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 13:34:16 as follows: raxml-ng --ancestral --msa /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/Q9BYX4/2_msa/Q9BYX4_nogap_msa.fasta --tree /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/Q9BYX4/3_mltree/Q9BYX4.raxml.bestTree_unrooted --model LG4X --prefix /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/Q9BYX4/4_raxmlng_ancestral/Q9BYX4 --threads 4 Analysis options: run mode: Ancestral state reconstruction start tree(s): user random seed: 1622802856 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/Q9BYX4/2_msa/Q9BYX4_nogap_msa.fasta [00:00:00] Loaded alignment with 1001 taxa and 1025 sites WARNING: Sequences tr_F1NJX0_F1NJX0_CHICK_9031 and sp_Q25BN1_DICER_CHICK_9031 are exactly identical! WARNING: Sequences tr_M3XVJ9_M3XVJ9_MUSPF_9669 and tr_A0A2Y9JJN5_A0A2Y9JJN5_ENHLU_391180 are exactly identical! WARNING: Sequences tr_G1S694_G1S694_NOMLE_61853 and tr_G3QMF9_G3QMF9_GORGO_9595 are exactly identical! WARNING: Sequences tr_G1S694_G1S694_NOMLE_61853 and tr_A0A2J8TLN5_A0A2J8TLN5_PONAB_9601 are exactly identical! WARNING: Sequences tr_G1S694_G1S694_NOMLE_61853 and tr_H2R458_H2R458_PANTR_9598 are exactly identical! WARNING: Sequences tr_G1S694_G1S694_NOMLE_61853 and sp_Q9UPY3_DICER_HUMAN_9606 are exactly identical! WARNING: Sequences tr_G1S694_G1S694_NOMLE_61853 and tr_A0A2R9B9T3_A0A2R9B9T3_PANPA_9597 are exactly identical! WARNING: Sequences tr_H2QX44_H2QX44_PANTR_9598 and sp_O95786_DDX58_HUMAN_9606 are exactly identical! WARNING: Sequences sp_Q2U6C4_DCL1_ASPOR_510516 and tr_A0A1S9D8N7_A0A1S9D8N7_ASPOZ_5062 are exactly identical! WARNING: Sequences tr_A0A0E0GB96_A0A0E0GB96_ORYNI_4536 and sp_Q8LMR2_DCL1_ORYSJ_39947 are exactly identical! WARNING: Sequences tr_F6SLC3_F6SLC3_MACMU_9544 and tr_G7PBE6_G7PBE6_MACFA_9541 are exactly identical! WARNING: Sequences tr_F6SLC3_F6SLC3_MACMU_9544 and tr_A0A096NJK7_A0A096NJK7_PAPAN_9555 are exactly identical! WARNING: Sequences tr_F6SLC3_F6SLC3_MACMU_9544 and tr_A0A0D9RE71_A0A0D9RE71_CHLSB_60711 are exactly identical! WARNING: Sequences tr_F6SLC3_F6SLC3_MACMU_9544 and tr_A0A2K5LPA7_A0A2K5LPA7_CERAT_9531 are exactly identical! WARNING: Sequences tr_F6SLC3_F6SLC3_MACMU_9544 and tr_A0A2K6AZM0_A0A2K6AZM0_MACNE_9545 are exactly identical! WARNING: Sequences tr_F6SLC3_F6SLC3_MACMU_9544 and tr_A0A2K5Z076_A0A2K5Z076_MANLE_9568 are exactly identical! WARNING: Sequences tr_F7FKQ9_F7FKQ9_MACMU_9544 and tr_G7PS60_G7PS60_MACFA_9541 are exactly identical! WARNING: Sequences tr_Q0GBW6_Q0GBW6_MACMU_9544 and tr_G7PKP2_G7PKP2_MACFA_9541 are exactly identical! WARNING: Sequences tr_I1PMX4_I1PMX4_ORYGL_4538 and sp_A7LFZ6_DCL4_ORYSJ_39947 are exactly identical! WARNING: Sequences tr_H0ZQZ5_H0ZQZ5_TAEGU_59729 and tr_A0A091K0X4_A0A091K0X4_EGRGA_188379 are exactly identical! WARNING: Sequences tr_H0ZQZ5_H0ZQZ5_TAEGU_59729 and tr_A0A091V8N7_A0A091V8N7_NIPNI_128390 are exactly identical! WARNING: Sequences tr_F2PUS1_F2PUS1_TRIEC_559882 and tr_A0A059JF71_A0A059JF71_9EURO_1215338 are exactly identical! WARNING: Sequences tr_A0A096P5R6_A0A096P5R6_PAPAN_9555 and tr_A0A2K6AAE6_A0A2K6AAE6_MANLE_9568 are exactly identical! WARNING: Sequences tr_A0A0W8DRF4_A0A0W8DRF4_PHYNI_4790 and tr_W2LQ40_W2LQ40_PHYPR_4792 are exactly identical! WARNING: Sequences tr_A0A1S3VFI9_A0A1S3VFI9_VIGRR_3916 and tr_A0A3Q0FIS0_A0A3Q0FIS0_VIGRR_3916 are exactly identical! WARNING: Sequences tr_A0A226NKG3_A0A226NKG3_CALSU_9009 and tr_A0A226NYI5_A0A226NYI5_COLVI_9014 are exactly identical! WARNING: Sequences tr_A0A2D0RQ94_A0A2D0RQ94_ICTPU_7998 and tr_A0A2D0RRT8_A0A2D0RRT8_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2U3ZZ05_A0A2U3ZZ05_TURTR_9739 and tr_A0A2Y9T7K5_A0A2Y9T7K5_PHYCD_9755 are exactly identical! WARNING: Sequences tr_A0A2U3ZZ05_A0A2U3ZZ05_TURTR_9739 and tr_A0A383ZV00_A0A383ZV00_BALAS_310752 are exactly identical! WARNING: Duplicate sequences found: 29 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/Q9BYX4/4_raxmlng_ancestral/Q9BYX4.raxml.reduced.phy Alignment comprises 1 partitions and 1025 sites Partition 0: noname Model: LG4X+R4 Alignment sites: 1025 Gaps: 37.21 % Invariant sites: 0.00 % NOTE: Binary MSA file created: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/Q9BYX4/4_raxmlng_ancestral/Q9BYX4.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/Q9BYX4/3_mltree/Q9BYX4.raxml.bestTree_unrooted [00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 257 / 20560 [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: -500621.057977 [00:00:00 -500621.057977] Initial branch length optimization [00:00:02 -498063.159026] Model parameter optimization (eps = 0.100000) [00:01:00] Tree #1, final logLikelihood: -496751.407801 Optimized model parameters: Partition 0: noname Rate heterogeneity: FREE (4 cats, mean), weights&rates: (0.104233,0.306933) (0.108450,0.318318) (0.315134,0.686278) (0.472183,1.518938) 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/Q9BYX4/4_raxmlng_ancestral/Q9BYX4.raxml.ancestralProbs Reconstructed ancestral sequences saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/Q9BYX4/4_raxmlng_ancestral/Q9BYX4.raxml.ancestralStates Node-labeled tree saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/Q9BYX4/4_raxmlng_ancestral/Q9BYX4.raxml.ancestralTree Execution log saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/Q9BYX4/4_raxmlng_ancestral/Q9BYX4.raxml.log Analysis started: 04-Jun-2021 13:34:16 / finished: 04-Jun-2021 13:35:26 Elapsed time: 69.928 seconds