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 04-Jul-2021 12:14:08 as follows: raxml-ng --msa /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/P24468/2_msa/P24468_trimmed_msa.fasta --data-type AA --model LG4X --prefix /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/P24468/3_mltree/P24468 --seed 2 --threads 5 --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 (5 threads), thread pinning: OFF [00:00:00] Reading alignment from file: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/P24468/2_msa/P24468_trimmed_msa.fasta [00:00:00] Loaded alignment with 1001 taxa and 341 sites WARNING: Sequences tr_E9HV90_E9HV90_DAPPU_6669 and tr_A1XQQ1_A1XQQ1_9CRUS_35525 are exactly identical! WARNING: Sequences sp_Q06725_N2F1A_DANRE_7955 and tr_A0A1S3NMC8_A0A1S3NMC8_SALSA_8030 are exactly identical! WARNING: Sequences sp_Q06725_N2F1A_DANRE_7955 and tr_W5USF1_W5USF1_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A1D5PVE2_A0A1D5PVE2_CHICK_9031 and sp_P28701_RXRG_CHICK_9031 are exactly identical! WARNING: Sequences tr_A0A1D5PVE2_A0A1D5PVE2_CHICK_9031 and tr_A0A226N1M4_A0A226N1M4_CALSU_9009 are exactly identical! WARNING: Sequences tr_F1NJL8_F1NJL8_CHICK_9031 and tr_A0A218V6Z9_A0A218V6Z9_9PASE_299123 are exactly identical! WARNING: Sequences tr_F1NJL8_F1NJL8_CHICK_9031 and tr_A0A226MYL0_A0A226MYL0_CALSU_9009 are exactly identical! WARNING: Sequences tr_F1NJL8_F1NJL8_CHICK_9031 and tr_A0A226P7M6_A0A226P7M6_COLVI_9014 are exactly identical! WARNING: Sequences tr_F1NTE7_F1NTE7_CHICK_9031 and sp_Q91379_NR2E1_CHICK_9031 are exactly identical! WARNING: Sequences tr_F1NZ15_F1NZ15_CHICK_9031 and tr_A0A226MI14_A0A226MI14_CALSU_9009 are exactly identical! WARNING: Sequences sp_Q90733_COT2_CHICK_9031 and tr_A0A226NNI5_A0A226NNI5_CALSU_9009 are exactly identical! WARNING: Sequences sp_Q90733_COT2_CHICK_9031 and tr_A0A226P2E4_A0A226P2E4_COLVI_9014 are exactly identical! WARNING: Sequences sp_P28704_RXRB_MOUSE_10090 and sp_P49743_RXRB_RAT_10116 are exactly identical! WARNING: Sequences sp_P43135_COT2_MOUSE_10090 and tr_A0A2I3HRX8_A0A2I3HRX8_NOMLE_61853 are exactly identical! WARNING: Sequences sp_P43135_COT2_MOUSE_10090 and tr_G3RXP9_G3RXP9_GORGO_9595 are exactly identical! WARNING: Sequences sp_P43135_COT2_MOUSE_10090 and tr_F1PX81_F1PX81_CANLF_9615 are exactly identical! WARNING: Sequences sp_P43135_COT2_MOUSE_10090 and tr_H2QA47_H2QA47_PANTR_9598 are exactly identical! WARNING: Sequences sp_P43135_COT2_MOUSE_10090 and sp_O09018_COT2_RAT_10116 are exactly identical! WARNING: Sequences sp_P43135_COT2_MOUSE_10090 and tr_I3N8M4_I3N8M4_ICTTR_43179 are exactly identical! WARNING: Sequences sp_P43135_COT2_MOUSE_10090 and tr_H0XPC9_H0XPC9_OTOGA_30611 are exactly identical! WARNING: Sequences sp_P43135_COT2_MOUSE_10090 and tr_A0A286XI75_A0A286XI75_CAVPO_10141 are exactly identical! WARNING: Sequences sp_P43135_COT2_MOUSE_10090 and sp_P24468_COT2_HUMAN_9606 are exactly identical! WARNING: Sequences sp_P43135_COT2_MOUSE_10090 and tr_G3TD61_G3TD61_LOXAF_9785 are exactly identical! WARNING: Sequences sp_P43135_COT2_MOUSE_10090 and tr_F1SCJ6_F1SCJ6_PIG_9823 are exactly identical! WARNING: Sequences sp_P43135_COT2_MOUSE_10090 and sp_Q9TTR7_COT2_BOVIN_9913 are exactly identical! WARNING: Sequences sp_P43135_COT2_MOUSE_10090 and tr_A0A2I3N666_A0A2I3N666_PAPAN_9555 are exactly identical! WARNING: Sequences sp_P43135_COT2_MOUSE_10090 and tr_A0A0D9RWN2_A0A0D9RWN2_CHLSB_60711 are exactly identical! WARNING: Sequences sp_P43135_COT2_MOUSE_10090 and tr_A0A1S2ZEU9_A0A1S2ZEU9_ERIEU_9365 are exactly identical! WARNING: Sequences sp_P43135_COT2_MOUSE_10090 and tr_A0A1S3ET11_A0A1S3ET11_DIPOR_10020 are exactly identical! WARNING: Sequences sp_P43135_COT2_MOUSE_10090 and tr_A0A1U7R1X2_A0A1U7R1X2_MESAU_10036 are exactly identical! WARNING: Sequences sp_P43135_COT2_MOUSE_10090 and tr_A0A2K5LN11_A0A2K5LN11_CERAT_9531 are exactly identical! WARNING: Sequences sp_P43135_COT2_MOUSE_10090 and tr_A0A2K6CL30_A0A2K6CL30_MACNE_9545 are exactly identical! WARNING: Sequences sp_P43135_COT2_MOUSE_10090 and tr_A0A2U3WBL5_A0A2U3WBL5_ODORO_9708 are exactly identical! WARNING: Sequences sp_P43135_COT2_MOUSE_10090 and tr_A0A2Y9DE54_A0A2Y9DE54_TRIMA_127582 are exactly identical! WARNING: Sequences sp_P43135_COT2_MOUSE_10090 and tr_A0A2Y9K0A8_A0A2Y9K0A8_ENHLU_391180 are exactly identical! WARNING: Sequences sp_P43135_COT2_MOUSE_10090 and tr_A0A2Y9QAH4_A0A2Y9QAH4_DELLE_9749 are exactly identical! WARNING: Sequences sp_P43135_COT2_MOUSE_10090 and tr_A0A2Y9S3G9_A0A2Y9S3G9_PHYCD_9755 are exactly identical! WARNING: Sequences sp_Q60632_COT1_MOUSE_10090 and tr_A0A2I3TGT9_A0A2I3TGT9_PANTR_9598 are exactly identical! WARNING: Sequences sp_Q60632_COT1_MOUSE_10090 and tr_F2Z3S9_F2Z3S9_RAT_10116 are exactly identical! WARNING: Sequences sp_Q60632_COT1_MOUSE_10090 and sp_P10589_COT1_HUMAN_9606 are exactly identical! WARNING: Sequences sp_Q60632_COT1_MOUSE_10090 and tr_A0A2R8M9U2_A0A2R8M9U2_CALJA_9483 are exactly identical! WARNING: Sequences sp_Q60632_COT1_MOUSE_10090 and tr_A0A287AV73_A0A287AV73_PIG_9823 are exactly identical! WARNING: Sequences sp_Q60632_COT1_MOUSE_10090 and sp_Q9TTR8_COT1_BOVIN_9913 are exactly identical! WARNING: Sequences sp_Q60632_COT1_MOUSE_10090 and tr_A0A337SRW0_A0A337SRW0_FELCA_9685 are exactly identical! WARNING: Sequences sp_Q60632_COT1_MOUSE_10090 and tr_A0A2I3LQB9_A0A2I3LQB9_PAPAN_9555 are exactly identical! WARNING: Sequences sp_Q60632_COT1_MOUSE_10090 and tr_A0A0D9RQ67_A0A0D9RQ67_CHLSB_60711 are exactly identical! WARNING: Sequences sp_Q60632_COT1_MOUSE_10090 and tr_A0A1S3AA55_A0A1S3AA55_ERIEU_9365 are exactly identical! WARNING: Sequences sp_Q60632_COT1_MOUSE_10090 and tr_A0A2K5P7P2_A0A2K5P7P2_CERAT_9531 are exactly identical! WARNING: Sequences sp_Q60632_COT1_MOUSE_10090 and tr_A0A2U3WYK9_A0A2U3WYK9_ODORO_9708 are exactly identical! WARNING: Sequences sp_Q60632_COT1_MOUSE_10090 and tr_A0A2Y9PNQ7_A0A2Y9PNQ7_DELLE_9749 are exactly identical! WARNING: Sequences sp_Q60632_COT1_MOUSE_10090 and tr_A0A2Y9SN18_A0A2Y9SN18_PHYCD_9755 are exactly identical! WARNING: Sequences tr_M3XT49_M3XT49_MUSPF_9669 and tr_A0A384CA25_A0A384CA25_URSMA_29073 are exactly identical! WARNING: Sequences tr_M3XXG4_M3XXG4_MUSPF_9669 and tr_G1LJ94_G1LJ94_AILME_9646 are exactly identical! WARNING: Sequences tr_M3XXG4_M3XXG4_MUSPF_9669 and tr_A0A2Y9JUH5_A0A2Y9JUH5_ENHLU_391180 are exactly identical! WARNING: Sequences tr_M3YEH4_M3YEH4_MUSPF_9669 and tr_F7AUI6_F7AUI6_HORSE_9796 are exactly identical! WARNING: Sequences tr_M3YEH4_M3YEH4_MUSPF_9669 and tr_A0A287DFI2_A0A287DFI2_ICTTR_43179 are exactly identical! WARNING: Sequences tr_M3YEH4_M3YEH4_MUSPF_9669 and tr_H0X5X6_H0X5X6_OTOGA_30611 are exactly identical! WARNING: Sequences tr_M3YEH4_M3YEH4_MUSPF_9669 and sp_Q9Y466_NR2E1_HUMAN_9606 are exactly identical! WARNING: Sequences tr_M3YEH4_M3YEH4_MUSPF_9669 and tr_G3TBK5_G3TBK5_LOXAF_9785 are exactly identical! WARNING: Sequences tr_M3YEH4_M3YEH4_MUSPF_9669 and tr_I3LU21_I3LU21_PIG_9823 are exactly identical! WARNING: Sequences tr_M3YEH4_M3YEH4_MUSPF_9669 and tr_A0A0D9RRH8_A0A0D9RRH8_CHLSB_60711 are exactly identical! WARNING: Sequences tr_M3YEH4_M3YEH4_MUSPF_9669 and tr_A0A2K6CE10_A0A2K6CE10_MACNE_9545 are exactly identical! WARNING: Sequences tr_M3YEH4_M3YEH4_MUSPF_9669 and tr_A0A2R9BUM6_A0A2R9BUM6_PANPA_9597 are exactly identical! WARNING: Sequences tr_M3YEH4_M3YEH4_MUSPF_9669 and tr_A0A2U3VRU3_A0A2U3VRU3_ODORO_9708 are exactly identical! WARNING: Sequences tr_M3YEH4_M3YEH4_MUSPF_9669 and tr_A0A2U3XDI7_A0A2U3XDI7_LEPWE_9713 are exactly identical! WARNING: Sequences tr_M3YEH4_M3YEH4_MUSPF_9669 and tr_A0A2Y9KX17_A0A2Y9KX17_ENHLU_391180 are exactly identical! WARNING: Sequences tr_M3YEH4_M3YEH4_MUSPF_9669 and tr_A0A2Y9FBE9_A0A2Y9FBE9_PHYCD_9755 are exactly identical! WARNING: Sequences tr_A0A3B3HFF6_A0A3B3HFF6_ORYLA_8090 and tr_I3K1B3_I3K1B3_ORENI_8128 are exactly identical! WARNING: Sequences tr_A0A3B3HFF6_A0A3B3HFF6_ORYLA_8090 and tr_G3P806_G3P806_GASAC_69293 are exactly identical! WARNING: Sequences tr_A0A3B3HFF6_A0A3B3HFF6_ORYLA_8090 and tr_A0A2U9BRU0_A0A2U9BRU0_SCOMX_52904 are exactly identical! WARNING: Sequences tr_H2M2X6_H2M2X6_ORYLA_8090 and tr_G3PIR5_G3PIR5_GASAC_69293 are exactly identical! WARNING: Sequences tr_G1R516_G1R516_NOMLE_61853 and tr_G3R2Y5_G3R2Y5_GORGO_9595 are exactly identical! WARNING: Sequences tr_G1R516_G1R516_NOMLE_61853 and tr_H2PL46_H2PL46_PONAB_9601 are exactly identical! WARNING: Sequences tr_G1R516_G1R516_NOMLE_61853 and tr_H2QSS5_H2QSS5_PANTR_9598 are exactly identical! WARNING: Sequences tr_G1R516_G1R516_NOMLE_61853 and tr_F6TN21_F6TN21_MACMU_9544 are exactly identical! WARNING: Sequences tr_G1R516_G1R516_NOMLE_61853 and tr_U3CF11_U3CF11_CALJA_9483 are exactly identical! WARNING: Sequences tr_G1R516_G1R516_NOMLE_61853 and tr_G7P2S1_G7P2S1_MACFA_9541 are exactly identical! WARNING: Sequences tr_G1R516_G1R516_NOMLE_61853 and tr_A0A2K5LC27_A0A2K5LC27_CERAT_9531 are exactly identical! WARNING: Sequences tr_G1R516_G1R516_NOMLE_61853 and tr_A0A2K6CBP5_A0A2K6CBP5_MACNE_9545 are exactly identical! WARNING: Sequences tr_G1R516_G1R516_NOMLE_61853 and tr_A0A2K5Y943_A0A2K5Y943_MANLE_9568 are exactly identical! WARNING: Sequences tr_G1R516_G1R516_NOMLE_61853 and tr_A0A2R9BXU1_A0A2R9BXU1_PANPA_9597 are exactly identical! WARNING: Sequences tr_G1PPF3_G1PPF3_MYOLU_59463 and tr_G1TH32_G1TH32_RABIT_9986 are exactly identical! WARNING: Sequences tr_G1PPF3_G1PPF3_MYOLU_59463 and tr_I3N272_I3N272_ICTTR_43179 are exactly identical! WARNING: Sequences tr_G1PPF3_G1PPF3_MYOLU_59463 and sp_P28702_RXRB_HUMAN_9606 are exactly identical! WARNING: Sequences tr_G1PPF3_G1PPF3_MYOLU_59463 and tr_L5L040_L5L040_PTEAL_9402 are exactly identical! WARNING: Sequences tr_G1PPF3_G1PPF3_MYOLU_59463 and tr_A0A096NHF9_A0A096NHF9_PAPAN_9555 are exactly identical! WARNING: Sequences tr_G1PPF3_G1PPF3_MYOLU_59463 and tr_A0A0D9RAX9_A0A0D9RAX9_CHLSB_60711 are exactly identical! WARNING: Sequences tr_G3GSD4_G3GSD4_CRIGR_10029 and tr_A0A2U4C7V2_A0A2U4C7V2_TURTR_9739 are exactly identical! WARNING: Sequences tr_G3IA21_G3IA21_CRIGR_10029 and tr_L5KL63_L5KL63_PTEAL_9402 are exactly identical! WARNING: Sequences tr_G3IDY0_G3IDY0_CRIGR_10029 and sp_Q05343_RXRA_RAT_10116 are exactly identical! WARNING: Sequences tr_G3IDY0_G3IDY0_CRIGR_10029 and tr_I3MWM6_I3MWM6_ICTTR_43179 are exactly identical! WARNING: Sequences tr_G3IDY0_G3IDY0_CRIGR_10029 and tr_A0A1S2ZM55_A0A1S2ZM55_ERIEU_9365 are exactly identical! WARNING: Sequences tr_G3IDY0_G3IDY0_CRIGR_10029 and tr_A0A1U7TEY7_A0A1U7TEY7_TARSY_1868482 are exactly identical! WARNING: Sequences tr_G3IDY0_G3IDY0_CRIGR_10029 and tr_A0A1U7RBT2_A0A1U7RBT2_MESAU_10036 are exactly identical! WARNING: Sequences tr_G3QP13_G3QP13_GORGO_9595 and tr_A0A2I3SFZ5_A0A2I3SFZ5_PANTR_9598 are exactly identical! WARNING: Sequences tr_G3QP13_G3QP13_GORGO_9595 and tr_A0A2R9CNL6_A0A2R9CNL6_PANPA_9597 are exactly identical! WARNING: Sequences tr_G3R3I4_G3R3I4_GORGO_9595 and tr_A0A2I3S7T8_A0A2I3S7T8_PANTR_9598 are exactly identical! WARNING: Sequences tr_G3S7Z4_G3S7Z4_GORGO_9595 and tr_A0A2I3SXI5_A0A2I3SXI5_PANTR_9598 are exactly identical! WARNING: Sequences tr_G3S7Z4_G3S7Z4_GORGO_9595 and sp_P48443_RXRG_HUMAN_9606 are exactly identical! WARNING: Sequences tr_G3S7Z4_G3S7Z4_GORGO_9595 and tr_A0A2R9AQF8_A0A2R9AQF8_PANPA_9597 are exactly identical! WARNING: Sequences sp_Q5REL6_RXRG_PONAB_9601 and tr_G1SP29_G1SP29_RABIT_9986 are exactly identical! WARNING: Sequences sp_Q5REL6_RXRG_PONAB_9601 and sp_Q0GFF6_RXRG_PIG_9823 are exactly identical! WARNING: Sequences sp_Q5REL6_RXRG_PONAB_9601 and tr_A0A096MW06_A0A096MW06_PAPAN_9555 are exactly identical! WARNING: Sequences sp_Q5REL6_RXRG_PONAB_9601 and tr_A0A0D9REB7_A0A0D9REB7_CHLSB_60711 are exactly identical! WARNING: Sequences sp_Q5REL6_RXRG_PONAB_9601 and tr_A0A1U7UAI0_A0A1U7UAI0_TARSY_1868482 are exactly identical! WARNING: Sequences sp_Q5REL6_RXRG_PONAB_9601 and tr_A0A2K5KI36_A0A2K5KI36_CERAT_9531 are exactly identical! WARNING: Sequences sp_Q5REL6_RXRG_PONAB_9601 and tr_A0A2K5XT39_A0A2K5XT39_MANLE_9568 are exactly identical! WARNING: Sequences sp_Q5REL6_RXRG_PONAB_9601 and tr_A0A2U3UZW3_A0A2U3UZW3_TURTR_9739 are exactly identical! WARNING: Sequences sp_Q5REL6_RXRG_PONAB_9601 and tr_A0A2Y9FR90_A0A2Y9FR90_PHYCD_9755 are exactly identical! WARNING: Sequences sp_Q5REL6_RXRG_PONAB_9601 and tr_A0A384AUR1_A0A384AUR1_BALAS_310752 are exactly identical! WARNING: Sequences tr_G1T5K1_G1T5K1_RABIT_9986 and tr_A0A1U7T9B9_A0A1U7T9B9_TARSY_1868482 are exactly identical! WARNING: Sequences tr_G1T5K1_G1T5K1_RABIT_9986 and tr_A0A2U3XHF6_A0A2U3XHF6_LEPWE_9713 are exactly identical! WARNING: Sequences tr_G1T5K1_G1T5K1_RABIT_9986 and tr_A0A384BUL0_A0A384BUL0_URSMA_29073 are exactly identical! WARNING: Sequences tr_G1T5K1_G1T5K1_RABIT_9986 and tr_A0A383YQR8_A0A383YQR8_BALAS_310752 are exactly identical! WARNING: Sequences tr_E2R3D0_E2R3D0_CANLF_9615 and tr_F1S962_F1S962_PIG_9823 are exactly identical! WARNING: Sequences tr_F1PUF6_F1PUF6_CANLF_9615 and tr_M3W6V1_M3W6V1_FELCA_9685 are exactly identical! WARNING: Sequences tr_F1PUF6_F1PUF6_CANLF_9615 and tr_A0A1U7TQ33_A0A1U7TQ33_TARSY_1868482 are exactly identical! WARNING: Sequences tr_H2R395_H2R395_PANTR_9598 and sp_P19793_RXRA_HUMAN_9606 are exactly identical! WARNING: Sequences tr_H2R395_H2R395_PANTR_9598 and tr_A0A2I3M8T5_A0A2I3M8T5_PAPAN_9555 are exactly identical! WARNING: Sequences tr_H2R395_H2R395_PANTR_9598 and tr_A0A2K5M5N8_A0A2K5M5N8_CERAT_9531 are exactly identical! WARNING: Sequences tr_H2R395_H2R395_PANTR_9598 and tr_A0A2K6BEY2_A0A2K6BEY2_MACNE_9545 are exactly identical! WARNING: Sequences tr_H2R395_H2R395_PANTR_9598 and tr_A0A2K5Y2K6_A0A2K5Y2K6_MANLE_9568 are exactly identical! WARNING: Sequences tr_H2R395_H2R395_PANTR_9598 and tr_A0A2R9CL53_A0A2R9CL53_PANPA_9597 are exactly identical! WARNING: Sequences tr_F6ZBP3_F6ZBP3_ORNAN_9258 and tr_F7AZG5_F7AZG5_MONDO_13616 are exactly identical! WARNING: Sequences tr_F6ZBP3_F6ZBP3_ORNAN_9258 and tr_G3WSM6_G3WSM6_SARHA_9305 are exactly identical! WARNING: Sequences tr_F6SHM9_F6SHM9_MONDO_13616 and tr_U3K355_U3K355_FICAL_59894 are exactly identical! WARNING: Sequences tr_F6V347_F6V347_HORSE_9796 and tr_G7P9I3_G7P9I3_MACFA_9541 are exactly identical! WARNING: Sequences tr_F6V347_F6V347_HORSE_9796 and tr_A0A2K5ZRB3_A0A2K5ZRB3_MANLE_9568 are exactly identical! WARNING: Sequences tr_W5PP44_W5PP44_SHEEP_9940 and sp_Q0VC20_RXRG_BOVIN_9913 are exactly identical! WARNING: Sequences tr_A0A3B5QAK7_A0A3B5QAK7_XIPMA_8083 and tr_A0A087YKJ2_A0A087YKJ2_POEFO_48698 are exactly identical! WARNING: Sequences tr_M4AG73_M4AG73_XIPMA_8083 and tr_A0A087XZF3_A0A087XZF3_POEFO_48698 are exactly identical! WARNING: Sequences tr_A0A158NB71_A0A158NB71_ATTCE_12957 and tr_A0A151ITL8_A0A151ITL8_9HYME_471704 are exactly identical! WARNING: Sequences tr_I3K5Q0_I3K5Q0_ORENI_8128 and tr_A0A087Y0Q4_A0A087Y0Q4_POEFO_48698 are exactly identical! WARNING: Sequences sp_P10588_NR2F6_HUMAN_9606 and tr_U3DJ91_U3DJ91_CALJA_9483 are exactly identical! WARNING: Sequences sp_P10588_NR2F6_HUMAN_9606 and tr_M3VVT5_M3VVT5_FELCA_9685 are exactly identical! WARNING: Sequences sp_P10588_NR2F6_HUMAN_9606 and tr_A0A0D9R023_A0A0D9R023_CHLSB_60711 are exactly identical! WARNING: Sequences tr_F6SBL7_F6SBL7_MACMU_9544 and tr_A0A096NML9_A0A096NML9_PAPAN_9555 are exactly identical! WARNING: Sequences tr_F6SBL7_F6SBL7_MACMU_9544 and tr_A0A2K6C6W8_A0A2K6C6W8_MACNE_9545 are exactly identical! WARNING: Sequences tr_F7HDB8_F7HDB8_MACMU_9544 and tr_G7NU27_G7NU27_MACFA_9541 are exactly identical! WARNING: Sequences tr_F7HDB8_F7HDB8_MACMU_9544 and tr_A0A2K6CSH7_A0A2K6CSH7_MACNE_9545 are exactly identical! WARNING: Sequences tr_G5AT97_G5AT97_HETGA_10181 and tr_A0A091CW78_A0A091CW78_FUKDA_885580 are exactly identical! WARNING: Sequences tr_K7FEV5_K7FEV5_PELSI_13735 and tr_A0A151MJX7_A0A151MJX7_ALLMI_8496 are exactly identical! WARNING: Sequences tr_H0Z247_H0Z247_TAEGU_59729 and tr_A0A218UYD4_A0A218UYD4_9PASE_299123 are exactly identical! WARNING: Sequences tr_H0Z605_H0Z605_TAEGU_59729 and tr_A0A091FAL0_A0A091FAL0_CORBR_85066 are exactly identical! WARNING: Sequences tr_H0Z605_H0Z605_TAEGU_59729 and tr_A0A093Q422_A0A093Q422_9PASS_328815 are exactly identical! WARNING: Sequences tr_H0ZE46_H0ZE46_TAEGU_59729 and tr_A0A091F445_A0A091F445_CORBR_85066 are exactly identical! WARNING: Sequences tr_H0ZE46_H0ZE46_TAEGU_59729 and tr_A0A091JMA1_A0A091JMA1_EGRGA_188379 are exactly identical! WARNING: Sequences tr_H0ZE46_H0ZE46_TAEGU_59729 and tr_A0A093PIU3_A0A093PIU3_9PASS_328815 are exactly identical! WARNING: Sequences tr_H0ZE46_H0ZE46_TAEGU_59729 and tr_A0A091VJA6_A0A091VJA6_NIPNI_128390 are exactly identical! WARNING: Sequences tr_H0ZE46_H0ZE46_TAEGU_59729 and tr_A0A087QWW8_A0A087QWW8_APTFO_9233 are exactly identical! WARNING: Sequences tr_H0ZE46_H0ZE46_TAEGU_59729 and tr_A0A093HYF6_A0A093HYF6_STRCA_441894 are exactly identical! WARNING: Sequences tr_H0ZE46_H0ZE46_TAEGU_59729 and tr_A0A091XIL6_A0A091XIL6_OPIHO_30419 are exactly identical! WARNING: Sequences tr_H0ZE46_H0ZE46_TAEGU_59729 and tr_A0A091GBD0_A0A091GBD0_9AVES_55661 are exactly identical! WARNING: Sequences tr_H0ZE46_H0ZE46_TAEGU_59729 and tr_A0A099ZXY6_A0A099ZXY6_CHAVO_50402 are exactly identical! WARNING: Sequences tr_H0ZE46_H0ZE46_TAEGU_59729 and tr_A0A093IHM3_A0A093IHM3_DRYPU_118200 are exactly identical! WARNING: Sequences tr_H0ZE46_H0ZE46_TAEGU_59729 and tr_A0A091IHZ4_A0A091IHZ4_CALAN_9244 are exactly identical! WARNING: Sequences tr_A5D9P3_A5D9P3_PIG_9823 and tr_A6H7I6_A6H7I6_BOVIN_9913 are exactly identical! WARNING: Sequences tr_B3RN76_B3RN76_TRIAD_10228 and tr_A0A369SD08_A0A369SD08_9METZ_287889 are exactly identical! WARNING: Sequences tr_A0A337SPZ3_A0A337SPZ3_FELCA_9685 and tr_A0A2U3ZRS6_A0A2U3ZRS6_ODORO_9708 are exactly identical! WARNING: Sequences tr_A0A337SPZ3_A0A337SPZ3_FELCA_9685 and tr_A0A2U3YXK0_A0A2U3YXK0_LEPWE_9713 are exactly identical! WARNING: Sequences tr_U3K704_U3K704_FICAL_59894 and tr_A0A0Q3PFI8_A0A0Q3PFI8_AMAAE_12930 are exactly identical! WARNING: Sequences tr_A0A151MFT6_A0A151MFT6_ALLMI_8496 and tr_A0A1U7SDP6_A0A1U7SDP6_ALLSI_38654 are exactly identical! WARNING: Sequences tr_A0A151NZY1_A0A151NZY1_ALLMI_8496 and tr_A0A1U7RM14_A0A1U7RM14_ALLSI_38654 are exactly identical! WARNING: Sequences tr_A0A091JE53_A0A091JE53_EGRGA_188379 and tr_A0A091UQP9_A0A091UQP9_NIPNI_128390 are exactly identical! WARNING: Sequences tr_A0A091JE53_A0A091JE53_EGRGA_188379 and tr_A0A087R4Q8_A0A087R4Q8_APTFO_9233 are exactly identical! WARNING: Sequences tr_A0A091JE53_A0A091JE53_EGRGA_188379 and tr_A0A093H9R3_A0A093H9R3_STRCA_441894 are exactly identical! WARNING: Sequences tr_A0A091JE53_A0A091JE53_EGRGA_188379 and tr_A0A091V921_A0A091V921_OPIHO_30419 are exactly identical! WARNING: Sequences tr_A0A091JE53_A0A091JE53_EGRGA_188379 and tr_A0A2I0M3Q9_A0A2I0M3Q9_COLLI_8932 are exactly identical! WARNING: Sequences tr_A0A091JE53_A0A091JE53_EGRGA_188379 and tr_A0A091I5Q5_A0A091I5Q5_CALAN_9244 are exactly identical! WARNING: Sequences tr_A0A091JE53_A0A091JE53_EGRGA_188379 and tr_A0A1V4J7B0_A0A1V4J7B0_PATFA_372326 are exactly identical! WARNING: Sequences tr_A0A091JE53_A0A091JE53_EGRGA_188379 and tr_A0A226NNV0_A0A226NNV0_CALSU_9009 are exactly identical! WARNING: Sequences tr_A0A091JE53_A0A091JE53_EGRGA_188379 and tr_A0A226P8I1_A0A226P8I1_COLVI_9014 are exactly identical! WARNING: Sequences tr_A0A0V1CFD7_A0A0V1CFD7_TRIBR_45882 and tr_A0A0V0VJD4_A0A0V0VJD4_9BILA_181606 are exactly identical! WARNING: Sequences tr_A0A0V1CFD7_A0A0V1CFD7_TRIBR_45882 and tr_A0A0V0ZZR4_A0A0V0ZZR4_9BILA_990121 are exactly identical! WARNING: Sequences tr_A0A0V1CFD7_A0A0V1CFD7_TRIBR_45882 and tr_A0A0V0TI79_A0A0V0TI79_9BILA_144512 are exactly identical! WARNING: Sequences tr_A0A1S3FM97_A0A1S3FM97_DIPOR_10020 and tr_A0A2Y9DHY7_A0A2Y9DHY7_TRIMA_127582 are exactly identical! WARNING: Sequences tr_A0A1S3MGS7_A0A1S3MGS7_SALSA_8030 and tr_A0A060X563_A0A060X563_ONCMY_8022 are exactly identical! WARNING: Sequences tr_A0A1S3PYL1_A0A1S3PYL1_SALSA_8030 and tr_A0A060WZU0_A0A060WZU0_ONCMY_8022 are exactly identical! WARNING: Sequences tr_A0A1S3S9G7_A0A1S3S9G7_SALSA_8030 and tr_A0A060XPC6_A0A060XPC6_ONCMY_8022 are exactly identical! WARNING: Sequences tr_A0A226MWG0_A0A226MWG0_CALSU_9009 and tr_A0A226PPE0_A0A226PPE0_COLVI_9014 are exactly identical! WARNING: Sequences tr_A0A2D0PY04_A0A2D0PY04_ICTPU_7998 and tr_A0A2D0PZA2_A0A2D0PZA2_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0QWS9_A0A2D0QWS9_ICTPU_7998 and tr_A0A2D0QXH6_A0A2D0QXH6_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0S1W1_A0A2D0S1W1_ICTPU_7998 and tr_A0A2D0S1X8_A0A2D0S1X8_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0S1W1_A0A2D0S1W1_ICTPU_7998 and tr_A0A2D0S2S1_A0A2D0S2S1_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0S1W1_A0A2D0S1W1_ICTPU_7998 and tr_A0A2D0S3F2_A0A2D0S3F2_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0T0F2_A0A2D0T0F2_ICTPU_7998 and tr_A0A2D0T0F7_A0A2D0T0F7_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0T0F2_A0A2D0T0F2_ICTPU_7998 and tr_A0A2D0T0F9_A0A2D0T0F9_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0T0F2_A0A2D0T0F2_ICTPU_7998 and tr_A0A2D0T0G0_A0A2D0T0G0_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0T0F2_A0A2D0T0F2_ICTPU_7998 and tr_A0A2D0T0G3_A0A2D0T0G3_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0T0F2_A0A2D0T0F2_ICTPU_7998 and tr_A0A2D0T0G4_A0A2D0T0G4_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0T0F2_A0A2D0T0F2_ICTPU_7998 and tr_A0A2D0T0U4_A0A2D0T0U4_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0T0F2_A0A2D0T0F2_ICTPU_7998 and tr_A0A2D0T0V0_A0A2D0T0V0_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0T0F2_A0A2D0T0F2_ICTPU_7998 and tr_A0A2D0T1D2_A0A2D0T1D2_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0T0F2_A0A2D0T0F2_ICTPU_7998 and tr_A0A2D0T1D8_A0A2D0T1D8_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2K5LVL8_A0A2K5LVL8_CERAT_9531 and tr_A0A2K6D3X3_A0A2K6D3X3_MACNE_9545 are exactly identical! WARNING: Sequences tr_A0A2K5NF86_A0A2K5NF86_CERAT_9531 and tr_A0A2K6A7F8_A0A2K6A7F8_MANLE_9568 are exactly identical! WARNING: Sequences tr_A0A2U3Y320_A0A2U3Y320_LEPWE_9713 and tr_A0A2Y9K9Z1_A0A2Y9K9Z1_ENHLU_391180 are exactly identical! WARNING: Sequences tr_A0A2Y9G3W5_A0A2Y9G3W5_TRIMA_127582 and tr_A0A2Y9P552_A0A2Y9P552_DELLE_9749 are exactly identical! WARNING: Sequences tr_A0A2Y9G3W5_A0A2Y9G3W5_TRIMA_127582 and tr_A0A2Y9ETG3_A0A2Y9ETG3_PHYCD_9755 are exactly identical! WARNING: Sequences tr_A0A2Y9G3W5_A0A2Y9G3W5_TRIMA_127582 and tr_A0A384AIB7_A0A384AIB7_BALAS_310752 are exactly identical! WARNING: Sequences tr_A0A2Y9J2P6_A0A2Y9J2P6_ENHLU_391180 and tr_A0A2Y9TL48_A0A2Y9TL48_PHYCD_9755 are exactly identical! WARNING: Sequences tr_A0A2Y9NM79_A0A2Y9NM79_DELLE_9749 and tr_A0A2Y9EZW5_A0A2Y9EZW5_PHYCD_9755 are exactly identical! WARNING: Duplicate sequences found: 202 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/P24468/3_mltree/P24468.raxml.reduced.phy Alignment comprises 1 partitions and 341 patterns Partition 0: noname Model: LG4X+R4 Alignment sites / patterns: 341 / 341 Gaps: 8.63 % Invariant sites: 0.00 % NOTE: Binary MSA file created: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/P24468/3_mltree/P24468.raxml.rba Parallelization scheme autoconfig: 5 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 / 341 / 27280 [00:00:00] Data distribution: max. searches per worker: 4 Starting ML tree search with 20 distinct starting trees [00:00:00 -452302.460208] Initial branch length optimization [00:00:07 -354944.055678] Model parameter optimization (eps = 10.000000) [00:01:17 -354050.996391] AUTODETECT spr round 1 (radius: 5) [00:05:48 -198948.469215] AUTODETECT spr round 2 (radius: 10) [00:10:11 -133589.200423] AUTODETECT spr round 3 (radius: 15) [00:15:07 -103362.251018] AUTODETECT spr round 4 (radius: 20) [00:20:14 -96322.101366] AUTODETECT spr round 5 (radius: 25) [00:27:55 -85662.949907] SPR radius for FAST iterations: 25 (autodetect) [00:27:55 -85662.949907] Model parameter optimization (eps = 3.000000) [00:28:35 -85543.393302] FAST spr round 1 (radius: 25) [00:33:47 -72366.274409] FAST spr round 2 (radius: 25) [00:37:26 -71576.116030] FAST spr round 3 (radius: 25) [00:40:35 -71505.144512] FAST spr round 4 (radius: 25) [00:43:31 -71486.991442] FAST spr round 5 (radius: 25) [00:46:07 -71484.753372] FAST spr round 6 (radius: 25) [00:48:37 -71484.753344] Model parameter optimization (eps = 1.000000) [00:49:08 -71459.606126] SLOW spr round 1 (radius: 5) [00:52:26 -71446.089361] SLOW spr round 2 (radius: 5) [00:55:50 -71445.585891] SLOW spr round 3 (radius: 5) [00:59:15 -71445.584727] SLOW spr round 4 (radius: 10) [01:02:53 -71445.584524] SLOW spr round 5 (radius: 15) [01:08:20 -71444.420189] SLOW spr round 6 (radius: 5) [01:12:41 -71439.758721] SLOW spr round 7 (radius: 5) [01:16:50 -71439.224555] SLOW spr round 8 (radius: 5) [01:20:33 -71439.224182] SLOW spr round 9 (radius: 10) [01:24:12 -71439.224109] SLOW spr round 10 (radius: 15) [01:29:36 -71439.224081] SLOW spr round 11 (radius: 20) [01:37:58 -71439.224074] SLOW spr round 12 (radius: 25) [01:48:33 -71439.069477] SLOW spr round 13 (radius: 5) [01:51:20] [worker #1] ML tree search #2, logLikelihood: -71443.316195 [01:53:15 -71439.068879] SLOW spr round 14 (radius: 10) [01:57:41 -71439.068837] SLOW spr round 15 (radius: 15) [02:02:52 -71439.068823] SLOW spr round 16 (radius: 20) [02:11:06 -71439.068819] SLOW spr round 17 (radius: 25) [02:16:30] [worker #3] ML tree search #4, logLikelihood: -71449.952436 [02:17:27] [worker #2] ML tree search #3, logLikelihood: -71423.413750 [02:21:24 -71439.068815] Model parameter optimization (eps = 0.100000) [02:21:35] [worker #0] ML tree search #1, logLikelihood: -71439.021955 [02:21:35 -457619.068402] Initial branch length optimization [02:21:43 -361414.056863] Model parameter optimization (eps = 10.000000) [02:22:53 -360397.954227] AUTODETECT spr round 1 (radius: 5) [02:26:05] [worker #4] ML tree search #5, logLikelihood: -71435.016057 [02:27:24 -199054.869618] AUTODETECT spr round 2 (radius: 10) [02:31:47 -139254.239423] AUTODETECT spr round 3 (radius: 15) [02:36:25 -116796.949283] AUTODETECT spr round 4 (radius: 20) [02:41:56 -99946.387118] AUTODETECT spr round 5 (radius: 25) [02:47:19 -90627.428100] SPR radius for FAST iterations: 25 (autodetect) [02:47:19 -90627.428100] Model parameter optimization (eps = 3.000000) [02:47:56 -90501.842393] FAST spr round 1 (radius: 25) [02:53:08 -73171.002335] FAST spr round 2 (radius: 25) [02:57:05 -71746.533048] FAST spr round 3 (radius: 25) [03:00:30 -71631.560859] FAST spr round 4 (radius: 25) [03:03:39 -71526.816963] FAST spr round 5 (radius: 25) [03:06:28 -71514.333628] FAST spr round 6 (radius: 25) [03:09:12 -71511.373648] FAST spr round 7 (radius: 25) [03:11:50 -71511.373251] Model parameter optimization (eps = 1.000000) [03:12:23 -71488.604585] SLOW spr round 1 (radius: 5) [03:15:47 -71466.681826] SLOW spr round 2 (radius: 5) [03:19:17 -71461.196537] SLOW spr round 3 (radius: 5) [03:22:48 -71461.194962] SLOW spr round 4 (radius: 10) [03:26:38 -71455.910836] SLOW spr round 5 (radius: 5) [03:31:04 -71455.909252] SLOW spr round 6 (radius: 10) [03:35:10 -71454.164499] SLOW spr round 7 (radius: 5) [03:38:42] [worker #1] ML tree search #7, logLikelihood: -71473.028569 [03:39:32 -71447.047084] SLOW spr round 8 (radius: 5) [03:43:20 -71447.046102] SLOW spr round 9 (radius: 10) [03:47:03 -71447.045858] SLOW spr round 10 (radius: 15) [03:52:27 -71446.844418] SLOW spr round 11 (radius: 5) [03:54:02] [worker #3] ML tree search #9, logLikelihood: -71429.711851 [03:57:02 -71446.843923] SLOW spr round 12 (radius: 10) [04:01:19 -71446.843598] SLOW spr round 13 (radius: 15) [04:06:33 -71446.843428] SLOW spr round 14 (radius: 20) [04:15:01 -71446.843255] SLOW spr round 15 (radius: 25) [04:26:41 -71443.350089] SLOW spr round 16 (radius: 5) [04:27:42] [worker #2] ML tree search #8, logLikelihood: -71438.886397 [04:31:19 -71443.348574] SLOW spr round 17 (radius: 10) [04:35:43 -71443.348224] SLOW spr round 18 (radius: 15) [04:37:41] [worker #4] ML tree search #10, logLikelihood: -71428.684478 [04:40:57 -71443.348034] SLOW spr round 19 (radius: 20) [04:49:18 -71443.347844] SLOW spr round 20 (radius: 25) [05:00:48 -71443.347648] Model parameter optimization (eps = 0.100000) [05:01:09] [worker #0] ML tree search #6, logLikelihood: -71442.856523 [05:01:09 -458402.190726] Initial branch length optimization [05:01:17 -363516.408121] Model parameter optimization (eps = 10.000000) [05:02:33 -362424.313039] AUTODETECT spr round 1 (radius: 5) [05:07:01 -199147.633993] AUTODETECT spr round 2 (radius: 10) [05:11:29 -127961.630662] AUTODETECT spr round 3 (radius: 15) [05:16:25 -97966.192848] AUTODETECT spr round 4 (radius: 20) [05:19:40] [worker #1] ML tree search #12, logLikelihood: -72152.462899 [05:21:43 -88662.754863] AUTODETECT spr round 5 (radius: 25) [05:29:31 -84035.225168] SPR radius for FAST iterations: 25 (autodetect) [05:29:31 -84035.225168] Model parameter optimization (eps = 3.000000) [05:30:02 -83885.343097] FAST spr round 1 (radius: 25) [05:35:05 -72285.963175] FAST spr round 2 (radius: 25) [05:38:47 -71582.865698] FAST spr round 3 (radius: 25) [05:41:56 -71523.970482] FAST spr round 4 (radius: 25) [05:44:40 -71491.575360] FAST spr round 5 (radius: 25) [05:47:06 -71490.581899] FAST spr round 6 (radius: 25) [05:49:26 -71490.581720] Model parameter optimization (eps = 1.000000) [05:49:52 -71473.249589] SLOW spr round 1 (radius: 5) [05:53:01 -71456.924557] SLOW spr round 2 (radius: 5) [05:56:14 -71453.559688] SLOW spr round 3 (radius: 5) [05:59:26 -71453.553387] SLOW spr round 4 (radius: 10) [06:02:53 -71453.220830] SLOW spr round 5 (radius: 5) [06:06:56 -71453.219934] SLOW spr round 6 (radius: 10) [06:10:37 -71452.064377] SLOW spr round 7 (radius: 5) [06:14:33 -71452.064178] SLOW spr round 8 (radius: 10) [06:18:12 -71452.064138] SLOW spr round 9 (radius: 15) [06:18:40] [worker #3] ML tree search #14, logLikelihood: -71422.644445 [06:23:09 -71452.064130] SLOW spr round 10 (radius: 20) [06:30:42 -71452.064122] SLOW spr round 11 (radius: 25) [06:39:03] [worker #2] ML tree search #13, logLikelihood: -71478.634489 [06:40:11 -71452.064119] Model parameter optimization (eps = 0.100000) [06:40:18] [worker #0] ML tree search #11, logLikelihood: -71452.034864 [06:40:18 -457089.036356] Initial branch length optimization [06:40:25 -360790.891031] Model parameter optimization (eps = 10.000000) [06:41:20 -359832.947647] AUTODETECT spr round 1 (radius: 5) [06:45:42 -199943.493049] AUTODETECT spr round 2 (radius: 10) [06:49:50 -135285.358996] AUTODETECT spr round 3 (radius: 15) [06:54:21 -103214.497759] AUTODETECT spr round 4 (radius: 20) [06:58:00] [worker #4] ML tree search #15, logLikelihood: -71433.130149 [06:59:46 -91919.279879] AUTODETECT spr round 5 (radius: 25) [07:07:03 -82777.596262] SPR radius for FAST iterations: 25 (autodetect) [07:07:03 -82777.596262] Model parameter optimization (eps = 3.000000) [07:07:27 -82685.192988] FAST spr round 1 (radius: 25) [07:11:34 -72113.440740] FAST spr round 2 (radius: 25) [07:14:42 -71620.466937] FAST spr round 3 (radius: 25) [07:17:18 -71548.729972] FAST spr round 4 (radius: 25) [07:19:42 -71530.292824] FAST spr round 5 (radius: 25) [07:22:00 -71529.978799] FAST spr round 6 (radius: 25) [07:24:12 -71529.978492] Model parameter optimization (eps = 1.000000) [07:24:35 -71510.748676] SLOW spr round 1 (radius: 5) [07:27:26 -71483.206964] SLOW spr round 2 (radius: 5) [07:30:53 -71476.723003] SLOW spr round 3 (radius: 5) [07:34:17 -71476.247759] SLOW spr round 4 (radius: 5) [07:37:37 -71476.247539] SLOW spr round 5 (radius: 10) [07:41:16 -71474.787672] SLOW spr round 6 (radius: 5) [07:45:27 -71473.463887] SLOW spr round 7 (radius: 5) [07:49:05 -71473.463870] SLOW spr round 8 (radius: 10) [07:52:36 -71473.463857] SLOW spr round 9 (radius: 15) [07:56:39] [worker #1] ML tree search #17, logLikelihood: -71419.666916 [07:57:24 -71473.463843] SLOW spr round 10 (radius: 20) [08:04:36 -71473.463841] SLOW spr round 11 (radius: 25) [08:14:02 -71472.613467] SLOW spr round 12 (radius: 5) [08:18:25 -71472.613157] SLOW spr round 13 (radius: 10) [08:22:35 -71472.613137] SLOW spr round 14 (radius: 15) [08:27:15 -71472.613134] SLOW spr round 15 (radius: 20) [08:34:26 -71472.613131] SLOW spr round 16 (radius: 25) [08:43:45 -71472.613129] Model parameter optimization (eps = 0.100000) [08:44:05] [worker #0] ML tree search #16, logLikelihood: -71471.958820 [08:52:20] [worker #2] ML tree search #18, logLikelihood: -71441.172110 [08:57:13] [worker #3] ML tree search #19, logLikelihood: -71427.970564 [09:11:16] [worker #4] ML tree search #20, logLikelihood: -71451.406833 Optimized model parameters: Partition 0: noname Rate heterogeneity: FREE (4 cats, mean), weights&rates: (0.262855,0.484821) (0.214230,0.471355) (0.343113,0.918306) (0.179802,2.538916) 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: -71419.666916 AIC score: 146849.333833 / AICc score: 8190909.333833 / BIC score: 154532.258200 Free parameters (model + branch lengths): 2005 WARNING: Number of free parameters (K=2005) is larger than alignment size (n=341). 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/P24468/3_mltree/P24468.raxml.bestTreeCollapsed Best ML tree saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/P24468/3_mltree/P24468.raxml.bestTree All ML trees saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/P24468/3_mltree/P24468.raxml.mlTrees Optimized model saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/P24468/3_mltree/P24468.raxml.bestModel Execution log saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/P24468/3_mltree/P24468.raxml.log Analysis started: 04-Jul-2021 12:14:08 / finished: 04-Jul-2021 21:25:24 Elapsed time: 33076.325 seconds Consumed energy: 3182.569 Wh (= 16 km in an electric car, or 80 km with an e-scooter!)