RAxML-NG v. 1.0.2 released on 22.02.2021 by The Exelixis Lab. Developed by: Alexey M. Kozlov and Alexandros Stamatakis. Contributors: Diego Darriba, Tomas Flouri, Benoit Morel, Sarah Lutteropp, Ben Bettisworth. Latest version: https://github.com/amkozlov/raxml-ng Questions/problems/suggestions? Please visit: https://groups.google.com/forum/#!forum/raxml System: Intel(R) Xeon(R) Gold 6140 CPU @ 2.30GHz, 36 cores, 251 GB RAM RAxML-NG was called at 04-Jun-2021 13:38:45 as follows: raxml-ng --ancestral --msa /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/P23025/2_msa/P23025_nogap_msa.fasta --tree /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/P23025/3_mltree/P23025.raxml.bestTree_unrooted --model LG4X --prefix /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/P23025/4_raxmlng_ancestral/P23025 --threads 4 Analysis options: run mode: Ancestral state reconstruction start tree(s): user random seed: 1622803125 tip-inner: ON pattern compression: OFF per-rate scalers: OFF site repeats: OFF branch lengths: proportional (ML estimate, algorithm: NR-FAST) SIMD kernels: AVX2 parallelization: coarse-grained (auto), PTHREADS (4 threads), thread pinning: OFF [00:00:00] Reading alignment from file: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/P23025/2_msa/P23025_nogap_msa.fasta [00:00:00] Loaded alignment with 641 taxa and 273 sites WARNING: Sequences tr_A0A0D8JT84_A0A0D8JT84_COCIM_246410 and tr_A0A0J7B126_A0A0J7B126_COCIT_404692 are exactly identical! WARNING: Sequences tr_B2VUI3_B2VUI3_PYRTR_426418 and tr_A0A2W1DBJ5_A0A2W1DBJ5_9PLEO_45151 are exactly identical! WARNING: Sequences tr_A0A2I2YWK6_A0A2I2YWK6_GORGO_9595 and tr_A0A2I3TJL9_A0A2I3TJL9_PANTR_9598 are exactly identical! WARNING: Sequences tr_A0A2I2YWK6_A0A2I2YWK6_GORGO_9595 and sp_Q6PML9_ZNT9_HUMAN_9606 are exactly identical! WARNING: Sequences tr_A0A2I2YWK6_A0A2I2YWK6_GORGO_9595 and tr_A0A2R9BDM9_A0A2R9BDM9_PANPA_9597 are exactly identical! WARNING: Sequences tr_A0A179UH55_A0A179UH55_BLAGS_559298 and tr_C5G8Y6_C5G8Y6_AJEDR_559297 are exactly identical! WARNING: Sequences tr_H2QXJ4_H2QXJ4_PANTR_9598 and tr_A0A2R9C0L1_A0A2R9C0L1_PANPA_9597 are exactly identical! WARNING: Sequences tr_F9FA69_F9FA69_FUSOF_660025 and tr_N4UBU5_N4UBU5_FUSC1_1229664 are exactly identical! WARNING: Sequences tr_F9FA69_F9FA69_FUSOF_660025 and tr_X0CQA1_X0CQA1_FUSOX_1089458 are exactly identical! WARNING: Sequences tr_F9FA69_F9FA69_FUSOF_660025 and tr_A0A2H3TBW0_A0A2H3TBW0_FUSOX_5507 are exactly identical! WARNING: Sequences tr_F9FA69_F9FA69_FUSOF_660025 and tr_A0A2H3HR39_A0A2H3HR39_FUSOX_327505 are exactly identical! WARNING: Sequences tr_C6HGW6_C6HGW6_AJECH_544712 and tr_F0UVY3_F0UVY3_AJEC8_544711 are exactly identical! WARNING: Sequences tr_G9NLQ5_G9NLQ5_HYPAI_452589 and tr_A0A2P4ZFB7_A0A2P4ZFB7_9HYPO_398673 are exactly identical! WARNING: Sequences tr_H9FNR2_H9FNR2_MACMU_9544 and tr_G7P5H4_G7P5H4_MACFA_9541 are exactly identical! WARNING: Sequences tr_H9FNR2_H9FNR2_MACMU_9544 and tr_A0A2I3ML78_A0A2I3ML78_PAPAN_9555 are exactly identical! WARNING: Sequences tr_H9FNR2_H9FNR2_MACMU_9544 and tr_A0A2K6DLL1_A0A2K6DLL1_MACNE_9545 are exactly identical! WARNING: Sequences tr_F4NUG4_F4NUG4_BATDJ_684364 and tr_A0A177WCL6_A0A177WCL6_BATDE_403673 are exactly identical! WARNING: Sequences tr_H0ZE43_H0ZE43_TAEGU_59729 and tr_A0A093SMJ2_A0A093SMJ2_9PASS_328815 are exactly identical! WARNING: Sequences tr_G2Y0U1_G2Y0U1_BOTF4_999810 and tr_M7U315_M7U315_BOTF1_1290391 are exactly identical! WARNING: Sequences tr_F2PQJ5_F2PQJ5_TRIEC_559882 and tr_A0A059JAD5_A0A059JAD5_9EURO_1215338 are exactly identical! WARNING: Sequences tr_L0P8Q1_L0P8Q1_PNEJ8_1209962 and tr_A0A0W4ZQC6_A0A0W4ZQC6_PNEJ7_1408657 are exactly identical! WARNING: Sequences tr_A0A091JNV2_A0A091JNV2_EGRGA_188379 and tr_A0A091UNH0_A0A091UNH0_NIPNI_128390 are exactly identical! WARNING: Sequences tr_A0A091JNV2_A0A091JNV2_EGRGA_188379 and tr_A0A087RD87_A0A087RD87_APTFO_9233 are exactly identical! WARNING: Sequences tr_A0A091JNV2_A0A091JNV2_EGRGA_188379 and tr_A0A091VJF1_A0A091VJF1_OPIHO_30419 are exactly identical! WARNING: Sequences tr_A0A091JNV2_A0A091JNV2_EGRGA_188379 and tr_A0A099ZZC6_A0A099ZZC6_CHAVO_50402 are exactly identical! WARNING: Sequences tr_A0A091W7M1_A0A091W7M1_OPIHO_30419 and tr_A0A0A0AIC8_A0A0A0AIC8_CHAVO_50402 are exactly identical! WARNING: Sequences tr_A0A0V1CA18_A0A0V1CA18_TRIBR_45882 and tr_A0A0V0X4J4_A0A0V0X4J4_9BILA_92179 are exactly identical! WARNING: Sequences tr_A0A0V1CA18_A0A0V1CA18_TRIBR_45882 and tr_A0A0V1L015_A0A0V1L015_9BILA_6335 are exactly identical! WARNING: Sequences tr_A0A0V1CA18_A0A0V1CA18_TRIBR_45882 and tr_A0A0V1NJ05_A0A0V1NJ05_9BILA_92180 are exactly identical! WARNING: Sequences tr_A0A0V1CA18_A0A0V1CA18_TRIBR_45882 and tr_A0A0V0TSE8_A0A0V0TSE8_9BILA_144512 are exactly identical! WARNING: Sequences tr_A0A0V1D8Q9_A0A0V1D8Q9_TRIBR_45882 and tr_A0A0V0V6R7_A0A0V0V6R7_9BILA_181606 are exactly identical! WARNING: Sequences tr_A0A0V0WT35_A0A0V0WT35_9BILA_92179 and tr_A0A0V1NZK3_A0A0V1NZK3_9BILA_92180 are exactly identical! WARNING: Sequences tr_I1RDH0_I1RDH0_GIBZE_229533 and tr_A0A2T4H7Z9_A0A2T4H7Z9_FUSCU_5516 are exactly identical! WARNING: Duplicate sequences found: 33 NOTE: Reduced alignment (with duplicates and gap-only sites/taxa removed) NOTE: was saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/P23025/4_raxmlng_ancestral/P23025.raxml.reduced.phy Alignment comprises 1 partitions and 273 sites Partition 0: noname Model: LG4X+R4 Alignment sites: 273 Gaps: 19.10 % Invariant sites: 0.00 % NOTE: Binary MSA file created: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/P23025/4_raxmlng_ancestral/P23025.raxml.rba Parallelization scheme autoconfig: 1 worker(s) x 4 thread(s) Parallel reduction/worker buffer size: 1 KB / 0 KB [00:00:00] Loading user starting tree(s) from: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/P23025/3_mltree/P23025.raxml.bestTree_unrooted [00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 69 / 5520 [00:00:00] Data distribution: max. searches per worker: 1 Starting ML tree search with 1 distinct starting trees [00:00:00] Tree #1, initial LogLikelihood: -94741.028485 [00:00:00 -94741.028485] Initial branch length optimization [00:00:00 -93238.967172] Model parameter optimization (eps = 0.100000) [00:00:20] Tree #1, final logLikelihood: -92952.999404 Optimized model parameters: Partition 0: noname Rate heterogeneity: FREE (4 cats, mean), weights&rates: (0.159898,0.218537) (0.060694,0.238807) (0.321118,0.655306) (0.458290,1.614985) Base frequencies (model): M0: 0.147383 0.017579 0.058208 0.017707 0.026331 0.041582 0.017494 0.027859 0.011849 0.076971 0.147823 0.019535 0.037132 0.029940 0.008059 0.088179 0.089653 0.006477 0.032308 0.097931 M1: 0.063139 0.066357 0.011586 0.066571 0.010800 0.009276 0.053984 0.146986 0.034214 0.088822 0.098196 0.032390 0.021263 0.072697 0.016761 0.020711 0.020797 0.025463 0.045615 0.094372 M2: 0.062457 0.066826 0.049332 0.065270 0.006513 0.041231 0.058965 0.080852 0.028024 0.037024 0.075925 0.064131 0.019620 0.028710 0.104579 0.056388 0.062027 0.008241 0.033124 0.050760 M3: 0.106471 0.074171 0.044513 0.096390 0.002148 0.066733 0.158908 0.037625 0.020691 0.014608 0.028797 0.105352 0.007864 0.007477 0.083595 0.055726 0.047711 0.003975 0.010088 0.027159 Substitution rates (model): M 0: 0.295719 0.067388 0.253712 1.029289 0.107964 0.514644 10.868848 0.380498 0.084223 0.086976 0.188789 0.286389 0.155567 1.671061 2.132922 0.529591 0.115551 0.102453 0.916683 0.448317 0.457483 0.576016 1.741924 0.736017 0.704334 5.658311 0.123387 0.221777 93.433377 0.382175 0.235965 6.535048 0.525521 0.303537 0.641259 0.289466 0.102065 2.358429 0.251987 0.216561 0.503084 0.435271 4.873453 0.090748 0.033310 0.746537 0.128905 0.127321 0.904011 0.939733 0.435450 0.046646 0.262076 0.043986 0.189008 0.599450 109.901504 1.070052 5.229858 0.052764 0.021407 0.621146 0.081091 0.205164 5.164456 0.747330 0.308078 0.260889 0.185083 0.080708 0.029955 0.084794 1.862626 0.553477 0.151733 0.230320 0.096955 0.352526 0.590018 0.386853 1.559564 0.606648 0.587531 0.592318 0.885230 4.117654 0.246260 6.508329 0.054187 0.195703 1.669092 0.810168 0.066081 2.437439 0.165666 0.106333 0.093417 0.035149 0.072549 1.202023 1.634845 0.060194 0.069359 2.448827 0.232297 0.064822 3.537387 0.435384 0.290413 0.280695 0.105999 0.206603 0.404968 0.048984 0.069963 0.256662 0.228519 0.241077 4.320442 3.656545 0.290216 0.307466 0.096556 0.306067 0.204296 0.504221 1.991533 0.655465 6.799829 11.291065 0.961142 0.448965 6.227274 20.304886 0.205944 1.495537 0.091940 1.994320 0.754940 0.170343 0.050315 0.372166 0.206332 0.097050 5.381403 0.122332 3.256485 2.261319 0.848067 0.064441 0.102493 0.459041 0.133091 0.561215 0.457430 0.163849 5.260446 0.360946 0.389413 0.033291 0.115301 0.112593 1.559944 0.426508 0.132547 0.498634 0.559069 0.264728 0.693307 0.438856 0.306683 0.109129 18.392863 66.647302 0.400021 4.586081 2.099355 0.411347 0.476350 0.584622 3.634276 0.101797 0.148995 0.089177 0.034710 0.063603 0.755865 20.561407 0.133790 0.154902 M 1: 0.066142 0.590377 0.069930 9.850951 1.101363 0.150375 0.568586 0.051668 0.127170 0.292429 0.071458 1.218562 0.075144 7.169085 30.139501 13.461692 0.021372 0.045779 4.270235 0.468325 0.013688 0.302287 1.353957 0.028386 0.037750 0.262130 0.016923 0.064289 0.855973 0.079621 0.011169 0.161937 0.276530 0.161053 0.081472 0.036742 0.030342 2.851667 3.932151 8.159169 0.219934 0.421974 2.468752 0.344765 0.210724 1.172204 0.763553 0.082464 0.726566 11.149790 4.782635 0.058046 0.498072 0.258487 0.146882 0.249672 0.560142 0.046719 0.106259 0.003656 0.004200 0.014189 0.009876 0.002656 0.040244 0.267322 0.053740 0.006597 0.027639 0.012745 0.582670 0.005035 0.275844 0.098208 0.445038 1.217010 0.033969 1.988516 0.681161 0.825960 18.762977 11.949233 0.286794 0.534219 4.336817 3.054085 0.129551 4.210126 0.165753 1.088704 1.889645 3.344809 0.111063 2.067758 3.547017 2.466507 0.188236 0.203493 0.281953 0.037250 0.029788 0.008541 0.014768 0.125869 0.056702 0.004186 0.110993 0.201148 0.139705 0.009201 0.012095 0.043812 0.013513 0.002533 0.005848 0.031390 0.021612 0.004854 0.129497 0.976631 0.053397 0.019475 0.004964 0.015539 0.031779 0.064558 0.065585 0.079927 0.095591 0.196886 0.408834 0.126088 0.037226 0.452302 0.016212 7.278994 0.029917 7.918203 0.450964 0.169797 0.104288 1.578530 0.015909 0.094365 16.179952 0.042762 14.799537 1.506485 0.637893 0.123793 0.641351 0.154810 0.140750 3.416059 0.259400 0.009457 0.090576 0.292108 0.297913 0.017172 0.021976 0.032578 1.375871 0.457399 0.598048 4.418398 0.239749 0.168432 2.950318 0.143327 0.328689 0.125011 0.562720 1.414883 0.227807 3.478333 2.984862 0.061299 0.077470 1.050562 13.974326 0.154326 0.224675 0.112000 0.060703 0.123480 5.294490 0.447011 0.033381 0.045528 M 2: 0.733336 0.558955 0.503360 4.149599 1.415369 1.367574 1.263002 0.994098 0.517204 0.775054 0.763094 1.890137 0.540460 0.200122 4.972745 1.825593 0.450842 0.526135 3.839269 0.597671 0.058964 2.863355 2.872594 0.258365 0.366868 2.578946 0.358350 0.672023 5.349861 0.691594 0.063347 0.032875 0.821562 0.580847 0.661866 0.265730 0.395134 5.581680 1.279881 1.335650 0.397108 1.840061 5.739035 0.284730 0.109781 1.612642 0.466979 0.141582 0.019509 4.670980 1.967383 0.088064 0.581928 0.145401 0.225860 0.434096 2.292917 1.024707 0.821921 0.027824 0.021443 0.088850 0.060820 0.018288 0.042687 1.199607 0.420710 0.037642 0.141233 0.090101 1.043232 0.209978 0.823594 3.039380 1.463390 1.983693 0.397640 2.831098 4.102068 0.059723 5.901348 2.034980 2.600668 5.413080 4.193725 4.534772 0.377181 4.877840 0.370939 1.298542 3.509873 2.646440 0.087872 0.072299 1.139018 0.864479 0.390688 0.322761 0.625409 0.496780 0.532488 0.232460 0.169219 0.755219 0.379926 0.020447 0.023282 0.503875 0.577513 0.109318 0.153776 0.696533 0.398817 0.008940 0.043707 0.436013 0.087640 0.064863 0.036426 1.673207 0.124068 0.218118 0.039217 0.104335 0.349195 0.838324 0.888693 0.488389 1.385133 0.050226 0.962470 0.502294 1.065585 8.351808 0.377304 5.102837 0.561690 7.010411 3.054968 0.039318 0.204155 2.653232 0.564368 0.854294 15.559906 0.401070 8.929538 5.525874 0.067505 0.273372 0.437116 1.927515 0.940458 2.508169 1.357738 0.043394 0.023126 0.567639 1.048288 0.120994 0.180650 0.449074 3.135353 0.012695 0.570771 2.319555 1.856122 0.975427 3.404087 0.015631 0.458799 0.151684 4.154750 11.429924 1.457957 0.233109 0.077004 0.011074 0.026268 0.052132 8.113282 0.377578 0.429221 0.260296 0.222293 0.273138 2.903836 4.731579 0.564762 0.681215 M 3: 0.658412 0.566269 0.854111 0.884454 1.309554 1.272639 1.874713 0.552007 0.227683 0.581512 0.695190 0.967985 0.344015 0.978992 3.427163 2.333253 0.154701 0.221089 2.088785 0.540749 0.058015 5.851132 2.294145 0.182966 0.684164 3.192521 0.528161 1.128882 3.010922 1.012866 0.227296 0.156635 0.878405 0.802754 0.830884 0.431617 0.456530 3.060574 1.279257 1.438430 0.431464 2.075952 4.840271 0.644656 0.266076 2.084975 0.720060 0.291854 0.028961 4.071574 2.258357 0.073037 1.238426 0.199728 0.160296 0.482619 2.992763 1.296206 0.841829 0.031467 0.048542 0.132774 0.133055 0.056045 0.209188 0.925172 0.360522 0.094591 0.313945 0.118104 0.992259 0.086318 2.149634 5.103188 3.775817 3.954021 0.190734 1.776095 4.495841 0.264277 7.063879 2.221150 3.017954 8.558815 4.310199 2.130054 0.571406 4.137385 0.437589 2.071689 2.498630 1.763546 0.116381 0.296578 1.033710 1.283423 0.312579 0.305772 0.681277 0.507160 0.351381 0.189152 0.217780 0.767361 0.278392 0.092075 0.177263 0.451893 0.653836 0.074620 0.181992 0.752277 0.679853 0.025780 0.082005 0.326441 0.343977 0.195877 0.217424 3.057583 0.377558 0.401252 0.072258 0.241015 0.665865 1.266791 0.680174 0.717301 4.001286 0.362942 1.189259 0.964545 1.350568 12.869737 0.531100 8.904999 0.652629 10.091413 2.671718 0.086367 0.359932 4.797423 0.336801 1.021885 23.029406 0.440178 14.013035 5.069337 0.539010 0.742569 0.780580 1.331875 1.531589 4.414850 1.082703 0.091278 0.172734 0.693405 1.422571 0.068958 0.163829 0.481711 4.643214 0.121821 0.584083 4.216178 1.677263 1.575754 5.046403 0.161015 1.531223 0.599244 5.832025 33.873091 1.914768 1.287474 0.444362 0.076328 0.079916 0.466823 5.231362 0.548763 0.831890 0.382271 0.208791 0.307846 3.717971 5.910440 0.282540 0.964421 Marginal ancestral probabilities saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/P23025/4_raxmlng_ancestral/P23025.raxml.ancestralProbs Reconstructed ancestral sequences saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/P23025/4_raxmlng_ancestral/P23025.raxml.ancestralStates Node-labeled tree saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/P23025/4_raxmlng_ancestral/P23025.raxml.ancestralTree Execution log saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/P23025/4_raxmlng_ancestral/P23025.raxml.log Analysis started: 04-Jun-2021 13:38:45 / finished: 04-Jun-2021 13:39:08 Elapsed time: 22.301 seconds