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 19-Jul-2021 13:12:14 as follows: raxml-ng --ancestral --msa /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q9UPP2/2_msa/Q9UPP2_nogap_msa.fasta --tree /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q9UPP2/3_mltree/Q9UPP2.raxml.bestTree_unrooted --model LG4X --prefix /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q9UPP2/4_raxmlng_ancestral/Q9UPP2 --threads 4 Analysis options: run mode: Ancestral state reconstruction start tree(s): user random seed: 1626689534 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_300621/phylogeny-snakemake/results/Q9UPP2/2_msa/Q9UPP2_nogap_msa.fasta [00:00:00] Loaded alignment with 993 taxa and 1182 sites WARNING: Sequences sp_O08967_CYH3_MOUSE_10090 and tr_A0A1U7R5Q6_A0A1U7R5Q6_MESAU_10036 are exactly identical! WARNING: Sequences sp_Q9QX11_CYH1_MOUSE_10090 and sp_P97694_CYH1_RAT_10116 are exactly identical! WARNING: Sequences tr_A0A2I3GQR7_A0A2I3GQR7_NOMLE_61853 and tr_A0A2I3MG92_A0A2I3MG92_PAPAN_9555 are exactly identical! WARNING: Sequences tr_G1QKE0_G1QKE0_NOMLE_61853 and tr_H2PLF5_H2PLF5_PONAB_9601 are exactly identical! WARNING: Sequences tr_G1QKE0_G1QKE0_NOMLE_61853 and tr_H2QU58_H2QU58_PANTR_9598 are exactly identical! WARNING: Sequences tr_G1QKE0_G1QKE0_NOMLE_61853 and tr_I0FH74_I0FH74_MACMU_9544 are exactly identical! WARNING: Sequences tr_G1QKE0_G1QKE0_NOMLE_61853 and tr_U3ELQ7_U3ELQ7_CALJA_9483 are exactly identical! WARNING: Sequences tr_G1QKE0_G1QKE0_NOMLE_61853 and tr_A0A0D9RYP9_A0A0D9RYP9_CHLSB_60711 are exactly identical! WARNING: Sequences tr_G1QKE0_G1QKE0_NOMLE_61853 and tr_A0A2K5KTX7_A0A2K5KTX7_CERAT_9531 are exactly identical! WARNING: Sequences tr_G1QKE0_G1QKE0_NOMLE_61853 and tr_A0A2K6BVL9_A0A2K6BVL9_MACNE_9545 are exactly identical! WARNING: Sequences tr_D8RRX5_D8RRX5_SELML_88036 and tr_D8SJM0_D8SJM0_SELML_88036 are exactly identical! WARNING: Sequences tr_A0A2I2YN83_A0A2I2YN83_GORGO_9595 and tr_W5PQD9_W5PQD9_SHEEP_9940 are exactly identical! WARNING: Sequences tr_G3S1P5_G3S1P5_GORGO_9595 and tr_H2NUW9_H2NUW9_PONAB_9601 are exactly identical! WARNING: Sequences tr_H2NZG5_H2NZG5_PONAB_9601 and tr_A0A1S3G3T7_A0A1S3G3T7_DIPOR_10020 are exactly identical! WARNING: Sequences tr_H2NZG5_H2NZG5_PONAB_9601 and tr_A0A2Y9DV91_A0A2Y9DV91_TRIMA_127582 are exactly identical! WARNING: Sequences tr_H2NZG5_H2NZG5_PONAB_9601 and tr_A0A2Y9PE76_A0A2Y9PE76_DELLE_9749 are exactly identical! WARNING: Sequences tr_A0A2I3SU11_A0A2I3SU11_PANTR_9598 and tr_A0A2R9BSN1_A0A2R9BSN1_PANPA_9597 are exactly identical! WARNING: Sequences tr_F9F376_F9F376_FUSOF_660025 and tr_A0A2H3TLV2_A0A2H3TLV2_FUSOX_5507 are exactly identical! WARNING: Sequences tr_M3ZG07_M3ZG07_XIPMA_8083 and tr_A0A087XH38_A0A087XH38_POEFO_48698 are exactly identical! WARNING: Sequences tr_I3LWA2_I3LWA2_ICTTR_43179 and sp_Q99418_CYH2_HUMAN_9606 are exactly identical! WARNING: Sequences tr_I3LWA2_I3LWA2_ICTTR_43179 and tr_G3TY44_G3TY44_LOXAF_9785 are exactly identical! WARNING: Sequences tr_I3LWA2_I3LWA2_ICTTR_43179 and sp_Q2KI41_CYH2_BOVIN_9913 are exactly identical! WARNING: Sequences tr_I3LWA2_I3LWA2_ICTTR_43179 and tr_A0A1S3AKC2_A0A1S3AKC2_ERIEU_9365 are exactly identical! WARNING: Sequences tr_I3LWA2_I3LWA2_ICTTR_43179 and tr_A0A2K5L818_A0A2K5L818_CERAT_9531 are exactly identical! WARNING: Sequences tr_I3LWA2_I3LWA2_ICTTR_43179 and tr_A0A2K6DW18_A0A2K6DW18_MACNE_9545 are exactly identical! WARNING: Sequences sp_O43739_CYH3_HUMAN_9606 and tr_A0A096NQ83_A0A096NQ83_PAPAN_9555 are exactly identical! WARNING: Sequences tr_A0A1D5QFG0_A0A1D5QFG0_MACMU_9544 and tr_A0A2I3MVV0_A0A2I3MVV0_PAPAN_9555 are exactly identical! WARNING: Sequences tr_A0A1D5QFG0_A0A1D5QFG0_MACMU_9544 and tr_A0A2K6EBL6_A0A2K6EBL6_MACNE_9545 are exactly identical! WARNING: Sequences tr_F7B954_F7B954_MACMU_9544 and tr_A0A2K6DSD5_A0A2K6DSD5_MACNE_9545 are exactly identical! WARNING: Sequences tr_H0ZEX0_H0ZEX0_TAEGU_59729 and tr_A0A218V7G8_A0A218V7G8_9PASE_299123 are exactly identical! WARNING: Sequences tr_A0JLZ9_A0JLZ9_XENTR_8364 and tr_A0A1L8EY25_A0A1L8EY25_XENLA_8355 are exactly identical! WARNING: Sequences tr_A0A0D2Y5B0_A0A0D2Y5B0_FUSO4_426428 and tr_N4UIV6_N4UIV6_FUSC1_1229664 are exactly identical! WARNING: Sequences tr_A0A0D2Y5B0_A0A0D2Y5B0_FUSO4_426428 and tr_X0CGD7_X0CGD7_FUSOX_1089458 are exactly identical! WARNING: Sequences tr_A0A0D2Y5B0_A0A0D2Y5B0_FUSO4_426428 and tr_A0A2H3GQW0_A0A2H3GQW0_FUSOX_327505 are exactly identical! WARNING: Sequences tr_A0A067H1X1_A0A067H1X1_CITSI_2711 and tr_V4U325_V4U325_9ROSI_85681 are exactly identical! WARNING: Sequences tr_A0A0Q3X395_A0A0Q3X395_AMAAE_12930 and tr_A0A091ITQ0_A0A091ITQ0_EGRGA_188379 are exactly identical! WARNING: Sequences tr_A0A0Q3X395_A0A0Q3X395_AMAAE_12930 and tr_A0A093Q5X5_A0A093Q5X5_9PASS_328815 are exactly identical! WARNING: Sequences tr_A0A0Q3X395_A0A0Q3X395_AMAAE_12930 and tr_A0A091WDT0_A0A091WDT0_NIPNI_128390 are exactly identical! WARNING: Sequences tr_A0A0Q3X395_A0A0Q3X395_AMAAE_12930 and tr_A0A087RFS5_A0A087RFS5_APTFO_9233 are exactly identical! WARNING: Sequences tr_A0A0Q3X395_A0A0Q3X395_AMAAE_12930 and tr_A0A093HVJ6_A0A093HVJ6_STRCA_441894 are exactly identical! WARNING: Sequences tr_A0A0Q3X395_A0A0Q3X395_AMAAE_12930 and tr_A0A091W5H7_A0A091W5H7_OPIHO_30419 are exactly identical! WARNING: Sequences tr_A0A0Q3X395_A0A0Q3X395_AMAAE_12930 and tr_A0A099ZQA1_A0A099ZQA1_TINGU_94827 are exactly identical! WARNING: Sequences tr_A0A0Q3X395_A0A0Q3X395_AMAAE_12930 and tr_A0A0A0A0Q8_A0A0A0A0Q8_CHAVO_50402 are exactly identical! WARNING: Sequences tr_A0A093S8P2_A0A093S8P2_9PASS_328815 and tr_A0A091VQA5_A0A091VQA5_NIPNI_128390 are exactly identical! WARNING: Sequences tr_A0A093S8P2_A0A093S8P2_9PASS_328815 and tr_A0A087QX99_A0A087QX99_APTFO_9233 are exactly identical! WARNING: Sequences tr_A0A093S8P2_A0A093S8P2_9PASS_328815 and tr_A0A093HXA3_A0A093HXA3_STRCA_441894 are exactly identical! WARNING: Sequences tr_A0A093S8P2_A0A093S8P2_9PASS_328815 and tr_A0A093GF11_A0A093GF11_DRYPU_118200 are exactly identical! WARNING: Sequences tr_A0A093S8P2_A0A093S8P2_9PASS_328815 and tr_A0A091HZZ3_A0A091HZZ3_CALAN_9244 are exactly identical! WARNING: Sequences tr_I1RJY4_I1RJY4_GIBZE_229533 and tr_A0A2T4GTK6_A0A2T4GTK6_FUSCU_5516 are exactly identical! WARNING: Duplicate sequences found: 49 NOTE: Reduced alignment (with duplicates and gap-only sites/taxa removed) NOTE: was saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q9UPP2/4_raxmlng_ancestral/Q9UPP2.raxml.reduced.phy Alignment comprises 1 partitions and 1182 sites Partition 0: noname Model: LG4X+R4 Alignment sites: 1182 Gaps: 49.17 % Invariant sites: 0.00 % NOTE: Binary MSA file created: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q9UPP2/4_raxmlng_ancestral/Q9UPP2.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_300621/phylogeny-snakemake/results/Q9UPP2/3_mltree/Q9UPP2.raxml.bestTree_unrooted [00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 296 / 23680 [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: -415252.457719 [00:00:00 -415252.457719] Initial branch length optimization [00:00:03 -283946.091099] Model parameter optimization (eps = 0.100000) [00:01:38] Tree #1, final logLikelihood: -282921.593645 Optimized model parameters: Partition 0: noname Rate heterogeneity: FREE (4 cats, mean), weights&rates: (0.151703,0.397986) (0.113885,0.519291) (0.335116,0.604292) (0.399296,1.697930) 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_300621/phylogeny-snakemake/results/Q9UPP2/4_raxmlng_ancestral/Q9UPP2.raxml.ancestralProbs Reconstructed ancestral sequences saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q9UPP2/4_raxmlng_ancestral/Q9UPP2.raxml.ancestralStates Node-labeled tree saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q9UPP2/4_raxmlng_ancestral/Q9UPP2.raxml.ancestralTree Execution log saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q9UPP2/4_raxmlng_ancestral/Q9UPP2.raxml.log Analysis started: 19-Jul-2021 13:12:14 / finished: 19-Jul-2021 13:14:03 Elapsed time: 109.298 seconds