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 6148 CPU @ 2.40GHz, 40 cores, 376 GB RAM RAxML-NG was called at 12-Jul-2021 16:39:04 as follows: raxml-ng --ancestral --msa /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q9UQ88/2_msa/Q9UQ88_nogap_msa.fasta --tree /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q9UQ88/3_mltree/Q9UQ88.raxml.bestTree_unrooted --model LG4X --prefix /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q9UQ88/4_raxmlng_ancestral/Q9UQ88 --threads 4 Analysis options: run mode: Ancestral state reconstruction start tree(s): user random seed: 1626097144 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: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q9UQ88/2_msa/Q9UQ88_nogap_msa.fasta [00:00:00] Loaded alignment with 1001 taxa and 783 sites WARNING: Sequences tr_J3K4B2_J3K4B2_COCIM_246410 and tr_A0A0J6YGP0_A0A0J6YGP0_COCIT_404692 are exactly identical! WARNING: Sequences tr_Q290T0_Q290T0_DROPS_46245 and tr_B4GBA4_B4GBA4_DROPE_7234 are exactly identical! WARNING: Sequences tr_F9GBP1_F9GBP1_FUSOF_660025 and tr_N4USL9_N4USL9_FUSC1_1229664 are exactly identical! WARNING: Sequences tr_F9GBP1_F9GBP1_FUSOF_660025 and tr_X0DKB7_X0DKB7_FUSOX_1089458 are exactly identical! WARNING: Sequences tr_A0A088ATD3_A0A088ATD3_APIME_7460 and tr_A0A2A3EIH3_A0A2A3EIH3_APICC_94128 are exactly identical! WARNING: Sequences sp_Q15131_CDK10_HUMAN_9606 and tr_A0A2R9A3I8_A0A2R9A3I8_PANPA_9597 are exactly identical! WARNING: Sequences tr_A0A0E0G9J5_A0A0E0G9J5_ORYNI_4536 and sp_A2X6X1_CDKG1_ORYSI_39946 are exactly identical! WARNING: Sequences tr_A0A0E0H2D9_A0A0E0H2D9_ORYNI_4536 and sp_A2XUW1_CDKG2_ORYSI_39946 are exactly identical! WARNING: Sequences tr_A0A0E0H2D9_A0A0E0H2D9_ORYNI_4536 and tr_A0A0D9ZMF4_A0A0D9ZMF4_9ORYZ_40148 are exactly identical! WARNING: Sequences tr_A0A0E0H2D9_A0A0E0H2D9_ORYNI_4536 and sp_Q7XUF4_CDKG2_ORYSJ_39947 are exactly identical! WARNING: Sequences tr_G7XD11_G7XD11_ASPKW_1033177 and tr_A0A146FEG1_A0A146FEG1_9EURO_1069201 are exactly identical! WARNING: Sequences tr_F4PAM0_F4PAM0_BATDJ_684364 and tr_A0A177WUI0_A0A177WUI0_BATDE_403673 are exactly identical! WARNING: Sequences tr_I1PMG9_I1PMG9_ORYGL_4538 and tr_A0A0D3FXA7_A0A0D3FXA7_9ORYZ_65489 are exactly identical! WARNING: Sequences tr_G2XWQ2_G2XWQ2_BOTF4_999810 and tr_M7TLW1_M7TLW1_BOTF1_1290391 are exactly identical! WARNING: Sequences tr_A0A0D2XZR6_A0A0D2XZR6_FUSO4_426428 and tr_A0A2H3GK44_A0A2H3GK44_FUSOX_327505 are exactly identical! WARNING: Sequences tr_M7Z0W2_M7Z0W2_TRIUA_4572 and tr_A0A3B6NQJ9_A0A3B6NQJ9_WHEAT_4565 are exactly identical! WARNING: Sequences tr_V2XX61_V2XX61_MONRO_1381753 and tr_A0A0W0G2R9_A0A0W0G2R9_9AGAR_221103 are exactly identical! WARNING: Sequences tr_A0A015M5X6_A0A015M5X6_9GLOM_1432141 and tr_A0A2H5UE38_A0A2H5UE38_RHIID_747089 are exactly identical! WARNING: Sequences tr_A0A044R0Y9_A0A044R0Y9_ONCVO_6282 and tr_A0A182E261_A0A182E261_ONCOC_42157 are exactly identical! WARNING: Sequences tr_A0A087X8S3_A0A087X8S3_POEFO_48698 and tr_A0A087XTA3_A0A087XTA3_POEFO_48698 are exactly identical! WARNING: Sequences tr_A0A2I3M6E2_A0A2I3M6E2_PAPAN_9555 and tr_A0A2K6AYT5_A0A2K6AYT5_MACNE_9545 are exactly identical! WARNING: Sequences tr_A0A094GHX1_A0A094GHX1_9PEZI_1420912 and tr_A0A2P2SWA8_A0A2P2SWA8_9PEZI_342668 are exactly identical! WARNING: Sequences tr_V4VFQ7_V4VFQ7_9ROSI_85681 and tr_A0A2H5NV91_A0A2H5NV91_CITUN_55188 are exactly identical! WARNING: Sequences tr_A0A0F8V5J2_A0A0F8V5J2_9EURO_308745 and tr_A0A2T5LQD0_A0A2T5LQD0_9EURO_1392256 are exactly identical! WARNING: Duplicate sequences found: 24 NOTE: Reduced alignment (with duplicates and gap-only sites/taxa removed) NOTE: was saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q9UQ88/4_raxmlng_ancestral/Q9UQ88.raxml.reduced.phy Alignment comprises 1 partitions and 783 sites Partition 0: noname Model: LG4X+R4 Alignment sites: 783 Gaps: 41.48 % Invariant sites: 0.38 % NOTE: Binary MSA file created: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q9UQ88/4_raxmlng_ancestral/Q9UQ88.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: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q9UQ88/3_mltree/Q9UQ88.raxml.bestTree_unrooted [00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 196 / 15680 [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: -251829.762896 [00:00:00 -251829.762896] Initial branch length optimization [00:00:01 -245133.110853] Model parameter optimization (eps = 0.100000) 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 6148 CPU @ 2.40GHz, 40 cores, 376 GB RAM RAxML-NG was called at 12-Jul-2021 17:32:13 as follows: raxml-ng --ancestral --msa /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q9UQ88/2_msa/Q9UQ88_nogap_msa.fasta --tree /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q9UQ88/3_mltree/Q9UQ88.raxml.bestTree_unrooted --model LG4X --prefix /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q9UQ88/4_raxmlng_ancestral/Q9UQ88 --threads 4 Analysis options: run mode: Ancestral state reconstruction start tree(s): user random seed: 1626100333 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 WARNING: The model you specified on the command line (LG4X) will be ignored since the binary MSA file already contains a model definition. If you want to change the model, please re-run RAxML-NG with the original PHYLIP/FASTA alignment and --redo option. [00:00:00] Loading binary alignment from file: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q9UQ88/4_raxmlng_ancestral/Q9UQ88.raxml.rba [00:00:00] Alignment comprises 1001 taxa, 1 partitions and 783 patterns Partition 0: noname Model: LG4X+R4 Alignment sites: 783 Gaps: 41.48 % Invariant sites: 0.38 % Parallelization scheme autoconfig: 1 worker(s) x 4 thread(s) Parallel reduction/worker buffer size: 1 KB / 0 KB [00:00:00] NOTE: Resuming execution from checkpoint (logLH: -245133.11, ML trees: 0, bootstraps: 0) [00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 196 / 15680 [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: -245133.110853 [00:00:00 -245133.110853] Model parameter optimization (eps = 0.100000) [00:00:47] Tree #1, final logLikelihood: -244241.645903 Optimized model parameters: Partition 0: noname Rate heterogeneity: FREE (4 cats, mean), weights&rates: (0.127343,0.160088) (0.122665,0.189608) (0.237059,0.572312) (0.512933,1.599983) 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: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q9UQ88/4_raxmlng_ancestral/Q9UQ88.raxml.ancestralProbs Reconstructed ancestral sequences saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q9UQ88/4_raxmlng_ancestral/Q9UQ88.raxml.ancestralStates Node-labeled tree saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q9UQ88/4_raxmlng_ancestral/Q9UQ88.raxml.ancestralTree Execution log saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q9UQ88/4_raxmlng_ancestral/Q9UQ88.raxml.log Analysis started: 12-Jul-2021 17:32:13 / finished: 12-Jul-2021 17:33:08 Elapsed time: 54.425 seconds (this run) / 56.215 seconds (total with restarts) Consumed energy: 3.940 Wh