Starting /dee2/code/volunteer_pipeline.sh SRR8096890 current disk space = 1511444676608 free memory = 1403605332 SRR8096890 SRAfilesize 9124c26cf0418a38c436139c5a7c998d SRR8096890.sra SRR8096890.sra file validated SRR8096890 is paired end SRR8096890 is conventional basespace SRR8096890 read1 length is 150 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR8096890_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 48 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 31.59925 34.0 33.0 34.0 32.0 34.0 2 33.0535 34.0 33.0 34.0 32.0 34.0 3 33.11925 34.0 33.0 34.0 32.0 34.0 4 33.18525 34.0 33.0 34.0 32.0 34.0 5 33.23475 34.0 33.0 34.0 33.0 34.0 6 36.97575 38.0 37.0 38.0 35.0 38.0 7 37.26675 38.0 38.0 38.0 36.0 38.0 8 37.32825 38.0 38.0 38.0 37.0 38.0 9 37.352 38.0 38.0 38.0 37.0 38.0 10-14 37.44175 38.0 38.0 38.0 37.0 38.0 15-19 37.2558 38.0 38.0 38.0 36.6 38.0 20-24 37.391 38.0 38.0 38.0 37.0 38.0 25-29 37.35445 38.0 38.0 38.0 37.0 38.0 30-34 37.303200000000004 38.0 38.0 38.0 37.0 38.0 35-39 37.22735 38.0 38.0 38.0 36.8 38.0 40-44 37.075100000000006 38.0 38.0 38.0 36.6 38.0 45-49 37.0764 38.0 38.0 38.0 36.2 38.0 50-54 37.07855 38.0 38.0 38.0 36.4 38.0 55-59 37.0105 38.0 38.0 38.0 36.0 38.0 60-64 36.915350000000004 38.0 38.0 38.0 36.2 38.0 65-69 36.83515 38.0 38.0 38.0 36.0 38.0 70-74 36.61175 38.0 38.0 38.0 35.4 38.0 75-79 35.989450000000005 38.0 38.0 38.0 34.0 38.0 80-84 36.0368 38.0 38.0 38.0 34.6 38.0 85-89 35.977549999999994 38.0 38.0 38.0 34.0 38.0 90-94 35.86405 38.0 38.0 38.0 34.0 38.0 95-99 35.8078 38.0 38.0 38.0 34.0 38.0 100-104 35.57629999999999 38.0 38.0 38.0 32.6 38.0 105-109 35.41780000000001 38.0 38.0 38.0 31.8 38.0 110-114 35.3456 38.0 38.0 38.0 31.4 38.0 115-119 35.26255 38.0 38.0 38.0 31.6 38.0 120-124 35.2442 38.0 38.0 38.0 31.4 38.0 125-129 34.9755 38.0 37.6 38.0 30.6 38.0 130-134 34.7517 38.0 36.8 38.0 28.6 38.0 135-139 34.52135 38.0 36.2 38.0 26.8 38.0 140-144 34.2716 38.0 36.2 38.0 24.8 38.0 145-149 33.60365 38.0 35.4 38.0 18.4 38.0 150 28.058 35.0 23.0 38.0 2.0 38.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 5 1.0 6 1.0 7 0.0 8 3.0 9 6.0 10 1.0 11 2.0 12 4.0 13 1.0 14 3.0 15 2.0 16 3.0 17 6.0 18 29.0 19 51.0 20 6.0 21 13.0 22 13.0 23 11.0 24 7.0 25 13.0 26 19.0 27 21.0 28 26.0 29 36.0 30 42.0 31 53.0 32 51.0 33 68.0 34 126.0 35 185.0 36 424.0 37 2773.0 >>END_MODULE >>Per base sequence content warn #Base G A T C 1 42.84582893347413 11.536430834213306 7.946145723336853 37.671594508975716 2 22.75 18.375 34.849999999999994 24.025 3 21.7 18.975 27.224999999999998 32.1 4 26.575 25.674999999999997 20.8 26.950000000000003 5 27.625 30.5 23.425 18.45 6 23.400000000000002 30.475 24.3 21.825 7 16.3 23.65 40.6 19.45 8 18.2 25.224999999999998 29.575000000000003 27.0 9 22.875 20.150000000000002 32.875 24.099999999999998 10-14 22.63 26.974999999999998 25.35 25.045 15-19 22.384999999999998 25.130000000000003 26.815 25.669999999999998 20-24 22.225 26.029999999999998 26.815 24.93 25-29 22.58 25.790000000000003 25.929999999999996 25.7 30-34 21.915000000000003 24.68 27.584999999999997 25.82 35-39 22.455 24.855 27.200000000000003 25.490000000000002 40-44 21.584999999999997 25.45 27.150000000000002 25.814999999999998 45-49 23.335 24.97 26.88 24.815 50-54 22.13 24.905 26.224999999999998 26.740000000000002 55-59 23.35 24.7 27.339999999999996 24.610000000000003 60-64 23.225 25.645 26.135 24.995 65-69 22.035 28.115000000000002 25.230000000000004 24.62 70-74 22.395 27.994999999999997 25.27 24.34 75-79 22.259999999999998 27.08 25.34 25.319999999999997 80-84 22.675 25.505 26.450000000000003 25.369999999999997 85-89 22.62 25.905 26.025 25.45 90-94 22.95 24.575 26.700000000000003 25.775 95-99 22.755 25.71 26.115 25.419999999999998 100-104 21.88 26.284999999999997 26.555 25.28 105-109 22.89 26.08 25.724999999999998 25.305 110-114 22.675 26.31 25.61 25.405 115-119 22.775000000000002 26.395000000000003 26.040000000000003 24.79 120-124 23.244999999999997 25.8 25.835 25.119999999999997 125-129 22.759999999999998 26.06 25.83 25.35 130-134 23.185 25.985000000000003 25.715 25.115 135-139 23.16 26.340000000000003 25.305 25.195 140-144 23.161158057902895 25.726286314315715 25.76128806440322 25.351267563378173 145-149 22.985 26.27 24.985 25.759999999999998 150 23.075000000000003 26.200000000000003 25.474999999999998 25.25 >>END_MODULE >>Per sequence GC content warn #GC Content Count 0 9.0 1 5.5 2 1.5 3 1.5 4 2.0 5 1.5 6 1.5 7 2.0 8 1.0 9 0.0 10 0.0 11 0.0 12 1.5 13 1.5 14 0.0 15 0.0 16 0.0 17 0.5 18 1.0 19 0.5 20 0.5 21 1.5 22 1.5 23 1.0 24 1.0 25 0.5 26 3.5 27 8.0 28 9.5 29 8.5 30 10.0 31 12.0 32 16.0 33 23.5 34 33.0 35 42.5 36 51.0 37 73.0 38 93.0 39 109.5 40 133.0 41 166.0 42 181.0 43 182.0 44 189.5 45 193.0 46 206.0 47 213.5 48 200.0 49 166.5 50 161.0 51 146.5 52 127.0 53 120.0 54 101.0 55 104.5 56 96.5 57 85.0 58 83.0 59 72.5 60 69.0 61 64.5 62 60.0 63 57.0 64 51.5 65 52.0 66 47.0 67 40.0 68 31.0 69 22.0 70 14.0 71 10.0 72 9.5 73 7.0 74 5.5 75 4.5 76 2.5 77 0.5 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 warn #Base N-Count 1 5.3 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 0.005 145-149 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 95.025 #Duplication Level Percentage of deduplicated Percentage of total 1 98.55301236516706 93.65 2 1.2102078400420941 2.3 3 0.13154433043935806 0.375 4 0.0 0.0 5 0.0 0.0 6 0.0 0.0 7 0.0 0.0 8 0.026308866087871613 0.2 9 0.026308866087871613 0.22499999999999998 >10 0.026308866087871613 0.325 >50 0.0 0.0 >100 0.026308866087871613 2.9250000000000003 >500 0.0 0.0 >1k 0.0 0.0 >5k 0.0 0.0 >10k+ 0.0 0.0 >>END_MODULE >>Overrepresented sequences fail #Sequence Count Percentage Possible Source GATCGGAAGAGCACACGTCTGAACTCCAGTCACTAGCTTATCTCGTATGC 117 2.9250000000000003 TruSeq Adapter, Index 10 (100% over 50bp) TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 13 0.325 No Hit AGATCGGAAGAGCACACGTCTGAACTCCAGTCACTAGCTTATCTCGTATG 9 0.22499999999999998 TruSeq Adapter, Index 10 (100% over 49bp) NATCGGAAGAGCACACGTCTGAACTCCAGTCACTAGCTTATCTCGTATGC 8 0.2 TruSeq Adapter, Index 10 (98% over 50bp) >>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 0.225 0.0 0.0 0.0 0.0 2 0.225 0.0 0.0 0.0 0.0 3 0.225 0.0 0.0 0.0 0.0 4 0.225 0.0 0.0 0.0 0.0 5 0.225 0.0 0.0 0.0 0.0 6 0.225 0.0 0.0 0.0 0.0 7 0.225 0.0 0.0 0.0 0.0 8 0.225 0.0 0.0 0.0 0.0 9 0.225 0.0 0.0 0.0 0.0 10-11 0.225 0.0 0.0 0.0 0.0 12-13 0.225 0.0 0.0 0.0 0.0 14-15 0.225 0.0 0.0 0.0 0.0 16-17 0.225 0.0 0.0 0.0 0.0 18-19 0.225 0.0 0.0 0.0 0.0 20-21 0.25 0.0 0.0 0.0 0.0 22-23 0.25 0.0 0.0 0.0 0.0 24-25 0.25 0.0 0.0 0.0 0.0 26-27 0.25 0.0 0.0 0.0 0.0 28-29 0.25 0.0 0.0 0.0 0.0 30-31 0.25 0.0 0.0 0.0 0.0 32-33 0.25 0.0 0.0 0.0 0.0 34-35 0.25 0.0 0.0 0.0 0.0 36-37 0.25 0.0 0.0 0.0 0.0 38-39 0.25 0.0 0.0 0.0 0.0 40-41 0.25 0.0 0.0 0.0 0.0 42-43 0.25 0.0 0.0 0.0 0.0 44-45 0.25 0.0 0.0 0.0 0.0 46-47 0.25 0.0 0.0 0.0 0.0 48-49 0.25 0.0 0.0 0.0 0.0 50-51 0.25 0.0 0.0 0.0 0.0 52-53 0.25 0.0 0.0 0.0 0.0 54-55 0.25 0.0 0.0 0.0 0.0 56-57 0.25 0.0 0.0 0.0 0.0 58-59 0.25 0.0 0.0 0.0 0.0 60-61 0.25 0.0 0.0 0.0 0.0 62-63 0.25 0.0 0.0 0.0 0.0 64-65 0.25 0.0 0.0 0.0 0.0 66-67 0.25 0.0 0.0 0.0 0.0 68-69 0.25 0.0 0.0 0.0 0.0 70-71 0.25 0.0 0.0 0.0 0.0 72-73 0.25 0.0 0.0 0.0 0.0 74-75 0.25 0.0 0.0 0.0 0.0 76-77 0.25 0.0 0.0 0.0 0.0 78-79 0.2875 0.0 0.0 0.0 0.0 80-81 0.3 0.0 0.0 0.0 0.0 82-83 0.3 0.0 0.0 0.0 0.0 84-85 0.3 0.0 0.0 0.0 0.0 86-87 0.3 0.0 0.0 0.0 0.0 88-89 0.3125 0.0 0.0 0.0 0.0 90-91 0.325 0.0 0.0 0.0 0.0 92-93 0.325 0.0 0.0 0.0 0.0 94-95 0.375 0.0 0.0 0.0 0.0 96-97 0.425 0.0 0.0 0.0 0.0 98-99 0.425 0.0 0.0 0.0 0.0 100-101 0.44999999999999996 0.0 0.0 0.0 0.0 102-103 0.4875 0.0 0.0 0.0 0.0 104-105 0.5125 0.0 0.0 0.0 0.0 106-107 0.5375000000000001 0.0 0.0 0.0 0.0 108-109 0.65 0.0 0.0 0.0 0.0 110-111 0.7375 0.0 0.0 0.0 0.0 112-113 0.8125 0.0 0.0 0.0 0.0 114-115 0.95 0.0 0.0 0.0 0.0 116-117 1.0625 0.0 0.0 0.0 0.0 118-119 1.25 0.0 0.0 0.0 0.0 120-121 1.3875000000000002 0.0 0.0 0.0 0.0 122-123 1.55 0.0 0.0 0.0 0.0 124-125 1.8125 0.0 0.0 0.0 0.0 126-127 1.9375 0.0 0.0 0.0 0.0 128-129 2.075 0.0 0.0 0.0 0.0 130-131 2.3125 0.0 0.0 0.0 0.0 132-133 2.5 0.0 0.0 0.0 0.0 134-135 2.7249999999999996 0.0 0.0 0.0 0.0 136-137 3.0 0.0 0.0 0.0 0.0 138 3.175 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position CGAAGCC 10 0.00621615 149.57143 1 CTTCGAT 10 0.00621615 149.57143 1 ATGATGC 10 0.0069790767 143.96251 9 GAACTTA 10 0.0069790767 143.96251 5 AGCCGAT 10 0.0069790767 143.96251 4 GCCGATG 10 0.0069790767 143.96251 5 >>END_MODULE SRR8096890 read2 length is 150 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR8096890_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 49 >>END_MODULE >>Per base sequence quality fail #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 30.72375 33.0 32.0 33.0 25.0 34.0 2 31.15125 33.0 32.0 33.0 27.0 34.0 3 30.9275 33.0 31.0 34.0 25.0 34.0 4 30.99475 33.0 32.0 34.0 27.0 34.0 5 30.72425 33.0 31.0 34.0 25.0 34.0 6 34.5395 38.0 36.0 38.0 26.0 38.0 7 34.6895 38.0 36.0 38.0 27.0 38.0 8 34.7855 38.0 36.0 38.0 27.0 38.0 9 34.7395 38.0 36.0 38.0 27.0 38.0 10-14 34.561550000000004 38.0 36.2 38.0 26.6 38.0 15-19 34.338800000000006 38.0 36.0 38.0 25.4 38.0 20-24 34.19345 38.0 35.8 38.0 21.4 38.0 25-29 33.955949999999994 38.0 35.2 38.0 17.8 38.0 30-34 33.73725 38.0 34.8 38.0 16.0 38.0 35-39 33.373850000000004 38.0 34.0 38.0 16.0 38.0 40-44 33.325599999999994 38.0 34.2 38.0 16.0 38.0 45-49 32.95605 38.0 33.8 38.0 16.0 38.0 50-54 32.7386 38.0 33.2 38.0 16.0 38.0 55-59 32.3593 38.0 32.2 38.0 16.0 38.0 60-64 32.13855000000001 37.2 31.4 38.0 15.2 38.0 65-69 31.68555 37.0 29.2 38.0 15.0 38.0 70-74 31.240250000000003 37.0 29.0 38.0 14.4 38.0 75-79 30.569849999999995 36.4 27.6 38.0 14.0 38.0 80-84 30.023500000000002 36.0 26.6 38.0 13.2 38.0 85-89 29.5048 35.8 24.8 38.0 13.2 38.0 90-94 28.8613 35.0 22.6 38.0 4.2 38.0 95-99 28.337200000000003 34.8 19.0 38.0 2.0 38.0 100-104 27.3385 34.0 15.0 38.0 2.0 38.0 105-109 26.545650000000002 33.6 15.0 38.0 2.0 38.0 110-114 25.815049999999996 32.8 15.0 37.4 2.0 38.0 115-119 24.681199999999997 31.0 14.0 37.0 2.0 38.0 120-124 23.5759 28.4 13.0 36.4 2.0 38.0 125-129 22.19325 25.8 6.4 35.4 2.0 38.0 130-134 20.640800000000002 22.4 2.0 35.0 2.0 38.0 135-139 19.0582 17.4 2.0 34.4 2.0 38.0 140-144 17.04105 13.8 2.0 34.0 2.0 37.8 145-149 14.45675 4.2 2.0 32.8 2.0 37.4 150 9.72025 2.0 2.0 15.0 2.0 35.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 2 95.0 3 21.0 4 14.0 5 16.0 6 14.0 7 11.0 8 12.0 9 16.0 10 19.0 11 22.0 12 23.0 13 35.0 14 25.0 15 46.0 16 37.0 17 38.0 18 40.0 19 45.0 20 54.0 21 71.0 22 64.0 23 85.0 24 103.0 25 106.0 26 125.0 27 136.0 28 172.0 29 205.0 30 251.0 31 263.0 32 328.0 33 382.0 34 418.0 35 401.0 36 250.0 37 57.0 >>END_MODULE >>Per base sequence content warn #Base G A T C 1 39.9748743718593 19.396984924623116 8.366834170854272 32.26130653266331 2 24.94313874147081 28.380085923679555 29.36568107151883 17.311094263330805 3 24.04551201011378 23.640960809102403 30.11378002528445 22.19974715549937 4 26.032953105196448 31.128010139416983 18.935361216730037 23.903675538656525 5 28.802834725385978 33.33333333333333 18.88129587446216 18.98253606681853 6 23.859026369168358 34.53346855983773 20.892494929006087 20.71501014198783 7 22.027883396704688 20.785804816223067 34.93029150823828 22.25602027883397 8 22.00253485424588 25.906210392902405 24.486692015209126 27.604562737642585 9 25.373891001267427 22.357414448669203 27.17363751584284 25.09505703422053 10-14 26.04441289799229 26.252281484485906 22.946663962685054 24.75664165483675 15-19 25.8327840592202 24.84916087816255 25.249708462201493 24.068346600415758 20-24 26.80961070559611 26.47506082725061 23.874695863746958 22.840632603406327 25-29 26.0790273556231 27.097264437689972 23.541033434650455 23.282674772036476 30-34 26.513961384482847 25.485227791009983 24.79602695991486 23.204783864592308 35-39 25.139184127948173 26.19192225933799 24.612815062253265 24.056078550460573 40-44 27.438870045056447 25.297423176226395 24.153293170657623 23.110413608059535 45-49 25.92705167173252 24.848024316109424 24.473150962512666 24.75177304964539 50-54 25.797130835910174 25.781923252395195 24.56531657119684 23.855629340497796 55-59 25.211574519839864 26.706532204935897 24.481832463386205 23.600060811838038 60-64 25.00887198986058 27.792141951837767 24.010139416983524 23.188846641318126 65-69 24.85675168601998 28.71558237411896 23.64484559606511 22.782820343795954 70-74 25.197768762677487 27.5709939148073 23.899594320486816 23.3316430020284 75-79 24.546100010143014 26.9297088954255 24.581600568008927 23.942590526422556 80-84 24.871911936285702 26.941612134124686 24.38492365444123 23.80155227514838 85-89 25.382898874125164 27.13256922608784 23.886803935490413 23.597727964296585 90-94 24.72491252979058 27.0625221844734 24.415597586329294 23.796967699406725 95-99 24.928991681882735 26.86650436193954 24.340637046053967 23.863866910123757 100-104 25.651688812252765 26.944923420225177 23.790445278425803 23.61294248909626 105-109 25.098894411197893 27.72593569327518 23.40501065016736 23.770159245359572 110-114 25.03804402962362 27.462716850968853 23.8155625443847 23.683676575022826 115-119 24.774226281075595 27.701674277016743 23.61237950279046 23.911719939117198 120-124 25.58092338914257 27.71182141045155 23.36884830035515 23.338406900050735 125-129 25.13062446101557 27.509765129609903 23.456602242175215 23.90300816719931 130-134 25.143320988280653 28.019887372533102 23.322002942519404 23.514788696666837 135-139 25.608642726719417 28.048285656319738 22.94583079732197 23.397240819638874 140-144 25.33982552241834 28.3323189287888 23.148711706228443 23.179143842564415 145-149 24.932689865379732 29.33705867411735 22.509525019050038 23.220726441452882 150 24.321582551356833 30.053258939893485 23.20568095358864 22.419477555161045 >>END_MODULE >>Per sequence GC content fail #GC Content Count 0 25.0 1 22.5 2 11.5 3 2.0 4 0.5 5 0.5 6 0.5 7 0.0 8 0.5 9 0.5 10 0.0 11 0.0 12 0.5 13 1.0 14 1.0 15 1.0 16 0.5 17 1.0 18 1.0 19 0.5 20 1.0 21 2.5 22 2.5 23 1.0 24 2.0 25 1.5 26 1.0 27 5.5 28 8.0 29 8.0 30 9.0 31 16.5 32 26.5 33 24.0 34 34.0 35 47.0 36 52.5 37 65.5 38 80.0 39 100.5 40 120.0 41 123.5 42 146.0 43 170.5 44 184.0 45 188.0 46 169.5 47 170.5 48 179.0 49 174.0 50 145.0 51 134.5 52 138.5 53 123.5 54 105.0 55 94.5 56 108.0 57 106.0 58 95.0 59 84.5 60 85.5 61 89.0 62 79.0 63 70.5 64 64.0 65 61.5 66 53.5 67 44.5 68 38.0 69 30.5 70 24.0 71 18.0 72 12.0 73 11.0 74 6.0 75 2.5 76 2.0 77 1.0 78 0.5 79 0.5 80 0.5 81 0.5 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 0.5 2 1.075 3 1.125 4 1.375 5 1.225 6 1.4000000000000001 7 1.375 8 1.375 9 1.375 10-14 1.38 15-19 1.385 20-24 1.3599999999999999 25-29 1.3 30-34 1.335 35-39 1.21 40-44 1.2349999999999999 45-49 1.3 50-54 1.365 55-59 1.335 60-64 1.375 65-69 1.395 70-74 1.4000000000000001 75-79 1.41 80-84 1.435 85-89 1.41 90-94 1.395 95-99 1.4200000000000002 100-104 1.41 105-109 1.41 110-114 1.43 115-119 1.4500000000000002 120-124 1.4500000000000002 125-129 1.435 130-134 1.4449999999999998 135-139 1.4200000000000002 140-144 1.4200000000000002 145-149 1.575 150 1.425 >>END_MODULE >>Sequence Length Distribution pass #Length Count 150 4000.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 96.975 #Duplication Level Percentage of deduplicated Percentage of total 1 98.65944831142048 95.675 2 1.082753286929621 2.1 3 0.10311936065996391 0.3 4 0.051559680329981955 0.2 5 0.025779840164990978 0.125 6 0.0 0.0 7 0.0 0.0 8 0.0 0.0 9 0.0 0.0 >10 0.07733952049497293 1.6 >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 GATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCG 30 0.75 Illumina Single End PCR Primer 1 (100% over 50bp) NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN 20 0.5 No Hit GNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN 14 0.35000000000000003 No Hit CTGCAATTGCAAGCTTGTGTCAAAGAAGAGGGTAGCACCTGATCCTCTTG 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 0.225 0.0 0.0 0.0 0.0 2 0.225 0.0 0.0 0.0 0.0 3 0.225 0.0 0.0 0.0 0.0 4 0.225 0.0 0.0 0.0 0.0 5 0.225 0.0 0.0 0.0 0.0 6 0.225 0.0 0.0 0.0 0.0 7 0.225 0.0 0.0 0.0 0.0 8 0.225 0.0 0.0 0.0 0.0 9 0.225 0.0 0.0 0.0 0.0 10-11 0.225 0.0 0.0 0.0 0.0 12-13 0.225 0.0 0.0 0.0 0.0 14-15 0.225 0.0 0.0 0.0 0.0 16-17 0.225 0.0 0.0 0.0 0.0 18-19 0.225 0.0 0.0 0.0 0.0 20-21 0.25 0.0 0.0 0.0 0.0 22-23 0.25 0.0 0.0 0.0 0.0 24-25 0.25 0.0 0.0 0.0 0.0 26-27 0.25 0.0 0.0 0.0 0.0 28-29 0.25 0.0 0.0 0.0 0.0 30-31 0.25 0.0 0.0 0.0 0.0 32-33 0.25 0.0 0.0 0.0 0.0 34-35 0.25 0.0 0.0 0.0 0.0 36-37 0.25 0.0 0.0 0.0 0.0 38-39 0.25 0.0 0.0 0.0 0.0 40-41 0.25 0.0 0.0 0.0 0.0 42-43 0.25 0.0 0.0 0.0 0.0 44-45 0.25 0.0 0.0 0.0 0.0 46-47 0.25 0.0 0.0 0.0 0.0 48-49 0.25 0.0 0.0 0.0 0.0 50-51 0.25 0.0 0.0 0.0 0.0 52-53 0.25 0.0 0.0 0.0 0.0 54-55 0.25 0.0 0.0 0.0 0.0 56-57 0.25 0.0 0.0 0.0 0.0 58-59 0.25 0.0 0.0 0.0 0.0 60-61 0.25 0.0 0.0 0.0 0.0 62-63 0.25 0.0 0.0 0.0 0.0 64-65 0.25 0.0 0.0 0.0 0.0 66-67 0.25 0.0 0.0 0.0 0.0 68-69 0.25 0.0 0.0 0.0 0.0 70-71 0.25 0.0 0.0 0.0 0.0 72-73 0.25 0.0 0.0 0.0 0.0 74-75 0.25 0.0 0.0 0.0 0.0 76-77 0.25 0.0 0.0 0.0 0.0 78-79 0.2875 0.0 0.0 0.0 0.0 80-81 0.3 0.0 0.0 0.0 0.0 82-83 0.3 0.0 0.0 0.0 0.0 84-85 0.3 0.0 0.0 0.0 0.0 86-87 0.3 0.0 0.0 0.0 0.0 88-89 0.3 0.0 0.0 0.0 0.0 90-91 0.3 0.0 0.0 0.0 0.0 92-93 0.3 0.0 0.0 0.0 0.0 94-95 0.3375 0.0 0.0 0.0 0.0 96-97 0.375 0.0 0.0 0.0 0.0 98-99 0.375 0.0 0.0 0.0 0.0 100-101 0.375 0.0 0.0 0.0 0.0 102-103 0.3875 0.0 0.0 0.0 0.0 104-105 0.4 0.0 0.0 0.0 0.0 106-107 0.4125 0.0 0.0 0.0 0.0 108-109 0.4625 0.0 0.0 0.0 0.0 110-111 0.525 0.0 0.0 0.0 0.0 112-113 0.5375000000000001 0.0 0.0 0.0 0.0 114-115 0.575 0.0 0.0 0.0 0.0 116-117 0.6 0.0 0.0 0.0 0.0 118-119 0.6875 0.0 0.0 0.0 0.0 120-121 0.75 0.0 0.0 0.0 0.0 122-123 0.8125 0.0 0.0 0.0 0.0 124-125 0.85 0.0 0.0 0.0 0.0 126-127 0.9 0.0 0.0 0.0 0.0 128-129 0.9375 0.0 0.0 0.0 0.0 130-131 0.9875 0.0 0.0 0.0 0.0 132-133 1.0 0.0 0.0 0.0 0.0 134-135 1.025 0.0 0.0 0.0 0.0 136-137 1.0625 0.0 0.0 0.0 0.0 138 1.075 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position AAAAAAA 50 0.0013912604 17.279999 60-64 >>END_MODULE Read 2527778 spots for SRR8096890.sra Written 2527778 spots for SRR8096890.sra Read 2527778 spots for SRR8096890.sra Written 2527778 spots for SRR8096890.sra Read 2527778 spots for SRR8096890.sra Written 2527778 spots for SRR8096890.sra Read 2527778 spots for SRR8096890.sra Written 2527778 spots for SRR8096890.sra Read 2527778 spots for SRR8096890.sra Written 2527778 spots for SRR8096890.sra Read 2527778 spots for SRR8096890.sra Written 2527778 spots for SRR8096890.sra Read 2527797 spots for SRR8096890.sra Written 2527797 spots for SRR8096890.sra Read 2527778 spots for SRR8096890.sra Written 2527778 spots for SRR8096890.sra Read 2527778 spots for SRR8096890.sra Written 2527778 spots for SRR8096890.sra Read 2527778 spots for SRR8096890.sra Written 2527778 spots for SRR8096890.sra Read 2527778 spots for SRR8096890.sra Written 2527778 spots for SRR8096890.sra Read 2527778 spots for SRR8096890.sra Written 2527778 spots for SRR8096890.sra Read 2527778 spots for SRR8096890.sra Written 2527778 spots for SRR8096890.sra Read 2527778 spots for SRR8096890.sra Written 2527778 spots for SRR8096890.sra Read 2527778 spots for SRR8096890.sra Written 2527778 spots for SRR8096890.sra Read 2527778 spots for SRR8096890.sra Written 2527778 spots for SRR8096890.sra Read 2527778 spots for SRR8096890.sra Written 2527778 spots for SRR8096890.sra Read 2527778 spots for SRR8096890.sra Written 2527778 spots for SRR8096890.sra Read 2527778 spots for SRR8096890.sra Written 2527778 spots for SRR8096890.sra Read 2527778 spots for SRR8096890.sra Written 2527778 spots for SRR8096890.sra SRR ids: ['SRR8096890.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_oa2tz6rd SRR8096890.sra spots: 50555579 blocks: [[1, 2527778], [2527779, 5055556], [5055557, 7583334], [7583335, 10111112], [10111113, 12638890], [12638891, 15166668], [15166669, 17694446], [17694447, 20222224], [20222225, 22750002], [22750003, 25277780], [25277781, 27805558], [27805559, 30333336], [30333337, 32861114], [32861115, 35388892], [35388893, 37916670], [37916671, 40444448], [40444449, 42972226], [42972227, 45500004], [45500005, 48027782], [48027783, 50555579]] SRR8096890 file size 17011185 SRR8096890 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 SRR8096890 SRR8096890_1.fastq SRR8096890_2.fastq Input file: SRR8096890_1.fastq Paired file: SRR8096890_2.fastq trimmed: SRR8096890-trimmed-pair1.fastq, SRR8096890-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 Sun Dec 8 10:47:15 2024 >> started Sun Dec 8 10:53:46 2024 >> done (390.578s) 50555579 read pairs processed; of these: 195134 ( 0.39%) short read pairs filtered out after trimming by size control 2432016 ( 4.81%) empty read pairs filtered out after trimming by size control 47928429 (94.80%) read pairs available; of these: 27169661 (56.69%) trimmed read pairs available after processing 20758768 (43.31%) untrimmed read pairs available after processing Length distribution of reads after trimming: length count percentage 18 203 0.00% 19 154 0.00% 20 120 0.00% 21 151 0.00% 22 192 0.00% 23 178 0.00% 24 166 0.00% 25 115 0.00% 26 174 0.00% 27 156 0.00% 28 204 0.00% 29 166 0.00% 30 218 0.00% 31 221 0.00% 32 220 0.00% 33 171 0.00% 34 273 0.00% 35 366 0.00% 36 370 0.00% 37 362 0.00% 38 331 0.00% 39 538 0.00% 40 715 0.00% 41 779 0.00% 42 739 0.00% 43 688 0.00% 44 803 0.00% 45 1286 0.00% 46 1515 0.00% 47 1414 0.00% 48 1454 0.00% 49 1499 0.00% 50 1534 0.00% 51 1685 0.00% 52 1556 0.00% 53 1910 0.00% 54 1839 0.00% 55 2394 0.00% 56 2725 0.01% 57 2327 0.00% 58 3358 0.01% 59 4656 0.01% 60 4055 0.01% 61 14465 0.03% 62 4086 0.01% 63 2110 0.00% 64 2076 0.00% 65 2246 0.00% 66 2469 0.01% 67 2741 0.01% 68 3626 0.01% 69 5957 0.01% 70 5200 0.01% 71 3792 0.01% 72 3728 0.01% 73 4028 0.01% 74 4202 0.01% 75 4606 0.01% 76 4908 0.01% 77 5354 0.01% 78 6000 0.01% 79 6486 0.01% 80 7110 0.01% 81 7980 0.02% 82 9368 0.02% 83 12322 0.03% 84 23340 0.05% 85 24567 0.05% 86 27331 0.06% 87 29334 0.06% 88 29737 0.06% 89 30183 0.06% 90 29845 0.06% 91 29616 0.06% 92 29789 0.06% 93 30288 0.06% 94 32057 0.07% 95 33741 0.07% 96 35764 0.07% 97 38889 0.08% 98 42399 0.09% 99 45165 0.09% 100 46430 0.10% 101 49740 0.10% 102 53077 0.11% 103 56036 0.12% 104 59311 0.12% 105 61836 0.13% 106 66910 0.14% 107 69111 0.14% 108 73141 0.15% 109 74327 0.16% 110 78361 0.16% 111 81643 0.17% 112 85832 0.18% 113 90297 0.19% 114 93990 0.20% 115 98640 0.21% 116 103989 0.22% 117 108640 0.23% 118 115022 0.24% 119 122376 0.26% 120 129952 0.27% 121 136597 0.29% 122 143861 0.30% 123 153132 0.32% 124 160752 0.34% 125 170587 0.36% 126 179573 0.37% 127 190863 0.40% 128 203604 0.42% 129 214594 0.45% 130 230772 0.48% 131 246956 0.52% 132 261391 0.55% 133 277336 0.58% 134 294568 0.61% 135 318510 0.66% 136 349668 0.73% 137 376953 0.79% 138 405676 0.85% 139 436802 0.91% 140 478268 1.00% 141 528624 1.10% 142 582684 1.22% 143 663215 1.38% 144 755972 1.58% 145 932811 1.95% 146 1202460 2.51% 147 1702190 3.55% 148 2973800 6.20% 149 10197896 21.28% 150 20758768 43.31% 47928429 reads passed initial QC criterion=sequence-density sequence-density=0.92 sequence-density-rank=1 fanout-score=2.06 fanout-score-rank=32 prefix-density=0.94 prefix-fanout=2.0 sequence=AACATGGAGAACATGGCGAGGCGGCCGTTCTTGATCTCCTTCACCTTGAGCTCAGCGAA criterion=fanout-score sequence-density=0.01 sequence-density-rank=34 fanout-score=13.92 fanout-score-rank=1 prefix-density=0.02 prefix-fanout=3.9 sequence=CACCAAATGAATATACTCAATATCTTTATATATGAACAAAAACTTTTCATGCCCAGCAATTGCTTGGATGCAATGCGGTACTTAGGTACAAAGAGTGAAACATCAGAATAATTAAAGTGGCATGCTTAAAAGGTGTAAAGGCAGCTGCCGTCGTCACTCCTTGCTGTTGGGTCGTAGTTCTCGGCATTCCGGTCAGTGCAACCTTCTGGGACGGGCAAATTACCTTGTTGTGCTCCTTTACCTCCTCCTATGCAGCTAGAGATGGTGTGTGTATGAAGAGTGTTCTAACCGTAGAAGGAACCAGTCTTCATGGCATCTGAGTTAGCATCTCCCAGAGCAGCCTCGCTCATGTACTTGTCAGCAAGCTGCACACGCTTGACATTGTCCTGCTCTTGGACGAGCATGTGGCCGTACTCCAGGAGCTTCTCGATTGTCATCTTTGGCTGCTCAAAGGACACCGGTCCATCCTTCGAGTTCACCAGCTTCTTGCCGATGTTCTCTATTCCGGTTG criterion=sequence-density sequence-density=0.42 sequence-density-rank=1 fanout-score=2.20 fanout-score-rank=32 prefix-density=0.43 prefix-fanout=2.1 sequence=TTCGCTGAGCTCAAGGTGAAGGAGATCAAGAACGGCCGCCTCGCCATGTTCTCCATGTT criterion=fanout-score sequence-density=0.01 sequence-density-rank=34 fanout-score=42.55 fanout-score-rank=1 prefix-density=0.05 prefix-fanout=5.4 sequence=GTGCTCATCATCTTGTTTAATACCAAAGCTCTTCATATTCTCCTCCTTGATTTCATCAGCTTGAGGTTAGAGAGATTTGGAAGATGTCTTGCAGCTGTGGATCAAGCTGCAACTGTGGCTCAAACTGCACTTGCGGGAAGATGTACCCAGACCTGGCAGAGCAGGCCAGCACCACCAGCAGCACCCAGGCCCAGGTGGTGGTTCTCGGCATGGCGCCGGAGAAG SRR8096890 testing PE reads STAR mapping to Ensembl genome Started job on | Dec 08 10:58:51 Started mapping on | Dec 08 10:58:52 Finished on | Dec 08 11:57:13 Mapping speed, Million of reads per hour | 49.28 Number of input reads | 47928429 Average input read length | 289 UNIQUE READS: Uniquely mapped reads number | 45714197 Uniquely mapped reads % | 95.38% Average mapped length | 289.66 Number of splices: Total | 48702609 Number of splices: Annotated (sjdb) | 45921708 Number of splices: GT/AG | 48064898 Number of splices: GC/AG | 557531 Number of splices: AT/AC | 15596 Number of splices: Non-canonical | 64584 Mismatch rate per base, % | 0.34% Deletion rate per base | 0.01% Deletion average length | 1.99 Insertion rate per base | 0.01% Insertion average length | 1.88 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 645216 % of reads mapped to multiple loci | 1.35% Number of reads mapped to too many loci | 16671 % of reads mapped to too many loci | 0.03% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 2.98% % of reads unmapped: other | 0.26% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 1779965 1779965 1779965 N_multimapping 645216 645216 645216 N_noFeature 1810772 44332910 2159502 N_ambiguous 1234519 6214 206182 UnstrandedReadsAssigned:42668906 PositiveStrandReadsAssigned:1375073 NegativeStrandReadsAssigned:43348513 Dataset is classified negative stranded MeadianReadLen=150 20thPercentileLength=150 echo kmer=145 SRR8096890 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: SRR8096890-trimmed-pair1.fastq SRR8096890-trimmed-pair2.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 47,928,429 reads, 43,475,648 reads pseudoaligned [quant] estimated average fragment length: 286.527 [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,194 rounds 52973 SRR8096890.ke.tsv 35125 SRR8096890.se.tsv 88098 total ==> SRR8096890.ke.tsv <== target_id length eff_length est_counts tpm PNS24245 936 651.168 0 0 PNS24247 1044 758.473 134.963 5.78075 PNS24249 1928 1642.47 73.2623 1.44908 PNS24246 1044 758.473 134.963 5.78075 PNS24248 1044 758.473 134.963 5.78075 PNS24244 1471 1185.47 263.848 7.23055 PNS24243 293 78.5828 0 0 KQK14069 1603 1317.47 10933.7 269.609 KQK14071 474 212.3 181.168 27.723 ==> SRR8096890.se.tsv <== BRADI_1g14170v3 13098 BRADI_1g53295v3 53 BRADI_1g59795v3 1893 BRADI_1g07683v3 0 BRADI_1g00485v3 3 BRADI_1g20270v3 482 BRADI_1g74790v3 128 BRADI_1g09890v3 0 BRADI_1g77505v3 596 BRADI_1g48960v3 0 SRR8096890 completed mapping pipeline successfully