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 14:09:04 as follows: raxml-ng --ancestral --msa /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/O75891/2_msa/O75891_nogap_msa.fasta --tree /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/O75891/3_mltree/O75891.raxml.bestTree_unrooted --model LG4X --prefix /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/O75891/4_raxmlng_ancestral/O75891 --threads 4 Analysis options: run mode: Ancestral state reconstruction start tree(s): user random seed: 1622804944 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/O75891/2_msa/O75891_nogap_msa.fasta [00:00:00] Loaded alignment with 1001 taxa and 902 sites WARNING: Sequences sp_O93344_AL1A2_CHICK_9031 and tr_A0A226PKF6_A0A226PKF6_COLVI_9014 are exactly identical! WARNING: Sequences tr_M3XZ73_M3XZ73_MUSPF_9669 and tr_A0A2Y9K310_A0A2Y9K310_ENHLU_391180 are exactly identical! WARNING: Sequences tr_B8N8T4_B8N8T4_ASPFN_332952 and tr_Q2UHF6_Q2UHF6_ASPOR_510516 are exactly identical! WARNING: Sequences tr_F1PGT3_F1PGT3_CANLF_9615 and tr_H2Q9I2_H2Q9I2_PANTR_9598 are exactly identical! WARNING: Sequences tr_F1PGT3_F1PGT3_CANLF_9615 and tr_F7CVL4_F7CVL4_HORSE_9796 are exactly identical! WARNING: Sequences tr_F1PGT3_F1PGT3_CANLF_9615 and tr_A0A2R9B140_A0A2R9B140_PANPA_9597 are exactly identical! WARNING: Sequences tr_A0A2I3S2X8_A0A2I3S2X8_PANTR_9598 and tr_A0A2R9A203_A0A2R9A203_PANPA_9597 are exactly identical! WARNING: Sequences tr_H2Q6R9_H2Q6R9_PANTR_9598 and tr_A0A2R9B8M2_A0A2R9B8M2_PANPA_9597 are exactly identical! WARNING: Sequences tr_H2QA58_H2QA58_PANTR_9598 and tr_A0A2R9CDK5_A0A2R9CDK5_PANPA_9597 are exactly identical! WARNING: Sequences tr_H2QXA8_H2QXA8_PANTR_9598 and tr_A0A2R8ZAD4_A0A2R8ZAD4_PANPA_9597 are exactly identical! WARNING: Sequences tr_A2QRU8_A2QRU8_ASPNC_425011 and tr_G3YER8_G3YER8_ASPNA_380704 are exactly identical! WARNING: Sequences tr_F6USB4_F6USB4_MACMU_9544 and tr_G7PIP6_G7PIP6_MACFA_9541 are exactly identical! WARNING: Sequences tr_F6YY71_F6YY71_MACMU_9544 and tr_Q4R5G3_Q4R5G3_MACFA_9541 are exactly identical! WARNING: Sequences tr_F6YY71_F6YY71_MACMU_9544 and tr_A0A2K6DYN5_A0A2K6DYN5_MACNE_9545 are exactly identical! WARNING: Sequences tr_F7FAR5_F7FAR5_MACMU_9544 and tr_G7NYF0_G7NYF0_MACFA_9541 are exactly identical! WARNING: Sequences tr_F7FAR5_F7FAR5_MACMU_9544 and tr_A0A2K6D0A5_A0A2K6D0A5_MACNE_9545 are exactly identical! WARNING: Sequences tr_F7H3Z0_F7H3Z0_MACMU_9544 and tr_A0A2K6AC29_A0A2K6AC29_MANLE_9568 are exactly identical! WARNING: Sequences tr_I2CVL1_I2CVL1_MACMU_9544 and tr_A0A0D9RHQ6_A0A0D9RHQ6_CHLSB_60711 are exactly identical! WARNING: Sequences tr_G7XKE2_G7XKE2_ASPKW_1033177 and tr_A0A146FSW7_A0A146FSW7_9EURO_1069201 are exactly identical! WARNING: Sequences tr_A2WS18_A2WS18_ORYSI_39946 and tr_Q94JC6_Q94JC6_ORYSJ_39947 are exactly identical! WARNING: Sequences tr_I1NPA6_I1NPA6_ORYGL_4538 and tr_A0A0D3EQR1_A0A0D3EQR1_9ORYZ_65489 are exactly identical! WARNING: Sequences tr_A8Y3G4_A8Y3G4_CAEBR_6238 and tr_A0A2G5UL98_A0A2G5UL98_9PELO_1611254 are exactly identical! WARNING: Sequences tr_B3RUH8_B3RUH8_TRIAD_10228 and tr_A0A369SHV5_A0A369SHV5_9METZ_287889 are exactly identical! WARNING: Sequences tr_U3KCL4_U3KCL4_FICAL_59894 and tr_A0A218UN47_A0A218UN47_9PASE_299123 are exactly identical! WARNING: Sequences tr_A0A015KR72_A0A015KR72_9GLOM_1432141 and tr_A0A2H5TYG6_A0A2H5TYG6_RHIID_747089 are exactly identical! WARNING: Sequences tr_A0A2I3MYH5_A0A2I3MYH5_PAPAN_9555 and tr_A0A2K5P1R7_A0A2K5P1R7_CERAT_9531 are exactly identical! WARNING: Sequences tr_A0A2I3MYH5_A0A2I3MYH5_PAPAN_9555 and tr_A0A2K6CMN2_A0A2K6CMN2_MACNE_9545 are exactly identical! WARNING: Sequences tr_A0A0D9S3S0_A0A0D9S3S0_CHLSB_60711 and tr_A0A2K5N4C2_A0A2K5N4C2_CERAT_9531 are exactly identical! WARNING: Sequences tr_A0A0D2U7N0_A0A0D2U7N0_GOSRA_29730 and tr_A0A1U8J332_A0A1U8J332_GOSHI_3635 are exactly identical! WARNING: Sequences tr_A0A0A1NWH0_A0A0A1NWH0_9FUNG_58291 and tr_A0A367J4V5_A0A367J4V5_9FUNG_86630 are exactly identical! WARNING: Sequences tr_A0A0A1P307_A0A0A1P307_9FUNG_58291 and tr_A0A367KG59_A0A367KG59_9FUNG_86630 are exactly identical! WARNING: Sequences tr_A0A091JHV5_A0A091JHV5_EGRGA_188379 and tr_A0A093QB80_A0A093QB80_9PASS_328815 are exactly identical! WARNING: Sequences tr_A0A091JHV5_A0A091JHV5_EGRGA_188379 and tr_A0A087R468_A0A087R468_APTFO_9233 are exactly identical! WARNING: Sequences tr_A0A091JHV5_A0A091JHV5_EGRGA_188379 and tr_A0A091G7A0_A0A091G7A0_9AVES_55661 are exactly identical! WARNING: Sequences tr_A0A091WLZ1_A0A091WLZ1_NIPNI_128390 and tr_A0A099ZXX6_A0A099ZXX6_CHAVO_50402 are exactly identical! WARNING: Sequences tr_A0A0G4PQ94_A0A0G4PQ94_PENCA_1429867 and tr_A0A101M936_A0A101M936_9EURO_48697 are exactly identical! WARNING: Sequences tr_A0A100IJL1_A0A100IJL1_ASPNG_5061 and tr_A0A1L9NPK9_A0A1L9NPK9_ASPTU_767770 are exactly identical! WARNING: Sequences tr_A0A1U7QDB4_A0A1U7QDB4_MESAU_10036 and sp_P86886_AL1A1_MESAU_10036 are exactly identical! WARNING: Sequences tr_A0A226NNL0_A0A226NNL0_CALSU_9009 and tr_A0A226PE42_A0A226PE42_COLVI_9014 are exactly identical! WARNING: Sequences tr_A0A2H3C4M1_A0A2H3C4M1_9AGAR_1076256 and tr_A0A284RUQ7_A0A284RUQ7_9AGAR_47428 are exactly identical! WARNING: Sequences tr_A0A2K5KYV1_A0A2K5KYV1_CERAT_9531 and tr_A0A2K5ZM37_A0A2K5ZM37_MANLE_9568 are exactly identical! WARNING: Sequences tr_A0A2U4BAL8_A0A2U4BAL8_TURTR_9739 and tr_A0A2Y9NIU5_A0A2Y9NIU5_DELLE_9749 are exactly identical! WARNING: Duplicate sequences found: 42 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/O75891/4_raxmlng_ancestral/O75891.raxml.reduced.phy Alignment comprises 1 partitions and 902 sites Partition 0: noname Model: LG4X+R4 Alignment sites: 902 Gaps: 35.34 % Invariant sites: 2.33 % NOTE: Binary MSA file created: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/O75891/4_raxmlng_ancestral/O75891.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/O75891/3_mltree/O75891.raxml.bestTree_unrooted [00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 226 / 18080 [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: -223503.157307 [00:00:00 -223503.157307] Initial branch length optimization [00:00:01 -223364.005637] Model parameter optimization (eps = 0.100000) [00:00:41] Tree #1, final logLikelihood: -222773.044316 Optimized model parameters: Partition 0: noname Rate heterogeneity: FREE (4 cats, mean), weights&rates: (0.182297,0.336953) (0.300707,0.463312) (0.266204,0.996932) (0.250792,2.128723) 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/O75891/4_raxmlng_ancestral/O75891.raxml.ancestralProbs Reconstructed ancestral sequences saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/O75891/4_raxmlng_ancestral/O75891.raxml.ancestralStates Node-labeled tree saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/O75891/4_raxmlng_ancestral/O75891.raxml.ancestralTree Execution log saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/O75891/4_raxmlng_ancestral/O75891.raxml.log Analysis started: 04-Jun-2021 14:09:04 / finished: 04-Jun-2021 14:09:54 Elapsed time: 49.750 seconds