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 04-Jun-2021 13:39:20 as follows: raxml-ng --ancestral --msa /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/P41235/2_msa/P41235_nogap_msa.fasta --tree /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/P41235/3_mltree/P41235.raxml.bestTree_unrooted --model LG4X --prefix /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/P41235/4_raxmlng_ancestral/P41235 --threads 4 Analysis options: run mode: Ancestral state reconstruction start tree(s): user random seed: 1622803160 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_020621/phylogeny-snakemake/results/P41235/2_msa/P41235_nogap_msa.fasta [00:00:00] Loaded alignment with 1001 taxa and 474 sites WARNING: Sequences tr_E9HV90_E9HV90_DAPPU_6669 and tr_A1XQQ1_A1XQQ1_9CRUS_35525 are exactly identical! WARNING: Sequences sp_Q06725_N2F1A_DANRE_7955 and tr_W5USF1_W5USF1_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A1D5PVE2_A0A1D5PVE2_CHICK_9031 and tr_A0A226N1M4_A0A226N1M4_CALSU_9009 are exactly identical! WARNING: Sequences tr_F1NJL8_F1NJL8_CHICK_9031 and tr_A0A226MYL0_A0A226MYL0_CALSU_9009 are exactly identical! WARNING: Sequences tr_F1NJL8_F1NJL8_CHICK_9031 and tr_A0A226P7M6_A0A226P7M6_COLVI_9014 are exactly identical! WARNING: Sequences sp_Q90733_COT2_CHICK_9031 and tr_A0A226NNI5_A0A226NNI5_CALSU_9009 are exactly identical! WARNING: Sequences sp_Q90733_COT2_CHICK_9031 and tr_A0A226P2E4_A0A226P2E4_COLVI_9014 are exactly identical! WARNING: Sequences sp_P28704_RXRB_MOUSE_10090 and sp_P49743_RXRB_RAT_10116 are exactly identical! WARNING: Sequences sp_P43135_COT2_MOUSE_10090 and tr_A0A2I3HRX8_A0A2I3HRX8_NOMLE_61853 are exactly identical! WARNING: Sequences sp_P43135_COT2_MOUSE_10090 and tr_G3RXP9_G3RXP9_GORGO_9595 are exactly identical! WARNING: Sequences sp_P43135_COT2_MOUSE_10090 and tr_F1PX81_F1PX81_CANLF_9615 are exactly identical! WARNING: Sequences sp_P43135_COT2_MOUSE_10090 and tr_H2QA47_H2QA47_PANTR_9598 are exactly identical! WARNING: Sequences sp_P43135_COT2_MOUSE_10090 and sp_O09018_COT2_RAT_10116 are exactly identical! WARNING: Sequences sp_P43135_COT2_MOUSE_10090 and tr_I3N8M4_I3N8M4_ICTTR_43179 are exactly identical! WARNING: Sequences sp_P43135_COT2_MOUSE_10090 and tr_H0XPC9_H0XPC9_OTOGA_30611 are exactly identical! WARNING: Sequences sp_P43135_COT2_MOUSE_10090 and tr_A0A286XI75_A0A286XI75_CAVPO_10141 are exactly identical! WARNING: Sequences sp_P43135_COT2_MOUSE_10090 and sp_P24468_COT2_HUMAN_9606 are exactly identical! WARNING: Sequences sp_P43135_COT2_MOUSE_10090 and tr_G3TD61_G3TD61_LOXAF_9785 are exactly identical! WARNING: Sequences sp_P43135_COT2_MOUSE_10090 and tr_F1SCJ6_F1SCJ6_PIG_9823 are exactly identical! WARNING: Sequences sp_P43135_COT2_MOUSE_10090 and sp_Q9TTR7_COT2_BOVIN_9913 are exactly identical! WARNING: Sequences sp_P43135_COT2_MOUSE_10090 and tr_A0A2I3N666_A0A2I3N666_PAPAN_9555 are exactly identical! WARNING: Sequences sp_P43135_COT2_MOUSE_10090 and tr_A0A0D9RWN2_A0A0D9RWN2_CHLSB_60711 are exactly identical! WARNING: Sequences sp_P43135_COT2_MOUSE_10090 and tr_A0A1S2ZEU9_A0A1S2ZEU9_ERIEU_9365 are exactly identical! WARNING: Sequences sp_P43135_COT2_MOUSE_10090 and tr_A0A1S3ET11_A0A1S3ET11_DIPOR_10020 are exactly identical! WARNING: Sequences sp_P43135_COT2_MOUSE_10090 and tr_A0A1U7R1X2_A0A1U7R1X2_MESAU_10036 are exactly identical! WARNING: Sequences sp_P43135_COT2_MOUSE_10090 and tr_A0A2K5LN11_A0A2K5LN11_CERAT_9531 are exactly identical! WARNING: Sequences sp_P43135_COT2_MOUSE_10090 and tr_A0A2K6CL30_A0A2K6CL30_MACNE_9545 are exactly identical! WARNING: Sequences sp_P43135_COT2_MOUSE_10090 and tr_A0A2U3WBL5_A0A2U3WBL5_ODORO_9708 are exactly identical! WARNING: Sequences sp_P43135_COT2_MOUSE_10090 and tr_A0A2Y9DE54_A0A2Y9DE54_TRIMA_127582 are exactly identical! WARNING: Sequences sp_P43135_COT2_MOUSE_10090 and tr_A0A2Y9K0A8_A0A2Y9K0A8_ENHLU_391180 are exactly identical! WARNING: Sequences sp_P43135_COT2_MOUSE_10090 and tr_A0A2Y9QAH4_A0A2Y9QAH4_DELLE_9749 are exactly identical! WARNING: Sequences sp_P43135_COT2_MOUSE_10090 and tr_A0A2Y9S3G9_A0A2Y9S3G9_PHYCD_9755 are exactly identical! WARNING: Sequences sp_Q60632_COT1_MOUSE_10090 and tr_A0A2I3TGT9_A0A2I3TGT9_PANTR_9598 are exactly identical! WARNING: Sequences sp_Q60632_COT1_MOUSE_10090 and tr_F2Z3S9_F2Z3S9_RAT_10116 are exactly identical! WARNING: Sequences sp_Q60632_COT1_MOUSE_10090 and sp_P10589_COT1_HUMAN_9606 are exactly identical! WARNING: Sequences sp_Q60632_COT1_MOUSE_10090 and tr_A0A2R8M9U2_A0A2R8M9U2_CALJA_9483 are exactly identical! WARNING: Sequences sp_Q60632_COT1_MOUSE_10090 and tr_A0A287AV73_A0A287AV73_PIG_9823 are exactly identical! WARNING: Sequences sp_Q60632_COT1_MOUSE_10090 and sp_Q9TTR8_COT1_BOVIN_9913 are exactly identical! WARNING: Sequences sp_Q60632_COT1_MOUSE_10090 and tr_A0A337SRW0_A0A337SRW0_FELCA_9685 are exactly identical! WARNING: Sequences sp_Q60632_COT1_MOUSE_10090 and tr_A0A2I3LQB9_A0A2I3LQB9_PAPAN_9555 are exactly identical! WARNING: Sequences sp_Q60632_COT1_MOUSE_10090 and tr_A0A0D9RQ67_A0A0D9RQ67_CHLSB_60711 are exactly identical! WARNING: Sequences sp_Q60632_COT1_MOUSE_10090 and tr_A0A1S3AA55_A0A1S3AA55_ERIEU_9365 are exactly identical! WARNING: Sequences sp_Q60632_COT1_MOUSE_10090 and tr_A0A2K5P7P2_A0A2K5P7P2_CERAT_9531 are exactly identical! WARNING: Sequences sp_Q60632_COT1_MOUSE_10090 and tr_A0A2U3WYK9_A0A2U3WYK9_ODORO_9708 are exactly identical! WARNING: Sequences sp_Q60632_COT1_MOUSE_10090 and tr_A0A2Y9PNQ7_A0A2Y9PNQ7_DELLE_9749 are exactly identical! WARNING: Sequences sp_Q60632_COT1_MOUSE_10090 and tr_A0A2Y9SN18_A0A2Y9SN18_PHYCD_9755 are exactly identical! WARNING: Sequences tr_M3XT49_M3XT49_MUSPF_9669 and tr_G1PPF3_G1PPF3_MYOLU_59463 are exactly identical! WARNING: Sequences tr_M3XT49_M3XT49_MUSPF_9669 and tr_G1TH32_G1TH32_RABIT_9986 are exactly identical! WARNING: Sequences tr_M3XT49_M3XT49_MUSPF_9669 and tr_I3N272_I3N272_ICTTR_43179 are exactly identical! WARNING: Sequences tr_M3XT49_M3XT49_MUSPF_9669 and sp_P28702_RXRB_HUMAN_9606 are exactly identical! WARNING: Sequences tr_M3XT49_M3XT49_MUSPF_9669 and tr_A5D9P3_A5D9P3_PIG_9823 are exactly identical! WARNING: Sequences tr_M3XT49_M3XT49_MUSPF_9669 and tr_A0A096NHF9_A0A096NHF9_PAPAN_9555 are exactly identical! WARNING: Sequences tr_M3XT49_M3XT49_MUSPF_9669 and tr_A0A0D9RAX9_A0A0D9RAX9_CHLSB_60711 are exactly identical! WARNING: Sequences tr_M3XXG4_M3XXG4_MUSPF_9669 and tr_G1LJ94_G1LJ94_AILME_9646 are exactly identical! WARNING: Sequences tr_M3XXG4_M3XXG4_MUSPF_9669 and tr_A0A2Y9JUH5_A0A2Y9JUH5_ENHLU_391180 are exactly identical! WARNING: Sequences tr_G1R516_G1R516_NOMLE_61853 and tr_G3R2Y5_G3R2Y5_GORGO_9595 are exactly identical! WARNING: Sequences tr_G1R516_G1R516_NOMLE_61853 and tr_H2PL46_H2PL46_PONAB_9601 are exactly identical! WARNING: Sequences tr_G1R516_G1R516_NOMLE_61853 and tr_H2QSS5_H2QSS5_PANTR_9598 are exactly identical! WARNING: Sequences tr_G1R516_G1R516_NOMLE_61853 and tr_F6TN21_F6TN21_MACMU_9544 are exactly identical! WARNING: Sequences tr_G1R516_G1R516_NOMLE_61853 and tr_U3CF11_U3CF11_CALJA_9483 are exactly identical! WARNING: Sequences tr_G1R516_G1R516_NOMLE_61853 and tr_G7P2S1_G7P2S1_MACFA_9541 are exactly identical! WARNING: Sequences tr_G1R516_G1R516_NOMLE_61853 and tr_M3W6V1_M3W6V1_FELCA_9685 are exactly identical! WARNING: Sequences tr_G1R516_G1R516_NOMLE_61853 and tr_A0A1U7TQ33_A0A1U7TQ33_TARSY_1868482 are exactly identical! WARNING: Sequences tr_G1R516_G1R516_NOMLE_61853 and tr_A0A2K5LC27_A0A2K5LC27_CERAT_9531 are exactly identical! WARNING: Sequences tr_G1R516_G1R516_NOMLE_61853 and tr_A0A2K6CBP5_A0A2K6CBP5_MACNE_9545 are exactly identical! WARNING: Sequences tr_G1R516_G1R516_NOMLE_61853 and tr_A0A2K5Y943_A0A2K5Y943_MANLE_9568 are exactly identical! WARNING: Sequences tr_G1R516_G1R516_NOMLE_61853 and tr_A0A2R9BXU1_A0A2R9BXU1_PANPA_9597 are exactly identical! WARNING: Sequences tr_G1R516_G1R516_NOMLE_61853 and tr_A0A2U3Y320_A0A2U3Y320_LEPWE_9713 are exactly identical! WARNING: Sequences tr_G1R516_G1R516_NOMLE_61853 and tr_A0A2Y9G3W5_A0A2Y9G3W5_TRIMA_127582 are exactly identical! WARNING: Sequences tr_G1R516_G1R516_NOMLE_61853 and tr_A0A2Y9K9Z1_A0A2Y9K9Z1_ENHLU_391180 are exactly identical! WARNING: Sequences tr_G1R516_G1R516_NOMLE_61853 and tr_A0A2Y9P552_A0A2Y9P552_DELLE_9749 are exactly identical! WARNING: Sequences tr_G1R516_G1R516_NOMLE_61853 and tr_A0A2Y9ETG3_A0A2Y9ETG3_PHYCD_9755 are exactly identical! WARNING: Sequences tr_G1R516_G1R516_NOMLE_61853 and tr_A0A384AIB7_A0A384AIB7_BALAS_310752 are exactly identical! WARNING: Sequences tr_G1RX84_G1RX84_NOMLE_61853 and tr_G3S7Z4_G3S7Z4_GORGO_9595 are exactly identical! WARNING: Sequences tr_G1RX84_G1RX84_NOMLE_61853 and sp_Q5REL6_RXRG_PONAB_9601 are exactly identical! WARNING: Sequences tr_G1RX84_G1RX84_NOMLE_61853 and tr_A0A2I3SXI5_A0A2I3SXI5_PANTR_9598 are exactly identical! WARNING: Sequences tr_G1RX84_G1RX84_NOMLE_61853 and sp_P48443_RXRG_HUMAN_9606 are exactly identical! WARNING: Sequences tr_G1RX84_G1RX84_NOMLE_61853 and tr_U3FF43_U3FF43_CALJA_9483 are exactly identical! WARNING: Sequences tr_G1RX84_G1RX84_NOMLE_61853 and sp_Q0GFF6_RXRG_PIG_9823 are exactly identical! WARNING: Sequences tr_G1RX84_G1RX84_NOMLE_61853 and tr_A0A096MW06_A0A096MW06_PAPAN_9555 are exactly identical! WARNING: Sequences tr_G1RX84_G1RX84_NOMLE_61853 and tr_A0A0D9REB7_A0A0D9REB7_CHLSB_60711 are exactly identical! WARNING: Sequences tr_G1RX84_G1RX84_NOMLE_61853 and tr_A0A1S3FKW1_A0A1S3FKW1_DIPOR_10020 are exactly identical! WARNING: Sequences tr_G1RX84_G1RX84_NOMLE_61853 and tr_A0A1U7UAI0_A0A1U7UAI0_TARSY_1868482 are exactly identical! WARNING: Sequences tr_G1RX84_G1RX84_NOMLE_61853 and tr_A0A2K5KI36_A0A2K5KI36_CERAT_9531 are exactly identical! WARNING: Sequences tr_G1RX84_G1RX84_NOMLE_61853 and tr_A0A2K5XT39_A0A2K5XT39_MANLE_9568 are exactly identical! WARNING: Sequences tr_G1RX84_G1RX84_NOMLE_61853 and tr_A0A2R9AQF8_A0A2R9AQF8_PANPA_9597 are exactly identical! WARNING: Sequences tr_G1RX84_G1RX84_NOMLE_61853 and tr_A0A2U3UZW3_A0A2U3UZW3_TURTR_9739 are exactly identical! WARNING: Sequences tr_G1RX84_G1RX84_NOMLE_61853 and tr_A0A2Y9FR90_A0A2Y9FR90_PHYCD_9755 are exactly identical! WARNING: Sequences tr_G1RX84_G1RX84_NOMLE_61853 and tr_A0A384AUR1_A0A384AUR1_BALAS_310752 are exactly identical! WARNING: Sequences tr_G3IDY0_G3IDY0_CRIGR_10029 and tr_A0A1U7RBT2_A0A1U7RBT2_MESAU_10036 are exactly identical! WARNING: Sequences tr_A0A2I2YNN8_A0A2I2YNN8_GORGO_9595 and tr_A0A2I3S4G5_A0A2I3S4G5_PANTR_9598 are exactly identical! WARNING: Sequences tr_A0A2I2YNN8_A0A2I2YNN8_GORGO_9595 and tr_A0A2R9AZR3_A0A2R9AZR3_PANPA_9597 are exactly identical! WARNING: Sequences tr_E2R3D0_E2R3D0_CANLF_9615 and tr_F1S962_F1S962_PIG_9823 are exactly identical! WARNING: Sequences tr_A0A2I3TE66_A0A2I3TE66_PANTR_9598 and tr_A0A2R9BKJ5_A0A2R9BKJ5_PANPA_9597 are exactly identical! WARNING: Sequences tr_H2R395_H2R395_PANTR_9598 and sp_P19793_RXRA_HUMAN_9606 are exactly identical! WARNING: Sequences tr_H2R395_H2R395_PANTR_9598 and tr_A0A2I3M8T5_A0A2I3M8T5_PAPAN_9555 are exactly identical! WARNING: Sequences tr_H2R395_H2R395_PANTR_9598 and tr_A0A2K5M5N8_A0A2K5M5N8_CERAT_9531 are exactly identical! WARNING: Sequences tr_H2R395_H2R395_PANTR_9598 and tr_A0A2K6BEY2_A0A2K6BEY2_MACNE_9545 are exactly identical! WARNING: Sequences tr_H2R395_H2R395_PANTR_9598 and tr_A0A2K5Y2K6_A0A2K5Y2K6_MANLE_9568 are exactly identical! WARNING: Sequences tr_H2R395_H2R395_PANTR_9598 and tr_A0A2R9CL53_A0A2R9CL53_PANPA_9597 are exactly identical! WARNING: Sequences tr_F7AZG5_F7AZG5_MONDO_13616 and tr_G3WSM6_G3WSM6_SARHA_9305 are exactly identical! WARNING: Sequences tr_W5PP44_W5PP44_SHEEP_9940 and sp_Q0VC20_RXRG_BOVIN_9913 are exactly identical! WARNING: Sequences tr_A0A158NB71_A0A158NB71_ATTCE_12957 and tr_A0A151ITL8_A0A151ITL8_9HYME_471704 are exactly identical! WARNING: Sequences tr_I3K1B3_I3K1B3_ORENI_8128 and tr_G3P806_G3P806_GASAC_69293 are exactly identical! WARNING: Sequences tr_I3K1B3_I3K1B3_ORENI_8128 and tr_A0A2U9BRU0_A0A2U9BRU0_SCOMX_52904 are exactly identical! WARNING: Sequences tr_F7HBP3_F7HBP3_MACMU_9544 and tr_A0A0D9RNS6_A0A0D9RNS6_CHLSB_60711 are exactly identical! WARNING: Sequences tr_F7HBP3_F7HBP3_MACMU_9544 and tr_A0A2K5NHD6_A0A2K5NHD6_CERAT_9531 are exactly identical! WARNING: Sequences tr_F7HBP3_F7HBP3_MACMU_9544 and tr_A0A2K6E2F4_A0A2K6E2F4_MACNE_9545 are exactly identical! WARNING: Sequences tr_F7HDB8_F7HDB8_MACMU_9544 and tr_G7NU27_G7NU27_MACFA_9541 are exactly identical! WARNING: Sequences tr_F7HDB8_F7HDB8_MACMU_9544 and tr_A0A2K6CSH7_A0A2K6CSH7_MACNE_9545 are exactly identical! WARNING: Sequences tr_H0Z605_H0Z605_TAEGU_59729 and tr_A0A091FAL0_A0A091FAL0_CORBR_85066 are exactly identical! WARNING: Sequences tr_H0Z605_H0Z605_TAEGU_59729 and tr_A0A093Q422_A0A093Q422_9PASS_328815 are exactly identical! WARNING: Sequences tr_H0ZE46_H0ZE46_TAEGU_59729 and tr_A0A091F445_A0A091F445_CORBR_85066 are exactly identical! WARNING: Sequences tr_H0ZE46_H0ZE46_TAEGU_59729 and tr_A0A091JMA1_A0A091JMA1_EGRGA_188379 are exactly identical! WARNING: Sequences tr_H0ZE46_H0ZE46_TAEGU_59729 and tr_A0A093PIU3_A0A093PIU3_9PASS_328815 are exactly identical! WARNING: Sequences tr_H0ZE46_H0ZE46_TAEGU_59729 and tr_A0A091VJA6_A0A091VJA6_NIPNI_128390 are exactly identical! WARNING: Sequences tr_H0ZE46_H0ZE46_TAEGU_59729 and tr_A0A087QWW8_A0A087QWW8_APTFO_9233 are exactly identical! WARNING: Sequences tr_H0ZE46_H0ZE46_TAEGU_59729 and tr_A0A093HYF6_A0A093HYF6_STRCA_441894 are exactly identical! WARNING: Sequences tr_H0ZE46_H0ZE46_TAEGU_59729 and tr_A0A091XIL6_A0A091XIL6_OPIHO_30419 are exactly identical! WARNING: Sequences tr_H0ZE46_H0ZE46_TAEGU_59729 and tr_A0A091GBD0_A0A091GBD0_9AVES_55661 are exactly identical! WARNING: Sequences tr_H0ZE46_H0ZE46_TAEGU_59729 and tr_A0A099ZXY6_A0A099ZXY6_CHAVO_50402 are exactly identical! WARNING: Sequences tr_H0ZE46_H0ZE46_TAEGU_59729 and tr_A0A093IHM3_A0A093IHM3_DRYPU_118200 are exactly identical! WARNING: Sequences tr_H0ZE46_H0ZE46_TAEGU_59729 and tr_A0A091IHZ4_A0A091IHZ4_CALAN_9244 are exactly identical! WARNING: Sequences tr_G0MFM1_G0MFM1_CAEBE_135651 and tr_G0P1R0_G0P1R0_CAEBE_135651 are exactly identical! WARNING: Sequences tr_A0A2R8M4N9_A0A2R8M4N9_CALJA_9483 and tr_G7PGB7_G7PGB7_MACFA_9541 are exactly identical! WARNING: Sequences tr_U3DJ91_U3DJ91_CALJA_9483 and tr_A0A0D9R023_A0A0D9R023_CHLSB_60711 are exactly identical! WARNING: Sequences tr_G7P9I3_G7P9I3_MACFA_9541 and tr_A0A2K5ZRB3_A0A2K5ZRB3_MANLE_9568 are exactly identical! WARNING: Sequences tr_F1N3S3_F1N3S3_BOVIN_9913 and tr_A0A2U3W8Q8_A0A2U3W8Q8_ODORO_9708 are exactly identical! WARNING: Sequences tr_F1N3S3_F1N3S3_BOVIN_9913 and tr_A0A2Y9J2P6_A0A2Y9J2P6_ENHLU_391180 are exactly identical! WARNING: Sequences tr_F1N3S3_F1N3S3_BOVIN_9913 and tr_A0A2Y9MA33_A0A2Y9MA33_DELLE_9749 are exactly identical! WARNING: Sequences tr_F1N3S3_F1N3S3_BOVIN_9913 and tr_A0A2Y9TL48_A0A2Y9TL48_PHYCD_9755 are exactly identical! WARNING: Sequences tr_A0A337SPZ3_A0A337SPZ3_FELCA_9685 and tr_A0A2U3ZRS6_A0A2U3ZRS6_ODORO_9708 are exactly identical! WARNING: Sequences tr_A0A096NFL0_A0A096NFL0_PAPAN_9555 and tr_A0A0D9RLZ4_A0A0D9RLZ4_CHLSB_60711 are exactly identical! WARNING: Sequences tr_A0A096NFL0_A0A096NFL0_PAPAN_9555 and tr_A0A2K5KPG4_A0A2K5KPG4_CERAT_9531 are exactly identical! WARNING: Sequences tr_A0A151MFT6_A0A151MFT6_ALLMI_8496 and tr_A0A0Q3RD29_A0A0Q3RD29_AMAAE_12930 are exactly identical! WARNING: Sequences tr_A0A151MFT6_A0A151MFT6_ALLMI_8496 and tr_A0A091JE53_A0A091JE53_EGRGA_188379 are exactly identical! WARNING: Sequences tr_A0A151MFT6_A0A151MFT6_ALLMI_8496 and tr_A0A091UQP9_A0A091UQP9_NIPNI_128390 are exactly identical! WARNING: Sequences tr_A0A151MFT6_A0A151MFT6_ALLMI_8496 and tr_A0A087R4Q8_A0A087R4Q8_APTFO_9233 are exactly identical! WARNING: Sequences tr_A0A151MFT6_A0A151MFT6_ALLMI_8496 and tr_A0A093H9R3_A0A093H9R3_STRCA_441894 are exactly identical! WARNING: Sequences tr_A0A151MFT6_A0A151MFT6_ALLMI_8496 and tr_A0A091V921_A0A091V921_OPIHO_30419 are exactly identical! WARNING: Sequences tr_A0A151MFT6_A0A151MFT6_ALLMI_8496 and tr_A0A091I5Q5_A0A091I5Q5_CALAN_9244 are exactly identical! WARNING: Sequences tr_A0A151MFT6_A0A151MFT6_ALLMI_8496 and tr_A0A1U7SDP6_A0A1U7SDP6_ALLSI_38654 are exactly identical! WARNING: Sequences tr_A0A151MFT6_A0A151MFT6_ALLMI_8496 and tr_A0A1V4J7B0_A0A1V4J7B0_PATFA_372326 are exactly identical! WARNING: Sequences tr_A0A151MFT6_A0A151MFT6_ALLMI_8496 and tr_A0A226NNV0_A0A226NNV0_CALSU_9009 are exactly identical! WARNING: Sequences tr_A0A151MFT6_A0A151MFT6_ALLMI_8496 and tr_A0A226P8I1_A0A226P8I1_COLVI_9014 are exactly identical! WARNING: Sequences tr_A0A151MIK8_A0A151MIK8_ALLMI_8496 and tr_A0A3Q0FYR5_A0A3Q0FYR5_ALLSI_38654 are exactly identical! WARNING: Sequences tr_A0A151NZY1_A0A151NZY1_ALLMI_8496 and tr_A0A1U7RM14_A0A1U7RM14_ALLSI_38654 are exactly identical! WARNING: Sequences tr_A0A087QY68_A0A087QY68_APTFO_9233 and tr_A0A0A0A7U8_A0A0A0A7U8_CHAVO_50402 are exactly identical! WARNING: Sequences tr_A0A0V1P5J1_A0A0V1P5J1_9BILA_92180 and tr_A0A0V0TIC9_A0A0V0TIC9_9BILA_144512 are exactly identical! WARNING: Sequences tr_A0A1S3NMC8_A0A1S3NMC8_SALSA_8030 and tr_A0A1S3PKK2_A0A1S3PKK2_SALSA_8030 are exactly identical! WARNING: Sequences tr_A0A1D1W4L8_A0A1D1W4L8_RAMVA_947166 and tr_A0A1D1W581_A0A1D1W581_RAMVA_947166 are exactly identical! WARNING: Sequences tr_A0A2D0PY04_A0A2D0PY04_ICTPU_7998 and tr_A0A2D0PZA2_A0A2D0PZA2_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0QWS9_A0A2D0QWS9_ICTPU_7998 and tr_A0A2D0QXH6_A0A2D0QXH6_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0S1X8_A0A2D0S1X8_ICTPU_7998 and tr_A0A2D0S2S1_A0A2D0S2S1_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0S1X8_A0A2D0S1X8_ICTPU_7998 and tr_A0A2D0S3F2_A0A2D0S3F2_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0T0F2_A0A2D0T0F2_ICTPU_7998 and tr_A0A2D0T0F7_A0A2D0T0F7_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0T0F2_A0A2D0T0F2_ICTPU_7998 and tr_A0A2D0T0G0_A0A2D0T0G0_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0T0F2_A0A2D0T0F2_ICTPU_7998 and tr_A0A2D0T0G3_A0A2D0T0G3_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0T0F2_A0A2D0T0F2_ICTPU_7998 and tr_A0A2D0T0G4_A0A2D0T0G4_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0T0F2_A0A2D0T0F2_ICTPU_7998 and tr_A0A2D0T0U4_A0A2D0T0U4_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0T0F2_A0A2D0T0F2_ICTPU_7998 and tr_A0A2D0T0V0_A0A2D0T0V0_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0T0F2_A0A2D0T0F2_ICTPU_7998 and tr_A0A2D0T1D2_A0A2D0T1D2_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0T0F2_A0A2D0T0F2_ICTPU_7998 and tr_A0A2D0T1D8_A0A2D0T1D8_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2K5LVL8_A0A2K5LVL8_CERAT_9531 and tr_A0A2K6D3X3_A0A2K6D3X3_MACNE_9545 are exactly identical! WARNING: Duplicate sequences found: 164 NOTE: Reduced alignment (with duplicates and gap-only sites/taxa removed) NOTE: was saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/P41235/4_raxmlng_ancestral/P41235.raxml.reduced.phy Alignment comprises 1 partitions and 474 sites Partition 0: noname Model: LG4X+R4 Alignment sites: 474 Gaps: 24.48 % Invariant sites: 0.21 % NOTE: Binary MSA file created: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/P41235/4_raxmlng_ancestral/P41235.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_020621/phylogeny-snakemake/results/P41235/3_mltree/P41235.raxml.bestTree_unrooted [00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 119 / 9520 [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: -100926.942689 [00:00:00 -100926.942689] Initial branch length optimization [00:00:01 -99227.772856] Model parameter optimization (eps = 0.100000) [00:00:41] Tree #1, final logLikelihood: -98964.903873 Optimized model parameters: Partition 0: noname Rate heterogeneity: FREE (4 cats, mean), weights&rates: (0.177533,0.244501) (0.220476,0.296485) (0.241968,0.754832) (0.360022,1.968154) 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_020621/phylogeny-snakemake/results/P41235/4_raxmlng_ancestral/P41235.raxml.ancestralProbs Reconstructed ancestral sequences saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/P41235/4_raxmlng_ancestral/P41235.raxml.ancestralStates Node-labeled tree saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/P41235/4_raxmlng_ancestral/P41235.raxml.ancestralTree Execution log saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/P41235/4_raxmlng_ancestral/P41235.raxml.log Analysis started: 04-Jun-2021 13:39:20 / finished: 04-Jun-2021 13:40:06 Elapsed time: 45.609 seconds