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 13:34:38 as follows: raxml-ng --ancestral --msa /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/Q9Y5C1/2_msa/Q9Y5C1_nogap_msa.fasta --tree /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/Q9Y5C1/3_mltree/Q9Y5C1.raxml.bestTree_unrooted --model LG4X --prefix /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/Q9Y5C1/4_raxmlng_ancestral/Q9Y5C1 --threads 4 Analysis options: run mode: Ancestral state reconstruction start tree(s): user random seed: 1622802878 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/Q9Y5C1/2_msa/Q9Y5C1_nogap_msa.fasta [00:00:00] Loaded alignment with 1001 taxa and 460 sites WARNING: Sequences sp_Q9R045_ANGL2_MOUSE_10090 and tr_G3V862_G3V862_RAT_10116 are exactly identical! WARNING: Sequences tr_G1S061_G1S061_NOMLE_61853 and tr_H2Q0P0_H2Q0P0_PANTR_9598 are exactly identical! WARNING: Sequences tr_G1S061_G1S061_NOMLE_61853 and tr_H9EU04_H9EU04_MACMU_9544 are exactly identical! WARNING: Sequences tr_G1S061_G1S061_NOMLE_61853 and tr_A0A096MLA3_A0A096MLA3_PAPAN_9555 are exactly identical! WARNING: Sequences tr_G1S061_G1S061_NOMLE_61853 and tr_A0A0D9RI18_A0A0D9RI18_CHLSB_60711 are exactly identical! WARNING: Sequences tr_G1S061_G1S061_NOMLE_61853 and tr_A0A2K5NMC3_A0A2K5NMC3_CERAT_9531 are exactly identical! WARNING: Sequences tr_G1S061_G1S061_NOMLE_61853 and tr_A0A2R9A861_A0A2R9A861_PANPA_9597 are exactly identical! WARNING: Sequences tr_G3S307_G3S307_GORGO_9595 and tr_H2PR10_H2PR10_PONAB_9601 are exactly identical! WARNING: Sequences tr_G3S307_G3S307_GORGO_9595 and tr_A0A2I3TSA7_A0A2I3TSA7_PANTR_9598 are exactly identical! WARNING: Sequences tr_G3S307_G3S307_GORGO_9595 and sp_Q15389_ANGP1_HUMAN_9606 are exactly identical! WARNING: Sequences tr_G3S307_G3S307_GORGO_9595 and tr_G7PCH7_G7PCH7_MACFA_9541 are exactly identical! WARNING: Sequences tr_G3S307_G3S307_GORGO_9595 and tr_A0A096N0L3_A0A096N0L3_PAPAN_9555 are exactly identical! WARNING: Sequences tr_G3S307_G3S307_GORGO_9595 and tr_A0A2K5LRM5_A0A2K5LRM5_CERAT_9531 are exactly identical! WARNING: Sequences tr_G3S307_G3S307_GORGO_9595 and tr_A0A2K5Z4J5_A0A2K5Z4J5_MANLE_9568 are exactly identical! WARNING: Sequences tr_E2RB01_E2RB01_CANLF_9615 and tr_A0A2K5Z7E9_A0A2K5Z7E9_MANLE_9568 are exactly identical! WARNING: Sequences tr_H2QVQ1_H2QVQ1_PANTR_9598 and tr_A0A2R9AJA4_A0A2R9AJA4_PANPA_9597 are exactly identical! WARNING: Sequences tr_H2R582_H2R582_PANTR_9598 and tr_A0A2R9AY17_A0A2R9AY17_PANPA_9597 are exactly identical! WARNING: Sequences tr_A0A1D5Q8V4_A0A1D5Q8V4_MACMU_9544 and tr_A0A2K5KR59_A0A2K5KR59_CERAT_9531 are exactly identical! WARNING: Sequences tr_A0A1D5Q8V4_A0A1D5Q8V4_MACMU_9544 and tr_A0A2K6BRM6_A0A2K6BRM6_MACNE_9545 are exactly identical! WARNING: Sequences tr_A0A1D5QWA9_A0A1D5QWA9_MACMU_9544 and tr_G7P6F8_G7P6F8_MACFA_9541 are exactly identical! WARNING: Sequences tr_F7DFG3_F7DFG3_MACMU_9544 and tr_G7PRB6_G7PRB6_MACFA_9541 are exactly identical! WARNING: Sequences tr_F7HKS2_F7HKS2_MACMU_9544 and tr_A0A096MZL6_A0A096MZL6_PAPAN_9555 are exactly identical! WARNING: Sequences tr_F7HKS2_F7HKS2_MACMU_9544 and tr_A0A0D9RH86_A0A0D9RH86_CHLSB_60711 are exactly identical! WARNING: Sequences tr_F7HKS2_F7HKS2_MACMU_9544 and tr_A0A2K6BNT8_A0A2K6BNT8_MACNE_9545 are exactly identical! WARNING: Sequences tr_F7HQR6_F7HQR6_MACMU_9544 and tr_A0A096MX05_A0A096MX05_PAPAN_9555 are exactly identical! WARNING: Sequences tr_F7HQR6_F7HQR6_MACMU_9544 and tr_A0A2K6DZQ6_A0A2K6DZQ6_MACNE_9545 are exactly identical! WARNING: Sequences tr_F7HQR6_F7HQR6_MACMU_9544 and tr_A0A2K6AAY2_A0A2K6AAY2_MANLE_9568 are exactly identical! WARNING: Sequences tr_H0YWZ9_H0YWZ9_TAEGU_59729 and tr_A0A218UAW2_A0A218UAW2_9PASE_299123 are exactly identical! WARNING: Sequences tr_A0A096MP49_A0A096MP49_PAPAN_9555 and tr_A0A2K6AHI8_A0A2K6AHI8_MANLE_9568 are exactly identical! WARNING: Sequences tr_A0A096NXK9_A0A096NXK9_PAPAN_9555 and tr_A0A2K5MBM0_A0A2K5MBM0_CERAT_9531 are exactly identical! WARNING: Sequences tr_A0A096NXK9_A0A096NXK9_PAPAN_9555 and tr_A0A2K5Y8Q7_A0A2K5Y8Q7_MANLE_9568 are exactly identical! WARNING: Sequences tr_A0A096P0F6_A0A096P0F6_PAPAN_9555 and tr_A0A2K5LFN1_A0A2K5LFN1_CERAT_9531 are exactly identical! WARNING: Sequences tr_A0A151MXT8_A0A151MXT8_ALLMI_8496 and tr_A0A1U7RZZ2_A0A1U7RZZ2_ALLSI_38654 are exactly identical! WARNING: Sequences tr_A0A091IKF7_A0A091IKF7_EGRGA_188379 and tr_A0A091W1Z5_A0A091W1Z5_NIPNI_128390 are exactly identical! WARNING: Sequences tr_A0A091IKF7_A0A091IKF7_EGRGA_188379 and tr_A0A087QVH7_A0A087QVH7_APTFO_9233 are exactly identical! WARNING: Sequences tr_A0A091IKF7_A0A091IKF7_EGRGA_188379 and tr_A0A0A0B078_A0A0A0B078_CHAVO_50402 are exactly identical! WARNING: Sequences tr_A0A226N2D7_A0A226N2D7_CALSU_9009 and tr_A0A226NXC5_A0A226NXC5_COLVI_9014 are exactly identical! WARNING: Sequences tr_A0A2D0QL56_A0A2D0QL56_ICTPU_7998 and tr_W5UEM6_W5UEM6_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2K5LEN0_A0A2K5LEN0_CERAT_9531 and tr_A0A2K5YQP3_A0A2K5YQP3_MANLE_9568 are exactly identical! WARNING: Sequences tr_A0A2U3V7E1_A0A2U3V7E1_TURTR_9739 and tr_A0A2Y9F952_A0A2Y9F952_PHYCD_9755 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/Q9Y5C1/4_raxmlng_ancestral/Q9Y5C1.raxml.reduced.phy Alignment comprises 1 partitions and 460 sites Partition 0: noname Model: LG4X+R4 Alignment sites: 460 Gaps: 26.93 % Invariant sites: 0.87 % NOTE: Binary MSA file created: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/Q9Y5C1/4_raxmlng_ancestral/Q9Y5C1.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/Q9Y5C1/3_mltree/Q9Y5C1.raxml.bestTree_unrooted [00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 115 / 9200 [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: -178075.133135 [00:00:00 -178075.133135] Initial branch length optimization [00:00:01 -177394.857152] Model parameter optimization (eps = 0.100000) [00:00:35] Tree #1, final logLikelihood: -176926.431074 Optimized model parameters: Partition 0: noname Rate heterogeneity: FREE (4 cats, mean), weights&rates: (0.087714,0.304504) (0.119438,0.330041) (0.397624,0.851142) (0.395225,1.506578) 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/Q9Y5C1/4_raxmlng_ancestral/Q9Y5C1.raxml.ancestralProbs Reconstructed ancestral sequences saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/Q9Y5C1/4_raxmlng_ancestral/Q9Y5C1.raxml.ancestralStates Node-labeled tree saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/Q9Y5C1/4_raxmlng_ancestral/Q9Y5C1.raxml.ancestralTree Execution log saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/Q9Y5C1/4_raxmlng_ancestral/Q9Y5C1.raxml.log Analysis started: 04-Jun-2021 13:34:38 / finished: 04-Jun-2021 13:35:18 Elapsed time: 39.468 seconds