nohup: ignoring input 11737886 reads; of these: 11737886 (100.00%) were paired; of these: 3773098 (32.14%) aligned concordantly 0 times 7757209 (66.09%) aligned concordantly exactly 1 time 207579 (1.77%) aligned concordantly >1 times ---- 3773098 pairs aligned concordantly 0 times; of these: 657690 (17.43%) aligned discordantly 1 time ---- 3115408 pairs aligned 0 times concordantly or discordantly; of these: 6230816 mates make up the pairs; of these: 6136660 (98.49%) aligned 0 times 55109 (0.88%) aligned exactly 1 time 39047 (0.63%) aligned >1 times 73.86% overall alignment rate 2238 GFF lines processed. 100000 alignment record pairs processed. 200000 alignment record pairs processed. 300000 alignment record pairs processed. 400000 alignment record pairs processed. 500000 alignment record pairs processed. 600000 alignment record pairs processed. 700000 alignment record pairs processed. 800000 alignment record pairs processed. 900000 alignment record pairs processed. 1000000 alignment record pairs processed. 1100000 alignment record pairs processed. 1200000 alignment record pairs processed. 1300000 alignment record pairs processed. 1400000 alignment record pairs processed. 1500000 alignment record pairs processed. 1600000 alignment record pairs processed. 1700000 alignment record pairs processed. 1800000 alignment record pairs processed. 1900000 alignment record pairs processed. 2000000 alignment record pairs processed. 2100000 alignment record pairs processed. 2200000 alignment record pairs processed. 2300000 alignment record pairs processed. 2400000 alignment record pairs processed. 2500000 alignment record pairs processed. 2600000 alignment record pairs processed. 2700000 alignment record pairs processed. 2800000 alignment record pairs processed. 2900000 alignment record pairs processed. 3000000 alignment record pairs processed. 3100000 alignment record pairs processed. 3200000 alignment record pairs processed. 3300000 alignment record pairs processed. 3400000 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processed. 8200000 alignment record pairs processed. 8300000 alignment record pairs processed. 8400000 alignment record pairs processed. 8500000 alignment record pairs processed. 8600000 alignment record pairs processed. 8700000 alignment record pairs processed. 8800000 alignment record pairs processed. 8900000 alignment record pairs processed. 9000000 alignment record pairs processed. 9100000 alignment record pairs processed. 9200000 alignment record pairs processed. 9300000 alignment record pairs processed. 9400000 alignment record pairs processed. 9500000 alignment record pairs processed. 9600000 alignment record pairs processed. 9700000 alignment record pairs processed. 9800000 alignment record pairs processed. 9900000 alignment record pairs processed. 10000000 alignment record pairs processed. 10100000 alignment record pairs processed. 10200000 alignment record pairs processed. 10300000 alignment record pairs processed. 10400000 alignment record pairs processed. 10500000 alignment record pairs processed. 10600000 alignment record pairs processed. 10700000 alignment record pairs processed. 10800000 alignment record pairs processed. 10900000 alignment record pairs processed. 11000000 alignment record pairs processed. 11100000 alignment record pairs processed. 11200000 alignment record pairs processed. 11300000 alignment record pairs processed. 11400000 alignment record pairs processed. 11500000 alignment record pairs processed. 11600000 alignment record pairs processed. 11700000 alignment record pairs processed. 11737886 alignment record pairs processed. 11405131 reads; of these: 11405131 (100.00%) were paired; of these: 3540693 (31.04%) aligned concordantly 0 times 7653278 (67.10%) aligned concordantly exactly 1 time 211160 (1.85%) aligned concordantly >1 times ---- 3540693 pairs aligned concordantly 0 times; of these: 741587 (20.94%) aligned discordantly 1 time ---- 2799106 pairs aligned 0 times concordantly or discordantly; of these: 5598212 mates make up the pairs; of these: 5493182 (98.12%) aligned 0 times 60133 (1.07%) aligned exactly 1 time 44897 (0.80%) aligned >1 times 75.92% overall alignment rate 2238 GFF lines processed. 100000 alignment record pairs processed. 200000 alignment record pairs processed. 300000 alignment record pairs processed. 400000 alignment record pairs processed. 500000 alignment record pairs processed. 600000 alignment record pairs processed. 700000 alignment record pairs processed. 800000 alignment record pairs processed. 900000 alignment record pairs processed. 1000000 alignment record pairs processed. 1100000 alignment record pairs processed. 1200000 alignment record pairs processed. 1300000 alignment record pairs processed. 1400000 alignment record pairs processed. 1500000 alignment record pairs processed. 1600000 alignment record pairs processed. 1700000 alignment record pairs processed. 1800000 alignment record pairs processed. 1900000 alignment record pairs processed. 2000000 alignment record pairs 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alignment record pairs processed. 6900000 alignment record pairs processed. 7000000 alignment record pairs processed. 7100000 alignment record pairs processed. 7200000 alignment record pairs processed. 7300000 alignment record pairs processed. 7400000 alignment record pairs processed. 7500000 alignment record pairs processed. 7600000 alignment record pairs processed. 7700000 alignment record pairs processed. 7800000 alignment record pairs processed. 7900000 alignment record pairs processed. 8000000 alignment record pairs processed. 8100000 alignment record pairs processed. 8200000 alignment record pairs processed. 8300000 alignment record pairs processed. 8400000 alignment record pairs processed. 8500000 alignment record pairs processed. 8600000 alignment record pairs processed. 8700000 alignment record pairs processed. 8800000 alignment record pairs processed. 8900000 alignment record pairs processed. 9000000 alignment record pairs processed. 9100000 alignment record pairs processed. 9200000 alignment record pairs processed. 9300000 alignment record pairs processed. 9400000 alignment record pairs processed. 9500000 alignment record pairs processed. 9600000 alignment record pairs processed. 9700000 alignment record pairs processed. 9800000 alignment record pairs processed. 9900000 alignment record pairs processed. 10000000 alignment record pairs processed. 10100000 alignment record pairs processed. 10200000 alignment record pairs processed. 10300000 alignment record pairs processed. 10400000 alignment record pairs processed. 10500000 alignment record pairs processed. 10600000 alignment record pairs processed. 10700000 alignment record pairs processed. 10800000 alignment record pairs processed. 10900000 alignment record pairs processed. 11000000 alignment record pairs processed. 11100000 alignment record pairs processed. 11200000 alignment record pairs processed. 11300000 alignment record pairs processed. 11400000 alignment record pairs processed. 11405131 alignment record pairs processed. 10596032 reads; of these: 10596032 (100.00%) were paired; of these: 2877332 (27.15%) aligned concordantly 0 times 7516225 (70.93%) aligned concordantly exactly 1 time 202475 (1.91%) aligned concordantly >1 times ---- 2877332 pairs aligned concordantly 0 times; of these: 736645 (25.60%) aligned discordantly 1 time ---- 2140687 pairs aligned 0 times concordantly or discordantly; of these: 4281374 mates make up the pairs; of these: 4181581 (97.67%) aligned 0 times 55097 (1.29%) aligned exactly 1 time 44696 (1.04%) aligned >1 times 80.27% overall alignment rate 2238 GFF lines processed. 100000 alignment record pairs processed. 200000 alignment record pairs processed. 300000 alignment record pairs processed. 400000 alignment record pairs processed. 500000 alignment record pairs processed. 600000 alignment record pairs processed. 700000 alignment record pairs processed. 800000 alignment record pairs processed. 900000 alignment record pairs processed. 1000000 alignment record pairs processed. 1100000 alignment record pairs processed. 1200000 alignment record pairs processed. 1300000 alignment record pairs processed. 1400000 alignment record pairs processed. 1500000 alignment record pairs processed. 1600000 alignment record pairs processed. 1700000 alignment record pairs processed. 1800000 alignment record pairs processed. 1900000 alignment record pairs processed. 2000000 alignment record pairs processed. 2100000 alignment record pairs processed. 2200000 alignment record pairs processed. 2300000 alignment record pairs processed. 2400000 alignment record pairs processed. 2500000 alignment record pairs processed. 2600000 alignment record pairs processed. 2700000 alignment record pairs processed. 2800000 alignment record pairs processed. 2900000 alignment record pairs processed. 3000000 alignment record pairs processed. 3100000 alignment record pairs processed. 3200000 alignment record pairs processed. 3300000 alignment record pairs processed. 3400000 alignment record pairs processed. 3500000 alignment record pairs processed. 3600000 alignment record pairs processed. 3700000 alignment record pairs processed. 3800000 alignment record pairs processed. 3900000 alignment record pairs processed. 4000000 alignment record pairs processed. 4100000 alignment record pairs processed. 4200000 alignment record pairs processed. 4300000 alignment record pairs processed. 4400000 alignment record pairs processed. 4500000 alignment record pairs processed. 4600000 alignment record pairs processed. 4700000 alignment record pairs processed. 4800000 alignment record pairs processed. 4900000 alignment record pairs processed. 5000000 alignment record pairs processed. 5100000 alignment record pairs processed. 5200000 alignment record pairs processed. 5300000 alignment record pairs processed. 5400000 alignment record pairs processed. 5500000 alignment record pairs processed. 5600000 alignment record pairs processed. 5700000 alignment record pairs processed. 5800000 alignment record pairs processed. 5900000 alignment record pairs processed. 6000000 alignment record pairs processed. 6100000 alignment record pairs processed. 6200000 alignment record pairs processed. 6300000 alignment record pairs processed. 6400000 alignment record pairs processed. 6500000 alignment record pairs processed. 6600000 alignment record pairs processed. 6700000 alignment record pairs processed. 6800000 alignment record pairs processed. 6900000 alignment record pairs processed. 7000000 alignment record pairs processed. 7100000 alignment record pairs processed. 7200000 alignment record pairs processed. 7300000 alignment record pairs processed. 7400000 alignment record pairs processed. 7500000 alignment record pairs processed. 7600000 alignment record pairs processed. 7700000 alignment record pairs processed. 7800000 alignment record pairs processed. 7900000 alignment record pairs processed. 8000000 alignment record pairs processed. 8100000 alignment record pairs processed. 8200000 alignment record pairs processed. 8300000 alignment record pairs processed. 8400000 alignment record pairs processed. 8500000 alignment record pairs processed. 8600000 alignment record pairs processed. 8700000 alignment record pairs processed. 8800000 alignment record pairs processed. 8900000 alignment record pairs processed. 9000000 alignment record pairs processed. 9100000 alignment record pairs processed. 9200000 alignment record pairs processed. 9300000 alignment record pairs processed. 9400000 alignment record pairs processed. 9500000 alignment record pairs processed. 9600000 alignment record pairs processed. 9700000 alignment record pairs processed. 9800000 alignment record pairs processed. 9900000 alignment record pairs processed. 10000000 alignment record pairs processed. 10100000 alignment record pairs processed. 10200000 alignment record pairs processed. 10300000 alignment record pairs processed. 10400000 alignment record pairs processed. 10500000 alignment record pairs processed. 10596032 alignment record pairs processed. 9452928 reads; of these: 9452928 (100.00%) were paired; of these: 2946185 (31.17%) aligned concordantly 0 times 6348494 (67.16%) aligned concordantly exactly 1 time 158249 (1.67%) aligned concordantly >1 times ---- 2946185 pairs aligned concordantly 0 times; of these: 698305 (23.70%) aligned discordantly 1 time ---- 2247880 pairs aligned 0 times concordantly or discordantly; of these: 4495760 mates make up the pairs; of these: 4401828 (97.91%) aligned 0 times 52388 (1.17%) aligned exactly 1 time 41544 (0.92%) aligned >1 times 76.72% overall alignment rate 2238 GFF lines processed. 100000 alignment record pairs processed. 200000 alignment record pairs processed. 300000 alignment record pairs processed. 400000 alignment record pairs processed. 500000 alignment record pairs processed. 600000 alignment record pairs processed. 700000 alignment record pairs processed. 800000 alignment record pairs processed. 900000 alignment record pairs processed. 1000000 alignment record pairs processed. 1100000 alignment record pairs processed. 1200000 alignment record pairs processed. 1300000 alignment record pairs processed. 1400000 alignment record pairs processed. 1500000 alignment record pairs processed. 1600000 alignment record pairs processed. 1700000 alignment record pairs processed. 1800000 alignment record pairs processed. 1900000 alignment record pairs processed. 2000000 alignment record pairs processed. 2100000 alignment record pairs processed. 2200000 alignment record pairs processed. 2300000 alignment record pairs processed. 2400000 alignment record pairs processed. 2500000 alignment record pairs processed. 2600000 alignment record pairs processed. 2700000 alignment record pairs processed. 2800000 alignment record pairs processed. 2900000 alignment record pairs processed. 3000000 alignment record pairs processed. 3100000 alignment record pairs processed. 3200000 alignment record pairs processed. 3300000 alignment record pairs processed. 3400000 alignment record pairs processed. 3500000 alignment record pairs processed. 3600000 alignment record pairs processed. 3700000 alignment record pairs processed. 3800000 alignment record pairs processed. 3900000 alignment record pairs processed. 4000000 alignment record pairs processed. 4100000 alignment record pairs processed. 4200000 alignment record pairs processed. 4300000 alignment record pairs processed. 4400000 alignment record pairs processed. 4500000 alignment record pairs processed. 4600000 alignment record pairs processed. 4700000 alignment record pairs processed. 4800000 alignment record pairs processed. 4900000 alignment record pairs processed. 5000000 alignment record pairs processed. 5100000 alignment record pairs processed. 5200000 alignment record pairs processed. 5300000 alignment record pairs processed. 5400000 alignment record pairs processed. 5500000 alignment record pairs processed. 5600000 alignment record pairs processed. 5700000 alignment record pairs processed. 5800000 alignment record pairs processed. 5900000 alignment record pairs processed. 6000000 alignment record pairs processed. 6100000 alignment record pairs processed. 6200000 alignment record pairs processed. 6300000 alignment record pairs processed. 6400000 alignment record pairs processed. 6500000 alignment record pairs processed. 6600000 alignment record pairs processed. 6700000 alignment record pairs processed. 6800000 alignment record pairs processed. 6900000 alignment record pairs processed. 7000000 alignment record pairs processed. 7100000 alignment record pairs processed. 7200000 alignment record pairs processed. 7300000 alignment record pairs processed. 7400000 alignment record pairs processed. 7500000 alignment record pairs processed. 7600000 alignment record pairs processed. 7700000 alignment record pairs processed. 7800000 alignment record pairs processed. 7900000 alignment record pairs processed. 8000000 alignment record pairs processed. 8100000 alignment record pairs processed. 8200000 alignment record pairs processed. 8300000 alignment record pairs processed. 8400000 alignment record pairs processed. 8500000 alignment record pairs processed. 8600000 alignment record pairs processed. 8700000 alignment record pairs processed. 8800000 alignment record pairs processed. 8900000 alignment record pairs processed. 9000000 alignment record pairs processed. 9100000 alignment record pairs processed. 9200000 alignment record pairs processed. 9300000 alignment record pairs processed. 9400000 alignment record pairs processed. 9452928 alignment record pairs processed. 10989863 reads; of these: 10989863 (100.00%) were paired; of these: 3942334 (35.87%) aligned concordantly 0 times 6898326 (62.77%) aligned concordantly exactly 1 time 149203 (1.36%) aligned concordantly >1 times ---- 3942334 pairs aligned concordantly 0 times; of these: 830587 (21.07%) aligned discordantly 1 time ---- 3111747 pairs aligned 0 times concordantly or discordantly; of these: 6223494 mates make up the pairs; of these: 6112767 (98.22%) aligned 0 times 67277 (1.08%) aligned exactly 1 time 43450 (0.70%) aligned >1 times 72.19% overall alignment rate 2238 GFF lines processed. 100000 alignment record pairs processed. 200000 alignment record pairs processed. 300000 alignment record pairs processed. 400000 alignment record pairs processed. 500000 alignment record pairs processed. 600000 alignment record pairs processed. 700000 alignment record pairs processed. 800000 alignment record pairs processed. 900000 alignment record pairs processed. 1000000 alignment record pairs processed. 1100000 alignment record pairs processed. 1200000 alignment record pairs processed. 1300000 alignment record pairs processed. 1400000 alignment record pairs processed. 1500000 alignment record pairs processed. 1600000 alignment record pairs processed. 1700000 alignment record pairs processed. 1800000 alignment record pairs processed. 1900000 alignment record pairs processed. 2000000 alignment record pairs processed. 2100000 alignment record pairs processed. 2200000 alignment record pairs processed. 2300000 alignment record pairs processed. 2400000 alignment record pairs processed. 2500000 alignment record pairs processed. 2600000 alignment record pairs processed. 2700000 alignment record pairs processed. 2800000 alignment record pairs processed. 2900000 alignment record pairs processed. 3000000 alignment record pairs processed. 3100000 alignment record pairs processed. 3200000 alignment record pairs processed. 3300000 alignment record pairs processed. 3400000 alignment record pairs processed. 3500000 alignment record pairs processed. 3600000 alignment record pairs processed. 3700000 alignment record pairs processed. 3800000 alignment record pairs processed. 3900000 alignment record pairs processed. 4000000 alignment record pairs processed. 4100000 alignment record pairs processed. 4200000 alignment record pairs processed. 4300000 alignment record pairs processed. 4400000 alignment record pairs processed. 4500000 alignment record pairs processed. 4600000 alignment record pairs processed. 4700000 alignment record pairs processed. 4800000 alignment record pairs processed. 4900000 alignment record pairs processed. 5000000 alignment record pairs processed. 5100000 alignment record pairs processed. 5200000 alignment record pairs processed. 5300000 alignment record pairs processed. 5400000 alignment record pairs processed. 5500000 alignment record pairs processed. 5600000 alignment record pairs processed. 5700000 alignment record pairs processed. 5800000 alignment record pairs processed. 5900000 alignment record pairs processed. 6000000 alignment record pairs processed. 6100000 alignment record pairs processed. 6200000 alignment record pairs processed. 6300000 alignment record pairs processed. 6400000 alignment record pairs processed. 6500000 alignment record pairs processed. 6600000 alignment record pairs processed. 6700000 alignment record pairs processed. 6800000 alignment record pairs processed. 6900000 alignment record pairs processed. 7000000 alignment record pairs processed. 7100000 alignment record pairs processed. 7200000 alignment record pairs processed. 7300000 alignment record pairs processed. 7400000 alignment record pairs processed. 7500000 alignment record pairs processed. 7600000 alignment record pairs processed. 7700000 alignment record pairs processed. 7800000 alignment record pairs processed. 7900000 alignment record pairs processed. 8000000 alignment record pairs processed. 8100000 alignment record pairs processed. 8200000 alignment record pairs processed. 8300000 alignment record pairs processed. 8400000 alignment record pairs processed. 8500000 alignment record pairs processed. 8600000 alignment record pairs processed. 8700000 alignment record pairs processed. 8800000 alignment record pairs processed. 8900000 alignment record pairs processed. 9000000 alignment record pairs processed. 9100000 alignment record pairs processed. 9200000 alignment record pairs processed. 9300000 alignment record pairs processed. 9400000 alignment record pairs processed. 9500000 alignment record pairs processed. 9600000 alignment record pairs processed. 9700000 alignment record pairs processed. 9800000 alignment record pairs processed. 9900000 alignment record pairs processed. 10000000 alignment record pairs processed. 10100000 alignment record pairs processed. 10200000 alignment record pairs processed. 10300000 alignment record pairs processed. 10400000 alignment record pairs processed. 10500000 alignment record pairs processed. 10600000 alignment record pairs processed. 10700000 alignment record pairs processed. 10800000 alignment record pairs processed. 10900000 alignment record pairs processed. 10989863 alignment record pairs processed. 11220662 reads; of these: 11220662 (100.00%) were paired; of these: 3679542 (32.79%) aligned concordantly 0 times 7344104 (65.45%) aligned concordantly exactly 1 time 197016 (1.76%) aligned concordantly >1 times ---- 3679542 pairs aligned concordantly 0 times; of these: 702591 (19.09%) aligned discordantly 1 time ---- 2976951 pairs aligned 0 times concordantly or discordantly; of these: 5953902 mates make up the pairs; of these: 5852607 (98.30%) aligned 0 times 58013 (0.97%) aligned exactly 1 time 43282 (0.73%) aligned >1 times 73.92% overall alignment rate 2238 GFF lines processed. 100000 alignment record pairs processed. 200000 alignment record pairs processed. 300000 alignment record pairs processed. 400000 alignment record pairs processed. 500000 alignment record pairs processed. 600000 alignment record pairs processed. 700000 alignment record pairs processed. 800000 alignment record pairs processed. 900000 alignment record pairs processed. 1000000 alignment record pairs processed. 1100000 alignment record pairs processed. 1200000 alignment record pairs processed. 1300000 alignment record pairs processed. 1400000 alignment record pairs processed. 1500000 alignment record pairs processed. 1600000 alignment record pairs processed. 1700000 alignment record pairs processed. 1800000 alignment record pairs processed. 1900000 alignment record pairs processed. 2000000 alignment record pairs processed. 2100000 alignment record pairs processed. 2200000 alignment record pairs processed. 2300000 alignment record pairs processed. 2400000 alignment record pairs processed. 2500000 alignment record pairs processed. 2600000 alignment record pairs processed. 2700000 alignment record pairs processed. 2800000 alignment record pairs processed. 2900000 alignment record pairs processed. 3000000 alignment record pairs processed. 3100000 alignment record pairs processed. 3200000 alignment record pairs processed. 3300000 alignment record pairs processed. 3400000 alignment record pairs processed. 3500000 alignment record pairs processed. 3600000 alignment record pairs processed. 3700000 alignment record pairs processed. 3800000 alignment record pairs processed. 3900000 alignment record pairs processed. 4000000 alignment record pairs processed. 4100000 alignment record pairs processed. 4200000 alignment record pairs processed. 4300000 alignment record pairs processed. 4400000 alignment record pairs processed. 4500000 alignment record pairs processed. 4600000 alignment record pairs processed. 4700000 alignment record pairs processed. 4800000 alignment record pairs processed. 4900000 alignment record pairs processed. 5000000 alignment record pairs processed. 5100000 alignment record pairs processed. 5200000 alignment record pairs processed. 5300000 alignment record pairs processed. 5400000 alignment record pairs processed. 5500000 alignment record pairs processed. 5600000 alignment record pairs processed. 5700000 alignment record pairs processed. 5800000 alignment record pairs processed. 5900000 alignment record pairs processed. 6000000 alignment record pairs processed. 6100000 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8500000 alignment record pairs processed. 8600000 alignment record pairs processed. 8700000 alignment record pairs processed. 8800000 alignment record pairs processed. 8900000 alignment record pairs processed. 9000000 alignment record pairs processed. 9100000 alignment record pairs processed. 9200000 alignment record pairs processed. 9300000 alignment record pairs processed. 9400000 alignment record pairs processed. 9500000 alignment record pairs processed. 9600000 alignment record pairs processed. 9700000 alignment record pairs processed. 9800000 alignment record pairs processed. 9900000 alignment record pairs processed. 10000000 alignment record pairs processed. 10100000 alignment record pairs processed. 10200000 alignment record pairs processed. 10300000 alignment record pairs processed. 10400000 alignment record pairs processed. 10500000 alignment record pairs processed. 10600000 alignment record pairs processed. 10700000 alignment record pairs processed. 10800000 alignment record pairs processed. 10900000 alignment record pairs processed. 11000000 alignment record pairs processed. 11100000 alignment record pairs processed. 11200000 alignment record pairs processed. 11220662 alignment record pairs processed. Loading required package: S4Vectors Loading required package: stats4 Loading required package: BiocGenerics Attaching package: ‘BiocGenerics’ The following objects are masked from ‘package:stats’: IQR, mad, sd, var, xtabs The following objects are masked from ‘package:base’: anyDuplicated, aperm, append, as.data.frame, basename, cbind, colnames, dirname, do.call, duplicated, eval, evalq, Filter, Find, get, grep, grepl, intersect, is.unsorted, lapply, Map, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, Position, rank, rbind, Reduce, rownames, sapply, setdiff, sort, table, tapply, union, unique, unsplit, which.max, which.min Attaching package: ‘S4Vectors’ The following object is masked from ‘package:utils’: findMatches The following objects are masked from ‘package:base’: expand.grid, I, unname Loading required package: IRanges Loading required package: GenomicRanges Loading required package: GenomeInfoDb Loading required package: SummarizedExperiment Loading required package: MatrixGenerics Loading required package: matrixStats Attaching package: ‘MatrixGenerics’ The following objects are masked from ‘package:matrixStats’: colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse, colCounts, colCummaxs, colCummins, colCumprods, colCumsums, colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs, colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats, colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds, colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads, colWeightedMeans, colWeightedMedians, colWeightedSds, colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet, rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods, rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps, rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins, rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks, rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars, rowWeightedMads, rowWeightedMeans, rowWeightedMedians, rowWeightedSds, rowWeightedVars Loading required package: Biobase Welcome to Bioconductor Vignettes contain introductory material; view with 'browseVignettes()'. To cite Bioconductor, see 'citation("Biobase")', and for packages 'citation("pkgname")'. Attaching package: ‘Biobase’ The following object is masked from ‘package:MatrixGenerics’: rowMedians The following objects are masked from ‘package:matrixStats’: anyMissing, rowMedians Warning message: In DESeqDataSet(se, design = design, ignoreRank) : some variables in design formula are characters, converting to factors estimating size factors estimating dispersions gene-wise dispersion estimates mean-dispersion relationship final dispersion estimates fitting model and testing using ntop=500 top features by variance Warning message: `aes_string()` was deprecated in ggplot2 3.0.0. ℹ Please use tidy evaluation idioms with `aes()`. ℹ See also `vignette("ggplot2-in-packages")` for more information. ℹ The deprecated feature was likely used in the DESeq2 package. Please report the issue to the authors. null device 1 Loading required package: ggplot2 Loading required package: ggrepel Warning messages: 1: Using `size` aesthetic for lines was deprecated in ggplot2 3.4.0. ℹ Please use `linewidth` instead. ℹ The deprecated feature was likely used in the EnhancedVolcano package. Please report the issue to the authors. 2: The `size` argument of `element_line()` is deprecated as of ggplot2 3.4.0. ℹ Please use the `linewidth` argument instead. ℹ The deprecated feature was likely used in the EnhancedVolcano package. Please report the issue to the authors. null device 1 Warning messages: 1: In type.convert.default(X[[i]], ...) : 'as.is' should be specified by the caller; using TRUE 2: In type.convert.default(X[[i]], ...) : 'as.is' should be specified by the caller; using TRUE 3: In type.convert.default(X[[i]], ...) : 'as.is' should be specified by the caller; using TRUE 4: In type.convert.default(X[[i]], ...) : 'as.is' should be specified by the caller; using TRUE Warning messages: 1: In type.convert.default(X[[i]], ...) : 'as.is' should be specified by the caller; using TRUE 2: In type.convert.default(X[[i]], ...) : 'as.is' should be specified by the caller; using TRUE Attaching package: ‘dplyr’ The following object is masked from ‘package:Biobase’: combine The following object is masked from ‘package:matrixStats’: count The following objects are masked from ‘package:GenomicRanges’: intersect, setdiff, union The following object is masked from ‘package:GenomeInfoDb’: intersect The following objects are masked from ‘package:IRanges’: collapse, desc, intersect, setdiff, slice, union The following objects are masked from ‘package:S4Vectors’: first, intersect, rename, setdiff, setequal, union The following objects are masked from ‘package:BiocGenerics’: combine, intersect, setdiff, union The following objects are masked from ‘package:stats’: filter, lag The following objects are masked from ‘package:base’: intersect, setdiff, setequal, union [1] "fold_change" "id" "pvalue" "padj" [5] "log2FoldChange" "gff_annotation" Warning message: In inner_join(kegg_data, ko_numbers, by = "ko") : Detected an unexpected many-to-many relationship between `x` and `y`. ℹ Row 4 of `x` matches multiple rows in `y`. ℹ Row 14 of `y` matches multiple rows in `x`. ℹ If a many-to-many relationship is expected, set `relationship = "many-to-many"` to silence this warning. null device 1 null device 1 null device 1 null device 1 Attaching package: ‘plyr’ The following object is masked from ‘package:matrixStats’: count The following object is masked from ‘package:IRanges’: desc The following object is masked from ‘package:S4Vectors’: rename