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 13:33:56 as follows: raxml-ng --ancestral --msa /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/Q5T481/2_msa/Q5T481_nogap_msa.fasta --tree /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/Q5T481/3_mltree/Q5T481.raxml.bestTree_unrooted --model LG4X --prefix /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/Q5T481/4_raxmlng_ancestral/Q5T481 --threads 4 Analysis options: run mode: Ancestral state reconstruction start tree(s): user random seed: 1622802836 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/Q5T481/2_msa/Q5T481_nogap_msa.fasta [00:00:00] Loaded alignment with 719 taxa and 1227 sites WARNING: Sequences tr_B4QTB0_B4QTB0_DROSI_7240 and tr_B4IJ45_B4IJ45_DROSE_7238 are exactly identical! WARNING: Sequences sp_Q91Z31_PTBP2_MOUSE_10090 and sp_Q66H20_PTBP2_RAT_10116 are exactly identical! WARNING: Sequences sp_Q91Z31_PTBP2_MOUSE_10090 and tr_H0V1M7_H0V1M7_CAVPO_10141 are exactly identical! WARNING: Sequences tr_M3XW10_M3XW10_MUSPF_9669 and tr_A0A2I3GPV1_A0A2I3GPV1_NOMLE_61853 are exactly identical! WARNING: Sequences tr_M3XW10_M3XW10_MUSPF_9669 and tr_G3QEF5_G3QEF5_GORGO_9595 are exactly identical! WARNING: Sequences tr_M3XW10_M3XW10_MUSPF_9669 and tr_E2RSK4_E2RSK4_CANLF_9615 are exactly identical! WARNING: Sequences tr_M3XW10_M3XW10_MUSPF_9669 and tr_F6RWP2_F6RWP2_CALJA_9483 are exactly identical! WARNING: Sequences tr_M3XW10_M3XW10_MUSPF_9669 and tr_M3WR16_M3WR16_FELCA_9685 are exactly identical! WARNING: Sequences tr_M3XW10_M3XW10_MUSPF_9669 and tr_A0A2K5N306_A0A2K5N306_CERAT_9531 are exactly identical! WARNING: Sequences tr_M3XW10_M3XW10_MUSPF_9669 and tr_A0A2K6DCS0_A0A2K6DCS0_MACNE_9545 are exactly identical! WARNING: Sequences tr_M3XW10_M3XW10_MUSPF_9669 and tr_A0A2K5YIL1_A0A2K5YIL1_MANLE_9568 are exactly identical! WARNING: Sequences tr_M3XW10_M3XW10_MUSPF_9669 and tr_A0A2R9BX06_A0A2R9BX06_PANPA_9597 are exactly identical! WARNING: Sequences tr_M3XW10_M3XW10_MUSPF_9669 and tr_A0A2U3V6E0_A0A2U3V6E0_TURTR_9739 are exactly identical! WARNING: Sequences tr_M3XW10_M3XW10_MUSPF_9669 and tr_A0A2Y9FXP3_A0A2Y9FXP3_TRIMA_127582 are exactly identical! WARNING: Sequences tr_M3XW10_M3XW10_MUSPF_9669 and tr_A0A2Y9IWP8_A0A2Y9IWP8_ENHLU_391180 are exactly identical! WARNING: Sequences tr_G3S894_G3S894_GORGO_9595 and tr_A0A2I3S9B0_A0A2I3S9B0_PANTR_9598 are exactly identical! WARNING: Sequences tr_H2N6P6_H2N6P6_PONAB_9601 and sp_Q9UKA9_PTBP2_HUMAN_9606 are exactly identical! WARNING: Sequences tr_H2N6P6_H2N6P6_PONAB_9601 and tr_H9FXV6_H9FXV6_MACMU_9544 are exactly identical! WARNING: Sequences tr_H2N6P6_H2N6P6_PONAB_9601 and tr_F1S549_F1S549_PIG_9823 are exactly identical! WARNING: Sequences tr_H2N6P6_H2N6P6_PONAB_9601 and tr_A0A096N001_A0A096N001_PAPAN_9555 are exactly identical! WARNING: Sequences tr_H2N6P6_H2N6P6_PONAB_9601 and tr_A0A0D9S6P3_A0A0D9S6P3_CHLSB_60711 are exactly identical! WARNING: Sequences tr_H2N6P6_H2N6P6_PONAB_9601 and tr_A0A2Y9S9Q0_A0A2Y9S9Q0_PHYCD_9755 are exactly identical! WARNING: Sequences tr_H2PT24_H2PT24_PONAB_9601 and sp_O95758_PTBP3_HUMAN_9606 are exactly identical! WARNING: Sequences tr_F7BRN9_F7BRN9_MONDO_13616 and tr_G3VUA4_G3VUA4_SARHA_9305 are exactly identical! WARNING: Sequences tr_M4AW35_M4AW35_XIPMA_8083 and tr_A0A087XIN5_A0A087XIN5_POEFO_48698 are exactly identical! WARNING: Sequences tr_G3U458_G3U458_LOXAF_9785 and tr_G7NV16_G7NV16_MACFA_9541 are exactly identical! WARNING: Sequences tr_W2QZL1_W2QZL1_PHYPN_761204 and tr_W2I8V2_W2I8V2_PHYPR_4792 are exactly identical! WARNING: Sequences tr_A0A0A0MVE9_A0A0A0MVE9_PAPAN_9555 and tr_A0A0D9RJZ5_A0A0D9RJZ5_CHLSB_60711 are exactly identical! WARNING: Sequences tr_A0A2I3MNB2_A0A2I3MNB2_PAPAN_9555 and tr_A0A2K5LEI9_A0A2K5LEI9_CERAT_9531 are exactly identical! WARNING: Sequences tr_A0A091KHC0_A0A091KHC0_EGRGA_188379 and tr_A0A0A0AI53_A0A0A0AI53_CHAVO_50402 are exactly identical! WARNING: Sequences tr_A0A1S3J968_A0A1S3J968_LINUN_7574 and tr_A0A1S3JAN5_A0A1S3JAN5_LINUN_7574 are exactly identical! WARNING: Sequences tr_A0A1S3J973_A0A1S3J973_LINUN_7574 and tr_A0A1S3J9R1_A0A1S3J9R1_LINUN_7574 are exactly identical! WARNING: Sequences tr_A0A1S3NCJ5_A0A1S3NCJ5_SALSA_8030 and tr_A0A060WNE3_A0A060WNE3_ONCMY_8022 are exactly identical! WARNING: Sequences tr_A0A1U7UN83_A0A1U7UN83_TARSY_1868482 and tr_A0A384CM39_A0A384CM39_URSMA_29073 are exactly identical! WARNING: Sequences tr_A0A2D0REY6_A0A2D0REY6_ICTPU_7998 and tr_A0A2D0REZ5_A0A2D0REZ5_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2U3WK65_A0A2U3WK65_ODORO_9708 and tr_A0A2U3X9A7_A0A2U3X9A7_LEPWE_9713 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_020621/phylogeny-snakemake/results/Q5T481/4_raxmlng_ancestral/Q5T481.raxml.reduced.phy Alignment comprises 1 partitions and 1227 sites Partition 0: noname Model: LG4X+R4 Alignment sites: 1227 Gaps: 61.65 % Invariant sites: 0.00 % NOTE: Binary MSA file created: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/Q5T481/4_raxmlng_ancestral/Q5T481.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/Q5T481/3_mltree/Q5T481.raxml.bestTree_unrooted [00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 307 / 24560 [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: -216539.402600 [00:00:00 -216539.402600] Initial branch length optimization [00:00:02 -212290.939651] Model parameter optimization (eps = 0.100000) [00:01:35] Tree #1, final logLikelihood: -211163.454367 Optimized model parameters: Partition 0: noname Rate heterogeneity: FREE (4 cats, mean), weights&rates: (0.085393,0.566942) (0.060448,1.251740) (0.229483,0.552610) (0.624675,1.199194) 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/Q5T481/4_raxmlng_ancestral/Q5T481.raxml.ancestralProbs Reconstructed ancestral sequences saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/Q5T481/4_raxmlng_ancestral/Q5T481.raxml.ancestralStates Node-labeled tree saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/Q5T481/4_raxmlng_ancestral/Q5T481.raxml.ancestralTree Execution log saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/Q5T481/4_raxmlng_ancestral/Q5T481.raxml.log Analysis started: 04-Jun-2021 13:33:56 / finished: 04-Jun-2021 13:35:39 Elapsed time: 102.960 seconds