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 04-Jun-2021 14:02:08 as follows: raxml-ng --ancestral --msa /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/P54845/2_msa/P54845_nogap_msa.fasta --tree /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/P54845/3_mltree/P54845.raxml.bestTree_unrooted --model LG4X --prefix /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/P54845/4_raxmlng_ancestral/P54845 --threads 4 Analysis options: run mode: Ancestral state reconstruction start tree(s): user random seed: 1622804528 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_020621/phylogeny-snakemake/results/P54845/2_msa/P54845_nogap_msa.fasta [00:00:00] Loaded alignment with 788 taxa and 237 sites WARNING: Sequences tr_B4QF32_B4QF32_DROSI_7240 and tr_B4HQM6_B4HQM6_DROSE_7238 are exactly identical! WARNING: Sequences tr_E9GW74_E9GW74_DAPPU_6669 and tr_A0A0P5DW09_A0A0P5DW09_9CRUS_35525 are exactly identical! WARNING: Sequences sp_Q90595_MAFF_CHICK_9031 and tr_A0A093IQB7_A0A093IQB7_DRYPU_118200 are exactly identical! WARNING: Sequences sp_Q90595_MAFF_CHICK_9031 and tr_A0A226PBX3_A0A226PBX3_COLVI_9014 are exactly identical! WARNING: Sequences sp_Q90596_MAFK_CHICK_9031 and tr_G1MUM2_G1MUM2_MELGA_9103 are exactly identical! WARNING: Sequences sp_Q90596_MAFK_CHICK_9031 and tr_H9GHM0_H9GHM0_ANOCA_28377 are exactly identical! WARNING: Sequences sp_Q90596_MAFK_CHICK_9031 and tr_H0ZD20_H0ZD20_TAEGU_59729 are exactly identical! WARNING: Sequences sp_Q90596_MAFK_CHICK_9031 and tr_U3KHM0_U3KHM0_FICAL_59894 are exactly identical! WARNING: Sequences sp_Q90596_MAFK_CHICK_9031 and tr_U3J6X0_U3J6X0_ANAPL_8839 are exactly identical! WARNING: Sequences sp_Q90596_MAFK_CHICK_9031 and tr_A0A151N219_A0A151N219_ALLMI_8496 are exactly identical! WARNING: Sequences sp_Q90596_MAFK_CHICK_9031 and tr_A0A0Q3XBL9_A0A0Q3XBL9_AMAAE_12930 are exactly identical! WARNING: Sequences sp_Q90596_MAFK_CHICK_9031 and tr_A0A091ERY5_A0A091ERY5_CORBR_85066 are exactly identical! WARNING: Sequences sp_Q90596_MAFK_CHICK_9031 and tr_A0A091JFM6_A0A091JFM6_EGRGA_188379 are exactly identical! WARNING: Sequences sp_Q90596_MAFK_CHICK_9031 and tr_A0A093QK74_A0A093QK74_9PASS_328815 are exactly identical! WARNING: Sequences sp_Q90596_MAFK_CHICK_9031 and tr_A0A091VAP5_A0A091VAP5_NIPNI_128390 are exactly identical! WARNING: Sequences sp_Q90596_MAFK_CHICK_9031 and tr_A0A087RFW6_A0A087RFW6_APTFO_9233 are exactly identical! WARNING: Sequences sp_Q90596_MAFK_CHICK_9031 and tr_A0A093H857_A0A093H857_STRCA_441894 are exactly identical! WARNING: Sequences sp_Q90596_MAFK_CHICK_9031 and tr_A0A099YY25_A0A099YY25_TINGU_94827 are exactly identical! WARNING: Sequences sp_Q90596_MAFK_CHICK_9031 and tr_A0A091GIQ6_A0A091GIQ6_9AVES_55661 are exactly identical! WARNING: Sequences sp_Q90596_MAFK_CHICK_9031 and tr_A0A099ZZN8_A0A099ZZN8_CHAVO_50402 are exactly identical! WARNING: Sequences sp_Q90596_MAFK_CHICK_9031 and tr_A0A2I0M0P5_A0A2I0M0P5_COLLI_8932 are exactly identical! WARNING: Sequences sp_Q90596_MAFK_CHICK_9031 and tr_A0A093FWI7_A0A093FWI7_DRYPU_118200 are exactly identical! WARNING: Sequences sp_Q90596_MAFK_CHICK_9031 and tr_A0A091IAZ4_A0A091IAZ4_CALAN_9244 are exactly identical! WARNING: Sequences sp_Q90596_MAFK_CHICK_9031 and tr_A0A3Q0H7V6_A0A3Q0H7V6_ALLSI_38654 are exactly identical! WARNING: Sequences sp_Q90596_MAFK_CHICK_9031 and tr_A0A1V4KSA9_A0A1V4KSA9_PATFA_372326 are exactly identical! WARNING: Sequences sp_Q90596_MAFK_CHICK_9031 and tr_A0A218V7Q2_A0A218V7Q2_9PASE_299123 are exactly identical! WARNING: Sequences sp_Q90596_MAFK_CHICK_9031 and tr_A0A226NJN4_A0A226NJN4_CALSU_9009 are exactly identical! WARNING: Sequences sp_Q90596_MAFK_CHICK_9031 and tr_A0A226PSR7_A0A226PSR7_COLVI_9014 are exactly identical! WARNING: Sequences sp_Q90888_MAFB_CHICK_9031 and tr_G1MW90_G1MW90_MELGA_9103 are exactly identical! WARNING: Sequences sp_Q90888_MAFB_CHICK_9031 and tr_A0A0Q3R8K6_A0A0Q3R8K6_AMAAE_12930 are exactly identical! WARNING: Sequences sp_Q90888_MAFB_CHICK_9031 and tr_A0A2I0M237_A0A2I0M237_COLLI_8932 are exactly identical! WARNING: Sequences sp_Q90888_MAFB_CHICK_9031 and tr_A0A226MFT1_A0A226MFT1_CALSU_9009 are exactly identical! WARNING: Sequences sp_Q90888_MAFB_CHICK_9031 and tr_A0A226NX50_A0A226NX50_COLVI_9014 are exactly identical! WARNING: Sequences sp_Q90889_MAFG_CHICK_9031 and tr_G1N162_G1N162_MELGA_9103 are exactly identical! WARNING: Sequences sp_Q90889_MAFG_CHICK_9031 and tr_G1KK29_G1KK29_ANOCA_28377 are exactly identical! WARNING: Sequences sp_Q90889_MAFG_CHICK_9031 and tr_U3KBK7_U3KBK7_FICAL_59894 are exactly identical! WARNING: Sequences sp_Q90889_MAFG_CHICK_9031 and tr_R0LZB5_R0LZB5_ANAPL_8839 are exactly identical! WARNING: Sequences sp_Q90889_MAFG_CHICK_9031 and tr_A0A091IQR4_A0A091IQR4_EGRGA_188379 are exactly identical! WARNING: Sequences sp_Q90889_MAFG_CHICK_9031 and tr_A0A093PYD7_A0A093PYD7_9PASS_328815 are exactly identical! WARNING: Sequences sp_Q90889_MAFG_CHICK_9031 and tr_A0A091WAH1_A0A091WAH1_NIPNI_128390 are exactly identical! WARNING: Sequences sp_Q90889_MAFG_CHICK_9031 and tr_A0A087R2C2_A0A087R2C2_APTFO_9233 are exactly identical! WARNING: Sequences sp_Q90889_MAFG_CHICK_9031 and tr_A0A091V7A5_A0A091V7A5_OPIHO_30419 are exactly identical! WARNING: Sequences sp_Q90889_MAFG_CHICK_9031 and tr_A0A099Z0B7_A0A099Z0B7_TINGU_94827 are exactly identical! WARNING: Sequences sp_Q90889_MAFG_CHICK_9031 and tr_A0A091GKW2_A0A091GKW2_9AVES_55661 are exactly identical! WARNING: Sequences sp_Q90889_MAFG_CHICK_9031 and tr_A0A0A0A9V3_A0A0A0A9V3_CHAVO_50402 are exactly identical! WARNING: Sequences sp_Q90889_MAFG_CHICK_9031 and tr_R7VRJ3_R7VRJ3_COLLI_8932 are exactly identical! WARNING: Sequences sp_Q90889_MAFG_CHICK_9031 and tr_A0A093GEP9_A0A093GEP9_DRYPU_118200 are exactly identical! WARNING: Sequences sp_Q90889_MAFG_CHICK_9031 and tr_A0A091I004_A0A091I004_CALAN_9244 are exactly identical! WARNING: Sequences sp_Q90889_MAFG_CHICK_9031 and tr_A0A1V4K5D2_A0A1V4K5D2_PATFA_372326 are exactly identical! WARNING: Sequences sp_Q90889_MAFG_CHICK_9031 and tr_A0A226N1B2_A0A226N1B2_CALSU_9009 are exactly identical! WARNING: Sequences sp_Q90889_MAFG_CHICK_9031 and tr_A0A226PN21_A0A226PN21_COLVI_9014 are exactly identical! WARNING: Sequences sp_O54790_MAFG_MOUSE_10090 and tr_G3GXB7_G3GXB7_CRIGR_10029 are exactly identical! WARNING: Sequences sp_O54790_MAFG_MOUSE_10090 and tr_E2QZ90_E2QZ90_CANLF_9615 are exactly identical! WARNING: Sequences sp_O54790_MAFG_MOUSE_10090 and tr_F6PKB1_F6PKB1_HORSE_9796 are exactly identical! WARNING: Sequences sp_O54790_MAFG_MOUSE_10090 and tr_W5Q8N7_W5Q8N7_SHEEP_9940 are exactly identical! WARNING: Sequences sp_O54790_MAFG_MOUSE_10090 and tr_A0A286X8K6_A0A286X8K6_CAVPO_10141 are exactly identical! WARNING: Sequences sp_O54790_MAFG_MOUSE_10090 and tr_G5BJ84_G5BJ84_HETGA_10181 are exactly identical! WARNING: Sequences sp_O54790_MAFG_MOUSE_10090 and tr_G3W7Z2_G3W7Z2_SARHA_9305 are exactly identical! WARNING: Sequences sp_O54790_MAFG_MOUSE_10090 and tr_A0A287BA30_A0A287BA30_PIG_9823 are exactly identical! WARNING: Sequences sp_O54790_MAFG_MOUSE_10090 and sp_A5PJV0_MAFG_BOVIN_9913 are exactly identical! WARNING: Sequences sp_O54790_MAFG_MOUSE_10090 and tr_A0A2I2U7D0_A0A2I2U7D0_FELCA_9685 are exactly identical! WARNING: Sequences sp_O54790_MAFG_MOUSE_10090 and tr_A0A151LZD6_A0A151LZD6_ALLMI_8496 are exactly identical! WARNING: Sequences sp_O54790_MAFG_MOUSE_10090 and tr_A0A1S3ANN7_A0A1S3ANN7_ERIEU_9365 are exactly identical! WARNING: Sequences sp_O54790_MAFG_MOUSE_10090 and tr_A0A1S3GIP7_A0A1S3GIP7_DIPOR_10020 are exactly identical! WARNING: Sequences sp_O54790_MAFG_MOUSE_10090 and tr_A0A1U7SUH4_A0A1U7SUH4_ALLSI_38654 are exactly identical! WARNING: Sequences sp_O54790_MAFG_MOUSE_10090 and tr_A0A1U7QAT7_A0A1U7QAT7_MESAU_10036 are exactly identical! WARNING: Sequences sp_O54790_MAFG_MOUSE_10090 and tr_A0A2U3UYG7_A0A2U3UYG7_TURTR_9739 are exactly identical! WARNING: Sequences sp_O54790_MAFG_MOUSE_10090 and tr_A0A2U3W8G2_A0A2U3W8G2_ODORO_9708 are exactly identical! WARNING: Sequences sp_O54790_MAFG_MOUSE_10090 and tr_A0A2U3YHE7_A0A2U3YHE7_LEPWE_9713 are exactly identical! WARNING: Sequences sp_O54790_MAFG_MOUSE_10090 and tr_A0A2Y9PIB1_A0A2Y9PIB1_DELLE_9749 are exactly identical! WARNING: Sequences sp_O54790_MAFG_MOUSE_10090 and tr_A0A2Y9FMX5_A0A2Y9FMX5_PHYCD_9755 are exactly identical! WARNING: Sequences sp_O54790_MAFG_MOUSE_10090 and tr_A0A384AF44_A0A384AF44_BALAS_310752 are exactly identical! WARNING: Sequences sp_O54791_MAFF_MOUSE_10090 and tr_A0A1S3FUN7_A0A1S3FUN7_DIPOR_10020 are exactly identical! WARNING: Sequences sp_O54791_MAFF_MOUSE_10090 and tr_A0A3Q0CJY1_A0A3Q0CJY1_MESAU_10036 are exactly identical! WARNING: Sequences sp_P54841_MAFB_MOUSE_10090 and tr_G3HTK2_G3HTK2_CRIGR_10029 are exactly identical! WARNING: Sequences sp_P54841_MAFB_MOUSE_10090 and sp_P54842_MAFB_RAT_10116 are exactly identical! WARNING: Sequences sp_P54841_MAFB_MOUSE_10090 and tr_I3N660_I3N660_ICTTR_43179 are exactly identical! WARNING: Sequences sp_P54841_MAFB_MOUSE_10090 and tr_H0XUM7_H0XUM7_OTOGA_30611 are exactly identical! WARNING: Sequences sp_P54841_MAFB_MOUSE_10090 and tr_A0A286XAE4_A0A286XAE4_CAVPO_10141 are exactly identical! WARNING: Sequences sp_P54841_MAFB_MOUSE_10090 and tr_U3EBS2_U3EBS2_CALJA_9483 are exactly identical! WARNING: Sequences sp_P54841_MAFB_MOUSE_10090 and tr_A0A287B9Z0_A0A287B9Z0_PIG_9823 are exactly identical! WARNING: Sequences sp_P54841_MAFB_MOUSE_10090 and tr_F1N054_F1N054_BOVIN_9913 are exactly identical! WARNING: Sequences sp_P54841_MAFB_MOUSE_10090 and tr_M3WE15_M3WE15_FELCA_9685 are exactly identical! WARNING: Sequences sp_P54841_MAFB_MOUSE_10090 and tr_A0A1U7QNE0_A0A1U7QNE0_MESAU_10036 are exactly identical! WARNING: Sequences sp_P54841_MAFB_MOUSE_10090 and tr_A0A2U3UZB9_A0A2U3UZB9_TURTR_9739 are exactly identical! WARNING: Sequences sp_P54841_MAFB_MOUSE_10090 and tr_A0A2U3WRU6_A0A2U3WRU6_ODORO_9708 are exactly identical! WARNING: Sequences sp_P54841_MAFB_MOUSE_10090 and tr_A0A2U3YSK6_A0A2U3YSK6_LEPWE_9713 are exactly identical! WARNING: Sequences sp_P54841_MAFB_MOUSE_10090 and tr_A0A2Y9D9D4_A0A2Y9D9D4_TRIMA_127582 are exactly identical! WARNING: Sequences sp_P54841_MAFB_MOUSE_10090 and tr_A0A2Y9IV16_A0A2Y9IV16_ENHLU_391180 are exactly identical! WARNING: Sequences sp_P54841_MAFB_MOUSE_10090 and tr_A0A2Y9EEG5_A0A2Y9EEG5_PHYCD_9755 are exactly identical! WARNING: Sequences sp_P54843_MAF_MOUSE_10090 and sp_O75444_MAF_HUMAN_9606 are exactly identical! WARNING: Sequences sp_P54843_MAF_MOUSE_10090 and tr_A0A286ZJS9_A0A286ZJS9_PIG_9823 are exactly identical! WARNING: Sequences sp_P54843_MAF_MOUSE_10090 and sp_A7Z017_MAF_BOVIN_9913 are exactly identical! WARNING: Sequences sp_P54843_MAF_MOUSE_10090 and tr_A0A1U8C650_A0A1U8C650_MESAU_10036 are exactly identical! WARNING: Sequences sp_P54843_MAF_MOUSE_10090 and tr_A0A2Y9P663_A0A2Y9P663_DELLE_9749 are exactly identical! WARNING: Sequences sp_Q61827_MAFK_MOUSE_10090 and tr_G3GVG2_G3GVG2_CRIGR_10029 are exactly identical! WARNING: Sequences sp_Q61827_MAFK_MOUSE_10090 and tr_A0A2J8SR88_A0A2J8SR88_PONAB_9601 are exactly identical! WARNING: Sequences sp_Q61827_MAFK_MOUSE_10090 and tr_K7DIM0_K7DIM0_PANTR_9598 are exactly identical! WARNING: Sequences sp_Q61827_MAFK_MOUSE_10090 and tr_H0WGA3_H0WGA3_OTOGA_30611 are exactly identical! WARNING: Sequences sp_Q61827_MAFK_MOUSE_10090 and tr_F7BVR2_F7BVR2_CALJA_9483 are exactly identical! WARNING: Sequences sp_Q61827_MAFK_MOUSE_10090 and tr_A0A1U7R337_A0A1U7R337_MESAU_10036 are exactly identical! WARNING: Sequences sp_Q61827_MAFK_MOUSE_10090 and tr_A0A2R9AF98_A0A2R9AF98_PANPA_9597 are exactly identical! WARNING: Sequences sp_Q8CF90_MAFA_MOUSE_10090 and sp_D3ZNT6_MAFA_RAT_10116 are exactly identical! WARNING: Sequences tr_M3YNT2_M3YNT2_MUSPF_9669 and tr_A0A2Y9KPI9_A0A2Y9KPI9_ENHLU_391180 are exactly identical! WARNING: Sequences tr_M3Z2I5_M3Z2I5_MUSPF_9669 and tr_A0A2Y9JBW8_A0A2Y9JBW8_ENHLU_391180 are exactly identical! WARNING: Sequences tr_M9PG80_M9PG80_DROME_7227 and tr_B4I5V7_B4I5V7_DROSE_7238 are exactly identical! WARNING: Sequences tr_G1R3T7_G1R3T7_NOMLE_61853 and tr_G3QFX4_G3QFX4_GORGO_9595 are exactly identical! WARNING: Sequences tr_G1R3T7_G1R3T7_NOMLE_61853 and tr_H2P1X7_H2P1X7_PONAB_9601 are exactly identical! WARNING: Sequences tr_G1R3T7_G1R3T7_NOMLE_61853 and tr_H2R8Y7_H2R8Y7_PANTR_9598 are exactly identical! WARNING: Sequences tr_G1R3T7_G1R3T7_NOMLE_61853 and sp_Q9Y5Q3_MAFB_HUMAN_9606 are exactly identical! WARNING: Sequences tr_G1R3T7_G1R3T7_NOMLE_61853 and tr_H9EPT2_H9EPT2_MACMU_9544 are exactly identical! WARNING: Sequences tr_G1R3T7_G1R3T7_NOMLE_61853 and tr_A0A096NXE7_A0A096NXE7_PAPAN_9555 are exactly identical! WARNING: Sequences tr_G1R3T7_G1R3T7_NOMLE_61853 and tr_A0A0D9SBN6_A0A0D9SBN6_CHLSB_60711 are exactly identical! WARNING: Sequences tr_G1R3T7_G1R3T7_NOMLE_61853 and tr_A0A2K5NL37_A0A2K5NL37_CERAT_9531 are exactly identical! WARNING: Sequences tr_G1R3T7_G1R3T7_NOMLE_61853 and tr_A0A2K6DB92_A0A2K6DB92_MACNE_9545 are exactly identical! WARNING: Sequences tr_G1R3T7_G1R3T7_NOMLE_61853 and tr_A0A2K5XCS8_A0A2K5XCS8_MANLE_9568 are exactly identical! WARNING: Sequences tr_G1R3T7_G1R3T7_NOMLE_61853 and tr_A0A2R8ZJJ7_A0A2R8ZJJ7_PANPA_9597 are exactly identical! WARNING: Sequences tr_G1R7G2_G1R7G2_NOMLE_61853 and tr_G3SIT8_G3SIT8_GORGO_9595 are exactly identical! WARNING: Sequences tr_G1R7G2_G1R7G2_NOMLE_61853 and tr_A0A2J8XZ41_A0A2J8XZ41_PONAB_9601 are exactly identical! WARNING: Sequences tr_G1R7G2_G1R7G2_NOMLE_61853 and tr_H2R9C1_H2R9C1_PANTR_9598 are exactly identical! WARNING: Sequences tr_G1R7G2_G1R7G2_NOMLE_61853 and sp_O15525_MAFG_HUMAN_9606 are exactly identical! WARNING: Sequences tr_G1R7G2_G1R7G2_NOMLE_61853 and tr_F6TMU6_F6TMU6_MACMU_9544 are exactly identical! WARNING: Sequences tr_G1R7G2_G1R7G2_NOMLE_61853 and tr_F6RJE6_F6RJE6_CALJA_9483 are exactly identical! WARNING: Sequences tr_G1R7G2_G1R7G2_NOMLE_61853 and tr_A0A096NTK8_A0A096NTK8_PAPAN_9555 are exactly identical! WARNING: Sequences tr_G1R7G2_G1R7G2_NOMLE_61853 and tr_A0A0D9S4P6_A0A0D9S4P6_CHLSB_60711 are exactly identical! WARNING: Sequences tr_G1R7G2_G1R7G2_NOMLE_61853 and tr_A0A2K5P376_A0A2K5P376_CERAT_9531 are exactly identical! WARNING: Sequences tr_G1R7G2_G1R7G2_NOMLE_61853 and tr_A0A2K6AXS0_A0A2K6AXS0_MACNE_9545 are exactly identical! WARNING: Sequences tr_G1R7G2_G1R7G2_NOMLE_61853 and tr_A0A2K5YYU4_A0A2K5YYU4_MANLE_9568 are exactly identical! WARNING: Sequences tr_G1RHH6_G1RHH6_NOMLE_61853 and tr_A0A2I3SE02_A0A2I3SE02_PANTR_9598 are exactly identical! WARNING: Sequences tr_G1RHH6_G1RHH6_NOMLE_61853 and tr_A0A2R8M8J9_A0A2R8M8J9_CALJA_9483 are exactly identical! WARNING: Sequences tr_G1RYI5_G1RYI5_NOMLE_61853 and tr_H2R6Z3_H2R6Z3_PANTR_9598 are exactly identical! WARNING: Sequences tr_G1RYI5_G1RYI5_NOMLE_61853 and sp_Q9ULX9_MAFF_HUMAN_9606 are exactly identical! WARNING: Sequences tr_G1RYI5_G1RYI5_NOMLE_61853 and tr_A0A1D5QFZ7_A0A1D5QFZ7_MACMU_9544 are exactly identical! WARNING: Sequences tr_G1RYI5_G1RYI5_NOMLE_61853 and tr_A0A096NK11_A0A096NK11_PAPAN_9555 are exactly identical! WARNING: Sequences tr_G1RYI5_G1RYI5_NOMLE_61853 and tr_A0A2K5L866_A0A2K5L866_CERAT_9531 are exactly identical! WARNING: Sequences tr_G1RYI5_G1RYI5_NOMLE_61853 and tr_A0A2K6E387_A0A2K6E387_MACNE_9545 are exactly identical! WARNING: Sequences tr_G1RYI5_G1RYI5_NOMLE_61853 and tr_A0A2K5YNK9_A0A2K5YNK9_MANLE_9568 are exactly identical! WARNING: Sequences tr_G1NK14_G1NK14_MELGA_9103 and tr_A0A226N120_A0A226N120_CALSU_9009 are exactly identical! WARNING: Sequences tr_G1NK14_G1NK14_MELGA_9103 and tr_A0A226PFB8_A0A226PFB8_COLVI_9014 are exactly identical! WARNING: Sequences tr_Q28ZP4_Q28ZP4_DROPS_46245 and tr_B4GGZ7_B4GGZ7_DROPE_7234 are exactly identical! WARNING: Sequences tr_Q29K55_Q29K55_DROPS_46245 and tr_B4GWX3_B4GWX3_DROPE_7234 are exactly identical! WARNING: Sequences tr_A0A2J8QKH2_A0A2J8QKH2_PANTR_9598 and sp_P54845_NRL_HUMAN_9606 are exactly identical! WARNING: Sequences tr_A0A2J8QKH2_A0A2J8QKH2_PANTR_9598 and tr_A0A2R9AIR4_A0A2R9AIR4_PANPA_9597 are exactly identical! WARNING: Sequences tr_H2QXS2_H2QXS2_PANTR_9598 and tr_H0XY68_H0XY68_OTOGA_30611 are exactly identical! WARNING: Sequences tr_H2QXS2_H2QXS2_PANTR_9598 and sp_Q8NHW3_MAFA_HUMAN_9606 are exactly identical! WARNING: Sequences tr_Q6IRI7_Q6IRI7_RAT_10116 and tr_G7MNF3_G7MNF3_MACMU_9544 are exactly identical! WARNING: Sequences tr_Q6IRI7_Q6IRI7_RAT_10116 and tr_G7P257_G7P257_MACFA_9541 are exactly identical! WARNING: Sequences tr_Q6IRI7_Q6IRI7_RAT_10116 and tr_A0A2I3NAX8_A0A2I3NAX8_PAPAN_9555 are exactly identical! WARNING: Sequences tr_Q6IRI7_Q6IRI7_RAT_10116 and tr_A0A0D9RYB3_A0A0D9RYB3_CHLSB_60711 are exactly identical! WARNING: Sequences tr_Q6IRI7_Q6IRI7_RAT_10116 and tr_A0A2K5MWJ3_A0A2K5MWJ3_CERAT_9531 are exactly identical! WARNING: Sequences tr_Q6IRI7_Q6IRI7_RAT_10116 and tr_A0A2K6CA48_A0A2K6CA48_MACNE_9545 are exactly identical! WARNING: Sequences tr_Q6IRI7_Q6IRI7_RAT_10116 and tr_A0A2K5Y4L3_A0A2K5Y4L3_MANLE_9568 are exactly identical! WARNING: Sequences tr_A0A3B5PNU9_A0A3B5PNU9_XIPMA_8083 and tr_A0A096MES6_A0A096MES6_POEFO_48698 are exactly identical! WARNING: Sequences tr_A0A3B5QUT6_A0A3B5QUT6_XIPMA_8083 and tr_A0A087XIP7_A0A087XIP7_POEFO_48698 are exactly identical! WARNING: Sequences tr_A0A3B5R2D0_A0A3B5R2D0_XIPMA_8083 and tr_A0A087YHM7_A0A087YHM7_POEFO_48698 are exactly identical! WARNING: Sequences tr_M3ZRA8_M3ZRA8_XIPMA_8083 and tr_A0A2I4BJ47_A0A2I4BJ47_9TELE_52670 are exactly identical! WARNING: Sequences tr_M4AEU5_M4AEU5_XIPMA_8083 and tr_A0A087XAR1_A0A087XAR1_POEFO_48698 are exactly identical! WARNING: Sequences tr_M4AZR6_M4AZR6_XIPMA_8083 and tr_A0A087XNJ6_A0A087XNJ6_POEFO_48698 are exactly identical! WARNING: Sequences tr_A0A158NJF3_A0A158NJF3_ATTCE_12957 and tr_F4W9J9_F4W9J9_ACREC_103372 are exactly identical! WARNING: Sequences tr_A0A158NTQ2_A0A158NTQ2_ATTCE_12957 and tr_A0A195B881_A0A195B881_9HYME_520822 are exactly identical! WARNING: Sequences tr_I3N6N1_I3N6N1_ICTTR_43179 and tr_A0A091DXE6_A0A091DXE6_FUKDA_885580 are exactly identical! WARNING: Sequences tr_F7E9A6_F7E9A6_MACMU_9544 and tr_A0A2K6ASV5_A0A2K6ASV5_MACNE_9545 are exactly identical! WARNING: Sequences tr_G3U6M7_G3U6M7_LOXAF_9785 and tr_A0A2Y9E4E9_A0A2Y9E4E9_TRIMA_127582 are exactly identical! WARNING: Sequences tr_H0YZC9_H0YZC9_TAEGU_59729 and tr_A0A093HFG6_A0A093HFG6_STRCA_441894 are exactly identical! WARNING: Sequences tr_H0YZC9_H0YZC9_TAEGU_59729 and tr_A0A218UM30_A0A218UM30_9PASE_299123 are exactly identical! WARNING: Sequences tr_H0ZJI9_H0ZJI9_TAEGU_59729 and tr_U3KDQ9_U3KDQ9_FICAL_59894 are exactly identical! WARNING: Sequences tr_H0ZJI9_H0ZJI9_TAEGU_59729 and tr_A0A091EWA3_A0A091EWA3_CORBR_85066 are exactly identical! WARNING: Sequences tr_H0ZJI9_H0ZJI9_TAEGU_59729 and tr_A0A091W0E4_A0A091W0E4_NIPNI_128390 are exactly identical! WARNING: Sequences tr_H0ZJI9_H0ZJI9_TAEGU_59729 and tr_A0A091GH69_A0A091GH69_9AVES_55661 are exactly identical! WARNING: Sequences tr_H0ZJI9_H0ZJI9_TAEGU_59729 and tr_A0A1V4J9G5_A0A1V4J9G5_PATFA_372326 are exactly identical! WARNING: Sequences tr_E3LW39_E3LW39_CAERE_31234 and tr_A0A261CEH5_A0A261CEH5_9PELO_1503980 are exactly identical! WARNING: Sequences tr_B3RJE1_B3RJE1_TRIAD_10228 and tr_A0A369S3B2_A0A369S3B2_9METZ_287889 are exactly identical! WARNING: Sequences sp_A7YY73_MAFF_BOVIN_9913 and tr_A0A2Y9QB23_A0A2Y9QB23_DELLE_9749 are exactly identical! WARNING: Sequences sp_A7YY73_MAFF_BOVIN_9913 and tr_A0A2Y9SYK1_A0A2Y9SYK1_PHYCD_9755 are exactly identical! WARNING: Sequences tr_G3MXT0_G3MXT0_BOVIN_9913 and tr_A0A2U3VYW3_A0A2U3VYW3_ODORO_9708 are exactly identical! WARNING: Sequences tr_G3MXT0_G3MXT0_BOVIN_9913 and tr_A0A2Y9JAQ6_A0A2Y9JAQ6_ENHLU_391180 are exactly identical! WARNING: Sequences tr_L5JXY0_L5JXY0_PTEAL_9402 and tr_A0A384B198_A0A384B198_BALAS_310752 are exactly identical! WARNING: Sequences tr_A0A096NX63_A0A096NX63_PAPAN_9555 and tr_A0A2K5N5X7_A0A2K5N5X7_CERAT_9531 are exactly identical! WARNING: Sequences tr_A0A0D9SBC1_A0A0D9SBC1_CHLSB_60711 and tr_A0A2K5KYK9_A0A2K5KYK9_CERAT_9531 are exactly identical! WARNING: Sequences tr_A0A0D9SBC1_A0A0D9SBC1_CHLSB_60711 and tr_A0A2K6C6Y3_A0A2K6C6Y3_MACNE_9545 are exactly identical! WARNING: Sequences tr_A0A151NHP4_A0A151NHP4_ALLMI_8496 and tr_A0A1U7RVE8_A0A1U7RVE8_ALLSI_38654 are exactly identical! WARNING: Sequences tr_A0A091ING0_A0A091ING0_EGRGA_188379 and tr_A0A218UZ80_A0A218UZ80_9PASE_299123 are exactly identical! WARNING: Sequences tr_A0A093Q424_A0A093Q424_9PASS_328815 and tr_A0A091HVM2_A0A091HVM2_CALAN_9244 are exactly identical! WARNING: Sequences tr_A0A0N1IBR4_A0A0N1IBR4_PAPXU_66420 and tr_A0A194PKD5_A0A194PKD5_PAPXU_66420 are exactly identical! WARNING: Sequences tr_A0A1S3W383_A0A1S3W383_ERIEU_9365 and tr_A0A384A632_A0A384A632_BALAS_310752 are exactly identical! WARNING: Sequences tr_A0A1S3EUR9_A0A1S3EUR9_DIPOR_10020 and tr_A0A3Q0EI08_A0A3Q0EI08_TARSY_1868482 are exactly identical! WARNING: Sequences tr_A0A1S3Q5D6_A0A1S3Q5D6_SALSA_8030 and tr_B5DFY8_B5DFY8_SALSA_8030 are exactly identical! WARNING: Sequences tr_A0A1S3Q5D6_A0A1S3Q5D6_SALSA_8030 and tr_A0A060X8K5_A0A060X8K5_ONCMY_8022 are exactly identical! WARNING: Sequences tr_A0A1S3Q5D6_A0A1S3Q5D6_SALSA_8030 and tr_A0A060XEA4_A0A060XEA4_ONCMY_8022 are exactly identical! WARNING: Sequences tr_A0A1S3QGC2_A0A1S3QGC2_SALSA_8030 and tr_A0A060ZJX5_A0A060ZJX5_ONCMY_8022 are exactly identical! WARNING: Sequences tr_A0A1S3RDK0_A0A1S3RDK0_SALSA_8030 and tr_A0A1S3S1G3_A0A1S3S1G3_SALSA_8030 are exactly identical! WARNING: Sequences tr_A0A226MN88_A0A226MN88_CALSU_9009 and tr_A0A226PIW9_A0A226PIW9_COLVI_9014 are exactly identical! WARNING: Sequences tr_A0A2D0RTW7_A0A2D0RTW7_ICTPU_7998 and tr_W5UI06_W5UI06_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0SQ65_A0A2D0SQ65_ICTPU_7998 and tr_A0A2D0SQ79_A0A2D0SQ79_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0SQ65_A0A2D0SQ65_ICTPU_7998 and tr_A0A2D0SRC7_A0A2D0SRC7_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2K5NLZ1_A0A2K5NLZ1_CERAT_9531 and tr_A0A2K6CUS8_A0A2K6CUS8_MACNE_9545 are exactly identical! WARNING: Sequences tr_A0A2U4B3Q2_A0A2U4B3Q2_TURTR_9739 and tr_A0A2Y9LP49_A0A2Y9LP49_DELLE_9749 are exactly identical! WARNING: Sequences tr_A0A2U4B3Q2_A0A2U4B3Q2_TURTR_9739 and tr_A0A2Y9S593_A0A2Y9S593_PHYCD_9755 are exactly identical! WARNING: Sequences tr_A0A2U3VH95_A0A2U3VH95_ODORO_9708 and tr_A0A2U3Y0I3_A0A2U3Y0I3_LEPWE_9713 are exactly identical! WARNING: Duplicate sequences found: 199 NOTE: Reduced alignment (with duplicates and gap-only sites/taxa removed) NOTE: was saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/P54845/4_raxmlng_ancestral/P54845.raxml.reduced.phy Alignment comprises 1 partitions and 237 sites Partition 0: noname Model: LG4X+R4 Alignment sites: 237 Gaps: 33.35 % Invariant sites: 0.00 % NOTE: Binary MSA file created: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/P54845/4_raxmlng_ancestral/P54845.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_020621/phylogeny-snakemake/results/P54845/3_mltree/P54845.raxml.bestTree_unrooted [00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 60 / 4800 [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: -42459.829823 [00:00:00 -42459.829823] Initial branch length optimization [00:00:00 -40370.253494] Model parameter optimization (eps = 0.100000) [00:00:27] Tree #1, final logLikelihood: -40276.324841 Optimized model parameters: Partition 0: noname Rate heterogeneity: FREE (4 cats, mean), weights&rates: (0.135394,0.323508) (0.108186,0.757729) (0.349410,0.626410) (0.407010,1.610156) 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_020621/phylogeny-snakemake/results/P54845/4_raxmlng_ancestral/P54845.raxml.ancestralProbs Reconstructed ancestral sequences saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/P54845/4_raxmlng_ancestral/P54845.raxml.ancestralStates Node-labeled tree saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/P54845/4_raxmlng_ancestral/P54845.raxml.ancestralTree Execution log saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/P54845/4_raxmlng_ancestral/P54845.raxml.log Analysis started: 04-Jun-2021 14:02:08 / finished: 04-Jun-2021 14:02:38 Elapsed time: 29.252 seconds