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 07:23:53 as follows: raxml-ng --ancestral --msa /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/A8MT65/2_msa/A8MT65_nogap_msa.fasta --tree /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/A8MT65/3_mltree/A8MT65.raxml.bestTree_unrooted --model LG4X --prefix /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/A8MT65/4_raxmlng_ancestral/A8MT65 --threads 4 Analysis options: run mode: Ancestral state reconstruction start tree(s): user random seed: 1626495833 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/A8MT65/2_msa/A8MT65_nogap_msa.fasta [00:00:00] Loaded alignment with 999 taxa and 544 sites WARNING: Sequences tr_M3YWT0_M3YWT0_MUSPF_9669 and tr_A0A2Y9KFZ4_A0A2Y9KFZ4_ENHLU_391180 are exactly identical! WARNING: Sequences tr_A0A2I2YDK3_A0A2I2YDK3_GORGO_9595 and tr_A0A2J8R638_A0A2J8R638_PONAB_9601 are exactly identical! WARNING: Sequences tr_A0A2I2YMB8_A0A2I2YMB8_GORGO_9595 and tr_H2QG72_H2QG72_PANTR_9598 are exactly identical! WARNING: Sequences tr_A0A2I2YYI0_A0A2I2YYI0_GORGO_9595 and sp_Q8TAQ5_ZN420_HUMAN_9606 are exactly identical! WARNING: Sequences tr_A0A2I2Z5M2_A0A2I2Z5M2_GORGO_9595 and tr_A0A2J8SJ28_A0A2J8SJ28_PONAB_9601 are exactly identical! WARNING: Sequences tr_G3S228_G3S228_GORGO_9595 and tr_A0A2I3T1I2_A0A2I3T1I2_PANTR_9598 are exactly identical! WARNING: Sequences tr_G3S228_G3S228_GORGO_9595 and tr_A0A2K5XY05_A0A2K5XY05_MANLE_9568 are exactly identical! WARNING: Sequences tr_G3S228_G3S228_GORGO_9595 and tr_A0A2R9C8X5_A0A2R9C8X5_PANPA_9597 are exactly identical! WARNING: Sequences tr_G3SCV4_G3SCV4_GORGO_9595 and tr_H2R5T2_H2R5T2_PANTR_9598 are exactly identical! WARNING: Sequences tr_A0A2I3S1M4_A0A2I3S1M4_PANTR_9598 and tr_A0A2R9A1Z5_A0A2R9A1Z5_PANPA_9597 are exactly identical! WARNING: Sequences tr_A0A2I3SNE8_A0A2I3SNE8_PANTR_9598 and tr_A0A2R9C8V9_A0A2R9C8V9_PANPA_9597 are exactly identical! WARNING: Sequences tr_A0A2I3TN33_A0A2I3TN33_PANTR_9598 and tr_A0A2R9AAF9_A0A2R9AAF9_PANPA_9597 are exactly identical! WARNING: Sequences tr_A0A2J8JLI6_A0A2J8JLI6_PANTR_9598 and sp_Q96ND8_ZN583_HUMAN_9606 are exactly identical! WARNING: Sequences tr_A0A2J8JLK3_A0A2J8JLK3_PANTR_9598 and tr_A0A2R9A954_A0A2R9A954_PANPA_9597 are exactly identical! WARNING: Sequences tr_H2R0W5_H2R0W5_PANTR_9598 and tr_A0A2R9BGK0_A0A2R9BGK0_PANPA_9597 are exactly identical! WARNING: Sequences tr_W5PCH7_W5PCH7_SHEEP_9940 and tr_E1BMZ4_E1BMZ4_BOVIN_9913 are exactly identical! WARNING: Sequences sp_Q96RE9_ZN300_HUMAN_9606 and tr_A0A2R9AP07_A0A2R9AP07_PANPA_9597 are exactly identical! WARNING: Sequences tr_A0A1D5QXZ3_A0A1D5QXZ3_MACMU_9544 and tr_G7PZ52_G7PZ52_MACFA_9541 are exactly identical! WARNING: Sequences tr_A0A1D5QXZ3_A0A1D5QXZ3_MACMU_9544 and tr_A0A2K6D4T1_A0A2K6D4T1_MACNE_9545 are exactly identical! WARNING: Sequences tr_A0A1D5R3C7_A0A1D5R3C7_MACMU_9544 and tr_A0A2K6DA83_A0A2K6DA83_MACNE_9545 are exactly identical! WARNING: Sequences tr_F6QVW9_F6QVW9_MACMU_9544 and tr_A0A0A0MUP5_A0A0A0MUP5_PAPAN_9555 are exactly identical! WARNING: Sequences tr_F6QVW9_F6QVW9_MACMU_9544 and tr_A0A2K5MYE8_A0A2K5MYE8_CERAT_9531 are exactly identical! WARNING: Sequences tr_F6QVW9_F6QVW9_MACMU_9544 and tr_A0A2K5ZQH5_A0A2K5ZQH5_MANLE_9568 are exactly identical! WARNING: Sequences tr_F6UR85_F6UR85_MACMU_9544 and tr_A0A2K6ADH3_A0A2K6ADH3_MANLE_9568 are exactly identical! WARNING: Sequences tr_F6XBT3_F6XBT3_MACMU_9544 and tr_A0A096NA69_A0A096NA69_PAPAN_9555 are exactly identical! WARNING: Sequences tr_F7C0L6_F7C0L6_MACMU_9544 and tr_G7PTR0_G7PTR0_MACFA_9541 are exactly identical! WARNING: Sequences tr_F7C0L6_F7C0L6_MACMU_9544 and tr_A0A096P2Z7_A0A096P2Z7_PAPAN_9555 are exactly identical! WARNING: Sequences tr_F7C0L6_F7C0L6_MACMU_9544 and tr_A0A2K5ZSE2_A0A2K5ZSE2_MANLE_9568 are exactly identical! WARNING: Sequences tr_F7DJ47_F7DJ47_MACMU_9544 and tr_A0A0A0MX45_A0A0A0MX45_PAPAN_9555 are exactly identical! WARNING: Sequences tr_F7DJ47_F7DJ47_MACMU_9544 and tr_A0A2K5LZU4_A0A2K5LZU4_CERAT_9531 are exactly identical! WARNING: Sequences tr_F7DJ47_F7DJ47_MACMU_9544 and tr_A0A2K6BPR5_A0A2K6BPR5_MACNE_9545 are exactly identical! WARNING: Sequences tr_F7GB84_F7GB84_MACMU_9544 and tr_A0A2K6BN44_A0A2K6BN44_MACNE_9545 are exactly identical! WARNING: Sequences tr_F7GDG2_F7GDG2_MACMU_9544 and tr_A0A096MVU8_A0A096MVU8_PAPAN_9555 are exactly identical! WARNING: Sequences tr_F7GDG2_F7GDG2_MACMU_9544 and tr_A0A0D9S896_A0A0D9S896_CHLSB_60711 are exactly identical! WARNING: Sequences tr_F7GDG2_F7GDG2_MACMU_9544 and tr_A0A2K5LPR7_A0A2K5LPR7_CERAT_9531 are exactly identical! WARNING: Sequences tr_F7GDG2_F7GDG2_MACMU_9544 and tr_A0A2K6BKJ1_A0A2K6BKJ1_MACNE_9545 are exactly identical! WARNING: Sequences tr_F7H5I5_F7H5I5_MACMU_9544 and tr_G7PXE5_G7PXE5_MACFA_9541 are exactly identical! WARNING: Sequences tr_F7HGS7_F7HGS7_MACMU_9544 and tr_G7P726_G7P726_MACFA_9541 are exactly identical! WARNING: Sequences tr_F7HGS7_F7HGS7_MACMU_9544 and tr_A0A2K6CE40_A0A2K6CE40_MACNE_9545 are exactly identical! WARNING: Sequences tr_G7MUI1_G7MUI1_MACMU_9544 and tr_A0A2K6AN26_A0A2K6AN26_MACNE_9545 are exactly identical! WARNING: Sequences tr_G7NNB5_G7NNB5_MACMU_9544 and tr_A0A096NPJ6_A0A096NPJ6_PAPAN_9555 are exactly identical! WARNING: Sequences tr_G7NNB5_G7NNB5_MACMU_9544 and tr_A0A2K6B331_A0A2K6B331_MACNE_9545 are exactly identical! WARNING: Sequences tr_G1LSL0_G1LSL0_AILME_9646 and tr_A0A384CDE3_A0A384CDE3_URSMA_29073 are exactly identical! WARNING: Sequences tr_G7PXE8_G7PXE8_MACFA_9541 and tr_A0A2K5XDE6_A0A2K5XDE6_MANLE_9568 are exactly identical! WARNING: Sequences tr_A0A2K5LAJ0_A0A2K5LAJ0_CERAT_9531 and tr_A0A2K5Y6G8_A0A2K5Y6G8_MANLE_9568 are exactly identical! WARNING: Sequences tr_A0A2K5M013_A0A2K5M013_CERAT_9531 and tr_A0A2K5YYE3_A0A2K5YYE3_MANLE_9568 are exactly identical! WARNING: Sequences tr_A0A2U3VJB5_A0A2U3VJB5_ODORO_9708 and tr_A0A2U3Y1N2_A0A2U3Y1N2_LEPWE_9713 are exactly identical! WARNING: Sequences tr_A0A2Y9LKY1_A0A2Y9LKY1_DELLE_9749 and tr_A0A383ZJ36_A0A383ZJ36_BALAS_310752 are exactly identical! WARNING: Sequences tr_A0A2Y9F4V4_A0A2Y9F4V4_PHYCD_9755 and tr_A0A383ZK52_A0A383ZK52_BALAS_310752 are exactly identical! WARNING: Duplicate sequences found: 49 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/A8MT65/4_raxmlng_ancestral/A8MT65.raxml.reduced.phy Alignment comprises 1 partitions and 544 sites Partition 0: noname Model: LG4X+R4 Alignment sites: 544 Gaps: 20.05 % Invariant sites: 2.39 % NOTE: Binary MSA file created: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/A8MT65/4_raxmlng_ancestral/A8MT65.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/A8MT65/3_mltree/A8MT65.raxml.bestTree_unrooted [00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 136 / 10880 [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: -300901.932111 [00:00:00 -300901.932111] Initial branch length optimization [00:00:02 -224895.636384] Model parameter optimization (eps = 0.100000) [00:00:32] Tree #1, final logLikelihood: -224583.442508 Optimized model parameters: Partition 0: noname Rate heterogeneity: FREE (4 cats, mean), weights&rates: (0.154101,0.224862) (0.144471,0.497678) (0.372440,0.833364) (0.328988,1.772316) 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/A8MT65/4_raxmlng_ancestral/A8MT65.raxml.ancestralProbs Reconstructed ancestral sequences saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/A8MT65/4_raxmlng_ancestral/A8MT65.raxml.ancestralStates Node-labeled tree saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/A8MT65/4_raxmlng_ancestral/A8MT65.raxml.ancestralTree Execution log saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/A8MT65/4_raxmlng_ancestral/A8MT65.raxml.log Analysis started: 17-Jul-2021 07:23:53 / finished: 17-Jul-2021 07:24:30 Elapsed time: 37.319 seconds