RAxML-NG v. 1.0.2 released on 22.02.2021 by The Exelixis Lab. Developed by: Alexey M. Kozlov and Alexandros Stamatakis. Contributors: Diego Darriba, Tomas Flouri, Benoit Morel, Sarah Lutteropp, Ben Bettisworth. Latest version: https://github.com/amkozlov/raxml-ng Questions/problems/suggestions? Please visit: https://groups.google.com/forum/#!forum/raxml System: Intel(R) Xeon(R) Gold 6140 CPU @ 2.30GHz, 36 cores, 251 GB RAM RAxML-NG was called at 19-Jul-2021 11:22:27 as follows: raxml-ng --msa /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q8WVJ9/2_msa/Q8WVJ9_trimmed_msa.fasta --data-type AA --model LG4X --prefix /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q8WVJ9/3_mltree/Q8WVJ9 --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: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q8WVJ9/2_msa/Q8WVJ9_trimmed_msa.fasta [00:00:00] Loaded alignment with 1001 taxa and 211 sites WARNING: Sequences tr_B4QZ09_B4QZ09_DROSI_7240 and tr_A0A0B4KFD8_A0A0B4KFD8_DROME_7227 are exactly identical! WARNING: Sequences tr_A0A1D5NZZ0_A0A1D5NZZ0_CHICK_9031 and tr_A0A226MUJ4_A0A226MUJ4_CALSU_9009 are exactly identical! WARNING: Sequences tr_A0A1D5NZZ0_A0A1D5NZZ0_CHICK_9031 and tr_A0A226PWR7_A0A226PWR7_COLVI_9014 are exactly identical! WARNING: Sequences tr_Q9PVG4_Q9PVG4_CHICK_9031 and tr_A0A226N5P0_A0A226N5P0_CALSU_9009 are exactly identical! WARNING: Sequences tr_Q9PVG4_Q9PVG4_CHICK_9031 and tr_A0A226PBT9_A0A226PBT9_COLVI_9014 are exactly identical! WARNING: Sequences tr_Q9YH69_Q9YH69_CHICK_9031 and tr_G1MTL8_G1MTL8_MELGA_9103 are exactly identical! WARNING: Sequences tr_Q9YH69_Q9YH69_CHICK_9031 and tr_H0YYB1_H0YYB1_TAEGU_59729 are exactly identical! WARNING: Sequences tr_Q9YH69_Q9YH69_CHICK_9031 and tr_U3KKQ1_U3KKQ1_FICAL_59894 are exactly identical! WARNING: Sequences tr_Q9YH69_Q9YH69_CHICK_9031 and tr_R0LCC1_R0LCC1_ANAPL_8839 are exactly identical! WARNING: Sequences tr_Q9YH69_Q9YH69_CHICK_9031 and tr_A0A151N9K1_A0A151N9K1_ALLMI_8496 are exactly identical! WARNING: Sequences tr_Q9YH69_Q9YH69_CHICK_9031 and tr_A0A0Q3PTK2_A0A0Q3PTK2_AMAAE_12930 are exactly identical! WARNING: Sequences tr_Q9YH69_Q9YH69_CHICK_9031 and tr_A0A091FT95_A0A091FT95_CORBR_85066 are exactly identical! WARNING: Sequences tr_Q9YH69_Q9YH69_CHICK_9031 and tr_A0A091IY88_A0A091IY88_EGRGA_188379 are exactly identical! WARNING: Sequences tr_Q9YH69_Q9YH69_CHICK_9031 and tr_A0A093QDZ1_A0A093QDZ1_9PASS_328815 are exactly identical! WARNING: Sequences tr_Q9YH69_Q9YH69_CHICK_9031 and tr_A0A091UVC6_A0A091UVC6_NIPNI_128390 are exactly identical! WARNING: Sequences tr_Q9YH69_Q9YH69_CHICK_9031 and tr_A0A087QJ16_A0A087QJ16_APTFO_9233 are exactly identical! WARNING: Sequences tr_Q9YH69_Q9YH69_CHICK_9031 and tr_A0A093JKN7_A0A093JKN7_STRCA_441894 are exactly identical! WARNING: Sequences tr_Q9YH69_Q9YH69_CHICK_9031 and tr_A0A091V648_A0A091V648_OPIHO_30419 are exactly identical! WARNING: Sequences tr_Q9YH69_Q9YH69_CHICK_9031 and tr_A0A099Z081_A0A099Z081_TINGU_94827 are exactly identical! WARNING: Sequences tr_Q9YH69_Q9YH69_CHICK_9031 and tr_A0A091GNP4_A0A091GNP4_9AVES_55661 are exactly identical! WARNING: Sequences tr_Q9YH69_Q9YH69_CHICK_9031 and tr_A0A0A0A1E9_A0A0A0A1E9_CHAVO_50402 are exactly identical! WARNING: Sequences tr_Q9YH69_Q9YH69_CHICK_9031 and tr_R7VQU6_R7VQU6_COLLI_8932 are exactly identical! WARNING: Sequences tr_Q9YH69_Q9YH69_CHICK_9031 and tr_A0A093GK80_A0A093GK80_DRYPU_118200 are exactly identical! WARNING: Sequences tr_Q9YH69_Q9YH69_CHICK_9031 and tr_A0A091I2Y0_A0A091I2Y0_CALAN_9244 are exactly identical! WARNING: Sequences tr_Q9YH69_Q9YH69_CHICK_9031 and tr_A0A1U7RL07_A0A1U7RL07_ALLSI_38654 are exactly identical! WARNING: Sequences tr_Q9YH69_Q9YH69_CHICK_9031 and tr_A0A226MIN4_A0A226MIN4_CALSU_9009 are exactly identical! WARNING: Sequences tr_Q9YH69_Q9YH69_CHICK_9031 and tr_A0A226P842_A0A226P842_COLVI_9014 are exactly identical! WARNING: Sequences tr_R4GFH4_R4GFH4_CHICK_9031 and tr_G1N775_G1N775_MELGA_9103 are exactly identical! WARNING: Sequences tr_R4GLC9_R4GLC9_CHICK_9031 and tr_A0A1V4JMR8_A0A1V4JMR8_PATFA_372326 are exactly identical! WARNING: Sequences sp_P26687_TWST1_MOUSE_10090 and tr_Q9EPJ1_Q9EPJ1_RAT_10116 are exactly identical! WARNING: Sequences sp_Q60756_TCF15_MOUSE_10090 and tr_D3ZEK9_D3ZEK9_RAT_10116 are exactly identical! WARNING: Sequences sp_Q61039_HAND2_MOUSE_10090 and tr_G1Q011_G1Q011_MYOLU_59463 are exactly identical! WARNING: Sequences sp_Q61039_HAND2_MOUSE_10090 and tr_H2R7W4_H2R7W4_PANTR_9598 are exactly identical! WARNING: Sequences sp_Q61039_HAND2_MOUSE_10090 and sp_P61295_HAND2_RAT_10116 are exactly identical! WARNING: Sequences sp_Q61039_HAND2_MOUSE_10090 and tr_I3N8C3_I3N8C3_ICTTR_43179 are exactly identical! WARNING: Sequences sp_Q61039_HAND2_MOUSE_10090 and tr_A0A286Y4K2_A0A286Y4K2_CAVPO_10141 are exactly identical! WARNING: Sequences sp_Q61039_HAND2_MOUSE_10090 and sp_P61296_HAND2_HUMAN_9606 are exactly identical! WARNING: Sequences sp_Q61039_HAND2_MOUSE_10090 and tr_A0A1D5QY03_A0A1D5QY03_MACMU_9544 are exactly identical! WARNING: Sequences sp_Q61039_HAND2_MOUSE_10090 and tr_G3U0Y6_G3U0Y6_LOXAF_9785 are exactly identical! WARNING: Sequences sp_Q61039_HAND2_MOUSE_10090 and tr_A0A337S0W3_A0A337S0W3_FELCA_9685 are exactly identical! WARNING: Sequences sp_Q61039_HAND2_MOUSE_10090 and tr_A0A0D9S255_A0A0D9S255_CHLSB_60711 are exactly identical! WARNING: Sequences sp_Q61039_HAND2_MOUSE_10090 and tr_A0A1S2ZQN8_A0A1S2ZQN8_ERIEU_9365 are exactly identical! WARNING: Sequences sp_Q61039_HAND2_MOUSE_10090 and tr_A0A1S3FVY5_A0A1S3FVY5_DIPOR_10020 are exactly identical! WARNING: Sequences sp_Q61039_HAND2_MOUSE_10090 and tr_A0A1U7QB47_A0A1U7QB47_MESAU_10036 are exactly identical! WARNING: Sequences sp_Q61039_HAND2_MOUSE_10090 and tr_A0A2K5NYJ7_A0A2K5NYJ7_CERAT_9531 are exactly identical! WARNING: Sequences sp_Q61039_HAND2_MOUSE_10090 and tr_A0A2U3V4G6_A0A2U3V4G6_TURTR_9739 are exactly identical! WARNING: Sequences sp_Q61039_HAND2_MOUSE_10090 and tr_A0A2U3VK63_A0A2U3VK63_ODORO_9708 are exactly identical! WARNING: Sequences sp_Q61039_HAND2_MOUSE_10090 and tr_A0A2U3Z5T9_A0A2U3Z5T9_LEPWE_9713 are exactly identical! WARNING: Sequences sp_Q61039_HAND2_MOUSE_10090 and tr_A0A2Y9KP92_A0A2Y9KP92_ENHLU_391180 are exactly identical! WARNING: Sequences sp_Q61039_HAND2_MOUSE_10090 and tr_A0A2Y9PZH1_A0A2Y9PZH1_DELLE_9749 are exactly identical! WARNING: Sequences sp_Q64124_SCX_MOUSE_10090 and tr_G3V8X3_G3V8X3_RAT_10116 are exactly identical! WARNING: Sequences tr_M3YTM9_M3YTM9_MUSPF_9669 and tr_D2HJ40_D2HJ40_AILME_9646 are exactly identical! WARNING: Sequences tr_M3YTM9_M3YTM9_MUSPF_9669 and tr_A0A2U3W061_A0A2U3W061_ODORO_9708 are exactly identical! WARNING: Sequences tr_M3YTM9_M3YTM9_MUSPF_9669 and tr_A0A2U3Y9R6_A0A2U3Y9R6_LEPWE_9713 are exactly identical! WARNING: Sequences tr_M3YTM9_M3YTM9_MUSPF_9669 and tr_A0A2Y9JGS3_A0A2Y9JGS3_ENHLU_391180 are exactly identical! WARNING: Sequences tr_M3YTM9_M3YTM9_MUSPF_9669 and tr_A0A384C384_A0A384C384_URSMA_29073 are exactly identical! WARNING: Sequences tr_M3Z6T8_M3Z6T8_MUSPF_9669 and tr_G1RKM7_G1RKM7_NOMLE_61853 are exactly identical! WARNING: Sequences tr_M3Z6T8_M3Z6T8_MUSPF_9669 and tr_G1QCG6_G1QCG6_MYOLU_59463 are exactly identical! WARNING: Sequences tr_M3Z6T8_M3Z6T8_MUSPF_9669 and tr_E2RQT1_E2RQT1_CANLF_9615 are exactly identical! WARNING: Sequences tr_M3Z6T8_M3Z6T8_MUSPF_9669 and tr_W5NQ13_W5NQ13_SHEEP_9940 are exactly identical! WARNING: Sequences tr_M3Z6T8_M3Z6T8_MUSPF_9669 and sp_P97831_TWST2_RAT_10116 are exactly identical! WARNING: Sequences tr_M3Z6T8_M3Z6T8_MUSPF_9669 and tr_I3M4K6_I3M4K6_ICTTR_43179 are exactly identical! WARNING: Sequences tr_M3Z6T8_M3Z6T8_MUSPF_9669 and sp_Q8WVJ9_TWST2_HUMAN_9606 are exactly identical! WARNING: Sequences tr_M3Z6T8_M3Z6T8_MUSPF_9669 and tr_F6V9S4_F6V9S4_MACMU_9544 are exactly identical! WARNING: Sequences tr_M3Z6T8_M3Z6T8_MUSPF_9669 and tr_F7FTJ2_F7FTJ2_CALJA_9483 are exactly identical! WARNING: Sequences tr_M3Z6T8_M3Z6T8_MUSPF_9669 and tr_F2Z5R9_F2Z5R9_PIG_9823 are exactly identical! WARNING: Sequences tr_M3Z6T8_M3Z6T8_MUSPF_9669 and tr_A4IFM6_A4IFM6_BOVIN_9913 are exactly identical! WARNING: Sequences tr_M3Z6T8_M3Z6T8_MUSPF_9669 and tr_L5KSL9_L5KSL9_PTEAL_9402 are exactly identical! WARNING: Sequences tr_M3Z6T8_M3Z6T8_MUSPF_9669 and tr_A0A096NXQ0_A0A096NXQ0_PAPAN_9555 are exactly identical! WARNING: Sequences tr_M3Z6T8_M3Z6T8_MUSPF_9669 and tr_A0A0D9SBT2_A0A0D9SBT2_CHLSB_60711 are exactly identical! WARNING: Sequences tr_M3Z6T8_M3Z6T8_MUSPF_9669 and tr_A0A1U7SZY3_A0A1U7SZY3_TARSY_1868482 are exactly identical! WARNING: Sequences tr_M3Z6T8_M3Z6T8_MUSPF_9669 and tr_A0A1U8CDQ9_A0A1U8CDQ9_MESAU_10036 are exactly identical! WARNING: Sequences tr_M3Z6T8_M3Z6T8_MUSPF_9669 and tr_A0A2K5L1V4_A0A2K5L1V4_CERAT_9531 are exactly identical! WARNING: Sequences tr_M3Z6T8_M3Z6T8_MUSPF_9669 and tr_A0A2K6B6S3_A0A2K6B6S3_MACNE_9545 are exactly identical! WARNING: Sequences tr_M3Z6T8_M3Z6T8_MUSPF_9669 and tr_A0A2K5XL67_A0A2K5XL67_MANLE_9568 are exactly identical! WARNING: Sequences tr_M3Z6T8_M3Z6T8_MUSPF_9669 and tr_A0A2U4ADZ7_A0A2U4ADZ7_TURTR_9739 are exactly identical! WARNING: Sequences tr_M3Z6T8_M3Z6T8_MUSPF_9669 and tr_A0A2Y9J3V1_A0A2Y9J3V1_ENHLU_391180 are exactly identical! WARNING: Sequences tr_M3Z6T8_M3Z6T8_MUSPF_9669 and tr_A0A2Y9MSF0_A0A2Y9MSF0_DELLE_9749 are exactly identical! WARNING: Sequences tr_M3Z6T8_M3Z6T8_MUSPF_9669 and tr_A0A384AC75_A0A384AC75_BALAS_310752 are exactly identical! WARNING: Sequences tr_A0A2I3GMF4_A0A2I3GMF4_NOMLE_61853 and tr_G3QRT2_G3QRT2_GORGO_9595 are exactly identical! WARNING: Sequences tr_A0A2I3GMF4_A0A2I3GMF4_NOMLE_61853 and tr_A0A2J8X998_A0A2J8X998_PONAB_9601 are exactly identical! WARNING: Sequences tr_A0A2I3GMF4_A0A2I3GMF4_NOMLE_61853 and tr_H2QTS0_H2QTS0_PANTR_9598 are exactly identical! WARNING: Sequences tr_A0A2I3GMF4_A0A2I3GMF4_NOMLE_61853 and tr_H0W7D6_H0W7D6_CAVPO_10141 are exactly identical! WARNING: Sequences tr_A0A2I3GMF4_A0A2I3GMF4_NOMLE_61853 and sp_O43680_TCF21_HUMAN_9606 are exactly identical! WARNING: Sequences tr_A0A2I3GMF4_A0A2I3GMF4_NOMLE_61853 and tr_F7HFW2_F7HFW2_MACMU_9544 are exactly identical! WARNING: Sequences tr_A0A2I3GMF4_A0A2I3GMF4_NOMLE_61853 and tr_G5AS64_G5AS64_HETGA_10181 are exactly identical! WARNING: Sequences tr_A0A2I3GMF4_A0A2I3GMF4_NOMLE_61853 and tr_G7P344_G7P344_MACFA_9541 are exactly identical! WARNING: Sequences tr_A0A2I3GMF4_A0A2I3GMF4_NOMLE_61853 and tr_A0A096NDT5_A0A096NDT5_PAPAN_9555 are exactly identical! WARNING: Sequences tr_A0A2I3GMF4_A0A2I3GMF4_NOMLE_61853 and tr_A0A0D9RVX4_A0A0D9RVX4_CHLSB_60711 are exactly identical! WARNING: Sequences tr_A0A2I3GMF4_A0A2I3GMF4_NOMLE_61853 and tr_A0A2K5MR37_A0A2K5MR37_CERAT_9531 are exactly identical! WARNING: Sequences tr_A0A2I3GMF4_A0A2I3GMF4_NOMLE_61853 and tr_A0A2K6ARZ8_A0A2K6ARZ8_MACNE_9545 are exactly identical! WARNING: Sequences tr_A0A2I3GMF4_A0A2I3GMF4_NOMLE_61853 and tr_A0A2K5ZBA3_A0A2K5ZBA3_MANLE_9568 are exactly identical! WARNING: Sequences tr_A0A2I3GMF4_A0A2I3GMF4_NOMLE_61853 and tr_A0A2R9CR00_A0A2R9CR00_PANPA_9597 are exactly identical! WARNING: Sequences tr_G1SBD4_G1SBD4_NOMLE_61853 and tr_G3QV69_G3QV69_GORGO_9595 are exactly identical! WARNING: Sequences tr_G1SBD4_G1SBD4_NOMLE_61853 and tr_H2QXM9_H2QXM9_PANTR_9598 are exactly identical! WARNING: Sequences tr_G1SBD4_G1SBD4_NOMLE_61853 and sp_Q16559_TAL2_HUMAN_9606 are exactly identical! WARNING: Sequences tr_G1SBD4_G1SBD4_NOMLE_61853 and tr_A0A2R8Z8D5_A0A2R8Z8D5_PANPA_9597 are exactly identical! WARNING: Sequences tr_G3RGL3_G3RGL3_GORGO_9595 and tr_H2R966_H2R966_PANTR_9598 are exactly identical! WARNING: Sequences tr_G3RGL3_G3RGL3_GORGO_9595 and tr_F6Y9N4_F6Y9N4_MACMU_9544 are exactly identical! WARNING: Sequences tr_G3RGL3_G3RGL3_GORGO_9595 and tr_A0A2I3LXX9_A0A2I3LXX9_PAPAN_9555 are exactly identical! WARNING: Sequences tr_G3RGL3_G3RGL3_GORGO_9595 and tr_A0A0D9RDK4_A0A0D9RDK4_CHLSB_60711 are exactly identical! WARNING: Sequences tr_G3RGL3_G3RGL3_GORGO_9595 and tr_A0A2K5NLF2_A0A2K5NLF2_CERAT_9531 are exactly identical! WARNING: Sequences tr_G3RGL3_G3RGL3_GORGO_9595 and tr_A0A2K6DRP7_A0A2K6DRP7_MACNE_9545 are exactly identical! WARNING: Sequences tr_H2PMQ9_H2PMQ9_PONAB_9601 and sp_Q15672_TWST1_HUMAN_9606 are exactly identical! WARNING: Sequences tr_H2PMQ9_H2PMQ9_PONAB_9601 and tr_F6VAC2_F6VAC2_MACMU_9544 are exactly identical! WARNING: Sequences tr_H2PMQ9_H2PMQ9_PONAB_9601 and tr_A0A2I2U7P8_A0A2I2U7P8_FELCA_9685 are exactly identical! WARNING: Sequences tr_H2PMQ9_H2PMQ9_PONAB_9601 and tr_A0A0D9SE20_A0A0D9SE20_CHLSB_60711 are exactly identical! WARNING: Sequences tr_H2PMQ9_H2PMQ9_PONAB_9601 and tr_A0A2U3X0Q8_A0A2U3X0Q8_ODORO_9708 are exactly identical! WARNING: Sequences tr_H2PMQ9_H2PMQ9_PONAB_9601 and tr_A0A2Y9JML2_A0A2Y9JML2_ENHLU_391180 are exactly identical! WARNING: Sequences tr_H2PQJ5_H2PQJ5_PONAB_9601 and tr_A0A096NE13_A0A096NE13_PAPAN_9555 are exactly identical! WARNING: Sequences tr_H2PQJ5_H2PQJ5_PONAB_9601 and tr_A0A2K6B470_A0A2K6B470_MACNE_9545 are exactly identical! WARNING: Sequences tr_H2PQJ5_H2PQJ5_PONAB_9601 and tr_A0A2K5XU68_A0A2K5XU68_MANLE_9568 are exactly identical! WARNING: Sequences tr_B5DW91_B5DW91_DROPS_46245 and tr_B4GMP5_B4GMP5_DROPE_7234 are exactly identical! WARNING: Sequences tr_Q292I0_Q292I0_DROPS_46245 and tr_B4GDG2_B4GDG2_DROPE_7234 are exactly identical! WARNING: Sequences tr_Q29CX1_Q29CX1_DROPS_46245 and tr_B4G7J0_B4G7J0_DROPE_7234 are exactly identical! WARNING: Sequences tr_E2RI49_E2RI49_CANLF_9615 and tr_F6VFW8_F6VFW8_HORSE_9796 are exactly identical! WARNING: Sequences tr_E2RI49_E2RI49_CANLF_9615 and tr_A0A2U3VEE2_A0A2U3VEE2_ODORO_9708 are exactly identical! WARNING: Sequences tr_E2RI49_E2RI49_CANLF_9615 and tr_A0A2Y9ILK8_A0A2Y9ILK8_ENHLU_391180 are exactly identical! WARNING: Sequences tr_A0A2I3T1M0_A0A2I3T1M0_PANTR_9598 and sp_Q7RTS3_PTF1A_HUMAN_9606 are exactly identical! WARNING: Sequences tr_F7GBK5_F7GBK5_MONDO_13616 and tr_G3WCC8_G3WCC8_SARHA_9305 are exactly identical! WARNING: Sequences tr_W5Q182_W5Q182_SHEEP_9940 and tr_A0A093PU63_A0A093PU63_9PASS_328815 are exactly identical! WARNING: Sequences tr_W5Q182_W5Q182_SHEEP_9940 and tr_A0A093GKS1_A0A093GKS1_DRYPU_118200 are exactly identical! WARNING: Sequences tr_W5Q182_W5Q182_SHEEP_9940 and tr_A0A091J729_A0A091J729_CALAN_9244 are exactly identical! WARNING: Sequences tr_W5Q182_W5Q182_SHEEP_9940 and tr_A0A384AZL3_A0A384AZL3_BALAS_310752 are exactly identical! WARNING: Sequences tr_M4AZD9_M4AZD9_XIPMA_8083 and tr_A0A087YPR1_A0A087YPR1_POEFO_48698 are exactly identical! WARNING: Sequences tr_M4AZV8_M4AZV8_XIPMA_8083 and tr_A0A087YRH4_A0A087YRH4_POEFO_48698 are exactly identical! WARNING: Sequences tr_M4B0E4_M4B0E4_XIPMA_8083 and tr_A0A087YQ76_A0A087YQ76_POEFO_48698 are exactly identical! WARNING: Sequences tr_A0A088A452_A0A088A452_APIME_7460 and tr_A0A2A3EKD8_A0A2A3EKD8_APICC_94128 are exactly identical! WARNING: Sequences tr_A0A158NUL2_A0A158NUL2_ATTCE_12957 and tr_F4WNL1_F4WNL1_ACREC_103372 are exactly identical! WARNING: Sequences tr_A0A158NUL2_A0A158NUL2_ATTCE_12957 and tr_A0A195B8H8_A0A195B8H8_9HYME_520822 are exactly identical! WARNING: Sequences tr_I3NFZ6_I3NFZ6_ICTTR_43179 and tr_F7IM24_F7IM24_CALJA_9483 are exactly identical! WARNING: Sequences tr_H0XD97_H0XD97_OTOGA_30611 and tr_A0A2R8MQ58_A0A2R8MQ58_CALJA_9483 are exactly identical! WARNING: Sequences sp_Q7RTU7_SCX_HUMAN_9606 and tr_A0A096NFP0_A0A096NFP0_PAPAN_9555 are exactly identical! WARNING: Sequences sp_Q7RTU7_SCX_HUMAN_9606 and tr_A0A0D9R8G4_A0A0D9R8G4_CHLSB_60711 are exactly identical! WARNING: Sequences sp_Q7RTU7_SCX_HUMAN_9606 and tr_A0A2K5KID7_A0A2K5KID7_CERAT_9531 are exactly identical! WARNING: Sequences tr_F7H2P2_F7H2P2_MACMU_9544 and tr_G7PRR5_G7PRR5_MACFA_9541 are exactly identical! WARNING: Sequences tr_F7H2P2_F7H2P2_MACMU_9544 and tr_A0A096NRK8_A0A096NRK8_PAPAN_9555 are exactly identical! WARNING: Sequences tr_F7H2P2_F7H2P2_MACMU_9544 and tr_A0A0D9S9J8_A0A0D9S9J8_CHLSB_60711 are exactly identical! WARNING: Sequences tr_F7H2P2_F7H2P2_MACMU_9544 and tr_A0A2K5NRT0_A0A2K5NRT0_CERAT_9531 are exactly identical! WARNING: Sequences tr_F7H2P2_F7H2P2_MACMU_9544 and tr_A0A2K6B6W3_A0A2K6B6W3_MACNE_9545 are exactly identical! WARNING: Sequences tr_F7H2P2_F7H2P2_MACMU_9544 and tr_A0A2K5XUV4_A0A2K5XUV4_MANLE_9568 are exactly identical! WARNING: Sequences tr_G5B403_G5B403_HETGA_10181 and tr_G1M6N4_G1M6N4_AILME_9646 are exactly identical! WARNING: Sequences tr_G5B403_G5B403_HETGA_10181 and tr_L5L2Q9_L5L2Q9_PTEAL_9402 are exactly identical! WARNING: Sequences tr_G5BZJ0_G5BZJ0_HETGA_10181 and tr_L5KLN1_L5KLN1_PTEAL_9402 are exactly identical! WARNING: Sequences tr_G5BZJ0_G5BZJ0_HETGA_10181 and tr_A0A091D3L0_A0A091D3L0_FUKDA_885580 are exactly identical! WARNING: Sequences tr_G5BZJ0_G5BZJ0_HETGA_10181 and tr_A0A1V4KBQ3_A0A1V4KBQ3_PATFA_372326 are exactly identical! WARNING: Sequences tr_H0Z797_H0Z797_TAEGU_59729 and tr_A0A218VFH8_A0A218VFH8_9PASE_299123 are exactly identical! WARNING: Sequences tr_H0Z7F0_H0Z7F0_TAEGU_59729 and tr_A0A091J0A2_A0A091J0A2_EGRGA_188379 are exactly identical! WARNING: Sequences tr_H0Z7F0_H0Z7F0_TAEGU_59729 and tr_A0A0A0APS1_A0A0A0APS1_CHAVO_50402 are exactly identical! WARNING: Sequences tr_H0ZMT1_H0ZMT1_TAEGU_59729 and tr_U3KBH7_U3KBH7_FICAL_59894 are exactly identical! WARNING: Sequences tr_A0A286ZU17_A0A286ZU17_PIG_9823 and tr_A2VE98_A2VE98_BOVIN_9913 are exactly identical! WARNING: Sequences tr_A0A287B8H6_A0A287B8H6_PIG_9823 and tr_A0A2U4CPW6_A0A2U4CPW6_TURTR_9739 are exactly identical! WARNING: Sequences tr_A0A287B8H6_A0A287B8H6_PIG_9823 and tr_A0A2Y9LTL8_A0A2Y9LTL8_DELLE_9749 are exactly identical! WARNING: Sequences tr_A0A287B8H6_A0A287B8H6_PIG_9823 and tr_A0A384AU86_A0A384AU86_BALAS_310752 are exactly identical! WARNING: Sequences tr_F1SEI1_F1SEI1_PIG_9823 and tr_G3N341_G3N341_BOVIN_9913 are exactly identical! WARNING: Sequences tr_F1SEI1_F1SEI1_PIG_9823 and tr_A0A2U4B1E9_A0A2U4B1E9_TURTR_9739 are exactly identical! WARNING: Sequences tr_F1SEI1_F1SEI1_PIG_9823 and tr_A0A2Y9PS80_A0A2Y9PS80_DELLE_9749 are exactly identical! WARNING: Sequences tr_A0A337SE52_A0A337SE52_FELCA_9685 and tr_A0A2U3VYU7_A0A2U3VYU7_ODORO_9708 are exactly identical! WARNING: Sequences tr_A0A0D9RJ18_A0A0D9RJ18_CHLSB_60711 and tr_A0A2K5NIE3_A0A2K5NIE3_CERAT_9531 are exactly identical! WARNING: Sequences tr_A0A0D9RJ18_A0A0D9RJ18_CHLSB_60711 and tr_A0A2K6BF97_A0A2K6BF97_MACNE_9545 are exactly identical! WARNING: Sequences tr_A0A0N4TQ46_A0A0N4TQ46_BRUPA_6280 and tr_A0A0R3QST8_A0A0R3QST8_9BILA_42155 are exactly identical! WARNING: Sequences tr_A0A151M3C4_A0A151M3C4_ALLMI_8496 and tr_A0A1U7SH66_A0A1U7SH66_ALLSI_38654 are exactly identical! WARNING: Sequences tr_A0A151M665_A0A151M665_ALLMI_8496 and tr_A0A1U7S5Z9_A0A1U7S5Z9_ALLSI_38654 are exactly identical! WARNING: Sequences tr_A0A0Q3VBT9_A0A0Q3VBT9_AMAAE_12930 and tr_A0A091V0A5_A0A091V0A5_NIPNI_128390 are exactly identical! WARNING: Sequences tr_A0A091W3L5_A0A091W3L5_NIPNI_128390 and tr_A0A087QSR2_A0A087QSR2_APTFO_9233 are exactly identical! WARNING: Sequences tr_A0A091FQ63_A0A091FQ63_9AVES_55661 and tr_A0A091HYV6_A0A091HYV6_CALAN_9244 are exactly identical! WARNING: Sequences tr_A0A195EHR7_A0A195EHR7_9HYME_471704 and tr_A0A195FC79_A0A195FC79_9HYME_34720 are exactly identical! WARNING: Sequences tr_A0A1S3MFS1_A0A1S3MFS1_SALSA_8030 and tr_A0A060Y8Y0_A0A060Y8Y0_ONCMY_8022 are exactly identical! WARNING: Sequences tr_A0A1S3REA6_A0A1S3REA6_SALSA_8030 and tr_A0A060WEU4_A0A060WEU4_ONCMY_8022 are exactly identical! WARNING: Sequences tr_A0A1S3SKG6_A0A1S3SKG6_SALSA_8030 and tr_A0A060XKS2_A0A060XKS2_ONCMY_8022 are exactly identical! WARNING: Sequences tr_A0A1D1UCE4_A0A1D1UCE4_RAMVA_947166 and tr_A0A1D1UG30_A0A1D1UG30_RAMVA_947166 are exactly identical! WARNING: Sequences tr_A0A1U7Q332_A0A1U7Q332_MESAU_10036 and sp_Q60539_TCF15_MESAU_10036 are exactly identical! WARNING: Sequences tr_A0A226MFN7_A0A226MFN7_CALSU_9009 and tr_A0A226MG06_A0A226MG06_COLVI_9014 are exactly identical! WARNING: Sequences tr_A0A226NL40_A0A226NL40_CALSU_9009 and tr_A0A226P0S5_A0A226P0S5_COLVI_9014 are exactly identical! WARNING: Sequences tr_A0A226NLV0_A0A226NLV0_CALSU_9009 and tr_A0A226PH78_A0A226PH78_COLVI_9014 are exactly identical! WARNING: Sequences tr_A0A2U3V3A1_A0A2U3V3A1_TURTR_9739 and tr_A0A2Y9PNP7_A0A2Y9PNP7_DELLE_9749 are exactly identical! WARNING: Sequences tr_A0A2U3V3A1_A0A2U3V3A1_TURTR_9739 and tr_A0A2Y9T0I9_A0A2Y9T0I9_PHYCD_9755 are exactly identical! WARNING: Sequences tr_A0A2U3VAD1_A0A2U3VAD1_TURTR_9739 and tr_A0A2Y9NPL1_A0A2Y9NPL1_DELLE_9749 are exactly identical! WARNING: Sequences tr_A0A2U4CGP5_A0A2U4CGP5_TURTR_9739 and tr_A0A2Y9FGV4_A0A2Y9FGV4_PHYCD_9755 are exactly identical! WARNING: Sequences tr_A0A2U4CGP5_A0A2U4CGP5_TURTR_9739 and tr_A0A383ZTB4_A0A383ZTB4_BALAS_310752 are exactly identical! WARNING: Sequences tr_A0A2U3WNC0_A0A2U3WNC0_ODORO_9708 and tr_A0A2U3YC91_A0A2U3YC91_LEPWE_9713 are exactly identical! WARNING: Duplicate sequences found: 181 NOTE: Reduced alignment (with duplicates and gap-only sites/taxa removed) NOTE: was saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q8WVJ9/3_mltree/Q8WVJ9.raxml.reduced.phy Alignment comprises 1 partitions and 211 patterns Partition 0: noname Model: LG4X+R4 Alignment sites / patterns: 211 / 211 Gaps: 33.03 % Invariant sites: 3.32 % NOTE: Binary MSA file created: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q8WVJ9/3_mltree/Q8WVJ9.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 / 211 / 16880 [00:00:00] Data distribution: max. searches per worker: 5 Starting ML tree search with 20 distinct starting trees [00:00:00 -272377.052148] Initial branch length optimization [00:00:05 -226261.146642] Model parameter optimization (eps = 10.000000) [00:00:53 -226174.134263] AUTODETECT spr round 1 (radius: 5) [00:04:03 -152851.062810] AUTODETECT spr round 2 (radius: 10) [00:07:31 -105587.633354] AUTODETECT spr round 3 (radius: 15) [00:11:28 -78981.630784] AUTODETECT spr round 4 (radius: 20) [00:15:30 -69633.185133] AUTODETECT spr round 5 (radius: 25) [00:20:23 -64931.499064] SPR radius for FAST iterations: 25 (autodetect) [00:20:23 -64931.499064] Model parameter optimization (eps = 3.000000) [00:20:49 -64859.491779] FAST spr round 1 (radius: 25) [00:24:10 -57320.126109] FAST spr round 2 (radius: 25) [00:26:52 -56821.148893] FAST spr round 3 (radius: 25) [00:29:24 -56692.619150] FAST spr round 4 (radius: 25) [00:31:44 -56674.898996] FAST spr round 5 (radius: 25) [00:34:01 -56673.636555] FAST spr round 6 (radius: 25) [00:36:12 -56671.750473] FAST spr round 7 (radius: 25) [00:38:24 -56666.392310] FAST spr round 8 (radius: 25) [00:40:33 -56666.392162] Model parameter optimization (eps = 1.000000) [00:40:54 -56664.240836] SLOW spr round 1 (radius: 5) [00:43:32 -56658.222656] SLOW spr round 2 (radius: 5) [00:46:14 -56657.679375] SLOW spr round 3 (radius: 5) [00:48:57 -56657.665373] SLOW spr round 4 (radius: 10) [00:51:45 -56655.751628] SLOW spr round 5 (radius: 5) [00:55:06 -56655.721838] SLOW spr round 6 (radius: 10) [00:58:09 -56655.566680] SLOW spr round 7 (radius: 5) [01:01:21 -56655.565186] SLOW spr round 8 (radius: 10) [01:04:18 -56655.564846] SLOW spr round 9 (radius: 15) [01:07:06] [worker #3] ML tree search #4, logLikelihood: -57989.182985 [01:08:25 -56655.564768] SLOW spr round 10 (radius: 20) [01:12:09] [worker #2] ML tree search #3, logLikelihood: -56662.243333 [01:14:46 -56655.564749] SLOW spr round 11 (radius: 25) [01:22:01 -56655.402972] SLOW spr round 12 (radius: 5) [01:25:35 -56655.138120] SLOW spr round 13 (radius: 5) [01:28:43 -56655.064141] SLOW spr round 14 (radius: 10) [01:30:13] [worker #1] ML tree search #2, logLikelihood: -56891.165435 [01:31:37 -56655.063774] SLOW spr round 15 (radius: 15) [01:35:46 -56655.063609] SLOW spr round 16 (radius: 20) [01:42:11 -56655.063522] SLOW spr round 17 (radius: 25) [01:49:32 -56655.063476] Model parameter optimization (eps = 0.100000) [01:49:43] [worker #0] ML tree search #1, logLikelihood: -56654.946092 [01:49:43 -274073.059445] Initial branch length optimization [01:49:48 -228946.592889] Model parameter optimization (eps = 10.000000) [01:50:32 -228830.919751] AUTODETECT spr round 1 (radius: 5) [01:53:37 -156888.985604] AUTODETECT spr round 2 (radius: 10) [01:57:07 -108659.909761] AUTODETECT spr round 3 (radius: 15) [02:00:52 -85906.479931] AUTODETECT spr round 4 (radius: 20) [02:04:47 -76698.808364] AUTODETECT spr round 5 (radius: 25) [02:09:13 -69361.014690] SPR radius for FAST iterations: 25 (autodetect) [02:09:13 -69361.014690] Model parameter optimization (eps = 3.000000) [02:09:41 -69271.693145] FAST spr round 1 (radius: 25) [02:13:07 -58044.593284] FAST spr round 2 (radius: 25) [02:15:57 -56789.836900] FAST spr round 3 (radius: 25) [02:18:37 -56696.133425] FAST spr round 4 (radius: 25) [02:20:58 -56680.416857] FAST spr round 5 (radius: 25) [02:23:12 -56677.859266] FAST spr round 6 (radius: 25) [02:25:16] [worker #3] ML tree search #8, logLikelihood: -56625.985945 [02:25:22 -56677.859107] Model parameter optimization (eps = 1.000000) [02:25:45 -56675.165698] SLOW spr round 1 (radius: 5) [02:28:20 -56653.976207] SLOW spr round 2 (radius: 5) [02:31:03 -56646.429260] SLOW spr round 3 (radius: 5) [02:33:46 -56643.706442] SLOW spr round 4 (radius: 5) [02:36:30 -56642.972872] SLOW spr round 5 (radius: 5) [02:39:12 -56642.803153] SLOW spr round 6 (radius: 5) [02:41:53 -56642.800647] SLOW spr round 7 (radius: 10) [02:44:39 -56642.548946] SLOW spr round 8 (radius: 5) [02:47:56 -56642.548470] SLOW spr round 9 (radius: 10) [02:50:52 -56642.548455] SLOW spr round 10 (radius: 15) [02:54:51 -56642.548450] SLOW spr round 11 (radius: 20) [03:00:48 -56642.548448] SLOW spr round 12 (radius: 25) [03:08:09 -56642.348254] SLOW spr round 13 (radius: 5) [03:08:58] [worker #1] ML tree search #6, logLikelihood: -56666.995255 [03:11:42 -56642.347094] SLOW spr round 14 (radius: 10) [03:14:59 -56642.347081] SLOW spr round 15 (radius: 15) [03:18:56 -56642.347079] SLOW spr round 16 (radius: 20) [03:24:55 -56642.347077] SLOW spr round 17 (radius: 25) [03:32:15 -56642.347076] Model parameter optimization (eps = 0.100000) [03:32:27] [worker #0] ML tree search #5, logLikelihood: -56642.203453 [03:32:27 -273448.973998] Initial branch length optimization [03:32:34 -228199.389981] Model parameter optimization (eps = 10.000000) [03:32:34] [worker #2] ML tree search #7, logLikelihood: -56629.176234 [03:33:32 -228120.974018] AUTODETECT spr round 1 (radius: 5) [03:36:42 -155377.278658] AUTODETECT spr round 2 (radius: 10) [03:40:15 -103810.976185] AUTODETECT spr round 3 (radius: 15) [03:44:03 -85875.323794] AUTODETECT spr round 4 (radius: 20) [03:48:11 -73283.327953] AUTODETECT spr round 5 (radius: 25) [03:53:03 -67488.956582] SPR radius for FAST iterations: 25 (autodetect) [03:53:03 -67488.956582] Model parameter optimization (eps = 3.000000) [03:53:27 -67407.801640] FAST spr round 1 (radius: 25) [03:54:59] [worker #3] ML tree search #12, logLikelihood: -56634.106062 [03:57:08 -57388.497631] FAST spr round 2 (radius: 25) [04:00:00 -56857.779922] FAST spr round 3 (radius: 25) [04:02:28 -56793.470686] FAST spr round 4 (radius: 25) [04:04:46 -56779.655565] FAST spr round 5 (radius: 25) [04:06:54 -56773.672634] FAST spr round 6 (radius: 25) [04:09:00 -56773.672391] Model parameter optimization (eps = 1.000000) [04:09:25 -56762.768015] SLOW spr round 1 (radius: 5) [04:12:03 -56729.994502] SLOW spr round 2 (radius: 5) [04:14:42 -56721.877238] SLOW spr round 3 (radius: 5) [04:17:22 -56717.028252] SLOW spr round 4 (radius: 5) [04:20:03 -56717.026403] SLOW spr round 5 (radius: 10) [04:22:50 -56714.717725] SLOW spr round 6 (radius: 5) [04:26:08 -56713.272093] SLOW spr round 7 (radius: 5) [04:29:01 -56713.271949] SLOW spr round 8 (radius: 10) [04:31:46 -56713.271942] SLOW spr round 9 (radius: 15) [04:36:00 -56711.821132] SLOW spr round 10 (radius: 5) [04:39:32 -56704.761121] SLOW spr round 11 (radius: 5) [04:42:36 -56704.679511] SLOW spr round 12 (radius: 10) [04:45:26 -56704.679131] SLOW spr round 13 (radius: 15) [04:49:36 -56704.679082] SLOW spr round 14 (radius: 20) [04:50:43] [worker #1] ML tree search #10, logLikelihood: -57053.221023 [04:56:03 -56704.679077] SLOW spr round 15 (radius: 25) [05:04:12 -56704.270371] SLOW spr round 16 (radius: 5) [05:07:44 -56704.269296] SLOW spr round 17 (radius: 10) [05:10:54 -56704.269267] SLOW spr round 18 (radius: 15) [05:12:27] [worker #3] ML tree search #16, logLikelihood: -56639.830831 [05:14:56 -56704.080576] SLOW spr round 19 (radius: 5) [05:18:24 -56704.079382] SLOW spr round 20 (radius: 10) [05:21:31 -56704.079353] SLOW spr round 21 (radius: 15) [05:25:33 -56704.079325] SLOW spr round 22 (radius: 20) [05:32:04 -56704.079317] SLOW spr round 23 (radius: 25) [05:40:11 -56704.079310] Model parameter optimization (eps = 0.100000) [05:40:29] [worker #0] ML tree search #9, logLikelihood: -56703.187959 [05:40:29 -274349.704315] Initial branch length optimization [05:40:35 -228433.358387] Model parameter optimization (eps = 10.000000) [05:41:33 -228268.531942] AUTODETECT spr round 1 (radius: 5) [05:44:43 -149968.691769] AUTODETECT spr round 2 (radius: 10) [05:48:11 -104650.026943] AUTODETECT spr round 3 (radius: 15) [05:51:55 -83895.499373] AUTODETECT spr round 4 (radius: 20) [05:55:40 -74359.991917] AUTODETECT spr round 5 (radius: 25) [06:00:14 -69011.931445] SPR radius for FAST iterations: 25 (autodetect) [06:00:14 -69011.931445] Model parameter optimization (eps = 3.000000) [06:00:41 -68921.209751] FAST spr round 1 (radius: 25) [06:02:23] [worker #2] ML tree search #11, logLikelihood: -56629.737694 [06:04:20 -58381.711262] FAST spr round 2 (radius: 25) [06:07:16 -56786.727148] FAST spr round 3 (radius: 25) [06:09:54 -56670.205010] FAST spr round 4 (radius: 25) [06:12:07 -56666.540137] FAST spr round 5 (radius: 25) [06:14:12 -56666.489314] Model parameter optimization (eps = 1.000000) [06:14:33 -56661.925828] SLOW spr round 1 (radius: 5) [06:17:06 -56651.104726] SLOW spr round 2 (radius: 5) [06:19:42 -56646.559153] SLOW spr round 3 (radius: 5) [06:22:17 -56646.399686] SLOW spr round 4 (radius: 5) [06:24:53 -56645.659258] SLOW spr round 5 (radius: 5) [06:27:30 -56642.516451] SLOW spr round 6 (radius: 5) [06:28:52] [worker #3] ML tree search #20, logLikelihood: -56701.835959 [06:29:58 -56642.516416] SLOW spr round 7 (radius: 10) [06:32:38 -56639.460919] SLOW spr round 8 (radius: 5) [06:35:48 -56638.811402] SLOW spr round 9 (radius: 5) [06:38:35 -56638.811230] SLOW spr round 10 (radius: 10) [06:39:33] [worker #1] ML tree search #14, logLikelihood: -56637.777332 [06:41:16 -56637.476550] SLOW spr round 11 (radius: 5) [06:44:23 -56637.192194] SLOW spr round 12 (radius: 5) [06:47:09 -56637.191482] SLOW spr round 13 (radius: 10) [06:49:48 -56637.191447] SLOW spr round 14 (radius: 15) [06:53:50 -56636.455814] SLOW spr round 15 (radius: 5) [06:57:13 -56636.454066] SLOW spr round 16 (radius: 10) [07:00:15 -56636.453830] SLOW spr round 17 (radius: 15) [07:04:11 -56636.453795] SLOW spr round 18 (radius: 20) [07:10:53 -56636.453789] SLOW spr round 19 (radius: 25) [07:14:01] [worker #2] ML tree search #15, logLikelihood: -56842.575444 [07:19:18 -56636.085890] SLOW spr round 20 (radius: 5) [07:22:42 -56636.085711] SLOW spr round 21 (radius: 10) [07:25:51 -56636.085711] SLOW spr round 22 (radius: 15) [07:29:46 -56636.085710] SLOW spr round 23 (radius: 20) [07:36:30 -56636.085710] SLOW spr round 24 (radius: 25) [07:44:54 -56636.085710] Model parameter optimization (eps = 0.100000) [07:45:09] [worker #0] ML tree search #13, logLikelihood: -56635.634417 [07:45:09 -271569.054862] Initial branch length optimization [07:45:15 -225440.218905] Model parameter optimization (eps = 10.000000) [07:46:03 -225373.954244] AUTODETECT spr round 1 (radius: 5) [07:49:12 -150463.173997] AUTODETECT spr round 2 (radius: 10) [07:52:39 -104187.981852] AUTODETECT spr round 3 (radius: 15) [07:56:29 -83234.734637] AUTODETECT spr round 4 (radius: 20) [08:00:34 -76770.114794] AUTODETECT spr round 5 (radius: 25) [08:04:44 -72505.136634] SPR radius for FAST iterations: 25 (autodetect) [08:04:44 -72505.136634] Model parameter optimization (eps = 3.000000) [08:05:13 -72403.959520] FAST spr round 1 (radius: 25) [08:08:33 -59961.059248] FAST spr round 2 (radius: 25) [08:11:19 -57770.033778] FAST spr round 3 (radius: 25) [08:13:49 -57319.458845] FAST spr round 4 (radius: 25) [08:16:11 -57281.009811] FAST spr round 5 (radius: 25) [08:18:24 -57278.734465] FAST spr round 6 (radius: 25) [08:20:32 -57278.683775] Model parameter optimization (eps = 1.000000) [08:20:54 -57269.912055] SLOW spr round 1 (radius: 5) [08:22:59] [worker #1] ML tree search #18, logLikelihood: -58299.172907 [08:23:31 -57262.959815] SLOW spr round 2 (radius: 5) [08:26:11 -57262.958420] SLOW spr round 3 (radius: 10) [08:28:59 -57262.403962] SLOW spr round 4 (radius: 5) [08:32:18 -57262.403744] SLOW spr round 5 (radius: 10) [08:35:13 -57262.403743] SLOW spr round 6 (radius: 15) [08:37:20] [worker #2] ML tree search #19, logLikelihood: -56657.185795 [08:38:54 -57262.058511] SLOW spr round 7 (radius: 5) [08:42:16 -57262.058197] SLOW spr round 8 (radius: 10) [08:45:24 -57262.058104] SLOW spr round 9 (radius: 15) [08:49:00 -57262.058068] SLOW spr round 10 (radius: 20) [08:53:33 -57262.058052] SLOW spr round 11 (radius: 25) [08:58:30 -57262.058047] Model parameter optimization (eps = 0.100000) [08:58:37] [worker #0] ML tree search #17, logLikelihood: -57262.002331 Optimized model parameters: Partition 0: noname Rate heterogeneity: FREE (4 cats, mean), weights&rates: (0.142578,0.112841) (0.099135,0.161924) (0.237728,0.622104) (0.520559,1.575168) 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: -56625.985945 AIC score: 117261.971891 / AICc score: 8161321.971891 / BIC score: 123982.447448 Free parameters (model + branch lengths): 2005 WARNING: Number of free parameters (K=2005) is larger than alignment size (n=211). This might lead to overfitting and compromise tree inference results! Best ML tree saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q8WVJ9/3_mltree/Q8WVJ9.raxml.bestTree All ML trees saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q8WVJ9/3_mltree/Q8WVJ9.raxml.mlTrees Optimized model saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q8WVJ9/3_mltree/Q8WVJ9.raxml.bestModel Execution log saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q8WVJ9/3_mltree/Q8WVJ9.raxml.log Analysis started: 19-Jul-2021 11:22:27 / finished: 19-Jul-2021 20:21:05 Elapsed time: 32317.903 seconds