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 18:04:40 as follows: raxml-ng --ancestral --msa /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/P14867/2_msa/P14867_nogap_msa.fasta --tree /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/P14867/3_mltree/P14867.raxml.bestTree_unrooted --model LG4X --prefix /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/P14867/4_raxmlng_ancestral/P14867 --threads 4 Analysis options: run mode: Ancestral state reconstruction start tree(s): user random seed: 1626102280 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/P14867/2_msa/P14867_nogap_msa.fasta [00:00:00] Loaded alignment with 1001 taxa and 456 sites WARNING: Sequences sp_P19150_GBRA1_CHICK_9031 and tr_G1MUV7_G1MUV7_MELGA_9103 are exactly identical! WARNING: Sequences tr_Q7LZ70_Q7LZ70_CHICK_9031 and tr_A0A226PWQ0_A0A226PWQ0_COLVI_9014 are exactly identical! WARNING: Sequences sp_P62812_GBRA1_MOUSE_10090 and sp_P62813_GBRA1_RAT_10116 are exactly identical! WARNING: Sequences tr_M3XNJ0_M3XNJ0_MUSPF_9669 and tr_A0A2Y9LJ41_A0A2Y9LJ41_ENHLU_391180 are exactly identical! WARNING: Sequences tr_M3YJX4_M3YJX4_MUSPF_9669 and tr_A0A2Y9IEE7_A0A2Y9IEE7_ENHLU_391180 are exactly identical! WARNING: Sequences tr_A0A2I3GX20_A0A2I3GX20_NOMLE_61853 and tr_A0A2I2ZHK1_A0A2I2ZHK1_GORGO_9595 are exactly identical! WARNING: Sequences tr_A0A2I3GX20_A0A2I3GX20_NOMLE_61853 and tr_A0A2J8SEU5_A0A2J8SEU5_PONAB_9601 are exactly identical! WARNING: Sequences tr_A0A2I3GX20_A0A2I3GX20_NOMLE_61853 and tr_H2Q919_H2Q919_PANTR_9598 are exactly identical! WARNING: Sequences tr_A0A2I3GX20_A0A2I3GX20_NOMLE_61853 and sp_P31644_GBRA5_HUMAN_9606 are exactly identical! WARNING: Sequences tr_A0A2I3GX20_A0A2I3GX20_NOMLE_61853 and tr_A0A2R9BFW8_A0A2R9BFW8_PANPA_9597 are exactly identical! WARNING: Sequences tr_A0A2I3HA40_A0A2I3HA40_NOMLE_61853 and tr_G3R5Q4_G3R5Q4_GORGO_9595 are exactly identical! WARNING: Sequences tr_A0A2I3HA40_A0A2I3HA40_NOMLE_61853 and tr_H2RDJ9_H2RDJ9_PANTR_9598 are exactly identical! WARNING: Sequences tr_A0A2I3HA40_A0A2I3HA40_NOMLE_61853 and tr_A0A2I3MQB3_A0A2I3MQB3_PAPAN_9555 are exactly identical! WARNING: Sequences tr_A0A2I3HA40_A0A2I3HA40_NOMLE_61853 and tr_A0A2K5MKN6_A0A2K5MKN6_CERAT_9531 are exactly identical! WARNING: Sequences tr_A0A2I3HA40_A0A2I3HA40_NOMLE_61853 and tr_A0A2K6BAT3_A0A2K6BAT3_MACNE_9545 are exactly identical! WARNING: Sequences tr_A0A2I3HA40_A0A2I3HA40_NOMLE_61853 and tr_A0A2K5XNZ6_A0A2K5XNZ6_MANLE_9568 are exactly identical! WARNING: Sequences tr_G1RU38_G1RU38_NOMLE_61853 and tr_A0A2J8S433_A0A2J8S433_PONAB_9601 are exactly identical! WARNING: Sequences tr_G1RU38_G1RU38_NOMLE_61853 and tr_G7Q1Y0_G7Q1Y0_MACFA_9541 are exactly identical! WARNING: Sequences tr_G1RU38_G1RU38_NOMLE_61853 and tr_A0A0D9R3U7_A0A0D9R3U7_CHLSB_60711 are exactly identical! WARNING: Sequences tr_G1RU38_G1RU38_NOMLE_61853 and tr_A0A2K5MJG0_A0A2K5MJG0_CERAT_9531 are exactly identical! WARNING: Sequences tr_G1RU38_G1RU38_NOMLE_61853 and tr_A0A2K5ZSS5_A0A2K5ZSS5_MANLE_9568 are exactly identical! WARNING: Sequences tr_A0A2I2YVQ9_A0A2I2YVQ9_GORGO_9595 and tr_A0A2I3RA39_A0A2I3RA39_PANTR_9598 are exactly identical! WARNING: Sequences tr_A0A2I2YVQ9_A0A2I2YVQ9_GORGO_9595 and tr_A0A2R9A081_A0A2R9A081_PANPA_9597 are exactly identical! WARNING: Sequences tr_A0A2I2ZBY0_A0A2I2ZBY0_GORGO_9595 and tr_H2QPE4_H2QPE4_PANTR_9598 are exactly identical! WARNING: Sequences tr_A0A2I2ZBY0_A0A2I2ZBY0_GORGO_9595 and sp_Q8N1C3_GBRG1_HUMAN_9606 are exactly identical! WARNING: Sequences tr_A0A2I2ZBY0_A0A2I2ZBY0_GORGO_9595 and tr_A0A2R9A1L5_A0A2R9A1L5_PANPA_9597 are exactly identical! WARNING: Sequences tr_A0A2I2ZXT7_A0A2I2ZXT7_GORGO_9595 and tr_H2NMM1_H2NMM1_PONAB_9601 are exactly identical! WARNING: Sequences tr_A0A2I2ZXT7_A0A2I2ZXT7_GORGO_9595 and tr_A0A2I3TTK9_A0A2I3TTK9_PANTR_9598 are exactly identical! WARNING: Sequences tr_A0A2I2ZXT7_A0A2I2ZXT7_GORGO_9595 and sp_Q99928_GBRG3_HUMAN_9606 are exactly identical! WARNING: Sequences tr_G3QGA7_G3QGA7_GORGO_9595 and sp_P78334_GBRE_HUMAN_9606 are exactly identical! WARNING: Sequences tr_G3R6I1_G3R6I1_GORGO_9595 and tr_H2PHA2_H2PHA2_PONAB_9601 are exactly identical! WARNING: Sequences tr_G3R6I1_G3R6I1_GORGO_9595 and tr_A0A2I3SDV7_A0A2I3SDV7_PANTR_9598 are exactly identical! WARNING: Sequences tr_G3R6I1_G3R6I1_GORGO_9595 and sp_P14867_GBRA1_HUMAN_9606 are exactly identical! WARNING: Sequences tr_G3R6I1_G3R6I1_GORGO_9595 and tr_A0A2R9AU65_A0A2R9AU65_PANPA_9597 are exactly identical! WARNING: Sequences tr_G3RPF4_G3RPF4_GORGO_9595 and tr_H2QPE7_H2QPE7_PANTR_9598 are exactly identical! WARNING: Sequences tr_G3RPF4_G3RPF4_GORGO_9595 and sp_P48169_GBRA4_HUMAN_9606 are exactly identical! WARNING: Sequences tr_G3RPF4_G3RPF4_GORGO_9595 and tr_A0A2R9C6M3_A0A2R9C6M3_PANPA_9597 are exactly identical! WARNING: Sequences tr_G3SKG8_G3SKG8_GORGO_9595 and tr_H2QZ88_H2QZ88_PANTR_9598 are exactly identical! WARNING: Sequences tr_G3SKG8_G3SKG8_GORGO_9595 and sp_P34903_GBRA3_HUMAN_9606 are exactly identical! WARNING: Sequences tr_G3SKG8_G3SKG8_GORGO_9595 and tr_A0A2R9AHX2_A0A2R9AHX2_PANPA_9597 are exactly identical! WARNING: Sequences sp_Q5RCC5_GBRA2_PONAB_9601 and tr_F6U2C0_F6U2C0_MACMU_9544 are exactly identical! WARNING: Sequences sp_Q5RCC5_GBRA2_PONAB_9601 and tr_G8F2J4_G8F2J4_MACFA_9541 are exactly identical! WARNING: Sequences sp_Q5REA1_GBRG2_PONAB_9601 and sp_P18507_GBRG2_HUMAN_9606 are exactly identical! WARNING: Sequences tr_F6YYW0_F6YYW0_HORSE_9796 and tr_A0A2U4C645_A0A2U4C645_TURTR_9739 are exactly identical! WARNING: Sequences tr_W5PWY6_W5PWY6_SHEEP_9940 and sp_P08219_GBRA1_BOVIN_9913 are exactly identical! WARNING: Sequences tr_A0A1D5RL15_A0A1D5RL15_MACMU_9544 and tr_G7P6T6_G7P6T6_MACFA_9541 are exactly identical! WARNING: Sequences tr_A0A1D5RL15_A0A1D5RL15_MACMU_9544 and tr_A0A096ND56_A0A096ND56_PAPAN_9555 are exactly identical! WARNING: Sequences tr_F6PX98_F6PX98_MACMU_9544 and tr_G7P5I4_G7P5I4_MACFA_9541 are exactly identical! WARNING: Sequences tr_F6PX98_F6PX98_MACMU_9544 and tr_A0A096NZ00_A0A096NZ00_PAPAN_9555 are exactly identical! WARNING: Sequences tr_F6PX98_F6PX98_MACMU_9544 and tr_A0A0D9RX31_A0A0D9RX31_CHLSB_60711 are exactly identical! WARNING: Sequences tr_F6PX98_F6PX98_MACMU_9544 and tr_A0A2K5NYG4_A0A2K5NYG4_CERAT_9531 are exactly identical! WARNING: Sequences tr_F6PX98_F6PX98_MACMU_9544 and tr_A0A2K5Y3I5_A0A2K5Y3I5_MANLE_9568 are exactly identical! WARNING: Sequences tr_F6YLN4_F6YLN4_MACMU_9544 and tr_G7P5I6_G7P5I6_MACFA_9541 are exactly identical! WARNING: Sequences tr_F6YLN4_F6YLN4_MACMU_9544 and tr_A0A096N4I2_A0A096N4I2_PAPAN_9555 are exactly identical! WARNING: Sequences tr_F6YLN4_F6YLN4_MACMU_9544 and tr_A0A0D9RX37_A0A0D9RX37_CHLSB_60711 are exactly identical! WARNING: Sequences tr_F6YLN4_F6YLN4_MACMU_9544 and tr_A0A2K5LLS9_A0A2K5LLS9_CERAT_9531 are exactly identical! WARNING: Sequences tr_F6YLN4_F6YLN4_MACMU_9544 and tr_A0A2K5Z3P0_A0A2K5Z3P0_MANLE_9568 are exactly identical! WARNING: Sequences tr_F7GJ80_F7GJ80_MACMU_9544 and tr_G7Q1X8_G7Q1X8_MACFA_9541 are exactly identical! WARNING: Sequences tr_F7GJ80_F7GJ80_MACMU_9544 and tr_A0A096N046_A0A096N046_PAPAN_9555 are exactly identical! WARNING: Sequences tr_G7MW76_G7MW76_MACMU_9544 and tr_A0A096NSX8_A0A096NSX8_PAPAN_9555 are exactly identical! WARNING: Sequences tr_G7MW76_G7MW76_MACMU_9544 and tr_A0A2K5MIV3_A0A2K5MIV3_CERAT_9531 are exactly identical! WARNING: Sequences tr_G7MW76_G7MW76_MACMU_9544 and tr_A0A2K6AN58_A0A2K6AN58_MACNE_9545 are exactly identical! WARNING: Sequences tr_G7MW76_G7MW76_MACMU_9544 and tr_A0A2K5YHP0_A0A2K5YHP0_MANLE_9568 are exactly identical! WARNING: Sequences tr_H0YT92_H0YT92_TAEGU_59729 and tr_U3KGH7_U3KGH7_FICAL_59894 are exactly identical! WARNING: Sequences tr_H0YT92_H0YT92_TAEGU_59729 and tr_A0A218V2Y9_A0A218V2Y9_9PASE_299123 are exactly identical! WARNING: Sequences tr_F7I411_F7I411_CALJA_9483 and tr_A0A2I3LYD3_A0A2I3LYD3_PAPAN_9555 are exactly identical! WARNING: Sequences tr_F7I411_F7I411_CALJA_9483 and tr_A0A2K6BEQ5_A0A2K6BEQ5_MACNE_9545 are exactly identical! WARNING: Sequences tr_F7I411_F7I411_CALJA_9483 and tr_A0A2K5YVQ8_A0A2K5YVQ8_MANLE_9568 are exactly identical! WARNING: Sequences tr_D2GUJ9_D2GUJ9_AILME_9646 and tr_A0A384C738_A0A384C738_URSMA_29073 are exactly identical! WARNING: Sequences tr_D2HI26_D2HI26_AILME_9646 and tr_A0A2U3XA10_A0A2U3XA10_LEPWE_9713 are exactly identical! WARNING: Sequences tr_D2HI26_D2HI26_AILME_9646 and tr_A0A384DBX8_A0A384DBX8_URSMA_29073 are exactly identical! WARNING: Sequences tr_G1LJN5_G1LJN5_AILME_9646 and tr_A0A337SG73_A0A337SG73_FELCA_9685 are exactly identical! WARNING: Sequences tr_G1MC80_G1MC80_AILME_9646 and tr_A0A384CXZ4_A0A384CXZ4_URSMA_29073 are exactly identical! WARNING: Sequences tr_G7P6T7_G7P6T7_MACFA_9541 and tr_A0A2I3LGH8_A0A2I3LGH8_PAPAN_9555 are exactly identical! WARNING: Sequences tr_G7P6T7_G7P6T7_MACFA_9541 and tr_A0A0D9RD73_A0A0D9RD73_CHLSB_60711 are exactly identical! WARNING: Sequences tr_G7P6T7_G7P6T7_MACFA_9541 and tr_A0A2K5NIN7_A0A2K5NIN7_CERAT_9531 are exactly identical! WARNING: Sequences tr_G7P6T7_G7P6T7_MACFA_9541 and tr_A0A2K6D8E4_A0A2K6D8E4_MACNE_9545 are exactly identical! WARNING: Sequences tr_G7P6T7_G7P6T7_MACFA_9541 and tr_A0A2K6A7F7_A0A2K6A7F7_MANLE_9568 are exactly identical! WARNING: Sequences tr_L5L1N8_L5L1N8_PTEAL_9402 and tr_A0A2U3XH15_A0A2U3XH15_LEPWE_9713 are exactly identical! WARNING: Sequences tr_U3JJY8_U3JJY8_FICAL_59894 and tr_A0A218VFM1_A0A218VFM1_9PASE_299123 are exactly identical! WARNING: Sequences tr_A0A2I3NBF3_A0A2I3NBF3_PAPAN_9555 and tr_A0A2K5P6J3_A0A2K5P6J3_CERAT_9531 are exactly identical! WARNING: Sequences tr_A0A2I3NBF3_A0A2I3NBF3_PAPAN_9555 and tr_A0A2K6D794_A0A2K6D794_MACNE_9545 are exactly identical! WARNING: Sequences tr_A0A151NMV3_A0A151NMV3_ALLMI_8496 and tr_A0A1U7RQQ1_A0A1U7RQQ1_ALLSI_38654 are exactly identical! WARNING: Sequences tr_A0A151PAK3_A0A151PAK3_ALLMI_8496 and tr_A0A1U7RZJ0_A0A1U7RZJ0_ALLSI_38654 are exactly identical! WARNING: Sequences tr_A0A091F4A4_A0A091F4A4_CORBR_85066 and tr_A0A091JBQ4_A0A091JBQ4_EGRGA_188379 are exactly identical! WARNING: Sequences tr_A0A091F4A4_A0A091F4A4_CORBR_85066 and tr_A0A091VXD3_A0A091VXD3_NIPNI_128390 are exactly identical! WARNING: Sequences tr_A0A091F4A4_A0A091F4A4_CORBR_85066 and tr_A0A087RAC8_A0A087RAC8_APTFO_9233 are exactly identical! WARNING: Sequences tr_A0A091F4A4_A0A091F4A4_CORBR_85066 and tr_A0A093HTL6_A0A093HTL6_STRCA_441894 are exactly identical! WARNING: Sequences tr_A0A091F4A4_A0A091F4A4_CORBR_85066 and tr_A0A0A0AID7_A0A0A0AID7_CHAVO_50402 are exactly identical! WARNING: Sequences tr_A0A091F8T1_A0A091F8T1_CORBR_85066 and tr_A0A091K2L4_A0A091K2L4_EGRGA_188379 are exactly identical! WARNING: Sequences tr_A0A091F8T1_A0A091F8T1_CORBR_85066 and tr_A0A091VYG2_A0A091VYG2_NIPNI_128390 are exactly identical! WARNING: Sequences tr_A0A091F8T1_A0A091F8T1_CORBR_85066 and tr_A0A087RAC9_A0A087RAC9_APTFO_9233 are exactly identical! WARNING: Sequences tr_A0A091F8T1_A0A091F8T1_CORBR_85066 and tr_A0A091WB10_A0A091WB10_OPIHO_30419 are exactly identical! WARNING: Sequences tr_A0A091F8T1_A0A091F8T1_CORBR_85066 and tr_A0A091G2W3_A0A091G2W3_9AVES_55661 are exactly identical! WARNING: Sequences tr_A0A091F8T1_A0A091F8T1_CORBR_85066 and tr_A0A0A0AFG3_A0A0A0AFG3_CHAVO_50402 are exactly identical! WARNING: Sequences tr_A0A091FHY5_A0A091FHY5_CORBR_85066 and tr_A0A093Q0H9_A0A093Q0H9_9PASS_328815 are exactly identical! WARNING: Sequences tr_A0A091J5L2_A0A091J5L2_EGRGA_188379 and tr_A0A091VSB3_A0A091VSB3_NIPNI_128390 are exactly identical! WARNING: Sequences tr_A0A091J5L2_A0A091J5L2_EGRGA_188379 and tr_A0A087R5Z0_A0A087R5Z0_APTFO_9233 are exactly identical! WARNING: Sequences tr_A0A091JP51_A0A091JP51_EGRGA_188379 and tr_A0A091VLK9_A0A091VLK9_OPIHO_30419 are exactly identical! WARNING: Sequences tr_A0A091JP51_A0A091JP51_EGRGA_188379 and tr_A0A0A0A340_A0A0A0A340_CHAVO_50402 are exactly identical! WARNING: Sequences tr_A0A091JQB3_A0A091JQB3_EGRGA_188379 and tr_A0A091VFC3_A0A091VFC3_NIPNI_128390 are exactly identical! WARNING: Sequences tr_A0A091JQB3_A0A091JQB3_EGRGA_188379 and tr_A0A087REJ4_A0A087REJ4_APTFO_9233 are exactly identical! WARNING: Sequences tr_A0A093Q4I3_A0A093Q4I3_9PASS_328815 and tr_A0A091HTV3_A0A091HTV3_CALAN_9244 are exactly identical! WARNING: Sequences tr_A0A091WEY6_A0A091WEY6_NIPNI_128390 and tr_A0A093HAR6_A0A093HAR6_STRCA_441894 are exactly identical! WARNING: Sequences tr_A0A091WEY6_A0A091WEY6_NIPNI_128390 and tr_A0A091W6K5_A0A091W6K5_OPIHO_30419 are exactly identical! WARNING: Sequences tr_A0A091WEY6_A0A091WEY6_NIPNI_128390 and tr_A0A099ZAE7_A0A099ZAE7_TINGU_94827 are exactly identical! WARNING: Sequences tr_A0A091WEY6_A0A091WEY6_NIPNI_128390 and tr_A0A0A0AT20_A0A0A0AT20_CHAVO_50402 are exactly identical! WARNING: Sequences tr_A0A087REJ3_A0A087REJ3_APTFO_9233 and tr_A0A093GYL5_A0A093GYL5_STRCA_441894 are exactly identical! WARNING: Sequences tr_A0A087REJ3_A0A087REJ3_APTFO_9233 and tr_A0A099YQQ5_A0A099YQQ5_TINGU_94827 are exactly identical! WARNING: Sequences tr_A0A2I0M4K5_A0A2I0M4K5_COLLI_8932 and tr_A0A1V4KYA2_A0A1V4KYA2_PATFA_372326 are exactly identical! WARNING: Sequences tr_A0A2I0MA56_A0A2I0MA56_COLLI_8932 and tr_A0A1V4KUZ3_A0A1V4KUZ3_PATFA_372326 are exactly identical! WARNING: Sequences tr_A0A2I0MMV6_A0A2I0MMV6_COLLI_8932 and tr_A0A1V4JFV1_A0A1V4JFV1_PATFA_372326 are exactly identical! WARNING: Sequences tr_A0A2U3UYL9_A0A2U3UYL9_TURTR_9739 and tr_A0A2U3UYM3_A0A2U3UYM3_TURTR_9739 are exactly identical! WARNING: Sequences tr_A0A2U3UYL9_A0A2U3UYL9_TURTR_9739 and tr_A0A2Y9PZG0_A0A2Y9PZG0_DELLE_9749 are exactly identical! WARNING: Sequences tr_A0A2U3UYL9_A0A2U3UYL9_TURTR_9739 and tr_A0A2Y9FDX8_A0A2Y9FDX8_PHYCD_9755 are exactly identical! WARNING: Sequences tr_A0A2U3UYL9_A0A2U3UYL9_TURTR_9739 and tr_A0A383Z8F9_A0A383Z8F9_BALAS_310752 are exactly identical! WARNING: Sequences tr_A0A2U3V438_A0A2U3V438_TURTR_9739 and tr_A0A2Y9MTZ7_A0A2Y9MTZ7_DELLE_9749 are exactly identical! WARNING: Sequences tr_A0A2U4AS56_A0A2U4AS56_TURTR_9739 and tr_A0A2Y9MFS9_A0A2Y9MFS9_DELLE_9749 are exactly identical! WARNING: Sequences tr_A0A2U4C654_A0A2U4C654_TURTR_9739 and tr_A0A2Y9Q610_A0A2Y9Q610_DELLE_9749 are exactly identical! WARNING: Sequences tr_A0A2U3VC31_A0A2U3VC31_ODORO_9708 and tr_A0A2U3XHD7_A0A2U3XHD7_LEPWE_9713 are exactly identical! WARNING: Sequences tr_A0A2U3VC31_A0A2U3VC31_ODORO_9708 and tr_A0A2Y9ISV4_A0A2Y9ISV4_ENHLU_391180 are exactly identical! WARNING: Sequences tr_A0A2U3VC31_A0A2U3VC31_ODORO_9708 and tr_A0A384C829_A0A384C829_URSMA_29073 are exactly identical! WARNING: Sequences tr_A0A2U3VMS3_A0A2U3VMS3_ODORO_9708 and tr_A0A2U3X7F4_A0A2U3X7F4_LEPWE_9713 are exactly identical! WARNING: Sequences tr_A0A2Y9FA62_A0A2Y9FA62_PHYCD_9755 and tr_A0A384A0D0_A0A384A0D0_BALAS_310752 are exactly identical! WARNING: Sequences tr_A0A2Y9RWR0_A0A2Y9RWR0_PHYCD_9755 and tr_A0A383ZW90_A0A383ZW90_BALAS_310752 are exactly identical! WARNING: Sequences tr_A0A2Y9S5C5_A0A2Y9S5C5_PHYCD_9755 and tr_A0A383ZV80_A0A383ZV80_BALAS_310752 are exactly identical! WARNING: Duplicate sequences found: 126 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/P14867/4_raxmlng_ancestral/P14867.raxml.reduced.phy Alignment comprises 1 partitions and 456 sites Partition 0: noname Model: LG4X+R4 Alignment sites: 456 Gaps: 11.58 % Invariant sites: 1.54 % NOTE: Binary MSA file created: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/P14867/4_raxmlng_ancestral/P14867.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/P14867/3_mltree/P14867.raxml.bestTree_unrooted [00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 114 / 9120 [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: -119584.190431 [00:00:00 -119584.190431] Initial branch length optimization [00:00:01 -84574.458177] Model parameter optimization (eps = 0.100000) [00:01:07] Tree #1, final logLikelihood: -84045.354259 Optimized model parameters: Partition 0: noname Rate heterogeneity: FREE (4 cats, mean), weights&rates: (0.301812,0.160287) (0.214905,0.247073) (0.280596,0.724781) (0.202687,3.429694) 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/P14867/4_raxmlng_ancestral/P14867.raxml.ancestralProbs Reconstructed ancestral sequences saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/P14867/4_raxmlng_ancestral/P14867.raxml.ancestralStates Node-labeled tree saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/P14867/4_raxmlng_ancestral/P14867.raxml.ancestralTree Execution log saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/P14867/4_raxmlng_ancestral/P14867.raxml.log Analysis started: 12-Jul-2021 18:04:40 / finished: 12-Jul-2021 18:05:51 Elapsed time: 71.372 seconds Consumed energy: 4.411 Wh