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 16:39:09 as follows: raxml-ng --ancestral --msa /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/P35711/2_msa/P35711_nogap_msa.fasta --tree /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/P35711/3_mltree/P35711.raxml.bestTree_unrooted --model LG4X --prefix /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/P35711/4_raxmlng_ancestral/P35711 --threads 4 Analysis options: run mode: Ancestral state reconstruction start tree(s): user random seed: 1626097149 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/P35711/2_msa/P35711_nogap_msa.fasta [00:00:00] Loaded alignment with 991 taxa and 763 sites WARNING: Sequences sp_Q32PP9_SOX14_DANRE_7955 and tr_A0A087YSU3_A0A087YSU3_POEFO_48698 are exactly identical! WARNING: Sequences sp_Q9W7R6_SOX14_CHICK_9031 and tr_H0Z8W5_H0Z8W5_TAEGU_59729 are exactly identical! WARNING: Sequences sp_Q9W7R6_SOX14_CHICK_9031 and tr_U3KIG3_U3KIG3_FICAL_59894 are exactly identical! WARNING: Sequences sp_Q9W7R6_SOX14_CHICK_9031 and tr_U3HYI1_U3HYI1_ANAPL_8839 are exactly identical! WARNING: Sequences sp_Q9W7R6_SOX14_CHICK_9031 and tr_A0A151NGX8_A0A151NGX8_ALLMI_8496 are exactly identical! WARNING: Sequences sp_Q9W7R6_SOX14_CHICK_9031 and tr_A0A0Q3PLH6_A0A0Q3PLH6_AMAAE_12930 are exactly identical! WARNING: Sequences sp_Q9W7R6_SOX14_CHICK_9031 and tr_A0A093Q8L4_A0A093Q8L4_9PASS_328815 are exactly identical! WARNING: Sequences sp_Q9W7R6_SOX14_CHICK_9031 and tr_A0A093J9H0_A0A093J9H0_STRCA_441894 are exactly identical! WARNING: Sequences sp_Q9W7R6_SOX14_CHICK_9031 and tr_A0A091XRL3_A0A091XRL3_OPIHO_30419 are exactly identical! WARNING: Sequences sp_Q9W7R6_SOX14_CHICK_9031 and tr_A0A0A0AMQ0_A0A0A0AMQ0_CHAVO_50402 are exactly identical! WARNING: Sequences sp_Q9W7R6_SOX14_CHICK_9031 and tr_A0A093GCB4_A0A093GCB4_DRYPU_118200 are exactly identical! WARNING: Sequences sp_Q9W7R6_SOX14_CHICK_9031 and tr_A0A091HR26_A0A091HR26_CALAN_9244 are exactly identical! WARNING: Sequences sp_Q9W7R6_SOX14_CHICK_9031 and tr_A0A1U7RC23_A0A1U7RC23_ALLSI_38654 are exactly identical! WARNING: Sequences sp_Q9W7R6_SOX14_CHICK_9031 and tr_A0A1V4KQX0_A0A1V4KQX0_PATFA_372326 are exactly identical! WARNING: Sequences sp_Q9W7R6_SOX14_CHICK_9031 and tr_A0A226NCN2_A0A226NCN2_CALSU_9009 are exactly identical! WARNING: Sequences sp_Q9W7R6_SOX14_CHICK_9031 and tr_A0A226PUW5_A0A226PUW5_COLVI_9014 are exactly identical! WARNING: Sequences sp_Q04892_SOX14_MOUSE_10090 and tr_M3Z4N2_M3Z4N2_MUSPF_9669 are exactly identical! WARNING: Sequences sp_Q04892_SOX14_MOUSE_10090 and tr_G1SBJ0_G1SBJ0_NOMLE_61853 are exactly identical! WARNING: Sequences sp_Q04892_SOX14_MOUSE_10090 and tr_G3RDD2_G3RDD2_GORGO_9595 are exactly identical! WARNING: Sequences sp_Q04892_SOX14_MOUSE_10090 and tr_H2PBI9_H2PBI9_PONAB_9601 are exactly identical! WARNING: Sequences sp_Q04892_SOX14_MOUSE_10090 and tr_A0A2I3TV57_A0A2I3TV57_PANTR_9598 are exactly identical! WARNING: Sequences sp_Q04892_SOX14_MOUSE_10090 and tr_W5Q1Z3_W5Q1Z3_SHEEP_9940 are exactly identical! WARNING: Sequences sp_Q04892_SOX14_MOUSE_10090 and tr_B7SZV3_B7SZV3_RAT_10116 are exactly identical! WARNING: Sequences sp_Q04892_SOX14_MOUSE_10090 and tr_A0A287D385_A0A287D385_ICTTR_43179 are exactly identical! WARNING: Sequences sp_Q04892_SOX14_MOUSE_10090 and tr_H0WE30_H0WE30_CAVPO_10141 are exactly identical! WARNING: Sequences sp_Q04892_SOX14_MOUSE_10090 and sp_O95416_SOX14_HUMAN_9606 are exactly identical! WARNING: Sequences sp_Q04892_SOX14_MOUSE_10090 and tr_F7HQE3_F7HQE3_MACMU_9544 are exactly identical! WARNING: Sequences sp_Q04892_SOX14_MOUSE_10090 and tr_G5BC40_G5BC40_HETGA_10181 are exactly identical! WARNING: Sequences sp_Q04892_SOX14_MOUSE_10090 and tr_A0A2R8P701_A0A2R8P701_CALJA_9483 are exactly identical! WARNING: Sequences sp_Q04892_SOX14_MOUSE_10090 and tr_G7P040_G7P040_MACFA_9541 are exactly identical! WARNING: Sequences sp_Q04892_SOX14_MOUSE_10090 and tr_L5KZV5_L5KZV5_PTEAL_9402 are exactly identical! WARNING: Sequences sp_Q04892_SOX14_MOUSE_10090 and tr_A0A2I2U9L9_A0A2I2U9L9_FELCA_9685 are exactly identical! WARNING: Sequences sp_Q04892_SOX14_MOUSE_10090 and tr_A0A096MSU2_A0A096MSU2_PAPAN_9555 are exactly identical! WARNING: Sequences sp_Q04892_SOX14_MOUSE_10090 and tr_A0A0D9SC48_A0A0D9SC48_CHLSB_60711 are exactly identical! WARNING: Sequences sp_Q04892_SOX14_MOUSE_10090 and tr_A0A1U7QSF6_A0A1U7QSF6_MESAU_10036 are exactly identical! WARNING: Sequences sp_Q04892_SOX14_MOUSE_10090 and tr_A0A2K5KS53_A0A2K5KS53_CERAT_9531 are exactly identical! WARNING: Sequences sp_Q04892_SOX14_MOUSE_10090 and tr_A0A2K6ANL6_A0A2K6ANL6_MACNE_9545 are exactly identical! WARNING: Sequences sp_Q04892_SOX14_MOUSE_10090 and tr_A0A2K5XVC7_A0A2K5XVC7_MANLE_9568 are exactly identical! WARNING: Sequences sp_Q04892_SOX14_MOUSE_10090 and tr_A0A2R8ZCF2_A0A2R8ZCF2_PANPA_9597 are exactly identical! WARNING: Sequences sp_Q04892_SOX14_MOUSE_10090 and tr_A0A2U4B8W6_A0A2U4B8W6_TURTR_9739 are exactly identical! WARNING: Sequences sp_Q04892_SOX14_MOUSE_10090 and tr_A0A2U3WV20_A0A2U3WV20_ODORO_9708 are exactly identical! WARNING: Sequences sp_Q04892_SOX14_MOUSE_10090 and tr_A0A2U3X925_A0A2U3X925_LEPWE_9713 are exactly identical! WARNING: Sequences sp_Q04892_SOX14_MOUSE_10090 and tr_A0A2Y9KGL2_A0A2Y9KGL2_ENHLU_391180 are exactly identical! WARNING: Sequences sp_Q04892_SOX14_MOUSE_10090 and tr_A0A2Y9NT43_A0A2Y9NT43_DELLE_9749 are exactly identical! WARNING: Sequences sp_Q04892_SOX14_MOUSE_10090 and tr_A0A2Y9FBD0_A0A2Y9FBD0_PHYCD_9755 are exactly identical! WARNING: Sequences sp_Q04892_SOX14_MOUSE_10090 and tr_A0A384DHB9_A0A384DHB9_URSMA_29073 are exactly identical! WARNING: Sequences sp_Q04892_SOX14_MOUSE_10090 and tr_A0A383Z5H6_A0A383Z5H6_BALAS_310752 are exactly identical! WARNING: Sequences sp_Q7M6Y2_SOX11_MOUSE_10090 and sp_P0C1G9_SOX11_RAT_10116 are exactly identical! WARNING: Sequences sp_Q7M6Y2_SOX11_MOUSE_10090 and tr_A0A1U8CDB4_A0A1U8CDB4_MESAU_10036 are exactly identical! WARNING: Sequences tr_M3Y0P3_M3Y0P3_MUSPF_9669 and tr_H2PI18_H2PI18_PONAB_9601 are exactly identical! WARNING: Sequences tr_G1QYX6_G1QYX6_NOMLE_61853 and tr_A0A1D5Q680_A0A1D5Q680_MACMU_9544 are exactly identical! WARNING: Sequences tr_G1S7L5_G1S7L5_NOMLE_61853 and tr_G3R5N3_G3R5N3_GORGO_9595 are exactly identical! WARNING: Sequences tr_G1S7L5_G1S7L5_NOMLE_61853 and tr_A0A2R9BNC8_A0A2R9BNC8_PANPA_9597 are exactly identical! WARNING: Sequences tr_A0A2I2ZX24_A0A2I2ZX24_GORGO_9595 and tr_A0A2I3TNT6_A0A2I3TNT6_PANTR_9598 are exactly identical! WARNING: Sequences tr_A0A2I2ZX24_A0A2I2ZX24_GORGO_9595 and tr_H0XGP9_H0XGP9_OTOGA_30611 are exactly identical! WARNING: Sequences tr_A0A2I2ZX24_A0A2I2ZX24_GORGO_9595 and sp_P35716_SOX11_HUMAN_9606 are exactly identical! WARNING: Sequences tr_A0A2I2ZX24_A0A2I2ZX24_GORGO_9595 and tr_A0A1D5R7Q8_A0A1D5R7Q8_MACMU_9544 are exactly identical! WARNING: Sequences tr_A0A2I2ZX24_A0A2I2ZX24_GORGO_9595 and tr_A0A0D9S9T7_A0A0D9S9T7_CHLSB_60711 are exactly identical! WARNING: Sequences tr_A0A2I2ZX24_A0A2I2ZX24_GORGO_9595 and tr_A0A2K5L0J2_A0A2K5L0J2_CERAT_9531 are exactly identical! WARNING: Sequences tr_A0A2I2ZX24_A0A2I2ZX24_GORGO_9595 and tr_A0A2K6AS12_A0A2K6AS12_MACNE_9545 are exactly identical! WARNING: Sequences tr_G3RJI1_G3RJI1_GORGO_9595 and sp_P35711_SOX5_HUMAN_9606 are exactly identical! WARNING: Sequences tr_G3RJI1_G3RJI1_GORGO_9595 and tr_A0A2R8MLZ2_A0A2R8MLZ2_CALJA_9483 are exactly identical! WARNING: Sequences tr_G3RJI1_G3RJI1_GORGO_9595 and tr_G7PK14_G7PK14_MACFA_9541 are exactly identical! WARNING: Sequences tr_G3RJI1_G3RJI1_GORGO_9595 and tr_A0A096NBX8_A0A096NBX8_PAPAN_9555 are exactly identical! WARNING: Sequences tr_G3RJI1_G3RJI1_GORGO_9595 and tr_A0A0D9R691_A0A0D9R691_CHLSB_60711 are exactly identical! WARNING: Sequences tr_G3RJI1_G3RJI1_GORGO_9595 and tr_A0A2K6CHF3_A0A2K6CHF3_MACNE_9545 are exactly identical! WARNING: Sequences tr_G3RJI1_G3RJI1_GORGO_9595 and tr_A0A2K5YPH0_A0A2K5YPH0_MANLE_9568 are exactly identical! WARNING: Sequences tr_E2RH58_E2RH58_CANLF_9615 and tr_I3LK63_I3LK63_PIG_9823 are exactly identical! WARNING: Sequences tr_H2Q5L7_H2Q5L7_PANTR_9598 and tr_A0A2R9B349_A0A2R9B349_PANPA_9597 are exactly identical! WARNING: Sequences tr_K7BLF6_K7BLF6_PANTR_9598 and tr_A0A2R9A6Q0_A0A2R9A6Q0_PANPA_9597 are exactly identical! WARNING: Sequences tr_K7CW19_K7CW19_PANTR_9598 and sp_O15370_SOX12_HUMAN_9606 are exactly identical! WARNING: Sequences tr_F6XNT3_F6XNT3_MONDO_13616 and tr_G3WHS5_G3WHS5_SARHA_9305 are exactly identical! WARNING: Sequences tr_M4ACG0_M4ACG0_XIPMA_8083 and tr_A0A087XTM4_A0A087XTM4_POEFO_48698 are exactly identical! WARNING: Sequences tr_Q6WNT8_Q6WNT8_TAKRU_31033 and tr_Q4SV91_Q4SV91_TETNG_99883 are exactly identical! WARNING: Sequences tr_F6UUG1_F6UUG1_MACMU_9544 and tr_G7NVE7_G7NVE7_MACFA_9541 are exactly identical! WARNING: Sequences tr_F6UUG1_F6UUG1_MACMU_9544 and tr_A0A096MUS4_A0A096MUS4_PAPAN_9555 are exactly identical! WARNING: Sequences tr_F6UUG1_F6UUG1_MACMU_9544 and tr_A0A2K5P3H3_A0A2K5P3H3_CERAT_9531 are exactly identical! WARNING: Sequences tr_F6UUG1_F6UUG1_MACMU_9544 and tr_A0A2K6B5V1_A0A2K6B5V1_MACNE_9545 are exactly identical! WARNING: Sequences tr_F6UUG1_F6UUG1_MACMU_9544 and tr_A0A2K5XIF8_A0A2K5XIF8_MANLE_9568 are exactly identical! WARNING: Sequences tr_F7H4A5_F7H4A5_MACMU_9544 and tr_G7PQM9_G7PQM9_MACFA_9541 are exactly identical! WARNING: Sequences tr_F7H4A5_F7H4A5_MACMU_9544 and tr_A0A2I3N9Z5_A0A2I3N9Z5_PAPAN_9555 are exactly identical! WARNING: Sequences tr_F7H4A5_F7H4A5_MACMU_9544 and tr_A0A2K5NCM9_A0A2K5NCM9_CERAT_9531 are exactly identical! WARNING: Sequences tr_F7H4A5_F7H4A5_MACMU_9544 and tr_A0A2K5Z3M0_A0A2K5Z3M0_MANLE_9568 are exactly identical! WARNING: Sequences tr_G3SSE7_G3SSE7_LOXAF_9785 and tr_A0A2Y9DUM9_A0A2Y9DUM9_TRIMA_127582 are exactly identical! WARNING: Sequences tr_H0YXE0_H0YXE0_TAEGU_59729 and tr_A0A091E8L7_A0A091E8L7_CORBR_85066 are exactly identical! WARNING: Sequences tr_E3LDW7_E3LDW7_CAERE_31234 and tr_A0A261CSR9_A0A261CSR9_9PELO_1503980 are exactly identical! WARNING: Sequences tr_G1LMD6_G1LMD6_AILME_9646 and tr_A0A2U3ZSY1_A0A2U3ZSY1_ODORO_9708 are exactly identical! WARNING: Sequences tr_A0A337RVV8_A0A337RVV8_FELCA_9685 and tr_A0A2U3VEI1_A0A2U3VEI1_ODORO_9708 are exactly identical! WARNING: Sequences tr_A0A337RVV8_A0A337RVV8_FELCA_9685 and tr_A0A2Y9IPI9_A0A2Y9IPI9_ENHLU_391180 are exactly identical! WARNING: Sequences tr_U3KJG5_U3KJG5_FICAL_59894 and tr_A0A1V4JN48_A0A1V4JN48_PATFA_372326 are exactly identical! WARNING: Sequences tr_A0A096MZ97_A0A096MZ97_PAPAN_9555 and tr_A0A2K5M610_A0A2K5M610_CERAT_9531 are exactly identical! WARNING: Sequences tr_A0A096MZ97_A0A096MZ97_PAPAN_9555 and tr_A0A2K6CKJ3_A0A2K6CKJ3_MACNE_9545 are exactly identical! WARNING: Sequences tr_A0A096N4N0_A0A096N4N0_PAPAN_9555 and tr_A0A2K5L3D6_A0A2K5L3D6_CERAT_9531 are exactly identical! WARNING: Sequences tr_A0A096N4N0_A0A096N4N0_PAPAN_9555 and tr_A0A2K6ATW4_A0A2K6ATW4_MACNE_9545 are exactly identical! WARNING: Sequences tr_A0A0D9RQ99_A0A0D9RQ99_CHLSB_60711 and tr_A0A2K5LZ51_A0A2K5LZ51_CERAT_9531 are exactly identical! WARNING: Sequences tr_A0A0D9RQ99_A0A0D9RQ99_CHLSB_60711 and tr_A0A2K6CCT3_A0A2K6CCT3_MACNE_9545 are exactly identical! WARNING: Sequences tr_A0A0V1CTP4_A0A0V1CTP4_TRIBR_45882 and tr_A0A0V0WVR9_A0A0V0WVR9_9BILA_92179 are exactly identical! WARNING: Sequences tr_A0A0V1CTP4_A0A0V1CTP4_TRIBR_45882 and tr_A0A0V1LB14_A0A0V1LB14_9BILA_6335 are exactly identical! WARNING: Sequences tr_A0A0V1CTP4_A0A0V1CTP4_TRIBR_45882 and tr_A0A0V1PCW0_A0A0V1PCW0_9BILA_92180 are exactly identical! WARNING: Sequences tr_A0A0V1CTP4_A0A0V1CTP4_TRIBR_45882 and tr_A0A0V0UCJ5_A0A0V0UCJ5_9BILA_144512 are exactly identical! WARNING: Sequences tr_A0A1S3KK65_A0A1S3KK65_SALSA_8030 and tr_A0A060Y4B1_A0A060Y4B1_ONCMY_8022 are exactly identical! WARNING: Sequences tr_A0A1S3PMG1_A0A1S3PMG1_SALSA_8030 and tr_A0A060WTL2_A0A060WTL2_ONCMY_8022 are exactly identical! WARNING: Sequences tr_A0A226NDZ2_A0A226NDZ2_CALSU_9009 and tr_A0A226P3V3_A0A226P3V3_COLVI_9014 are exactly identical! WARNING: Sequences tr_A0A2D0PIH8_A0A2D0PIH8_ICTPU_7998 and tr_A0A2D0PMN1_A0A2D0PMN1_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2U3VAD4_A0A2U3VAD4_TURTR_9739 and tr_A0A2Y9PZ92_A0A2Y9PZ92_DELLE_9749 are exactly identical! WARNING: Sequences tr_A0A2U3VAD4_A0A2U3VAD4_TURTR_9739 and tr_A0A2Y9T670_A0A2Y9T670_PHYCD_9755 are exactly identical! WARNING: Sequences tr_A0A2U4AJ34_A0A2U4AJ34_TURTR_9739 and tr_A0A2Y9M570_A0A2Y9M570_DELLE_9749 are exactly identical! WARNING: Sequences tr_A0A2U4CF42_A0A2U4CF42_TURTR_9739 and tr_A0A2Y9LWT3_A0A2Y9LWT3_DELLE_9749 are exactly identical! WARNING: Duplicate sequences found: 108 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/P35711/4_raxmlng_ancestral/P35711.raxml.reduced.phy Alignment comprises 1 partitions and 763 sites Partition 0: noname Model: LG4X+R4 Alignment sites: 763 Gaps: 55.23 % Invariant sites: 0.13 % NOTE: Binary MSA file created: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/P35711/4_raxmlng_ancestral/P35711.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/P35711/3_mltree/P35711.raxml.bestTree_unrooted [00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 191 / 15280 [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: -349870.931551 [00:00:00 -349870.931551] Initial branch length optimization [00:00:03 -176452.106306] Model parameter optimization (eps = 0.100000) 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 18:12:26 as follows: raxml-ng --ancestral --msa /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/P35711/2_msa/P35711_nogap_msa.fasta --tree /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/P35711/3_mltree/P35711.raxml.bestTree_unrooted --model LG4X --prefix /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/P35711/4_raxmlng_ancestral/P35711 --threads 4 Analysis options: run mode: Ancestral state reconstruction start tree(s): user random seed: 1626102746 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 WARNING: The model you specified on the command line (LG4X) will be ignored since the binary MSA file already contains a model definition. If you want to change the model, please re-run RAxML-NG with the original PHYLIP/FASTA alignment and --redo option. [00:00:00] Loading binary alignment from file: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/P35711/4_raxmlng_ancestral/P35711.raxml.rba [00:00:00] Alignment comprises 991 taxa, 1 partitions and 763 patterns Partition 0: noname Model: LG4X+R4 Alignment sites: 763 Gaps: 55.23 % Invariant sites: 0.13 % Parallelization scheme autoconfig: 1 worker(s) x 4 thread(s) Parallel reduction/worker buffer size: 1 KB / 0 KB [00:00:00] NOTE: Resuming execution from checkpoint (logLH: -176452.11, ML trees: 0, bootstraps: 0) [00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 191 / 15280 [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: -176452.106306 [00:00:00 -176452.106306] Model parameter optimization (eps = 0.100000) [00:00:56] Tree #1, final logLikelihood: -176182.277625 Optimized model parameters: Partition 0: noname Rate heterogeneity: FREE (4 cats, mean), weights&rates: (0.053950,0.082720) (0.077178,0.282835) (0.352506,0.664995) (0.516366,1.431726) 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/P35711/4_raxmlng_ancestral/P35711.raxml.ancestralProbs Reconstructed ancestral sequences saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/P35711/4_raxmlng_ancestral/P35711.raxml.ancestralStates Node-labeled tree saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/P35711/4_raxmlng_ancestral/P35711.raxml.ancestralTree Execution log saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/P35711/4_raxmlng_ancestral/P35711.raxml.log Analysis started: 12-Jul-2021 18:12:26 / finished: 12-Jul-2021 18:13:30 Elapsed time: 64.049 seconds (this run) / 67.802 seconds (total with restarts) Consumed energy: 5.051 Wh