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) CPU E5-2690 v4 @ 2.60GHz, 28 cores, 251 GB RAM RAxML-NG was called at 07-Jul-2021 16:38:52 as follows: raxml-ng --msa /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/O43318/2_msa/O43318_trimmed_msa.fasta --data-type AA --model LG4X --prefix /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/O43318/3_mltree/O43318 --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: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/O43318/2_msa/O43318_trimmed_msa.fasta [00:00:00] Loaded alignment with 999 taxa and 238 sites WARNING: Sequences tr_A0A1D5NUC4_A0A1D5NUC4_CHICK_9031 and tr_U3JKK0_U3JKK0_FICAL_59894 are exactly identical! WARNING: Sequences tr_A0A1D5NUC4_A0A1D5NUC4_CHICK_9031 and tr_A0A091F5M8_A0A091F5M8_CORBR_85066 are exactly identical! WARNING: Sequences tr_A0A1D5NUC4_A0A1D5NUC4_CHICK_9031 and tr_A0A091FLF6_A0A091FLF6_9AVES_55661 are exactly identical! WARNING: Sequences tr_A0A1D5NUC4_A0A1D5NUC4_CHICK_9031 and tr_A0A218VC23_A0A218VC23_9PASE_299123 are exactly identical! WARNING: Sequences tr_A0A1D5P4R5_A0A1D5P4R5_CHICK_9031 and tr_A0A226NH32_A0A226NH32_CALSU_9009 are exactly identical! WARNING: Sequences tr_A0A1D5P4R5_A0A1D5P4R5_CHICK_9031 and tr_A0A226P568_A0A226P568_COLVI_9014 are exactly identical! WARNING: Sequences tr_A0A1D5PT46_A0A1D5PT46_CHICK_9031 and tr_G1NC02_G1NC02_MELGA_9103 are exactly identical! WARNING: Sequences tr_A0A1D5PT46_A0A1D5PT46_CHICK_9031 and tr_A0A093I100_A0A093I100_STRCA_441894 are exactly identical! WARNING: Sequences tr_A0A1D5PT46_A0A1D5PT46_CHICK_9031 and tr_A0A099ZIF3_A0A099ZIF3_TINGU_94827 are exactly identical! WARNING: Sequences sp_Q62073_M3K7_MOUSE_10090 and tr_M3YCF7_M3YCF7_MUSPF_9669 are exactly identical! WARNING: Sequences sp_Q62073_M3K7_MOUSE_10090 and tr_G1RSQ0_G1RSQ0_NOMLE_61853 are exactly identical! WARNING: Sequences sp_Q62073_M3K7_MOUSE_10090 and tr_G3RXU7_G3RXU7_GORGO_9595 are exactly identical! WARNING: Sequences sp_Q62073_M3K7_MOUSE_10090 and tr_H2PJU2_H2PJU2_PONAB_9601 are exactly identical! WARNING: Sequences sp_Q62073_M3K7_MOUSE_10090 and sp_Q5RFL3_M3K7_PONAB_9601 are exactly identical! WARNING: Sequences sp_Q62073_M3K7_MOUSE_10090 and tr_G1SFY3_G1SFY3_RABIT_9986 are exactly identical! WARNING: Sequences sp_Q62073_M3K7_MOUSE_10090 and tr_E2R3R6_E2R3R6_CANLF_9615 are exactly identical! WARNING: Sequences sp_Q62073_M3K7_MOUSE_10090 and tr_H2RCY2_H2RCY2_PANTR_9598 are exactly identical! WARNING: Sequences sp_Q62073_M3K7_MOUSE_10090 and tr_F7CCD5_F7CCD5_MONDO_13616 are exactly identical! WARNING: Sequences sp_Q62073_M3K7_MOUSE_10090 and tr_F7BAU3_F7BAU3_HORSE_9796 are exactly identical! WARNING: Sequences sp_Q62073_M3K7_MOUSE_10090 and tr_W5PRX8_W5PRX8_SHEEP_9940 are exactly identical! WARNING: Sequences sp_Q62073_M3K7_MOUSE_10090 and sp_P0C8E4_M3K7_RAT_10116 are exactly identical! WARNING: Sequences sp_Q62073_M3K7_MOUSE_10090 and tr_A0A287DFR1_A0A287DFR1_ICTTR_43179 are exactly identical! WARNING: Sequences sp_Q62073_M3K7_MOUSE_10090 and tr_H0WTC8_H0WTC8_OTOGA_30611 are exactly identical! WARNING: Sequences sp_Q62073_M3K7_MOUSE_10090 and sp_O43318_M3K7_HUMAN_9606 are exactly identical! WARNING: Sequences sp_Q62073_M3K7_MOUSE_10090 and tr_F7H6S1_F7H6S1_MACMU_9544 are exactly identical! WARNING: Sequences sp_Q62073_M3K7_MOUSE_10090 and tr_G5AL97_G5AL97_HETGA_10181 are exactly identical! WARNING: Sequences sp_Q62073_M3K7_MOUSE_10090 and tr_G3TL77_G3TL77_LOXAF_9785 are exactly identical! WARNING: Sequences sp_Q62073_M3K7_MOUSE_10090 and tr_G3WZI8_G3WZI8_SARHA_9305 are exactly identical! WARNING: Sequences sp_Q62073_M3K7_MOUSE_10090 and tr_U3CBH8_U3CBH8_CALJA_9483 are exactly identical! WARNING: Sequences sp_Q62073_M3K7_MOUSE_10090 and tr_B0LXP5_B0LXP5_PIG_9823 are exactly identical! WARNING: Sequences sp_Q62073_M3K7_MOUSE_10090 and tr_D2HRF5_D2HRF5_AILME_9646 are exactly identical! WARNING: Sequences sp_Q62073_M3K7_MOUSE_10090 and tr_G7P421_G7P421_MACFA_9541 are exactly identical! WARNING: Sequences sp_Q62073_M3K7_MOUSE_10090 and sp_A2VDU3_M3K7_BOVIN_9913 are exactly identical! WARNING: Sequences sp_Q62073_M3K7_MOUSE_10090 and tr_L5JL43_L5JL43_PTEAL_9402 are exactly identical! WARNING: Sequences sp_Q62073_M3K7_MOUSE_10090 and tr_M3WSG5_M3WSG5_FELCA_9685 are exactly identical! WARNING: Sequences sp_Q62073_M3K7_MOUSE_10090 and tr_A0A2I3LYE7_A0A2I3LYE7_PAPAN_9555 are exactly identical! WARNING: Sequences sp_Q62073_M3K7_MOUSE_10090 and tr_A0A091E2U7_A0A091E2U7_FUKDA_885580 are exactly identical! WARNING: Sequences sp_Q62073_M3K7_MOUSE_10090 and tr_A0A0D9RXG7_A0A0D9RXG7_CHLSB_60711 are exactly identical! WARNING: Sequences sp_Q62073_M3K7_MOUSE_10090 and tr_A0A1U7TCL6_A0A1U7TCL6_TARSY_1868482 are exactly identical! WARNING: Sequences sp_Q62073_M3K7_MOUSE_10090 and tr_A0A3Q0D412_A0A3Q0D412_MESAU_10036 are exactly identical! WARNING: Sequences sp_Q62073_M3K7_MOUSE_10090 and tr_A0A2K6D8Q7_A0A2K6D8Q7_MACNE_9545 are exactly identical! WARNING: Sequences sp_Q62073_M3K7_MOUSE_10090 and tr_A0A2K5ZSU5_A0A2K5ZSU5_MANLE_9568 are exactly identical! WARNING: Sequences sp_Q62073_M3K7_MOUSE_10090 and tr_A0A2R8ZZW1_A0A2R8ZZW1_PANPA_9597 are exactly identical! WARNING: Sequences sp_Q62073_M3K7_MOUSE_10090 and tr_A0A2U4AVL4_A0A2U4AVL4_TURTR_9739 are exactly identical! WARNING: Sequences sp_Q62073_M3K7_MOUSE_10090 and tr_A0A2U4AVN0_A0A2U4AVN0_TURTR_9739 are exactly identical! WARNING: Sequences sp_Q62073_M3K7_MOUSE_10090 and tr_A0A2U3X6I3_A0A2U3X6I3_LEPWE_9713 are exactly identical! WARNING: Sequences sp_Q62073_M3K7_MOUSE_10090 and tr_A0A2Y9E8P5_A0A2Y9E8P5_TRIMA_127582 are exactly identical! WARNING: Sequences sp_Q62073_M3K7_MOUSE_10090 and tr_A0A2Y9KSQ6_A0A2Y9KSQ6_ENHLU_391180 are exactly identical! WARNING: Sequences sp_Q62073_M3K7_MOUSE_10090 and tr_A0A2Y9LI75_A0A2Y9LI75_DELLE_9749 are exactly identical! WARNING: Sequences sp_Q62073_M3K7_MOUSE_10090 and tr_A0A2Y9FM10_A0A2Y9FM10_PHYCD_9755 are exactly identical! WARNING: Sequences sp_Q62073_M3K7_MOUSE_10090 and tr_A0A384BTK6_A0A384BTK6_URSMA_29073 are exactly identical! WARNING: Sequences sp_Q62073_M3K7_MOUSE_10090 and tr_A0A384B8N5_A0A384B8N5_BALAS_310752 are exactly identical! WARNING: Sequences sp_Q95UN8_M3KSL_DROME_7227 and tr_B4IKY6_B4IKY6_DROSE_7238 are exactly identical! WARNING: Sequences tr_A0A2I3FR90_A0A2I3FR90_NOMLE_61853 and tr_A0A2J8VQZ7_A0A2J8VQZ7_PONAB_9601 are exactly identical! WARNING: Sequences tr_A0A2I3FR90_A0A2I3FR90_NOMLE_61853 and tr_I3MCR4_I3MCR4_ICTTR_43179 are exactly identical! WARNING: Sequences tr_A0A2I3FR90_A0A2I3FR90_NOMLE_61853 and tr_H0XAF1_H0XAF1_OTOGA_30611 are exactly identical! WARNING: Sequences tr_A0A2I3FR90_A0A2I3FR90_NOMLE_61853 and sp_Q9NYL2_M3K20_HUMAN_9606 are exactly identical! WARNING: Sequences tr_A0A2I3FR90_A0A2I3FR90_NOMLE_61853 and tr_F7BN69_F7BN69_MACMU_9544 are exactly identical! WARNING: Sequences tr_A0A2I3FR90_A0A2I3FR90_NOMLE_61853 and tr_G7PKU5_G7PKU5_MACFA_9541 are exactly identical! WARNING: Sequences tr_A0A2I3FR90_A0A2I3FR90_NOMLE_61853 and tr_L5K038_L5K038_PTEAL_9402 are exactly identical! WARNING: Sequences tr_A0A2I3FR90_A0A2I3FR90_NOMLE_61853 and tr_A0A096NZL7_A0A096NZL7_PAPAN_9555 are exactly identical! WARNING: Sequences tr_A0A2I3FR90_A0A2I3FR90_NOMLE_61853 and tr_A0A1S3A038_A0A1S3A038_ERIEU_9365 are exactly identical! WARNING: Sequences tr_A0A2I3FR90_A0A2I3FR90_NOMLE_61853 and tr_A0A3Q0D4Y6_A0A3Q0D4Y6_MESAU_10036 are exactly identical! WARNING: Sequences tr_A0A2I3FR90_A0A2I3FR90_NOMLE_61853 and tr_A0A2K5Z3R4_A0A2K5Z3R4_MANLE_9568 are exactly identical! WARNING: Sequences tr_G1QMU3_G1QMU3_NOMLE_61853 and tr_H2NLP2_H2NLP2_PONAB_9601 are exactly identical! WARNING: Sequences tr_G1QMU3_G1QMU3_NOMLE_61853 and tr_H2Q8J6_H2Q8J6_PANTR_9598 are exactly identical! WARNING: Sequences tr_G1QMU3_G1QMU3_NOMLE_61853 and sp_P80192_M3K9_HUMAN_9606 are exactly identical! WARNING: Sequences tr_G1QMU3_G1QMU3_NOMLE_61853 and tr_F7H042_F7H042_CALJA_9483 are exactly identical! WARNING: Sequences tr_G1QMU3_G1QMU3_NOMLE_61853 and tr_G1LN14_G1LN14_AILME_9646 are exactly identical! WARNING: Sequences tr_G1QMU3_G1QMU3_NOMLE_61853 and tr_A0A2I2U1R9_A0A2I2U1R9_FELCA_9685 are exactly identical! WARNING: Sequences tr_G1QMU3_G1QMU3_NOMLE_61853 and tr_A0A2R8ZZF8_A0A2R8ZZF8_PANPA_9597 are exactly identical! WARNING: Sequences tr_G1QMU3_G1QMU3_NOMLE_61853 and tr_A0A2U3X2N8_A0A2U3X2N8_ODORO_9708 are exactly identical! WARNING: Sequences tr_G1QMU3_G1QMU3_NOMLE_61853 and tr_A0A2U3XSU7_A0A2U3XSU7_LEPWE_9713 are exactly identical! WARNING: Sequences tr_G1QMU3_G1QMU3_NOMLE_61853 and tr_A0A2Y9DBN4_A0A2Y9DBN4_TRIMA_127582 are exactly identical! WARNING: Sequences tr_G1QMU3_G1QMU3_NOMLE_61853 and tr_A0A2Y9JSK6_A0A2Y9JSK6_ENHLU_391180 are exactly identical! WARNING: Sequences tr_G3QGC1_G3QGC1_GORGO_9595 and tr_H2NYU5_H2NYU5_PONAB_9601 are exactly identical! WARNING: Sequences tr_G3QGC1_G3QGC1_GORGO_9595 and tr_H2QGC0_H2QGC0_PANTR_9598 are exactly identical! WARNING: Sequences tr_G3QGC1_G3QGC1_GORGO_9595 and sp_Q02779_M3K10_HUMAN_9606 are exactly identical! WARNING: Sequences tr_G3QGC1_G3QGC1_GORGO_9595 and tr_A0A2R9CMA2_A0A2R9CMA2_PANPA_9597 are exactly identical! WARNING: Sequences tr_G1NLK0_G1NLK0_MELGA_9103 and tr_A0A091IRF8_A0A091IRF8_EGRGA_188379 are exactly identical! WARNING: Sequences tr_G1NLK0_G1NLK0_MELGA_9103 and tr_A0A093QAL5_A0A093QAL5_9PASS_328815 are exactly identical! WARNING: Sequences tr_G1NLK0_G1NLK0_MELGA_9103 and tr_A0A091W3E3_A0A091W3E3_NIPNI_128390 are exactly identical! WARNING: Sequences tr_G1NLK0_G1NLK0_MELGA_9103 and tr_A0A093JRR1_A0A093JRR1_STRCA_441894 are exactly identical! WARNING: Sequences tr_G1NLK0_G1NLK0_MELGA_9103 and tr_A0A091WEW8_A0A091WEW8_OPIHO_30419 are exactly identical! WARNING: Sequences tr_G1NLK0_G1NLK0_MELGA_9103 and tr_A0A099ZLV2_A0A099ZLV2_TINGU_94827 are exactly identical! WARNING: Sequences tr_G1NLK0_G1NLK0_MELGA_9103 and tr_A0A0A0AP87_A0A0A0AP87_CHAVO_50402 are exactly identical! WARNING: Sequences tr_G1SJ83_G1SJ83_RABIT_9986 and tr_F1P626_F1P626_CANLF_9615 are exactly identical! WARNING: Sequences tr_Q29GL6_Q29GL6_DROPS_46245 and tr_B4H0S1_B4H0S1_DROPE_7234 are exactly identical! WARNING: Sequences tr_E2REE9_E2REE9_CANLF_9615 and tr_G1L0B9_G1L0B9_AILME_9646 are exactly identical! WARNING: Sequences tr_E2REE9_E2REE9_CANLF_9615 and tr_A0A337SLR8_A0A337SLR8_FELCA_9685 are exactly identical! WARNING: Sequences tr_E2REE9_E2REE9_CANLF_9615 and tr_A0A2U3WG81_A0A2U3WG81_ODORO_9708 are exactly identical! WARNING: Sequences tr_E2REE9_E2REE9_CANLF_9615 and tr_A0A2Y9IWE3_A0A2Y9IWE3_ENHLU_391180 are exactly identical! WARNING: Sequences tr_E2REE9_E2REE9_CANLF_9615 and tr_A0A384BT67_A0A384BT67_URSMA_29073 are exactly identical! WARNING: Sequences sp_D3ZG83_M3K10_RAT_10116 and tr_I3LT36_I3LT36_PIG_9823 are exactly identical! WARNING: Sequences sp_D3ZG83_M3K10_RAT_10116 and tr_E1B7H4_E1B7H4_BOVIN_9913 are exactly identical! WARNING: Sequences tr_M3ZS20_M3ZS20_XIPMA_8083 and tr_A0A096M5P1_A0A096M5P1_POEFO_48698 are exactly identical! WARNING: Sequences tr_A0A088A795_A0A088A795_APIME_7460 and tr_A0A0M8ZN83_A0A0M8ZN83_9HYME_166423 are exactly identical! WARNING: Sequences tr_A0A088A795_A0A088A795_APIME_7460 and tr_A0A0L7QNJ2_A0A0L7QNJ2_9HYME_597456 are exactly identical! WARNING: Sequences tr_A0A088A795_A0A088A795_APIME_7460 and tr_A0A2A3ED90_A0A2A3ED90_APICC_94128 are exactly identical! WARNING: Sequences tr_A0A158NH59_A0A158NH59_ATTCE_12957 and tr_F4WZI8_F4WZI8_ACREC_103372 are exactly identical! WARNING: Sequences tr_A0A158NH59_A0A158NH59_ATTCE_12957 and tr_A0A195DQE3_A0A195DQE3_9HYME_471704 are exactly identical! WARNING: Sequences tr_A0A158NH59_A0A158NH59_ATTCE_12957 and tr_A0A195BW05_A0A195BW05_9HYME_520822 are exactly identical! WARNING: Sequences tr_A0A158NKD5_A0A158NKD5_ATTCE_12957 and tr_A0A195AZZ8_A0A195AZZ8_9HYME_520822 are exactly identical! WARNING: Sequences tr_J3LA18_J3LA18_ORYBR_4533 and tr_A0A0E0G240_A0A0E0G240_ORYNI_4536 are exactly identical! WARNING: Sequences tr_J3LA18_J3LA18_ORYBR_4533 and tr_A2X1G7_A2X1G7_ORYSI_39946 are exactly identical! WARNING: Sequences tr_J3LA18_J3LA18_ORYBR_4533 and tr_I1NXQ9_I1NXQ9_ORYGL_4538 are exactly identical! WARNING: Sequences tr_J3LA18_J3LA18_ORYBR_4533 and tr_A0A0E0CGF6_A0A0E0CGF6_9ORYZ_40149 are exactly identical! WARNING: Sequences tr_J3LA18_J3LA18_ORYBR_4533 and tr_A0A0E0NAK3_A0A0E0NAK3_ORYRU_4529 are exactly identical! WARNING: Sequences tr_J3LA18_J3LA18_ORYBR_4533 and tr_A0A0D3F1D9_A0A0D3F1D9_9ORYZ_65489 are exactly identical! WARNING: Sequences tr_J3LA18_J3LA18_ORYBR_4533 and tr_A0A0D9YN18_A0A0D9YN18_9ORYZ_40148 are exactly identical! WARNING: Sequences tr_J3LA18_J3LA18_ORYBR_4533 and tr_A0A0D9VCS8_A0A0D9VCS8_9ORYZ_77586 are exactly identical! WARNING: Sequences tr_J3LA18_J3LA18_ORYBR_4533 and tr_Q8GV28_Q8GV28_ORYSJ_39947 are exactly identical! WARNING: Sequences tr_A0A0E0H5R9_A0A0E0H5R9_ORYNI_4536 and tr_A2XXC2_A2XXC2_ORYSI_39946 are exactly identical! WARNING: Sequences tr_A0A0E0H5R9_A0A0E0H5R9_ORYNI_4536 and tr_I1PPK1_I1PPK1_ORYGL_4538 are exactly identical! WARNING: Sequences tr_A0A0E0H5R9_A0A0E0H5R9_ORYNI_4536 and tr_A0A0E0DI28_A0A0E0DI28_9ORYZ_40149 are exactly identical! WARNING: Sequences tr_A0A0E0H5R9_A0A0E0H5R9_ORYNI_4536 and tr_A0A0D9ZQF6_A0A0D9ZQF6_9ORYZ_40148 are exactly identical! WARNING: Sequences tr_A0A0E0H5R9_A0A0E0H5R9_ORYNI_4536 and tr_Q8GV29_Q8GV29_ORYSJ_39947 are exactly identical! WARNING: Sequences tr_A0A0E0HUK1_A0A0E0HUK1_ORYNI_4536 and tr_A2YFW8_A2YFW8_ORYSI_39946 are exactly identical! WARNING: Sequences tr_A0A0E0HUK1_A0A0E0HUK1_ORYNI_4536 and tr_I1Q4D5_I1Q4D5_ORYGL_4538 are exactly identical! WARNING: Sequences tr_A0A0E0HUK1_A0A0E0HUK1_ORYNI_4536 and tr_A0A0E0E4V8_A0A0E0E4V8_9ORYZ_40149 are exactly identical! WARNING: Sequences tr_A0A0E0HUK1_A0A0E0HUK1_ORYNI_4536 and tr_A0A0E0Q194_A0A0E0Q194_ORYRU_4529 are exactly identical! WARNING: Sequences tr_A0A0E0HUK1_A0A0E0HUK1_ORYNI_4536 and tr_A0A0D3GJL4_A0A0D3GJL4_9ORYZ_65489 are exactly identical! WARNING: Sequences tr_A0A0E0HUK1_A0A0E0HUK1_ORYNI_4536 and tr_A0A0E0ACW3_A0A0E0ACW3_9ORYZ_40148 are exactly identical! WARNING: Sequences tr_A0A0E0HUK1_A0A0E0HUK1_ORYNI_4536 and tr_Q653Z6_Q653Z6_ORYSJ_39947 are exactly identical! WARNING: Sequences tr_A0A0E0I705_A0A0E0I705_ORYNI_4536 and tr_Q6DTV6_Q6DTV6_ORYSI_39946 are exactly identical! WARNING: Sequences tr_A0A0E0I705_A0A0E0I705_ORYNI_4536 and tr_I1QGL4_I1QGL4_ORYGL_4538 are exactly identical! WARNING: Sequences tr_A0A0E0I705_A0A0E0I705_ORYNI_4536 and tr_A0A0E0EJ71_A0A0E0EJ71_9ORYZ_40149 are exactly identical! WARNING: Sequences tr_A0A0E0I705_A0A0E0I705_ORYNI_4536 and tr_A0A0E0QFT0_A0A0E0QFT0_ORYRU_4529 are exactly identical! WARNING: Sequences tr_A0A0E0I705_A0A0E0I705_ORYNI_4536 and tr_A0A0D3GXK0_A0A0D3GXK0_9ORYZ_65489 are exactly identical! WARNING: Sequences tr_A0A0E0I705_A0A0E0I705_ORYNI_4536 and tr_Q8GV30_Q8GV30_ORYSJ_39947 are exactly identical! WARNING: Sequences tr_A0A0E0IN43_A0A0E0IN43_ORYNI_4536 and tr_A2Z3N4_A2Z3N4_ORYSI_39946 are exactly identical! WARNING: Sequences tr_A0A0E0IN43_A0A0E0IN43_ORYNI_4536 and tr_I1QQW9_I1QQW9_ORYGL_4538 are exactly identical! WARNING: Sequences tr_A0A0E0IN43_A0A0E0IN43_ORYNI_4536 and tr_A0A0E0EUH7_A0A0E0EUH7_9ORYZ_40149 are exactly identical! WARNING: Sequences tr_A0A0E0IN43_A0A0E0IN43_ORYNI_4536 and tr_A0A0D3H9K3_A0A0D3H9K3_9ORYZ_65489 are exactly identical! WARNING: Sequences tr_A0A0E0IN43_A0A0E0IN43_ORYNI_4536 and tr_A0A0E0B5Z4_A0A0E0B5Z4_9ORYZ_40148 are exactly identical! WARNING: Sequences tr_A0A0E0IN43_A0A0E0IN43_ORYNI_4536 and tr_Q7XXN2_Q7XXN2_ORYSJ_39947 are exactly identical! WARNING: Sequences tr_D0NUE0_D0NUE0_PHYIT_403677 and tr_W2Q694_W2Q694_PHYPN_761204 are exactly identical! WARNING: Sequences tr_D0NUE0_D0NUE0_PHYIT_403677 and tr_A0A0W8CIY8_A0A0W8CIY8_PHYNI_4790 are exactly identical! WARNING: Sequences tr_D0NUE0_D0NUE0_PHYIT_403677 and tr_W2L7T2_W2L7T2_PHYPR_4792 are exactly identical! WARNING: Sequences tr_F6VUC2_F6VUC2_MACMU_9544 and tr_A0A2I3LNV8_A0A2I3LNV8_PAPAN_9555 are exactly identical! WARNING: Sequences tr_F6VUC2_F6VUC2_MACMU_9544 and tr_A0A2K5LGI1_A0A2K5LGI1_CERAT_9531 are exactly identical! WARNING: Sequences tr_F6VUC2_F6VUC2_MACMU_9544 and tr_A0A2K6CZF3_A0A2K6CZF3_MACNE_9545 are exactly identical! WARNING: Sequences tr_F6XQC8_F6XQC8_MACMU_9544 and tr_A0A0A0MV36_A0A0A0MV36_PAPAN_9555 are exactly identical! WARNING: Sequences tr_F6XQC8_F6XQC8_MACMU_9544 and tr_A0A0D9QUU1_A0A0D9QUU1_CHLSB_60711 are exactly identical! WARNING: Sequences tr_F6XQC8_F6XQC8_MACMU_9544 and tr_A0A2K5NJ63_A0A2K5NJ63_CERAT_9531 are exactly identical! WARNING: Sequences tr_F6XQC8_F6XQC8_MACMU_9544 and tr_A0A2K6BFN1_A0A2K6BFN1_MACNE_9545 are exactly identical! WARNING: Sequences tr_H0ZEB6_H0ZEB6_TAEGU_59729 and tr_U3JJT0_U3JJT0_FICAL_59894 are exactly identical! WARNING: Sequences tr_H0ZEB6_H0ZEB6_TAEGU_59729 and tr_A0A0Q3U273_A0A0Q3U273_AMAAE_12930 are exactly identical! WARNING: Sequences tr_H0ZEB6_H0ZEB6_TAEGU_59729 and tr_A0A218V151_A0A218V151_9PASE_299123 are exactly identical! WARNING: Sequences tr_H0ZM86_H0ZM86_TAEGU_59729 and tr_A0A091F310_A0A091F310_CORBR_85066 are exactly identical! WARNING: Sequences tr_F4X1B8_F4X1B8_ACREC_103372 and tr_A0A151WNW5_A0A151WNW5_9HYME_64791 are exactly identical! WARNING: Sequences tr_F4X1B8_F4X1B8_ACREC_103372 and tr_A0A195DP70_A0A195DP70_9HYME_471704 are exactly identical! WARNING: Sequences tr_F4X1B8_F4X1B8_ACREC_103372 and tr_A0A195BDQ6_A0A195BDQ6_9HYME_520822 are exactly identical! WARNING: Sequences tr_G1M1R5_G1M1R5_AILME_9646 and tr_M3WGG8_M3WGG8_FELCA_9685 are exactly identical! WARNING: Sequences tr_G1M1R5_G1M1R5_AILME_9646 and tr_A0A2U3VMZ1_A0A2U3VMZ1_ODORO_9708 are exactly identical! WARNING: Sequences tr_G1M1R5_G1M1R5_AILME_9646 and tr_A0A384BXL3_A0A384BXL3_URSMA_29073 are exactly identical! WARNING: Sequences tr_B3S0S9_B3S0S9_TRIAD_10228 and tr_A0A369SCR0_A0A369SCR0_9METZ_287889 are exactly identical! WARNING: Sequences tr_G7PAS1_G7PAS1_MACFA_9541 and tr_A0A2K5XHH3_A0A2K5XHH3_MANLE_9568 are exactly identical! WARNING: Sequences tr_M4D446_M4D446_BRARP_51351 and tr_A0A078GSW5_A0A078GSW5_BRANA_3708 are exactly identical! WARNING: Sequences tr_M4E5G6_M4E5G6_BRARP_51351 and tr_A0A078FKC3_A0A078FKC3_BRANA_3708 are exactly identical! WARNING: Sequences tr_W2PW01_W2PW01_PHYPN_761204 and tr_W2KRX8_W2KRX8_PHYPR_4792 are exactly identical! WARNING: Sequences tr_W2PYG7_W2PYG7_PHYPN_761204 and tr_A0A0W8C9C0_A0A0W8C9C0_PHYNI_4790 are exactly identical! WARNING: Sequences tr_W2PYG7_W2PYG7_PHYPN_761204 and tr_W2IMN9_W2IMN9_PHYPR_4792 are exactly identical! WARNING: Sequences tr_W2R4S5_W2R4S5_PHYPN_761204 and tr_A0A0W8D2L1_A0A0W8D2L1_PHYNI_4790 are exactly identical! WARNING: Sequences tr_W2R4S5_W2R4S5_PHYPN_761204 and tr_W2KJ21_W2KJ21_PHYPR_4792 are exactly identical! WARNING: Sequences tr_A0A3B6LRR0_A0A3B6LRR0_WHEAT_4565 and tr_A0A3B6MVS1_A0A3B6MVS1_WHEAT_4565 are exactly identical! WARNING: Sequences tr_A0A3B6NUY0_A0A3B6NUY0_WHEAT_4565 and tr_A0A3B6PNX1_A0A3B6PNX1_WHEAT_4565 are exactly identical! WARNING: Sequences tr_A0A067FLE1_A0A067FLE1_CITSI_2711 and tr_V4U926_V4U926_9ROSI_85681 are exactly identical! WARNING: Sequences tr_A0A067GNN3_A0A067GNN3_CITSI_2711 and tr_V4TBN8_V4TBN8_9ROSI_85681 are exactly identical! WARNING: Sequences tr_A0A078GD42_A0A078GD42_BRANA_3708 and tr_A0A078HI36_A0A078HI36_BRANA_3708 are exactly identical! WARNING: Sequences tr_A0A078GD42_A0A078GD42_BRANA_3708 and tr_A0A0D3BM14_A0A0D3BM14_BRAOL_109376 are exactly identical! WARNING: Sequences tr_A0A0A0LML1_A0A0A0LML1_CUCSA_3659 and tr_A0A1S3BQ63_A0A1S3BQ63_CUCME_3656 are exactly identical! WARNING: Sequences tr_A0A0D2M4W2_A0A0D2M4W2_GOSRA_29730 and tr_A0A1U8LM17_A0A1U8LM17_GOSHI_3635 are exactly identical! WARNING: Sequences tr_A0A0D2REG1_A0A0D2REG1_GOSRA_29730 and tr_A0A1U8MLC5_A0A1U8MLC5_GOSHI_3635 are exactly identical! WARNING: Sequences tr_A0A151M001_A0A151M001_ALLMI_8496 and tr_A0A1U7SG77_A0A1U7SG77_ALLSI_38654 are exactly identical! WARNING: Sequences tr_A0A091JCK4_A0A091JCK4_EGRGA_188379 and tr_A0A091UV93_A0A091UV93_NIPNI_128390 are exactly identical! WARNING: Sequences tr_A0A091JCK4_A0A091JCK4_EGRGA_188379 and tr_A0A087R0N1_A0A087R0N1_APTFO_9233 are exactly identical! WARNING: Sequences tr_A0A091JCK4_A0A091JCK4_EGRGA_188379 and tr_A0A091FSW6_A0A091FSW6_9AVES_55661 are exactly identical! WARNING: Sequences tr_A0A091JCK4_A0A091JCK4_EGRGA_188379 and tr_A0A091IBC5_A0A091IBC5_CALAN_9244 are exactly identical! WARNING: Sequences tr_A0A091K5V7_A0A091K5V7_EGRGA_188379 and tr_A0A099ZWS2_A0A099ZWS2_CHAVO_50402 are exactly identical! WARNING: Sequences tr_A0A091K5V7_A0A091K5V7_EGRGA_188379 and tr_A0A093GL16_A0A093GL16_DRYPU_118200 are exactly identical! WARNING: Sequences tr_A0A0L9THB5_A0A0L9THB5_PHAAN_3914 and tr_A0A1S3USP9_A0A1S3USP9_VIGRR_3916 are exactly identical! WARNING: Sequences tr_A0A194RMF3_A0A194RMF3_PAPMA_76193 and tr_A0A194Q2Z4_A0A194Q2Z4_PAPXU_66420 are exactly identical! WARNING: Sequences tr_A0A2I0MJ01_A0A2I0MJ01_COLLI_8932 and tr_A0A1V4K6K4_A0A1V4K6K4_PATFA_372326 are exactly identical! WARNING: Sequences tr_A0A0V0WVM8_A0A0V0WVM8_9BILA_92179 and tr_A0A0V1LRQ9_A0A0V1LRQ9_9BILA_6335 are exactly identical! WARNING: Sequences tr_A0A1S3XTN8_A0A1S3XTN8_TOBAC_4097 and tr_A0A1U7YJI0_A0A1U7YJI0_NICSY_4096 are exactly identical! WARNING: Sequences tr_A0A1S3ZVF4_A0A1S3ZVF4_TOBAC_4097 and tr_A0A314L368_A0A314L368_NICAT_49451 are exactly identical! WARNING: Sequences tr_A0A1S4AA74_A0A1S4AA74_TOBAC_4097 and tr_A0A1U7YTV3_A0A1U7YTV3_NICSY_4096 are exactly identical! WARNING: Sequences tr_A0A1S4AGT4_A0A1S4AGT4_TOBAC_4097 and tr_A0A1U7VYT6_A0A1U7VYT6_NICSY_4096 are exactly identical! WARNING: Sequences tr_A0A1S4AL66_A0A1S4AL66_TOBAC_4097 and tr_A0A1S4D257_A0A1S4D257_TOBAC_4097 are exactly identical! WARNING: Sequences tr_A0A1S4AL66_A0A1S4AL66_TOBAC_4097 and tr_A0A314KZV3_A0A314KZV3_NICAT_49451 are exactly identical! WARNING: Sequences tr_A0A1S4AL66_A0A1S4AL66_TOBAC_4097 and tr_A0A1U7Y7C5_A0A1U7Y7C5_NICSY_4096 are exactly identical! WARNING: Sequences tr_A0A1S4CIV7_A0A1S4CIV7_TOBAC_4097 and tr_A0A1U7X550_A0A1U7X550_NICSY_4096 are exactly identical! WARNING: Sequences tr_A0A1S3I3B9_A0A1S3I3B9_LINUN_7574 and tr_A0A1S3IIJ3_A0A1S3IIJ3_LINUN_7574 are exactly identical! WARNING: Sequences tr_A0A1S3Q5Z6_A0A1S3Q5Z6_SALSA_8030 and tr_A0A060WH32_A0A060WH32_ONCMY_8022 are exactly identical! WARNING: Sequences tr_A0A1S3S7Y3_A0A1S3S7Y3_SALSA_8030 and tr_C0H8V1_C0H8V1_SALSA_8030 are exactly identical! WARNING: Sequences tr_A0A1L8G366_A0A1L8G366_XENLA_8355 and tr_O73613_O73613_XENLA_8355 are exactly identical! WARNING: Sequences tr_A0A2D0QP22_A0A2D0QP22_ICTPU_7998 and tr_A0A2D0QRF0_A0A2D0QRF0_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A1U8E0Q9_A0A1U8E0Q9_CAPAN_4072 and tr_A0A2G3BW57_A0A2G3BW57_CAPCH_80379 are exactly identical! WARNING: Sequences tr_A0A2G2Z1K5_A0A2G2Z1K5_CAPAN_4072 and tr_A0A2G3BZP5_A0A2G3BZP5_CAPCH_80379 are exactly identical! WARNING: Sequences tr_A0A2G3A9X9_A0A2G3A9X9_CAPAN_4072 and tr_A0A2G3D7F5_A0A2G3D7F5_CAPCH_80379 are exactly identical! WARNING: Sequences tr_A0A2G8JYE4_A0A2G8JYE4_STIJA_307972 and tr_A0A2G8K2I4_A0A2G8K2I4_STIJA_307972 are exactly identical! WARNING: Sequences tr_A0A2J6JMT0_A0A2J6JMT0_LACSA_4236 and tr_A0A2J6JQU8_A0A2J6JQU8_LACSA_4236 are exactly identical! WARNING: Sequences tr_A0A2J6JMT0_A0A2J6JMT0_LACSA_4236 and tr_A0A2J6MI55_A0A2J6MI55_LACSA_4236 are exactly identical! WARNING: Sequences tr_A0A2U4A929_A0A2U4A929_TURTR_9739 and tr_A0A2Y9N3G2_A0A2Y9N3G2_DELLE_9749 are exactly identical! WARNING: Sequences tr_A0A2U4A929_A0A2U4A929_TURTR_9739 and tr_A0A384AAU1_A0A384AAU1_BALAS_310752 are exactly identical! WARNING: Sequences tr_A0A2U4ABX3_A0A2U4ABX3_TURTR_9739 and tr_A0A2U4AC80_A0A2U4AC80_TURTR_9739 are exactly identical! WARNING: Sequences tr_A0A2Y9PFF5_A0A2Y9PFF5_DELLE_9749 and tr_A0A2Y9TDW0_A0A2Y9TDW0_PHYCD_9755 are exactly identical! WARNING: Duplicate sequences found: 208 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/O43318/3_mltree/O43318.raxml.reduced.phy Alignment comprises 1 partitions and 238 patterns Partition 0: noname Model: LG4X+R4 Alignment sites / patterns: 238 / 238 Gaps: 1.68 % Invariant sites: 0.00 % NOTE: Binary MSA file created: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/O43318/3_mltree/O43318.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 999 taxa [00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 238 / 19040 [00:00:00] Data distribution: max. searches per worker: 4 Starting ML tree search with 20 distinct starting trees [00:00:00 -414456.713099] Initial branch length optimization [00:00:06 -342499.290674] Model parameter optimization (eps = 10.000000) [00:01:10 -340748.934504] AUTODETECT spr round 1 (radius: 5) [00:05:11 -204120.905792] AUTODETECT spr round 2 (radius: 10) [00:09:21 -146088.294119] AUTODETECT spr round 3 (radius: 15) [00:13:33 -121407.432869] AUTODETECT spr round 4 (radius: 20) [00:18:10 -106374.333112] AUTODETECT spr round 5 (radius: 25) [00:23:27 -97982.005830] SPR radius for FAST iterations: 25 (autodetect) [00:23:27 -97982.005830] Model parameter optimization (eps = 3.000000) [00:23:55 -97927.221336] FAST spr round 1 (radius: 25) [00:27:59 -80557.506002] FAST spr round 2 (radius: 25) [00:30:51 -79490.285349] FAST spr round 3 (radius: 25) [00:33:22 -79397.809338] FAST spr round 4 (radius: 25) [00:35:41 -79392.606990] FAST spr round 5 (radius: 25) [00:37:53 -79390.397886] FAST spr round 6 (radius: 25) [00:40:03 -79388.548351] FAST spr round 7 (radius: 25) [00:42:12 -79383.915702] FAST spr round 8 (radius: 25) [00:44:17 -79383.324939] FAST spr round 9 (radius: 25) [00:46:23 -79383.323574] Model parameter optimization (eps = 1.000000) [00:46:50 -79376.031375] SLOW spr round 1 (radius: 5) [00:49:34 -79353.590146] SLOW spr round 2 (radius: 5) [00:52:23 -79352.561830] SLOW spr round 3 (radius: 5) [00:55:11 -79352.561137] SLOW spr round 4 (radius: 10) [00:58:13 -79351.016675] SLOW spr round 5 (radius: 5) [01:01:59 -79347.192178] SLOW spr round 6 (radius: 5) [01:05:14 -79346.499203] SLOW spr round 7 (radius: 5) [01:08:12 -79346.255934] SLOW spr round 8 (radius: 5) [01:11:01 -79346.255444] SLOW spr round 9 (radius: 10) [01:13:59 -79343.686908] SLOW spr round 10 (radius: 5) [01:17:39 -79339.295486] SLOW spr round 11 (radius: 5) [01:18:03] [worker #2] ML tree search #3, logLikelihood: -79379.033309 [01:20:49 -79339.295412] SLOW spr round 12 (radius: 10) [01:21:12] [worker #3] ML tree search #4, logLikelihood: -79369.432586 [01:23:54 -79339.295327] SLOW spr round 13 (radius: 15) [01:26:36] [worker #4] ML tree search #5, logLikelihood: -79353.891839 [01:28:15 -79339.295272] SLOW spr round 14 (radius: 20) [01:34:44 -79339.295256] SLOW spr round 15 (radius: 25) [01:38:50] [worker #1] ML tree search #2, logLikelihood: -79380.679737 [01:43:06 -79339.295240] Model parameter optimization (eps = 0.100000) [01:43:31] [worker #0] ML tree search #1, logLikelihood: -79337.294743 [01:43:31 -412375.263705] Initial branch length optimization [01:43:37 -338401.686293] Model parameter optimization (eps = 10.000000) [01:44:40 -337031.958760] AUTODETECT spr round 1 (radius: 5) [01:48:40 -202285.939830] AUTODETECT spr round 2 (radius: 10) [01:52:37 -152058.944905] AUTODETECT spr round 3 (radius: 15) [01:56:52 -126393.857216] AUTODETECT spr round 4 (radius: 20) [02:01:44 -108623.655777] AUTODETECT spr round 5 (radius: 25) [02:06:46 -100181.373675] SPR radius for FAST iterations: 25 (autodetect) [02:06:46 -100181.373675] Model parameter optimization (eps = 3.000000) [02:07:11 -100129.653683] FAST spr round 1 (radius: 25) [02:11:05 -80391.027320] FAST spr round 2 (radius: 25) [02:13:52 -79464.518705] FAST spr round 3 (radius: 25) [02:16:20 -79396.571090] FAST spr round 4 (radius: 25) [02:18:35 -79385.373604] FAST spr round 5 (radius: 25) [02:20:43 -79385.373244] Model parameter optimization (eps = 1.000000) [02:21:13 -79379.764856] SLOW spr round 1 (radius: 5) [02:24:02 -79357.502501] SLOW spr round 2 (radius: 5) [02:26:52 -79351.621527] SLOW spr round 3 (radius: 5) [02:29:35 -79351.603020] SLOW spr round 4 (radius: 10) [02:30:03] [worker #2] ML tree search #8, logLikelihood: -79369.460919 [02:32:27 -79351.602588] SLOW spr round 5 (radius: 15) [02:36:57 -79351.602365] SLOW spr round 6 (radius: 20) [02:43:30 -79351.602250] SLOW spr round 7 (radius: 25) [02:49:55] [worker #4] ML tree search #10, logLikelihood: -79377.783634 [02:51:55 -79351.602188] Model parameter optimization (eps = 0.100000) [02:52:13] [worker #0] ML tree search #6, logLikelihood: -79348.901882 [02:52:13 -412424.015177] Initial branch length optimization [02:52:19 -339718.630093] Model parameter optimization (eps = 10.000000) [02:53:22 -338114.969981] AUTODETECT spr round 1 (radius: 5) [02:57:20 -205525.651613] AUTODETECT spr round 2 (radius: 10) [03:01:21 -152953.143109] AUTODETECT spr round 3 (radius: 15) [03:03:29] [worker #1] ML tree search #7, logLikelihood: -79366.132293 [03:05:41 -127227.022298] AUTODETECT spr round 4 (radius: 20) [03:07:22] [worker #3] ML tree search #9, logLikelihood: -79357.631890 [03:10:09 -114060.359515] AUTODETECT spr round 5 (radius: 25) [03:15:13 -107469.126269] SPR radius for FAST iterations: 25 (autodetect) [03:15:13 -107469.126269] Model parameter optimization (eps = 3.000000) [03:15:41 -107448.430226] FAST spr round 1 (radius: 25) [03:19:48 -82647.534935] FAST spr round 2 (radius: 25) [03:22:40 -79765.928516] FAST spr round 3 (radius: 25) [03:25:13 -79417.035306] FAST spr round 4 (radius: 25) [03:27:36 -79401.934400] FAST spr round 5 (radius: 25) [03:29:49 -79399.443065] FAST spr round 6 (radius: 25) [03:31:54 -79399.442463] Model parameter optimization (eps = 1.000000) [03:32:13 -79389.357061] SLOW spr round 1 (radius: 5) [03:34:58 -79361.998284] SLOW spr round 2 (radius: 5) [03:37:46 -79358.068650] SLOW spr round 3 (radius: 5) [03:40:34 -79358.067342] SLOW spr round 4 (radius: 10) [03:43:31 -79357.774719] SLOW spr round 5 (radius: 5) [03:45:30] [worker #2] ML tree search #13, logLikelihood: -79336.402511 [03:47:14 -79356.754459] SLOW spr round 6 (radius: 5) [03:50:27 -79356.754186] SLOW spr round 7 (radius: 10) [03:53:28 -79356.754125] SLOW spr round 8 (radius: 15) [03:57:53 -79356.754045] SLOW spr round 9 (radius: 20) [04:04:16 -79356.516713] SLOW spr round 10 (radius: 5) [04:08:07 -79356.516594] SLOW spr round 11 (radius: 10) [04:11:37 -79354.547946] SLOW spr round 12 (radius: 5) [04:13:44] [worker #4] ML tree search #15, logLikelihood: -79351.280375 [04:15:07 -79354.547498] SLOW spr round 13 (radius: 10) [04:18:17 -79354.547351] SLOW spr round 14 (radius: 15) [04:22:34 -79354.021970] SLOW spr round 15 (radius: 5) [04:26:24 -79354.021562] SLOW spr round 16 (radius: 10) [04:29:45 -79354.021533] SLOW spr round 17 (radius: 15) [04:33:59 -79354.021525] SLOW spr round 18 (radius: 20) [04:40:28 -79354.021523] SLOW spr round 19 (radius: 25) [04:48:31 -79354.021521] Model parameter optimization (eps = 0.100000) [04:48:47] [worker #0] ML tree search #11, logLikelihood: -79353.585094 [04:48:47 -417571.755611] Initial branch length optimization [04:48:53 -341431.172019] Model parameter optimization (eps = 10.000000) [04:49:46 -340038.452503] AUTODETECT spr round 1 (radius: 5) [04:53:38 -206014.025496] AUTODETECT spr round 2 (radius: 10) [04:56:37] [worker #3] ML tree search #14, logLikelihood: -79354.597504 [04:57:44 -149962.357537] AUTODETECT spr round 3 (radius: 15) [05:01:44 -118423.998340] AUTODETECT spr round 4 (radius: 20) [05:05:40] [worker #2] ML tree search #18, logLikelihood: -79372.206154 [05:05:57 -110149.792476] AUTODETECT spr round 5 (radius: 25) [05:10:52 -102968.747324] SPR radius for FAST iterations: 25 (autodetect) [05:10:52 -102968.747324] Model parameter optimization (eps = 3.000000) [05:11:29 -102939.715730] FAST spr round 1 (radius: 25) [05:14:01] [worker #1] ML tree search #12, logLikelihood: -79363.495538 [05:15:35 -81277.441674] FAST spr round 2 (radius: 25) [05:18:37 -79464.963720] FAST spr round 3 (radius: 25) [05:21:08 -79410.160860] FAST spr round 4 (radius: 25) [05:23:27 -79398.262535] FAST spr round 5 (radius: 25) [05:25:36 -79395.581756] FAST spr round 6 (radius: 25) [05:27:41 -79395.581675] Model parameter optimization (eps = 1.000000) [05:27:58 -79392.476438] SLOW spr round 1 (radius: 5) [05:30:41 -79381.148463] SLOW spr round 2 (radius: 5) [05:31:35] [worker #4] ML tree search #20, logLikelihood: -79360.708212 [05:33:28 -79374.393650] SLOW spr round 3 (radius: 5) [05:36:16 -79374.338209] SLOW spr round 4 (radius: 10) [05:39:17 -79368.914309] SLOW spr round 5 (radius: 5) [05:43:00 -79365.923778] SLOW spr round 6 (radius: 5) [05:46:09 -79365.783174] SLOW spr round 7 (radius: 5) [05:49:02 -79365.783070] SLOW spr round 8 (radius: 10) [05:51:58 -79365.661123] SLOW spr round 9 (radius: 5) [05:55:30 -79365.660151] SLOW spr round 10 (radius: 10) [05:58:39 -79365.660103] SLOW spr round 11 (radius: 15) [06:02:57 -79365.660093] SLOW spr round 12 (radius: 20) [06:09:37 -79365.660034] SLOW spr round 13 (radius: 25) [06:17:47 -79365.660033] Model parameter optimization (eps = 0.100000) [06:17:54] [worker #0] ML tree search #16, logLikelihood: -79365.635356 [06:34:52] [worker #1] ML tree search #17, logLikelihood: -79351.124192 [06:37:39] [worker #3] ML tree search #19, logLikelihood: -79349.884728 Optimized model parameters: Partition 0: noname Rate heterogeneity: FREE (4 cats, mean), weights&rates: (0.140662,0.208398) (0.338142,0.302611) (0.298781,1.085044) (0.222415,2.446644) 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: -79336.402511 AIC score: 162674.805023 / AICc score: 8174678.805023 / BIC score: 169622.818641 Free parameters (model + branch lengths): 2001 WARNING: Number of free parameters (K=2001) is larger than alignment size (n=238). 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/O43318/3_mltree/O43318.raxml.bestTree All ML trees saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/O43318/3_mltree/O43318.raxml.mlTrees Optimized model saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/O43318/3_mltree/O43318.raxml.bestModel Execution log saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/O43318/3_mltree/O43318.raxml.log Analysis started: 07-Jul-2021 16:38:52 / finished: 07-Jul-2021 23:16:31 Elapsed time: 23859.165 seconds Consumed energy: 1622.884 Wh (= 8 km in an electric car, or 41 km with an e-scooter!)