RAxML-NG v. 1.0.2 released on 22.02.2021 by The Exelixis Lab. Developed by: Alexey M. Kozlov and Alexandros Stamatakis. Contributors: Diego Darriba, Tomas Flouri, Benoit Morel, Sarah Lutteropp, Ben Bettisworth. Latest version: https://github.com/amkozlov/raxml-ng Questions/problems/suggestions? Please visit: https://groups.google.com/forum/#!forum/raxml System: Intel(R) Xeon(R) Gold 6148 CPU @ 2.40GHz, 40 cores, 376 GB RAM RAxML-NG was called at 03-Jun-2021 02:00:38 as follows: raxml-ng --ancestral --msa /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P10828/2_msa/P10828_nogap_msa.fasta --tree /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P10828/3_mltree/P10828.raxml.bestTree_unrooted --model LG4X --prefix /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P10828/4_raxmlng_ancestral/P10828 --threads 4 Analysis options: run mode: Ancestral state reconstruction start tree(s): user random seed: 1622674838 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: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P10828/2_msa/P10828_nogap_msa.fasta [00:00:00] Loaded alignment with 1001 taxa and 461 sites WARNING: Sequences sp_P22448_RARB_CHICK_9031 and tr_G3UUU2_G3UUU2_MELGA_9103 are exactly identical! WARNING: Sequences sp_P22448_RARB_CHICK_9031 and tr_U3IFR1_U3IFR1_ANAPL_8839 are exactly identical! WARNING: Sequences sp_P68306_THB_CHICK_9031 and tr_U3K3J5_U3K3J5_FICAL_59894 are exactly identical! WARNING: Sequences sp_P68306_THB_CHICK_9031 and tr_A0A218VE64_A0A218VE64_9PASE_299123 are exactly identical! WARNING: Sequences tr_Q8JHU1_Q8JHU1_CHICK_9031 and tr_G1NE58_G1NE58_MELGA_9103 are exactly identical! WARNING: Sequences tr_Q8JHU1_Q8JHU1_CHICK_9031 and tr_A0A226MEB0_A0A226MEB0_CALSU_9009 are exactly identical! WARNING: Sequences sp_P18911_RARG_MOUSE_10090 and tr_F1PN60_F1PN60_CANLF_9615 are exactly identical! WARNING: Sequences sp_P18911_RARG_MOUSE_10090 and tr_A0A2I3T1N3_A0A2I3T1N3_PANTR_9598 are exactly identical! WARNING: Sequences sp_P18911_RARG_MOUSE_10090 and tr_I3N6K5_I3N6K5_ICTTR_43179 are exactly identical! WARNING: Sequences sp_P18911_RARG_MOUSE_10090 and tr_H0VRX3_H0VRX3_CAVPO_10141 are exactly identical! WARNING: Sequences sp_P18911_RARG_MOUSE_10090 and sp_P13631_RARG_HUMAN_9606 are exactly identical! WARNING: Sequences sp_P18911_RARG_MOUSE_10090 and tr_F6RB79_F6RB79_MACMU_9544 are exactly identical! WARNING: Sequences sp_P18911_RARG_MOUSE_10090 and tr_A0A2R8MMD9_A0A2R8MMD9_CALJA_9483 are exactly identical! WARNING: Sequences sp_P18911_RARG_MOUSE_10090 and tr_A0A286ZM53_A0A286ZM53_PIG_9823 are exactly identical! WARNING: Sequences sp_P18911_RARG_MOUSE_10090 and tr_G7PHU3_G7PHU3_MACFA_9541 are exactly identical! WARNING: Sequences sp_P18911_RARG_MOUSE_10090 and tr_Q08DD4_Q08DD4_BOVIN_9913 are exactly identical! WARNING: Sequences sp_P18911_RARG_MOUSE_10090 and tr_A0A2K6BUA5_A0A2K6BUA5_MACNE_9545 are exactly identical! WARNING: Sequences sp_P18911_RARG_MOUSE_10090 and tr_A0A2Y9MZ66_A0A2Y9MZ66_DELLE_9749 are exactly identical! WARNING: Sequences sp_P18911_RARG_MOUSE_10090 and tr_A0A384D720_A0A384D720_URSMA_29073 are exactly identical! WARNING: Sequences sp_P18911_RARG_MOUSE_10090 and tr_A0A383ZWI9_A0A383ZWI9_BALAS_310752 are exactly identical! WARNING: Sequences tr_G9KK78_G9KK78_MUSPF_9669 and tr_G1QML8_G1QML8_NOMLE_61853 are exactly identical! WARNING: Sequences tr_G9KK78_G9KK78_MUSPF_9669 and tr_H2NU79_H2NU79_PONAB_9601 are exactly identical! WARNING: Sequences tr_G9KK78_G9KK78_MUSPF_9669 and tr_G1TI43_G1TI43_RABIT_9986 are exactly identical! WARNING: Sequences tr_G9KK78_G9KK78_MUSPF_9669 and tr_W5PXH0_W5PXH0_SHEEP_9940 are exactly identical! WARNING: Sequences tr_G9KK78_G9KK78_MUSPF_9669 and tr_I3M4V2_I3M4V2_ICTTR_43179 are exactly identical! WARNING: Sequences tr_G9KK78_G9KK78_MUSPF_9669 and sp_P10276_RARA_HUMAN_9606 are exactly identical! WARNING: Sequences tr_G9KK78_G9KK78_MUSPF_9669 and tr_F1RXC9_F1RXC9_PIG_9823 are exactly identical! WARNING: Sequences tr_G9KK78_G9KK78_MUSPF_9669 and tr_G1LMX4_G1LMX4_AILME_9646 are exactly identical! WARNING: Sequences tr_G9KK78_G9KK78_MUSPF_9669 and tr_F1MWQ3_F1MWQ3_BOVIN_9913 are exactly identical! WARNING: Sequences tr_G9KK78_G9KK78_MUSPF_9669 and tr_L5JQ51_L5JQ51_PTEAL_9402 are exactly identical! WARNING: Sequences tr_G9KK78_G9KK78_MUSPF_9669 and tr_A0A0D9S321_A0A0D9S321_CHLSB_60711 are exactly identical! WARNING: Sequences tr_G9KK78_G9KK78_MUSPF_9669 and tr_A0A1U7UH95_A0A1U7UH95_TARSY_1868482 are exactly identical! WARNING: Sequences tr_G9KK78_G9KK78_MUSPF_9669 and tr_A0A2U3VJK3_A0A2U3VJK3_ODORO_9708 are exactly identical! WARNING: Sequences tr_G9KK78_G9KK78_MUSPF_9669 and tr_A0A383ZRW1_A0A383ZRW1_BALAS_310752 are exactly identical! WARNING: Sequences tr_M3YL24_M3YL24_MUSPF_9669 and tr_G1QU20_G1QU20_NOMLE_61853 are exactly identical! WARNING: Sequences tr_M3YL24_M3YL24_MUSPF_9669 and tr_G3S8K4_G3S8K4_GORGO_9595 are exactly identical! WARNING: Sequences tr_M3YL24_M3YL24_MUSPF_9669 and tr_H2PBB6_H2PBB6_PONAB_9601 are exactly identical! WARNING: Sequences tr_M3YL24_M3YL24_MUSPF_9669 and tr_E2R2A6_E2R2A6_CANLF_9615 are exactly identical! WARNING: Sequences tr_M3YL24_M3YL24_MUSPF_9669 and tr_A0A2I3T0W6_A0A2I3T0W6_PANTR_9598 are exactly identical! WARNING: Sequences tr_M3YL24_M3YL24_MUSPF_9669 and tr_F6YXU9_F6YXU9_HORSE_9796 are exactly identical! WARNING: Sequences tr_M3YL24_M3YL24_MUSPF_9669 and tr_D3ZFD9_D3ZFD9_RAT_10116 are exactly identical! WARNING: Sequences tr_M3YL24_M3YL24_MUSPF_9669 and tr_I3MAT4_I3MAT4_ICTTR_43179 are exactly identical! WARNING: Sequences tr_M3YL24_M3YL24_MUSPF_9669 and tr_A0A1D5QJY1_A0A1D5QJY1_MACMU_9544 are exactly identical! WARNING: Sequences tr_M3YL24_M3YL24_MUSPF_9669 and tr_M3WD77_M3WD77_FELCA_9685 are exactly identical! WARNING: Sequences tr_M3YL24_M3YL24_MUSPF_9669 and tr_A0A2I3MGX5_A0A2I3MGX5_PAPAN_9555 are exactly identical! WARNING: Sequences tr_M3YL24_M3YL24_MUSPF_9669 and tr_A0A2K5NBP9_A0A2K5NBP9_CERAT_9531 are exactly identical! WARNING: Sequences tr_M3YL24_M3YL24_MUSPF_9669 and tr_A0A2K6DR22_A0A2K6DR22_MACNE_9545 are exactly identical! WARNING: Sequences tr_M3YL24_M3YL24_MUSPF_9669 and tr_A0A2K5Z0E7_A0A2K5Z0E7_MANLE_9568 are exactly identical! WARNING: Sequences tr_M3YL24_M3YL24_MUSPF_9669 and tr_A0A2R9BQB5_A0A2R9BQB5_PANPA_9597 are exactly identical! WARNING: Sequences tr_M3Z0G0_M3Z0G0_MUSPF_9669 and tr_A0A2Y9J2B4_A0A2Y9J2B4_ENHLU_391180 are exactly identical! WARNING: Sequences tr_A0A2I3FV35_A0A2I3FV35_NOMLE_61853 and tr_G3QWF5_G3QWF5_GORGO_9595 are exactly identical! WARNING: Sequences tr_A0A2I3FV35_A0A2I3FV35_NOMLE_61853 and tr_A0A2I3SVN9_A0A2I3SVN9_PANTR_9598 are exactly identical! WARNING: Sequences tr_A0A2I3FV35_A0A2I3FV35_NOMLE_61853 and tr_F6S9P7_F6S9P7_CALJA_9483 are exactly identical! WARNING: Sequences tr_A0A2I3FV35_A0A2I3FV35_NOMLE_61853 and tr_G7NY92_G7NY92_MACFA_9541 are exactly identical! WARNING: Sequences tr_A0A2I3FV35_A0A2I3FV35_NOMLE_61853 and tr_A0A2I3NB61_A0A2I3NB61_PAPAN_9555 are exactly identical! WARNING: Sequences tr_A0A2I3FV35_A0A2I3FV35_NOMLE_61853 and tr_A0A2K5MKR8_A0A2K5MKR8_CERAT_9531 are exactly identical! WARNING: Sequences tr_A0A2I3FV35_A0A2I3FV35_NOMLE_61853 and tr_A0A2K6E1L8_A0A2K6E1L8_MACNE_9545 are exactly identical! WARNING: Sequences tr_A0A2I3FV35_A0A2I3FV35_NOMLE_61853 and tr_A0A2K5YHL0_A0A2K5YHL0_MANLE_9568 are exactly identical! WARNING: Sequences tr_A0A2I3FV35_A0A2I3FV35_NOMLE_61853 and tr_A0A2R9A5N1_A0A2R9A5N1_PANPA_9597 are exactly identical! WARNING: Sequences tr_A0A2I3H0K9_A0A2I3H0K9_NOMLE_61853 and tr_A0A2I2YCE9_A0A2I2YCE9_GORGO_9595 are exactly identical! WARNING: Sequences tr_A0A2I3H0K9_A0A2I3H0K9_NOMLE_61853 and tr_A0A2I3SI31_A0A2I3SI31_PANTR_9598 are exactly identical! WARNING: Sequences tr_A0A2I3H0K9_A0A2I3H0K9_NOMLE_61853 and tr_G1K373_G1K373_MACMU_9544 are exactly identical! WARNING: Sequences tr_A0A2I3H0K9_A0A2I3H0K9_NOMLE_61853 and sp_O18924_PPARG_MACMU_9544 are exactly identical! WARNING: Sequences tr_A0A2I3H0K9_A0A2I3H0K9_NOMLE_61853 and tr_F6T9U1_F6T9U1_CALJA_9483 are exactly identical! WARNING: Sequences tr_A0A2I3H0K9_A0A2I3H0K9_NOMLE_61853 and tr_G7NYH4_G7NYH4_MACFA_9541 are exactly identical! WARNING: Sequences tr_A0A2I3H0K9_A0A2I3H0K9_NOMLE_61853 and tr_A0A0D9RBU3_A0A0D9RBU3_CHLSB_60711 are exactly identical! WARNING: Sequences tr_A0A2I3H0K9_A0A2I3H0K9_NOMLE_61853 and tr_A0A2K5L4H2_A0A2K5L4H2_CERAT_9531 are exactly identical! WARNING: Sequences tr_A0A2I3H0K9_A0A2I3H0K9_NOMLE_61853 and tr_A0A2K6B7D4_A0A2K6B7D4_MACNE_9545 are exactly identical! WARNING: Sequences tr_A0A2I3H0K9_A0A2I3H0K9_NOMLE_61853 and tr_A0A2K6AFG8_A0A2K6AFG8_MANLE_9568 are exactly identical! WARNING: Sequences tr_A0A2I3H0K9_A0A2I3H0K9_NOMLE_61853 and tr_A0A2R9A8K3_A0A2R9A8K3_PANPA_9597 are exactly identical! WARNING: Sequences tr_G3QKS9_G3QKS9_GORGO_9595 and tr_H2R9N8_H2R9N8_PANTR_9598 are exactly identical! WARNING: Sequences tr_G3QKS9_G3QKS9_GORGO_9595 and tr_A0A2R9CKX4_A0A2R9CKX4_PANPA_9597 are exactly identical! WARNING: Sequences tr_A0A0A0MPB6_A0A0A0MPB6_CANLF_9615 and sp_Q4U3Q4_PPARG_CANLF_9615 are exactly identical! WARNING: Sequences tr_A0A0A0MPB6_A0A0A0MPB6_CANLF_9615 and tr_G1LDR7_G1LDR7_AILME_9646 are exactly identical! WARNING: Sequences tr_A0A2I3S5L3_A0A2I3S5L3_PANTR_9598 and sp_Q96RI1_NR1H4_HUMAN_9606 are exactly identical! WARNING: Sequences tr_A0A2I3S5L3_A0A2I3S5L3_PANTR_9598 and tr_A0A2R8ZRX6_A0A2R8ZRX6_PANPA_9597 are exactly identical! WARNING: Sequences tr_A0A2I3SPS8_A0A2I3SPS8_PANTR_9598 and tr_A0A2R9BRK5_A0A2R9BRK5_PANPA_9597 are exactly identical! WARNING: Sequences tr_H2QCV7_H2QCV7_PANTR_9598 and tr_A0A2R9BJJ5_A0A2R9BJJ5_PANPA_9597 are exactly identical! WARNING: Sequences tr_F6ZL91_F6ZL91_HORSE_9796 and tr_A0A287CW18_A0A287CW18_ICTTR_43179 are exactly identical! WARNING: Sequences tr_F6ZL91_F6ZL91_HORSE_9796 and sp_O97716_THA_PIG_9823 are exactly identical! WARNING: Sequences tr_A0A0G2JW78_A0A0G2JW78_RAT_10116 and tr_A0A1U8CBR3_A0A1U8CBR3_MESAU_10036 are exactly identical! WARNING: Sequences tr_M3ZHC5_M3ZHC5_XIPMA_8083 and tr_A0A096M8G6_A0A096M8G6_POEFO_48698 are exactly identical! WARNING: Sequences tr_H0WSU1_H0WSU1_OTOGA_30611 and tr_L5JS23_L5JS23_PTEAL_9402 are exactly identical! WARNING: Sequences tr_H0WSU1_H0WSU1_OTOGA_30611 and tr_A0A1S3A8J3_A0A1S3A8J3_ERIEU_9365 are exactly identical! WARNING: Sequences tr_H0WSU1_H0WSU1_OTOGA_30611 and tr_A0A1S3GX10_A0A1S3GX10_DIPOR_10020 are exactly identical! WARNING: Sequences tr_H0WSU1_H0WSU1_OTOGA_30611 and tr_A0A1U8CBE0_A0A1U8CBE0_MESAU_10036 are exactly identical! WARNING: Sequences tr_H0WSU1_H0WSU1_OTOGA_30611 and tr_A0A2U3VJY3_A0A2U3VJY3_ODORO_9708 are exactly identical! WARNING: Sequences tr_H0WSU1_H0WSU1_OTOGA_30611 and tr_A0A2U3YR99_A0A2U3YR99_LEPWE_9713 are exactly identical! WARNING: Sequences tr_H0WSU1_H0WSU1_OTOGA_30611 and tr_A0A2Y9JVU8_A0A2Y9JVU8_ENHLU_391180 are exactly identical! WARNING: Sequences tr_H0WSU1_H0WSU1_OTOGA_30611 and tr_A0A2Y9LYM2_A0A2Y9LYM2_DELLE_9749 are exactly identical! WARNING: Sequences tr_H0WSU1_H0WSU1_OTOGA_30611 and tr_A0A2Y9F266_A0A2Y9F266_PHYCD_9755 are exactly identical! WARNING: Sequences tr_H0WSU1_H0WSU1_OTOGA_30611 and tr_A0A384BYE0_A0A384BYE0_URSMA_29073 are exactly identical! WARNING: Sequences tr_H0WSU1_H0WSU1_OTOGA_30611 and tr_A0A383ZR94_A0A383ZR94_BALAS_310752 are exactly identical! WARNING: Sequences tr_H0VTA6_H0VTA6_CAVPO_10141 and tr_F6RB49_F6RB49_CALJA_9483 are exactly identical! WARNING: Sequences tr_H0VTA6_H0VTA6_CAVPO_10141 and tr_L5L3F0_L5L3F0_PTEAL_9402 are exactly identical! WARNING: Sequences tr_H0VTA6_H0VTA6_CAVPO_10141 and tr_A0A091D601_A0A091D601_FUKDA_885580 are exactly identical! WARNING: Sequences tr_H0VTA6_H0VTA6_CAVPO_10141 and tr_A0A1S3ENE9_A0A1S3ENE9_DIPOR_10020 are exactly identical! WARNING: Sequences sp_P10826_RARB_HUMAN_9606 and tr_A0A1U7TWI3_A0A1U7TWI3_TARSY_1868482 are exactly identical! WARNING: Sequences sp_P10826_RARB_HUMAN_9606 and tr_A0A2Y9KCT9_A0A2Y9KCT9_ENHLU_391180 are exactly identical! WARNING: Sequences sp_P10827_THA_HUMAN_9606 and tr_A0A0D9S339_A0A0D9S339_CHLSB_60711 are exactly identical! WARNING: Sequences tr_F6U1W4_F6U1W4_MACMU_9544 and tr_G7PJA3_G7PJA3_MACFA_9541 are exactly identical! WARNING: Sequences tr_F6U1W4_F6U1W4_MACMU_9544 and tr_A0A096NC34_A0A096NC34_PAPAN_9555 are exactly identical! WARNING: Sequences tr_F6U1W4_F6U1W4_MACMU_9544 and tr_A0A0D9S162_A0A0D9S162_CHLSB_60711 are exactly identical! WARNING: Sequences tr_F6U1W4_F6U1W4_MACMU_9544 and tr_A0A2K5NPA3_A0A2K5NPA3_CERAT_9531 are exactly identical! WARNING: Sequences tr_F6U1W4_F6U1W4_MACMU_9544 and tr_A0A2K6BCT3_A0A2K6BCT3_MACNE_9545 are exactly identical! WARNING: Sequences tr_F6U1W4_F6U1W4_MACMU_9544 and tr_A0A2K5XS38_A0A2K5XS38_MANLE_9568 are exactly identical! WARNING: Sequences tr_F7G9B9_F7G9B9_MACMU_9544 and tr_A0A0D9RBL0_A0A0D9RBL0_CHLSB_60711 are exactly identical! WARNING: Sequences tr_I0FG12_I0FG12_MACMU_9544 and tr_A0A2Y9JV20_A0A2Y9JV20_ENHLU_391180 are exactly identical! WARNING: Sequences sp_Q8MIM3_NR1I3_MACMU_9544 and tr_A0A096N2Y4_A0A096N2Y4_PAPAN_9555 are exactly identical! WARNING: Sequences sp_Q8MIM3_NR1I3_MACMU_9544 and tr_A0A2K6BPR6_A0A2K6BPR6_MACNE_9545 are exactly identical! WARNING: Sequences tr_G3W3E2_G3W3E2_SARHA_9305 and sp_O62807_PPARG_PIG_9823 are exactly identical! WARNING: Sequences tr_H0YYW9_H0YYW9_TAEGU_59729 and tr_U3K3J3_U3K3J3_FICAL_59894 are exactly identical! WARNING: Sequences tr_H0ZJP2_H0ZJP2_TAEGU_59729 and tr_A0A091VV96_A0A091VV96_NIPNI_128390 are exactly identical! WARNING: Sequences tr_H0ZJP2_H0ZJP2_TAEGU_59729 and tr_A0A218V9F4_A0A218V9F4_9PASE_299123 are exactly identical! WARNING: Sequences tr_F1MTT1_F1MTT1_BOVIN_9913 and sp_Q3SZL0_NR1H4_BOVIN_9913 are exactly identical! WARNING: Sequences tr_U3JUY4_U3JUY4_FICAL_59894 and tr_A0A087QYK9_A0A087QYK9_APTFO_9233 are exactly identical! WARNING: Sequences tr_A0A2I3LZ58_A0A2I3LZ58_PAPAN_9555 and tr_A0A2K5KQN8_A0A2K5KQN8_CERAT_9531 are exactly identical! WARNING: Sequences tr_A0A2I3LZ58_A0A2I3LZ58_PAPAN_9555 and tr_A0A2K5Z439_A0A2K5Z439_MANLE_9568 are exactly identical! WARNING: Sequences tr_A0A2I3MWU2_A0A2I3MWU2_PAPAN_9555 and tr_A0A2K5N2P2_A0A2K5N2P2_CERAT_9531 are exactly identical! WARNING: Sequences tr_A0A2I3N6C1_A0A2I3N6C1_PAPAN_9555 and tr_A0A2K5P3R2_A0A2K5P3R2_CERAT_9531 are exactly identical! WARNING: Sequences tr_A0A2I3N6C1_A0A2I3N6C1_PAPAN_9555 and tr_A0A2K6BFY8_A0A2K6BFY8_MACNE_9545 are exactly identical! WARNING: Sequences tr_A0A2I3N6C1_A0A2I3N6C1_PAPAN_9555 and tr_A0A2K6A937_A0A2K6A937_MANLE_9568 are exactly identical! WARNING: Sequences tr_A0A151PCR3_A0A151PCR3_ALLMI_8496 and tr_A0A1U8DB42_A0A1U8DB42_ALLSI_38654 are exactly identical! WARNING: Sequences tr_A0A091EMJ6_A0A091EMJ6_CORBR_85066 and tr_A0A093PVM7_A0A093PVM7_9PASS_328815 are exactly identical! WARNING: Sequences tr_A0A2I0MQP2_A0A2I0MQP2_COLLI_8932 and tr_A0A1V4KDS9_A0A1V4KDS9_PATFA_372326 are exactly identical! WARNING: Sequences tr_A0A0V1CSX1_A0A0V1CSX1_TRIBR_45882 and tr_A0A0V0U9D4_A0A0V0U9D4_9BILA_144512 are exactly identical! WARNING: Sequences tr_A0A0V1CX65_A0A0V1CX65_TRIBR_45882 and tr_A0A0V0VYE3_A0A0V0VYE3_9BILA_181606 are exactly identical! WARNING: Sequences tr_A0A0V1CX65_A0A0V1CX65_TRIBR_45882 and tr_A0A0V1PEM8_A0A0V1PEM8_9BILA_92180 are exactly identical! WARNING: Sequences tr_A0A0V1CX65_A0A0V1CX65_TRIBR_45882 and tr_A0A0V0U7W0_A0A0V0U7W0_9BILA_144512 are exactly identical! WARNING: Sequences tr_A0A0V1D4X9_A0A0V1D4X9_TRIBR_45882 and tr_A0A0V0VJE8_A0A0V0VJE8_9BILA_181606 are exactly identical! WARNING: Sequences tr_A0A0V1D4X9_A0A0V1D4X9_TRIBR_45882 and tr_A0A0V1P7W6_A0A0V1P7W6_9BILA_92180 are exactly identical! WARNING: Sequences tr_A0A0V1D4X9_A0A0V1D4X9_TRIBR_45882 and tr_A0A0V0TQG9_A0A0V0TQG9_9BILA_144512 are exactly identical! WARNING: Sequences tr_A0A0V1DC20_A0A0V1DC20_TRIBR_45882 and tr_A0A0V0UM22_A0A0V0UM22_9BILA_181606 are exactly identical! WARNING: Sequences tr_A0A0V1DC20_A0A0V1DC20_TRIBR_45882 and tr_A0A0V0TLL1_A0A0V0TLL1_9BILA_144512 are exactly identical! WARNING: Sequences tr_A0A0V0WPT1_A0A0V0WPT1_9BILA_92179 and tr_A0A0V1KN98_A0A0V1KN98_9BILA_6335 are exactly identical! WARNING: Sequences tr_A0A0V0VIS1_A0A0V0VIS1_9BILA_181606 and tr_A0A0V1PEM3_A0A0V1PEM3_9BILA_92180 are exactly identical! WARNING: Sequences tr_A0A0V1LAZ7_A0A0V1LAZ7_9BILA_6335 and tr_A0A0V1A7P5_A0A0V1A7P5_9BILA_990121 are exactly identical! WARNING: Sequences tr_A0A1S3JVH9_A0A1S3JVH9_LINUN_7574 and tr_A0A1S3JVP8_A0A1S3JVP8_LINUN_7574 are exactly identical! WARNING: Sequences tr_A0A1S2WZ42_A0A1S2WZ42_SALSA_8030 and sp_Q9W785_THA_SALSA_8030 are exactly identical! WARNING: Sequences tr_Q90Y21_Q90Y21_SALSA_8030 and tr_Q90Y22_Q90Y22_SALSA_8030 are exactly identical! WARNING: Sequences tr_Q8K473_Q8K473_MESAU_10036 and tr_Q8K474_Q8K474_MESAU_10036 are exactly identical! WARNING: Sequences tr_Q8K473_Q8K473_MESAU_10036 and tr_Q8K476_Q8K476_MESAU_10036 are exactly identical! WARNING: Sequences tr_A0A2I4BA78_A0A2I4BA78_9TELE_52670 and tr_A0A2I4C1P4_A0A2I4C1P4_9TELE_52670 are exactly identical! WARNING: Sequences tr_A0A2D0PLB2_A0A2D0PLB2_ICTPU_7998 and tr_W5ULB6_W5ULB6_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0Q8R6_A0A2D0Q8R6_ICTPU_7998 and tr_A0A2D0QBB9_A0A2D0QBB9_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0RRC0_A0A2D0RRC0_ICTPU_7998 and tr_A0A2D0RRY2_A0A2D0RRY2_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0S2R1_A0A2D0S2R1_ICTPU_7998 and tr_A0A2D0S3K9_A0A2D0S3K9_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2U3WCR8_A0A2U3WCR8_ODORO_9708 and tr_A0A2U3YD47_A0A2U3YD47_LEPWE_9713 are exactly identical! WARNING: Duplicate sequences found: 148 NOTE: Reduced alignment (with duplicates and gap-only sites/taxa removed) NOTE: was saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P10828/4_raxmlng_ancestral/P10828.raxml.reduced.phy Alignment comprises 1 partitions and 461 sites Partition 0: noname Model: LG4X+R4 Alignment sites: 461 Gaps: 26.27 % Invariant sites: 0.00 % NOTE: Binary MSA file created: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P10828/4_raxmlng_ancestral/P10828.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: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P10828/3_mltree/P10828.raxml.bestTree_unrooted [00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 116 / 9280 [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: -117087.916942 [00:00:00 -117087.916942] Initial branch length optimization [00:00:00 -113561.905961] Model parameter optimization (eps = 0.100000) [00:00:49] Tree #1, final logLikelihood: -113174.503183 Optimized model parameters: Partition 0: noname Rate heterogeneity: FREE (4 cats, mean), weights&rates: (0.142501,0.273133) (0.170186,0.322609) (0.397536,0.661920) (0.289777,2.219077) 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: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P10828/4_raxmlng_ancestral/P10828.raxml.ancestralProbs Reconstructed ancestral sequences saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P10828/4_raxmlng_ancestral/P10828.raxml.ancestralStates Node-labeled tree saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P10828/4_raxmlng_ancestral/P10828.raxml.ancestralTree Execution log saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P10828/4_raxmlng_ancestral/P10828.raxml.log Analysis started: 03-Jun-2021 02:00:38 / finished: 03-Jun-2021 02:01:31 Elapsed time: 53.065 seconds Consumed energy: 3.282 Wh