Starting /dee2/code/volunteer_pipeline.sh SRR7172117 current disk space = 3085593608192 free memory = 1449510492 SRR7172117 SRAfilesize e1360085946796cb845e4a642edc203e SRR7172117.sra SRR7172117.sra file validated SRR7172117 is paired end SRR7172117 is conventional basespace SRR7172117 read1 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR7172117_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 43 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 32.8595 33.0 33.0 34.0 32.0 34.0 2 33.1095 34.0 33.0 34.0 32.0 34.0 3 33.1665 34.0 33.0 34.0 32.0 34.0 4 32.70375 33.0 33.0 34.0 32.0 34.0 5 33.09275 34.0 33.0 34.0 32.0 34.0 6 37.15975 38.0 37.0 38.0 36.0 38.0 7 37.41925 38.0 38.0 38.0 37.0 38.0 8 37.57825 38.0 38.0 38.0 37.0 38.0 9 37.512 38.0 38.0 38.0 38.0 38.0 10-14 37.276050000000005 38.0 38.0 38.0 37.2 38.0 15-19 37.493249999999996 38.0 38.0 38.0 37.8 38.0 20-24 37.4407 38.0 38.0 38.0 37.4 38.0 25-29 37.3841 38.0 38.0 38.0 37.0 38.0 30-34 37.4083 38.0 38.0 38.0 37.4 38.0 35-39 37.2907 38.0 38.0 38.0 37.0 38.0 40-44 37.25465 38.0 38.0 38.0 37.0 38.0 45-49 36.9246 38.0 38.0 38.0 35.6 38.0 50-54 37.24345 38.0 38.0 38.0 36.8 38.0 55-59 37.32375 38.0 38.0 38.0 37.0 38.0 60-64 37.3046 38.0 38.0 38.0 37.0 38.0 65-69 37.2315 38.0 38.0 38.0 37.0 38.0 70-74 37.12405 38.0 38.0 38.0 36.2 38.0 75-79 36.981449999999995 38.0 38.0 38.0 36.0 38.0 80-84 37.02025 38.0 38.0 38.0 36.0 38.0 85-89 36.89105 38.0 38.0 38.0 35.6 38.0 90-94 36.828500000000005 38.0 38.0 38.0 35.2 38.0 95-99 36.72625 38.0 38.0 38.0 35.0 38.0 100-104 36.731750000000005 38.0 38.0 38.0 34.8 38.0 105-109 36.54445 38.0 38.0 38.0 34.0 38.0 110-114 36.43085000000001 38.0 38.0 38.0 34.0 38.0 115-119 36.24855 38.0 37.6 38.0 33.8 38.0 120-124 36.09734999999999 38.0 37.4 38.0 33.4 38.0 125-129 35.88665 38.0 36.8 38.0 32.8 38.0 130-134 35.5834 38.0 36.2 38.0 31.4 38.0 135-139 35.20145 38.0 36.0 38.0 31.0 38.0 140-144 34.75185 38.0 35.2 38.0 28.0 38.0 145-149 34.0233 38.0 34.8 38.0 24.8 38.0 150-151 28.970125 35.5 25.5 38.0 2.0 38.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 5 1.0 6 0.0 7 0.0 8 0.0 9 1.0 10 0.0 11 0.0 12 0.0 13 0.0 14 1.0 15 0.0 16 1.0 17 2.0 18 1.0 19 3.0 20 2.0 21 5.0 22 5.0 23 4.0 24 6.0 25 9.0 26 14.0 27 19.0 28 22.0 29 35.0 30 30.0 31 69.0 32 70.0 33 85.0 34 150.0 35 252.0 36 615.0 37 2598.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 31.574999999999996 15.9 15.975 36.55 2 20.0 23.225 37.925 18.85 3 18.7 29.575000000000003 26.424999999999997 25.3 4 20.674999999999997 36.025 22.225 21.075 5 20.525 38.7 22.825 17.95 6 16.575 36.9 24.625 21.9 7 12.8 19.25 46.225 21.725 8 17.7 20.625 29.075 32.6 9 18.925 21.75 31.075000000000003 28.249999999999996 10-14 19.258775674182697 30.392206096519864 26.289358710390196 24.059659518907246 15-19 19.675 28.74 27.529999999999998 24.055 20-24 19.54 28.88 27.295 24.285 25-29 19.675 29.054999999999996 27.61 23.66 30-34 19.61 28.854999999999997 27.845 23.69 35-39 20.27 28.23 27.650000000000002 23.849999999999998 40-44 20.349999999999998 28.735 27.834999999999997 23.080000000000002 45-49 19.744999999999997 28.249999999999996 27.950000000000003 24.055 50-54 19.715 28.625 28.185 23.474999999999998 55-59 19.665 29.020000000000003 27.41 23.905 60-64 20.055 28.599999999999998 27.265 24.08 65-69 20.02 28.970000000000002 27.865000000000002 23.145 70-74 20.044999999999998 29.255 27.384999999999998 23.315 75-79 20.06 28.595 27.54 23.805 80-84 20.36 28.23 28.08 23.330000000000002 85-89 20.064999999999998 28.48 28.02 23.435 90-94 20.335 27.765 28.38 23.52 95-99 20.115 28.77 27.744999999999997 23.369999999999997 100-104 20.26 27.83 28.360000000000003 23.549999999999997 105-109 20.405 27.884999999999998 28.17 23.54 110-114 20.712249287250536 28.810083529235232 26.98944630620717 23.488220877307057 115-119 20.49 28.455000000000002 27.644999999999996 23.41 120-124 20.505252626313155 28.47423711855928 27.243621810905456 23.77688844422211 125-129 20.382516397136133 28.45841886546838 27.316877785009762 23.84218695238572 130-134 20.91 28.285 27.32 23.485 135-139 21.0 28.299999999999997 26.93 23.77 140-144 20.849999999999998 28.465 26.71 23.974999999999998 145-149 20.885 28.754999999999995 26.8 23.56 150-151 20.3 28.237499999999997 26.9125 24.55 >>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 0.0 13 0.0 14 0.5 15 0.5 16 0.0 17 0.0 18 0.5 19 1.0 20 0.5 21 0.5 22 2.0 23 3.0 24 4.0 25 4.5 26 6.5 27 8.0 28 10.0 29 12.0 30 18.5 31 30.0 32 40.5 33 49.0 34 57.5 35 80.0 36 95.0 37 121.5 38 155.5 39 179.5 40 220.5 41 227.0 42 240.0 43 260.5 44 258.5 45 266.5 46 251.5 47 231.5 48 220.0 49 184.5 50 154.5 51 132.0 52 102.5 53 85.5 54 63.0 55 49.5 56 44.0 57 30.5 58 24.0 59 19.0 60 12.5 61 9.0 62 6.0 63 6.0 64 6.0 65 5.5 66 4.5 67 2.0 68 0.5 69 1.0 70 1.0 71 0.5 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 0.43499999999999994 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 0.034999999999999996 115-119 0.0 120-124 0.05 125-129 0.135 130-134 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 99.8 #Duplication Level Percentage of deduplicated Percentage of total 1 99.8246492985972 99.625 2 0.15030060120240482 0.3 3 0.0250501002004008 0.075 4 0.0 0.0 5 0.0 0.0 6 0.0 0.0 7 0.0 0.0 8 0.0 0.0 9 0.0 0.0 >10 0.0 0.0 >50 0.0 0.0 >100 0.0 0.0 >500 0.0 0.0 >1k 0.0 0.0 >5k 0.0 0.0 >10k+ 0.0 0.0 >>END_MODULE >>Overrepresented sequences pass >>END_MODULE >>Adapter Content warn #Position Illumina Universal Adapter Illumina Small RNA 3' Adapter Illumina Small RNA 5' Adapter Nextera Transposase Sequence SOLID Small RNA Adapter 1 0.025 0.0 0.0 0.0 0.0 2 0.025 0.0 0.0 0.0 0.0 3 0.025 0.0 0.0 0.0 0.0 4 0.025 0.0 0.0 0.0 0.0 5 0.025 0.0 0.0 0.0 0.0 6 0.025 0.0 0.0 0.0 0.0 7 0.025 0.0 0.0 0.0 0.0 8 0.025 0.0 0.0 0.0 0.0 9 0.025 0.0 0.0 0.0 0.0 10-11 0.025 0.0 0.0 0.0 0.0 12-13 0.025 0.0 0.0 0.0 0.0 14-15 0.025 0.0 0.0 0.0 0.0 16-17 0.025 0.0 0.0 0.0 0.0 18-19 0.025 0.0 0.0 0.0 0.0 20-21 0.025 0.0 0.0 0.0 0.0 22-23 0.025 0.0 0.0 0.0 0.0 24-25 0.025 0.0 0.0 0.0 0.0 26-27 0.025 0.0 0.0 0.0 0.0 28-29 0.025 0.0 0.0 0.0 0.0 30-31 0.025 0.0 0.0 0.0 0.0 32-33 0.025 0.0 0.0 0.0 0.0 34-35 0.025 0.0 0.0 0.0 0.0 36-37 0.025 0.0 0.0 0.0 0.0 38-39 0.025 0.0 0.0 0.0 0.0 40-41 0.025 0.0 0.0 0.0 0.0 42-43 0.025 0.0 0.0 0.0 0.0 44-45 0.025 0.0 0.0 0.0 0.0 46-47 0.025 0.0 0.0 0.0 0.0 48-49 0.025 0.0 0.0 0.0 0.0 50-51 0.025 0.0 0.0 0.0 0.0 52-53 0.025 0.0 0.0 0.0 0.0 54-55 0.025 0.0 0.0 0.0 0.0 56-57 0.025 0.0 0.0 0.0 0.0 58-59 0.025 0.0 0.0 0.0 0.0 60-61 0.025 0.0 0.0 0.0 0.0 62-63 0.025 0.0 0.0 0.0 0.0 64-65 0.025 0.0 0.0 0.0 0.0 66-67 0.025 0.0 0.0 0.0 0.0 68-69 0.025 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 0.05 0.0 0.0 0.0 0.0 78-79 0.05 0.0 0.0 0.0 0.0 80-81 0.05 0.0 0.0 0.0 0.0 82-83 0.1 0.0 0.0 0.0 0.0 84-85 0.1 0.0 0.0 0.0 0.0 86-87 0.15 0.0 0.0 0.0 0.0 88-89 0.16249999999999998 0.0 0.0 0.0 0.0 90-91 0.2375 0.0 0.0 0.0 0.0 92-93 0.275 0.0 0.0 0.0 0.0 94-95 0.3375 0.0 0.0 0.0 0.0 96-97 0.4375 0.0 0.0 0.0 0.0 98-99 0.5125 0.0 0.0 0.0 0.0 100-101 0.575 0.0 0.0 0.0 0.0 102-103 0.6625000000000001 0.0 0.0 0.0 0.0 104-105 0.7375 0.0 0.0 0.0 0.0 106-107 0.8999999999999999 0.0 0.0 0.0 0.0 108-109 1.0875 0.0 0.0 0.0 0.0 110-111 1.2625000000000002 0.0 0.0 0.0 0.0 112-113 1.45 0.0 0.0 0.0 0.0 114-115 1.6625 0.0 0.0 0.0 0.0 116-117 1.8624999999999998 0.0 0.0 0.0 0.0 118-119 2.025 0.0 0.0 0.0 0.0 120-121 2.2750000000000004 0.0 0.0 0.0 0.0 122-123 2.5625 0.0 0.0 0.0 0.0 124-125 2.7625 0.0 0.0 0.0 0.0 126-127 3.0625 0.0 0.0 0.0 0.0 128-129 3.5250000000000004 0.0 0.0 0.0 0.0 130-131 3.9375 0.0 0.0 0.0 0.0 132-133 4.3625 0.0 0.0 0.0 0.0 134-135 4.825 0.0 0.0 0.0 0.0 136-137 5.25 0.0 0.0 0.0 0.0 138-139 5.7875 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content pass >>END_MODULE SRR7172117 read2 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR7172117_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 44 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 32.9855 33.0 33.0 34.0 32.0 34.0 2 33.02725 34.0 33.0 34.0 32.0 34.0 3 33.059 34.0 33.0 34.0 32.0 34.0 4 33.00675 34.0 33.0 34.0 32.0 34.0 5 33.04025 34.0 33.0 34.0 33.0 34.0 6 37.2365 38.0 38.0 38.0 37.0 38.0 7 37.26575 38.0 38.0 38.0 37.0 38.0 8 37.2855 38.0 38.0 38.0 37.0 38.0 9 37.305 38.0 38.0 38.0 37.0 38.0 10-14 37.27175 38.0 38.0 38.0 37.2 38.0 15-19 37.21825 38.0 38.0 38.0 37.0 38.0 20-24 37.1647 38.0 38.0 38.0 37.0 38.0 25-29 37.1074 38.0 38.0 38.0 37.0 38.0 30-34 37.1324 38.0 38.0 38.0 36.8 38.0 35-39 37.03915 38.0 38.0 38.0 36.4 38.0 40-44 36.99765 38.0 38.0 38.0 36.4 38.0 45-49 37.0379 38.0 38.0 38.0 36.6 38.0 50-54 37.05605 38.0 38.0 38.0 36.4 38.0 55-59 37.03025 38.0 38.0 38.0 36.4 38.0 60-64 36.9832 38.0 38.0 38.0 36.2 38.0 65-69 36.9528 38.0 38.0 38.0 36.0 38.0 70-74 36.90725 38.0 38.0 38.0 36.0 38.0 75-79 36.82745 38.0 38.0 38.0 36.0 38.0 80-84 36.70195 38.0 38.0 38.0 35.4 38.0 85-89 36.595000000000006 38.0 38.0 38.0 35.2 38.0 90-94 36.4418 38.0 38.0 38.0 34.4 38.0 95-99 36.2636 38.0 38.0 38.0 34.0 38.0 100-104 36.2365 38.0 38.0 38.0 34.0 38.0 105-109 36.179100000000005 38.0 38.0 38.0 34.0 38.0 110-114 36.180899999999994 38.0 38.0 38.0 33.8 38.0 115-119 36.0 38.0 37.8 38.0 33.4 38.0 120-124 35.74060000000001 38.0 37.2 38.0 32.4 38.0 125-129 35.5979 38.0 37.0 38.0 31.8 38.0 130-134 35.24325 38.0 36.4 38.0 31.0 38.0 135-139 34.885149999999996 38.0 36.0 38.0 28.8 38.0 140-144 34.334 38.0 35.0 38.0 25.8 38.0 145-149 33.55185 38.0 33.8 38.0 19.8 38.0 150-151 28.975125 35.5 18.5 38.0 2.0 38.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 2 3.0 3 5.0 4 2.0 5 2.0 6 1.0 7 0.0 8 0.0 9 1.0 10 2.0 11 1.0 12 4.0 13 3.0 14 1.0 15 2.0 16 2.0 17 4.0 18 3.0 19 2.0 20 11.0 21 10.0 22 6.0 23 5.0 24 12.0 25 17.0 26 18.0 27 23.0 28 25.0 29 26.0 30 55.0 31 40.0 32 68.0 33 96.0 34 145.0 35 219.0 36 558.0 37 2628.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 34.109691960931634 13.348359629351364 19.333834209867266 33.20811419984974 2 23.50288148333751 20.846905537459286 38.2610874467552 17.38912553244801 3 20.29566524680531 25.331996993234778 31.01979453770985 23.352543222250063 4 24.774549098196395 33.19138276553106 21.34268537074148 20.691382765531063 5 23.42184368737475 36.97394789579158 22.044088176352705 17.560120240480963 6 17.329332333083272 37.88447111777945 24.20605151287822 20.580145036259065 7 17.075000000000003 15.425 46.725 20.775 8 20.95 21.125 28.025 29.9 9 20.974999999999998 23.875 28.625 26.525 10-14 22.94229422942294 27.77777777777778 26.63766376637664 22.642264226422643 15-19 22.895 27.334999999999997 28.17 21.6 20-24 22.85 28.435 28.105000000000004 20.61 25-29 23.39 27.395000000000003 28.01 21.205 30-34 22.945 27.955000000000002 28.065 21.035 35-39 22.884999999999998 28.59 27.715 20.810000000000002 40-44 23.29 28.185 28.035 20.49 45-49 22.99 27.855 28.444999999999997 20.71 50-54 22.575 28.12 28.1 21.205 55-59 23.595 28.275 27.375 20.755000000000003 60-64 23.555 28.15 27.644999999999996 20.65 65-69 22.895 28.005000000000003 28.525 20.575 70-74 23.365 28.199999999999996 27.584999999999997 20.849999999999998 75-79 23.195 27.92 27.975 20.91 80-84 23.735 27.685 27.994999999999997 20.585 85-89 23.915 27.515 27.96 20.61 90-94 23.595 27.860000000000003 27.634999999999998 20.91 95-99 23.51 28.110000000000003 27.665 20.715 100-104 23.715 27.865000000000002 27.935 20.485 105-109 23.68 27.800000000000004 27.845 20.674999999999997 110-114 23.66 28.01 27.474999999999998 20.855 115-119 23.925 27.72 28.025 20.330000000000002 120-124 23.77 28.01 27.675 20.544999999999998 125-129 24.224999999999998 28.605000000000004 27.22 19.950000000000003 130-134 24.02 28.08 27.395000000000003 20.505000000000003 135-139 24.2 28.389999999999997 28.1 19.31 140-144 25.005 27.560000000000002 27.405 20.03 145-149 24.39 28.24 27.37 20.0 150-151 24.85 27.1125 29.025000000000002 19.0125 >>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 0.0 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 1.5 23 1.5 24 1.0 25 1.5 26 3.0 27 2.5 28 4.0 29 9.0 30 12.0 31 17.0 32 25.5 33 37.0 34 51.5 35 66.5 36 85.0 37 111.0 38 135.5 39 164.0 40 181.5 41 218.5 42 264.5 43 279.5 44 287.0 45 281.0 46 270.5 47 264.0 48 234.5 49 200.0 50 164.5 51 128.5 52 99.5 53 85.0 54 79.5 55 50.5 56 36.5 57 33.5 58 25.5 59 18.5 60 16.5 61 13.0 62 7.5 63 6.0 64 6.5 65 5.0 66 2.0 67 1.5 68 1.5 69 2.0 70 2.0 71 2.5 72 1.5 73 0.5 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 0.17500000000000002 2 0.22499999999999998 3 0.22499999999999998 4 0.2 5 0.2 6 0.025 7 0.0 8 0.0 9 0.0 10-14 0.01 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 99.6 #Duplication Level Percentage of deduplicated Percentage of total 1 99.62349397590361 99.225 2 0.3514056224899598 0.7000000000000001 3 0.0251004016064257 0.075 4 0.0 0.0 5 0.0 0.0 6 0.0 0.0 7 0.0 0.0 8 0.0 0.0 9 0.0 0.0 >10 0.0 0.0 >50 0.0 0.0 >100 0.0 0.0 >500 0.0 0.0 >1k 0.0 0.0 >5k 0.0 0.0 >10k+ 0.0 0.0 >>END_MODULE >>Overrepresented sequences pass >>END_MODULE >>Adapter Content warn #Position Illumina Universal Adapter Illumina Small RNA 3' Adapter Illumina Small RNA 5' Adapter Nextera Transposase Sequence SOLID Small RNA Adapter 1 0.025 0.0 0.0 0.0 0.0 2 0.025 0.0 0.0 0.0 0.0 3 0.025 0.0 0.0 0.0 0.0 4 0.025 0.0 0.0 0.0 0.0 5 0.025 0.0 0.0 0.0 0.0 6 0.025 0.0 0.0 0.0 0.0 7 0.025 0.0 0.0 0.0 0.0 8 0.025 0.0 0.0 0.0 0.0 9 0.025 0.0 0.0 0.0 0.0 10-11 0.025 0.0 0.0 0.0 0.0 12-13 0.025 0.0 0.0 0.0 0.0 14-15 0.025 0.0 0.0 0.0 0.0 16-17 0.025 0.0 0.0 0.0 0.0 18-19 0.025 0.0 0.0 0.0 0.0 20-21 0.025 0.0 0.0 0.0 0.0 22-23 0.025 0.0 0.0 0.0 0.0 24-25 0.025 0.0 0.0 0.0 0.0 26-27 0.025 0.0 0.0 0.0 0.0 28-29 0.025 0.0 0.0 0.0 0.0 30-31 0.025 0.0 0.0 0.0 0.0 32-33 0.025 0.0 0.0 0.0 0.0 34-35 0.025 0.0 0.0 0.0 0.0 36-37 0.025 0.0 0.0 0.0 0.0 38-39 0.025 0.0 0.0 0.0 0.0 40-41 0.025 0.0 0.0 0.0 0.0 42-43 0.025 0.0 0.0 0.0 0.0 44-45 0.025 0.0 0.0 0.0 0.0 46-47 0.025 0.0 0.0 0.0 0.0 48-49 0.025 0.0 0.0 0.0 0.0 50-51 0.025 0.0 0.0 0.0 0.0 52-53 0.025 0.0 0.0 0.0 0.0 54-55 0.025 0.0 0.0 0.0 0.0 56-57 0.025 0.0 0.0 0.0 0.0 58-59 0.025 0.0 0.0 0.0 0.0 60-61 0.025 0.0 0.0 0.0 0.0 62-63 0.025 0.0 0.0 0.0 0.0 64-65 0.025 0.0 0.0 0.0 0.0 66-67 0.025 0.0 0.0 0.0 0.0 68-69 0.025 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 0.05 0.0 0.0 0.0 0.0 78-79 0.05 0.0 0.0 0.0 0.0 80-81 0.05 0.0 0.0 0.0 0.0 82-83 0.1 0.0 0.0 0.0 0.0 84-85 0.1 0.0 0.0 0.0 0.0 86-87 0.15 0.0 0.0 0.0 0.0 88-89 0.16249999999999998 0.0 0.0 0.0 0.0 90-91 0.2375 0.0 0.0 0.0 0.0 92-93 0.275 0.0 0.0 0.0 0.0 94-95 0.325 0.0 0.0 0.0 0.0 96-97 0.4125 0.0 0.0 0.0 0.0 98-99 0.4875 0.0 0.0 0.0 0.0 100-101 0.55 0.0 0.0 0.0 0.0 102-103 0.6375 0.0 0.0 0.0 0.0 104-105 0.7124999999999999 0.0 0.0 0.0 0.0 106-107 0.875 0.0 0.0 0.0 0.0 108-109 1.0625 0.0 0.0 0.0 0.0 110-111 1.2374999999999998 0.0 0.0 0.0 0.0 112-113 1.425 0.0 0.0 0.0 0.0 114-115 1.6375 0.0 0.0 0.0 0.0 116-117 1.825 0.0 0.0 0.0 0.0 118-119 2.0 0.0 0.0 0.0 0.0 120-121 2.25 0.0 0.0 0.0 0.0 122-123 2.5374999999999996 0.0 0.0 0.0 0.0 124-125 2.75 0.0 0.0 0.0 0.0 126-127 3.0625 0.0 0.0 0.0 0.0 128-129 3.55 0.0 0.0 0.0 0.0 130-131 3.9625000000000004 0.0 0.0 0.0 0.0 132-133 4.375 0.0 0.0 0.0 0.0 134-135 4.825 0.0 0.0 0.0 0.0 136-137 5.25 0.0 0.0 0.0 0.0 138-139 5.7875 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content pass >>END_MODULE Read 890699 spots for SRR7172117.sra Written 890699 spots for SRR7172117.sra Read 890699 spots for SRR7172117.sra Written 890699 spots for SRR7172117.sra Read 890699 spots for SRR7172117.sra Written 890699 spots for SRR7172117.sra Read 890699 spots for SRR7172117.sra Written 890699 spots for SRR7172117.sra Read 890699 spots for SRR7172117.sra Written 890699 spots for SRR7172117.sra Read 890699 spots for SRR7172117.sra Written 890699 spots for SRR7172117.sra Read 890699 spots for SRR7172117.sra Written 890699 spots for SRR7172117.sra Read 890699 spots for SRR7172117.sra Written 890699 spots for SRR7172117.sra Read 890699 spots for SRR7172117.sra Written 890699 spots for SRR7172117.sra Read 890699 spots for SRR7172117.sra Written 890699 spots for SRR7172117.sra Read 890699 spots for SRR7172117.sra Written 890699 spots for SRR7172117.sra Read 890699 spots for SRR7172117.sra Written 890699 spots for SRR7172117.sra Read 890699 spots for SRR7172117.sra Written 890699 spots for SRR7172117.sra Read 890699 spots for SRR7172117.sra Written 890699 spots for SRR7172117.sra Read 890699 spots for SRR7172117.sra Written 890699 spots for SRR7172117.sra Read 890699 spots for SRR7172117.sra Written 890699 spots for SRR7172117.sra Read 890699 spots for SRR7172117.sra Written 890699 spots for SRR7172117.sra Read 890699 spots for SRR7172117.sra Written 890699 spots for SRR7172117.sra Read 890699 spots for SRR7172117.sra Written 890699 spots for SRR7172117.sra Read 890715 spots for SRR7172117.sra Written 890715 spots for SRR7172117.sra SRR ids: ['SRR7172117.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_5qizb3wg SRR7172117.sra spots: 17813996 blocks: [[1, 890699], [890700, 1781398], [1781399, 2672097], [2672098, 3562796], [3562797, 4453495], [4453496, 5344194], [5344195, 6234893], [6234894, 7125592], [7125593, 8016291], [8016292, 8906990], [8906991, 9797689], [9797690, 10688388], [10688389, 11579087], [11579088, 12469786], [12469787, 13360485], [13360486, 14251184], [14251185, 15141883], [15141884, 16032582], [16032583, 16923281], [16923282, 17813996]] SRR7172117 file size 6014878 SRR7172117 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 SRR7172117 SRR7172117_1.fastq SRR7172117_2.fastq Input file: SRR7172117_1.fastq Paired file: SRR7172117_2.fastq trimmed: SRR7172117-trimmed-pair1.fastq, SRR7172117-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 Feb 14 05:56:10 2025 >> started Fri Feb 14 05:56:39 2025 >> done (29.069s) 17813996 read pairs processed; of these: 15478 ( 0.09%) short read pairs filtered out after trimming by size control 16177 ( 0.09%) empty read pairs filtered out after trimming by size control 17782341 (99.82%) read pairs available; of these: 8768098 (49.31%) trimmed read pairs available after processing 9014243 (50.69%) untrimmed read pairs available after processing Length distribution of reads after trimming: length count percentage 18 3 0.00% 19 0 0.00% 20 6 0.00% 21 4 0.00% 22 8 0.00% 23 7 0.00% 24 8 0.00% 25 2 0.00% 26 3 0.00% 27 5 0.00% 28 5 0.00% 29 6 0.00% 30 4 0.00% 31 9 0.00% 32 5 0.00% 33 2 0.00% 34 3 0.00% 35 15 0.00% 36 7 0.00% 37 5 0.00% 38 11 0.00% 39 11 0.00% 40 9 0.00% 41 7 0.00% 42 13 0.00% 43 9 0.00% 44 7 0.00% 45 22 0.00% 46 20 0.00% 47 19 0.00% 48 20 0.00% 49 30 0.00% 50 28 0.00% 51 39 0.00% 52 43 0.00% 53 52 0.00% 54 37 0.00% 55 67 0.00% 56 55 0.00% 57 73 0.00% 58 95 0.00% 59 110 0.00% 60 141 0.00% 61 152 0.00% 62 168 0.00% 63 192 0.00% 64 192 0.00% 65 230 0.00% 66 293 0.00% 67 302 0.00% 68 355 0.00% 69 367 0.00% 70 424 0.00% 71 481 0.00% 72 609 0.00% 73 667 0.00% 74 767 0.00% 75 846 0.00% 76 1006 0.01% 77 1202 0.01% 78 1282 0.01% 79 1517 0.01% 80 1687 0.01% 81 1864 0.01% 82 2228 0.01% 83 2631 0.01% 84 3999 0.02% 85 4707 0.03% 86 4875 0.03% 87 5365 0.03% 88 5675 0.03% 89 5811 0.03% 90 5939 0.03% 91 6612 0.04% 92 7092 0.04% 93 7552 0.04% 94 8110 0.05% 95 8870 0.05% 96 9461 0.05% 97 10278 0.06% 98 10731 0.06% 99 12034 0.07% 100 13179 0.07% 101 13431 0.08% 102 13934 0.08% 103 15208 0.09% 104 15924 0.09% 105 16684 0.09% 106 17633 0.10% 107 18469 0.10% 108 19498 0.11% 109 20680 0.12% 110 21411 0.12% 111 22733 0.13% 112 23362 0.13% 113 24355 0.14% 114 25772 0.14% 115 27155 0.15% 116 28447 0.16% 117 29493 0.17% 118 30812 0.17% 119 32184 0.18% 120 33251 0.19% 121 34726 0.20% 122 35966 0.20% 123 37979 0.21% 124 39353 0.22% 125 41227 0.23% 126 43208 0.24% 127 44611 0.25% 128 46572 0.26% 129 48479 0.27% 130 50805 0.29% 131 53004 0.30% 132 55265 0.31% 133 58822 0.33% 134 61977 0.35% 135 65831 0.37% 136 70979 0.40% 137 74093 0.42% 138 78703 0.44% 139 86905 0.49% 140 97564 0.55% 141 102928 0.58% 142 113441 0.64% 143 126122 0.71% 144 146407 0.82% 145 173361 0.97% 146 215323 1.21% 147 289148 1.63% 148 437665 2.46% 149 869216 4.89% 150 4567205 25.68% 151 9014243 50.69% 17782341 reads passed initial QC criterion=sequence-density sequence-density=0.17 sequence-density-rank=1 fanout-score=3.55 fanout-score-rank=18 prefix-density=0.27 prefix-fanout=2.3 sequence=CATCTCAGACCTCTC criterion=fanout-score sequence-density=0.02 sequence-density-rank=33 fanout-score=116.71 fanout-score-rank=1 prefix-density=0.16 prefix-fanout=12.1 sequence=CTCCTTCCTCTAAATGATAAGGTTCAGTGGACTTCTCGCGACGTCGCCGGCGGCGAACCGCCCACGTCGCCGCGATCCGAACACTTCACCGGACCATTCAATCGGTAGGAGCGACGGGCGGTGTGTACAAAGGGCAGGGACGTAGTCAACGCGAGCTGATGACTCGCGCTTACTAGGAATTCCTCGTTGAAGACCAACAATTGCAATGATCTATCCCCATCACGATGAAATTTCAAAGATTACCCGGGCCTGTCGGCCAAGGCTATAGACTCGTTGAATACATCAGTGTAGCGCGCGTGCGGCCCAGAACATCTAAGGGCATCACAGACCTGTTATTGCCTCAAACTTCCTTGGCCTGGAAGGCCATAGTCCCTCTAAGAAGCTGGCCGCGGAGGGTCACCTCCGCATAGCTAGTTAGCAGGCTGAGGTCTCGTTCGTTAACGGAATTAACCAGACAAATCGCTCCACCAACTAAGAACGGCCATGCACCACCACCCATA criterion=sequence-density sequence-density=0.24 sequence-density-rank=1 fanout-score=2.47 fanout-score-rank=25 prefix-density=0.25 prefix-fanout=2.3 sequence=ATGTACCCTGACTT criterion=fanout-score sequence-density=0.01 sequence-density-rank=29 fanout-score=86.49 fanout-score-rank=1 prefix-density=0.07 prefix-fanout=8.5 sequence=CTTCCATTTCCGCCCAAGCTGCTCACAGTATACGGGCGTCGGCATCCAGACCGTCGGCTGATCGTGGTTTTACTAGGCTAGACTAGCGTACGAGCACTATGGTCAGTAATTCCTGGAGGAATAGGTACCAAGAAAAAAACGAACCTTTGGGTTCCAGAGCTGTACGGTCGCACTGAACTCGGATAGGTCTCAGAAAAACGAAATATAGGCTTACGGTAGGTCCGAATGGCACAAAGCTTGTTCCGTTAGCTGGCATAAGATTCCATGCCTAGATGTGATACACGTTTCTGGAAACTGCCTCGTCATGCGACTGTTCCCCGGGGTCAGGGCCGCTGGTATTTGCTGTAAAGAGGGGCGTTGAGTCCGTCCGACTTCACTGCCCCCTTTCAGCCTTTTGGGTCCTGTATCCCAATTCTCAGAGGTCCCGCCGTACGCTGAGGACCACCTGAAACGGGCATCGTCGCTCTTCGTTGTTCGTCGACTTCTAGTGTGGAGACGAATTGCCAGAATT SRR7172117 testing PE reads STAR mapping to Ensembl genome Started job on | Feb 14 05:57:28 Started mapping on | Feb 14 05:57:28 Finished on | Feb 14 06:01:03 Mapping speed, Million of reads per hour | 297.75 Number of input reads | 17782341 Average input read length | 295 UNIQUE READS: Uniquely mapped reads number | 15968613 Uniquely mapped reads % | 89.80% Average mapped length | 294.44 Number of splices: Total | 15694885 Number of splices: Annotated (sjdb) | 15408253 Number of splices: GT/AG | 15430831 Number of splices: GC/AG | 203036 Number of splices: AT/AC | 13094 Number of splices: Non-canonical | 47924 Mismatch rate per base, % | 0.39% Deletion rate per base | 0.04% Deletion average length | 2.11 Insertion rate per base | 0.03% Insertion average length | 2.13 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 452497 % of reads mapped to multiple loci | 2.54% Number of reads mapped to too many loci | 98869 % of reads mapped to too many loci | 0.56% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 6.93% % of reads unmapped: other | 0.17% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 1375993 1375993 1375993 N_multimapping 452497 452497 452497 N_noFeature 463438 15824243 526135 N_ambiguous 166361 792 84197 UnstrandedReadsAssigned:15338814 PositiveStrandReadsAssigned:143578 NegativeStrandReadsAssigned:15358281 Dataset is classified negative stranded MeadianReadLen=151 20thPercentileLength=150 echo kmer=145 SRR7172117 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: SRR7172117-trimmed-pair1.fastq SRR7172117-trimmed-pair2.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 17,782,341 reads, 15,284,265 reads pseudoaligned [quant] estimated average fragment length: 238.793 [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,113 rounds 52401 SRR7172117.ke.tsv 34699 SRR7172117.se.tsv 87100 total ==> SRR7172117.ke.tsv <== target_id length eff_length est_counts tpm Potri.005G200100.1.v4.1 2018 1780.21 1336 49.0061 Potri.005G024800.1.v4.1 1035 797.207 286 23.4266 Potri.004G059700.1.v4.1 961 723.212 40 3.61167 Potri.007G009000.2.v4.1 1416 1178.21 0 0 Potri.003G141000.2.v4.1 2943 2705.21 424.379 10.2439 Potri.016G087400.1.v4.1 270 79.4406 1065 875.429 Potri.015G069301.1.v4.1 564 329.547 0 0 Potri.010G195200.1.v4.1 1773 1535.21 269 11.4419 Potri.012G127500.1.v4.1 977 739.207 15559 1374.45 ==> SRR7172117.se.tsv <== Potri.001G166300.v4.1 0 Potri.001G448400.v4.1 9 Potri.001G233950.v4.1 0 Potri.001G122700.v4.1 340 Potri.001G212900.v4.1 0 Potri.001G182400.v4.1 1 Potri.001G256600.v4.1 0 Potri.001G040500.v4.1 0 Potri.001G416900.v4.1 2 Potri.001G452600.v4.1 419 SRR7172117 completed mapping pipeline successfully