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 05-Jul-2021 23:37:23 as follows: raxml-ng --msa /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q5TH74/2_msa/Q5TH74_trimmed_msa.fasta --data-type AA --model LG4X --prefix /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q5TH74/3_mltree/Q5TH74 --seed 2 --threads 5 --tree rand{20} pars{20} Analysis options: run mode: ML tree search start tree(s): random (20) random seed: 2 tip-inner: OFF pattern compression: ON per-rate scalers: OFF site repeats: ON fast spr radius: AUTO spr subtree cutoff: 1.000000 branch lengths: proportional (ML estimate, algorithm: NR-FAST) SIMD kernels: AVX2 parallelization: coarse-grained (auto), PTHREADS (5 threads), thread pinning: OFF [00:00:00] Reading alignment from file: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q5TH74/2_msa/Q5TH74_trimmed_msa.fasta [00:00:00] Loaded alignment with 90 taxa and 333 sites WARNING: Sequences tr_A0A2J8K3V6_A0A2J8K3V6_PANTR_9598 and tr_A0A2R8ZDR7_A0A2R8ZDR7_PANPA_9597 are exactly identical! WARNING: Sequences tr_B3S188_B3S188_TRIAD_10228 and tr_A0A369S9S5_A0A369S9S5_9METZ_287889 are exactly identical! WARNING: Sequences tr_A0A2I4D424_A0A2I4D424_9TELE_52670 and tr_A0A2I4D546_A0A2I4D546_9TELE_52670 are exactly identical! WARNING: Sequences tr_A0A2K5LF57_A0A2K5LF57_CERAT_9531 and tr_A0A2K5ZXQ5_A0A2K5ZXQ5_MANLE_9568 are exactly identical! WARNING: Duplicate sequences found: 4 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/Q5TH74/3_mltree/Q5TH74.raxml.reduced.phy Alignment comprises 1 partitions and 333 patterns Partition 0: noname Model: LG4X+R4 Alignment sites / patterns: 333 / 333 Gaps: 10.45 % Invariant sites: 3.00 % NOTE: Binary MSA file created: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q5TH74/3_mltree/Q5TH74.raxml.rba Parallelization scheme autoconfig: 5 worker(s) x 1 thread(s) Parallel reduction/worker buffer size: 1 KB / 0 KB [00:00:00] Generating 20 random starting tree(s) with 90 taxa [00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 333 / 26640 [00:00:00] Data distribution: max. searches per worker: 4 Starting ML tree search with 20 distinct starting trees [00:00:00 -42108.127383] Initial branch length optimization [00:00:00 -33340.236653] Model parameter optimization (eps = 10.000000) [00:00:04 -33252.063774] AUTODETECT spr round 1 (radius: 5) [00:00:09 -28449.317067] AUTODETECT spr round 2 (radius: 10) [00:00:15 -24018.309230] AUTODETECT spr round 3 (radius: 15) [00:00:21 -24017.921520] AUTODETECT spr round 4 (radius: 20) [00:00:26 -24017.910314] SPR radius for FAST iterations: 15 (autodetect) [00:00:26 -24017.910314] Model parameter optimization (eps = 3.000000) [00:00:32 -23954.399363] FAST spr round 1 (radius: 15) [00:00:39 -23196.531845] FAST spr round 2 (radius: 15) [00:00:46 -23060.544625] FAST spr round 3 (radius: 15) [00:00:51 -23055.907124] FAST spr round 4 (radius: 15) [00:00:56 -23055.361815] FAST spr round 5 (radius: 15) [00:01:01 -23054.841848] FAST spr round 6 (radius: 15) [00:01:06 -23050.401586] FAST spr round 7 (radius: 15) [00:01:11 -23050.399648] Model parameter optimization (eps = 1.000000) [00:01:12 -23049.755714] SLOW spr round 1 (radius: 5) [00:01:24 -23047.061483] SLOW spr round 2 (radius: 5) [00:01:34 -23047.061047] SLOW spr round 3 (radius: 10) [00:01:44 -23045.641747] SLOW spr round 4 (radius: 5) [00:01:58 -23045.641680] SLOW spr round 5 (radius: 10) [00:02:09 -23045.641679] SLOW spr round 6 (radius: 15) [00:02:10] [worker #4] ML tree search #5, logLikelihood: -23045.631071 [00:02:10] [worker #3] ML tree search #4, logLikelihood: -23038.320445 [00:02:14] [worker #2] ML tree search #3, logLikelihood: -23041.512883 [00:02:15] [worker #1] ML tree search #2, logLikelihood: -23038.904279 [00:02:19 -23045.641679] SLOW spr round 7 (radius: 20) [00:02:29 -23045.641679] SLOW spr round 8 (radius: 25) [00:02:39 -23045.641679] Model parameter optimization (eps = 0.100000) [00:02:40] [worker #0] ML tree search #1, logLikelihood: -23045.604106 [00:02:40 -43146.189207] Initial branch length optimization [00:02:40 -33416.832283] Model parameter optimization (eps = 10.000000) [00:02:46 -33324.804610] AUTODETECT spr round 1 (radius: 5) [00:02:50 -28058.884048] AUTODETECT spr round 2 (radius: 10) [00:02:57 -25696.838612] AUTODETECT spr round 3 (radius: 15) [00:03:05 -25539.210720] AUTODETECT spr round 4 (radius: 20) [00:03:11 -25538.177604] AUTODETECT spr round 5 (radius: 25) [00:03:16 -25538.116330] SPR radius for FAST iterations: 20 (autodetect) [00:03:16 -25538.116330] Model parameter optimization (eps = 3.000000) [00:03:20 -25484.274632] FAST spr round 1 (radius: 20) [00:03:28 -23112.013404] FAST spr round 2 (radius: 20) [00:03:34 -23062.776309] FAST spr round 3 (radius: 20) [00:03:39 -23054.260790] FAST spr round 4 (radius: 20) [00:03:44 -23052.295828] FAST spr round 5 (radius: 20) [00:03:48 -23052.295466] Model parameter optimization (eps = 1.000000) [00:03:52 -23044.171187] SLOW spr round 1 (radius: 5) [00:04:05 -23038.382795] SLOW spr round 2 (radius: 5) [00:04:09] [worker #1] ML tree search #7, logLikelihood: -23042.048675 [00:04:13] [worker #4] ML tree search #10, logLikelihood: -23041.508538 [00:04:15 -23038.382682] SLOW spr round 3 (radius: 10) [00:04:20] [worker #2] ML tree search #8, logLikelihood: -23046.446439 [00:04:25 -23038.382671] SLOW spr round 4 (radius: 15) [00:04:35 -23038.382670] SLOW spr round 5 (radius: 20) [00:04:45 -23038.382670] SLOW spr round 6 (radius: 25) [00:04:48] [worker #3] ML tree search #9, logLikelihood: -23045.866257 [00:04:55 -23038.382670] Model parameter optimization (eps = 0.100000) [00:04:57] [worker #0] ML tree search #6, logLikelihood: -23038.316544 [00:04:57 -42774.190547] Initial branch length optimization [00:04:57 -33210.907398] Model parameter optimization (eps = 10.000000) [00:05:02 -33126.111981] AUTODETECT spr round 1 (radius: 5) [00:05:07 -27986.277472] AUTODETECT spr round 2 (radius: 10) [00:05:13 -24889.617070] AUTODETECT spr round 3 (radius: 15) [00:05:20 -24637.460223] AUTODETECT spr round 4 (radius: 20) [00:05:24 -24637.453399] SPR radius for FAST iterations: 15 (autodetect) [00:05:24 -24637.453399] Model parameter optimization (eps = 3.000000) [00:05:29 -24585.770938] FAST spr round 1 (radius: 15) [00:05:37 -23066.833747] FAST spr round 2 (radius: 15) [00:05:42 -23059.329590] FAST spr round 3 (radius: 15) [00:05:47 -23053.913702] FAST spr round 4 (radius: 15) [00:05:52 -23051.350180] FAST spr round 5 (radius: 15) [00:05:57 -23051.115440] FAST spr round 6 (radius: 15) [00:06:02 -23051.076867] Model parameter optimization (eps = 1.000000) [00:06:05 -23049.064081] SLOW spr round 1 (radius: 5) [00:06:14] [worker #1] ML tree search #12, logLikelihood: -23045.820627 [00:06:17 -23049.060559] SLOW spr round 2 (radius: 10) [00:06:21] [worker #2] ML tree search #13, logLikelihood: -23038.473641 [00:06:26 -23042.765876] SLOW spr round 3 (radius: 5) [00:06:33] [worker #4] ML tree search #15, logLikelihood: -23038.473611 [00:06:42 -23040.272767] SLOW spr round 4 (radius: 5) [00:06:54 -23040.271937] SLOW spr round 5 (radius: 10) [00:06:57] [worker #3] ML tree search #14, logLikelihood: -23047.025125 [00:07:04 -23040.271847] SLOW spr round 6 (radius: 15) [00:07:14 -23040.271822] SLOW spr round 7 (radius: 20) [00:07:25 -23040.271817] SLOW spr round 8 (radius: 25) [00:07:34 -23040.271816] Model parameter optimization (eps = 0.100000) [00:07:35] [worker #0] ML tree search #11, logLikelihood: -23040.249270 [00:07:35 -42026.943820] Initial branch length optimization [00:07:36 -33201.737864] Model parameter optimization (eps = 10.000000) [00:07:41 -33103.079323] AUTODETECT spr round 1 (radius: 5) [00:07:45 -28254.717615] AUTODETECT spr round 2 (radius: 10) [00:07:52 -25551.690187] AUTODETECT spr round 3 (radius: 15) [00:07:59 -25350.900761] AUTODETECT spr round 4 (radius: 20) [00:08:04 -25349.327346] AUTODETECT spr round 5 (radius: 25) [00:08:07 -25349.258097] SPR radius for FAST iterations: 20 (autodetect) [00:08:07 -25349.258097] Model parameter optimization (eps = 3.000000) [00:08:13 -25315.082184] FAST spr round 1 (radius: 20) [00:08:21 -23078.735230] FAST spr round 2 (radius: 20) [00:08:27 -23053.838193] FAST spr round 3 (radius: 20) [00:08:28] [worker #1] ML tree search #17, logLikelihood: -23038.473809 [00:08:31 -23051.546680] FAST spr round 4 (radius: 20) [00:08:36 -23046.933087] FAST spr round 5 (radius: 20) [00:08:38] [worker #2] ML tree search #18, logLikelihood: -23038.320481 [00:08:41 -23046.732871] FAST spr round 6 (radius: 20) [00:08:46 -23046.732771] Model parameter optimization (eps = 1.000000) [00:08:49 -23039.029131] SLOW spr round 1 (radius: 5) [00:08:52] [worker #4] ML tree search #20, logLikelihood: -23038.316180 [00:09:00 -23038.474971] SLOW spr round 2 (radius: 5) [00:09:05] [worker #3] ML tree search #19, logLikelihood: -23038.316462 [00:09:11 -23038.474063] SLOW spr round 3 (radius: 10) [00:09:20 -23038.473955] SLOW spr round 4 (radius: 15) [00:09:31 -23038.473942] SLOW spr round 5 (radius: 20) [00:09:41 -23038.473941] SLOW spr round 6 (radius: 25) [00:09:51 -23038.473941] Model parameter optimization (eps = 0.100000) [00:09:51] [worker #0] ML tree search #16, logLikelihood: -23038.473576 Optimized model parameters: Partition 0: noname Rate heterogeneity: FREE (4 cats, mean), weights&rates: (0.162559,0.422556) (0.169874,0.493613) (0.386302,0.907857) (0.281265,1.766131) 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 Final LogLikelihood: -23038.316180 AIC score: 46442.632360 / AICc score: 46894.605514 / BIC score: 47139.522436 Free parameters (model + branch lengths): 183 WARNING: Best ML tree contains 4 near-zero branches! Best ML tree with collapsed near-zero branches saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q5TH74/3_mltree/Q5TH74.raxml.bestTreeCollapsed Best ML tree saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q5TH74/3_mltree/Q5TH74.raxml.bestTree All ML trees saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q5TH74/3_mltree/Q5TH74.raxml.mlTrees Optimized model saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q5TH74/3_mltree/Q5TH74.raxml.bestModel Execution log saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q5TH74/3_mltree/Q5TH74.raxml.log Analysis started: 05-Jul-2021 23:37:23 / finished: 05-Jul-2021 23:47:14 Elapsed time: 591.479 seconds