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 30-Jun-2021 17:55:15 as follows: raxml-ng --msa /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/P84022/2_msa/P84022_trimmed_msa.fasta --data-type AA --model LG4X --prefix /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/P84022/3_mltree/P84022 --seed 2 --threads 8 --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 (8 threads), thread pinning: OFF [00:00:00] Reading alignment from file: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/P84022/2_msa/P84022_trimmed_msa.fasta [00:00:00] Loaded alignment with 1001 taxa and 691 sites WARNING: Sequences sp_P84023_SMAD3_CHICK_9031 and tr_A0A0Q3PU66_A0A0Q3PU66_AMAAE_12930 are exactly identical! WARNING: Sequences sp_P84023_SMAD3_CHICK_9031 and tr_A0A1V4JDJ5_A0A1V4JDJ5_PATFA_372326 are exactly identical! WARNING: Sequences sp_Q56I99_SMAD5_CHICK_9031 and tr_G1N7K9_G1N7K9_MELGA_9103 are exactly identical! WARNING: Sequences sp_Q8BUN5_SMAD3_MOUSE_10090 and tr_H2NNK3_H2NNK3_PONAB_9601 are exactly identical! WARNING: Sequences sp_Q8BUN5_SMAD3_MOUSE_10090 and sp_P84025_SMAD3_RAT_10116 are exactly identical! WARNING: Sequences sp_Q8BUN5_SMAD3_MOUSE_10090 and tr_I3MF72_I3MF72_ICTTR_43179 are exactly identical! WARNING: Sequences sp_Q8BUN5_SMAD3_MOUSE_10090 and tr_H0XAS3_H0XAS3_OTOGA_30611 are exactly identical! WARNING: Sequences sp_Q8BUN5_SMAD3_MOUSE_10090 and sp_P84022_SMAD3_HUMAN_9606 are exactly identical! WARNING: Sequences sp_Q8BUN5_SMAD3_MOUSE_10090 and sp_P84024_SMAD3_PIG_9823 are exactly identical! WARNING: Sequences sp_Q8BUN5_SMAD3_MOUSE_10090 and tr_A0A2I2UP85_A0A2I2UP85_FELCA_9685 are exactly identical! WARNING: Sequences sp_Q8BUN5_SMAD3_MOUSE_10090 and tr_A0A1S3EP13_A0A1S3EP13_DIPOR_10020 are exactly identical! WARNING: Sequences sp_Q8BUN5_SMAD3_MOUSE_10090 and tr_A0A2R9AV36_A0A2R9AV36_PANPA_9597 are exactly identical! WARNING: Sequences sp_Q8BUN5_SMAD3_MOUSE_10090 and tr_A0A2U3WYA5_A0A2U3WYA5_ODORO_9708 are exactly identical! WARNING: Sequences sp_Q8BUN5_SMAD3_MOUSE_10090 and tr_A0A2Y9DIB4_A0A2Y9DIB4_TRIMA_127582 are exactly identical! WARNING: Sequences sp_Q8BUN5_SMAD3_MOUSE_10090 and tr_A0A2Y9K3C9_A0A2Y9K3C9_ENHLU_391180 are exactly identical! WARNING: Sequences sp_Q8BUN5_SMAD3_MOUSE_10090 and tr_A0A2Y9NWL7_A0A2Y9NWL7_DELLE_9749 are exactly identical! WARNING: Sequences sp_Q8BUN5_SMAD3_MOUSE_10090 and tr_A0A2Y9FQZ8_A0A2Y9FQZ8_PHYCD_9755 are exactly identical! WARNING: Sequences sp_Q8BUN5_SMAD3_MOUSE_10090 and tr_A0A383YTC5_A0A383YTC5_BALAS_310752 are exactly identical! WARNING: Sequences tr_M3XRX1_M3XRX1_MUSPF_9669 and tr_A0A2Y9KT65_A0A2Y9KT65_ENHLU_391180 are exactly identical! WARNING: Sequences tr_M3Y661_M3Y661_MUSPF_9669 and tr_E2QZF1_E2QZF1_CANLF_9615 are exactly identical! WARNING: Sequences tr_M3Y661_M3Y661_MUSPF_9669 and tr_D2H3Q3_D2H3Q3_AILME_9646 are exactly identical! WARNING: Sequences tr_M3Y661_M3Y661_MUSPF_9669 and tr_M3W1M8_M3W1M8_FELCA_9685 are exactly identical! WARNING: Sequences tr_M3Y661_M3Y661_MUSPF_9669 and tr_A0A2U3WRB8_A0A2U3WRB8_ODORO_9708 are exactly identical! WARNING: Sequences tr_M3Y661_M3Y661_MUSPF_9669 and tr_A0A2Y9K6L2_A0A2Y9K6L2_ENHLU_391180 are exactly identical! WARNING: Sequences tr_M3Y661_M3Y661_MUSPF_9669 and tr_A0A384BM65_A0A384BM65_URSMA_29073 are exactly identical! WARNING: Sequences tr_M3YBJ8_M3YBJ8_MUSPF_9669 and tr_D2H520_D2H520_AILME_9646 are exactly identical! WARNING: Sequences tr_M3YBJ8_M3YBJ8_MUSPF_9669 and tr_A0A2U3WNE2_A0A2U3WNE2_ODORO_9708 are exactly identical! WARNING: Sequences tr_M3YBJ8_M3YBJ8_MUSPF_9669 and tr_A0A2U3XTK1_A0A2U3XTK1_LEPWE_9713 are exactly identical! WARNING: Sequences tr_M3YBJ8_M3YBJ8_MUSPF_9669 and tr_A0A2Y9ISJ5_A0A2Y9ISJ5_ENHLU_391180 are exactly identical! WARNING: Sequences tr_M3YEV3_M3YEV3_MUSPF_9669 and tr_G3RTX4_G3RTX4_GORGO_9595 are exactly identical! WARNING: Sequences tr_M3YEV3_M3YEV3_MUSPF_9669 and sp_Q5R6H7_SMAD5_PONAB_9601 are exactly identical! WARNING: Sequences tr_M3YEV3_M3YEV3_MUSPF_9669 and tr_E2RCX7_E2RCX7_CANLF_9615 are exactly identical! WARNING: Sequences tr_M3YEV3_M3YEV3_MUSPF_9669 and tr_K7B6A4_K7B6A4_PANTR_9598 are exactly identical! WARNING: Sequences tr_M3YEV3_M3YEV3_MUSPF_9669 and tr_F7A120_F7A120_HORSE_9796 are exactly identical! WARNING: Sequences tr_M3YEV3_M3YEV3_MUSPF_9669 and tr_H0X0W6_H0X0W6_OTOGA_30611 are exactly identical! WARNING: Sequences tr_M3YEV3_M3YEV3_MUSPF_9669 and sp_Q99717_SMAD5_HUMAN_9606 are exactly identical! WARNING: Sequences tr_M3YEV3_M3YEV3_MUSPF_9669 and tr_F6YMS3_F6YMS3_MACMU_9544 are exactly identical! WARNING: Sequences tr_M3YEV3_M3YEV3_MUSPF_9669 and tr_G5BX13_G5BX13_HETGA_10181 are exactly identical! WARNING: Sequences tr_M3YEV3_M3YEV3_MUSPF_9669 and tr_U3FCQ3_U3FCQ3_CALJA_9483 are exactly identical! WARNING: Sequences tr_M3YEV3_M3YEV3_MUSPF_9669 and tr_A0A286ZNF5_A0A286ZNF5_PIG_9823 are exactly identical! WARNING: Sequences tr_M3YEV3_M3YEV3_MUSPF_9669 and tr_D2GVL2_D2GVL2_AILME_9646 are exactly identical! WARNING: Sequences tr_M3YEV3_M3YEV3_MUSPF_9669 and tr_F1MD43_F1MD43_BOVIN_9913 are exactly identical! WARNING: Sequences tr_M3YEV3_M3YEV3_MUSPF_9669 and tr_M3X9P2_M3X9P2_FELCA_9685 are exactly identical! WARNING: Sequences tr_M3YEV3_M3YEV3_MUSPF_9669 and tr_A0A096MMR6_A0A096MMR6_PAPAN_9555 are exactly identical! WARNING: Sequences tr_M3YEV3_M3YEV3_MUSPF_9669 and tr_A0A091D8T3_A0A091D8T3_FUKDA_885580 are exactly identical! WARNING: Sequences tr_M3YEV3_M3YEV3_MUSPF_9669 and tr_A0A0D9RLM2_A0A0D9RLM2_CHLSB_60711 are exactly identical! WARNING: Sequences tr_M3YEV3_M3YEV3_MUSPF_9669 and tr_A0A2K6DUF7_A0A2K6DUF7_MACNE_9545 are exactly identical! WARNING: Sequences tr_M3YEV3_M3YEV3_MUSPF_9669 and tr_A0A2K5YSA7_A0A2K5YSA7_MANLE_9568 are exactly identical! WARNING: Sequences tr_M3YEV3_M3YEV3_MUSPF_9669 and tr_A0A2R9BFQ2_A0A2R9BFQ2_PANPA_9597 are exactly identical! WARNING: Sequences tr_M3YEV3_M3YEV3_MUSPF_9669 and tr_A0A2U3WAY5_A0A2U3WAY5_ODORO_9708 are exactly identical! WARNING: Sequences tr_M3YEV3_M3YEV3_MUSPF_9669 and tr_A0A2Y9E278_A0A2Y9E278_TRIMA_127582 are exactly identical! WARNING: Sequences tr_M3YEV3_M3YEV3_MUSPF_9669 and tr_A0A384C4K2_A0A384C4K2_URSMA_29073 are exactly identical! WARNING: Sequences tr_O96660_O96660_DROME_7227 and tr_B4IKX2_B4IKX2_DROSE_7238 are exactly identical! WARNING: Sequences sp_P42003_MAD_DROME_7227 and tr_B4I2W3_B4I2W3_DROSE_7238 are exactly identical! WARNING: Sequences tr_G1QM38_G1QM38_NOMLE_61853 and tr_A0A2I2ZI57_A0A2I2ZI57_GORGO_9595 are exactly identical! WARNING: Sequences tr_G1QM38_G1QM38_NOMLE_61853 and tr_H2RCQ5_H2RCQ5_PANTR_9598 are exactly identical! WARNING: Sequences tr_G1QM38_G1QM38_NOMLE_61853 and tr_F6YCR1_F6YCR1_MACMU_9544 are exactly identical! WARNING: Sequences tr_G1QM38_G1QM38_NOMLE_61853 and tr_G7PW13_G7PW13_MACFA_9541 are exactly identical! WARNING: Sequences tr_G1QM38_G1QM38_NOMLE_61853 and tr_A0A2K6CF91_A0A2K6CF91_MACNE_9545 are exactly identical! WARNING: Sequences tr_G1QM38_G1QM38_NOMLE_61853 and tr_A0A2R9A3J1_A0A2R9A3J1_PANPA_9597 are exactly identical! WARNING: Sequences tr_G1RL59_G1RL59_NOMLE_61853 and tr_G1PCD2_G1PCD2_MYOLU_59463 are exactly identical! WARNING: Sequences tr_G1RL59_G1RL59_NOMLE_61853 and tr_G3QPV6_G3QPV6_GORGO_9595 are exactly identical! WARNING: Sequences tr_G1RL59_G1RL59_NOMLE_61853 and tr_A0A2J8UE82_A0A2J8UE82_PONAB_9601 are exactly identical! WARNING: Sequences tr_G1RL59_G1RL59_NOMLE_61853 and tr_G1T109_G1T109_RABIT_9986 are exactly identical! WARNING: Sequences tr_G1RL59_G1RL59_NOMLE_61853 and tr_E2RP23_E2RP23_CANLF_9615 are exactly identical! WARNING: Sequences tr_G1RL59_G1RL59_NOMLE_61853 and tr_H2QEH9_H2QEH9_PANTR_9598 are exactly identical! WARNING: Sequences tr_G1RL59_G1RL59_NOMLE_61853 and tr_W5P0F2_W5P0F2_SHEEP_9940 are exactly identical! WARNING: Sequences tr_G1RL59_G1RL59_NOMLE_61853 and tr_I3M2Z7_I3M2Z7_ICTTR_43179 are exactly identical! WARNING: Sequences tr_G1RL59_G1RL59_NOMLE_61853 and tr_H0WGF2_H0WGF2_OTOGA_30611 are exactly identical! WARNING: Sequences tr_G1RL59_G1RL59_NOMLE_61853 and tr_H0VNM6_H0VNM6_CAVPO_10141 are exactly identical! WARNING: Sequences tr_G1RL59_G1RL59_NOMLE_61853 and sp_Q15796_SMAD2_HUMAN_9606 are exactly identical! WARNING: Sequences tr_G1RL59_G1RL59_NOMLE_61853 and tr_F7CP27_F7CP27_MACMU_9544 are exactly identical! WARNING: Sequences tr_G1RL59_G1RL59_NOMLE_61853 and tr_G3SL58_G3SL58_LOXAF_9785 are exactly identical! WARNING: Sequences tr_G1RL59_G1RL59_NOMLE_61853 and tr_F7HWK8_F7HWK8_CALJA_9483 are exactly identical! WARNING: Sequences tr_G1RL59_G1RL59_NOMLE_61853 and tr_A0A287AE86_A0A287AE86_PIG_9823 are exactly identical! WARNING: Sequences tr_G1RL59_G1RL59_NOMLE_61853 and tr_G7PWR4_G7PWR4_MACFA_9541 are exactly identical! WARNING: Sequences tr_G1RL59_G1RL59_NOMLE_61853 and tr_E1BE92_E1BE92_BOVIN_9913 are exactly identical! WARNING: Sequences tr_G1RL59_G1RL59_NOMLE_61853 and tr_A0A0D9RZJ6_A0A0D9RZJ6_CHLSB_60711 are exactly identical! WARNING: Sequences tr_G1RL59_G1RL59_NOMLE_61853 and tr_A0A2K5KKF5_A0A2K5KKF5_CERAT_9531 are exactly identical! WARNING: Sequences tr_G1RL59_G1RL59_NOMLE_61853 and tr_A0A2K6CWF8_A0A2K6CWF8_MACNE_9545 are exactly identical! WARNING: Sequences tr_G1RL59_G1RL59_NOMLE_61853 and tr_A0A2R9B4S1_A0A2R9B4S1_PANPA_9597 are exactly identical! WARNING: Sequences tr_G1RL59_G1RL59_NOMLE_61853 and tr_A0A2U4BH90_A0A2U4BH90_TURTR_9739 are exactly identical! WARNING: Sequences tr_G1RL59_G1RL59_NOMLE_61853 and tr_A0A2U3WII2_A0A2U3WII2_ODORO_9708 are exactly identical! WARNING: Sequences tr_G1RL59_G1RL59_NOMLE_61853 and tr_A0A2Y9EBA5_A0A2Y9EBA5_TRIMA_127582 are exactly identical! WARNING: Sequences tr_G1RL59_G1RL59_NOMLE_61853 and tr_A0A2Y9IZB1_A0A2Y9IZB1_ENHLU_391180 are exactly identical! WARNING: Sequences tr_G1RL59_G1RL59_NOMLE_61853 and tr_A0A2Y9NZF1_A0A2Y9NZF1_DELLE_9749 are exactly identical! WARNING: Sequences tr_G1RL59_G1RL59_NOMLE_61853 and tr_A0A2Y9TEE0_A0A2Y9TEE0_PHYCD_9755 are exactly identical! WARNING: Sequences tr_G1RMF1_G1RMF1_NOMLE_61853 and tr_G3RCU6_G3RCU6_GORGO_9595 are exactly identical! WARNING: Sequences tr_G1RMF1_G1RMF1_NOMLE_61853 and tr_A0A2J8UEM2_A0A2J8UEM2_PONAB_9601 are exactly identical! WARNING: Sequences tr_G1RMF1_G1RMF1_NOMLE_61853 and tr_H2QEJ6_H2QEJ6_PANTR_9598 are exactly identical! WARNING: Sequences tr_G1RMF1_G1RMF1_NOMLE_61853 and sp_Q13485_SMAD4_HUMAN_9606 are exactly identical! WARNING: Sequences tr_G1RMF1_G1RMF1_NOMLE_61853 and tr_A0A1D5QTT6_A0A1D5QTT6_MACMU_9544 are exactly identical! WARNING: Sequences tr_G1RMF1_G1RMF1_NOMLE_61853 and tr_A0A2R8MAR1_A0A2R8MAR1_CALJA_9483 are exactly identical! WARNING: Sequences tr_G1RMF1_G1RMF1_NOMLE_61853 and tr_G7PWS9_G7PWS9_MACFA_9541 are exactly identical! WARNING: Sequences tr_G1RMF1_G1RMF1_NOMLE_61853 and tr_A0A096N2U8_A0A096N2U8_PAPAN_9555 are exactly identical! WARNING: Sequences tr_G1RMF1_G1RMF1_NOMLE_61853 and tr_A0A2K5NH42_A0A2K5NH42_CERAT_9531 are exactly identical! WARNING: Sequences tr_G1RMF1_G1RMF1_NOMLE_61853 and tr_A0A2K6BPF5_A0A2K6BPF5_MACNE_9545 are exactly identical! WARNING: Sequences tr_G1RMF1_G1RMF1_NOMLE_61853 and tr_A0A2K5XWF3_A0A2K5XWF3_MANLE_9568 are exactly identical! WARNING: Sequences tr_G1RMF1_G1RMF1_NOMLE_61853 and tr_A0A2R9A0M1_A0A2R9A0M1_PANPA_9597 are exactly identical! WARNING: Sequences tr_B5DJI3_B5DJI3_DROPS_46245 and tr_B4GSG1_B4GSG1_DROPE_7234 are exactly identical! WARNING: Sequences tr_Q29HD9_Q29HD9_DROPS_46245 and tr_B4GXV7_B4GXV7_DROPE_7234 are exactly identical! WARNING: Sequences tr_W5PH38_W5PH38_SHEEP_9940 and tr_I3MG69_I3MG69_ICTTR_43179 are exactly identical! WARNING: Sequences tr_W5PH38_W5PH38_SHEEP_9940 and sp_Q1JQA2_SMAD1_BOVIN_9913 are exactly identical! WARNING: Sequences tr_A0A087ZZ35_A0A087ZZ35_APIME_7460 and tr_A0A2A3EFX4_A0A2A3EFX4_APICC_94128 are exactly identical! WARNING: Sequences tr_A0A158NI66_A0A158NI66_ATTCE_12957 and tr_A0A195B694_A0A195B694_9HYME_520822 are exactly identical! WARNING: Sequences tr_I3MX09_I3MX09_ICTTR_43179 and tr_H0V7V1_H0V7V1_CAVPO_10141 are exactly identical! WARNING: Sequences tr_I3MX09_I3MX09_ICTTR_43179 and tr_A0A2I2V1Y5_A0A2I2V1Y5_FELCA_9685 are exactly identical! WARNING: Sequences sp_Q15797_SMAD1_HUMAN_9606 and tr_A0A1D5Q7V1_A0A1D5Q7V1_MACMU_9544 are exactly identical! WARNING: Sequences sp_Q15797_SMAD1_HUMAN_9606 and tr_G7P6D2_G7P6D2_MACFA_9541 are exactly identical! WARNING: Sequences sp_Q15797_SMAD1_HUMAN_9606 and tr_A0A2K5NE45_A0A2K5NE45_CERAT_9531 are exactly identical! WARNING: Sequences sp_Q15797_SMAD1_HUMAN_9606 and tr_A0A2K6B401_A0A2K6B401_MACNE_9545 are exactly identical! WARNING: Sequences sp_Q15797_SMAD1_HUMAN_9606 and tr_A0A2K5YVF0_A0A2K5YVF0_MANLE_9568 are exactly identical! WARNING: Sequences tr_H0YSJ2_H0YSJ2_TAEGU_59729 and tr_A0A091ENW8_A0A091ENW8_CORBR_85066 are exactly identical! WARNING: Sequences tr_F4WG94_F4WG94_ACREC_103372 and tr_A0A151JXB1_A0A151JXB1_9HYME_34720 are exactly identical! WARNING: Sequences tr_E3LSQ5_E3LSQ5_CAERE_31234 and tr_A0A261BT04_A0A261BT04_9PELO_1503980 are exactly identical! WARNING: Sequences tr_G7P8C6_G7P8C6_MACFA_9541 and tr_L5JUU0_L5JUU0_PTEAL_9402 are exactly identical! WARNING: Sequences tr_U3K056_U3K056_FICAL_59894 and tr_A0A218V374_A0A218V374_9PASE_299123 are exactly identical! WARNING: Sequences tr_A0A044S541_A0A044S541_ONCVO_6282 and tr_A0A182EMM9_A0A182EMM9_ONCOC_42157 are exactly identical! WARNING: Sequences tr_A0A044V1C1_A0A044V1C1_ONCVO_6282 and tr_A0A182DZ65_A0A182DZ65_ONCOC_42157 are exactly identical! WARNING: Sequences tr_A0A096NMF6_A0A096NMF6_PAPAN_9555 and tr_A0A0D9RLF4_A0A0D9RLF4_CHLSB_60711 are exactly identical! WARNING: Sequences tr_A0A096NMF6_A0A096NMF6_PAPAN_9555 and tr_A0A2K6C3Y4_A0A2K6C3Y4_MACNE_9545 are exactly identical! WARNING: Sequences tr_A0A096NMF6_A0A096NMF6_PAPAN_9555 and tr_A0A2K5YMS3_A0A2K5YMS3_MANLE_9568 are exactly identical! WARNING: Sequences tr_A0A151PBL1_A0A151PBL1_ALLMI_8496 and tr_A0A1U7RI03_A0A1U7RI03_ALLSI_38654 are exactly identical! WARNING: Sequences tr_A0A091EX42_A0A091EX42_CORBR_85066 and tr_A0A087QRI5_A0A087QRI5_APTFO_9233 are exactly identical! WARNING: Sequences tr_A0A091JFG5_A0A091JFG5_EGRGA_188379 and tr_A0A091V382_A0A091V382_NIPNI_128390 are exactly identical! WARNING: Sequences tr_A0A091JFG5_A0A091JFG5_EGRGA_188379 and tr_A0A087RF12_A0A087RF12_APTFO_9233 are exactly identical! WARNING: Sequences tr_A0A091JFG5_A0A091JFG5_EGRGA_188379 and tr_A0A099ZZ81_A0A099ZZ81_CHAVO_50402 are exactly identical! WARNING: Sequences tr_A0A091JFG5_A0A091JFG5_EGRGA_188379 and tr_A0A093FWU2_A0A093FWU2_DRYPU_118200 are exactly identical! WARNING: Sequences tr_A0A091JFG5_A0A091JFG5_EGRGA_188379 and tr_A0A091I6W7_A0A091I6W7_CALAN_9244 are exactly identical! WARNING: Sequences tr_A0A093RTB4_A0A093RTB4_9PASS_328815 and tr_A0A091VD87_A0A091VD87_NIPNI_128390 are exactly identical! WARNING: Sequences tr_A0A093RTB4_A0A093RTB4_9PASS_328815 and tr_A0A091XWI6_A0A091XWI6_OPIHO_30419 are exactly identical! WARNING: Sequences tr_A0A2I0M0M7_A0A2I0M0M7_COLLI_8932 and tr_A0A3Q0FQ23_A0A3Q0FQ23_ALLSI_38654 are exactly identical! WARNING: Sequences tr_A0A2I0MAB5_A0A2I0MAB5_COLLI_8932 and tr_A0A1V4KUQ2_A0A1V4KUQ2_PATFA_372326 are exactly identical! WARNING: Sequences tr_A0A0V1DDL3_A0A0V1DDL3_TRIBR_45882 and tr_A0A0V0X7R0_A0A0V0X7R0_9BILA_92179 are exactly identical! WARNING: Sequences tr_A0A0V1DDL3_A0A0V1DDL3_TRIBR_45882 and tr_A0A0V0ULF1_A0A0V0ULF1_9BILA_181606 are exactly identical! WARNING: Sequences tr_A0A0V1DDL3_A0A0V1DDL3_TRIBR_45882 and tr_A0A0V1KLY9_A0A0V1KLY9_9BILA_6335 are exactly identical! WARNING: Sequences tr_A0A0V1DDL3_A0A0V1DDL3_TRIBR_45882 and tr_A0A0V1A9E7_A0A0V1A9E7_9BILA_990121 are exactly identical! WARNING: Sequences tr_A0A0V1DDL3_A0A0V1DDL3_TRIBR_45882 and tr_A0A0V1NY85_A0A0V1NY85_9BILA_92180 are exactly identical! WARNING: Sequences tr_A0A0V1DDL3_A0A0V1DDL3_TRIBR_45882 and tr_A0A0V0T9X0_A0A0V0T9X0_9BILA_144512 are exactly identical! WARNING: Sequences tr_A0A0V1DI95_A0A0V1DI95_TRIBR_45882 and tr_A0A0V0X8M8_A0A0V0X8M8_9BILA_92179 are exactly identical! WARNING: Sequences tr_A0A0V0VTJ4_A0A0V0VTJ4_9BILA_181606 and tr_A0A0V1LSP4_A0A0V1LSP4_9BILA_6335 are exactly identical! WARNING: Sequences tr_A0A0V0VTJ4_A0A0V0VTJ4_9BILA_181606 and tr_A0A0V1NQ88_A0A0V1NQ88_9BILA_92180 are exactly identical! WARNING: Sequences tr_A0A0V0VTJ4_A0A0V0VTJ4_9BILA_181606 and tr_A0A0V0TVR7_A0A0V0TVR7_9BILA_144512 are exactly identical! WARNING: Sequences tr_A0A0V1ME55_A0A0V1ME55_9BILA_268474 and tr_A0A0V1HB83_A0A0V1HB83_9BILA_268475 are exactly identical! WARNING: Sequences tr_A0A1U7UBQ1_A0A1U7UBQ1_TARSY_1868482 and tr_A0A2R8ZY67_A0A2R8ZY67_PANPA_9597 are exactly identical! WARNING: Sequences tr_A0A2U3V5W2_A0A2U3V5W2_TURTR_9739 and tr_A0A2Y9PH18_A0A2Y9PH18_DELLE_9749 are exactly identical! WARNING: Sequences tr_A0A2U3V5W2_A0A2U3V5W2_TURTR_9739 and tr_A0A2Y9SI56_A0A2Y9SI56_PHYCD_9755 are exactly identical! WARNING: Sequences tr_A0A2U3V5W2_A0A2U3V5W2_TURTR_9739 and tr_A0A383ZAR7_A0A383ZAR7_BALAS_310752 are exactly identical! WARNING: Sequences tr_A0A2U4BGU5_A0A2U4BGU5_TURTR_9739 and tr_A0A2Y9N811_A0A2Y9N811_DELLE_9749 are exactly identical! WARNING: Sequences tr_A0A2U4BHD1_A0A2U4BHD1_TURTR_9739 and tr_A0A2Y9NZ77_A0A2Y9NZ77_DELLE_9749 are exactly identical! WARNING: Sequences tr_A0A2U4BHD1_A0A2U4BHD1_TURTR_9739 and tr_A0A2Y9EKH2_A0A2Y9EKH2_PHYCD_9755 are exactly identical! WARNING: Duplicate sequences found: 151 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/P84022/3_mltree/P84022.raxml.reduced.phy Alignment comprises 1 partitions and 691 patterns Partition 0: noname Model: LG4X+R4 Alignment sites / patterns: 691 / 691 Gaps: 37.89 % Invariant sites: 0.29 % NOTE: Binary MSA file created: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/P84022/3_mltree/P84022.raxml.rba Parallelization scheme autoconfig: 2 worker(s) x 4 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 / 173 / 13840 [00:00:00] Data distribution: max. searches per worker: 10 Starting ML tree search with 20 distinct starting trees [00:00:00 -533282.120586] Initial branch length optimization [00:00:06 -433414.023483] Model parameter optimization (eps = 10.000000) [00:01:36 -430896.984141] AUTODETECT spr round 1 (radius: 5) [00:04:40 -275482.216389] AUTODETECT spr round 2 (radius: 10) [00:08:00 -200654.301414] AUTODETECT spr round 3 (radius: 15) [00:11:28 -163184.717137] AUTODETECT spr round 4 (radius: 20) [00:15:22 -145051.622747] AUTODETECT spr round 5 (radius: 25) [00:20:19 -141204.556277] SPR radius for FAST iterations: 25 (autodetect) [00:20:19 -141204.556277] Model parameter optimization (eps = 3.000000) [00:21:12 -140592.822872] FAST spr round 1 (radius: 25) [00:25:04 -117415.405784] FAST spr round 2 (radius: 25) [00:28:04 -115238.312407] FAST spr round 3 (radius: 25) [00:30:44 -115157.441443] FAST spr round 4 (radius: 25) [00:33:09 -115145.685629] FAST spr round 5 (radius: 25) [00:35:27 -115144.010173] FAST spr round 6 (radius: 25) [00:37:37 -115144.009071] Model parameter optimization (eps = 1.000000) [00:38:04 -115139.164270] SLOW spr round 1 (radius: 5) [00:40:47 -115120.070346] SLOW spr round 2 (radius: 5) [00:43:31 -115117.692063] SLOW spr round 3 (radius: 5) [00:46:17 -115116.251372] SLOW spr round 4 (radius: 5) [00:49:01 -115114.937668] SLOW spr round 5 (radius: 5) [00:51:42 -115114.003196] SLOW spr round 6 (radius: 5) [00:54:48 -115114.001902] SLOW spr round 7 (radius: 10) [00:57:32 -115114.001301] SLOW spr round 8 (radius: 15) [01:01:59 -115113.631639] SLOW spr round 9 (radius: 5) [01:06:48 -115111.488186] SLOW spr round 10 (radius: 5) [01:12:12 -115111.487996] SLOW spr round 11 (radius: 10) [01:17:47 -115111.487844] SLOW spr round 12 (radius: 15) [01:26:15 -115111.487709] SLOW spr round 13 (radius: 20) [01:38:48 -115101.502225] SLOW spr round 14 (radius: 5) [01:45:43 -115095.472210] SLOW spr round 15 (radius: 5) [01:51:10 -115094.684756] SLOW spr round 16 (radius: 5) [01:55:02 -115094.672929] SLOW spr round 17 (radius: 10) [01:58:52 -115094.671918] SLOW spr round 18 (radius: 15) [02:05:47 -115092.803156] SLOW spr round 19 (radius: 5) [02:07:26] [worker #1] ML tree search #2, logLikelihood: -115084.641015 [02:11:04 -115092.744759] SLOW spr round 20 (radius: 10) [02:16:26 -115091.866638] SLOW spr round 21 (radius: 5) [02:21:05 -115091.862615] SLOW spr round 22 (radius: 10) [02:26:25 -115091.862185] SLOW spr round 23 (radius: 15) [02:34:43 -115091.862162] SLOW spr round 24 (radius: 20) [02:46:18 -115091.862140] SLOW spr round 25 (radius: 25) [02:56:39 -115091.862119] Model parameter optimization (eps = 0.100000) [02:57:01] [worker #0] ML tree search #1, logLikelihood: -115091.651509 [02:57:01 -535370.220239] Initial branch length optimization [02:57:11 -434718.923763] Model parameter optimization (eps = 10.000000) [03:00:16 -432005.604961] AUTODETECT spr round 1 (radius: 5) [03:05:46 -268283.777882] AUTODETECT spr round 2 (radius: 10) [03:11:52 -194697.857350] AUTODETECT spr round 3 (radius: 15) [03:18:48 -164277.423415] AUTODETECT spr round 4 (radius: 20) [03:26:25 -143900.945670] AUTODETECT spr round 5 (radius: 25) [03:35:34 -136562.012664] SPR radius for FAST iterations: 25 (autodetect) [03:35:34 -136562.012664] Model parameter optimization (eps = 3.000000) [03:37:04 -135899.677065] FAST spr round 1 (radius: 25) [03:44:32 -115989.954217] FAST spr round 2 (radius: 25) [03:50:18 -115241.222505] FAST spr round 3 (radius: 25) [03:54:54 -115140.014567] FAST spr round 4 (radius: 25) [03:59:04 -115138.232721] FAST spr round 5 (radius: 25) [04:02:54 -115137.787933] FAST spr round 6 (radius: 25) [04:06:36 -115137.787323] Model parameter optimization (eps = 1.000000) [04:07:14 -115126.115045] SLOW spr round 1 (radius: 5) [04:12:01 -115101.801018] SLOW spr round 2 (radius: 5) [04:16:54 -115097.656572] SLOW spr round 3 (radius: 5) [04:21:48 -115097.246903] SLOW spr round 4 (radius: 5) [04:23:39] [worker #1] ML tree search #4, logLikelihood: -115073.668472 [04:26:35 -115097.246841] SLOW spr round 5 (radius: 10) [04:31:35 -115097.221672] SLOW spr round 6 (radius: 15) [04:40:11 -115094.946857] SLOW spr round 7 (radius: 5) [04:46:39 -115091.174263] SLOW spr round 8 (radius: 5) [04:52:20 -115090.881724] SLOW spr round 9 (radius: 5) [04:57:28 -115090.881217] SLOW spr round 10 (radius: 10) [05:02:37 -115090.230497] SLOW spr round 11 (radius: 5) [05:08:37 -115090.229981] SLOW spr round 12 (radius: 10) [05:14:16 -115090.229735] SLOW spr round 13 (radius: 15) [05:22:48 -115070.920647] SLOW spr round 14 (radius: 5) [05:29:33 -115064.061481] SLOW spr round 15 (radius: 5) [05:35:24 -115064.011335] SLOW spr round 16 (radius: 10) [05:40:55 -115064.010879] SLOW spr round 17 (radius: 15) [05:49:16 -115064.010799] SLOW spr round 18 (radius: 20) [06:01:24 -115064.010757] SLOW spr round 19 (radius: 25) [06:17:10 -115063.996904] Model parameter optimization (eps = 0.100000) [06:17:30] [worker #0] ML tree search #3, logLikelihood: -115063.902348 [06:17:30 -528799.773812] Initial branch length optimization [06:17:38 -430287.428226] Model parameter optimization (eps = 10.000000) [06:19:51 -427878.077216] AUTODETECT spr round 1 (radius: 5) [06:25:31 -271627.994942] AUTODETECT spr round 2 (radius: 10) [06:31:37 -201911.745138] AUTODETECT spr round 3 (radius: 15) [06:38:18 -167787.663738] AUTODETECT spr round 4 (radius: 20) [06:43:41 -146615.096167] AUTODETECT spr round 5 (radius: 25) [06:48:36 -135129.168550] SPR radius for FAST iterations: 25 (autodetect) [06:48:36 -135129.168550] Model parameter optimization (eps = 3.000000) [06:49:36 -134594.615471] FAST spr round 1 (radius: 25) [06:53:42 -116138.777162] FAST spr round 2 (radius: 25) [06:58:13 -115233.166498] FAST spr round 3 (radius: 25) [07:02:52 -115174.373437] FAST spr round 4 (radius: 25) [07:07:15 -115172.680208] FAST spr round 5 (radius: 25) [07:08:46] [worker #1] ML tree search #6, logLikelihood: -115081.223010 [07:11:16 -115171.118097] FAST spr round 6 (radius: 25) [07:15:19 -115171.113275] Model parameter optimization (eps = 1.000000) [07:16:22 -115139.642771] SLOW spr round 1 (radius: 5) [07:21:13 -115109.467070] SLOW spr round 2 (radius: 5) [07:24:52 -115106.463891] SLOW spr round 3 (radius: 5) [07:27:38 -115104.842932] SLOW spr round 4 (radius: 5) [07:30:20 -115104.842811] SLOW spr round 5 (radius: 10) [07:33:05 -115104.842632] SLOW spr round 6 (radius: 15) [07:37:31 -115104.842586] SLOW spr round 7 (radius: 20) [07:43:40 -115104.842541] SLOW spr round 8 (radius: 25) [07:51:44 -115104.242565] SLOW spr round 9 (radius: 5) [07:55:13 -115104.242456] SLOW spr round 10 (radius: 10) [07:58:35 -115104.242389] SLOW spr round 11 (radius: 15) [08:02:42 -115104.242342] SLOW spr round 12 (radius: 20) [08:08:51 -115104.242294] SLOW spr round 13 (radius: 25) [08:18:17 -115104.242246] Model parameter optimization (eps = 0.100000) [08:18:38] [worker #0] ML tree search #5, logLikelihood: -115104.152114 [08:18:38 -531114.681505] Initial branch length optimization [08:18:46 -430619.094395] Model parameter optimization (eps = 10.000000) [08:20:38 -428231.874149] AUTODETECT spr round 1 (radius: 5) [08:26:23 -266726.801846] AUTODETECT spr round 2 (radius: 10) [08:32:16 -191888.692079] AUTODETECT spr round 3 (radius: 15) [08:38:07 -153059.211841] AUTODETECT spr round 4 (radius: 20) [08:44:57 -146162.823138] AUTODETECT spr round 5 (radius: 25) [08:53:42 -134489.134163] SPR radius for FAST iterations: 25 (autodetect) [08:53:42 -134489.134163] Model parameter optimization (eps = 3.000000) [08:55:28 -134026.516025] FAST spr round 1 (radius: 25) [09:02:25 -116335.962622] FAST spr round 2 (radius: 25) [09:07:38 -115397.120322] FAST spr round 3 (radius: 25) [09:08:47] [worker #1] ML tree search #8, logLikelihood: -115111.439484 [09:12:18 -115202.591769] FAST spr round 4 (radius: 25) [09:14:38 -115173.652694] FAST spr round 5 (radius: 25) [09:16:50 -115164.584328] FAST spr round 6 (radius: 25) [09:18:53 -115164.583818] Model parameter optimization (eps = 1.000000) [09:19:22 -115140.405738] SLOW spr round 1 (radius: 5) [09:21:57 -115108.573394] SLOW spr round 2 (radius: 5) [09:24:35 -115091.137593] SLOW spr round 3 (radius: 5) [09:27:10 -115083.629091] SLOW spr round 4 (radius: 5) [09:29:43 -115083.215661] SLOW spr round 5 (radius: 5) [09:32:12 -115083.215542] SLOW spr round 6 (radius: 10) [09:34:53 -115078.884661] SLOW spr round 7 (radius: 5) [09:38:01 -115078.884000] SLOW spr round 8 (radius: 10) [09:40:57 -115078.883956] SLOW spr round 9 (radius: 15) [09:45:01 -115077.032956] SLOW spr round 10 (radius: 5) [09:48:15 -115077.015439] SLOW spr round 11 (radius: 10) [09:51:19 -115077.014611] SLOW spr round 12 (radius: 15) [09:55:20 -115077.014499] SLOW spr round 13 (radius: 20) [10:01:20 -115077.014384] SLOW spr round 14 (radius: 25) [10:09:02 -115077.014353] Model parameter optimization (eps = 0.100000) [10:09:19] [worker #0] ML tree search #7, logLikelihood: -115076.628769 [10:09:19 -529068.311302] Initial branch length optimization [10:09:24 -432297.380743] Model parameter optimization (eps = 10.000000) [10:10:42 -429926.415563] AUTODETECT spr round 1 (radius: 5) [10:13:36 -272325.637090] AUTODETECT spr round 2 (radius: 10) [10:16:46 -194002.472464] AUTODETECT spr round 3 (radius: 15) [10:20:02 -162385.591051] AUTODETECT spr round 4 (radius: 20) [10:23:47 -141429.465538] AUTODETECT spr round 5 (radius: 25) [10:28:02 -134523.740808] SPR radius for FAST iterations: 25 (autodetect) [10:28:03 -134523.740808] Model parameter optimization (eps = 3.000000) [10:28:49 -134001.743694] FAST spr round 1 (radius: 25) [10:32:30 -117808.794687] FAST spr round 2 (radius: 25) [10:35:18 -116052.913059] FAST spr round 3 (radius: 25) [10:37:50 -115940.232167] FAST spr round 4 (radius: 25) [10:40:12 -115248.599786] FAST spr round 5 (radius: 25) [10:42:30 -115228.975711] FAST spr round 6 (radius: 25) [10:44:36 -115228.975195] Model parameter optimization (eps = 1.000000) [10:45:04 -115207.589498] SLOW spr round 1 (radius: 5) [10:47:39 -115179.262347] SLOW spr round 2 (radius: 5) [10:50:18 -115179.123591] SLOW spr round 3 (radius: 5) [10:52:58 -115179.122341] SLOW spr round 4 (radius: 10) [10:55:41 -115179.121449] SLOW spr round 5 (radius: 15) [11:00:04 -115176.484816] SLOW spr round 6 (radius: 5) [11:03:46 -115175.900610] SLOW spr round 7 (radius: 5) [11:09:19 -115175.899717] SLOW spr round 8 (radius: 10) [11:14:30 -115175.899157] SLOW spr round 9 (radius: 15) [11:22:37 -115175.898654] SLOW spr round 10 (radius: 20) [11:34:23 -115175.898185] SLOW spr round 11 (radius: 25) [11:49:47 -115175.897747] Model parameter optimization (eps = 0.100000) [11:50:19] [worker #0] ML tree search #9, logLikelihood: -115175.357119 [11:50:19 -534466.316225] Initial branch length optimization [11:50:27 -435548.141257] Model parameter optimization (eps = 10.000000) [11:52:38 -432938.413443] AUTODETECT spr round 1 (radius: 5) [11:57:57 -267244.277463] AUTODETECT spr round 2 (radius: 10) [12:03:50 -191053.833651] AUTODETECT spr round 3 (radius: 15) [12:10:19 -153194.083139] AUTODETECT spr round 4 (radius: 20) [12:17:28 -135238.991603] AUTODETECT spr round 5 (radius: 25) [12:25:40] [worker #1] ML tree search #10, logLikelihood: -115083.861344 [12:26:15 -131216.155234] SPR radius for FAST iterations: 25 (autodetect) [12:26:15 -131216.155234] Model parameter optimization (eps = 3.000000) [12:27:44 -130644.700275] FAST spr round 1 (radius: 25) [12:34:30 -116451.609519] FAST spr round 2 (radius: 25) [12:39:31 -115288.728276] FAST spr round 3 (radius: 25) [12:43:48 -115146.985603] FAST spr round 4 (radius: 25) [12:47:50 -115140.868000] FAST spr round 5 (radius: 25) [12:51:37 -115139.573548] FAST spr round 6 (radius: 25) [12:55:13 -115139.573071] Model parameter optimization (eps = 1.000000) [12:55:51 -115131.760821] SLOW spr round 1 (radius: 5) [13:00:33 -115103.048963] SLOW spr round 2 (radius: 5) [13:05:23 -115096.898647] SLOW spr round 3 (radius: 5) [13:10:13 -115096.876070] SLOW spr round 4 (radius: 10) [13:15:08 -115096.265413] SLOW spr round 5 (radius: 5) [13:21:00 -115096.265385] SLOW spr round 6 (radius: 10) [13:26:35 -115096.265363] SLOW spr round 7 (radius: 15) [13:34:29 -115096.265344] SLOW spr round 8 (radius: 20) [13:46:35 -115096.265306] SLOW spr round 9 (radius: 25) [13:48:57] [worker #1] ML tree search #12, logLikelihood: -115610.686952 [14:02:28 -115096.265287] Model parameter optimization (eps = 0.100000) [14:02:52] [worker #0] ML tree search #11, logLikelihood: -115096.080174 [14:02:52 -535590.277530] Initial branch length optimization [14:02:58 -434463.324945] Model parameter optimization (eps = 10.000000) [14:04:57 -432135.913430] AUTODETECT spr round 1 (radius: 5) [14:10:17 -273899.459216] AUTODETECT spr round 2 (radius: 10) [14:16:14 -200696.246835] AUTODETECT spr round 3 (radius: 15) [14:22:43 -169021.520534] AUTODETECT spr round 4 (radius: 20) [14:30:43 -145565.624335] AUTODETECT spr round 5 (radius: 25) [14:38:39 -136468.919072] SPR radius for FAST iterations: 25 (autodetect) [14:38:39 -136468.919072] Model parameter optimization (eps = 3.000000) [14:39:58 -135928.430842] FAST spr round 1 (radius: 25) [14:46:52 -117219.457051] FAST spr round 2 (radius: 25) [14:52:09 -115344.759117] FAST spr round 3 (radius: 25) [14:55:01] [worker #1] ML tree search #14, logLikelihood: -115075.801870 [14:56:33 -115266.714520] FAST spr round 4 (radius: 25) [15:00:46 -115232.643285] FAST spr round 5 (radius: 25) [15:04:35 -115232.642845] Model parameter optimization (eps = 1.000000) [15:05:09 -115203.473036] SLOW spr round 1 (radius: 5) [15:10:01 -115179.891195] SLOW spr round 2 (radius: 5) [15:14:59 -115174.227389] SLOW spr round 3 (radius: 5) [15:19:49 -115171.591507] SLOW spr round 4 (radius: 5) [15:24:33 -115171.589960] SLOW spr round 5 (radius: 10) [15:29:39 -115166.210730] SLOW spr round 6 (radius: 5) [15:35:55 -115159.471140] SLOW spr round 7 (radius: 5) [15:41:19 -115159.469330] SLOW spr round 8 (radius: 10) [15:46:33 -115159.468876] SLOW spr round 9 (radius: 15) [15:54:47 -115158.140684] SLOW spr round 10 (radius: 5) [16:01:06 -115157.712092] SLOW spr round 11 (radius: 5) [16:06:37 -115157.710899] SLOW spr round 12 (radius: 10) [16:11:57 -115157.710800] SLOW spr round 13 (radius: 15) [16:20:09 -115157.710775] SLOW spr round 14 (radius: 20) [16:32:11 -115157.710754] SLOW spr round 15 (radius: 25) [16:48:25 -115155.940047] SLOW spr round 16 (radius: 5) [16:50:24] [worker #1] ML tree search #16, logLikelihood: -115077.645188 [16:55:01 -115154.884530] SLOW spr round 17 (radius: 5) [17:00:43 -115154.879558] SLOW spr round 18 (radius: 10) [17:06:05 -115154.879463] SLOW spr round 19 (radius: 15) [17:14:14 -115154.879356] SLOW spr round 20 (radius: 20) [17:26:27 -115154.879318] SLOW spr round 21 (radius: 25) [17:42:42 -115154.879298] Model parameter optimization (eps = 0.100000) [17:43:04] [worker #0] ML tree search #13, logLikelihood: -115154.743139 [17:43:04 -532899.500119] Initial branch length optimization [17:43:12 -431742.533256] Model parameter optimization (eps = 10.000000) [17:46:13 -429078.968579] AUTODETECT spr round 1 (radius: 5) [17:51:35 -281371.660176] AUTODETECT spr round 2 (radius: 10) [17:57:32 -200387.239724] AUTODETECT spr round 3 (radius: 15) [18:03:47 -163661.153425] AUTODETECT spr round 4 (radius: 20) [18:10:47 -145734.442066] AUTODETECT spr round 5 (radius: 25) [18:19:16 -136301.764630] SPR radius for FAST iterations: 25 (autodetect) [18:19:16 -136301.764630] Model parameter optimization (eps = 3.000000) [18:20:33 -135676.807829] FAST spr round 1 (radius: 25) [18:28:23 -116735.960719] FAST spr round 2 (radius: 25) [18:33:56 -115201.155172] FAST spr round 3 (radius: 25) [18:38:23 -115142.688899] FAST spr round 4 (radius: 25) [18:42:28 -115127.622547] FAST spr round 5 (radius: 25) [18:46:08 -115127.621647] Model parameter optimization (eps = 1.000000) [18:46:41 -115121.480756] SLOW spr round 1 (radius: 5) [18:51:29 -115100.278599] SLOW spr round 2 (radius: 5) [18:56:16 -115096.541361] SLOW spr round 3 (radius: 5) [19:00:51 -115096.540422] SLOW spr round 4 (radius: 10) [19:05:49 -115095.267135] SLOW spr round 5 (radius: 5) [19:11:47 -115095.266442] SLOW spr round 6 (radius: 10) [19:17:28 -115095.266085] SLOW spr round 7 (radius: 15) [19:25:33 -115093.989423] SLOW spr round 8 (radius: 5) [19:31:43 -115093.988746] SLOW spr round 9 (radius: 10) [19:37:32 -115093.988488] SLOW spr round 10 (radius: 15) [19:45:15 -115093.988306] SLOW spr round 11 (radius: 20) [19:57:16 -115093.988148] SLOW spr round 12 (radius: 25) [20:01:10] [worker #1] ML tree search #18, logLikelihood: -115081.521529 [20:13:07 -115093.461007] SLOW spr round 13 (radius: 5) [20:19:30 -115093.460680] SLOW spr round 14 (radius: 10) [20:25:48 -115093.460367] SLOW spr round 15 (radius: 15) [20:33:46 -115093.460062] SLOW spr round 16 (radius: 20) [20:46:10 -115093.459765] SLOW spr round 17 (radius: 25) [21:01:57 -115093.459475] Model parameter optimization (eps = 0.100000) [21:02:24] [worker #0] ML tree search #15, logLikelihood: -115093.124920 [21:02:24 -534237.679884] Initial branch length optimization [21:02:33 -436161.662363] Model parameter optimization (eps = 10.000000) [21:05:01 -433745.077209] AUTODETECT spr round 1 (radius: 5) [21:10:01 -273144.035351] AUTODETECT spr round 2 (radius: 10) [21:15:32 -201346.406097] AUTODETECT spr round 3 (radius: 15) [21:21:47 -157273.611715] AUTODETECT spr round 4 (radius: 20) [21:29:04 -141429.630991] AUTODETECT spr round 5 (radius: 25) [21:37:40 -134236.376675] SPR radius for FAST iterations: 25 (autodetect) [21:37:40 -134236.376675] Model parameter optimization (eps = 3.000000) [21:39:09 -133669.391654] FAST spr round 1 (radius: 25) [21:45:47 -116968.878804] FAST spr round 2 (radius: 25) [21:51:00 -115403.828140] FAST spr round 3 (radius: 25) [21:55:38 -115262.231268] FAST spr round 4 (radius: 25) [22:00:01 -115253.282370] FAST spr round 5 (radius: 25) [22:04:03 -115253.281630] Model parameter optimization (eps = 1.000000) [22:04:45 -115250.828095] SLOW spr round 1 (radius: 5) [22:09:49 -115229.785284] SLOW spr round 2 (radius: 5) [22:14:58 -115228.321997] SLOW spr round 3 (radius: 5) [22:20:05 -115228.321648] SLOW spr round 4 (radius: 10) [22:25:16 -115228.321587] SLOW spr round 5 (radius: 15) [22:33:40 -115228.279387] SLOW spr round 6 (radius: 20) [22:44:01 -115228.277801] SLOW spr round 7 (radius: 25) [22:56:09 -115227.660665] SLOW spr round 8 (radius: 5) [23:02:51 -115227.660495] SLOW spr round 9 (radius: 10) [23:04:06] [worker #1] ML tree search #20, logLikelihood: -115061.144894 [23:09:14 -115227.660468] SLOW spr round 10 (radius: 15) [23:17:00 -115227.660446] SLOW spr round 11 (radius: 20) [23:24:38 -115227.660426] SLOW spr round 12 (radius: 25) [23:32:27 -115227.660408] Model parameter optimization (eps = 0.100000) [23:32:46] [worker #0] ML tree search #17, logLikelihood: -115227.518284 [23:32:46 -536931.060539] Initial branch length optimization [23:32:52 -435543.003763] Model parameter optimization (eps = 10.000000) [23:33:53 -433133.382373] AUTODETECT spr round 1 (radius: 5) [23:36:50 -275139.389517] AUTODETECT spr round 2 (radius: 10) [23:40:11 -201029.834523] AUTODETECT spr round 3 (radius: 15) [23:44:13 -157433.965025] AUTODETECT spr round 4 (radius: 20) [23:48:52 -144135.125653] AUTODETECT spr round 5 (radius: 25) [23:54:37 -139281.019341] SPR radius for FAST iterations: 25 (autodetect) [23:54:37 -139281.019341] Model parameter optimization (eps = 3.000000) [23:55:15 -138748.345555] FAST spr round 1 (radius: 25) [23:59:55 -118052.254536] FAST spr round 2 (radius: 25) [24:03:04 -115376.073326] FAST spr round 3 (radius: 25) [24:05:48 -115131.492538] FAST spr round 4 (radius: 25) [24:08:12 -115120.842405] FAST spr round 5 (radius: 25) [24:10:24 -115120.841439] Model parameter optimization (eps = 1.000000) [24:10:49 -115114.457453] SLOW spr round 1 (radius: 5) [24:13:49 -115090.871469] SLOW spr round 2 (radius: 5) [24:16:50 -115083.575788] SLOW spr round 3 (radius: 5) [24:19:48 -115083.059745] SLOW spr round 4 (radius: 5) [24:22:41 -115083.058149] SLOW spr round 5 (radius: 10) [24:25:45 -115083.057788] SLOW spr round 6 (radius: 15) [24:31:22 -115079.279757] SLOW spr round 7 (radius: 5) [24:35:28 -115076.507613] SLOW spr round 8 (radius: 5) [24:38:54 -115076.506377] SLOW spr round 9 (radius: 10) [24:42:23 -115076.506199] SLOW spr round 10 (radius: 15) [24:48:26 -115076.506032] SLOW spr round 11 (radius: 20) [24:57:46 -115076.505875] SLOW spr round 12 (radius: 25) [25:09:16 -115076.505727] Model parameter optimization (eps = 0.100000) [25:09:39] [worker #0] ML tree search #19, logLikelihood: -115075.829666 Optimized model parameters: Partition 0: noname Rate heterogeneity: FREE (4 cats, mean), weights&rates: (0.209595,0.383267) (0.121840,0.684606) (0.300131,0.561293) (0.368434,1.812524) 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: -115061.144894 AIC score: 234132.289788 / AICc score: 8278192.289788 / BIC score: 243231.260135 Free parameters (model + branch lengths): 2005 WARNING: Number of free parameters (K=2005) is larger than alignment size (n=691). This might lead to overfitting and compromise tree inference results! WARNING: Best ML tree contains 264 near-zero branches! Best ML tree with collapsed near-zero branches saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/P84022/3_mltree/P84022.raxml.bestTreeCollapsed Best ML tree saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/P84022/3_mltree/P84022.raxml.bestTree All ML trees saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/P84022/3_mltree/P84022.raxml.mlTrees Optimized model saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/P84022/3_mltree/P84022.raxml.bestModel Execution log saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/P84022/3_mltree/P84022.raxml.log Analysis started: 30-Jun-2021 17:55:15 / finished: 01-Jul-2021 19:04:55 Elapsed time: 90579.883 seconds Consumed energy: 6376.844 Wh (= 32 km in an electric car, or 159 km with an e-scooter!)