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) CPU E5-2690 v4 @ 2.60GHz, 28 cores, 251 GB RAM RAxML-NG was called at 02-Jun-2021 18:44:48 as follows: raxml-ng --ancestral --msa /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P49638/2_msa/P49638_nogap_msa.fasta --tree /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P49638/3_mltree/P49638.raxml.bestTree_unrooted --model LG4X --prefix /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P49638/4_raxmlng_ancestral/P49638 --threads 4 Analysis options: run mode: Ancestral state reconstruction start tree(s): user random seed: 1622648688 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/020621_run/phylogeny-snakemake/results/P49638/2_msa/P49638_nogap_msa.fasta [00:00:00] Loaded alignment with 889 taxa and 278 sites WARNING: Sequences tr_E1C6S0_E1C6S0_CHICK_9031 and tr_G1K9P4_G1K9P4_ANOCA_28377 are exactly identical! WARNING: Sequences tr_E1C6S0_E1C6S0_CHICK_9031 and tr_H0ZNJ9_H0ZNJ9_TAEGU_59729 are exactly identical! WARNING: Sequences tr_E1C6S0_E1C6S0_CHICK_9031 and tr_U3KA56_U3KA56_FICAL_59894 are exactly identical! WARNING: Sequences tr_E1C6S0_E1C6S0_CHICK_9031 and tr_R0LRA5_R0LRA5_ANAPL_8839 are exactly identical! WARNING: Sequences tr_E1C6S0_E1C6S0_CHICK_9031 and tr_A0A151M3A1_A0A151M3A1_ALLMI_8496 are exactly identical! WARNING: Sequences tr_E1C6S0_E1C6S0_CHICK_9031 and tr_A0A091EWS4_A0A091EWS4_CORBR_85066 are exactly identical! WARNING: Sequences tr_E1C6S0_E1C6S0_CHICK_9031 and tr_A0A091JMV0_A0A091JMV0_EGRGA_188379 are exactly identical! WARNING: Sequences tr_E1C6S0_E1C6S0_CHICK_9031 and tr_A0A091UTE5_A0A091UTE5_NIPNI_128390 are exactly identical! WARNING: Sequences tr_E1C6S0_E1C6S0_CHICK_9031 and tr_A0A087RKU6_A0A087RKU6_APTFO_9233 are exactly identical! WARNING: Sequences tr_E1C6S0_E1C6S0_CHICK_9031 and tr_A0A093HVK8_A0A093HVK8_STRCA_441894 are exactly identical! WARNING: Sequences tr_E1C6S0_E1C6S0_CHICK_9031 and tr_A0A091VVC1_A0A091VVC1_OPIHO_30419 are exactly identical! WARNING: Sequences tr_E1C6S0_E1C6S0_CHICK_9031 and tr_A0A099ZU75_A0A099ZU75_TINGU_94827 are exactly identical! WARNING: Sequences tr_E1C6S0_E1C6S0_CHICK_9031 and tr_A0A091GH63_A0A091GH63_9AVES_55661 are exactly identical! WARNING: Sequences tr_E1C6S0_E1C6S0_CHICK_9031 and tr_A0A2I0MTY2_A0A2I0MTY2_COLLI_8932 are exactly identical! WARNING: Sequences tr_E1C6S0_E1C6S0_CHICK_9031 and tr_A0A093H3P4_A0A093H3P4_DRYPU_118200 are exactly identical! WARNING: Sequences tr_E1C6S0_E1C6S0_CHICK_9031 and tr_A0A1U7RQ02_A0A1U7RQ02_ALLSI_38654 are exactly identical! WARNING: Sequences tr_E1C6S0_E1C6S0_CHICK_9031 and tr_A0A1V4JLP9_A0A1V4JLP9_PATFA_372326 are exactly identical! WARNING: Sequences tr_E1C6S0_E1C6S0_CHICK_9031 and tr_A0A218V4X3_A0A218V4X3_9PASE_299123 are exactly identical! WARNING: Sequences sp_Q9D4C9_CLVS1_MOUSE_10090 and tr_M3XTB1_M3XTB1_MUSPF_9669 are exactly identical! WARNING: Sequences sp_Q9D4C9_CLVS1_MOUSE_10090 and tr_G1QNX3_G1QNX3_NOMLE_61853 are exactly identical! WARNING: Sequences sp_Q9D4C9_CLVS1_MOUSE_10090 and tr_G3QXB8_G3QXB8_GORGO_9595 are exactly identical! WARNING: Sequences sp_Q9D4C9_CLVS1_MOUSE_10090 and sp_Q5RCA6_CLVS1_PONAB_9601 are exactly identical! WARNING: Sequences sp_Q9D4C9_CLVS1_MOUSE_10090 and tr_E2RE25_E2RE25_CANLF_9615 are exactly identical! WARNING: Sequences sp_Q9D4C9_CLVS1_MOUSE_10090 and tr_H2QW80_H2QW80_PANTR_9598 are exactly identical! WARNING: Sequences sp_Q9D4C9_CLVS1_MOUSE_10090 and tr_F7D5B5_F7D5B5_HORSE_9796 are exactly identical! WARNING: Sequences sp_Q9D4C9_CLVS1_MOUSE_10090 and tr_W5Q4N0_W5Q4N0_SHEEP_9940 are exactly identical! WARNING: Sequences sp_Q9D4C9_CLVS1_MOUSE_10090 and sp_A6JFQ6_CLVS1_RAT_10116 are exactly identical! WARNING: Sequences sp_Q9D4C9_CLVS1_MOUSE_10090 and tr_I3MIX7_I3MIX7_ICTTR_43179 are exactly identical! WARNING: Sequences sp_Q9D4C9_CLVS1_MOUSE_10090 and tr_H0V9W2_H0V9W2_CAVPO_10141 are exactly identical! WARNING: Sequences sp_Q9D4C9_CLVS1_MOUSE_10090 and sp_Q8IUQ0_CLVS1_HUMAN_9606 are exactly identical! WARNING: Sequences sp_Q9D4C9_CLVS1_MOUSE_10090 and tr_F7DKJ0_F7DKJ0_MACMU_9544 are exactly identical! WARNING: Sequences sp_Q9D4C9_CLVS1_MOUSE_10090 and tr_A0A2R8MV56_A0A2R8MV56_CALJA_9483 are exactly identical! WARNING: Sequences sp_Q9D4C9_CLVS1_MOUSE_10090 and tr_A0A287AHW7_A0A287AHW7_PIG_9823 are exactly identical! WARNING: Sequences sp_Q9D4C9_CLVS1_MOUSE_10090 and tr_D2H2C3_D2H2C3_AILME_9646 are exactly identical! WARNING: Sequences sp_Q9D4C9_CLVS1_MOUSE_10090 and tr_G7PBX0_G7PBX0_MACFA_9541 are exactly identical! WARNING: Sequences sp_Q9D4C9_CLVS1_MOUSE_10090 and tr_L5JSG0_L5JSG0_PTEAL_9402 are exactly identical! WARNING: Sequences sp_Q9D4C9_CLVS1_MOUSE_10090 and tr_A0A096N535_A0A096N535_PAPAN_9555 are exactly identical! WARNING: Sequences sp_Q9D4C9_CLVS1_MOUSE_10090 and tr_A0A091ENX7_A0A091ENX7_FUKDA_885580 are exactly identical! WARNING: Sequences sp_Q9D4C9_CLVS1_MOUSE_10090 and tr_A0A0D9RPC1_A0A0D9RPC1_CHLSB_60711 are exactly identical! WARNING: Sequences sp_Q9D4C9_CLVS1_MOUSE_10090 and tr_A0A1S3ELC0_A0A1S3ELC0_DIPOR_10020 are exactly identical! WARNING: Sequences sp_Q9D4C9_CLVS1_MOUSE_10090 and tr_A0A2K5LH14_A0A2K5LH14_CERAT_9531 are exactly identical! WARNING: Sequences sp_Q9D4C9_CLVS1_MOUSE_10090 and tr_A0A2K6CK59_A0A2K6CK59_MACNE_9545 are exactly identical! WARNING: Sequences sp_Q9D4C9_CLVS1_MOUSE_10090 and tr_A0A2K5XB32_A0A2K5XB32_MANLE_9568 are exactly identical! WARNING: Sequences sp_Q9D4C9_CLVS1_MOUSE_10090 and tr_A0A2R9ASN8_A0A2R9ASN8_PANPA_9597 are exactly identical! WARNING: Sequences sp_Q9D4C9_CLVS1_MOUSE_10090 and tr_A0A2U3VU94_A0A2U3VU94_ODORO_9708 are exactly identical! WARNING: Sequences sp_Q9D4C9_CLVS1_MOUSE_10090 and tr_A0A2U3XDF6_A0A2U3XDF6_LEPWE_9713 are exactly identical! WARNING: Sequences sp_Q9D4C9_CLVS1_MOUSE_10090 and tr_A0A2Y9KCM1_A0A2Y9KCM1_ENHLU_391180 are exactly identical! WARNING: Sequences sp_Q9D4C9_CLVS1_MOUSE_10090 and tr_A0A2Y9Q674_A0A2Y9Q674_DELLE_9749 are exactly identical! WARNING: Sequences sp_Q9D4C9_CLVS1_MOUSE_10090 and tr_A0A2Y9F6G4_A0A2Y9F6G4_PHYCD_9755 are exactly identical! WARNING: Sequences sp_Q9D4C9_CLVS1_MOUSE_10090 and tr_A0A383Z0E9_A0A383Z0E9_BALAS_310752 are exactly identical! WARNING: Sequences tr_M3YSR0_M3YSR0_MUSPF_9669 and tr_G1RUB2_G1RUB2_NOMLE_61853 are exactly identical! WARNING: Sequences tr_M3YSR0_M3YSR0_MUSPF_9669 and tr_G1PCM7_G1PCM7_MYOLU_59463 are exactly identical! WARNING: Sequences tr_M3YSR0_M3YSR0_MUSPF_9669 and tr_G3HKL3_G3HKL3_CRIGR_10029 are exactly identical! WARNING: Sequences tr_M3YSR0_M3YSR0_MUSPF_9669 and tr_G3SAF3_G3SAF3_GORGO_9595 are exactly identical! WARNING: Sequences tr_M3YSR0_M3YSR0_MUSPF_9669 and tr_H2PK87_H2PK87_PONAB_9601 are exactly identical! WARNING: Sequences tr_M3YSR0_M3YSR0_MUSPF_9669 and tr_G1SV96_G1SV96_RABIT_9986 are exactly identical! WARNING: Sequences tr_M3YSR0_M3YSR0_MUSPF_9669 and tr_F1PL15_F1PL15_CANLF_9615 are exactly identical! WARNING: Sequences tr_M3YSR0_M3YSR0_MUSPF_9669 and tr_H2QTP1_H2QTP1_PANTR_9598 are exactly identical! WARNING: Sequences tr_M3YSR0_M3YSR0_MUSPF_9669 and tr_F7ELG1_F7ELG1_MONDO_13616 are exactly identical! WARNING: Sequences tr_M3YSR0_M3YSR0_MUSPF_9669 and tr_F6ZKU2_F6ZKU2_HORSE_9796 are exactly identical! WARNING: Sequences tr_M3YSR0_M3YSR0_MUSPF_9669 and tr_W5PE41_W5PE41_SHEEP_9940 are exactly identical! WARNING: Sequences tr_M3YSR0_M3YSR0_MUSPF_9669 and sp_A6JUQ6_CLVS2_RAT_10116 are exactly identical! WARNING: Sequences tr_M3YSR0_M3YSR0_MUSPF_9669 and tr_I3LYK8_I3LYK8_ICTTR_43179 are exactly identical! WARNING: Sequences tr_M3YSR0_M3YSR0_MUSPF_9669 and tr_H0XBA6_H0XBA6_OTOGA_30611 are exactly identical! WARNING: Sequences tr_M3YSR0_M3YSR0_MUSPF_9669 and sp_Q5SYC1_CLVS2_HUMAN_9606 are exactly identical! WARNING: Sequences tr_M3YSR0_M3YSR0_MUSPF_9669 and tr_F7EDV5_F7EDV5_MACMU_9544 are exactly identical! WARNING: Sequences tr_M3YSR0_M3YSR0_MUSPF_9669 and tr_G5B3W2_G5B3W2_HETGA_10181 are exactly identical! WARNING: Sequences tr_M3YSR0_M3YSR0_MUSPF_9669 and tr_G3T080_G3T080_LOXAF_9785 are exactly identical! WARNING: Sequences tr_M3YSR0_M3YSR0_MUSPF_9669 and tr_F6TT00_F6TT00_CALJA_9483 are exactly identical! WARNING: Sequences tr_M3YSR0_M3YSR0_MUSPF_9669 and tr_F1S2T8_F1S2T8_PIG_9823 are exactly identical! WARNING: Sequences tr_M3YSR0_M3YSR0_MUSPF_9669 and tr_G1LLQ7_G1LLQ7_AILME_9646 are exactly identical! WARNING: Sequences tr_M3YSR0_M3YSR0_MUSPF_9669 and tr_G7P389_G7P389_MACFA_9541 are exactly identical! WARNING: Sequences tr_M3YSR0_M3YSR0_MUSPF_9669 and tr_E1BHP4_E1BHP4_BOVIN_9913 are exactly identical! WARNING: Sequences tr_M3YSR0_M3YSR0_MUSPF_9669 and tr_L5JPL1_L5JPL1_PTEAL_9402 are exactly identical! WARNING: Sequences tr_M3YSR0_M3YSR0_MUSPF_9669 and tr_M3WE10_M3WE10_FELCA_9685 are exactly identical! WARNING: Sequences tr_M3YSR0_M3YSR0_MUSPF_9669 and tr_A0A096MV83_A0A096MV83_PAPAN_9555 are exactly identical! WARNING: Sequences tr_M3YSR0_M3YSR0_MUSPF_9669 and tr_A0A091DA05_A0A091DA05_FUKDA_885580 are exactly identical! WARNING: Sequences tr_M3YSR0_M3YSR0_MUSPF_9669 and tr_A0A0D9RUR6_A0A0D9RUR6_CHLSB_60711 are exactly identical! WARNING: Sequences tr_M3YSR0_M3YSR0_MUSPF_9669 and tr_A0A1S2ZLT7_A0A1S2ZLT7_ERIEU_9365 are exactly identical! WARNING: Sequences tr_M3YSR0_M3YSR0_MUSPF_9669 and tr_A0A1U7TS25_A0A1U7TS25_TARSY_1868482 are exactly identical! WARNING: Sequences tr_M3YSR0_M3YSR0_MUSPF_9669 and tr_A0A1U8BDY1_A0A1U8BDY1_MESAU_10036 are exactly identical! WARNING: Sequences tr_M3YSR0_M3YSR0_MUSPF_9669 and tr_A0A2K5LQS4_A0A2K5LQS4_CERAT_9531 are exactly identical! WARNING: Sequences tr_M3YSR0_M3YSR0_MUSPF_9669 and tr_A0A2K6CGF4_A0A2K6CGF4_MACNE_9545 are exactly identical! WARNING: Sequences tr_M3YSR0_M3YSR0_MUSPF_9669 and tr_A0A2K5YT24_A0A2K5YT24_MANLE_9568 are exactly identical! WARNING: Sequences tr_M3YSR0_M3YSR0_MUSPF_9669 and tr_A0A2R9BFT0_A0A2R9BFT0_PANPA_9597 are exactly identical! WARNING: Sequences tr_M3YSR0_M3YSR0_MUSPF_9669 and tr_A0A2U4CPU5_A0A2U4CPU5_TURTR_9739 are exactly identical! WARNING: Sequences tr_M3YSR0_M3YSR0_MUSPF_9669 and tr_A0A2U3W6A1_A0A2U3W6A1_ODORO_9708 are exactly identical! WARNING: Sequences tr_M3YSR0_M3YSR0_MUSPF_9669 and tr_A0A2Y9RHD5_A0A2Y9RHD5_TRIMA_127582 are exactly identical! WARNING: Sequences tr_M3YSR0_M3YSR0_MUSPF_9669 and tr_A0A2Y9JF16_A0A2Y9JF16_ENHLU_391180 are exactly identical! WARNING: Sequences tr_M3YSR0_M3YSR0_MUSPF_9669 and tr_A0A2Y9LPZ0_A0A2Y9LPZ0_DELLE_9749 are exactly identical! WARNING: Sequences tr_M3YSR0_M3YSR0_MUSPF_9669 and tr_A0A2Y9FBE4_A0A2Y9FBE4_PHYCD_9755 are exactly identical! WARNING: Sequences tr_M3YSR0_M3YSR0_MUSPF_9669 and tr_A0A384C3E1_A0A384C3E1_URSMA_29073 are exactly identical! WARNING: Sequences tr_M3YSR0_M3YSR0_MUSPF_9669 and tr_A0A384ATX4_A0A384ATX4_BALAS_310752 are exactly identical! WARNING: Sequences tr_G3QQ35_G3QQ35_GORGO_9595 and sp_Q5RFR0_TTPAL_PONAB_9601 are exactly identical! WARNING: Sequences tr_G3QQ35_G3QQ35_GORGO_9595 and tr_H2QKE4_H2QKE4_PANTR_9598 are exactly identical! WARNING: Sequences tr_G3QQ35_G3QQ35_GORGO_9595 and sp_Q9BTX7_TTPAL_HUMAN_9606 are exactly identical! WARNING: Sequences tr_G3QQ35_G3QQ35_GORGO_9595 and tr_A0A2R9AKS5_A0A2R9AKS5_PANPA_9597 are exactly identical! WARNING: Sequences tr_Q29K50_Q29K50_DROPS_46245 and tr_B4GWW5_B4GWW5_DROPE_7234 are exactly identical! WARNING: Sequences tr_F7CDW7_F7CDW7_MONDO_13616 and tr_G3VUR9_G3VUR9_SARHA_9305 are exactly identical! WARNING: Sequences tr_A0A088APW8_A0A088APW8_APIME_7460 and tr_A0A2A3EJ91_A0A2A3EJ91_APICC_94128 are exactly identical! WARNING: Sequences tr_A0A158NQM1_A0A158NQM1_ATTCE_12957 and tr_A0A195BRZ1_A0A195BRZ1_9HYME_520822 are exactly identical! WARNING: Sequences tr_I3KWF5_I3KWF5_ORENI_8128 and tr_H2TWM5_H2TWM5_TAKRU_31033 are exactly identical! WARNING: Sequences tr_A0A1D5R6N4_A0A1D5R6N4_MACMU_9544 and tr_A0A2K6CQ30_A0A2K6CQ30_MACNE_9545 are exactly identical! WARNING: Sequences tr_F6S6M9_F6S6M9_MACMU_9544 and tr_G7PGB6_G7PGB6_MACFA_9541 are exactly identical! WARNING: Sequences tr_F6S6M9_F6S6M9_MACMU_9544 and tr_A0A096NX98_A0A096NX98_PAPAN_9555 are exactly identical! WARNING: Sequences tr_F6S6M9_F6S6M9_MACMU_9544 and tr_A0A0D9RNS9_A0A0D9RNS9_CHLSB_60711 are exactly identical! WARNING: Sequences tr_F6S6M9_F6S6M9_MACMU_9544 and tr_A0A2K5MPC7_A0A2K5MPC7_CERAT_9531 are exactly identical! WARNING: Sequences tr_F6S6M9_F6S6M9_MACMU_9544 and tr_A0A2K6C3Z2_A0A2K6C3Z2_MACNE_9545 are exactly identical! WARNING: Sequences tr_F6S6M9_F6S6M9_MACMU_9544 and tr_A0A2K5YE60_A0A2K5YE60_MANLE_9568 are exactly identical! WARNING: Sequences tr_F7BIL0_F7BIL0_MACMU_9544 and tr_G7P9E6_G7P9E6_MACFA_9541 are exactly identical! WARNING: Sequences tr_F7BIL0_F7BIL0_MACMU_9544 and tr_A0A0D9RX71_A0A0D9RX71_CHLSB_60711 are exactly identical! WARNING: Sequences tr_F7BIL0_F7BIL0_MACMU_9544 and tr_A0A2K5KZI9_A0A2K5KZI9_CERAT_9531 are exactly identical! WARNING: Sequences tr_F7BIL0_F7BIL0_MACMU_9544 and tr_A0A2K5XKA3_A0A2K5XKA3_MANLE_9568 are exactly identical! WARNING: Sequences tr_K7G3J8_K7G3J8_PELSI_13735 and tr_A0A2U3Y0Q2_A0A2U3Y0Q2_LEPWE_9713 are exactly identical! WARNING: Sequences tr_H0Z4B8_H0Z4B8_TAEGU_59729 and tr_A0A218USI9_A0A218USI9_9PASE_299123 are exactly identical! WARNING: Sequences tr_H0ZLU6_H0ZLU6_TAEGU_59729 and tr_U3JSM4_U3JSM4_FICAL_59894 are exactly identical! WARNING: Sequences tr_H0ZLU6_H0ZLU6_TAEGU_59729 and tr_R0M155_R0M155_ANAPL_8839 are exactly identical! WARNING: Sequences tr_H0ZLU6_H0ZLU6_TAEGU_59729 and tr_A0A091EAX2_A0A091EAX2_CORBR_85066 are exactly identical! WARNING: Sequences tr_H0ZLU6_H0ZLU6_TAEGU_59729 and tr_A0A091IQ56_A0A091IQ56_EGRGA_188379 are exactly identical! WARNING: Sequences tr_H0ZLU6_H0ZLU6_TAEGU_59729 and tr_A0A093PXB0_A0A093PXB0_9PASS_328815 are exactly identical! WARNING: Sequences tr_H0ZLU6_H0ZLU6_TAEGU_59729 and tr_A0A091VSN2_A0A091VSN2_NIPNI_128390 are exactly identical! WARNING: Sequences tr_H0ZLU6_H0ZLU6_TAEGU_59729 and tr_A0A093JP84_A0A093JP84_STRCA_441894 are exactly identical! WARNING: Sequences tr_H0ZLU6_H0ZLU6_TAEGU_59729 and tr_A0A091WC14_A0A091WC14_OPIHO_30419 are exactly identical! WARNING: Sequences tr_H0ZLU6_H0ZLU6_TAEGU_59729 and tr_A0A091GUZ9_A0A091GUZ9_9AVES_55661 are exactly identical! WARNING: Sequences tr_H0ZLU6_H0ZLU6_TAEGU_59729 and tr_A0A0A0ATA1_A0A0A0ATA1_CHAVO_50402 are exactly identical! WARNING: Sequences tr_H0ZLU6_H0ZLU6_TAEGU_59729 and tr_A0A2I0MWZ9_A0A2I0MWZ9_COLLI_8932 are exactly identical! WARNING: Sequences tr_H0ZLU6_H0ZLU6_TAEGU_59729 and tr_A0A093ITP4_A0A093ITP4_DRYPU_118200 are exactly identical! WARNING: Sequences tr_H0ZLU6_H0ZLU6_TAEGU_59729 and tr_A0A091HWU3_A0A091HWU3_CALAN_9244 are exactly identical! WARNING: Sequences tr_H0ZLU6_H0ZLU6_TAEGU_59729 and tr_A0A1V4KGD8_A0A1V4KGD8_PATFA_372326 are exactly identical! WARNING: Sequences tr_H0ZLU6_H0ZLU6_TAEGU_59729 and tr_A0A218VCQ0_A0A218VCQ0_9PASE_299123 are exactly identical! WARNING: Sequences tr_F6S4Y7_F6S4Y7_XENTR_8364 and tr_A0A1L8FZ40_A0A1L8FZ40_XENLA_8355 are exactly identical! WARNING: Sequences tr_F6TJX3_F6TJX3_XENTR_8364 and tr_A0A1L8G910_A0A1L8G910_XENLA_8355 are exactly identical! WARNING: Sequences tr_A0A2I3M0Z7_A0A2I3M0Z7_PAPAN_9555 and tr_A0A2K6DEV2_A0A2K6DEV2_MACNE_9545 are exactly identical! WARNING: Sequences tr_A0A0Q3QNF6_A0A0Q3QNF6_AMAAE_12930 and tr_A0A087QKE6_A0A087QKE6_APTFO_9233 are exactly identical! WARNING: Sequences tr_A0A091J4S4_A0A091J4S4_EGRGA_188379 and tr_A0A087R7L8_A0A087R7L8_APTFO_9233 are exactly identical! WARNING: Sequences tr_A0A2I0MD32_A0A2I0MD32_COLLI_8932 and tr_A0A1V4JE65_A0A1V4JE65_PATFA_372326 are exactly identical! WARNING: Sequences tr_A0A1S3M9U9_A0A1S3M9U9_SALSA_8030 and tr_A0A060W595_A0A060W595_ONCMY_8022 are exactly identical! WARNING: Sequences tr_A0A1S3NIN0_A0A1S3NIN0_SALSA_8030 and tr_A0A060WFI8_A0A060WFI8_ONCMY_8022 are exactly identical! WARNING: Sequences tr_A0A226MQH7_A0A226MQH7_CALSU_9009 and tr_A0A226PH52_A0A226PH52_COLVI_9014 are exactly identical! WARNING: Sequences tr_A0A2U4C292_A0A2U4C292_TURTR_9739 and tr_A0A2U4C2A0_A0A2U4C2A0_TURTR_9739 are exactly identical! WARNING: Sequences tr_A0A2U4C292_A0A2U4C292_TURTR_9739 and tr_A0A384B0C4_A0A384B0C4_BALAS_310752 are exactly identical! WARNING: Sequences tr_A0A2U3WX77_A0A2U3WX77_ODORO_9708 and tr_A0A2U3XSX1_A0A2U3XSX1_LEPWE_9713 are exactly identical! WARNING: Sequences tr_A0A2Y9ML49_A0A2Y9ML49_DELLE_9749 and tr_A0A384B3W2_A0A384B3W2_BALAS_310752 are exactly identical! WARNING: Duplicate sequences found: 143 NOTE: Reduced alignment (with duplicates and gap-only sites/taxa removed) NOTE: was saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P49638/4_raxmlng_ancestral/P49638.raxml.reduced.phy Alignment comprises 1 partitions and 278 sites Partition 0: noname Model: LG4X+R4 Alignment sites: 278 Gaps: 14.67 % Invariant sites: 0.00 % NOTE: Binary MSA file created: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P49638/4_raxmlng_ancestral/P49638.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/020621_run/phylogeny-snakemake/results/P49638/3_mltree/P49638.raxml.bestTree_unrooted [00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 70 / 5600 [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: -126978.888947 [00:00:00 -126978.888947] Initial branch length optimization [00:00:00 -126286.516399] Model parameter optimization (eps = 0.100000) [00:00:48] Tree #1, final logLikelihood: -125934.727143 Optimized model parameters: Partition 0: noname Rate heterogeneity: FREE (4 cats, mean), weights&rates: (0.081219,0.668823) (0.168168,0.675038) (0.440336,0.724739) (0.310277,1.653459) 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/020621_run/phylogeny-snakemake/results/P49638/4_raxmlng_ancestral/P49638.raxml.ancestralProbs Reconstructed ancestral sequences saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P49638/4_raxmlng_ancestral/P49638.raxml.ancestralStates Node-labeled tree saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P49638/4_raxmlng_ancestral/P49638.raxml.ancestralTree Execution log saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P49638/4_raxmlng_ancestral/P49638.raxml.log Analysis started: 02-Jun-2021 18:44:48 / finished: 02-Jun-2021 18:45:38 Elapsed time: 50.613 seconds Consumed energy: 2.948 Wh