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 08-Jul-2021 21:27:15 as follows: raxml-ng --msa /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/P09651/2_msa/P09651_trimmed_msa.fasta --data-type AA --model LG4X --prefix /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/P09651/3_mltree/P09651 --seed 2 --threads 6 --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 (6 threads), thread pinning: OFF [00:00:00] Reading alignment from file: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/P09651/2_msa/P09651_trimmed_msa.fasta [00:00:00] Loaded alignment with 1001 taxa and 282 sites WARNING: Sequences tr_B4QWS9_B4QWS9_DROSI_7240 and tr_B4IC01_B4IC01_DROSE_7238 are exactly identical! WARNING: Sequences tr_E1BZE6_E1BZE6_CHICK_9031 and tr_G1NBB9_G1NBB9_MELGA_9103 are exactly identical! WARNING: Sequences tr_E1BZE6_E1BZE6_CHICK_9031 and tr_U3IQ39_U3IQ39_ANAPL_8839 are exactly identical! WARNING: Sequences tr_E1BZE6_E1BZE6_CHICK_9031 and tr_A0A218V0B2_A0A218V0B2_9PASE_299123 are exactly identical! WARNING: Sequences sp_O88569_ROA2_MOUSE_10090 and tr_M3XZL8_M3XZL8_MUSPF_9669 are exactly identical! WARNING: Sequences sp_O88569_ROA2_MOUSE_10090 and tr_G1RY30_G1RY30_NOMLE_61853 are exactly identical! WARNING: Sequences sp_O88569_ROA2_MOUSE_10090 and tr_G3RLL0_G3RLL0_GORGO_9595 are exactly identical! WARNING: Sequences sp_O88569_ROA2_MOUSE_10090 and tr_A0A2J8VDV7_A0A2J8VDV7_PONAB_9601 are exactly identical! WARNING: Sequences sp_O88569_ROA2_MOUSE_10090 and tr_F1Q1K6_F1Q1K6_CANLF_9615 are exactly identical! WARNING: Sequences sp_O88569_ROA2_MOUSE_10090 and tr_H2QUA8_H2QUA8_PANTR_9598 are exactly identical! WARNING: Sequences sp_O88569_ROA2_MOUSE_10090 and tr_F6VYB1_F6VYB1_HORSE_9796 are exactly identical! WARNING: Sequences sp_O88569_ROA2_MOUSE_10090 and tr_W5PK95_W5PK95_SHEEP_9940 are exactly identical! WARNING: Sequences sp_O88569_ROA2_MOUSE_10090 and tr_A0A287D861_A0A287D861_ICTTR_43179 are exactly identical! WARNING: Sequences sp_O88569_ROA2_MOUSE_10090 and tr_H0XD32_H0XD32_OTOGA_30611 are exactly identical! WARNING: Sequences sp_O88569_ROA2_MOUSE_10090 and tr_A0A286XS96_A0A286XS96_CAVPO_10141 are exactly identical! WARNING: Sequences sp_O88569_ROA2_MOUSE_10090 and sp_P22626_ROA2_HUMAN_9606 are exactly identical! WARNING: Sequences sp_O88569_ROA2_MOUSE_10090 and tr_I2CYL4_I2CYL4_MACMU_9544 are exactly identical! WARNING: Sequences sp_O88569_ROA2_MOUSE_10090 and tr_G5BD43_G5BD43_HETGA_10181 are exactly identical! WARNING: Sequences sp_O88569_ROA2_MOUSE_10090 and tr_F7HPZ0_F7HPZ0_CALJA_9483 are exactly identical! WARNING: Sequences sp_O88569_ROA2_MOUSE_10090 and tr_A0A286ZI52_A0A286ZI52_PIG_9823 are exactly identical! WARNING: Sequences sp_O88569_ROA2_MOUSE_10090 and tr_G1LHD9_G1LHD9_AILME_9646 are exactly identical! WARNING: Sequences sp_O88569_ROA2_MOUSE_10090 and tr_G7P0P7_G7P0P7_MACFA_9541 are exactly identical! WARNING: Sequences sp_O88569_ROA2_MOUSE_10090 and tr_M3XCQ1_M3XCQ1_FELCA_9685 are exactly identical! WARNING: Sequences sp_O88569_ROA2_MOUSE_10090 and tr_A0A2I3LGK2_A0A2I3LGK2_PAPAN_9555 are exactly identical! WARNING: Sequences sp_O88569_ROA2_MOUSE_10090 and tr_A0A0D9RNX3_A0A0D9RNX3_CHLSB_60711 are exactly identical! WARNING: Sequences sp_O88569_ROA2_MOUSE_10090 and tr_A0A1S3FV39_A0A1S3FV39_DIPOR_10020 are exactly identical! WARNING: Sequences sp_O88569_ROA2_MOUSE_10090 and tr_A0A1U7U6Y2_A0A1U7U6Y2_TARSY_1868482 are exactly identical! WARNING: Sequences sp_O88569_ROA2_MOUSE_10090 and tr_A0A1U8CXE8_A0A1U8CXE8_MESAU_10036 are exactly identical! WARNING: Sequences sp_O88569_ROA2_MOUSE_10090 and tr_A0A2K5M1J4_A0A2K5M1J4_CERAT_9531 are exactly identical! WARNING: Sequences sp_O88569_ROA2_MOUSE_10090 and tr_A0A2K6BDJ1_A0A2K6BDJ1_MACNE_9545 are exactly identical! WARNING: Sequences sp_O88569_ROA2_MOUSE_10090 and tr_A0A2K5ZZW9_A0A2K5ZZW9_MANLE_9568 are exactly identical! WARNING: Sequences sp_O88569_ROA2_MOUSE_10090 and tr_A0A2R9BIQ7_A0A2R9BIQ7_PANPA_9597 are exactly identical! WARNING: Sequences sp_O88569_ROA2_MOUSE_10090 and tr_A0A2U4AMA3_A0A2U4AMA3_TURTR_9739 are exactly identical! WARNING: Sequences sp_O88569_ROA2_MOUSE_10090 and tr_A0A2U3ZCU7_A0A2U3ZCU7_ODORO_9708 are exactly identical! WARNING: Sequences sp_O88569_ROA2_MOUSE_10090 and tr_A0A2U3XJB9_A0A2U3XJB9_LEPWE_9713 are exactly identical! WARNING: Sequences sp_O88569_ROA2_MOUSE_10090 and tr_A0A2Y9JGP4_A0A2Y9JGP4_ENHLU_391180 are exactly identical! WARNING: Sequences sp_O88569_ROA2_MOUSE_10090 and tr_A0A2Y9P0C4_A0A2Y9P0C4_DELLE_9749 are exactly identical! WARNING: Sequences sp_O88569_ROA2_MOUSE_10090 and tr_A0A2Y9FFJ7_A0A2Y9FFJ7_PHYCD_9755 are exactly identical! WARNING: Sequences sp_O88569_ROA2_MOUSE_10090 and tr_A0A384BPW4_A0A384BPW4_URSMA_29073 are exactly identical! WARNING: Sequences sp_O88569_ROA2_MOUSE_10090 and tr_A0A383Z8Q9_A0A383Z8Q9_BALAS_310752 are exactly identical! WARNING: Sequences sp_P49312_ROA1_MOUSE_10090 and tr_G1S7F5_G1S7F5_NOMLE_61853 are exactly identical! WARNING: Sequences sp_P49312_ROA1_MOUSE_10090 and tr_G3QKL5_G3QKL5_GORGO_9595 are exactly identical! WARNING: Sequences sp_P49312_ROA1_MOUSE_10090 and sp_A5A6H4_ROA1_PANTR_9598 are exactly identical! WARNING: Sequences sp_P49312_ROA1_MOUSE_10090 and tr_F6YZ44_F6YZ44_HORSE_9796 are exactly identical! WARNING: Sequences sp_P49312_ROA1_MOUSE_10090 and tr_W5Q400_W5Q400_SHEEP_9940 are exactly identical! WARNING: Sequences sp_P49312_ROA1_MOUSE_10090 and tr_I3M849_I3M849_ICTTR_43179 are exactly identical! WARNING: Sequences sp_P49312_ROA1_MOUSE_10090 and sp_P09651_ROA1_HUMAN_9606 are exactly identical! WARNING: Sequences sp_P49312_ROA1_MOUSE_10090 and tr_F7HT55_F7HT55_MACMU_9544 are exactly identical! WARNING: Sequences sp_P49312_ROA1_MOUSE_10090 and tr_G3W829_G3W829_SARHA_9305 are exactly identical! WARNING: Sequences sp_P49312_ROA1_MOUSE_10090 and tr_F7IDN2_F7IDN2_CALJA_9483 are exactly identical! WARNING: Sequences sp_P49312_ROA1_MOUSE_10090 and tr_A0A286ZPE3_A0A286ZPE3_PIG_9823 are exactly identical! WARNING: Sequences sp_P49312_ROA1_MOUSE_10090 and sp_P09867_ROA1_BOVIN_9913 are exactly identical! WARNING: Sequences sp_P49312_ROA1_MOUSE_10090 and tr_M3X7W8_M3X7W8_FELCA_9685 are exactly identical! WARNING: Sequences sp_P49312_ROA1_MOUSE_10090 and tr_A0A096MSQ8_A0A096MSQ8_PAPAN_9555 are exactly identical! WARNING: Sequences sp_P49312_ROA1_MOUSE_10090 and tr_A0A0D9QZF1_A0A0D9QZF1_CHLSB_60711 are exactly identical! WARNING: Sequences sp_P49312_ROA1_MOUSE_10090 and tr_A0A1S3W5B1_A0A1S3W5B1_ERIEU_9365 are exactly identical! WARNING: Sequences sp_P49312_ROA1_MOUSE_10090 and tr_A0A1S3GGH5_A0A1S3GGH5_DIPOR_10020 are exactly identical! WARNING: Sequences sp_P49312_ROA1_MOUSE_10090 and tr_A0A3Q0E366_A0A3Q0E366_TARSY_1868482 are exactly identical! WARNING: Sequences sp_P49312_ROA1_MOUSE_10090 and tr_A0A1U8BTE0_A0A1U8BTE0_MESAU_10036 are exactly identical! WARNING: Sequences sp_P49312_ROA1_MOUSE_10090 and tr_A0A2K5NWS6_A0A2K5NWS6_CERAT_9531 are exactly identical! WARNING: Sequences sp_P49312_ROA1_MOUSE_10090 and tr_A0A2K6DWA3_A0A2K6DWA3_MACNE_9545 are exactly identical! WARNING: Sequences sp_P49312_ROA1_MOUSE_10090 and tr_A0A2K6AL43_A0A2K6AL43_MANLE_9568 are exactly identical! WARNING: Sequences sp_P49312_ROA1_MOUSE_10090 and tr_A0A2R8ZHP5_A0A2R8ZHP5_PANPA_9597 are exactly identical! WARNING: Sequences sp_P49312_ROA1_MOUSE_10090 and tr_A0A2U4CBH8_A0A2U4CBH8_TURTR_9739 are exactly identical! WARNING: Sequences sp_P49312_ROA1_MOUSE_10090 and tr_A0A2U3WCM7_A0A2U3WCM7_ODORO_9708 are exactly identical! WARNING: Sequences sp_P49312_ROA1_MOUSE_10090 and tr_A0A2Y9KE10_A0A2Y9KE10_ENHLU_391180 are exactly identical! WARNING: Sequences sp_P49312_ROA1_MOUSE_10090 and tr_A0A2Y9KQE4_A0A2Y9KQE4_ENHLU_391180 are exactly identical! WARNING: Sequences sp_P49312_ROA1_MOUSE_10090 and tr_A0A2Y9N0I4_A0A2Y9N0I4_DELLE_9749 are exactly identical! WARNING: Sequences sp_P49312_ROA1_MOUSE_10090 and tr_A0A2Y9FN35_A0A2Y9FN35_PHYCD_9755 are exactly identical! WARNING: Sequences sp_P49312_ROA1_MOUSE_10090 and tr_A0A384D809_A0A384D809_URSMA_29073 are exactly identical! WARNING: Sequences sp_P49312_ROA1_MOUSE_10090 and tr_A0A383ZWS1_A0A383ZWS1_BALAS_310752 are exactly identical! WARNING: Sequences sp_Q61474_MSI1H_MOUSE_10090 and sp_Q8K3P4_MSI1H_RAT_10116 are exactly identical! WARNING: Sequences sp_Q8BG05_ROA3_MOUSE_10090 and tr_W5Q7M7_W5Q7M7_SHEEP_9940 are exactly identical! WARNING: Sequences sp_Q8BG05_ROA3_MOUSE_10090 and sp_Q6URK4_ROA3_RAT_10116 are exactly identical! WARNING: Sequences sp_Q8BG05_ROA3_MOUSE_10090 and tr_A0A1D5QW22_A0A1D5QW22_MACMU_9544 are exactly identical! WARNING: Sequences sp_Q8BG05_ROA3_MOUSE_10090 and tr_F2Z5B4_F2Z5B4_PIG_9823 are exactly identical! WARNING: Sequences sp_Q8BG05_ROA3_MOUSE_10090 and tr_A0A096NPT5_A0A096NPT5_PAPAN_9555 are exactly identical! WARNING: Sequences sp_Q8BG05_ROA3_MOUSE_10090 and tr_A0A0D9RPE9_A0A0D9RPE9_CHLSB_60711 are exactly identical! WARNING: Sequences sp_Q8BG05_ROA3_MOUSE_10090 and tr_A0A1S3G8F9_A0A1S3G8F9_DIPOR_10020 are exactly identical! WARNING: Sequences sp_Q8BG05_ROA3_MOUSE_10090 and tr_A0A1U7TRL5_A0A1U7TRL5_TARSY_1868482 are exactly identical! WARNING: Sequences sp_Q8BG05_ROA3_MOUSE_10090 and tr_A0A3Q0D147_A0A3Q0D147_MESAU_10036 are exactly identical! WARNING: Sequences sp_Q8BG05_ROA3_MOUSE_10090 and tr_A0A2K5LU55_A0A2K5LU55_CERAT_9531 are exactly identical! WARNING: Sequences sp_Q8BG05_ROA3_MOUSE_10090 and tr_A0A2U4AAR0_A0A2U4AAR0_TURTR_9739 are exactly identical! WARNING: Sequences sp_Q8BG05_ROA3_MOUSE_10090 and tr_A0A2Y9MTW7_A0A2Y9MTW7_DELLE_9749 are exactly identical! WARNING: Sequences sp_Q8BG05_ROA3_MOUSE_10090 and tr_A0A2Y9SHV3_A0A2Y9SHV3_PHYCD_9755 are exactly identical! WARNING: Sequences sp_Q920Q6_MSI2H_MOUSE_10090 and tr_A0A1S2ZYV7_A0A1S2ZYV7_ERIEU_9365 are exactly identical! WARNING: Sequences sp_Q920Q6_MSI2H_MOUSE_10090 and tr_A0A2U3ZKI9_A0A2U3ZKI9_ODORO_9708 are exactly identical! WARNING: Sequences sp_Q920Q6_MSI2H_MOUSE_10090 and tr_A0A2Y9JVE8_A0A2Y9JVE8_ENHLU_391180 are exactly identical! WARNING: Sequences tr_M3YTL3_M3YTL3_MUSPF_9669 and tr_G3SB22_G3SB22_GORGO_9595 are exactly identical! WARNING: Sequences tr_M3YTL3_M3YTL3_MUSPF_9669 and tr_G1SF95_G1SF95_RABIT_9986 are exactly identical! WARNING: Sequences tr_M3YTL3_M3YTL3_MUSPF_9669 and tr_G3TH39_G3TH39_LOXAF_9785 are exactly identical! WARNING: Sequences tr_M3YTL3_M3YTL3_MUSPF_9669 and tr_G3WJL6_G3WJL6_SARHA_9305 are exactly identical! WARNING: Sequences tr_M3YVA7_M3YVA7_MUSPF_9669 and tr_G1SZA1_G1SZA1_RABIT_9986 are exactly identical! WARNING: Sequences tr_M3Z7U9_M3Z7U9_MUSPF_9669 and tr_E2RBV8_E2RBV8_CANLF_9615 are exactly identical! WARNING: Sequences tr_M3Z7U9_M3Z7U9_MUSPF_9669 and tr_L5JUT4_L5JUT4_PTEAL_9402 are exactly identical! WARNING: Sequences tr_M3Z7U9_M3Z7U9_MUSPF_9669 and tr_A0A337SGC5_A0A337SGC5_FELCA_9685 are exactly identical! WARNING: Sequences tr_M3Z7U9_M3Z7U9_MUSPF_9669 and tr_A0A2U3VRZ0_A0A2U3VRZ0_ODORO_9708 are exactly identical! WARNING: Sequences tr_M3Z7U9_M3Z7U9_MUSPF_9669 and tr_A0A2U3Y0M5_A0A2U3Y0M5_LEPWE_9713 are exactly identical! WARNING: Sequences tr_M3Z7U9_M3Z7U9_MUSPF_9669 and tr_A0A2Y9INC3_A0A2Y9INC3_ENHLU_391180 are exactly identical! WARNING: Sequences tr_G1RAY6_G1RAY6_NOMLE_61853 and tr_H2R5B8_H2R5B8_PANTR_9598 are exactly identical! WARNING: Sequences tr_G1RAY6_G1RAY6_NOMLE_61853 and tr_A0A096N9I0_A0A096N9I0_PAPAN_9555 are exactly identical! WARNING: Sequences tr_G1RAY6_G1RAY6_NOMLE_61853 and tr_A0A2K6AWA5_A0A2K6AWA5_MACNE_9545 are exactly identical! WARNING: Sequences tr_G1RAY6_G1RAY6_NOMLE_61853 and tr_A0A2K5XT04_A0A2K5XT04_MANLE_9568 are exactly identical! WARNING: Sequences tr_G1RAY6_G1RAY6_NOMLE_61853 and tr_A0A2R8ZCG6_A0A2R8ZCG6_PANPA_9597 are exactly identical! WARNING: Sequences tr_G3I782_G3I782_CRIGR_10029 and tr_A0A1U7T6B9_A0A1U7T6B9_TARSY_1868482 are exactly identical! WARNING: Sequences tr_G3QTH6_G3QTH6_GORGO_9595 and tr_K7DJX6_K7DJX6_PANTR_9598 are exactly identical! WARNING: Sequences tr_G3QTH6_G3QTH6_GORGO_9595 and tr_I3NCR3_I3NCR3_ICTTR_43179 are exactly identical! WARNING: Sequences tr_G3QTH6_G3QTH6_GORGO_9595 and sp_P51991_ROA3_HUMAN_9606 are exactly identical! WARNING: Sequences tr_G3QTH6_G3QTH6_GORGO_9595 and tr_A0A2R8ZSN7_A0A2R8ZSN7_PANPA_9597 are exactly identical! WARNING: Sequences tr_G1NDW3_G1NDW3_MELGA_9103 and tr_A0A093HHH7_A0A093HHH7_STRCA_441894 are exactly identical! WARNING: Sequences tr_E2RFV7_E2RFV7_CANLF_9615 and tr_M3WGE6_M3WGE6_FELCA_9685 are exactly identical! WARNING: Sequences tr_E2RFV7_E2RFV7_CANLF_9615 and tr_A0A2U3W6J9_A0A2U3W6J9_ODORO_9708 are exactly identical! WARNING: Sequences tr_E2RFV7_E2RFV7_CANLF_9615 and tr_A0A2U3XYT1_A0A2U3XYT1_LEPWE_9713 are exactly identical! WARNING: Sequences tr_A0A2I3RM80_A0A2I3RM80_PANTR_9598 and tr_A0A2R9BGG8_A0A2R9BGG8_PANPA_9597 are exactly identical! WARNING: Sequences tr_A0A2I3SD00_A0A2I3SD00_PANTR_9598 and sp_O43347_MSI1H_HUMAN_9606 are exactly identical! WARNING: Sequences tr_A0A2I3SD00_A0A2I3SD00_PANTR_9598 and tr_A0A287BPE3_A0A287BPE3_PIG_9823 are exactly identical! WARNING: Sequences tr_A0A2I3SD00_A0A2I3SD00_PANTR_9598 and tr_A0A1U8CHM7_A0A1U8CHM7_MESAU_10036 are exactly identical! WARNING: Sequences tr_A0A2I3SD00_A0A2I3SD00_PANTR_9598 and tr_A0A2K5LF81_A0A2K5LF81_CERAT_9531 are exactly identical! WARNING: Sequences tr_A0A2I3SD00_A0A2I3SD00_PANTR_9598 and tr_A0A2K6DCC8_A0A2K6DCC8_MACNE_9545 are exactly identical! WARNING: Sequences tr_A0A2I3SD00_A0A2I3SD00_PANTR_9598 and tr_A0A2U3VNQ8_A0A2U3VNQ8_ODORO_9708 are exactly identical! WARNING: Sequences tr_A0A2I3SD00_A0A2I3SD00_PANTR_9598 and tr_A0A2Y9KVG4_A0A2Y9KVG4_ENHLU_391180 are exactly identical! WARNING: Sequences tr_A0A2I3SD00_A0A2I3SD00_PANTR_9598 and tr_A0A2Y9LAF6_A0A2Y9LAF6_DELLE_9749 are exactly identical! WARNING: Sequences tr_A0A2I3SD00_A0A2I3SD00_PANTR_9598 and tr_A0A2Y9SK96_A0A2Y9SK96_PHYCD_9755 are exactly identical! WARNING: Sequences tr_A0A2I3TCU7_A0A2I3TCU7_PANTR_9598 and tr_A0A2R9C0Z6_A0A2R9C0Z6_PANPA_9597 are exactly identical! WARNING: Sequences tr_F6WHS3_F6WHS3_HORSE_9796 and tr_H0WP41_H0WP41_OTOGA_30611 are exactly identical! WARNING: Sequences tr_F6WHS3_F6WHS3_HORSE_9796 and tr_G1LEX1_G1LEX1_AILME_9646 are exactly identical! WARNING: Sequences tr_F6WHS3_F6WHS3_HORSE_9796 and tr_G8F5B0_G8F5B0_MACFA_9541 are exactly identical! WARNING: Sequences tr_F6WHS3_F6WHS3_HORSE_9796 and tr_A6H6Y0_A6H6Y0_BOVIN_9913 are exactly identical! WARNING: Sequences tr_F6WHS3_F6WHS3_HORSE_9796 and tr_A0A1S3W5N6_A0A1S3W5N6_ERIEU_9365 are exactly identical! WARNING: Sequences tr_F6WHS3_F6WHS3_HORSE_9796 and tr_A0A2R9B755_A0A2R9B755_PANPA_9597 are exactly identical! WARNING: Sequences tr_F6WHS3_F6WHS3_HORSE_9796 and tr_A0A2U3VAZ8_A0A2U3VAZ8_ODORO_9708 are exactly identical! WARNING: Sequences sp_Q96DH6_MSI2H_HUMAN_9606 and tr_U3EKM7_U3EKM7_CALJA_9483 are exactly identical! WARNING: Sequences sp_Q96DH6_MSI2H_HUMAN_9606 and tr_A0A337SE56_A0A337SE56_FELCA_9685 are exactly identical! WARNING: Sequences sp_Q96DH6_MSI2H_HUMAN_9606 and tr_A0A096P4R9_A0A096P4R9_PAPAN_9555 are exactly identical! WARNING: Sequences sp_Q96DH6_MSI2H_HUMAN_9606 and tr_A0A0D9R002_A0A0D9R002_CHLSB_60711 are exactly identical! WARNING: Sequences sp_Q96DH6_MSI2H_HUMAN_9606 and tr_A0A2K6EBJ8_A0A2K6EBJ8_MACNE_9545 are exactly identical! WARNING: Sequences sp_Q96DH6_MSI2H_HUMAN_9606 and tr_A0A2Y9DNH3_A0A2Y9DNH3_TRIMA_127582 are exactly identical! WARNING: Sequences tr_A0A0K0JCT4_A0A0K0JCT4_BRUMA_6279 and tr_A0A044SIW0_A0A044SIW0_ONCVO_6282 are exactly identical! WARNING: Sequences tr_G5ALN8_G5ALN8_HETGA_10181 and tr_A0A099ZP95_A0A099ZP95_TINGU_94827 are exactly identical! WARNING: Sequences tr_E5RYW6_E5RYW6_TRISP_6334 and tr_A0A0V0S2L5_A0A0V0S2L5_9BILA_6336 are exactly identical! WARNING: Sequences tr_E5RYW6_E5RYW6_TRISP_6334 and tr_A0A0V1LD58_A0A0V1LD58_9BILA_6335 are exactly identical! WARNING: Sequences tr_A0A287ATA8_A0A287ATA8_PIG_9823 and tr_A0A2Y9LMN4_A0A2Y9LMN4_DELLE_9749 are exactly identical! WARNING: Sequences tr_U3JKP4_U3JKP4_FICAL_59894 and tr_A0A2I0MIX2_A0A2I0MIX2_COLLI_8932 are exactly identical! WARNING: Sequences tr_U3K4H6_U3K4H6_FICAL_59894 and tr_A0A218VDQ1_A0A218VDQ1_9PASE_299123 are exactly identical! WARNING: Sequences tr_U3IWL4_U3IWL4_ANAPL_8839 and tr_A0A091F6N9_A0A091F6N9_CORBR_85066 are exactly identical! WARNING: Sequences tr_U3IWL4_U3IWL4_ANAPL_8839 and tr_A0A091JQ08_A0A091JQ08_EGRGA_188379 are exactly identical! WARNING: Sequences tr_U3IWL4_U3IWL4_ANAPL_8839 and tr_A0A093PIF9_A0A093PIF9_9PASS_328815 are exactly identical! WARNING: Sequences tr_U3IWL4_U3IWL4_ANAPL_8839 and tr_A0A091VSK1_A0A091VSK1_NIPNI_128390 are exactly identical! WARNING: Sequences tr_U3IWL4_U3IWL4_ANAPL_8839 and tr_A0A087RAJ4_A0A087RAJ4_APTFO_9233 are exactly identical! WARNING: Sequences tr_U3IWL4_U3IWL4_ANAPL_8839 and tr_A0A0A0AMX3_A0A0A0AMX3_CHAVO_50402 are exactly identical! WARNING: Sequences tr_A0A091F5Y3_A0A091F5Y3_CORBR_85066 and tr_A0A091J7L1_A0A091J7L1_EGRGA_188379 are exactly identical! WARNING: Sequences tr_A0A091F5Y3_A0A091F5Y3_CORBR_85066 and tr_A0A093PNP0_A0A093PNP0_9PASS_328815 are exactly identical! WARNING: Sequences tr_A0A091F5Y3_A0A091F5Y3_CORBR_85066 and tr_A0A091V4H5_A0A091V4H5_NIPNI_128390 are exactly identical! WARNING: Sequences tr_A0A091F5Y3_A0A091F5Y3_CORBR_85066 and tr_A0A087R7B2_A0A087R7B2_APTFO_9233 are exactly identical! WARNING: Sequences tr_A0A091F5Y3_A0A091F5Y3_CORBR_85066 and tr_A0A091XSY2_A0A091XSY2_OPIHO_30419 are exactly identical! WARNING: Sequences tr_A0A091F5Y3_A0A091F5Y3_CORBR_85066 and tr_A0A091FL74_A0A091FL74_9AVES_55661 are exactly identical! WARNING: Sequences tr_A0A091F5Y3_A0A091F5Y3_CORBR_85066 and tr_A0A0A0A6W7_A0A0A0A6W7_CHAVO_50402 are exactly identical! WARNING: Sequences tr_A0A091F5Y3_A0A091F5Y3_CORBR_85066 and tr_A0A091I173_A0A091I173_CALAN_9244 are exactly identical! WARNING: Sequences tr_A0A0V0SKC0_A0A0V0SKC0_9BILA_6336 and tr_A0A0V1DFS3_A0A0V1DFS3_TRIBR_45882 are exactly identical! WARNING: Sequences tr_A0A0V0SKC0_A0A0V0SKC0_9BILA_6336 and tr_A0A0V0X1R8_A0A0V0X1R8_9BILA_92179 are exactly identical! WARNING: Sequences tr_A0A0V0SKC0_A0A0V0SKC0_9BILA_6336 and tr_A0A0V0VGQ9_A0A0V0VGQ9_9BILA_181606 are exactly identical! WARNING: Sequences tr_A0A0V0SKC0_A0A0V0SKC0_9BILA_6336 and tr_A0A0V1LSC1_A0A0V1LSC1_9BILA_6335 are exactly identical! WARNING: Sequences tr_A0A0V0SKC0_A0A0V0SKC0_9BILA_6336 and tr_A0A0V1AA05_A0A0V1AA05_9BILA_990121 are exactly identical! WARNING: Sequences tr_A0A0V0SKC0_A0A0V0SKC0_9BILA_6336 and tr_A0A0V1PK46_A0A0V1PK46_9BILA_92180 are exactly identical! WARNING: Sequences tr_A0A0V0SKC0_A0A0V0SKC0_9BILA_6336 and tr_A0A0V0U7U5_A0A0V0U7U5_9BILA_144512 are exactly identical! WARNING: Sequences tr_A0A0V1A6K6_A0A0V1A6K6_9BILA_990121 and tr_A0A0V0U018_A0A0V0U018_9BILA_144512 are exactly identical! WARNING: Sequences tr_A0A0V1F8R0_A0A0V1F8R0_TRIPS_6337 and tr_A0A0V1MX13_A0A0V1MX13_9BILA_268474 are exactly identical! WARNING: Sequences tr_A0A1S3MH19_A0A1S3MH19_SALSA_8030 and tr_C0H8N3_C0H8N3_SALSA_8030 are exactly identical! WARNING: Sequences tr_A0A1U7SPR5_A0A1U7SPR5_ALLSI_38654 and tr_A0A218V3V1_A0A218V3V1_9PASE_299123 are exactly identical! WARNING: Sequences tr_A0A2D0SP75_A0A2D0SP75_ICTPU_7998 and tr_A0A2D0SQE3_A0A2D0SQE3_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2U3V853_A0A2U3V853_TURTR_9739 and tr_A0A2U3V861_A0A2U3V861_TURTR_9739 are exactly identical! WARNING: Duplicate sequences found: 171 NOTE: Reduced alignment (with duplicates and gap-only sites/taxa removed) NOTE: was saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/P09651/3_mltree/P09651.raxml.reduced.phy Alignment comprises 1 partitions and 282 patterns Partition 0: noname Model: LG4X+R4 Alignment sites / patterns: 282 / 282 Gaps: 13.51 % Invariant sites: 0.00 % NOTE: Binary MSA file created: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/P09651/3_mltree/P09651.raxml.rba Parallelization scheme autoconfig: 6 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 1001 taxa [00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 282 / 22560 [00:00:00] Data distribution: max. searches per worker: 4 Starting ML tree search with 20 distinct starting trees [00:00:00 -330887.823692] Initial branch length optimization [00:00:06 -267794.713259] Model parameter optimization (eps = 10.000000) [00:00:55 -264694.971045] AUTODETECT spr round 1 (radius: 5) [00:04:48 -205390.956424] AUTODETECT spr round 2 (radius: 10) [00:08:56 -168458.050106] AUTODETECT spr round 3 (radius: 15) [00:13:34 -138148.060883] AUTODETECT spr round 4 (radius: 20) [00:19:02 -122520.508919] AUTODETECT spr round 5 (radius: 25) [00:24:54 -113953.945220] SPR radius for FAST iterations: 25 (autodetect) [00:24:54 -113953.945220] Model parameter optimization (eps = 3.000000) [00:26:13 -113698.773986] FAST spr round 1 (radius: 25) [00:32:36 -97390.600171] FAST spr round 2 (radius: 25) [00:37:38 -95882.001087] FAST spr round 3 (radius: 25) [00:42:08 -95717.612787] FAST spr round 4 (radius: 25) [00:46:04 -95698.918662] FAST spr round 5 (radius: 25) [00:49:35 -95694.802681] FAST spr round 6 (radius: 25) [00:52:53 -95689.058154] FAST spr round 7 (radius: 25) [00:55:58 -95689.057985] Model parameter optimization (eps = 1.000000) [00:56:46 -95676.094765] SLOW spr round 1 (radius: 5) [01:00:18 -95637.972417] SLOW spr round 2 (radius: 5) [01:03:52 -95634.307855] SLOW spr round 3 (radius: 5) [01:07:24 -95634.171838] SLOW spr round 4 (radius: 5) [01:10:54 -95634.171641] SLOW spr round 5 (radius: 10) [01:14:55 -95617.548190] SLOW spr round 6 (radius: 5) [01:19:02 -95616.886661] SLOW spr round 7 (radius: 5) [01:22:50 -95615.439079] SLOW spr round 8 (radius: 5) [01:26:29 -95612.688482] SLOW spr round 9 (radius: 5) [01:30:04 -95612.571526] SLOW spr round 10 (radius: 5) [01:33:32 -95612.571387] SLOW spr round 11 (radius: 10) [01:37:27 -95612.571334] SLOW spr round 12 (radius: 15) [01:44:04 -95602.331810] SLOW spr round 13 (radius: 5) [01:48:18 -95602.331631] SLOW spr round 14 (radius: 10) [01:53:12 -95590.110887] SLOW spr round 15 (radius: 5) [01:57:20 -95577.953688] SLOW spr round 16 (radius: 5) [02:01:06 -95574.524549] SLOW spr round 17 (radius: 5) [02:04:42 -95573.160217] SLOW spr round 18 (radius: 5) [02:08:14 -95568.825968] SLOW spr round 19 (radius: 5) [02:11:42 -95568.824873] SLOW spr round 20 (radius: 10) [02:15:40 -95567.016635] SLOW spr round 21 (radius: 5) [02:19:44 -95565.801603] SLOW spr round 22 (radius: 5) [02:23:27 -95565.801556] SLOW spr round 23 (radius: 10) [02:27:40 -95559.936413] SLOW spr round 24 (radius: 5) [02:31:42 -95558.612549] SLOW spr round 25 (radius: 5) [02:35:29 -95556.959597] SLOW spr round 26 (radius: 5) [02:39:02 -95556.959527] SLOW spr round 27 (radius: 10) [02:43:01 -95556.959524] SLOW spr round 28 (radius: 15) [02:49:40 -95553.206745] SLOW spr round 29 (radius: 5) [02:53:52 -95553.206703] SLOW spr round 30 (radius: 10) [02:58:42 -95553.206700] SLOW spr round 31 (radius: 15) [03:05:09 -95553.206697] SLOW spr round 32 (radius: 20) [03:13:49 -95435.443965] SLOW spr round 33 (radius: 5) [03:17:45] [worker #5] ML tree search #6, logLikelihood: -95389.333976 [03:18:22 -95431.157514] SLOW spr round 34 (radius: 5) [03:22:23 -95427.269671] SLOW spr round 35 (radius: 5) [03:26:03 -95427.269445] SLOW spr round 36 (radius: 10) [03:30:09 -95426.861094] SLOW spr round 37 (radius: 5) [03:34:10 -95426.861055] SLOW spr round 38 (radius: 10) [03:38:40 -95426.286440] SLOW spr round 39 (radius: 5) [03:42:39 -95426.286342] SLOW spr round 40 (radius: 10) [03:47:05 -95426.286336] SLOW spr round 41 (radius: 15) [03:47:58] [worker #4] ML tree search #5, logLikelihood: -95406.740887 [03:53:36 -95425.883285] SLOW spr round 42 (radius: 5) [03:57:50 -95425.883200] SLOW spr round 43 (radius: 10) [04:02:37 -95425.883196] SLOW spr round 44 (radius: 15) [04:09:08 -95425.883193] SLOW spr round 45 (radius: 20) [04:17:40 -95423.050371] SLOW spr round 46 (radius: 5) [04:22:04 -95422.030424] SLOW spr round 47 (radius: 5) [04:25:59 -95422.030395] SLOW spr round 48 (radius: 10) [04:30:19 -95422.030392] SLOW spr round 49 (radius: 15) [04:36:52 -95422.030389] SLOW spr round 50 (radius: 20) [04:40:11] [worker #2] ML tree search #3, logLikelihood: -95616.331317 [04:45:22 -95421.274171] SLOW spr round 51 (radius: 5) [04:49:44 -95421.274139] SLOW spr round 52 (radius: 10) [04:54:45 -95421.274135] SLOW spr round 53 (radius: 15) [05:01:16 -95420.557046] SLOW spr round 54 (radius: 5) [05:05:30 -95420.556863] SLOW spr round 55 (radius: 10) [05:10:17 -95420.556858] SLOW spr round 56 (radius: 15) [05:16:44 -95420.556855] SLOW spr round 57 (radius: 20) [05:24:43] [worker #3] ML tree search #4, logLikelihood: -95511.067273 [05:25:14 -95420.556852] SLOW spr round 58 (radius: 25) [05:34:43 -95418.789972] SLOW spr round 59 (radius: 5) [05:39:14 -95416.938138] SLOW spr round 60 (radius: 5) [05:43:11 -95416.937235] SLOW spr round 61 (radius: 10) [05:47:33 -95416.937232] SLOW spr round 62 (radius: 15) [05:54:03 -95416.937228] SLOW spr round 63 (radius: 20) [05:58:25] [worker #1] ML tree search #2, logLikelihood: -95438.996475 [06:02:31 -95416.937225] SLOW spr round 64 (radius: 25) [06:11:51 -95416.937221] Model parameter optimization (eps = 0.100000) [06:12:05] [worker #0] ML tree search #1, logLikelihood: -95416.870147 [06:12:06 -329922.571188] Initial branch length optimization [06:12:11 -266713.155131] Model parameter optimization (eps = 10.000000) [06:13:11 -263663.271620] AUTODETECT spr round 1 (radius: 5) [06:17:00 -202307.916587] AUTODETECT spr round 2 (radius: 10) [06:21:13 -159577.036505] AUTODETECT spr round 3 (radius: 15) [06:25:55 -137916.358396] AUTODETECT spr round 4 (radius: 20) [06:31:27 -117944.912886] AUTODETECT spr round 5 (radius: 25) [06:37:45 -108965.528325] SPR radius for FAST iterations: 25 (autodetect) [06:37:45 -108965.528325] Model parameter optimization (eps = 3.000000) [06:38:44 -108739.603972] FAST spr round 1 (radius: 25) [06:44:59 -96923.348250] FAST spr round 2 (radius: 25) [06:49:56 -95857.090219] FAST spr round 3 (radius: 25) [06:54:14 -95573.215820] FAST spr round 4 (radius: 25) [06:58:06 -95551.400730] FAST spr round 5 (radius: 25) [07:01:41 -95537.353111] FAST spr round 6 (radius: 25) [07:04:54 -95531.802570] FAST spr round 7 (radius: 25) [07:07:59 -95531.802274] Model parameter optimization (eps = 1.000000) [07:08:28 -95521.621288] SLOW spr round 1 (radius: 5) [07:12:00 -95499.849270] SLOW spr round 2 (radius: 5) [07:15:34 -95498.923746] SLOW spr round 3 (radius: 5) [07:19:11 -95498.922699] SLOW spr round 4 (radius: 10) [07:23:12 -95492.554436] SLOW spr round 5 (radius: 5) [07:27:23 -95491.153290] SLOW spr round 6 (radius: 5) [07:31:12 -95491.153099] SLOW spr round 7 (radius: 10) [07:35:14 -95491.153041] SLOW spr round 8 (radius: 15) [07:41:08 -95487.540660] SLOW spr round 9 (radius: 5) [07:45:33 -95476.930611] SLOW spr round 10 (radius: 5) [07:49:24 -95476.929965] SLOW spr round 11 (radius: 10) [07:53:34 -95476.249648] SLOW spr round 12 (radius: 5) [07:57:34 -95476.249411] SLOW spr round 13 (radius: 10) [08:01:51 -95473.621433] SLOW spr round 14 (radius: 5) [08:05:50 -95473.621287] SLOW spr round 15 (radius: 10) [08:10:04 -95473.621215] SLOW spr round 16 (radius: 15) [08:15:58 -95471.377022] SLOW spr round 17 (radius: 5) [08:20:11 -95471.376934] SLOW spr round 18 (radius: 10) [08:24:49 -95471.376912] SLOW spr round 19 (radius: 15) [08:30:41 -95471.188366] SLOW spr round 20 (radius: 5) [08:34:54 -95471.188353] SLOW spr round 21 (radius: 10) [08:39:31 -95469.884104] SLOW spr round 22 (radius: 5) [08:43:28 -95469.884079] SLOW spr round 23 (radius: 10) [08:47:41 -95469.884071] SLOW spr round 24 (radius: 15) [08:53:03] [worker #5] ML tree search #12, logLikelihood: -95441.435666 [08:53:33 -95469.884064] SLOW spr round 25 (radius: 20) [08:57:22] [worker #2] ML tree search #9, logLikelihood: -95382.547504 [09:00:45 -95469.734206] SLOW spr round 26 (radius: 5) [09:05:07 -95469.734194] SLOW spr round 27 (radius: 10) [09:09:59 -95469.734187] SLOW spr round 28 (radius: 15) [09:15:52 -95469.734171] SLOW spr round 29 (radius: 20) [09:23:03 -95469.734164] SLOW spr round 30 (radius: 25) [09:31:32 -95455.574128] SLOW spr round 31 (radius: 5) [09:35:58 -95455.573874] SLOW spr round 32 (radius: 10) [09:40:54 -95455.082687] SLOW spr round 33 (radius: 5) [09:44:19] [worker #4] ML tree search #11, logLikelihood: -95363.937836 [09:44:52 -95455.082679] SLOW spr round 34 (radius: 10) [09:49:05 -95455.082673] SLOW spr round 35 (radius: 15) [09:55:00 -95455.082603] SLOW spr round 36 (radius: 20) [10:02:14 -95455.082597] SLOW spr round 37 (radius: 25) [10:03:11] [worker #1] ML tree search #8, logLikelihood: -95442.565206 [10:10:39 -95452.581359] SLOW spr round 38 (radius: 5) [10:15:06 -95452.581342] SLOW spr round 39 (radius: 10) [10:20:00 -95450.566547] SLOW spr round 40 (radius: 5) [10:24:00 -95450.245991] SLOW spr round 41 (radius: 5) [10:27:42 -95450.245983] SLOW spr round 42 (radius: 10) [10:31:39 -95450.245976] SLOW spr round 43 (radius: 15) [10:37:34 -95450.245968] SLOW spr round 44 (radius: 20) [10:44:45 -95450.245961] SLOW spr round 45 (radius: 25) [10:53:06 -95450.245955] Model parameter optimization (eps = 0.100000) [10:53:21] [worker #0] ML tree search #7, logLikelihood: -95450.149938 [10:53:21 -330658.946768] Initial branch length optimization [10:53:27 -267785.496574] Model parameter optimization (eps = 10.000000) [10:54:12 -264757.568745] AUTODETECT spr round 1 (radius: 5) [10:58:07 -204621.817078] AUTODETECT spr round 2 (radius: 10) [11:02:15 -165662.989840] AUTODETECT spr round 3 (radius: 15) [11:06:58 -137902.323287] AUTODETECT spr round 4 (radius: 20) [11:12:45 -126055.008759] AUTODETECT spr round 5 (radius: 25) [11:15:31] [worker #3] ML tree search #10, logLikelihood: -95955.270996 [11:18:24 -113112.673894] SPR radius for FAST iterations: 25 (autodetect) [11:18:24 -113112.673894] Model parameter optimization (eps = 3.000000) [11:19:35 -112821.363763] FAST spr round 1 (radius: 25) [11:26:29 -96476.062736] FAST spr round 2 (radius: 25) [11:32:06 -95621.454541] FAST spr round 3 (radius: 25) [11:36:52 -95549.943667] FAST spr round 4 (radius: 25) [11:41:03 -95539.323421] FAST spr round 5 (radius: 25) [11:44:42 -95536.868921] FAST spr round 6 (radius: 25) [11:48:06 -95519.147601] FAST spr round 7 (radius: 25) [11:51:20 -95516.377118] FAST spr round 8 (radius: 25) [11:54:26 -95516.376793] Model parameter optimization (eps = 1.000000) [11:54:55 -95500.976063] SLOW spr round 1 (radius: 5) [11:58:34 -95472.094169] SLOW spr round 2 (radius: 5) [12:02:15 -95464.123449] SLOW spr round 3 (radius: 5) [12:05:56 -95464.120569] SLOW spr round 4 (radius: 10) [12:10:04 -95453.000933] SLOW spr round 5 (radius: 5) [12:14:22 -95450.906216] SLOW spr round 6 (radius: 5) [12:18:18 -95450.905747] SLOW spr round 7 (radius: 10) [12:22:29 -95448.997579] SLOW spr round 8 (radius: 5) [12:26:42 -95448.639372] SLOW spr round 9 (radius: 5) [12:30:34 -95448.639268] SLOW spr round 10 (radius: 10) [12:34:40 -95448.639225] SLOW spr round 11 (radius: 15) [12:35:28] [worker #5] ML tree search #18, logLikelihood: -95625.600881 [12:41:31 -95431.898869] SLOW spr round 12 (radius: 5) [12:45:57 -95421.334399] SLOW spr round 13 (radius: 5) [12:49:57 -95420.741092] SLOW spr round 14 (radius: 5) [12:53:41 -95420.740804] SLOW spr round 15 (radius: 10) [12:57:43 -95420.325682] SLOW spr round 16 (radius: 5) [13:01:55 -95419.275858] SLOW spr round 17 (radius: 5) [13:05:45 -95419.275846] SLOW spr round 18 (radius: 10) [13:09:51 -95419.275842] SLOW spr round 19 (radius: 15) [13:16:32 -95416.340401] SLOW spr round 20 (radius: 5) [13:21:01 -95411.688828] SLOW spr round 21 (radius: 5) [13:25:00 -95411.650182] SLOW spr round 22 (radius: 10) [13:29:15 -95408.702728] SLOW spr round 23 (radius: 5) [13:33:25 -95408.367747] SLOW spr round 24 (radius: 5) [13:37:13 -95408.367739] SLOW spr round 25 (radius: 10) [13:41:19 -95408.367735] SLOW spr round 26 (radius: 15) [13:48:03 -95407.029674] SLOW spr round 27 (radius: 5) [13:52:23 -95406.431226] SLOW spr round 28 (radius: 5) [13:56:21 -95405.237933] SLOW spr round 29 (radius: 5) [14:00:04 -95405.237926] SLOW spr round 30 (radius: 10) [14:04:08 -95405.237914] SLOW spr round 31 (radius: 15) [14:10:45 -95401.556589] SLOW spr round 32 (radius: 5) [14:15:05 -95401.374949] SLOW spr round 33 (radius: 5) [14:19:02 -95401.374945] SLOW spr round 34 (radius: 10) [14:19:39] [worker #2] ML tree search #15, logLikelihood: -95391.488241 [14:23:16 -95401.374941] SLOW spr round 35 (radius: 15) [14:29:48 -95401.374938] SLOW spr round 36 (radius: 20) [14:38:00 -95399.012969] SLOW spr round 37 (radius: 5) [14:42:29 -95398.782919] SLOW spr round 38 (radius: 5) [14:46:30 -95398.782914] SLOW spr round 39 (radius: 10) [14:50:51 -95398.782822] SLOW spr round 40 (radius: 15) [14:57:17 -95398.782774] SLOW spr round 41 (radius: 20) [15:05:29 -95398.782771] SLOW spr round 42 (radius: 25) [15:08:46] [worker #4] ML tree search #17, logLikelihood: -95385.789566 [15:14:49 -95392.675811] SLOW spr round 43 (radius: 5) [15:15:58] [worker #1] ML tree search #14, logLikelihood: -95392.037335 [15:19:33 -95386.413215] SLOW spr round 44 (radius: 5) [15:23:36 -95386.413209] SLOW spr round 45 (radius: 10) [15:27:58 -95386.413205] SLOW spr round 46 (radius: 15) [15:34:25 -95386.413200] SLOW spr round 47 (radius: 20) [15:42:38 -95386.412926] SLOW spr round 48 (radius: 25) [15:51:59 -95386.045569] SLOW spr round 49 (radius: 5) [15:56:33 -95385.366659] SLOW spr round 50 (radius: 5) [16:00:35 -95385.366643] SLOW spr round 51 (radius: 10) [16:04:57 -95385.366639] SLOW spr round 52 (radius: 15) [16:11:24 -95385.366636] SLOW spr round 53 (radius: 20) [16:14:40] [worker #3] ML tree search #16, logLikelihood: -95432.936677 [16:19:39 -95384.826845] SLOW spr round 54 (radius: 5) [16:24:08 -95384.826839] SLOW spr round 55 (radius: 10) [16:29:08 -95384.826835] SLOW spr round 56 (radius: 15) [16:35:33 -95384.826831] SLOW spr round 57 (radius: 20) [16:43:46 -95384.826827] SLOW spr round 58 (radius: 25) [16:53:05 -95384.155056] SLOW spr round 59 (radius: 5) [16:57:37 -95384.155052] SLOW spr round 60 (radius: 10) [17:02:42 -95384.155017] SLOW spr round 61 (radius: 15) [17:09:07 -95384.154982] SLOW spr round 62 (radius: 20) [17:17:19 -95384.154947] SLOW spr round 63 (radius: 25) [17:26:37 -95384.154911] Model parameter optimization (eps = 0.100000) [17:27:00] [worker #0] ML tree search #13, logLikelihood: -95383.295778 [17:27:01 -333302.608717] Initial branch length optimization [17:27:07 -269982.200590] Model parameter optimization (eps = 10.000000) [17:28:05 -266776.477687] AUTODETECT spr round 1 (radius: 5) [17:31:57 -203256.751072] AUTODETECT spr round 2 (radius: 10) [17:36:03 -160531.019225] AUTODETECT spr round 3 (radius: 15) [17:40:38 -140443.146696] AUTODETECT spr round 4 (radius: 20) [17:46:00 -134399.506455] AUTODETECT spr round 5 (radius: 25) [17:52:22 -119039.317434] SPR radius for FAST iterations: 25 (autodetect) [17:52:22 -119039.317434] Model parameter optimization (eps = 3.000000) [17:53:12 -118677.815865] FAST spr round 1 (radius: 25) [18:00:48 -97817.835020] FAST spr round 2 (radius: 25) [18:06:22 -95800.574580] FAST spr round 3 (radius: 25) [18:11:12 -95671.339751] FAST spr round 4 (radius: 25) [18:15:32 -95652.744893] FAST spr round 5 (radius: 25) [18:19:22 -95630.181826] FAST spr round 6 (radius: 25) [18:22:50 -95628.910689] FAST spr round 7 (radius: 25) [18:26:06 -95628.808656] FAST spr round 8 (radius: 25) [18:29:14 -95628.808526] Model parameter optimization (eps = 1.000000) [18:29:48 -95614.712218] SLOW spr round 1 (radius: 5) [18:33:25 -95587.100148] SLOW spr round 2 (radius: 5) [18:37:04 -95579.675254] SLOW spr round 3 (radius: 5) [18:40:41 -95573.491786] SLOW spr round 4 (radius: 5) [18:44:15 -95572.747325] SLOW spr round 5 (radius: 5) [18:47:45 -95572.747129] SLOW spr round 6 (radius: 10) [18:51:54 -95565.519322] SLOW spr round 7 (radius: 5) [18:56:03 -95564.700091] SLOW spr round 8 (radius: 5) [18:59:51 -95564.699890] SLOW spr round 9 (radius: 10) [19:04:06 -95562.938309] SLOW spr round 10 (radius: 5) [19:08:09 -95562.855285] SLOW spr round 11 (radius: 10) [19:12:44 -95562.855281] SLOW spr round 12 (radius: 15) [19:19:59 -95528.631145] SLOW spr round 13 (radius: 5) [19:24:23 -95522.367243] SLOW spr round 14 (radius: 5) [19:28:25 -95520.581180] SLOW spr round 15 (radius: 5) [19:32:13 -95517.894224] SLOW spr round 16 (radius: 5) [19:35:49 -95517.501760] SLOW spr round 17 (radius: 5) [19:39:20 -95517.501756] SLOW spr round 18 (radius: 10) [19:43:23 -95511.907335] SLOW spr round 19 (radius: 5) [19:47:34 -95510.124511] SLOW spr round 20 (radius: 5) [19:51:23 -95510.124347] SLOW spr round 21 (radius: 10) [19:55:31 -95510.124333] SLOW spr round 22 (radius: 15) [19:56:50] [worker #1] ML tree search #20, logLikelihood: -95472.455370 [20:02:08 -95508.741228] SLOW spr round 23 (radius: 5) [20:06:22 -95508.741189] SLOW spr round 24 (radius: 10) [20:11:14 -95508.741188] SLOW spr round 25 (radius: 15) [20:17:47 -95508.741095] SLOW spr round 26 (radius: 20) [20:26:17 -95500.899134] SLOW spr round 27 (radius: 5) [20:30:45 -95498.626225] SLOW spr round 28 (radius: 5) [20:34:42 -95498.625194] SLOW spr round 29 (radius: 10) [20:39:08 -95498.162185] SLOW spr round 30 (radius: 5) [20:43:12 -95497.662223] SLOW spr round 31 (radius: 5) [20:46:56 -95497.662218] SLOW spr round 32 (radius: 10) [20:51:04 -95497.662131] SLOW spr round 33 (radius: 15) [20:57:46 -95496.912503] SLOW spr round 34 (radius: 5) [21:02:03 -95496.912342] SLOW spr round 35 (radius: 10) [21:06:57 -95496.912341] SLOW spr round 36 (radius: 15) [21:13:31 -95496.912340] SLOW spr round 37 (radius: 20) [21:21:50 -95496.912340] SLOW spr round 38 (radius: 25) [21:31:13 -95494.712855] SLOW spr round 39 (radius: 5) [21:35:46 -95494.710860] SLOW spr round 40 (radius: 10) [21:41:02 -95494.710772] SLOW spr round 41 (radius: 15) [21:47:37 -95492.723267] SLOW spr round 42 (radius: 5) [21:51:54 -95492.723265] SLOW spr round 43 (radius: 10) [21:56:50 -95492.723265] SLOW spr round 44 (radius: 15) [22:03:23 -95492.723264] SLOW spr round 45 (radius: 20) [22:11:44 -95492.723263] SLOW spr round 46 (radius: 25) [22:21:08 -95492.723263] Model parameter optimization (eps = 0.100000) [22:21:29] [worker #0] ML tree search #19, logLikelihood: -95491.926027 Optimized model parameters: Partition 0: noname Rate heterogeneity: FREE (4 cats, mean), weights&rates: (0.060061,0.667698) (0.059167,0.492118) (0.366831,0.674683) (0.513941,1.329502) 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: -95363.937836 AIC score: 194737.875672 / AICc score: 8238797.875672 / BIC score: 202039.899349 Free parameters (model + branch lengths): 2005 WARNING: Number of free parameters (K=2005) is larger than alignment size (n=282). This might lead to overfitting and compromise tree inference results! Best ML tree saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/P09651/3_mltree/P09651.raxml.bestTree All ML trees saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/P09651/3_mltree/P09651.raxml.mlTrees Optimized model saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/P09651/3_mltree/P09651.raxml.bestModel Execution log saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/P09651/3_mltree/P09651.raxml.log Analysis started: 08-Jul-2021 21:27:15 / finished: 09-Jul-2021 19:48:45 Elapsed time: 80490.119 seconds