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 06-Jul-2021 07:16:07 as follows: raxml-ng --msa /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/A5D8T8/2_msa/A5D8T8_trimmed_msa.fasta --data-type AA --model LG4X --prefix /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/A5D8T8/3_mltree/A5D8T8 --seed 2 --threads 4 --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 (4 threads), thread pinning: OFF [00:00:00] Reading alignment from file: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/A5D8T8/2_msa/A5D8T8_trimmed_msa.fasta [00:00:00] Loaded alignment with 1001 taxa and 194 sites WARNING: Sequences tr_A0A1D5PAF5_A0A1D5PAF5_CHICK_9031 and sp_Q98ST5_CRLD1_CHICK_9031 are exactly identical! WARNING: Sequences tr_M3YFG6_M3YFG6_MUSPF_9669 and tr_F6XHZ9_F6XHZ9_CANLF_9615 are exactly identical! WARNING: Sequences tr_M3YFG6_M3YFG6_MUSPF_9669 and tr_A0A2U3X7E6_A0A2U3X7E6_LEPWE_9713 are exactly identical! WARNING: Sequences tr_M3YFG6_M3YFG6_MUSPF_9669 and tr_A0A2Y9KJ43_A0A2Y9KJ43_ENHLU_391180 are exactly identical! WARNING: Sequences tr_M3YFH8_M3YFH8_MUSPF_9669 and tr_A0A2Y9KWW0_A0A2Y9KWW0_ENHLU_391180 are exactly identical! WARNING: Sequences tr_G1QMW8_G1QMW8_NOMLE_61853 and tr_G3SC07_G3SC07_GORGO_9595 are exactly identical! WARNING: Sequences tr_G1QMW8_G1QMW8_NOMLE_61853 and tr_H2PQL5_H2PQL5_PONAB_9601 are exactly identical! WARNING: Sequences tr_G1QMW8_G1QMW8_NOMLE_61853 and tr_A0A2J8M9V0_A0A2J8M9V0_PANTR_9598 are exactly identical! WARNING: Sequences tr_G1QMW8_G1QMW8_NOMLE_61853 and sp_Q9H336_CRLD1_HUMAN_9606 are exactly identical! WARNING: Sequences tr_G1QMW8_G1QMW8_NOMLE_61853 and tr_A0A2R9BDU4_A0A2R9BDU4_PANPA_9597 are exactly identical! WARNING: Sequences tr_A0A2I2Z403_A0A2I2Z403_GORGO_9595 and tr_G1TNH6_G1TNH6_RABIT_9986 are exactly identical! WARNING: Sequences tr_A0A2I2Z403_A0A2I2Z403_GORGO_9595 and tr_A0A2I3RX55_A0A2I3RX55_PANTR_9598 are exactly identical! WARNING: Sequences tr_A0A2I2Z403_A0A2I2Z403_GORGO_9595 and tr_I3MKK0_I3MKK0_ICTTR_43179 are exactly identical! WARNING: Sequences tr_A0A2I2Z403_A0A2I2Z403_GORGO_9595 and sp_O43692_PI15_HUMAN_9606 are exactly identical! WARNING: Sequences tr_A0A2I2Z403_A0A2I2Z403_GORGO_9595 and tr_F7GZU6_F7GZU6_MACMU_9544 are exactly identical! WARNING: Sequences tr_A0A2I2Z403_A0A2I2Z403_GORGO_9595 and tr_G8F5A2_G8F5A2_MACFA_9541 are exactly identical! WARNING: Sequences tr_A0A2I2Z403_A0A2I2Z403_GORGO_9595 and tr_A0A096N9D7_A0A096N9D7_PAPAN_9555 are exactly identical! WARNING: Sequences tr_A0A2I2Z403_A0A2I2Z403_GORGO_9595 and tr_A0A0D9RM12_A0A0D9RM12_CHLSB_60711 are exactly identical! WARNING: Sequences tr_A0A2I2Z403_A0A2I2Z403_GORGO_9595 and tr_A0A2K5XRL6_A0A2K5XRL6_MANLE_9568 are exactly identical! WARNING: Sequences tr_A0A2I2Z403_A0A2I2Z403_GORGO_9595 and tr_A0A2R9AJD5_A0A2R9AJD5_PANPA_9597 are exactly identical! WARNING: Sequences tr_G3RCM0_G3RCM0_GORGO_9595 and tr_H2Q6I0_H2Q6I0_PANTR_9598 are exactly identical! WARNING: Sequences tr_G3RCM0_G3RCM0_GORGO_9595 and sp_P48060_GLIP1_HUMAN_9606 are exactly identical! WARNING: Sequences tr_G3RCM0_G3RCM0_GORGO_9595 and tr_A0A2R9BRE0_A0A2R9BRE0_PANPA_9597 are exactly identical! WARNING: Sequences tr_G3S1V3_G3S1V3_GORGO_9595 and tr_A0A2J8Y3N9_A0A2J8Y3N9_PONAB_9601 are exactly identical! WARNING: Sequences tr_G3SI65_G3SI65_GORGO_9595 and tr_K7A8K8_K7A8K8_PANTR_9598 are exactly identical! WARNING: Sequences tr_G3SI65_G3SI65_GORGO_9595 and sp_Q9H0B8_CRLD2_HUMAN_9606 are exactly identical! WARNING: Sequences tr_G3SI65_G3SI65_GORGO_9595 and tr_A0A2R8ZGN8_A0A2R8ZGN8_PANPA_9597 are exactly identical! WARNING: Sequences tr_G1NGB8_G1NGB8_MELGA_9103 and tr_A0A0Q3X735_A0A0Q3X735_AMAAE_12930 are exactly identical! WARNING: Sequences tr_G1NGB8_G1NGB8_MELGA_9103 and tr_A0A091VD85_A0A091VD85_NIPNI_128390 are exactly identical! WARNING: Sequences tr_G1NGB8_G1NGB8_MELGA_9103 and tr_A0A091WIQ7_A0A091WIQ7_OPIHO_30419 are exactly identical! WARNING: Sequences tr_G1NGB8_G1NGB8_MELGA_9103 and tr_A0A091FNI8_A0A091FNI8_9AVES_55661 are exactly identical! WARNING: Sequences tr_G1NGB8_G1NGB8_MELGA_9103 and tr_A0A0A0AXZ7_A0A0A0AXZ7_CHAVO_50402 are exactly identical! WARNING: Sequences tr_G1NGB8_G1NGB8_MELGA_9103 and tr_A0A091HZJ7_A0A091HZJ7_CALAN_9244 are exactly identical! WARNING: Sequences tr_G3UQ03_G3UQ03_MELGA_9103 and tr_U3K1N7_U3K1N7_FICAL_59894 are exactly identical! WARNING: Sequences tr_G3UQ03_G3UQ03_MELGA_9103 and tr_A0A091JKZ9_A0A091JKZ9_EGRGA_188379 are exactly identical! WARNING: Sequences tr_G3UQ03_G3UQ03_MELGA_9103 and tr_A0A2I0MVT4_A0A2I0MVT4_COLLI_8932 are exactly identical! WARNING: Sequences tr_F1PIU3_F1PIU3_CANLF_9615 and tr_W5P9U9_W5P9U9_SHEEP_9940 are exactly identical! WARNING: Sequences tr_F1PIU3_F1PIU3_CANLF_9615 and tr_F1RWK2_F1RWK2_PIG_9823 are exactly identical! WARNING: Sequences tr_F1PIU3_F1PIU3_CANLF_9615 and tr_A0A2I2UJP1_A0A2I2UJP1_FELCA_9685 are exactly identical! WARNING: Sequences tr_F1PIU3_F1PIU3_CANLF_9615 and tr_A0A2U3WE50_A0A2U3WE50_ODORO_9708 are exactly identical! WARNING: Sequences tr_F1PIU3_F1PIU3_CANLF_9615 and tr_A0A2U3X7N3_A0A2U3X7N3_LEPWE_9713 are exactly identical! WARNING: Sequences tr_H2QSX2_H2QSX2_PANTR_9598 and tr_A0A2R9BJ53_A0A2R9BJ53_PANPA_9597 are exactly identical! WARNING: Sequences tr_M4A7N1_M4A7N1_XIPMA_8083 and tr_A0A087Y5R6_A0A087Y5R6_POEFO_48698 are exactly identical! WARNING: Sequences tr_A0A0E0HYP0_A0A0E0HYP0_ORYNI_4536 and tr_Q8H5R0_Q8H5R0_ORYSJ_39947 are exactly identical! WARNING: Sequences tr_F6RSK7_F6RSK7_MACMU_9544 and tr_G7P3C5_G7P3C5_MACFA_9541 are exactly identical! WARNING: Sequences tr_F6RSK7_F6RSK7_MACMU_9544 and tr_A0A2K6B571_A0A2K6B571_MACNE_9545 are exactly identical! WARNING: Sequences tr_F7FY55_F7FY55_MACMU_9544 and tr_G7P4U1_G7P4U1_MACFA_9541 are exactly identical! WARNING: Sequences tr_F7FY55_F7FY55_MACMU_9544 and tr_A0A2K6CKD5_A0A2K6CKD5_MACNE_9545 are exactly identical! WARNING: Sequences tr_F7GPA7_F7GPA7_MACMU_9544 and tr_G7PC22_G7PC22_MACFA_9541 are exactly identical! WARNING: Sequences tr_F7GPA7_F7GPA7_MACMU_9544 and tr_A0A2K6D6C5_A0A2K6D6C5_MACNE_9545 are exactly identical! WARNING: Sequences sp_Q9XSD3_CRIS1_MACMU_9544 and tr_G8F5W7_G8F5W7_MACFA_9541 are exactly identical! WARNING: Sequences tr_A2YJU7_A2YJU7_ORYSI_39946 and tr_A0A0E0AHL2_A0A0E0AHL2_9ORYZ_40148 are exactly identical! WARNING: Sequences tr_D2HUM9_D2HUM9_AILME_9646 and tr_A0A384DQH8_A0A384DQH8_URSMA_29073 are exactly identical! WARNING: Sequences tr_M4F7C1_M4F7C1_BRARP_51351 and tr_A0A078IJX4_A0A078IJX4_BRANA_3708 are exactly identical! WARNING: Sequences tr_M4F7C8_M4F7C8_BRARP_51351 and tr_A0A078I8C5_A0A078I8C5_BRANA_3708 are exactly identical! WARNING: Sequences tr_A0A096NEQ2_A0A096NEQ2_PAPAN_9555 and tr_A0A2K5MQH8_A0A2K5MQH8_CERAT_9531 are exactly identical! WARNING: Sequences tr_A0A096NEQ2_A0A096NEQ2_PAPAN_9555 and tr_A0A2K5XA39_A0A2K5XA39_MANLE_9568 are exactly identical! WARNING: Sequences tr_A0A096NHT4_A0A096NHT4_PAPAN_9555 and tr_A0A2K5MI88_A0A2K5MI88_CERAT_9531 are exactly identical! WARNING: Sequences tr_A0A096NHT4_A0A096NHT4_PAPAN_9555 and tr_A0A2K5Y9E5_A0A2K5Y9E5_MANLE_9568 are exactly identical! WARNING: Sequences tr_A0A096P090_A0A096P090_PAPAN_9555 and tr_A0A2K5N6E4_A0A2K5N6E4_CERAT_9531 are exactly identical! WARNING: Sequences tr_A0A096P090_A0A096P090_PAPAN_9555 and tr_A0A2K5Z6X3_A0A2K5Z6X3_MANLE_9568 are exactly identical! WARNING: Sequences tr_A0A0D9S1Z0_A0A0D9S1Z0_CHLSB_60711 and tr_A0A2K6C0N7_A0A2K6C0N7_MACNE_9545 are exactly identical! WARNING: Sequences tr_A0A091EJQ5_A0A091EJQ5_CORBR_85066 and tr_A0A093QHN8_A0A093QHN8_9PASS_328815 are exactly identical! WARNING: Sequences tr_A0A091JIB6_A0A091JIB6_EGRGA_188379 and tr_A0A2I0LMN0_A0A2I0LMN0_COLLI_8932 are exactly identical! WARNING: Sequences tr_A0A2I0MVT7_A0A2I0MVT7_COLLI_8932 and tr_A0A1V4KIB2_A0A1V4KIB2_PATFA_372326 are exactly identical! WARNING: Sequences tr_A0A1S3XBU5_A0A1S3XBU5_TOBAC_4097 and sp_P09042_PR1C_TOBAC_4097 are exactly identical! WARNING: Sequences tr_A0A1S3XBU5_A0A1S3XBU5_TOBAC_4097 and tr_A0A1U7VS72_A0A1U7VS72_NICSY_4096 are exactly identical! WARNING: Sequences tr_A0A1S4AM21_A0A1S4AM21_TOBAC_4097 and tr_A0A1U7XML8_A0A1U7XML8_NICSY_4096 are exactly identical! WARNING: Sequences tr_A0A2D0SKW7_A0A2D0SKW7_ICTPU_7998 and tr_A0A2D0SLH1_A0A2D0SLH1_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A1U8HM42_A0A1U8HM42_CAPAN_4072 and tr_A0A2G3BV51_A0A2G3BV51_CAPCH_80379 are exactly identical! WARNING: Sequences tr_A0A2K5N688_A0A2K5N688_CERAT_9531 and tr_A0A2K5XGN4_A0A2K5XGN4_MANLE_9568 are exactly identical! WARNING: Sequences tr_A0A2L1DGY3_A0A2L1DGY3_ARTAN_35608 and tr_A0A2U1L8L8_A0A2U1L8L8_ARTAN_35608 are exactly identical! WARNING: Sequences tr_A0A2U4AJ26_A0A2U4AJ26_TURTR_9739 and tr_A0A2Y9PVW0_A0A2Y9PVW0_DELLE_9749 are exactly identical! WARNING: Sequences tr_A0A2Y9Q031_A0A2Y9Q031_DELLE_9749 and tr_A0A2Y9EP59_A0A2Y9EP59_PHYCD_9755 are exactly identical! WARNING: Duplicate sequences found: 74 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/A5D8T8/3_mltree/A5D8T8.raxml.reduced.phy Alignment comprises 1 partitions and 194 patterns Partition 0: noname Model: LG4X+R4 Alignment sites / patterns: 194 / 194 Gaps: 11.89 % Invariant sites: 0.00 % NOTE: Binary MSA file created: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/A5D8T8/3_mltree/A5D8T8.raxml.rba Parallelization scheme autoconfig: 4 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 / 194 / 15520 [00:00:00] Data distribution: max. searches per worker: 5 Starting ML tree search with 20 distinct starting trees [00:00:00 -328998.080517] Initial branch length optimization [00:00:04 -271432.526849] Model parameter optimization (eps = 10.000000) [00:00:39 -271222.320766] AUTODETECT spr round 1 (radius: 5) [00:03:21 -200706.607029] AUTODETECT spr round 2 (radius: 10) [00:06:23 -154544.682275] AUTODETECT spr round 3 (radius: 15) [00:09:48 -133601.452201] AUTODETECT spr round 4 (radius: 20) [00:13:44 -125492.507355] AUTODETECT spr round 5 (radius: 25) [00:18:27 -116456.054551] SPR radius for FAST iterations: 25 (autodetect) [00:18:27 -116456.054551] Model parameter optimization (eps = 3.000000) [00:18:36 -116451.568819] FAST spr round 1 (radius: 25) [00:22:31 -100571.868324] FAST spr round 2 (radius: 25) [00:25:13 -99767.792905] FAST spr round 3 (radius: 25) [00:27:21 -99707.454582] FAST spr round 4 (radius: 25) [00:29:13 -99698.588054] FAST spr round 5 (radius: 25) [00:30:59 -99693.092582] FAST spr round 6 (radius: 25) [00:32:45 -99680.319887] FAST spr round 7 (radius: 25) [00:34:34 -99673.223865] FAST spr round 8 (radius: 25) [00:36:19 -99673.223816] Model parameter optimization (eps = 1.000000) [00:36:39 -99465.546695] SLOW spr round 1 (radius: 5) [00:39:06 -99415.955576] SLOW spr round 2 (radius: 5) [00:41:28 -99403.882400] SLOW spr round 3 (radius: 5) [00:43:47 -99403.084111] SLOW spr round 4 (radius: 5) [00:46:03 -99402.627674] SLOW spr round 5 (radius: 5) [00:48:18 -99402.625963] SLOW spr round 6 (radius: 10) [00:50:34 -99401.825109] SLOW spr round 7 (radius: 5) [00:53:20 -99401.824277] SLOW spr round 8 (radius: 10) [00:55:45 -99401.823826] SLOW spr round 9 (radius: 15) [00:59:20 -99401.823518] SLOW spr round 10 (radius: 20) [01:01:57] [worker #3] ML tree search #4, logLikelihood: -99423.684764 [01:06:04 -99401.823307] SLOW spr round 11 (radius: 25) [01:08:08] [worker #2] ML tree search #3, logLikelihood: -99401.507770 [01:14:37 -99401.823162] Model parameter optimization (eps = 0.100000) [01:14:45] [worker #0] ML tree search #1, logLikelihood: -99401.717832 [01:14:45 -327118.983941] Initial branch length optimization [01:14:46] [worker #1] ML tree search #2, logLikelihood: -99409.652499 [01:14:49 -269473.484892] Model parameter optimization (eps = 10.000000) [01:15:25 -269316.550478] AUTODETECT spr round 1 (radius: 5) [01:18:02 -197933.872913] AUTODETECT spr round 2 (radius: 10) [01:20:57 -157639.606099] AUTODETECT spr round 3 (radius: 15) [01:24:26 -135427.995682] AUTODETECT spr round 4 (radius: 20) [01:27:58 -122470.364942] AUTODETECT spr round 5 (radius: 25) [01:32:24 -115020.471053] SPR radius for FAST iterations: 25 (autodetect) [01:32:24 -115020.471053] Model parameter optimization (eps = 3.000000) [01:32:49 -114761.883730] FAST spr round 1 (radius: 25) [01:36:26 -100194.112411] FAST spr round 2 (radius: 25) [01:38:57 -99496.912292] FAST spr round 3 (radius: 25) [01:41:11 -99449.044278] FAST spr round 4 (radius: 25) [01:43:06 -99437.544961] FAST spr round 5 (radius: 25) [01:44:52 -99437.543341] Model parameter optimization (eps = 1.000000) [01:44:57 -99437.307230] SLOW spr round 1 (radius: 5) [01:47:22 -99418.094762] SLOW spr round 2 (radius: 5) [01:49:45 -99409.571977] SLOW spr round 3 (radius: 5) [01:52:03 -99409.512562] SLOW spr round 4 (radius: 10) [01:54:21 -99407.772386] SLOW spr round 5 (radius: 5) [01:57:13 -99407.289942] SLOW spr round 6 (radius: 5) [01:59:46 -99407.289883] SLOW spr round 7 (radius: 10) [02:02:02 -99407.289841] SLOW spr round 8 (radius: 15) [02:05:45 -99407.258427] SLOW spr round 9 (radius: 20) [02:11:49 -99407.258401] SLOW spr round 10 (radius: 25) [02:12:05] [worker #3] ML tree search #8, logLikelihood: -99386.115950 [02:15:00] [worker #2] ML tree search #7, logLikelihood: -99409.935180 [02:19:19 -99407.258376] Model parameter optimization (eps = 0.100000) [02:19:23] [worker #0] ML tree search #5, logLikelihood: -99407.257183 [02:19:23 -328831.703349] Initial branch length optimization [02:19:27 -270525.189384] Model parameter optimization (eps = 10.000000) [02:20:01 -270398.714820] AUTODETECT spr round 1 (radius: 5) [02:22:34 -198014.356345] AUTODETECT spr round 2 (radius: 10) [02:25:28 -152535.061550] AUTODETECT spr round 3 (radius: 15) [02:29:23 -130362.288909] AUTODETECT spr round 4 (radius: 20) [02:33:16 -115647.735922] AUTODETECT spr round 5 (radius: 25) [02:36:38] [worker #1] ML tree search #6, logLikelihood: -99387.679092 [02:38:29 -113372.584978] SPR radius for FAST iterations: 25 (autodetect) [02:38:29 -113372.584978] Model parameter optimization (eps = 3.000000) [02:38:49 -112985.189408] FAST spr round 1 (radius: 25) [02:42:26 -100218.340155] FAST spr round 2 (radius: 25) [02:44:53 -99521.712509] FAST spr round 3 (radius: 25) [02:47:01 -99479.514863] FAST spr round 4 (radius: 25) [02:48:53 -99475.906122] FAST spr round 5 (radius: 25) [02:50:39 -99475.906017] Model parameter optimization (eps = 1.000000) [02:50:56 -99466.489137] SLOW spr round 1 (radius: 5) [02:53:19 -99439.688340] SLOW spr round 2 (radius: 5) [02:55:39 -99435.078519] SLOW spr round 3 (radius: 5) [02:58:01 -99429.422958] SLOW spr round 4 (radius: 5) [03:00:21 -99420.997060] SLOW spr round 5 (radius: 5) [03:02:43 -99416.598028] SLOW spr round 6 (radius: 5) [03:05:01 -99416.239481] SLOW spr round 7 (radius: 5) [03:07:11 -99416.238640] SLOW spr round 8 (radius: 10) [03:09:27 -99413.071151] SLOW spr round 9 (radius: 5) [03:12:23 -99404.818576] SLOW spr round 10 (radius: 5) [03:14:52 -99404.308247] SLOW spr round 11 (radius: 5) [03:17:11 -99404.307528] SLOW spr round 12 (radius: 10) [03:19:24 -99404.307491] SLOW spr round 13 (radius: 15) [03:23:00 -99404.178519] SLOW spr round 14 (radius: 5) [03:25:44] [worker #2] ML tree search #11, logLikelihood: -99385.052378 [03:25:59 -99400.023502] SLOW spr round 15 (radius: 5) [03:28:40 -99399.435346] SLOW spr round 16 (radius: 5) [03:30:44] [worker #3] ML tree search #12, logLikelihood: -99378.519374 [03:30:59 -99399.434797] SLOW spr round 17 (radius: 10) [03:33:14 -99399.434703] SLOW spr round 18 (radius: 15) [03:36:53 -99399.434682] SLOW spr round 19 (radius: 20) [03:43:01 -99399.434677] SLOW spr round 20 (radius: 25) [03:51:03 -99399.434676] Model parameter optimization (eps = 0.100000) [03:51:09] [worker #0] ML tree search #9, logLikelihood: -99399.392682 [03:51:09 -327599.424561] Initial branch length optimization [03:51:13 -268392.009559] Model parameter optimization (eps = 10.000000) [03:51:39] [worker #1] ML tree search #10, logLikelihood: -99417.216025 [03:51:43 -268283.899805] AUTODETECT spr round 1 (radius: 5) [03:54:21 -201683.555835] AUTODETECT spr round 2 (radius: 10) [03:57:19 -162638.174732] AUTODETECT spr round 3 (radius: 15) [04:00:46 -139689.405845] AUTODETECT spr round 4 (radius: 20) [04:04:30 -118056.031906] AUTODETECT spr round 5 (radius: 25) [04:08:55 -115016.145787] SPR radius for FAST iterations: 25 (autodetect) [04:08:55 -115016.145787] Model parameter optimization (eps = 3.000000) [04:09:04 -115012.261492] FAST spr round 1 (radius: 25) [04:12:53 -100712.048280] FAST spr round 2 (radius: 25) [04:15:26 -99792.029583] FAST spr round 3 (radius: 25) [04:17:41 -99701.755663] FAST spr round 4 (radius: 25) [04:19:37 -99682.062845] FAST spr round 5 (radius: 25) [04:21:21 -99679.571164] FAST spr round 6 (radius: 25) [04:23:04 -99679.570636] Model parameter optimization (eps = 1.000000) [04:23:11 -99678.433232] SLOW spr round 1 (radius: 5) [04:25:35 -99644.274896] SLOW spr round 2 (radius: 5) [04:26:26] [worker #2] ML tree search #15, logLikelihood: -99378.469402 [04:27:51 -99643.594310] SLOW spr round 3 (radius: 5) [04:30:03 -99643.593392] SLOW spr round 4 (radius: 10) [04:32:19 -99642.965952] SLOW spr round 5 (radius: 5) [04:35:10 -99642.965861] SLOW spr round 6 (radius: 10) [04:37:43 -99642.965857] SLOW spr round 7 (radius: 15) [04:41:25 -99642.597739] SLOW spr round 8 (radius: 5) [04:44:23 -99642.592173] SLOW spr round 9 (radius: 10) [04:47:01 -99642.592173] SLOW spr round 10 (radius: 15) [04:50:32 -99642.592173] SLOW spr round 11 (radius: 20) [04:53:22] [worker #3] ML tree search #16, logLikelihood: -99375.756902 [04:56:44 -99642.592173] SLOW spr round 12 (radius: 25) [05:04:38 -99642.592173] Model parameter optimization (eps = 0.100000) [05:04:40] [worker #0] ML tree search #13, logLikelihood: -99642.592094 [05:04:40 -328393.589188] Initial branch length optimization [05:04:44 -270394.454421] Model parameter optimization (eps = 10.000000) [05:05:19 -270251.724561] AUTODETECT spr round 1 (radius: 5) [05:08:01 -192671.981195] AUTODETECT spr round 2 (radius: 10) [05:08:47] [worker #1] ML tree search #14, logLikelihood: -99368.710747 [05:10:56 -151162.056397] AUTODETECT spr round 3 (radius: 15) [05:14:18 -123144.586245] AUTODETECT spr round 4 (radius: 20) [05:17:55 -116159.055211] AUTODETECT spr round 5 (radius: 25) [05:21:49 -113414.363177] SPR radius for FAST iterations: 25 (autodetect) [05:21:49 -113414.363177] Model parameter optimization (eps = 3.000000) [05:22:13 -113158.556951] FAST spr round 1 (radius: 25) [05:25:53 -100841.512283] FAST spr round 2 (radius: 25) [05:28:35 -99527.919074] FAST spr round 3 (radius: 25) [05:30:47 -99456.212444] FAST spr round 4 (radius: 25) [05:32:43 -99450.129190] FAST spr round 5 (radius: 25) [05:34:36 -99444.253086] FAST spr round 6 (radius: 25) [05:36:26 -99441.299944] FAST spr round 7 (radius: 25) [05:38:13 -99441.299739] Model parameter optimization (eps = 1.000000) [05:38:26] [worker #2] ML tree search #19, logLikelihood: -99394.976667 [05:38:35 -99437.043811] SLOW spr round 1 (radius: 5) [05:41:05 -99411.511844] SLOW spr round 2 (radius: 5) [05:43:30 -99401.623111] SLOW spr round 3 (radius: 5) [05:45:50 -99399.452599] SLOW spr round 4 (radius: 5) [05:48:08 -99399.023787] SLOW spr round 5 (radius: 5) [05:50:22 -99399.021800] SLOW spr round 6 (radius: 10) [05:52:41 -99395.850776] SLOW spr round 7 (radius: 5) [05:55:33 -99395.849853] SLOW spr round 8 (radius: 10) [05:58:05 -99395.849444] SLOW spr round 9 (radius: 15) [06:01:53 -99395.197703] SLOW spr round 10 (radius: 5) [06:02:02] [worker #3] ML tree search #20, logLikelihood: -99376.294524 [06:04:52 -99394.295017] SLOW spr round 11 (radius: 5) [06:07:26 -99394.293973] SLOW spr round 12 (radius: 10) [06:09:51 -99394.293902] SLOW spr round 13 (radius: 15) [06:13:42 -99394.293892] SLOW spr round 14 (radius: 20) [06:15:45] [worker #1] ML tree search #18, logLikelihood: -99401.359748 [06:20:00 -99394.293889] SLOW spr round 15 (radius: 25) [06:28:01 -99394.293888] Model parameter optimization (eps = 0.100000) [06:28:09] [worker #0] ML tree search #17, logLikelihood: -99394.162176 Optimized model parameters: Partition 0: noname Rate heterogeneity: FREE (4 cats, mean), weights&rates: (0.184068,0.314910) (0.159262,0.466756) (0.355038,1.023210) (0.301632,1.672303) 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: -99368.710747 AIC score: 202747.421494 / AICc score: 8246807.421494 / BIC score: 209299.477103 Free parameters (model + branch lengths): 2005 WARNING: Number of free parameters (K=2005) is larger than alignment size (n=194). This might lead to overfitting and compromise tree inference results! Best ML tree saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/A5D8T8/3_mltree/A5D8T8.raxml.bestTree All ML trees saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/A5D8T8/3_mltree/A5D8T8.raxml.mlTrees Optimized model saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/A5D8T8/3_mltree/A5D8T8.raxml.bestModel Execution log saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/A5D8T8/3_mltree/A5D8T8.raxml.log Analysis started: 06-Jul-2021 07:16:07 / finished: 06-Jul-2021 13:44:16 Elapsed time: 23289.752 seconds Consumed energy: 1766.736 Wh (= 9 km in an electric car, or 44 km with an e-scooter!)