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 01-Jul-2021 22:54:41 as follows: raxml-ng --msa /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q70Z35/2_msa/Q70Z35_trimmed_msa.fasta --data-type AA --model LG4X --prefix /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q70Z35/3_mltree/Q70Z35 --seed 2 --threads 4 --tree rand{20} pars{20} Analysis options: run mode: ML tree search start tree(s): random (20) random seed: 2 tip-inner: OFF pattern compression: ON per-rate scalers: OFF site repeats: ON fast spr radius: AUTO spr subtree cutoff: 1.000000 branch lengths: proportional (ML estimate, algorithm: NR-FAST) SIMD kernels: AVX2 parallelization: coarse-grained (auto), PTHREADS (4 threads), thread pinning: OFF [00:00:00] Reading alignment from file: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q70Z35/2_msa/Q70Z35_trimmed_msa.fasta [00:00:00] Loaded alignment with 995 taxa and 208 sites WARNING: Sequences tr_A0A2R8QHV5_A0A2R8QHV5_DANRE_7955 and tr_A0A2R8QRI5_A0A2R8QRI5_DANRE_7955 are exactly identical! WARNING: Sequences tr_A0A1D5NVQ5_A0A1D5NVQ5_CHICK_9031 and tr_G3UP34_G3UP34_MELGA_9103 are exactly identical! WARNING: Sequences tr_A0A1D5NVQ5_A0A1D5NVQ5_CHICK_9031 and tr_A0A226NNF6_A0A226NNF6_CALSU_9009 are exactly identical! WARNING: Sequences tr_A0A1D5PL02_A0A1D5PL02_CHICK_9031 and tr_A0A091JPH0_A0A091JPH0_EGRGA_188379 are exactly identical! WARNING: Sequences tr_A0A1D5PL02_A0A1D5PL02_CHICK_9031 and tr_A0A0A0A7Y7_A0A0A0A7Y7_CHAVO_50402 are exactly identical! WARNING: Sequences tr_A0A1D5PL02_A0A1D5PL02_CHICK_9031 and tr_A0A2I0MW97_A0A2I0MW97_COLLI_8932 are exactly identical! WARNING: Sequences tr_A0A1D5PL02_A0A1D5PL02_CHICK_9031 and tr_A0A1V4KHD6_A0A1V4KHD6_PATFA_372326 are exactly identical! WARNING: Sequences tr_A0A1D5PL02_A0A1D5PL02_CHICK_9031 and tr_A0A226N1X1_A0A226N1X1_CALSU_9009 are exactly identical! WARNING: Sequences tr_E1C9C1_E1C9C1_CHICK_9031 and tr_G1N216_G1N216_MELGA_9103 are exactly identical! WARNING: Sequences tr_E1C9C1_E1C9C1_CHICK_9031 and tr_H0Z5F9_H0Z5F9_TAEGU_59729 are exactly identical! WARNING: Sequences tr_E1C9C1_E1C9C1_CHICK_9031 and tr_U3K9G3_U3K9G3_FICAL_59894 are exactly identical! WARNING: Sequences tr_E1C9C1_E1C9C1_CHICK_9031 and tr_A0A091JPX8_A0A091JPX8_EGRGA_188379 are exactly identical! WARNING: Sequences tr_E1C9C1_E1C9C1_CHICK_9031 and tr_A0A091X471_A0A091X471_NIPNI_128390 are exactly identical! WARNING: Sequences tr_E1C9C1_E1C9C1_CHICK_9031 and tr_A0A087QQS5_A0A087QQS5_APTFO_9233 are exactly identical! WARNING: Sequences tr_E1C9C1_E1C9C1_CHICK_9031 and tr_A0A091WNE9_A0A091WNE9_OPIHO_30419 are exactly identical! WARNING: Sequences tr_E1C9C1_E1C9C1_CHICK_9031 and tr_A0A091H1D7_A0A091H1D7_9AVES_55661 are exactly identical! WARNING: Sequences tr_E1C9C1_E1C9C1_CHICK_9031 and tr_A0A0A0AJ58_A0A0A0AJ58_CHAVO_50402 are exactly identical! WARNING: Sequences tr_E1C9C1_E1C9C1_CHICK_9031 and tr_A0A2I0MB49_A0A2I0MB49_COLLI_8932 are exactly identical! WARNING: Sequences tr_E1C9C1_E1C9C1_CHICK_9031 and tr_A0A093GAT2_A0A093GAT2_DRYPU_118200 are exactly identical! WARNING: Sequences tr_E1C9C1_E1C9C1_CHICK_9031 and tr_A0A091J1J7_A0A091J1J7_CALAN_9244 are exactly identical! WARNING: Sequences tr_E1C9C1_E1C9C1_CHICK_9031 and tr_A0A1V4KZC6_A0A1V4KZC6_PATFA_372326 are exactly identical! WARNING: Sequences tr_E1C9C1_E1C9C1_CHICK_9031 and tr_A0A218UTV5_A0A218UTV5_9PASE_299123 are exactly identical! WARNING: Sequences tr_F1NVB0_F1NVB0_CHICK_9031 and tr_A0A226MJ62_A0A226MJ62_CALSU_9009 are exactly identical! WARNING: Sequences tr_F1NVB0_F1NVB0_CHICK_9031 and tr_A0A226PV87_A0A226PV87_COLVI_9014 are exactly identical! WARNING: Sequences sp_Q3UTH8_ARHG9_MOUSE_10090 and tr_A0A1U8CBG9_A0A1U8CBG9_MESAU_10036 are exactly identical! WARNING: Sequences sp_Q7TNR9_ARHG4_MOUSE_10090 and tr_D3ZKB4_D3ZKB4_RAT_10116 are exactly identical! WARNING: Sequences tr_M3XNJ2_M3XNJ2_MUSPF_9669 and tr_A0A2Y9L3R5_A0A2Y9L3R5_ENHLU_391180 are exactly identical! WARNING: Sequences tr_M3YES4_M3YES4_MUSPF_9669 and tr_A0A2I3HNT1_A0A2I3HNT1_NOMLE_61853 are exactly identical! WARNING: Sequences tr_M3YES4_M3YES4_MUSPF_9669 and tr_A0A2I2ZY53_A0A2I2ZY53_GORGO_9595 are exactly identical! WARNING: Sequences tr_M3YES4_M3YES4_MUSPF_9669 and tr_H2PVU3_H2PVU3_PONAB_9601 are exactly identical! WARNING: Sequences tr_M3YES4_M3YES4_MUSPF_9669 and sp_Q5RDK0_ARHG9_PONAB_9601 are exactly identical! WARNING: Sequences tr_M3YES4_M3YES4_MUSPF_9669 and tr_G1T0Z0_G1T0Z0_RABIT_9986 are exactly identical! WARNING: Sequences tr_M3YES4_M3YES4_MUSPF_9669 and tr_E2QY09_E2QY09_CANLF_9615 are exactly identical! WARNING: Sequences tr_M3YES4_M3YES4_MUSPF_9669 and tr_A0A2I3TQA2_A0A2I3TQA2_PANTR_9598 are exactly identical! WARNING: Sequences tr_M3YES4_M3YES4_MUSPF_9669 and tr_F7DVN5_F7DVN5_HORSE_9796 are exactly identical! WARNING: Sequences tr_M3YES4_M3YES4_MUSPF_9669 and tr_W5P3T1_W5P3T1_SHEEP_9940 are exactly identical! WARNING: Sequences tr_M3YES4_M3YES4_MUSPF_9669 and tr_A0A287CTU2_A0A287CTU2_ICTTR_43179 are exactly identical! WARNING: Sequences tr_M3YES4_M3YES4_MUSPF_9669 and sp_O43307_ARHG9_HUMAN_9606 are exactly identical! WARNING: Sequences tr_M3YES4_M3YES4_MUSPF_9669 and tr_A0A1D5Q059_A0A1D5Q059_MACMU_9544 are exactly identical! WARNING: Sequences tr_M3YES4_M3YES4_MUSPF_9669 and tr_A0A2R8M3M0_A0A2R8M3M0_CALJA_9483 are exactly identical! WARNING: Sequences tr_M3YES4_M3YES4_MUSPF_9669 and tr_G1L052_G1L052_AILME_9646 are exactly identical! WARNING: Sequences tr_M3YES4_M3YES4_MUSPF_9669 and sp_Q58DL7_ARHG9_BOVIN_9913 are exactly identical! WARNING: Sequences tr_M3YES4_M3YES4_MUSPF_9669 and tr_A0A2I2UV85_A0A2I2UV85_FELCA_9685 are exactly identical! WARNING: Sequences tr_M3YES4_M3YES4_MUSPF_9669 and tr_A0A2I3LP44_A0A2I3LP44_PAPAN_9555 are exactly identical! WARNING: Sequences tr_M3YES4_M3YES4_MUSPF_9669 and tr_A0A0D9RI01_A0A0D9RI01_CHLSB_60711 are exactly identical! WARNING: Sequences tr_M3YES4_M3YES4_MUSPF_9669 and tr_A0A2K5NIF0_A0A2K5NIF0_CERAT_9531 are exactly identical! WARNING: Sequences tr_M3YES4_M3YES4_MUSPF_9669 and tr_A0A2K6AMZ0_A0A2K6AMZ0_MACNE_9545 are exactly identical! WARNING: Sequences tr_M3YES4_M3YES4_MUSPF_9669 and tr_A0A2K5XW67_A0A2K5XW67_MANLE_9568 are exactly identical! WARNING: Sequences tr_M3YES4_M3YES4_MUSPF_9669 and tr_A0A2R8ZLA9_A0A2R8ZLA9_PANPA_9597 are exactly identical! WARNING: Sequences tr_M3YES4_M3YES4_MUSPF_9669 and tr_A0A2U4CGZ8_A0A2U4CGZ8_TURTR_9739 are exactly identical! WARNING: Sequences tr_M3YES4_M3YES4_MUSPF_9669 and tr_A0A2U3Y2Q5_A0A2U3Y2Q5_LEPWE_9713 are exactly identical! WARNING: Sequences tr_M3YES4_M3YES4_MUSPF_9669 and tr_A0A2Y9IMR9_A0A2Y9IMR9_ENHLU_391180 are exactly identical! WARNING: Sequences tr_M3YES4_M3YES4_MUSPF_9669 and tr_A0A2Y9MDE1_A0A2Y9MDE1_DELLE_9749 are exactly identical! WARNING: Sequences tr_M3YES4_M3YES4_MUSPF_9669 and tr_A0A2Y9S6X6_A0A2Y9S6X6_PHYCD_9755 are exactly identical! WARNING: Sequences tr_M3YM31_M3YM31_MUSPF_9669 and tr_A0A1S3GPN9_A0A1S3GPN9_DIPOR_10020 are exactly identical! WARNING: Sequences tr_M3YM31_M3YM31_MUSPF_9669 and tr_A0A060YLP1_A0A060YLP1_ONCMY_8022 are exactly identical! WARNING: Sequences tr_M3Z1L6_M3Z1L6_MUSPF_9669 and tr_K7B9U0_K7B9U0_PANTR_9598 are exactly identical! WARNING: Sequences tr_M3Z1L6_M3Z1L6_MUSPF_9669 and sp_Q8TCU6_PREX1_HUMAN_9606 are exactly identical! WARNING: Sequences tr_M3Z1L6_M3Z1L6_MUSPF_9669 and tr_G1M5M0_G1M5M0_AILME_9646 are exactly identical! WARNING: Sequences tr_M3Z1L6_M3Z1L6_MUSPF_9669 and tr_A0A1S2ZYX1_A0A1S2ZYX1_ERIEU_9365 are exactly identical! WARNING: Sequences tr_M3Z1L6_M3Z1L6_MUSPF_9669 and tr_A0A2U4C1K0_A0A2U4C1K0_TURTR_9739 are exactly identical! WARNING: Sequences tr_M3Z1L6_M3Z1L6_MUSPF_9669 and tr_A0A2U3WT90_A0A2U3WT90_ODORO_9708 are exactly identical! WARNING: Sequences tr_M3Z1L6_M3Z1L6_MUSPF_9669 and tr_A0A2Y9IUD8_A0A2Y9IUD8_ENHLU_391180 are exactly identical! WARNING: Sequences tr_M3Z1L6_M3Z1L6_MUSPF_9669 and tr_A0A2Y9Q781_A0A2Y9Q781_DELLE_9749 are exactly identical! WARNING: Sequences tr_A0A3B3I0E8_A0A3B3I0E8_ORYLA_8090 and tr_A0A3B5Q4B6_A0A3B5Q4B6_XIPMA_8083 are exactly identical! WARNING: Sequences tr_A0A3B3I0E8_A0A3B3I0E8_ORYLA_8090 and tr_H2SRC8_H2SRC8_TAKRU_31033 are exactly identical! WARNING: Sequences tr_A0A3B3I0E8_A0A3B3I0E8_ORYLA_8090 and tr_H3DEB6_H3DEB6_TETNG_99883 are exactly identical! WARNING: Sequences tr_A0A3B3I0E8_A0A3B3I0E8_ORYLA_8090 and tr_A0A087XK17_A0A087XK17_POEFO_48698 are exactly identical! WARNING: Sequences tr_A0A2I3G8L6_A0A2I3G8L6_NOMLE_61853 and tr_G3QP24_G3QP24_GORGO_9595 are exactly identical! WARNING: Sequences tr_A0A2I3G8L6_A0A2I3G8L6_NOMLE_61853 and tr_H2PR36_H2PR36_PONAB_9601 are exactly identical! WARNING: Sequences tr_A0A2I3G8L6_A0A2I3G8L6_NOMLE_61853 and tr_H2QWM8_H2QWM8_PANTR_9598 are exactly identical! WARNING: Sequences tr_A0A2I3G8L6_A0A2I3G8L6_NOMLE_61853 and sp_Q8TB45_DPTOR_HUMAN_9606 are exactly identical! WARNING: Sequences tr_A0A2I3G8L6_A0A2I3G8L6_NOMLE_61853 and tr_A0A1D5R627_A0A1D5R627_MACMU_9544 are exactly identical! WARNING: Sequences tr_A0A2I3G8L6_A0A2I3G8L6_NOMLE_61853 and tr_F7BCX8_F7BCX8_CALJA_9483 are exactly identical! WARNING: Sequences tr_A0A2I3G8L6_A0A2I3G8L6_NOMLE_61853 and tr_G1L5X3_G1L5X3_AILME_9646 are exactly identical! WARNING: Sequences tr_A0A2I3G8L6_A0A2I3G8L6_NOMLE_61853 and tr_G7PCQ6_G7PCQ6_MACFA_9541 are exactly identical! WARNING: Sequences tr_A0A2I3G8L6_A0A2I3G8L6_NOMLE_61853 and tr_M3WE84_M3WE84_FELCA_9685 are exactly identical! WARNING: Sequences tr_A0A2I3G8L6_A0A2I3G8L6_NOMLE_61853 and tr_A0A096MUT4_A0A096MUT4_PAPAN_9555 are exactly identical! WARNING: Sequences tr_A0A2I3G8L6_A0A2I3G8L6_NOMLE_61853 and tr_A0A0D9RED8_A0A0D9RED8_CHLSB_60711 are exactly identical! WARNING: Sequences tr_A0A2I3G8L6_A0A2I3G8L6_NOMLE_61853 and tr_A0A2K5P3K8_A0A2K5P3K8_CERAT_9531 are exactly identical! WARNING: Sequences tr_A0A2I3G8L6_A0A2I3G8L6_NOMLE_61853 and tr_A0A2K6B8F4_A0A2K6B8F4_MACNE_9545 are exactly identical! WARNING: Sequences tr_A0A2I3G8L6_A0A2I3G8L6_NOMLE_61853 and tr_A0A2R9BYL3_A0A2R9BYL3_PANPA_9597 are exactly identical! WARNING: Sequences tr_A0A2I3G8L6_A0A2I3G8L6_NOMLE_61853 and tr_A0A2U3WSL2_A0A2U3WSL2_ODORO_9708 are exactly identical! WARNING: Sequences tr_A0A2I3G8L6_A0A2I3G8L6_NOMLE_61853 and tr_A0A2Y9JAE7_A0A2Y9JAE7_ENHLU_391180 are exactly identical! WARNING: Sequences tr_G1S1J0_G1S1J0_NOMLE_61853 and tr_A0A096MVA5_A0A096MVA5_PAPAN_9555 are exactly identical! WARNING: Sequences tr_G1S1J0_G1S1J0_NOMLE_61853 and tr_A0A2K5KU83_A0A2K5KU83_CERAT_9531 are exactly identical! WARNING: Sequences tr_G1S1J0_G1S1J0_NOMLE_61853 and tr_A0A2K6B4N1_A0A2K6B4N1_MACNE_9545 are exactly identical! WARNING: Sequences tr_G1S1J0_G1S1J0_NOMLE_61853 and tr_A0A2R9AGC8_A0A2R9AGC8_PANPA_9597 are exactly identical! WARNING: Sequences tr_A0A2I2YRE4_A0A2I2YRE4_GORGO_9595 and tr_H2P777_H2P777_PONAB_9601 are exactly identical! WARNING: Sequences tr_A0A2I2YRE4_A0A2I2YRE4_GORGO_9595 and tr_H2QIQ7_H2QIQ7_PANTR_9598 are exactly identical! WARNING: Sequences tr_A0A2I2YRE4_A0A2I2YRE4_GORGO_9595 and sp_Q9NR80_ARHG4_HUMAN_9606 are exactly identical! WARNING: Sequences tr_A0A2I2YRE4_A0A2I2YRE4_GORGO_9595 and tr_G8F2P2_G8F2P2_MACFA_9541 are exactly identical! WARNING: Sequences tr_A0A2I2YRE4_A0A2I2YRE4_GORGO_9595 and tr_A0A0D9RYR7_A0A0D9RYR7_CHLSB_60711 are exactly identical! WARNING: Sequences tr_A0A2I2YRE4_A0A2I2YRE4_GORGO_9595 and tr_A0A2K5ZYG7_A0A2K5ZYG7_MANLE_9568 are exactly identical! WARNING: Sequences tr_A0A2I2Z1R5_A0A2I2Z1R5_GORGO_9595 and tr_K7BJ16_K7BJ16_PANTR_9598 are exactly identical! WARNING: Sequences tr_A0A2I2Z1R5_A0A2I2Z1R5_GORGO_9595 and sp_Q96N96_SPT13_HUMAN_9606 are exactly identical! WARNING: Sequences tr_A0A2I2Z1R5_A0A2I2Z1R5_GORGO_9595 and tr_A0A2R9BI86_A0A2R9BI86_PANPA_9597 are exactly identical! WARNING: Sequences tr_G3RRP5_G3RRP5_GORGO_9595 and tr_H2PQI3_H2PQI3_PONAB_9601 are exactly identical! WARNING: Sequences tr_G3RRP5_G3RRP5_GORGO_9595 and tr_A0A2I3SC96_A0A2I3SC96_PANTR_9598 are exactly identical! WARNING: Sequences tr_G3RRP5_G3RRP5_GORGO_9595 and sp_Q70Z35_PREX2_HUMAN_9606 are exactly identical! WARNING: Sequences tr_G3RRP5_G3RRP5_GORGO_9595 and tr_G7PBZ7_G7PBZ7_MACFA_9541 are exactly identical! WARNING: Sequences tr_G3RRP5_G3RRP5_GORGO_9595 and tr_A0A096MWT3_A0A096MWT3_PAPAN_9555 are exactly identical! WARNING: Sequences tr_G3RRP5_G3RRP5_GORGO_9595 and tr_A0A0D9RN74_A0A0D9RN74_CHLSB_60711 are exactly identical! WARNING: Sequences tr_G3RRP5_G3RRP5_GORGO_9595 and tr_A0A2K5KK59_A0A2K5KK59_CERAT_9531 are exactly identical! WARNING: Sequences tr_G3RRP5_G3RRP5_GORGO_9595 and tr_A0A2K6DAT5_A0A2K6DAT5_MACNE_9545 are exactly identical! WARNING: Sequences tr_G1MQQ3_G1MQQ3_MELGA_9103 and tr_A0A093HAA5_A0A093HAA5_STRCA_441894 are exactly identical! WARNING: Sequences tr_F1P6T3_F1P6T3_CANLF_9615 and tr_F1N6T8_F1N6T8_BOVIN_9913 are exactly identical! WARNING: Sequences tr_H2R6W0_H2R6W0_PANTR_9598 and tr_F7G8P7_F7G8P7_MACMU_9544 are exactly identical! WARNING: Sequences tr_H2R6W0_H2R6W0_PANTR_9598 and tr_G7P4Y8_G7P4Y8_MACFA_9541 are exactly identical! WARNING: Sequences tr_H2R6W0_H2R6W0_PANTR_9598 and tr_A0A2R9BZW5_A0A2R9BZW5_PANPA_9597 are exactly identical! WARNING: Sequences tr_W5Q2V9_W5Q2V9_SHEEP_9940 and tr_A0A287BGI4_A0A287BGI4_PIG_9823 are exactly identical! WARNING: Sequences tr_A0A158NIZ6_A0A158NIZ6_ATTCE_12957 and tr_F4WWT0_F4WWT0_ACREC_103372 are exactly identical! WARNING: Sequences tr_A0A158NIZ6_A0A158NIZ6_ATTCE_12957 and tr_A0A195DVB3_A0A195DVB3_9HYME_471704 are exactly identical! WARNING: Sequences tr_A0A158P3R1_A0A158P3R1_ATTCE_12957 and tr_F4X211_F4X211_ACREC_103372 are exactly identical! WARNING: Sequences tr_A0A158P3R1_A0A158P3R1_ATTCE_12957 and tr_A0A195BCT4_A0A195BCT4_9HYME_520822 are exactly identical! WARNING: Sequences tr_A0A158P3R1_A0A158P3R1_ATTCE_12957 and tr_A0A195F086_A0A195F086_9HYME_34720 are exactly identical! WARNING: Sequences tr_A0A286XFU5_A0A286XFU5_CAVPO_10141 and tr_A0A091DHC4_A0A091DHC4_FUKDA_885580 are exactly identical! WARNING: Sequences tr_A0A1D5Q1F9_A0A1D5Q1F9_MACMU_9544 and tr_A0A096NYR6_A0A096NYR6_PAPAN_9555 are exactly identical! WARNING: Sequences tr_A0A1D5Q1F9_A0A1D5Q1F9_MACMU_9544 and tr_A0A2K6BFV7_A0A2K6BFV7_MACNE_9545 are exactly identical! WARNING: Sequences tr_F6WVV6_F6WVV6_MACMU_9544 and tr_A0A096NSD2_A0A096NSD2_PAPAN_9555 are exactly identical! WARNING: Sequences tr_F6WVV6_F6WVV6_MACMU_9544 and tr_A0A2K5MW44_A0A2K5MW44_CERAT_9531 are exactly identical! WARNING: Sequences tr_F6WVV6_F6WVV6_MACMU_9544 and tr_A0A2K6E6G3_A0A2K6E6G3_MACNE_9545 are exactly identical! WARNING: Sequences tr_K7FI56_K7FI56_PELSI_13735 and tr_A0A093I625_A0A093I625_STRCA_441894 are exactly identical! WARNING: Sequences tr_K7FI56_K7FI56_PELSI_13735 and tr_A0A099Z0Q8_A0A099Z0Q8_TINGU_94827 are exactly identical! WARNING: Sequences tr_H0Z5E1_H0Z5E1_TAEGU_59729 and tr_A0A218UVF0_A0A218UVF0_9PASE_299123 are exactly identical! WARNING: Sequences tr_H0ZB40_H0ZB40_TAEGU_59729 and tr_A0A091ENY4_A0A091ENY4_CORBR_85066 are exactly identical! WARNING: Sequences tr_A0A1B8YA71_A0A1B8YA71_XENTR_8364 and tr_F6WZD6_F6WZD6_XENTR_8364 are exactly identical! WARNING: Sequences tr_G1M007_G1M007_AILME_9646 and tr_M3VUH5_M3VUH5_FELCA_9685 are exactly identical! WARNING: Sequences tr_G1M8D4_G1M8D4_AILME_9646 and tr_A0A2Y9FVE5_A0A2Y9FVE5_TRIMA_127582 are exactly identical! WARNING: Sequences tr_G7PR79_G7PR79_MACFA_9541 and tr_A0A0D9RSP6_A0A0D9RSP6_CHLSB_60711 are exactly identical! WARNING: Sequences tr_F1MRP8_F1MRP8_BOVIN_9913 and tr_A0A2U4CNT7_A0A2U4CNT7_TURTR_9739 are exactly identical! WARNING: Sequences tr_F1MRP8_F1MRP8_BOVIN_9913 and tr_A0A2Y9M6V5_A0A2Y9M6V5_DELLE_9749 are exactly identical! WARNING: Sequences tr_F1MRP8_F1MRP8_BOVIN_9913 and tr_A0A2Y9EK92_A0A2Y9EK92_PHYCD_9755 are exactly identical! WARNING: Sequences tr_U3JLT8_U3JLT8_FICAL_59894 and tr_A0A091USM1_A0A091USM1_NIPNI_128390 are exactly identical! WARNING: Sequences tr_U3JLT8_U3JLT8_FICAL_59894 and tr_A0A087RBT4_A0A087RBT4_APTFO_9233 are exactly identical! WARNING: Sequences tr_U3JLT8_U3JLT8_FICAL_59894 and tr_A0A091FRY2_A0A091FRY2_9AVES_55661 are exactly identical! WARNING: Sequences tr_U3JLT8_U3JLT8_FICAL_59894 and tr_A0A0A0AA36_A0A0A0AA36_CHAVO_50402 are exactly identical! WARNING: Sequences tr_U3JLT8_U3JLT8_FICAL_59894 and tr_A0A2I0LTU3_A0A2I0LTU3_COLLI_8932 are exactly identical! WARNING: Sequences tr_U3JRY0_U3JRY0_FICAL_59894 and tr_A0A218VC28_A0A218VC28_9PASE_299123 are exactly identical! WARNING: Sequences tr_U3IRE2_U3IRE2_ANAPL_8839 and tr_A0A091IUE9_A0A091IUE9_CALAN_9244 are exactly identical! WARNING: Sequences tr_U3IRE2_U3IRE2_ANAPL_8839 and tr_A0A226MZ09_A0A226MZ09_CALSU_9009 are exactly identical! WARNING: Sequences tr_U3IRE2_U3IRE2_ANAPL_8839 and tr_A0A226PWK4_A0A226PWK4_COLVI_9014 are exactly identical! WARNING: Sequences tr_U3IRE7_U3IRE7_ANAPL_8839 and tr_A0A093HCD2_A0A093HCD2_STRCA_441894 are exactly identical! WARNING: Sequences tr_A0A3B1IV85_A0A3B1IV85_ASTMX_7994 and tr_A0A2D0R9E4_A0A2D0R9E4_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A3B1IV85_A0A3B1IV85_ASTMX_7994 and tr_A0A2D0R9X6_A0A2D0R9X6_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A3B1IV85_A0A3B1IV85_ASTMX_7994 and tr_A0A2D0RAL6_A0A2D0RAL6_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A151MFS8_A0A151MFS8_ALLMI_8496 and tr_A0A3Q0FYS9_A0A3Q0FYS9_ALLSI_38654 are exactly identical! WARNING: Sequences tr_A0A151MN91_A0A151MN91_ALLMI_8496 and tr_A0A3Q0H1V0_A0A3Q0H1V0_ALLSI_38654 are exactly identical! WARNING: Sequences tr_A0A151MSF4_A0A151MSF4_ALLMI_8496 and tr_A0A3Q0G2T6_A0A3Q0G2T6_ALLSI_38654 are exactly identical! WARNING: Sequences tr_A0A151NPD5_A0A151NPD5_ALLMI_8496 and tr_A0A3Q0HGE8_A0A3Q0HGE8_ALLSI_38654 are exactly identical! WARNING: Sequences tr_A0A151NUI5_A0A151NUI5_ALLMI_8496 and tr_A0A3Q0H118_A0A3Q0H118_ALLSI_38654 are exactly identical! WARNING: Sequences tr_A0A151NZ14_A0A151NZ14_ALLMI_8496 and tr_A0A3Q0FJK0_A0A3Q0FJK0_ALLSI_38654 are exactly identical! WARNING: Sequences tr_A0A091F9T3_A0A091F9T3_CORBR_85066 and tr_A0A091JG13_A0A091JG13_EGRGA_188379 are exactly identical! WARNING: Sequences tr_A0A091F9T3_A0A091F9T3_CORBR_85066 and tr_A0A093QBC7_A0A093QBC7_9PASS_328815 are exactly identical! WARNING: Sequences tr_A0A091F9T3_A0A091F9T3_CORBR_85066 and tr_A0A091VTK4_A0A091VTK4_NIPNI_128390 are exactly identical! WARNING: Sequences tr_A0A091F9T3_A0A091F9T3_CORBR_85066 and tr_A0A091GMV2_A0A091GMV2_9AVES_55661 are exactly identical! WARNING: Sequences tr_A0A091JI65_A0A091JI65_EGRGA_188379 and tr_A0A093PQV6_A0A093PQV6_9PASS_328815 are exactly identical! WARNING: Sequences tr_A0A091JI65_A0A091JI65_EGRGA_188379 and tr_A0A091IWX7_A0A091IWX7_CALAN_9244 are exactly identical! WARNING: Sequences tr_A0A091V6J0_A0A091V6J0_NIPNI_128390 and tr_A0A087R646_A0A087R646_APTFO_9233 are exactly identical! WARNING: Sequences tr_A0A091XXB1_A0A091XXB1_OPIHO_30419 and tr_A0A2I0MCV8_A0A2I0MCV8_COLLI_8932 are exactly identical! WARNING: Sequences tr_A0A091XXB1_A0A091XXB1_OPIHO_30419 and tr_A0A1V4K9I1_A0A1V4K9I1_PATFA_372326 are exactly identical! WARNING: Sequences tr_A0A2I0M626_A0A2I0M626_COLLI_8932 and tr_A0A1V4KKK5_A0A1V4KKK5_PATFA_372326 are exactly identical! WARNING: Sequences tr_A0A2I0MVC5_A0A2I0MVC5_COLLI_8932 and tr_A0A1V4JL29_A0A1V4JL29_PATFA_372326 are exactly identical! WARNING: Sequences tr_A0A091IV92_A0A091IV92_CALAN_9244 and tr_A0A1V4J6P5_A0A1V4J6P5_PATFA_372326 are exactly identical! WARNING: Sequences tr_A0A1S3IGW1_A0A1S3IGW1_LINUN_7574 and tr_A0A1S3JA49_A0A1S3JA49_LINUN_7574 are exactly identical! WARNING: Sequences tr_A0A1S3LQZ8_A0A1S3LQZ8_SALSA_8030 and tr_A0A060VZ21_A0A060VZ21_ONCMY_8022 are exactly identical! WARNING: Sequences tr_A0A1S3QBA9_A0A1S3QBA9_SALSA_8030 and tr_C0H9S6_C0H9S6_SALSA_8030 are exactly identical! WARNING: Sequences tr_A0A1S3SW76_A0A1S3SW76_SALSA_8030 and tr_A0A1S3SW89_A0A1S3SW89_SALSA_8030 are exactly identical! WARNING: Sequences tr_A0A226MU35_A0A226MU35_CALSU_9009 and tr_A0A226PPF1_A0A226PPF1_COLVI_9014 are exactly identical! WARNING: Sequences tr_A0A226NJK5_A0A226NJK5_CALSU_9009 and tr_A0A226PEJ0_A0A226PEJ0_COLVI_9014 are exactly identical! WARNING: Sequences tr_A0A2D0PYG6_A0A2D0PYG6_ICTPU_7998 and tr_A0A2D0Q057_A0A2D0Q057_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0Q9N4_A0A2D0Q9N4_ICTPU_7998 and tr_W5UB82_W5UB82_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0R9I5_A0A2D0R9I5_ICTPU_7998 and tr_A0A2D0R9J5_A0A2D0R9J5_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0SST6_A0A2D0SST6_ICTPU_7998 and tr_A0A2D0STC4_A0A2D0STC4_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0SYT5_A0A2D0SYT5_ICTPU_7998 and tr_A0A2D0SYU6_A0A2D0SYU6_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0SYT5_A0A2D0SYT5_ICTPU_7998 and tr_A0A2D0SZ82_A0A2D0SZ82_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0T6X2_A0A2D0T6X2_ICTPU_7998 and tr_A0A2D0T6X3_A0A2D0T6X3_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0T6X2_A0A2D0T6X2_ICTPU_7998 and tr_A0A2D0T7M4_A0A2D0T7M4_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2K5L4V7_A0A2K5L4V7_CERAT_9531 and tr_A0A2K5ZTJ0_A0A2K5ZTJ0_MANLE_9568 are exactly identical! WARNING: Sequences tr_A0A2K5XCV2_A0A2K5XCV2_MANLE_9568 and tr_A0A2R9AV48_A0A2R9AV48_PANPA_9597 are exactly identical! WARNING: Sequences tr_A0A2U3V699_A0A2U3V699_TURTR_9739 and tr_A0A2Y9LNN9_A0A2Y9LNN9_DELLE_9749 are exactly identical! WARNING: Sequences tr_A0A2U4AIF3_A0A2U4AIF3_TURTR_9739 and tr_A0A2Y9PVR0_A0A2Y9PVR0_DELLE_9749 are exactly identical! WARNING: Sequences tr_A0A2U4B2G8_A0A2U4B2G8_TURTR_9739 and tr_A0A2Y9PTE3_A0A2Y9PTE3_DELLE_9749 are exactly identical! WARNING: Duplicate sequences found: 183 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/Q70Z35/3_mltree/Q70Z35.raxml.reduced.phy Alignment comprises 1 partitions and 208 patterns Partition 0: noname Model: LG4X+R4 Alignment sites / patterns: 208 / 208 Gaps: 8.50 % Invariant sites: 0.00 % NOTE: Binary MSA file created: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q70Z35/3_mltree/Q70Z35.raxml.rba Parallelization scheme autoconfig: 4 worker(s) x 1 thread(s) Parallel reduction/worker buffer size: 1 KB / 0 KB [00:00:00] Generating 20 random starting tree(s) with 995 taxa [00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 208 / 16640 [00:00:00] Data distribution: max. searches per worker: 5 Starting ML tree search with 20 distinct starting trees [00:00:00 -357728.952972] Initial branch length optimization [00:00:07 -286766.975009] Model parameter optimization (eps = 10.000000) [00:01:13 -285948.018261] AUTODETECT spr round 1 (radius: 5) [00:04:06 -180162.049107] AUTODETECT spr round 2 (radius: 10) [00:07:13 -127460.982682] AUTODETECT spr round 3 (radius: 15) [00:11:00 -97987.413165] AUTODETECT spr round 4 (radius: 20) [00:14:41 -86378.084459] AUTODETECT spr round 5 (radius: 25) [00:19:13 -78193.316385] SPR radius for FAST iterations: 25 (autodetect) [00:19:13 -78193.316385] Model parameter optimization (eps = 3.000000) [00:19:57 -77493.259971] FAST spr round 1 (radius: 25) [00:23:03 -64941.496684] FAST spr round 2 (radius: 25) [00:25:24 -64095.632802] FAST spr round 3 (radius: 25) [00:27:34 -64046.935090] FAST spr round 4 (radius: 25) [00:29:29 -64044.727250] FAST spr round 5 (radius: 25) [00:31:21 -64041.064619] FAST spr round 6 (radius: 25) [00:33:08 -64041.063918] Model parameter optimization (eps = 1.000000) [00:33:24 -64037.435878] SLOW spr round 1 (radius: 5) [00:35:42 -64009.438028] SLOW spr round 2 (radius: 5) [00:38:01 -64007.880391] SLOW spr round 3 (radius: 5) [00:40:17 -64007.680596] SLOW spr round 4 (radius: 5) [00:42:30 -64007.672675] SLOW spr round 5 (radius: 10) [00:44:54 -64005.738800] SLOW spr round 6 (radius: 5) [00:47:45 -64004.451086] SLOW spr round 7 (radius: 5) [00:50:15 -64004.450657] SLOW spr round 8 (radius: 10) [00:52:42 -64004.450615] SLOW spr round 9 (radius: 15) [00:56:10 -64003.729485] SLOW spr round 10 (radius: 5) [00:59:07 -64003.727763] SLOW spr round 11 (radius: 10) [01:01:54 -64003.725990] SLOW spr round 12 (radius: 15) [01:05:16 -64003.725191] SLOW spr round 13 (radius: 20) [01:07:00] [worker #3] ML tree search #4, logLikelihood: -64013.588752 [01:07:39] [worker #1] ML tree search #2, logLikelihood: -64007.232004 [01:10:29] [worker #2] ML tree search #3, logLikelihood: -64009.824188 [01:10:59 -64003.725141] SLOW spr round 14 (radius: 25) [01:18:14 -64003.725135] Model parameter optimization (eps = 0.100000) [01:18:28] [worker #0] ML tree search #1, logLikelihood: -64003.204150 [01:18:29 -357561.690414] Initial branch length optimization [01:18:33 -286110.498231] Model parameter optimization (eps = 10.000000) [01:19:58 -285220.400018] AUTODETECT spr round 1 (radius: 5) [01:22:50 -185269.273777] AUTODETECT spr round 2 (radius: 10) [01:26:02 -125672.815254] AUTODETECT spr round 3 (radius: 15) [01:29:38 -98273.508112] AUTODETECT spr round 4 (radius: 20) [01:33:12 -90395.014421] AUTODETECT spr round 5 (radius: 25) [01:37:42 -82995.939946] SPR radius for FAST iterations: 25 (autodetect) [01:37:42 -82995.939946] Model parameter optimization (eps = 3.000000) [01:38:42 -82434.561832] FAST spr round 1 (radius: 25) [01:41:52 -65755.357218] FAST spr round 2 (radius: 25) [01:44:17 -64103.269029] FAST spr round 3 (radius: 25) [01:46:24 -64039.189039] FAST spr round 4 (radius: 25) [01:48:25 -64037.258813] FAST spr round 5 (radius: 25) [01:50:19 -64037.256927] Model parameter optimization (eps = 1.000000) [01:50:28 -64036.386906] SLOW spr round 1 (radius: 5) [01:52:47 -64014.529684] SLOW spr round 2 (radius: 5) [01:55:08 -64012.489703] SLOW spr round 3 (radius: 5) [01:57:22 -64012.489484] SLOW spr round 4 (radius: 10) [01:59:49 -64009.154761] SLOW spr round 5 (radius: 5) [02:02:43 -64007.794345] SLOW spr round 6 (radius: 5) [02:05:12 -64007.794325] SLOW spr round 7 (radius: 10) [02:07:40 -64007.794322] SLOW spr round 8 (radius: 15) [02:11:13 -64007.676244] SLOW spr round 9 (radius: 5) [02:14:13 -64006.914221] SLOW spr round 10 (radius: 5) [02:14:31] [worker #3] ML tree search #8, logLikelihood: -64019.413777 [02:16:49 -64006.913968] SLOW spr round 11 (radius: 10) [02:19:19 -64006.913916] SLOW spr round 12 (radius: 15) [02:22:47 -64006.913898] SLOW spr round 13 (radius: 20) [02:27:19] [worker #2] ML tree search #7, logLikelihood: -64016.241831 [02:27:59 -64006.289088] SLOW spr round 14 (radius: 5) [02:31:01 -64006.288596] SLOW spr round 15 (radius: 10) [02:33:49 -64006.288563] SLOW spr round 16 (radius: 15) [02:37:11 -64006.288355] SLOW spr round 17 (radius: 20) [02:42:28 -64006.288354] SLOW spr round 18 (radius: 25) [02:42:41] [worker #1] ML tree search #6, logLikelihood: -64011.585608 [02:49:24 -64006.288354] Model parameter optimization (eps = 0.100000) [02:49:31] [worker #0] ML tree search #5, logLikelihood: -64006.248538 [02:49:31 -358565.889199] Initial branch length optimization [02:49:35 -288807.354518] Model parameter optimization (eps = 10.000000) [02:50:37 -287949.903298] AUTODETECT spr round 1 (radius: 5) [02:53:42 -181977.141165] AUTODETECT spr round 2 (radius: 10) [02:57:02 -128613.267798] AUTODETECT spr round 3 (radius: 15) [03:00:51 -103428.739174] AUTODETECT spr round 4 (radius: 20) [03:04:34 -89824.538624] AUTODETECT spr round 5 (radius: 25) [03:09:07 -84370.768414] SPR radius for FAST iterations: 25 (autodetect) [03:09:07 -84370.768414] Model parameter optimization (eps = 3.000000) [03:09:54 -83581.833397] FAST spr round 1 (radius: 25) [03:13:34 -66112.828195] FAST spr round 2 (radius: 25) [03:16:21 -64182.706412] FAST spr round 3 (radius: 25) [03:18:41 -64097.225526] FAST spr round 4 (radius: 25) [03:20:54 -64045.713401] FAST spr round 5 (radius: 25) [03:22:57 -64039.856051] FAST spr round 6 (radius: 25) [03:23:52] [worker #3] ML tree search #12, logLikelihood: -64018.507860 [03:24:55 -64039.855879] Model parameter optimization (eps = 1.000000) [03:25:11 -64034.444668] SLOW spr round 1 (radius: 5) [03:27:41 -64020.012595] SLOW spr round 2 (radius: 5) [03:30:14 -64015.764163] SLOW spr round 3 (radius: 5) [03:32:43 -64015.200818] SLOW spr round 4 (radius: 5) [03:35:07 -64015.198743] SLOW spr round 5 (radius: 10) [03:37:46 -64013.860589] SLOW spr round 6 (radius: 5) [03:40:50 -64012.741431] SLOW spr round 7 (radius: 5) [03:43:31 -64012.741418] SLOW spr round 8 (radius: 10) [03:46:05 -64012.741407] SLOW spr round 9 (radius: 15) [03:49:44 -64012.624987] SLOW spr round 10 (radius: 5) [03:52:11] [worker #2] ML tree search #11, logLikelihood: -64015.047033 [03:52:54 -64012.624920] SLOW spr round 11 (radius: 10) [03:55:55 -64012.624915] SLOW spr round 12 (radius: 15) [03:59:35 -64012.624911] SLOW spr round 13 (radius: 20) [04:05:15 -64012.624907] SLOW spr round 14 (radius: 25) [04:12:01 -64012.624902] Model parameter optimization (eps = 0.100000) [04:12:13] [worker #0] ML tree search #9, logLikelihood: -64012.474297 [04:12:13 -360140.106547] Initial branch length optimization [04:12:18 -289179.120995] Model parameter optimization (eps = 10.000000) [04:13:37 -288183.619071] AUTODETECT spr round 1 (radius: 5) [04:16:45 -191065.582581] AUTODETECT spr round 2 (radius: 10) [04:20:06 -131094.475074] AUTODETECT spr round 3 (radius: 15) [04:23:50 -96854.180044] AUTODETECT spr round 4 (radius: 20) [04:27:55] [worker #1] ML tree search #10, logLikelihood: -64004.388608 [04:27:58 -80837.588188] AUTODETECT spr round 5 (radius: 25) [04:31:58 -77392.583231] SPR radius for FAST iterations: 25 (autodetect) [04:31:58 -77392.583231] Model parameter optimization (eps = 3.000000) [04:32:50 -76699.114999] FAST spr round 1 (radius: 25) [04:35:51 -64560.975393] FAST spr round 2 (radius: 25) [04:38:08 -64119.679316] FAST spr round 3 (radius: 25) [04:40:15 -64058.742437] FAST spr round 4 (radius: 25) [04:42:13 -64052.328752] FAST spr round 5 (radius: 25) [04:44:03 -64050.827950] FAST spr round 6 (radius: 25) [04:45:50 -64050.827806] Model parameter optimization (eps = 1.000000) [04:46:04 -64047.665608] SLOW spr round 1 (radius: 5) [04:48:23 -64028.045867] SLOW spr round 2 (radius: 5) [04:50:42 -64015.852677] SLOW spr round 3 (radius: 5) [04:53:02 -64011.721024] SLOW spr round 4 (radius: 5) [04:55:17 -64011.720462] SLOW spr round 5 (radius: 10) [04:57:41 -64010.921385] SLOW spr round 6 (radius: 5) [05:00:30 -64010.919294] SLOW spr round 7 (radius: 10) [05:03:19 -64010.917594] SLOW spr round 8 (radius: 15) [05:06:13] [worker #3] ML tree search #16, logLikelihood: -64008.003269 [05:07:07 -64010.518532] SLOW spr round 9 (radius: 5) [05:10:20 -64010.518052] SLOW spr round 10 (radius: 10) [05:13:16 -64010.517824] SLOW spr round 11 (radius: 15) [05:17:00 -64010.517819] SLOW spr round 12 (radius: 20) [05:23:08 -64010.517814] SLOW spr round 13 (radius: 25) [05:27:45] [worker #2] ML tree search #15, logLikelihood: -64009.057432 [05:31:02 -64010.517809] Model parameter optimization (eps = 0.100000) [05:31:08] [worker #0] ML tree search #13, logLikelihood: -64010.464163 [05:31:09 -358202.793362] Initial branch length optimization [05:31:13 -289174.570534] Model parameter optimization (eps = 10.000000) [05:32:37 -288363.761095] AUTODETECT spr round 1 (radius: 5) [05:35:46 -189874.806208] AUTODETECT spr round 2 (radius: 10) [05:39:05 -129173.867407] AUTODETECT spr round 3 (radius: 15) [05:42:52 -109127.645309] AUTODETECT spr round 4 (radius: 20) [05:47:05 -95408.577382] AUTODETECT spr round 5 (radius: 25) [05:51:33 -92151.235035] SPR radius for FAST iterations: 25 (autodetect) [05:51:33 -92151.235035] Model parameter optimization (eps = 3.000000) [05:52:12 -91436.748111] FAST spr round 1 (radius: 25) [05:55:33 -69118.099222] FAST spr round 2 (radius: 25) [05:55:36] [worker #1] ML tree search #14, logLikelihood: -64014.145949 [05:58:16 -64580.508265] FAST spr round 3 (radius: 25) [06:00:22 -64091.746199] FAST spr round 4 (radius: 25) [06:02:28 -64036.313857] FAST spr round 5 (radius: 25) [06:04:20 -64032.993018] FAST spr round 6 (radius: 25) [06:06:08 -64032.992974] Model parameter optimization (eps = 1.000000) [06:06:24 -64031.169784] SLOW spr round 1 (radius: 5) [06:08:42 -64012.762660] SLOW spr round 2 (radius: 5) [06:10:38] [worker #3] ML tree search #20, logLikelihood: -64004.693165 [06:11:01 -64009.853976] SLOW spr round 3 (radius: 5) [06:13:17 -64009.597027] SLOW spr round 4 (radius: 5) [06:15:32 -64009.595263] SLOW spr round 5 (radius: 10) [06:17:57 -64008.677434] SLOW spr round 6 (radius: 5) [06:20:43 -64007.944688] SLOW spr round 7 (radius: 5) [06:23:11 -64007.943924] SLOW spr round 8 (radius: 10) [06:25:37 -64007.943852] SLOW spr round 9 (radius: 15) [06:29:06 -64007.943849] SLOW spr round 10 (radius: 20) [06:34:26 -64007.943849] SLOW spr round 11 (radius: 25) [06:41:29 -64007.943848] Model parameter optimization (eps = 0.100000) [06:41:41] [worker #0] ML tree search #17, logLikelihood: -64007.561647 [07:02:21] [worker #2] ML tree search #19, logLikelihood: -64012.923669 [07:46:33] [worker #1] ML tree search #18, logLikelihood: -64007.139951 Optimized model parameters: Partition 0: noname Rate heterogeneity: FREE (4 cats, mean), weights&rates: (0.163056,0.417386) (0.165947,0.493834) (0.371999,0.819845) (0.298999,1.822788) 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: -64003.204150 AIC score: 131992.408300 / AICc score: 8080076.408300 / BIC score: 138644.121693 Free parameters (model + branch lengths): 1993 WARNING: Number of free parameters (K=1993) is larger than alignment size (n=208). This might lead to overfitting and compromise tree inference results! WARNING: Best ML tree contains 1 near-zero branches! Best ML tree with collapsed near-zero branches saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q70Z35/3_mltree/Q70Z35.raxml.bestTreeCollapsed Best ML tree saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q70Z35/3_mltree/Q70Z35.raxml.bestTree All ML trees saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q70Z35/3_mltree/Q70Z35.raxml.mlTrees Optimized model saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q70Z35/3_mltree/Q70Z35.raxml.bestModel Execution log saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q70Z35/3_mltree/Q70Z35.raxml.log Analysis started: 01-Jul-2021 22:54:41 / finished: 02-Jul-2021 06:41:15 Elapsed time: 27993.706 seconds Consumed energy: 2260.793 Wh (= 11 km in an electric car, or 57 km with an e-scooter!)