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 6258R CPU @ 2.70GHz, 56 cores, 187 GB RAM RAxML-NG was called at 26-Jul-2021 00:10:22 as follows: raxml-ng --msa /truba/home/emrah/WORKFOLDER/PROD/250721_run/phylogeny-snakemake/results/O15049/2_msa/O15049_trimmed_msa.fasta --data-type AA --model LG4X --prefix /truba/home/emrah/WORKFOLDER/PROD/250721_run/phylogeny-snakemake/results/O15049/3_mltree/O15049 --seed 2 --threads 6 --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 (6 threads), thread pinning: OFF [00:00:00] Reading alignment from file: /truba/home/emrah/WORKFOLDER/PROD/250721_run/phylogeny-snakemake/results/O15049/2_msa/O15049_trimmed_msa.fasta [00:00:00] Loaded alignment with 260 taxa and 419 sites WARNING: Sequences tr_A0A1D5PKA5_A0A1D5PKA5_CHICK_9031 and sp_Q5ZLT3_N4BP3_CHICK_9031 are exactly identical! WARNING: Sequences tr_G3QZX8_G3QZX8_GORGO_9595 and tr_H2QJV4_H2QJV4_PANTR_9598 are exactly identical! WARNING: Sequences tr_G3QZX8_G3QZX8_GORGO_9595 and sp_O60299_LZTS3_HUMAN_9606 are exactly identical! WARNING: Sequences tr_G3QZX8_G3QZX8_GORGO_9595 and tr_A0A2R9AK69_A0A2R9AK69_PANPA_9597 are exactly identical! WARNING: Sequences tr_K7CH82_K7CH82_PANTR_9598 and sp_Q9BRK4_LZTS2_HUMAN_9606 are exactly identical! WARNING: Sequences tr_F6QR40_F6QR40_MACMU_9544 and tr_A0A0D9RLH1_A0A0D9RLH1_CHLSB_60711 are exactly identical! WARNING: Sequences tr_F6QR40_F6QR40_MACMU_9544 and tr_A0A2K5P433_A0A2K5P433_CERAT_9531 are exactly identical! WARNING: Sequences tr_F6QR40_F6QR40_MACMU_9544 and tr_A0A2K6B0E1_A0A2K6B0E1_MACNE_9545 are exactly identical! WARNING: Sequences tr_F6QR40_F6QR40_MACMU_9544 and tr_A0A2K5ZXD5_A0A2K5ZXD5_MANLE_9568 are exactly identical! WARNING: Sequences tr_G7P713_G7P713_MACFA_9541 and tr_A0A2K6D085_A0A2K6D085_MACNE_9545 are exactly identical! WARNING: Sequences tr_G7PDS3_G7PDS3_MACFA_9541 and tr_A0A096P6A7_A0A096P6A7_PAPAN_9555 are exactly identical! WARNING: Sequences tr_G7PDS3_G7PDS3_MACFA_9541 and tr_A0A0D9QZR8_A0A0D9QZR8_CHLSB_60711 are exactly identical! WARNING: Sequences tr_G7PDS3_G7PDS3_MACFA_9541 and tr_A0A2K5MC83_A0A2K5MC83_CERAT_9531 are exactly identical! WARNING: Sequences tr_G7PDS3_G7PDS3_MACFA_9541 and tr_A0A2K6B0C4_A0A2K6B0C4_MACNE_9545 are exactly identical! WARNING: Sequences tr_G7PDS3_G7PDS3_MACFA_9541 and tr_A0A2K6ACT0_A0A2K6ACT0_MANLE_9568 are exactly identical! WARNING: Sequences tr_A0A0D9R8M4_A0A0D9R8M4_CHLSB_60711 and tr_A0A2K5M5U5_A0A2K5M5U5_CERAT_9531 are exactly identical! WARNING: Sequences tr_A0A2Y9PSM0_A0A2Y9PSM0_DELLE_9749 and tr_A0A2Y9SAS0_A0A2Y9SAS0_PHYCD_9755 are exactly identical! WARNING: Sequences tr_A0A2Y9PSM0_A0A2Y9PSM0_DELLE_9749 and tr_A0A384B869_A0A384B869_BALAS_310752 are exactly identical! WARNING: Duplicate sequences found: 18 NOTE: Reduced alignment (with duplicates and gap-only sites/taxa removed) NOTE: was saved to: /truba/home/emrah/WORKFOLDER/PROD/250721_run/phylogeny-snakemake/results/O15049/3_mltree/O15049.raxml.reduced.phy Alignment comprises 1 partitions and 419 patterns Partition 0: noname Model: LG4X+R4 Alignment sites / patterns: 419 / 419 Gaps: 7.98 % Invariant sites: 1.43 % NOTE: Binary MSA file created: /truba/home/emrah/WORKFOLDER/PROD/250721_run/phylogeny-snakemake/results/O15049/3_mltree/O15049.raxml.rba Parallelization scheme autoconfig: 3 worker(s) x 2 thread(s) Parallel reduction/worker buffer size: 1 KB / 0 KB [00:00:00] Generating 20 random starting tree(s) with 260 taxa [00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 210 / 16800 [00:00:00] Data distribution: max. searches per worker: 7 Starting ML tree search with 20 distinct starting trees [00:00:00 -171009.473822] Initial branch length optimization [00:00:01 -139861.028810] Model parameter optimization (eps = 10.000000) [00:00:19 -139466.942274] AUTODETECT spr round 1 (radius: 5) [00:00:46 -75828.392903] AUTODETECT spr round 2 (radius: 10) [00:01:20 -58534.531373] AUTODETECT spr round 3 (radius: 15) [00:02:09 -47693.118080] AUTODETECT spr round 4 (radius: 20) [00:02:59 -45294.203459] AUTODETECT spr round 5 (radius: 25) [00:03:49 -45263.098594] SPR radius for FAST iterations: 25 (autodetect) [00:03:49 -45263.098594] Model parameter optimization (eps = 3.000000) [00:04:04 -45149.594085] FAST spr round 1 (radius: 25) [00:04:42 -40520.374771] FAST spr round 2 (radius: 25) [00:05:13 -40293.490090] FAST spr round 3 (radius: 25) [00:05:41 -40271.259878] FAST spr round 4 (radius: 25) [00:06:01 -40268.391431] FAST spr round 5 (radius: 25) [00:06:21 -40268.368006] Model parameter optimization (eps = 1.000000) [00:06:28 -40265.726605] SLOW spr round 1 (radius: 5) [00:07:10 -40263.404174] SLOW spr round 2 (radius: 5) [00:07:47 -40263.403878] SLOW spr round 3 (radius: 10) [00:08:26 -40263.119567] SLOW spr round 4 (radius: 5) [00:09:24 -40263.119461] SLOW spr round 5 (radius: 10) [00:10:15 -40263.119458] SLOW spr round 6 (radius: 15) [00:11:04] [worker #1] ML tree search #2, logLikelihood: -40266.820900 [00:11:28 -40263.003781] SLOW spr round 7 (radius: 5) [00:12:31 -40263.003754] SLOW spr round 8 (radius: 10) [00:13:16] [worker #2] ML tree search #3, logLikelihood: -40257.403718 [00:13:29 -40263.003754] SLOW spr round 9 (radius: 15) [00:14:41 -40263.003754] SLOW spr round 10 (radius: 20) [00:16:04 -40263.003754] SLOW spr round 11 (radius: 25) [00:17:19 -40263.003754] Model parameter optimization (eps = 0.100000) [00:17:22] [worker #0] ML tree search #1, logLikelihood: -40262.983075 [00:17:22 -170079.193617] Initial branch length optimization [00:17:24 -139207.413146] Model parameter optimization (eps = 10.000000) [00:17:42 -138864.832869] AUTODETECT spr round 1 (radius: 5) [00:18:09 -75428.246662] AUTODETECT spr round 2 (radius: 10) [00:18:40 -53705.700590] AUTODETECT spr round 3 (radius: 15) [00:19:31 -45384.632077] AUTODETECT spr round 4 (radius: 20) [00:20:16 -45279.858483] AUTODETECT spr round 5 (radius: 25) [00:20:59 -45279.849562] SPR radius for FAST iterations: 20 (autodetect) [00:20:59 -45279.849562] Model parameter optimization (eps = 3.000000) [00:21:15 -45124.048703] FAST spr round 1 (radius: 20) [00:21:53 -40498.111442] FAST spr round 2 (radius: 20) [00:22:22 -40292.584185] FAST spr round 3 (radius: 20) [00:22:45 -40278.876189] FAST spr round 4 (radius: 20) [00:23:05 -40278.876122] Model parameter optimization (eps = 1.000000) [00:23:13 -40273.035326] SLOW spr round 1 (radius: 5) [00:23:53 -40270.542753] SLOW spr round 2 (radius: 5) [00:24:27] [worker #1] ML tree search #5, logLikelihood: -40256.657642 [00:24:29 -40270.542486] SLOW spr round 3 (radius: 10) [00:25:08 -40270.369126] SLOW spr round 4 (radius: 5) [00:26:07 -40270.369047] SLOW spr round 5 (radius: 10) [00:26:53] [worker #2] ML tree search #6, logLikelihood: -40261.458042 [00:27:01 -40270.369018] SLOW spr round 6 (radius: 15) [00:28:16 -40270.369005] SLOW spr round 7 (radius: 20) [00:29:35 -40270.368999] SLOW spr round 8 (radius: 25) [00:30:54 -40270.368996] Model parameter optimization (eps = 0.100000) [00:30:57] [worker #0] ML tree search #4, logLikelihood: -40270.363318 [00:30:57 -168223.767690] Initial branch length optimization [00:30:59 -137636.348574] Model parameter optimization (eps = 10.000000) [00:31:17 -137308.923218] AUTODETECT spr round 1 (radius: 5) [00:31:44 -70778.942972] AUTODETECT spr round 2 (radius: 10) [00:32:16 -55324.588894] AUTODETECT spr round 3 (radius: 15) [00:33:01 -46001.804887] AUTODETECT spr round 4 (radius: 20) [00:33:50 -44665.112548] AUTODETECT spr round 5 (radius: 25) [00:34:35 -44665.108423] SPR radius for FAST iterations: 20 (autodetect) [00:34:35 -44665.108423] Model parameter optimization (eps = 3.000000) [00:34:53 -44539.942098] FAST spr round 1 (radius: 20) [00:35:29 -40547.048896] FAST spr round 2 (radius: 20) [00:36:00 -40290.963625] FAST spr round 3 (radius: 20) [00:36:23 -40280.784489] FAST spr round 4 (radius: 20) [00:36:43 -40276.862745] FAST spr round 5 (radius: 20) [00:37:02 -40276.862611] Model parameter optimization (eps = 1.000000) [00:37:09 -40274.329196] SLOW spr round 1 (radius: 5) [00:37:51 -40267.446326] SLOW spr round 2 (radius: 5) [00:38:32 -40262.292051] SLOW spr round 3 (radius: 5) [00:38:58] [worker #1] ML tree search #8, logLikelihood: -40256.308378 [00:39:09 -40262.291963] SLOW spr round 4 (radius: 10) [00:39:47 -40262.160681] SLOW spr round 5 (radius: 5) [00:39:59] [worker #2] ML tree search #9, logLikelihood: -40257.015385 [00:40:47 -40262.160653] SLOW spr round 6 (radius: 10) [00:41:39 -40262.160653] SLOW spr round 7 (radius: 15) [00:42:52 -40262.160653] SLOW spr round 8 (radius: 20) [00:44:14 -40262.160653] SLOW spr round 9 (radius: 25) [00:45:34 -40262.160653] Model parameter optimization (eps = 0.100000) [00:45:37] [worker #0] ML tree search #7, logLikelihood: -40262.111148 [00:45:37 -167461.555899] Initial branch length optimization [00:45:38 -136807.437378] Model parameter optimization (eps = 10.000000) [00:45:59 -136420.288917] AUTODETECT spr round 1 (radius: 5) [00:46:27 -75240.194602] AUTODETECT spr round 2 (radius: 10) [00:47:01 -55619.840356] AUTODETECT spr round 3 (radius: 15) [00:47:37 -49920.041865] AUTODETECT spr round 4 (radius: 20) [00:48:48 -45714.792346] AUTODETECT spr round 5 (radius: 25) [00:49:46 -45688.527480] SPR radius for FAST iterations: 25 (autodetect) [00:49:46 -45688.527480] Model parameter optimization (eps = 3.000000) [00:50:02 -45596.057693] FAST spr round 1 (radius: 25) [00:50:32 -40640.229891] FAST spr round 2 (radius: 25) [00:51:00 -40318.447816] FAST spr round 3 (radius: 25) [00:51:25 -40297.464419] FAST spr round 4 (radius: 25) [00:51:44 -40297.464072] Model parameter optimization (eps = 1.000000) [00:51:56 -40277.005834] SLOW spr round 1 (radius: 5) [00:52:35] [worker #1] ML tree search #11, logLikelihood: -40264.943840 [00:52:36 -40273.068037] SLOW spr round 2 (radius: 5) [00:53:14 -40273.067918] SLOW spr round 3 (radius: 10) [00:53:53 -40270.151007] SLOW spr round 4 (radius: 5) [00:54:35] [worker #2] ML tree search #12, logLikelihood: -40262.904240 [00:54:53 -40270.150953] SLOW spr round 5 (radius: 10) [00:55:46 -40270.150953] SLOW spr round 6 (radius: 15) [00:57:00 -40270.150953] SLOW spr round 7 (radius: 20) [00:58:17 -40270.150953] SLOW spr round 8 (radius: 25) [00:59:38 -40270.150953] Model parameter optimization (eps = 0.100000) [00:59:41] [worker #0] ML tree search #10, logLikelihood: -40270.146176 [00:59:41 -168606.194556] Initial branch length optimization [00:59:42 -136481.069106] Model parameter optimization (eps = 10.000000) [01:00:04 -136195.268010] AUTODETECT spr round 1 (radius: 5) [01:00:31 -76643.770772] AUTODETECT spr round 2 (radius: 10) [01:01:07 -53902.764391] AUTODETECT spr round 3 (radius: 15) [01:01:52 -46584.775409] AUTODETECT spr round 4 (radius: 20) [01:02:41 -46418.344725] AUTODETECT spr round 5 (radius: 25) [01:03:34 -46418.315140] SPR radius for FAST iterations: 20 (autodetect) [01:03:34 -46418.315140] Model parameter optimization (eps = 3.000000) [01:03:50 -46339.991464] FAST spr round 1 (radius: 20) [01:04:28 -40470.742034] FAST spr round 2 (radius: 20) [01:04:58 -40312.043686] FAST spr round 3 (radius: 20) [01:05:19 -40300.331639] FAST spr round 4 (radius: 20) [01:05:38 -40300.331628] Model parameter optimization (eps = 1.000000) [01:05:47 -40276.766439] SLOW spr round 1 (radius: 5) [01:06:23] [worker #2] ML tree search #15, logLikelihood: -40262.442510 [01:06:30 -40260.352609] SLOW spr round 2 (radius: 5) [01:06:42] [worker #1] ML tree search #14, logLikelihood: -40257.162938 [01:07:07 -40259.930620] SLOW spr round 3 (radius: 5) [01:07:43 -40259.930580] SLOW spr round 4 (radius: 10) [01:08:23 -40257.238570] SLOW spr round 5 (radius: 5) [01:09:23 -40257.070706] SLOW spr round 6 (radius: 5) [01:10:11 -40257.070626] SLOW spr round 7 (radius: 10) [01:10:55 -40257.070605] SLOW spr round 8 (radius: 15) [01:12:08 -40257.070597] SLOW spr round 9 (radius: 20) [01:13:26 -40257.070594] SLOW spr round 10 (radius: 25) [01:14:43 -40257.070593] Model parameter optimization (eps = 0.100000) [01:14:48] [worker #0] ML tree search #13, logLikelihood: -40257.015416 [01:14:48 -165867.869444] Initial branch length optimization [01:14:49 -134010.761342] Model parameter optimization (eps = 10.000000) [01:15:10 -133607.399196] AUTODETECT spr round 1 (radius: 5) [01:15:37 -75432.432620] AUTODETECT spr round 2 (radius: 10) [01:16:09 -55204.582960] AUTODETECT spr round 3 (radius: 15) [01:16:55 -46644.058662] AUTODETECT spr round 4 (radius: 20) [01:17:55 -45907.703666] AUTODETECT spr round 5 (radius: 25) [01:18:51 -45907.676500] SPR radius for FAST iterations: 20 (autodetect) [01:18:51 -45907.676500] Model parameter optimization (eps = 3.000000) [01:19:05 -45778.378321] FAST spr round 1 (radius: 20) [01:19:43 -40442.796083] FAST spr round 2 (radius: 20) [01:20:15 -40291.993220] FAST spr round 3 (radius: 20) [01:20:25] [worker #2] ML tree search #18, logLikelihood: -40256.010946 [01:20:40 -40269.878135] FAST spr round 4 (radius: 20) [01:20:45] [worker #1] ML tree search #17, logLikelihood: -40259.617606 [01:21:00 -40269.877944] Model parameter optimization (eps = 1.000000) [01:21:07 -40265.514551] SLOW spr round 1 (radius: 5) [01:21:51 -40260.443479] SLOW spr round 2 (radius: 5) [01:22:29 -40260.443199] SLOW spr round 3 (radius: 10) [01:23:07 -40260.339078] SLOW spr round 4 (radius: 5) [01:24:06 -40260.339016] SLOW spr round 5 (radius: 10) [01:24:58 -40260.338994] SLOW spr round 6 (radius: 15) [01:26:10 -40260.338983] SLOW spr round 7 (radius: 20) [01:27:28 -40260.338979] SLOW spr round 8 (radius: 25) [01:28:48 -40260.338977] Model parameter optimization (eps = 0.100000) [01:28:51] [worker #0] ML tree search #16, logLikelihood: -40260.333799 [01:28:51 -167570.672936] Initial branch length optimization [01:28:52 -136253.666850] Model parameter optimization (eps = 10.000000) [01:29:11 -135912.840151] AUTODETECT spr round 1 (radius: 5) [01:29:38 -70807.552952] AUTODETECT spr round 2 (radius: 10) [01:30:14 -52958.412985] AUTODETECT spr round 3 (radius: 15) [01:31:01 -45837.841031] AUTODETECT spr round 4 (radius: 20) [01:31:55 -44519.483842] AUTODETECT spr round 5 (radius: 25) [01:32:46 -44509.382000] SPR radius for FAST iterations: 25 (autodetect) [01:32:46 -44509.382000] Model parameter optimization (eps = 3.000000) [01:32:58 -44345.536229] FAST spr round 1 (radius: 25) [01:33:39 -40401.110051] FAST spr round 2 (radius: 25) [01:34:08 -40270.787965] FAST spr round 3 (radius: 25) [01:34:30 -40267.443052] FAST spr round 4 (radius: 25) [01:34:49 -40267.442967] Model parameter optimization (eps = 1.000000) [01:34:56 -40266.419087] SLOW spr round 1 (radius: 5) [01:34:58] [worker #1] ML tree search #20, logLikelihood: -40256.643139 [01:35:37 -40264.003167] SLOW spr round 2 (radius: 5) [01:36:13 -40264.002834] SLOW spr round 3 (radius: 10) [01:36:52 -40263.895658] SLOW spr round 4 (radius: 5) [01:37:52 -40263.895539] SLOW spr round 5 (radius: 10) [01:38:45 -40263.895510] SLOW spr round 6 (radius: 15) [01:39:55 -40263.895497] SLOW spr round 7 (radius: 20) [01:41:12 -40263.895491] SLOW spr round 8 (radius: 25) [01:42:35 -40263.895489] Model parameter optimization (eps = 0.100000) [01:42:39] [worker #0] ML tree search #19, logLikelihood: -40263.885345 Optimized model parameters: Partition 0: noname Rate heterogeneity: FREE (4 cats, mean), weights&rates: (0.216615,0.461852) (0.094946,0.904248) (0.402893,0.788268) (0.285546,1.738820) 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: -40256.010946 AIC score: 81558.021891 / AICc score: 629662.021891 / BIC score: 83669.828382 Free parameters (model + branch lengths): 523 WARNING: Number of free parameters (K=523) is larger than alignment size (n=419). This might lead to overfitting and compromise tree inference results! WARNING: Best ML tree contains 40 near-zero branches! Best ML tree with collapsed near-zero branches saved to: /truba/home/emrah/WORKFOLDER/PROD/250721_run/phylogeny-snakemake/results/O15049/3_mltree/O15049.raxml.bestTreeCollapsed Best ML tree saved to: /truba/home/emrah/WORKFOLDER/PROD/250721_run/phylogeny-snakemake/results/O15049/3_mltree/O15049.raxml.bestTree All ML trees saved to: /truba/home/emrah/WORKFOLDER/PROD/250721_run/phylogeny-snakemake/results/O15049/3_mltree/O15049.raxml.mlTrees Optimized model saved to: /truba/home/emrah/WORKFOLDER/PROD/250721_run/phylogeny-snakemake/results/O15049/3_mltree/O15049.raxml.bestModel Execution log saved to: /truba/home/emrah/WORKFOLDER/PROD/250721_run/phylogeny-snakemake/results/O15049/3_mltree/O15049.raxml.log Analysis started: 26-Jul-2021 00:10:22 / finished: 26-Jul-2021 01:53:01 Elapsed time: 6159.428 seconds Consumed energy: 359.222 Wh (= 2 km in an electric car, or 9 km with an e-scooter!)