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 17-Jul-2021 07:31:47 as follows: raxml-ng --ancestral --msa /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/P49711/2_msa/P49711_nogap_msa.fasta --tree /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/P49711/3_mltree/P49711.raxml.bestTree_unrooted --model LG4X --prefix /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/P49711/4_raxmlng_ancestral/P49711 --threads 4 Analysis options: run mode: Ancestral state reconstruction start tree(s): user random seed: 1626496307 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/P49711/2_msa/P49711_nogap_msa.fasta [00:00:00] Loaded alignment with 1001 taxa and 727 sites WARNING: Sequences tr_A0A1D5PYS0_A0A1D5PYS0_CHICK_9031 and tr_G1MTM5_G1MTM5_MELGA_9103 are exactly identical! WARNING: Sequences tr_G3QFH5_G3QFH5_GORGO_9595 and tr_H2NR83_H2NR83_PONAB_9601 are exactly identical! WARNING: Sequences tr_G3QFH5_G3QFH5_GORGO_9595 and tr_H2QBB9_H2QBB9_PANTR_9598 are exactly identical! WARNING: Sequences tr_G3QFH5_G3QFH5_GORGO_9595 and sp_P49711_CTCF_HUMAN_9606 are exactly identical! WARNING: Sequences tr_G3QFH5_G3QFH5_GORGO_9595 and tr_A0A2R9CRW2_A0A2R9CRW2_PANPA_9597 are exactly identical! WARNING: Sequences tr_G3RKQ6_G3RKQ6_GORGO_9595 and tr_H2NQQ0_H2NQQ0_PONAB_9601 are exactly identical! WARNING: Sequences tr_H2NXU3_H2NXU3_PONAB_9601 and tr_H2RBZ2_H2RBZ2_PANTR_9598 are exactly identical! WARNING: Sequences tr_Q29E70_Q29E70_DROPS_46245 and tr_B4HAU6_B4HAU6_DROPE_7234 are exactly identical! WARNING: Sequences tr_A0A2J8JH70_A0A2J8JH70_PANTR_9598 and tr_A0A2R9BXM1_A0A2R9BXM1_PANPA_9597 are exactly identical! WARNING: Sequences tr_H2PYV9_H2PYV9_PANTR_9598 and sp_P17025_ZN182_HUMAN_9606 are exactly identical! WARNING: Sequences tr_H2QAY6_H2QAY6_PANTR_9598 and tr_A0A2R8ZSQ2_A0A2R8ZSQ2_PANPA_9597 are exactly identical! WARNING: Sequences tr_H2QWY0_H2QWY0_PANTR_9598 and tr_A0A2R9AP39_A0A2R9AP39_PANPA_9597 are exactly identical! WARNING: Sequences tr_A0A1D5Q7Q1_A0A1D5Q7Q1_MACMU_9544 and tr_A0A2K6CMR4_A0A2K6CMR4_MACNE_9545 are exactly identical! WARNING: Sequences tr_A0A1D5QC17_A0A1D5QC17_MACMU_9544 and tr_A0A2K6BUH3_A0A2K6BUH3_MACNE_9545 are exactly identical! WARNING: Sequences tr_A0A1D5QFU4_A0A1D5QFU4_MACMU_9544 and tr_A0A0A0MVY8_A0A0A0MVY8_PAPAN_9555 are exactly identical! WARNING: Sequences tr_A0A1D5QFU4_A0A1D5QFU4_MACMU_9544 and tr_A0A2K5M0K3_A0A2K5M0K3_CERAT_9531 are exactly identical! WARNING: Sequences tr_A0A1D5QJK0_A0A1D5QJK0_MACMU_9544 and tr_G7PZM3_G7PZM3_MACFA_9541 are exactly identical! WARNING: Sequences tr_A0A1D5R7W1_A0A1D5R7W1_MACMU_9544 and tr_G7PZZ5_G7PZZ5_MACFA_9541 are exactly identical! WARNING: Sequences tr_F6U3U0_F6U3U0_MACMU_9544 and tr_G7PXU7_G7PXU7_MACFA_9541 are exactly identical! WARNING: Sequences tr_F6VIB6_F6VIB6_MACMU_9544 and tr_G7PZB3_G7PZB3_MACFA_9541 are exactly identical! WARNING: Sequences tr_F6VIB6_F6VIB6_MACMU_9544 and tr_A0A2K6BZF6_A0A2K6BZF6_MACNE_9545 are exactly identical! WARNING: Sequences tr_F6WQ38_F6WQ38_MACMU_9544 and tr_G7PRN1_G7PRN1_MACFA_9541 are exactly identical! WARNING: Sequences tr_F6WQ38_F6WQ38_MACMU_9544 and tr_A0A2K6DYU0_A0A2K6DYU0_MACNE_9545 are exactly identical! WARNING: Sequences tr_F7D328_F7D328_MACMU_9544 and tr_A0A2I3N8I2_A0A2I3N8I2_PAPAN_9555 are exactly identical! WARNING: Sequences tr_F7D328_F7D328_MACMU_9544 and tr_A0A2K5XRB6_A0A2K5XRB6_MANLE_9568 are exactly identical! WARNING: Sequences tr_G7NQ61_G7NQ61_MACMU_9544 and tr_G8F4K8_G8F4K8_MACFA_9541 are exactly identical! WARNING: Sequences tr_G7NQ61_G7NQ61_MACMU_9544 and tr_A0A096NZP9_A0A096NZP9_PAPAN_9555 are exactly identical! WARNING: Sequences tr_G7NQ61_G7NQ61_MACMU_9544 and tr_A0A2K5NS86_A0A2K5NS86_CERAT_9531 are exactly identical! WARNING: Sequences tr_G7NQ61_G7NQ61_MACMU_9544 and tr_A0A2K6CQN4_A0A2K6CQN4_MACNE_9545 are exactly identical! WARNING: Sequences tr_G7NQ61_G7NQ61_MACMU_9544 and tr_A0A2K6A1T9_A0A2K6A1T9_MANLE_9568 are exactly identical! WARNING: Sequences tr_G1MGF9_G1MGF9_AILME_9646 and tr_A0A2U3ZQP0_A0A2U3ZQP0_ODORO_9708 are exactly identical! WARNING: Sequences tr_G1MGF9_G1MGF9_AILME_9646 and tr_A0A2Y9K1L7_A0A2Y9K1L7_ENHLU_391180 are exactly identical! WARNING: Sequences tr_G7PXE0_G7PXE0_MACFA_9541 and tr_A0A2K6D0J3_A0A2K6D0J3_MACNE_9545 are exactly identical! WARNING: Sequences tr_G7Q0Y7_G7Q0Y7_MACFA_9541 and tr_A0A096NHV6_A0A096NHV6_PAPAN_9555 are exactly identical! WARNING: Sequences tr_G7Q0Y7_G7Q0Y7_MACFA_9541 and tr_A0A2K6E406_A0A2K6E406_MACNE_9545 are exactly identical! WARNING: Sequences tr_G7Q0Y7_G7Q0Y7_MACFA_9541 and tr_A0A2K5Z431_A0A2K5Z431_MANLE_9568 are exactly identical! WARNING: Sequences tr_G7Q2M0_G7Q2M0_MACFA_9541 and tr_A0A0D9RM98_A0A0D9RM98_CHLSB_60711 are exactly identical! WARNING: Sequences tr_G8F4M9_G8F4M9_MACFA_9541 and tr_A0A096P208_A0A096P208_PAPAN_9555 are exactly identical! WARNING: Sequences tr_G8F4M9_G8F4M9_MACFA_9541 and tr_A0A2K5Y921_A0A2K5Y921_MANLE_9568 are exactly identical! WARNING: Sequences tr_A0A096NXU9_A0A096NXU9_PAPAN_9555 and tr_A0A2K5MDY3_A0A2K5MDY3_CERAT_9531 are exactly identical! WARNING: Sequences tr_A0A2I3MEB8_A0A2I3MEB8_PAPAN_9555 and tr_A0A2K5NZC2_A0A2K5NZC2_CERAT_9531 are exactly identical! WARNING: Sequences tr_A0A2I3MEB8_A0A2I3MEB8_PAPAN_9555 and tr_A0A2K6E8I7_A0A2K6E8I7_MACNE_9545 are exactly identical! WARNING: Sequences tr_A0A151NJM4_A0A151NJM4_ALLMI_8496 and tr_A0A1U7S702_A0A1U7S702_ALLSI_38654 are exactly identical! WARNING: Sequences tr_A0A091WN93_A0A091WN93_NIPNI_128390 and tr_A0A0A0AX99_A0A0A0AX99_CHAVO_50402 are exactly identical! WARNING: Sequences tr_A0A2I0LMM1_A0A2I0LMM1_COLLI_8932 and tr_A0A1V4K2C3_A0A1V4K2C3_PATFA_372326 are exactly identical! WARNING: Sequences tr_A0A226MPP6_A0A226MPP6_CALSU_9009 and tr_A0A226P1V1_A0A226P1V1_COLVI_9014 are exactly identical! WARNING: Sequences tr_A0A2D0QSV0_A0A2D0QSV0_ICTPU_7998 and tr_A0A2D0QUG8_A0A2D0QUG8_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2K5LAJ0_A0A2K5LAJ0_CERAT_9531 and tr_A0A2K5Y6G8_A0A2K5Y6G8_MANLE_9568 are exactly identical! WARNING: Sequences tr_A0A2K5MN45_A0A2K5MN45_CERAT_9531 and tr_A0A2K5ZVZ6_A0A2K5ZVZ6_MANLE_9568 are exactly identical! WARNING: Sequences tr_A0A2U4BDE5_A0A2U4BDE5_TURTR_9739 and tr_A0A2Y9NYV3_A0A2Y9NYV3_DELLE_9749 are exactly identical! WARNING: Sequences tr_A0A2Y9P4L2_A0A2Y9P4L2_DELLE_9749 and tr_A0A383YQX4_A0A383YQX4_BALAS_310752 are exactly identical! WARNING: Sequences tr_A0A2Y9EGH1_A0A2Y9EGH1_PHYCD_9755 and tr_A0A384B4Y9_A0A384B4Y9_BALAS_310752 are exactly identical! WARNING: Sequences tr_A0A2Y9SXZ5_A0A2Y9SXZ5_PHYCD_9755 and tr_A0A384BEM0_A0A384BEM0_BALAS_310752 are exactly identical! WARNING: Duplicate sequences found: 53 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/P49711/4_raxmlng_ancestral/P49711.raxml.reduced.phy Alignment comprises 1 partitions and 727 sites Partition 0: noname Model: LG4X+R4 Alignment sites: 727 Gaps: 37.17 % Invariant sites: 0.28 % NOTE: Binary MSA file created: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/P49711/4_raxmlng_ancestral/P49711.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/P49711/3_mltree/P49711.raxml.bestTree_unrooted [00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 182 / 14560 [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: -230603.155192 [00:00:00 -230603.155192] Initial branch length optimization [00:00:01 -228432.508748] Model parameter optimization (eps = 0.100000) [00:00:44] Tree #1, final logLikelihood: -228096.828879 Optimized model parameters: Partition 0: noname Rate heterogeneity: FREE (4 cats, mean), weights&rates: (0.102987,0.141243) (0.073862,0.374805) (0.319225,0.668293) (0.503926,1.477269) 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/P49711/4_raxmlng_ancestral/P49711.raxml.ancestralProbs Reconstructed ancestral sequences saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/P49711/4_raxmlng_ancestral/P49711.raxml.ancestralStates Node-labeled tree saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/P49711/4_raxmlng_ancestral/P49711.raxml.ancestralTree Execution log saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/P49711/4_raxmlng_ancestral/P49711.raxml.log Analysis started: 17-Jul-2021 07:31:47 / finished: 17-Jul-2021 07:32:38 Elapsed time: 51.188 seconds