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 6148 CPU @ 2.40GHz, 40 cores, 376 GB RAM

RAxML-NG was called at 02-Jun-2021 18:13:01 as follows:

raxml-ng --ancestral --msa /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q9Y6H1/2_msa/Q9Y6H1_nogap_msa.fasta --tree /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q9Y6H1/3_mltree/Q9Y6H1.raxml.bestTree_unrooted --model LG4X --prefix /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q9Y6H1/4_raxmlng_ancestral/Q9Y6H1 --threads 4

Analysis options:
  run mode: Ancestral state reconstruction
  start tree(s): user
  random seed: 1622646781
  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/Q9Y6H1/2_msa/Q9Y6H1_nogap_msa.fasta
[00:00:00] Loaded alignment with 759 taxa and 151 sites

WARNING: Sequences tr_E3RS54_E3RS54_PYRTT_861557 and tr_B2WAU3_B2WAU3_PYRTR_426418 are exactly identical!
WARNING: Sequences tr_E3RS54_E3RS54_PYRTT_861557 and tr_A0A2W1EAH6_A0A2W1EAH6_9PLEO_45151 are exactly identical!
WARNING: Sequences tr_J3KH00_J3KH00_COCIM_246410 and tr_A0A0J7ASP1_A0A0J7ASP1_COCIT_404692 are exactly identical!
WARNING: Sequences tr_B6QTE7_B6QTE7_TALMQ_441960 and tr_A0A093VAB4_A0A093VAB4_TALMA_1077442 are exactly identical!
WARNING: Sequences tr_G3S809_G3S809_GORGO_9595 and tr_H2QUM2_H2QUM2_PANTR_9598 are exactly identical!
WARNING: Sequences tr_G3S809_G3S809_GORGO_9595 and sp_Q9Y6H1_CHCH2_HUMAN_9606 are exactly identical!
WARNING: Sequences tr_G3S809_G3S809_GORGO_9595 and tr_A0A2R9CDN1_A0A2R9CDN1_PANPA_9597 are exactly identical!
WARNING: Sequences tr_H2P3S7_H2P3S7_PONAB_9601 and sp_Q8WYQ3_CHC10_HUMAN_9606 are exactly identical!
WARNING: Sequences tr_Q29CD1_Q29CD1_DROPS_46245 and tr_B4GN89_B4GN89_DROPE_7234 are exactly identical!
WARNING: Sequences tr_K7E3Y9_K7E3Y9_MONDO_13616 and tr_G3W4V2_G3W4V2_SARHA_9305 are exactly identical!
WARNING: Sequences tr_E9EUQ7_E9EUQ7_METRA_655844 and tr_A0A0B4HSE4_A0A0B4HSE4_METMF_1276143 are exactly identical!
WARNING: Sequences tr_E9EUQ7_E9EUQ7_METRA_655844 and tr_A0A0D9NP84_A0A0D9NP84_METAN_1291518 are exactly identical!
WARNING: Sequences tr_A1D875_A1D875_NEOFI_331117 and tr_A0A0K8LCG4_A0A0K8LCG4_9EURO_91492 are exactly identical!
WARNING: Sequences tr_A1D875_A1D875_NEOFI_331117 and tr_A0A0S7DIF2_A0A0S7DIF2_9EURO_293939 are exactly identical!
WARNING: Sequences tr_G9MR39_G9MR39_HYPVG_413071 and tr_A0A0F9X837_A0A0F9X837_TRIHA_5544 are exactly identical!
WARNING: Sequences tr_F4NY17_F4NY17_BATDJ_684364 and tr_A0A177WKP6_A0A177WKP6_BATDE_403673 are exactly identical!
WARNING: Sequences tr_H3C8B8_H3C8B8_TETNG_99883 and tr_Q4REM5_Q4REM5_TETNG_99883 are exactly identical!
WARNING: Sequences tr_F9XQF4_F9XQF4_ZYMTI_336722 and tr_A0A1X7S9X3_A0A1X7S9X3_ZYMTR_1276538 are exactly identical!
WARNING: Sequences tr_F2SH76_F2SH76_TRIRC_559305 and tr_A0A178F2A4_A0A178F2A4_TRIRU_5551 are exactly identical!
WARNING: Sequences tr_W7LW60_W7LW60_GIBM7_334819 and tr_N4UI81_N4UI81_FUSC1_1229664 are exactly identical!
WARNING: Sequences tr_W7LW60_W7LW60_GIBM7_334819 and tr_X0D3S6_X0D3S6_FUSOX_1089458 are exactly identical!
WARNING: Sequences tr_W7LW60_W7LW60_GIBM7_334819 and tr_A0A2H3TEN2_A0A2H3TEN2_FUSOX_5507 are exactly identical!
WARNING: Sequences tr_W7LW60_W7LW60_GIBM7_334819 and tr_A0A2H3GUK6_A0A2H3GUK6_FUSOX_327505 are exactly identical!
WARNING: Sequences tr_F2Q5Z1_F2Q5Z1_TRIEC_559882 and tr_A0A059J584_A0A059J584_9EURO_1215338 are exactly identical!
WARNING: Sequences tr_M2SXM6_M2SXM6_COCH5_701091 and tr_W6XZL0_W6XZL0_COCCA_930089 are exactly identical!
WARNING: Sequences tr_U5H227_U5H227_USTV1_683840 and tr_A0A2X0MQ49_A0A2X0MQ49_9BASI_796604 are exactly identical!
WARNING: Sequences tr_V2XE19_V2XE19_MONRO_1381753 and tr_A0A0W0EXB4_A0A0W0EXB4_9AGAR_221103 are exactly identical!
WARNING: Sequences tr_A0A015N7M6_A0A015N7M6_9GLOM_1432141 and tr_A0A2I1DS38_A0A2I1DS38_9GLOM_588596 are exactly identical!
WARNING: Sequences tr_A0A015N7M6_A0A015N7M6_9GLOM_1432141 and tr_A0A2H5SJC6_A0A2H5SJC6_RHIID_747089 are exactly identical!
WARNING: Sequences tr_A0A2K6WJQ8_A0A2K6WJQ8_ONCVO_6282 and tr_A0A182EK97_A0A182EK97_ONCOC_42157 are exactly identical!
WARNING: Sequences tr_A0A094F4J2_A0A094F4J2_9PEZI_1420912 and tr_A0A1B8GU25_A0A1B8GU25_9PEZI_342668 are exactly identical!
WARNING: Sequences tr_A0A0D9RG88_A0A0D9RG88_CHLSB_60711 and tr_A0A2K5KQM5_A0A2K5KQM5_CERAT_9531 are exactly identical!
WARNING: Sequences tr_A0A0D9RG88_A0A0D9RG88_CHLSB_60711 and tr_A0A2K5Z0Q2_A0A2K5Z0Q2_MANLE_9568 are exactly identical!
WARNING: Sequences tr_A0A0A2I4I3_A0A0A2I4I3_PENEN_27334 and tr_A0A0M8NZT8_A0A0M8NZT8_9EURO_229535 are exactly identical!
WARNING: Sequences tr_A0A0F8UZH5_A0A0F8UZH5_9EURO_308745 and tr_A0A2T5M066_A0A2T5M066_9EURO_1392256 are exactly identical!
WARNING: Sequences tr_A0A0M9EZC9_A0A0M9EZC9_FUSLA_179993 and tr_I1RX21_I1RX21_GIBZE_229533 are exactly identical!
WARNING: Sequences tr_A0A0A1PK51_A0A0A1PK51_9FUNG_58291 and tr_A0A367JD66_A0A367JD66_9FUNG_86630 are exactly identical!
WARNING: Sequences tr_A0A0V1CT71_A0A0V1CT71_TRIBR_45882 and tr_A0A0V0VIY9_A0A0V0VIY9_9BILA_181606 are exactly identical!
WARNING: Sequences tr_A0A0V1CT71_A0A0V1CT71_TRIBR_45882 and tr_A0A0V1PEL6_A0A0V1PEL6_9BILA_92180 are exactly identical!
WARNING: Sequences tr_A0A0V1CT71_A0A0V1CT71_TRIBR_45882 and tr_A0A0V0U9E4_A0A0V0U9E4_9BILA_144512 are exactly identical!
WARNING: Sequences tr_A0A0V0WSU1_A0A0V0WSU1_9BILA_92179 and tr_A0A0V1L9Z1_A0A0V1L9Z1_9BILA_6335 are exactly identical!
WARNING: Sequences tr_A0A0P1BKM4_A0A0P1BKM4_9BASI_401625 and tr_A0A316W226_A0A316W226_9BASI_1522189 are exactly identical!
WARNING: Sequences tr_A0A166XFM7_A0A166XFM7_9PEZI_708197 and tr_A0A167DS87_A0A167DS87_9PEZI_1573173 are exactly identical!
WARNING: Sequences tr_A0A194WBK3_A0A194WBK3_9PEZI_105487 and tr_A0A194VFG5_A0A194VFG5_9PEZI_694573 are exactly identical!
WARNING: Sequences tr_A0A1S9DIA3_A0A1S9DIA3_ASPOZ_5062 and tr_A0A2G7FSQ1_A0A2G7FSQ1_9EURO_656916 are exactly identical!
WARNING: Sequences tr_A0A1Y2AZX1_A0A1Y2AZX1_9FUNG_329046 and tr_A0A1Y2BYW3_A0A1Y2BYW3_9FUNG_329046 are exactly identical!
WARNING: Sequences tr_A0A2S7NVY4_A0A2S7NVY4_9HELO_2070414 and tr_A0A2S7PGN4_A0A2S7PGN4_9HELO_2070412 are exactly identical!
WARNING: Sequences tr_A0A2U3V8B9_A0A2U3V8B9_TURTR_9739 and tr_A0A2Y9PD43_A0A2Y9PD43_DELLE_9749 are exactly identical!
WARNING: Sequences tr_A0A2Y9JD31_A0A2Y9JD31_ENHLU_391180 and tr_A0A2Y9JIJ3_A0A2Y9JIJ3_ENHLU_391180 are exactly identical!
WARNING: Sequences tr_A0A384AI86_A0A384AI86_BALAS_310752 and tr_A0A384ASE4_A0A384ASE4_BALAS_310752 are exactly identical!
WARNING: Duplicate sequences found: 50

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/Q9Y6H1/4_raxmlng_ancestral/Q9Y6H1.raxml.reduced.phy

Alignment comprises 1 partitions and 151 sites

Partition 0: noname
Model: LG4X+R4
Alignment sites: 151
Gaps: 19.06 %
Invariant sites: 0.00 %


NOTE: Binary MSA file created: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q9Y6H1/4_raxmlng_ancestral/Q9Y6H1.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/Q9Y6H1/3_mltree/Q9Y6H1.raxml.bestTree_unrooted
[00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 38 / 3040
[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: -51418.659612

[00:00:00 -51418.659612] Initial branch length optimization
[00:00:00 -51007.828749] Model parameter optimization (eps = 0.100000)

[00:00:13] Tree #1, final logLikelihood: -50825.633646


Optimized model parameters:

   Partition 0: noname
   Rate heterogeneity: FREE (4 cats, mean),  weights&rates: (0.145760,0.264046) (0.160313,0.486918) (0.274308,0.743448) (0.419619,1.619373) 
   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/Q9Y6H1/4_raxmlng_ancestral/Q9Y6H1.raxml.ancestralProbs
Reconstructed ancestral sequences saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q9Y6H1/4_raxmlng_ancestral/Q9Y6H1.raxml.ancestralStates
Node-labeled tree saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q9Y6H1/4_raxmlng_ancestral/Q9Y6H1.raxml.ancestralTree

Execution log saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q9Y6H1/4_raxmlng_ancestral/Q9Y6H1.raxml.log

Analysis started: 02-Jun-2021 18:13:01 / finished: 02-Jun-2021 18:13:16

Elapsed time: 14.532 seconds

Consumed energy: 1.254 Wh