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 02-Jun-2021 14:08:53 as follows: raxml-ng --ancestral --msa /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/Q16637/2_msa/Q16637_nogap_msa.fasta --tree /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/Q16637/3_mltree/Q16637.raxml.bestTree_unrooted --model LG4X --prefix /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/Q16637/4_raxmlng_ancestral/Q16637 --threads 4 Analysis options: run mode: Ancestral state reconstruction start tree(s): user random seed: 1622632133 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/Q16637/2_msa/Q16637_nogap_msa.fasta [00:00:00] Loaded alignment with 466 taxa and 294 sites WARNING: Sequences tr_E1BQK7_E1BQK7_CHICK_9031 and tr_H0ZK11_H0ZK11_TAEGU_59729 are exactly identical! WARNING: Sequences tr_E1BQK7_E1BQK7_CHICK_9031 and tr_U3JHZ7_U3JHZ7_FICAL_59894 are exactly identical! WARNING: Sequences tr_E1BQK7_E1BQK7_CHICK_9031 and tr_A0A091EP67_A0A091EP67_CORBR_85066 are exactly identical! WARNING: Sequences tr_E1BQK7_E1BQK7_CHICK_9031 and tr_A0A218V9F7_A0A218V9F7_9PASE_299123 are exactly identical! WARNING: Sequences tr_M3XSL8_M3XSL8_MUSPF_9669 and tr_G1RZV3_G1RZV3_NOMLE_61853 are exactly identical! WARNING: Sequences tr_M3XSL8_M3XSL8_MUSPF_9669 and tr_G3R3J9_G3R3J9_GORGO_9595 are exactly identical! WARNING: Sequences tr_M3XSL8_M3XSL8_MUSPF_9669 and sp_Q5R591_SPF30_PONAB_9601 are exactly identical! WARNING: Sequences tr_M3XSL8_M3XSL8_MUSPF_9669 and tr_H2Q2K2_H2Q2K2_PANTR_9598 are exactly identical! WARNING: Sequences tr_M3XSL8_M3XSL8_MUSPF_9669 and tr_W5PID0_W5PID0_SHEEP_9940 are exactly identical! WARNING: Sequences tr_M3XSL8_M3XSL8_MUSPF_9669 and tr_I3M792_I3M792_ICTTR_43179 are exactly identical! WARNING: Sequences tr_M3XSL8_M3XSL8_MUSPF_9669 and tr_H0WGQ2_H0WGQ2_OTOGA_30611 are exactly identical! WARNING: Sequences tr_M3XSL8_M3XSL8_MUSPF_9669 and tr_F7CVM3_F7CVM3_MACMU_9544 are exactly identical! WARNING: Sequences tr_M3XSL8_M3XSL8_MUSPF_9669 and tr_G3TD30_G3TD30_LOXAF_9785 are exactly identical! WARNING: Sequences tr_M3XSL8_M3XSL8_MUSPF_9669 and tr_F7HMY9_F7HMY9_CALJA_9483 are exactly identical! WARNING: Sequences tr_M3XSL8_M3XSL8_MUSPF_9669 and tr_D2I6J0_D2I6J0_AILME_9646 are exactly identical! WARNING: Sequences tr_M3XSL8_M3XSL8_MUSPF_9669 and tr_F1MS68_F1MS68_BOVIN_9913 are exactly identical! WARNING: Sequences tr_M3XSL8_M3XSL8_MUSPF_9669 and tr_M3XF47_M3XF47_FELCA_9685 are exactly identical! WARNING: Sequences tr_M3XSL8_M3XSL8_MUSPF_9669 and tr_A0A096P6K0_A0A096P6K0_PAPAN_9555 are exactly identical! WARNING: Sequences tr_M3XSL8_M3XSL8_MUSPF_9669 and tr_A0A0D9QYP6_A0A0D9QYP6_CHLSB_60711 are exactly identical! WARNING: Sequences tr_M3XSL8_M3XSL8_MUSPF_9669 and tr_A0A1S3FBA8_A0A1S3FBA8_DIPOR_10020 are exactly identical! WARNING: Sequences tr_M3XSL8_M3XSL8_MUSPF_9669 and tr_A0A1U7U422_A0A1U7U422_TARSY_1868482 are exactly identical! WARNING: Sequences tr_M3XSL8_M3XSL8_MUSPF_9669 and tr_A0A1U7Q2M9_A0A1U7Q2M9_MESAU_10036 are exactly identical! WARNING: Sequences tr_M3XSL8_M3XSL8_MUSPF_9669 and tr_A0A2K6DW37_A0A2K6DW37_MACNE_9545 are exactly identical! WARNING: Sequences tr_M3XSL8_M3XSL8_MUSPF_9669 and tr_A0A2R9A1R7_A0A2R9A1R7_PANPA_9597 are exactly identical! WARNING: Sequences tr_M3XSL8_M3XSL8_MUSPF_9669 and tr_A0A2U3V0J0_A0A2U3V0J0_TURTR_9739 are exactly identical! WARNING: Sequences tr_M3XSL8_M3XSL8_MUSPF_9669 and tr_A0A2Y9QQF7_A0A2Y9QQF7_TRIMA_127582 are exactly identical! WARNING: Sequences tr_M3XSL8_M3XSL8_MUSPF_9669 and tr_A0A2Y9J3W6_A0A2Y9J3W6_ENHLU_391180 are exactly identical! WARNING: Sequences tr_M3XSL8_M3XSL8_MUSPF_9669 and tr_A0A2Y9N5L7_A0A2Y9N5L7_DELLE_9749 are exactly identical! WARNING: Sequences tr_M3XSL8_M3XSL8_MUSPF_9669 and tr_A0A2Y9F4C6_A0A2Y9F4C6_PHYCD_9755 are exactly identical! WARNING: Sequences tr_M3XSL8_M3XSL8_MUSPF_9669 and tr_A0A384BKF4_A0A384BKF4_URSMA_29073 are exactly identical! WARNING: Sequences tr_M3XSL8_M3XSL8_MUSPF_9669 and tr_A0A383ZE34_A0A383ZE34_BALAS_310752 are exactly identical! WARNING: Sequences tr_A0A2I3TMK9_A0A2I3TMK9_PANTR_9598 and sp_Q16637_SMN_HUMAN_9606 are exactly identical! WARNING: Sequences tr_F6ZET6_F6ZET6_MONDO_13616 and sp_O75940_SPF30_HUMAN_9606 are exactly identical! WARNING: Sequences tr_F6ZET6_F6ZET6_MONDO_13616 and tr_G3WR38_G3WR38_SARHA_9305 are exactly identical! WARNING: Sequences tr_A0A0E0I6G5_A0A0E0I6G5_ORYNI_4536 and tr_A2YQI7_A2YQI7_ORYSI_39946 are exactly identical! WARNING: Sequences tr_A0A0E0I6G5_A0A0E0I6G5_ORYNI_4536 and tr_I1QF09_I1QF09_ORYGL_4538 are exactly identical! WARNING: Sequences tr_A0A0E0I6G5_A0A0E0I6G5_ORYNI_4536 and tr_A0A0E0QDH1_A0A0E0QDH1_ORYRU_4529 are exactly identical! WARNING: Sequences tr_A0A0E0I6G5_A0A0E0I6G5_ORYNI_4536 and tr_A0A0D3GVM8_A0A0D3GVM8_9ORYZ_65489 are exactly identical! WARNING: Sequences tr_A0A0E0I6G5_A0A0E0I6G5_ORYNI_4536 and tr_A0A0E0AQ11_A0A0E0AQ11_9ORYZ_40148 are exactly identical! WARNING: Sequences tr_F4WC80_F4WC80_ACREC_103372 and tr_A0A195BKA3_A0A195BKA3_9HYME_520822 are exactly identical! WARNING: Sequences tr_F9X7K9_F9X7K9_ZYMTI_336722 and tr_A0A0F4GYU2_A0A0F4GYU2_9PEZI_1047168 are exactly identical! WARNING: Sequences tr_A0A091K7M5_A0A091K7M5_EGRGA_188379 and tr_A0A091UQP5_A0A091UQP5_NIPNI_128390 are exactly identical! WARNING: Sequences tr_A0A091K7M5_A0A091K7M5_EGRGA_188379 and tr_A0A087QZF6_A0A087QZF6_APTFO_9233 are exactly identical! WARNING: Sequences tr_A0A091K7M5_A0A091K7M5_EGRGA_188379 and tr_A0A091VES8_A0A091VES8_OPIHO_30419 are exactly identical! WARNING: Sequences tr_A0A091K7M5_A0A091K7M5_EGRGA_188379 and tr_A0A0A0AC09_A0A0A0AC09_CHAVO_50402 are exactly identical! WARNING: Sequences tr_A0A091H5D9_A0A091H5D9_9AVES_55661 and tr_A0A2I0MEF0_A0A2I0MEF0_COLLI_8932 are exactly identical! WARNING: Sequences tr_A0A0V0RUR3_A0A0V0RUR3_9BILA_6336 and tr_A0A0V1CW87_A0A0V1CW87_TRIBR_45882 are exactly identical! WARNING: Sequences tr_A0A0V0RUR3_A0A0V0RUR3_9BILA_6336 and tr_A0A0V0X0R5_A0A0V0X0R5_9BILA_92179 are exactly identical! WARNING: Sequences tr_A0A0V0RUR3_A0A0V0RUR3_9BILA_6336 and tr_A0A0V1PE85_A0A0V1PE85_9BILA_92180 are exactly identical! WARNING: Sequences tr_A0A0V0RUR3_A0A0V0RUR3_9BILA_6336 and tr_A0A0V0U8E7_A0A0V0U8E7_9BILA_144512 are exactly identical! WARNING: Sequences tr_B5X7J7_B5X7J7_SALSA_8030 and tr_C1BEV6_C1BEV6_ONCMY_8022 are exactly identical! WARNING: Sequences tr_A0A226MX29_A0A226MX29_CALSU_9009 and tr_A0A226PQK7_A0A226PQK7_COLVI_9014 are exactly identical! WARNING: Sequences tr_A0A2H3CPQ3_A0A2H3CPQ3_9AGAR_1076256 and tr_A0A284RAG2_A0A284RAG2_9AGAR_47428 are exactly identical! WARNING: Duplicate sequences found: 53 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/Q16637/4_raxmlng_ancestral/Q16637.raxml.reduced.phy Alignment comprises 1 partitions and 294 sites Partition 0: noname Model: LG4X+R4 Alignment sites: 294 Gaps: 34.40 % Invariant sites: 0.00 % NOTE: Binary MSA file created: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/Q16637/4_raxmlng_ancestral/Q16637.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/Q16637/3_mltree/Q16637.raxml.bestTree_unrooted [00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 74 / 5920 [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: -65049.875613 [00:00:00 -65049.875613] Initial branch length optimization [00:00:00 -64396.375297] Model parameter optimization (eps = 0.100000) [00:00:29] Tree #1, final logLikelihood: -64122.546515 Optimized model parameters: Partition 0: noname Rate heterogeneity: FREE (4 cats, mean), weights&rates: (0.105159,0.508187) (0.082807,0.798827) (0.273657,0.783606) (0.538378,1.236998) 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/Q16637/4_raxmlng_ancestral/Q16637.raxml.ancestralProbs Reconstructed ancestral sequences saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/Q16637/4_raxmlng_ancestral/Q16637.raxml.ancestralStates Node-labeled tree saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/Q16637/4_raxmlng_ancestral/Q16637.raxml.ancestralTree Execution log saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/Q16637/4_raxmlng_ancestral/Q16637.raxml.log Analysis started: 02-Jun-2021 14:08:53 / finished: 02-Jun-2021 14:09:25 Elapsed time: 31.246 seconds