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 12-Jul-2021 17:41:22 as follows: raxml-ng --ancestral --msa /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q8IX07/2_msa/Q8IX07_nogap_msa.fasta --tree /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q8IX07/3_mltree/Q8IX07.raxml.bestTree_unrooted --model LG4X --prefix /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q8IX07/4_raxmlng_ancestral/Q8IX07 --threads 4 Analysis options: run mode: Ancestral state reconstruction start tree(s): user random seed: 1626100882 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/Q8IX07/2_msa/Q8IX07_nogap_msa.fasta [00:00:00] Loaded alignment with 1001 taxa and 1006 sites WARNING: Sequences sp_Q9JHX2_SP5_MOUSE_10090 and tr_A0A0G2JUC1_A0A0G2JUC1_RAT_10116 are exactly identical! WARNING: Sequences tr_G3RPP3_G3RPP3_GORGO_9595 and tr_H2QUK7_H2QUK7_PANTR_9598 are exactly identical! WARNING: Sequences tr_G3RPP3_G3RPP3_GORGO_9595 and sp_Q13422_IKZF1_HUMAN_9606 are exactly identical! WARNING: Sequences tr_G3RPP3_G3RPP3_GORGO_9595 and tr_F6YC72_F6YC72_MACMU_9544 are exactly identical! WARNING: Sequences tr_G3RPP3_G3RPP3_GORGO_9595 and tr_G7P1S2_G7P1S2_MACFA_9541 are exactly identical! WARNING: Sequences tr_G3RPP3_G3RPP3_GORGO_9595 and tr_A0A096NWV9_A0A096NWV9_PAPAN_9555 are exactly identical! WARNING: Sequences tr_G3RPP3_G3RPP3_GORGO_9595 and tr_A0A0D9RTY8_A0A0D9RTY8_CHLSB_60711 are exactly identical! WARNING: Sequences tr_G3RPP3_G3RPP3_GORGO_9595 and tr_A0A2K5NH61_A0A2K5NH61_CERAT_9531 are exactly identical! WARNING: Sequences tr_G3RPP3_G3RPP3_GORGO_9595 and tr_A0A2K6C676_A0A2K6C676_MACNE_9545 are exactly identical! WARNING: Sequences tr_G3RPP3_G3RPP3_GORGO_9595 and tr_A0A2K5ZPN0_A0A2K5ZPN0_MANLE_9568 are exactly identical! WARNING: Sequences tr_G3RPP3_G3RPP3_GORGO_9595 and tr_A0A2R9B7I4_A0A2R9B7I4_PANPA_9597 are exactly identical! WARNING: Sequences tr_Q28Z81_Q28Z81_DROPS_46245 and tr_B4GI51_B4GI51_DROPE_7234 are exactly identical! WARNING: Sequences tr_A0A2J8JLM8_A0A2J8JLM8_PANTR_9598 and sp_Q8NHY6_ZFP28_HUMAN_9606 are exactly identical! WARNING: Sequences tr_A0A2J8JLM8_A0A2J8JLM8_PANTR_9598 and tr_A0A2R9BYG1_A0A2R9BYG1_PANPA_9597 are exactly identical! WARNING: Sequences tr_A0A2J8KGX5_A0A2J8KGX5_PANTR_9598 and tr_A0A2R8ZNQ3_A0A2R8ZNQ3_PANPA_9597 are exactly identical! WARNING: Sequences tr_F6S913_F6S913_HORSE_9796 and tr_D2H553_D2H553_AILME_9646 are exactly identical! WARNING: Sequences tr_F6S913_F6S913_HORSE_9796 and tr_A0A1S3A6E3_A0A1S3A6E3_ERIEU_9365 are exactly identical! WARNING: Sequences tr_M4ATS7_M4ATS7_XIPMA_8083 and tr_A0A087XNQ0_A0A087XNQ0_POEFO_48698 are exactly identical! WARNING: Sequences tr_A0A158NXH8_A0A158NXH8_ATTCE_12957 and tr_A0A195B6W8_A0A195B6W8_9HYME_520822 are exactly identical! WARNING: Sequences sp_Q6BEB4_SP5_HUMAN_9606 and tr_F6SBI0_F6SBI0_CALJA_9483 are exactly identical! WARNING: Sequences tr_F6VNV7_F6VNV7_MACMU_9544 and tr_A0A096N980_A0A096N980_PAPAN_9555 are exactly identical! WARNING: Sequences tr_F6VNV7_F6VNV7_MACMU_9544 and tr_A0A0D9SCG4_A0A0D9SCG4_CHLSB_60711 are exactly identical! WARNING: Sequences tr_F6VNV7_F6VNV7_MACMU_9544 and tr_A0A2K5L0G8_A0A2K5L0G8_CERAT_9531 are exactly identical! WARNING: Sequences tr_F6VNV7_F6VNV7_MACMU_9544 and tr_A0A2K6B1E0_A0A2K6B1E0_MACNE_9545 are exactly identical! WARNING: Sequences tr_F6VNV7_F6VNV7_MACMU_9544 and tr_A0A2K5XTR3_A0A2K5XTR3_MANLE_9568 are exactly identical! WARNING: Sequences tr_F7HGH1_F7HGH1_MACMU_9544 and tr_G7PUM7_G7PUM7_MACFA_9541 are exactly identical! WARNING: Sequences tr_F7HGH1_F7HGH1_MACMU_9544 and tr_A0A0D9S376_A0A0D9S376_CHLSB_60711 are exactly identical! WARNING: Sequences tr_F7HGH1_F7HGH1_MACMU_9544 and tr_A0A2K5LW35_A0A2K5LW35_CERAT_9531 are exactly identical! WARNING: Sequences tr_F7HGH1_F7HGH1_MACMU_9544 and tr_A0A2K5YZH0_A0A2K5YZH0_MANLE_9568 are exactly identical! WARNING: Sequences tr_F7HPZ3_F7HPZ3_MACMU_9544 and tr_A0A0D9RR78_A0A0D9RR78_CHLSB_60711 are exactly identical! WARNING: Sequences tr_F7HPZ3_F7HPZ3_MACMU_9544 and tr_A0A2K5NKQ4_A0A2K5NKQ4_CERAT_9531 are exactly identical! WARNING: Sequences tr_F7HPZ3_F7HPZ3_MACMU_9544 and tr_A0A2K6D4H8_A0A2K6D4H8_MACNE_9545 are exactly identical! WARNING: Sequences tr_A0A2I3MEB8_A0A2I3MEB8_PAPAN_9555 and tr_A0A2K5NZC2_A0A2K5NZC2_CERAT_9531 are exactly identical! WARNING: Sequences tr_A0A091VQM4_A0A091VQM4_NIPNI_128390 and tr_A0A0A0ACN0_A0A0A0ACN0_CHAVO_50402 are exactly identical! WARNING: Sequences tr_A0A1S3PWM5_A0A1S3PWM5_SALSA_8030 and tr_A0A060WWC2_A0A060WWC2_ONCMY_8022 are exactly identical! WARNING: Sequences tr_A0A2Y9LUV3_A0A2Y9LUV3_DELLE_9749 and tr_A0A2Y9F1H3_A0A2Y9F1H3_PHYCD_9755 are exactly identical! WARNING: Duplicate sequences found: 36 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/Q8IX07/4_raxmlng_ancestral/Q8IX07.raxml.reduced.phy Alignment comprises 1 partitions and 1006 sites Partition 0: noname Model: LG4X+R4 Alignment sites: 1006 Gaps: 64.24 % Invariant sites: 0.00 % NOTE: Binary MSA file created: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q8IX07/4_raxmlng_ancestral/Q8IX07.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/Q8IX07/3_mltree/Q8IX07.raxml.bestTree_unrooted [00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 252 / 20160 [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: -270122.945616 [00:00:00 -270122.945616] Initial branch length optimization [00:00:02 -264892.821778] Model parameter optimization (eps = 0.100000) [00:01:21] Tree #1, final logLikelihood: -263702.877864 Optimized model parameters: Partition 0: noname Rate heterogeneity: FREE (4 cats, mean), weights&rates: (0.066573,0.229867) (0.098241,0.853100) (0.269352,0.687562) (0.565835,1.264843) 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/Q8IX07/4_raxmlng_ancestral/Q8IX07.raxml.ancestralProbs Reconstructed ancestral sequences saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q8IX07/4_raxmlng_ancestral/Q8IX07.raxml.ancestralStates Node-labeled tree saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q8IX07/4_raxmlng_ancestral/Q8IX07.raxml.ancestralTree Execution log saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q8IX07/4_raxmlng_ancestral/Q8IX07.raxml.log Analysis started: 12-Jul-2021 17:41:22 / finished: 12-Jul-2021 17:42:52 Elapsed time: 90.468 seconds