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 18-Jun-2021 15:46:14 as follows: raxml-ng --msa /cta/users/eakkoyun/WORKFOLDER/PROD/run_040621/phylogeny-snakemake/results/P43403/2_msa/P43403_trimmed_msa.fasta --data-type AA --model LG4X --prefix /cta/users/eakkoyun/WORKFOLDER/PROD/run_040621/phylogeny-snakemake/results/P43403/3_mltree/P43403 --seed 2 --threads 7 --tree rand{20} pars{20} Analysis options: run mode: ML tree search start tree(s): random (20) random seed: 2 tip-inner: OFF pattern compression: ON per-rate scalers: OFF site repeats: ON fast spr radius: AUTO spr subtree cutoff: 1.000000 branch lengths: proportional (ML estimate, algorithm: NR-FAST) SIMD kernels: AVX2 parallelization: coarse-grained (auto), PTHREADS (7 threads), thread pinning: OFF [00:00:00] Reading alignment from file: /cta/users/eakkoyun/WORKFOLDER/PROD/run_040621/phylogeny-snakemake/results/P43403/2_msa/P43403_trimmed_msa.fasta [00:00:00] Loaded alignment with 1001 taxa and 476 sites WARNING: Sequences tr_F1NCD9_F1NCD9_CHICK_9031 and tr_U3IYV8_U3IYV8_ANAPL_8839 are exactly identical! WARNING: Sequences tr_M3Z238_M3Z238_MUSPF_9669 and tr_E2RSH8_E2RSH8_CANLF_9615 are exactly identical! WARNING: Sequences tr_M3Z238_M3Z238_MUSPF_9669 and tr_G1M0W5_G1M0W5_AILME_9646 are exactly identical! WARNING: Sequences tr_M3Z238_M3Z238_MUSPF_9669 and tr_A0A337RYE7_A0A337RYE7_FELCA_9685 are exactly identical! WARNING: Sequences tr_M3Z238_M3Z238_MUSPF_9669 and tr_A0A2U3XQI2_A0A2U3XQI2_LEPWE_9713 are exactly identical! WARNING: Sequences tr_M3Z238_M3Z238_MUSPF_9669 and tr_A0A2Y9IRF1_A0A2Y9IRF1_ENHLU_391180 are exactly identical! WARNING: Sequences tr_M3Z238_M3Z238_MUSPF_9669 and tr_A0A384CND9_A0A384CND9_URSMA_29073 are exactly identical! WARNING: Sequences tr_G1P8R6_G1P8R6_MYOLU_59463 and tr_W5Q539_W5Q539_SHEEP_9940 are exactly identical! WARNING: Sequences tr_G3HD26_G3HD26_CRIGR_10029 and tr_A0A091DKV7_A0A091DKV7_FUKDA_885580 are exactly identical! WARNING: Sequences tr_G3QJK0_G3QJK0_GORGO_9595 and tr_A0A2I3TWE6_A0A2I3TWE6_PANTR_9598 are exactly identical! WARNING: Sequences tr_G3QJK0_G3QJK0_GORGO_9595 and sp_P42684_ABL2_HUMAN_9606 are exactly identical! WARNING: Sequences tr_G3QJK0_G3QJK0_GORGO_9595 and tr_F7AU70_F7AU70_MACMU_9544 are exactly identical! WARNING: Sequences tr_G3QJK0_G3QJK0_GORGO_9595 and tr_A0A2R8MYN3_A0A2R8MYN3_CALJA_9483 are exactly identical! WARNING: Sequences tr_G3QJK0_G3QJK0_GORGO_9595 and tr_A0A2I3MIM0_A0A2I3MIM0_PAPAN_9555 are exactly identical! WARNING: Sequences tr_G3QJK0_G3QJK0_GORGO_9595 and tr_A0A1U7TZR0_A0A1U7TZR0_TARSY_1868482 are exactly identical! WARNING: Sequences tr_G3QJK0_G3QJK0_GORGO_9595 and tr_A0A2K6CR83_A0A2K6CR83_MACNE_9545 are exactly identical! WARNING: Sequences tr_G3S1C3_G3S1C3_GORGO_9595 and tr_A0A2I3N5G5_A0A2I3N5G5_PAPAN_9555 are exactly identical! WARNING: Sequences tr_G3S1C3_G3S1C3_GORGO_9595 and tr_A0A2K5YHF7_A0A2K5YHF7_MANLE_9568 are exactly identical! WARNING: Sequences tr_H2N4J6_H2N4J6_PONAB_9601 and tr_I3LP68_I3LP68_PIG_9823 are exactly identical! WARNING: Sequences tr_H2N4J6_H2N4J6_PONAB_9601 and tr_F1MWH8_F1MWH8_BOVIN_9913 are exactly identical! WARNING: Sequences tr_H2N4J6_H2N4J6_PONAB_9601 and tr_A0A2Y9LZ58_A0A2Y9LZ58_DELLE_9749 are exactly identical! WARNING: Sequences tr_H2N4J6_H2N4J6_PONAB_9601 and tr_A0A2Y9TJX0_A0A2Y9TJX0_PHYCD_9755 are exactly identical! WARNING: Sequences tr_H2P1V4_H2P1V4_PONAB_9601 and tr_A0A2I3SIH9_A0A2I3SIH9_PANTR_9598 are exactly identical! WARNING: Sequences tr_H2P1V4_H2P1V4_PONAB_9601 and tr_A0A286X7I1_A0A286X7I1_CAVPO_10141 are exactly identical! WARNING: Sequences tr_H2P1V4_H2P1V4_PONAB_9601 and sp_P12931_SRC_HUMAN_9606 are exactly identical! WARNING: Sequences tr_H2P1V4_H2P1V4_PONAB_9601 and tr_F7FWN9_F7FWN9_MACMU_9544 are exactly identical! WARNING: Sequences tr_H2P1V4_H2P1V4_PONAB_9601 and tr_F7IJA5_F7IJA5_CALJA_9483 are exactly identical! WARNING: Sequences tr_H2P1V4_H2P1V4_PONAB_9601 and tr_A0A2I3M0W2_A0A2I3M0W2_PAPAN_9555 are exactly identical! WARNING: Sequences tr_H2P1V4_H2P1V4_PONAB_9601 and tr_A0A0D9RML6_A0A0D9RML6_CHLSB_60711 are exactly identical! WARNING: Sequences tr_H2P1V4_H2P1V4_PONAB_9601 and tr_A0A2K5KTV3_A0A2K5KTV3_CERAT_9531 are exactly identical! WARNING: Sequences tr_H2P1V4_H2P1V4_PONAB_9601 and tr_A0A2K6B4I3_A0A2K6B4I3_MACNE_9545 are exactly identical! WARNING: Sequences tr_G1MUH1_G1MUH1_MELGA_9103 and tr_H1A456_H1A456_TAEGU_59729 are exactly identical! WARNING: Sequences tr_G1MUH1_G1MUH1_MELGA_9103 and tr_A0A091EWN1_A0A091EWN1_CORBR_85066 are exactly identical! WARNING: Sequences tr_G1MUH1_G1MUH1_MELGA_9103 and tr_A0A091IJE8_A0A091IJE8_EGRGA_188379 are exactly identical! WARNING: Sequences tr_G1MUH1_G1MUH1_MELGA_9103 and tr_A0A091UYW5_A0A091UYW5_NIPNI_128390 are exactly identical! WARNING: Sequences tr_G1MUH1_G1MUH1_MELGA_9103 and tr_A0A093HBT4_A0A093HBT4_STRCA_441894 are exactly identical! WARNING: Sequences tr_G3UTK7_G3UTK7_MELGA_9103 and tr_A0A226NBZ5_A0A226NBZ5_COLVI_9014 are exactly identical! WARNING: Sequences tr_E2RGQ1_E2RGQ1_CANLF_9615 and tr_A0A384CR38_A0A384CR38_URSMA_29073 are exactly identical! WARNING: Sequences tr_F1PEX6_F1PEX6_CANLF_9615 and tr_G3SZ92_G3SZ92_LOXAF_9785 are exactly identical! WARNING: Sequences tr_F1PEX6_F1PEX6_CANLF_9615 and tr_D2H177_D2H177_AILME_9646 are exactly identical! WARNING: Sequences tr_F1PEX6_F1PEX6_CANLF_9615 and tr_M3W3H7_M3W3H7_FELCA_9685 are exactly identical! WARNING: Sequences tr_F1PEX6_F1PEX6_CANLF_9615 and tr_A0A2U3VD43_A0A2U3VD43_ODORO_9708 are exactly identical! WARNING: Sequences tr_F1PEX6_F1PEX6_CANLF_9615 and tr_A0A2Y9DJL9_A0A2Y9DJL9_TRIMA_127582 are exactly identical! WARNING: Sequences tr_F1PEX6_F1PEX6_CANLF_9615 and tr_A0A2Y9NX24_A0A2Y9NX24_DELLE_9749 are exactly identical! WARNING: Sequences tr_A0A2I3RAJ1_A0A2I3RAJ1_PANTR_9598 and tr_A0A2I3S7G9_A0A2I3S7G9_PANTR_9598 are exactly identical! WARNING: Sequences tr_A0A2I3RAJ1_A0A2I3RAJ1_PANTR_9598 and tr_H9YUX8_H9YUX8_MACMU_9544 are exactly identical! WARNING: Sequences tr_A0A2I3RAJ1_A0A2I3RAJ1_PANTR_9598 and tr_G7PRB8_G7PRB8_MACFA_9541 are exactly identical! WARNING: Sequences tr_A0A2I3RAJ1_A0A2I3RAJ1_PANTR_9598 and tr_A0A2K5LX70_A0A2K5LX70_CERAT_9531 are exactly identical! WARNING: Sequences tr_A0A2I3RAJ1_A0A2I3RAJ1_PANTR_9598 and tr_A0A2K6B7I9_A0A2K6B7I9_MACNE_9545 are exactly identical! WARNING: Sequences tr_A0A2I3RAJ1_A0A2I3RAJ1_PANTR_9598 and tr_A0A2K5XNT4_A0A2K5XNT4_MANLE_9568 are exactly identical! WARNING: Sequences tr_A0A2I3RAJ1_A0A2I3RAJ1_PANTR_9598 and tr_A0A2R9BA11_A0A2R9BA11_PANPA_9597 are exactly identical! WARNING: Sequences tr_A0A2I3T3L8_A0A2I3T3L8_PANTR_9598 and tr_A0A2R9CGB2_A0A2R9CGB2_PANPA_9597 are exactly identical! WARNING: Sequences tr_A0A2J8KTF6_A0A2J8KTF6_PANTR_9598 and sp_P43405_KSYK_HUMAN_9606 are exactly identical! WARNING: Sequences tr_A0A2J8KTF6_A0A2J8KTF6_PANTR_9598 and tr_A0A2R9BI29_A0A2R9BI29_PANPA_9597 are exactly identical! WARNING: Sequences tr_A0A2J8PYX8_A0A2J8PYX8_PANTR_9598 and sp_P08631_HCK_HUMAN_9606 are exactly identical! WARNING: Sequences tr_H2QIE3_H2QIE3_PANTR_9598 and sp_P43403_ZAP70_HUMAN_9606 are exactly identical! WARNING: Sequences tr_H2QIE3_H2QIE3_PANTR_9598 and tr_A0A2R8ZE55_A0A2R8ZE55_PANPA_9597 are exactly identical! WARNING: Sequences tr_H2QTL3_H2QTL3_PANTR_9598 and sp_P42685_FRK_HUMAN_9606 are exactly identical! WARNING: Sequences tr_H2QTL3_H2QTL3_PANTR_9598 and tr_A0A2R9BRU0_A0A2R9BRU0_PANPA_9597 are exactly identical! WARNING: Sequences tr_E9PT20_E9PT20_RAT_10116 and tr_A0A1U7R1K5_A0A1U7R1K5_MESAU_10036 are exactly identical! WARNING: Sequences tr_A0A3B5PV91_A0A3B5PV91_XIPMA_8083 and tr_A0A087YPJ4_A0A087YPJ4_POEFO_48698 are exactly identical! WARNING: Sequences tr_A0A158NUM9_A0A158NUM9_ATTCE_12957 and tr_F4WV60_F4WV60_ACREC_103372 are exactly identical! WARNING: Sequences tr_A0A158NUM9_A0A158NUM9_ATTCE_12957 and tr_A0A151WUC9_A0A151WUC9_9HYME_64791 are exactly identical! WARNING: Sequences tr_A0A158NUM9_A0A158NUM9_ATTCE_12957 and tr_A0A195DS06_A0A195DS06_9HYME_471704 are exactly identical! WARNING: Sequences tr_A0A158NUM9_A0A158NUM9_ATTCE_12957 and tr_A0A195BS54_A0A195BS54_9HYME_520822 are exactly identical! WARNING: Sequences tr_A0A158NUM9_A0A158NUM9_ATTCE_12957 and tr_A0A195EXC2_A0A195EXC2_9HYME_34720 are exactly identical! WARNING: Sequences tr_A0A158NUM9_A0A158NUM9_ATTCE_12957 and tr_A0A195C704_A0A195C704_9HYME_456900 are exactly identical! WARNING: Sequences tr_I3MRX6_I3MRX6_ICTTR_43179 and tr_G3TDK8_G3TDK8_LOXAF_9785 are exactly identical! WARNING: Sequences sp_P00519_ABL1_HUMAN_9606 and tr_A0A0D9RQJ3_A0A0D9RQJ3_CHLSB_60711 are exactly identical! WARNING: Sequences tr_A0A1D5QGC6_A0A1D5QGC6_MACMU_9544 and tr_A0A1U7SLU4_A0A1U7SLU4_TARSY_1868482 are exactly identical! WARNING: Sequences tr_F7FAI7_F7FAI7_MACMU_9544 and tr_A0A096NGT8_A0A096NGT8_PAPAN_9555 are exactly identical! WARNING: Sequences tr_F7FAI7_F7FAI7_MACMU_9544 and tr_A0A0D9RXH6_A0A0D9RXH6_CHLSB_60711 are exactly identical! WARNING: Sequences tr_F7FAI7_F7FAI7_MACMU_9544 and tr_A0A2K5MYN1_A0A2K5MYN1_CERAT_9531 are exactly identical! WARNING: Sequences tr_F7FAI7_F7FAI7_MACMU_9544 and tr_A0A2K6CVN0_A0A2K6CVN0_MACNE_9545 are exactly identical! WARNING: Sequences tr_F7H8A7_F7H8A7_MACMU_9544 and tr_G7PGN2_G7PGN2_MACFA_9541 are exactly identical! WARNING: Sequences tr_F7H8A7_F7H8A7_MACMU_9544 and tr_A0A2K6DQ69_A0A2K6DQ69_MACNE_9545 are exactly identical! WARNING: Sequences tr_E5SRE0_E5SRE0_TRISP_6334 and tr_A0A0V0X1S4_A0A0V0X1S4_9BILA_92179 are exactly identical! WARNING: Sequences tr_E5SRE0_E5SRE0_TRISP_6334 and tr_A0A0V0VJ28_A0A0V0VJ28_9BILA_181606 are exactly identical! WARNING: Sequences tr_E5SRE0_E5SRE0_TRISP_6334 and tr_A0A0V1ACR2_A0A0V1ACR2_9BILA_990121 are exactly identical! WARNING: Sequences tr_E5SRE0_E5SRE0_TRISP_6334 and tr_A0A0V0TUN5_A0A0V0TUN5_9BILA_144512 are exactly identical! WARNING: Sequences tr_H0YPY8_H0YPY8_TAEGU_59729 and tr_A0A218UCB5_A0A218UCB5_9PASE_299123 are exactly identical! WARNING: Sequences tr_H0Z2V6_H0Z2V6_TAEGU_59729 and tr_A0A091FAS5_A0A091FAS5_CORBR_85066 are exactly identical! WARNING: Sequences tr_H0Z2V6_H0Z2V6_TAEGU_59729 and tr_A0A091JHP5_A0A091JHP5_EGRGA_188379 are exactly identical! WARNING: Sequences tr_H0Z2V6_H0Z2V6_TAEGU_59729 and tr_A0A093PK85_A0A093PK85_9PASS_328815 are exactly identical! WARNING: Sequences tr_H0Z2V6_H0Z2V6_TAEGU_59729 and tr_A0A091URD2_A0A091URD2_NIPNI_128390 are exactly identical! WARNING: Sequences tr_H0Z2V6_H0Z2V6_TAEGU_59729 and tr_A0A087RGY7_A0A087RGY7_APTFO_9233 are exactly identical! WARNING: Sequences tr_H0Z2V6_H0Z2V6_TAEGU_59729 and tr_A0A093HB20_A0A093HB20_STRCA_441894 are exactly identical! WARNING: Sequences tr_H0Z2V6_H0Z2V6_TAEGU_59729 and tr_A0A091V7N8_A0A091V7N8_OPIHO_30419 are exactly identical! WARNING: Sequences tr_H0Z2V6_H0Z2V6_TAEGU_59729 and tr_A0A091GMR3_A0A091GMR3_9AVES_55661 are exactly identical! WARNING: Sequences tr_H0Z2V6_H0Z2V6_TAEGU_59729 and tr_A0A218V5K2_A0A218V5K2_9PASE_299123 are exactly identical! WARNING: Sequences tr_H0ZR18_H0ZR18_TAEGU_59729 and tr_A0A093PND3_A0A093PND3_9PASS_328815 are exactly identical! WARNING: Sequences tr_A8WXQ5_A8WXQ5_CAEBR_6238 and tr_A0A2G5SPS2_A0A2G5SPS2_9PELO_1611254 are exactly identical! WARNING: Sequences tr_G7PSP1_G7PSP1_MACFA_9541 and tr_A0A096P223_A0A096P223_PAPAN_9555 are exactly identical! WARNING: Sequences tr_E1BIM8_E1BIM8_BOVIN_9913 and tr_A0A2Y9PSD7_A0A2Y9PSD7_DELLE_9749 are exactly identical! WARNING: Sequences tr_E1BIM8_E1BIM8_BOVIN_9913 and tr_A0A2Y9EJT6_A0A2Y9EJT6_PHYCD_9755 are exactly identical! WARNING: Sequences tr_A0A0D9RI41_A0A0D9RI41_CHLSB_60711 and tr_A0A2R9CMZ1_A0A2R9CMZ1_PANPA_9597 are exactly identical! WARNING: Sequences tr_A0A151MFN4_A0A151MFN4_ALLMI_8496 and tr_A0A1U7S4W8_A0A1U7S4W8_ALLSI_38654 are exactly identical! WARNING: Sequences tr_A0A091ETM4_A0A091ETM4_CORBR_85066 and tr_A0A091JKD8_A0A091JKD8_EGRGA_188379 are exactly identical! WARNING: Sequences tr_A0A091ETM4_A0A091ETM4_CORBR_85066 and tr_A0A087QKE4_A0A087QKE4_APTFO_9233 are exactly identical! WARNING: Sequences tr_A0A091ETM4_A0A091ETM4_CORBR_85066 and tr_A0A093GYT7_A0A093GYT7_STRCA_441894 are exactly identical! WARNING: Sequences tr_A0A091ETM4_A0A091ETM4_CORBR_85066 and tr_A0A099YTB5_A0A099YTB5_TINGU_94827 are exactly identical! WARNING: Sequences tr_A0A091ETM4_A0A091ETM4_CORBR_85066 and tr_A0A091GTJ3_A0A091GTJ3_9AVES_55661 are exactly identical! WARNING: Sequences tr_A0A091ETM4_A0A091ETM4_CORBR_85066 and tr_A0A0A0AT41_A0A0A0AT41_CHAVO_50402 are exactly identical! WARNING: Sequences tr_A0A091ETM4_A0A091ETM4_CORBR_85066 and tr_A0A093G492_A0A093G492_DRYPU_118200 are exactly identical! WARNING: Sequences tr_A0A091ETM4_A0A091ETM4_CORBR_85066 and tr_A0A091HUP1_A0A091HUP1_CALAN_9244 are exactly identical! WARNING: Sequences tr_A0A091EUJ1_A0A091EUJ1_CORBR_85066 and tr_A0A091IT27_A0A091IT27_EGRGA_188379 are exactly identical! WARNING: Sequences tr_A0A091EUJ1_A0A091EUJ1_CORBR_85066 and tr_A0A091VYQ6_A0A091VYQ6_NIPNI_128390 are exactly identical! WARNING: Sequences tr_A0A091EUJ1_A0A091EUJ1_CORBR_85066 and tr_A0A087QR73_A0A087QR73_APTFO_9233 are exactly identical! WARNING: Sequences tr_A0A091EUJ1_A0A091EUJ1_CORBR_85066 and tr_A0A093HY04_A0A093HY04_STRCA_441894 are exactly identical! WARNING: Sequences tr_A0A091EUJ1_A0A091EUJ1_CORBR_85066 and tr_A0A091XV06_A0A091XV06_OPIHO_30419 are exactly identical! WARNING: Sequences tr_A0A091EUJ1_A0A091EUJ1_CORBR_85066 and tr_A0A091GHA4_A0A091GHA4_9AVES_55661 are exactly identical! WARNING: Sequences tr_A0A091EUJ1_A0A091EUJ1_CORBR_85066 and tr_A0A0A0AGC2_A0A0A0AGC2_CHAVO_50402 are exactly identical! WARNING: Sequences tr_A0A091EUJ1_A0A091EUJ1_CORBR_85066 and tr_A0A091J0E6_A0A091J0E6_CALAN_9244 are exactly identical! WARNING: Sequences tr_A0A091IVD5_A0A091IVD5_EGRGA_188379 and tr_A0A091VW16_A0A091VW16_NIPNI_128390 are exactly identical! WARNING: Sequences tr_A0A091JHY2_A0A091JHY2_EGRGA_188379 and tr_A0A091UWV7_A0A091UWV7_NIPNI_128390 are exactly identical! WARNING: Sequences tr_A0A091JHY2_A0A091JHY2_EGRGA_188379 and tr_A0A087RD36_A0A087RD36_APTFO_9233 are exactly identical! WARNING: Sequences tr_A0A091JHY2_A0A091JHY2_EGRGA_188379 and tr_A0A093H843_A0A093H843_STRCA_441894 are exactly identical! WARNING: Sequences tr_A0A091JHY2_A0A091JHY2_EGRGA_188379 and tr_A0A091G8V1_A0A091G8V1_9AVES_55661 are exactly identical! WARNING: Sequences tr_A0A091JHY2_A0A091JHY2_EGRGA_188379 and tr_A0A091IG63_A0A091IG63_CALAN_9244 are exactly identical! WARNING: Sequences tr_A0A091JMK4_A0A091JMK4_EGRGA_188379 and tr_A0A091W9U3_A0A091W9U3_NIPNI_128390 are exactly identical! WARNING: Sequences tr_A0A091JMK4_A0A091JMK4_EGRGA_188379 and tr_A0A093HFK6_A0A093HFK6_STRCA_441894 are exactly identical! WARNING: Sequences tr_A0A091JMK4_A0A091JMK4_EGRGA_188379 and tr_A0A091WJZ2_A0A091WJZ2_OPIHO_30419 are exactly identical! WARNING: Sequences tr_A0A091JMK4_A0A091JMK4_EGRGA_188379 and tr_A0A091GH19_A0A091GH19_9AVES_55661 are exactly identical! WARNING: Sequences tr_A0A091JMK4_A0A091JMK4_EGRGA_188379 and tr_A0A0A0ARF2_A0A0A0ARF2_CHAVO_50402 are exactly identical! WARNING: Sequences tr_A0A091FUW7_A0A091FUW7_9AVES_55661 and tr_A0A093J8P3_A0A093J8P3_DRYPU_118200 are exactly identical! WARNING: Sequences tr_A0A091FUW7_A0A091FUW7_9AVES_55661 and tr_A0A091HS58_A0A091HS58_CALAN_9244 are exactly identical! WARNING: Sequences tr_A0A0A0A444_A0A0A0A444_CHAVO_50402 and tr_A0A091HZD7_A0A091HZD7_CALAN_9244 are exactly identical! WARNING: Sequences tr_A0A0V0RXG8_A0A0V0RXG8_9BILA_6336 and tr_A0A0V1CKI0_A0A0V1CKI0_TRIBR_45882 are exactly identical! WARNING: Sequences tr_A0A0V0S006_A0A0V0S006_9BILA_6336 and tr_A0A0V1CHZ0_A0A0V1CHZ0_TRIBR_45882 are exactly identical! WARNING: Sequences tr_A0A0V0S006_A0A0V0S006_9BILA_6336 and tr_A0A0V0VPU7_A0A0V0VPU7_9BILA_181606 are exactly identical! WARNING: Sequences tr_A0A0V0S006_A0A0V0S006_9BILA_6336 and tr_A0A0V1KW03_A0A0V1KW03_9BILA_6335 are exactly identical! WARNING: Sequences tr_A0A0V0S006_A0A0V0S006_9BILA_6336 and tr_A0A0V1NZC5_A0A0V1NZC5_9BILA_92180 are exactly identical! WARNING: Sequences tr_A0A0V0S006_A0A0V0S006_9BILA_6336 and tr_A0A0V0TSD2_A0A0V0TSD2_9BILA_144512 are exactly identical! WARNING: Sequences tr_A0A151X6R4_A0A151X6R4_9HYME_64791 and tr_A0A195EHE4_A0A195EHE4_9HYME_471704 are exactly identical! WARNING: Sequences tr_A0A151X6R4_A0A151X6R4_9HYME_64791 and tr_A0A195FER6_A0A195FER6_9HYME_34720 are exactly identical! WARNING: Sequences tr_A0A1S3MBP8_A0A1S3MBP8_SALSA_8030 and tr_C0HA59_C0HA59_SALSA_8030 are exactly identical! WARNING: Sequences tr_A0A2D0PSX8_A0A2D0PSX8_ICTPU_7998 and tr_A0A2D0PUH5_A0A2D0PUH5_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0PUF6_A0A2D0PUF6_ICTPU_7998 and tr_A0A2D0PW58_A0A2D0PW58_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0PUF6_A0A2D0PUF6_ICTPU_7998 and tr_A0A2D0PW63_A0A2D0PW63_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0PUF6_A0A2D0PUF6_ICTPU_7998 and tr_A0A2D0PX14_A0A2D0PX14_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0PUF6_A0A2D0PUF6_ICTPU_7998 and tr_A0A2D0PX19_A0A2D0PX19_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0RBJ8_A0A2D0RBJ8_ICTPU_7998 and tr_A0A2D0RBL1_A0A2D0RBL1_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0RBJ8_A0A2D0RBJ8_ICTPU_7998 and tr_A0A2D0RBR4_A0A2D0RBR4_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0RBJ8_A0A2D0RBJ8_ICTPU_7998 and tr_A0A2D0RBS3_A0A2D0RBS3_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0RBJ8_A0A2D0RBJ8_ICTPU_7998 and tr_A0A2D0RCT4_A0A2D0RCT4_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0RBJ8_A0A2D0RBJ8_ICTPU_7998 and tr_A0A2D0RCU1_A0A2D0RCU1_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0RBJ8_A0A2D0RBJ8_ICTPU_7998 and tr_A0A2D0RCV2_A0A2D0RCV2_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0RBP7_A0A2D0RBP7_ICTPU_7998 and tr_A0A2D0RBU8_A0A2D0RBU8_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0SJ06_A0A2D0SJ06_ICTPU_7998 and tr_W5U9K8_W5U9K8_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0SR82_A0A2D0SR82_ICTPU_7998 and tr_A0A2D0SSC0_A0A2D0SSC0_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2U4B0F7_A0A2U4B0F7_TURTR_9739 and tr_A0A2Y9Q6T4_A0A2Y9Q6T4_DELLE_9749 are exactly identical! WARNING: Sequences tr_A0A2U4B2R3_A0A2U4B2R3_TURTR_9739 and tr_A0A2Y9T6F6_A0A2Y9T6F6_PHYCD_9755 are exactly identical! WARNING: Sequences tr_A0A2U3VSL4_A0A2U3VSL4_ODORO_9708 and tr_A0A2Y9JSJ0_A0A2Y9JSJ0_ENHLU_391180 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/P43403/3_mltree/P43403.raxml.reduced.phy Alignment comprises 1 partitions and 474 patterns Partition 0: noname Model: LG4X+R4 Alignment sites / patterns: 476 / 474 Gaps: 10.39 % Invariant sites: 2.10 % NOTE: Binary MSA file created: /cta/users/eakkoyun/WORKFOLDER/PROD/run_040621/phylogeny-snakemake/results/P43403/3_mltree/P43403.raxml.rba Parallelization scheme autoconfig: 1 worker(s) x 7 thread(s) Parallel reduction/worker buffer size: 1 KB / 0 KB [00:00:00] Generating 20 random starting tree(s) with 1001 taxa [00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 68 / 5440 [00:00:00] Data distribution: max. searches per worker: 20 Starting ML tree search with 20 distinct starting trees [00:00:00 -775727.595360] Initial branch length optimization [00:00:04 -626620.854761] Model parameter optimization (eps = 10.000000) [00:03:52 -625886.369439] AUTODETECT spr round 1 (radius: 5) [00:50:17 -369587.882270] AUTODETECT spr round 2 (radius: 10) [01:43:13 -254102.800863] AUTODETECT spr round 3 (radius: 15) [02:36:52 -204692.550565] AUTODETECT spr round 4 (radius: 20) [03:30:20 -182906.940915] AUTODETECT spr round 5 (radius: 25) [04:44:36 -168736.218333] SPR radius for FAST iterations: 25 (autodetect) [04:44:36 -168736.218333] Model parameter optimization (eps = 3.000000) [04:46:19 -168634.122602] FAST spr round 1 (radius: 25) [05:29:09 -136340.674793] FAST spr round 2 (radius: 25) [06:13:04 -134070.538777] FAST spr round 3 (radius: 25) [07:23:24 -133936.241929] FAST spr round 4 (radius: 25) [07:54:15 -133928.709055] FAST spr round 5 (radius: 25) [08:15:34 -133923.370388] FAST spr round 6 (radius: 25) [08:39:02 -133923.370134] Model parameter optimization (eps = 1.000000) [08:39:16 -133920.848726] SLOW spr round 1 (radius: 5) [09:11:58 -133896.811943] SLOW spr round 2 (radius: 5) [10:14:24 -133896.251220] SLOW spr round 3 (radius: 5) [11:00:09 -133896.251121] SLOW spr round 4 (radius: 10) [12:04:57 -133895.798175] SLOW spr round 5 (radius: 5) [12:42:37 -133895.798100] SLOW spr round 6 (radius: 10) [13:11:54 -133895.798040] SLOW spr round 7 (radius: 15) [14:24:52 -133895.797979] SLOW spr round 8 (radius: 20) [15:21:20 -133895.574005] SLOW spr round 9 (radius: 5) [15:41:06 -133893.854730] SLOW spr round 10 (radius: 5) [16:05:26 -133893.854668] SLOW spr round 11 (radius: 10) [16:44:28 -133893.854607] SLOW spr round 12 (radius: 15) [19:37:58 -133893.854545] SLOW spr round 13 (radius: 20) [26:55:59 -133893.854483] SLOW spr round 14 (radius: 25) 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 23-Jun-2021 08:52:58 as follows: raxml-ng --msa /cta/users/eakkoyun/WORKFOLDER/PROD/run_040621/phylogeny-snakemake/results/P43403/2_msa/P43403_trimmed_msa.fasta --data-type AA --model LG4X --prefix /cta/users/eakkoyun/WORKFOLDER/PROD/run_040621/phylogeny-snakemake/results/P43403/3_mltree/P43403 --seed 2 --threads 7 --tree rand{20} pars{20} Analysis options: run mode: ML tree search start tree(s): random (20) random seed: 2 tip-inner: OFF pattern compression: ON per-rate scalers: OFF site repeats: ON fast spr radius: AUTO spr subtree cutoff: 1.000000 branch lengths: proportional (ML estimate, algorithm: NR-FAST) SIMD kernels: AVX2 parallelization: coarse-grained (auto), PTHREADS (7 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: /cta/users/eakkoyun/WORKFOLDER/PROD/run_040621/phylogeny-snakemake/results/P43403/3_mltree/P43403.raxml.rba [00:00:00] Alignment comprises 1001 taxa, 1 partitions and 474 patterns Partition 0: noname Model: LG4X+R4 Alignment sites / patterns: 476 / 474 Gaps: 10.39 % Invariant sites: 2.10 % Parallelization scheme autoconfig: 1 worker(s) x 7 thread(s) Parallel reduction/worker buffer size: 1 KB / 0 KB [00:00:00] NOTE: Resuming execution from checkpoint (logLH: -133893.85, ML trees: 0, bootstraps: 0) [00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 68 / 5440 [00:00:00] Data distribution: max. searches per worker: 20 Starting ML tree search with 20 distinct starting trees [00:00:00 -133893.854483] SPR radius for FAST iterations: 25 (autodetect) [00:00:00 -133893.854483] SLOW spr round 14 (radius: 25) [00:03:45 -133893.854421] Model parameter optimization (eps = 0.100000) [00:03:52] ML tree search #1, logLikelihood: -133893.598704 [00:03:52 -773550.071737] Initial branch length optimization [00:03:56 -631911.089979] Model parameter optimization (eps = 10.000000) [00:04:26 -631288.379724] AUTODETECT spr round 1 (radius: 5) [00:06:13 -378282.482173] AUTODETECT spr round 2 (radius: 10) [00:08:13 -259777.878240] AUTODETECT spr round 3 (radius: 15) [00:10:21 -208174.956506] AUTODETECT spr round 4 (radius: 20) [00:12:42 -182937.056990] AUTODETECT spr round 5 (radius: 25) [00:15:04 -171549.535732] SPR radius for FAST iterations: 25 (autodetect) [00:15:04 -171549.535732] Model parameter optimization (eps = 3.000000) [00:15:23 -171463.718072] FAST spr round 1 (radius: 25) [00:17:21 -136457.688007] FAST spr round 2 (radius: 25) [00:19:04 -134163.958514] FAST spr round 3 (radius: 25) [00:20:42 -133943.790939] FAST spr round 4 (radius: 25) [00:22:16 -133937.727083] FAST spr round 5 (radius: 25) [00:23:49 -133937.726529] Model parameter optimization (eps = 1.000000) [00:24:04 -133934.144669] SLOW spr round 1 (radius: 5) [00:25:54 -133906.931376] SLOW spr round 2 (radius: 5) [00:27:43 -133902.846433] SLOW spr round 3 (radius: 5) [00:29:32 -133902.429658] SLOW spr round 4 (radius: 5) [00:31:17 -133902.429442] SLOW spr round 5 (radius: 10) [00:33:04 -133902.429391] SLOW spr round 6 (radius: 15) [00:35:34 -133902.429368] SLOW spr round 7 (radius: 20) [00:38:50 -133902.429345] SLOW spr round 8 (radius: 25) [00:42:53 -133902.429322] Model parameter optimization (eps = 0.100000) [00:43:03] ML tree search #2, logLikelihood: -133901.952881 [00:43:04 -780214.885411] Initial branch length optimization [00:43:07 -636535.680072] Model parameter optimization (eps = 10.000000) [00:43:37 -636029.910402] AUTODETECT spr round 1 (radius: 5) [00:45:31 -366286.516412] AUTODETECT spr round 2 (radius: 10) [00:47:33 -267450.426622] AUTODETECT spr round 3 (radius: 15) [00:49:38 -212239.242728] AUTODETECT spr round 4 (radius: 20) [00:51:52 -192853.663448] AUTODETECT spr round 5 (radius: 25) [00:54:03 -178745.836991] SPR radius for FAST iterations: 25 (autodetect) [00:54:03 -178745.836991] Model parameter optimization (eps = 3.000000) [00:54:25 -178679.707091] FAST spr round 1 (radius: 25) [00:56:23 -140495.450656] FAST spr round 2 (radius: 25) [00:58:03 -134923.113951] FAST spr round 3 (radius: 25) [00:59:37 -134107.009018] FAST spr round 4 (radius: 25) [01:01:06 -134004.120361] FAST spr round 5 (radius: 25) [01:02:40 -133928.362765] FAST spr round 6 (radius: 25) [01:04:12 -133928.362465] Model parameter optimization (eps = 1.000000) [01:04:29 -133925.173163] SLOW spr round 1 (radius: 5) [01:06:17 -133898.180777] SLOW spr round 2 (radius: 5) [01:08:03 -133891.403844] SLOW spr round 3 (radius: 5) [01:09:50 -133889.708084] SLOW spr round 4 (radius: 5) [01:11:34 -133889.707944] SLOW spr round 5 (radius: 10) [01:13:22 -133889.707562] SLOW spr round 6 (radius: 15) [01:15:54 -133889.707517] SLOW spr round 7 (radius: 20) [01:19:08 -133889.707472] SLOW spr round 8 (radius: 25) [01:23:23 -133889.707427] Model parameter optimization (eps = 0.100000) [01:23:27] ML tree search #3, logLikelihood: -133889.687500 [01:23:27 -777727.301135] Initial branch length optimization [01:23:31 -631169.612407] Model parameter optimization (eps = 10.000000) [01:23:59 -630580.245692] AUTODETECT spr round 1 (radius: 5) [01:25:51 -364040.188384] AUTODETECT spr round 2 (radius: 10) [01:27:57 -245511.260422] AUTODETECT spr round 3 (radius: 15) [01:30:04 -199223.799792] AUTODETECT spr round 4 (radius: 20) [01:32:18 -179287.947050] AUTODETECT spr round 5 (radius: 25) [01:34:54 -162044.221106] SPR radius for FAST iterations: 25 (autodetect) [01:34:54 -162044.221106] Model parameter optimization (eps = 3.000000) [01:35:12 -161982.527481] FAST spr round 1 (radius: 25) [01:37:19 -135493.733816] FAST spr round 2 (radius: 25) [01:39:05 -134013.468904] FAST spr round 3 (radius: 25) [01:40:40 -133935.178823] FAST spr round 4 (radius: 25) [01:42:08 -133927.062810] FAST spr round 5 (radius: 25) [01:43:33 -133927.062601] Model parameter optimization (eps = 1.000000) [01:43:47 -133923.498764] SLOW spr round 1 (radius: 5) [01:45:31 -133889.670349] SLOW spr round 2 (radius: 5) [01:47:11 -133888.258094] SLOW spr round 3 (radius: 5) [01:48:50 -133888.257823] SLOW spr round 4 (radius: 10) [01:50:32 -133887.449963] SLOW spr round 5 (radius: 5) [01:52:36 -133887.449636] SLOW spr round 6 (radius: 10) [01:54:34 -133887.449627] SLOW spr round 7 (radius: 15) [01:57:01 -133886.477801] SLOW spr round 8 (radius: 5) [01:59:11 -133886.477697] SLOW spr round 9 (radius: 10) [02:01:13 -133886.477689] SLOW spr round 10 (radius: 15) [02:03:37 -133886.477681] SLOW spr round 11 (radius: 20) [02:06:58 -133886.477672] SLOW spr round 12 (radius: 25) [02:11:10 -133886.477664] Model parameter optimization (eps = 0.100000) [02:11:15] ML tree search #4, logLikelihood: -133886.460437 [02:11:15 -780203.986413] Initial branch length optimization [02:11:18 -637284.912742] Model parameter optimization (eps = 10.000000) [02:11:46 -636618.859801] AUTODETECT spr round 1 (radius: 5) [02:13:40 -366486.824582] AUTODETECT spr round 2 (radius: 10) [02:15:51 -261202.766594] AUTODETECT spr round 3 (radius: 15) [02:18:02 -205010.209035] AUTODETECT spr round 4 (radius: 20) [02:20:23 -186977.692992] AUTODETECT spr round 5 (radius: 25) [02:22:58 -164666.346604] SPR radius for FAST iterations: 25 (autodetect) [02:22:58 -164666.346604] Model parameter optimization (eps = 3.000000) [02:23:17 -164612.431816] FAST spr round 1 (radius: 25) [02:25:20 -135739.903061] FAST spr round 2 (radius: 25) [02:27:11 -134310.294469] FAST spr round 3 (radius: 25) [02:28:48 -134137.732312] FAST spr round 4 (radius: 25) [02:30:24 -134112.550789] FAST spr round 5 (radius: 25) [02:31:56 -134111.789668] FAST spr round 6 (radius: 25) [02:33:28 -134111.789081] Model parameter optimization (eps = 1.000000) [02:33:40 -134109.961695] SLOW spr round 1 (radius: 5) [02:35:30 -134086.029450] SLOW spr round 2 (radius: 5) [02:37:15 -134081.620245] SLOW spr round 3 (radius: 5) [02:38:57 -134081.619498] SLOW spr round 4 (radius: 10) [02:40:42 -134081.344745] SLOW spr round 5 (radius: 5) [02:42:42 -134081.344465] SLOW spr round 6 (radius: 10) [02:44:35 -134081.344229] SLOW spr round 7 (radius: 15) [02:46:53 -134081.343992] SLOW spr round 8 (radius: 20) [02:50:11 -134081.343752] SLOW spr round 9 (radius: 25) [02:54:27 -134081.343512] Model parameter optimization (eps = 0.100000) [02:54:32] ML tree search #5, logLikelihood: -134081.285780 [02:54:32 -774887.147259] Initial branch length optimization [02:54:36 -626252.296395] Model parameter optimization (eps = 10.000000) [02:55:01 -625648.971415] AUTODETECT spr round 1 (radius: 5) [02:56:56 -371314.438704] AUTODETECT spr round 2 (radius: 10) [02:59:02 -251585.102247] AUTODETECT spr round 3 (radius: 15) [03:01:14 -192538.992808] AUTODETECT spr round 4 (radius: 20) [03:03:33 -173931.927864] AUTODETECT spr round 5 (radius: 25) [03:05:54 -161001.998796] SPR radius for FAST iterations: 25 (autodetect) [03:05:54 -161001.998796] Model parameter optimization (eps = 3.000000) [03:06:13 -160920.559152] FAST spr round 1 (radius: 25) [03:08:23 -136589.583228] FAST spr round 2 (radius: 25) [03:10:14 -134509.032880] FAST spr round 3 (radius: 25) [03:11:57 -134066.974076] FAST spr round 4 (radius: 25) [03:13:39 -133940.779204] FAST spr round 5 (radius: 25) [03:15:14 -133935.264036] FAST spr round 6 (radius: 25) [03:16:48 -133933.996183] FAST spr round 7 (radius: 25) [03:18:20 -133933.996082] Model parameter optimization (eps = 1.000000) [03:18:32 -133932.494080] SLOW spr round 1 (radius: 5) [03:20:23 -133901.361996] SLOW spr round 2 (radius: 5) [03:22:07 -133898.818564] SLOW spr round 3 (radius: 5) [03:23:53 -133894.333259] SLOW spr round 4 (radius: 5) [03:25:38 -133894.333118] SLOW spr round 5 (radius: 10) [03:27:26 -133894.333093] SLOW spr round 6 (radius: 15) [03:29:52 -133894.332869] SLOW spr round 7 (radius: 20) [03:32:59 -133894.332859] SLOW spr round 8 (radius: 25) [03:36:59 -133894.332850] Model parameter optimization (eps = 0.100000) [03:37:06] ML tree search #6, logLikelihood: -133894.221789 [03:37:06 -776121.924272] Initial branch length optimization [03:37:10 -630810.976970] Model parameter optimization (eps = 10.000000) [03:37:31 -630265.501489] AUTODETECT spr round 1 (radius: 5) [03:39:19 -370567.586329] AUTODETECT spr round 2 (radius: 10) [03:41:23 -253988.668443] AUTODETECT spr round 3 (radius: 15) [03:43:34 -206875.400099] AUTODETECT spr round 4 (radius: 20) [03:45:50 -188623.623526] AUTODETECT spr round 5 (radius: 25) [03:48:30 -164949.837324] SPR radius for FAST iterations: 25 (autodetect) [03:48:30 -164949.837324] Model parameter optimization (eps = 3.000000) [03:48:48 -164806.637770] FAST spr round 1 (radius: 25) [03:50:56 -136410.987861] FAST spr round 2 (radius: 25) [03:52:41 -134524.161530] FAST spr round 3 (radius: 25) [03:54:22 -134161.827454] FAST spr round 4 (radius: 25) [03:55:59 -133982.474483] FAST spr round 5 (radius: 25) [03:57:33 -133949.442108] FAST spr round 6 (radius: 25) [03:59:05 -133946.952563] FAST spr round 7 (radius: 25) [04:00:37 -133946.952097] Model parameter optimization (eps = 1.000000) [04:00:47 -133946.050736] SLOW spr round 1 (radius: 5) [04:02:37 -133917.490949] SLOW spr round 2 (radius: 5) [04:04:26 -133913.028955] SLOW spr round 3 (radius: 5) [04:06:09 -133913.028867] SLOW spr round 4 (radius: 10) [04:07:56 -133913.028808] SLOW spr round 5 (radius: 15) [04:10:30 -133904.448900] SLOW spr round 6 (radius: 5) [04:12:40 -133902.955796] SLOW spr round 7 (radius: 5) [04:14:34 -133902.955729] SLOW spr round 8 (radius: 10) [04:16:23 -133881.093136] SLOW spr round 9 (radius: 5) [04:18:21 -133881.093070] SLOW spr round 10 (radius: 10) [04:20:12 -133881.093010] SLOW spr round 11 (radius: 15) [04:22:32 -133881.092950] SLOW spr round 12 (radius: 20) [04:25:37 -133881.092891] SLOW spr round 13 (radius: 25) [04:29:41 -133881.092832] Model parameter optimization (eps = 0.100000) [04:29:53] ML tree search #7, logLikelihood: -133880.566765 [04:29:53 -772799.448515] Initial branch length optimization [04:29:56 -627201.804060] Model parameter optimization (eps = 10.000000) [04:30:24 -626538.506055] AUTODETECT spr round 1 (radius: 5) [04:32:19 -354898.661006] AUTODETECT spr round 2 (radius: 10) [04:34:22 -242580.296673] AUTODETECT spr round 3 (radius: 15) [04:36:29 -187054.909216] AUTODETECT spr round 4 (radius: 20) [04:38:55 -161769.443565] AUTODETECT spr round 5 (radius: 25) [04:41:34 -157622.214652] SPR radius for FAST iterations: 25 (autodetect) [04:41:34 -157622.214652] Model parameter optimization (eps = 3.000000) [04:41:53 -157553.392553] FAST spr round 1 (radius: 25) [04:43:59 -135006.641844] FAST spr round 2 (radius: 25) [04:45:51 -134037.896957] FAST spr round 3 (radius: 25) [04:47:31 -133944.662351] FAST spr round 4 (radius: 25) [04:49:08 -133935.984370] FAST spr round 5 (radius: 25) [04:50:42 -133935.982344] Model parameter optimization (eps = 1.000000) [04:50:55 -133931.181111] SLOW spr round 1 (radius: 5) [04:52:47 -133895.399788] SLOW spr round 2 (radius: 5) [04:54:36 -133890.021361] SLOW spr round 3 (radius: 5) [04:56:19 -133890.020744] SLOW spr round 4 (radius: 10) [04:58:05 -133889.320653] SLOW spr round 5 (radius: 5) [05:00:09 -133889.320290] SLOW spr round 6 (radius: 10) [05:02:06 -133889.320223] SLOW spr round 7 (radius: 15) [05:04:31 -133889.320155] SLOW spr round 8 (radius: 20) [05:07:40 -133889.320088] SLOW spr round 9 (radius: 25) [05:11:45 -133889.320020] Model parameter optimization (eps = 0.100000) [05:11:53] ML tree search #8, logLikelihood: -133889.147392 [05:11:53 -781693.071041] Initial branch length optimization [05:11:56 -630023.518820] Model parameter optimization (eps = 10.000000) [05:12:31 -629297.675399] AUTODETECT spr round 1 (radius: 5) [05:14:20 -379786.495331] AUTODETECT spr round 2 (radius: 10) [05:16:17 -274795.863611] AUTODETECT spr round 3 (radius: 15) [05:18:17 -217067.370628] AUTODETECT spr round 4 (radius: 20) [05:20:29 -188806.548953] AUTODETECT spr round 5 (radius: 25) [05:23:06 -171592.022694] SPR radius for FAST iterations: 25 (autodetect) [05:23:06 -171592.022694] Model parameter optimization (eps = 3.000000) [05:23:25 -171450.180003] FAST spr round 1 (radius: 25) [05:25:24 -137842.376199] FAST spr round 2 (radius: 25) [05:27:16 -134161.955991] FAST spr round 3 (radius: 25) [05:28:55 -133991.615587] FAST spr round 4 (radius: 25) [05:30:31 -133950.967598] FAST spr round 5 (radius: 25) [05:32:01 -133950.956861] Model parameter optimization (eps = 1.000000) [05:32:14 -133949.362253] SLOW spr round 1 (radius: 5) [05:34:00 -133926.525863] SLOW spr round 2 (radius: 5) [05:35:47 -133922.085257] SLOW spr round 3 (radius: 5) [05:37:34 -133920.476439] SLOW spr round 4 (radius: 5) [05:39:20 -133920.476101] SLOW spr round 5 (radius: 10) [05:41:10 -133920.475749] SLOW spr round 6 (radius: 15) [05:43:39 -133920.475677] SLOW spr round 7 (radius: 20) [05:46:51 -133920.475611] SLOW spr round 8 (radius: 25) [05:50:56 -133920.475545] Model parameter optimization (eps = 0.100000) [05:51:07] ML tree search #9, logLikelihood: -133919.978357 [05:51:07 -778813.891713] Initial branch length optimization [05:51:11 -630609.138121] Model parameter optimization (eps = 10.000000) [05:51:38 -629967.527665] AUTODETECT spr round 1 (radius: 5) [05:53:33 -372038.327446] AUTODETECT spr round 2 (radius: 10) [05:55:38 -253035.142708] AUTODETECT spr round 3 (radius: 15) [05:57:43 -215553.390819] AUTODETECT spr round 4 (radius: 20) [05:59:59 -202167.993510] AUTODETECT spr round 5 (radius: 25) [06:02:19 -195736.244464] SPR radius for FAST iterations: 25 (autodetect) [06:02:19 -195736.244464] Model parameter optimization (eps = 3.000000) [06:02:37 -195657.106812] FAST spr round 1 (radius: 25) [06:04:44 -154148.541664] FAST spr round 2 (radius: 25) [06:06:35 -144856.026950] FAST spr round 3 (radius: 25) [06:08:20 -136016.537883] FAST spr round 4 (radius: 25) [06:09:57 -134092.861136] FAST spr round 5 (radius: 25) [06:11:30 -133969.905993] FAST spr round 6 (radius: 25) [06:12:58 -133966.724236] FAST spr round 7 (radius: 25) [06:14:24 -133966.724122] Model parameter optimization (eps = 1.000000) [06:14:39 -133960.307706] SLOW spr round 1 (radius: 5) [06:16:25 -133935.402298] SLOW spr round 2 (radius: 5) [06:18:09 -133921.011152] SLOW spr round 3 (radius: 5) [06:19:52 -133913.728505] SLOW spr round 4 (radius: 5) [06:21:30 -133911.213124] SLOW spr round 5 (radius: 5) [06:23:13 -133909.317118] SLOW spr round 6 (radius: 5) [06:25:00 -133909.316864] SLOW spr round 7 (radius: 10) [06:26:50 -133903.692079] SLOW spr round 8 (radius: 5) [06:28:55 -133903.692077] SLOW spr round 9 (radius: 10) [06:30:53 -133903.692076] SLOW spr round 10 (radius: 15) [06:33:19 -133903.692074] SLOW spr round 11 (radius: 20) [06:36:47 -133903.692073] SLOW spr round 12 (radius: 25) [06:41:07 -133903.692072] Model parameter optimization (eps = 0.100000) [06:41:15] ML tree search #10, logLikelihood: -133903.349825 [06:41:15 -777456.692339] Initial branch length optimization [06:41:18 -632478.302732] Model parameter optimization (eps = 10.000000) [06:41:46 -631764.814415] AUTODETECT spr round 1 (radius: 5) [06:43:40 -371657.640193] AUTODETECT spr round 2 (radius: 10) [06:45:47 -262635.770174] AUTODETECT spr round 3 (radius: 15) [06:47:59 -191791.750750] AUTODETECT spr round 4 (radius: 20) [06:50:11 -168867.290678] AUTODETECT spr round 5 (radius: 25) [06:52:45 -158071.695332] SPR radius for FAST iterations: 25 (autodetect) [06:52:46 -158071.695332] Model parameter optimization (eps = 3.000000) [06:53:06 -158000.754835] FAST spr round 1 (radius: 25) [06:55:13 -135278.336225] FAST spr round 2 (radius: 25) [06:57:00 -134024.738982] FAST spr round 3 (radius: 25) [06:58:37 -133941.048594] FAST spr round 4 (radius: 25) [07:00:09 -133933.671239] FAST spr round 5 (radius: 25) [07:01:41 -133933.670567] Model parameter optimization (eps = 1.000000) [07:01:55 -133930.600386] SLOW spr round 1 (radius: 5) [07:03:46 -133890.901358] SLOW spr round 2 (radius: 5) [07:05:30 -133885.692347] SLOW spr round 3 (radius: 5) [07:07:11 -133885.691839] SLOW spr round 4 (radius: 10) [07:08:53 -133885.691729] SLOW spr round 5 (radius: 15) [07:11:15 -133884.860471] SLOW spr round 6 (radius: 5) [07:13:20 -133883.563200] SLOW spr round 7 (radius: 5) [07:15:11 -133883.563073] SLOW spr round 8 (radius: 10) [07:16:55 -133883.563013] SLOW spr round 9 (radius: 15) [07:19:15 -133883.562954] SLOW spr round 10 (radius: 20) [07:22:21 -133883.562894] SLOW spr round 11 (radius: 25) [07:26:31 -133883.562835] Model parameter optimization (eps = 0.100000) [07:26:36] ML tree search #11, logLikelihood: -133883.493742 [07:26:37 -773660.919149] Initial branch length optimization [07:26:40 -631788.592895] Model parameter optimization (eps = 10.000000) [07:27:08 -631253.492574] AUTODETECT spr round 1 (radius: 5) [07:29:00 -382392.967048] AUTODETECT spr round 2 (radius: 10) [07:31:01 -264382.383170] AUTODETECT spr round 3 (radius: 15) [07:33:23 -204748.937367] AUTODETECT spr round 4 (radius: 20) [07:35:48 -185298.516751] AUTODETECT spr round 5 (radius: 25) [07:38:36 -163388.629873] SPR radius for FAST iterations: 25 (autodetect) [07:38:36 -163388.629873] Model parameter optimization (eps = 3.000000) [07:39:00 -163309.786156] FAST spr round 1 (radius: 25) [07:41:05 -136131.505634] FAST spr round 2 (radius: 25) [07:42:50 -134075.073760] FAST spr round 3 (radius: 25) [07:44:30 -133961.415591] FAST spr round 4 (radius: 25) [07:46:07 -133950.171774] FAST spr round 5 (radius: 25) [07:47:41 -133950.171102] Model parameter optimization (eps = 1.000000) [07:47:47 -133949.355641] SLOW spr round 1 (radius: 5) [07:49:40 -133915.029198] SLOW spr round 2 (radius: 5) [07:51:29 -133913.507804] SLOW spr round 3 (radius: 5) [07:53:13 -133913.507110] SLOW spr round 4 (radius: 10) [07:55:01 -133913.507059] SLOW spr round 5 (radius: 15) [07:57:31 -133913.507037] SLOW spr round 6 (radius: 20) [08:00:40 -133912.581636] SLOW spr round 7 (radius: 5) [08:02:54 -133912.581518] SLOW spr round 8 (radius: 10) [08:04:59 -133912.581497] SLOW spr round 9 (radius: 15) [08:07:23 -133912.581477] SLOW spr round 10 (radius: 20) [08:10:35 -133912.581221] SLOW spr round 11 (radius: 25) [08:14:31 -133912.581201] Model parameter optimization (eps = 0.100000) [08:14:41] ML tree search #12, logLikelihood: -133912.312110 [08:14:41 -773436.036095] Initial branch length optimization [08:14:44 -622631.479276] Model parameter optimization (eps = 10.000000) [08:15:13 -622043.750343] AUTODETECT spr round 1 (radius: 5) [08:17:08 -377222.286066] AUTODETECT spr round 2 (radius: 10) [08:19:13 -261843.239433] AUTODETECT spr round 3 (radius: 15) [08:21:22 -209724.347674] AUTODETECT spr round 4 (radius: 20) [08:23:47 -186835.353732] AUTODETECT spr round 5 (radius: 25) [08:26:15 -171845.887006] SPR radius for FAST iterations: 25 (autodetect) [08:26:15 -171845.887006] Model parameter optimization (eps = 3.000000) [08:26:34 -171747.338483] FAST spr round 1 (radius: 25) [08:28:44 -138902.181678] FAST spr round 2 (radius: 25) [08:30:31 -134594.158472] FAST spr round 3 (radius: 25) [08:32:14 -133975.360099] FAST spr round 4 (radius: 25) [08:33:50 -133940.069754] FAST spr round 5 (radius: 25) [08:35:21 -133939.756824] FAST spr round 6 (radius: 25) [08:36:51 -133939.756110] Model parameter optimization (eps = 1.000000) [08:37:04 -133935.483541] SLOW spr round 1 (radius: 5) [08:38:50 -133896.103037] SLOW spr round 2 (radius: 5) [08:40:32 -133884.966564] SLOW spr round 3 (radius: 5) [08:42:17 -133884.965745] SLOW spr round 4 (radius: 10) [08:44:06 -133884.965681] SLOW spr round 5 (radius: 15) [08:46:38 -133884.965656] SLOW spr round 6 (radius: 20) [08:49:48 -133884.965632] SLOW spr round 7 (radius: 25) [08:54:00 -133884.965609] Model parameter optimization (eps = 0.100000) [08:54:12] ML tree search #13, logLikelihood: -133883.936604 [08:54:12 -781866.970943] Initial branch length optimization [08:54:17 -638324.905543] Model parameter optimization (eps = 10.000000) [08:54:44 -637735.583159] AUTODETECT spr round 1 (radius: 5) [08:56:36 -373727.283459] AUTODETECT spr round 2 (radius: 10) [08:58:40 -254805.426792] AUTODETECT spr round 3 (radius: 15) [09:00:52 -194885.877575] AUTODETECT spr round 4 (radius: 20) [09:03:12 -176079.765937] AUTODETECT spr round 5 (radius: 25) [09:05:49 -159137.660242] SPR radius for FAST iterations: 25 (autodetect) [09:05:49 -159137.660242] Model parameter optimization (eps = 3.000000) [09:06:07 -159067.711884] FAST spr round 1 (radius: 25) [09:08:16 -135070.354326] FAST spr round 2 (radius: 25) [09:10:10 -134036.515608] FAST spr round 3 (radius: 25) [09:11:50 -133937.616906] FAST spr round 4 (radius: 25) [09:13:28 -133921.445817] FAST spr round 5 (radius: 25) [09:15:04 -133919.985978] FAST spr round 6 (radius: 25) [09:16:35 -133919.985282] Model parameter optimization (eps = 1.000000) [09:16:49 -133915.305889] SLOW spr round 1 (radius: 5) [09:18:41 -133890.408058] SLOW spr round 2 (radius: 5) [09:20:30 -133889.720293] SLOW spr round 3 (radius: 5) [09:22:13 -133889.720218] SLOW spr round 4 (radius: 10) [09:24:05 -133889.719971] SLOW spr round 5 (radius: 15) [09:26:37 -133889.719722] SLOW spr round 6 (radius: 20) [09:29:50 -133889.719709] SLOW spr round 7 (radius: 25) [09:33:56 -133889.719697] Model parameter optimization (eps = 0.100000) [09:34:02] ML tree search #14, logLikelihood: -133889.615864 [09:34:02 -783428.430840] Initial branch length optimization [09:34:06 -637968.824933] Model parameter optimization (eps = 10.000000) [09:34:30 -637207.025550] AUTODETECT spr round 1 (radius: 5) [09:36:25 -363276.196268] AUTODETECT spr round 2 (radius: 10) [09:38:32 -250906.810115] AUTODETECT spr round 3 (radius: 15) [09:40:41 -203251.878559] AUTODETECT spr round 4 (radius: 20) [09:43:02 -178273.915449] AUTODETECT spr round 5 (radius: 25) [09:45:37 -158384.998385] SPR radius for FAST iterations: 25 (autodetect) [09:45:37 -158384.998385] Model parameter optimization (eps = 3.000000) [09:45:59 -158294.023309] FAST spr round 1 (radius: 25) [09:48:04 -135300.474756] FAST spr round 2 (radius: 25) [09:49:55 -134144.185630] FAST spr round 3 (radius: 25) [09:51:38 -133942.114371] FAST spr round 4 (radius: 25) [09:53:09 -133935.697123] FAST spr round 5 (radius: 25) [09:54:38 -133935.696575] Model parameter optimization (eps = 1.000000) [09:54:48 -133935.212414] SLOW spr round 1 (radius: 5) [09:56:35 -133907.183663] SLOW spr round 2 (radius: 5) [09:58:20 -133906.325197] SLOW spr round 3 (radius: 5) [10:00:03 -133906.324559] SLOW spr round 4 (radius: 10) [10:01:48 -133906.324169] SLOW spr round 5 (radius: 15) [10:04:17 -133906.324152] SLOW spr round 6 (radius: 20) [10:07:33 -133906.324137] SLOW spr round 7 (radius: 25) [10:11:34 -133906.324121] Model parameter optimization (eps = 0.100000) [10:11:39] ML tree search #15, logLikelihood: -133906.245380 [10:11:39 -783379.232190] Initial branch length optimization [10:11:43 -630494.384829] Model parameter optimization (eps = 10.000000) [10:12:07 -629951.114203] AUTODETECT spr round 1 (radius: 5) [10:14:05 -382658.991652] AUTODETECT spr round 2 (radius: 10) [10:16:10 -278368.016669] AUTODETECT spr round 3 (radius: 15) [10:18:26 -204604.809560] AUTODETECT spr round 4 (radius: 20) [10:20:50 -170188.587789] AUTODETECT spr round 5 (radius: 25) [10:23:35 -161986.663214] SPR radius for FAST iterations: 25 (autodetect) [10:23:35 -161986.663214] Model parameter optimization (eps = 3.000000) [10:23:56 -161892.102079] FAST spr round 1 (radius: 25) [10:26:04 -134988.983232] FAST spr round 2 (radius: 25) [10:27:49 -134004.698879] FAST spr round 3 (radius: 25) [10:29:29 -133947.611400] FAST spr round 4 (radius: 25) [10:31:05 -133940.145094] FAST spr round 5 (radius: 25) [10:32:37 -133940.144930] Model parameter optimization (eps = 1.000000) [10:32:46 -133939.279996] SLOW spr round 1 (radius: 5) [10:34:37 -133912.557810] SLOW spr round 2 (radius: 5) [10:36:26 -133910.783492] SLOW spr round 3 (radius: 5) [10:38:15 -133910.782848] SLOW spr round 4 (radius: 10) [10:40:06 -133905.135523] SLOW spr round 5 (radius: 5) [10:42:11 -133905.135354] SLOW spr round 6 (radius: 10) [10:44:07 -133905.135082] SLOW spr round 7 (radius: 15) [10:46:30 -133905.135068] SLOW spr round 8 (radius: 20) [10:49:42 -133905.135054] SLOW spr round 9 (radius: 25) [10:53:47 -133905.135040] Model parameter optimization (eps = 0.100000) [10:53:59] ML tree search #16, logLikelihood: -133903.790782 [10:53:59 -779921.118916] Initial branch length optimization [10:54:02 -630342.756886] Model parameter optimization (eps = 10.000000) [10:54:34 -629707.518425] AUTODETECT spr round 1 (radius: 5) [10:56:25 -372526.187817] AUTODETECT spr round 2 (radius: 10) [10:58:29 -256177.822467] AUTODETECT spr round 3 (radius: 15) [11:00:33 -195220.812741] AUTODETECT spr round 4 (radius: 20) [11:02:38 -173980.693575] AUTODETECT spr round 5 (radius: 25) [11:05:06 -161849.312815] SPR radius for FAST iterations: 25 (autodetect) [11:05:06 -161849.312815] Model parameter optimization (eps = 3.000000) [11:05:23 -161775.215498] FAST spr round 1 (radius: 25) [11:07:24 -135743.142498] FAST spr round 2 (radius: 25) [11:09:07 -134087.500903] FAST spr round 3 (radius: 25) [11:10:39 -133950.825940] FAST spr round 4 (radius: 25) [11:12:10 -133924.175204] FAST spr round 5 (radius: 25) [11:13:40 -133918.354743] FAST spr round 6 (radius: 25) [11:15:06 -133912.429416] FAST spr round 7 (radius: 25) [11:16:32 -133911.512140] FAST spr round 8 (radius: 25) [11:17:58 -133911.511877] Model parameter optimization (eps = 1.000000) [11:18:06 -133911.064141] SLOW spr round 1 (radius: 5) [11:19:47 -133893.980273] SLOW spr round 2 (radius: 5) [11:21:28 -133893.977291] SLOW spr round 3 (radius: 10) [11:23:12 -133892.791069] SLOW spr round 4 (radius: 5) [11:25:14 -133892.790763] SLOW spr round 5 (radius: 10) [11:27:08 -133892.790672] SLOW spr round 6 (radius: 15) [11:29:27 -133892.790370] SLOW spr round 7 (radius: 20) [11:32:31 -133892.790314] SLOW spr round 8 (radius: 25) [11:36:32 -133892.790259] Model parameter optimization (eps = 0.100000) [11:36:37] ML tree search #17, logLikelihood: -133892.769123 [11:36:37 -781617.767110] Initial branch length optimization [11:36:41 -629383.083273] Model parameter optimization (eps = 10.000000) [11:37:12 -628802.395512] AUTODETECT spr round 1 (radius: 5) [11:39:02 -375252.903939] AUTODETECT spr round 2 (radius: 10) [11:41:01 -262372.970873] AUTODETECT spr round 3 (radius: 15) [11:43:06 -199573.217994] AUTODETECT spr round 4 (radius: 20) [11:45:20 -177273.740246] AUTODETECT spr round 5 (radius: 25) [11:48:18 -156668.257931] SPR radius for FAST iterations: 25 (autodetect) [11:48:18 -156668.257931] Model parameter optimization (eps = 3.000000) [11:48:44 -156609.063129] FAST spr round 1 (radius: 25) [11:50:55 -135458.022256] FAST spr round 2 (radius: 25) [11:52:51 -134024.482738] FAST spr round 3 (radius: 25) [11:54:43 -133937.702585] FAST spr round 4 (radius: 25) [11:56:18 -133935.012368] FAST spr round 5 (radius: 25) [11:57:55 -133935.011697] Model parameter optimization (eps = 1.000000) [11:58:08 -133931.491010] SLOW spr round 1 (radius: 5) [12:00:04 -133908.088813] SLOW spr round 2 (radius: 5) [12:01:52 -133908.088269] SLOW spr round 3 (radius: 10) [12:03:45 -133901.755790] SLOW spr round 4 (radius: 5) [12:05:53 -133896.292519] SLOW spr round 5 (radius: 5) [12:07:50 -133896.292465] SLOW spr round 6 (radius: 10) [12:09:43 -133896.292455] SLOW spr round 7 (radius: 15) [12:12:11 -133895.235645] SLOW spr round 8 (radius: 5) [12:14:23 -133890.489882] SLOW spr round 9 (radius: 5) [12:16:19 -133890.145948] SLOW spr round 10 (radius: 5) [12:18:09 -133890.145162] SLOW spr round 11 (radius: 10) [12:19:57 -133890.144792] SLOW spr round 12 (radius: 15) [12:22:24 -133890.144612] SLOW spr round 13 (radius: 20) [12:25:33 -133890.144521] SLOW spr round 14 (radius: 25) [12:29:38 -133890.144473] Model parameter optimization (eps = 0.100000) [12:29:43] ML tree search #18, logLikelihood: -133890.060315 [12:29:43 -779015.124535] Initial branch length optimization [12:29:46 -632146.968495] Model parameter optimization (eps = 10.000000) [12:30:11 -631534.904447] AUTODETECT spr round 1 (radius: 5) [12:32:09 -368659.181329] AUTODETECT spr round 2 (radius: 10) [12:34:19 -271232.693045] AUTODETECT spr round 3 (radius: 15) [12:36:34 -207673.151691] AUTODETECT spr round 4 (radius: 20) [12:39:01 -174596.248746] AUTODETECT spr round 5 (radius: 25) [12:41:33 -166642.494406] SPR radius for FAST iterations: 25 (autodetect) [12:41:33 -166642.494406] Model parameter optimization (eps = 3.000000) [12:41:50 -166553.352816] FAST spr round 1 (radius: 25) [12:44:00 -136527.426409] FAST spr round 2 (radius: 25) [12:45:48 -134813.706290] FAST spr round 3 (radius: 25) [12:47:28 -133941.724223] FAST spr round 4 (radius: 25) [12:49:06 -133935.132084] FAST spr round 5 (radius: 25) [12:50:34 -133934.378202] FAST spr round 6 (radius: 25) [12:52:07 -133934.378023] Model parameter optimization (eps = 1.000000) [12:52:23 -133929.456616] SLOW spr round 1 (radius: 5) [12:54:17 -133901.734527] SLOW spr round 2 (radius: 5) [12:56:09 -133901.733465] SLOW spr round 3 (radius: 10) [12:57:57 -133896.049831] SLOW spr round 4 (radius: 5) [13:00:03 -133896.049745] SLOW spr round 5 (radius: 10) [13:02:06 -133896.049679] SLOW spr round 6 (radius: 15) [13:04:33 -133896.049613] SLOW spr round 7 (radius: 20) [13:07:55 -133895.823841] SLOW spr round 8 (radius: 5) [13:10:13 -133894.108904] SLOW spr round 9 (radius: 5) [13:12:15 -133894.108837] SLOW spr round 10 (radius: 10) [13:14:13 -133894.108772] SLOW spr round 11 (radius: 15) [13:16:43 -133894.108707] SLOW spr round 12 (radius: 20) [13:20:06 -133894.108642] SLOW spr round 13 (radius: 25) [13:24:18 -133892.576930] SLOW spr round 14 (radius: 5) [13:26:38 -133892.335985] SLOW spr round 15 (radius: 5) [13:28:43 -133892.335694] SLOW spr round 16 (radius: 10) [13:30:41 -133892.335668] SLOW spr round 17 (radius: 15) [13:33:09 -133892.335661] SLOW spr round 18 (radius: 20) [13:36:30 -133892.335656] SLOW spr round 19 (radius: 25) [13:40:40 -133892.335651] Model parameter optimization (eps = 0.100000) [13:40:47] ML tree search #19, logLikelihood: -133892.263981 [13:40:47 -787041.899621] Initial branch length optimization [13:40:50 -638828.782855] Model parameter optimization (eps = 10.000000) [13:41:16 -638237.638285] AUTODETECT spr round 1 (radius: 5) [13:43:15 -371722.717983] AUTODETECT spr round 2 (radius: 10) [13:45:26 -274595.000069] AUTODETECT spr round 3 (radius: 15) [13:47:34 -217305.468600] AUTODETECT spr round 4 (radius: 20) [13:50:04 -197352.204125] AUTODETECT spr round 5 (radius: 25) [13:52:50 -179202.715937] SPR radius for FAST iterations: 25 (autodetect) [13:52:50 -179202.715937] Model parameter optimization (eps = 3.000000) [13:53:10 -179103.274125] FAST spr round 1 (radius: 25) [13:55:26 -139651.344161] FAST spr round 2 (radius: 25) [13:57:15 -134291.642897] FAST spr round 3 (radius: 25) [13:58:56 -133957.363236] FAST spr round 4 (radius: 25) [14:00:38 -133928.492324] FAST spr round 5 (radius: 25) [14:02:11 -133928.491251] Model parameter optimization (eps = 1.000000) [14:02:25 -133926.041789] SLOW spr round 1 (radius: 5) [14:04:18 -133897.797080] SLOW spr round 2 (radius: 5) [14:06:09 -133896.202468] SLOW spr round 3 (radius: 5) [14:07:58 -133892.971727] SLOW spr round 4 (radius: 5) [14:09:47 -133892.914243] SLOW spr round 5 (radius: 10) [14:11:37 -133892.106631] SLOW spr round 6 (radius: 5) [14:13:40 -133892.106280] SLOW spr round 7 (radius: 10) [14:15:36 -133892.106270] SLOW spr round 8 (radius: 15) [14:18:00 -133892.106017] SLOW spr round 9 (radius: 20) [14:21:13 -133892.106008] SLOW spr round 10 (radius: 25) [14:25:19 -133892.106000] Model parameter optimization (eps = 0.100000) [14:25:23] ML tree search #20, logLikelihood: -133892.077008 Optimized model parameters: Partition 0: noname Rate heterogeneity: FREE (4 cats, mean), weights&rates: (0.157267,0.243997) (0.208730,0.329528) (0.348935,0.936719) (0.285069,1.985453) 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 Final LogLikelihood: -133880.566765 AIC score: 271771.133530 / AICc score: 8315831.133530 / BIC score: 280122.796327 Free parameters (model + branch lengths): 2005 WARNING: Number of free parameters (K=2005) is larger than alignment size (n=476). This might lead to overfitting and compromise tree inference results! WARNING: Best ML tree contains 253 near-zero branches! Best ML tree with collapsed near-zero branches saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_040621/phylogeny-snakemake/results/P43403/3_mltree/P43403.raxml.bestTreeCollapsed Best ML tree saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_040621/phylogeny-snakemake/results/P43403/3_mltree/P43403.raxml.bestTree All ML trees saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_040621/phylogeny-snakemake/results/P43403/3_mltree/P43403.raxml.mlTrees Optimized model saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_040621/phylogeny-snakemake/results/P43403/3_mltree/P43403.raxml.bestModel Execution log saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_040621/phylogeny-snakemake/results/P43403/3_mltree/P43403.raxml.log Analysis started: 23-Jun-2021 08:52:58 / finished: 23-Jun-2021 23:18:22 Elapsed time: 51924.253 seconds (this run) / 148883.549 seconds (total with restarts)