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 13:50:42 as follows: raxml-ng --ancestral --msa /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/P14868/2_msa/P14868_nogap_msa.fasta --tree /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/P14868/3_mltree/P14868.raxml.bestTree_unrooted --model LG4X --prefix /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/P14868/4_raxmlng_ancestral/P14868 --threads 4 Analysis options: run mode: Ancestral state reconstruction start tree(s): user random seed: 1622803842 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/P14868/2_msa/P14868_nogap_msa.fasta [00:00:00] Loaded alignment with 1001 taxa and 501 sites WARNING: Sequences tr_J3KJZ2_J3KJZ2_COCIM_246410 and tr_A0A0J6XZQ0_A0A0J6XZQ0_COCIT_404692 are exactly identical! WARNING: Sequences tr_B2WAP2_B2WAP2_PYRTR_426418 and tr_A0A2W1GPC5_A0A2W1GPC5_9PLEO_45151 are exactly identical! WARNING: Sequences tr_B2WCS5_B2WCS5_PYRTR_426418 and tr_A0A2W1HK31_A0A2W1HK31_9PLEO_45151 are exactly identical! WARNING: Sequences tr_C0NGY7_C0NGY7_AJECG_447093 and tr_C6H6Z8_C6H6Z8_AJECH_544712 are exactly identical! WARNING: Sequences tr_C0NGY7_C0NGY7_AJECG_447093 and tr_F0U7C3_F0U7C3_AJEC8_544711 are exactly identical! WARNING: Sequences tr_B8MYF2_B8MYF2_ASPFN_332952 and tr_Q2URG4_Q2URG4_ASPOR_510516 are exactly identical! WARNING: Sequences tr_B8MYF2_B8MYF2_ASPFN_332952 and tr_A0A1S9DV48_A0A1S9DV48_ASPOZ_5062 are exactly identical! WARNING: Sequences tr_B8NFS0_B8NFS0_ASPFN_332952 and tr_Q2UEI6_Q2UEI6_ASPOR_510516 are exactly identical! WARNING: Sequences tr_B8NFS0_B8NFS0_ASPFN_332952 and tr_A0A1S9E072_A0A1S9E072_ASPOZ_5062 are exactly identical! WARNING: Sequences tr_B8NFS0_B8NFS0_ASPFN_332952 and tr_A0A2G7FJD8_A0A2G7FJD8_9EURO_656916 are exactly identical! WARNING: Sequences tr_A0A179U6T3_A0A179U6T3_BLAGS_559298 and tr_C5GX94_C5GX94_AJEDR_559297 are exactly identical! WARNING: Sequences sp_P14868_SYDC_HUMAN_9606 and tr_A0A2R9BVT7_A0A2R9BVT7_PANPA_9597 are exactly identical! WARNING: Sequences tr_A0A0E0GBF6_A0A0E0GBF6_ORYNI_4536 and tr_B8AGR5_B8AGR5_ORYSI_39946 are exactly identical! WARNING: Sequences tr_A0A0E0GBF6_A0A0E0GBF6_ORYNI_4536 and tr_I1P375_I1P375_ORYGL_4538 are exactly identical! WARNING: Sequences tr_A0A0E0GBF6_A0A0E0GBF6_ORYNI_4536 and tr_A0A0E0NJD2_A0A0E0NJD2_ORYRU_4529 are exactly identical! WARNING: Sequences tr_E2PSR7_E2PSR7_ASPNC_425011 and tr_G3XYX9_G3XYX9_ASPNA_380704 are exactly identical! WARNING: Sequences tr_G7NB00_G7NB00_MACMU_9544 and tr_G7PN28_G7PN28_MACFA_9541 are exactly identical! WARNING: Sequences tr_G7NB00_G7NB00_MACMU_9544 and tr_A0A096MWD1_A0A096MWD1_PAPAN_9555 are exactly identical! WARNING: Sequences tr_G7NB00_G7NB00_MACMU_9544 and tr_A0A0D9RUT2_A0A0D9RUT2_CHLSB_60711 are exactly identical! WARNING: Sequences tr_G7NB00_G7NB00_MACMU_9544 and tr_A0A2K5MZJ5_A0A2K5MZJ5_CERAT_9531 are exactly identical! WARNING: Sequences tr_G7NB00_G7NB00_MACMU_9544 and tr_A0A2K6B9R9_A0A2K6B9R9_MACNE_9545 are exactly identical! WARNING: Sequences tr_G7XE92_G7XE92_ASPKW_1033177 and tr_A0A146F111_A0A146F111_9EURO_1069201 are exactly identical! WARNING: Sequences tr_F2SEN6_F2SEN6_TRIRC_559305 and tr_A0A178ESN2_A0A178ESN2_TRIRU_5551 are exactly identical! WARNING: Sequences tr_B3RYB0_B3RYB0_TRIAD_10228 and tr_A0A369SGN5_A0A369SGN5_9METZ_287889 are exactly identical! WARNING: Sequences tr_F2PIU1_F2PIU1_TRIEC_559882 and tr_A0A059J2T2_A0A059J2T2_9EURO_1215338 are exactly identical! WARNING: Sequences tr_L0P7R1_L0P7R1_PNEJ8_1209962 and tr_A0A0W4ZSK7_A0A0W4ZSK7_PNEJ7_1408657 are exactly identical! WARNING: Sequences tr_M4D447_M4D447_BRARP_51351 and tr_A0A078GUB6_A0A078GUB6_BRANA_3708 are exactly identical! WARNING: Sequences tr_M4E5G4_M4E5G4_BRARP_51351 and tr_A0A078FM60_A0A078FM60_BRANA_3708 are exactly identical! WARNING: Sequences tr_M2UQB7_M2UQB7_COCH5_701091 and tr_W6ZDJ8_W6ZDJ8_COCMI_930090 are exactly identical! WARNING: Sequences tr_V2WM13_V2WM13_MONRO_1381753 and tr_A0A0W0G329_A0A0W0G329_9AGAR_221103 are exactly identical! WARNING: Sequences tr_A0A015IEL3_A0A015IEL3_9GLOM_1432141 and tr_U9SMM9_U9SMM9_RHIID_747089 are exactly identical! WARNING: Sequences tr_A0A044V4G8_A0A044V4G8_ONCVO_6282 and tr_A0A182ECN4_A0A182ECN4_ONCOC_42157 are exactly identical! WARNING: Sequences tr_A0A067DVC8_A0A067DVC8_CITSI_2711 and tr_V4SEI1_V4SEI1_9ROSI_85681 are exactly identical! WARNING: Sequences tr_A0A0F8WNB8_A0A0F8WNB8_9EURO_308745 and tr_A0A2T5M9A5_A0A2T5M9A5_9EURO_1392256 are exactly identical! WARNING: Sequences tr_A0A124BWH7_A0A124BWH7_ASPNG_5061 and tr_A0A1L9MYF6_A0A1L9MYF6_ASPTU_767770 are exactly identical! WARNING: Sequences tr_A0A164UQ82_A0A164UQ82_9HOMO_1314777 and tr_A0A166IHH6_A0A166IHH6_9HOMO_1314776 are exactly identical! WARNING: Sequences tr_A0A1S4APY2_A0A1S4APY2_TOBAC_4097 and tr_A0A1U7XK50_A0A1U7XK50_NICSY_4096 are exactly identical! WARNING: Sequences tr_A0A226NK10_A0A226NK10_CALSU_9009 and tr_A0A226P5H4_A0A226P5H4_COLVI_9014 are exactly identical! WARNING: Sequences tr_A0A2G4SHF7_A0A2G4SHF7_9FUNG_1340429 and tr_A0A367JL39_A0A367JL39_9FUNG_86630 are exactly identical! WARNING: Sequences tr_A0A2V5J787_A0A2V5J787_9EURO_1450541 and tr_A0A2V5I2F7_A0A2V5I2F7_9EURO_1450538 are exactly identical! WARNING: Duplicate sequences found: 40 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/P14868/4_raxmlng_ancestral/P14868.raxml.reduced.phy Alignment comprises 1 partitions and 501 sites Partition 0: noname Model: LG4X+R4 Alignment sites: 501 Gaps: 3.42 % Invariant sites: 1.80 % NOTE: Binary MSA file created: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/P14868/4_raxmlng_ancestral/P14868.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/P14868/3_mltree/P14868.raxml.bestTree_unrooted [00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 126 / 10080 [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: -222639.420506 [00:00:00 -222639.420506] Initial branch length optimization [00:00:01 -222381.694492] Model parameter optimization (eps = 0.100000) [00:00:30] Tree #1, final logLikelihood: -221638.053863 Optimized model parameters: Partition 0: noname Rate heterogeneity: FREE (4 cats, mean), weights&rates: (0.219112,0.350760) (0.334398,0.474602) (0.222844,1.087807) (0.223646,2.334165) 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/P14868/4_raxmlng_ancestral/P14868.raxml.ancestralProbs Reconstructed ancestral sequences saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/P14868/4_raxmlng_ancestral/P14868.raxml.ancestralStates Node-labeled tree saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/P14868/4_raxmlng_ancestral/P14868.raxml.ancestralTree Execution log saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/P14868/4_raxmlng_ancestral/P14868.raxml.log Analysis started: 04-Jun-2021 13:50:42 / finished: 04-Jun-2021 13:51:18 Elapsed time: 35.318 seconds