Starting /dee2/code/volunteer_pipeline.sh SRR7170000 current disk space = 3049618214912 free memory = 1581206704 SRR7170000 SRAfilesize 02acf624a84917a7cb590823501c12f4 SRR7170000.sra SRR7170000.sra file validated SRR7170000 is paired end SRR7170000 is conventional basespace SRR7170000 read1 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR7170000_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 42 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 33.545 34.0 34.0 34.0 33.0 34.0 2 33.61625 34.0 34.0 34.0 33.0 34.0 3 33.6895 34.0 34.0 34.0 33.0 34.0 4 33.683 34.0 34.0 34.0 33.0 34.0 5 33.68825 34.0 34.0 34.0 33.0 34.0 6 37.318 38.0 38.0 38.0 36.0 38.0 7 37.5935 38.0 38.0 38.0 37.0 38.0 8 37.726 38.0 38.0 38.0 38.0 38.0 9 37.676 38.0 38.0 38.0 38.0 38.0 10-14 37.652 38.0 38.0 38.0 38.0 38.0 15-19 37.6325 38.0 38.0 38.0 38.0 38.0 20-24 37.606700000000004 38.0 38.0 38.0 38.0 38.0 25-29 37.55989999999999 38.0 38.0 38.0 38.0 38.0 30-34 37.54645000000001 38.0 38.0 38.0 38.0 38.0 35-39 37.4506 38.0 38.0 38.0 37.6 38.0 40-44 36.96265 38.0 38.0 38.0 36.0 38.0 45-49 37.062149999999995 38.0 38.0 38.0 36.0 38.0 50-54 36.91025 38.0 38.0 38.0 35.6 38.0 55-59 36.930099999999996 38.0 38.0 38.0 36.0 38.0 60-64 36.816649999999996 38.0 38.0 38.0 35.4 38.0 65-69 36.7209 38.0 38.0 38.0 35.0 38.0 70-74 36.438 38.0 38.0 38.0 34.4 38.0 75-79 35.201 38.0 38.0 38.0 31.0 38.0 80-84 35.0231 38.0 37.4 38.0 30.2 38.0 85-89 34.88925 38.0 37.2 38.0 28.8 38.0 90-94 34.662549999999996 38.0 37.0 38.0 27.6 38.0 95-99 34.575199999999995 38.0 37.0 38.0 27.2 38.0 100-104 34.54260000000001 38.0 36.6 38.0 27.2 38.0 105-109 34.24114999999999 38.0 36.2 38.0 24.2 38.0 110-114 33.90214999999999 38.0 35.4 38.0 21.4 38.0 115-119 33.593650000000004 38.0 35.0 38.0 16.2 38.0 120-124 33.4019 38.0 35.0 38.0 15.0 38.0 125-129 32.90625 38.0 34.0 38.0 15.0 38.0 130-134 32.7063 38.0 34.0 38.0 14.4 38.0 135-139 32.1251 38.0 33.4 38.0 13.6 38.0 140-144 31.348300000000002 37.8 31.8 38.0 10.8 38.0 145-149 30.500049999999998 36.2 31.0 38.0 2.0 38.0 150-151 25.972375 33.5 16.5 37.0 2.0 38.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 8 1.0 9 0.0 10 1.0 11 4.0 12 6.0 13 5.0 14 11.0 15 15.0 16 13.0 17 16.0 18 47.0 19 84.0 20 12.0 21 7.0 22 10.0 23 9.0 24 15.0 25 25.0 26 29.0 27 23.0 28 19.0 29 27.0 30 41.0 31 49.0 32 72.0 33 89.0 34 171.0 35 324.0 36 956.0 37 1919.0 >>END_MODULE >>Per base sequence content warn #Base G A T C 1 43.29819277108434 15.311244979919678 9.713855421686747 31.676706827309236 2 23.175 16.950000000000003 29.15 30.725 3 19.175 16.925 28.375 35.525 4 21.475 22.325 23.150000000000002 33.050000000000004 5 25.174999999999997 27.275 23.674999999999997 23.875 6 22.15 31.474999999999998 25.85 20.525 7 15.174999999999999 32.425 36.275 16.125 8 16.1 32.925 29.525000000000002 21.45 9 19.175 28.525 32.824999999999996 19.475 10-14 18.605 32.26 26.735 22.400000000000002 15-19 18.895 30.264999999999997 27.334999999999997 23.505000000000003 20-24 19.305 31.255 26.784999999999997 22.655 25-29 18.8 30.759999999999998 26.875 23.565 30-34 18.54 31.19 26.650000000000002 23.62 35-39 19.57 30.625000000000004 27.034999999999997 22.770000000000003 40-44 18.355 30.455 27.205000000000002 23.985 45-49 20.48 29.275000000000002 27.955000000000002 22.29 50-54 19.415 29.535 26.39 24.66 55-59 19.405 29.21 28.155 23.23 60-64 19.919999999999998 28.765 28.32 22.994999999999997 65-69 18.59 33.115 26.115 22.18 70-74 18.415 33.095 25.865 22.625 75-79 18.375 32.195 25.905 23.525 80-84 19.585 30.959999999999997 26.279999999999998 23.175 85-89 20.345 29.99 26.179999999999996 23.485 90-94 20.153137824041636 29.576618957061356 27.129416474827345 23.140826744069663 95-99 18.88794354636905 30.704168960512483 27.175817026174865 23.232070466943597 100-104 19.455 31.990000000000002 25.629999999999995 22.925 105-109 19.220000000000002 31.775 26.26 22.745 110-114 19.405 32.015 25.7 22.88 115-119 19.390969548477425 31.386569328466425 26.126306315315766 23.096154807740387 120-124 19.647859143657463 31.362545018007204 25.470188075230094 23.519407763105242 125-129 20.0 31.6 25.535000000000004 22.865 130-134 19.576851898164357 31.541039363777323 25.653978892612418 23.228129845445906 135-139 19.790937281184355 31.309392817845357 25.187556266880062 23.712113634090226 140-144 20.292102235782526 31.275946581303455 24.618616515780523 23.813334667133496 145-149 19.955975786682675 30.701886037320524 25.43899144529491 23.903146730701884 150-151 19.432287107665374 30.674002751031637 25.034387895460796 24.85932224584219 >>END_MODULE >>Per sequence GC content warn #GC Content Count 0 1.0 1 0.5 2 0.0 3 0.0 4 0.0 5 0.0 6 0.5 7 0.5 8 0.0 9 0.0 10 0.0 11 0.5 12 1.0 13 0.5 14 0.5 15 1.5 16 2.0 17 1.0 18 1.0 19 3.0 20 2.5 21 2.5 22 4.0 23 3.0 24 4.0 25 8.0 26 11.0 27 13.0 28 15.5 29 27.5 30 36.0 31 46.5 32 63.5 33 78.5 34 95.0 35 106.0 36 131.0 37 154.5 38 174.5 39 195.0 40 191.5 41 212.5 42 233.0 43 218.5 44 207.5 45 225.0 46 223.0 47 192.5 48 168.5 49 152.0 50 134.0 51 105.5 52 101.5 53 103.0 54 87.0 55 62.0 56 45.0 57 35.5 58 24.0 59 22.0 60 18.0 61 13.5 62 14.0 63 8.0 64 3.5 65 4.0 66 5.0 67 2.0 68 1.5 69 1.5 70 0.5 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 0.4 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 0.09 95-99 0.095 100-104 0.0 105-109 0.0 110-114 0.0 115-119 0.005 120-124 0.04 125-129 0.0 130-134 0.034999999999999996 135-139 0.03 140-144 0.034999999999999996 145-149 0.055 150-151 0.0375 >>END_MODULE >>Sequence Length Distribution pass #Length Count 151 4000.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 93.575 #Duplication Level Percentage of deduplicated Percentage of total 1 97.46192893401016 91.2 2 2.2709056906224956 4.25 3 0.13358268768367618 0.375 4 0.05343307507347048 0.2 5 0.02671653753673524 0.125 6 0.0 0.0 7 0.0 0.0 8 0.0 0.0 9 0.0 0.0 >10 0.02671653753673524 0.475 >50 0.0 0.0 >100 0.02671653753673524 3.375 >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 GATCGGAAGAGCACACGTCTGAACTCCAGTCACACAGTGATCTCGTATGC 135 3.375 TruSeq Adapter, Index 5 (100% over 50bp) ATCGGAAGAGCACACGTCTGAACTCCAGTCACACAGTGATCTCGTATGCC 19 0.475 TruSeq Adapter, Index 5 (100% over 50bp) CCCCACTGCTGCCTCCCGTAGGAGTCTGGACCGTGTCTCAGTTCCAGTGT 5 0.125 No Hit >>END_MODULE >>Adapter Content fail #Position Illumina Universal Adapter Illumina Small RNA 3' Adapter Illumina Small RNA 5' Adapter Nextera Transposase Sequence SOLID Small RNA Adapter 1 0.075 0.0 0.0 0.0 0.0 2 0.075 0.0 0.0 0.0 0.0 3 0.075 0.0 0.0 0.0 0.0 4 0.075 0.0 0.0 0.0 0.0 5 0.075 0.0 0.0 0.0 0.0 6 0.075 0.0 0.0 0.0 0.0 7 0.075 0.0 0.0 0.0 0.0 8 0.075 0.0 0.0 0.0 0.0 9 0.075 0.0 0.0 0.0 0.0 10-11 0.075 0.0 0.0 0.0 0.0 12-13 0.075 0.0 0.0 0.0 0.0 14-15 0.075 0.0 0.0 0.0 0.0 16-17 0.075 0.0 0.0 0.0 0.0 18-19 0.075 0.0 0.0 0.0 0.0 20-21 0.075 0.0 0.0 0.0 0.0 22-23 0.075 0.0 0.0 0.0 0.0 24-25 0.075 0.0 0.0 0.0 0.0 26-27 0.075 0.0 0.0 0.0 0.0 28-29 0.075 0.0 0.0 0.0 0.0 30-31 0.075 0.0 0.0 0.0 0.0 32-33 0.075 0.0 0.0 0.0 0.0 34-35 0.075 0.0 0.0 0.0 0.0 36-37 0.075 0.0 0.0 0.0 0.0 38-39 0.075 0.0 0.0 0.0 0.0 40-41 0.075 0.0 0.0 0.0 0.0 42-43 0.075 0.0 0.0 0.0 0.0 44-45 0.0875 0.0 0.0 0.0 0.0 46-47 0.1 0.0 0.0 0.0 0.0 48-49 0.1 0.0 0.0 0.0 0.0 50-51 0.1 0.0 0.0 0.0 0.0 52-53 0.1 0.0 0.0 0.0 0.0 54-55 0.1 0.0 0.0 0.0 0.0 56-57 0.1 0.0 0.0 0.0 0.0 58-59 0.1 0.0 0.0 0.0 0.0 60-61 0.125 0.0 0.0 0.0 0.0 62-63 0.125 0.0 0.0 0.0 0.0 64-65 0.15 0.0 0.0 0.0 0.0 66-67 0.175 0.0 0.0 0.0 0.0 68-69 0.2 0.0 0.0 0.0 0.0 70-71 0.225 0.0 0.0 0.0 0.0 72-73 0.225 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 0.25 0.0 0.0 0.0 0.0 80-81 0.3125 0.0 0.0 0.0 0.0 82-83 0.3875 0.0 0.0 0.0 0.0 84-85 0.44999999999999996 0.0 0.0 0.0 0.0 86-87 0.575 0.0 0.0 0.0 0.0 88-89 0.6625 0.0 0.0 0.0 0.0 90-91 0.95 0.0 0.0 0.0 0.0 92-93 1.0875 0.0 0.0 0.0 0.0 94-95 1.2125 0.0 0.0 0.0 0.0 96-97 1.3375 0.0 0.0 0.0 0.0 98-99 1.4875 0.0 0.0 0.0 0.0 100-101 1.6625 0.0 0.0 0.0 0.0 102-103 1.8875 0.0 0.0 0.0 0.0 104-105 2.175 0.0 0.0 0.0 0.0 106-107 2.6500000000000004 0.0 0.0 0.0 0.0 108-109 2.8625 0.0 0.0 0.0 0.0 110-111 3.075 0.0 0.0 0.0 0.0 112-113 3.3499999999999996 0.0 0.0 0.0 0.0 114-115 3.6125 0.0 0.0 0.0 0.0 116-117 4.074999999999999 0.0 0.0 0.0 0.0 118-119 4.6875 0.0 0.0 0.0 0.0 120-121 5.262499999999999 0.0 0.0 0.0 0.0 122-123 5.775 0.0 0.0 0.0 0.0 124-125 6.1875 0.0 0.0 0.0 0.0 126-127 6.675000000000001 0.0 0.0 0.0 0.0 128-129 7.2 0.0 0.0 0.0 0.0 130-131 7.737500000000001 0.0 0.0 0.0 0.0 132-133 8.25 0.0 0.0 0.0 0.0 134-135 8.912500000000001 0.0 0.0 0.0 0.0 136-137 9.649999999999999 0.0 0.0 0.0 0.0 138-139 10.375 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position GAGCACA 55 2.8476407E-4 52.72273 9 AGAGCAC 55 2.8476407E-4 52.72273 8 AAGAGCA 60 4.376127E-4 48.32917 7 GATCGGA 65 6.0945144E-4 45.17624 1 GAAGAGC 70 9.357257E-4 41.425 6 TCGGAAG 70 9.357257E-4 41.425 3 CGGAAGA 70 9.357257E-4 41.425 4 ATCGGAA 70 9.357257E-4 41.425 2 GGAAGAG 85 0.002430757 34.114704 5 TGCTTGA 20 0.0059376103 28.9975 55-59 CTGCTTG 20 0.0059376103 28.9975 55-59 CTTGAAA 20 0.0059376103 28.9975 60-64 TGAAAAA 20 0.0059376103 28.9975 60-64 TGCCGTC 30 0.0014445208 24.164585 45-49 AAAAAAA 470 3.6299243E-6 5.861197 65-69 >>END_MODULE SRR7170000 read2 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR7170000_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 43 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 33.0485 34.0 33.0 34.0 33.0 34.0 2 33.18675 34.0 33.0 34.0 33.0 34.0 3 33.07875 34.0 33.0 34.0 33.0 34.0 4 32.94475 34.0 33.0 34.0 33.0 34.0 5 33.06575 34.0 33.0 34.0 33.0 34.0 6 37.153 38.0 38.0 38.0 38.0 38.0 7 37.2365 38.0 38.0 38.0 38.0 38.0 8 37.1975 38.0 38.0 38.0 38.0 38.0 9 37.25525 38.0 38.0 38.0 38.0 38.0 10-14 37.080949999999994 38.0 38.0 38.0 38.0 38.0 15-19 37.0033 38.0 38.0 38.0 37.8 38.0 20-24 37.04325 38.0 38.0 38.0 37.8 38.0 25-29 37.001099999999994 38.0 38.0 38.0 38.0 38.0 30-34 37.026650000000004 38.0 38.0 38.0 38.0 38.0 35-39 36.9384 38.0 38.0 38.0 37.6 38.0 40-44 36.873149999999995 38.0 38.0 38.0 37.6 38.0 45-49 36.76174999999999 38.0 38.0 38.0 37.0 38.0 50-54 36.8701 38.0 38.0 38.0 37.0 38.0 55-59 36.932849999999995 38.0 38.0 38.0 37.0 38.0 60-64 36.8142 38.0 38.0 38.0 37.0 38.0 65-69 36.35155 38.0 38.0 38.0 36.0 38.0 70-74 35.377449999999996 38.0 38.0 38.0 34.0 38.0 75-79 35.3487 38.0 38.0 38.0 34.0 38.0 80-84 35.19585 38.0 38.0 38.0 33.4 38.0 85-89 34.9413 38.0 38.0 38.0 32.2 38.0 90-94 34.80965 38.0 38.0 38.0 30.0 38.0 95-99 34.984950000000005 38.0 38.0 38.0 31.2 38.0 100-104 34.9388 38.0 38.0 38.0 31.2 38.0 105-109 34.79225 38.0 38.0 38.0 30.6 38.0 110-114 34.65985 38.0 38.0 38.0 28.4 38.0 115-119 34.499199999999995 38.0 38.0 38.0 27.0 38.0 120-124 34.31425 38.0 37.0 38.0 24.6 38.0 125-129 33.94315 38.0 36.6 38.0 20.6 38.0 130-134 33.16995 38.0 35.6 38.0 13.8 38.0 135-139 32.5034 38.0 34.8 38.0 4.2 38.0 140-144 31.859699999999997 38.0 33.4 38.0 2.0 38.0 145-149 31.328449999999997 38.0 33.0 38.0 2.0 38.0 150-151 27.419375 34.5 17.5 38.0 2.0 38.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 2 31.0 3 11.0 4 1.0 5 4.0 6 1.0 7 1.0 8 1.0 9 2.0 10 3.0 11 0.0 12 1.0 13 4.0 14 6.0 15 17.0 16 26.0 17 92.0 18 39.0 19 8.0 20 7.0 21 8.0 22 13.0 23 11.0 24 12.0 25 8.0 26 6.0 27 16.0 28 26.0 29 29.0 30 30.0 31 39.0 32 74.0 33 89.0 34 95.0 35 167.0 36 413.0 37 2709.0 >>END_MODULE >>Per base sequence content warn #Base G A T C 1 41.36807817589577 22.62590829366074 14.332247557003258 21.67376597344024 2 26.960661488348787 30.19293410172889 25.95840641443247 16.887997995489854 3 20.699195171026158 30.030181086519114 30.331991951710265 18.938631790744466 4 26.31711620872196 31.383917317872445 22.53592135114696 19.763045122258635 5 28.733031674208142 32.32780291603821 22.021116138763198 16.918049270990448 6 24.55390801708972 36.29052525760241 23.07112339783865 16.084443327469213 7 21.155778894472363 27.060301507537687 34.07035175879397 17.713567839195978 8 22.702159718734304 29.432446007031643 24.81165243596183 23.053741838272224 9 25.879396984924625 26.28140703517588 27.28643216080402 20.552763819095475 10-14 24.967254408060455 27.4911838790932 26.332493702770783 21.209068010075566 15-19 24.800726465543335 27.05075169004137 27.893249924326508 20.25527192008879 20-24 25.99456138583946 29.267801389868065 25.566522308389565 19.17111491590291 25-29 25.051624276001007 29.3679174011584 26.300679929488798 19.2797783933518 30-34 25.091879373709915 28.021950359965764 27.14091526959674 19.745254996727585 35-39 23.18518892195934 27.25621752509711 28.31054835292337 21.24804520002018 40-44 26.652516676773804 26.278552658176675 27.223569840307256 19.84536082474227 45-49 24.003435558025565 26.736725104835042 27.575405446369928 21.684433890769466 50-54 23.1908143224052 28.16638968625674 28.382938006748248 20.259857984589818 55-59 22.91268002820022 28.995870681841073 28.628260650619396 19.46318863933931 60-64 22.73667221465678 30.75603974378373 26.917839310031777 19.589448731527714 65-69 23.02774001913105 30.549262447767205 26.97477722398429 19.448220309117453 70-74 23.37766624843162 30.429109159347554 26.419071518193228 19.774153074027602 75-79 22.920118491740723 29.597830998644376 27.44891298890395 20.03313752071095 80-84 23.381331185177725 29.302185077031517 27.66085993354144 19.65562380424932 85-89 23.93765548053003 29.481646951312385 27.049804538762245 19.530893029395337 90-94 24.264407467532468 28.657670454545453 27.800324675324678 19.2775974025974 95-99 23.451883897580363 29.362643996176867 27.767996378087428 19.41747572815534 100-104 23.47410759175465 29.66817496229261 27.36551030668678 19.492207139265965 105-109 23.269965801649565 30.11466505733253 27.499497083081874 19.115872057936027 110-114 23.081184528605963 30.14705882352941 27.48791297340854 19.283843674456083 115-119 23.644949012910033 29.788516602200232 27.34716431406038 19.219370070829356 120-124 24.27647088328234 29.783819029944326 27.23077694738426 18.708933139389075 125-129 23.79387073935471 29.91301709315263 27.08101547486599 19.21209669262668 130-134 24.514077645007436 29.898969177906558 26.878301451356478 18.708651725729524 135-139 25.12812548532381 29.228141015685665 26.986592120929753 18.657141378060775 140-144 24.91410723581468 29.656428943258717 26.517438833940655 18.912024986985944 145-149 25.17468251134799 29.73937879328811 26.332432294588664 18.753506400775233 150-151 25.413249211356465 30.195583596214508 25.55205047318612 18.839116719242902 >>END_MODULE >>Per sequence GC content warn #GC Content Count 0 8.0 1 4.5 2 2.0 3 2.5 4 3.0 5 2.5 6 0.5 7 1.0 8 1.5 9 0.5 10 0.0 11 1.0 12 1.0 13 1.5 14 1.5 15 0.0 16 1.0 17 1.0 18 0.0 19 0.0 20 0.0 21 1.0 22 2.0 23 2.0 24 1.5 25 1.0 26 3.0 27 8.5 28 11.0 29 12.5 30 14.5 31 23.0 32 34.5 33 43.0 34 57.5 35 72.5 36 91.0 37 117.0 38 142.5 39 170.5 40 213.0 41 233.5 42 241.5 43 254.5 44 261.5 45 271.5 46 264.5 47 231.5 48 201.5 49 178.0 50 145.5 51 122.5 52 106.5 53 93.5 54 78.5 55 60.5 56 49.0 57 40.0 58 32.5 59 24.0 60 17.0 61 14.5 62 10.5 63 7.5 64 3.5 65 1.0 66 2.0 67 2.0 68 1.0 69 0.0 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 0.22499999999999998 2 0.22499999999999998 3 0.6 4 0.8250000000000001 5 0.5499999999999999 6 0.525 7 0.5 8 0.44999999999999996 9 0.5 10-14 0.75 15-19 0.89 20-24 0.7100000000000001 25-29 0.7250000000000001 30-34 0.685 35-39 0.885 40-44 1.06 45-49 1.035 50-54 0.715 55-59 0.7100000000000001 60-64 0.865 65-69 0.685 70-74 0.375 75-79 0.415 80-84 0.69 85-89 1.5150000000000001 90-94 1.44 95-99 0.605 100-104 0.5499999999999999 105-109 0.58 110-114 0.72 115-119 0.46499999999999997 120-124 0.315 125-129 1.13 130-134 2.505 135-139 3.415 140-144 3.95 145-149 1.965 150-151 0.9375 >>END_MODULE >>Sequence Length Distribution pass #Length Count 151 4000.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 93.0 #Duplication Level Percentage of deduplicated Percentage of total 1 97.36559139784946 90.55 2 2.204301075268817 4.1000000000000005 3 0.24193548387096775 0.675 4 0.053763440860215055 0.2 5 0.053763440860215055 0.25 6 0.026881720430107527 0.15 7 0.0 0.0 8 0.0 0.0 9 0.0 0.0 >10 0.026881720430107527 0.675 >50 0.0 0.0 >100 0.026881720430107527 3.4000000000000004 >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 GATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCG 136 3.4000000000000004 Illumina Single End PCR Primer 1 (100% over 50bp) ATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGT 27 0.675 Illumina Single End PCR Primer 1 (100% over 50bp) CATTAATTAGGGCTGAAAGCCCTAACTTAATGGACGGGAGGTATCCCAAT 6 0.15 No Hit GCTGAAAGCCCTAACTTAATGGACGGGAGGTATCCCAATAGGAGGTTTCC 5 0.125 No Hit NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN 5 0.125 No Hit >>END_MODULE >>Adapter Content fail #Position Illumina Universal Adapter Illumina Small RNA 3' Adapter Illumina Small RNA 5' Adapter Nextera Transposase Sequence SOLID Small RNA Adapter 1 0.075 0.0 0.0 0.0 0.0 2 0.075 0.0 0.0 0.0 0.0 3 0.075 0.0 0.0 0.0 0.0 4 0.075 0.0 0.0 0.0 0.0 5 0.075 0.0 0.0 0.0 0.0 6 0.075 0.0 0.0 0.0 0.0 7 0.075 0.0 0.0 0.0 0.0 8 0.075 0.0 0.0 0.0 0.0 9 0.075 0.0 0.0 0.0 0.0 10-11 0.075 0.0 0.0 0.0 0.0 12-13 0.075 0.0 0.0 0.0 0.0 14-15 0.075 0.0 0.0 0.0 0.0 16-17 0.075 0.0 0.0 0.0 0.0 18-19 0.075 0.0 0.0 0.0 0.0 20-21 0.075 0.0 0.0 0.0 0.0 22-23 0.075 0.0 0.0 0.0 0.0 24-25 0.075 0.0 0.0 0.0 0.0 26-27 0.075 0.0 0.0 0.0 0.0 28-29 0.075 0.0 0.0 0.0 0.0 30-31 0.075 0.0 0.0 0.0 0.0 32-33 0.075 0.0 0.0 0.0 0.0 34-35 0.075 0.0 0.0 0.0 0.0 36-37 0.075 0.0 0.0 0.0 0.0 38-39 0.075 0.0 0.0 0.0 0.0 40-41 0.075 0.0 0.0 0.0 0.0 42-43 0.075 0.0 0.0 0.0 0.0 44-45 0.0875 0.0 0.0 0.0 0.0 46-47 0.1 0.0 0.0 0.0 0.0 48-49 0.1 0.0 0.0 0.0 0.0 50-51 0.1 0.0 0.0 0.0 0.0 52-53 0.1 0.0 0.0 0.0 0.0 54-55 0.1 0.0 0.0 0.0 0.0 56-57 0.1 0.0 0.0 0.0 0.0 58-59 0.1 0.0 0.0 0.0 0.0 60-61 0.125 0.0 0.0 0.0 0.0 62-63 0.125 0.0 0.0 0.0 0.0 64-65 0.15 0.0 0.0 0.0 0.0 66-67 0.175 0.0 0.0 0.0 0.0 68-69 0.2 0.0 0.0 0.0 0.0 70-71 0.225 0.0 0.0 0.0 0.0 72-73 0.225 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 0.2625 0.0 0.0 0.0 0.0 80-81 0.36250000000000004 0.0 0.0 0.0 0.0 82-83 0.4375 0.0 0.0 0.0 0.0 84-85 0.5 0.0 0.0 0.0 0.0 86-87 0.625 0.0 0.0 0.0 0.0 88-89 0.7250000000000001 0.0 0.0 0.0 0.0 90-91 1.0125 0.0 0.0 0.0 0.0 92-93 1.1375000000000002 0.0 0.0 0.0 0.0 94-95 1.2625000000000002 0.0 0.0 0.0 0.0 96-97 1.4125 0.0 0.0 0.0 0.0 98-99 1.5625 0.0 0.0 0.0 0.0 100-101 1.7125 0.0 0.0 0.0 0.0 102-103 1.9125 0.0 0.0 0.0 0.0 104-105 2.2125 0.0 0.0 0.0 0.0 106-107 2.6500000000000004 0.0 0.0 0.0 0.0 108-109 2.8875 0.0 0.0 0.0 0.0 110-111 3.0999999999999996 0.0 0.0 0.0 0.0 112-113 3.3875 0.0 0.0 0.0 0.0 114-115 3.725 0.0 0.0 0.0 0.0 116-117 4.199999999999999 0.0 0.0 0.0 0.0 118-119 4.762499999999999 0.0 0.0 0.0 0.0 120-121 5.3375 0.0 0.0 0.0 0.0 122-123 5.8125 0.0 0.0 0.0 0.0 124-125 6.25 0.0 0.0 0.0 0.0 126-127 6.699999999999999 0.0 0.0 0.0 0.0 128-129 7.2375 0.0 0.0 0.0 0.0 130-131 7.775 0.0 0.0 0.0 0.0 132-133 8.225 0.0 0.0 0.0 0.0 134-135 8.8625 0.0 0.0 0.0 0.0 136-137 9.537500000000001 0.0 0.0 0.0 0.0 138-139 10.2375 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position CTGAAAG 10 0.0068963906 144.5375 5 GAGCGTC 55 2.8917132E-4 52.55909 9 AAGAGCG 55 2.8917132E-4 52.55909 7 AGAGCGT 55 2.8917132E-4 52.55909 8 GATCGGA 65 6.595053E-4 44.473076 1 CGGAAGA 70 9.5016026E-4 41.29643 4 ATCGGAA 70 9.5016026E-4 41.29643 2 GGAAGAG 70 9.5016026E-4 41.29643 5 GAAGAGC 75 0.0013343456 38.543335 6 TCGGAAG 75 0.0013343456 38.543335 3 >>END_MODULE Read 411473 spots for SRR7170000.sra Written 411473 spots for SRR7170000.sra Read 411473 spots for SRR7170000.sra Written 411473 spots for SRR7170000.sra Read 411473 spots for SRR7170000.sra Written 411473 spots for SRR7170000.sra Read 411473 spots for SRR7170000.sra Written 411473 spots for SRR7170000.sra Read 411473 spots for SRR7170000.sra Written 411473 spots for SRR7170000.sra Read 411473 spots for SRR7170000.sra Written 411473 spots for SRR7170000.sra Read 411473 spots for SRR7170000.sra Written 411473 spots for SRR7170000.sra Read 411473 spots for SRR7170000.sra Written 411473 spots for SRR7170000.sra Read 411473 spots for SRR7170000.sra Written 411473 spots for SRR7170000.sra Read 411473 spots for SRR7170000.sra Written 411473 spots for SRR7170000.sra Read 411480 spots for SRR7170000.sra Written 411480 spots for SRR7170000.sra Read 411473 spots for SRR7170000.sra Written 411473 spots for SRR7170000.sra Read 411473 spots for SRR7170000.sra Written 411473 spots for SRR7170000.sra Read 411473 spots for SRR7170000.sra Written 411473 spots for SRR7170000.sra Read 411473 spots for SRR7170000.sra Written 411473 spots for SRR7170000.sra Read 411473 spots for SRR7170000.sra Written 411473 spots for SRR7170000.sra Read 411473 spots for SRR7170000.sra Written 411473 spots for SRR7170000.sra Read 411473 spots for SRR7170000.sra Written 411473 spots for SRR7170000.sra Read 411473 spots for SRR7170000.sra Written 411473 spots for SRR7170000.sra Read 411473 spots for SRR7170000.sra Written 411473 spots for SRR7170000.sra SRR ids: ['SRR7170000.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_f82z6sii SRR7170000.sra spots: 8229467 blocks: [[1, 411473], [411474, 822946], [822947, 1234419], [1234420, 1645892], [1645893, 2057365], [2057366, 2468838], [2468839, 2880311], [2880312, 3291784], [3291785, 3703257], [3703258, 4114730], [4114731, 4526203], [4526204, 4937676], [4937677, 5349149], [5349150, 5760622], [5760623, 6172095], [6172096, 6583568], [6583569, 6995041], [6995042, 7406514], [7406515, 7817987], [7817988, 8229467]] SRR7170000 file size 2770454 SRR7170000 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 SRR7170000 SRR7170000_1.fastq SRR7170000_2.fastq Input file: SRR7170000_1.fastq Paired file: SRR7170000_2.fastq trimmed: SRR7170000-trimmed-pair1.fastq, SRR7170000-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 Wed Feb 12 09:34:36 2025 >> started Wed Feb 12 09:34:49 2025 >> done (13.312s) 8229467 read pairs processed; of these: 20948 ( 0.25%) short read pairs filtered out after trimming by size control 275751 ( 3.35%) empty read pairs filtered out after trimming by size control 7932768 (96.39%) read pairs available; of these: 4618275 (58.22%) trimmed read pairs available after processing 3314493 (41.78%) untrimmed read pairs available after processing Length distribution of reads after trimming: length count percentage 18 10 0.00% 19 11 0.00% 20 11 0.00% 21 13 0.00% 22 16 0.00% 23 7 0.00% 24 30 0.00% 25 14 0.00% 26 12 0.00% 27 22 0.00% 28 27 0.00% 29 32 0.00% 30 26 0.00% 31 22 0.00% 32 27 0.00% 33 35 0.00% 34 33 0.00% 35 23 0.00% 36 29 0.00% 37 24 0.00% 38 57 0.00% 39 50 0.00% 40 51 0.00% 41 54 0.00% 42 70 0.00% 43 68 0.00% 44 88 0.00% 45 134 0.00% 46 136 0.00% 47 143 0.00% 48 180 0.00% 49 172 0.00% 50 187 0.00% 51 234 0.00% 52 209 0.00% 53 236 0.00% 54 243 0.00% 55 282 0.00% 56 285 0.00% 57 311 0.00% 58 384 0.00% 59 355 0.00% 60 412 0.01% 61 450 0.01% 62 529 0.01% 63 630 0.01% 64 694 0.01% 65 1261 0.02% 66 2004 0.03% 67 2643 0.03% 68 4235 0.05% 69 8264 0.10% 70 17299 0.22% 71 9061 0.11% 72 4577 0.06% 73 3305 0.04% 74 2721 0.03% 75 2738 0.03% 76 2459 0.03% 77 2550 0.03% 78 2534 0.03% 79 2679 0.03% 80 2816 0.04% 81 3252 0.04% 82 3532 0.04% 83 4027 0.05% 84 5228 0.07% 85 5888 0.07% 86 6696 0.08% 87 7220 0.09% 88 8001 0.10% 89 8710 0.11% 90 9124 0.12% 91 9261 0.12% 92 9473 0.12% 93 10138 0.13% 94 10704 0.13% 95 11473 0.14% 96 12064 0.15% 97 12337 0.16% 98 12885 0.16% 99 13076 0.16% 100 13703 0.17% 101 14421 0.18% 102 15217 0.19% 103 15797 0.20% 104 16496 0.21% 105 17559 0.22% 106 18085 0.23% 107 19038 0.24% 108 19884 0.25% 109 20700 0.26% 110 20758 0.26% 111 20377 0.26% 112 21242 0.27% 113 22506 0.28% 114 22940 0.29% 115 24107 0.30% 116 24530 0.31% 117 25290 0.32% 118 25436 0.32% 119 25391 0.32% 120 26524 0.33% 121 26906 0.34% 122 27524 0.35% 123 28189 0.36% 124 29576 0.37% 125 30429 0.38% 126 31827 0.40% 127 32857 0.41% 128 33450 0.42% 129 34568 0.44% 130 35561 0.45% 131 36466 0.46% 132 38165 0.48% 133 39833 0.50% 134 41454 0.52% 135 44095 0.56% 136 45847 0.58% 137 48407 0.61% 138 51054 0.64% 139 54245 0.68% 140 56682 0.71% 141 61136 0.77% 142 66787 0.84% 143 72914 0.92% 144 81177 1.02% 145 93507 1.18% 146 115381 1.45% 147 154503 1.95% 148 227718 2.87% 149 431557 5.44% 150 1875156 23.64% 151 3314493 41.78% 7932768 reads passed initial QC criterion=sequence-density sequence-density=0.15 sequence-density-rank=1 fanout-score=3.97 fanout-score-rank=31 prefix-density=0.20 prefix-fanout=3.0 sequence=GGCTTCTCCCATTTGAGGGGCTTGACAAC criterion=fanout-score sequence-density=0.04 sequence-density-rank=33 fanout-score=43.48 fanout-score-rank=1 prefix-density=0.33 prefix-fanout=5.1 sequence=ATCTCCTTCATGGGAAACTGCAGCTTCAGGGGAAACATGTTCAGGAGCTGGAGGAGGGACCTCGTCAGCTTTCTTATGTCCTGGCAATTTCTCCTTGATTTTGTCAAGGAAACCCTTCTTATCCTCTGGTTCGTGGGGTGTCTCTGTATGGACTACCTCGACAGGAACACTAGTATCCTCGTGTTCCTTCTCCTC criterion=sequence-density sequence-density=0.52 sequence-density-rank=1 fanout-score=3.56 fanout-score-rank=30 prefix-density=0.66 prefix-fanout=2.8 sequence=GCTGACGAGTGGCGGACGGGTGAGTAATGTCTGGGAAACTGCCTGATGGAGGGGGATAACTACTGGAAACGGTAGCTAATACCGCATAACGTCGCAAGACCAAAGAGGGGGACCTTCGGGCCTCTTGCCATCGGATGTGCCCAGATGGGATTAGCTAGTAGGTGGGGTAACGGCTCACCTAGGCGACGATCCCTAGCTGGTCTGAGAGGATGACCAGCCACACTGGAACTGAGACACGGTCCAGACTCCTACGGGAGGCAGCAGTGGGGAATATTGCACAATGGGCGCAAGCCTGATGCAGCCATGCCGCGTGTATGAAGAAGGCCTTCGGGTTGTAAAGTACTTTCAGCGGGGAGGAAGGGAGTAAAGTTAATACCTTTGCTCATTGACGTTACCCGCAGAAGAAGCACCGGCTAACTCCGTGCCAGCAGCCGCGGTAATACGGAGGGTGCAAGCGTTAATCGGAATTACTGGGCGTAAAGCGCACGCAGGCGGTTTGTTAAGTCAGATG criterion=fanout-score sequence-density=0.04 sequence-density-rank=32 fanout-score=69.39 fanout-score-rank=1 prefix-density=0.26 prefix-fanout=10.2 sequence=GAAAATGGAGGCAATGAAAATGAAGATCTTTGTTGTGTTGATGGTGGTCTTGATGGCCTTCTCAACCATGCAAAAGGCTGCAGCTGCCGATGCACCAGCACCA SRR7170000 testing PE reads STAR mapping to Ensembl genome Started job on | Feb 12 09:35:42 Started mapping on | Feb 12 09:35:43 Finished on | Feb 12 09:37:55 Mapping speed, Million of reads per hour | 216.35 Number of input reads | 7932768 Average input read length | 288 UNIQUE READS: Uniquely mapped reads number | 6775464 Uniquely mapped reads % | 85.41% Average mapped length | 289.57 Number of splices: Total | 4952753 Number of splices: Annotated (sjdb) | 4851127 Number of splices: GT/AG | 4874474 Number of splices: GC/AG | 59201 Number of splices: AT/AC | 4313 Number of splices: Non-canonical | 14765 Mismatch rate per base, % | 0.38% Deletion rate per base | 0.04% Deletion average length | 2.53 Insertion rate per base | 0.03% Insertion average length | 2.39 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 126744 % of reads mapped to multiple loci | 1.60% Number of reads mapped to too many loci | 15335 % of reads mapped to too many loci | 0.19% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 12.71% % of reads unmapped: other | 0.08% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 1043235 1043235 1043235 N_multimapping 126744 126744 126744 N_noFeature 170250 6668201 218134 N_ambiguous 88044 577 28329 UnstrandedReadsAssigned:6517170 PositiveStrandReadsAssigned:106686 NegativeStrandReadsAssigned:6529001 Dataset is classified negative stranded MeadianReadLen=151 20thPercentileLength=144 echo kmer=139 SRR7170000 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: SRR7170000-trimmed-pair1.fastq SRR7170000-trimmed-pair2.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 7,932,768 reads, 6,545,965 reads pseudoaligned [quant] estimated average fragment length: 215.657 [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,113 rounds 52401 SRR7170000.ke.tsv 34699 SRR7170000.se.tsv 87100 total ==> SRR7170000.ke.tsv <== target_id length eff_length est_counts tpm Potri.005G200100.1.v4.1 2018 1803.34 83 6.06638 Potri.005G024800.1.v4.1 1035 820.343 18 2.89206 Potri.004G059700.1.v4.1 961 746.343 3 0.529801 Potri.007G009000.2.v4.1 1416 1201.34 0 0 Potri.003G141000.2.v4.1 2943 2728.34 91 4.39615 Potri.016G087400.1.v4.1 270 88.2709 871 1300.56 Potri.015G069301.1.v4.1 564 351.169 0 0 Potri.010G195200.1.v4.1 1773 1558.34 8 0.676639 Potri.012G127500.1.v4.1 977 762.343 2558 442.263 ==> SRR7170000.se.tsv <== Potri.001G166300.v4.1 0 Potri.001G448400.v4.1 436 Potri.001G233950.v4.1 0 Potri.001G122700.v4.1 166 Potri.001G212900.v4.1 0 Potri.001G182400.v4.1 4 Potri.001G256600.v4.1 0 Potri.001G040500.v4.1 0 Potri.001G416900.v4.1 0 Potri.001G452600.v4.1 0 SRR7170000 completed mapping pipeline successfully