Starting /dee2/code/volunteer_pipeline.sh SRR14639611 current disk space = 3058653343744 free memory = 1377305012 SRR14639611 SRAfilesize ebfb237de4969e76a135bc60e3f782da SRR14639611.sra SRR14639611.sra file validated SRR14639611 is paired end SRR14639611 is conventional basespace SRR14639611 read1 length is 150 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR14639611_1.fastq File type Conventional base calls Encoding Sanger / Illumina 1.9 Total Sequences 4000 Sequences flagged as poor quality 0 Sequence length 150 %GC 43 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 31.57625 32.0 32.0 32.0 32.0 32.0 2 31.58375 32.0 32.0 32.0 32.0 32.0 3 35.15375 37.0 32.0 37.0 32.0 37.0 4 36.07375 37.0 37.0 37.0 32.0 37.0 5 36.35875 37.0 37.0 37.0 37.0 37.0 6 39.75775 41.0 41.0 41.0 37.0 41.0 7 39.7915 41.0 41.0 41.0 37.0 41.0 8 39.9695 41.0 41.0 41.0 37.0 41.0 9 40.10375 41.0 41.0 41.0 37.0 41.0 10-14 40.0979 41.0 41.0 41.0 37.0 41.0 15-19 40.178200000000004 41.0 41.0 41.0 37.0 41.0 20-24 40.13075 41.0 41.0 41.0 37.0 41.0 25-29 40.13955 41.0 41.0 41.0 37.0 41.0 30-34 40.11755 41.0 41.0 41.0 37.0 41.0 35-39 39.98870000000001 41.0 41.0 41.0 37.0 41.0 40-44 39.98694999999999 41.0 41.0 41.0 37.0 41.0 45-49 39.94584999999999 41.0 41.0 41.0 37.0 41.0 50-54 39.91180000000001 41.0 41.0 41.0 37.0 41.0 55-59 39.86515 41.0 41.0 41.0 37.0 41.0 60-64 39.722300000000004 41.0 41.0 41.0 37.0 41.0 65-69 39.63185 41.0 41.0 41.0 37.0 41.0 70-74 39.46745 41.0 41.0 41.0 37.0 41.0 75-79 39.04174999999999 41.0 40.2 41.0 36.0 41.0 80-84 39.5077 41.0 41.0 41.0 37.0 41.0 85-89 39.44725 41.0 41.0 41.0 37.0 41.0 90-94 39.48315 41.0 41.0 41.0 37.0 41.0 95-99 39.349549999999994 41.0 41.0 41.0 37.0 41.0 100-104 39.2885 41.0 41.0 41.0 37.0 41.0 105-109 39.1591 41.0 41.0 41.0 37.0 41.0 110-114 39.107600000000005 41.0 41.0 41.0 37.0 41.0 115-119 39.08155000000001 41.0 41.0 41.0 36.0 41.0 120-124 39.033300000000004 41.0 41.0 41.0 37.0 41.0 125-129 39.108450000000005 41.0 41.0 41.0 37.0 41.0 130-134 38.81705 41.0 41.0 41.0 34.0 41.0 135-139 38.575450000000004 41.0 41.0 41.0 32.0 41.0 140-144 38.3342 41.0 39.4 41.0 32.0 41.0 145-149 38.03775 41.0 37.0 41.0 32.0 41.0 150 37.918 41.0 37.0 41.0 32.0 41.0 >>END_MODULE >>Per tile sequence quality pass #Tile Base Mean 1101 1 0.0 1101 2 0.0 1101 3 0.0 1101 4 0.0 1101 5 0.0 1101 6 0.0 1101 7 0.0 1101 8 0.0 1101 9 0.0 1101 10-14 0.0 1101 15-19 0.0 1101 20-24 0.0 1101 25-29 0.0 1101 30-34 0.0 1101 35-39 0.0 1101 40-44 0.0 1101 45-49 0.0 1101 50-54 0.0 1101 55-59 0.0 1101 60-64 0.0 1101 65-69 0.0 1101 70-74 0.0 1101 75-79 0.0 1101 80-84 0.0 1101 85-89 0.0 1101 90-94 0.0 1101 95-99 0.0 1101 100-104 0.0 1101 105-109 0.0 1101 110-114 0.0 1101 115-119 0.0 1101 120-124 0.0 1101 125-129 0.0 1101 130-134 0.0 1101 135-139 0.0 1101 140-144 0.0 1101 145-149 0.0 1101 150 0.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 21 2.0 22 0.0 23 1.0 24 2.0 25 4.0 26 4.0 27 13.0 28 15.0 29 28.0 30 28.0 31 35.0 32 43.0 33 51.0 34 70.0 35 91.0 36 113.0 37 166.0 38 278.0 39 545.0 40 2511.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 33.675 13.5 13.15 39.675 2 14.774999999999999 12.9 42.325 30.0 3 15.525 18.35 29.9 36.225 4 21.275 26.25 25.4 27.075 5 23.275000000000002 32.875 25.85 18.0 6 16.375 32.550000000000004 29.75 21.325 7 16.625 27.224999999999998 38.25 17.9 8 13.750000000000002 25.15 38.625 22.475 9 16.1 26.174999999999997 34.325 23.400000000000002 10-14 18.845 28.57 28.705000000000002 23.880000000000003 15-19 19.075 28.915000000000003 27.92 24.09 20-24 19.189999999999998 28.904999999999998 28.044999999999998 23.86 25-29 19.29 28.925 27.865000000000002 23.919999999999998 30-34 19.81 28.555000000000003 28.115000000000002 23.52 35-39 19.835 28.665000000000003 27.925 23.575 40-44 20.080000000000002 28.610000000000003 27.644999999999996 23.665 45-49 19.814999999999998 28.275 28.205000000000002 23.705000000000002 50-54 19.400000000000002 28.73 27.85 24.02 55-59 20.175 28.42 27.665 23.74 60-64 19.345000000000002 28.744999999999997 27.445000000000004 24.465 65-69 19.42 28.64 28.115000000000002 23.825 70-74 20.53 27.975 27.72 23.775 75-79 20.185 28.03 27.845 23.94 80-84 20.16 28.21 27.665 23.965 85-89 19.950000000000003 28.060000000000002 28.07 23.919999999999998 90-94 20.45 27.765 27.725 24.060000000000002 95-99 19.63 28.634999999999998 27.529999999999998 24.205 100-104 20.195 27.67 28.035 24.099999999999998 105-109 20.15701570157016 28.862886288628864 27.27272727272727 23.707370737073706 110-114 20.119999999999997 27.894999999999996 27.894999999999996 24.09 115-119 20.549999999999997 28.525 28.075 22.85 120-124 20.65 27.66 27.82 23.87 125-129 20.645 27.694999999999997 27.465 24.195 130-134 20.015 27.905 28.21 23.87 135-139 20.925 27.195000000000004 27.615000000000002 24.265 140-144 20.612061206120615 27.51775177517752 27.71777177717772 24.152415241524153 145-149 20.035 28.02 27.825 24.12 150 20.75 26.424999999999997 28.725 24.099999999999998 >>END_MODULE >>Per sequence GC content pass #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 0.5 8 0.5 9 0.5 10 0.5 11 0.5 12 0.5 13 0.5 14 0.5 15 0.5 16 0.5 17 1.0 18 0.5 19 0.5 20 1.0 21 1.0 22 4.5 23 5.0 24 3.0 25 3.5 26 5.0 27 10.0 28 10.5 29 16.0 30 21.0 31 21.5 32 36.5 33 51.0 34 59.5 35 80.0 36 99.5 37 120.5 38 144.5 39 171.0 40 200.5 41 217.0 42 252.0 43 269.5 44 262.5 45 271.0 46 257.0 47 239.0 48 210.5 49 162.0 50 141.5 51 119.0 52 100.0 53 89.0 54 69.5 55 60.5 56 48.0 57 36.5 58 29.0 59 22.0 60 20.5 61 16.0 62 8.0 63 4.0 64 4.0 65 5.5 66 5.5 67 4.5 68 3.0 69 1.0 70 0.0 71 0.0 72 0.0 73 0.0 74 0.0 75 0.0 76 0.0 77 0.0 78 0.0 79 0.0 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 0.01 110-114 0.0 115-119 0.0 120-124 0.0 125-129 0.0 130-134 0.0 135-139 0.0 140-144 0.01 145-149 0.0 150 0.0 >>END_MODULE >>Sequence Length Distribution pass #Length Count 150 4000.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 95.325 #Duplication Level Percentage of deduplicated Percentage of total 1 95.3842119066352 90.925 2 4.327301337529504 8.25 3 0.2884867558353003 0.8250000000000001 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 0.025 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 0.037500000000000006 0.0 0.0 0.0 0.0 94-95 0.05 0.0 0.0 0.0 0.0 96-97 0.05 0.0 0.0 0.0 0.0 98-99 0.0625 0.0 0.0 0.0 0.0 100-101 0.075 0.0 0.0 0.0 0.0 102-103 0.075 0.0 0.0 0.0 0.0 104-105 0.0875 0.0 0.0 0.0 0.0 106-107 0.1 0.0 0.0 0.0 0.0 108-109 0.1 0.0 0.0 0.0 0.0 110-111 0.1 0.0 0.0 0.0 0.0 112-113 0.1 0.0 0.0 0.0 0.0 114-115 0.1 0.0 0.0 0.0 0.0 116-117 0.125 0.0 0.0 0.0 0.0 118-119 0.1375 0.0 0.0 0.0 0.0 120-121 0.16249999999999998 0.0 0.0 0.0 0.0 122-123 0.175 0.0 0.0 0.0 0.0 124-125 0.175 0.0 0.0 0.0 0.0 126-127 0.175 0.0 0.0 0.0 0.0 128-129 0.175 0.0 0.0 0.0 0.0 130-131 0.175 0.0 0.0 0.0 0.0 132-133 0.2 0.0 0.0 0.0 0.0 134-135 0.21250000000000002 0.0 0.0 0.0 0.0 136-137 0.25 0.0 0.0 0.0 0.0 138 0.25 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position CACAGAT 10 0.006973645 144.0 1 >>END_MODULE SRR14639611 read2 length is 150 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR14639611_2.fastq File type Conventional base calls Encoding Sanger / Illumina 1.9 Total Sequences 4000 Sequences flagged as poor quality 0 Sequence length 150 %GC 44 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 30.74 32.0 32.0 32.0 32.0 32.0 2 30.6625 32.0 32.0 32.0 27.0 32.0 3 33.575 37.0 32.0 37.0 27.0 37.0 4 34.695 37.0 37.0 37.0 32.0 37.0 5 35.09 37.0 37.0 37.0 32.0 37.0 6 37.9295 41.0 37.0 41.0 32.0 41.0 7 37.99975 41.0 37.0 41.0 32.0 41.0 8 38.059 41.0 37.0 41.0 32.0 41.0 9 38.3225 41.0 41.0 41.0 32.0 41.0 10-14 38.3069 41.0 41.0 41.0 32.0 41.0 15-19 38.053250000000006 41.0 39.4 41.0 29.0 41.0 20-24 37.8497 41.0 37.0 41.0 27.0 41.0 25-29 37.64315 41.0 37.0 41.0 28.0 41.0 30-34 37.529849999999996 41.0 37.0 41.0 27.0 41.0 35-39 37.41175 41.0 37.0 41.0 27.0 41.0 40-44 37.2475 41.0 37.0 41.0 27.0 41.0 45-49 37.09845 41.0 37.0 41.0 27.0 41.0 50-54 36.89445 41.0 37.0 41.0 25.0 41.0 55-59 36.915499999999994 41.0 37.0 41.0 27.0 41.0 60-64 36.9015 41.0 37.0 41.0 27.0 41.0 65-69 36.59779999999999 41.0 37.0 41.0 23.0 41.0 70-74 36.348349999999996 41.0 37.0 41.0 22.0 41.0 75-79 35.490899999999996 40.2 34.0 41.0 22.0 41.0 80-84 36.523849999999996 41.0 37.0 41.0 22.0 41.0 85-89 36.570550000000004 41.0 37.0 41.0 22.0 41.0 90-94 36.11895 41.0 37.0 41.0 22.0 41.0 95-99 36.2766 41.0 37.0 41.0 22.0 41.0 100-104 35.934549999999994 41.0 36.0 41.0 20.0 41.0 105-109 35.89795 41.0 36.0 41.0 22.0 41.0 110-114 35.81885 41.0 34.0 41.0 22.0 41.0 115-119 35.458000000000006 41.0 33.0 41.0 20.0 41.0 120-124 35.432 41.0 32.0 41.0 20.0 41.0 125-129 34.9186 41.0 32.0 41.0 18.0 41.0 130-134 34.88865 41.0 32.0 41.0 18.0 41.0 135-139 34.5227 40.2 31.0 41.0 16.0 41.0 140-144 34.103 37.0 32.0 41.0 12.0 41.0 145-149 33.823449999999994 37.0 31.0 41.0 12.0 41.0 150 33.5765 37.0 27.0 41.0 12.0 41.0 >>END_MODULE >>Per tile sequence quality pass #Tile Base Mean 1101 1 0.0 1101 2 0.0 1101 3 0.0 1101 4 0.0 1101 5 0.0 1101 6 0.0 1101 7 0.0 1101 8 0.0 1101 9 0.0 1101 10-14 0.0 1101 15-19 0.0 1101 20-24 0.0 1101 25-29 0.0 1101 30-34 0.0 1101 35-39 0.0 1101 40-44 0.0 1101 45-49 0.0 1101 50-54 0.0 1101 55-59 0.0 1101 60-64 0.0 1101 65-69 0.0 1101 70-74 0.0 1101 75-79 0.0 1101 80-84 0.0 1101 85-89 0.0 1101 90-94 0.0 1101 95-99 0.0 1101 100-104 0.0 1101 105-109 0.0 1101 110-114 0.0 1101 115-119 0.0 1101 120-124 0.0 1101 125-129 0.0 1101 130-134 0.0 1101 135-139 0.0 1101 140-144 0.0 1101 145-149 0.0 1101 150 0.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 14 2.0 15 1.0 16 11.0 17 16.0 18 23.0 19 28.0 20 32.0 21 26.0 22 41.0 23 29.0 24 43.0 25 49.0 26 67.0 27 53.0 28 74.0 29 84.0 30 89.0 31 98.0 32 105.0 33 128.0 34 158.0 35 173.0 36 188.0 37 266.0 38 329.0 39 599.0 40 1288.0 >>END_MODULE >>Per base sequence content warn #Base G A T C 1 33.08289506636614 26.646631605309288 12.121212121212121 28.149261207112446 2 17.549999999999997 26.775 37.75 17.925 3 16.25 25.575 36.225 21.95 4 21.3 32.625 25.025 21.05 5 21.975 38.05 23.175 16.8 6 18.2 35.65 26.875 19.275000000000002 7 20.175 22.900000000000002 36.15 20.775 8 15.950000000000001 23.625 34.075 26.35 9 19.35 25.7 31.125000000000004 23.825 10-14 22.28 27.915 27.384999999999998 22.42 15-19 21.555 27.525 28.535 22.384999999999998 20-24 21.89 28.249999999999996 28.060000000000002 21.8 25-29 21.37 28.035 28.244999999999997 22.35 30-34 22.2 27.355 28.294999999999998 22.15 35-39 22.095000000000002 27.439999999999998 28.255000000000003 22.21 40-44 21.97 28.065 28.125 21.84 45-49 22.25 27.525 28.1 22.125 50-54 21.72 28.845 27.889999999999997 21.545 55-59 22.845 27.935 27.97 21.25 60-64 22.57 27.805000000000003 28.189999999999998 21.435000000000002 65-69 23.435 27.715 27.265 21.584999999999997 70-74 22.93 28.060000000000002 27.66 21.349999999999998 75-79 22.52 27.68 27.950000000000003 21.85 80-84 22.939999999999998 28.050000000000004 27.36 21.65 85-89 22.84 27.865000000000002 27.755000000000003 21.54 90-94 23.26 28.294999999999998 27.125 21.32 95-99 23.11 28.055000000000003 27.700000000000003 21.135 100-104 22.95 27.544999999999998 27.845 21.66 105-109 22.975 27.735 27.915 21.375 110-114 22.98 27.805000000000003 27.96 21.255 115-119 23.477347734773478 27.86278627862786 27.20772077207721 21.45214521452145 120-124 23.3 27.634999999999998 28.005000000000003 21.060000000000002 125-129 23.335 27.755000000000003 27.1 21.81 130-134 23.215 27.615000000000002 27.889999999999997 21.279999999999998 135-139 22.945 27.67 27.525 21.86 140-144 23.305 27.339999999999996 27.834999999999997 21.52 145-149 23.425 27.88 27.395000000000003 21.3 150 21.925 27.575 28.599999999999998 21.9 >>END_MODULE >>Per sequence GC content pass #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 0.5 13 0.5 14 0.0 15 0.0 16 0.5 17 2.0 18 2.5 19 1.0 20 1.5 21 3.0 22 1.5 23 0.5 24 1.0 25 5.0 26 11.0 27 10.5 28 11.5 29 15.0 30 17.5 31 28.0 32 39.0 33 40.0 34 45.5 35 74.0 36 95.0 37 114.5 38 159.5 39 174.0 40 174.0 41 229.5 42 254.0 43 247.5 44 260.0 45 276.5 46 248.0 47 216.5 48 223.0 49 192.0 50 161.0 51 127.0 52 100.5 53 85.5 54 66.0 55 59.5 56 52.0 57 39.0 58 28.0 59 22.5 60 17.5 61 13.0 62 11.0 63 10.0 64 7.5 65 5.0 66 4.5 67 3.0 68 2.0 69 1.5 70 1.0 71 1.0 72 0.5 73 0.5 74 0.5 75 1.0 76 1.0 77 0.5 78 1.0 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 0.17500000000000002 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 0.01 120-124 0.0 125-129 0.0 130-134 0.0 135-139 0.0 140-144 0.0 145-149 0.0 150 0.0 >>END_MODULE >>Sequence Length Distribution pass #Length Count 150 4000.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 96.15 #Duplication Level Percentage of deduplicated Percentage of total 1 96.20384815392615 92.5 2 3.58814352574103 6.9 3 0.20800832033281333 0.6 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 0.025 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 0.037500000000000006 0.0 0.0 0.0 0.0 94-95 0.05 0.0 0.0 0.0 0.0 96-97 0.05 0.0 0.0 0.0 0.0 98-99 0.0625 0.0 0.0 0.0 0.0 100-101 0.075 0.0 0.0 0.0 0.0 102-103 0.075 0.0 0.0 0.0 0.0 104-105 0.1125 0.0 0.0 0.0 0.0 106-107 0.125 0.0 0.0 0.0 0.0 108-109 0.125 0.0 0.0 0.0 0.0 110-111 0.125 0.0 0.0 0.0 0.0 112-113 0.125 0.0 0.0 0.0 0.0 114-115 0.125 0.0 0.0 0.0 0.0 116-117 0.125 0.0 0.0 0.0 0.0 118-119 0.1375 0.0 0.0 0.0 0.0 120-121 0.16249999999999998 0.0 0.0 0.0 0.0 122-123 0.1875 0.0 0.0 0.0 0.0 124-125 0.2 0.0 0.0 0.0 0.0 126-127 0.2 0.0 0.0 0.0 0.0 128-129 0.2 0.0 0.0 0.0 0.0 130-131 0.2 0.0 0.0 0.0 0.0 132-133 0.225 0.0 0.0 0.0 0.0 134-135 0.2375 0.0 0.0 0.0 0.0 136-137 0.25 0.0 0.0 0.0 0.0 138 0.275 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content pass >>END_MODULE Read 1209571 spots for SRR14639611.sra Written 1209571 spots for SRR14639611.sra Read 1209571 spots for SRR14639611.sra Written 1209571 spots for SRR14639611.sra Read 1209571 spots for SRR14639611.sra Written 1209571 spots for SRR14639611.sra Read 1209571 spots for SRR14639611.sra Written 1209571 spots for SRR14639611.sra Read 1209571 spots for SRR14639611.sra Written 1209571 spots for SRR14639611.sra Read 1209571 spots for SRR14639611.sra Written 1209571 spots for SRR14639611.sra Read 1209571 spots for SRR14639611.sra Written 1209571 spots for SRR14639611.sra Read 1209571 spots for SRR14639611.sra Written 1209571 spots for SRR14639611.sra Read 1209571 spots for SRR14639611.sra Written 1209571 spots for SRR14639611.sra Read 1209571 spots for SRR14639611.sra Written 1209571 spots for SRR14639611.sra Read 1209571 spots for SRR14639611.sra Written 1209571 spots for SRR14639611.sra Read 1209571 spots for SRR14639611.sra Written 1209571 spots for SRR14639611.sra Read 1209571 spots for SRR14639611.sra Written 1209571 spots for SRR14639611.sra Read 1209571 spots for SRR14639611.sra Written 1209571 spots for SRR14639611.sra Read 1209571 spots for SRR14639611.sra Written 1209571 spots for SRR14639611.sra Read 1209571 spots for SRR14639611.sra Written 1209571 spots for SRR14639611.sra Read 1209571 spots for SRR14639611.sra Written 1209571 spots for SRR14639611.sra Read 1209571 spots for SRR14639611.sra Written 1209571 spots for SRR14639611.sra Read 1209571 spots for SRR14639611.sra Written 1209571 spots for SRR14639611.sra Read 1209571 spots for SRR14639611.sra Written 1209571 spots for SRR14639611.sra SRR ids: ['SRR14639611.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_4msd_hkh SRR14639611.sra spots: 24191420 blocks: [[1, 1209571], [1209572, 2419142], [2419143, 3628713], [3628714, 4838284], [4838285, 6047855], [6047856, 7257426], [7257427, 8466997], [8466998, 9676568], [9676569, 10886139], [10886140, 12095710], [12095711, 13305281], [13305282, 14514852], [14514853, 15724423], [15724424, 16933994], [16933995, 18143565], [18143566, 19353136], [19353137, 20562707], [20562708, 21772278], [21772279, 22981849], [22981850, 24191420]] SRR14639611 file size 8955471 SRR14639611 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 SRR14639611 SRR14639611_1.fastq SRR14639611_2.fastq Input file: SRR14639611_1.fastq Paired file: SRR14639611_2.fastq trimmed: SRR14639611-trimmed-pair1.fastq, SRR14639611-trimmed-pair2.fastq Parameters used: -- 3' end adapter sequence (-x): AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC -- paired 3' end adapter sequence (-y): AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTA -- maximum error ratio allowed (-r): 0.100 -- maximum indel error ratio allowed (-d): 0.030 -- end quality threshold (-q): 10 -- minimum read length allowed after trimming (-l): 18 -- file format (-f): Sanger/Illumina 1.8+ FASTQ -- number of concurrent threads (-t): 20 Mon Feb 10 12:38:08 2025 >> started Mon Feb 10 12:38:36 2025 >> done (27.521s) 24191420 read pairs processed; of these: 80 ( 0.00%) short read pairs filtered out after trimming by size control 31 ( 0.00%) empty read pairs filtered out after trimming by size control 24191309 (100.00%) read pairs available; of these: 539840 ( 2.23%) trimmed read pairs available after processing 23651469 (97.77%) untrimmed read pairs available after processing Length distribution of reads after trimming: length count percentage 18 20 0.00% 19 13 0.00% 20 10 0.00% 21 23 0.00% 22 6 0.00% 23 29 0.00% 24 24 0.00% 25 19 0.00% 26 18 0.00% 27 22 0.00% 28 21 0.00% 29 27 0.00% 30 36 0.00% 31 40 0.00% 32 34 0.00% 33 30 0.00% 34 31 0.00% 35 40 0.00% 36 51 0.00% 37 36 0.00% 38 55 0.00% 39 50 0.00% 40 50 0.00% 41 59 0.00% 42 65 0.00% 43 57 0.00% 44 70 0.00% 45 56 0.00% 46 70 0.00% 47 72 0.00% 48 66 0.00% 49 44 0.00% 50 80 0.00% 51 71 0.00% 52 70 0.00% 53 63 0.00% 54 89 0.00% 55 108 0.00% 56 100 0.00% 57 96 0.00% 58 89 0.00% 59 92 0.00% 60 123 0.00% 61 103 0.00% 62 100 0.00% 63 125 0.00% 64 140 0.00% 65 132 0.00% 66 143 0.00% 67 165 0.00% 68 167 0.00% 69 188 0.00% 70 192 0.00% 71 185 0.00% 72 208 0.00% 73 220 0.00% 74 224 0.00% 75 233 0.00% 76 237 0.00% 77 251 0.00% 78 333 0.00% 79 291 0.00% 80 297 0.00% 81 353 0.00% 82 347 0.00% 83 342 0.00% 84 406 0.00% 85 420 0.00% 86 459 0.00% 87 441 0.00% 88 433 0.00% 89 488 0.00% 90 493 0.00% 91 487 0.00% 92 576 0.00% 93 511 0.00% 94 593 0.00% 95 634 0.00% 96 670 0.00% 97 705 0.00% 98 731 0.00% 99 776 0.00% 100 774 0.00% 101 883 0.00% 102 877 0.00% 103 987 0.00% 104 925 0.00% 105 1030 0.00% 106 1041 0.00% 107 1081 0.00% 108 1118 0.00% 109 1182 0.00% 110 1194 0.00% 111 1359 0.01% 112 1355 0.01% 113 1333 0.01% 114 1409 0.01% 115 1479 0.01% 116 1588 0.01% 117 1722 0.01% 118 1823 0.01% 119 1837 0.01% 120 1781 0.01% 121 1929 0.01% 122 2088 0.01% 123 2111 0.01% 124 2197 0.01% 125 2290 0.01% 126 2336 0.01% 127 2451 0.01% 128 2510 0.01% 129 2662 0.01% 130 2605 0.01% 131 2698 0.01% 132 2720 0.01% 133 2828 0.01% 134 2965 0.01% 135 3002 0.01% 136 3055 0.01% 137 3162 0.01% 138 3369 0.01% 139 3315 0.01% 140 3528 0.01% 141 3585 0.01% 142 3686 0.02% 143 3806 0.02% 144 4048 0.02% 145 4246 0.02% 146 4870 0.02% 147 7893 0.03% 148 27188 0.11% 149 383895 1.59% 150 23651469 97.77% 24191309 reads passed initial QC criterion=sequence-density sequence-density=0.27 sequence-density-rank=1 fanout-score=3.77 fanout-score-rank=19 prefix-density=0.33 prefix-fanout=3.1 sequence=GTTTTCTCATTTGCA criterion=fanout-score sequence-density=0.01 sequence-density-rank=31 fanout-score=174.08 fanout-score-rank=1 prefix-density=0.16 prefix-fanout=14.5 sequence=CTCCTTCCTCTAAATGATAAGGTTCAGTGGACTTCTCGCGACGTCGCCGGCGGCGAACCGCCCACGTCGCCGCGATCCGAACACTTCACCGGACCATTCAATCGGTAGGAGCGACGGGCGGTGTGTACAAAGGGCAGGGACGTAGTCAACGCGAGCTGATGACTCGCGCTTACTAGGAATTCCTCGTTGAAGACCAACAATTGCAATGATCTATCCCCATCACGATGAAATTTCAAAGATTACCCGGGCCTGTCGGCCAAGGCTATAGACTCGTTGAATACATCAGTGTAGCGCGCGTGCGGCCCAGAACATCTAAGGGCATCACAGACCTGTTATTGCCTCAAACTTCCTTGGCCTGGAAGGCCATAGTCCCTCTAAGAAGCTGGCCGCGGAGGGTCACCTCCGCATAGCTAGTTAGCAGGCTGAGGTCTCGTTCGTTAACGGAATTAACCAGACAAATCGCTCCACCAACT criterion=sequence-density sequence-density=0.36 sequence-density-rank=1 fanout-score=4.49 fanout-score-rank=15 prefix-density=0.49 prefix-fanout=3.3 sequence=CTGCAAATGTGG criterion=fanout-score sequence-density=0.09 sequence-density-rank=22 fanout-score=125.25 fanout-score-rank=1 prefix-density=0.51 prefix-fanout=22.4 sequence=TCTCTCTCTCTA SRR14639611 testing PE reads STAR mapping to Ensembl genome Started job on | Feb 10 12:39:29 Started mapping on | Feb 10 12:39:29 Finished on | Feb 10 12:45:20 Mapping speed, Million of reads per hour | 248.12 Number of input reads | 24191309 Average input read length | 299 UNIQUE READS: Uniquely mapped reads number | 20977526 Uniquely mapped reads % | 86.72% Average mapped length | 297.00 Number of splices: Total | 17722872 Number of splices: Annotated (sjdb) | 17352026 Number of splices: GT/AG | 17428248 Number of splices: GC/AG | 218990 Number of splices: AT/AC | 15623 Number of splices: Non-canonical | 60011 Mismatch rate per base, % | 0.61% Deletion rate per base | 0.03% Deletion average length | 3.01 Insertion rate per base | 0.02% Insertion average length | 2.60 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 644567 % of reads mapped to multiple loci | 2.66% Number of reads mapped to too many loci | 163790 % of reads mapped to too many loci | 0.68% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 9.64% % of reads unmapped: other | 0.30% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 2569216 2569216 2569216 N_multimapping 644567 644567 644567 N_noFeature 644536 20792563 724566 N_ambiguous 265889 1621 160061 UnstrandedReadsAssigned:20067101 PositiveStrandReadsAssigned:183342 NegativeStrandReadsAssigned:20092899 Dataset is classified negative stranded MeadianReadLen=150 20thPercentileLength=150 echo kmer=145 SRR14639611 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: 52,400 [index] number of k-mers: 62,057,036 [index] number of equivalence classes: 130,681 [quant] running in paired-end mode [quant] will process pair 1: SRR14639611-trimmed-pair1.fastq SRR14639611-trimmed-pair2.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 24,191,309 reads, 20,675,615 reads pseudoaligned [quant] estimated average fragment length: 388.333 [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 991 rounds 52401 SRR14639611.ke.tsv 34699 SRR14639611.se.tsv 87100 total ==> SRR14639611.ke.tsv <== target_id length eff_length est_counts tpm Potri.005G200100.1.v4.1 2018 1630.67 3922 100.935 Potri.005G024800.1.v4.1 1035 647.667 720 46.6532 Potri.004G059700.1.v4.1 961 574.214 263 19.2213 Potri.007G009000.2.v4.1 1416 1028.67 0 0 Potri.003G141000.2.v4.1 2943 2555.67 1113 18.2764 Potri.016G087400.1.v4.1 270 48.5524 1294.72 1119.09 Potri.015G069301.1.v4.1 564 212.698 0 0 Potri.010G195200.1.v4.1 1773 1385.67 56 1.69601 Potri.012G127500.1.v4.1 977 589.996 2715 193.117 ==> SRR14639611.se.tsv <== Potri.001G166300.v4.1 0 Potri.001G448400.v4.1 21 Potri.001G233950.v4.1 0 Potri.001G122700.v4.1 241 Potri.001G212900.v4.1 0 Potri.001G182400.v4.1 0 Potri.001G256600.v4.1 0 Potri.001G040500.v4.1 9 Potri.001G416900.v4.1 0 Potri.001G452600.v4.1 343 SRR14639611 completed mapping pipeline successfully