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 04-Jul-2021 04:40:48 as follows: raxml-ng --msa /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q03252/2_msa/Q03252_trimmed_msa.fasta --data-type AA --model LG4X --prefix /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q03252/3_mltree/Q03252 --seed 2 --threads 5 --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 (5 threads), thread pinning: OFF [00:00:00] Reading alignment from file: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q03252/2_msa/Q03252_trimmed_msa.fasta [00:00:00] Loaded alignment with 1001 taxa and 342 sites WARNING: Sequences tr_E1C5R3_E1C5R3_CHICK_9031 and tr_G1MQS0_G1MQS0_MELGA_9103 are exactly identical! WARNING: Sequences tr_E1C5R3_E1C5R3_CHICK_9031 and tr_A0A226P4S0_A0A226P4S0_COLVI_9014 are exactly identical! WARNING: Sequences sp_P20152_VIME_MOUSE_10090 and tr_G3HHR3_G3HHR3_CRIGR_10029 are exactly identical! WARNING: Sequences sp_P20152_VIME_MOUSE_10090 and sp_P31000_VIME_RAT_10116 are exactly identical! WARNING: Sequences sp_P20152_VIME_MOUSE_10090 and tr_A0A1U7QL88_A0A1U7QL88_MESAU_10036 are exactly identical! WARNING: Sequences sp_P20152_VIME_MOUSE_10090 and sp_P02544_VIME_MESAU_10036 are exactly identical! WARNING: Sequences tr_M3Y072_M3Y072_MUSPF_9669 and tr_A0A2Y9IE42_A0A2Y9IE42_ENHLU_391180 are exactly identical! WARNING: Sequences tr_M3YKP4_M3YKP4_MUSPF_9669 and tr_A0A2Y9IKN8_A0A2Y9IKN8_ENHLU_391180 are exactly identical! WARNING: Sequences tr_M3YT34_M3YT34_MUSPF_9669 and tr_A0A2U3ZG72_A0A2U3ZG72_ODORO_9708 are exactly identical! WARNING: Sequences tr_M3YT34_M3YT34_MUSPF_9669 and tr_A0A2Y9KVQ1_A0A2Y9KVQ1_ENHLU_391180 are exactly identical! WARNING: Sequences tr_A0A2I3HSS5_A0A2I3HSS5_NOMLE_61853 and tr_G3QEU9_G3QEU9_GORGO_9595 are exactly identical! WARNING: Sequences tr_A0A2I3HSS5_A0A2I3HSS5_NOMLE_61853 and tr_A0A2J8VGR7_A0A2J8VGR7_PONAB_9601 are exactly identical! WARNING: Sequences tr_A0A2I3HSS5_A0A2I3HSS5_NOMLE_61853 and tr_H2Q091_H2Q091_PANTR_9598 are exactly identical! WARNING: Sequences tr_A0A2I3HSS5_A0A2I3HSS5_NOMLE_61853 and sp_P02545_LMNA_HUMAN_9606 are exactly identical! WARNING: Sequences tr_A0A2I3HSS5_A0A2I3HSS5_NOMLE_61853 and tr_A0A1D5QQZ2_A0A1D5QQZ2_MACMU_9544 are exactly identical! WARNING: Sequences tr_A0A2I3HSS5_A0A2I3HSS5_NOMLE_61853 and tr_G7NV78_G7NV78_MACFA_9541 are exactly identical! WARNING: Sequences tr_A0A2I3HSS5_A0A2I3HSS5_NOMLE_61853 and tr_A0A096MQV4_A0A096MQV4_PAPAN_9555 are exactly identical! WARNING: Sequences tr_A0A2I3HSS5_A0A2I3HSS5_NOMLE_61853 and tr_A0A0D9S4Z6_A0A0D9S4Z6_CHLSB_60711 are exactly identical! WARNING: Sequences tr_A0A2I3HSS5_A0A2I3HSS5_NOMLE_61853 and tr_A0A2K5M323_A0A2K5M323_CERAT_9531 are exactly identical! WARNING: Sequences tr_A0A2I3HSS5_A0A2I3HSS5_NOMLE_61853 and tr_A0A2K6ED46_A0A2K6ED46_MACNE_9545 are exactly identical! WARNING: Sequences tr_A0A2I3HSS5_A0A2I3HSS5_NOMLE_61853 and tr_A0A2K5YDB4_A0A2K5YDB4_MANLE_9568 are exactly identical! WARNING: Sequences tr_A0A2I3HSS5_A0A2I3HSS5_NOMLE_61853 and tr_A0A2R9BK07_A0A2R9BK07_PANPA_9597 are exactly identical! WARNING: Sequences tr_G1S823_G1S823_NOMLE_61853 and tr_H2NH69_H2NH69_PONAB_9601 are exactly identical! WARNING: Sequences tr_A0A2I2Y3K0_A0A2I2Y3K0_GORGO_9595 and tr_A0A2I3RCP5_A0A2I3RCP5_PANTR_9598 are exactly identical! WARNING: Sequences tr_A0A2I2Y3K0_A0A2I2Y3K0_GORGO_9595 and tr_A0A2R9CBG0_A0A2R9CBG0_PANPA_9597 are exactly identical! WARNING: Sequences tr_G3QJS0_G3QJS0_GORGO_9595 and sp_P17661_DESM_HUMAN_9606 are exactly identical! WARNING: Sequences tr_G3QJS0_G3QJS0_GORGO_9595 and tr_F7ERR2_F7ERR2_MACMU_9544 are exactly identical! WARNING: Sequences tr_G3QJS0_G3QJS0_GORGO_9595 and tr_B0CM49_B0CM49_PAPAN_9555 are exactly identical! WARNING: Sequences tr_G3QJS0_G3QJS0_GORGO_9595 and tr_A0A0D9R6T4_A0A0D9R6T4_CHLSB_60711 are exactly identical! WARNING: Sequences tr_G3QJS0_G3QJS0_GORGO_9595 and tr_A0A2K5LDT7_A0A2K5LDT7_CERAT_9531 are exactly identical! WARNING: Sequences tr_G3QJS0_G3QJS0_GORGO_9595 and tr_A0A2K6D3R9_A0A2K6D3R9_MACNE_9545 are exactly identical! WARNING: Sequences tr_G3QJS0_G3QJS0_GORGO_9595 and tr_A0A2K5YQE7_A0A2K5YQE7_MANLE_9568 are exactly identical! WARNING: Sequences tr_G3QK94_G3QK94_GORGO_9595 and tr_H2Q2I4_H2Q2I4_PANTR_9598 are exactly identical! WARNING: Sequences tr_G3QK94_G3QK94_GORGO_9595 and sp_Q16352_AINX_HUMAN_9606 are exactly identical! WARNING: Sequences tr_G3QK94_G3QK94_GORGO_9595 and tr_A0A2R9BN98_A0A2R9BN98_PANPA_9597 are exactly identical! WARNING: Sequences tr_G3R2A8_G3R2A8_GORGO_9595 and tr_G2HJ38_G2HJ38_PANTR_9598 are exactly identical! WARNING: Sequences tr_G3R2A8_G3R2A8_GORGO_9595 and sp_P08670_VIME_HUMAN_9606 are exactly identical! WARNING: Sequences tr_G3R2A8_G3R2A8_GORGO_9595 and tr_A0A2R9BXN0_A0A2R9BXN0_PANPA_9597 are exactly identical! WARNING: Sequences tr_G3R335_G3R335_GORGO_9595 and sp_P07197_NFM_HUMAN_9606 are exactly identical! WARNING: Sequences tr_G3RWL2_G3RWL2_GORGO_9595 and tr_H2PGE3_H2PGE3_PONAB_9601 are exactly identical! WARNING: Sequences tr_G3SHE6_G3SHE6_GORGO_9595 and tr_H2Q5V1_H2Q5V1_PANTR_9598 are exactly identical! WARNING: Sequences tr_G3SHE6_G3SHE6_GORGO_9595 and sp_P41219_PERI_HUMAN_9606 are exactly identical! WARNING: Sequences tr_G3SHE6_G3SHE6_GORGO_9595 and tr_A0A2R9AZE7_A0A2R9AZE7_PANPA_9597 are exactly identical! WARNING: Sequences tr_G1N6W4_G1N6W4_MELGA_9103 and tr_A0A091JIL7_A0A091JIL7_EGRGA_188379 are exactly identical! WARNING: Sequences tr_F1PLS4_F1PLS4_CANLF_9615 and tr_G1LVM5_G1LVM5_AILME_9646 are exactly identical! WARNING: Sequences tr_F1PLS4_F1PLS4_CANLF_9615 and tr_A0A2U3VET8_A0A2U3VET8_ODORO_9708 are exactly identical! WARNING: Sequences tr_F1PLS4_F1PLS4_CANLF_9615 and tr_A0A384C7E5_A0A384C7E5_URSMA_29073 are exactly identical! WARNING: Sequences tr_H2QEX0_H2QEX0_PANTR_9598 and sp_Q03252_LMNB2_HUMAN_9606 are exactly identical! WARNING: Sequences tr_H2QEX0_H2QEX0_PANTR_9598 and tr_F6R7X5_F6R7X5_MACMU_9544 are exactly identical! WARNING: Sequences tr_H2QEX0_H2QEX0_PANTR_9598 and tr_A0A0A0MV39_A0A0A0MV39_PAPAN_9555 are exactly identical! WARNING: Sequences tr_H2QEX0_H2QEX0_PANTR_9598 and tr_A0A2K6DZV2_A0A2K6DZV2_MACNE_9545 are exactly identical! WARNING: Sequences tr_H2QLG1_H2QLG1_PANTR_9598 and sp_P12036_NFH_HUMAN_9606 are exactly identical! WARNING: Sequences tr_H2QRE7_H2QRE7_PANTR_9598 and tr_A0A2R9BUC3_A0A2R9BUC3_PANPA_9597 are exactly identical! WARNING: Sequences tr_W5Q9T3_W5Q9T3_SHEEP_9940 and tr_F1RKM0_F1RKM0_PIG_9823 are exactly identical! WARNING: Sequences tr_W5Q9T3_W5Q9T3_SHEEP_9940 and tr_A0A2Y9SDA7_A0A2Y9SDA7_PHYCD_9755 are exactly identical! WARNING: Sequences tr_W5QG29_W5QG29_SHEEP_9940 and sp_P02540_DESM_PIG_9823 are exactly identical! WARNING: Sequences tr_W5QG29_W5QG29_SHEEP_9940 and sp_O62654_DESM_BOVIN_9913 are exactly identical! WARNING: Sequences tr_W5QG29_W5QG29_SHEEP_9940 and tr_A0A337SLT6_A0A337SLT6_FELCA_9685 are exactly identical! WARNING: Sequences tr_A0A088AD32_A0A088AD32_APIME_7460 and tr_A0A2A3EM64_A0A2A3EM64_APICC_94128 are exactly identical! WARNING: Sequences tr_A0A158NSD7_A0A158NSD7_ATTCE_12957 and tr_A0A151HYG0_A0A151HYG0_9HYME_520822 are exactly identical! WARNING: Sequences tr_A0A1D5QRV5_A0A1D5QRV5_MACMU_9544 and tr_G7PCX0_G7PCX0_MACFA_9541 are exactly identical! WARNING: Sequences tr_A0A1D5QRV5_A0A1D5QRV5_MACMU_9544 and tr_A0A2I3LJD5_A0A2I3LJD5_PAPAN_9555 are exactly identical! WARNING: Sequences tr_A0A1D5QRV5_A0A1D5QRV5_MACMU_9544 and tr_A0A0D9RUC0_A0A0D9RUC0_CHLSB_60711 are exactly identical! WARNING: Sequences tr_A0A1D5QRV5_A0A1D5QRV5_MACMU_9544 and tr_A0A2K5NQS4_A0A2K5NQS4_CERAT_9531 are exactly identical! WARNING: Sequences tr_A0A1D5QRV5_A0A1D5QRV5_MACMU_9544 and tr_A0A2K6BBU8_A0A2K6BBU8_MACNE_9545 are exactly identical! WARNING: Sequences tr_A0A1D5QRV5_A0A1D5QRV5_MACMU_9544 and tr_A0A2K6ACN1_A0A2K6ACN1_MANLE_9568 are exactly identical! WARNING: Sequences tr_F6Q273_F6Q273_MACMU_9544 and tr_A0A096MS49_A0A096MS49_PAPAN_9555 are exactly identical! WARNING: Sequences tr_F6Q273_F6Q273_MACMU_9544 and tr_A0A0D9RPS0_A0A0D9RPS0_CHLSB_60711 are exactly identical! WARNING: Sequences tr_F6Q273_F6Q273_MACMU_9544 and tr_A0A2K5MBU6_A0A2K5MBU6_CERAT_9531 are exactly identical! WARNING: Sequences tr_F6Q273_F6Q273_MACMU_9544 and tr_A0A2K6CEN3_A0A2K6CEN3_MACNE_9545 are exactly identical! WARNING: Sequences tr_F7G5S6_F7G5S6_MACMU_9544 and tr_A0A096NJD8_A0A096NJD8_PAPAN_9555 are exactly identical! WARNING: Sequences tr_F7G5S6_F7G5S6_MACMU_9544 and tr_A0A0D9RBE3_A0A0D9RBE3_CHLSB_60711 are exactly identical! WARNING: Sequences tr_F7G5S6_F7G5S6_MACMU_9544 and tr_A0A2K6DE45_A0A2K6DE45_MACNE_9545 are exactly identical! WARNING: Sequences tr_F7GW66_F7GW66_MACMU_9544 and tr_A0A096NAQ5_A0A096NAQ5_PAPAN_9555 are exactly identical! WARNING: Sequences tr_F7GW66_F7GW66_MACMU_9544 and tr_A0A0D9R1E9_A0A0D9R1E9_CHLSB_60711 are exactly identical! WARNING: Sequences tr_F7GW66_F7GW66_MACMU_9544 and tr_A0A2K5N8A5_A0A2K5N8A5_CERAT_9531 are exactly identical! WARNING: Sequences tr_F7GW66_F7GW66_MACMU_9544 and tr_A0A2K6C7C4_A0A2K6C7C4_MACNE_9545 are exactly identical! WARNING: Sequences tr_F7GW66_F7GW66_MACMU_9544 and tr_A0A2K5Y3J4_A0A2K5Y3J4_MANLE_9568 are exactly identical! WARNING: Sequences tr_G7N1N6_G7N1N6_MACMU_9544 and tr_G7PEG3_G7PEG3_MACFA_9541 are exactly identical! WARNING: Sequences tr_G7N1N6_G7N1N6_MACMU_9544 and tr_A0A096NQ21_A0A096NQ21_PAPAN_9555 are exactly identical! WARNING: Sequences tr_G7N1N6_G7N1N6_MACMU_9544 and tr_A0A0D9RJU1_A0A0D9RJU1_CHLSB_60711 are exactly identical! WARNING: Sequences tr_G7N1N6_G7N1N6_MACMU_9544 and tr_A0A2K5KZZ4_A0A2K5KZZ4_CERAT_9531 are exactly identical! WARNING: Sequences tr_G7N1N6_G7N1N6_MACMU_9544 and tr_A0A2K6CXT7_A0A2K6CXT7_MACNE_9545 are exactly identical! WARNING: Sequences tr_G7N1N6_G7N1N6_MACMU_9544 and tr_A0A2K5ZIJ1_A0A2K5ZIJ1_MANLE_9568 are exactly identical! WARNING: Sequences tr_E5SDW6_E5SDW6_TRISP_6334 and tr_A0A0V0SLF9_A0A0V0SLF9_9BILA_6336 are exactly identical! WARNING: Sequences tr_E5SDW6_E5SDW6_TRISP_6334 and tr_A0A0V1C9H0_A0A0V1C9H0_TRIBR_45882 are exactly identical! WARNING: Sequences tr_E5SDW6_E5SDW6_TRISP_6334 and tr_A0A0V0W622_A0A0V0W622_9BILA_92179 are exactly identical! WARNING: Sequences tr_E5SDW6_E5SDW6_TRISP_6334 and tr_A0A0V0UPW5_A0A0V0UPW5_9BILA_181606 are exactly identical! WARNING: Sequences tr_E5SDW6_E5SDW6_TRISP_6334 and tr_A0A0V1KUW3_A0A0V1KUW3_9BILA_6335 are exactly identical! WARNING: Sequences tr_E5SDW6_E5SDW6_TRISP_6334 and tr_A0A0V0Z9L9_A0A0V0Z9L9_9BILA_990121 are exactly identical! WARNING: Sequences tr_E5SDW6_E5SDW6_TRISP_6334 and tr_A0A0V1NHJ1_A0A0V1NHJ1_9BILA_92180 are exactly identical! WARNING: Sequences tr_E5SDW6_E5SDW6_TRISP_6334 and tr_A0A0V0TH75_A0A0V0TH75_9BILA_144512 are exactly identical! WARNING: Sequences sp_B4F721_NFL_XENTR_8364 and tr_F6TRE5_F6TRE5_XENTR_8364 are exactly identical! WARNING: Sequences tr_F6YTV2_F6YTV2_CALJA_9483 and tr_G1M6X1_G1M6X1_AILME_9646 are exactly identical! WARNING: Sequences tr_F6YTV2_F6YTV2_CALJA_9483 and tr_M3WFR2_M3WFR2_FELCA_9685 are exactly identical! WARNING: Sequences tr_F6YTV2_F6YTV2_CALJA_9483 and tr_A0A1S3F3P7_A0A1S3F3P7_DIPOR_10020 are exactly identical! WARNING: Sequences tr_D2GZ83_D2GZ83_AILME_9646 and tr_M3WV73_M3WV73_FELCA_9685 are exactly identical! WARNING: Sequences tr_A0A2I3NFW1_A0A2I3NFW1_PAPAN_9555 and tr_A0A2K6BAT9_A0A2K6BAT9_MACNE_9545 are exactly identical! WARNING: Sequences tr_A0A2I3NFW1_A0A2I3NFW1_PAPAN_9555 and tr_A0A2K5ZFI5_A0A2K5ZFI5_MANLE_9568 are exactly identical! WARNING: Sequences tr_A0A0V0RHE3_A0A0V0RHE3_9BILA_6336 and tr_A0A0V1CK15_A0A0V1CK15_TRIBR_45882 are exactly identical! WARNING: Sequences tr_A0A0V0RHE3_A0A0V0RHE3_9BILA_6336 and tr_A0A0V0W5T3_A0A0V0W5T3_9BILA_92179 are exactly identical! WARNING: Sequences tr_A0A0V0RHE3_A0A0V0RHE3_9BILA_6336 and tr_A0A0V0VIX6_A0A0V0VIX6_9BILA_181606 are exactly identical! WARNING: Sequences tr_A0A0V0RHE3_A0A0V0RHE3_9BILA_6336 and tr_A0A0V1KPB8_A0A0V1KPB8_9BILA_6335 are exactly identical! WARNING: Sequences tr_A0A0V0RHE3_A0A0V0RHE3_9BILA_6336 and tr_A0A0V0ZJC8_A0A0V0ZJC8_9BILA_990121 are exactly identical! WARNING: Sequences tr_A0A0V0RHE3_A0A0V0RHE3_9BILA_6336 and tr_A0A0V1NQ44_A0A0V1NQ44_9BILA_92180 are exactly identical! WARNING: Sequences tr_A0A0V0RHE3_A0A0V0RHE3_9BILA_6336 and tr_A0A0V0TDR8_A0A0V0TDR8_9BILA_144512 are exactly identical! WARNING: Sequences tr_A0A0V0XSU2_A0A0V0XSU2_TRIPS_6337 and tr_A0A0V1M9V9_A0A0V1M9V9_9BILA_268474 are exactly identical! WARNING: Sequences tr_A0A0V0XSU2_A0A0V0XSU2_TRIPS_6337 and tr_A0A0V1HA06_A0A0V1HA06_9BILA_268475 are exactly identical! WARNING: Sequences tr_A0A1S3GYA9_A0A1S3GYA9_LINUN_7574 and tr_A0A1S3GYJ9_A0A1S3GYJ9_LINUN_7574 are exactly identical! WARNING: Sequences tr_A0A226NJV5_A0A226NJV5_CALSU_9009 and tr_A0A226PH92_A0A226PH92_COLVI_9014 are exactly identical! WARNING: Sequences tr_A0A226NN62_A0A226NN62_CALSU_9009 and tr_A0A226PAN0_A0A226PAN0_COLVI_9014 are exactly identical! WARNING: Sequences tr_A0A2D0PL39_A0A2D0PL39_ICTPU_7998 and tr_A0A2D0PMV1_A0A2D0PMV1_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0SRK4_A0A2D0SRK4_ICTPU_7998 and tr_A0A2D0SRK8_A0A2D0SRK8_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0SRK4_A0A2D0SRK4_ICTPU_7998 and tr_A0A2D0SSP3_A0A2D0SSP3_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2U3V0C3_A0A2U3V0C3_TURTR_9739 and tr_A0A2Y9NTL3_A0A2Y9NTL3_DELLE_9749 are exactly identical! WARNING: Sequences tr_A0A2U3V0C3_A0A2U3V0C3_TURTR_9739 and tr_A0A2Y9FAX4_A0A2Y9FAX4_PHYCD_9755 are exactly identical! WARNING: Sequences tr_A0A2U3V3D7_A0A2U3V3D7_TURTR_9739 and tr_A0A2U4BA02_A0A2U4BA02_TURTR_9739 are exactly identical! WARNING: Sequences tr_A0A2U4BAE0_A0A2U4BAE0_TURTR_9739 and tr_A0A2Y9N997_A0A2Y9N997_DELLE_9749 are exactly identical! WARNING: Sequences tr_A0A2U4BMP4_A0A2U4BMP4_TURTR_9739 and tr_A0A2Y9MMG6_A0A2Y9MMG6_DELLE_9749 are exactly identical! WARNING: Sequences tr_A0A2U3XCY0_A0A2U3XCY0_LEPWE_9713 and tr_A0A2U3Z699_A0A2U3Z699_LEPWE_9713 are exactly identical! WARNING: Sequences tr_A0A2Y9EX49_A0A2Y9EX49_PHYCD_9755 and tr_A0A383ZA52_A0A383ZA52_BALAS_310752 are exactly identical! WARNING: Duplicate sequences found: 121 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/Q03252/3_mltree/Q03252.raxml.reduced.phy Alignment comprises 1 partitions and 342 patterns Partition 0: noname Model: LG4X+R4 Alignment sites / patterns: 342 / 342 Gaps: 12.01 % Invariant sites: 0.00 % NOTE: Binary MSA file created: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q03252/3_mltree/Q03252.raxml.rba Parallelization scheme autoconfig: 5 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 / 342 / 27360 [00:00:00] Data distribution: max. searches per worker: 4 Starting ML tree search with 20 distinct starting trees [00:00:00 -569173.036583] Initial branch length optimization [00:00:08 -471220.985312] Model parameter optimization (eps = 10.000000) [00:01:47 -469759.091193] AUTODETECT spr round 1 (radius: 5) [00:06:24 -314515.890444] AUTODETECT spr round 2 (radius: 10) [00:10:35 -208030.595160] AUTODETECT spr round 3 (radius: 15) [00:15:40 -173004.315099] AUTODETECT spr round 4 (radius: 20) [00:22:09 -149751.740549] AUTODETECT spr round 5 (radius: 25) [00:29:13 -142558.057601] SPR radius for FAST iterations: 25 (autodetect) [00:29:13 -142558.057601] Model parameter optimization (eps = 3.000000) [00:29:52 -142372.580527] FAST spr round 1 (radius: 25) [00:34:42 -121785.613164] FAST spr round 2 (radius: 25) [00:38:24 -120420.971383] FAST spr round 3 (radius: 25) [00:41:45 -120242.201574] FAST spr round 4 (radius: 25) [00:44:50 -120217.026099] FAST spr round 5 (radius: 25) [00:47:43 -120212.734437] FAST spr round 6 (radius: 25) [00:50:31 -120212.734193] Model parameter optimization (eps = 1.000000) [00:50:58 -120209.849560] SLOW spr round 1 (radius: 5) [00:54:49 -120184.075937] SLOW spr round 2 (radius: 5) [00:58:40 -120183.150135] SLOW spr round 3 (radius: 5) [01:02:19 -120183.149202] SLOW spr round 4 (radius: 10) [01:06:15 -120182.402439] SLOW spr round 5 (radius: 5) [01:10:57 -120182.396990] SLOW spr round 6 (radius: 10) [01:15:26 -120182.396801] SLOW spr round 7 (radius: 15) [01:21:47 -120179.067438] SLOW spr round 8 (radius: 5) [01:26:51 -120179.067406] SLOW spr round 9 (radius: 10) [01:31:36 -120179.067403] SLOW spr round 10 (radius: 15) [01:37:55 -120178.976857] SLOW spr round 11 (radius: 20) [01:49:47 -120178.976820] SLOW spr round 12 (radius: 25) [02:04:46 -120178.976815] Model parameter optimization (eps = 0.100000) [02:04:56] [worker #0] ML tree search #1, logLikelihood: -120178.938702 [02:04:56 -569277.948200] Initial branch length optimization [02:05:05 -472159.024003] Model parameter optimization (eps = 10.000000) [02:06:41 -470634.626980] AUTODETECT spr round 1 (radius: 5) [02:07:45] [worker #1] ML tree search #2, logLikelihood: -120153.780891 [02:09:51] [worker #4] ML tree search #5, logLikelihood: -120178.843748 [02:11:11 -311098.553256] AUTODETECT spr round 2 (radius: 10) [02:14:55] [worker #2] ML tree search #3, logLikelihood: -120169.928143 [02:15:41] [worker #3] ML tree search #4, logLikelihood: -120179.594451 [02:15:55 -223619.737359] AUTODETECT spr round 3 (radius: 15) [02:21:16 -170640.983106] AUTODETECT spr round 4 (radius: 20) [02:27:53 -150368.126127] AUTODETECT spr round 5 (radius: 25) [02:36:08 -141628.898077] SPR radius for FAST iterations: 25 (autodetect) [02:36:08 -141628.898077] Model parameter optimization (eps = 3.000000) [02:36:46 -141435.691702] FAST spr round 1 (radius: 25) [02:41:55 -122310.904466] FAST spr round 2 (radius: 25) [02:45:54 -120448.869216] FAST spr round 3 (radius: 25) [02:49:20 -120252.385981] FAST spr round 4 (radius: 25) [02:52:27 -120232.198099] FAST spr round 5 (radius: 25) [02:55:20 -120228.354248] FAST spr round 6 (radius: 25) [02:58:09 -120228.262476] Model parameter optimization (eps = 1.000000) [02:58:33 -120226.163326] SLOW spr round 1 (radius: 5) [03:02:29 -120191.455976] SLOW spr round 2 (radius: 5) [03:06:21 -120177.133103] SLOW spr round 3 (radius: 5) [03:10:08 -120177.132746] SLOW spr round 4 (radius: 10) [03:14:02 -120176.936727] SLOW spr round 5 (radius: 5) [03:18:49 -120176.759743] SLOW spr round 6 (radius: 5) [03:22:55 -120176.759668] SLOW spr round 7 (radius: 10) [03:27:02 -120176.255428] SLOW spr round 8 (radius: 5) [03:31:39 -120176.255338] SLOW spr round 9 (radius: 10) [03:36:05 -120176.255279] SLOW spr round 10 (radius: 15) [03:42:22 -120176.255244] SLOW spr round 11 (radius: 20) [03:53:07] [worker #1] ML tree search #7, logLikelihood: -120181.688718 [03:54:09 -120176.255210] SLOW spr round 12 (radius: 25) [04:08:24 -120176.255177] Model parameter optimization (eps = 0.100000) [04:08:43] [worker #0] ML tree search #6, logLikelihood: -120176.063389 [04:08:43 -572458.706301] Initial branch length optimization [04:08:50 -473848.771467] Model parameter optimization (eps = 10.000000) [04:10:36 -472438.436070] AUTODETECT spr round 1 (radius: 5) [04:15:10 -312397.138594] AUTODETECT spr round 2 (radius: 10) [04:17:01] [worker #3] ML tree search #9, logLikelihood: -120166.299852 [04:19:49 -218782.887221] AUTODETECT spr round 3 (radius: 15) [04:24:15] [worker #4] ML tree search #10, logLikelihood: -120167.838074 [04:25:02 -176806.099405] AUTODETECT spr round 4 (radius: 20) [04:31:31 -150539.880172] AUTODETECT spr round 5 (radius: 25) [04:40:19 -146026.843113] SPR radius for FAST iterations: 25 (autodetect) [04:40:19 -146026.843113] Model parameter optimization (eps = 3.000000) [04:41:05 -145854.201883] FAST spr round 1 (radius: 25) [04:46:26 -121685.890294] FAST spr round 2 (radius: 25) [04:50:15 -120320.685288] FAST spr round 3 (radius: 25) [04:53:28 -120226.838180] FAST spr round 4 (radius: 25) [04:56:32 -120221.890587] FAST spr round 5 (radius: 25) [04:59:28 -120211.852150] FAST spr round 6 (radius: 25) [05:02:16 -120209.234318] FAST spr round 7 (radius: 25) [05:04:59 -120209.233661] Model parameter optimization (eps = 1.000000) [05:05:14] [worker #2] ML tree search #8, logLikelihood: -120162.490233 [05:05:18 -120207.700705] SLOW spr round 1 (radius: 5) [05:09:10 -120172.371453] SLOW spr round 2 (radius: 5) [05:12:58 -120167.617679] SLOW spr round 3 (radius: 5) [05:16:37 -120167.616962] SLOW spr round 4 (radius: 10) [05:20:28 -120167.522628] SLOW spr round 5 (radius: 15) [05:27:13 -120167.140791] SLOW spr round 6 (radius: 5) [05:32:20 -120167.001037] SLOW spr round 7 (radius: 5) [05:36:39 -120167.000592] SLOW spr round 8 (radius: 10) [05:40:56 -120167.000553] SLOW spr round 9 (radius: 15) [05:47:26 -120166.976975] SLOW spr round 10 (radius: 20) [05:59:22 -120166.976920] SLOW spr round 11 (radius: 25) [06:14:25 -120166.976912] Model parameter optimization (eps = 0.100000) [06:14:37] [worker #0] ML tree search #11, logLikelihood: -120166.934378 [06:14:37 -572103.856210] Initial branch length optimization [06:14:44 -472421.021918] Model parameter optimization (eps = 10.000000) [06:16:17 -470978.458336] AUTODETECT spr round 1 (radius: 5) [06:18:48] [worker #4] ML tree search #15, logLikelihood: -120194.531827 [06:20:52 -317285.199696] AUTODETECT spr round 2 (radius: 10) [06:25:38 -226376.877335] AUTODETECT spr round 3 (radius: 15) [06:30:56 -181852.631683] AUTODETECT spr round 4 (radius: 20) [06:33:10] [worker #1] ML tree search #12, logLikelihood: -120173.244016 [06:36:55] [worker #3] ML tree search #14, logLikelihood: -120155.604546 [06:37:19 -159837.963063] AUTODETECT spr round 5 (radius: 25) [06:45:45 -144451.571170] SPR radius for FAST iterations: 25 (autodetect) [06:45:45 -144451.571170] Model parameter optimization (eps = 3.000000) [06:46:22 -144213.531822] FAST spr round 1 (radius: 25) [06:51:16 -121779.075864] FAST spr round 2 (radius: 25) [06:54:54 -120500.516427] FAST spr round 3 (radius: 25) [06:58:00 -120281.218587] FAST spr round 4 (radius: 25) [07:01:06 -120234.676645] FAST spr round 5 (radius: 25) [07:04:04 -120223.398665] FAST spr round 6 (radius: 25) [07:06:48 -120223.397380] Model parameter optimization (eps = 1.000000) [07:07:11 -120219.573699] SLOW spr round 1 (radius: 5) [07:11:00 -120188.739675] SLOW spr round 2 (radius: 5) [07:12:58] [worker #2] ML tree search #13, logLikelihood: -120168.126295 [07:14:49 -120177.324467] SLOW spr round 3 (radius: 5) [07:18:39 -120173.746433] SLOW spr round 4 (radius: 5) [07:22:22 -120173.745487] SLOW spr round 5 (radius: 10) [07:26:19 -120172.100475] SLOW spr round 6 (radius: 5) [07:31:03 -120172.100168] SLOW spr round 7 (radius: 10) [07:35:35 -120172.033677] SLOW spr round 8 (radius: 15) [07:41:46 -120172.033664] SLOW spr round 9 (radius: 20) [07:53:05 -120172.033653] SLOW spr round 10 (radius: 25) [08:07:19 -120172.033642] Model parameter optimization (eps = 0.100000) [08:07:32] [worker #0] ML tree search #16, logLikelihood: -120171.963792 [08:22:23] [worker #1] ML tree search #17, logLikelihood: -120168.254103 [08:37:54] [worker #4] ML tree search #20, logLikelihood: -120164.771244 [08:54:38] [worker #3] ML tree search #19, logLikelihood: -120169.780301 [09:03:03] [worker #2] ML tree search #18, logLikelihood: -120153.300527 Optimized model parameters: Partition 0: noname Rate heterogeneity: FREE (4 cats, mean), weights&rates: (0.125833,0.457493) (0.101763,0.677469) (0.510764,0.848261) (0.261640,1.682578) 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: -120153.300527 AIC score: 244316.601054 / AICc score: 8288376.601054 / BIC score: 252005.396582 Free parameters (model + branch lengths): 2005 WARNING: Number of free parameters (K=2005) is larger than alignment size (n=342). 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/Q03252/3_mltree/Q03252.raxml.bestTree All ML trees saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q03252/3_mltree/Q03252.raxml.mlTrees Optimized model saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q03252/3_mltree/Q03252.raxml.bestModel Execution log saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q03252/3_mltree/Q03252.raxml.log Analysis started: 04-Jul-2021 04:40:48 / finished: 04-Jul-2021 13:43:52 Elapsed time: 32583.646 seconds Consumed energy: 2537.251 Wh (= 13 km in an electric car, or 63 km with an e-scooter!)