 52 121.5 53 114.5 54 107.0 55 104.0 56 97.5 57 85.0 58 82.0 59 86.5 60 88.0 61 80.5 62 69.0 63 64.5 64 62.0 65 48.5 66 39.5 67 38.5 68 32.5 69 28.5 70 28.5 71 23.5 72 19.0 73 16.0 74 9.0 75 4.5 76 2.0 77 2.5 78 3.5 79 1.5 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 0.0 130-134 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 99.4 #Duplication Level Percentage of deduplicated Percentage of total 1 99.57243460764587 98.97500000000001 2 0.35211267605633806 0.7000000000000001 3 0.025150905432595575 0.075 4 0.0 0.0 5 0.05030181086519115 0.25 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 warn #Sequence Count Percentage Possible Source CTGCAATTGCAAGCTTGTGTCAAAGAAGAGGGTAGCACCTGATCCTCTTG 5 0.125 No Hit CTTGATCATCTGAAAAATCTTAATCCAGATCAGACCAAGCAGAGCAGAGA 5 0.125 No Hit >>END_MODULE >>Adapter Content warn #Position Illumina Universal Adapter Illumina Small RNA 3' Adapter Illumina Small RNA 5' Adapter Nextera Transposase Sequence SOLID Small RNA Adapter 1 0.0 0.0 0.0 0.0 0.0 2 0.0 0.0 0.0 0.0 0.0 3 0.0 0.0 0.0 0.0 0.0 4 0.0 0.0 0.0 0.0 0.0 5 0.0 0.0 0.0 0.0 0.0 6 0.0 0.0 0.0 0.0 0.0 7 0.0 0.0 0.0 0.0 0.0 8 0.0 0.0 0.0 0.0 0.0 9 0.0 0.0 0.0 0.0 0.0 10-11 0.0 0.0 0.0 0.0 0.0 12-13 0.0 0.0 0.0 0.0 0.0 14-15 0.0 0.0 0.0 0.0 0.0 16-17 0.0 0.0 0.0 0.0 0.0 18-19 0.0 0.0 0.0 0.0 0.0 20-21 0.0 0.0 0.0 0.0 0.0 22-23 0.0 0.0 0.0 0.0 0.0 24-25 0.0 0.0 0.0 0.0 0.0 26-27 0.0 0.0 0.0 0.0 0.0 28-29 0.0 0.0 0.0 0.0 0.0 30-31 0.0 0.0 0.0 0.0 0.0 32-33 0.0 0.0 0.0 0.0 0.0 34-35 0.0 0.0 0.0 0.0 0.0 36-37 0.0 0.0 0.0 0.0 0.0 38-39 0.0 0.0 0.0 0.0 0.0 40-41 0.0 0.0 0.0 0.0 0.0 42-43 0.0 0.0 0.0 0.0 0.0 44-45 0.0 0.0 0.0 0.0 0.0 46-47 0.0 0.0 0.0 0.0 0.0 48-49 0.0 0.0 0.0 0.0 0.0 50-51 0.0 0.0 0.0 0.0 0.0 52-53 0.0 0.0 0.0 0.0 0.0 54-55 0.0 0.0 0.0 0.0 0.0 56-57 0.0 0.0 0.0 0.0 0.0 58-59 0.0 0.0 0.0 0.0 0.0 60-61 0.0 0.0 0.0 0.0 0.0 62-63 0.0 0.0 0.0 0.0 0.0 64-65 0.0 0.0 0.0 0.0 0.0 66-67 0.0 0.0 0.0 0.0 0.0 68-69 0.0125 0.0 0.0 0.0 0.0 70-71 0.025 0.0 0.0 0.0 0.0 72-73 0.025 0.0 0.0 0.0 0.0 74-75 0.025 0.0 0.0 0.0 0.0 76-77 0.0875 0.0 0.0 0.0 0.0 78-79 0.1 0.0 0.0 0.0 0.0 80-81 0.1 0.0 0.0 0.0 0.0 82-83 0.1 0.0 0.0 0.0 0.0 84-85 0.1125 0.0 0.0 0.0 0.0 86-87 0.16249999999999998 0.0 0.0 0.0 0.0 88-89 0.2 0.0 0.0 0.0 0.0 90-91 0.3125 0.0 0.0 0.0 0.0 92-93 0.3875 0.0 0.0 0.0 0.0 94-95 0.45 0.0 0.0 0.0 0.0 96-97 0.65 0.0 0.0 0.0 0.0 98-99 0.7375 0.0 0.0 0.0 0.0 100-101 0.85 0.0 0.0 0.0 0.0 102-103 0.9875 0.0 0.0 0.0 0.0 104-105 1.175 0.0 0.0 0.0 0.0 106-107 1.4 0.0 0.0 0.0 0.0 108-109 1.6875 0.0 0.0 0.0 0.0 110-111 1.85 0.0 0.0 0.0 0.0 112-113 2.15 0.0 0.0 0.0 0.0 114-115 2.4000000000000004 0.0 0.0 0.0 0.0 116-117 2.625 0.0 0.0 0.0 0.0 118-119 2.8875 0.0 0.0 0.0 0.0 120-121 3.1625 0.0 0.0 0.0 0.0 122-123 3.425 0.0 0.0 0.0 0.0 124-125 3.8125 0.0 0.0 0.0 0.0 126-127 4.2375 0.0 0.0 0.0 0.0 128-129 4.5875 0.0 0.0 0.0 0.0 130-131 5.0625 0.0 0.0 0.0 0.0 132-133 5.475 0.0 0.0 0.0 0.0 134-135 6.0375 0.0 0.0 0.0 0.0 136-137 6.6125 0.0 0.0 0.0 0.0 138-139 7.262499999999999 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position GAGTGAT 10 0.006830828 145.0 9 >>END_MODULE Read 1311207 spots for SRR6958420.sra Written 1311207 spots for SRR6958420.sra Read 1311207 spots for SRR6958420.sra Written 1311207 spots for SRR6958420.sra Read 1311207 spots for SRR6958420.sra Written 1311207 spots for SRR6958420.sra Read 1311207 spots for SRR6958420.sra Written 1311207 spots for SRR6958420.sra Read 1311207 spots for SRR6958420.sra Written 1311207 spots for SRR6958420.sra Read 1311207 spots for SRR6958420.sra Written 1311207 spots for SRR6958420.sra Read 1311207 spots for SRR6958420.sra Written 1311207 spots for SRR6958420.sra Read 1311207 spots for SRR6958420.sra Written 1311207 spots for SRR6958420.sra Read 1311207 spots for SRR6958420.sra Written 1311207 spots for SRR6958420.sra Read 1311207 spots for SRR6958420.sra Written 1311207 spots for SRR6958420.sra Read 1311221 spots for SRR6958420.sra Written 1311221 spots for SRR6958420.sra Read 1311207 spots for SRR6958420.sra Written 1311207 spots for SRR6958420.sra Read 1311207 spots for SRR6958420.sra Written 1311207 spots for SRR6958420.sra Read 1311207 spots for SRR6958420.sra Written 1311207 spots for SRR6958420.sra Read 1311207 spots for SRR6958420.sra Written 1311207 spots for SRR6958420.sra Read 1311207 spots for SRR6958420.sra Written 1311207 spots for SRR6958420.sra Read 1311207 spots for SRR6958420.sra Written 1311207 spots for SRR6958420.sra Read 1311207 spots for SRR6958420.sra Written 1311207 spots for SRR6958420.sra Read 1311207 spots for SRR6958420.sra Written 1311207 spots for SRR6958420.sra Read 1311207 spots for SRR6958420.sra Written 1311207 spots for SRR6958420.sra SRR ids: ['SRR6958420.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_tmmzt4bd SRR6958420.sra spots: 26224154 blocks: [[1, 1311207], [1311208, 2622414], [2622415, 3933621], [3933622, 5244828], [5244829, 6556035], [6556036, 7867242], [7867243, 9178449], [9178450, 10489656], [10489657, 11800863], [11800864, 13112070], [13112071, 14423277], [14423278, 15734484], [15734485, 17045691], [17045692, 18356898], [18356899, 19668105], [19668106, 20979312], [20979313, 22290519], [22290520, 23601726], [23601727, 24912933], [24912934, 26224154]] SRR6958420 file size 8864804 SRR6958420 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 SRR6958420 SRR6958420_1.fastq SRR6958420_2.fastq Input file: SRR6958420_1.fastq Paired file: SRR6958420_2.fastq trimmed: SRR6958420-trimmed-pair1.fastq, SRR6958420-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 22:43:07 2024 >> started Fri Dec 6 22:43:34 2024 >> done (26.770s) 26224154 read pairs processed; of these: 21917 ( 0.08%) short read pairs filtered out after trimming by size control 19814 ( 0.08%) empty read pairs filtered out after trimming by size control 26182423 (99.84%) read pairs available; of these: 10232264 (39.08%) trimmed read pairs available after processing 15950159 (60.92%) untrimmed read pairs available after processing Length distribution of reads after trimming: length count percentage 18 10 0.00% 19 13 0.00% 20 14 0.00% 21 15 0.00% 22 10 0.00% 23 16 0.00% 24 15 0.00% 25 16 0.00% 26 15 0.00% 27 18 0.00% 28 21 0.00% 29 16 0.00% 30 19 0.00% 31 27 0.00% 32 18 0.00% 33 23 0.00% 34 31 0.00% 35 19 0.00% 36 19 0.00% 37 32 0.00% 38 25 0.00% 39 38 0.00% 40 43 0.00% 41 40 0.00% 42 51 0.00% 43 47 0.00% 44 53 0.00% 45 61 0.00% 46 63 0.00% 47 78 0.00% 48 68 0.00% 49 97 0.00% 50 85 0.00% 51 106 0.00% 52 129 0.00% 53 109 0.00% 54 150 0.00% 55 143 0.00% 56 165 0.00% 57 185 0.00% 58 226 0.00% 59 233 0.00% 60 324 0.00% 61 341 0.00% 62 420 0.00% 63 428 0.00% 64 482 0.00% 65 549 0.00% 66 570 0.00% 67 686 0.00% 68 711 0.00% 69 850 0.00% 70 1003 0.00% 71 1128 0.00% 72 1361 0.01% 73 1480 0.01% 74 1584 0.01% 75 1867 0.01% 76 2001 0.01% 77 2310 0.01% 78 2535 0.01% 79 2941 0.01% 80 3320 0.01% 81 3860 0.01% 82 4341 0.02% 83 4957 0.02% 84 6352 0.02% 85 7535 0.03% 86 8012 0.03% 87 8734 0.03% 88 9150 0.03% 89 9955 0.04% 90 10681 0.04% 91 11485 0.04% 92 12754 0.05% 93 14000 0.05% 94 14776 0.06% 95 15748 0.06% 96 16879 0.06% 97 17925 0.07% 98 19055 0.07% 99 20548 0.08% 100 22074 0.08% 101 23323 0.09% 102 25420 0.10% 103 27375 0.10% 104 29325 0.11% 105 30286 0.12% 106 32005 0.12% 107 33421 0.13% 108 34747 0.13% 109 36349 0.14% 110 37804 0.14% 111 40351 0.15% 112 42547 0.16% 113 44751 0.17% 114 47133 0.18% 115 50022 0.19% 116 50872 0.19% 117 52189 0.20% 118 53845 0.21% 119 55442 0.21% 120 57582 0.22% 121 59723 0.23% 122 62446 0.24% 123 65086 0.25% 124 68174 0.26% 125 71026 0.27% 126 72876 0.28% 127 73977 0.28% 128 75286 0.29% 129 77486 0.30% 130 80399 0.31% 131 82930 0.32% 132 87164 0.33% 133 90256 0.34% 134 93040 0.36% 135 97797 0.37% 136 100812 0.39% 137 103630 0.40% 138 107206 0.41% 139 113530 0.43% 140 117857 0.45% 141 124924 0.48% 142 135013 0.52% 143 146253 0.56% 144 165307 0.63% 145 187473 0.72% 146 222783 0.85% 147 283930 1.08% 148 403656 1.54% 149 759234 2.90% 150 5029927 19.21% 151 15950159 60.92% 26182423 reads passed initial QC criterion=sequence-density sequence-density=0.45 sequence-density-rank=1 fanout-score=3.21 fanout-score-rank=25 prefix-density=0.49 prefix-fanout=2.9 sequence=GGTGTTGTCGAAG criterion=fanout-score sequence-density=0.01 sequence-density-rank=31 fanout-score=22.69 fanout-score-rank=1 prefix-density=0.04 prefix-fanout=3.9 sequence=CCTTGTTACGACTTCTCCTTCCTCTAAATGATAAGGTTCAATGGACTTCTCGCGACGTCGGCGGCGGCGAACCGCCCCCGTCGCCGCGATCCGAACACTTCACCGGACCATTCAATCGGTAGGAGCGACGGGCGGTGTGTACAAAGGGCAGGGACGTAGTCAACGCGAGCTGATGACTCGCGCTTACTAGGCATTCCTCGTTGAAGACCAACAATTGCAATGATCTATCCCCATCACGATGAAATTTCCCAAGATTACCCGGGCCTGTCGGCCAAGGCTATATACTCGTTGAATACATCAGTGTAGCGCGCGTGCGGCCCAGAACATCTAAGGGCATCACAGACCTGTTATTGCCTCAAACTTCCGTCGCCTAAACGGCGATAGTCCCTCTAAGAAGCTAGCTGCGGAGGGATGGCTCCGCATAGCTAGTTAGCAGGCTGAGGTCTCGTTCGTTAACGGAATTAACCAGACAAATCGCTCCACCAACTAAGAACGGCCATGCACCACCACC criterion=sequence-density sequence-density=0.33 sequence-density-rank=1 fanout-score=3.42 fanout-score-rank=23 prefix-density=0.40 prefix-fanout=2.8 sequence=CTTCGACAACACCATGGGAGGCTTCTACATCGCCCCAGCCTTCATGGACAAGCTCGTCGTCCACCTCTCCAAGAACTTCATGACCCTGCCCAACATCAAGGTGCCACTCATCTTGGGTATCTGGGGAGGCAAGGGTCAAGGAAAATCCTTCCAATGTGAGCTTGTCTTCGCCAAGATGGGCATCAACCCAATCATGATGAGTGCCGGAGAGCTGGAGAGCGGAAACGCCGGAGAGCCAGCCAAGCTGATCAGGCAGCGGTACCGTGAGGCCGCAGACTTGATCAAGAAGGGTAAGATGTGCTGCCTCTTCATCAACGATCTCGACGCTGGTGCGGGTCGGATGGGCGGGACCACCCAGTACACTGTCAACAACCAGATGGTTAACGCCACCCTGATGAACATCGCGGATGCCCCCACCAACGTGCAGCTCCCTGGGATGTACAACAAGGAGGAAAACCCCCGTGTGCCCATCATCGTCACTGGTAACGATTTCTCCACGCTCTACGCGCCA criterion=fanout-score sequence-density=0.11 sequence-density-rank=25 fanout-score=60.75 fanout-score-rank=1 prefix-density=0.55 prefix-fanout=11.7 sequence=GCCGCCGCCGCCAAGGAAGGC SRR6958420 testing PE reads STAR mapping to Ensembl genome Started job on | Dec 06 22:44:13 Started mapping on | Dec 06 22:44:14 Finished on | Dec 06 22:46:11 Mapping speed, Million of reads per hour | 805.61 Number of input reads | 26182423 Average input read length | 294 UNIQUE READS: Uniquely mapped reads number | 25223559 Uniquely mapped reads % | 96.34% Average mapped length | 294.40 Number of splices: Total | 28447123 Number of splices: Annotated (sjdb) | 26739812 Number of splices: GT/AG | 28075097 Number of splices: GC/AG | 335431 Number of splices: AT/AC | 12314 Number of splices: Non-canonical | 24281 Mismatch rate per base, % | 0.10% Deletion rate per base | 0.00% Deletion average length | 1.43 Insertion rate per base | 0.00% Insertion average length | 1.33 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 292814 % of reads mapped to multiple loci | 1.12% Number of reads mapped to too many loci | 55906 % of reads mapped to too many loci | 0.21% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 1.17% % of reads unmapped: other | 1.16% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 682529 682529 682529 N_multimapping 292814 292814 292814 N_noFeature 1158453 24533104 1381437 N_ambiguous 558707 3178 93123 UnstrandedReadsAssigned:23506399 PositiveStrandReadsAssigned:687277 NegativeStrandReadsAssigned:23748999 Dataset is classified negative stranded MeadianReadLen=151 20thPercentileLength=150 echo kmer=145 SRR6958420 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: SRR6958420-trimmed-pair1.fastq SRR6958420-trimmed-pair2.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 26,182,423 reads, 23,857,971 reads pseudoaligned [quant] estimated average fragment length: 254.894 [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,208 rounds 52973 SRR6958420.ke.tsv 35125 SRR6958420.se.tsv 88098 total ==> SRR6958420.ke.tsv <== target_id length eff_length est_counts tpm PNS24245 936 682.566 0 0 PNS24247 1044 790.106 82.6746 6.78057 PNS24249 1928 1674.11 41.004 1.58717 PNS24246 1044 790.106 82.6746 6.78057 PNS24248 1044 790.106 82.6746 6.78057 PNS24244 1471 1217.11 91.9723 4.89675 PNS24243 293 96.2583 0 0 KQK14069 1603 1349.11 2363.26 113.513 KQK14071 474 238.555 48.0673 13.0569 ==> SRR6958420.se.tsv <== BRADI_1g14170v3 2784 BRADI_1g53295v3 527 BRADI_1g59795v3 586 BRADI_1g07683v3 0 BRADI_1g00485v3 1 BRADI_1g20270v3 407 BRADI_1g74790v3 112 BRADI_1g09890v3 0 BRADI_1g77505v3 368 BRADI_1g48960v3 0 SRR6958420 completed mapping pipeline successfully