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 03-Jul-2021 01:07:04 as follows: raxml-ng --msa /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q9BT40/2_msa/Q9BT40_trimmed_msa.fasta --data-type AA --model LG4X --prefix /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q9BT40/3_mltree/Q9BT40 --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/Q9BT40/2_msa/Q9BT40_trimmed_msa.fasta [00:00:00] Loaded alignment with 1001 taxa and 273 sites WARNING: Sequences tr_A0A1D5NT69_A0A1D5NT69_CHICK_9031 and tr_G1NNW3_G1NNW3_MELGA_9103 are exactly identical! WARNING: Sequences sp_Q8CHC4_SYNJ1_MOUSE_10090 and sp_Q62910_SYNJ1_RAT_10116 are exactly identical! WARNING: Sequences tr_M3XPZ2_M3XPZ2_MUSPF_9669 and tr_J9JHK8_J9JHK8_CANLF_9615 are exactly identical! WARNING: Sequences tr_M3XPZ2_M3XPZ2_MUSPF_9669 and tr_H0WTB4_H0WTB4_OTOGA_30611 are exactly identical! WARNING: Sequences tr_M3XPZ2_M3XPZ2_MUSPF_9669 and tr_F7GAV4_F7GAV4_CALJA_9483 are exactly identical! WARNING: Sequences tr_M3XPZ2_M3XPZ2_MUSPF_9669 and tr_G1M962_G1M962_AILME_9646 are exactly identical! WARNING: Sequences tr_M3XPZ2_M3XPZ2_MUSPF_9669 and tr_G7P133_G7P133_MACFA_9541 are exactly identical! WARNING: Sequences tr_M3XPZ2_M3XPZ2_MUSPF_9669 and tr_A0A096NBU6_A0A096NBU6_PAPAN_9555 are exactly identical! WARNING: Sequences tr_M3XPZ2_M3XPZ2_MUSPF_9669 and tr_A0A0D9RBB3_A0A0D9RBB3_CHLSB_60711 are exactly identical! WARNING: Sequences tr_M3XPZ2_M3XPZ2_MUSPF_9669 and tr_A0A2K5M5X1_A0A2K5M5X1_CERAT_9531 are exactly identical! WARNING: Sequences tr_M3XPZ2_M3XPZ2_MUSPF_9669 and tr_A0A2K6DER4_A0A2K6DER4_MACNE_9545 are exactly identical! WARNING: Sequences tr_M3XPZ2_M3XPZ2_MUSPF_9669 and tr_A0A2K5ZED0_A0A2K5ZED0_MANLE_9568 are exactly identical! WARNING: Sequences tr_M3XPZ2_M3XPZ2_MUSPF_9669 and tr_A0A2U3WCW7_A0A2U3WCW7_ODORO_9708 are exactly identical! WARNING: Sequences tr_M3XPZ2_M3XPZ2_MUSPF_9669 and tr_A0A2U3YDF9_A0A2U3YDF9_LEPWE_9713 are exactly identical! WARNING: Sequences tr_M3XPZ2_M3XPZ2_MUSPF_9669 and tr_A0A2Y9KE01_A0A2Y9KE01_ENHLU_391180 are exactly identical! WARNING: Sequences tr_M3XPZ2_M3XPZ2_MUSPF_9669 and tr_A0A2Y9LJ10_A0A2Y9LJ10_DELLE_9749 are exactly identical! WARNING: Sequences tr_M3XPZ2_M3XPZ2_MUSPF_9669 and tr_A0A384CZW3_A0A384CZW3_URSMA_29073 are exactly identical! WARNING: Sequences tr_M3YN28_M3YN28_MUSPF_9669 and tr_G1LKY8_G1LKY8_AILME_9646 are exactly identical! WARNING: Sequences tr_M3YN28_M3YN28_MUSPF_9669 and tr_A0A2U3XQ79_A0A2U3XQ79_LEPWE_9713 are exactly identical! WARNING: Sequences tr_M3YN28_M3YN28_MUSPF_9669 and tr_A0A384DP80_A0A384DP80_URSMA_29073 are exactly identical! WARNING: Sequences tr_M3Z152_M3Z152_MUSPF_9669 and tr_A0A2U3VXK3_A0A2U3VXK3_ODORO_9708 are exactly identical! WARNING: Sequences tr_M3Z152_M3Z152_MUSPF_9669 and tr_A0A2Y9KYQ1_A0A2Y9KYQ1_ENHLU_391180 are exactly identical! WARNING: Sequences tr_G1QW39_G1QW39_NOMLE_61853 and tr_H2P436_H2P436_PONAB_9601 are exactly identical! WARNING: Sequences tr_G1QW39_G1QW39_NOMLE_61853 and sp_Q15735_PI5PA_HUMAN_9606 are exactly identical! WARNING: Sequences tr_G3QEV9_G3QEV9_GORGO_9595 and tr_K7B232_K7B232_PANTR_9598 are exactly identical! WARNING: Sequences tr_G3QEV9_G3QEV9_GORGO_9595 and sp_Q01968_OCRL_HUMAN_9606 are exactly identical! WARNING: Sequences tr_G3QEV9_G3QEV9_GORGO_9595 and tr_A0A2R8ZNA7_A0A2R8ZNA7_PANPA_9597 are exactly identical! WARNING: Sequences tr_G3RIQ1_G3RIQ1_GORGO_9595 and tr_H2RAJ6_H2RAJ6_PANTR_9598 are exactly identical! WARNING: Sequences tr_G3RIQ1_G3RIQ1_GORGO_9595 and tr_A0A2R8ZRH4_A0A2R8ZRH4_PANPA_9597 are exactly identical! WARNING: Sequences tr_H2P2Z6_H2P2Z6_PONAB_9601 and tr_A0A1S3G2E5_A0A1S3G2E5_DIPOR_10020 are exactly identical! WARNING: Sequences tr_H9GUB2_H9GUB2_ANOCA_28377 and tr_H9GUU7_H9GUU7_ANOCA_28377 are exactly identical! WARNING: Sequences tr_A0A179UC23_A0A179UC23_BLAGS_559298 and tr_C5GGF1_C5GGF1_AJEDR_559297 are exactly identical! WARNING: Sequences tr_A0A2I3S416_A0A2I3S416_PANTR_9598 and tr_A0A2R9BVC7_A0A2R9BVC7_PANPA_9597 are exactly identical! WARNING: Sequences tr_K7D6H2_K7D6H2_PANTR_9598 and tr_A0A2R9CCA5_A0A2R9CCA5_PANPA_9597 are exactly identical! WARNING: Sequences tr_F9F189_F9F189_FUSOF_660025 and tr_X0D3R0_X0D3R0_FUSOX_1089458 are exactly identical! WARNING: Sequences tr_F9F189_F9F189_FUSOF_660025 and tr_A0A2H3SUA7_A0A2H3SUA7_FUSOX_5507 are exactly identical! WARNING: Sequences tr_D4A2N2_D4A2N2_RAT_10116 and tr_F1LP71_F1LP71_RAT_10116 are exactly identical! WARNING: Sequences tr_A0A158NRT8_A0A158NRT8_ATTCE_12957 and tr_A0A195BR14_A0A195BR14_9HYME_520822 are exactly identical! WARNING: Sequences tr_I3MQE5_I3MQE5_ICTTR_43179 and tr_A0A2Y9RTX7_A0A2Y9RTX7_TRIMA_127582 are exactly identical! WARNING: Sequences tr_A2R155_A2R155_ASPNC_425011 and tr_G3XPM5_G3XPM5_ASPNA_380704 are exactly identical! WARNING: Sequences tr_A2R155_A2R155_ASPNC_425011 and tr_A0A319BTX4_A0A319BTX4_9EURO_1450533 are exactly identical! WARNING: Sequences tr_A0A1D5Q176_A0A1D5Q176_MACMU_9544 and tr_A0A096NZ70_A0A096NZ70_PAPAN_9555 are exactly identical! WARNING: Sequences tr_A0A1D5Q176_A0A1D5Q176_MACMU_9544 and tr_A0A2K5MVG4_A0A2K5MVG4_CERAT_9531 are exactly identical! WARNING: Sequences tr_A0A1D5Q176_A0A1D5Q176_MACMU_9544 and tr_A0A2K5YXR0_A0A2K5YXR0_MANLE_9568 are exactly identical! WARNING: Sequences tr_F6QC29_F6QC29_MACMU_9544 and tr_A0A096NJL7_A0A096NJL7_PAPAN_9555 are exactly identical! WARNING: Sequences tr_F6QC29_F6QC29_MACMU_9544 and tr_A0A0D9R8X1_A0A0D9R8X1_CHLSB_60711 are exactly identical! WARNING: Sequences tr_F6QC29_F6QC29_MACMU_9544 and tr_A0A2K6APN3_A0A2K6APN3_MACNE_9545 are exactly identical! WARNING: Sequences tr_F6QC29_F6QC29_MACMU_9544 and tr_A0A2K5Z0F7_A0A2K5Z0F7_MANLE_9568 are exactly identical! WARNING: Sequences tr_F7DSU6_F7DSU6_MACMU_9544 and tr_M3WH24_M3WH24_FELCA_9685 are exactly identical! WARNING: Sequences tr_F7EWY7_F7EWY7_MACMU_9544 and tr_A0A096MP77_A0A096MP77_PAPAN_9555 are exactly identical! WARNING: Sequences tr_F7EWY7_F7EWY7_MACMU_9544 and tr_A0A0D9R7S0_A0A0D9R7S0_CHLSB_60711 are exactly identical! WARNING: Sequences tr_F7EWY7_F7EWY7_MACMU_9544 and tr_A0A2K5MU43_A0A2K5MU43_CERAT_9531 are exactly identical! WARNING: Sequences tr_F7EWY7_F7EWY7_MACMU_9544 and tr_A0A2K6D9Y0_A0A2K6D9Y0_MACNE_9545 are exactly identical! WARNING: Sequences tr_F7EWY7_F7EWY7_MACMU_9544 and tr_A0A2K5YQ40_A0A2K5YQ40_MANLE_9568 are exactly identical! WARNING: Sequences tr_B8AZH3_B8AZH3_ORYSI_39946 and tr_Q6AVN0_Q6AVN0_ORYSJ_39947 are exactly identical! WARNING: Sequences tr_H0YTD1_H0YTD1_TAEGU_59729 and tr_H0ZX01_H0ZX01_TAEGU_59729 are exactly identical! WARNING: Sequences tr_H0ZT98_H0ZT98_TAEGU_59729 and tr_A0A218U9H3_A0A218U9H3_9PASE_299123 are exactly identical! WARNING: Sequences tr_L0PBL0_L0PBL0_PNEJ8_1209962 and tr_A0A0W4ZUU3_A0A0W4ZUU3_PNEJ7_1408657 are exactly identical! WARNING: Sequences tr_L0PDZ7_L0PDZ7_PNEJ8_1209962 and tr_A0A0W4ZVI3_A0A0W4ZVI3_PNEJ7_1408657 are exactly identical! WARNING: Sequences tr_S0DL35_S0DL35_GIBF5_1279085 and tr_A0A365MSZ1_A0A365MSZ1_GIBIN_948311 are exactly identical! WARNING: Sequences tr_A0A044R8U2_A0A044R8U2_ONCVO_6282 and tr_A0A182EE54_A0A182EE54_ONCOC_42157 are exactly identical! WARNING: Sequences tr_A0A2I3N5G4_A0A2I3N5G4_PAPAN_9555 and tr_A0A0D9RNJ2_A0A0D9RNJ2_CHLSB_60711 are exactly identical! WARNING: Sequences tr_A0A2I3N5G4_A0A2I3N5G4_PAPAN_9555 and tr_A0A2K5NS91_A0A2K5NS91_CERAT_9531 are exactly identical! WARNING: Sequences tr_A0A2I3N5G4_A0A2I3N5G4_PAPAN_9555 and tr_A0A2K5ZK10_A0A2K5ZK10_MANLE_9568 are exactly identical! WARNING: Sequences tr_A0A0F8WV40_A0A0F8WV40_9EURO_308745 and tr_A0A2T5LSE2_A0A2T5LSE2_9EURO_1392256 are exactly identical! WARNING: Sequences tr_A0A151NDF4_A0A151NDF4_ALLMI_8496 and tr_A0A3Q0HKA7_A0A3Q0HKA7_ALLSI_38654 are exactly identical! WARNING: Sequences tr_A0A0V1CNI4_A0A0V1CNI4_TRIBR_45882 and tr_A0A0V0WK25_A0A0V0WK25_9BILA_92179 are exactly identical! WARNING: Sequences tr_A0A0V1CNI4_A0A0V1CNI4_TRIBR_45882 and tr_A0A0V0UXL8_A0A0V0UXL8_9BILA_181606 are exactly identical! WARNING: Sequences tr_A0A0V1CNI4_A0A0V1CNI4_TRIBR_45882 and tr_A0A0V0ZRE7_A0A0V0ZRE7_9BILA_990121 are exactly identical! WARNING: Sequences tr_A0A0V1CNI4_A0A0V1CNI4_TRIBR_45882 and tr_A0A0V1NQK0_A0A0V1NQK0_9BILA_92180 are exactly identical! WARNING: Sequences tr_A0A0V1CNI4_A0A0V1CNI4_TRIBR_45882 and tr_A0A0V0UBD9_A0A0V0UBD9_9BILA_144512 are exactly identical! WARNING: Sequences tr_A0A0V0WZD4_A0A0V0WZD4_9BILA_92179 and tr_A0A0V1L7R6_A0A0V1L7R6_9BILA_6335 are exactly identical! WARNING: Sequences tr_A0A0V0WZD4_A0A0V0WZD4_9BILA_92179 and tr_A0A0V1A4S9_A0A0V1A4S9_9BILA_990121 are exactly identical! WARNING: Sequences tr_A0A0V0VQC3_A0A0V0VQC3_9BILA_181606 and tr_A0A0V0U0F5_A0A0V0U0F5_9BILA_144512 are exactly identical! WARNING: Sequences tr_A0A0V1MF23_A0A0V1MF23_9BILA_268474 and tr_A0A0V1HIN3_A0A0V1HIN3_9BILA_268475 are exactly identical! WARNING: Sequences tr_A0A151X3Z7_A0A151X3Z7_9HYME_64791 and tr_A0A195EEZ0_A0A195EEZ0_9HYME_471704 are exactly identical! WARNING: Sequences tr_A0A151XBV7_A0A151XBV7_9HYME_64791 and tr_A0A195B7N6_A0A195B7N6_9HYME_520822 are exactly identical! WARNING: Sequences tr_A0A1S3L2W4_A0A1S3L2W4_SALSA_8030 and tr_A0A1S3L2Y8_A0A1S3L2Y8_SALSA_8030 are exactly identical! WARNING: Sequences tr_A0A0M4EHP2_A0A0M4EHP2_DROBS_30019 and tr_A0A0M4ELI0_A0A0M4ELI0_DROBS_30019 are exactly identical! WARNING: Sequences tr_A0A226MPF9_A0A226MPF9_CALSU_9009 and tr_A0A226PJS0_A0A226PJS0_COLVI_9014 are exactly identical! WARNING: Sequences tr_A0A226NE92_A0A226NE92_CALSU_9009 and tr_A0A226P938_A0A226P938_COLVI_9014 are exactly identical! WARNING: Sequences tr_A0A2D0RHF8_A0A2D0RHF8_ICTPU_7998 and tr_A0A2D0RHG1_A0A2D0RHG1_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0RHF8_A0A2D0RHF8_ICTPU_7998 and tr_A0A2D0RJ71_A0A2D0RJ71_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0RJR3_A0A2D0RJR3_ICTPU_7998 and tr_A0A2D0RJR4_A0A2D0RJR4_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0RJR3_A0A2D0RJR3_ICTPU_7998 and tr_A0A2D0RJU0_A0A2D0RJU0_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0SUY5_A0A2D0SUY5_ICTPU_7998 and tr_A0A2D0SUZ6_A0A2D0SUZ6_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2I1GVX0_A0A2I1GVX0_9GLOM_588596 and tr_A0A2H5RNG7_A0A2H5RNG7_RHIID_747089 are exactly identical! WARNING: Sequences tr_A0A2N5SEY2_A0A2N5SEY2_9BASI_200324 and tr_A0A2N5UM15_A0A2N5UM15_9BASI_200324 are exactly identical! WARNING: Sequences tr_A0A2A3ESY5_A0A2A3ESY5_APICC_94128 and tr_A0A2A3ET12_A0A2A3ET12_APICC_94128 are exactly identical! WARNING: Sequences tr_A0A2U4ABZ8_A0A2U4ABZ8_TURTR_9739 and tr_A0A2Y9SB89_A0A2Y9SB89_PHYCD_9755 are exactly identical! WARNING: Sequences tr_A0A2U4BKB8_A0A2U4BKB8_TURTR_9739 and tr_A0A2Y9N8A0_A0A2Y9N8A0_DELLE_9749 are exactly identical! WARNING: Sequences tr_A0A2Y9M567_A0A2Y9M567_DELLE_9749 and tr_A0A2Y9SYY4_A0A2Y9SYY4_PHYCD_9755 are exactly identical! WARNING: Sequences tr_A0A2Y9M567_A0A2Y9M567_DELLE_9749 and tr_A0A384A1J0_A0A384A1J0_BALAS_310752 are exactly identical! WARNING: Duplicate sequences found: 93 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/Q9BT40/3_mltree/Q9BT40.raxml.reduced.phy Alignment comprises 1 partitions and 273 patterns Partition 0: noname Model: LG4X+R4 Alignment sites / patterns: 273 / 273 Gaps: 2.18 % Invariant sites: 2.20 % NOTE: Binary MSA file created: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q9BT40/3_mltree/Q9BT40.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 / 273 / 21840 [00:00:00] Data distribution: max. searches per worker: 4 Starting ML tree search with 20 distinct starting trees [00:00:00 -506505.604053] Initial branch length optimization [00:00:07 -423007.990874] Model parameter optimization (eps = 10.000000) [00:01:07 -422436.560285] AUTODETECT spr round 1 (radius: 5) [00:05:01 -292745.607239] AUTODETECT spr round 2 (radius: 10) [00:09:21 -217803.099846] AUTODETECT spr round 3 (radius: 15) [00:14:03 -183003.604996] AUTODETECT spr round 4 (radius: 20) [00:19:48 -169775.194319] AUTODETECT spr round 5 (radius: 25) [00:26:29 -154075.840169] SPR radius for FAST iterations: 25 (autodetect) [00:26:29 -154075.840169] Model parameter optimization (eps = 3.000000) [00:27:07 -153913.514769] FAST spr round 1 (radius: 25) [00:31:37 -130202.446256] FAST spr round 2 (radius: 25) [00:34:59 -128656.473640] FAST spr round 3 (radius: 25) [00:37:45 -128383.221079] FAST spr round 4 (radius: 25) [00:40:03 -128372.282412] FAST spr round 5 (radius: 25) [00:42:15 -128368.739713] FAST spr round 6 (radius: 25) [00:44:28 -128368.738622] Model parameter optimization (eps = 1.000000) [00:44:44 -128363.485129] SLOW spr round 1 (radius: 5) [00:48:00 -128325.973802] SLOW spr round 2 (radius: 5) [00:51:10 -128319.750823] SLOW spr round 3 (radius: 5) [00:54:09 -128318.218524] SLOW spr round 4 (radius: 5) [00:57:06 -128318.218428] SLOW spr round 5 (radius: 10) [01:00:01 -128318.218428] SLOW spr round 6 (radius: 15) [01:04:54 -128318.218385] SLOW spr round 7 (radius: 20) [01:12:37 -128318.218385] SLOW spr round 8 (radius: 25) [01:19:38] [worker #3] ML tree search #4, logLikelihood: -128309.328858 [01:20:05] [worker #2] ML tree search #3, logLikelihood: -128323.502296 [01:22:12 -128318.218385] Model parameter optimization (eps = 0.100000) [01:22:19] [worker #0] ML tree search #1, logLikelihood: -128318.208269 [01:22:19 -501361.458024] Initial branch length optimization [01:22:26 -420088.798153] Model parameter optimization (eps = 10.000000) [01:22:50] [worker #4] ML tree search #5, logLikelihood: -128316.377778 [01:23:10] [worker #1] ML tree search #2, logLikelihood: -128341.491008 [01:23:37 -419447.832730] AUTODETECT spr round 1 (radius: 5) [01:27:31 -288170.410851] AUTODETECT spr round 2 (radius: 10) [01:31:50 -202260.437928] AUTODETECT spr round 3 (radius: 15) [01:36:01 -164764.877402] AUTODETECT spr round 4 (radius: 20) [01:41:15 -154943.606886] AUTODETECT spr round 5 (radius: 25) [01:47:12 -147533.333757] SPR radius for FAST iterations: 25 (autodetect) [01:47:12 -147533.333757] Model parameter optimization (eps = 3.000000) [01:47:45 -147451.165454] FAST spr round 1 (radius: 25) [01:52:01 -129401.394258] FAST spr round 2 (radius: 25) [01:55:15 -128500.028812] FAST spr round 3 (radius: 25) [01:58:02 -128401.479942] FAST spr round 4 (radius: 25) [02:00:37 -128372.128330] FAST spr round 5 (radius: 25) [02:02:58 -128370.038019] FAST spr round 6 (radius: 25) [02:05:13 -128370.036571] Model parameter optimization (eps = 1.000000) [02:05:28 -128366.937230] SLOW spr round 1 (radius: 5) [02:08:44 -128334.516849] SLOW spr round 2 (radius: 5) [02:11:55 -128328.725009] SLOW spr round 3 (radius: 5) [02:15:03 -128325.456433] SLOW spr round 4 (radius: 5) [02:18:09 -128323.922068] SLOW spr round 5 (radius: 5) [02:21:12 -128320.871143] SLOW spr round 6 (radius: 5) [02:24:10 -128320.088759] SLOW spr round 7 (radius: 5) [02:27:08 -128319.081698] SLOW spr round 8 (radius: 5) [02:30:05 -128319.081637] SLOW spr round 9 (radius: 10) [02:33:05 -128316.890295] SLOW spr round 10 (radius: 5) [02:36:56 -128312.214790] SLOW spr round 11 (radius: 5) [02:37:37] [worker #4] ML tree search #10, logLikelihood: -128336.048271 [02:39:09] [worker #1] ML tree search #7, logLikelihood: -128337.369825 [02:40:19 -128311.050006] SLOW spr round 12 (radius: 5) [02:40:27] [worker #2] ML tree search #8, logLikelihood: -128339.929650 [02:43:27 -128311.049975] SLOW spr round 13 (radius: 10) [02:43:53] [worker #3] ML tree search #9, logLikelihood: -128342.120146 [02:46:28 -128311.049975] SLOW spr round 14 (radius: 15) [02:51:16 -128311.049975] SLOW spr round 15 (radius: 20) [02:58:35 -128311.049975] SLOW spr round 16 (radius: 25) [03:08:05 -128311.049975] Model parameter optimization (eps = 0.100000) [03:08:15] [worker #0] ML tree search #6, logLikelihood: -128310.922386 [03:08:16 -506805.212170] Initial branch length optimization [03:08:25 -423813.204312] Model parameter optimization (eps = 10.000000) [03:09:19 -423203.625673] AUTODETECT spr round 1 (radius: 5) [03:13:19 -286492.201311] AUTODETECT spr round 2 (radius: 10) [03:17:41 -211014.349736] AUTODETECT spr round 3 (radius: 15) [03:22:30 -178828.926124] AUTODETECT spr round 4 (radius: 20) [03:27:39 -161862.114852] AUTODETECT spr round 5 (radius: 25) [03:33:19 -151690.889881] SPR radius for FAST iterations: 25 (autodetect) [03:33:19 -151690.889881] Model parameter optimization (eps = 3.000000) [03:33:47 -151605.690979] FAST spr round 1 (radius: 25) [03:37:58 -129739.976140] FAST spr round 2 (radius: 25) [03:41:00 -128479.195732] FAST spr round 3 (radius: 25) [03:43:43 -128408.092982] FAST spr round 4 (radius: 25) [03:46:09 -128392.045675] FAST spr round 5 (radius: 25) [03:48:27 -128390.363227] FAST spr round 6 (radius: 25) [03:50:41 -128390.363195] Model parameter optimization (eps = 1.000000) [03:51:01 -128381.310997] SLOW spr round 1 (radius: 5) [03:54:18 -128338.390047] SLOW spr round 2 (radius: 5) [03:57:27 -128331.489060] SLOW spr round 3 (radius: 5) [03:57:32] [worker #1] ML tree search #12, logLikelihood: -128317.148704 [03:58:23] [worker #4] ML tree search #15, logLikelihood: -128319.799744 [04:00:37 -128322.135983] SLOW spr round 4 (radius: 5) [04:03:37 -128322.135049] SLOW spr round 5 (radius: 10) [04:06:38 -128319.816056] SLOW spr round 6 (radius: 5) [04:10:29 -128319.036329] SLOW spr round 7 (radius: 5) [04:11:22] [worker #2] ML tree search #13, logLikelihood: -128317.605294 [04:13:50 -128319.036329] SLOW spr round 8 (radius: 10) [04:15:02] [worker #3] ML tree search #14, logLikelihood: -128314.642445 [04:16:56 -128319.036329] SLOW spr round 9 (radius: 15) [04:21:44 -128319.036329] SLOW spr round 10 (radius: 20) [04:29:27 -128319.036329] SLOW spr round 11 (radius: 25) [04:39:53 -128319.036329] Model parameter optimization (eps = 0.100000) [04:40:00] [worker #0] ML tree search #11, logLikelihood: -128319.002996 [04:40:00 -503967.280389] Initial branch length optimization [04:40:07 -421569.726034] Model parameter optimization (eps = 10.000000) [04:41:02 -420994.528666] AUTODETECT spr round 1 (radius: 5) [04:44:53 -288578.301087] AUTODETECT spr round 2 (radius: 10) [04:48:47 -227606.889084] AUTODETECT spr round 3 (radius: 15) [04:53:02 -181364.230120] AUTODETECT spr round 4 (radius: 20) [04:57:51 -157526.903600] AUTODETECT spr round 5 (radius: 25) [05:03:48 -152271.514531] SPR radius for FAST iterations: 25 (autodetect) [05:03:48 -152271.514531] Model parameter optimization (eps = 3.000000) [05:04:17 -152168.104213] FAST spr round 1 (radius: 25) [05:08:58 -130129.835756] FAST spr round 2 (radius: 25) [05:12:15 -128487.108043] FAST spr round 3 (radius: 25) [05:14:56 -128372.059193] FAST spr round 4 (radius: 25) [05:17:18 -128369.547960] FAST spr round 5 (radius: 25) [05:17:46] [worker #1] ML tree search #17, logLikelihood: -128311.823636 [05:19:33 -128369.547878] Model parameter optimization (eps = 1.000000) [05:19:54 -128360.336711] SLOW spr round 1 (radius: 5) [05:23:06 -128334.598123] SLOW spr round 2 (radius: 5) [05:26:12 -128333.555856] SLOW spr round 3 (radius: 5) [05:26:48] [worker #2] ML tree search #18, logLikelihood: -128315.600931 [05:28:08] [worker #4] ML tree search #20, logLikelihood: -128325.376440 [05:29:12 -128333.555621] SLOW spr round 4 (radius: 10) [05:32:10 -128329.838496] SLOW spr round 5 (radius: 5) [05:35:58 -128329.838054] SLOW spr round 6 (radius: 10) [05:39:15 -128329.837855] SLOW spr round 7 (radius: 15) [05:43:49 -128329.837658] SLOW spr round 8 (radius: 20) [05:48:46] [worker #3] ML tree search #19, logLikelihood: -128331.918571 [05:51:37 -128329.837462] SLOW spr round 9 (radius: 25) [06:01:35 -128329.837266] Model parameter optimization (eps = 0.100000) [06:01:46] [worker #0] ML tree search #16, logLikelihood: -128329.791928 Optimized model parameters: Partition 0: noname Rate heterogeneity: FREE (4 cats, mean), weights&rates: (0.175232,0.361692) (0.323358,0.502006) (0.300439,1.044637) (0.200971,2.291093) 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: -128309.328858 AIC score: 260628.657716 / AICc score: 8304688.657716 / BIC score: 267865.648665 Free parameters (model + branch lengths): 2005 WARNING: Number of free parameters (K=2005) is larger than alignment size (n=273). 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/Q9BT40/3_mltree/Q9BT40.raxml.bestTree All ML trees saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q9BT40/3_mltree/Q9BT40.raxml.mlTrees Optimized model saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q9BT40/3_mltree/Q9BT40.raxml.bestModel Execution log saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q9BT40/3_mltree/Q9BT40.raxml.log Analysis started: 03-Jul-2021 01:07:04 / finished: 03-Jul-2021 07:08:51 Elapsed time: 21707.095 seconds Consumed energy: 2036.362 Wh (= 10 km in an electric car, or 51 km with an e-scooter!)