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) CPU E5-2690 v4 @ 2.60GHz, 28 cores, 251 GB RAM RAxML-NG was called at 02-Jun-2021 18:06:00 as follows: raxml-ng --ancestral --msa /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/O43175/2_msa/O43175_nogap_msa.fasta --tree /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/O43175/3_mltree/O43175.raxml.bestTree_unrooted --model LG4X --prefix /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/O43175/4_raxmlng_ancestral/O43175 --threads 4 Analysis options: run mode: Ancestral state reconstruction start tree(s): user random seed: 1622646360 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: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/O43175/2_msa/O43175_nogap_msa.fasta [00:00:00] Loaded alignment with 1001 taxa and 533 sites WARNING: Sequences tr_A0A0D8JW95_A0A0D8JW95_COCIM_246410 and tr_A0A0J7B0Z5_A0A0J7B0Z5_COCIT_404692 are exactly identical! WARNING: Sequences tr_J3KIR7_J3KIR7_COCIM_246410 and tr_A0A0J6XY62_A0A0J6XY62_COCIT_404692 are exactly identical! WARNING: Sequences tr_B2VUF1_B2VUF1_PYRTR_426418 and tr_A0A2W1HDG9_A0A2W1HDG9_9PLEO_45151 are exactly identical! WARNING: Sequences tr_C0NE90_C0NE90_AJECG_447093 and tr_F0UG03_F0UG03_AJEC8_544711 are exactly identical! WARNING: Sequences tr_A0A0R3NZ30_A0A0R3NZ30_DROPS_46245 and tr_B4G9U8_B4G9U8_DROPE_7234 are exactly identical! WARNING: Sequences tr_A0A179UW17_A0A179UW17_BLAGS_559298 and tr_C5GM12_C5GM12_AJEDR_559297 are exactly identical! WARNING: Sequences tr_J9P120_J9P120_CANLF_9615 and tr_L7N0I9_L7N0I9_CANLF_9615 are exactly identical! WARNING: Sequences tr_K7DD09_K7DD09_PANTR_9598 and tr_A0A2R9C2H1_A0A2R9C2H1_PANPA_9597 are exactly identical! WARNING: Sequences tr_F9FL55_F9FL55_FUSOF_660025 and tr_A0A2H3T9R9_A0A2H3T9R9_FUSOX_5507 are exactly identical! WARNING: Sequences tr_E9F3T2_E9F3T2_METRA_655844 and tr_A0A0D9NZH3_A0A0D9NZH3_METAN_1291518 are exactly identical! WARNING: Sequences tr_C6HCU8_C6HCU8_AJECH_544712 and tr_F0UTL5_F0UTL5_AJEC8_544711 are exactly identical! WARNING: Sequences tr_A0A0E0GDR7_A0A0E0GDR7_ORYNI_4536 and tr_A2YVQ8_A2YVQ8_ORYSI_39946 are exactly identical! WARNING: Sequences tr_A0A0E0GDR7_A0A0E0GDR7_ORYNI_4536 and tr_I1QJ44_I1QJ44_ORYGL_4538 are exactly identical! WARNING: Sequences tr_A0A0E0HUF0_A0A0E0HUF0_ORYNI_4536 and tr_A2YFS1_A2YFS1_ORYSI_39946 are exactly identical! WARNING: Sequences tr_A0A0E0HUF0_A0A0E0HUF0_ORYNI_4536 and tr_I1Q485_I1Q485_ORYGL_4538 are exactly identical! WARNING: Sequences tr_A0A0E0HUF0_A0A0E0HUF0_ORYNI_4536 and tr_A0A0E0ACQ1_A0A0E0ACQ1_9ORYZ_40148 are exactly identical! WARNING: Sequences tr_A2XYC2_A2XYC2_ORYSI_39946 and tr_A0A0E0PEY8_A0A0E0PEY8_ORYRU_4529 are exactly identical! WARNING: Sequences tr_A2XYC2_A2XYC2_ORYSI_39946 and tr_Q7XMP6_Q7XMP6_ORYSJ_39947 are exactly identical! WARNING: Sequences tr_I1PQC4_I1PQC4_ORYGL_4538 and tr_A0A0D9ZRP3_A0A0D9ZRP3_9ORYZ_40148 are exactly identical! WARNING: Sequences tr_F9X171_F9X171_ZYMTI_336722 and tr_A0A1X7RFU1_A0A1X7RFU1_ZYMTR_1276538 are exactly identical! WARNING: Sequences tr_F9XHB9_F9XHB9_ZYMTI_336722 and tr_A0A0F4GPE3_A0A0F4GPE3_9PEZI_1047168 are exactly identical! WARNING: Sequences tr_F9XHB9_F9XHB9_ZYMTI_336722 and tr_A0A1X7S212_A0A1X7S212_ZYMTR_1276538 are exactly identical! WARNING: Sequences tr_G2Y361_G2Y361_BOTF4_999810 and tr_M7TRI3_M7TRI3_BOTF1_1290391 are exactly identical! WARNING: Sequences tr_B3RTC6_B3RTC6_TRIAD_10228 and tr_A0A369S215_A0A369S215_9METZ_287889 are exactly identical! WARNING: Sequences tr_A0A0D2XQD3_A0A0D2XQD3_FUSO4_426428 and tr_N4UDU5_N4UDU5_FUSC1_1229664 are exactly identical! WARNING: Sequences tr_V2XZE6_V2XZE6_MONRO_1381753 and tr_A0A0W0F5R4_A0A0W0F5R4_9AGAR_221103 are exactly identical! WARNING: Sequences tr_W2PWM4_W2PWM4_PHYPN_761204 and tr_W2KN63_W2KN63_PHYPR_4792 are exactly identical! WARNING: Sequences tr_A0A044TZU3_A0A044TZU3_ONCVO_6282 and tr_A0A182EBT6_A0A182EBT6_ONCOC_42157 are exactly identical! WARNING: Sequences tr_A0A067F9E7_A0A067F9E7_CITSI_2711 and tr_V4SBI8_V4SBI8_9ROSI_85681 are exactly identical! WARNING: Sequences tr_A0A067GWF5_A0A067GWF5_CITSI_2711 and tr_V4V765_V4V765_9ROSI_85681 are exactly identical! WARNING: Sequences tr_A0A078IH14_A0A078IH14_BRANA_3708 and tr_A0A0D3DHM5_A0A0D3DHM5_BRAOL_109376 are exactly identical! WARNING: Sequences tr_A0A094GSP5_A0A094GSP5_9PEZI_1420912 and tr_A0A1B8GAI9_A0A1B8GAI9_9PEZI_342668 are exactly identical! WARNING: Sequences tr_V4SPV9_V4SPV9_9ROSI_85681 and tr_A0A2H5PAP2_A0A2H5PAP2_CITUN_55188 are exactly identical! WARNING: Sequences tr_A0A100IQ66_A0A100IQ66_ASPNG_5061 and tr_A0A1L9N595_A0A1L9N595_ASPTU_767770 are exactly identical! WARNING: Sequences tr_A0A100IQ66_A0A100IQ66_ASPNG_5061 and tr_A0A317VJ79_A0A317VJ79_9EURO_1448314 are exactly identical! WARNING: Sequences tr_A0A164XH58_A0A164XH58_9HOMO_1314777 and tr_A0A166CG10_A0A166CG10_9HOMO_1314776 are exactly identical! WARNING: Sequences tr_A0A1S4A5W5_A0A1S4A5W5_TOBAC_4097 and tr_A0A1U7UZI5_A0A1U7UZI5_NICSY_4096 are exactly identical! WARNING: Sequences tr_A0A1F5L7H6_A0A1F5L7H6_9EURO_1835702 and tr_A0A1V6PUT4_A0A1V6PUT4_9EURO_416450 are exactly identical! WARNING: Sequences tr_A0A1V8USG4_A0A1V8USG4_9PEZI_1974281 and tr_A0A1V8SZ56_A0A1V8SZ56_9PEZI_1507870 are exactly identical! WARNING: Sequences tr_A0A2D0R592_A0A2D0R592_ICTPU_7998 and tr_A0A2D0R5A4_A0A2D0R5A4_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A1U8FY27_A0A1U8FY27_CAPAN_4072 and tr_A0A2G3CY74_A0A2G3CY74_CAPCH_80379 are exactly identical! WARNING: Duplicate sequences found: 41 NOTE: Reduced alignment (with duplicates and gap-only sites/taxa removed) NOTE: was saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/O43175/4_raxmlng_ancestral/O43175.raxml.reduced.phy Alignment comprises 1 partitions and 533 sites Partition 0: noname Model: LG4X+R4 Alignment sites: 533 Gaps: 16.43 % Invariant sites: 0.19 % NOTE: Binary MSA file created: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/O43175/4_raxmlng_ancestral/O43175.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: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/O43175/3_mltree/O43175.raxml.bestTree_unrooted [00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 134 / 10720 [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: -183764.535459 [00:00:00 -183764.535459] Initial branch length optimization [00:00:01 -182663.380963] Model parameter optimization (eps = 0.100000) [00:00:47] Tree #1, final logLikelihood: -182172.806778 Optimized model parameters: Partition 0: noname Rate heterogeneity: FREE (4 cats, mean), weights&rates: (0.186428,0.307315) (0.251054,0.392612) (0.313957,0.922130) (0.248560,2.231375) 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: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/O43175/4_raxmlng_ancestral/O43175.raxml.ancestralProbs Reconstructed ancestral sequences saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/O43175/4_raxmlng_ancestral/O43175.raxml.ancestralStates Node-labeled tree saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/O43175/4_raxmlng_ancestral/O43175.raxml.ancestralTree Execution log saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/O43175/4_raxmlng_ancestral/O43175.raxml.log Analysis started: 02-Jun-2021 18:06:00 / finished: 02-Jun-2021 18:06:52 Elapsed time: 52.771 seconds Consumed energy: 3.765 Wh