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 19-Jul-2021 20:21:38 as follows: raxml-ng --ancestral --msa /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q9NQX0/2_msa/Q9NQX0_nogap_msa.fasta --tree /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q9NQX0/3_mltree/Q9NQX0.raxml.bestTree_unrooted --model LG4X --prefix /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q9NQX0/4_raxmlng_ancestral/Q9NQX0 --threads 4 Analysis options: run mode: Ancestral state reconstruction start tree(s): user random seed: 1626715298 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_300621/phylogeny-snakemake/results/Q9NQX0/2_msa/Q9NQX0_nogap_msa.fasta [00:00:00] Loaded alignment with 1001 taxa and 595 sites WARNING: Sequences tr_E1C6K0_E1C6K0_CHICK_9031 and tr_G1N1G5_G1N1G5_MELGA_9103 are exactly identical! WARNING: Sequences tr_E1C6K0_E1C6K0_CHICK_9031 and tr_A0A1V4J6C7_A0A1V4J6C7_PATFA_372326 are exactly identical! WARNING: Sequences tr_E1C6K0_E1C6K0_CHICK_9031 and tr_A0A218V159_A0A218V159_9PASE_299123 are exactly identical! WARNING: Sequences tr_E1C6K0_E1C6K0_CHICK_9031 and tr_A0A226NP02_A0A226NP02_CALSU_9009 are exactly identical! WARNING: Sequences tr_E1C6K0_E1C6K0_CHICK_9031 and tr_A0A226P0G4_A0A226P0G4_COLVI_9014 are exactly identical! WARNING: Sequences sp_A2AJ77_PRD12_MOUSE_10090 and tr_D3ZEJ0_D3ZEJ0_RAT_10116 are exactly identical! WARNING: Sequences sp_A2AJ77_PRD12_MOUSE_10090 and tr_I3M725_I3M725_ICTTR_43179 are exactly identical! WARNING: Sequences sp_A2AJ77_PRD12_MOUSE_10090 and tr_G3SZ86_G3SZ86_LOXAF_9785 are exactly identical! WARNING: Sequences sp_A2AJ77_PRD12_MOUSE_10090 and tr_F1S0X7_F1S0X7_PIG_9823 are exactly identical! WARNING: Sequences sp_A2AJ77_PRD12_MOUSE_10090 and tr_A0A337SEE4_A0A337SEE4_FELCA_9685 are exactly identical! WARNING: Sequences sp_A2AJ77_PRD12_MOUSE_10090 and tr_A0A1U7REI9_A0A1U7REI9_MESAU_10036 are exactly identical! WARNING: Sequences sp_A2AJ77_PRD12_MOUSE_10090 and tr_A0A2Y9J523_A0A2Y9J523_ENHLU_391180 are exactly identical! WARNING: Sequences tr_G1QL70_G1QL70_NOMLE_61853 and tr_G3S2S2_G3S2S2_GORGO_9595 are exactly identical! WARNING: Sequences tr_G1QL70_G1QL70_NOMLE_61853 and sp_B4DU55_ZN879_HUMAN_9606 are exactly identical! WARNING: Sequences tr_G1RPQ6_G1RPQ6_NOMLE_61853 and tr_A0A2K5Z9L2_A0A2K5Z9L2_MANLE_9568 are exactly identical! WARNING: Sequences tr_A0A2I2YBD3_A0A2I2YBD3_GORGO_9595 and sp_Q6ZN57_ZFP2_HUMAN_9606 are exactly identical! WARNING: Sequences tr_G3QU29_G3QU29_GORGO_9595 and tr_H2NXU3_H2NXU3_PONAB_9601 are exactly identical! WARNING: Sequences tr_G3QU29_G3QU29_GORGO_9595 and tr_H2RBZ2_H2RBZ2_PANTR_9598 are exactly identical! WARNING: Sequences tr_G3SAJ5_G3SAJ5_GORGO_9595 and tr_K7DBH8_K7DBH8_PANTR_9598 are exactly identical! WARNING: Sequences tr_A0A2J8JTT0_A0A2J8JTT0_PANTR_9598 and tr_A0A2R8ZF15_A0A2R8ZF15_PANPA_9597 are exactly identical! WARNING: Sequences tr_H2QHA2_H2QHA2_PANTR_9598 and sp_Q9BWM5_ZN416_HUMAN_9606 are exactly identical! WARNING: Sequences tr_H2QHB7_H2QHB7_PANTR_9598 and tr_A0A2R9AFG9_A0A2R9AFG9_PANPA_9597 are exactly identical! WARNING: Sequences tr_H2QY20_H2QY20_PANTR_9598 and sp_Q9H4Q4_PRD12_HUMAN_9606 are exactly identical! WARNING: Sequences tr_H2QY20_H2QY20_PANTR_9598 and tr_F7I4S5_F7I4S5_CALJA_9483 are exactly identical! WARNING: Sequences tr_H2QY20_H2QY20_PANTR_9598 and tr_A0A096P0F9_A0A096P0F9_PAPAN_9555 are exactly identical! WARNING: Sequences tr_H2QY20_H2QY20_PANTR_9598 and tr_A0A0D9RQI6_A0A0D9RQI6_CHLSB_60711 are exactly identical! WARNING: Sequences tr_H2QY20_H2QY20_PANTR_9598 and tr_A0A2K5L0P9_A0A2K5L0P9_CERAT_9531 are exactly identical! WARNING: Sequences tr_H2QY20_H2QY20_PANTR_9598 and tr_A0A2K6CVC9_A0A2K6CVC9_MACNE_9545 are exactly identical! WARNING: Sequences tr_H2REH7_H2REH7_PANTR_9598 and tr_A0A2R9ACJ3_A0A2R9ACJ3_PANPA_9597 are exactly identical! WARNING: Sequences tr_A0A1D5QJK0_A0A1D5QJK0_MACMU_9544 and tr_G7PZM3_G7PZM3_MACFA_9541 are exactly identical! WARNING: Sequences tr_F7H1A1_F7H1A1_MACMU_9544 and tr_G7PZB8_G7PZB8_MACFA_9541 are exactly identical! WARNING: Sequences tr_H0Z2N4_H0Z2N4_TAEGU_59729 and tr_A0A093PSR3_A0A093PSR3_9PASS_328815 are exactly identical! WARNING: Sequences tr_H0Z2N4_H0Z2N4_TAEGU_59729 and tr_A0A091UPR0_A0A091UPR0_NIPNI_128390 are exactly identical! WARNING: Sequences tr_H0Z2N4_H0Z2N4_TAEGU_59729 and tr_A0A093JBE6_A0A093JBE6_STRCA_441894 are exactly identical! WARNING: Sequences tr_H0Z2N4_H0Z2N4_TAEGU_59729 and tr_A0A091V8C5_A0A091V8C5_OPIHO_30419 are exactly identical! WARNING: Sequences tr_H0Z2N4_H0Z2N4_TAEGU_59729 and tr_A0A099YZK0_A0A099YZK0_TINGU_94827 are exactly identical! WARNING: Sequences tr_H0Z2N4_H0Z2N4_TAEGU_59729 and tr_A0A091H882_A0A091H882_9AVES_55661 are exactly identical! WARNING: Sequences tr_H0Z2N4_H0Z2N4_TAEGU_59729 and tr_A0A0A0AP02_A0A0A0AP02_CHAVO_50402 are exactly identical! WARNING: Sequences tr_H0Z2N4_H0Z2N4_TAEGU_59729 and tr_A0A093IBH6_A0A093IBH6_DRYPU_118200 are exactly identical! WARNING: Sequences tr_H0Z2N4_H0Z2N4_TAEGU_59729 and tr_A0A091HRY8_A0A091HRY8_CALAN_9244 are exactly identical! WARNING: Sequences tr_A0A091JR11_A0A091JR11_EGRGA_188379 and tr_A0A093I2Y2_A0A093I2Y2_STRCA_441894 are exactly identical! WARNING: Sequences tr_A0A1S3PRF7_A0A1S3PRF7_SALSA_8030 and tr_A0A060XNB8_A0A060XNB8_ONCMY_8022 are exactly identical! WARNING: Sequences tr_A0A2D0QW48_A0A2D0QW48_ICTPU_7998 and tr_A0A2D0QWG6_A0A2D0QWG6_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2K5MX30_A0A2K5MX30_CERAT_9531 and tr_A0A2K5YJ92_A0A2K5YJ92_MANLE_9568 are exactly identical! WARNING: Sequences tr_A0A2Y9MA68_A0A2Y9MA68_DELLE_9749 and tr_A0A383Z4X8_A0A383Z4X8_BALAS_310752 are exactly identical! WARNING: Duplicate sequences found: 45 NOTE: Reduced alignment (with duplicates and gap-only sites/taxa removed) NOTE: was saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q9NQX0/4_raxmlng_ancestral/Q9NQX0.raxml.reduced.phy Alignment comprises 1 partitions and 595 sites Partition 0: noname Model: LG4X+R4 Alignment sites: 595 Gaps: 56.78 % Invariant sites: 0.00 % NOTE: Binary MSA file created: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q9NQX0/4_raxmlng_ancestral/Q9NQX0.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_300621/phylogeny-snakemake/results/Q9NQX0/3_mltree/Q9NQX0.raxml.bestTree_unrooted [00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 149 / 11920 [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: -184382.810486 [00:00:00 -184382.810486] Initial branch length optimization [00:00:02 -182612.183906] Model parameter optimization (eps = 0.100000) [00:00:52] Tree #1, final logLikelihood: -181881.889827 Optimized model parameters: Partition 0: noname Rate heterogeneity: FREE (4 cats, mean), weights&rates: (0.105772,0.223297) (0.042682,0.358161) (0.408797,0.773091) (0.442749,1.456937) 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_300621/phylogeny-snakemake/results/Q9NQX0/4_raxmlng_ancestral/Q9NQX0.raxml.ancestralProbs Reconstructed ancestral sequences saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q9NQX0/4_raxmlng_ancestral/Q9NQX0.raxml.ancestralStates Node-labeled tree saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q9NQX0/4_raxmlng_ancestral/Q9NQX0.raxml.ancestralTree Execution log saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q9NQX0/4_raxmlng_ancestral/Q9NQX0.raxml.log Analysis started: 19-Jul-2021 20:21:38 / finished: 19-Jul-2021 20:22:36 Elapsed time: 57.558 seconds