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 03-Jul-2021 11:06:54 as follows: raxml-ng --msa /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q7Z5L7/2_msa/Q7Z5L7_trimmed_msa.fasta --data-type AA --model LG4X --prefix /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q7Z5L7/3_mltree/Q7Z5L7 --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/Q7Z5L7/2_msa/Q7Z5L7_trimmed_msa.fasta [00:00:00] Loaded alignment with 1001 taxa and 182 sites WARNING: Sequences tr_A0A1D5NTY7_A0A1D5NTY7_CHICK_9031 and sp_P51887_FMOD_CHICK_9031 are exactly identical! WARNING: Sequences tr_E1C4H4_E1C4H4_CHICK_9031 and tr_G3UUK4_G3UUK4_MELGA_9103 are exactly identical! WARNING: Sequences tr_E1C4H4_E1C4H4_CHICK_9031 and tr_A0A226NAE6_A0A226NAE6_CALSU_9009 are exactly identical! WARNING: Sequences tr_E1C4H4_E1C4H4_CHICK_9031 and tr_A0A226PPY8_A0A226PPY8_COLVI_9014 are exactly identical! WARNING: Sequences sp_F1NUK7_FLRT3_CHICK_9031 and tr_G1NRU8_G1NRU8_MELGA_9103 are exactly identical! WARNING: Sequences sp_F1NUK7_FLRT3_CHICK_9031 and tr_A0A226MZ26_A0A226MZ26_CALSU_9009 are exactly identical! WARNING: Sequences sp_O42235_KERA_CHICK_9031 and tr_G1NFL4_G1NFL4_MELGA_9103 are exactly identical! WARNING: Sequences sp_O42235_KERA_CHICK_9031 and tr_U3J2N3_U3J2N3_ANAPL_8839 are exactly identical! WARNING: Sequences sp_Q8BGT1_FLRT3_MOUSE_10090 and tr_G3HX58_G3HX58_CRIGR_10029 are exactly identical! WARNING: Sequences sp_Q8BGT1_FLRT3_MOUSE_10090 and sp_B1H234_FLRT3_RAT_10116 are exactly identical! WARNING: Sequences sp_Q8BLU0_FLRT2_MOUSE_10090 and tr_A0A2I3GQF0_A0A2I3GQF0_NOMLE_61853 are exactly identical! WARNING: Sequences sp_Q8BLU0_FLRT2_MOUSE_10090 and tr_G3GUD7_G3GUD7_CRIGR_10029 are exactly identical! WARNING: Sequences sp_Q8BLU0_FLRT2_MOUSE_10090 and tr_A0A2J8W5J4_A0A2J8W5J4_PONAB_9601 are exactly identical! WARNING: Sequences sp_Q8BLU0_FLRT2_MOUSE_10090 and tr_H2Q8Q8_H2Q8Q8_PANTR_9598 are exactly identical! WARNING: Sequences sp_Q8BLU0_FLRT2_MOUSE_10090 and sp_O43155_FLRT2_HUMAN_9606 are exactly identical! WARNING: Sequences sp_Q8BLU0_FLRT2_MOUSE_10090 and tr_A0A2R8MR44_A0A2R8MR44_CALJA_9483 are exactly identical! WARNING: Sequences sp_Q8BLU0_FLRT2_MOUSE_10090 and tr_A0A1U8BND3_A0A1U8BND3_MESAU_10036 are exactly identical! WARNING: Sequences sp_Q8BLU0_FLRT2_MOUSE_10090 and tr_A0A2R8Z827_A0A2R8Z827_PANPA_9597 are exactly identical! WARNING: Sequences tr_M3Y5Y1_M3Y5Y1_MUSPF_9669 and tr_A0A2Y9J4Z6_A0A2Y9J4Z6_ENHLU_391180 are exactly identical! WARNING: Sequences tr_M3Y828_M3Y828_MUSPF_9669 and tr_E2R423_E2R423_CANLF_9615 are exactly identical! WARNING: Sequences tr_M3Y828_M3Y828_MUSPF_9669 and tr_G1M7Y0_G1M7Y0_AILME_9646 are exactly identical! WARNING: Sequences tr_M3Y828_M3Y828_MUSPF_9669 and tr_M3W0X2_M3W0X2_FELCA_9685 are exactly identical! WARNING: Sequences tr_M3YJH3_M3YJH3_MUSPF_9669 and tr_A0A2Y9JXX6_A0A2Y9JXX6_ENHLU_391180 are exactly identical! WARNING: Sequences tr_M3Z6D8_M3Z6D8_MUSPF_9669 and tr_A0A2I3HXW8_A0A2I3HXW8_NOMLE_61853 are exactly identical! WARNING: Sequences tr_M3Z6D8_M3Z6D8_MUSPF_9669 and tr_G3SB88_G3SB88_GORGO_9595 are exactly identical! WARNING: Sequences tr_M3Z6D8_M3Z6D8_MUSPF_9669 and tr_G1SFR2_G1SFR2_RABIT_9986 are exactly identical! WARNING: Sequences tr_M3Z6D8_M3Z6D8_MUSPF_9669 and tr_E2RKY7_E2RKY7_CANLF_9615 are exactly identical! WARNING: Sequences tr_M3Z6D8_M3Z6D8_MUSPF_9669 and tr_A0A2J8MSW9_A0A2J8MSW9_PANTR_9598 are exactly identical! WARNING: Sequences tr_M3Z6D8_M3Z6D8_MUSPF_9669 and tr_F6VGZ3_F6VGZ3_HORSE_9796 are exactly identical! WARNING: Sequences tr_M3Z6D8_M3Z6D8_MUSPF_9669 and tr_W5P2P4_W5P2P4_SHEEP_9940 are exactly identical! WARNING: Sequences tr_M3Z6D8_M3Z6D8_MUSPF_9669 and tr_I3MCQ8_I3MCQ8_ICTTR_43179 are exactly identical! WARNING: Sequences tr_M3Z6D8_M3Z6D8_MUSPF_9669 and tr_A0A286XMF9_A0A286XMF9_CAVPO_10141 are exactly identical! WARNING: Sequences tr_M3Z6D8_M3Z6D8_MUSPF_9669 and sp_Q9NZU0_FLRT3_HUMAN_9606 are exactly identical! WARNING: Sequences tr_M3Z6D8_M3Z6D8_MUSPF_9669 and tr_F6SUY7_F6SUY7_MACMU_9544 are exactly identical! WARNING: Sequences tr_M3Z6D8_M3Z6D8_MUSPF_9669 and tr_F1SBJ0_F1SBJ0_PIG_9823 are exactly identical! WARNING: Sequences tr_M3Z6D8_M3Z6D8_MUSPF_9669 and tr_D2H9J6_D2H9J6_AILME_9646 are exactly identical! WARNING: Sequences tr_M3Z6D8_M3Z6D8_MUSPF_9669 and tr_G7PH00_G7PH00_MACFA_9541 are exactly identical! WARNING: Sequences tr_M3Z6D8_M3Z6D8_MUSPF_9669 and tr_F1N0R7_F1N0R7_BOVIN_9913 are exactly identical! WARNING: Sequences tr_M3Z6D8_M3Z6D8_MUSPF_9669 and tr_A0A096MYT7_A0A096MYT7_PAPAN_9555 are exactly identical! WARNING: Sequences tr_M3Z6D8_M3Z6D8_MUSPF_9669 and tr_A0A0D9SBF4_A0A0D9SBF4_CHLSB_60711 are exactly identical! WARNING: Sequences tr_M3Z6D8_M3Z6D8_MUSPF_9669 and tr_A0A1S3ESS3_A0A1S3ESS3_DIPOR_10020 are exactly identical! WARNING: Sequences tr_M3Z6D8_M3Z6D8_MUSPF_9669 and tr_A0A2K5L1A1_A0A2K5L1A1_CERAT_9531 are exactly identical! WARNING: Sequences tr_M3Z6D8_M3Z6D8_MUSPF_9669 and tr_A0A2K6ASW6_A0A2K6ASW6_MACNE_9545 are exactly identical! WARNING: Sequences tr_M3Z6D8_M3Z6D8_MUSPF_9669 and tr_A0A2K5XWH9_A0A2K5XWH9_MANLE_9568 are exactly identical! WARNING: Sequences tr_M3Z6D8_M3Z6D8_MUSPF_9669 and tr_A0A2R8ZD86_A0A2R8ZD86_PANPA_9597 are exactly identical! WARNING: Sequences tr_M3Z6D8_M3Z6D8_MUSPF_9669 and tr_A0A2U4AQQ1_A0A2U4AQQ1_TURTR_9739 are exactly identical! WARNING: Sequences tr_M3Z6D8_M3Z6D8_MUSPF_9669 and tr_A0A2U3WU36_A0A2U3WU36_ODORO_9708 are exactly identical! WARNING: Sequences tr_M3Z6D8_M3Z6D8_MUSPF_9669 and tr_A0A2Y9IMJ0_A0A2Y9IMJ0_ENHLU_391180 are exactly identical! WARNING: Sequences tr_M3Z6D8_M3Z6D8_MUSPF_9669 and tr_A0A2Y9PWH9_A0A2Y9PWH9_DELLE_9749 are exactly identical! WARNING: Sequences tr_M3Z6D8_M3Z6D8_MUSPF_9669 and tr_A0A2Y9FMJ1_A0A2Y9FMJ1_PHYCD_9755 are exactly identical! WARNING: Sequences tr_M3Z6D8_M3Z6D8_MUSPF_9669 and tr_A0A384D471_A0A384D471_URSMA_29073 are exactly identical! WARNING: Sequences tr_M3Z7G9_M3Z7G9_MUSPF_9669 and tr_H0XFK0_H0XFK0_OTOGA_30611 are exactly identical! WARNING: Sequences tr_M3Z7G9_M3Z7G9_MUSPF_9669 and tr_A0A2Y9JTN9_A0A2Y9JTN9_ENHLU_391180 are exactly identical! WARNING: Sequences tr_G1R0P1_G1R0P1_NOMLE_61853 and tr_G3R2H4_G3R2H4_GORGO_9595 are exactly identical! WARNING: Sequences tr_G1R0P1_G1R0P1_NOMLE_61853 and tr_H2NI86_H2NI86_PONAB_9601 are exactly identical! WARNING: Sequences tr_G1R0P1_G1R0P1_NOMLE_61853 and tr_H2Q6L2_H2Q6L2_PANTR_9598 are exactly identical! WARNING: Sequences tr_G1R0P1_G1R0P1_NOMLE_61853 and sp_O60938_KERA_HUMAN_9606 are exactly identical! WARNING: Sequences tr_G1R0P1_G1R0P1_NOMLE_61853 and tr_G7PJ12_G7PJ12_MACFA_9541 are exactly identical! WARNING: Sequences tr_G1R0P1_G1R0P1_NOMLE_61853 and tr_A0A096MYY6_A0A096MYY6_PAPAN_9555 are exactly identical! WARNING: Sequences tr_G1R0P1_G1R0P1_NOMLE_61853 and tr_A0A0D9QUS5_A0A0D9QUS5_CHLSB_60711 are exactly identical! WARNING: Sequences tr_G1R0P1_G1R0P1_NOMLE_61853 and tr_A0A2K5NKG3_A0A2K5NKG3_CERAT_9531 are exactly identical! WARNING: Sequences tr_G1R0P1_G1R0P1_NOMLE_61853 and tr_A0A2K6C599_A0A2K6C599_MACNE_9545 are exactly identical! WARNING: Sequences tr_G1R0P1_G1R0P1_NOMLE_61853 and tr_A0A2K6AAK7_A0A2K6AAK7_MANLE_9568 are exactly identical! WARNING: Sequences tr_G1R0P1_G1R0P1_NOMLE_61853 and tr_A0A2R9CE75_A0A2R9CE75_PANPA_9597 are exactly identical! WARNING: Sequences tr_G1RS72_G1RS72_NOMLE_61853 and tr_A0A2I2YJ91_A0A2I2YJ91_GORGO_9595 are exactly identical! WARNING: Sequences tr_G1RS72_G1RS72_NOMLE_61853 and tr_H2R1R5_H2R1R5_PANTR_9598 are exactly identical! WARNING: Sequences tr_G1RS72_G1RS72_NOMLE_61853 and sp_P21810_PGS1_HUMAN_9606 are exactly identical! WARNING: Sequences tr_G1RS72_G1RS72_NOMLE_61853 and tr_F7ESZ3_F7ESZ3_MACMU_9544 are exactly identical! WARNING: Sequences tr_G1RS72_G1RS72_NOMLE_61853 and tr_G7Q1Z4_G7Q1Z4_MACFA_9541 are exactly identical! WARNING: Sequences tr_G1RS72_G1RS72_NOMLE_61853 and tr_A0A096NEE7_A0A096NEE7_PAPAN_9555 are exactly identical! WARNING: Sequences tr_G1RS72_G1RS72_NOMLE_61853 and tr_A0A0D9R3Q0_A0A0D9R3Q0_CHLSB_60711 are exactly identical! WARNING: Sequences tr_G1RS72_G1RS72_NOMLE_61853 and tr_A0A2K5MLL7_A0A2K5MLL7_CERAT_9531 are exactly identical! WARNING: Sequences tr_G1RS72_G1RS72_NOMLE_61853 and tr_A0A2K6DUP2_A0A2K6DUP2_MACNE_9545 are exactly identical! WARNING: Sequences tr_G1RS72_G1RS72_NOMLE_61853 and tr_A0A2K5Y2J9_A0A2K5Y2J9_MANLE_9568 are exactly identical! WARNING: Sequences tr_G1RS72_G1RS72_NOMLE_61853 and tr_A0A2R9ARY7_A0A2R9ARY7_PANPA_9597 are exactly identical! WARNING: Sequences tr_G1S8L8_G1S8L8_NOMLE_61853 and tr_G3QS91_G3QS91_GORGO_9595 are exactly identical! WARNING: Sequences tr_G1S8L8_G1S8L8_NOMLE_61853 and tr_A0A2I3TRP8_A0A2I3TRP8_PANTR_9598 are exactly identical! WARNING: Sequences tr_G1S8L8_G1S8L8_NOMLE_61853 and tr_A0A2R8ZZ95_A0A2R8ZZ95_PANPA_9597 are exactly identical! WARNING: Sequences tr_G1S8Z2_G1S8Z2_NOMLE_61853 and tr_F7HMU6_F7HMU6_CALJA_9483 are exactly identical! WARNING: Sequences tr_G1S8Z2_G1S8Z2_NOMLE_61853 and tr_A0A2R9A3B0_A0A2R9A3B0_PANPA_9597 are exactly identical! WARNING: Sequences tr_G1S918_G1S918_NOMLE_61853 and tr_G3RIQ2_G3RIQ2_GORGO_9595 are exactly identical! WARNING: Sequences tr_G1S918_G1S918_NOMLE_61853 and tr_F7FA61_F7FA61_MACMU_9544 are exactly identical! WARNING: Sequences tr_G1S918_G1S918_NOMLE_61853 and tr_G7NVF5_G7NVF5_MACFA_9541 are exactly identical! WARNING: Sequences tr_G1S918_G1S918_NOMLE_61853 and tr_A0A096NPR2_A0A096NPR2_PAPAN_9555 are exactly identical! WARNING: Sequences tr_G1S918_G1S918_NOMLE_61853 and tr_A0A0D9RPE4_A0A0D9RPE4_CHLSB_60711 are exactly identical! WARNING: Sequences tr_G1S918_G1S918_NOMLE_61853 and tr_A0A2K6CNC7_A0A2K6CNC7_MACNE_9545 are exactly identical! WARNING: Sequences tr_G1S918_G1S918_NOMLE_61853 and tr_A0A2K6A943_A0A2K6A943_MANLE_9568 are exactly identical! WARNING: Sequences tr_G3SGU5_G3SGU5_GORGO_9595 and tr_A0A2I3S402_A0A2I3S402_PANTR_9598 are exactly identical! WARNING: Sequences tr_G3SGU5_G3SGU5_GORGO_9595 and sp_Q6PEZ8_PONL1_HUMAN_9606 are exactly identical! WARNING: Sequences tr_G3SJH4_G3SJH4_GORGO_9595 and tr_H2PSP4_H2PSP4_PONAB_9601 are exactly identical! WARNING: Sequences tr_G3SJH4_G3SJH4_GORGO_9595 and tr_H2QXG6_H2QXG6_PANTR_9598 are exactly identical! WARNING: Sequences tr_G3SJH4_G3SJH4_GORGO_9595 and sp_Q9BXN1_ASPN_HUMAN_9606 are exactly identical! WARNING: Sequences tr_G3SJH4_G3SJH4_GORGO_9595 and tr_A0A2R9B818_A0A2R9B818_PANPA_9597 are exactly identical! WARNING: Sequences tr_H2N7D1_H2N7D1_PONAB_9601 and sp_Q7Z5L7_PODN_HUMAN_9606 are exactly identical! WARNING: Sequences tr_U3KML1_U3KML1_RABIT_9986 and tr_G5B4W9_G5B4W9_HETGA_10181 are exactly identical! WARNING: Sequences tr_U3KML1_U3KML1_RABIT_9986 and tr_A0A091DKN2_A0A091DKN2_FUKDA_885580 are exactly identical! WARNING: Sequences tr_Q291L6_Q291L6_DROPS_46245 and tr_B4GAJ5_B4GAJ5_DROPE_7234 are exactly identical! WARNING: Sequences tr_Q29K98_Q29K98_DROPS_46245 and tr_B4GX48_B4GX48_DROPE_7234 are exactly identical! WARNING: Sequences tr_G1K2D8_G1K2D8_CANLF_9615 and sp_O02678_PGS1_CANLF_9615 are exactly identical! WARNING: Sequences tr_G1K2D8_G1K2D8_CANLF_9615 and sp_O46390_PGS1_SHEEP_9940 are exactly identical! WARNING: Sequences tr_G1K2D8_G1K2D8_CANLF_9615 and tr_W5PCP8_W5PCP8_SHEEP_9940 are exactly identical! WARNING: Sequences tr_G1K2D8_G1K2D8_CANLF_9615 and sp_P21809_PGS1_BOVIN_9913 are exactly identical! WARNING: Sequences tr_G1K2D8_G1K2D8_CANLF_9615 and tr_L5KDR6_L5KDR6_PTEAL_9402 are exactly identical! WARNING: Sequences tr_G1K2D8_G1K2D8_CANLF_9615 and tr_A0A2I2UTN2_A0A2I2UTN2_FELCA_9685 are exactly identical! WARNING: Sequences tr_G1K2D8_G1K2D8_CANLF_9615 and tr_A0A2U3Y9V6_A0A2U3Y9V6_LEPWE_9713 are exactly identical! WARNING: Sequences tr_H2QXG5_H2QXG5_PANTR_9598 and tr_A0A2R9CG56_A0A2R9CG56_PANPA_9597 are exactly identical! WARNING: Sequences tr_H2R1T6_H2R1T6_PANTR_9598 and sp_P51888_PRELP_HUMAN_9606 are exactly identical! WARNING: Sequences tr_H2R1T6_H2R1T6_PANTR_9598 and tr_A0A2R9APH9_A0A2R9APH9_PANPA_9597 are exactly identical! WARNING: Sequences tr_F7E6S6_F7E6S6_MONDO_13616 and tr_G3X3M0_G3X3M0_SARHA_9305 are exactly identical! WARNING: Sequences tr_F6R830_F6R830_HORSE_9796 and tr_L5JP27_L5JP27_PTEAL_9402 are exactly identical! WARNING: Sequences tr_F6R830_F6R830_HORSE_9796 and tr_A0A1U7UWG9_A0A1U7UWG9_TARSY_1868482 are exactly identical! WARNING: Sequences sp_D3ZTV3_FLRT2_RAT_10116 and tr_F7BEN4_F7BEN4_MACMU_9544 are exactly identical! WARNING: Sequences sp_D3ZTV3_FLRT2_RAT_10116 and tr_G7PB44_G7PB44_MACFA_9541 are exactly identical! WARNING: Sequences sp_D3ZTV3_FLRT2_RAT_10116 and tr_A0A096MMQ8_A0A096MMQ8_PAPAN_9555 are exactly identical! WARNING: Sequences sp_D3ZTV3_FLRT2_RAT_10116 and tr_A0A0D9SDY6_A0A0D9SDY6_CHLSB_60711 are exactly identical! WARNING: Sequences sp_D3ZTV3_FLRT2_RAT_10116 and tr_A0A2K5KVR0_A0A2K5KVR0_CERAT_9531 are exactly identical! WARNING: Sequences sp_D3ZTV3_FLRT2_RAT_10116 and tr_A0A2K6AU17_A0A2K6AU17_MACNE_9545 are exactly identical! WARNING: Sequences sp_D3ZTV3_FLRT2_RAT_10116 and tr_A0A2K5XT54_A0A2K5XT54_MANLE_9568 are exactly identical! WARNING: Sequences tr_M3ZLM9_M3ZLM9_XIPMA_8083 and tr_A0A087XVD4_A0A087XVD4_POEFO_48698 are exactly identical! WARNING: Sequences tr_M4AZ31_M4AZ31_XIPMA_8083 and tr_A0A087Y268_A0A087Y268_POEFO_48698 are exactly identical! WARNING: Sequences tr_A0A158NJP2_A0A158NJP2_ATTCE_12957 and tr_A0A195DX90_A0A195DX90_9HYME_471704 are exactly identical! WARNING: Sequences tr_A0A158NJP2_A0A158NJP2_ATTCE_12957 and tr_A0A195BCJ9_A0A195BCJ9_9HYME_520822 are exactly identical! WARNING: Sequences tr_A0A158NYH4_A0A158NYH4_ATTCE_12957 and tr_A0A195AYH6_A0A195AYH6_9HYME_520822 are exactly identical! WARNING: Sequences tr_A0A158NZT8_A0A158NZT8_ATTCE_12957 and tr_A0A195BMH4_A0A195BMH4_9HYME_520822 are exactly identical! WARNING: Sequences tr_A0A158NZT8_A0A158NZT8_ATTCE_12957 and tr_A0A195F3I7_A0A195F3I7_9HYME_34720 are exactly identical! WARNING: Sequences tr_F6Y7Q4_F6Y7Q4_MACMU_9544 and tr_A0A0D9RG22_A0A0D9RG22_CHLSB_60711 are exactly identical! WARNING: Sequences tr_F6Y7Q4_F6Y7Q4_MACMU_9544 and tr_A0A2K5N083_A0A2K5N083_CERAT_9531 are exactly identical! WARNING: Sequences tr_F6Y7Q4_F6Y7Q4_MACMU_9544 and tr_A0A2K6BZH9_A0A2K6BZH9_MACNE_9545 are exactly identical! WARNING: Sequences tr_F6YEA0_F6YEA0_MACMU_9544 and tr_G7NVP9_G7NVP9_MACFA_9541 are exactly identical! WARNING: Sequences tr_F6YEA0_F6YEA0_MACMU_9544 and tr_A0A2I3N6L5_A0A2I3N6L5_PAPAN_9555 are exactly identical! WARNING: Sequences tr_F6YEA0_F6YEA0_MACMU_9544 and tr_A0A2K5YPV4_A0A2K5YPV4_MANLE_9568 are exactly identical! WARNING: Sequences tr_G5B364_G5B364_HETGA_10181 and tr_A0A091D1K5_A0A091D1K5_FUKDA_885580 are exactly identical! WARNING: Sequences tr_H0YW34_H0YW34_TAEGU_59729 and tr_A0A091F858_A0A091F858_CORBR_85066 are exactly identical! WARNING: Sequences tr_H0YW34_H0YW34_TAEGU_59729 and tr_A0A218US11_A0A218US11_9PASE_299123 are exactly identical! WARNING: Sequences tr_H0ZFQ3_H0ZFQ3_TAEGU_59729 and tr_A0A091EPV3_A0A091EPV3_CORBR_85066 are exactly identical! WARNING: Sequences tr_H0ZFQ3_H0ZFQ3_TAEGU_59729 and tr_A0A218VET4_A0A218VET4_9PASE_299123 are exactly identical! WARNING: Sequences tr_H0ZQ68_H0ZQ68_TAEGU_59729 and tr_U3KJD9_U3KJD9_FICAL_59894 are exactly identical! WARNING: Sequences tr_H0ZQ68_H0ZQ68_TAEGU_59729 and tr_A0A091F2M4_A0A091F2M4_CORBR_85066 are exactly identical! WARNING: Sequences tr_H0ZQ68_H0ZQ68_TAEGU_59729 and tr_A0A218VE72_A0A218VE72_9PASE_299123 are exactly identical! WARNING: Sequences tr_H1A4C1_H1A4C1_TAEGU_59729 and tr_A0A218UGR9_A0A218UGR9_9PASE_299123 are exactly identical! WARNING: Sequences tr_D2HLH8_D2HLH8_AILME_9646 and tr_A0A384CRX7_A0A384CRX7_URSMA_29073 are exactly identical! WARNING: Sequences tr_G1LSE4_G1LSE4_AILME_9646 and tr_M3WQJ6_M3WQJ6_FELCA_9685 are exactly identical! WARNING: Sequences tr_G1LSE4_G1LSE4_AILME_9646 and tr_A0A2U3ZFP9_A0A2U3ZFP9_ODORO_9708 are exactly identical! WARNING: Sequences tr_G1LSE4_G1LSE4_AILME_9646 and tr_A0A384CSZ7_A0A384CSZ7_URSMA_29073 are exactly identical! WARNING: Sequences tr_G3MY74_G3MY74_BOVIN_9913 and tr_A0A2U4B0Z6_A0A2U4B0Z6_TURTR_9739 are exactly identical! WARNING: Sequences tr_G3MY74_G3MY74_BOVIN_9913 and tr_A0A2Y9PQ70_A0A2Y9PQ70_DELLE_9749 are exactly identical! WARNING: Sequences tr_G3MY74_G3MY74_BOVIN_9913 and tr_A0A2Y9EHT4_A0A2Y9EHT4_PHYCD_9755 are exactly identical! WARNING: Sequences tr_G3MY74_G3MY74_BOVIN_9913 and tr_A0A383ZGX0_A0A383ZGX0_BALAS_310752 are exactly identical! WARNING: Sequences tr_R0LFR8_R0LFR8_ANAPL_8839 and tr_A0A091JH13_A0A091JH13_EGRGA_188379 are exactly identical! WARNING: Sequences tr_R0LFR8_R0LFR8_ANAPL_8839 and tr_A0A091UNC1_A0A091UNC1_NIPNI_128390 are exactly identical! WARNING: Sequences tr_R0LFR8_R0LFR8_ANAPL_8839 and tr_A0A087R504_A0A087R504_APTFO_9233 are exactly identical! WARNING: Sequences tr_R0LFR8_R0LFR8_ANAPL_8839 and tr_A0A091WBX1_A0A091WBX1_OPIHO_30419 are exactly identical! WARNING: Sequences tr_R0LFR8_R0LFR8_ANAPL_8839 and tr_A0A099YTI8_A0A099YTI8_TINGU_94827 are exactly identical! WARNING: Sequences tr_R0LFR8_R0LFR8_ANAPL_8839 and tr_A0A091GQQ5_A0A091GQQ5_9AVES_55661 are exactly identical! WARNING: Sequences tr_R0LFR8_R0LFR8_ANAPL_8839 and tr_A0A0A0A6N9_A0A0A0A6N9_CHAVO_50402 are exactly identical! WARNING: Sequences tr_A0A087YRL4_A0A087YRL4_POEFO_48698 and tr_A0A087YRL5_A0A087YRL5_POEFO_48698 are exactly identical! WARNING: Sequences tr_A0A096P237_A0A096P237_PAPAN_9555 and tr_A0A2K5KVB4_A0A2K5KVB4_CERAT_9531 are exactly identical! WARNING: Sequences tr_A0A096P237_A0A096P237_PAPAN_9555 and tr_A0A2K5YFD9_A0A2K5YFD9_MANLE_9568 are exactly identical! WARNING: Sequences tr_A0A2I3NIE0_A0A2I3NIE0_PAPAN_9555 and tr_A0A2K5L616_A0A2K5L616_CERAT_9531 are exactly identical! WARNING: Sequences tr_A0A2I3NIE0_A0A2I3NIE0_PAPAN_9555 and tr_A0A2K6BCY4_A0A2K6BCY4_MACNE_9545 are exactly identical! WARNING: Sequences tr_A0A091DFG8_A0A091DFG8_FUKDA_885580 and tr_A0A1U7TYA5_A0A1U7TYA5_TARSY_1868482 are exactly identical! WARNING: Sequences tr_A0A0D9S791_A0A0D9S791_CHLSB_60711 and tr_A0A2K5NS67_A0A2K5NS67_CERAT_9531 are exactly identical! WARNING: Sequences tr_A0A151MKF4_A0A151MKF4_ALLMI_8496 and tr_A0A1U7RQW2_A0A1U7RQW2_ALLSI_38654 are exactly identical! WARNING: Sequences tr_A0A151NBR6_A0A151NBR6_ALLMI_8496 and tr_A0A1U7S3S2_A0A1U7S3S2_ALLSI_38654 are exactly identical! WARNING: Sequences tr_A0A151NBS5_A0A151NBS5_ALLMI_8496 and tr_A0A1U7S688_A0A1U7S688_ALLSI_38654 are exactly identical! WARNING: Sequences tr_A0A151NLG0_A0A151NLG0_ALLMI_8496 and tr_A0A1U7SFS0_A0A1U7SFS0_ALLSI_38654 are exactly identical! WARNING: Sequences tr_A0A151P9H4_A0A151P9H4_ALLMI_8496 and tr_A0A1U7SM99_A0A1U7SM99_ALLSI_38654 are exactly identical! WARNING: Sequences tr_A0A091JLF4_A0A091JLF4_EGRGA_188379 and tr_A0A087R8A8_A0A087R8A8_APTFO_9233 are exactly identical! WARNING: Sequences tr_A0A091JLF4_A0A091JLF4_EGRGA_188379 and tr_A0A091FR17_A0A091FR17_9AVES_55661 are exactly identical! WARNING: Sequences tr_A0A091JLF4_A0A091JLF4_EGRGA_188379 and tr_A0A0A0A5M7_A0A0A0A5M7_CHAVO_50402 are exactly identical! WARNING: Sequences tr_A0A091JLF4_A0A091JLF4_EGRGA_188379 and tr_A0A2I0M9J1_A0A2I0M9J1_COLLI_8932 are exactly identical! WARNING: Sequences tr_A0A091JLF4_A0A091JLF4_EGRGA_188379 and tr_A0A1U7RVR2_A0A1U7RVR2_ALLSI_38654 are exactly identical! WARNING: Sequences tr_A0A091JLF4_A0A091JLF4_EGRGA_188379 and tr_A0A1V4IGN9_A0A1V4IGN9_PATFA_372326 are exactly identical! WARNING: Sequences tr_A0A091JLH4_A0A091JLH4_EGRGA_188379 and tr_A0A091VWR1_A0A091VWR1_NIPNI_128390 are exactly identical! WARNING: Sequences tr_A0A091JLH4_A0A091JLH4_EGRGA_188379 and tr_A0A087RHS7_A0A087RHS7_APTFO_9233 are exactly identical! WARNING: Sequences tr_A0A091JLH4_A0A091JLH4_EGRGA_188379 and tr_A0A091WIZ4_A0A091WIZ4_OPIHO_30419 are exactly identical! WARNING: Sequences tr_A0A093PIM8_A0A093PIM8_9PASS_328815 and tr_A0A2I0LML3_A0A2I0LML3_COLLI_8932 are exactly identical! WARNING: Sequences tr_A0A093PIM8_A0A093PIM8_9PASS_328815 and tr_A0A1V4KWV7_A0A1V4KWV7_PATFA_372326 are exactly identical! WARNING: Sequences tr_A0A093QKL0_A0A093QKL0_9PASS_328815 and tr_A0A099YVV7_A0A099YVV7_TINGU_94827 are exactly identical! WARNING: Sequences tr_A0A2I0MC38_A0A2I0MC38_COLLI_8932 and tr_A0A1V4JY81_A0A1V4JY81_PATFA_372326 are exactly identical! WARNING: Sequences tr_A0A2I0MP77_A0A2I0MP77_COLLI_8932 and tr_A0A1V4KAS9_A0A1V4KAS9_PATFA_372326 are exactly identical! WARNING: Sequences tr_A0A093J0C3_A0A093J0C3_DRYPU_118200 and tr_A0A091IDM2_A0A091IDM2_CALAN_9244 are exactly identical! WARNING: Sequences tr_A0A1S3SAC9_A0A1S3SAC9_SALSA_8030 and tr_A0A060YRP1_A0A060YRP1_ONCMY_8022 are exactly identical! WARNING: Sequences tr_A0A226MBC1_A0A226MBC1_CALSU_9009 and tr_A0A226MCT9_A0A226MCT9_COLVI_9014 are exactly identical! WARNING: Sequences tr_A0A226MHT1_A0A226MHT1_CALSU_9009 and tr_A0A226NWF3_A0A226NWF3_COLVI_9014 are exactly identical! WARNING: Sequences tr_A0A226MHU1_A0A226MHU1_CALSU_9009 and tr_A0A226NVP3_A0A226NVP3_COLVI_9014 are exactly identical! WARNING: Sequences tr_A0A2D0T2T3_A0A2D0T2T3_ICTPU_7998 and tr_A0A2D0T2T4_A0A2D0T2T4_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0T2T3_A0A2D0T2T3_ICTPU_7998 and tr_A0A2D0T334_A0A2D0T334_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2U4BS36_A0A2U4BS36_TURTR_9739 and tr_A0A2Y9MT45_A0A2Y9MT45_DELLE_9749 are exactly identical! WARNING: Sequences tr_A0A2U4BS36_A0A2U4BS36_TURTR_9739 and tr_A0A2Y9EY63_A0A2Y9EY63_PHYCD_9755 are exactly identical! WARNING: Sequences tr_A0A2U3ZW94_A0A2U3ZW94_ODORO_9708 and tr_A0A2U3YSW8_A0A2U3YSW8_LEPWE_9713 are exactly identical! WARNING: Sequences tr_A0A2Y9LM87_A0A2Y9LM87_DELLE_9749 and tr_A0A2Y9FIE4_A0A2Y9FIE4_PHYCD_9755 are exactly identical! WARNING: Sequences tr_A0A2Y9MWU6_A0A2Y9MWU6_DELLE_9749 and tr_A0A384A8B8_A0A384A8B8_BALAS_310752 are exactly identical! WARNING: Sequences tr_A0A2Y9EXQ3_A0A2Y9EXQ3_PHYCD_9755 and tr_A0A383YTI1_A0A383YTI1_BALAS_310752 are exactly identical! WARNING: Sequences tr_A0A2Y9SB35_A0A2Y9SB35_PHYCD_9755 and tr_A0A383YNR2_A0A383YNR2_BALAS_310752 are exactly identical! WARNING: Duplicate sequences found: 195 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/Q7Z5L7/3_mltree/Q7Z5L7.raxml.reduced.phy Alignment comprises 1 partitions and 182 patterns Partition 0: noname Model: LG4X+R4 Alignment sites / patterns: 182 / 182 Gaps: 1.37 % Invariant sites: 0.00 % NOTE: Binary MSA file created: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q7Z5L7/3_mltree/Q7Z5L7.raxml.rba Parallelization scheme autoconfig: 4 worker(s) x 1 thread(s) Parallel reduction/worker buffer size: 1 KB / 0 KB [00:00:00] Generating 20 random starting tree(s) with 1001 taxa [00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 182 / 14560 [00:00:00] Data distribution: max. searches per worker: 5 Starting ML tree search with 20 distinct starting trees [00:00:00 -368523.185587] Initial branch length optimization [00:00:06 -302583.948400] Model parameter optimization (eps = 10.000000) [00:01:00 -301654.448038] AUTODETECT spr round 1 (radius: 5) [00:04:13 -209335.448405] AUTODETECT spr round 2 (radius: 10) [00:07:43 -152676.584997] AUTODETECT spr round 3 (radius: 15) [00:11:41 -122781.804075] AUTODETECT spr round 4 (radius: 20) [00:15:45 -99238.475753] AUTODETECT spr round 5 (radius: 25) [00:19:39 -94385.053823] SPR radius for FAST iterations: 25 (autodetect) [00:19:40 -94385.053823] Model parameter optimization (eps = 3.000000) [00:20:09 -94310.448964] FAST spr round 1 (radius: 25) [00:23:29 -79047.975640] FAST spr round 2 (radius: 25) [00:26:04 -76080.521776] FAST spr round 3 (radius: 25) [00:28:21 -75250.639982] FAST spr round 4 (radius: 25) [00:30:29 -75066.657610] FAST spr round 5 (radius: 25) [00:32:29 -75064.021440] FAST spr round 6 (radius: 25) [00:34:24 -75064.020756] Model parameter optimization (eps = 1.000000) [00:34:42 -75051.554014] SLOW spr round 1 (radius: 5) [00:37:17 -75033.188674] SLOW spr round 2 (radius: 5) [00:39:48 -75025.089367] SLOW spr round 3 (radius: 5) [00:42:23 -75017.375948] SLOW spr round 4 (radius: 5) [00:44:48 -75017.375170] SLOW spr round 5 (radius: 10) [00:47:23 -75013.405941] SLOW spr round 6 (radius: 5) [00:50:26 -75012.909551] SLOW spr round 7 (radius: 5) [00:53:07 -75012.906838] SLOW spr round 8 (radius: 10) [00:55:44 -75012.906292] SLOW spr round 9 (radius: 15) [00:59:31 -75012.495138] SLOW spr round 10 (radius: 5) [01:02:42 -75012.495022] SLOW spr round 11 (radius: 10) [01:05:41 -75012.494976] SLOW spr round 12 (radius: 15) [01:09:22 -75012.494954] SLOW spr round 13 (radius: 20) [01:15:00 -75011.132189] SLOW spr round 14 (radius: 5) [01:15:27] [worker #2] ML tree search #3, logLikelihood: -75001.229342 [01:16:09] [worker #3] ML tree search #4, logLikelihood: -75041.098646 [01:18:12 -75011.131955] SLOW spr round 15 (radius: 10) [01:18:45] [worker #1] ML tree search #2, logLikelihood: -74997.592564 [01:21:13 -75011.131948] SLOW spr round 16 (radius: 15) [01:24:51 -75011.131947] SLOW spr round 17 (radius: 20) [01:30:23 -75010.967573] SLOW spr round 18 (radius: 5) [01:33:36 -75010.378302] SLOW spr round 19 (radius: 5) [01:36:24 -75010.378262] SLOW spr round 20 (radius: 10) [01:39:05 -75010.378258] SLOW spr round 21 (radius: 15) [01:42:48 -75010.378257] SLOW spr round 22 (radius: 20) [01:48:16 -75010.378257] SLOW spr round 23 (radius: 25) [01:55:20 -75010.378257] Model parameter optimization (eps = 0.100000) [01:55:34] [worker #0] ML tree search #1, logLikelihood: -75010.155870 [01:55:35 -366089.404679] Initial branch length optimization [01:55:41 -301710.397455] Model parameter optimization (eps = 10.000000) [01:56:38 -300430.994605] AUTODETECT spr round 1 (radius: 5) [01:59:49 -203119.584419] AUTODETECT spr round 2 (radius: 10) [02:03:20 -141376.926087] AUTODETECT spr round 3 (radius: 15) [02:07:05 -114289.668982] AUTODETECT spr round 4 (radius: 20) [02:10:37 -102678.271620] AUTODETECT spr round 5 (radius: 25) [02:13:05] [worker #1] ML tree search #6, logLikelihood: -75023.327888 [02:15:27 -92588.626687] SPR radius for FAST iterations: 25 (autodetect) [02:15:27 -92588.626687] Model parameter optimization (eps = 3.000000) [02:16:01 -92491.260554] FAST spr round 1 (radius: 25) [02:19:21 -76392.623427] FAST spr round 2 (radius: 25) [02:21:55 -75157.163241] FAST spr round 3 (radius: 25) [02:24:16 -75056.812091] FAST spr round 4 (radius: 25) [02:26:20 -75045.476431] FAST spr round 5 (radius: 25) [02:28:16 -75042.608461] FAST spr round 6 (radius: 25) [02:30:09 -75042.607270] Model parameter optimization (eps = 1.000000) [02:30:25 -75037.037607] SLOW spr round 1 (radius: 5) [02:30:32] [worker #3] ML tree search #8, logLikelihood: -75006.012449 [02:30:56] [worker #2] ML tree search #7, logLikelihood: -74989.846733 [02:32:59 -75022.168802] SLOW spr round 2 (radius: 5) [02:35:25 -75015.857668] SLOW spr round 3 (radius: 5) [02:37:47 -75015.856939] SLOW spr round 4 (radius: 10) [02:40:16 -75013.281875] SLOW spr round 5 (radius: 5) [02:43:13 -75013.196194] SLOW spr round 6 (radius: 10) [02:45:58 -75013.195942] SLOW spr round 7 (radius: 15) [02:49:47 -75009.509669] SLOW spr round 8 (radius: 5) [02:52:55 -75008.426090] SLOW spr round 9 (radius: 5) [02:55:39 -75008.425793] SLOW spr round 10 (radius: 10) [02:58:16 -75008.185829] SLOW spr round 11 (radius: 5) [03:01:09 -75008.185277] SLOW spr round 12 (radius: 10) [03:03:52 -75008.185274] SLOW spr round 13 (radius: 15) [03:07:43 -75008.185274] SLOW spr round 14 (radius: 20) [03:13:37 -75008.185274] SLOW spr round 15 (radius: 25) [03:21:31 -75008.185274] Model parameter optimization (eps = 0.100000) [03:21:43] [worker #0] ML tree search #5, logLikelihood: -75007.978664 [03:21:43 -369931.229194] Initial branch length optimization [03:21:51 -306692.625233] Model parameter optimization (eps = 10.000000) [03:22:51 -305643.683782] AUTODETECT spr round 1 (radius: 5) [03:25:56 -203663.122369] AUTODETECT spr round 2 (radius: 10) [03:29:28 -140549.864053] AUTODETECT spr round 3 (radius: 15) [03:33:08 -115483.217476] AUTODETECT spr round 4 (radius: 20) [03:37:34 -92943.868505] AUTODETECT spr round 5 (radius: 25) [03:41:39] [worker #1] ML tree search #10, logLikelihood: -75008.753519 [03:42:00 -89824.422111] SPR radius for FAST iterations: 25 (autodetect) [03:42:00 -89824.422111] Model parameter optimization (eps = 3.000000) [03:42:29 -89742.540431] FAST spr round 1 (radius: 25) [03:45:51 -76113.204796] FAST spr round 2 (radius: 25) [03:48:17 -75159.019615] FAST spr round 3 (radius: 25) [03:49:53] [worker #2] ML tree search #11, logLikelihood: -75005.678920 [03:50:21 -75059.024536] FAST spr round 4 (radius: 25) [03:51:52 -75054.960088] FAST spr round 5 (radius: 25) [03:53:18 -75054.958593] Model parameter optimization (eps = 1.000000) [03:53:32 -75041.946507] SLOW spr round 1 (radius: 5) [03:55:26 -75028.752809] SLOW spr round 2 (radius: 5) [03:57:17 -75025.220869] SLOW spr round 3 (radius: 5) [03:58:25] [worker #3] ML tree search #12, logLikelihood: -74989.340855 [03:59:07 -75019.742072] SLOW spr round 4 (radius: 5) [04:00:56 -75018.547295] SLOW spr round 5 (radius: 5) [04:02:41 -75018.547220] SLOW spr round 6 (radius: 10) [04:04:32 -75016.570841] SLOW spr round 7 (radius: 5) [04:06:45 -75016.570727] SLOW spr round 8 (radius: 10) [04:08:49 -75016.257885] SLOW spr round 9 (radius: 5) [04:10:58 -75016.257882] SLOW spr round 10 (radius: 10) [04:12:59 -75016.257881] SLOW spr round 11 (radius: 15) [04:15:51 -75014.295140] SLOW spr round 12 (radius: 5) [04:18:13 -75013.645332] SLOW spr round 13 (radius: 5) [04:20:16 -75013.644763] SLOW spr round 14 (radius: 10) [04:22:16 -75012.840012] SLOW spr round 15 (radius: 5) [04:24:28 -75011.362872] SLOW spr round 16 (radius: 5) [04:26:25 -75011.362581] SLOW spr round 17 (radius: 10) [04:28:20 -75011.362552] SLOW spr round 18 (radius: 15) [04:31:48 -75011.362543] SLOW spr round 19 (radius: 20) [04:37:25 -75010.479803] SLOW spr round 20 (radius: 5) [04:40:40 -75010.319095] SLOW spr round 21 (radius: 5) [04:43:29 -75010.318831] SLOW spr round 22 (radius: 10) [04:46:10 -75010.318824] SLOW spr round 23 (radius: 15) [04:49:55 -75010.318823] SLOW spr round 24 (radius: 20) [04:55:02] [worker #2] ML tree search #15, logLikelihood: -75000.972242 [04:55:32 -75010.318822] SLOW spr round 25 (radius: 25) [04:56:37] [worker #3] ML tree search #16, logLikelihood: -75006.481677 [05:02:00] [worker #1] ML tree search #14, logLikelihood: -75013.596916 [05:02:59 -75010.318822] Model parameter optimization (eps = 0.100000) [05:03:14] [worker #0] ML tree search #9, logLikelihood: -75010.142722 [05:03:14 -369016.113206] Initial branch length optimization [05:03:19 -303763.412813] Model parameter optimization (eps = 10.000000) [05:04:17 -302505.644132] AUTODETECT spr round 1 (radius: 5) [05:07:30 -206741.965626] AUTODETECT spr round 2 (radius: 10) [05:11:03 -145186.474099] AUTODETECT spr round 3 (radius: 15) [05:14:57 -111112.436933] AUTODETECT spr round 4 (radius: 20) [05:18:55 -98855.658233] AUTODETECT spr round 5 (radius: 25) [05:22:58 -92751.777359] SPR radius for FAST iterations: 25 (autodetect) [05:22:58 -92751.777359] Model parameter optimization (eps = 3.000000) [05:23:26 -92637.324144] FAST spr round 1 (radius: 25) [05:26:57 -76975.078254] FAST spr round 2 (radius: 25) [05:29:43 -75141.707624] FAST spr round 3 (radius: 25) [05:32:11 -75065.167217] FAST spr round 4 (radius: 25) [05:34:20 -75050.576215] FAST spr round 5 (radius: 25) [05:36:19 -75050.573722] Model parameter optimization (eps = 1.000000) [05:36:37 -75038.402993] SLOW spr round 1 (radius: 5) [05:39:20 -75019.032935] SLOW spr round 2 (radius: 5) [05:41:54 -75011.374195] SLOW spr round 3 (radius: 5) [05:44:19 -75011.374125] SLOW spr round 4 (radius: 10) [05:46:54 -75009.101434] SLOW spr round 5 (radius: 5) [05:49:56 -75009.101320] SLOW spr round 6 (radius: 10) [05:52:47 -75009.101306] SLOW spr round 7 (radius: 15) [05:56:31 -75009.101302] SLOW spr round 8 (radius: 20) [06:02:32 -75009.101300] SLOW spr round 9 (radius: 25) [06:10:44 -75009.101300] Model parameter optimization (eps = 0.100000) [06:10:53] [worker #0] ML tree search #13, logLikelihood: -75008.991101 [06:10:53 -368254.750353] Initial branch length optimization [06:10:59 -304915.498477] Model parameter optimization (eps = 10.000000) [06:11:47 -303869.070854] AUTODETECT spr round 1 (radius: 5) [06:14:14] [worker #2] ML tree search #19, logLikelihood: -74997.714444 [06:15:02 -202699.338549] AUTODETECT spr round 2 (radius: 10) [06:18:36 -152211.638582] AUTODETECT spr round 3 (radius: 15) [06:22:27 -132284.025630] AUTODETECT spr round 4 (radius: 20) [06:26:22 -118497.226334] AUTODETECT spr round 5 (radius: 25) [06:28:47] [worker #1] ML tree search #18, logLikelihood: -74997.984085 [06:30:34 -107210.418240] SPR radius for FAST iterations: 25 (autodetect) [06:30:34 -107210.418240] Model parameter optimization (eps = 3.000000) [06:31:02 -107040.699329] FAST spr round 1 (radius: 25) [06:34:40 -77805.246832] FAST spr round 2 (radius: 25) [06:36:35] [worker #3] ML tree search #20, logLikelihood: -75013.513337 [06:37:30 -75277.509487] FAST spr round 3 (radius: 25) [06:39:56 -75067.647580] FAST spr round 4 (radius: 25) [06:42:04 -75046.801124] FAST spr round 5 (radius: 25) [06:44:03 -75045.149890] FAST spr round 6 (radius: 25) [06:45:57 -75045.148720] Model parameter optimization (eps = 1.000000) [06:46:14 -75040.025592] SLOW spr round 1 (radius: 5) [06:48:45 -75026.804262] SLOW spr round 2 (radius: 5) [06:51:12 -75024.317708] SLOW spr round 3 (radius: 5) [06:53:33 -75024.218789] SLOW spr round 4 (radius: 10) [06:56:05 -75021.746782] SLOW spr round 5 (radius: 5) [06:59:04 -75021.623569] SLOW spr round 6 (radius: 5) [07:01:41 -75021.623470] SLOW spr round 7 (radius: 10) [07:04:16 -75021.623469] SLOW spr round 8 (radius: 15) [07:08:10 -75021.623467] SLOW spr round 9 (radius: 20) [07:14:15 -75021.623467] SLOW spr round 10 (radius: 25) [07:22:44 -75021.623466] Model parameter optimization (eps = 0.100000) [07:22:51] [worker #0] ML tree search #17, logLikelihood: -75021.560323 Optimized model parameters: Partition 0: noname Rate heterogeneity: FREE (4 cats, mean), weights&rates: (0.235263,0.423010) (0.124521,0.363154) (0.392150,1.091321) (0.248067,1.722521) 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: -74989.340855 AIC score: 153988.681710 / AICc score: 8198048.681710 / BIC score: 160412.715117 Free parameters (model + branch lengths): 2005 WARNING: Number of free parameters (K=2005) is larger than alignment size (n=182). 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/Q7Z5L7/3_mltree/Q7Z5L7.raxml.bestTree All ML trees saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q7Z5L7/3_mltree/Q7Z5L7.raxml.mlTrees Optimized model saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q7Z5L7/3_mltree/Q7Z5L7.raxml.bestModel Execution log saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q7Z5L7/3_mltree/Q7Z5L7.raxml.log Analysis started: 03-Jul-2021 11:06:54 / finished: 03-Jul-2021 18:29:47 Elapsed time: 26572.222 seconds Consumed energy: 2045.086 Wh (= 10 km in an electric car, or 51 km with an e-scooter!)