> ## this script takes the semistrict data and applies RAxML utility to make maximal likelihood tree > ## requires RAxML installation an dthe presence of working "raxmlHPC" binary > > library(shipunov) package 'shipunov', version 1.3-1 > library(ips) # this package contains raxml() function to call RAxML from within R Loading required package: ape > DATE <- format(Sys.time(), "%Y%m%d_%H%M%S") # timestamp > treesp <- read.table("_kubricks_treesp.txt", sep="\t", h=TRUE, as.is=TRUE) # is needed to understand outgroups and outliers > outgroups <- treesp$SPECIES.NEW[treesp$TYPE == "outgroup" & treesp$USE == 1] > outgroups <- gsub(" ", "_", outgroups) > conc <- read.dna("40_concatenated/semistrict.fasta", format="fasta") > LAB <- sub("__.*$", "", labels(conc)) > OUT <- labels(conc)[LAB %in% outgroups] > outliers <- treesp$SPECIES.NEW[treesp$TYPE == "outlier" & treesp$USE == 1] > if (length(outliers) > 0) { + outliers <- gsub(" ", "_", outliers) + EXC <- labels(conc)[LAB %in% outliers] + conc <- conc[!labels(conc) %in% EXC, ] # remove outliers, if any + } > setwd("70_raxml_working") # go to RAxML working directory > tr <- raxml(conc, m="GTRGAMMAI", # change the model if needed + f="a", # change RAxML algorithm if needed + N=100, # change bootstrap options if needed + p=1234, x=1234, exec="raxmlHPC", # change name of RAxML binary; on Windows, you will _need_ to change it + outgroup=OUT) [1] "raxmlHPC -f a -p 1234 -x 1234 -m GTRGAMMAI -o Kubrickus_heus__K-008 -N 100 -s fromR_2019-11-27.phy -n fromR_2019-11-27" Use raxml with AVX support (2 cpus) You are using a proportion of Invariable sites estimate, although I don't like it. The likelihood epsilon "-f e" will be automatically lowered to 0.001 to avoid unfavorable effects caused by simultaneous optimization of alpha and P-Invar Using BFGS method to optimize GTR rate parameters, to disable this specify "--no-bfgs" This is the RAxML Master Pthread This is RAxML Worker Pthread Number: 1 This is RAxML version 8.2.4 released by Alexandros Stamatakis on October 02 2015. With greatly appreciated code contributions by: Andre Aberer (HITS) Simon Berger (HITS) Alexey Kozlov (HITS) Kassian Kobert (HITS) David Dao (KIT and HITS) Nick Pattengale (Sandia) Wayne Pfeiffer (SDSC) Akifumi S. Tanabe (NRIFS) Alignment has 83 distinct alignment patterns Found 0 invariant alignment patterns that correspond to 0 columns Proportion of gaps and completely undetermined characters in this alignment: 14.79% RAxML rapid bootstrapping and subsequent ML search Using 1 distinct models/data partitions with joint branch length optimization Executing 100 rapid bootstrap inferences and thereafter a thorough ML search All free model parameters will be estimated by RAxML GAMMA+P-Invar model of rate heteorgeneity, ML estimate of alpha-parameter GAMMA+P-Invar Model parameters will be estimated up to an accuracy of 0.0010000000 Log Likelihood units Partition: 0 Alignment Patterns: 83 Name: No Name Provided DataType: DNA Substitution Matrix: GTR RAxML was called as follows: /usr/bin/raxmlHPC-PTHREADS-AVX -T 2 -f a -p 1234 -x 1234 -m GTRGAMMAI -o Kubrickus_heus__K-008 -N 100 -s fromR_2019-11-27.phy -n fromR_2019-11-27 Time for BS model parameter optimization 0.017010 Bootstrap[0]: Time 0.064108 seconds, bootstrap likelihood -2164.789117, best rearrangement setting 10 Bootstrap[1]: Time 0.031831 seconds, bootstrap likelihood -2268.198942, best rearrangement setting 15 Bootstrap[2]: Time 0.045079 seconds, bootstrap likelihood -2241.080238, best rearrangement setting 15 Bootstrap[3]: Time 0.030880 seconds, bootstrap likelihood -2161.098499, best rearrangement setting 12 Bootstrap[4]: Time 0.041027 seconds, bootstrap likelihood -2291.031584, best rearrangement setting 9 Bootstrap[5]: Time 0.031682 seconds, bootstrap likelihood -2146.447469, best rearrangement setting 12 Bootstrap[6]: Time 0.012679 seconds, bootstrap likelihood -2224.764323, best rearrangement setting 14 Bootstrap[7]: Time 0.028843 seconds, bootstrap likelihood -2183.323661, best rearrangement setting 10 Bootstrap[8]: Time 0.041780 seconds, bootstrap likelihood -2165.289470, best rearrangement setting 13 Bootstrap[9]: Time 0.043447 seconds, bootstrap likelihood -2137.134612, best rearrangement setting 14 Bootstrap[10]: Time 0.027205 seconds, bootstrap likelihood -2111.369952, best rearrangement setting 14 Bootstrap[11]: Time 0.045818 seconds, bootstrap likelihood -2299.153401, best rearrangement setting 5 Bootstrap[12]: Time 0.038914 seconds, bootstrap likelihood -2215.208993, best rearrangement setting 9 Bootstrap[13]: Time 0.030314 seconds, bootstrap likelihood -2201.160103, best rearrangement setting 10 Bootstrap[14]: Time 0.033931 seconds, bootstrap likelihood -2078.560725, best rearrangement setting 13 Bootstrap[15]: Time 0.031472 seconds, bootstrap likelihood -2196.048911, best rearrangement setting 6 Bootstrap[16]: Time 0.030222 seconds, bootstrap likelihood -2165.396001, best rearrangement setting 15 Bootstrap[17]: Time 0.040590 seconds, bootstrap likelihood -2152.202204, best rearrangement setting 13 Bootstrap[18]: Time 0.030231 seconds, bootstrap likelihood -2094.952538, best rearrangement setting 9 Bootstrap[19]: Time 0.025203 seconds, bootstrap likelihood -2223.951849, best rearrangement setting 8 Bootstrap[20]: Time 0.032311 seconds, bootstrap likelihood -2146.763856, best rearrangement setting 13 Bootstrap[21]: Time 0.020911 seconds, bootstrap likelihood -2104.342207, best rearrangement setting 10 Bootstrap[22]: Time 0.013743 seconds, bootstrap likelihood -2135.351694, best rearrangement setting 5 Bootstrap[23]: Time 0.035002 seconds, bootstrap likelihood -2285.910283, best rearrangement setting 10 Bootstrap[24]: Time 0.033597 seconds, bootstrap likelihood -2111.153639, best rearrangement setting 14 Bootstrap[25]: Time 0.033517 seconds, bootstrap likelihood -2102.955280, best rearrangement setting 7 Bootstrap[26]: Time 0.042135 seconds, bootstrap likelihood -2133.296040, best rearrangement setting 11 Bootstrap[27]: Time 0.037690 seconds, bootstrap likelihood -2178.895077, best rearrangement setting 11 Bootstrap[28]: Time 0.034531 seconds, bootstrap likelihood -2237.230120, best rearrangement setting 8 Bootstrap[29]: Time 0.037157 seconds, bootstrap likelihood -2155.599867, best rearrangement setting 13 Bootstrap[30]: Time 0.031258 seconds, bootstrap likelihood -2154.511785, best rearrangement setting 6 Bootstrap[31]: Time 0.039228 seconds, bootstrap likelihood -2114.033844, best rearrangement setting 9 Bootstrap[32]: Time 0.026458 seconds, bootstrap likelihood -2155.588622, best rearrangement setting 13 Bootstrap[33]: Time 0.034768 seconds, bootstrap likelihood -2207.067455, best rearrangement setting 8 Bootstrap[34]: Time 0.029432 seconds, bootstrap likelihood -2200.865547, best rearrangement setting 8 Bootstrap[35]: Time 0.031249 seconds, bootstrap likelihood -2137.725150, best rearrangement setting 12 Bootstrap[36]: Time 0.037434 seconds, bootstrap likelihood -2180.430155, best rearrangement setting 5 Bootstrap[37]: Time 0.032843 seconds, bootstrap likelihood -2170.410555, best rearrangement setting 8 Bootstrap[38]: Time 0.030955 seconds, bootstrap likelihood -2044.245831, best rearrangement setting 12 Bootstrap[39]: Time 0.029903 seconds, bootstrap likelihood -2215.467483, best rearrangement setting 13 Bootstrap[40]: Time 0.032635 seconds, bootstrap likelihood -2228.077075, best rearrangement setting 14 Bootstrap[41]: Time 0.032734 seconds, bootstrap likelihood -2112.862357, best rearrangement setting 13 Bootstrap[42]: Time 0.026308 seconds, bootstrap likelihood -2157.311395, best rearrangement setting 10 Bootstrap[43]: Time 0.024636 seconds, bootstrap likelihood -2093.473494, best rearrangement setting 13 Bootstrap[44]: Time 0.031911 seconds, bootstrap likelihood -2131.311530, best rearrangement setting 7 Bootstrap[45]: Time 0.036785 seconds, bootstrap likelihood -2128.230769, best rearrangement setting 14 Bootstrap[46]: Time 0.013444 seconds, bootstrap likelihood -2221.489834, best rearrangement setting 14 Bootstrap[47]: Time 0.031632 seconds, bootstrap likelihood -2184.385398, best rearrangement setting 11 Bootstrap[48]: Time 0.038137 seconds, bootstrap likelihood -2173.660947, best rearrangement setting 11 Bootstrap[49]: Time 0.038909 seconds, bootstrap likelihood -2102.199885, best rearrangement setting 15 Bootstrap[50]: Time 0.013347 seconds, bootstrap likelihood -2126.355442, best rearrangement setting 8 Bootstrap[51]: Time 0.014213 seconds, bootstrap likelihood -2170.996253, best rearrangement setting 5 Bootstrap[52]: Time 0.028688 seconds, bootstrap likelihood -2193.789407, best rearrangement setting 7 Bootstrap[53]: Time 0.032731 seconds, bootstrap likelihood -2240.176495, best rearrangement setting 10 Bootstrap[54]: Time 0.029918 seconds, bootstrap likelihood -2268.934967, best rearrangement setting 7 Bootstrap[55]: Time 0.031730 seconds, bootstrap likelihood -2189.483050, best rearrangement setting 8 Bootstrap[56]: Time 0.029619 seconds, bootstrap likelihood -2073.997393, best rearrangement setting 5 Bootstrap[57]: Time 0.037692 seconds, bootstrap likelihood -2187.288000, best rearrangement setting 12 Bootstrap[58]: Time 0.028441 seconds, bootstrap likelihood -2217.795062, best rearrangement setting 15 Bootstrap[59]: Time 0.032466 seconds, bootstrap likelihood -2120.057442, best rearrangement setting 6 Bootstrap[60]: Time 0.033980 seconds, bootstrap likelihood -2204.033638, best rearrangement setting 9 Bootstrap[61]: Time 0.031241 seconds, bootstrap likelihood -2182.894186, best rearrangement setting 9 Bootstrap[62]: Time 0.039949 seconds, bootstrap likelihood -2203.144416, best rearrangement setting 10 Bootstrap[63]: Time 0.031404 seconds, bootstrap likelihood -2101.592819, best rearrangement setting 12 Bootstrap[64]: Time 0.031857 seconds, bootstrap likelihood -2097.887276, best rearrangement setting 11 Bootstrap[65]: Time 0.030337 seconds, bootstrap likelihood -2057.121464, best rearrangement setting 8 Bootstrap[66]: Time 0.031388 seconds, bootstrap likelihood -2124.074026, best rearrangement setting 13 Bootstrap[67]: Time 0.031656 seconds, bootstrap likelihood -2127.980214, best rearrangement setting 15 Bootstrap[68]: Time 0.032285 seconds, bootstrap likelihood -2144.230425, best rearrangement setting 10 Bootstrap[69]: Time 0.032119 seconds, bootstrap likelihood -2202.957615, best rearrangement setting 13 Bootstrap[70]: Time 0.036257 seconds, bootstrap likelihood -2141.371771, best rearrangement setting 11 Bootstrap[71]: Time 0.033763 seconds, bootstrap likelihood -2135.521467, best rearrangement setting 11 Bootstrap[72]: Time 0.029669 seconds, bootstrap likelihood -2154.606682, best rearrangement setting 13 Bootstrap[73]: Time 0.030082 seconds, bootstrap likelihood -2054.692398, best rearrangement setting 5 Bootstrap[74]: Time 0.033591 seconds, bootstrap likelihood -2121.587241, best rearrangement setting 6 Bootstrap[75]: Time 0.032493 seconds, bootstrap likelihood -2211.966697, best rearrangement setting 11 Bootstrap[76]: Time 0.031586 seconds, bootstrap likelihood -2157.019797, best rearrangement setting 6 Bootstrap[77]: Time 0.030865 seconds, bootstrap likelihood -2157.769669, best rearrangement setting 8 Bootstrap[78]: Time 0.035917 seconds, bootstrap likelihood -2215.272864, best rearrangement setting 13 Bootstrap[79]: Time 0.031882 seconds, bootstrap likelihood -2149.318994, best rearrangement setting 13 Bootstrap[80]: Time 0.032937 seconds, bootstrap likelihood -2204.833933, best rearrangement setting 9 Bootstrap[81]: Time 0.012997 seconds, bootstrap likelihood -2169.369118, best rearrangement setting 10 Bootstrap[82]: Time 0.034076 seconds, bootstrap likelihood -2246.310136, best rearrangement setting 7 Bootstrap[83]: Time 0.033712 seconds, bootstrap likelihood -2154.255306, best rearrangement setting 6 Bootstrap[84]: Time 0.033484 seconds, bootstrap likelihood -2201.559870, best rearrangement setting 15 Bootstrap[85]: Time 0.030540 seconds, bootstrap likelihood -2180.574686, best rearrangement setting 10 Bootstrap[86]: Time 0.029537 seconds, bootstrap likelihood -2214.982757, best rearrangement setting 9 Bootstrap[87]: Time 0.029029 seconds, bootstrap likelihood -2145.823479, best rearrangement setting 5 Bootstrap[88]: Time 0.030891 seconds, bootstrap likelihood -2126.196892, best rearrangement setting 12 Bootstrap[89]: Time 0.033162 seconds, bootstrap likelihood -2195.270708, best rearrangement setting 6 Bootstrap[90]: Time 0.037869 seconds, bootstrap likelihood -2198.451568, best rearrangement setting 13 Bootstrap[91]: Time 0.029570 seconds, bootstrap likelihood -2238.914547, best rearrangement setting 8 Bootstrap[92]: Time 0.033669 seconds, bootstrap likelihood -2126.569791, best rearrangement setting 7 Bootstrap[93]: Time 0.035832 seconds, bootstrap likelihood -2310.011816, best rearrangement setting 11 Bootstrap[94]: Time 0.029165 seconds, bootstrap likelihood -2186.817177, best rearrangement setting 15 Bootstrap[95]: Time 0.036609 seconds, bootstrap likelihood -2196.728738, best rearrangement setting 15 Bootstrap[96]: Time 0.028156 seconds, bootstrap likelihood -2170.289422, best rearrangement setting 5 Bootstrap[97]: Time 0.040139 seconds, bootstrap likelihood -2129.166878, best rearrangement setting 14 Bootstrap[98]: Time 0.034528 seconds, bootstrap likelihood -2176.616021, best rearrangement setting 7 Bootstrap[99]: Time 0.022163 seconds, bootstrap likelihood -2198.785616, best rearrangement setting 10 Overall Time for 100 Rapid Bootstraps 3.221029 seconds Average Time per Rapid Bootstrap 0.032210 seconds Starting ML Search ... Fast ML optimization finished Fast ML search Time: 1.672859 seconds Slow ML Search 0 Likelihood: -2186.697667 Slow ML Search 1 Likelihood: -2186.697668 Slow ML Search 2 Likelihood: -2186.697667 Slow ML Search 3 Likelihood: -2186.697667 Slow ML Search 4 Likelihood: -2186.697668 Slow ML Search 5 Likelihood: -2186.697685 Slow ML Search 6 Likelihood: -2186.697685 Slow ML Search 7 Likelihood: -2186.697685 Slow ML Search 8 Likelihood: -2186.697685 Slow ML Search 9 Likelihood: -2186.697685 Slow ML optimization finished Slow ML search Time: 0.461240 seconds Thorough ML search Time: 0.103885 seconds Final ML Optimization Likelihood: -2186.697682 Model Information: Model Parameters of Partition 0, Name: No Name Provided, Type of Data: DNA alpha: 0.875736 invar: 0.541245 Tree-Length: 0.123322 rate A <-> C: 3.524215 rate A <-> G: 1.695321 rate A <-> T: 0.431917 rate C <-> G: 0.661875 rate C <-> T: 4.320300 rate G <-> T: 1.000000 freq pi(A): 0.325642 freq pi(C): 0.171561 freq pi(G): 0.233438 freq pi(T): 0.269358 ML search took 2.238297 secs or 0.000622 hours Combined Bootstrap and ML search took 5.459343 secs or 0.001516 hours Drawing Bootstrap Support Values on best-scoring ML tree ... Found 1 tree in File /home/alexey/wrk/dev/r/ripeline/70_raxml_working/RAxML_bestTree.fromR_2019-11-27 Found 1 tree in File /home/alexey/wrk/dev/r/ripeline/70_raxml_working/RAxML_bestTree.fromR_2019-11-27 Program execution info written to /home/alexey/wrk/dev/r/ripeline/70_raxml_working/RAxML_info.fromR_2019-11-27 All 100 bootstrapped trees written to: /home/alexey/wrk/dev/r/ripeline/70_raxml_working/RAxML_bootstrap.fromR_2019-11-27 Best-scoring ML tree written to: /home/alexey/wrk/dev/r/ripeline/70_raxml_working/RAxML_bestTree.fromR_2019-11-27 Best-scoring ML tree with support values written to: /home/alexey/wrk/dev/r/ripeline/70_raxml_working/RAxML_bipartitions.fromR_2019-11-27 Best-scoring ML tree with support values as branch labels written to: /home/alexey/wrk/dev/r/ripeline/70_raxml_working/RAxML_bipartitionsBranchLabels.fromR_2019-11-27 Overall execution time for full ML analysis: 5.461653 secs or 0.001517 hours or 0.000063 days > setwd("..") # go out of RAxML working directory > ## print "bipartitions" tree to PDF > pdf(paste0("99_trees/", DATE, "_semistrict_raxml_kubricks.pdf"), height=8, width=12) # change PDF size if needed > oldpar <- par(mar=rep(0, 4)) > plot(tr$bipartitions) > nodelabels(tr$bipartitions$node.label, frame="none", bg="transparent", adj=-0.1) > mtext("semistrict RAxML", font=2, line=-1) > add.scale.bar() > dev.off() null device 1 > ## also save it as Newick > tr$node.label[tr$node.label == "NA"] <- "" # useful for some Newick reading software > write.tree(tr$bipartitions, file=paste0("99_trees/", DATE, "_semistrict_raxml_kubricks.tre"))