RAxML-NG v. 1.0.2 released on 22.02.2021 by The Exelixis Lab. Developed by: Alexey M. Kozlov and Alexandros Stamatakis. Contributors: Diego Darriba, Tomas Flouri, Benoit Morel, Sarah Lutteropp, Ben Bettisworth. Latest version: https://github.com/amkozlov/raxml-ng Questions/problems/suggestions? Please visit: https://groups.google.com/forum/#!forum/raxml System: Intel(R) Xeon(R) Gold 6148 CPU @ 2.40GHz, 40 cores, 376 GB RAM RAxML-NG was called at 06-Jul-2021 08:52:16 as follows: raxml-ng --msa /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q96D31/2_msa/Q96D31_trimmed_msa.fasta --data-type AA --model LG4X --prefix /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q96D31/3_mltree/Q96D31 --seed 2 --threads 2 --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 (2 threads), thread pinning: OFF [00:00:00] Reading alignment from file: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q96D31/2_msa/Q96D31_trimmed_msa.fasta [00:00:00] Loaded alignment with 427 taxa and 124 sites WARNING: Sequences tr_B4QBS3_B4QBS3_DROSI_7240 and sp_Q9U6B8_CRCM1_DROME_7227 are exactly identical! WARNING: Sequences tr_B4QBS3_B4QBS3_DROSI_7240 and tr_B4HN91_B4HN91_DROSE_7238 are exactly identical! WARNING: Sequences tr_F1NZH8_F1NZH8_CHICK_9031 and sp_Q5ZL05_CRCM1_CHICK_9031 are exactly identical! WARNING: Sequences tr_F1NZH8_F1NZH8_CHICK_9031 and tr_G1MYT3_G1MYT3_MELGA_9103 are exactly identical! WARNING: Sequences tr_F1NZH8_F1NZH8_CHICK_9031 and tr_U3IB20_U3IB20_ANAPL_8839 are exactly identical! WARNING: Sequences tr_F1NZH8_F1NZH8_CHICK_9031 and tr_A0A226N985_A0A226N985_CALSU_9009 are exactly identical! WARNING: Sequences tr_F1NZH8_F1NZH8_CHICK_9031 and tr_A0A226PZ61_A0A226PZ61_COLVI_9014 are exactly identical! WARNING: Sequences sp_Q5ZLW2_ORAI2_CHICK_9031 and tr_G1MWN0_G1MWN0_MELGA_9103 are exactly identical! WARNING: Sequences sp_Q5ZLW2_ORAI2_CHICK_9031 and tr_F6VVM2_F6VVM2_MONDO_13616 are exactly identical! WARNING: Sequences sp_Q5ZLW2_ORAI2_CHICK_9031 and tr_G3W963_G3W963_SARHA_9305 are exactly identical! WARNING: Sequences sp_Q5ZLW2_ORAI2_CHICK_9031 and tr_U3I6U0_U3I6U0_ANAPL_8839 are exactly identical! WARNING: Sequences sp_Q5ZLW2_ORAI2_CHICK_9031 and tr_A0A093HVE8_A0A093HVE8_STRCA_441894 are exactly identical! WARNING: Sequences sp_Q5ZLW2_ORAI2_CHICK_9031 and tr_A0A099YTK7_A0A099YTK7_TINGU_94827 are exactly identical! WARNING: Sequences sp_Q5ZLW2_ORAI2_CHICK_9031 and tr_A0A226NB30_A0A226NB30_CALSU_9009 are exactly identical! WARNING: Sequences sp_Q5ZLW2_ORAI2_CHICK_9031 and tr_A0A226PGN0_A0A226PGN0_COLVI_9014 are exactly identical! WARNING: Sequences sp_Q6P8G8_ORAI3_MOUSE_10090 and tr_G3I7C3_G3I7C3_CRIGR_10029 are exactly identical! WARNING: Sequences sp_Q6P8G8_ORAI3_MOUSE_10090 and sp_Q6AXR8_ORAI3_RAT_10116 are exactly identical! WARNING: Sequences sp_Q6P8G8_ORAI3_MOUSE_10090 and tr_A0A1U7Q568_A0A1U7Q568_MESAU_10036 are exactly identical! WARNING: Sequences sp_Q6P8G8_ORAI3_MOUSE_10090 and tr_A0A2U4A8J2_A0A2U4A8J2_TURTR_9739 are exactly identical! WARNING: Sequences sp_Q6P8G8_ORAI3_MOUSE_10090 and tr_A0A2Y9E475_A0A2Y9E475_TRIMA_127582 are exactly identical! WARNING: Sequences sp_Q6P8G8_ORAI3_MOUSE_10090 and tr_A0A2Y9PL09_A0A2Y9PL09_DELLE_9749 are exactly identical! WARNING: Sequences sp_Q6P8G8_ORAI3_MOUSE_10090 and tr_A0A2Y9ESJ2_A0A2Y9ESJ2_PHYCD_9755 are exactly identical! WARNING: Sequences sp_Q6P8G8_ORAI3_MOUSE_10090 and tr_A0A384AGL9_A0A384AGL9_BALAS_310752 are exactly identical! WARNING: Sequences sp_Q8BH10_ORAI2_MOUSE_10090 and tr_G3HA36_G3HA36_CRIGR_10029 are exactly identical! WARNING: Sequences sp_Q8BH10_ORAI2_MOUSE_10090 and tr_B2ZDP9_B2ZDP9_RAT_10116 are exactly identical! WARNING: Sequences sp_Q8BWG9_CRCM1_MOUSE_10090 and tr_G3H247_G3H247_CRIGR_10029 are exactly identical! WARNING: Sequences sp_Q8BWG9_CRCM1_MOUSE_10090 and sp_Q5M848_CRCM1_RAT_10116 are exactly identical! WARNING: Sequences sp_Q8BWG9_CRCM1_MOUSE_10090 and tr_A0A1S3FRS3_A0A1S3FRS3_DIPOR_10020 are exactly identical! WARNING: Sequences sp_Q8BWG9_CRCM1_MOUSE_10090 and tr_A0A1U7R471_A0A1U7R471_MESAU_10036 are exactly identical! WARNING: Sequences tr_M3XSM9_M3XSM9_MUSPF_9669 and tr_G1PMJ1_G1PMJ1_MYOLU_59463 are exactly identical! WARNING: Sequences tr_M3XSM9_M3XSM9_MUSPF_9669 and tr_G1TJL6_G1TJL6_RABIT_9986 are exactly identical! WARNING: Sequences tr_M3XSM9_M3XSM9_MUSPF_9669 and tr_E2QZ47_E2QZ47_CANLF_9615 are exactly identical! WARNING: Sequences tr_M3XSM9_M3XSM9_MUSPF_9669 and tr_F6Q0G2_F6Q0G2_ORNAN_9258 are exactly identical! WARNING: Sequences tr_M3XSM9_M3XSM9_MUSPF_9669 and tr_F7G4P2_F7G4P2_MONDO_13616 are exactly identical! WARNING: Sequences tr_M3XSM9_M3XSM9_MUSPF_9669 and tr_F6Q600_F6Q600_HORSE_9796 are exactly identical! WARNING: Sequences tr_M3XSM9_M3XSM9_MUSPF_9669 and tr_G5AWN3_G5AWN3_HETGA_10181 are exactly identical! WARNING: Sequences tr_M3XSM9_M3XSM9_MUSPF_9669 and tr_G3TT70_G3TT70_LOXAF_9785 are exactly identical! WARNING: Sequences tr_M3XSM9_M3XSM9_MUSPF_9669 and tr_G1M735_G1M735_AILME_9646 are exactly identical! WARNING: Sequences tr_M3XSM9_M3XSM9_MUSPF_9669 and tr_L5KTR0_L5KTR0_PTEAL_9402 are exactly identical! WARNING: Sequences tr_M3XSM9_M3XSM9_MUSPF_9669 and tr_M3XCI4_M3XCI4_FELCA_9685 are exactly identical! WARNING: Sequences tr_M3XSM9_M3XSM9_MUSPF_9669 and tr_A0A1S3ASV2_A0A1S3ASV2_ERIEU_9365 are exactly identical! WARNING: Sequences tr_M3XSM9_M3XSM9_MUSPF_9669 and tr_A0A2U3VLQ3_A0A2U3VLQ3_ODORO_9708 are exactly identical! WARNING: Sequences tr_M3XSM9_M3XSM9_MUSPF_9669 and tr_A0A2U3YZH7_A0A2U3YZH7_LEPWE_9713 are exactly identical! WARNING: Sequences tr_M3XSM9_M3XSM9_MUSPF_9669 and tr_A0A2Y9DQT1_A0A2Y9DQT1_TRIMA_127582 are exactly identical! WARNING: Sequences tr_M3XSM9_M3XSM9_MUSPF_9669 and tr_A0A2Y9KP19_A0A2Y9KP19_ENHLU_391180 are exactly identical! WARNING: Sequences tr_M3YKK5_M3YKK5_MUSPF_9669 and tr_G1TRG3_G1TRG3_RABIT_9986 are exactly identical! WARNING: Sequences tr_M3YKK5_M3YKK5_MUSPF_9669 and tr_F6USF8_F6USF8_CANLF_9615 are exactly identical! WARNING: Sequences tr_M3YKK5_M3YKK5_MUSPF_9669 and tr_F6QFL4_F6QFL4_HORSE_9796 are exactly identical! WARNING: Sequences tr_M3YKK5_M3YKK5_MUSPF_9669 and tr_W5PE76_W5PE76_SHEEP_9940 are exactly identical! WARNING: Sequences tr_M3YKK5_M3YKK5_MUSPF_9669 and tr_A0A287D005_A0A287D005_ICTTR_43179 are exactly identical! WARNING: Sequences tr_M3YKK5_M3YKK5_MUSPF_9669 and tr_H0X506_H0X506_OTOGA_30611 are exactly identical! WARNING: Sequences tr_M3YKK5_M3YKK5_MUSPF_9669 and tr_G1LLZ7_G1LLZ7_AILME_9646 are exactly identical! WARNING: Sequences tr_M3YKK5_M3YKK5_MUSPF_9669 and tr_E1BLX3_E1BLX3_BOVIN_9913 are exactly identical! WARNING: Sequences tr_M3YKK5_M3YKK5_MUSPF_9669 and tr_A0A2I2V0U1_A0A2I2V0U1_FELCA_9685 are exactly identical! WARNING: Sequences tr_M3YKK5_M3YKK5_MUSPF_9669 and tr_A0A1S3A6B5_A0A1S3A6B5_ERIEU_9365 are exactly identical! WARNING: Sequences tr_M3YKK5_M3YKK5_MUSPF_9669 and tr_A0A1S3EQH2_A0A1S3EQH2_DIPOR_10020 are exactly identical! WARNING: Sequences tr_M3YKK5_M3YKK5_MUSPF_9669 and tr_A0A1U7U2V8_A0A1U7U2V8_TARSY_1868482 are exactly identical! WARNING: Sequences tr_M3YKK5_M3YKK5_MUSPF_9669 and tr_A0A2U3VQ40_A0A2U3VQ40_ODORO_9708 are exactly identical! WARNING: Sequences tr_M3YKK5_M3YKK5_MUSPF_9669 and tr_A0A2U3XEM0_A0A2U3XEM0_LEPWE_9713 are exactly identical! WARNING: Sequences tr_M3YKK5_M3YKK5_MUSPF_9669 and tr_A0A2Y9LET3_A0A2Y9LET3_ENHLU_391180 are exactly identical! WARNING: Sequences tr_M3YKK5_M3YKK5_MUSPF_9669 and tr_A0A384BN39_A0A384BN39_URSMA_29073 are exactly identical! WARNING: Sequences tr_G1RAA1_G1RAA1_NOMLE_61853 and tr_G3RIY1_G3RIY1_GORGO_9595 are exactly identical! WARNING: Sequences tr_G1RAA1_G1RAA1_NOMLE_61853 and tr_A0A2J8XU32_A0A2J8XU32_PONAB_9601 are exactly identical! WARNING: Sequences tr_G1RAA1_G1RAA1_NOMLE_61853 and tr_G1U3B1_G1U3B1_RABIT_9986 are exactly identical! WARNING: Sequences tr_G1RAA1_G1RAA1_NOMLE_61853 and tr_F6UZN2_F6UZN2_CANLF_9615 are exactly identical! WARNING: Sequences tr_G1RAA1_G1RAA1_NOMLE_61853 and tr_A0A2I3SMW8_A0A2I3SMW8_PANTR_9598 are exactly identical! WARNING: Sequences tr_G1RAA1_G1RAA1_NOMLE_61853 and tr_F7BG69_F7BG69_HORSE_9796 are exactly identical! WARNING: Sequences tr_G1RAA1_G1RAA1_NOMLE_61853 and tr_W5PYG5_W5PYG5_SHEEP_9940 are exactly identical! WARNING: Sequences tr_G1RAA1_G1RAA1_NOMLE_61853 and tr_A0A286XX89_A0A286XX89_CAVPO_10141 are exactly identical! WARNING: Sequences tr_G1RAA1_G1RAA1_NOMLE_61853 and sp_Q96SN7_ORAI2_HUMAN_9606 are exactly identical! WARNING: Sequences tr_G1RAA1_G1RAA1_NOMLE_61853 and tr_F7GY76_F7GY76_MACMU_9544 are exactly identical! WARNING: Sequences tr_G1RAA1_G1RAA1_NOMLE_61853 and tr_G5AXA7_G5AXA7_HETGA_10181 are exactly identical! WARNING: Sequences tr_G1RAA1_G1RAA1_NOMLE_61853 and tr_G3SV66_G3SV66_LOXAF_9785 are exactly identical! WARNING: Sequences tr_G1RAA1_G1RAA1_NOMLE_61853 and tr_F7I542_F7I542_CALJA_9483 are exactly identical! WARNING: Sequences tr_G1RAA1_G1RAA1_NOMLE_61853 and tr_F1RKF5_F1RKF5_PIG_9823 are exactly identical! WARNING: Sequences tr_G1RAA1_G1RAA1_NOMLE_61853 and tr_G1MAC9_G1MAC9_AILME_9646 are exactly identical! WARNING: Sequences tr_G1RAA1_G1RAA1_NOMLE_61853 and tr_G7P152_G7P152_MACFA_9541 are exactly identical! WARNING: Sequences tr_G1RAA1_G1RAA1_NOMLE_61853 and tr_E1BD39_E1BD39_BOVIN_9913 are exactly identical! WARNING: Sequences tr_G1RAA1_G1RAA1_NOMLE_61853 and tr_L5K8T7_L5K8T7_PTEAL_9402 are exactly identical! WARNING: Sequences tr_G1RAA1_G1RAA1_NOMLE_61853 and tr_M3XDP2_M3XDP2_FELCA_9685 are exactly identical! WARNING: Sequences tr_G1RAA1_G1RAA1_NOMLE_61853 and tr_A0A2I3LPN3_A0A2I3LPN3_PAPAN_9555 are exactly identical! WARNING: Sequences tr_G1RAA1_G1RAA1_NOMLE_61853 and tr_A0A091DTJ1_A0A091DTJ1_FUKDA_885580 are exactly identical! WARNING: Sequences tr_G1RAA1_G1RAA1_NOMLE_61853 and tr_A0A0D9RZQ9_A0A0D9RZQ9_CHLSB_60711 are exactly identical! WARNING: Sequences tr_G1RAA1_G1RAA1_NOMLE_61853 and tr_A0A2K5LVR3_A0A2K5LVR3_CERAT_9531 are exactly identical! WARNING: Sequences tr_G1RAA1_G1RAA1_NOMLE_61853 and tr_A0A2K6AMG3_A0A2K6AMG3_MACNE_9545 are exactly identical! WARNING: Sequences tr_G1RAA1_G1RAA1_NOMLE_61853 and tr_A0A2K5XH72_A0A2K5XH72_MANLE_9568 are exactly identical! WARNING: Sequences tr_G1RAA1_G1RAA1_NOMLE_61853 and tr_A0A2R9BE06_A0A2R9BE06_PANPA_9597 are exactly identical! WARNING: Sequences tr_G1RAA1_G1RAA1_NOMLE_61853 and tr_A0A2U3V2B0_A0A2U3V2B0_TURTR_9739 are exactly identical! WARNING: Sequences tr_G1RAA1_G1RAA1_NOMLE_61853 and tr_A0A2U3ZEG0_A0A2U3ZEG0_ODORO_9708 are exactly identical! WARNING: Sequences tr_G1RAA1_G1RAA1_NOMLE_61853 and tr_A0A2U3XR99_A0A2U3XR99_LEPWE_9713 are exactly identical! WARNING: Sequences tr_G1RAA1_G1RAA1_NOMLE_61853 and tr_A0A2Y9E2X5_A0A2Y9E2X5_TRIMA_127582 are exactly identical! WARNING: Sequences tr_G1RAA1_G1RAA1_NOMLE_61853 and tr_A0A2Y9SRX3_A0A2Y9SRX3_PHYCD_9755 are exactly identical! WARNING: Sequences tr_G1RAA1_G1RAA1_NOMLE_61853 and tr_A0A384AH20_A0A384AH20_BALAS_310752 are exactly identical! WARNING: Sequences tr_G1PZU7_G1PZU7_MYOLU_59463 and tr_I3LXM3_I3LXM3_ICTTR_43179 are exactly identical! WARNING: Sequences tr_G3SBY4_G3SBY4_GORGO_9595 and tr_H2NQQ8_H2NQQ8_PONAB_9601 are exactly identical! WARNING: Sequences tr_G3SBY4_G3SBY4_GORGO_9595 and tr_K7B6T1_K7B6T1_PANTR_9598 are exactly identical! WARNING: Sequences tr_G3SBY4_G3SBY4_GORGO_9595 and sp_Q9BRQ5_ORAI3_HUMAN_9606 are exactly identical! WARNING: Sequences tr_G3SBY4_G3SBY4_GORGO_9595 and tr_A0A1D5RK59_A0A1D5RK59_MACMU_9544 are exactly identical! WARNING: Sequences tr_G3SBY4_G3SBY4_GORGO_9595 and tr_F7I315_F7I315_CALJA_9483 are exactly identical! WARNING: Sequences tr_G3SBY4_G3SBY4_GORGO_9595 and tr_G7Q0Z1_G7Q0Z1_MACFA_9541 are exactly identical! WARNING: Sequences tr_G3SBY4_G3SBY4_GORGO_9595 and tr_A0A2I3MGP9_A0A2I3MGP9_PAPAN_9555 are exactly identical! WARNING: Sequences tr_G3SBY4_G3SBY4_GORGO_9595 and tr_A0A0D9R0H3_A0A0D9R0H3_CHLSB_60711 are exactly identical! WARNING: Sequences tr_G3SBY4_G3SBY4_GORGO_9595 and tr_A0A2K5MQE4_A0A2K5MQE4_CERAT_9531 are exactly identical! WARNING: Sequences tr_G3SBY4_G3SBY4_GORGO_9595 and tr_A0A2K6CAQ5_A0A2K6CAQ5_MACNE_9545 are exactly identical! WARNING: Sequences tr_G3SBY4_G3SBY4_GORGO_9595 and tr_A0A2K5Z8S0_A0A2K5Z8S0_MANLE_9568 are exactly identical! WARNING: Sequences tr_G3SBY4_G3SBY4_GORGO_9595 and tr_A0A2R9CSQ9_A0A2R9CSQ9_PANPA_9597 are exactly identical! WARNING: Sequences tr_H2NIX8_H2NIX8_PONAB_9601 and tr_H2Q730_H2Q730_PANTR_9598 are exactly identical! WARNING: Sequences tr_H2NIX8_H2NIX8_PONAB_9601 and tr_W5PVM9_W5PVM9_SHEEP_9940 are exactly identical! WARNING: Sequences tr_H2NIX8_H2NIX8_PONAB_9601 and sp_Q96D31_CRCM1_HUMAN_9606 are exactly identical! WARNING: Sequences tr_H2NIX8_H2NIX8_PONAB_9601 and tr_F7BNH0_F7BNH0_MACMU_9544 are exactly identical! WARNING: Sequences tr_H2NIX8_H2NIX8_PONAB_9601 and tr_F7IAH3_F7IAH3_CALJA_9483 are exactly identical! WARNING: Sequences tr_H2NIX8_H2NIX8_PONAB_9601 and tr_D3U7X2_D3U7X2_PIG_9823 are exactly identical! WARNING: Sequences tr_H2NIX8_H2NIX8_PONAB_9601 and tr_G8F4U5_G8F4U5_MACFA_9541 are exactly identical! WARNING: Sequences tr_H2NIX8_H2NIX8_PONAB_9601 and tr_A5PKA7_A5PKA7_BOVIN_9913 are exactly identical! WARNING: Sequences tr_H2NIX8_H2NIX8_PONAB_9601 and tr_A0A096N8L4_A0A096N8L4_PAPAN_9555 are exactly identical! WARNING: Sequences tr_H2NIX8_H2NIX8_PONAB_9601 and tr_A0A0D9S4P8_A0A0D9S4P8_CHLSB_60711 are exactly identical! WARNING: Sequences tr_H2NIX8_H2NIX8_PONAB_9601 and tr_A0A2K5P4D9_A0A2K5P4D9_CERAT_9531 are exactly identical! WARNING: Sequences tr_H2NIX8_H2NIX8_PONAB_9601 and tr_A0A2K5YR15_A0A2K5YR15_MANLE_9568 are exactly identical! WARNING: Sequences tr_H2NIX8_H2NIX8_PONAB_9601 and tr_A0A2R8ZXK4_A0A2R8ZXK4_PANPA_9597 are exactly identical! WARNING: Sequences tr_H2NIX8_H2NIX8_PONAB_9601 and tr_A0A2U3VAN5_A0A2U3VAN5_TURTR_9739 are exactly identical! WARNING: Sequences tr_H2NIX8_H2NIX8_PONAB_9601 and tr_A0A2Y9Q7S0_A0A2Y9Q7S0_DELLE_9749 are exactly identical! WARNING: Sequences tr_H2NIX8_H2NIX8_PONAB_9601 and tr_A0A2Y9FST4_A0A2Y9FST4_PHYCD_9755 are exactly identical! WARNING: Sequences tr_H2NIX8_H2NIX8_PONAB_9601 and tr_A0A384AQH0_A0A384AQH0_BALAS_310752 are exactly identical! WARNING: Sequences tr_N6W572_N6W572_DROPS_46245 and tr_B4GIU1_B4GIU1_DROPE_7234 are exactly identical! WARNING: Sequences tr_F6T596_F6T596_ORNAN_9258 and tr_F6XS98_F6XS98_MONDO_13616 are exactly identical! WARNING: Sequences tr_F6T596_F6T596_ORNAN_9258 and tr_G3WAU9_G3WAU9_SARHA_9305 are exactly identical! WARNING: Sequences tr_M4A2Y5_M4A2Y5_XIPMA_8083 and tr_A0A087YFH8_A0A087YFH8_POEFO_48698 are exactly identical! WARNING: Sequences tr_M4AI04_M4AI04_XIPMA_8083 and tr_A0A3B5KCH5_A0A3B5KCH5_TAKRU_31033 are exactly identical! WARNING: Sequences tr_M4AI04_M4AI04_XIPMA_8083 and tr_H3CUL1_H3CUL1_TETNG_99883 are exactly identical! WARNING: Sequences tr_M4AI04_M4AI04_XIPMA_8083 and tr_G3PXZ0_G3PXZ0_GASAC_69293 are exactly identical! WARNING: Sequences tr_M4AI04_M4AI04_XIPMA_8083 and tr_A0A087YPD7_A0A087YPD7_POEFO_48698 are exactly identical! WARNING: Sequences tr_M4AI04_M4AI04_XIPMA_8083 and tr_A0A2I4AUP9_A0A2I4AUP9_9TELE_52670 are exactly identical! WARNING: Sequences tr_M4AL64_M4AL64_XIPMA_8083 and tr_A0A087YG47_A0A087YG47_POEFO_48698 are exactly identical! WARNING: Sequences tr_A0A087ZUN8_A0A087ZUN8_APIME_7460 and tr_A0A2A3E6L3_A0A2A3E6L3_APICC_94128 are exactly identical! WARNING: Sequences tr_A0A088A6F8_A0A088A6F8_APIME_7460 and tr_A0A0N0BC83_A0A0N0BC83_9HYME_166423 are exactly identical! WARNING: Sequences tr_A0A088A6F8_A0A088A6F8_APIME_7460 and tr_A0A0L7R8M8_A0A0L7R8M8_9HYME_597456 are exactly identical! WARNING: Sequences tr_A0A088A6F8_A0A088A6F8_APIME_7460 and tr_A0A154PPF8_A0A154PPF8_9HYME_178035 are exactly identical! WARNING: Sequences tr_A0A088A6F8_A0A088A6F8_APIME_7460 and tr_A0A2A3E349_A0A2A3E349_APICC_94128 are exactly identical! WARNING: Sequences tr_A0A158NR30_A0A158NR30_ATTCE_12957 and tr_A0A151HYU7_A0A151HYU7_9HYME_520822 are exactly identical! WARNING: Sequences tr_I3JXM6_I3JXM6_ORENI_8128 and tr_H2SLE0_H2SLE0_TAKRU_31033 are exactly identical! WARNING: Sequences tr_A0A0K0J4G5_A0A0K0J4G5_BRUMA_6279 and tr_A0A0N4TT13_A0A0N4TT13_BRUPA_6280 are exactly identical! WARNING: Sequences tr_A0A0K0J4G5_A0A0K0J4G5_BRUMA_6279 and tr_A0A0R3QB02_A0A0R3QB02_9BILA_42155 are exactly identical! WARNING: Sequences tr_K7EWW1_K7EWW1_PELSI_13735 and tr_W5MCR0_W5MCR0_LEPOC_7918 are exactly identical! WARNING: Sequences tr_H0Z205_H0Z205_TAEGU_59729 and tr_U3K4E8_U3K4E8_FICAL_59894 are exactly identical! WARNING: Sequences tr_H0Z205_H0Z205_TAEGU_59729 and tr_A0A0Q3Q1W0_A0A0Q3Q1W0_AMAAE_12930 are exactly identical! WARNING: Sequences tr_H0Z205_H0Z205_TAEGU_59729 and tr_A0A091F6Q1_A0A091F6Q1_CORBR_85066 are exactly identical! WARNING: Sequences tr_H0Z205_H0Z205_TAEGU_59729 and tr_A0A091KBI6_A0A091KBI6_EGRGA_188379 are exactly identical! WARNING: Sequences tr_H0Z205_H0Z205_TAEGU_59729 and tr_A0A093QJ02_A0A093QJ02_9PASS_328815 are exactly identical! WARNING: Sequences tr_H0Z205_H0Z205_TAEGU_59729 and tr_A0A091VET8_A0A091VET8_NIPNI_128390 are exactly identical! WARNING: Sequences tr_H0Z205_H0Z205_TAEGU_59729 and tr_A0A087QHV0_A0A087QHV0_APTFO_9233 are exactly identical! WARNING: Sequences tr_H0Z205_H0Z205_TAEGU_59729 and tr_A0A091V7K1_A0A091V7K1_OPIHO_30419 are exactly identical! WARNING: Sequences tr_H0Z205_H0Z205_TAEGU_59729 and tr_A0A091GNE0_A0A091GNE0_9AVES_55661 are exactly identical! WARNING: Sequences tr_H0Z205_H0Z205_TAEGU_59729 and tr_A0A0A0AIS4_A0A0A0AIS4_CHAVO_50402 are exactly identical! WARNING: Sequences tr_H0Z205_H0Z205_TAEGU_59729 and tr_A0A091I2Z5_A0A091I2Z5_CALAN_9244 are exactly identical! WARNING: Sequences tr_H0Z205_H0Z205_TAEGU_59729 and tr_A0A218V1R2_A0A218V1R2_9PASE_299123 are exactly identical! WARNING: Sequences tr_H0Z6J9_H0Z6J9_TAEGU_59729 and tr_U3K3E0_U3K3E0_FICAL_59894 are exactly identical! WARNING: Sequences tr_H0Z6J9_H0Z6J9_TAEGU_59729 and tr_A0A0Q3PRG2_A0A0Q3PRG2_AMAAE_12930 are exactly identical! WARNING: Sequences tr_H0Z6J9_H0Z6J9_TAEGU_59729 and tr_A0A091FCF2_A0A091FCF2_CORBR_85066 are exactly identical! WARNING: Sequences tr_H0Z6J9_H0Z6J9_TAEGU_59729 and tr_A0A093Q3S1_A0A093Q3S1_9PASS_328815 are exactly identical! WARNING: Sequences tr_H0Z6J9_H0Z6J9_TAEGU_59729 and tr_A0A091UMH3_A0A091UMH3_NIPNI_128390 are exactly identical! WARNING: Sequences tr_H0Z6J9_H0Z6J9_TAEGU_59729 and tr_A0A087RB20_A0A087RB20_APTFO_9233 are exactly identical! WARNING: Sequences tr_H0Z6J9_H0Z6J9_TAEGU_59729 and tr_A0A091VN96_A0A091VN96_OPIHO_30419 are exactly identical! WARNING: Sequences tr_H0Z6J9_H0Z6J9_TAEGU_59729 and tr_A0A099ZGB6_A0A099ZGB6_TINGU_94827 are exactly identical! WARNING: Sequences tr_H0Z6J9_H0Z6J9_TAEGU_59729 and tr_A0A091G3K0_A0A091G3K0_9AVES_55661 are exactly identical! WARNING: Sequences tr_H0Z6J9_H0Z6J9_TAEGU_59729 and tr_A0A093HD03_A0A093HD03_DRYPU_118200 are exactly identical! WARNING: Sequences tr_H0Z6J9_H0Z6J9_TAEGU_59729 and tr_A0A091HIW0_A0A091HIW0_CALAN_9244 are exactly identical! WARNING: Sequences tr_H0Z6J9_H0Z6J9_TAEGU_59729 and tr_A0A218UMU5_A0A218UMU5_9PASE_299123 are exactly identical! WARNING: Sequences tr_F4WBV4_F4WBV4_ACREC_103372 and tr_A0A151XB59_A0A151XB59_9HYME_64791 are exactly identical! WARNING: Sequences tr_F4WBV4_F4WBV4_ACREC_103372 and tr_A0A195DI95_A0A195DI95_9HYME_471704 are exactly identical! WARNING: Sequences tr_F4WBV4_F4WBV4_ACREC_103372 and tr_A0A195BD97_A0A195BD97_9HYME_520822 are exactly identical! WARNING: Sequences tr_F4WBV4_F4WBV4_ACREC_103372 and tr_A0A195D4X5_A0A195D4X5_9HYME_456900 are exactly identical! WARNING: Sequences tr_F4WPB0_F4WPB0_ACREC_103372 and tr_A0A151WMB2_A0A151WMB2_9HYME_64791 are exactly identical! WARNING: Sequences tr_F4WPB0_F4WPB0_ACREC_103372 and tr_A0A195E5M5_A0A195E5M5_9HYME_471704 are exactly identical! WARNING: Sequences tr_F4WPB0_F4WPB0_ACREC_103372 and tr_A0A195EU86_A0A195EU86_9HYME_34720 are exactly identical! WARNING: Sequences tr_F4WPB0_F4WPB0_ACREC_103372 and tr_A0A195CAD3_A0A195CAD3_9HYME_456900 are exactly identical! WARNING: Sequences tr_E3MLB4_E3MLB4_CAERE_31234 and tr_A0A261AQW4_A0A261AQW4_9PELO_1503980 are exactly identical! WARNING: Sequences sp_Q616J1_ORAI_CAEBR_6238 and tr_A0A2G5UME7_A0A2G5UME7_9PELO_1611254 are exactly identical! WARNING: Sequences tr_Q17KQ6_Q17KQ6_AEDAE_7159 and tr_Q1DGX6_Q1DGX6_AEDAE_7159 are exactly identical! WARNING: Sequences tr_B3RJW9_B3RJW9_TRIAD_10228 and tr_A0A369S941_A0A369S941_9METZ_287889 are exactly identical! WARNING: Sequences tr_A0A044VCV3_A0A044VCV3_ONCVO_6282 and tr_A0A182EE33_A0A182EE33_ONCOC_42157 are exactly identical! WARNING: Sequences tr_A0A067RI76_A0A067RI76_ZOONE_136037 and tr_A0A2J7PX12_A0A2J7PX12_9NEOP_105785 are exactly identical! WARNING: Sequences tr_A0A0K0EYC8_A0A0K0EYC8_STRVS_75913 and tr_A0A0N5BJF6_A0A0N5BJF6_STREA_174720 are exactly identical! WARNING: Sequences tr_A0A0K0FCP0_A0A0K0FCP0_STRVS_75913 and tr_A0A0N5CGD7_A0A0N5CGD7_STREA_174720 are exactly identical! WARNING: Sequences tr_A0A151NSH5_A0A151NSH5_ALLMI_8496 and tr_A0A1U7RJ36_A0A1U7RJ36_ALLSI_38654 are exactly identical! WARNING: Sequences tr_A0A0N0PDJ4_A0A0N0PDJ4_PAPMA_76193 and tr_A0A0N1PHX0_A0A0N1PHX0_PAPXU_66420 are exactly identical! WARNING: Sequences tr_A0A0N0PDJ4_A0A0N0PDJ4_PAPMA_76193 and tr_A0A2A4JR04_A0A2A4JR04_HELVI_7102 are exactly identical! WARNING: Sequences tr_A0A194RNY3_A0A194RNY3_PAPMA_76193 and tr_A0A194QHP9_A0A194QHP9_PAPXU_66420 are exactly identical! WARNING: Sequences tr_A0A2I0M1T8_A0A2I0M1T8_COLLI_8932 and tr_A0A1V4K2Q6_A0A1V4K2Q6_PATFA_372326 are exactly identical! WARNING: Sequences tr_A0A2I0M8L0_A0A2I0M8L0_COLLI_8932 and tr_A0A1V4JSA0_A0A1V4JSA0_PATFA_372326 are exactly identical! WARNING: Sequences tr_A0A0V0RKB5_A0A0V0RKB5_9BILA_6336 and tr_A0A0V1D277_A0A0V1D277_TRIBR_45882 are exactly identical! WARNING: Sequences tr_A0A0V0RKB5_A0A0V0RKB5_9BILA_6336 and tr_A0A0V0WME7_A0A0V0WME7_9BILA_92179 are exactly identical! WARNING: Sequences tr_A0A0V0RKB5_A0A0V0RKB5_9BILA_6336 and tr_A0A0V0VIN1_A0A0V0VIN1_9BILA_181606 are exactly identical! WARNING: Sequences tr_A0A0V0RKB5_A0A0V0RKB5_9BILA_6336 and tr_A0A0V1LPV8_A0A0V1LPV8_9BILA_6335 are exactly identical! WARNING: Sequences tr_A0A0V0RKB5_A0A0V0RKB5_9BILA_6336 and tr_A0A0V0ZNY3_A0A0V0ZNY3_9BILA_990121 are exactly identical! WARNING: Sequences tr_A0A0V0RKB5_A0A0V0RKB5_9BILA_6336 and tr_A0A0V1P396_A0A0V1P396_9BILA_92180 are exactly identical! WARNING: Sequences tr_A0A0V0RKB5_A0A0V0RKB5_9BILA_6336 and tr_A0A0V0TUI4_A0A0V0TUI4_9BILA_144512 are exactly identical! WARNING: Sequences tr_A0A0V0YEF6_A0A0V0YEF6_TRIPS_6337 and tr_A0A0V1MRF4_A0A0V1MRF4_9BILA_268474 are exactly identical! WARNING: Sequences tr_A0A0V0YEF6_A0A0V0YEF6_TRIPS_6337 and tr_A0A0V1I901_A0A0V1I901_9BILA_268475 are exactly identical! WARNING: Sequences tr_A0A1S3CTZ2_A0A1S3CTZ2_DIACI_121845 and tr_A0A3Q0IJD5_A0A3Q0IJD5_DIACI_121845 are exactly identical! WARNING: Sequences tr_A0A1S3LPE6_A0A1S3LPE6_SALSA_8030 and tr_A0A060WB79_A0A060WB79_ONCMY_8022 are exactly identical! WARNING: Sequences tr_A0A1S3LSK7_A0A1S3LSK7_SALSA_8030 and tr_A0A060VQD5_A0A060VQD5_ONCMY_8022 are exactly identical! WARNING: Sequences tr_A0A1S3LSK7_A0A1S3LSK7_SALSA_8030 and tr_A0A060YMN1_A0A060YMN1_ONCMY_8022 are exactly identical! WARNING: Sequences tr_A0A1S3NK77_A0A1S3NK77_SALSA_8030 and tr_A0A060VN40_A0A060VN40_ONCMY_8022 are exactly identical! WARNING: Sequences tr_A0A1S3PHW9_A0A1S3PHW9_SALSA_8030 and tr_A0A060WEB6_A0A060WEB6_ONCMY_8022 are exactly identical! WARNING: Sequences tr_A0A1L8H616_A0A1L8H616_XENLA_8355 and tr_A0A1L8HDQ3_A0A1L8HDQ3_XENLA_8355 are exactly identical! WARNING: Duplicate sequences found: 205 NOTE: Reduced alignment (with duplicates and gap-only sites/taxa removed) NOTE: was saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q96D31/3_mltree/Q96D31.raxml.reduced.phy Alignment comprises 1 partitions and 124 patterns Partition 0: noname Model: LG4X+R4 Alignment sites / patterns: 124 / 124 Gaps: 1.68 % Invariant sites: 0.81 % NOTE: Binary MSA file created: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q96D31/3_mltree/Q96D31.raxml.rba Parallelization scheme autoconfig: 2 worker(s) x 1 thread(s) Parallel reduction/worker buffer size: 1 KB / 0 KB [00:00:00] Generating 20 random starting tree(s) with 427 taxa [00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 124 / 9920 [00:00:00] Data distribution: max. searches per worker: 10 Starting ML tree search with 20 distinct starting trees [00:00:00 -55862.378280] Initial branch length optimization [00:00:01 -43426.480633] Model parameter optimization (eps = 10.000000) [00:00:22 -43224.564841] AUTODETECT spr round 1 (radius: 5) [00:00:49 -26227.255568] AUTODETECT spr round 2 (radius: 10) [00:01:16 -18917.281666] AUTODETECT spr round 3 (radius: 15) [00:01:47 -14796.310569] AUTODETECT spr round 4 (radius: 20) [00:02:22 -13257.308140] AUTODETECT spr round 5 (radius: 25) [00:03:00 -13044.146070] SPR radius for FAST iterations: 25 (autodetect) [00:03:00 -13044.146070] Model parameter optimization (eps = 3.000000) [00:03:11 -12958.295435] FAST spr round 1 (radius: 25) [00:03:40 -11596.826107] FAST spr round 2 (radius: 25) [00:04:03 -11435.012931] FAST spr round 3 (radius: 25) [00:04:22 -11432.433196] FAST spr round 4 (radius: 25) [00:04:40 -11432.432815] Model parameter optimization (eps = 1.000000) [00:04:48 -11430.359897] SLOW spr round 1 (radius: 5) [00:05:13 -11426.668351] SLOW spr round 2 (radius: 5) [00:05:36 -11426.667065] SLOW spr round 3 (radius: 10) [00:06:03 -11424.970076] SLOW spr round 4 (radius: 5) [00:06:38 -11424.636575] SLOW spr round 5 (radius: 5) [00:07:07 -11424.636561] SLOW spr round 6 (radius: 10) [00:07:35 -11423.818520] SLOW spr round 7 (radius: 5) [00:08:09 -11423.729223] SLOW spr round 8 (radius: 10) [00:08:42 -11423.728439] SLOW spr round 9 (radius: 15) [00:09:26 -11423.463484] SLOW spr round 10 (radius: 5) [00:10:01 -11423.463421] SLOW spr round 11 (radius: 10) [00:10:34 -11423.463413] SLOW spr round 12 (radius: 15) [00:11:16 -11423.463408] SLOW spr round 13 (radius: 20) [00:12:07 -11421.874193] SLOW spr round 14 (radius: 5) [00:12:16] [worker #1] ML tree search #2, logLikelihood: -11415.262719 [00:12:42 -11421.868303] SLOW spr round 15 (radius: 10) [00:13:18 -11421.867870] SLOW spr round 16 (radius: 15) [00:13:59 -11421.867846] SLOW spr round 17 (radius: 20) [00:14:49 -11421.867842] SLOW spr round 18 (radius: 25) [00:15:42 -11421.867839] Model parameter optimization (eps = 0.100000) [00:15:45] [worker #0] ML tree search #1, logLikelihood: -11421.830019 [00:15:45 -55492.099484] Initial branch length optimization [00:15:46 -43077.527131] Model parameter optimization (eps = 10.000000) [00:16:14 -42688.000248] AUTODETECT spr round 1 (radius: 5) [00:16:42 -24982.793767] AUTODETECT spr round 2 (radius: 10) [00:17:10 -18376.058401] AUTODETECT spr round 3 (radius: 15) [00:17:44 -14374.074357] AUTODETECT spr round 4 (radius: 20) [00:18:22 -13276.687984] AUTODETECT spr round 5 (radius: 25) [00:18:59 -13220.691320] SPR radius for FAST iterations: 25 (autodetect) [00:18:59 -13220.691320] Model parameter optimization (eps = 3.000000) [00:19:10 -13191.294628] FAST spr round 1 (radius: 25) [00:19:40 -11617.627377] FAST spr round 2 (radius: 25) [00:20:06 -11437.739885] FAST spr round 3 (radius: 25) [00:20:26 -11431.871590] FAST spr round 4 (radius: 25) [00:20:45 -11428.587337] FAST spr round 5 (radius: 25) [00:21:03 -11428.586969] Model parameter optimization (eps = 1.000000) [00:21:11 -11426.506724] SLOW spr round 1 (radius: 5) [00:21:37 -11422.203908] SLOW spr round 2 (radius: 5) [00:21:38] [worker #1] ML tree search #4, logLikelihood: -11418.677700 [00:22:01 -11422.089705] SLOW spr round 3 (radius: 5) [00:22:24 -11422.089383] SLOW spr round 4 (radius: 10) [00:22:50 -11422.089298] SLOW spr round 5 (radius: 15) [00:23:35 -11422.089272] SLOW spr round 6 (radius: 20) [00:24:22 -11421.944357] SLOW spr round 7 (radius: 5) [00:24:59 -11421.578897] SLOW spr round 8 (radius: 5) [00:25:30 -11421.578896] SLOW spr round 9 (radius: 10) [00:26:01 -11419.168655] SLOW spr round 10 (radius: 5) [00:26:36 -11418.877688] SLOW spr round 11 (radius: 5) [00:27:05 -11418.877223] SLOW spr round 12 (radius: 10) [00:27:32 -11418.876997] SLOW spr round 13 (radius: 15) [00:28:19 -11418.876995] SLOW spr round 14 (radius: 20) [00:29:09 -11418.876993] SLOW spr round 15 (radius: 25) [00:30:02 -11418.876991] Model parameter optimization (eps = 0.100000) [00:30:05] [worker #0] ML tree search #3, logLikelihood: -11418.859582 [00:30:05 -55241.551057] Initial branch length optimization [00:30:06 -43118.695083] Model parameter optimization (eps = 10.000000) [00:30:25 -42758.300188] AUTODETECT spr round 1 (radius: 5) [00:30:52 -25972.320163] AUTODETECT spr round 2 (radius: 10) [00:31:19 -19600.633564] AUTODETECT spr round 3 (radius: 15) [00:31:49 -14576.084561] AUTODETECT spr round 4 (radius: 20) [00:32:25 -13430.783511] AUTODETECT spr round 5 (radius: 25) [00:33:09 -13115.584539] SPR radius for FAST iterations: 25 (autodetect) [00:33:09 -13115.584539] Model parameter optimization (eps = 3.000000) [00:33:19 -13077.043686] FAST spr round 1 (radius: 25) [00:33:44 -11492.871812] FAST spr round 2 (radius: 25) [00:33:48] [worker #1] ML tree search #6, logLikelihood: -11421.097180 [00:34:06 -11431.688461] FAST spr round 3 (radius: 25) [00:34:25 -11429.112065] FAST spr round 4 (radius: 25) [00:34:44 -11429.004184] FAST spr round 5 (radius: 25) [00:35:03 -11428.750781] FAST spr round 6 (radius: 25) [00:35:21 -11428.750607] Model parameter optimization (eps = 1.000000) [00:35:30 -11426.792799] SLOW spr round 1 (radius: 5) [00:35:56 -11425.249950] SLOW spr round 2 (radius: 5) [00:36:21 -11424.579793] SLOW spr round 3 (radius: 5) [00:36:45 -11424.579516] SLOW spr round 4 (radius: 10) [00:37:12 -11424.399852] SLOW spr round 5 (radius: 5) [00:37:47 -11424.126696] SLOW spr round 6 (radius: 5) [00:38:17 -11424.126694] SLOW spr round 7 (radius: 10) [00:38:44 -11424.126694] SLOW spr round 8 (radius: 15) [00:39:31 -11424.014688] SLOW spr round 9 (radius: 5) [00:40:06 -11424.014688] SLOW spr round 10 (radius: 10) [00:40:39 -11423.953088] SLOW spr round 11 (radius: 15) [00:41:23 -11423.953087] SLOW spr round 12 (radius: 20) [00:42:17 -11423.953086] SLOW spr round 13 (radius: 25) [00:42:50] [worker #1] ML tree search #8, logLikelihood: -11412.314612 [00:43:11 -11423.953086] Model parameter optimization (eps = 0.100000) [00:43:15] [worker #0] ML tree search #5, logLikelihood: -11423.906120 [00:43:15 -55547.199023] Initial branch length optimization [00:43:15 -42974.988589] Model parameter optimization (eps = 10.000000) [00:43:36 -42651.871061] AUTODETECT spr round 1 (radius: 5) [00:44:03 -26626.428771] AUTODETECT spr round 2 (radius: 10) [00:44:30 -19146.016109] AUTODETECT spr round 3 (radius: 15) [00:45:02 -16486.875498] AUTODETECT spr round 4 (radius: 20) [00:45:40 -14703.119316] AUTODETECT spr round 5 (radius: 25) [00:46:19 -13744.750500] SPR radius for FAST iterations: 25 (autodetect) [00:46:19 -13744.750500] Model parameter optimization (eps = 3.000000) [00:46:29 -13689.467588] FAST spr round 1 (radius: 25) [00:47:00 -11559.498827] FAST spr round 2 (radius: 25) [00:47:23 -11455.239033] FAST spr round 3 (radius: 25) [00:47:43 -11451.024779] FAST spr round 4 (radius: 25) [00:48:05 -11446.130358] FAST spr round 5 (radius: 25) [00:48:24 -11446.130223] Model parameter optimization (eps = 1.000000) [00:48:28 -11445.354220] SLOW spr round 1 (radius: 5) [00:48:53 -11443.819639] SLOW spr round 2 (radius: 5) [00:49:17 -11443.818030] SLOW spr round 3 (radius: 10) [00:49:43 -11443.777558] SLOW spr round 4 (radius: 15) [00:50:26 -11421.870666] SLOW spr round 5 (radius: 5) [00:51:00 -11421.510914] SLOW spr round 6 (radius: 5) [00:51:30 -11421.510902] SLOW spr round 7 (radius: 10) [00:51:59 -11421.510880] SLOW spr round 8 (radius: 15) [00:52:40 -11421.510880] SLOW spr round 9 (radius: 20) [00:53:33 -11421.510880] SLOW spr round 10 (radius: 25) [00:54:26 -11421.510880] Model parameter optimization (eps = 0.100000) [00:54:30] [worker #0] ML tree search #7, logLikelihood: -11421.491323 [00:54:30 -55850.606063] Initial branch length optimization [00:54:31 -43665.687490] Model parameter optimization (eps = 10.000000) [00:54:45] [worker #1] ML tree search #10, logLikelihood: -11421.455869 [00:54:50 -43348.752389] AUTODETECT spr round 1 (radius: 5) [00:55:17 -23983.834630] AUTODETECT spr round 2 (radius: 10) [00:55:44 -19020.938814] AUTODETECT spr round 3 (radius: 15) [00:56:16 -15397.419700] AUTODETECT spr round 4 (radius: 20) [00:56:55 -13366.106347] AUTODETECT spr round 5 (radius: 25) [00:57:45 -13156.375398] SPR radius for FAST iterations: 25 (autodetect) [00:57:45 -13156.375398] Model parameter optimization (eps = 3.000000) [00:57:55 -13102.450030] FAST spr round 1 (radius: 25) [00:58:19 -11521.603562] FAST spr round 2 (radius: 25) [00:58:41 -11443.870766] FAST spr round 3 (radius: 25) [00:58:59 -11442.449636] FAST spr round 4 (radius: 25) [00:59:17 -11442.449571] Model parameter optimization (eps = 1.000000) [00:59:24 -11441.280040] SLOW spr round 1 (radius: 5) [00:59:48 -11437.441833] SLOW spr round 2 (radius: 5) [01:00:11 -11437.440235] SLOW spr round 3 (radius: 10) [01:00:37 -11437.440048] SLOW spr round 4 (radius: 15) [01:01:28 -11435.830992] SLOW spr round 5 (radius: 5) [01:02:04 -11435.514250] SLOW spr round 6 (radius: 5) [01:02:33 -11435.514249] SLOW spr round 7 (radius: 10) [01:03:02 -11435.514249] SLOW spr round 8 (radius: 15) [01:03:50 -11435.514249] SLOW spr round 9 (radius: 20) [01:04:49 -11435.514249] SLOW spr round 10 (radius: 25) [01:05:48 -11435.514249] Model parameter optimization (eps = 0.100000) [01:05:51] [worker #0] ML tree search #9, logLikelihood: -11435.482639 [01:05:51 -56139.306719] Initial branch length optimization [01:05:51 -43619.207864] Model parameter optimization (eps = 10.000000) [01:06:08 -43279.237455] AUTODETECT spr round 1 (radius: 5) [01:06:35 -26386.225390] AUTODETECT spr round 2 (radius: 10) [01:07:02 -20241.308853] AUTODETECT spr round 3 (radius: 15) [01:07:34 -15034.586493] AUTODETECT spr round 4 (radius: 20) [01:08:14 -13749.836923] AUTODETECT spr round 5 (radius: 25) [01:08:54 -13694.344186] SPR radius for FAST iterations: 25 (autodetect) [01:08:54 -13694.344186] Model parameter optimization (eps = 3.000000) [01:09:05 -13647.967102] FAST spr round 1 (radius: 25) [01:09:35 -11604.232679] FAST spr round 2 (radius: 25) [01:09:51] [worker #1] ML tree search #12, logLikelihood: -11416.483122 [01:10:01 -11437.816212] FAST spr round 3 (radius: 25) [01:10:22 -11429.269066] FAST spr round 4 (radius: 25) [01:10:43 -11429.022030] FAST spr round 5 (radius: 25) [01:11:03 -11429.021665] Model parameter optimization (eps = 1.000000) [01:11:10 -11426.080882] SLOW spr round 1 (radius: 5) [01:11:36 -11421.455234] SLOW spr round 2 (radius: 5) [01:12:00 -11416.507569] SLOW spr round 3 (radius: 5) [01:12:23 -11416.507156] SLOW spr round 4 (radius: 10) [01:12:49 -11416.316466] SLOW spr round 5 (radius: 5) [01:13:23 -11415.927703] SLOW spr round 6 (radius: 5) [01:13:51 -11415.927699] SLOW spr round 7 (radius: 10) [01:14:18 -11415.927698] SLOW spr round 8 (radius: 15) [01:15:04 -11415.927697] SLOW spr round 9 (radius: 20) [01:15:57 -11415.781352] SLOW spr round 10 (radius: 5) [01:16:33 -11415.781042] SLOW spr round 11 (radius: 10) [01:17:08 -11415.781013] SLOW spr round 12 (radius: 15) [01:17:49 -11415.781009] SLOW spr round 13 (radius: 20) [01:18:45 -11415.781008] SLOW spr round 14 (radius: 25) [01:19:44 -11414.765035] SLOW spr round 15 (radius: 5) [01:20:19 -11414.764971] SLOW spr round 16 (radius: 10) [01:20:55 -11414.764971] SLOW spr round 17 (radius: 15) [01:21:37 -11414.764971] SLOW spr round 18 (radius: 20) [01:22:33 -11414.442973] SLOW spr round 19 (radius: 5) [01:23:09 -11414.442972] SLOW spr round 20 (radius: 10) [01:23:45 -11411.364521] SLOW spr round 21 (radius: 5) [01:24:17 -11411.364059] SLOW spr round 22 (radius: 10) [01:24:48 -11411.364030] SLOW spr round 23 (radius: 15) [01:25:01] [worker #1] ML tree search #14, logLikelihood: -11415.332096 [01:25:30 -11411.364029] SLOW spr round 24 (radius: 20) [01:26:27 -11411.364029] SLOW spr round 25 (radius: 25) [01:27:27 -11411.364029] Model parameter optimization (eps = 0.100000) [01:27:31] [worker #0] ML tree search #11, logLikelihood: -11411.302268 [01:27:31 -55575.242479] Initial branch length optimization [01:27:32 -43032.930718] Model parameter optimization (eps = 10.000000) [01:27:49 -42769.758146] AUTODETECT spr round 1 (radius: 5) [01:28:15 -27070.270456] AUTODETECT spr round 2 (radius: 10) [01:28:41 -19517.069263] AUTODETECT spr round 3 (radius: 15) [01:29:14 -16212.659919] AUTODETECT spr round 4 (radius: 20) [01:29:52 -15732.747381] AUTODETECT spr round 5 (radius: 25) [01:30:32 -14432.326938] SPR radius for FAST iterations: 25 (autodetect) [01:30:32 -14432.326938] Model parameter optimization (eps = 3.000000) [01:30:41 -14386.672683] FAST spr round 1 (radius: 25) [01:31:12 -12032.933464] FAST spr round 2 (radius: 25) [01:31:38 -11481.220597] FAST spr round 3 (radius: 25) [01:32:02 -11427.897640] FAST spr round 4 (radius: 25) [01:32:21 -11425.972525] FAST spr round 5 (radius: 25) [01:32:39 -11424.756495] FAST spr round 6 (radius: 25) [01:32:57 -11424.756485] Model parameter optimization (eps = 1.000000) [01:33:04 -11421.741823] SLOW spr round 1 (radius: 5) [01:33:29 -11420.204464] SLOW spr round 2 (radius: 5) [01:33:52 -11420.128985] SLOW spr round 3 (radius: 10) [01:34:19 -11414.836901] SLOW spr round 4 (radius: 5) [01:34:52 -11414.450702] SLOW spr round 5 (radius: 5) [01:35:20 -11414.450679] SLOW spr round 6 (radius: 10) [01:35:49 -11414.450675] SLOW spr round 7 (radius: 15) [01:36:32] [worker #1] ML tree search #16, logLikelihood: -11413.307857 [01:36:35 -11414.450675] SLOW spr round 8 (radius: 20) [01:37:25 -11414.450674] SLOW spr round 9 (radius: 25) [01:38:19 -11414.450674] Model parameter optimization (eps = 0.100000) [01:38:24] [worker #0] ML tree search #13, logLikelihood: -11414.319185 [01:38:24 -55637.945495] Initial branch length optimization [01:38:25 -43399.235351] Model parameter optimization (eps = 10.000000) [01:38:42 -43044.769922] AUTODETECT spr round 1 (radius: 5) [01:39:09 -26017.777606] AUTODETECT spr round 2 (radius: 10) [01:39:37 -19647.430240] AUTODETECT spr round 3 (radius: 15) [01:40:10 -16477.832839] AUTODETECT spr round 4 (radius: 20) [01:40:47 -14025.619047] AUTODETECT spr round 5 (radius: 25) [01:41:25 -14003.651090] SPR radius for FAST iterations: 25 (autodetect) [01:41:25 -14003.651090] Model parameter optimization (eps = 3.000000) [01:41:35 -13963.246200] FAST spr round 1 (radius: 25) [01:42:02 -11567.887355] FAST spr round 2 (radius: 25) [01:42:24 -11449.095846] FAST spr round 3 (radius: 25) [01:42:45 -11428.757774] FAST spr round 4 (radius: 25) [01:43:03 -11426.693888] FAST spr round 5 (radius: 25) [01:43:20 -11426.693880] Model parameter optimization (eps = 1.000000) [01:43:25 -11425.533899] SLOW spr round 1 (radius: 5) [01:43:49 -11422.093679] SLOW spr round 2 (radius: 5) [01:44:12 -11422.091542] SLOW spr round 3 (radius: 10) [01:44:38 -11422.091236] SLOW spr round 4 (radius: 15) [01:45:25 -11421.253591] SLOW spr round 5 (radius: 5) [01:45:59 -11421.215524] SLOW spr round 6 (radius: 10) [01:46:32 -11419.312047] SLOW spr round 7 (radius: 5) [01:47:03 -11418.994455] SLOW spr round 8 (radius: 5) [01:47:31 -11418.994058] SLOW spr round 9 (radius: 10) [01:47:57 -11418.994045] SLOW spr round 10 (radius: 15) [01:48:42 -11418.993972] SLOW spr round 11 (radius: 20) [01:49:13] [worker #1] ML tree search #18, logLikelihood: -11419.558172 [01:49:35 -11418.993960] SLOW spr round 12 (radius: 25) [01:50:28 -11418.993949] Model parameter optimization (eps = 0.100000) [01:50:30] [worker #0] ML tree search #15, logLikelihood: -11418.959871 [01:50:30 -55495.277775] Initial branch length optimization [01:50:31 -43427.720856] Model parameter optimization (eps = 10.000000) [01:50:49 -43112.793298] AUTODETECT spr round 1 (radius: 5) [01:51:15 -25320.917686] AUTODETECT spr round 2 (radius: 10) [01:51:42 -19250.250754] AUTODETECT spr round 3 (radius: 15) [01:52:14 -16010.929465] AUTODETECT spr round 4 (radius: 20) [01:52:49 -15070.436323] AUTODETECT spr round 5 (radius: 25) [01:53:28 -14636.707316] SPR radius for FAST iterations: 25 (autodetect) [01:53:28 -14636.707316] Model parameter optimization (eps = 3.000000) [01:53:38 -14596.838560] FAST spr round 1 (radius: 25) [01:54:04 -11798.414924] FAST spr round 2 (radius: 25) [01:54:28 -11518.631820] FAST spr round 3 (radius: 25) [01:54:50 -11425.532747] FAST spr round 4 (radius: 25) [01:55:10 -11425.532462] Model parameter optimization (eps = 1.000000) [01:55:15 -11424.588327] SLOW spr round 1 (radius: 5) [01:55:41 -11421.523404] SLOW spr round 2 (radius: 5) [01:56:05 -11421.494644] SLOW spr round 3 (radius: 10) [01:56:31 -11420.833080] SLOW spr round 4 (radius: 5) [01:57:06 -11420.481566] SLOW spr round 5 (radius: 5) [01:57:35 -11420.481529] SLOW spr round 6 (radius: 10) [01:58:03 -11420.481519] SLOW spr round 7 (radius: 15) [01:58:47 -11418.853414] SLOW spr round 8 (radius: 5) [01:59:22 -11418.853395] SLOW spr round 9 (radius: 10) [01:59:55 -11418.853390] SLOW spr round 10 (radius: 15) [02:00:36 -11418.853389] SLOW spr round 11 (radius: 20) [02:01:28 -11418.853388] SLOW spr round 12 (radius: 25) [02:02:21 -11418.853386] Model parameter optimization (eps = 0.100000) [02:02:26] [worker #0] ML tree search #17, logLikelihood: -11418.817756 [02:02:26 -55906.756483] Initial branch length optimization [02:02:26 -43556.839186] Model parameter optimization (eps = 10.000000) [02:02:43 -43184.534576] AUTODETECT spr round 1 (radius: 5) [02:03:11 -26631.795891] AUTODETECT spr round 2 (radius: 10) [02:03:38 -19878.705093] AUTODETECT spr round 3 (radius: 15) [02:04:10 -16946.790865] AUTODETECT spr round 4 (radius: 20) [02:04:48 -14038.551969] AUTODETECT spr round 5 (radius: 25) [02:05:25 -13735.126549] SPR radius for FAST iterations: 25 (autodetect) [02:05:25 -13735.126549] Model parameter optimization (eps = 3.000000) [02:05:34 -13664.859615] FAST spr round 1 (radius: 25) [02:05:52] [worker #1] ML tree search #20, logLikelihood: -11421.270776 [02:05:59 -11743.491290] FAST spr round 2 (radius: 25) [02:06:22 -11441.127024] FAST spr round 3 (radius: 25) [02:06:43 -11426.660858] FAST spr round 4 (radius: 25) [02:07:00 -11425.806468] FAST spr round 5 (radius: 25) [02:07:18 -11425.806204] Model parameter optimization (eps = 1.000000) [02:07:27 -11421.142596] SLOW spr round 1 (radius: 5) [02:07:52 -11420.487007] SLOW spr round 2 (radius: 5) [02:08:15 -11420.484641] SLOW spr round 3 (radius: 10) [02:08:40 -11420.484307] SLOW spr round 4 (radius: 15) [02:09:24 -11420.484274] SLOW spr round 5 (radius: 20) [02:10:15 -11420.484270] SLOW spr round 6 (radius: 25) [02:11:08 -11420.484268] Model parameter optimization (eps = 0.100000) [02:11:09] [worker #0] ML tree search #19, logLikelihood: -11420.481982 Optimized model parameters: Partition 0: noname Rate heterogeneity: FREE (4 cats, mean), weights&rates: (0.322047,0.418318) (0.457230,0.775102) (0.204599,1.844844) (0.016124,8.274895) 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: -11411.302268 AIC score: 24536.604535 / AICc score: 1495148.604535 / BIC score: 26953.585837 Free parameters (model + branch lengths): 857 WARNING: Number of free parameters (K=857) is larger than alignment size (n=124). This might lead to overfitting and compromise tree inference results! Best ML tree saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q96D31/3_mltree/Q96D31.raxml.bestTree All ML trees saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q96D31/3_mltree/Q96D31.raxml.mlTrees Optimized model saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q96D31/3_mltree/Q96D31.raxml.bestModel Execution log saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q96D31/3_mltree/Q96D31.raxml.log Analysis started: 06-Jul-2021 08:52:16 / finished: 06-Jul-2021 11:03:26 Elapsed time: 7869.646 seconds Consumed energy: 605.450 Wh (= 3 km in an electric car, or 15 km with an e-scooter!)