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 30-Jun-2021 17:32:27 as follows: raxml-ng --msa /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/P61266/2_msa/P61266_trimmed_msa.fasta --data-type AA --model LG4X --prefix /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/P61266/3_mltree/P61266 --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/300621_run/phylogeny-snakemake/results/P61266/2_msa/P61266_trimmed_msa.fasta [00:00:00] Loaded alignment with 1001 taxa and 286 sites WARNING: Sequences sp_P61264_STX1B_MOUSE_10090 and tr_H2NQR3_H2NQR3_PONAB_9601 are exactly identical! WARNING: Sequences sp_P61264_STX1B_MOUSE_10090 and sp_P61265_STX1B_RAT_10116 are exactly identical! WARNING: Sequences sp_P61264_STX1B_MOUSE_10090 and tr_A0A286Y5U2_A0A286Y5U2_CAVPO_10141 are exactly identical! WARNING: Sequences sp_P61264_STX1B_MOUSE_10090 and sp_P61266_STX1B_HUMAN_9606 are exactly identical! WARNING: Sequences sp_P61264_STX1B_MOUSE_10090 and tr_G3WBG9_G3WBG9_SARHA_9305 are exactly identical! WARNING: Sequences sp_P61264_STX1B_MOUSE_10090 and tr_F7IJH5_F7IJH5_CALJA_9483 are exactly identical! WARNING: Sequences sp_P61264_STX1B_MOUSE_10090 and tr_I3LIF3_I3LIF3_PIG_9823 are exactly identical! WARNING: Sequences sp_P61264_STX1B_MOUSE_10090 and tr_M3VYT5_M3VYT5_FELCA_9685 are exactly identical! WARNING: Sequences sp_P61264_STX1B_MOUSE_10090 and tr_A0A096NHX1_A0A096NHX1_PAPAN_9555 are exactly identical! WARNING: Sequences sp_P61264_STX1B_MOUSE_10090 and tr_A0A1S3A6C4_A0A1S3A6C4_ERIEU_9365 are exactly identical! WARNING: Sequences sp_P61264_STX1B_MOUSE_10090 and tr_A0A1U7QEE5_A0A1U7QEE5_MESAU_10036 are exactly identical! WARNING: Sequences sp_P61264_STX1B_MOUSE_10090 and tr_A0A2K5LR11_A0A2K5LR11_CERAT_9531 are exactly identical! WARNING: Sequences sp_P61264_STX1B_MOUSE_10090 and tr_A0A2K6C390_A0A2K6C390_MACNE_9545 are exactly identical! WARNING: Sequences sp_P61264_STX1B_MOUSE_10090 and tr_A0A2U3VQ61_A0A2U3VQ61_ODORO_9708 are exactly identical! WARNING: Sequences sp_P61264_STX1B_MOUSE_10090 and tr_A0A2Y9E5F4_A0A2Y9E5F4_TRIMA_127582 are exactly identical! WARNING: Sequences sp_P61264_STX1B_MOUSE_10090 and tr_A0A2Y9LFG8_A0A2Y9LFG8_ENHLU_391180 are exactly identical! WARNING: Sequences sp_P61264_STX1B_MOUSE_10090 and tr_A0A2Y9PMM4_A0A2Y9PMM4_DELLE_9749 are exactly identical! WARNING: Sequences sp_P61264_STX1B_MOUSE_10090 and tr_A0A384AGM1_A0A384AGM1_BALAS_310752 are exactly identical! WARNING: Sequences tr_M3YXB5_M3YXB5_MUSPF_9669 and tr_A0A2U3YJM9_A0A2U3YJM9_LEPWE_9713 are exactly identical! WARNING: Sequences sp_Q24547_STX1A_DROME_7227 and tr_B3MST1_B3MST1_DROAN_7217 are exactly identical! WARNING: Sequences sp_Q24547_STX1A_DROME_7227 and tr_A0A1W4V491_A0A1W4V491_DROFC_30025 are exactly identical! WARNING: Sequences tr_A0A2I3GV88_A0A2I3GV88_NOMLE_61853 and tr_G3RW61_G3RW61_GORGO_9595 are exactly identical! WARNING: Sequences tr_A0A2I3GV88_A0A2I3GV88_NOMLE_61853 and tr_A0A2R9C857_A0A2R9C857_PANPA_9597 are exactly identical! WARNING: Sequences tr_G3HA06_G3HA06_CRIGR_10029 and tr_A0A091DYF5_A0A091DYF5_FUKDA_885580 are exactly identical! WARNING: Sequences tr_D8STJ9_D8STJ9_SELML_88036 and tr_D8T570_D8T570_SELML_88036 are exactly identical! WARNING: Sequences tr_G3QGI1_G3QGI1_GORGO_9595 and tr_A0A2R9CKT4_A0A2R9CKT4_PANPA_9597 are exactly identical! WARNING: Sequences tr_G3QJH0_G3QJH0_GORGO_9595 and tr_K7BT43_K7BT43_PANTR_9598 are exactly identical! WARNING: Sequences tr_G3QJH0_G3QJH0_GORGO_9595 and sp_Q12846_STX4_HUMAN_9606 are exactly identical! WARNING: Sequences tr_G3QJH0_G3QJH0_GORGO_9595 and tr_A0A2R9AY94_A0A2R9AY94_PANPA_9597 are exactly identical! WARNING: Sequences tr_G3R0G3_G3R0G3_GORGO_9595 and sp_Q8N4C7_STX19_HUMAN_9606 are exactly identical! WARNING: Sequences tr_Q298K6_Q298K6_DROPS_46245 and tr_B4G427_B4G427_DROPE_7234 are exactly identical! WARNING: Sequences tr_F1PGE7_F1PGE7_CANLF_9615 and tr_F6WJB1_F6WJB1_MONDO_13616 are exactly identical! WARNING: Sequences tr_F1PGE7_F1PGE7_CANLF_9615 and tr_A0A091DZ25_A0A091DZ25_FUKDA_885580 are exactly identical! WARNING: Sequences tr_A0A2I3TFT0_A0A2I3TFT0_PANTR_9598 and tr_H2QUQ1_H2QUQ1_PANTR_9598 are exactly identical! WARNING: Sequences tr_A0A2I3TFT0_A0A2I3TFT0_PANTR_9598 and sp_Q16623_STX1A_HUMAN_9606 are exactly identical! WARNING: Sequences tr_A0A2I3TFT0_A0A2I3TFT0_PANTR_9598 and tr_F6Z4V9_F6Z4V9_CALJA_9483 are exactly identical! WARNING: Sequences tr_H2Q3R5_H2Q3R5_PANTR_9598 and tr_A0A2R8ZBM7_A0A2R8ZBM7_PANPA_9597 are exactly identical! WARNING: Sequences tr_H2QTV4_H2QTV4_PANTR_9598 and tr_A0A2R8ZCY5_A0A2R8ZCY5_PANPA_9597 are exactly identical! WARNING: Sequences sp_P61268_STX1B_SHEEP_9940 and sp_P61267_STX1B_BOVIN_9913 are exactly identical! WARNING: Sequences tr_A0A3B5PSS4_A0A3B5PSS4_XIPMA_8083 and tr_A0A087XQV4_A0A087XQV4_POEFO_48698 are exactly identical! WARNING: Sequences tr_A0A1D5QEM1_A0A1D5QEM1_MACMU_9544 and tr_A0A2I3MB23_A0A2I3MB23_PAPAN_9555 are exactly identical! WARNING: Sequences tr_A0A1D5QEM1_A0A1D5QEM1_MACMU_9544 and tr_A0A0D9S008_A0A0D9S008_CHLSB_60711 are exactly identical! WARNING: Sequences tr_A0A1D5QEM1_A0A1D5QEM1_MACMU_9544 and tr_A0A2K5MJQ5_A0A2K5MJQ5_CERAT_9531 are exactly identical! WARNING: Sequences tr_A0A1D5QEM1_A0A1D5QEM1_MACMU_9544 and tr_A0A2K6C982_A0A2K6C982_MACNE_9545 are exactly identical! WARNING: Sequences tr_A0A1D5QEM1_A0A1D5QEM1_MACMU_9544 and tr_A0A2K6A3C5_A0A2K6A3C5_MANLE_9568 are exactly identical! WARNING: Sequences tr_F6R0Q4_F6R0Q4_MACMU_9544 and tr_G7P509_G7P509_MACFA_9541 are exactly identical! WARNING: Sequences tr_F6R0Q4_F6R0Q4_MACMU_9544 and tr_A0A2K6B0J8_A0A2K6B0J8_MACNE_9545 are exactly identical! WARNING: Sequences tr_G7NQX9_G7NQX9_MACMU_9544 and tr_G7Q0Z6_G7Q0Z6_MACFA_9541 are exactly identical! WARNING: Sequences tr_B3S4L6_B3S4L6_TRIAD_10228 and tr_A0A369S0F8_A0A369S0F8_9METZ_287889 are exactly identical! WARNING: Sequences tr_A0A096MQU3_A0A096MQU3_PAPAN_9555 and tr_A0A2K5P8A1_A0A2K5P8A1_CERAT_9531 are exactly identical! WARNING: Sequences tr_A0A096NHX2_A0A096NHX2_PAPAN_9555 and tr_A0A2K5P0F0_A0A2K5P0F0_CERAT_9531 are exactly identical! WARNING: Sequences tr_A0A151N9H8_A0A151N9H8_ALLMI_8496 and tr_A0A1U7S2C0_A0A1U7S2C0_ALLSI_38654 are exactly identical! WARNING: Sequences tr_A0A091ET27_A0A091ET27_CORBR_85066 and tr_A0A087QWG8_A0A087QWG8_APTFO_9233 are exactly identical! WARNING: Sequences tr_A0A091ET27_A0A091ET27_CORBR_85066 and tr_A0A093HMZ5_A0A093HMZ5_STRCA_441894 are exactly identical! WARNING: Sequences tr_A0A091ET27_A0A091ET27_CORBR_85066 and tr_A0A091FVG8_A0A091FVG8_9AVES_55661 are exactly identical! WARNING: Sequences tr_A0A091ET27_A0A091ET27_CORBR_85066 and tr_A0A091J5R2_A0A091J5R2_CALAN_9244 are exactly identical! WARNING: Sequences tr_A0A093PT31_A0A093PT31_9PASS_328815 and tr_A0A091V0F4_A0A091V0F4_NIPNI_128390 are exactly identical! WARNING: Sequences tr_A0A093PT31_A0A093PT31_9PASS_328815 and tr_A0A0A0ATI4_A0A0A0ATI4_CHAVO_50402 are exactly identical! WARNING: Sequences tr_A0A093PT31_A0A093PT31_9PASS_328815 and tr_A0A093GH22_A0A093GH22_DRYPU_118200 are exactly identical! WARNING: Sequences tr_A0A0V1D337_A0A0V1D337_TRIBR_45882 and tr_A0A0V1NT07_A0A0V1NT07_9BILA_92180 are exactly identical! WARNING: Sequences tr_A0A0V1L670_A0A0V1L670_9BILA_6335 and tr_A0A0V1M3Z7_A0A0V1M3Z7_9BILA_268474 are exactly identical! WARNING: Sequences tr_B5XA81_B5XA81_SALSA_8030 and tr_A0A060WK22_A0A060WK22_ONCMY_8022 are exactly identical! WARNING: Sequences tr_A0A1D1VSU3_A0A1D1VSU3_RAMVA_947166 and tr_A0A1D1VWJ3_A0A1D1VWJ3_RAMVA_947166 are exactly identical! WARNING: Sequences tr_A0A218UF57_A0A218UF57_9PASE_299123 and tr_A0A226MLR2_A0A226MLR2_CALSU_9009 are exactly identical! WARNING: Sequences tr_A0A218UF57_A0A218UF57_9PASE_299123 and tr_A0A226NUI6_A0A226NUI6_COLVI_9014 are exactly identical! WARNING: Sequences tr_A0A226M7T4_A0A226M7T4_CALSU_9009 and tr_A0A226MB33_A0A226MB33_COLVI_9014 are exactly identical! WARNING: Sequences tr_A0A226MQU7_A0A226MQU7_CALSU_9009 and tr_A0A226MBA0_A0A226MBA0_COLVI_9014 are exactly identical! WARNING: Sequences tr_A0A2A2JAB6_A0A2A2JAB6_9BILA_2018661 and tr_A0A2A2LZ22_A0A2A2LZ22_9BILA_2018661 are exactly identical! WARNING: Sequences tr_A0A2K6D7S9_A0A2K6D7S9_MACNE_9545 and tr_A0A2K5ZXS7_A0A2K5ZXS7_MANLE_9568 are exactly identical! WARNING: Duplicate sequences found: 69 NOTE: Reduced alignment (with duplicates and gap-only sites/taxa removed) NOTE: was saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/P61266/3_mltree/P61266.raxml.reduced.phy Alignment comprises 1 partitions and 286 patterns Partition 0: noname Model: LG4X+R4 Alignment sites / patterns: 286 / 286 Gaps: 12.16 % Invariant sites: 0.00 % NOTE: Binary MSA file created: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/P61266/3_mltree/P61266.raxml.rba Parallelization scheme autoconfig: 6 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 1001 taxa [00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 286 / 22880 [00:00:00] Data distribution: max. searches per worker: 4 Starting ML tree search with 20 distinct starting trees [00:00:00 -446727.894478] Initial branch length optimization [00:00:05 -365724.575964] Model parameter optimization (eps = 10.000000) [00:00:54 -362138.370618] AUTODETECT spr round 1 (radius: 5) [00:04:12 -272856.559062] AUTODETECT spr round 2 (radius: 10) [00:08:25 -216942.448248] AUTODETECT spr round 3 (radius: 15) [00:13:32 -184690.217388] AUTODETECT spr round 4 (radius: 20) [00:20:53 -157410.286886] AUTODETECT spr round 5 (radius: 25) [00:29:10 -154260.710873] SPR radius for FAST iterations: 25 (autodetect) [00:29:10 -154260.710873] Model parameter optimization (eps = 3.000000) [00:29:55 -153406.780734] FAST spr round 1 (radius: 25) [00:35:11 -134070.663403] FAST spr round 2 (radius: 25) [00:39:30 -132809.123661] FAST spr round 3 (radius: 25) [00:43:02 -132755.181442] FAST spr round 4 (radius: 25) [00:45:59 -132754.035397] FAST spr round 5 (radius: 25) [00:48:49 -132754.035371] Model parameter optimization (eps = 1.000000) [00:49:14 -132750.755602] SLOW spr round 1 (radius: 5) [00:53:08 -132706.710696] SLOW spr round 2 (radius: 5) [00:56:37 -132698.064427] SLOW spr round 3 (radius: 5) [01:00:14 -132694.084180] SLOW spr round 4 (radius: 5) [01:03:45 -132694.084163] SLOW spr round 5 (radius: 10) [01:07:26 -132687.438080] SLOW spr round 6 (radius: 5) [01:11:55 -132686.772169] SLOW spr round 7 (radius: 5) [01:15:52 -132686.771835] SLOW spr round 8 (radius: 10) [01:19:24 -132686.771819] SLOW spr round 9 (radius: 15) [01:25:40 -132683.834995] SLOW spr round 10 (radius: 5) [01:30:25 -132683.830892] SLOW spr round 11 (radius: 10) [01:34:53 -132683.741249] SLOW spr round 12 (radius: 15) [01:40:48 -132683.740438] SLOW spr round 13 (radius: 20) [01:49:20 -132683.740192] SLOW spr round 14 (radius: 25) [01:56:49] [worker #3] ML tree search #4, logLikelihood: -132715.914746 [01:58:36] [worker #1] ML tree search #2, logLikelihood: -132836.358967 [02:00:17] [worker #5] ML tree search #6, logLikelihood: -132860.765031 [02:02:32 -132683.740094] Model parameter optimization (eps = 0.100000) [02:02:46] [worker #0] ML tree search #1, logLikelihood: -132683.363852 [02:02:46 -443465.201389] Initial branch length optimization [02:02:51 -362118.184971] Model parameter optimization (eps = 10.000000) [02:03:55 -358599.519625] AUTODETECT spr round 1 (radius: 5) [02:07:18 -279608.373046] AUTODETECT spr round 2 (radius: 10) [02:11:07 -210969.539649] AUTODETECT spr round 3 (radius: 15) [02:15:00] [worker #4] ML tree search #5, logLikelihood: -132835.001242 [02:16:13 -188612.222705] AUTODETECT spr round 4 (radius: 20) [02:22:08 -160761.777820] AUTODETECT spr round 5 (radius: 25) [02:27:40 -153632.518370] SPR radius for FAST iterations: 25 (autodetect) [02:27:40 -153632.518370] Model parameter optimization (eps = 3.000000) [02:28:22 -152911.370501] FAST spr round 1 (radius: 25) [02:32:50 -134373.097298] FAST spr round 2 (radius: 25) [02:33:15] [worker #2] ML tree search #3, logLikelihood: -132708.659263 [02:36:06 -132914.878421] FAST spr round 3 (radius: 25) [02:38:52 -132769.375609] FAST spr round 4 (radius: 25) [02:41:22 -132767.021238] FAST spr round 5 (radius: 25) [02:43:43 -132767.021094] Model parameter optimization (eps = 1.000000) [02:44:05 -132758.582471] SLOW spr round 1 (radius: 5) [02:47:09 -132725.032689] SLOW spr round 2 (radius: 5) [02:50:11 -132714.752773] SLOW spr round 3 (radius: 5) [02:53:05 -132714.746815] SLOW spr round 4 (radius: 10) [02:56:04 -132714.637310] SLOW spr round 5 (radius: 5) [02:59:38 -132714.636988] SLOW spr round 6 (radius: 10) [03:02:56 -132714.636980] SLOW spr round 7 (radius: 15) [03:07:42 -132714.286114] SLOW spr round 8 (radius: 5) [03:11:27 -132714.286104] SLOW spr round 9 (radius: 10) [03:15:00 -132714.286099] SLOW spr round 10 (radius: 15) [03:19:43 -132714.286094] SLOW spr round 11 (radius: 20) [03:25:53] [worker #3] ML tree search #10, logLikelihood: -132834.777673 [03:28:12 -132712.633742] SLOW spr round 12 (radius: 5) [03:32:03 -132712.631394] SLOW spr round 13 (radius: 10) [03:33:52] [worker #1] ML tree search #8, logLikelihood: -132692.890114 [03:35:44 -132712.631085] SLOW spr round 14 (radius: 15) [03:40:26 -132712.631017] SLOW spr round 15 (radius: 20) [03:46:50] [worker #4] ML tree search #11, logLikelihood: -132728.208741 [03:48:56 -132712.630998] SLOW spr round 16 (radius: 25) [03:57:27] [worker #5] ML tree search #12, logLikelihood: -132818.814327 [04:00:11 -132712.086878] SLOW spr round 17 (radius: 5) [04:04:04 -132712.086712] SLOW spr round 18 (radius: 10) [04:07:48 -132712.086704] SLOW spr round 19 (radius: 15) [04:09:06] [worker #2] ML tree search #9, logLikelihood: -132704.630387 [04:12:32 -132712.086697] SLOW spr round 20 (radius: 20) [04:21:07 -132712.086690] SLOW spr round 21 (radius: 25) [04:32:32 -132712.086683] Model parameter optimization (eps = 0.100000) [04:32:39] [worker #0] ML tree search #7, logLikelihood: -132712.029583 [04:32:39 -443764.036583] Initial branch length optimization [04:32:44 -363001.334376] Model parameter optimization (eps = 10.000000) [04:33:31 -359392.522514] AUTODETECT spr round 1 (radius: 5) [04:36:50 -275903.832810] AUTODETECT spr round 2 (radius: 10) [04:40:25 -214722.549716] AUTODETECT spr round 3 (radius: 15) [04:44:25 -179647.215839] AUTODETECT spr round 4 (radius: 20) [04:49:14 -164724.437625] AUTODETECT spr round 5 (radius: 25) [04:55:40 -155985.547680] SPR radius for FAST iterations: 25 (autodetect) [04:55:40 -155985.547680] Model parameter optimization (eps = 3.000000) [04:56:15 -155555.522077] FAST spr round 1 (radius: 25) [05:00:56 -134273.340812] FAST spr round 2 (radius: 25) [05:04:16 -133087.274183] FAST spr round 3 (radius: 25) [05:06:51] [worker #3] ML tree search #16, logLikelihood: -132704.802931 [05:07:06 -133008.046110] FAST spr round 4 (radius: 25) [05:09:16] [worker #1] ML tree search #14, logLikelihood: -132837.289491 [05:09:40 -132995.065331] FAST spr round 5 (radius: 25) [05:12:03 -132983.299862] FAST spr round 6 (radius: 25) [05:14:21 -132979.792029] FAST spr round 7 (radius: 25) [05:16:34 -132979.791486] Model parameter optimization (eps = 1.000000) [05:16:58 -132901.849261] SLOW spr round 1 (radius: 5) [05:20:03 -132857.824579] SLOW spr round 2 (radius: 5) [05:23:05 -132850.201952] SLOW spr round 3 (radius: 5) [05:25:59 -132850.201196] SLOW spr round 4 (radius: 10) [05:28:58 -132848.622138] SLOW spr round 5 (radius: 5) [05:32:34 -132848.621804] SLOW spr round 6 (radius: 10) [05:35:52 -132848.621777] SLOW spr round 7 (radius: 15) [05:40:30 -132847.348442] SLOW spr round 8 (radius: 5) [05:44:17 -132847.348434] SLOW spr round 9 (radius: 10) [05:47:45 -132847.348428] SLOW spr round 10 (radius: 15) [05:48:48] [worker #4] ML tree search #17, logLikelihood: -132862.576959 [05:52:19 -132847.348422] SLOW spr round 11 (radius: 20) [05:54:03] [worker #2] ML tree search #15, logLikelihood: -132697.490939 [06:00:03 -132847.348416] SLOW spr round 12 (radius: 25) [06:06:44] [worker #5] ML tree search #18, logLikelihood: -132842.296873 [06:10:47 -132846.750027] SLOW spr round 13 (radius: 5) [06:14:40 -132846.750014] SLOW spr round 14 (radius: 10) [06:18:16 -132846.750005] SLOW spr round 15 (radius: 15) [06:22:50 -132846.749996] SLOW spr round 16 (radius: 20) [06:30:35 -132846.749987] SLOW spr round 17 (radius: 25) [06:41:13 -132846.749979] Model parameter optimization (eps = 0.100000) [06:41:23] [worker #0] ML tree search #13, logLikelihood: -132846.592822 [06:41:24 -447875.654375] Initial branch length optimization [06:41:28 -366015.955160] Model parameter optimization (eps = 10.000000) [06:42:16 -362480.391641] AUTODETECT spr round 1 (radius: 5) [06:45:32 -282089.539059] AUTODETECT spr round 2 (radius: 10) [06:49:05 -220293.705229] AUTODETECT spr round 3 (radius: 15) [06:51:49] [worker #1] ML tree search #20, logLikelihood: -132842.157588 [06:53:15 -175795.200304] AUTODETECT spr round 4 (radius: 20) [06:58:18 -163296.163593] AUTODETECT spr round 5 (radius: 25) [07:05:08 -157245.115792] SPR radius for FAST iterations: 25 (autodetect) [07:05:08 -157245.115792] Model parameter optimization (eps = 3.000000) [07:05:42 -156529.650046] FAST spr round 1 (radius: 25) [07:10:12 -134533.248392] FAST spr round 2 (radius: 25) [07:13:37 -132909.963742] FAST spr round 3 (radius: 25) [07:16:20 -132784.922892] FAST spr round 4 (radius: 25) [07:18:47 -132771.324677] FAST spr round 5 (radius: 25) [07:21:01 -132768.837223] FAST spr round 6 (radius: 25) [07:23:11 -132768.836676] Model parameter optimization (eps = 1.000000) [07:23:23 -132767.381292] SLOW spr round 1 (radius: 5) [07:26:23 -132718.292702] SLOW spr round 2 (radius: 5) [07:29:21 -132707.063434] SLOW spr round 3 (radius: 5) [07:32:15 -132703.394756] SLOW spr round 4 (radius: 5) [07:35:04 -132703.306851] SLOW spr round 5 (radius: 10) [07:38:03 -132697.647711] SLOW spr round 6 (radius: 5) [07:41:41 -132690.813493] SLOW spr round 7 (radius: 5) [07:44:50 -132690.377765] SLOW spr round 8 (radius: 5) [07:47:46 -132690.377705] SLOW spr round 9 (radius: 10) [07:50:43 -132690.377700] SLOW spr round 10 (radius: 15) [07:55:35 -132689.909362] SLOW spr round 11 (radius: 5) [07:59:18 -132689.763832] SLOW spr round 12 (radius: 5) [08:02:34 -132689.763439] SLOW spr round 13 (radius: 10) [08:05:39 -132689.763261] SLOW spr round 14 (radius: 15) [08:10:22 -132689.763180] SLOW spr round 15 (radius: 20) [08:18:03 -132689.763142] SLOW spr round 16 (radius: 25) [08:28:36 -132689.763123] Model parameter optimization (eps = 0.100000) [08:28:49] [worker #0] ML tree search #19, logLikelihood: -132689.123270 Optimized model parameters: Partition 0: noname Rate heterogeneity: FREE (4 cats, mean), weights&rates: (0.204779,0.541555) (0.105384,1.431110) (0.384805,0.706886) (0.305031,1.528600) 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: -132683.363852 AIC score: 269376.727704 / AICc score: 8313436.727704 / BIC score: 276706.991285 Free parameters (model + branch lengths): 2005 WARNING: Number of free parameters (K=2005) is larger than alignment size (n=286). This might lead to overfitting and compromise tree inference results! WARNING: Best ML tree contains 1 near-zero branches! Best ML tree with collapsed near-zero branches saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/P61266/3_mltree/P61266.raxml.bestTreeCollapsed Best ML tree saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/P61266/3_mltree/P61266.raxml.bestTree All ML trees saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/P61266/3_mltree/P61266.raxml.mlTrees Optimized model saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/P61266/3_mltree/P61266.raxml.bestModel Execution log saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/P61266/3_mltree/P61266.raxml.log Analysis started: 30-Jun-2021 17:32:27 / finished: 01-Jul-2021 02:01:17 Elapsed time: 30530.046 seconds Consumed energy: 2581.471 Wh (= 13 km in an electric car, or 65 km with an e-scooter!)