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 6140 CPU @ 2.30GHz, 36 cores, 251 GB RAM RAxML-NG was called at 18-Jun-2021 00:06:03 as follows: raxml-ng --msa /cta/users/eakkoyun/WORKFOLDER/PROD/run_040621/phylogeny-snakemake/results/Q96L73/2_msa/Q96L73_trimmed_msa.fasta --data-type AA --model LG4X --prefix /cta/users/eakkoyun/WORKFOLDER/PROD/run_040621/phylogeny-snakemake/results/Q96L73/3_mltree/Q96L73 --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: /cta/users/eakkoyun/WORKFOLDER/PROD/run_040621/phylogeny-snakemake/results/Q96L73/2_msa/Q96L73_trimmed_msa.fasta [00:00:00] Loaded alignment with 988 taxa and 252 sites WARNING: Sequences tr_A0A1D5PLB7_A0A1D5PLB7_CHICK_9031 and tr_G1MT77_G1MT77_MELGA_9103 are exactly identical! WARNING: Sequences tr_A0A1D5PLB7_A0A1D5PLB7_CHICK_9031 and tr_U3J251_U3J251_ANAPL_8839 are exactly identical! WARNING: Sequences tr_F1N972_F1N972_CHICK_9031 and tr_G1MYL5_G1MYL5_MELGA_9103 are exactly identical! WARNING: Sequences tr_F1N972_F1N972_CHICK_9031 and tr_U3I5W4_U3I5W4_ANAPL_8839 are exactly identical! WARNING: Sequences tr_F1N972_F1N972_CHICK_9031 and tr_A0A226PNP1_A0A226PNP1_COLVI_9014 are exactly identical! WARNING: Sequences tr_H9L0M3_H9L0M3_CHICK_9031 and tr_G1MQF3_G1MQF3_MELGA_9103 are exactly identical! WARNING: Sequences tr_M3YHZ0_M3YHZ0_MUSPF_9669 and tr_A0A2U3VML0_A0A2U3VML0_ODORO_9708 are exactly identical! WARNING: Sequences tr_M3YHZ0_M3YHZ0_MUSPF_9669 and tr_A0A2U3XYR8_A0A2U3XYR8_LEPWE_9713 are exactly identical! WARNING: Sequences tr_M3YHZ0_M3YHZ0_MUSPF_9669 and tr_A0A2Y9JLW3_A0A2Y9JLW3_ENHLU_391180 are exactly identical! WARNING: Sequences tr_M3YLH1_M3YLH1_MUSPF_9669 and tr_E2R3Q9_E2R3Q9_CANLF_9615 are exactly identical! WARNING: Sequences tr_M3YLH1_M3YLH1_MUSPF_9669 and tr_F7BGP4_F7BGP4_HORSE_9796 are exactly identical! WARNING: Sequences tr_M3YLH1_M3YLH1_MUSPF_9669 and tr_G1MIP9_G1MIP9_AILME_9646 are exactly identical! WARNING: Sequences tr_M3YLH1_M3YLH1_MUSPF_9669 and tr_M3VWU0_M3VWU0_FELCA_9685 are exactly identical! WARNING: Sequences tr_M3YLH1_M3YLH1_MUSPF_9669 and tr_A0A2U4BY81_A0A2U4BY81_TURTR_9739 are exactly identical! WARNING: Sequences tr_M3YLH1_M3YLH1_MUSPF_9669 and tr_A0A2U3W0P2_A0A2U3W0P2_ODORO_9708 are exactly identical! WARNING: Sequences tr_M3YLH1_M3YLH1_MUSPF_9669 and tr_A0A2Y9IMU0_A0A2Y9IMU0_ENHLU_391180 are exactly identical! WARNING: Sequences tr_M3YLH1_M3YLH1_MUSPF_9669 and tr_A0A2Y9MCX8_A0A2Y9MCX8_DELLE_9749 are exactly identical! WARNING: Sequences tr_M3YLH1_M3YLH1_MUSPF_9669 and tr_A0A2Y9S0F7_A0A2Y9S0F7_PHYCD_9755 are exactly identical! WARNING: Sequences tr_M3YLH1_M3YLH1_MUSPF_9669 and tr_A0A384C837_A0A384C837_URSMA_29073 are exactly identical! WARNING: Sequences tr_M3YLH1_M3YLH1_MUSPF_9669 and tr_A0A383Z435_A0A383Z435_BALAS_310752 are exactly identical! WARNING: Sequences tr_G1P8A1_G1P8A1_MYOLU_59463 and tr_L5JUK2_L5JUK2_PTEAL_9402 are exactly identical! WARNING: Sequences tr_G1PMX3_G1PMX3_MYOLU_59463 and tr_A0A2Y9RZF0_A0A2Y9RZF0_PHYCD_9755 are exactly identical! WARNING: Sequences tr_G3H180_G3H180_CRIGR_10029 and tr_D4AA06_D4AA06_RAT_10116 are exactly identical! WARNING: Sequences tr_G3H180_G3H180_CRIGR_10029 and tr_A0A1U8CGH1_A0A1U8CGH1_MESAU_10036 are exactly identical! WARNING: Sequences tr_G3HK75_G3HK75_CRIGR_10029 and tr_A0A1U8BP37_A0A1U8BP37_MESAU_10036 are exactly identical! WARNING: Sequences tr_G3HKR8_G3HKR8_CRIGR_10029 and tr_G1SIF6_G1SIF6_RABIT_9986 are exactly identical! WARNING: Sequences tr_G3HKR8_G3HKR8_CRIGR_10029 and tr_E2RMP9_E2RMP9_CANLF_9615 are exactly identical! WARNING: Sequences tr_G3HKR8_G3HKR8_CRIGR_10029 and tr_F6YTP3_F6YTP3_HORSE_9796 are exactly identical! WARNING: Sequences tr_G3HKR8_G3HKR8_CRIGR_10029 and tr_A0A0G2KB10_A0A0G2KB10_RAT_10116 are exactly identical! WARNING: Sequences tr_G3HKR8_G3HKR8_CRIGR_10029 and tr_G1M2A2_G1M2A2_AILME_9646 are exactly identical! WARNING: Sequences tr_G3HKR8_G3HKR8_CRIGR_10029 and tr_F1MDT8_F1MDT8_BOVIN_9913 are exactly identical! WARNING: Sequences tr_G3HKR8_G3HKR8_CRIGR_10029 and tr_L5KES2_L5KES2_PTEAL_9402 are exactly identical! WARNING: Sequences tr_G3HKR8_G3HKR8_CRIGR_10029 and tr_A0A2Y9N461_A0A2Y9N461_DELLE_9749 are exactly identical! WARNING: Sequences tr_G3HKR8_G3HKR8_CRIGR_10029 and tr_A0A384D5W9_A0A384D5W9_URSMA_29073 are exactly identical! WARNING: Sequences tr_G3HKR8_G3HKR8_CRIGR_10029 and tr_A0A383Z179_A0A383Z179_BALAS_310752 are exactly identical! WARNING: Sequences sp_Q1DU03_SET2_COCIM_246410 and tr_A0A0J6Y3S6_A0A0J6Y3S6_COCIT_404692 are exactly identical! WARNING: Sequences tr_A0A2I2Z1X0_A0A2I2Z1X0_GORGO_9595 and tr_H2PAW9_H2PAW9_PONAB_9601 are exactly identical! WARNING: Sequences tr_A0A2I2Z1X0_A0A2I2Z1X0_GORGO_9595 and tr_K7D2K6_K7D2K6_PANTR_9598 are exactly identical! WARNING: Sequences tr_A0A2I2Z1X0_A0A2I2Z1X0_GORGO_9595 and sp_Q9BYW2_SETD2_HUMAN_9606 are exactly identical! WARNING: Sequences tr_A0A2I2Z1X0_A0A2I2Z1X0_GORGO_9595 and tr_F7HU62_F7HU62_MACMU_9544 are exactly identical! WARNING: Sequences tr_A0A2I2Z1X0_A0A2I2Z1X0_GORGO_9595 and tr_F6YPZ8_F6YPZ8_CALJA_9483 are exactly identical! WARNING: Sequences tr_A0A2I2Z1X0_A0A2I2Z1X0_GORGO_9595 and tr_A0A096MU20_A0A096MU20_PAPAN_9555 are exactly identical! WARNING: Sequences tr_A0A2I2Z1X0_A0A2I2Z1X0_GORGO_9595 and tr_A0A0D9RUB5_A0A0D9RUB5_CHLSB_60711 are exactly identical! WARNING: Sequences tr_A0A2I2Z1X0_A0A2I2Z1X0_GORGO_9595 and tr_A0A2K5NXJ5_A0A2K5NXJ5_CERAT_9531 are exactly identical! WARNING: Sequences tr_A0A2I2Z1X0_A0A2I2Z1X0_GORGO_9595 and tr_A0A2R8ZXQ2_A0A2R8ZXQ2_PANPA_9597 are exactly identical! WARNING: Sequences tr_G3RE37_G3RE37_GORGO_9595 and tr_H2PCP9_H2PCP9_PONAB_9601 are exactly identical! WARNING: Sequences tr_G3RE37_G3RE37_GORGO_9595 and tr_H2QP41_H2QP41_PANTR_9598 are exactly identical! WARNING: Sequences tr_G3RE37_G3RE37_GORGO_9595 and sp_O96028_NSD2_HUMAN_9606 are exactly identical! WARNING: Sequences tr_G3RE37_G3RE37_GORGO_9595 and tr_I0FUW4_I0FUW4_MACMU_9544 are exactly identical! WARNING: Sequences tr_G3RE37_G3RE37_GORGO_9595 and tr_G7NWN9_G7NWN9_MACFA_9541 are exactly identical! WARNING: Sequences tr_G3RE37_G3RE37_GORGO_9595 and tr_A0A0D9RT07_A0A0D9RT07_CHLSB_60711 are exactly identical! WARNING: Sequences tr_G3RE37_G3RE37_GORGO_9595 and tr_A0A2K6BMC0_A0A2K6BMC0_MACNE_9545 are exactly identical! WARNING: Sequences tr_G3RE37_G3RE37_GORGO_9595 and tr_A0A2R9A256_A0A2R9A256_PANPA_9597 are exactly identical! WARNING: Sequences tr_G3SHI3_G3SHI3_GORGO_9595 and tr_H2PQ33_H2PQ33_PONAB_9601 are exactly identical! WARNING: Sequences tr_G3SHI3_G3SHI3_GORGO_9595 and tr_H2R3Q8_H2R3Q8_PANTR_9598 are exactly identical! WARNING: Sequences tr_G3SHI3_G3SHI3_GORGO_9595 and sp_Q9BZ95_NSD3_HUMAN_9606 are exactly identical! WARNING: Sequences tr_G3SHI3_G3SHI3_GORGO_9595 and tr_H9FW89_H9FW89_MACMU_9544 are exactly identical! WARNING: Sequences tr_G3SHI3_G3SHI3_GORGO_9595 and tr_F6YM48_F6YM48_CALJA_9483 are exactly identical! WARNING: Sequences tr_G3SHI3_G3SHI3_GORGO_9595 and tr_A0A096NGC0_A0A096NGC0_PAPAN_9555 are exactly identical! WARNING: Sequences tr_G3SHI3_G3SHI3_GORGO_9595 and tr_A0A0D9RSC6_A0A0D9RSC6_CHLSB_60711 are exactly identical! WARNING: Sequences tr_G3SHI3_G3SHI3_GORGO_9595 and tr_A0A2K5MBR0_A0A2K5MBR0_CERAT_9531 are exactly identical! WARNING: Sequences tr_G3SHI3_G3SHI3_GORGO_9595 and tr_A0A2K6CB53_A0A2K6CB53_MACNE_9545 are exactly identical! WARNING: Sequences tr_G3SHI3_G3SHI3_GORGO_9595 and tr_A0A2K5Y301_A0A2K5Y301_MANLE_9568 are exactly identical! WARNING: Sequences tr_G3SHI3_G3SHI3_GORGO_9595 and tr_A0A2R8ZBN9_A0A2R8ZBN9_PANPA_9597 are exactly identical! WARNING: Sequences tr_B8NSI5_B8NSI5_ASPFN_332952 and sp_Q2UTN6_SET2_ASPOR_510516 are exactly identical! WARNING: Sequences tr_B8NSI5_B8NSI5_ASPFN_332952 and tr_A0A1S9D4G5_A0A1S9D4G5_ASPOZ_5062 are exactly identical! WARNING: Sequences tr_A0A179UZB4_A0A179UZB4_BLAGS_559298 and tr_C5GXS6_C5GXS6_AJEDR_559297 are exactly identical! WARNING: Sequences tr_A0A2I3S9S5_A0A2I3S9S5_PANTR_9598 and sp_Q96L73_NSD1_HUMAN_9606 are exactly identical! WARNING: Sequences tr_A0A2I3S9S5_A0A2I3S9S5_PANTR_9598 and tr_F7FC92_F7FC92_MACMU_9544 are exactly identical! WARNING: Sequences tr_A0A2I3S9S5_A0A2I3S9S5_PANTR_9598 and tr_G7P6Z9_G7P6Z9_MACFA_9541 are exactly identical! WARNING: Sequences tr_A0A2I3S9S5_A0A2I3S9S5_PANTR_9598 and tr_A0A2I3MDD2_A0A2I3MDD2_PAPAN_9555 are exactly identical! WARNING: Sequences tr_A0A2I3S9S5_A0A2I3S9S5_PANTR_9598 and tr_A0A0D9R996_A0A0D9R996_CHLSB_60711 are exactly identical! WARNING: Sequences tr_A0A2I3S9S5_A0A2I3S9S5_PANTR_9598 and tr_A0A2K5NE00_A0A2K5NE00_CERAT_9531 are exactly identical! WARNING: Sequences tr_A0A2I3S9S5_A0A2I3S9S5_PANTR_9598 and tr_A0A2K6CGS5_A0A2K6CGS5_MACNE_9545 are exactly identical! WARNING: Sequences tr_A0A2I3S9S5_A0A2I3S9S5_PANTR_9598 and tr_A0A2K5ZJQ0_A0A2K5ZJQ0_MANLE_9568 are exactly identical! WARNING: Sequences tr_A0A2I3S9S5_A0A2I3S9S5_PANTR_9598 and tr_A0A2R8ZH47_A0A2R8ZH47_PANPA_9597 are exactly identical! WARNING: Sequences tr_H2Q081_H2Q081_PANTR_9598 and sp_Q9NR48_ASH1L_HUMAN_9606 are exactly identical! WARNING: Sequences tr_H2Q081_H2Q081_PANTR_9598 and tr_H9FX47_H9FX47_MACMU_9544 are exactly identical! WARNING: Sequences tr_H2Q081_H2Q081_PANTR_9598 and tr_A0A096N082_A0A096N082_PAPAN_9555 are exactly identical! WARNING: Sequences tr_H2Q081_H2Q081_PANTR_9598 and tr_A0A1U7TG65_A0A1U7TG65_TARSY_1868482 are exactly identical! WARNING: Sequences tr_H2Q081_H2Q081_PANTR_9598 and tr_A0A2K5KRL6_A0A2K5KRL6_CERAT_9531 are exactly identical! WARNING: Sequences tr_H2Q081_H2Q081_PANTR_9598 and tr_A0A2K5ZXP5_A0A2K5ZXP5_MANLE_9568 are exactly identical! WARNING: Sequences tr_F6Y040_F6Y040_MONDO_13616 and tr_G3W6D3_G3W6D3_SARHA_9305 are exactly identical! WARNING: Sequences tr_F6SK58_F6SK58_HORSE_9796 and tr_H0XRK2_H0XRK2_OTOGA_30611 are exactly identical! WARNING: Sequences tr_F6SK58_F6SK58_HORSE_9796 and tr_A0A2Y9SGI7_A0A2Y9SGI7_PHYCD_9755 are exactly identical! WARNING: Sequences tr_W5P112_W5P112_SHEEP_9940 and tr_G3SW93_G3SW93_LOXAF_9785 are exactly identical! WARNING: Sequences tr_W5P112_W5P112_SHEEP_9940 and tr_A0A287AA00_A0A287AA00_PIG_9823 are exactly identical! WARNING: Sequences tr_W5P112_W5P112_SHEEP_9940 and tr_E1BM66_E1BM66_BOVIN_9913 are exactly identical! WARNING: Sequences tr_W5P112_W5P112_SHEEP_9940 and tr_A0A2Y9QLA7_A0A2Y9QLA7_TRIMA_127582 are exactly identical! WARNING: Sequences tr_W5P2W7_W5P2W7_SHEEP_9940 and tr_E1BGA4_E1BGA4_BOVIN_9913 are exactly identical! WARNING: Sequences tr_F9G813_F9G813_FUSOF_660025 and tr_A0A0D2XZA8_A0A0D2XZA8_FUSO4_426428 are exactly identical! WARNING: Sequences tr_F9G813_F9G813_FUSOF_660025 and tr_N4UBN3_N4UBN3_FUSC1_1229664 are exactly identical! WARNING: Sequences tr_F9G813_F9G813_FUSOF_660025 and tr_X0CLS7_X0CLS7_FUSOX_1089458 are exactly identical! WARNING: Sequences tr_F9G813_F9G813_FUSOF_660025 and tr_A0A2H3THT3_A0A2H3THT3_FUSOX_5507 are exactly identical! WARNING: Sequences tr_J5JDJ5_J5JDJ5_BEAB2_655819 and tr_A0A0A2VJ52_A0A0A2VJ52_BEABA_1245745 are exactly identical! WARNING: Sequences tr_J5JDJ5_J5JDJ5_BEAB2_655819 and tr_A0A2N6NGM7_A0A2N6NGM7_BEABA_176275 are exactly identical! WARNING: Sequences tr_M4AID2_M4AID2_XIPMA_8083 and tr_A0A087X778_A0A087X778_POEFO_48698 are exactly identical! WARNING: Sequences tr_A0A088AJJ3_A0A088AJJ3_APIME_7460 and tr_A0A2A3E6P6_A0A2A3E6P6_APICC_94128 are exactly identical! WARNING: Sequences tr_A0A158NL86_A0A158NL86_ATTCE_12957 and tr_A0A151I1W6_A0A151I1W6_9HYME_520822 are exactly identical! WARNING: Sequences tr_A0A287CYD9_A0A287CYD9_ICTTR_43179 and tr_H0X4U4_H0X4U4_OTOGA_30611 are exactly identical! WARNING: Sequences tr_A0A287CYD9_A0A287CYD9_ICTTR_43179 and tr_H0VB70_H0VB70_CAVPO_10141 are exactly identical! WARNING: Sequences tr_A0A287CYD9_A0A287CYD9_ICTTR_43179 and tr_G5BQ01_G5BQ01_HETGA_10181 are exactly identical! WARNING: Sequences tr_A0A287CYD9_A0A287CYD9_ICTTR_43179 and tr_F6UCM0_F6UCM0_CALJA_9483 are exactly identical! WARNING: Sequences tr_A0A287CYD9_A0A287CYD9_ICTTR_43179 and tr_A0A091EFC1_A0A091EFC1_FUKDA_885580 are exactly identical! WARNING: Sequences tr_I3MXV7_I3MXV7_ICTTR_43179 and tr_A0A2Y9J8X5_A0A2Y9J8X5_ENHLU_391180 are exactly identical! WARNING: Sequences tr_A2R9L2_A2R9L2_ASPNC_425011 and tr_G7XSK3_G7XSK3_ASPKW_1033177 are exactly identical! WARNING: Sequences tr_A2R9L2_A2R9L2_ASPNC_425011 and tr_G3Y4Q1_G3Y4Q1_ASPNA_380704 are exactly identical! WARNING: Sequences tr_A2R9L2_A2R9L2_ASPNC_425011 and tr_A0A100IQV5_A0A100IQV5_ASPNG_5061 are exactly identical! WARNING: Sequences tr_A2R9L2_A2R9L2_ASPNC_425011 and tr_A0A146G0X1_A0A146G0X1_9EURO_1069201 are exactly identical! WARNING: Sequences tr_A2R9L2_A2R9L2_ASPNC_425011 and tr_A0A1L9N570_A0A1L9N570_ASPTU_767770 are exactly identical! WARNING: Sequences tr_A2R9L2_A2R9L2_ASPNC_425011 and tr_A0A317VJ74_A0A317VJ74_9EURO_1448314 are exactly identical! WARNING: Sequences tr_A2R9L2_A2R9L2_ASPNC_425011 and tr_A0A319A707_A0A319A707_9EURO_1450533 are exactly identical! WARNING: Sequences tr_A0A212F2X1_A0A212F2X1_DANPL_278856 and tr_A0A212FHL1_A0A212FHL1_DANPL_278856 are exactly identical! WARNING: Sequences tr_G3SS46_G3SS46_LOXAF_9785 and tr_A0A2Y9QL39_A0A2Y9QL39_TRIMA_127582 are exactly identical! WARNING: Sequences tr_H0YPH4_H0YPH4_TAEGU_59729 and tr_U3JGV3_U3JGV3_FICAL_59894 are exactly identical! WARNING: Sequences tr_H0YPH4_H0YPH4_TAEGU_59729 and tr_A0A093PRE7_A0A093PRE7_9PASS_328815 are exactly identical! WARNING: Sequences tr_H0YPH4_H0YPH4_TAEGU_59729 and tr_A0A218UDW7_A0A218UDW7_9PASE_299123 are exactly identical! WARNING: Sequences tr_H0YQ91_H0YQ91_TAEGU_59729 and tr_U3K226_U3K226_FICAL_59894 are exactly identical! WARNING: Sequences tr_H0YQ91_H0YQ91_TAEGU_59729 and tr_A0A093GTY1_A0A093GTY1_DRYPU_118200 are exactly identical! WARNING: Sequences tr_H0YQ91_H0YQ91_TAEGU_59729 and tr_A0A218UPB3_A0A218UPB3_9PASE_299123 are exactly identical! WARNING: Sequences tr_H0Z351_H0Z351_TAEGU_59729 and tr_U3JW35_U3JW35_FICAL_59894 are exactly identical! WARNING: Sequences tr_H0Z351_H0Z351_TAEGU_59729 and tr_A0A091E4P2_A0A091E4P2_CORBR_85066 are exactly identical! WARNING: Sequences tr_H0Z351_H0Z351_TAEGU_59729 and tr_A0A093QAI2_A0A093QAI2_9PASS_328815 are exactly identical! WARNING: Sequences tr_H0Z351_H0Z351_TAEGU_59729 and tr_A0A218UJC4_A0A218UJC4_9PASE_299123 are exactly identical! WARNING: Sequences tr_H0ZJX6_H0ZJX6_TAEGU_59729 and tr_A0A218V8N0_A0A218V8N0_9PASE_299123 are exactly identical! WARNING: Sequences tr_E6R923_E6R923_CRYGW_367775 and tr_A0A095CAB0_A0A095CAB0_CRYGR_294750 are exactly identical! WARNING: Sequences tr_F2SMP3_F2SMP3_TRIRC_559305 and tr_A0A178F368_A0A178F368_TRIRU_5551 are exactly identical! WARNING: Sequences tr_G1KZK0_G1KZK0_AILME_9646 and tr_A0A2U3W4G9_A0A2U3W4G9_ODORO_9708 are exactly identical! WARNING: Sequences tr_G1KZK0_G1KZK0_AILME_9646 and tr_A0A2U3XTV1_A0A2U3XTV1_LEPWE_9713 are exactly identical! WARNING: Sequences tr_G1KZK0_G1KZK0_AILME_9646 and tr_A0A384CJ04_A0A384CJ04_URSMA_29073 are exactly identical! WARNING: Sequences tr_B3RRG4_B3RRG4_TRIAD_10228 and tr_A0A369RSG8_A0A369RSG8_9METZ_287889 are exactly identical! WARNING: Sequences tr_B3S8Y2_B3S8Y2_TRIAD_10228 and tr_A0A369SC06_A0A369SC06_9METZ_287889 are exactly identical! WARNING: Sequences tr_L0PA24_L0PA24_PNEJ8_1209962 and tr_A0A0W4ZTQ7_A0A0W4ZTQ7_PNEJ7_1408657 are exactly identical! WARNING: Sequences tr_M4DGQ3_M4DGQ3_BRARP_51351 and tr_A0A0D3D1C9_A0A0D3D1C9_BRAOL_109376 are exactly identical! WARNING: Sequences tr_U3I7R1_U3I7R1_ANAPL_8839 and tr_A0A2I0MMZ0_A0A2I0MMZ0_COLLI_8932 are exactly identical! WARNING: Sequences tr_U3I7R1_U3I7R1_ANAPL_8839 and tr_A0A091J5I7_A0A091J5I7_CALAN_9244 are exactly identical! WARNING: Sequences tr_U3I7R1_U3I7R1_ANAPL_8839 and tr_A0A1V4JFB9_A0A1V4JFB9_PATFA_372326 are exactly identical! WARNING: Sequences tr_U3IB58_U3IB58_ANAPL_8839 and tr_A0A091JNA6_A0A091JNA6_EGRGA_188379 are exactly identical! WARNING: Sequences tr_U3IB58_U3IB58_ANAPL_8839 and tr_A0A087QJI3_A0A087QJI3_APTFO_9233 are exactly identical! WARNING: Sequences tr_U3IB58_U3IB58_ANAPL_8839 and tr_A0A091FTX7_A0A091FTX7_9AVES_55661 are exactly identical! WARNING: Sequences tr_U3IB58_U3IB58_ANAPL_8839 and tr_A0A0A0AQI0_A0A0A0AQI0_CHAVO_50402 are exactly identical! WARNING: Sequences tr_S0E8Q5_S0E8Q5_GIBF5_1279085 and tr_A0A2K0WHR5_A0A2K0WHR5_GIBNY_42673 are exactly identical! WARNING: Sequences tr_S0E8Q5_S0E8Q5_GIBF5_1279085 and tr_A0A365MWP9_A0A365MWP9_GIBIN_948311 are exactly identical! WARNING: Sequences tr_M2TZX0_M2TZX0_COCH5_701091 and tr_W6YPT4_W6YPT4_COCCA_930089 are exactly identical! WARNING: Sequences tr_M2TZX0_M2TZX0_COCH5_701091 and tr_W6Z016_W6Z016_COCMI_930090 are exactly identical! WARNING: Sequences tr_A0A3B6B0P3_A0A3B6B0P3_WHEAT_4565 and tr_A0A3B6DHE7_A0A3B6DHE7_WHEAT_4565 are exactly identical! WARNING: Sequences tr_A0A084QU38_A0A084QU38_STAC4_1283841 and tr_A0A084RG40_A0A084RG40_STACH_1283842 are exactly identical! WARNING: Sequences tr_A0A2I3LLC3_A0A2I3LLC3_PAPAN_9555 and tr_A0A2K5KSC7_A0A2K5KSC7_CERAT_9531 are exactly identical! WARNING: Sequences tr_A0A2I3LLC3_A0A2I3LLC3_PAPAN_9555 and tr_A0A2K5ZFP3_A0A2K5ZFP3_MANLE_9568 are exactly identical! WARNING: Sequences tr_A0A094EMQ3_A0A094EMQ3_9PEZI_1420912 and tr_A0A1B8GSS7_A0A1B8GSS7_9PEZI_342668 are exactly identical! WARNING: Sequences tr_A0A094EMQ3_A0A094EMQ3_9PEZI_1420912 and tr_A0A1B8CN12_A0A1B8CN12_9PEZI_1622147 are exactly identical! WARNING: Sequences tr_A0A0F0I6B1_A0A0F0I6B1_ASPPU_1403190 and tr_A0A2G7FQR6_A0A2G7FQR6_9EURO_656916 are exactly identical! WARNING: Sequences tr_A0A0A1NEM0_A0A0A1NEM0_9FUNG_58291 and tr_A0A367K7H2_A0A367K7H2_9FUNG_86630 are exactly identical! WARNING: Sequences tr_A0A151MUS7_A0A151MUS7_ALLMI_8496 and tr_A0A1U8D5X9_A0A1U8D5X9_ALLSI_38654 are exactly identical! WARNING: Sequences tr_A0A151NCN1_A0A151NCN1_ALLMI_8496 and tr_A0A1U7RS50_A0A1U7RS50_ALLSI_38654 are exactly identical! WARNING: Sequences tr_A0A151P974_A0A151P974_ALLMI_8496 and tr_A0A1U8D5E3_A0A1U8D5E3_ALLSI_38654 are exactly identical! WARNING: Sequences tr_A0A0S7DVU4_A0A0S7DVU4_9EURO_293939 and tr_A0A2I1CGP4_A0A2I1CGP4_9EURO_1392255 are exactly identical! WARNING: Sequences tr_A0A091F045_A0A091F045_CORBR_85066 and tr_A0A093PNT6_A0A093PNT6_9PASS_328815 are exactly identical! WARNING: Sequences tr_A0A091J6P4_A0A091J6P4_EGRGA_188379 and tr_A0A091VFH3_A0A091VFH3_NIPNI_128390 are exactly identical! WARNING: Sequences tr_A0A091J6P4_A0A091J6P4_EGRGA_188379 and tr_A0A087QGP1_A0A087QGP1_APTFO_9233 are exactly identical! WARNING: Sequences tr_A0A091J6P4_A0A091J6P4_EGRGA_188379 and tr_A0A091GBJ5_A0A091GBJ5_9AVES_55661 are exactly identical! WARNING: Sequences tr_A0A091J6P4_A0A091J6P4_EGRGA_188379 and tr_A0A0A0ABT6_A0A0A0ABT6_CHAVO_50402 are exactly identical! WARNING: Sequences tr_A0A091JCS7_A0A091JCS7_EGRGA_188379 and tr_A0A091WUG1_A0A091WUG1_NIPNI_128390 are exactly identical! WARNING: Sequences tr_A0A091JCS7_A0A091JCS7_EGRGA_188379 and tr_A0A091WBA5_A0A091WBA5_OPIHO_30419 are exactly identical! WARNING: Sequences tr_A0A091JCS7_A0A091JCS7_EGRGA_188379 and tr_A0A091GJF3_A0A091GJF3_9AVES_55661 are exactly identical! WARNING: Sequences tr_A0A0L9UFP6_A0A0L9UFP6_PHAAN_3914 and tr_A0A1S3U4P3_A0A1S3U4P3_VIGRR_3916 are exactly identical! WARNING: Sequences tr_A0A093GQ55_A0A093GQ55_STRCA_441894 and tr_A0A099YUM8_A0A099YUM8_TINGU_94827 are exactly identical! WARNING: Sequences tr_A0A093GQ55_A0A093GQ55_STRCA_441894 and tr_A0A2I0LK15_A0A2I0LK15_COLLI_8932 are exactly identical! WARNING: Sequences tr_A0A093GQ55_A0A093GQ55_STRCA_441894 and tr_A0A1V4KU80_A0A1V4KU80_PATFA_372326 are exactly identical! WARNING: Sequences tr_A0A2I0LJF2_A0A2I0LJF2_COLLI_8932 and tr_A0A1V4KHH6_A0A1V4KHH6_PATFA_372326 are exactly identical! WARNING: Sequences tr_A0A2I0LL04_A0A2I0LL04_COLLI_8932 and tr_A0A091HJ02_A0A091HJ02_CALAN_9244 are exactly identical! WARNING: Sequences tr_A0A2I0LM30_A0A2I0LM30_COLLI_8932 and tr_A0A1V4KDL6_A0A1V4KDL6_PATFA_372326 are exactly identical! WARNING: Sequences tr_A0A1S3IEK0_A0A1S3IEK0_LINUN_7574 and tr_A0A1S3JUZ0_A0A1S3JUZ0_LINUN_7574 are exactly identical! WARNING: Sequences tr_A0A1B8DT25_A0A1B8DT25_9PEZI_1524831 and tr_A0A1B8F577_A0A1B8F577_9PEZI_1622149 are exactly identical! WARNING: Sequences tr_A0A1U8JY44_A0A1U8JY44_GOSHI_3635 and tr_A0A1U8NSU5_A0A1U8NSU5_GOSHI_3635 are exactly identical! WARNING: Sequences tr_A0A226N665_A0A226N665_CALSU_9009 and tr_A0A226P5T6_A0A226P5T6_COLVI_9014 are exactly identical! WARNING: Sequences tr_A0A226N8E4_A0A226N8E4_CALSU_9009 and tr_A0A226P3L8_A0A226P3L8_COLVI_9014 are exactly identical! WARNING: Sequences tr_A0A2D0S1Y4_A0A2D0S1Y4_ICTPU_7998 and tr_A0A2D0S1Y9_A0A2D0S1Y9_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0S1Y4_A0A2D0S1Y4_ICTPU_7998 and tr_A0A2D0S1Z8_A0A2D0S1Z8_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0S1Y4_A0A2D0S1Y4_ICTPU_7998 and tr_A0A2D0S216_A0A2D0S216_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0SS08_A0A2D0SS08_ICTPU_7998 and tr_A0A2D0ST52_A0A2D0ST52_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0SZ48_A0A2D0SZ48_ICTPU_7998 and tr_A0A2D0SZ49_A0A2D0SZ49_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0SZ48_A0A2D0SZ48_ICTPU_7998 and tr_A0A2D0SZ66_A0A2D0SZ66_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0SZ48_A0A2D0SZ48_ICTPU_7998 and tr_A0A2D0SZK1_A0A2D0SZK1_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0SZ48_A0A2D0SZ48_ICTPU_7998 and tr_A0A2D0T032_A0A2D0T032_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A1U8GVV4_A0A1U8GVV4_CAPAN_4072 and tr_A0A2G3C7A5_A0A2G3C7A5_CAPCH_80379 are exactly identical! WARNING: Sequences tr_A0A2P5F194_A0A2P5F194_TREOI_63057 and tr_A0A2P5CGG6_A0A2P5CGG6_PARAD_3476 are exactly identical! WARNING: Sequences tr_A0A2U4A779_A0A2U4A779_TURTR_9739 and tr_A0A2Y9NCG9_A0A2Y9NCG9_DELLE_9749 are exactly identical! WARNING: Sequences tr_A0A2U4A779_A0A2U4A779_TURTR_9739 and tr_A0A2Y9FR09_A0A2Y9FR09_PHYCD_9755 are exactly identical! WARNING: Sequences tr_A0A2U4A779_A0A2U4A779_TURTR_9739 and tr_A0A383ZTM0_A0A383ZTM0_BALAS_310752 are exactly identical! WARNING: Sequences tr_A0A2U4B7D6_A0A2U4B7D6_TURTR_9739 and tr_A0A2Y9M8J4_A0A2Y9M8J4_DELLE_9749 are exactly identical! WARNING: Sequences tr_A0A2U3Z9S5_A0A2U3Z9S5_ODORO_9708 and tr_A0A2U3YCR4_A0A2U3YCR4_LEPWE_9713 are exactly identical! WARNING: Duplicate sequences found: 192 NOTE: Reduced alignment (with duplicates and gap-only sites/taxa removed) NOTE: was saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_040621/phylogeny-snakemake/results/Q96L73/3_mltree/Q96L73.raxml.reduced.phy Alignment comprises 1 partitions and 252 patterns Partition 0: noname Model: LG4X+R4 Alignment sites / patterns: 252 / 252 Gaps: 5.36 % Invariant sites: 0.00 % NOTE: Binary MSA file created: /cta/users/eakkoyun/WORKFOLDER/PROD/run_040621/phylogeny-snakemake/results/Q96L73/3_mltree/Q96L73.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 988 taxa [00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 252 / 20160 [00:00:00] Data distribution: max. searches per worker: 4 Starting ML tree search with 20 distinct starting trees [00:00:00 -409283.239623] Initial branch length optimization [00:00:06 -337947.824976] Model parameter optimization (eps = 10.000000) [00:01:18 -337226.302566] AUTODETECT spr round 1 (radius: 5) [00:04:58 -213149.476622] AUTODETECT spr round 2 (radius: 10) [00:08:45 -156842.068263] AUTODETECT spr round 3 (radius: 15) [00:12:41 -121937.990490] AUTODETECT spr round 4 (radius: 20) [00:17:06 -101076.829894] AUTODETECT spr round 5 (radius: 25) [00:22:38 -96978.969355] SPR radius for FAST iterations: 25 (autodetect) [00:22:38 -96978.969355] Model parameter optimization (eps = 3.000000) [00:23:06 -96928.998789] FAST spr round 1 (radius: 25) [00:26:54 -82311.725898] FAST spr round 2 (radius: 25) [00:29:43 -81667.044732] FAST spr round 3 (radius: 25) [00:32:08 -81639.163468] FAST spr round 4 (radius: 25) [00:34:21 -81627.424560] FAST spr round 5 (radius: 25) [00:36:28 -81627.423777] Model parameter optimization (eps = 1.000000) [00:36:50 -81624.098823] SLOW spr round 1 (radius: 5) [00:39:38 -81609.838798] SLOW spr round 2 (radius: 5) [00:42:16 -81609.838218] SLOW spr round 3 (radius: 10) [00:45:09 -81609.584628] SLOW spr round 4 (radius: 5) [00:48:31 -81609.584292] SLOW spr round 5 (radius: 10) [00:51:38 -81609.583957] SLOW spr round 6 (radius: 15) [00:55:42 -81607.483728] SLOW spr round 7 (radius: 5) [00:59:19 -81607.481137] SLOW spr round 8 (radius: 10) [01:02:34 -81607.480791] SLOW spr round 9 (radius: 15) [01:06:35 -81607.480447] SLOW spr round 10 (radius: 20) [01:12:51 -81607.480100] SLOW spr round 11 (radius: 25) [01:12:52] [worker #1] ML tree search #2, logLikelihood: -81589.153620 [01:18:52] [worker #3] ML tree search #4, logLikelihood: -81615.786872 [01:20:57 -81607.479736] Model parameter optimization (eps = 0.100000) [01:21:06] [worker #0] ML tree search #1, logLikelihood: -81607.379864 [01:21:06 -409240.142058] Initial branch length optimization [01:21:12 -336876.169285] Model parameter optimization (eps = 10.000000) [01:22:16 -336312.886667] AUTODETECT spr round 1 (radius: 5) [01:22:47] [worker #4] ML tree search #5, logLikelihood: -81604.152284 [01:25:58 -209450.079984] AUTODETECT spr round 2 (radius: 10) [01:29:45 -153135.300806] AUTODETECT spr round 3 (radius: 15) [01:33:47 -133735.318285] AUTODETECT spr round 4 (radius: 20) [01:38:47 -120150.860404] AUTODETECT spr round 5 (radius: 25) [01:44:24 -105699.093563] SPR radius for FAST iterations: 25 (autodetect) [01:44:24 -105699.093563] Model parameter optimization (eps = 3.000000) [01:44:48] [worker #2] ML tree search #3, logLikelihood: -81599.414236 [01:44:50 -105663.761304] FAST spr round 1 (radius: 25) [01:48:27 -83682.922162] FAST spr round 2 (radius: 25) [01:51:07 -81709.680441] FAST spr round 3 (radius: 25) [01:53:35 -81636.838727] FAST spr round 4 (radius: 25) [01:55:54 -81627.007890] FAST spr round 5 (radius: 25) [01:58:03 -81623.899570] FAST spr round 6 (radius: 25) [02:00:07 -81623.898638] Model parameter optimization (eps = 1.000000) [02:00:26 -81621.626039] SLOW spr round 1 (radius: 5) [02:03:14 -81600.077198] SLOW spr round 2 (radius: 5) [02:06:02 -81593.814451] SLOW spr round 3 (radius: 5) [02:08:43 -81593.813818] SLOW spr round 4 (radius: 10) [02:11:32 -81592.746100] SLOW spr round 5 (radius: 5) [02:14:57 -81592.745646] SLOW spr round 6 (radius: 10) [02:18:04 -81592.745626] SLOW spr round 7 (radius: 15) [02:22:15 -81590.535262] SLOW spr round 8 (radius: 5) [02:25:55 -81590.532934] SLOW spr round 9 (radius: 10) [02:29:11 -81590.532912] SLOW spr round 10 (radius: 15) [02:33:15 -81590.532894] SLOW spr round 11 (radius: 20) [02:39:25 -81590.532876] SLOW spr round 12 (radius: 25) [02:47:25 -81590.288002] SLOW spr round 13 (radius: 5) [02:51:11 -81590.283935] SLOW spr round 14 (radius: 10) [02:54:34 -81590.282875] SLOW spr round 15 (radius: 15) [02:58:41 -81589.953058] SLOW spr round 16 (radius: 5) [02:59:45] [worker #4] ML tree search #10, logLikelihood: -81610.380860 [03:02:20 -81589.926045] SLOW spr round 17 (radius: 10) [03:05:42 -81589.893386] SLOW spr round 18 (radius: 15) [03:09:48 -81589.893051] SLOW spr round 19 (radius: 20) [03:14:21] [worker #3] ML tree search #9, logLikelihood: -81606.334533 [03:16:01 -81589.892963] SLOW spr round 20 (radius: 25) [03:16:22] [worker #1] ML tree search #7, logLikelihood: -81583.255368 [03:24:18 -81589.892926] Model parameter optimization (eps = 0.100000) [03:24:25] [worker #0] ML tree search #6, logLikelihood: -81589.873788 [03:24:26 -412235.625682] Initial branch length optimization [03:24:32 -338968.413374] Model parameter optimization (eps = 10.000000) [03:25:31 -338304.550170] AUTODETECT spr round 1 (radius: 5) [03:29:52 -212943.194903] AUTODETECT spr round 2 (radius: 10) [03:33:43 -145561.815180] AUTODETECT spr round 3 (radius: 15) [03:37:48 -116086.540648] AUTODETECT spr round 4 (radius: 20) [03:42:18 -102688.785687] AUTODETECT spr round 5 (radius: 25) [03:47:12 -95243.550192] SPR radius for FAST iterations: 25 (autodetect) [03:47:12 -95243.550192] Model parameter optimization (eps = 3.000000) [03:47:44 -95200.813921] FAST spr round 1 (radius: 25) [03:51:38 -82611.702689] FAST spr round 2 (radius: 25) [03:53:09] [worker #2] ML tree search #8, logLikelihood: -81596.559618 [03:54:33 -81693.534471] FAST spr round 3 (radius: 25) [03:56:59 -81635.950423] FAST spr round 4 (radius: 25) [03:59:17 -81630.556812] FAST spr round 5 (radius: 25) [04:01:24 -81630.325597] FAST spr round 6 (radius: 25) [04:03:27 -81630.323807] Model parameter optimization (eps = 1.000000) [04:03:37 -81629.690348] SLOW spr round 1 (radius: 5) [04:06:30 -81609.845006] SLOW spr round 2 (radius: 5) [04:09:09 -81608.816874] SLOW spr round 3 (radius: 5) [04:11:45 -81608.816314] SLOW spr round 4 (radius: 10) [04:14:35 -81605.502893] SLOW spr round 5 (radius: 5) [04:18:01 -81605.500467] SLOW spr round 6 (radius: 10) [04:21:06 -81605.500461] SLOW spr round 7 (radius: 15) [04:25:13 -81605.500461] SLOW spr round 8 (radius: 20) [04:25:59] [worker #4] ML tree search #15, logLikelihood: -81634.394638 [04:29:15] [worker #1] ML tree search #12, logLikelihood: -81615.441462 [04:31:37 -81605.500461] SLOW spr round 9 (radius: 25) [04:39:43 -81604.107636] SLOW spr round 10 (radius: 5) [04:43:29 -81604.107605] SLOW spr round 11 (radius: 10) [04:46:51 -81604.107605] SLOW spr round 12 (radius: 15) [04:50:58 -81604.107605] SLOW spr round 13 (radius: 20) [04:57:25 -81604.107605] SLOW spr round 14 (radius: 25) [05:05:32 -81604.107605] Model parameter optimization (eps = 0.100000) [05:05:38] [worker #0] ML tree search #11, logLikelihood: -81604.102270 [05:05:38 -410332.678318] Initial branch length optimization [05:05:43 -337805.877553] Model parameter optimization (eps = 10.000000) [05:07:01 -337133.099813] AUTODETECT spr round 1 (radius: 5) [05:10:29] [worker #2] ML tree search #13, logLikelihood: -81595.937969 [05:10:37 -209074.272900] AUTODETECT spr round 2 (radius: 10) [05:14:16 -143730.009233] AUTODETECT spr round 3 (radius: 15) [05:18:25 -113973.558329] AUTODETECT spr round 4 (radius: 20) [05:22:55 -101636.170760] AUTODETECT spr round 5 (radius: 25) [05:28:46 -95248.074678] SPR radius for FAST iterations: 25 (autodetect) [05:28:46 -95248.074678] Model parameter optimization (eps = 3.000000) [05:29:13 -95148.717084] FAST spr round 1 (radius: 25) [05:32:58 -82244.740602] FAST spr round 2 (radius: 25) [05:35:44 -81674.551957] FAST spr round 3 (radius: 25) [05:38:09 -81648.421391] FAST spr round 4 (radius: 25) [05:38:24] [worker #4] ML tree search #20, logLikelihood: -81594.410383 [05:40:33 -81641.006407] FAST spr round 5 (radius: 25) [05:42:39] [worker #1] ML tree search #17, logLikelihood: -81600.309858 [05:42:49 -81641.005909] Model parameter optimization (eps = 1.000000) [05:42:59 -81640.162107] SLOW spr round 1 (radius: 5) [05:46:42 -81629.898340] SLOW spr round 2 (radius: 5) [05:49:24 -81629.897942] SLOW spr round 3 (radius: 10) [05:52:48 -81629.644433] SLOW spr round 4 (radius: 5) [05:55:38] [worker #3] ML tree search #14, logLikelihood: -81595.602476 [05:56:12 -81629.644143] SLOW spr round 5 (radius: 10) [05:59:18 -81629.643853] SLOW spr round 6 (radius: 15) [06:03:15 -81629.643562] SLOW spr round 7 (radius: 20) [06:09:18 -81624.431748] SLOW spr round 8 (radius: 5) [06:13:01 -81623.518924] SLOW spr round 9 (radius: 5) [06:16:11 -81623.518614] SLOW spr round 10 (radius: 10) [06:19:08 -81623.518308] SLOW spr round 11 (radius: 15) [06:22:59] [worker #2] ML tree search #18, logLikelihood: -81601.896582 [06:23:21 -81623.518001] SLOW spr round 12 (radius: 20) [06:29:24 -81623.459771] SLOW spr round 13 (radius: 25) [06:37:19 -81623.459329] Model parameter optimization (eps = 0.100000) [06:37:24] [worker #0] ML tree search #16, logLikelihood: -81623.452809 [07:49:16] [worker #3] ML tree search #19, logLikelihood: -81621.397622 Optimized model parameters: Partition 0: noname Rate heterogeneity: FREE (4 cats, mean), weights&rates: (0.131329,0.185047) (0.255954,0.318379) (0.332734,0.907709) (0.279983,2.115066) 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: -81583.255368 AIC score: 167124.510735 / AICc score: 8003964.510735 / BIC score: 174109.250899 Free parameters (model + branch lengths): 1979 WARNING: Number of free parameters (K=1979) is larger than alignment size (n=252). This might lead to overfitting and compromise tree inference results! Best ML tree saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_040621/phylogeny-snakemake/results/Q96L73/3_mltree/Q96L73.raxml.bestTree All ML trees saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_040621/phylogeny-snakemake/results/Q96L73/3_mltree/Q96L73.raxml.mlTrees Optimized model saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_040621/phylogeny-snakemake/results/Q96L73/3_mltree/Q96L73.raxml.bestModel Execution log saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_040621/phylogeny-snakemake/results/Q96L73/3_mltree/Q96L73.raxml.log Analysis started: 18-Jun-2021 00:06:03 / finished: 18-Jun-2021 07:55:20 Elapsed time: 28156.693 seconds