RAxML-NG v. 1.0.2 released on 22.02.2021 by The Exelixis Lab. Developed by: Alexey M. Kozlov and Alexandros Stamatakis. Contributors: Diego Darriba, Tomas Flouri, Benoit Morel, Sarah Lutteropp, Ben Bettisworth. Latest version: https://github.com/amkozlov/raxml-ng Questions/problems/suggestions? Please visit: https://groups.google.com/forum/#!forum/raxml System: Intel(R) Xeon(R) Gold 6140 CPU @ 2.30GHz, 36 cores, 251 GB RAM RAxML-NG was called at 19-Jun-2021 20:01:05 as follows: raxml-ng --ancestral --msa /cta/users/eakkoyun/WORKFOLDER/PROD/run_040621/phylogeny-snakemake/results/P28069/2_msa/P28069_nogap_msa.fasta --tree /cta/users/eakkoyun/WORKFOLDER/PROD/run_040621/phylogeny-snakemake/results/P28069/3_mltree/P28069.raxml.bestTree_unrooted --model LG4X --prefix /cta/users/eakkoyun/WORKFOLDER/PROD/run_040621/phylogeny-snakemake/results/P28069/4_raxmlng_ancestral/P28069 --threads 4 Analysis options: run mode: Ancestral state reconstruction start tree(s): user random seed: 1624122065 tip-inner: ON pattern compression: OFF per-rate scalers: OFF site repeats: OFF branch lengths: proportional (ML estimate, algorithm: NR-FAST) SIMD kernels: AVX2 parallelization: coarse-grained (auto), PTHREADS (4 threads), thread pinning: OFF [00:00:00] Reading alignment from file: /cta/users/eakkoyun/WORKFOLDER/PROD/run_040621/phylogeny-snakemake/results/P28069/2_msa/P28069_nogap_msa.fasta [00:00:00] Loaded alignment with 1001 taxa and 291 sites WARNING: Sequences tr_B4Q476_B4Q476_DROSI_7240 and tr_B4IEA9_B4IEA9_DROSE_7238 are exactly identical! WARNING: Sequences tr_A0A1D5NY46_A0A1D5NY46_CHICK_9031 and sp_Q9YGL7_PIT1_CHICK_9031 are exactly identical! WARNING: Sequences tr_A0A1D5P0C8_A0A1D5P0C8_CHICK_9031 and sp_A7Y7W2_PO5F3_CHICK_9031 are exactly identical! WARNING: Sequences sp_P31360_PO3F2_MOUSE_10090 and tr_H0XMS3_H0XMS3_OTOGA_30611 are exactly identical! WARNING: Sequences sp_P31360_PO3F2_MOUSE_10090 and sp_P20265_PO3F2_HUMAN_9606 are exactly identical! WARNING: Sequences sp_P31360_PO3F2_MOUSE_10090 and tr_A0A2R8NBI2_A0A2R8NBI2_CALJA_9483 are exactly identical! WARNING: Sequences sp_P31360_PO3F2_MOUSE_10090 and tr_A0A1U7QHN3_A0A1U7QHN3_MESAU_10036 are exactly identical! WARNING: Sequences sp_P31360_PO3F2_MOUSE_10090 and tr_A0A2U3WEX5_A0A2U3WEX5_ODORO_9708 are exactly identical! WARNING: Sequences sp_P31360_PO3F2_MOUSE_10090 and tr_A0A2Y9KPU4_A0A2Y9KPU4_ENHLU_391180 are exactly identical! WARNING: Sequences sp_P31360_PO3F2_MOUSE_10090 and tr_A0A2Y9LGA6_A0A2Y9LGA6_DELLE_9749 are exactly identical! WARNING: Sequences sp_P31361_PO3F3_MOUSE_10090 and sp_Q63262_PO3F3_RAT_10116 are exactly identical! WARNING: Sequences sp_P31361_PO3F3_MOUSE_10090 and sp_P20264_PO3F3_HUMAN_9606 are exactly identical! WARNING: Sequences sp_P31361_PO3F3_MOUSE_10090 and tr_A0A337SVT6_A0A337SVT6_FELCA_9685 are exactly identical! WARNING: Sequences sp_P31361_PO3F3_MOUSE_10090 and tr_A0A2U3X1U4_A0A2U3X1U4_ODORO_9708 are exactly identical! WARNING: Sequences sp_P31361_PO3F3_MOUSE_10090 and tr_A0A2Y9KL31_A0A2Y9KL31_ENHLU_391180 are exactly identical! WARNING: Sequences sp_P62515_PO3F4_MOUSE_10090 and tr_G3HPU7_G3HPU7_CRIGR_10029 are exactly identical! WARNING: Sequences sp_P62515_PO3F4_MOUSE_10090 and sp_P62516_PO3F4_RAT_10116 are exactly identical! WARNING: Sequences sp_P62515_PO3F4_MOUSE_10090 and sp_Q812B1_PO3F4_MESAU_10036 are exactly identical! WARNING: Sequences sp_Q00196_PO2F2_MOUSE_10090 and tr_E2RFC4_E2RFC4_CANLF_9615 are exactly identical! WARNING: Sequences sp_Q63955_PO4F3_MOUSE_10090 and tr_A0A1U7QK11_A0A1U7QK11_MESAU_10036 are exactly identical! WARNING: Sequences tr_M3Y8W3_M3Y8W3_MUSPF_9669 and tr_E2QUY3_E2QUY3_CANLF_9615 are exactly identical! WARNING: Sequences tr_M3Y8W3_M3Y8W3_MUSPF_9669 and tr_W5NYL1_W5NYL1_SHEEP_9940 are exactly identical! WARNING: Sequences tr_M3Y8W3_M3Y8W3_MUSPF_9669 and tr_H0XQ64_H0XQ64_OTOGA_30611 are exactly identical! WARNING: Sequences tr_M3Y8W3_M3Y8W3_MUSPF_9669 and tr_H0W6C1_H0W6C1_CAVPO_10141 are exactly identical! WARNING: Sequences tr_M3Y8W3_M3Y8W3_MUSPF_9669 and tr_G5C842_G5C842_HETGA_10181 are exactly identical! WARNING: Sequences tr_M3Y8W3_M3Y8W3_MUSPF_9669 and tr_D2HQF8_D2HQF8_AILME_9646 are exactly identical! WARNING: Sequences tr_M3Y8W3_M3Y8W3_MUSPF_9669 and tr_E1BJ03_E1BJ03_BOVIN_9913 are exactly identical! WARNING: Sequences tr_M3Y8W3_M3Y8W3_MUSPF_9669 and tr_L5JWU3_L5JWU3_PTEAL_9402 are exactly identical! WARNING: Sequences tr_M3Y8W3_M3Y8W3_MUSPF_9669 and tr_A0A2U3WVX6_A0A2U3WVX6_ODORO_9708 are exactly identical! WARNING: Sequences tr_M3Y8W3_M3Y8W3_MUSPF_9669 and tr_A0A2Y9E2L3_A0A2Y9E2L3_TRIMA_127582 are exactly identical! WARNING: Sequences tr_M3Y8W3_M3Y8W3_MUSPF_9669 and tr_A0A2Y9KJ24_A0A2Y9KJ24_ENHLU_391180 are exactly identical! WARNING: Sequences tr_M3Y8W3_M3Y8W3_MUSPF_9669 and tr_A0A384C452_A0A384C452_URSMA_29073 are exactly identical! WARNING: Sequences sp_P16241_CF1A_DROME_7227 and tr_B4HUY1_B4HUY1_DROSE_7238 are exactly identical! WARNING: Sequences tr_A0A2I3HNQ3_A0A2I3HNQ3_NOMLE_61853 and tr_H2N4V6_H2N4V6_PONAB_9601 are exactly identical! WARNING: Sequences tr_A0A2I3HNQ3_A0A2I3HNQ3_NOMLE_61853 and tr_A0A1D5R2U1_A0A1D5R2U1_MACMU_9544 are exactly identical! WARNING: Sequences tr_A0A2I3HNQ3_A0A2I3HNQ3_NOMLE_61853 and tr_G7NU42_G7NU42_MACFA_9541 are exactly identical! WARNING: Sequences tr_A0A2I3HNQ3_A0A2I3HNQ3_NOMLE_61853 and tr_A0A2K5Z8W3_A0A2K5Z8W3_MANLE_9568 are exactly identical! WARNING: Sequences tr_G1RFQ1_G1RFQ1_NOMLE_61853 and tr_G3R9P3_G3R9P3_GORGO_9595 are exactly identical! WARNING: Sequences tr_G1RFQ1_G1RFQ1_NOMLE_61853 and tr_H2PGY6_H2PGY6_PONAB_9601 are exactly identical! WARNING: Sequences tr_G1RFQ1_G1RFQ1_NOMLE_61853 and tr_H2QRQ4_H2QRQ4_PANTR_9598 are exactly identical! WARNING: Sequences tr_G1RFQ1_G1RFQ1_NOMLE_61853 and sp_Q15319_PO4F3_HUMAN_9606 are exactly identical! WARNING: Sequences tr_G1RFQ1_G1RFQ1_NOMLE_61853 and tr_F7G4P3_F7G4P3_CALJA_9483 are exactly identical! WARNING: Sequences tr_G1RFQ1_G1RFQ1_NOMLE_61853 and tr_F1RM14_F1RM14_PIG_9823 are exactly identical! WARNING: Sequences tr_G1RFQ1_G1RFQ1_NOMLE_61853 and tr_A0A096N737_A0A096N737_PAPAN_9555 are exactly identical! WARNING: Sequences tr_G1RFQ1_G1RFQ1_NOMLE_61853 and tr_A0A0D9RIK6_A0A0D9RIK6_CHLSB_60711 are exactly identical! WARNING: Sequences tr_G1RFQ1_G1RFQ1_NOMLE_61853 and tr_A0A2K5MIM2_A0A2K5MIM2_CERAT_9531 are exactly identical! WARNING: Sequences tr_G1RFQ1_G1RFQ1_NOMLE_61853 and tr_A0A2K6DYF1_A0A2K6DYF1_MACNE_9545 are exactly identical! WARNING: Sequences tr_G1RFQ1_G1RFQ1_NOMLE_61853 and tr_A0A2K5Z3K2_A0A2K5Z3K2_MANLE_9568 are exactly identical! WARNING: Sequences tr_G1RFQ1_G1RFQ1_NOMLE_61853 and tr_A0A2R9CJG6_A0A2R9CJG6_PANPA_9597 are exactly identical! WARNING: Sequences tr_A0A2I2YJ72_A0A2I2YJ72_GORGO_9595 and tr_H2RGT3_H2RGT3_PANTR_9598 are exactly identical! WARNING: Sequences tr_A0A2I2YJ72_A0A2I2YJ72_GORGO_9595 and tr_U3EFU3_U3EFU3_CALJA_9483 are exactly identical! WARNING: Sequences tr_A0A2I2YJ72_A0A2I2YJ72_GORGO_9595 and tr_A0A2R8ZGB2_A0A2R8ZGB2_PANPA_9597 are exactly identical! WARNING: Sequences tr_A0A2I2ZGZ9_A0A2I2ZGZ9_GORGO_9595 and tr_A0A2I3NAR0_A0A2I3NAR0_PAPAN_9555 are exactly identical! WARNING: Sequences tr_A0A2I2ZGZ9_A0A2I2ZGZ9_GORGO_9595 and tr_A0A2K5MQX2_A0A2K5MQX2_CERAT_9531 are exactly identical! WARNING: Sequences tr_G3RJF8_G3RJF8_GORGO_9595 and tr_A0A2K5L0P4_A0A2K5L0P4_CERAT_9531 are exactly identical! WARNING: Sequences tr_G3RJF8_G3RJF8_GORGO_9595 and tr_A0A2K6BXL0_A0A2K6BXL0_MACNE_9545 are exactly identical! WARNING: Sequences tr_G3RJF8_G3RJF8_GORGO_9595 and tr_A0A2R9BCB2_A0A2R9BCB2_PANPA_9597 are exactly identical! WARNING: Sequences tr_H2NYZ9_H2NYZ9_PONAB_9601 and sp_P09086_PO2F2_HUMAN_9606 are exactly identical! WARNING: Sequences tr_H2NYZ9_H2NYZ9_PONAB_9601 and tr_A0A0D9S133_A0A0D9S133_CHLSB_60711 are exactly identical! WARNING: Sequences tr_H2NYZ9_H2NYZ9_PONAB_9601 and tr_A0A2Y9E7Z0_A0A2Y9E7Z0_TRIMA_127582 are exactly identical! WARNING: Sequences tr_H2NYZ9_H2NYZ9_PONAB_9601 and tr_A0A2Y9IG07_A0A2Y9IG07_ENHLU_391180 are exactly identical! WARNING: Sequences tr_F1P840_F1P840_CANLF_9615 and tr_H2R980_H2R980_PANTR_9598 are exactly identical! WARNING: Sequences tr_F1P840_F1P840_CANLF_9615 and sp_P20267_PO3F1_RAT_10116 are exactly identical! WARNING: Sequences tr_F1P840_F1P840_CANLF_9615 and sp_Q03052_PO3F1_HUMAN_9606 are exactly identical! WARNING: Sequences tr_F1P840_F1P840_CANLF_9615 and tr_A0A2R8MSJ4_A0A2R8MSJ4_CALJA_9483 are exactly identical! WARNING: Sequences tr_F1P840_F1P840_CANLF_9615 and tr_A0A337S059_A0A337S059_FELCA_9685 are exactly identical! WARNING: Sequences tr_F1P840_F1P840_CANLF_9615 and tr_A0A0D9SAG8_A0A0D9SAG8_CHLSB_60711 are exactly identical! WARNING: Sequences tr_F1P840_F1P840_CANLF_9615 and tr_A0A2K5KL41_A0A2K5KL41_CERAT_9531 are exactly identical! WARNING: Sequences tr_F1P840_F1P840_CANLF_9615 and tr_A0A2K6ASC7_A0A2K6ASC7_MACNE_9545 are exactly identical! WARNING: Sequences tr_F1P840_F1P840_CANLF_9615 and tr_A0A2U3W3T6_A0A2U3W3T6_ODORO_9708 are exactly identical! WARNING: Sequences tr_F1P840_F1P840_CANLF_9615 and tr_A0A2Y9J5C2_A0A2Y9J5C2_ENHLU_391180 are exactly identical! WARNING: Sequences tr_F1P840_F1P840_CANLF_9615 and tr_A0A2Y9SZZ9_A0A2Y9SZZ9_PHYCD_9755 are exactly identical! WARNING: Sequences tr_F1PZH7_F1PZH7_CANLF_9615 and sp_Q9TTI7_PIT1_CANLF_9615 are exactly identical! WARNING: Sequences tr_A0A2I3SUL3_A0A2I3SUL3_PANTR_9598 and tr_A0A2K6BDC1_A0A2K6BDC1_MACNE_9545 are exactly identical! WARNING: Sequences tr_H2QMY4_H2QMY4_PANTR_9598 and sp_P28069_PIT1_HUMAN_9606 are exactly identical! WARNING: Sequences tr_H2QMY4_H2QMY4_PANTR_9598 and tr_A0A1D5RB42_A0A1D5RB42_MACMU_9544 are exactly identical! WARNING: Sequences tr_H2QMY4_H2QMY4_PANTR_9598 and tr_G7NZ53_G7NZ53_MACFA_9541 are exactly identical! WARNING: Sequences tr_H2QMY4_H2QMY4_PANTR_9598 and tr_A0A096MTC6_A0A096MTC6_PAPAN_9555 are exactly identical! WARNING: Sequences tr_H2QMY4_H2QMY4_PANTR_9598 and tr_A0A0D9R0U5_A0A0D9R0U5_CHLSB_60711 are exactly identical! WARNING: Sequences tr_H2QMY4_H2QMY4_PANTR_9598 and tr_A0A2K6BC13_A0A2K6BC13_MACNE_9545 are exactly identical! WARNING: Sequences tr_B0XIM7_B0XIM7_CULQU_7176 and tr_Q17F60_Q17F60_AEDAE_7159 are exactly identical! WARNING: Sequences tr_W5PJV9_W5PJV9_SHEEP_9940 and tr_F1N017_F1N017_BOVIN_9913 are exactly identical! WARNING: Sequences tr_W5PJV9_W5PJV9_SHEEP_9940 and sp_O97552_PO5F1_BOVIN_9913 are exactly identical! WARNING: Sequences tr_M4AYN1_M4AYN1_XIPMA_8083 and tr_A0A087YRX5_A0A087YRX5_POEFO_48698 are exactly identical! WARNING: Sequences tr_M4AYN1_M4AYN1_XIPMA_8083 and tr_A0A2I4BVK4_A0A2I4BVK4_9TELE_52670 are exactly identical! WARNING: Sequences tr_A0A158NG23_A0A158NG23_ATTCE_12957 and tr_F4WTK7_F4WTK7_ACREC_103372 are exactly identical! WARNING: Sequences tr_A0A158NG23_A0A158NG23_ATTCE_12957 and tr_A0A151XB75_A0A151XB75_9HYME_64791 are exactly identical! WARNING: Sequences tr_A0A158NG23_A0A158NG23_ATTCE_12957 and tr_A0A195E819_A0A195E819_9HYME_471704 are exactly identical! WARNING: Sequences tr_A0A158NG23_A0A158NG23_ATTCE_12957 and tr_A0A151I195_A0A151I195_9HYME_520822 are exactly identical! WARNING: Sequences tr_A0A158NG23_A0A158NG23_ATTCE_12957 and tr_A0A195F253_A0A195F253_9HYME_34720 are exactly identical! WARNING: Sequences tr_I3MUG3_I3MUG3_ICTTR_43179 and tr_A0A2U3V0W2_A0A2U3V0W2_TURTR_9739 are exactly identical! WARNING: Sequences tr_I3MUG3_I3MUG3_ICTTR_43179 and tr_A0A2Y9PL45_A0A2Y9PL45_DELLE_9749 are exactly identical! WARNING: Sequences tr_I3MUG3_I3MUG3_ICTTR_43179 and tr_A0A2Y9F5W6_A0A2Y9F5W6_PHYCD_9755 are exactly identical! WARNING: Sequences tr_I3MUG3_I3MUG3_ICTTR_43179 and tr_A0A384B3E0_A0A384B3E0_BALAS_310752 are exactly identical! WARNING: Sequences sp_Q14863_PO6F1_HUMAN_9606 and tr_A0A286ZSS5_A0A286ZSS5_PIG_9823 are exactly identical! WARNING: Sequences sp_Q14863_PO6F1_HUMAN_9606 and tr_A0A0D9R0S3_A0A0D9R0S3_CHLSB_60711 are exactly identical! WARNING: Sequences tr_A0A0H5S102_A0A0H5S102_BRUMA_6279 and tr_A0A0N4TRL9_A0A0N4TRL9_BRUPA_6280 are exactly identical! WARNING: Sequences tr_A0A1D5QVM2_A0A1D5QVM2_MACMU_9544 and tr_G7PPB8_G7PPB8_MACFA_9541 are exactly identical! WARNING: Sequences tr_A0A1D5QVM2_A0A1D5QVM2_MACMU_9544 and tr_A0A2I3NEB5_A0A2I3NEB5_PAPAN_9555 are exactly identical! WARNING: Sequences tr_A0A1D5QVM2_A0A1D5QVM2_MACMU_9544 and tr_A0A2K6B9K7_A0A2K6B9K7_MACNE_9545 are exactly identical! WARNING: Sequences tr_A0A1D5QVM2_A0A1D5QVM2_MACMU_9544 and tr_A0A2K5XY16_A0A2K5XY16_MANLE_9568 are exactly identical! WARNING: Sequences tr_F7DRC1_F7DRC1_MACMU_9544 and tr_G7Q354_G7Q354_MACFA_9541 are exactly identical! WARNING: Sequences tr_F7DRC1_F7DRC1_MACMU_9544 and tr_A0A2K5KZM6_A0A2K5KZM6_CERAT_9531 are exactly identical! WARNING: Sequences tr_F7DRC1_F7DRC1_MACMU_9544 and tr_A0A2K5XPM1_A0A2K5XPM1_MANLE_9568 are exactly identical! WARNING: Sequences tr_G5AQ47_G5AQ47_HETGA_10181 and tr_A0A091DDG3_A0A091DDG3_FUKDA_885580 are exactly identical! WARNING: Sequences tr_H0YQ72_H0YQ72_TAEGU_59729 and tr_A0A091EZC7_A0A091EZC7_CORBR_85066 are exactly identical! WARNING: Sequences tr_H0YQ72_H0YQ72_TAEGU_59729 and tr_A0A091J3Q7_A0A091J3Q7_EGRGA_188379 are exactly identical! WARNING: Sequences tr_H0YQ72_H0YQ72_TAEGU_59729 and tr_A0A093QH88_A0A093QH88_9PASS_328815 are exactly identical! WARNING: Sequences tr_H0YQ72_H0YQ72_TAEGU_59729 and tr_A0A091VF12_A0A091VF12_NIPNI_128390 are exactly identical! WARNING: Sequences tr_H0YQ72_H0YQ72_TAEGU_59729 and tr_A0A091WP73_A0A091WP73_OPIHO_30419 are exactly identical! WARNING: Sequences tr_H0YQ72_H0YQ72_TAEGU_59729 and tr_A0A099Z789_A0A099Z789_TINGU_94827 are exactly identical! WARNING: Sequences tr_H0YQ72_H0YQ72_TAEGU_59729 and tr_A0A0A0A1Z1_A0A0A0A1Z1_CHAVO_50402 are exactly identical! WARNING: Sequences tr_H0YQ72_H0YQ72_TAEGU_59729 and tr_A0A093GMM3_A0A093GMM3_DRYPU_118200 are exactly identical! WARNING: Sequences tr_H0YQ72_H0YQ72_TAEGU_59729 and tr_A0A1V4J852_A0A1V4J852_PATFA_372326 are exactly identical! WARNING: Sequences tr_H0YW05_H0YW05_TAEGU_59729 and tr_A0A091EQH0_A0A091EQH0_CORBR_85066 are exactly identical! WARNING: Sequences tr_H0ZTG2_H0ZTG2_TAEGU_59729 and tr_A0A218V2B3_A0A218V2B3_9PASE_299123 are exactly identical! WARNING: Sequences tr_G0NK56_G0NK56_CAEBE_135651 and tr_G0PHV7_G0PHV7_CAEBE_135651 are exactly identical! WARNING: Sequences tr_D2I4C0_D2I4C0_AILME_9646 and tr_A0A2U3WMP6_A0A2U3WMP6_ODORO_9708 are exactly identical! WARNING: Sequences tr_D2I4C0_D2I4C0_AILME_9646 and tr_A0A2U3X6I4_A0A2U3X6I4_LEPWE_9713 are exactly identical! WARNING: Sequences tr_G1KZH3_G1KZH3_AILME_9646 and tr_A0A384CH73_A0A384CH73_URSMA_29073 are exactly identical! WARNING: Sequences tr_G1LL54_G1LL54_AILME_9646 and tr_A0A384D6Z8_A0A384D6Z8_URSMA_29073 are exactly identical! WARNING: Sequences tr_A0A2I2UGP5_A0A2I2UGP5_FELCA_9685 and tr_A0A383YYZ6_A0A383YYZ6_BALAS_310752 are exactly identical! WARNING: Sequences tr_U3I3X6_U3I3X6_ANAPL_8839 and tr_A0A091VPE2_A0A091VPE2_NIPNI_128390 are exactly identical! WARNING: Sequences tr_A0A091EWJ4_A0A091EWJ4_CORBR_85066 and tr_A0A093QUU3_A0A093QUU3_9PASS_328815 are exactly identical! WARNING: Sequences tr_A0A091EWJ4_A0A091EWJ4_CORBR_85066 and tr_A0A091W2M2_A0A091W2M2_NIPNI_128390 are exactly identical! WARNING: Sequences tr_A0A091EWJ4_A0A091EWJ4_CORBR_85066 and tr_A0A091GCI1_A0A091GCI1_9AVES_55661 are exactly identical! WARNING: Sequences tr_A0A091EWJ4_A0A091EWJ4_CORBR_85066 and tr_A0A0A0ASJ4_A0A0A0ASJ4_CHAVO_50402 are exactly identical! WARNING: Sequences tr_A0A091EWJ4_A0A091EWJ4_CORBR_85066 and tr_A0A091IAW7_A0A091IAW7_CALAN_9244 are exactly identical! WARNING: Sequences tr_A0A091V8N2_A0A091V8N2_NIPNI_128390 and tr_A0A087QT12_A0A087QT12_APTFO_9233 are exactly identical! WARNING: Sequences tr_A0A091V8N2_A0A091V8N2_NIPNI_128390 and tr_A0A091WPL0_A0A091WPL0_OPIHO_30419 are exactly identical! WARNING: Sequences tr_A0A093HMM7_A0A093HMM7_STRCA_441894 and tr_A0A099ZH01_A0A099ZH01_TINGU_94827 are exactly identical! WARNING: Sequences tr_A0A093HMM7_A0A093HMM7_STRCA_441894 and tr_A0A091FXR3_A0A091FXR3_9AVES_55661 are exactly identical! WARNING: Sequences tr_A0A0V1C996_A0A0V1C996_TRIBR_45882 and tr_A0A0V1LHA9_A0A0V1LHA9_9BILA_6335 are exactly identical! WARNING: Sequences tr_A0A0V1C996_A0A0V1C996_TRIBR_45882 and tr_A0A0V1NZ90_A0A0V1NZ90_9BILA_92180 are exactly identical! WARNING: Sequences tr_A0A0V0Z8Q2_A0A0V0Z8Q2_9BILA_990121 and tr_A0A0V0TRM5_A0A0V0TRM5_9BILA_144512 are exactly identical! WARNING: Sequences tr_A0A1S3FPA9_A0A1S3FPA9_DIPOR_10020 and tr_A0A383Z4B8_A0A383Z4B8_BALAS_310752 are exactly identical! WARNING: Sequences tr_A0A1S3MAB7_A0A1S3MAB7_SALSA_8030 and tr_A0A060YPT5_A0A060YPT5_ONCMY_8022 are exactly identical! WARNING: Sequences tr_A0A1S3P9R2_A0A1S3P9R2_SALSA_8030 and tr_A0A1S3RV76_A0A1S3RV76_SALSA_8030 are exactly identical! WARNING: Sequences tr_A0A1S3RMK4_A0A1S3RMK4_SALSA_8030 and tr_A0A060XPX0_A0A060XPX0_ONCMY_8022 are exactly identical! WARNING: Sequences tr_A0A060X9G4_A0A060X9G4_ONCMY_8022 and tr_A0A060YDG0_A0A060YDG0_ONCMY_8022 are exactly identical! WARNING: Sequences tr_A0A226N467_A0A226N467_CALSU_9009 and tr_A0A226PUR8_A0A226PUR8_COLVI_9014 are exactly identical! WARNING: Sequences tr_A0A226NGK7_A0A226NGK7_CALSU_9009 and tr_A0A226PLQ6_A0A226PLQ6_COLVI_9014 are exactly identical! WARNING: Sequences tr_A0A2D0R4J5_A0A2D0R4J5_ICTPU_7998 and tr_A0A2D0R4K4_A0A2D0R4K4_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0R4J5_A0A2D0R4J5_ICTPU_7998 and tr_A0A2D0R4N2_A0A2D0R4N2_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0R4J5_A0A2D0R4J5_ICTPU_7998 and tr_A0A2D0R6T5_A0A2D0R6T5_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2U3V534_A0A2U3V534_TURTR_9739 and tr_A0A2U3V535_A0A2U3V535_TURTR_9739 are exactly identical! WARNING: Sequences tr_A0A2U3V534_A0A2U3V534_TURTR_9739 and tr_A0A2Y9EJT5_A0A2Y9EJT5_PHYCD_9755 are exactly identical! WARNING: Sequences tr_A0A2U3V534_A0A2U3V534_TURTR_9739 and tr_A0A383YMV7_A0A383YMV7_BALAS_310752 are exactly identical! WARNING: Sequences tr_A0A2U4BK87_A0A2U4BK87_TURTR_9739 and tr_A0A2Y9NCL7_A0A2Y9NCL7_DELLE_9749 are exactly identical! WARNING: Sequences tr_A0A2U4CS41_A0A2U4CS41_TURTR_9739 and tr_A0A2Y9S872_A0A2Y9S872_PHYCD_9755 are exactly identical! WARNING: Sequences tr_A0A2U3WW45_A0A2U3WW45_ODORO_9708 and tr_A0A2U3X6R3_A0A2U3X6R3_LEPWE_9713 are exactly identical! WARNING: Sequences tr_A0A2Y9NMT1_A0A2Y9NMT1_DELLE_9749 and tr_A0A2Y9FCP4_A0A2Y9FCP4_PHYCD_9755 are exactly identical! WARNING: Sequences tr_A0A2Y9NMT1_A0A2Y9NMT1_DELLE_9749 and tr_A0A384AN72_A0A384AN72_BALAS_310752 are exactly identical! WARNING: Duplicate sequences found: 153 NOTE: Reduced alignment (with duplicates and gap-only sites/taxa removed) NOTE: was saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_040621/phylogeny-snakemake/results/P28069/4_raxmlng_ancestral/P28069.raxml.reduced.phy Alignment comprises 1 partitions and 291 sites Partition 0: noname Model: LG4X+R4 Alignment sites: 291 Gaps: 25.86 % Invariant sites: 3.78 % NOTE: Binary MSA file created: /cta/users/eakkoyun/WORKFOLDER/PROD/run_040621/phylogeny-snakemake/results/P28069/4_raxmlng_ancestral/P28069.raxml.rba Parallelization scheme autoconfig: 1 worker(s) x 4 thread(s) Parallel reduction/worker buffer size: 1 KB / 0 KB [00:00:00] Loading user starting tree(s) from: /cta/users/eakkoyun/WORKFOLDER/PROD/run_040621/phylogeny-snakemake/results/P28069/3_mltree/P28069.raxml.bestTree_unrooted [00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 73 / 5840 [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: -93328.851192 [00:00:00 -93328.851192] Initial branch length optimization [00:00:01 -58873.637812] Model parameter optimization (eps = 0.100000) [00:00:37] Tree #1, final logLikelihood: -58781.670710 Optimized model parameters: Partition 0: noname Rate heterogeneity: FREE (4 cats, mean), weights&rates: (0.206326,0.061607) (0.188563,0.170318) (0.197394,0.720024) (0.407717,1.994139) Base frequencies (model): M0: 0.147383 0.017579 0.058208 0.017707 0.026331 0.041582 0.017494 0.027859 0.011849 0.076971 0.147823 0.019535 0.037132 0.029940 0.008059 0.088179 0.089653 0.006477 0.032308 0.097931 M1: 0.063139 0.066357 0.011586 0.066571 0.010800 0.009276 0.053984 0.146986 0.034214 0.088822 0.098196 0.032390 0.021263 0.072697 0.016761 0.020711 0.020797 0.025463 0.045615 0.094372 M2: 0.062457 0.066826 0.049332 0.065270 0.006513 0.041231 0.058965 0.080852 0.028024 0.037024 0.075925 0.064131 0.019620 0.028710 0.104579 0.056388 0.062027 0.008241 0.033124 0.050760 M3: 0.106471 0.074171 0.044513 0.096390 0.002148 0.066733 0.158908 0.037625 0.020691 0.014608 0.028797 0.105352 0.007864 0.007477 0.083595 0.055726 0.047711 0.003975 0.010088 0.027159 Substitution rates (model): M 0: 0.295719 0.067388 0.253712 1.029289 0.107964 0.514644 10.868848 0.380498 0.084223 0.086976 0.188789 0.286389 0.155567 1.671061 2.132922 0.529591 0.115551 0.102453 0.916683 0.448317 0.457483 0.576016 1.741924 0.736017 0.704334 5.658311 0.123387 0.221777 93.433377 0.382175 0.235965 6.535048 0.525521 0.303537 0.641259 0.289466 0.102065 2.358429 0.251987 0.216561 0.503084 0.435271 4.873453 0.090748 0.033310 0.746537 0.128905 0.127321 0.904011 0.939733 0.435450 0.046646 0.262076 0.043986 0.189008 0.599450 109.901504 1.070052 5.229858 0.052764 0.021407 0.621146 0.081091 0.205164 5.164456 0.747330 0.308078 0.260889 0.185083 0.080708 0.029955 0.084794 1.862626 0.553477 0.151733 0.230320 0.096955 0.352526 0.590018 0.386853 1.559564 0.606648 0.587531 0.592318 0.885230 4.117654 0.246260 6.508329 0.054187 0.195703 1.669092 0.810168 0.066081 2.437439 0.165666 0.106333 0.093417 0.035149 0.072549 1.202023 1.634845 0.060194 0.069359 2.448827 0.232297 0.064822 3.537387 0.435384 0.290413 0.280695 0.105999 0.206603 0.404968 0.048984 0.069963 0.256662 0.228519 0.241077 4.320442 3.656545 0.290216 0.307466 0.096556 0.306067 0.204296 0.504221 1.991533 0.655465 6.799829 11.291065 0.961142 0.448965 6.227274 20.304886 0.205944 1.495537 0.091940 1.994320 0.754940 0.170343 0.050315 0.372166 0.206332 0.097050 5.381403 0.122332 3.256485 2.261319 0.848067 0.064441 0.102493 0.459041 0.133091 0.561215 0.457430 0.163849 5.260446 0.360946 0.389413 0.033291 0.115301 0.112593 1.559944 0.426508 0.132547 0.498634 0.559069 0.264728 0.693307 0.438856 0.306683 0.109129 18.392863 66.647302 0.400021 4.586081 2.099355 0.411347 0.476350 0.584622 3.634276 0.101797 0.148995 0.089177 0.034710 0.063603 0.755865 20.561407 0.133790 0.154902 M 1: 0.066142 0.590377 0.069930 9.850951 1.101363 0.150375 0.568586 0.051668 0.127170 0.292429 0.071458 1.218562 0.075144 7.169085 30.139501 13.461692 0.021372 0.045779 4.270235 0.468325 0.013688 0.302287 1.353957 0.028386 0.037750 0.262130 0.016923 0.064289 0.855973 0.079621 0.011169 0.161937 0.276530 0.161053 0.081472 0.036742 0.030342 2.851667 3.932151 8.159169 0.219934 0.421974 2.468752 0.344765 0.210724 1.172204 0.763553 0.082464 0.726566 11.149790 4.782635 0.058046 0.498072 0.258487 0.146882 0.249672 0.560142 0.046719 0.106259 0.003656 0.004200 0.014189 0.009876 0.002656 0.040244 0.267322 0.053740 0.006597 0.027639 0.012745 0.582670 0.005035 0.275844 0.098208 0.445038 1.217010 0.033969 1.988516 0.681161 0.825960 18.762977 11.949233 0.286794 0.534219 4.336817 3.054085 0.129551 4.210126 0.165753 1.088704 1.889645 3.344809 0.111063 2.067758 3.547017 2.466507 0.188236 0.203493 0.281953 0.037250 0.029788 0.008541 0.014768 0.125869 0.056702 0.004186 0.110993 0.201148 0.139705 0.009201 0.012095 0.043812 0.013513 0.002533 0.005848 0.031390 0.021612 0.004854 0.129497 0.976631 0.053397 0.019475 0.004964 0.015539 0.031779 0.064558 0.065585 0.079927 0.095591 0.196886 0.408834 0.126088 0.037226 0.452302 0.016212 7.278994 0.029917 7.918203 0.450964 0.169797 0.104288 1.578530 0.015909 0.094365 16.179952 0.042762 14.799537 1.506485 0.637893 0.123793 0.641351 0.154810 0.140750 3.416059 0.259400 0.009457 0.090576 0.292108 0.297913 0.017172 0.021976 0.032578 1.375871 0.457399 0.598048 4.418398 0.239749 0.168432 2.950318 0.143327 0.328689 0.125011 0.562720 1.414883 0.227807 3.478333 2.984862 0.061299 0.077470 1.050562 13.974326 0.154326 0.224675 0.112000 0.060703 0.123480 5.294490 0.447011 0.033381 0.045528 M 2: 0.733336 0.558955 0.503360 4.149599 1.415369 1.367574 1.263002 0.994098 0.517204 0.775054 0.763094 1.890137 0.540460 0.200122 4.972745 1.825593 0.450842 0.526135 3.839269 0.597671 0.058964 2.863355 2.872594 0.258365 0.366868 2.578946 0.358350 0.672023 5.349861 0.691594 0.063347 0.032875 0.821562 0.580847 0.661866 0.265730 0.395134 5.581680 1.279881 1.335650 0.397108 1.840061 5.739035 0.284730 0.109781 1.612642 0.466979 0.141582 0.019509 4.670980 1.967383 0.088064 0.581928 0.145401 0.225860 0.434096 2.292917 1.024707 0.821921 0.027824 0.021443 0.088850 0.060820 0.018288 0.042687 1.199607 0.420710 0.037642 0.141233 0.090101 1.043232 0.209978 0.823594 3.039380 1.463390 1.983693 0.397640 2.831098 4.102068 0.059723 5.901348 2.034980 2.600668 5.413080 4.193725 4.534772 0.377181 4.877840 0.370939 1.298542 3.509873 2.646440 0.087872 0.072299 1.139018 0.864479 0.390688 0.322761 0.625409 0.496780 0.532488 0.232460 0.169219 0.755219 0.379926 0.020447 0.023282 0.503875 0.577513 0.109318 0.153776 0.696533 0.398817 0.008940 0.043707 0.436013 0.087640 0.064863 0.036426 1.673207 0.124068 0.218118 0.039217 0.104335 0.349195 0.838324 0.888693 0.488389 1.385133 0.050226 0.962470 0.502294 1.065585 8.351808 0.377304 5.102837 0.561690 7.010411 3.054968 0.039318 0.204155 2.653232 0.564368 0.854294 15.559906 0.401070 8.929538 5.525874 0.067505 0.273372 0.437116 1.927515 0.940458 2.508169 1.357738 0.043394 0.023126 0.567639 1.048288 0.120994 0.180650 0.449074 3.135353 0.012695 0.570771 2.319555 1.856122 0.975427 3.404087 0.015631 0.458799 0.151684 4.154750 11.429924 1.457957 0.233109 0.077004 0.011074 0.026268 0.052132 8.113282 0.377578 0.429221 0.260296 0.222293 0.273138 2.903836 4.731579 0.564762 0.681215 M 3: 0.658412 0.566269 0.854111 0.884454 1.309554 1.272639 1.874713 0.552007 0.227683 0.581512 0.695190 0.967985 0.344015 0.978992 3.427163 2.333253 0.154701 0.221089 2.088785 0.540749 0.058015 5.851132 2.294145 0.182966 0.684164 3.192521 0.528161 1.128882 3.010922 1.012866 0.227296 0.156635 0.878405 0.802754 0.830884 0.431617 0.456530 3.060574 1.279257 1.438430 0.431464 2.075952 4.840271 0.644656 0.266076 2.084975 0.720060 0.291854 0.028961 4.071574 2.258357 0.073037 1.238426 0.199728 0.160296 0.482619 2.992763 1.296206 0.841829 0.031467 0.048542 0.132774 0.133055 0.056045 0.209188 0.925172 0.360522 0.094591 0.313945 0.118104 0.992259 0.086318 2.149634 5.103188 3.775817 3.954021 0.190734 1.776095 4.495841 0.264277 7.063879 2.221150 3.017954 8.558815 4.310199 2.130054 0.571406 4.137385 0.437589 2.071689 2.498630 1.763546 0.116381 0.296578 1.033710 1.283423 0.312579 0.305772 0.681277 0.507160 0.351381 0.189152 0.217780 0.767361 0.278392 0.092075 0.177263 0.451893 0.653836 0.074620 0.181992 0.752277 0.679853 0.025780 0.082005 0.326441 0.343977 0.195877 0.217424 3.057583 0.377558 0.401252 0.072258 0.241015 0.665865 1.266791 0.680174 0.717301 4.001286 0.362942 1.189259 0.964545 1.350568 12.869737 0.531100 8.904999 0.652629 10.091413 2.671718 0.086367 0.359932 4.797423 0.336801 1.021885 23.029406 0.440178 14.013035 5.069337 0.539010 0.742569 0.780580 1.331875 1.531589 4.414850 1.082703 0.091278 0.172734 0.693405 1.422571 0.068958 0.163829 0.481711 4.643214 0.121821 0.584083 4.216178 1.677263 1.575754 5.046403 0.161015 1.531223 0.599244 5.832025 33.873091 1.914768 1.287474 0.444362 0.076328 0.079916 0.466823 5.231362 0.548763 0.831890 0.382271 0.208791 0.307846 3.717971 5.910440 0.282540 0.964421 Marginal ancestral probabilities saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_040621/phylogeny-snakemake/results/P28069/4_raxmlng_ancestral/P28069.raxml.ancestralProbs Reconstructed ancestral sequences saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_040621/phylogeny-snakemake/results/P28069/4_raxmlng_ancestral/P28069.raxml.ancestralStates Node-labeled tree saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_040621/phylogeny-snakemake/results/P28069/4_raxmlng_ancestral/P28069.raxml.ancestralTree Execution log saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_040621/phylogeny-snakemake/results/P28069/4_raxmlng_ancestral/P28069.raxml.log Analysis started: 19-Jun-2021 20:01:05 / finished: 19-Jun-2021 20:01:45 Elapsed time: 40.542 seconds