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 22:47:59 as follows: raxml-ng --ancestral --msa /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/Q9Y4W6/2_msa/Q9Y4W6_nogap_msa.fasta --tree /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/Q9Y4W6/3_mltree/Q9Y4W6.raxml.bestTree_unrooted --model LG4X --prefix /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/Q9Y4W6/4_raxmlng_ancestral/Q9Y4W6 --threads 4 Analysis options: run mode: Ancestral state reconstruction start tree(s): user random seed: 1622663279 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/Q9Y4W6/2_msa/Q9Y4W6_nogap_msa.fasta [00:00:00] Loaded alignment with 1001 taxa and 797 sites WARNING: Sequences tr_J3KJY5_J3KJY5_COCIM_246410 and tr_E9DAF9_E9DAF9_COCPS_443226 are exactly identical! WARNING: Sequences tr_J3KJY5_J3KJY5_COCIM_246410 and tr_A0A0J6Y263_A0A0J6Y263_COCIT_404692 are exactly identical! WARNING: Sequences tr_B6QS08_B6QS08_TALMQ_441960 and tr_A0A093V9Z5_A0A093V9Z5_TALMA_1077442 are exactly identical! WARNING: Sequences tr_H2QEA1_H2QEA1_PANTR_9598 and tr_A0A2R8Z921_A0A2R8Z921_PANPA_9597 are exactly identical! WARNING: Sequences tr_J5JEI6_J5JEI6_BEAB2_655819 and tr_A0A0A2VM53_A0A0A2VM53_BEABA_1245745 are exactly identical! WARNING: Sequences tr_A0A158NAG8_A0A158NAG8_ATTCE_12957 and tr_A0A151I0W7_A0A151I0W7_9HYME_520822 are exactly identical! WARNING: Sequences tr_A0A0E0HFJ2_A0A0E0HFJ2_ORYNI_4536 and tr_B8AYZ7_B8AYZ7_ORYSI_39946 are exactly identical! WARNING: Sequences tr_A0A0E0HFJ2_A0A0E0HFJ2_ORYNI_4536 and sp_Q0DHL4_FTSH8_ORYSJ_39947 are exactly identical! WARNING: Sequences tr_A2QNU0_A2QNU0_ASPNC_425011 and tr_G3XZ47_G3XZ47_ASPNA_380704 are exactly identical! WARNING: Sequences tr_A2QNU0_A2QNU0_ASPNC_425011 and tr_A0A319ART0_A0A319ART0_9EURO_1450533 are exactly identical! WARNING: Sequences tr_G7XEX3_G7XEX3_ASPKW_1033177 and tr_A0A146F1A6_A0A146F1A6_9EURO_1069201 are exactly identical! WARNING: Sequences tr_F4NTN6_F4NTN6_BATDJ_684364 and tr_A0A177WD41_A0A177WD41_BATDE_403673 are exactly identical! WARNING: Sequences tr_G2XWR1_G2XWR1_BOTF4_999810 and tr_M7THM5_M7THM5_BOTF1_1290391 are exactly identical! WARNING: Sequences tr_F2SEP4_F2SEP4_TRIRC_559305 and tr_A0A178ESF3_A0A178ESF3_TRIRU_5551 are exactly identical! WARNING: Sequences tr_A0A0D2XDM8_A0A0D2XDM8_FUSO4_426428 and tr_X0D253_X0D253_FUSOX_1089458 are exactly identical! WARNING: Sequences tr_F2PIT3_F2PIT3_TRIEC_559882 and tr_A0A059J345_A0A059J345_9EURO_1215338 are exactly identical! WARNING: Sequences tr_N4U6Q0_N4U6Q0_FUSC1_1229664 and tr_A0A2H3T3X4_A0A2H3T3X4_FUSOX_5507 are exactly identical! WARNING: Sequences tr_W2Q8K1_W2Q8K1_PHYPN_761204 and tr_A0A0W8CIB5_A0A0W8CIB5_PHYNI_4790 are exactly identical! WARNING: Sequences tr_W2Q8K1_W2Q8K1_PHYPN_761204 and tr_W2NEC3_W2NEC3_PHYPR_4792 are exactly identical! WARNING: Sequences tr_A0A0D2QC48_A0A0D2QC48_GOSRA_29730 and tr_A0A1U8MSQ0_A0A1U8MSQ0_GOSHI_3635 are exactly identical! WARNING: Sequences tr_A0A0D2TME3_A0A0D2TME3_GOSRA_29730 and tr_A0A1U8JFS6_A0A1U8JFS6_GOSHI_3635 are exactly identical! WARNING: Sequences tr_A0A0V0WXB4_A0A0V0WXB4_9BILA_92179 and tr_A0A0V1L009_A0A0V1L009_9BILA_6335 are exactly identical! WARNING: Sequences tr_A0A117DYA6_A0A117DYA6_ASPNG_5061 and tr_A0A1L9MZ66_A0A1L9MZ66_ASPTU_767770 are exactly identical! WARNING: Sequences tr_A0A117DYA6_A0A117DYA6_ASPNG_5061 and tr_A0A317W226_A0A317W226_9EURO_1448314 are exactly identical! WARNING: Sequences tr_A0A164XFR6_A0A164XFR6_9HOMO_1314777 and tr_A0A166G5Z7_A0A166G5Z7_9HOMO_1314776 are exactly identical! WARNING: Sequences tr_A0A1S3ZF94_A0A1S3ZF94_TOBAC_4097 and tr_A0A1U7W629_A0A1U7W629_NICSY_4096 are exactly identical! WARNING: Sequences tr_A0A2I1GWN3_A0A2I1GWN3_9GLOM_588596 and tr_U9TAN1_U9TAN1_RHIID_747089 are exactly identical! WARNING: Sequences tr_A0A2N5SVP0_A0A2N5SVP0_9BASI_200324 and tr_A0A2N5VAP4_A0A2N5VAP4_9BASI_200324 are exactly identical! WARNING: Duplicate sequences found: 28 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/Q9Y4W6/4_raxmlng_ancestral/Q9Y4W6.raxml.reduced.phy Alignment comprises 1 partitions and 797 sites Partition 0: noname Model: LG4X+R4 Alignment sites: 797 Gaps: 13.02 % Invariant sites: 1.13 % NOTE: Binary MSA file already exists: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/Q9Y4W6/4_raxmlng_ancestral/Q9Y4W6.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/Q9Y4W6/3_mltree/Q9Y4W6.raxml.bestTree_unrooted [00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 200 / 16000 [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: -326197.348479 [00:00:00 -326197.348479] Initial branch length optimization [00:00:02 -318814.494604] Model parameter optimization (eps = 0.100000) [00:00:49] Tree #1, final logLikelihood: -317901.979080 Optimized model parameters: Partition 0: noname Rate heterogeneity: FREE (4 cats, mean), weights&rates: (0.229886,0.155216) (0.239520,0.239227) (0.296134,1.041699) (0.234460,2.552825) 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/Q9Y4W6/4_raxmlng_ancestral/Q9Y4W6.raxml.ancestralProbs Reconstructed ancestral sequences saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/Q9Y4W6/4_raxmlng_ancestral/Q9Y4W6.raxml.ancestralStates Node-labeled tree saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/Q9Y4W6/4_raxmlng_ancestral/Q9Y4W6.raxml.ancestralTree Execution log saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/Q9Y4W6/4_raxmlng_ancestral/Q9Y4W6.raxml.log Analysis started: 02-Jun-2021 22:47:59 / finished: 02-Jun-2021 22:48:56 Elapsed time: 56.930 seconds