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 14:07:38 as follows: raxml-ng --ancestral --msa /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/Q16394/2_msa/Q16394_nogap_msa.fasta --tree /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/Q16394/3_mltree/Q16394.raxml.bestTree_unrooted --model LG4X --prefix /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/Q16394/4_raxmlng_ancestral/Q16394 --threads 4 Analysis options: run mode: Ancestral state reconstruction start tree(s): user random seed: 1622804858 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/Q16394/2_msa/Q16394_nogap_msa.fasta [00:00:00] Loaded alignment with 1001 taxa and 746 sites WARNING: Sequences sp_P97464_EXT1_MOUSE_10090 and tr_G3V901_G3V901_RAT_10116 are exactly identical! WARNING: Sequences tr_M3XPI8_M3XPI8_MUSPF_9669 and tr_A0A2Y9K6P0_A0A2Y9K6P0_ENHLU_391180 are exactly identical! WARNING: Sequences tr_H2PR27_H2PR27_PONAB_9601 and tr_K7DAN3_K7DAN3_PANTR_9598 are exactly identical! WARNING: Sequences tr_H2PR27_H2PR27_PONAB_9601 and tr_F7F8Y3_F7F8Y3_MACMU_9544 are exactly identical! WARNING: Sequences tr_H2PR27_H2PR27_PONAB_9601 and sp_A9X1C8_EXT1_PAPAN_9555 are exactly identical! WARNING: Sequences tr_H2PR27_H2PR27_PONAB_9601 and tr_A0A2K6E3M4_A0A2K6E3M4_MACNE_9545 are exactly identical! WARNING: Sequences tr_H2PR27_H2PR27_PONAB_9601 and tr_A0A2R8ZLS5_A0A2R8ZLS5_PANPA_9597 are exactly identical! WARNING: Sequences tr_A0A2I3S6F0_A0A2I3S6F0_PANTR_9598 and tr_A0A2R9BBR6_A0A2R9BBR6_PANPA_9597 are exactly identical! WARNING: Sequences tr_A0A2I3SQC4_A0A2I3SQC4_PANTR_9598 and tr_A0A2R9C8L9_A0A2R9C8L9_PANPA_9597 are exactly identical! WARNING: Sequences tr_H2QVZ1_H2QVZ1_PANTR_9598 and sp_O43909_EXTL3_HUMAN_9606 are exactly identical! WARNING: Sequences tr_F6S245_F6S245_MACMU_9544 and tr_A0A2K6DSA0_A0A2K6DSA0_MACNE_9545 are exactly identical! WARNING: Sequences tr_G7N0T1_G7N0T1_MACMU_9544 and tr_G7PD46_G7PD46_MACFA_9541 are exactly identical! WARNING: Sequences tr_G7N0T1_G7N0T1_MACMU_9544 and tr_A0A096NYB3_A0A096NYB3_PAPAN_9555 are exactly identical! WARNING: Sequences tr_G7N0T1_G7N0T1_MACMU_9544 and tr_A0A2K6D518_A0A2K6D518_MACNE_9545 are exactly identical! WARNING: Sequences tr_G7N0T1_G7N0T1_MACMU_9544 and tr_A0A2K5ZV76_A0A2K5ZV76_MANLE_9568 are exactly identical! WARNING: Sequences tr_H0ZJ15_H0ZJ15_TAEGU_59729 and tr_A0A218VAL5_A0A218VAL5_9PASE_299123 are exactly identical! WARNING: Sequences tr_A0A067FSA3_A0A067FSA3_CITSI_2711 and tr_V4SMC2_V4SMC2_9ROSI_85681 are exactly identical! WARNING: Sequences tr_A0A067FSA3_A0A067FSA3_CITSI_2711 and tr_A0A2H5NJZ6_A0A2H5NJZ6_CITUN_55188 are exactly identical! WARNING: Sequences tr_A0A091VMZ4_A0A091VMZ4_NIPNI_128390 and tr_A0A087QY09_A0A087QY09_APTFO_9233 are exactly identical! WARNING: Sequences tr_A0A091VMZ4_A0A091VMZ4_NIPNI_128390 and tr_A0A093I4D1_A0A093I4D1_STRCA_441894 are exactly identical! WARNING: Sequences tr_A0A091VMZ4_A0A091VMZ4_NIPNI_128390 and tr_A0A093G3S3_A0A093G3S3_DRYPU_118200 are exactly identical! WARNING: Sequences tr_A0A091VMZ4_A0A091VMZ4_NIPNI_128390 and tr_A0A091HPY7_A0A091HPY7_CALAN_9244 are exactly identical! WARNING: Sequences tr_A0A0V0WEP0_A0A0V0WEP0_9BILA_92179 and tr_A0A0V1KWR1_A0A0V1KWR1_9BILA_6335 are exactly identical! WARNING: Sequences tr_A0A1S3Y224_A0A1S3Y224_TOBAC_4097 and tr_A0A1U7XBP3_A0A1U7XBP3_NICSY_4096 are exactly identical! WARNING: Sequences tr_A0A1S4B1L4_A0A1S4B1L4_TOBAC_4097 and tr_A0A1U7X8D1_A0A1U7X8D1_NICSY_4096 are exactly identical! WARNING: Sequences tr_A0A2D0PT25_A0A2D0PT25_ICTPU_7998 and tr_A0A2D0PVL3_A0A2D0PVL3_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2K5KHT3_A0A2K5KHT3_CERAT_9531 and tr_A0A2K6AXZ7_A0A2K6AXZ7_MACNE_9545 are exactly identical! WARNING: Sequences tr_A0A2U3V029_A0A2U3V029_TURTR_9739 and tr_A0A2Y9P9E7_A0A2Y9P9E7_DELLE_9749 are exactly identical! WARNING: Sequences tr_A0A2U3X598_A0A2U3X598_ODORO_9708 and tr_A0A2U3Y7L0_A0A2U3Y7L0_LEPWE_9713 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/Q16394/4_raxmlng_ancestral/Q16394.raxml.reduced.phy Alignment comprises 1 partitions and 746 sites Partition 0: noname Model: LG4X+R4 Alignment sites: 746 Gaps: 34.14 % Invariant sites: 0.00 % NOTE: Binary MSA file created: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/Q16394/4_raxmlng_ancestral/Q16394.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/Q16394/3_mltree/Q16394.raxml.bestTree_unrooted [00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 187 / 14960 [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: -247019.523703 [00:00:00 -247019.523703] Initial branch length optimization [00:00:01 -246159.755941] Model parameter optimization (eps = 0.100000) [00:01:02] Tree #1, final logLikelihood: -244731.919890 Optimized model parameters: Partition 0: noname Rate heterogeneity: FREE (4 cats, mean), weights&rates: (0.173901,0.537149) (0.140768,0.730027) (0.377346,0.773555) (0.307985,1.662182) 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/Q16394/4_raxmlng_ancestral/Q16394.raxml.ancestralProbs Reconstructed ancestral sequences saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/Q16394/4_raxmlng_ancestral/Q16394.raxml.ancestralStates Node-labeled tree saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/Q16394/4_raxmlng_ancestral/Q16394.raxml.ancestralTree Execution log saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/Q16394/4_raxmlng_ancestral/Q16394.raxml.log Analysis started: 04-Jun-2021 14:07:38 / finished: 04-Jun-2021 14:08:47 Elapsed time: 69.234 seconds