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 14-Jul-2021 17:54:33 as follows: raxml-ng --ancestral --msa /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/A6NGH8/2_msa/A6NGH8_nogap_msa.fasta --tree /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/A6NGH8/3_mltree/A6NGH8.raxml.bestTree_unrooted --model LG4X --prefix /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/A6NGH8/4_raxmlng_ancestral/A6NGH8 --threads 4 Analysis options: run mode: Ancestral state reconstruction start tree(s): user random seed: 1626274473 tip-inner: ON pattern compression: OFF per-rate scalers: OFF site repeats: OFF 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: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/A6NGH8/2_msa/A6NGH8_nogap_msa.fasta [00:00:00] Loaded alignment with 1001 taxa and 418 sites WARNING: Sequences tr_B4QVC8_B4QVC8_DROSI_7240 and sp_Q9VBP3_TNKS_DROME_7227 are exactly identical! WARNING: Sequences tr_B4QVC8_B4QVC8_DROSI_7240 and tr_B4ICC0_B4ICC0_DROSE_7238 are exactly identical! WARNING: Sequences tr_E9PUR0_E9PUR0_MOUSE_10090 and tr_A0A0G2K916_A0A0G2K916_RAT_10116 are exactly identical! WARNING: Sequences tr_E9PUR0_E9PUR0_MOUSE_10090 and tr_A0A1U8BL92_A0A1U8BL92_MESAU_10036 are exactly identical! WARNING: Sequences tr_G9KJ01_G9KJ01_MUSPF_9669 and tr_G3QKE5_G3QKE5_GORGO_9595 are exactly identical! WARNING: Sequences tr_G9KJ01_G9KJ01_MUSPF_9669 and tr_H2PWF9_H2PWF9_PONAB_9601 are exactly identical! WARNING: Sequences tr_G9KJ01_G9KJ01_MUSPF_9669 and tr_E2RA22_E2RA22_CANLF_9615 are exactly identical! WARNING: Sequences tr_G9KJ01_G9KJ01_MUSPF_9669 and tr_H2R235_H2R235_PANTR_9598 are exactly identical! WARNING: Sequences tr_G9KJ01_G9KJ01_MUSPF_9669 and tr_I3M2Y9_I3M2Y9_ICTTR_43179 are exactly identical! WARNING: Sequences tr_G9KJ01_G9KJ01_MUSPF_9669 and sp_O75832_PSD10_HUMAN_9606 are exactly identical! WARNING: Sequences tr_G9KJ01_G9KJ01_MUSPF_9669 and tr_A0A1D5QZ92_A0A1D5QZ92_MACMU_9544 are exactly identical! WARNING: Sequences tr_G9KJ01_G9KJ01_MUSPF_9669 and tr_A0A287BTN9_A0A287BTN9_PIG_9823 are exactly identical! WARNING: Sequences tr_G9KJ01_G9KJ01_MUSPF_9669 and tr_G1L817_G1L817_AILME_9646 are exactly identical! WARNING: Sequences tr_G9KJ01_G9KJ01_MUSPF_9669 and tr_M3X4N2_M3X4N2_FELCA_9685 are exactly identical! WARNING: Sequences tr_G9KJ01_G9KJ01_MUSPF_9669 and tr_A0A2I3LK46_A0A2I3LK46_PAPAN_9555 are exactly identical! WARNING: Sequences tr_G9KJ01_G9KJ01_MUSPF_9669 and tr_A0A0D9R9F2_A0A0D9R9F2_CHLSB_60711 are exactly identical! WARNING: Sequences tr_G9KJ01_G9KJ01_MUSPF_9669 and tr_A0A1U7UY97_A0A1U7UY97_TARSY_1868482 are exactly identical! WARNING: Sequences tr_G9KJ01_G9KJ01_MUSPF_9669 and tr_A0A2K5M286_A0A2K5M286_CERAT_9531 are exactly identical! WARNING: Sequences tr_G9KJ01_G9KJ01_MUSPF_9669 and tr_A0A2K6DZ99_A0A2K6DZ99_MACNE_9545 are exactly identical! WARNING: Sequences tr_G9KJ01_G9KJ01_MUSPF_9669 and tr_A0A2K5YL66_A0A2K5YL66_MANLE_9568 are exactly identical! WARNING: Sequences tr_G9KJ01_G9KJ01_MUSPF_9669 and tr_A0A2R9B2I6_A0A2R9B2I6_PANPA_9597 are exactly identical! WARNING: Sequences tr_G9KJ01_G9KJ01_MUSPF_9669 and tr_A0A2U3ZV10_A0A2U3ZV10_ODORO_9708 are exactly identical! WARNING: Sequences tr_G9KJ01_G9KJ01_MUSPF_9669 and tr_A0A2Y9L2W8_A0A2Y9L2W8_ENHLU_391180 are exactly identical! WARNING: Sequences tr_G9KJ01_G9KJ01_MUSPF_9669 and tr_A0A384B9U4_A0A384B9U4_BALAS_310752 are exactly identical! WARNING: Sequences tr_M3XMZ2_M3XMZ2_MUSPF_9669 and tr_G1PXK4_G1PXK4_MYOLU_59463 are exactly identical! WARNING: Sequences tr_M3XMZ2_M3XMZ2_MUSPF_9669 and tr_E2QST3_E2QST3_CANLF_9615 are exactly identical! WARNING: Sequences tr_M3XMZ2_M3XMZ2_MUSPF_9669 and tr_H0WS78_H0WS78_OTOGA_30611 are exactly identical! WARNING: Sequences tr_M3XMZ2_M3XMZ2_MUSPF_9669 and tr_D2HE78_D2HE78_AILME_9646 are exactly identical! WARNING: Sequences tr_M3XMZ2_M3XMZ2_MUSPF_9669 and tr_L5KAQ8_L5KAQ8_PTEAL_9402 are exactly identical! WARNING: Sequences tr_M3XMZ2_M3XMZ2_MUSPF_9669 and tr_A0A2I2U1I5_A0A2I2U1I5_FELCA_9685 are exactly identical! WARNING: Sequences tr_M3XMZ2_M3XMZ2_MUSPF_9669 and tr_A0A2U3ZBE6_A0A2U3ZBE6_ODORO_9708 are exactly identical! WARNING: Sequences tr_M3XMZ2_M3XMZ2_MUSPF_9669 and tr_A0A2Y9KVX7_A0A2Y9KVX7_ENHLU_391180 are exactly identical! WARNING: Sequences tr_M3XMZ2_M3XMZ2_MUSPF_9669 and tr_A0A384D7I2_A0A384D7I2_URSMA_29073 are exactly identical! WARNING: Sequences tr_M3XQF5_M3XQF5_MUSPF_9669 and tr_A0A2Y9LB94_A0A2Y9LB94_ENHLU_391180 are exactly identical! WARNING: Sequences tr_M3YHY9_M3YHY9_MUSPF_9669 and tr_F1PJ98_F1PJ98_CANLF_9615 are exactly identical! WARNING: Sequences tr_M3YHY9_M3YHY9_MUSPF_9669 and tr_G1L9X1_G1L9X1_AILME_9646 are exactly identical! WARNING: Sequences tr_M3YHY9_M3YHY9_MUSPF_9669 and tr_A0A2U3WCI4_A0A2U3WCI4_ODORO_9708 are exactly identical! WARNING: Sequences tr_M3YHY9_M3YHY9_MUSPF_9669 and tr_A0A2Y9J2Q3_A0A2Y9J2Q3_ENHLU_391180 are exactly identical! WARNING: Sequences tr_M3YHY9_M3YHY9_MUSPF_9669 and tr_A0A384CIA2_A0A384CIA2_URSMA_29073 are exactly identical! WARNING: Sequences tr_A0A2I3HLI6_A0A2I3HLI6_NOMLE_61853 and tr_A0A2I2YDH9_A0A2I2YDH9_GORGO_9595 are exactly identical! WARNING: Sequences tr_A0A2I3HLI6_A0A2I3HLI6_NOMLE_61853 and tr_A0A2I3MIE6_A0A2I3MIE6_PAPAN_9555 are exactly identical! WARNING: Sequences tr_A0A2I3HLI6_A0A2I3HLI6_NOMLE_61853 and tr_A0A2K5LPM7_A0A2K5LPM7_CERAT_9531 are exactly identical! WARNING: Sequences tr_A0A2I3HLI6_A0A2I3HLI6_NOMLE_61853 and tr_A0A2K6DJR0_A0A2K6DJR0_MACNE_9545 are exactly identical! WARNING: Sequences tr_A0A2I3HLI6_A0A2I3HLI6_NOMLE_61853 and tr_A0A2K5YP31_A0A2K5YP31_MANLE_9568 are exactly identical! WARNING: Sequences tr_G1RNN5_G1RNN5_NOMLE_61853 and tr_F7EBU2_F7EBU2_MACMU_9544 are exactly identical! WARNING: Sequences tr_G1RNN5_G1RNN5_NOMLE_61853 and tr_G7PDE9_G7PDE9_MACFA_9541 are exactly identical! WARNING: Sequences tr_G1RNN5_G1RNN5_NOMLE_61853 and tr_A0A2I3NH47_A0A2I3NH47_PAPAN_9555 are exactly identical! WARNING: Sequences tr_G1RNN5_G1RNN5_NOMLE_61853 and tr_A0A3Q0E3J7_A0A3Q0E3J7_TARSY_1868482 are exactly identical! WARNING: Sequences tr_G1RNN5_G1RNN5_NOMLE_61853 and tr_A0A2K5N412_A0A2K5N412_CERAT_9531 are exactly identical! WARNING: Sequences tr_G1RNN5_G1RNN5_NOMLE_61853 and tr_A0A2K6CI25_A0A2K6CI25_MACNE_9545 are exactly identical! WARNING: Sequences tr_G1RNN5_G1RNN5_NOMLE_61853 and tr_A0A2K6ACH1_A0A2K6ACH1_MANLE_9568 are exactly identical! WARNING: Sequences tr_G1RNN5_G1RNN5_NOMLE_61853 and tr_A0A2Y9RT58_A0A2Y9RT58_TRIMA_127582 are exactly identical! WARNING: Sequences tr_G1S889_G1S889_NOMLE_61853 and tr_A0A2I2YPI1_A0A2I2YPI1_GORGO_9595 are exactly identical! WARNING: Sequences tr_G1S889_G1S889_NOMLE_61853 and tr_H2Q5T1_H2Q5T1_PANTR_9598 are exactly identical! WARNING: Sequences tr_G1S889_G1S889_NOMLE_61853 and sp_Q9H765_ASB8_HUMAN_9606 are exactly identical! WARNING: Sequences tr_G1S889_G1S889_NOMLE_61853 and tr_F6WXQ9_F6WXQ9_MACMU_9544 are exactly identical! WARNING: Sequences tr_G1S889_G1S889_NOMLE_61853 and tr_G7PHQ2_G7PHQ2_MACFA_9541 are exactly identical! WARNING: Sequences tr_G1S889_G1S889_NOMLE_61853 and tr_A0A096MRB6_A0A096MRB6_PAPAN_9555 are exactly identical! WARNING: Sequences tr_G1S889_G1S889_NOMLE_61853 and tr_A0A0D9R1V8_A0A0D9R1V8_CHLSB_60711 are exactly identical! WARNING: Sequences tr_G1S889_G1S889_NOMLE_61853 and tr_A0A2K5LLD3_A0A2K5LLD3_CERAT_9531 are exactly identical! WARNING: Sequences tr_G1S889_G1S889_NOMLE_61853 and tr_A0A2K6CQ89_A0A2K6CQ89_MACNE_9545 are exactly identical! WARNING: Sequences tr_G1S889_G1S889_NOMLE_61853 and tr_A0A2K5Z4Y7_A0A2K5Z4Y7_MANLE_9568 are exactly identical! WARNING: Sequences tr_G1S889_G1S889_NOMLE_61853 and tr_A0A2R9B7R6_A0A2R9B7R6_PANPA_9597 are exactly identical! WARNING: Sequences tr_G1NZG4_G1NZG4_MYOLU_59463 and tr_G3SG36_G3SG36_GORGO_9595 are exactly identical! WARNING: Sequences tr_G1NZG4_G1NZG4_MYOLU_59463 and tr_H2PGS0_H2PGS0_PONAB_9601 are exactly identical! WARNING: Sequences tr_G1NZG4_G1NZG4_MYOLU_59463 and tr_F6W4W9_F6W4W9_HORSE_9796 are exactly identical! WARNING: Sequences tr_G1NZG4_G1NZG4_MYOLU_59463 and tr_I3LZI0_I3LZI0_ICTTR_43179 are exactly identical! WARNING: Sequences tr_G1NZG4_G1NZG4_MYOLU_59463 and tr_H0XAW3_H0XAW3_OTOGA_30611 are exactly identical! WARNING: Sequences tr_G1NZG4_G1NZG4_MYOLU_59463 and tr_H0VK14_H0VK14_CAVPO_10141 are exactly identical! WARNING: Sequences tr_G1NZG4_G1NZG4_MYOLU_59463 and sp_Q8IWZ3_ANKH1_HUMAN_9606 are exactly identical! WARNING: Sequences tr_G1NZG4_G1NZG4_MYOLU_59463 and tr_F7CJQ2_F7CJQ2_CALJA_9483 are exactly identical! WARNING: Sequences tr_G1NZG4_G1NZG4_MYOLU_59463 and tr_G1LX53_G1LX53_AILME_9646 are exactly identical! WARNING: Sequences tr_G1NZG4_G1NZG4_MYOLU_59463 and tr_A0A091CP42_A0A091CP42_FUKDA_885580 are exactly identical! WARNING: Sequences tr_G1NZG4_G1NZG4_MYOLU_59463 and tr_A0A2U3XJ53_A0A2U3XJ53_LEPWE_9713 are exactly identical! WARNING: Sequences tr_G3GR75_G3GR75_CRIGR_10029 and tr_A0A1U7QYQ7_A0A1U7QYQ7_MESAU_10036 are exactly identical! WARNING: Sequences tr_G3QMX5_G3QMX5_GORGO_9595 and tr_H2Q1Y0_H2Q1Y0_PANTR_9598 are exactly identical! WARNING: Sequences tr_G3QMX5_G3QMX5_GORGO_9595 and sp_Q12955_ANK3_HUMAN_9606 are exactly identical! WARNING: Sequences tr_G3QMX5_G3QMX5_GORGO_9595 and tr_A0A2R9BXS8_A0A2R9BXS8_PANPA_9597 are exactly identical! WARNING: Sequences tr_H2NAT9_H2NAT9_PONAB_9601 and tr_F7D3K5_F7D3K5_CALJA_9483 are exactly identical! WARNING: Sequences tr_H2NHP2_H2NHP2_PONAB_9601 and tr_K7CMT6_K7CMT6_PANTR_9598 are exactly identical! WARNING: Sequences tr_H2NHP2_H2NHP2_PONAB_9601 and tr_F6PH71_F6PH71_HORSE_9796 are exactly identical! WARNING: Sequences tr_H2NHP2_H2NHP2_PONAB_9601 and tr_D4ACT4_D4ACT4_RAT_10116 are exactly identical! WARNING: Sequences tr_H2NHP2_H2NHP2_PONAB_9601 and tr_H0WIT0_H0WIT0_OTOGA_30611 are exactly identical! WARNING: Sequences tr_H2NHP2_H2NHP2_PONAB_9601 and sp_Q8NB46_ANR52_HUMAN_9606 are exactly identical! WARNING: Sequences tr_H2NHP2_H2NHP2_PONAB_9601 and tr_H9EQD1_H9EQD1_MACMU_9544 are exactly identical! WARNING: Sequences tr_H2NHP2_H2NHP2_PONAB_9601 and tr_G3TE01_G3TE01_LOXAF_9785 are exactly identical! WARNING: Sequences tr_H2NHP2_H2NHP2_PONAB_9601 and tr_F6UX12_F6UX12_CALJA_9483 are exactly identical! WARNING: Sequences tr_H2NHP2_H2NHP2_PONAB_9601 and tr_E1BIQ7_E1BIQ7_BOVIN_9913 are exactly identical! WARNING: Sequences tr_H2NHP2_H2NHP2_PONAB_9601 and tr_M3WG66_M3WG66_FELCA_9685 are exactly identical! WARNING: Sequences tr_H2NHP2_H2NHP2_PONAB_9601 and tr_A0A096NH02_A0A096NH02_PAPAN_9555 are exactly identical! WARNING: Sequences tr_H2NHP2_H2NHP2_PONAB_9601 and tr_A0A091D0P5_A0A091D0P5_FUKDA_885580 are exactly identical! WARNING: Sequences tr_H2NHP2_H2NHP2_PONAB_9601 and tr_A0A0D9QYS1_A0A0D9QYS1_CHLSB_60711 are exactly identical! WARNING: Sequences tr_H2NHP2_H2NHP2_PONAB_9601 and tr_A0A1S3FNL5_A0A1S3FNL5_DIPOR_10020 are exactly identical! WARNING: Sequences tr_H2NHP2_H2NHP2_PONAB_9601 and tr_A0A2K5NLJ3_A0A2K5NLJ3_CERAT_9531 are exactly identical! WARNING: Sequences tr_H2NHP2_H2NHP2_PONAB_9601 and tr_A0A2K6AMX8_A0A2K6AMX8_MACNE_9545 are exactly identical! WARNING: Sequences tr_H2NHP2_H2NHP2_PONAB_9601 and tr_A0A2K5Y8N1_A0A2K5Y8N1_MANLE_9568 are exactly identical! WARNING: Sequences tr_H2NHP2_H2NHP2_PONAB_9601 and tr_A0A2R8ZGJ2_A0A2R8ZGJ2_PANPA_9597 are exactly identical! WARNING: Sequences tr_H2NHP2_H2NHP2_PONAB_9601 and tr_A0A2Y9SJN1_A0A2Y9SJN1_PHYCD_9755 are exactly identical! WARNING: Sequences tr_H2PBD8_H2PBD8_PONAB_9601 and sp_O15084_ANR28_HUMAN_9606 are exactly identical! WARNING: Sequences tr_H2PBD8_H2PBD8_PONAB_9601 and tr_F7E5S7_F7E5S7_MACMU_9544 are exactly identical! WARNING: Sequences tr_H2PBD8_H2PBD8_PONAB_9601 and tr_F7H6C7_F7H6C7_CALJA_9483 are exactly identical! WARNING: Sequences tr_H2PBD8_H2PBD8_PONAB_9601 and tr_G7NY15_G7NY15_MACFA_9541 are exactly identical! WARNING: Sequences tr_F6XSE4_F6XSE4_CANLF_9615 and tr_K7DU15_K7DU15_PANTR_9598 are exactly identical! WARNING: Sequences tr_F6XSE4_F6XSE4_CANLF_9615 and tr_F6ZH85_F6ZH85_MACMU_9544 are exactly identical! WARNING: Sequences tr_F6XSE4_F6XSE4_CANLF_9615 and tr_G7P8G5_G7P8G5_MACFA_9541 are exactly identical! WARNING: Sequences tr_F6XSE4_F6XSE4_CANLF_9615 and tr_A0A2I3N6E9_A0A2I3N6E9_PAPAN_9555 are exactly identical! WARNING: Sequences tr_F6XSE4_F6XSE4_CANLF_9615 and tr_A0A0D9RK88_A0A0D9RK88_CHLSB_60711 are exactly identical! WARNING: Sequences tr_F6XSE4_F6XSE4_CANLF_9615 and tr_A0A1S3W4I1_A0A1S3W4I1_ERIEU_9365 are exactly identical! WARNING: Sequences tr_F6XSE4_F6XSE4_CANLF_9615 and tr_A0A2K5Y5C2_A0A2K5Y5C2_MANLE_9568 are exactly identical! WARNING: Sequences tr_F6XSE4_F6XSE4_CANLF_9615 and tr_A0A2U4AGJ9_A0A2U4AGJ9_TURTR_9739 are exactly identical! WARNING: Sequences tr_F6XSE4_F6XSE4_CANLF_9615 and tr_A0A2U3ZD56_A0A2U3ZD56_ODORO_9708 are exactly identical! WARNING: Sequences tr_F6XSE4_F6XSE4_CANLF_9615 and tr_A0A2Y9IKB6_A0A2Y9IKB6_ENHLU_391180 are exactly identical! WARNING: Sequences tr_F6XSE4_F6XSE4_CANLF_9615 and tr_A0A2Y9PPE1_A0A2Y9PPE1_DELLE_9749 are exactly identical! WARNING: Sequences tr_F6XSE4_F6XSE4_CANLF_9615 and tr_A0A2Y9SX60_A0A2Y9SX60_PHYCD_9755 are exactly identical! WARNING: Sequences tr_F6XSE4_F6XSE4_CANLF_9615 and tr_A0A384B3D1_A0A384B3D1_BALAS_310752 are exactly identical! WARNING: Sequences tr_A0A2I3TF47_A0A2I3TF47_PANTR_9598 and tr_A0A2R9CIP4_A0A2R9CIP4_PANPA_9597 are exactly identical! WARNING: Sequences tr_F6UZC4_F6UZC4_MONDO_13616 and tr_A0A1U7TKP8_A0A1U7TKP8_TARSY_1868482 are exactly identical! WARNING: Sequences tr_F6YTT0_F6YTT0_HORSE_9796 and tr_W5QDB9_W5QDB9_SHEEP_9940 are exactly identical! WARNING: Sequences tr_F6YTT0_F6YTT0_HORSE_9796 and tr_I3LRC3_I3LRC3_PIG_9823 are exactly identical! WARNING: Sequences tr_F6YTT0_F6YTT0_HORSE_9796 and sp_Q08E43_ASB8_BOVIN_9913 are exactly identical! WARNING: Sequences tr_F6YTT0_F6YTT0_HORSE_9796 and tr_A0A2Y9EK66_A0A2Y9EK66_PHYCD_9755 are exactly identical! WARNING: Sequences tr_F6YTT0_F6YTT0_HORSE_9796 and tr_A0A383ZWL3_A0A383ZWL3_BALAS_310752 are exactly identical! WARNING: Sequences tr_F6ZXD3_F6ZXD3_HORSE_9796 and tr_A0A287AEE1_A0A287AEE1_PIG_9823 are exactly identical! WARNING: Sequences tr_W5NY88_W5NY88_SHEEP_9940 and tr_A0A384CKV5_A0A384CKV5_URSMA_29073 are exactly identical! WARNING: Sequences tr_W5PFX0_W5PFX0_SHEEP_9940 and tr_E1BJ12_E1BJ12_BOVIN_9913 are exactly identical! WARNING: Sequences tr_A0A088AN05_A0A088AN05_APIME_7460 and tr_A0A2A3EE44_A0A2A3EE44_APICC_94128 are exactly identical! WARNING: Sequences tr_A0A158NYD8_A0A158NYD8_ATTCE_12957 and tr_F4WSY2_F4WSY2_ACREC_103372 are exactly identical! WARNING: Sequences tr_A0A158NYD8_A0A158NYD8_ATTCE_12957 and tr_A0A151WTV0_A0A151WTV0_9HYME_64791 are exactly identical! WARNING: Sequences tr_A0A158NYD8_A0A158NYD8_ATTCE_12957 and tr_A0A195AYV4_A0A195AYV4_9HYME_520822 are exactly identical! WARNING: Sequences tr_A0A158NYD8_A0A158NYD8_ATTCE_12957 and tr_A0A195F6K1_A0A195F6K1_9HYME_34720 are exactly identical! WARNING: Sequences tr_A0A286XC52_A0A286XC52_CAVPO_10141 and tr_F1SLZ6_F1SLZ6_PIG_9823 are exactly identical! WARNING: Sequences sp_Q96DX5_ASB9_HUMAN_9606 and tr_A0A2R9CJ65_A0A2R9CJ65_PANPA_9597 are exactly identical! WARNING: Sequences tr_A0A0E0GU17_A0A0E0GU17_ORYNI_4536 and tr_A0A0E0P1K0_A0A0E0P1K0_ORYRU_4529 are exactly identical! WARNING: Sequences tr_G7XNR1_G7XNR1_ASPKW_1033177 and tr_A0A146FTL6_A0A146FTL6_9EURO_1069201 are exactly identical! WARNING: Sequences tr_H0YTV7_H0YTV7_TAEGU_59729 and tr_U3K3W2_U3K3W2_FICAL_59894 are exactly identical! WARNING: Sequences tr_H0YTV7_H0YTV7_TAEGU_59729 and tr_A0A087R3L6_A0A087R3L6_APTFO_9233 are exactly identical! WARNING: Sequences tr_H0YTV7_H0YTV7_TAEGU_59729 and tr_A0A218UPF7_A0A218UPF7_9PASE_299123 are exactly identical! WARNING: Sequences tr_A0A091IT34_A0A091IT34_EGRGA_188379 and tr_A0A091UYI1_A0A091UYI1_NIPNI_128390 are exactly identical! WARNING: Sequences tr_A0A091IT34_A0A091IT34_EGRGA_188379 and tr_A0A087R8K2_A0A087R8K2_APTFO_9233 are exactly identical! WARNING: Sequences tr_A0A091IT34_A0A091IT34_EGRGA_188379 and tr_A0A093IKB2_A0A093IKB2_DRYPU_118200 are exactly identical! WARNING: Sequences tr_A0A091VKQ8_A0A091VKQ8_NIPNI_128390 and tr_A0A087QV92_A0A087QV92_APTFO_9233 are exactly identical! WARNING: Sequences tr_A0A087R3I8_A0A087R3I8_APTFO_9233 and tr_A0A0A0ACY5_A0A0A0ACY5_CHAVO_50402 are exactly identical! WARNING: Sequences tr_A0A091G6I9_A0A091G6I9_9AVES_55661 and tr_A0A0A0AC16_A0A0A0AC16_CHAVO_50402 are exactly identical! WARNING: Sequences tr_A0A0V1DH72_A0A0V1DH72_TRIBR_45882 and tr_A0A0V0XCI2_A0A0V0XCI2_9BILA_92179 are exactly identical! WARNING: Sequences tr_A0A0V1DH72_A0A0V1DH72_TRIBR_45882 and tr_A0A0V0VN75_A0A0V0VN75_9BILA_181606 are exactly identical! WARNING: Sequences tr_A0A0V1DH72_A0A0V1DH72_TRIBR_45882 and tr_A0A0V1LQP1_A0A0V1LQP1_9BILA_6335 are exactly identical! WARNING: Sequences tr_A0A0V1DH72_A0A0V1DH72_TRIBR_45882 and tr_A0A0V1P9M3_A0A0V1P9M3_9BILA_92180 are exactly identical! WARNING: Sequences tr_A0A0V1DH72_A0A0V1DH72_TRIBR_45882 and tr_A0A0V0UCC5_A0A0V0UCC5_9BILA_144512 are exactly identical! WARNING: Sequences tr_A0A1S3J476_A0A1S3J476_LINUN_7574 and tr_A0A1S3J5H3_A0A1S3J5H3_LINUN_7574 are exactly identical! WARNING: Sequences tr_A0A1S3QZF8_A0A1S3QZF8_SALSA_8030 and tr_A0A1S3QZL6_A0A1S3QZL6_SALSA_8030 are exactly identical! WARNING: Sequences tr_A0A226MK97_A0A226MK97_CALSU_9009 and tr_A0A226PHS7_A0A226PHS7_COLVI_9014 are exactly identical! WARNING: Sequences tr_A0A2D0SZG3_A0A2D0SZG3_ICTPU_7998 and tr_A0A2D0SZG8_A0A2D0SZG8_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0SZG3_A0A2D0SZG3_ICTPU_7998 and tr_A0A2D0SZG9_A0A2D0SZG9_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0SZG3_A0A2D0SZG3_ICTPU_7998 and tr_A0A2D0SZH1_A0A2D0SZH1_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0SZG3_A0A2D0SZG3_ICTPU_7998 and tr_A0A2D0SZW2_A0A2D0SZW2_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0SZG3_A0A2D0SZG3_ICTPU_7998 and tr_A0A2D0SZW7_A0A2D0SZW7_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0SZG3_A0A2D0SZG3_ICTPU_7998 and tr_A0A2D0T0E7_A0A2D0T0E7_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0SZG3_A0A2D0SZG3_ICTPU_7998 and tr_A0A2D0T0F3_A0A2D0T0F3_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2K5MMH2_A0A2K5MMH2_CERAT_9531 and tr_A0A2K5ZVY1_A0A2K5ZVY1_MANLE_9568 are exactly identical! WARNING: Sequences tr_A0A2U4BEB4_A0A2U4BEB4_TURTR_9739 and tr_A0A2Y9M5I2_A0A2Y9M5I2_DELLE_9749 are exactly identical! WARNING: Duplicate sequences found: 160 NOTE: Reduced alignment (with duplicates and gap-only sites/taxa removed) NOTE: was saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/A6NGH8/4_raxmlng_ancestral/A6NGH8.raxml.reduced.phy Alignment comprises 1 partitions and 418 sites Partition 0: noname Model: LG4X+R4 Alignment sites: 418 Gaps: 38.11 % Invariant sites: 0.00 % NOTE: Binary MSA file created: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/A6NGH8/4_raxmlng_ancestral/A6NGH8.raxml.rba Parallelization scheme autoconfig: 1 worker(s) x 4 thread(s) Parallel reduction/worker buffer size: 1 KB / 0 KB [00:00:00] Loading user starting tree(s) from: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/A6NGH8/3_mltree/A6NGH8.raxml.bestTree_unrooted [00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 105 / 8400 [00:00:00] Data distribution: max. searches per worker: 1 Starting ML tree search with 1 distinct starting trees [00:00:00] Tree #1, initial LogLikelihood: -205912.662539 [00:00:00 -205912.662539] Initial branch length optimization [00:00:01 -204624.953771] Model parameter optimization (eps = 0.100000) [00:00:32] Tree #1, final logLikelihood: -203365.717453 Optimized model parameters: Partition 0: noname Rate heterogeneity: FREE (4 cats, mean), weights&rates: (0.134504,0.428051) (0.135061,0.475946) (0.377634,0.862458) (0.352800,1.565899) 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 Marginal ancestral probabilities saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/A6NGH8/4_raxmlng_ancestral/A6NGH8.raxml.ancestralProbs Reconstructed ancestral sequences saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/A6NGH8/4_raxmlng_ancestral/A6NGH8.raxml.ancestralStates Node-labeled tree saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/A6NGH8/4_raxmlng_ancestral/A6NGH8.raxml.ancestralTree Execution log saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/A6NGH8/4_raxmlng_ancestral/A6NGH8.raxml.log Analysis started: 14-Jul-2021 17:54:33 / finished: 14-Jul-2021 17:55:09 Elapsed time: 36.330 seconds