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 12-Jul-2021 18:02:34 as follows: raxml-ng --ancestral --msa /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q5JT82/2_msa/Q5JT82_nogap_msa.fasta --tree /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q5JT82/3_mltree/Q5JT82.raxml.bestTree_unrooted --model LG4X --prefix /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q5JT82/4_raxmlng_ancestral/Q5JT82 --threads 4 Analysis options: run mode: Ancestral state reconstruction start tree(s): user random seed: 1626102154 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/300621_run/phylogeny-snakemake/results/Q5JT82/2_msa/Q5JT82_nogap_msa.fasta [00:00:00] Loaded alignment with 1001 taxa and 389 sites WARNING: Sequences tr_A0A1D5PLW4_A0A1D5PLW4_CHICK_9031 and tr_G1ND65_G1ND65_MELGA_9103 are exactly identical! WARNING: Sequences tr_F1NAJ7_F1NAJ7_CHICK_9031 and tr_A0A1V4J4N4_A0A1V4J4N4_PATFA_372326 are exactly identical! WARNING: Sequences sp_Q62445_SP4_MOUSE_10090 and tr_Q63158_Q63158_RAT_10116 are exactly identical! WARNING: Sequences sp_Q99JB0_KLF7_MOUSE_10090 and tr_A0A3Q0CR77_A0A3Q0CR77_MESAU_10036 are exactly identical! WARNING: Sequences tr_M3XN27_M3XN27_MUSPF_9669 and tr_G3SWY8_G3SWY8_LOXAF_9785 are exactly identical! WARNING: Sequences tr_M3XN27_M3XN27_MUSPF_9669 and tr_I3LBA7_I3LBA7_PIG_9823 are exactly identical! WARNING: Sequences tr_M3XN27_M3XN27_MUSPF_9669 and tr_G1M9D9_G1M9D9_AILME_9646 are exactly identical! WARNING: Sequences tr_M3XN27_M3XN27_MUSPF_9669 and tr_A0A2U3WAS6_A0A2U3WAS6_ODORO_9708 are exactly identical! WARNING: Sequences tr_M3XN27_M3XN27_MUSPF_9669 and tr_A0A2U3Z1A2_A0A2U3Z1A2_LEPWE_9713 are exactly identical! WARNING: Sequences tr_M3Y3L6_M3Y3L6_MUSPF_9669 and tr_G1LU15_G1LU15_AILME_9646 are exactly identical! WARNING: Sequences tr_M3Y3L6_M3Y3L6_MUSPF_9669 and tr_M3WQR5_M3WQR5_FELCA_9685 are exactly identical! WARNING: Sequences tr_M3Y3L6_M3Y3L6_MUSPF_9669 and tr_A0A2U3VMG6_A0A2U3VMG6_ODORO_9708 are exactly identical! WARNING: Sequences tr_M3Y3L6_M3Y3L6_MUSPF_9669 and tr_A0A2Y9JV30_A0A2Y9JV30_ENHLU_391180 are exactly identical! WARNING: Sequences tr_M3Y772_M3Y772_MUSPF_9669 and tr_A0A2Y9J7G8_A0A2Y9J7G8_ENHLU_391180 are exactly identical! WARNING: Sequences tr_M3YFN5_M3YFN5_MUSPF_9669 and tr_G1S221_G1S221_NOMLE_61853 are exactly identical! WARNING: Sequences tr_M3YFN5_M3YFN5_MUSPF_9669 and tr_G1NY31_G1NY31_MYOLU_59463 are exactly identical! WARNING: Sequences tr_M3YFN5_M3YFN5_MUSPF_9669 and tr_G3QNE9_G3QNE9_GORGO_9595 are exactly identical! WARNING: Sequences tr_M3YFN5_M3YFN5_MUSPF_9669 and tr_H2NK20_H2NK20_PONAB_9601 are exactly identical! WARNING: Sequences tr_M3YFN5_M3YFN5_MUSPF_9669 and tr_J9P1H6_J9P1H6_CANLF_9615 are exactly identical! WARNING: Sequences tr_M3YFN5_M3YFN5_MUSPF_9669 and tr_A0A2I3TG93_A0A2I3TG93_PANTR_9598 are exactly identical! WARNING: Sequences tr_M3YFN5_M3YFN5_MUSPF_9669 and tr_F7BJ35_F7BJ35_HORSE_9796 are exactly identical! WARNING: Sequences tr_M3YFN5_M3YFN5_MUSPF_9669 and tr_A0A287CSJ2_A0A287CSJ2_ICTTR_43179 are exactly identical! WARNING: Sequences tr_M3YFN5_M3YFN5_MUSPF_9669 and tr_H0VJG8_H0VJG8_CAVPO_10141 are exactly identical! WARNING: Sequences tr_M3YFN5_M3YFN5_MUSPF_9669 and sp_Q9Y4X4_KLF12_HUMAN_9606 are exactly identical! WARNING: Sequences tr_M3YFN5_M3YFN5_MUSPF_9669 and tr_F6TF45_F6TF45_MACMU_9544 are exactly identical! WARNING: Sequences tr_M3YFN5_M3YFN5_MUSPF_9669 and tr_F7H530_F7H530_CALJA_9483 are exactly identical! WARNING: Sequences tr_M3YFN5_M3YFN5_MUSPF_9669 and tr_I3LN86_I3LN86_PIG_9823 are exactly identical! WARNING: Sequences tr_M3YFN5_M3YFN5_MUSPF_9669 and tr_G1M1J5_G1M1J5_AILME_9646 are exactly identical! WARNING: Sequences tr_M3YFN5_M3YFN5_MUSPF_9669 and tr_G7PVI4_G7PVI4_MACFA_9541 are exactly identical! WARNING: Sequences tr_M3YFN5_M3YFN5_MUSPF_9669 and tr_M3WD25_M3WD25_FELCA_9685 are exactly identical! WARNING: Sequences tr_M3YFN5_M3YFN5_MUSPF_9669 and tr_A0A096N0U2_A0A096N0U2_PAPAN_9555 are exactly identical! WARNING: Sequences tr_M3YFN5_M3YFN5_MUSPF_9669 and tr_A0A1S3WG98_A0A1S3WG98_ERIEU_9365 are exactly identical! WARNING: Sequences tr_M3YFN5_M3YFN5_MUSPF_9669 and tr_A0A1U7UQU4_A0A1U7UQU4_TARSY_1868482 are exactly identical! WARNING: Sequences tr_M3YFN5_M3YFN5_MUSPF_9669 and tr_A0A2K5KKE2_A0A2K5KKE2_CERAT_9531 are exactly identical! WARNING: Sequences tr_M3YFN5_M3YFN5_MUSPF_9669 and tr_A0A2K6D8D3_A0A2K6D8D3_MACNE_9545 are exactly identical! WARNING: Sequences tr_M3YFN5_M3YFN5_MUSPF_9669 and tr_A0A2K5YAM7_A0A2K5YAM7_MANLE_9568 are exactly identical! WARNING: Sequences tr_M3YFN5_M3YFN5_MUSPF_9669 and tr_A0A2R9ALE4_A0A2R9ALE4_PANPA_9597 are exactly identical! WARNING: Sequences tr_M3YFN5_M3YFN5_MUSPF_9669 and tr_A0A2U3WRI2_A0A2U3WRI2_ODORO_9708 are exactly identical! WARNING: Sequences tr_M3YFN5_M3YFN5_MUSPF_9669 and tr_A0A2Y9JDL5_A0A2Y9JDL5_ENHLU_391180 are exactly identical! WARNING: Sequences tr_M3YFN5_M3YFN5_MUSPF_9669 and tr_A0A384BRT7_A0A384BRT7_URSMA_29073 are exactly identical! WARNING: Sequences tr_M3YR48_M3YR48_MUSPF_9669 and tr_F1PLE5_F1PLE5_CANLF_9615 are exactly identical! WARNING: Sequences tr_A0A2I3FXG5_A0A2I3FXG5_NOMLE_61853 and tr_H2PVT3_H2PVT3_PONAB_9601 are exactly identical! WARNING: Sequences tr_A0A2I3FXG5_A0A2I3FXG5_NOMLE_61853 and tr_A0A2I3TQK3_A0A2I3TQK3_PANTR_9598 are exactly identical! WARNING: Sequences tr_A0A2I3FXG5_A0A2I3FXG5_NOMLE_61853 and sp_O95600_KLF8_HUMAN_9606 are exactly identical! WARNING: Sequences tr_A0A2I3FXG5_A0A2I3FXG5_NOMLE_61853 and tr_A0A2R9CQU0_A0A2R9CQU0_PANPA_9597 are exactly identical! WARNING: Sequences tr_A0A2I3GE53_A0A2I3GE53_NOMLE_61853 and tr_A0A2K5YA95_A0A2K5YA95_MANLE_9568 are exactly identical! WARNING: Sequences tr_G1S468_G1S468_NOMLE_61853 and tr_A0A2I2YXL1_A0A2I2YXL1_GORGO_9595 are exactly identical! WARNING: Sequences tr_G1S468_G1S468_NOMLE_61853 and tr_H2PMP9_H2PMP9_PONAB_9601 are exactly identical! WARNING: Sequences tr_G1S468_G1S468_NOMLE_61853 and tr_H2QU88_H2QU88_PANTR_9598 are exactly identical! WARNING: Sequences tr_G1S468_G1S468_NOMLE_61853 and sp_Q02446_SP4_HUMAN_9606 are exactly identical! WARNING: Sequences tr_G1S468_G1S468_NOMLE_61853 and tr_A0A1D5Q3F2_A0A1D5Q3F2_MACMU_9544 are exactly identical! WARNING: Sequences tr_G1S468_G1S468_NOMLE_61853 and tr_F7HQH5_F7HQH5_CALJA_9483 are exactly identical! WARNING: Sequences tr_G1S468_G1S468_NOMLE_61853 and tr_G7P0R8_G7P0R8_MACFA_9541 are exactly identical! WARNING: Sequences tr_G1S468_G1S468_NOMLE_61853 and tr_A0A2I3MD48_A0A2I3MD48_PAPAN_9555 are exactly identical! WARNING: Sequences tr_G1S468_G1S468_NOMLE_61853 and tr_A0A0D9RMD3_A0A0D9RMD3_CHLSB_60711 are exactly identical! WARNING: Sequences tr_G1S468_G1S468_NOMLE_61853 and tr_A0A2K5KXI9_A0A2K5KXI9_CERAT_9531 are exactly identical! WARNING: Sequences tr_G1S468_G1S468_NOMLE_61853 and tr_A0A2K6D095_A0A2K6D095_MACNE_9545 are exactly identical! WARNING: Sequences tr_G1S468_G1S468_NOMLE_61853 and tr_A0A2K6A806_A0A2K6A806_MANLE_9568 are exactly identical! WARNING: Sequences tr_G3GR84_G3GR84_CRIGR_10029 and tr_A0A1U7Q7G9_A0A1U7Q7G9_MESAU_10036 are exactly identical! WARNING: Sequences tr_G3QPS2_G3QPS2_GORGO_9595 and tr_H2PD38_H2PD38_PONAB_9601 are exactly identical! WARNING: Sequences tr_G3QPS2_G3QPS2_GORGO_9595 and tr_H2QPC1_H2QPC1_PANTR_9598 are exactly identical! WARNING: Sequences tr_G3QPS2_G3QPS2_GORGO_9595 and sp_P57682_KLF3_HUMAN_9606 are exactly identical! WARNING: Sequences tr_G3QPS2_G3QPS2_GORGO_9595 and tr_F7E8X0_F7E8X0_MACMU_9544 are exactly identical! WARNING: Sequences tr_G3QPS2_G3QPS2_GORGO_9595 and tr_G7P5E4_G7P5E4_MACFA_9541 are exactly identical! WARNING: Sequences tr_G3QPS2_G3QPS2_GORGO_9595 and tr_A0A096N246_A0A096N246_PAPAN_9555 are exactly identical! WARNING: Sequences tr_G3QPS2_G3QPS2_GORGO_9595 and tr_A0A0D9RWD1_A0A0D9RWD1_CHLSB_60711 are exactly identical! WARNING: Sequences tr_G3QPS2_G3QPS2_GORGO_9595 and tr_A0A2K5KRZ1_A0A2K5KRZ1_CERAT_9531 are exactly identical! WARNING: Sequences tr_G3QPS2_G3QPS2_GORGO_9595 and tr_A0A2K5ZGI8_A0A2K5ZGI8_MANLE_9568 are exactly identical! WARNING: Sequences tr_G3QPS2_G3QPS2_GORGO_9595 and tr_A0A2R8ZPC8_A0A2R8ZPC8_PANPA_9597 are exactly identical! WARNING: Sequences tr_G3R1P0_G3R1P0_GORGO_9595 and tr_H2P8F1_H2P8F1_PONAB_9601 are exactly identical! WARNING: Sequences tr_G3R1P0_G3R1P0_GORGO_9595 and tr_A0A2I3RAR5_A0A2I3RAR5_PANTR_9598 are exactly identical! WARNING: Sequences tr_G3R1P0_G3R1P0_GORGO_9595 and sp_O75840_KLF7_HUMAN_9606 are exactly identical! WARNING: Sequences tr_G3R1P0_G3R1P0_GORGO_9595 and tr_F7GTJ0_F7GTJ0_CALJA_9483 are exactly identical! WARNING: Sequences tr_G3R1P0_G3R1P0_GORGO_9595 and tr_G7PLA2_G7PLA2_MACFA_9541 are exactly identical! WARNING: Sequences tr_G3R1P0_G3R1P0_GORGO_9595 and tr_A0A096NXV9_A0A096NXV9_PAPAN_9555 are exactly identical! WARNING: Sequences tr_G3R1P0_G3R1P0_GORGO_9595 and tr_A0A0D9RCL3_A0A0D9RCL3_CHLSB_60711 are exactly identical! WARNING: Sequences tr_G3R1P0_G3R1P0_GORGO_9595 and tr_A0A2K5NKE7_A0A2K5NKE7_CERAT_9531 are exactly identical! WARNING: Sequences tr_G3R1P0_G3R1P0_GORGO_9595 and tr_A0A2K6B622_A0A2K6B622_MACNE_9545 are exactly identical! WARNING: Sequences tr_G3R1P0_G3R1P0_GORGO_9595 and tr_A0A2K5XC97_A0A2K5XC97_MANLE_9568 are exactly identical! WARNING: Sequences tr_H2QFH4_H2QFH4_PANTR_9598 and tr_A0A2R9BTB9_A0A2R9BTB9_PANPA_9597 are exactly identical! WARNING: Sequences tr_K7E6N1_K7E6N1_ORNAN_9258 and tr_A0A1U7TVA5_A0A1U7TVA5_TARSY_1868482 are exactly identical! WARNING: Sequences tr_F7DGJ3_F7DGJ3_MONDO_13616 and tr_G3WSS1_G3WSS1_SARHA_9305 are exactly identical! WARNING: Sequences tr_W5Q1P9_W5Q1P9_SHEEP_9940 and tr_F1MQF5_F1MQF5_BOVIN_9913 are exactly identical! WARNING: Sequences tr_D3ZG44_D3ZG44_RAT_10116 and tr_A0A1S3ENF5_A0A1S3ENF5_DIPOR_10020 are exactly identical! WARNING: Sequences tr_A0A3B5R4M9_A0A3B5R4M9_XIPMA_8083 and tr_A0A087X4S6_A0A087X4S6_POEFO_48698 are exactly identical! WARNING: Sequences tr_A0A158NF61_A0A158NF61_ATTCE_12957 and tr_A0A195BRF8_A0A195BRF8_9HYME_520822 are exactly identical! WARNING: Sequences tr_A0A286Y4T0_A0A286Y4T0_CAVPO_10141 and tr_A0A091DRF4_A0A091DRF4_FUKDA_885580 are exactly identical! WARNING: Sequences tr_A0A1D5QBM3_A0A1D5QBM3_MACMU_9544 and tr_G8F2K4_G8F2K4_MACFA_9541 are exactly identical! WARNING: Sequences tr_A0A1D5QBM3_A0A1D5QBM3_MACMU_9544 and tr_A0A0D9RI24_A0A0D9RI24_CHLSB_60711 are exactly identical! WARNING: Sequences tr_A0A1D5QBM3_A0A1D5QBM3_MACMU_9544 and tr_A0A2K5LP06_A0A2K5LP06_CERAT_9531 are exactly identical! WARNING: Sequences tr_A0A1D5QBM3_A0A1D5QBM3_MACMU_9544 and tr_A0A2K6BXQ6_A0A2K6BXQ6_MACNE_9545 are exactly identical! WARNING: Sequences tr_A0A1D5R292_A0A1D5R292_MACMU_9544 and tr_A0A2K6BZU6_A0A2K6BZU6_MACNE_9545 are exactly identical! WARNING: Sequences tr_F6VVB3_F6VVB3_MACMU_9544 and tr_A0A0D9RG89_A0A0D9RG89_CHLSB_60711 are exactly identical! WARNING: Sequences tr_F6VVB3_F6VVB3_MACMU_9544 and tr_A0A2K5KZK9_A0A2K5KZK9_CERAT_9531 are exactly identical! WARNING: Sequences tr_F6VVB3_F6VVB3_MACMU_9544 and tr_A0A2K6BXA2_A0A2K6BXA2_MACNE_9545 are exactly identical! WARNING: Sequences tr_F6WXX2_F6WXX2_MACMU_9544 and tr_A0A2K5NXD8_A0A2K5NXD8_CERAT_9531 are exactly identical! WARNING: Sequences tr_F6WXX2_F6WXX2_MACMU_9544 and tr_A0A2K5Y4V2_A0A2K5Y4V2_MANLE_9568 are exactly identical! WARNING: Sequences tr_H0ZIB7_H0ZIB7_TAEGU_59729 and tr_A0A218UHV8_A0A218UHV8_9PASE_299123 are exactly identical! WARNING: Sequences tr_H0ZV49_H0ZV49_TAEGU_59729 and tr_A0A091J4E6_A0A091J4E6_EGRGA_188379 are exactly identical! WARNING: Sequences tr_H0ZV49_H0ZV49_TAEGU_59729 and tr_A0A091V626_A0A091V626_NIPNI_128390 are exactly identical! WARNING: Sequences tr_H0ZV49_H0ZV49_TAEGU_59729 and tr_A0A087R7D4_A0A087R7D4_APTFO_9233 are exactly identical! WARNING: Sequences tr_H0ZV49_H0ZV49_TAEGU_59729 and tr_A0A091WYB0_A0A091WYB0_OPIHO_30419 are exactly identical! WARNING: Sequences tr_H0ZV49_H0ZV49_TAEGU_59729 and tr_A0A0A0A476_A0A0A0A476_CHAVO_50402 are exactly identical! WARNING: Sequences tr_H0ZV49_H0ZV49_TAEGU_59729 and tr_A0A093GUE7_A0A093GUE7_DRYPU_118200 are exactly identical! WARNING: Sequences tr_H0ZV49_H0ZV49_TAEGU_59729 and tr_A0A091HYW5_A0A091HYW5_CALAN_9244 are exactly identical! WARNING: Sequences tr_E1BIQ9_E1BIQ9_BOVIN_9913 and tr_A0A2U4ASJ0_A0A2U4ASJ0_TURTR_9739 are exactly identical! WARNING: Sequences tr_E1BIQ9_E1BIQ9_BOVIN_9913 and tr_A0A2Y9MLJ4_A0A2Y9MLJ4_DELLE_9749 are exactly identical! WARNING: Sequences tr_E1BIQ9_E1BIQ9_BOVIN_9913 and tr_A0A2Y9EIE1_A0A2Y9EIE1_PHYCD_9755 are exactly identical! WARNING: Sequences tr_U3JDZ6_U3JDZ6_FICAL_59894 and tr_A0A218V3M8_A0A218V3M8_9PASE_299123 are exactly identical! WARNING: Sequences tr_U3K3W9_U3K3W9_FICAL_59894 and tr_A0A218ULR7_A0A218ULR7_9PASE_299123 are exactly identical! WARNING: Sequences tr_U3K9P6_U3K9P6_FICAL_59894 and tr_A0A218UU13_A0A218UU13_9PASE_299123 are exactly identical! WARNING: Sequences tr_A0A0D9R0D3_A0A0D9R0D3_CHLSB_60711 and tr_A0A2K5NXJ2_A0A2K5NXJ2_CERAT_9531 are exactly identical! WARNING: Sequences tr_A0A151P7P2_A0A151P7P2_ALLMI_8496 and tr_A0A1U8DUU5_A0A1U8DUU5_ALLSI_38654 are exactly identical! WARNING: Sequences tr_A0A091F6S9_A0A091F6S9_CORBR_85066 and tr_A0A091J3I8_A0A091J3I8_EGRGA_188379 are exactly identical! WARNING: Sequences tr_A0A091F6S9_A0A091F6S9_CORBR_85066 and tr_A0A093QBM2_A0A093QBM2_9PASS_328815 are exactly identical! WARNING: Sequences tr_A0A091F6S9_A0A091F6S9_CORBR_85066 and tr_A0A091V171_A0A091V171_NIPNI_128390 are exactly identical! WARNING: Sequences tr_A0A091F6S9_A0A091F6S9_CORBR_85066 and tr_A0A087R6R2_A0A087R6R2_APTFO_9233 are exactly identical! WARNING: Sequences tr_A0A091F6S9_A0A091F6S9_CORBR_85066 and tr_A0A091WE98_A0A091WE98_OPIHO_30419 are exactly identical! WARNING: Sequences tr_A0A091F6S9_A0A091F6S9_CORBR_85066 and tr_A0A091FPX4_A0A091FPX4_9AVES_55661 are exactly identical! WARNING: Sequences tr_A0A091F6S9_A0A091F6S9_CORBR_85066 and tr_A0A0A0AEN8_A0A0A0AEN8_CHAVO_50402 are exactly identical! WARNING: Sequences tr_A0A091F6S9_A0A091F6S9_CORBR_85066 and tr_A0A093G393_A0A093G393_DRYPU_118200 are exactly identical! WARNING: Sequences tr_A0A091F6S9_A0A091F6S9_CORBR_85066 and tr_A0A091J4I0_A0A091J4I0_CALAN_9244 are exactly identical! WARNING: Sequences tr_A0A091FVA6_A0A091FVA6_CORBR_85066 and tr_A0A091UQ94_A0A091UQ94_NIPNI_128390 are exactly identical! WARNING: Sequences tr_A0A091FVA6_A0A091FVA6_CORBR_85066 and tr_A0A091V7Z2_A0A091V7Z2_OPIHO_30419 are exactly identical! WARNING: Sequences tr_A0A091FVA6_A0A091FVA6_CORBR_85066 and tr_A0A0A0ASZ6_A0A0A0ASZ6_CHAVO_50402 are exactly identical! WARNING: Sequences tr_A0A091JAI9_A0A091JAI9_EGRGA_188379 and tr_A0A093Q5F9_A0A093Q5F9_9PASS_328815 are exactly identical! WARNING: Sequences tr_A0A091JAL4_A0A091JAL4_EGRGA_188379 and tr_A0A091UP63_A0A091UP63_NIPNI_128390 are exactly identical! WARNING: Sequences tr_A0A091JAL4_A0A091JAL4_EGRGA_188379 and tr_A0A087R0T7_A0A087R0T7_APTFO_9233 are exactly identical! WARNING: Sequences tr_A0A091JAL4_A0A091JAL4_EGRGA_188379 and tr_A0A0A0A1V1_A0A0A0A1V1_CHAVO_50402 are exactly identical! WARNING: Sequences tr_A0A091JAL4_A0A091JAL4_EGRGA_188379 and tr_A0A2I0MQ45_A0A2I0MQ45_COLLI_8932 are exactly identical! WARNING: Sequences tr_A0A091JAL4_A0A091JAL4_EGRGA_188379 and tr_A0A1V4KLN9_A0A1V4KLN9_PATFA_372326 are exactly identical! WARNING: Sequences tr_A0A091VD14_A0A091VD14_NIPNI_128390 and tr_A0A093GNW9_A0A093GNW9_DRYPU_118200 are exactly identical! WARNING: Sequences tr_A0A091VD14_A0A091VD14_NIPNI_128390 and tr_A0A091HTT4_A0A091HTT4_CALAN_9244 are exactly identical! WARNING: Sequences tr_A0A091VI55_A0A091VI55_NIPNI_128390 and tr_A0A091GG62_A0A091GG62_9AVES_55661 are exactly identical! WARNING: Sequences tr_A0A2I0LXM2_A0A2I0LXM2_COLLI_8932 and tr_A0A1V4L0Q7_A0A1V4L0Q7_PATFA_372326 are exactly identical! WARNING: Sequences tr_A0A2I0MMK5_A0A2I0MMK5_COLLI_8932 and tr_A0A1V4JFV0_A0A1V4JFV0_PATFA_372326 are exactly identical! WARNING: Sequences tr_A0A0V1DEY9_A0A0V1DEY9_TRIBR_45882 and tr_A0A0V0X9L0_A0A0V0X9L0_9BILA_92179 are exactly identical! WARNING: Sequences tr_A0A0V1DEY9_A0A0V1DEY9_TRIBR_45882 and tr_A0A0V1NPD7_A0A0V1NPD7_9BILA_92180 are exactly identical! WARNING: Sequences tr_B5XF21_B5XF21_SALSA_8030 and tr_A0A060YD73_A0A060YD73_ONCMY_8022 are exactly identical! WARNING: Sequences tr_A0A226MTY2_A0A226MTY2_CALSU_9009 and tr_A0A226NZU7_A0A226NZU7_COLVI_9014 are exactly identical! WARNING: Sequences tr_A0A2U4ASN3_A0A2U4ASN3_TURTR_9739 and tr_A0A2Y9P9D9_A0A2Y9P9D9_DELLE_9749 are exactly identical! WARNING: Sequences tr_A0A2U4ASN3_A0A2U4ASN3_TURTR_9739 and tr_A0A2Y9FDZ5_A0A2Y9FDZ5_PHYCD_9755 are exactly identical! WARNING: Sequences tr_A0A2U4ASN3_A0A2U4ASN3_TURTR_9739 and tr_A0A384A9K6_A0A384A9K6_BALAS_310752 are exactly identical! WARNING: Sequences tr_A0A2U4CMW5_A0A2U4CMW5_TURTR_9739 and tr_A0A2Y9LXB9_A0A2Y9LXB9_DELLE_9749 are exactly identical! WARNING: Sequences tr_A0A2U4CMW5_A0A2U4CMW5_TURTR_9739 and tr_A0A2Y9TI56_A0A2Y9TI56_PHYCD_9755 are exactly identical! WARNING: Sequences tr_A0A2U3ZCT6_A0A2U3ZCT6_ODORO_9708 and tr_A0A2Y9JHH8_A0A2Y9JHH8_ENHLU_391180 are exactly identical! WARNING: Sequences tr_A0A2Y9NN28_A0A2Y9NN28_DELLE_9749 and tr_A0A384AG11_A0A384AG11_BALAS_310752 are exactly identical! WARNING: Duplicate sequences found: 147 NOTE: Reduced alignment (with duplicates and gap-only sites/taxa removed) NOTE: was saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q5JT82/4_raxmlng_ancestral/Q5JT82.raxml.reduced.phy Alignment comprises 1 partitions and 389 sites Partition 0: noname Model: LG4X+R4 Alignment sites: 389 Gaps: 45.70 % Invariant sites: 4.11 % NOTE: Binary MSA file created: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q5JT82/4_raxmlng_ancestral/Q5JT82.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/300621_run/phylogeny-snakemake/results/Q5JT82/3_mltree/Q5JT82.raxml.bestTree_unrooted [00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 98 / 7840 [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: -206738.242712 [00:00:00 -206738.242712] Initial branch length optimization [00:00:01 -115746.900012] Model parameter optimization (eps = 0.100000) [00:00:46] Tree #1, final logLikelihood: -115499.785118 Optimized model parameters: Partition 0: noname Rate heterogeneity: FREE (4 cats, mean), weights&rates: (0.082835,0.068015) (0.097195,0.142260) (0.262767,0.734411) (0.557202,1.413418) 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/300621_run/phylogeny-snakemake/results/Q5JT82/4_raxmlng_ancestral/Q5JT82.raxml.ancestralProbs Reconstructed ancestral sequences saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q5JT82/4_raxmlng_ancestral/Q5JT82.raxml.ancestralStates Node-labeled tree saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q5JT82/4_raxmlng_ancestral/Q5JT82.raxml.ancestralTree Execution log saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q5JT82/4_raxmlng_ancestral/Q5JT82.raxml.log Analysis started: 12-Jul-2021 18:02:34 / finished: 12-Jul-2021 18:03:24 Elapsed time: 49.661 seconds Consumed energy: 4.357 Wh