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 14:13:24 as follows: raxml-ng --ancestral --msa /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/O00142/2_msa/O00142_nogap_msa.fasta --tree /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/O00142/3_mltree/O00142.raxml.bestTree_unrooted --model LG4X --prefix /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/O00142/4_raxmlng_ancestral/O00142 --threads 4 Analysis options: run mode: Ancestral state reconstruction start tree(s): user random seed: 1622805204 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/O00142/2_msa/O00142_nogap_msa.fasta [00:00:00] Loaded alignment with 613 taxa and 265 sites WARNING: Sequences tr_B4QTW8_B4QTW8_DROSI_7240 and tr_B4IME5_B4IME5_DROSE_7238 are exactly identical! WARNING: Sequences tr_D8SK55_D8SK55_SELML_88036 and tr_D8T4G3_D8T4G3_SELML_88036 are exactly identical! WARNING: Sequences tr_A0A2I3RS78_A0A2I3RS78_PANTR_9598 and tr_A0A2R9B8P6_A0A2R9B8P6_PANPA_9597 are exactly identical! WARNING: Sequences tr_H2QI54_H2QI54_PANTR_9598 and tr_A0A2R9BLX3_A0A2R9BLX3_PANPA_9597 are exactly identical! WARNING: Sequences tr_A0A158NT48_A0A158NT48_ATTCE_12957 and tr_A0A195B780_A0A195B780_9HYME_520822 are exactly identical! WARNING: Sequences tr_A0A0E0FWE5_A0A0E0FWE5_ORYNI_4536 and tr_I1NTU7_I1NTU7_ORYGL_4538 are exactly identical! WARNING: Sequences tr_A0A0E0FWE5_A0A0E0FWE5_ORYNI_4536 and tr_A0A0E0CAZ0_A0A0E0CAZ0_9ORYZ_40149 are exactly identical! WARNING: Sequences tr_A0A0E0FWE5_A0A0E0FWE5_ORYNI_4536 and tr_A0A0E0N5P3_A0A0E0N5P3_ORYRU_4529 are exactly identical! WARNING: Sequences tr_A0A0E0FWE5_A0A0E0FWE5_ORYNI_4536 and tr_A0A0D3EWV4_A0A0D3EWV4_9ORYZ_65489 are exactly identical! WARNING: Sequences tr_A0A0E0FWE5_A0A0E0FWE5_ORYNI_4536 and tr_A0A0D9YI36_A0A0D9YI36_9ORYZ_40148 are exactly identical! WARNING: Sequences tr_A0A1D5R823_A0A1D5R823_MACMU_9544 and tr_A0A2I3M500_A0A2I3M500_PAPAN_9555 are exactly identical! WARNING: Sequences tr_A0A1D5R823_A0A1D5R823_MACMU_9544 and tr_A0A2K5LKP6_A0A2K5LKP6_CERAT_9531 are exactly identical! WARNING: Sequences tr_A0A1D5R823_A0A1D5R823_MACMU_9544 and tr_A0A2K6C8E3_A0A2K6C8E3_MACNE_9545 are exactly identical! WARNING: Sequences tr_A0A0E0PMV3_A0A0E0PMV3_ORYRU_4529 and tr_A0A0D3G7Z6_A0A0D3G7Z6_9ORYZ_65489 are exactly identical! WARNING: Sequences tr_B3RPM6_B3RPM6_TRIAD_10228 and tr_A0A369SH03_A0A369SH03_9METZ_287889 are exactly identical! WARNING: Sequences tr_G7PMI3_G7PMI3_MACFA_9541 and tr_A0A096NF31_A0A096NF31_PAPAN_9555 are exactly identical! WARNING: Sequences tr_G7PMI3_G7PMI3_MACFA_9541 and tr_A0A2K5NXI1_A0A2K5NXI1_CERAT_9531 are exactly identical! WARNING: Sequences tr_G7PMI3_G7PMI3_MACFA_9541 and tr_A0A2K6D5Q8_A0A2K6D5Q8_MACNE_9545 are exactly identical! WARNING: Sequences tr_A0A3B5YZQ3_A0A3B5YZQ3_WHEAT_4565 and tr_A0A3B5ZWC7_A0A3B5ZWC7_WHEAT_4565 are exactly identical! WARNING: Sequences tr_A0A067H8E5_A0A067H8E5_CITSI_2711 and tr_V4TDT2_V4TDT2_9ROSI_85681 are exactly identical! WARNING: Sequences tr_A0A067H8E5_A0A067H8E5_CITSI_2711 and tr_A0A2H5NHM9_A0A2H5NHM9_CITUN_55188 are exactly identical! WARNING: Sequences tr_A0A2I3LL71_A0A2I3LL71_PAPAN_9555 and tr_A0A2K5Y120_A0A2K5Y120_MANLE_9568 are exactly identical! WARNING: Sequences tr_A0A226MVD3_A0A226MVD3_CALSU_9009 and tr_A0A226P075_A0A226P075_COLVI_9014 are exactly identical! WARNING: Sequences tr_A0A2G2ZNL2_A0A2G2ZNL2_CAPAN_4072 and tr_A0A2G3CMF4_A0A2G3CMF4_CAPCH_80379 are exactly identical! WARNING: Sequences tr_A0A2P5DUM4_A0A2P5DUM4_TREOI_63057 and tr_A0A2P5ANC9_A0A2P5ANC9_PARAD_3476 are exactly identical! WARNING: Sequences tr_A0A2U4B4V3_A0A2U4B4V3_TURTR_9739 and tr_A0A2Y9QCG0_A0A2Y9QCG0_DELLE_9749 are exactly identical! WARNING: Sequences tr_A0A2U4B4V3_A0A2U4B4V3_TURTR_9739 and tr_A0A384B240_A0A384B240_BALAS_310752 are exactly identical! WARNING: Sequences tr_A0A2U3VE62_A0A2U3VE62_ODORO_9708 and tr_A0A2Y9JMJ6_A0A2Y9JMJ6_ENHLU_391180 are exactly identical! WARNING: Duplicate sequences found: 28 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/O00142/4_raxmlng_ancestral/O00142.raxml.reduced.phy Alignment comprises 1 partitions and 265 sites Partition 0: noname Model: LG4X+R4 Alignment sites: 265 Gaps: 21.90 % Invariant sites: 0.00 % NOTE: Binary MSA file created: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/O00142/4_raxmlng_ancestral/O00142.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/O00142/3_mltree/O00142.raxml.bestTree_unrooted [00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 67 / 5360 [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: -74711.047508 [00:00:00 -74711.047508] Initial branch length optimization [00:00:00 -70882.229913] Model parameter optimization (eps = 0.100000) [00:00:15] Tree #1, final logLikelihood: -70746.818228 Optimized model parameters: Partition 0: noname Rate heterogeneity: FREE (4 cats, mean), weights&rates: (0.106138,0.178407) (0.218268,0.269718) (0.273315,0.686247) (0.402280,1.826173) 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/O00142/4_raxmlng_ancestral/O00142.raxml.ancestralProbs Reconstructed ancestral sequences saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/O00142/4_raxmlng_ancestral/O00142.raxml.ancestralStates Node-labeled tree saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/O00142/4_raxmlng_ancestral/O00142.raxml.ancestralTree Execution log saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/O00142/4_raxmlng_ancestral/O00142.raxml.log Analysis started: 04-Jun-2021 14:13:24 / finished: 04-Jun-2021 14:13:41 Elapsed time: 17.204 seconds