Starting /dee2/code/volunteer_pipeline.sh SRR6958403 current disk space = 1548374806528 free memory = 1597337040 SRR6958403 SRAfilesize f4b3cf8a07e7946775a5a0cf9733f531 SRR6958403.sra SRR6958403.sra file validated SRR6958403 is paired end SRR6958403 is conventional basespace SRR6958403 read1 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR6958403_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 50 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 32.68375 33.0 33.0 34.0 32.0 34.0 2 31.336 33.0 31.0 33.0 28.0 34.0 3 32.21775 33.0 33.0 33.0 31.0 34.0 4 32.66875 33.0 33.0 34.0 31.0 34.0 5 33.08575 33.0 33.0 34.0 33.0 34.0 6 36.30075 38.0 36.0 38.0 33.0 38.0 7 36.6435 38.0 37.0 38.0 34.0 38.0 8 37.0825 38.0 38.0 38.0 36.0 38.0 9 37.42025 38.0 38.0 38.0 37.0 38.0 10-14 37.44805 38.0 38.0 38.0 37.0 38.0 15-19 37.4898 38.0 38.0 38.0 37.2 38.0 20-24 37.549850000000006 38.0 38.0 38.0 38.0 38.0 25-29 37.45745000000001 38.0 38.0 38.0 37.2 38.0 30-34 37.4936 38.0 38.0 38.0 37.6 38.0 35-39 37.4131 38.0 38.0 38.0 37.0 38.0 40-44 37.4327 38.0 38.0 38.0 37.0 38.0 45-49 37.398500000000006 38.0 38.0 38.0 37.0 38.0 50-54 37.310249999999996 38.0 38.0 38.0 37.0 38.0 55-59 37.08630000000001 38.0 38.0 38.0 36.6 38.0 60-64 36.85815 38.0 38.0 38.0 35.8 38.0 65-69 37.157599999999995 38.0 38.0 38.0 36.0 38.0 70-74 37.1668 38.0 38.0 38.0 36.0 38.0 75-79 37.11465 38.0 38.0 38.0 36.0 38.0 80-84 36.93935 38.0 38.0 38.0 35.6 38.0 85-89 36.888799999999996 38.0 38.0 38.0 35.0 38.0 90-94 36.7847 38.0 38.0 38.0 35.0 38.0 95-99 36.7112 38.0 38.0 38.0 34.6 38.0 100-104 36.59965 38.0 38.0 38.0 34.0 38.0 105-109 36.4531 38.0 38.0 38.0 34.0 38.0 110-114 36.28375 38.0 37.8 38.0 33.8 38.0 115-119 36.06805 38.0 37.2 38.0 32.6 38.0 120-124 35.71485 38.0 36.4 38.0 31.0 38.0 125-129 35.504599999999996 38.0 36.2 38.0 30.6 38.0 130-134 35.1288 38.0 36.0 38.0 29.0 38.0 135-139 34.564499999999995 38.0 34.8 38.0 27.2 38.0 140-144 34.352700000000006 38.0 34.4 38.0 26.6 38.0 145-149 33.40560000000001 38.0 33.0 38.0 21.6 38.0 150-151 27.861375000000002 33.5 17.5 37.0 2.0 38.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 7 1.0 8 0.0 9 0.0 10 0.0 11 0.0 12 1.0 13 0.0 14 1.0 15 0.0 16 0.0 17 2.0 18 1.0 19 3.0 20 7.0 21 2.0 22 3.0 23 4.0 24 10.0 25 10.0 26 17.0 27 17.0 28 21.0 29 27.0 30 57.0 31 56.0 32 62.0 33 105.0 34 153.0 35 324.0 36 771.0 37 2345.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 42.199999999999996 10.174999999999999 10.775 36.85 2 24.775 11.125 34.8 29.299999999999997 3 21.349999999999998 16.375 25.525 36.75 4 25.575 23.425 22.125 28.875 5 27.250000000000004 26.3 22.85 23.599999999999998 6 23.35 31.374999999999996 23.799999999999997 21.475 7 18.7 23.45 38.625 19.225 8 22.025 22.05 28.325 27.6 9 20.150000000000002 22.075 31.900000000000002 25.874999999999996 10-14 23.699479791916765 25.35514205682273 25.625250100040013 25.320128051220486 15-19 23.5 24.035 25.990000000000002 26.474999999999998 20-24 23.985 24.779999999999998 25.169999999999998 26.064999999999998 25-29 24.21 24.54 25.335 25.915 30-34 23.625 24.13 25.580000000000002 26.665 35-39 24.285 24.22 25.069999999999997 26.424999999999997 40-44 23.705000000000002 24.805 25.155 26.334999999999997 45-49 23.48 24.59 25.45 26.479999999999997 50-54 23.955000000000002 24.224999999999998 25.480000000000004 26.340000000000003 55-59 24.54650520074368 24.290236671524042 24.747500125621826 26.415758002110444 60-64 24.169184290030213 24.451158106747233 25.040281973816718 26.339375629405843 65-69 24.565 24.45 25.069999999999997 25.915 70-74 24.21 24.185000000000002 25.715 25.89 75-79 24.14 24.36 25.515 25.985000000000003 80-84 23.705000000000002 24.335 25.679999999999996 26.279999999999998 85-89 24.52 23.91 25.27 26.3 90-94 24.27 25.055 24.75 25.924999999999997 95-99 24.565 24.42 24.73 26.284999999999997 100-104 24.099999999999998 23.805 25.205 26.889999999999997 105-109 23.885 24.575 25.305 26.235000000000003 110-114 24.255 24.34 25.235000000000003 26.169999999999998 115-119 24.54 24.404999999999998 24.834999999999997 26.22 120-124 24.68 24.65 24.355 26.314999999999998 125-129 23.995 24.310000000000002 25.040000000000003 26.655 130-134 24.73 24.505 24.355 26.41 135-139 25.014999999999997 24.015 24.66 26.31 140-144 24.779999999999998 24.505 24.72 25.995 145-149 25.05 24.355 24.81 25.785000000000004 150-151 24.95 24.2 24.637500000000003 26.2125 >>END_MODULE >>Per sequence GC content fail #GC Content Count 0 0.0 1 0.0 2 0.0 3 0.0 4 0.0 5 0.0 6 0.0 7 0.0 8 0.0 9 0.0 10 0.0 11 0.0 12 0.0 13 0.0 14 0.0 15 0.0 16 0.0 17 0.0 18 0.0 19 0.0 20 0.0 21 0.0 22 1.0 23 1.5 24 0.5 25 0.0 26 0.5 27 1.0 28 1.0 29 2.0 30 4.0 31 7.5 32 12.0 33 13.5 34 12.0 35 23.0 36 35.5 37 52.0 38 69.0 39 77.5 40 97.5 41 124.5 42 158.0 43 181.0 44 183.5 45 185.0 46 196.5 47 196.5 48 199.0 49 190.5 50 163.5 51 156.5 52 147.0 53 124.5 54 113.5 55 105.5 56 100.0 57 96.5 58 95.0 59 94.0 60 83.0 61 78.0 62 74.5 63 70.0 64 70.0 65 72.0 66 65.5 67 51.0 68 42.5 69 34.5 70 28.5 71 25.0 72 18.0 73 16.5 74 17.0 75 14.0 76 6.5 77 4.0 78 4.0 79 1.0 80 0.5 81 1.0 82 0.5 83 0.0 84 0.5 85 0.5 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 0.04 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 0.49500000000000005 60-64 0.7000000000000001 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 99.3 #Duplication Level Percentage of deduplicated Percentage of total 1 99.34541792547836 98.65 2 0.6042296072507553 1.2 3 0.050352467270896276 0.15 4 0.0 0.0 5 0.0 0.0 6 0.0 0.0 7 0.0 0.0 8 0.0 0.0 9 0.0 0.0 >10 0.0 0.0 >50 0.0 0.0 >100 0.0 0.0 >500 0.0 0.0 >1k 0.0 0.0 >5k 0.0 0.0 >10k+ 0.0 0.0 >>END_MODULE >>Overrepresented sequences pass >>END_MODULE >>Adapter Content pass #Position Illumina Universal Adapter Illumina Small RNA 3' Adapter Illumina Small RNA 5' Adapter Nextera Transposase Sequence SOLID Small RNA Adapter 1 0.0 0.0 0.0 0.0 0.0 2 0.0 0.0 0.0 0.0 0.0 3 0.0 0.0 0.0 0.0 0.0 4 0.0 0.0 0.0 0.0 0.0 5 0.0 0.0 0.0 0.0 0.0 6 0.0 0.0 0.0 0.0 0.0 7 0.0 0.0 0.0 0.0 0.0 8 0.0 0.0 0.0 0.0 0.0 9 0.0 0.0 0.0 0.0 0.0 10-11 0.0 0.0 0.0 0.0 0.0 12-13 0.0 0.0 0.0 0.0 0.0 14-15 0.0 0.0 0.0 0.0 0.0 16-17 0.0 0.0 0.0 0.0 0.0 18-19 0.0 0.0 0.0 0.0 0.0 20-21 0.0 0.0 0.0 0.0 0.0 22-23 0.0 0.0 0.0 0.0 0.0 24-25 0.0 0.0 0.0 0.0 0.0 26-27 0.0 0.0 0.0 0.0 0.0 28-29 0.0 0.0 0.0 0.0 0.0 30-31 0.0 0.0 0.0 0.0 0.0 32-33 0.0 0.0 0.0 0.0 0.0 34-35 0.0 0.0 0.0 0.0 0.0 36-37 0.0 0.0 0.0 0.0 0.0 38-39 0.0 0.0 0.0 0.0 0.0 40-41 0.0 0.0 0.0 0.0 0.0 42-43 0.0 0.0 0.0 0.0 0.0 44-45 0.0 0.0 0.0 0.0 0.0 46-47 0.0 0.0 0.0 0.0 0.0 48-49 0.0 0.0 0.0 0.0 0.0 50-51 0.0 0.0 0.0 0.0 0.0 52-53 0.0 0.0 0.0 0.0 0.0 54-55 0.0 0.0 0.0 0.0 0.0 56-57 0.0 0.0 0.0 0.0 0.0 58-59 0.0 0.0 0.0 0.0 0.0 60-61 0.0 0.0 0.0 0.0 0.0 62-63 0.0 0.0 0.0 0.0 0.0 64-65 0.0 0.0 0.0 0.0 0.0 66-67 0.0 0.0 0.0 0.0 0.0 68-69 0.0 0.0 0.0 0.0 0.0 70-71 0.0 0.0 0.0 0.0 0.0 72-73 0.0 0.0 0.0 0.0 0.0 74-75 0.0 0.0 0.0 0.0 0.0 76-77 0.0 0.0 0.0 0.0 0.0 78-79 0.0 0.0 0.0 0.0 0.0 80-81 0.0 0.0 0.0 0.0 0.0 82-83 0.0 0.0 0.0 0.0 0.0 84-85 0.0 0.0 0.0 0.0 0.0 86-87 0.0 0.0 0.0 0.0 0.0 88-89 0.0 0.0 0.0 0.0 0.0 90-91 0.0 0.0 0.0 0.0 0.0 92-93 0.0 0.0 0.0 0.0 0.0 94-95 0.0875 0.0 0.0 0.0 0.0 96-97 0.1375 0.0 0.0 0.0 0.0 98-99 0.175 0.0 0.0 0.0 0.0 100-101 0.2 0.0 0.0 0.0 0.0 102-103 0.275 0.0 0.0 0.0 0.0 104-105 0.35 0.0 0.0 0.0 0.0 106-107 0.375 0.0 0.0 0.0 0.0 108-109 0.3875 0.0 0.0 0.0 0.0 110-111 0.42500000000000004 0.0 0.0 0.0 0.0 112-113 0.5125 0.0 0.0 0.0 0.0 114-115 0.625 0.0 0.0 0.0 0.0 116-117 0.7625 0.0 0.0 0.0 0.0 118-119 0.85 0.0 0.0 0.0 0.0 120-121 0.9874999999999999 0.0 0.0 0.0 0.0 122-123 1.0625 0.0 0.0 0.0 0.0 124-125 1.225 0.0 0.0 0.0 0.0 126-127 1.45 0.0 0.0 0.0 0.0 128-129 1.6375000000000002 0.0 0.0 0.0 0.0 130-131 1.7 0.0 0.0 0.0 0.0 132-133 1.7999999999999998 0.0 0.0 0.0 0.0 134-135 1.9625 0.0 0.0 0.0 0.0 136-137 2.2125 0.0 0.0 0.0 0.0 138-139 2.525 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position GGCAGTT 10 0.0068590776 144.79999 1 >>END_MODULE SRR6958403 read2 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR6958403_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 51 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 32.94925 33.0 33.0 34.0 32.0 34.0 2 33.05475 34.0 33.0 34.0 32.0 34.0 3 33.0375 34.0 33.0 34.0 32.0 34.0 4 33.087 34.0 33.0 34.0 32.0 34.0 5 33.06825 34.0 33.0 34.0 32.0 34.0 6 37.208 38.0 38.0 38.0 37.0 38.0 7 37.23075 38.0 38.0 38.0 37.0 38.0 8 37.26475 38.0 38.0 38.0 37.0 38.0 9 37.22275 38.0 38.0 38.0 37.0 38.0 10-14 37.2155 38.0 38.0 38.0 37.0 38.0 15-19 37.17925 38.0 38.0 38.0 37.0 38.0 20-24 37.1118 38.0 38.0 38.0 36.4 38.0 25-29 37.093450000000004 38.0 38.0 38.0 36.6 38.0 30-34 37.1161 38.0 38.0 38.0 36.4 38.0 35-39 37.10125 38.0 38.0 38.0 36.8 38.0 40-44 37.05845 38.0 38.0 38.0 36.6 38.0 45-49 37.0681 38.0 38.0 38.0 36.2 38.0 50-54 37.010349999999995 38.0 38.0 38.0 36.0 38.0 55-59 36.90775 38.0 38.0 38.0 35.8 38.0 60-64 36.91005 38.0 38.0 38.0 36.0 38.0 65-69 36.825700000000005 38.0 38.0 38.0 35.6 38.0 70-74 36.880199999999995 38.0 38.0 38.0 36.0 38.0 75-79 36.8276 38.0 38.0 38.0 35.4 38.0 80-84 36.7517 38.0 38.0 38.0 35.2 38.0 85-89 36.60685 38.0 38.0 38.0 34.8 38.0 90-94 36.53215 38.0 38.0 38.0 34.4 38.0 95-99 36.458099999999995 38.0 38.0 38.0 34.2 38.0 100-104 36.363099999999996 38.0 38.0 38.0 34.0 38.0 105-109 36.223600000000005 38.0 38.0 38.0 34.0 38.0 110-114 35.8759 38.0 37.6 38.0 32.6 38.0 115-119 35.80645 38.0 37.0 38.0 32.8 38.0 120-124 35.8032 38.0 37.2 38.0 33.0 38.0 125-129 35.79485 38.0 37.0 38.0 32.8 38.0 130-134 35.5747 38.0 36.2 38.0 31.6 38.0 135-139 35.323750000000004 38.0 36.0 38.0 31.0 38.0 140-144 34.91065 38.0 35.8 38.0 29.6 38.0 145-149 34.126450000000006 38.0 34.4 38.0 26.2 38.0 150-151 30.145000000000003 35.5 28.0 38.0 11.5 38.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 2 7.0 3 2.0 4 3.0 5 0.0 6 2.0 7 0.0 8 0.0 9 0.0 10 2.0 11 0.0 12 2.0 13 2.0 14 1.0 15 2.0 16 3.0 17 2.0 18 6.0 19 6.0 20 6.0 21 4.0 22 8.0 23 8.0 24 7.0 25 13.0 26 12.0 27 19.0 28 27.0 29 32.0 30 43.0 31 47.0 32 61.0 33 86.0 34 149.0 35 219.0 36 556.0 37 2663.0 >>END_MODULE >>Per base sequence content warn #Base G A T C 1 37.3 17.525 13.850000000000001 31.324999999999996 2 29.78723404255319 22.152690863579476 25.882352941176475 22.177722152690862 3 23.4984984984985 24.824824824824827 26.426426426426424 25.25025025025025 4 26.790185277916873 30.696044066099148 20.28042063094642 22.233350025037556 5 27.027027027027028 30.755755755755754 19.744744744744743 22.47247247247247 6 25.05005005005005 32.75775775775776 20.095095095095093 22.097097097097095 7 24.474474474474476 18.093093093093092 33.48348348348348 23.94894894894895 8 23.623623623623622 23.073073073073072 23.673673673673672 29.629629629629626 9 23.24824824824825 23.54854854854855 25.975975975975974 27.227227227227228 10-14 26.09109109109109 25.45045045045045 23.123123123123122 25.335335335335333 15-19 26.062365483757944 25.37664547775164 23.63982181290355 24.921167225586867 20-24 26.256507809371243 25.545654785742894 23.448137765318382 24.74969963956748 25-29 26.36295369211514 25.491864831038797 23.178973717146434 24.966207759699625 30-34 25.93371382797637 25.44808250725944 23.780915189746672 24.837288475017523 35-39 25.859566588258847 24.893648966518192 23.867674290576048 25.379110154646916 40-44 26.338972870157175 24.737210932025228 23.355691260386426 25.568124937431175 45-49 25.848093665565898 25.367757430201145 23.036125287701392 25.748023616531572 50-54 26.141763793707167 25.351408133660147 23.640638287229255 24.86618978540343 55-59 26.618957061355218 25.302772495245723 23.225903312981682 24.852367130417374 60-64 26.014713978279364 25.158900955908116 23.552374756018217 25.274010309794303 65-69 26.79179179179179 24.91991991991992 23.48848848848849 24.7997997997998 70-74 26.109804314098394 24.60837795906111 24.077873980281268 25.203943746559233 75-79 26.24148978774529 24.169002803364037 24.304164997997596 25.28534241089307 80-84 25.77046227736642 24.599759855913547 24.499699819891934 25.130078046828096 85-89 27.338201460438132 24.532359707912374 23.026908072421726 25.10253075922777 90-94 26.381104883907124 24.819855884707767 23.713971176941552 25.085068054443553 95-99 26.110888710968776 24.769815852682147 23.82405924739792 25.295236188951158 100-104 27.384168918242768 24.902431702191535 23.296307415190633 24.41709196437506 105-109 26.36477358018514 24.468351263447584 24.38829121841381 24.778583937953467 110-114 26.32105684547638 25.12510008006405 23.58386709367494 24.96997598078463 115-119 26.918264177386252 25.471745332599227 23.369538014915662 24.240452475098852 120-124 26.67967382060133 25.203862124168293 23.728050427735255 24.388413627495122 125-129 26.715036277207904 25.71428571428571 23.062296722541905 24.50838128596447 130-134 27.172227502376067 25.316392376569457 23.60562253013856 23.905757590915915 135-139 26.67100260156094 25.290174104462675 24.029417650590354 24.00940564338603 140-144 26.811086651991197 24.8198919351611 24.23954372623574 24.129477686611967 145-149 26.79107464478687 25.255153091855114 23.46908144886932 24.484690814488694 150-151 27.489989989989986 25.462962962962965 23.61111111111111 23.435935935935937 >>END_MODULE >>Per sequence GC content fail #GC Content Count 0 0.0 1 0.5 2 0.5 3 0.0 4 0.0 5 0.0 6 0.0 7 0.5 8 0.5 9 0.5 10 0.5 11 0.0 12 0.0 13 0.0 14 0.5 15 0.5 16 0.0 17 0.0 18 0.0 19 0.0 20 0.0 21 0.0 22 0.0 23 0.0 24 0.0 25 1.5 26 2.0 27 2.5 28 2.0 29 0.5 30 1.5 31 2.5 32 4.0 33 9.0 34 16.0 35 23.0 36 35.0 37 48.5 38 64.5 39 85.0 40 102.5 41 129.0 42 142.5 43 149.0 44 171.0 45 172.5 46 169.0 47 175.0 48 177.5 49 168.0 50 170.0 51 170.5 52 133.0 53 109.0 54 112.5 55 113.5 56 95.5 57 93.5 58 102.5 59 97.0 60 94.0 61 94.5 62 86.0 63 73.0 64 71.5 65 68.5 66 70.0 67 71.5 68 66.5 69 57.0 70 46.5 71 39.0 72 32.5 73 27.5 74 16.0 75 11.5 76 11.5 77 4.5 78 2.0 79 1.5 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 0.0 2 0.125 3 0.1 4 0.15 5 0.1 6 0.1 7 0.1 8 0.1 9 0.1 10-14 0.1 15-19 0.105 20-24 0.12 25-29 0.125 30-34 0.13 35-39 0.095 40-44 0.11 45-49 0.06999999999999999 50-54 0.045 55-59 0.09 60-64 0.095 65-69 0.1 70-74 0.095 75-79 0.12 80-84 0.06 85-89 0.03 90-94 0.08 95-99 0.08 100-104 0.06999999999999999 105-109 0.075 110-114 0.08 115-119 0.105 120-124 0.055 125-129 0.075 130-134 0.045 135-139 0.06 140-144 0.06 145-149 0.06 150-151 0.1 >>END_MODULE >>Sequence Length Distribution pass #Length Count 151 4000.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 98.225 #Duplication Level Percentage of deduplicated Percentage of total 1 98.80376686179689 97.05 2 0.8908119114278442 1.7500000000000002 3 0.17816238228556885 0.525 4 0.050903537795876815 0.2 5 0.025451768897938407 0.125 6 0.025451768897938407 0.15 7 0.0 0.0 8 0.025451768897938407 0.2 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 CTTGATCATCTGAAAAATCTTAATCCAGATCAGACCAAGCAGAGCAGAGA 8 0.2 No Hit CTGCAATTGCAAGCTTGTGTCAAAGAAGAGGGTAGCACCTGATCCTCTTG 6 0.15 No Hit CACACACAGGCAAAACACAGCTGATTCGTGTACTCGATCTCCCCAGCAAG 5 0.125 No Hit >>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 0.0 0.0 0.0 0.0 0.0 92-93 0.0 0.0 0.0 0.0 0.0 94-95 0.0875 0.0 0.0 0.0 0.0 96-97 0.1375 0.0 0.0 0.0 0.0 98-99 0.175 0.0 0.0 0.0 0.0 100-101 0.2 0.0 0.0 0.0 0.0 102-103 0.275 0.0 0.0 0.0 0.0 104-105 0.375 0.0 0.0 0.0 0.0 106-107 0.4 0.0 0.0 0.0 0.0 108-109 0.4125 0.0 0.0 0.0 0.0 110-111 0.4375 0.0 0.0 0.0 0.0 112-113 0.5125 0.0 0.0 0.0 0.0 114-115 0.625 0.0 0.0 0.0 0.0 116-117 0.7625 0.0 0.0 0.0 0.0 118-119 0.85 0.0 0.0 0.0 0.0 120-121 0.9874999999999999 0.0 0.0 0.0 0.0 122-123 1.0750000000000002 0.0 0.0 0.0 0.0 124-125 1.25 0.0 0.0 0.0 0.0 126-127 1.45 0.0 0.0 0.0 0.0 128-129 1.6375000000000002 0.0 0.0 0.0 0.0 130-131 1.7 0.0 0.0 0.0 0.0 132-133 1.7999999999999998 0.0 0.0 0.0 0.0 134-135 1.9625 0.0 0.0 0.0 0.0 136-137 2.2125 0.0 0.0 0.0 0.0 138-139 2.5375 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position TCCCTCC 10 0.006830828 145.0 9 >>END_MODULE Read 1349580 spots for SRR6958403.sra Written 1349580 spots for SRR6958403.sra Read 1349580 spots for SRR6958403.sra Written 1349580 spots for SRR6958403.sra Read 1349580 spots for SRR6958403.sra Written 1349580 spots for SRR6958403.sra Read 1349587 spots for SRR6958403.sra Written 1349587 spots for SRR6958403.sra Read 1349580 spots for SRR6958403.sra Written 1349580 spots for SRR6958403.sra Read 1349580 spots for SRR6958403.sra Written 1349580 spots for SRR6958403.sra Read 1349580 spots for SRR6958403.sra Written 1349580 spots for SRR6958403.sra Read 1349580 spots for SRR6958403.sra Written 1349580 spots for SRR6958403.sra Read 1349580 spots for SRR6958403.sra Written 1349580 spots for SRR6958403.sra Read 1349580 spots for SRR6958403.sra Written 1349580 spots for SRR6958403.sra Read 1349580 spots for SRR6958403.sra Written 1349580 spots for SRR6958403.sra Read 1349580 spots for SRR6958403.sra Written 1349580 spots for SRR6958403.sra Read 1349580 spots for SRR6958403.sra Written 1349580 spots for SRR6958403.sra Read 1349580 spots for SRR6958403.sra Written 1349580 spots for SRR6958403.sra Read 1349580 spots for SRR6958403.sra Written 1349580 spots for SRR6958403.sra Read 1349580 spots for SRR6958403.sra Written 1349580 spots for SRR6958403.sra Read 1349580 spots for SRR6958403.sra Written 1349580 spots for SRR6958403.sra Read 1349580 spots for SRR6958403.sra Written 1349580 spots for SRR6958403.sra Read 1349580 spots for SRR6958403.sra Written 1349580 spots for SRR6958403.sra Read 1349580 spots for SRR6958403.sra Written 1349580 spots for SRR6958403.sra SRR ids: ['SRR6958403.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_v23xsy59 SRR6958403.sra spots: 26991607 blocks: [[1, 1349580], [1349581, 2699160], [2699161, 4048740], [4048741, 5398320], [5398321, 6747900], [6747901, 8097480], [8097481, 9447060], [9447061, 10796640], [10796641, 12146220], [12146221, 13495800], [13495801, 14845380], [14845381, 16194960], [16194961, 17544540], [17544541, 18894120], [18894121, 20243700], [20243701, 21593280], [21593281, 22942860], [22942861, 24292440], [24292441, 25642020], [25642021, 26991607]] SRR6958403 file size 9124869 SRR6958403 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 SRR6958403 SRR6958403_1.fastq SRR6958403_2.fastq Input file: SRR6958403_1.fastq Paired file: SRR6958403_2.fastq trimmed: SRR6958403-trimmed-pair1.fastq, SRR6958403-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 22:14:31 2024 >> started Fri Dec 6 22:15:18 2024 >> done (46.516s) 26991607 read pairs processed; of these: 36842 ( 0.14%) short read pairs filtered out after trimming by size control 62480 ( 0.23%) empty read pairs filtered out after trimming by size control 26892285 (99.63%) read pairs available; of these: 11020718 (40.98%) trimmed read pairs available after processing 15871567 (59.02%) untrimmed read pairs available after processing Length distribution of reads after trimming: length count percentage 18 1 0.00% 19 6 0.00% 20 3 0.00% 21 5 0.00% 22 6 0.00% 23 3 0.00% 24 7 0.00% 25 5 0.00% 26 7 0.00% 27 5 0.00% 28 6 0.00% 29 8 0.00% 30 9 0.00% 31 11 0.00% 32 5 0.00% 33 7 0.00% 34 8 0.00% 35 6 0.00% 36 11 0.00% 37 11 0.00% 38 23 0.00% 39 13 0.00% 40 20 0.00% 41 18 0.00% 42 21 0.00% 43 19 0.00% 44 25 0.00% 45 19 0.00% 46 29 0.00% 47 22 0.00% 48 30 0.00% 49 39 0.00% 50 43 0.00% 51 41 0.00% 52 55 0.00% 53 43 0.00% 54 68 0.00% 55 70 0.00% 56 86 0.00% 57 82 0.00% 58 104 0.00% 59 112 0.00% 60 155 0.00% 61 142 0.00% 62 169 0.00% 63 222 0.00% 64 221 0.00% 65 235 0.00% 66 255 0.00% 67 289 0.00% 68 325 0.00% 69 340 0.00% 70 432 0.00% 71 484 0.00% 72 505 0.00% 73 611 0.00% 74 656 0.00% 75 736 0.00% 76 786 0.00% 77 900 0.00% 78 1050 0.00% 79 1211 0.00% 80 1305 0.00% 81 1521 0.01% 82 1689 0.01% 83 1942 0.01% 84 3242 0.01% 85 3983 0.01% 86 4114 0.02% 87 4228 0.02% 88 4422 0.02% 89 4647 0.02% 90 4773 0.02% 91 4999 0.02% 92 5337 0.02% 93 5782 0.02% 94 6103 0.02% 95 6366 0.02% 96 6652 0.02% 97 7297 0.03% 98 7552 0.03% 99 7994 0.03% 100 8289 0.03% 101 8920 0.03% 102 9605 0.04% 103 10218 0.04% 104 10642 0.04% 105 11197 0.04% 106 11888 0.04% 107 12591 0.05% 108 13013 0.05% 109 13638 0.05% 110 14378 0.05% 111 15533 0.06% 112 16237 0.06% 113 17059 0.06% 114 18278 0.07% 115 19310 0.07% 116 20291 0.08% 117 21653 0.08% 118 22223 0.08% 119 22794 0.08% 120 24367 0.09% 121 25237 0.09% 122 26534 0.10% 123 28051 0.10% 124 29519 0.11% 125 31662 0.12% 126 33132 0.12% 127 34613 0.13% 128 36163 0.13% 129 37702 0.14% 130 39467 0.15% 131 41721 0.16% 132 44560 0.17% 133 46967 0.17% 134 50254 0.19% 135 53719 0.20% 136 56571 0.21% 137 60502 0.22% 138 65265 0.24% 139 70123 0.26% 140 75933 0.28% 141 83700 0.31% 142 93475 0.35% 143 106981 0.40% 144 126087 0.47% 145 153636 0.57% 146 195763 0.73% 147 275930 1.03% 148 450965 1.68% 149 1006409 3.74% 150 7213169 26.82% 151 15871567 59.02% 26892285 reads passed initial QC criterion=sequence-density sequence-density=0.63 sequence-density-rank=1 fanout-score=3.28 fanout-score-rank=25 prefix-density=0.67 prefix-fanout=3.1 sequence=GGTGTTGTCGAAGCCGATGATGCGGACATAGGCGTCCGG criterion=fanout-score sequence-density=0.03 sequence-density-rank=34 fanout-score=165.99 fanout-score-rank=1 prefix-density=0.68 prefix-fanout=7.2 sequence=GGCGGCGGCGAACCGCCCCCGTCGCCGCGATCCGAACACTTCACCGGACCATTCAATCGGTAGGAGCGACGGGCGGTGTGTACAAAGGGCAGGGACGTAGTCAACGCGAGCTGATGACTCGCGCTTACTAGGCATTCCTCGTTGAAGACCAACAATTGCAATGATCTATCCCCATCACGATGAAATTTCCCAAGATTACCCGGGCCTGTCGGCCAAGGCTATATACTCGTTGAATACATCAGTGTAGCGCGCGTGCGGCCCAGAACATCTAAGGGCATCACAGACCTGTTATTGCCTCAAACTTCCGTCGCCTAAACGGCGATAGTCCCTCTAAGAAGCTAGCTGCGGAGGGATGGCTCCGCATAGCTAGTTAGCAGGCTGAGGTCTCGTTCGTTAACGGAATTAACCAGACAAATCGCTCCACCAACTAAGAACGGCCATGCACCACCACCCATAGAATCAAGAAAGAGCTCTCAGTCTGTCAATCCTTGCTATGTCTGGACCTGGTAAG criterion=sequence-density sequence-density=0.46 sequence-density-rank=1 fanout-score=3.91 fanout-score-rank=17 prefix-density=0.57 prefix-fanout=3.1 sequence=CTGCAAGTGCGGCA criterion=fanout-score sequence-density=0.14 sequence-density-rank=23 fanout-score=61.14 fanout-score-rank=1 prefix-density=0.76 prefix-fanout=11.6 sequence=GCCGCCGCCGCC SRR6958403 testing PE reads STAR mapping to Ensembl genome Started job on | Dec 06 22:16:04 Started mapping on | Dec 06 22:16:05 Finished on | Dec 06 22:18:19 Mapping speed, Million of reads per hour | 722.48 Number of input reads | 26892285 Average input read length | 298 UNIQUE READS: Uniquely mapped reads number | 25818618 Uniquely mapped reads % | 96.01% Average mapped length | 297.71 Number of splices: Total | 30012190 Number of splices: Annotated (sjdb) | 28187505 Number of splices: GT/AG | 29600125 Number of splices: GC/AG | 361844 Number of splices: AT/AC | 11050 Number of splices: Non-canonical | 39171 Mismatch rate per base, % | 0.18% Deletion rate per base | 0.01% Deletion average length | 2.51 Insertion rate per base | 0.01% Insertion average length | 2.55 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 274443 % of reads mapped to multiple loci | 1.02% Number of reads mapped to too many loci | 39396 % of reads mapped to too many loci | 0.15% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 1.86% % of reads unmapped: other | 0.97% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 817661 817661 817661 N_multimapping 274443 274443 274443 N_noFeature 792055 25115380 975953 N_ambiguous 628788 3496 110380 UnstrandedReadsAssigned:24397775 PositiveStrandReadsAssigned:699742 NegativeStrandReadsAssigned:24732285 Dataset is classified negative stranded MeadianReadLen=151 20thPercentileLength=150 echo kmer=145 SRR6958403 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: SRR6958403-trimmed-pair1.fastq SRR6958403-trimmed-pair2.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 26,892,285 reads, 24,730,962 reads pseudoaligned [quant] estimated average fragment length: 278.695 [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,139 rounds 52973 SRR6958403.ke.tsv 35125 SRR6958403.se.tsv 88098 total ==> SRR6958403.ke.tsv <== target_id length eff_length est_counts tpm PNS24245 936 658.97 18.5543 1.64425 PNS24247 1044 766.305 99.7776 7.60364 PNS24249 1928 1650.31 74.5044 2.63638 PNS24246 1044 766.305 99.7776 7.60364 PNS24248 1044 766.305 99.7776 7.60364 PNS24244 1471 1193.31 47.6086 2.32983 PNS24243 293 76.1336 0 0 KQK14069 1603 1325.31 11194.9 493.283 KQK14071 474 212.742 147.903 40.5991 ==> SRR6958403.se.tsv <== BRADI_1g14170v3 12195 BRADI_1g53295v3 224 BRADI_1g59795v3 332 BRADI_1g07683v3 0 BRADI_1g00485v3 6 BRADI_1g20270v3 289 BRADI_1g74790v3 109 BRADI_1g09890v3 0 BRADI_1g77505v3 262 BRADI_1g48960v3 0 SRR6958403 completed mapping pipeline successfully