RAxML-NG v. 1.0.2 released on 22.02.2021 by The Exelixis Lab. Developed by: Alexey M. Kozlov and Alexandros Stamatakis. Contributors: Diego Darriba, Tomas Flouri, Benoit Morel, Sarah Lutteropp, Ben Bettisworth. Latest version: https://github.com/amkozlov/raxml-ng Questions/problems/suggestions? Please visit: https://groups.google.com/forum/#!forum/raxml System: Intel(R) Xeon(R) Gold 6148 CPU @ 2.40GHz, 40 cores, 376 GB RAM RAxML-NG was called at 02-Jul-2021 09:57:52 as follows: raxml-ng --msa /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q6XPR3/2_msa/Q6XPR3_trimmed_msa.fasta --data-type AA --model LG4X --prefix /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q6XPR3/3_mltree/Q6XPR3 --seed 2 --threads 2 --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 (2 threads), thread pinning: OFF [00:00:00] Reading alignment from file: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q6XPR3/2_msa/Q6XPR3_trimmed_msa.fasta [00:00:00] Loaded alignment with 728 taxa and 85 sites WARNING: Sequences tr_A0A1D5PJJ4_A0A1D5PJJ4_CHICK_9031 and tr_A0A091ILC5_A0A091ILC5_EGRGA_188379 are exactly identical! WARNING: Sequences tr_A0A1D5PJJ4_A0A1D5PJJ4_CHICK_9031 and tr_A0A091VLU4_A0A091VLU4_NIPNI_128390 are exactly identical! WARNING: Sequences tr_A0A1D5PJJ4_A0A1D5PJJ4_CHICK_9031 and tr_A0A087QP91_A0A087QP91_APTFO_9233 are exactly identical! WARNING: Sequences tr_A0A1D5PJJ4_A0A1D5PJJ4_CHICK_9031 and tr_A0A2I0LLS9_A0A2I0LLS9_COLLI_8932 are exactly identical! WARNING: Sequences tr_A0A1D5PJJ4_A0A1D5PJJ4_CHICK_9031 and tr_A0A1V4JZG4_A0A1V4JZG4_PATFA_372326 are exactly identical! WARNING: Sequences tr_A0A1D5PJJ4_A0A1D5PJJ4_CHICK_9031 and tr_A0A226MEW3_A0A226MEW3_CALSU_9009 are exactly identical! WARNING: Sequences tr_A0A1D5PJJ4_A0A1D5PJJ4_CHICK_9031 and tr_A0A226NI21_A0A226NI21_COLVI_9014 are exactly identical! WARNING: Sequences tr_E1C251_E1C251_CHICK_9031 and tr_G1MRY2_G1MRY2_MELGA_9103 are exactly identical! WARNING: Sequences tr_E1C251_E1C251_CHICK_9031 and tr_A0A226N1K0_A0A226N1K0_CALSU_9009 are exactly identical! WARNING: Sequences tr_E1C251_E1C251_CHICK_9031 and tr_A0A226P850_A0A226P850_COLVI_9014 are exactly identical! WARNING: Sequences sp_P27003_S10AA_CHICK_9031 and tr_G1NK73_G1NK73_MELGA_9103 are exactly identical! WARNING: Sequences sp_P27003_S10AA_CHICK_9031 and tr_A0A226MES4_A0A226MES4_CALSU_9009 are exactly identical! WARNING: Sequences sp_P27003_S10AA_CHICK_9031 and tr_A0A226NUS8_A0A226NUS8_COLVI_9014 are exactly identical! WARNING: Sequences tr_B9EJL3_B9EJL3_MOUSE_10090 and tr_G3H328_G3H328_CRIGR_10029 are exactly identical! WARNING: Sequences tr_B9EJL3_B9EJL3_MOUSE_10090 and tr_A0A1U7Q6F1_A0A1U7Q6F1_MESAU_10036 are exactly identical! WARNING: Sequences tr_M3XUC8_M3XUC8_MUSPF_9669 and tr_I3L7I3_I3L7I3_PIG_9823 are exactly identical! WARNING: Sequences tr_M3XUC8_M3XUC8_MUSPF_9669 and tr_A0A337SKT0_A0A337SKT0_FELCA_9685 are exactly identical! WARNING: Sequences tr_M3XUC8_M3XUC8_MUSPF_9669 and tr_A0A2Y9LDZ9_A0A2Y9LDZ9_ENHLU_391180 are exactly identical! WARNING: Sequences tr_M3XWL0_M3XWL0_MUSPF_9669 and tr_A0A2Y9IR02_A0A2Y9IR02_ENHLU_391180 are exactly identical! WARNING: Sequences tr_M3YA96_M3YA96_MUSPF_9669 and tr_W5NRD4_W5NRD4_SHEEP_9940 are exactly identical! WARNING: Sequences tr_M3YA96_M3YA96_MUSPF_9669 and tr_I3LX39_I3LX39_ICTTR_43179 are exactly identical! WARNING: Sequences tr_M3YA96_M3YA96_MUSPF_9669 and tr_A0A286XNC8_A0A286XNC8_CAVPO_10141 are exactly identical! WARNING: Sequences tr_M3YA96_M3YA96_MUSPF_9669 and tr_G3SQW8_G3SQW8_LOXAF_9785 are exactly identical! WARNING: Sequences tr_M3YA96_M3YA96_MUSPF_9669 and tr_G1M0I1_G1M0I1_AILME_9646 are exactly identical! WARNING: Sequences tr_M3YA96_M3YA96_MUSPF_9669 and sp_P02639_S10A1_BOVIN_9913 are exactly identical! WARNING: Sequences tr_M3YA96_M3YA96_MUSPF_9669 and tr_M3XA34_M3XA34_FELCA_9685 are exactly identical! WARNING: Sequences tr_M3YA96_M3YA96_MUSPF_9669 and tr_A0A2U3W4T9_A0A2U3W4T9_ODORO_9708 are exactly identical! WARNING: Sequences tr_M3YA96_M3YA96_MUSPF_9669 and tr_A0A2U3YWQ1_A0A2U3YWQ1_LEPWE_9713 are exactly identical! WARNING: Sequences tr_M3YA96_M3YA96_MUSPF_9669 and tr_A0A2Y9IHF9_A0A2Y9IHF9_ENHLU_391180 are exactly identical! WARNING: Sequences tr_M3YA96_M3YA96_MUSPF_9669 and tr_A0A2Y9MD03_A0A2Y9MD03_DELLE_9749 are exactly identical! WARNING: Sequences tr_M3YA96_M3YA96_MUSPF_9669 and tr_A0A2Y9FVI4_A0A2Y9FVI4_PHYCD_9755 are exactly identical! WARNING: Sequences tr_M3YA96_M3YA96_MUSPF_9669 and tr_A0A383ZU35_A0A383ZU35_BALAS_310752 are exactly identical! WARNING: Sequences tr_A0A2I3GSV8_A0A2I3GSV8_NOMLE_61853 and tr_H2N5S8_H2N5S8_PONAB_9601 are exactly identical! WARNING: Sequences tr_G1RHH7_G1RHH7_NOMLE_61853 and tr_G3RL51_G3RL51_GORGO_9595 are exactly identical! WARNING: Sequences tr_G1RHH7_G1RHH7_NOMLE_61853 and tr_I6L539_I6L539_PONAB_9601 are exactly identical! WARNING: Sequences tr_G1RHH7_G1RHH7_NOMLE_61853 and sp_Q5RC36_S10A1_PONAB_9601 are exactly identical! WARNING: Sequences tr_G1RHH7_G1RHH7_NOMLE_61853 and tr_H2Q035_H2Q035_PANTR_9598 are exactly identical! WARNING: Sequences tr_G1RHH7_G1RHH7_NOMLE_61853 and sp_P23297_S10A1_HUMAN_9606 are exactly identical! WARNING: Sequences tr_G1RHH7_G1RHH7_NOMLE_61853 and tr_F7HGE0_F7HGE0_MACMU_9544 are exactly identical! WARNING: Sequences tr_G1RHH7_G1RHH7_NOMLE_61853 and tr_F6QF56_F6QF56_CALJA_9483 are exactly identical! WARNING: Sequences tr_G1RHH7_G1RHH7_NOMLE_61853 and tr_G7NUH2_G7NUH2_MACFA_9541 are exactly identical! WARNING: Sequences tr_G1RHH7_G1RHH7_NOMLE_61853 and tr_A0A096NYU6_A0A096NYU6_PAPAN_9555 are exactly identical! WARNING: Sequences tr_G1RHH7_G1RHH7_NOMLE_61853 and tr_A0A0D9S5N2_A0A0D9S5N2_CHLSB_60711 are exactly identical! WARNING: Sequences tr_G1RHH7_G1RHH7_NOMLE_61853 and tr_A0A2K5NH83_A0A2K5NH83_CERAT_9531 are exactly identical! WARNING: Sequences tr_G1RHH7_G1RHH7_NOMLE_61853 and tr_A0A2K6DJR8_A0A2K6DJR8_MACNE_9545 are exactly identical! WARNING: Sequences tr_G1RHH7_G1RHH7_NOMLE_61853 and tr_A0A2K5Y2G8_A0A2K5Y2G8_MANLE_9568 are exactly identical! WARNING: Sequences tr_G1RHH7_G1RHH7_NOMLE_61853 and tr_A0A2R9BUH5_A0A2R9BUH5_PANPA_9597 are exactly identical! WARNING: Sequences tr_G1RRP8_G1RRP8_NOMLE_61853 and tr_H2N5T7_H2N5T7_PONAB_9601 are exactly identical! WARNING: Sequences tr_G1RRP8_G1RRP8_NOMLE_61853 and sp_Q6SQH4_S10AA_RABIT_9986 are exactly identical! WARNING: Sequences tr_G1RRP8_G1RRP8_NOMLE_61853 and tr_E2RGM0_E2RGM0_CANLF_9615 are exactly identical! WARNING: Sequences tr_G1RRP8_G1RRP8_NOMLE_61853 and tr_J9NYC2_J9NYC2_CANLF_9615 are exactly identical! WARNING: Sequences tr_G1RRP8_G1RRP8_NOMLE_61853 and tr_H2Q001_H2Q001_PANTR_9598 are exactly identical! WARNING: Sequences tr_G1RRP8_G1RRP8_NOMLE_61853 and tr_F7BKY7_F7BKY7_HORSE_9796 are exactly identical! WARNING: Sequences tr_G1RRP8_G1RRP8_NOMLE_61853 and tr_W5QIU9_W5QIU9_SHEEP_9940 are exactly identical! WARNING: Sequences tr_G1RRP8_G1RRP8_NOMLE_61853 and tr_I3N1Z2_I3N1Z2_ICTTR_43179 are exactly identical! WARNING: Sequences tr_G1RRP8_G1RRP8_NOMLE_61853 and sp_P60903_S10AA_HUMAN_9606 are exactly identical! WARNING: Sequences tr_G1RRP8_G1RRP8_NOMLE_61853 and sp_P62504_S10AA_MACMU_9544 are exactly identical! WARNING: Sequences tr_G1RRP8_G1RRP8_NOMLE_61853 and tr_G3T711_G3T711_LOXAF_9785 are exactly identical! WARNING: Sequences tr_G1RRP8_G1RRP8_NOMLE_61853 and tr_G3WV01_G3WV01_SARHA_9305 are exactly identical! WARNING: Sequences tr_G1RRP8_G1RRP8_NOMLE_61853 and tr_F7FGI3_F7FGI3_CALJA_9483 are exactly identical! WARNING: Sequences tr_G1RRP8_G1RRP8_NOMLE_61853 and tr_F2Z5M2_F2Z5M2_PIG_9823 are exactly identical! WARNING: Sequences tr_G1RRP8_G1RRP8_NOMLE_61853 and sp_P04163_S10AA_PIG_9823 are exactly identical! WARNING: Sequences tr_G1RRP8_G1RRP8_NOMLE_61853 and tr_G7NTU2_G7NTU2_MACFA_9541 are exactly identical! WARNING: Sequences tr_G1RRP8_G1RRP8_NOMLE_61853 and sp_P60902_S10AA_BOVIN_9913 are exactly identical! WARNING: Sequences tr_G1RRP8_G1RRP8_NOMLE_61853 and tr_A0A096MSI7_A0A096MSI7_PAPAN_9555 are exactly identical! WARNING: Sequences tr_G1RRP8_G1RRP8_NOMLE_61853 and tr_A0A091CML6_A0A091CML6_FUKDA_885580 are exactly identical! WARNING: Sequences tr_G1RRP8_G1RRP8_NOMLE_61853 and tr_A0A0D9S5R0_A0A0D9S5R0_CHLSB_60711 are exactly identical! WARNING: Sequences tr_G1RRP8_G1RRP8_NOMLE_61853 and tr_A0A1U7U2W8_A0A1U7U2W8_TARSY_1868482 are exactly identical! WARNING: Sequences tr_G1RRP8_G1RRP8_NOMLE_61853 and tr_A0A2K5KUS4_A0A2K5KUS4_CERAT_9531 are exactly identical! WARNING: Sequences tr_G1RRP8_G1RRP8_NOMLE_61853 and tr_A0A2K6C8P3_A0A2K6C8P3_MACNE_9545 are exactly identical! WARNING: Sequences tr_G1RRP8_G1RRP8_NOMLE_61853 and tr_A0A2K5XGX7_A0A2K5XGX7_MANLE_9568 are exactly identical! WARNING: Sequences tr_G1RRP8_G1RRP8_NOMLE_61853 and tr_A0A2R9BHV8_A0A2R9BHV8_PANPA_9597 are exactly identical! WARNING: Sequences tr_G1RRP8_G1RRP8_NOMLE_61853 and tr_A0A2U4A278_A0A2U4A278_TURTR_9739 are exactly identical! WARNING: Sequences tr_G1RRP8_G1RRP8_NOMLE_61853 and tr_A0A2U3ZJL2_A0A2U3ZJL2_ODORO_9708 are exactly identical! WARNING: Sequences tr_G1RRP8_G1RRP8_NOMLE_61853 and tr_A0A2U3XAI3_A0A2U3XAI3_LEPWE_9713 are exactly identical! WARNING: Sequences tr_G1RRP8_G1RRP8_NOMLE_61853 and tr_A0A2Y9L6K7_A0A2Y9L6K7_ENHLU_391180 are exactly identical! WARNING: Sequences tr_G1RRP8_G1RRP8_NOMLE_61853 and tr_A0A2Y9MLC2_A0A2Y9MLC2_DELLE_9749 are exactly identical! WARNING: Sequences tr_G1RRP8_G1RRP8_NOMLE_61853 and tr_A0A2Y9FGV5_A0A2Y9FGV5_PHYCD_9755 are exactly identical! WARNING: Sequences tr_G1RRP8_G1RRP8_NOMLE_61853 and tr_A0A383ZSR8_A0A383ZSR8_BALAS_310752 are exactly identical! WARNING: Sequences tr_G1P4C9_G1P4C9_MYOLU_59463 and tr_D2HBQ5_D2HBQ5_AILME_9646 are exactly identical! WARNING: Sequences tr_G1P4C9_G1P4C9_MYOLU_59463 and tr_L5JWN7_L5JWN7_PTEAL_9402 are exactly identical! WARNING: Sequences tr_G1P4C9_G1P4C9_MYOLU_59463 and tr_M3WD86_M3WD86_FELCA_9685 are exactly identical! WARNING: Sequences tr_G1P4C9_G1P4C9_MYOLU_59463 and tr_A0A384CG76_A0A384CG76_URSMA_29073 are exactly identical! WARNING: Sequences tr_G1Q9C5_G1Q9C5_MYOLU_59463 and tr_A0A1U7T1U2_A0A1U7T1U2_TARSY_1868482 are exactly identical! WARNING: Sequences tr_G3HC24_G3HC24_CRIGR_10029 and tr_A0A1U7R3I4_A0A1U7R3I4_MESAU_10036 are exactly identical! WARNING: Sequences tr_G3SGV1_G3SGV1_GORGO_9595 and tr_H2QP64_H2QP64_PANTR_9598 are exactly identical! WARNING: Sequences tr_G3SGV1_G3SGV1_GORGO_9595 and tr_A0A2R8ZMX9_A0A2R8ZMX9_PANPA_9597 are exactly identical! WARNING: Sequences tr_A0A2J8RC22_A0A2J8RC22_PONAB_9601 and tr_G1SFI2_G1SFI2_RABIT_9986 are exactly identical! WARNING: Sequences tr_A0A2J8RC22_A0A2J8RC22_PONAB_9601 and sp_Q6YNR6_S100B_RABIT_9986 are exactly identical! WARNING: Sequences tr_A0A2J8RC22_A0A2J8RC22_PONAB_9601 and tr_F6RF49_F6RF49_HORSE_9796 are exactly identical! WARNING: Sequences tr_A0A2J8RC22_A0A2J8RC22_PONAB_9601 and sp_P04271_S100B_HUMAN_9606 are exactly identical! WARNING: Sequences tr_A0A2J8RC22_A0A2J8RC22_PONAB_9601 and tr_G1L2S1_G1L2S1_AILME_9646 are exactly identical! WARNING: Sequences tr_A0A2J8RC22_A0A2J8RC22_PONAB_9601 and tr_A0A2I2UW07_A0A2I2UW07_FELCA_9685 are exactly identical! WARNING: Sequences tr_A0A2J8RC22_A0A2J8RC22_PONAB_9601 and tr_A0A2Y9FKI7_A0A2Y9FKI7_PHYCD_9755 are exactly identical! WARNING: Sequences tr_A0A2J8RC22_A0A2J8RC22_PONAB_9601 and tr_A0A384DNP5_A0A384DNP5_URSMA_29073 are exactly identical! WARNING: Sequences tr_A0A2J8RC22_A0A2J8RC22_PONAB_9601 and tr_A0A383ZCB7_A0A383ZCB7_BALAS_310752 are exactly identical! WARNING: Sequences tr_H2PCU7_H2PCU7_PONAB_9601 and sp_P25815_S100P_HUMAN_9606 are exactly identical! WARNING: Sequences tr_H2PCU7_H2PCU7_PONAB_9601 and tr_F6PWQ7_F6PWQ7_MACMU_9544 are exactly identical! WARNING: Sequences tr_H2PCU7_H2PCU7_PONAB_9601 and tr_A0A096NZC3_A0A096NZC3_PAPAN_9555 are exactly identical! WARNING: Sequences tr_H2PCU7_H2PCU7_PONAB_9601 and tr_A0A0D9RU76_A0A0D9RU76_CHLSB_60711 are exactly identical! WARNING: Sequences tr_H2PCU7_H2PCU7_PONAB_9601 and tr_A0A2K5NID4_A0A2K5NID4_CERAT_9531 are exactly identical! WARNING: Sequences tr_H2PCU7_H2PCU7_PONAB_9601 and tr_A0A2K6DNK8_A0A2K6DNK8_MACNE_9545 are exactly identical! WARNING: Sequences tr_H2PCU7_H2PCU7_PONAB_9601 and tr_A0A2K5XH25_A0A2K5XH25_MANLE_9568 are exactly identical! WARNING: Sequences tr_G1SNF3_G1SNF3_RABIT_9986 and sp_P37709_TRHY_RABIT_9986 are exactly identical! WARNING: Sequences tr_B8NAU1_B8NAU1_ASPFN_332952 and tr_A0A1S9DCW6_A0A1S9DCW6_ASPOZ_5062 are exactly identical! WARNING: Sequences tr_B8NAU1_B8NAU1_ASPFN_332952 and tr_A0A2G7FEH0_A0A2G7FEH0_9EURO_656916 are exactly identical! WARNING: Sequences tr_J9PAI3_J9PAI3_CANLF_9615 and tr_A0A2U3W7Z5_A0A2U3W7Z5_ODORO_9708 are exactly identical! WARNING: Sequences tr_J9PAI3_J9PAI3_CANLF_9615 and tr_A0A2U3XAV6_A0A2U3XAV6_LEPWE_9713 are exactly identical! WARNING: Sequences tr_H2R8N3_H2R8N3_PANTR_9598 and sp_Q5QJ38_TCHL1_HUMAN_9606 are exactly identical! WARNING: Sequences tr_H2R8N3_H2R8N3_PANTR_9598 and tr_A0A2R9CDN5_A0A2R9CDN5_PANPA_9597 are exactly identical! WARNING: Sequences sp_P22793_TRHY_SHEEP_9940 and tr_W5QIV5_W5QIV5_SHEEP_9940 are exactly identical! WARNING: Sequences tr_W5PVB6_W5PVB6_SHEEP_9940 and tr_G7PWM2_G7PWM2_MACFA_9541 are exactly identical! WARNING: Sequences tr_W5PVB6_W5PVB6_SHEEP_9940 and tr_A0A0D9R407_A0A0D9R407_CHLSB_60711 are exactly identical! WARNING: Sequences tr_W5PVB6_W5PVB6_SHEEP_9940 and tr_A0A2U3VAA5_A0A2U3VAA5_TURTR_9739 are exactly identical! WARNING: Sequences tr_W5PVB6_W5PVB6_SHEEP_9940 and tr_A0A2U3X2C1_A0A2U3X2C1_ODORO_9708 are exactly identical! WARNING: Sequences tr_W5PVB6_W5PVB6_SHEEP_9940 and tr_A0A2U3Z3M3_A0A2U3Z3M3_LEPWE_9713 are exactly identical! WARNING: Sequences tr_W5PVB6_W5PVB6_SHEEP_9940 and tr_A0A2Y9Q578_A0A2Y9Q578_DELLE_9749 are exactly identical! WARNING: Sequences tr_W5QIW9_W5QIW9_SHEEP_9940 and tr_E1BB35_E1BB35_BOVIN_9913 are exactly identical! WARNING: Sequences tr_I3MDN4_I3MDN4_ICTTR_43179 and tr_A0A286XTU0_A0A286XTU0_CAVPO_10141 are exactly identical! WARNING: Sequences tr_A2QNR8_A2QNR8_ASPNC_425011 and tr_G7XEV0_G7XEV0_ASPKW_1033177 are exactly identical! WARNING: Sequences tr_A2QNR8_A2QNR8_ASPNC_425011 and tr_A0A1L9MYN8_A0A1L9MYN8_ASPTU_767770 are exactly identical! WARNING: Sequences tr_A2QNR8_A2QNR8_ASPNC_425011 and tr_A0A317W2F7_A0A317W2F7_9EURO_1448314 are exactly identical! WARNING: Sequences tr_A0A1D5QZ82_A0A1D5QZ82_MACMU_9544 and tr_A0A2K6C482_A0A2K6C482_MACNE_9545 are exactly identical! WARNING: Sequences tr_F6Q6L1_F6Q6L1_MACMU_9544 and tr_A0A096MPI8_A0A096MPI8_PAPAN_9555 are exactly identical! WARNING: Sequences tr_F6Q6L1_F6Q6L1_MACMU_9544 and tr_A0A2K5P568_A0A2K5P568_CERAT_9531 are exactly identical! WARNING: Sequences tr_F6Q6L1_F6Q6L1_MACMU_9544 and tr_A0A2K6DRF8_A0A2K6DRF8_MACNE_9545 are exactly identical! WARNING: Sequences tr_F6R3M7_F6R3M7_MACMU_9544 and tr_A0A0D9S5Q6_A0A0D9S5Q6_CHLSB_60711 are exactly identical! WARNING: Sequences tr_F6R3M7_F6R3M7_MACMU_9544 and tr_A0A2K6BR78_A0A2K6BR78_MACNE_9545 are exactly identical! WARNING: Sequences tr_F7FCK7_F7FCK7_MACMU_9544 and tr_G8F5R2_G8F5R2_MACFA_9541 are exactly identical! WARNING: Sequences tr_F7FCK7_F7FCK7_MACMU_9544 and tr_A0A0D9S5Q4_A0A0D9S5Q4_CHLSB_60711 are exactly identical! WARNING: Sequences tr_F7FCK7_F7FCK7_MACMU_9544 and tr_A0A2K6DK96_A0A2K6DK96_MACNE_9545 are exactly identical! WARNING: Sequences tr_G3TE57_G3TE57_LOXAF_9785 and tr_A0A2Y9E103_A0A2Y9E103_TRIMA_127582 are exactly identical! WARNING: Sequences tr_B5FXV2_B5FXV2_TAEGU_59729 and tr_U3KFS2_U3KFS2_FICAL_59894 are exactly identical! WARNING: Sequences tr_H1A485_H1A485_TAEGU_59729 and tr_A0A218UDX1_A0A218UDX1_9PASE_299123 are exactly identical! WARNING: Sequences sp_A6QP92_TCHL1_BOVIN_9913 and tr_F1MAV8_F1MAV8_BOVIN_9913 are exactly identical! WARNING: Sequences tr_A0A096MQV7_A0A096MQV7_PAPAN_9555 and tr_A0A2K5L0B3_A0A2K5L0B3_CERAT_9531 are exactly identical! WARNING: Sequences tr_A0A091DKG2_A0A091DKG2_FUKDA_885580 and tr_A0A3Q0D7D8_A0A3Q0D7D8_MESAU_10036 are exactly identical! WARNING: Sequences tr_A0A091V497_A0A091V497_NIPNI_128390 and tr_A0A087R9H8_A0A087R9H8_APTFO_9233 are exactly identical! WARNING: Sequences tr_A0A091V497_A0A091V497_NIPNI_128390 and tr_A0A091V676_A0A091V676_OPIHO_30419 are exactly identical! WARNING: Sequences tr_A0A091V497_A0A091V497_NIPNI_128390 and tr_A0A2I0LXI2_A0A2I0LXI2_COLLI_8932 are exactly identical! WARNING: Sequences tr_A0A091V497_A0A091V497_NIPNI_128390 and tr_A0A1V4L055_A0A1V4L055_PATFA_372326 are exactly identical! WARNING: Sequences tr_A0A091W6Y1_A0A091W6Y1_NIPNI_128390 and tr_A0A0A0AES4_A0A0A0AES4_CHAVO_50402 are exactly identical! WARNING: Sequences tr_A0A2I0M190_A0A2I0M190_COLLI_8932 and tr_A0A1V4L1H1_A0A1V4L1H1_PATFA_372326 are exactly identical! WARNING: Sequences tr_A0A2I0MMV3_A0A2I0MMV3_COLLI_8932 and tr_A0A1V4JFN9_A0A1V4JFN9_PATFA_372326 are exactly identical! WARNING: Sequences tr_A0A1S3RWW0_A0A1S3RWW0_SALSA_8030 and tr_A0A060WZ60_A0A060WZ60_ONCMY_8022 are exactly identical! WARNING: Sequences tr_M4UZZ7_M4UZZ7_SALSA_8030 and tr_A0A060YVE5_A0A060YVE5_ONCMY_8022 are exactly identical! WARNING: Sequences tr_A0A2D0QYR7_A0A2D0QYR7_ICTPU_7998 and tr_A0A2D0QYS7_A0A2D0QYS7_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0SZ10_A0A2D0SZ10_ICTPU_7998 and tr_A0A2D0SZ13_A0A2D0SZ13_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2I1GIE4_A0A2I1GIE4_9GLOM_588596 and tr_A0A2H5UHH8_A0A2H5UHH8_RHIID_747089 are exactly identical! WARNING: Duplicate sequences found: 149 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/Q6XPR3/3_mltree/Q6XPR3.raxml.reduced.phy Alignment comprises 1 partitions and 85 patterns Partition 0: noname Model: LG4X+R4 Alignment sites / patterns: 85 / 85 Gaps: 5.43 % Invariant sites: 0.00 % NOTE: Binary MSA file created: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q6XPR3/3_mltree/Q6XPR3.raxml.rba Parallelization scheme autoconfig: 2 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 728 taxa [00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 85 / 6800 [00:00:00] Data distribution: max. searches per worker: 10 Starting ML tree search with 20 distinct starting trees [00:00:00 -112365.832993] Initial branch length optimization [00:00:01 -93083.029393] Model parameter optimization (eps = 10.000000) [00:00:23 -92855.971395] AUTODETECT spr round 1 (radius: 5) [00:01:14 -63188.430396] AUTODETECT spr round 2 (radius: 10) [00:02:11 -46321.594734] AUTODETECT spr round 3 (radius: 15) [00:03:10 -37824.093311] AUTODETECT spr round 4 (radius: 20) [00:04:19 -34734.363787] AUTODETECT spr round 5 (radius: 25) [00:05:31 -32997.299146] SPR radius for FAST iterations: 25 (autodetect) [00:05:31 -32997.299146] Model parameter optimization (eps = 3.000000) [00:05:51 -32866.134617] FAST spr round 1 (radius: 25) [00:06:51 -27582.816441] FAST spr round 2 (radius: 25) [00:07:45 -26981.734623] FAST spr round 3 (radius: 25) [00:08:34 -26856.710147] FAST spr round 4 (radius: 25) [00:09:19 -26628.604107] FAST spr round 5 (radius: 25) [00:10:02 -26624.016416] FAST spr round 6 (radius: 25) [00:10:43 -26624.014641] Model parameter optimization (eps = 1.000000) [00:10:53 -26608.740773] SLOW spr round 1 (radius: 5) [00:11:46 -26596.628618] SLOW spr round 2 (radius: 5) [00:12:40 -26580.665761] SLOW spr round 3 (radius: 5) [00:13:31 -26576.344600] SLOW spr round 4 (radius: 5) [00:14:22 -26574.389934] SLOW spr round 5 (radius: 5) [00:15:11 -26572.648149] SLOW spr round 6 (radius: 5) [00:16:00 -26572.465717] SLOW spr round 7 (radius: 5) [00:16:49 -26572.465526] SLOW spr round 8 (radius: 10) [00:17:41 -26572.465347] SLOW spr round 9 (radius: 15) [00:19:04 -26571.024451] SLOW spr round 10 (radius: 5) [00:20:09 -26569.813667] SLOW spr round 11 (radius: 5) [00:21:06 -26569.648149] SLOW spr round 12 (radius: 5) [00:21:58 -26569.647974] SLOW spr round 13 (radius: 10) [00:22:52 -26562.759590] SLOW spr round 14 (radius: 5) [00:23:53 -26562.759177] SLOW spr round 15 (radius: 10) [00:24:49 -26562.759000] SLOW spr round 16 (radius: 15) [00:26:07 -26562.758899] SLOW spr round 17 (radius: 20) [00:26:34] [worker #1] ML tree search #2, logLikelihood: -26560.294085 [00:28:08 -26562.758890] SLOW spr round 18 (radius: 25) [00:30:40 -26562.758881] Model parameter optimization (eps = 0.100000) [00:30:46] [worker #0] ML tree search #1, logLikelihood: -26562.739169 [00:30:46 -112142.421060] Initial branch length optimization [00:30:47 -93483.720931] Model parameter optimization (eps = 10.000000) [00:31:02 -93232.180918] AUTODETECT spr round 1 (radius: 5) [00:31:54 -62546.776158] AUTODETECT spr round 2 (radius: 10) [00:32:52 -47594.524400] AUTODETECT spr round 3 (radius: 15) [00:33:58 -39541.761426] AUTODETECT spr round 4 (radius: 20) [00:35:13 -33571.085534] AUTODETECT spr round 5 (radius: 25) [00:36:48 -31502.469310] SPR radius for FAST iterations: 25 (autodetect) [00:36:48 -31502.469310] Model parameter optimization (eps = 3.000000) [00:37:04 -31402.002078] FAST spr round 1 (radius: 25) [00:38:03 -27092.811658] FAST spr round 2 (radius: 25) [00:38:55 -26702.762863] FAST spr round 3 (radius: 25) [00:39:42 -26643.210996] FAST spr round 4 (radius: 25) [00:40:27 -26625.491059] FAST spr round 5 (radius: 25) [00:41:09 -26623.444705] FAST spr round 6 (radius: 25) [00:41:52 -26617.404173] FAST spr round 7 (radius: 25) [00:42:35 -26614.420673] FAST spr round 8 (radius: 25) [00:43:16 -26614.029811] FAST spr round 9 (radius: 25) [00:43:57 -26614.028943] Model parameter optimization (eps = 1.000000) [00:44:09 -26586.087496] SLOW spr round 1 (radius: 5) [00:45:00 -26571.745215] SLOW spr round 2 (radius: 5) [00:45:51 -26569.287760] SLOW spr round 3 (radius: 5) [00:46:42 -26568.125175] SLOW spr round 4 (radius: 5) [00:47:33 -26567.877175] SLOW spr round 5 (radius: 5) [00:48:23 -26567.856020] SLOW spr round 6 (radius: 10) [00:49:16 -26563.438537] SLOW spr round 7 (radius: 5) [00:50:19 -26562.744768] SLOW spr round 8 (radius: 5) [00:51:14 -26562.744042] SLOW spr round 9 (radius: 10) [00:52:08 -26562.557979] SLOW spr round 10 (radius: 5) [00:53:08 -26562.464121] SLOW spr round 11 (radius: 10) [00:54:03 -26562.462463] SLOW spr round 12 (radius: 15) [00:55:20 -26559.722414] SLOW spr round 13 (radius: 5) [00:56:24 -26559.714601] SLOW spr round 14 (radius: 10) [00:57:22 -26559.713754] SLOW spr round 15 (radius: 15) [00:58:37 -26559.713324] SLOW spr round 16 (radius: 20) [01:00:30 -26548.979108] SLOW spr round 17 (radius: 5) [01:01:36 -26548.928714] SLOW spr round 18 (radius: 10) [01:02:35 -26548.927160] SLOW spr round 19 (radius: 15) [01:03:50 -26548.927051] SLOW spr round 20 (radius: 20) [01:05:42 -26548.927043] SLOW spr round 21 (radius: 25) [01:07:46] [worker #1] ML tree search #4, logLikelihood: -26533.694642 [01:08:03 -26548.603618] SLOW spr round 22 (radius: 5) [01:09:08 -26548.603614] SLOW spr round 23 (radius: 10) [01:10:08 -26548.603610] SLOW spr round 24 (radius: 15) [01:11:24 -26548.603609] SLOW spr round 25 (radius: 20) [01:13:15 -26548.603608] SLOW spr round 26 (radius: 25) [01:15:37 -26548.603606] Model parameter optimization (eps = 0.100000) [01:15:44] [worker #0] ML tree search #3, logLikelihood: -26547.800120 [01:15:44 -113211.867331] Initial branch length optimization [01:15:46 -93703.047849] Model parameter optimization (eps = 10.000000) [01:16:03 -93393.390486] AUTODETECT spr round 1 (radius: 5) [01:16:55 -62351.089506] AUTODETECT spr round 2 (radius: 10) [01:17:53 -44684.619539] AUTODETECT spr round 3 (radius: 15) [01:18:54 -36309.100129] AUTODETECT spr round 4 (radius: 20) [01:20:07 -33952.997183] AUTODETECT spr round 5 (radius: 25) [01:21:29 -32090.818756] SPR radius for FAST iterations: 25 (autodetect) [01:21:29 -32090.818756] Model parameter optimization (eps = 3.000000) [01:21:47 -31926.799412] FAST spr round 1 (radius: 25) [01:22:46 -27309.242850] FAST spr round 2 (radius: 25) [01:23:39 -26671.942506] FAST spr round 3 (radius: 25) [01:24:26 -26622.408752] FAST spr round 4 (radius: 25) [01:25:09 -26611.670804] FAST spr round 5 (radius: 25) [01:25:52 -26603.626640] FAST spr round 6 (radius: 25) [01:26:34 -26601.329714] FAST spr round 7 (radius: 25) [01:27:15 -26600.666542] FAST spr round 8 (radius: 25) [01:27:56 -26600.665868] Model parameter optimization (eps = 1.000000) [01:28:07 -26580.094783] SLOW spr round 1 (radius: 5) [01:28:58 -26551.100394] SLOW spr round 2 (radius: 5) [01:29:50 -26547.150584] SLOW spr round 3 (radius: 5) [01:30:28] [worker #1] ML tree search #6, logLikelihood: -26560.173856 [01:30:40 -26547.149759] SLOW spr round 4 (radius: 10) [01:31:32 -26547.149543] SLOW spr round 5 (radius: 15) [01:32:48 -26546.093769] SLOW spr round 6 (radius: 5) [01:33:54 -26545.140390] SLOW spr round 7 (radius: 5) [01:34:51 -26545.138330] SLOW spr round 8 (radius: 10) [01:35:45 -26545.137387] SLOW spr round 9 (radius: 15) [01:37:00 -26545.136841] SLOW spr round 10 (radius: 20) [01:38:39 -26545.136490] SLOW spr round 11 (radius: 25) [01:40:41 -26545.136232] Model parameter optimization (eps = 0.100000) [01:40:43] [worker #0] ML tree search #5, logLikelihood: -26545.042158 [01:40:43 -113103.612076] Initial branch length optimization [01:40:45 -93328.322671] Model parameter optimization (eps = 10.000000) [01:41:01 -93078.355060] AUTODETECT spr round 1 (radius: 5) [01:41:52 -63207.783336] AUTODETECT spr round 2 (radius: 10) [01:42:47 -47016.790003] AUTODETECT spr round 3 (radius: 15) [01:43:50 -39863.752172] AUTODETECT spr round 4 (radius: 20) [01:45:04 -33362.922301] AUTODETECT spr round 5 (radius: 25) [01:46:19 -31920.869723] SPR radius for FAST iterations: 25 (autodetect) [01:46:19 -31920.869723] Model parameter optimization (eps = 3.000000) [01:46:35 -31772.091311] FAST spr round 1 (radius: 25) [01:47:32 -27541.248106] FAST spr round 2 (radius: 25) [01:48:22 -26939.646151] FAST spr round 3 (radius: 25) [01:49:08 -26652.294838] FAST spr round 4 (radius: 25) [01:49:52 -26625.265904] FAST spr round 5 (radius: 25) [01:50:34 -26609.813401] FAST spr round 6 (radius: 25) [01:51:15 -26609.488861] FAST spr round 7 (radius: 25) [01:51:56 -26609.408027] Model parameter optimization (eps = 1.000000) [01:52:07 -26590.735069] SLOW spr round 1 (radius: 5) [01:52:59 -26578.753000] SLOW spr round 2 (radius: 5) [01:53:49 -26578.752087] SLOW spr round 3 (radius: 10) [01:54:41 -26575.457829] SLOW spr round 4 (radius: 5) [01:55:43 -26573.046381] SLOW spr round 5 (radius: 5) [01:56:39 -26573.044994] SLOW spr round 6 (radius: 10) [01:57:32 -26573.044703] SLOW spr round 7 (radius: 15) [01:58:46 -26568.589545] SLOW spr round 8 (radius: 5) [01:59:52 -26564.407909] SLOW spr round 9 (radius: 5) [02:00:50 -26564.334805] SLOW spr round 10 (radius: 10) [02:01:45 -26562.053453] SLOW spr round 11 (radius: 5) [02:02:46 -26560.884624] SLOW spr round 12 (radius: 5) [02:03:42 -26558.505436] SLOW spr round 13 (radius: 5) [02:04:35 -26558.467430] SLOW spr round 14 (radius: 10) [02:05:28 -26558.467178] SLOW spr round 15 (radius: 15) [02:06:44 -26558.467054] SLOW spr round 16 (radius: 20) [02:08:32 -26558.466998] SLOW spr round 17 (radius: 25) [02:10:55 -26550.669843] SLOW spr round 18 (radius: 5) [02:12:02 -26550.669339] SLOW spr round 19 (radius: 10) [02:13:02 -26550.669332] SLOW spr round 20 (radius: 15) [02:14:16 -26550.669330] SLOW spr round 21 (radius: 20) [02:15:07] [worker #1] ML tree search #8, logLikelihood: -26550.715455 [02:16:04 -26550.363266] SLOW spr round 22 (radius: 5) [02:17:11 -26549.270489] SLOW spr round 23 (radius: 5) [02:18:09 -26549.268278] SLOW spr round 24 (radius: 10) [02:19:04 -26549.268094] SLOW spr round 25 (radius: 15) [02:20:19 -26549.268079] SLOW spr round 26 (radius: 20) [02:22:08 -26549.268077] SLOW spr round 27 (radius: 25) [02:24:31 -26549.268076] Model parameter optimization (eps = 0.100000) [02:24:37] [worker #0] ML tree search #7, logLikelihood: -26549.078407 [02:24:37 -113131.710756] Initial branch length optimization [02:24:38 -93988.031271] Model parameter optimization (eps = 10.000000) [02:24:57 -93740.431664] AUTODETECT spr round 1 (radius: 5) [02:25:48 -62342.011536] AUTODETECT spr round 2 (radius: 10) [02:26:43 -44318.703185] AUTODETECT spr round 3 (radius: 15) [02:27:43 -38007.410765] AUTODETECT spr round 4 (radius: 20) [02:28:50 -33688.043117] AUTODETECT spr round 5 (radius: 25) [02:30:02 -32453.984145] SPR radius for FAST iterations: 25 (autodetect) [02:30:02 -32453.984145] Model parameter optimization (eps = 3.000000) [02:30:20 -32283.245164] FAST spr round 1 (radius: 25) [02:31:14 -27393.066873] FAST spr round 2 (radius: 25) [02:32:04 -26890.948332] FAST spr round 3 (radius: 25) [02:32:51 -26828.301121] FAST spr round 4 (radius: 25) [02:33:35 -26813.920399] FAST spr round 5 (radius: 25) [02:34:17 -26800.506315] FAST spr round 6 (radius: 25) [02:34:58 -26800.361805] FAST spr round 7 (radius: 25) [02:35:38 -26800.361372] Model parameter optimization (eps = 1.000000) [02:35:49 -26797.369814] SLOW spr round 1 (radius: 5) [02:36:40 -26790.217401] SLOW spr round 2 (radius: 5) [02:37:31 -26786.824179] SLOW spr round 3 (radius: 5) [02:38:20 -26786.758419] SLOW spr round 4 (radius: 10) [02:39:10 -26786.757256] SLOW spr round 5 (radius: 15) [02:40:31 -26783.823548] SLOW spr round 6 (radius: 5) [02:41:34 -26783.742399] SLOW spr round 7 (radius: 10) [02:42:32 -26783.741846] SLOW spr round 8 (radius: 15) [02:43:48 -26783.741789] SLOW spr round 9 (radius: 20) [02:45:46 -26783.741766] SLOW spr round 10 (radius: 25) [02:46:56] [worker #1] ML tree search #10, logLikelihood: -26560.944761 [02:48:17 -26783.741745] Model parameter optimization (eps = 0.100000) [02:48:26] [worker #0] ML tree search #9, logLikelihood: -26783.395321 [02:48:26 -112603.796156] Initial branch length optimization [02:48:28 -93281.223571] Model parameter optimization (eps = 10.000000) [02:48:50 -93041.789990] AUTODETECT spr round 1 (radius: 5) [02:49:40 -61864.746175] AUTODETECT spr round 2 (radius: 10) [02:50:37 -43128.271158] AUTODETECT spr round 3 (radius: 15) [02:51:39 -36439.270532] AUTODETECT spr round 4 (radius: 20) [02:52:59 -33407.606077] AUTODETECT spr round 5 (radius: 25) [02:54:26 -31319.823843] SPR radius for FAST iterations: 25 (autodetect) [02:54:26 -31319.823843] Model parameter optimization (eps = 3.000000) [02:54:39 -31219.945865] FAST spr round 1 (radius: 25) [02:55:33 -27031.158582] FAST spr round 2 (radius: 25) [02:56:22 -26725.996795] FAST spr round 3 (radius: 25) [02:57:09 -26658.214874] FAST spr round 4 (radius: 25) [02:57:53 -26640.719722] FAST spr round 5 (radius: 25) [02:58:35 -26636.697086] FAST spr round 6 (radius: 25) [02:59:17 -26636.697006] Model parameter optimization (eps = 1.000000) [02:59:28 -26606.689948] SLOW spr round 1 (radius: 5) [03:00:19 -26594.180566] SLOW spr round 2 (radius: 5) [03:01:11 -26588.910198] SLOW spr round 3 (radius: 5) [03:02:00 -26588.865773] SLOW spr round 4 (radius: 10) [03:02:53 -26586.129212] SLOW spr round 5 (radius: 5) [03:03:55 -26586.128769] SLOW spr round 6 (radius: 10) [03:04:52 -26586.128550] SLOW spr round 7 (radius: 15) [03:06:05 -26576.569350] SLOW spr round 8 (radius: 5) [03:07:10 -26576.569286] SLOW spr round 9 (radius: 10) [03:08:09 -26576.569237] SLOW spr round 10 (radius: 15) [03:09:19 -26574.778485] SLOW spr round 11 (radius: 5) [03:10:23 -26574.778439] SLOW spr round 12 (radius: 10) [03:11:22 -26574.778393] SLOW spr round 13 (radius: 15) [03:12:36 -26574.778347] SLOW spr round 14 (radius: 20) [03:14:19 -26573.799962] SLOW spr round 15 (radius: 5) [03:15:26 -26573.799918] SLOW spr round 16 (radius: 10) [03:16:26 -26573.799909] SLOW spr round 17 (radius: 15) [03:17:36 -26573.799905] SLOW spr round 18 (radius: 20) [03:19:19 -26573.799903] SLOW spr round 19 (radius: 25) [03:21:26 -26573.799902] Model parameter optimization (eps = 0.100000) [03:21:28] [worker #0] ML tree search #11, logLikelihood: -26573.789769 [03:21:28 -112360.353546] Initial branch length optimization [03:21:30 -92897.199133] Model parameter optimization (eps = 10.000000) [03:21:50 -92614.340648] AUTODETECT spr round 1 (radius: 5) [03:22:43 -61195.968780] AUTODETECT spr round 2 (radius: 10) [03:23:41 -44401.492812] AUTODETECT spr round 3 (radius: 15) [03:24:44 -36870.879398] AUTODETECT spr round 4 (radius: 20) [03:25:58 -33727.255522] AUTODETECT spr round 5 (radius: 25) [03:27:17 -32843.218602] SPR radius for FAST iterations: 25 (autodetect) [03:27:17 -32843.218602] Model parameter optimization (eps = 3.000000) [03:27:34 -32674.659726] FAST spr round 1 (radius: 25) [03:28:37 -27485.392450] FAST spr round 2 (radius: 25) [03:29:29 -27024.151619] FAST spr round 3 (radius: 25) [03:30:17 -26694.489034] FAST spr round 4 (radius: 25) [03:31:03 -26640.967701] FAST spr round 5 (radius: 25) [03:31:46 -26633.184145] FAST spr round 6 (radius: 25) [03:32:29 -26632.175098] FAST spr round 7 (radius: 25) [03:33:11 -26628.262930] FAST spr round 8 (radius: 25) [03:33:52 -26628.257167] Model parameter optimization (eps = 1.000000) [03:34:04 -26604.499463] SLOW spr round 1 (radius: 5) [03:34:54 -26596.682226] SLOW spr round 2 (radius: 5) [03:35:31] [worker #1] ML tree search #12, logLikelihood: -26537.954646 [03:35:44 -26594.960191] SLOW spr round 3 (radius: 5) [03:36:35 -26593.805538] SLOW spr round 4 (radius: 5) [03:37:26 -26593.805027] SLOW spr round 5 (radius: 10) [03:38:18 -26588.943668] SLOW spr round 6 (radius: 5) [03:39:21 -26580.815708] SLOW spr round 7 (radius: 5) [03:40:15 -26580.811970] SLOW spr round 8 (radius: 10) [03:41:07 -26580.811332] SLOW spr round 9 (radius: 15) [03:42:18 -26580.811017] SLOW spr round 10 (radius: 20) [03:44:03 -26580.323282] SLOW spr round 11 (radius: 5) [03:45:08 -26580.323107] SLOW spr round 12 (radius: 10) [03:46:06 -26580.323088] SLOW spr round 13 (radius: 15) [03:47:14 -26580.323083] SLOW spr round 14 (radius: 20) [03:48:57 -26580.323082] SLOW spr round 15 (radius: 25) [03:51:11 -26579.893607] SLOW spr round 16 (radius: 5) [03:52:17 -26579.893590] SLOW spr round 17 (radius: 10) [03:53:15 -26579.893572] SLOW spr round 18 (radius: 15) [03:54:23 -26579.893558] SLOW spr round 19 (radius: 20) [03:56:05 -26579.893544] SLOW spr round 20 (radius: 25) [03:58:21 -26579.893530] Model parameter optimization (eps = 0.100000) [03:58:25] [worker #0] ML tree search #13, logLikelihood: -26579.856687 [03:58:25 -112506.787292] Initial branch length optimization [03:58:27 -93384.502769] Model parameter optimization (eps = 10.000000) [03:58:47 -93100.106151] AUTODETECT spr round 1 (radius: 5) [03:59:38 -64243.840405] AUTODETECT spr round 2 (radius: 10) [04:00:34 -44584.377239] AUTODETECT spr round 3 (radius: 15) [04:01:38 -35003.512295] AUTODETECT spr round 4 (radius: 20) [04:02:47 -32018.446161] AUTODETECT spr round 5 (radius: 25) [04:04:07 -30635.138114] SPR radius for FAST iterations: 25 (autodetect) [04:04:07 -30635.138114] Model parameter optimization (eps = 3.000000) [04:04:26 -30519.305651] FAST spr round 1 (radius: 25) [04:04:43] [worker #1] ML tree search #14, logLikelihood: -26770.176736 [04:05:27 -26991.493781] FAST spr round 2 (radius: 25) [04:06:20 -26711.023909] FAST spr round 3 (radius: 25) [04:07:09 -26661.170162] FAST spr round 4 (radius: 25) [04:07:54 -26641.408163] FAST spr round 5 (radius: 25) [04:08:36 -26641.266489] FAST spr round 6 (radius: 25) [04:09:18 -26641.264806] Model parameter optimization (eps = 1.000000) [04:09:34 -26623.836201] SLOW spr round 1 (radius: 5) [04:10:32 -26608.244822] SLOW spr round 2 (radius: 5) [04:11:31 -26605.088955] SLOW spr round 3 (radius: 5) [04:12:30 -26605.088271] SLOW spr round 4 (radius: 10) [04:13:31 -26599.475750] SLOW spr round 5 (radius: 5) [04:14:42 -26599.338509] SLOW spr round 6 (radius: 5) [04:15:44 -26599.338014] SLOW spr round 7 (radius: 10) [04:16:44 -26599.337959] SLOW spr round 8 (radius: 15) [04:18:05 -26597.305287] SLOW spr round 9 (radius: 5) [04:19:19 -26588.446583] SLOW spr round 10 (radius: 5) [04:20:26 -26588.441079] SLOW spr round 11 (radius: 10) [04:21:26 -26588.440974] SLOW spr round 12 (radius: 15) [04:22:47 -26585.263956] SLOW spr round 13 (radius: 5) [04:24:01 -26584.524943] SLOW spr round 14 (radius: 5) [04:25:07 -26578.860867] SLOW spr round 15 (radius: 5) [04:26:07 -26578.858319] SLOW spr round 16 (radius: 10) [04:27:02 -26576.245328] SLOW spr round 17 (radius: 5) [04:28:03 -26575.918921] SLOW spr round 18 (radius: 5) [04:28:58 -26575.918539] SLOW spr round 19 (radius: 10) [04:29:50 -26575.918523] SLOW spr round 20 (radius: 15) [04:31:04 -26574.079341] SLOW spr round 21 (radius: 5) [04:32:08 -26574.078369] SLOW spr round 22 (radius: 10) [04:33:05 -26566.466515] SLOW spr round 23 (radius: 5) [04:34:06 -26555.039053] SLOW spr round 24 (radius: 5) [04:35:00 -26553.951585] SLOW spr round 25 (radius: 5) [04:35:51 -26553.948116] SLOW spr round 26 (radius: 10) [04:36:41 -26553.948109] SLOW spr round 27 (radius: 15) [04:37:55 -26553.948101] SLOW spr round 28 (radius: 20) [04:39:40 -26553.948094] SLOW spr round 29 (radius: 25) [04:40:48] [worker #1] ML tree search #16, logLikelihood: -26550.748121 [04:41:58 -26553.777671] SLOW spr round 30 (radius: 5) [04:43:04 -26553.776115] SLOW spr round 31 (radius: 10) [04:44:02 -26553.775969] SLOW spr round 32 (radius: 15) [04:45:14 -26553.775948] SLOW spr round 33 (radius: 20) [04:47:02 -26553.775939] SLOW spr round 34 (radius: 25) [04:49:19 -26553.775932] Model parameter optimization (eps = 0.100000) [04:49:28] [worker #0] ML tree search #15, logLikelihood: -26552.814692 [04:49:28 -112837.682801] Initial branch length optimization [04:49:30 -93679.183847] Model parameter optimization (eps = 10.000000) [04:49:44 -93349.580137] AUTODETECT spr round 1 (radius: 5) [04:50:36 -63069.639667] AUTODETECT spr round 2 (radius: 10) [04:51:33 -44217.839488] AUTODETECT spr round 3 (radius: 15) [04:52:30 -39122.341490] AUTODETECT spr round 4 (radius: 20) [04:53:44 -32322.481050] AUTODETECT spr round 5 (radius: 25) [04:54:56 -31412.192216] SPR radius for FAST iterations: 25 (autodetect) [04:54:56 -31412.192216] Model parameter optimization (eps = 3.000000) [04:55:11 -31280.007996] FAST spr round 1 (radius: 25) [04:56:10 -27027.948922] FAST spr round 2 (radius: 25) [04:57:01 -26665.282960] FAST spr round 3 (radius: 25) [04:57:48 -26618.922950] FAST spr round 4 (radius: 25) [04:58:33 -26613.250663] FAST spr round 5 (radius: 25) [04:59:15 -26613.213505] Model parameter optimization (eps = 1.000000) [04:59:28 -26591.449760] SLOW spr round 1 (radius: 5) [05:00:20 -26576.512853] SLOW spr round 2 (radius: 5) [05:01:12 -26564.773261] SLOW spr round 3 (radius: 5) [05:02:04 -26561.151173] SLOW spr round 4 (radius: 5) [05:02:57 -26560.039620] SLOW spr round 5 (radius: 5) [05:03:47 -26560.038385] SLOW spr round 6 (radius: 10) [05:04:40 -26558.888207] SLOW spr round 7 (radius: 5) [05:05:41 -26558.887806] SLOW spr round 8 (radius: 10) [05:06:38 -26558.887777] SLOW spr round 9 (radius: 15) [05:07:54 -26557.343108] SLOW spr round 10 (radius: 5) [05:08:58 -26557.342886] SLOW spr round 11 (radius: 10) [05:09:47] [worker #1] ML tree search #18, logLikelihood: -26559.020717 [05:09:58 -26556.662065] SLOW spr round 12 (radius: 5) [05:10:58 -26556.660953] SLOW spr round 13 (radius: 10) [05:11:53 -26556.660866] SLOW spr round 14 (radius: 15) [05:13:10 -26556.660859] SLOW spr round 15 (radius: 20) [05:15:05 -26554.966750] SLOW spr round 16 (radius: 5) [05:16:11 -26554.966524] SLOW spr round 17 (radius: 10) [05:17:11 -26554.966518] SLOW spr round 18 (radius: 15) [05:18:27 -26554.966518] SLOW spr round 19 (radius: 20) [05:20:23 -26554.966481] SLOW spr round 20 (radius: 25) [05:22:50 -26554.650789] SLOW spr round 21 (radius: 5) [05:23:56 -26554.648158] SLOW spr round 22 (radius: 10) [05:24:57 -26554.647901] SLOW spr round 23 (radius: 15) [05:26:12 -26554.647877] SLOW spr round 24 (radius: 20) [05:28:08 -26554.647875] SLOW spr round 25 (radius: 25) [05:30:35 -26554.647875] Model parameter optimization (eps = 0.100000) [05:30:43] [worker #0] ML tree search #17, logLikelihood: -26554.245748 [05:30:43 -112652.324504] Initial branch length optimization [05:30:45 -93573.728810] Model parameter optimization (eps = 10.000000) [05:31:00 -93322.424221] AUTODETECT spr round 1 (radius: 5) [05:31:51 -63276.307324] AUTODETECT spr round 2 (radius: 10) [05:32:48 -44453.970858] AUTODETECT spr round 3 (radius: 15) [05:33:47 -37904.167018] AUTODETECT spr round 4 (radius: 20) [05:34:55 -33540.741162] AUTODETECT spr round 5 (radius: 25) [05:36:09 -31133.875536] SPR radius for FAST iterations: 25 (autodetect) [05:36:09 -31133.875536] Model parameter optimization (eps = 3.000000) [05:36:23 -30984.824722] FAST spr round 1 (radius: 25) [05:37:22 -27003.103722] FAST spr round 2 (radius: 25) [05:38:14 -26726.390807] FAST spr round 3 (radius: 25) [05:39:03 -26664.078948] FAST spr round 4 (radius: 25) [05:39:46 -26641.448359] FAST spr round 5 (radius: 25) [05:40:27 -26641.447048] Model parameter optimization (eps = 1.000000) [05:40:38 -26614.275198] SLOW spr round 1 (radius: 5) [05:41:29 -26595.274203] SLOW spr round 2 (radius: 5) [05:42:20 -26590.138315] SLOW spr round 3 (radius: 5) [05:43:11 -26588.395779] SLOW spr round 4 (radius: 5) [05:43:58] [worker #1] ML tree search #20, logLikelihood: -26558.451166 [05:44:01 -26588.394006] SLOW spr round 5 (radius: 10) [05:44:52 -26584.607097] SLOW spr round 6 (radius: 5) [05:45:53 -26584.606897] SLOW spr round 7 (radius: 10) [05:46:49 -26584.606721] SLOW spr round 8 (radius: 15) [05:47:57 -26584.276329] SLOW spr round 9 (radius: 5) [05:49:00 -26584.233727] SLOW spr round 10 (radius: 10) [05:49:57 -26584.155784] SLOW spr round 11 (radius: 15) [05:51:06 -26584.155641] SLOW spr round 12 (radius: 20) [05:52:53 -26583.709308] SLOW spr round 13 (radius: 5) [05:53:57 -26583.709205] SLOW spr round 14 (radius: 10) [05:54:54 -26583.709189] SLOW spr round 15 (radius: 15) [05:56:03 -26583.709183] SLOW spr round 16 (radius: 20) [05:57:48 -26583.709177] SLOW spr round 17 (radius: 25) [05:59:53 -26583.709171] Model parameter optimization (eps = 0.100000) [05:59:57] [worker #0] ML tree search #19, logLikelihood: -26583.552074 Optimized model parameters: Partition 0: noname Rate heterogeneity: FREE (4 cats, mean), weights&rates: (0.133260,0.676937) (0.219779,0.474987) (0.423816,0.887726) (0.223145,1.923264) 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: -26533.694642 AIC score: 55985.389283 / AICc score: 4316265.389283 / BIC score: 59549.217467 Free parameters (model + branch lengths): 1459 WARNING: Number of free parameters (K=1459) is larger than alignment size (n=85). 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/Q6XPR3/3_mltree/Q6XPR3.raxml.bestTree All ML trees saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q6XPR3/3_mltree/Q6XPR3.raxml.mlTrees Optimized model saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q6XPR3/3_mltree/Q6XPR3.raxml.bestModel Execution log saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q6XPR3/3_mltree/Q6XPR3.raxml.log Analysis started: 02-Jul-2021 09:57:52 / finished: 02-Jul-2021 15:57:50 Elapsed time: 21598.015 seconds Consumed energy: 1916.205 Wh (= 10 km in an electric car, or 48 km with an e-scooter!)