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 05-Jul-2021 20:20:48 as follows: raxml-ng --msa /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q7Z5Y6/2_msa/Q7Z5Y6_trimmed_msa.fasta --data-type AA --model LG4X --prefix /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q7Z5Y6/3_mltree/Q7Z5Y6 --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: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q7Z5Y6/2_msa/Q7Z5Y6_trimmed_msa.fasta [00:00:00] Loaded alignment with 1001 taxa and 293 sites WARNING: Sequences tr_B4QB06_B4QB06_DROSI_7240 and sp_P27091_60A_DROME_7227 are exactly identical! WARNING: Sequences tr_B4QB06_B4QB06_DROSI_7240 and tr_B4I8U4_B4I8U4_DROSE_7238 are exactly identical! WARNING: Sequences tr_E1C0T2_E1C0T2_CHICK_9031 and tr_A0A226MNG7_A0A226MNG7_CALSU_9009 are exactly identical! WARNING: Sequences tr_E1C0T2_E1C0T2_CHICK_9031 and tr_A0A226P2H3_A0A226P2H3_COLVI_9014 are exactly identical! WARNING: Sequences tr_P87373_P87373_CHICK_9031 and tr_G1NMB0_G1NMB0_MELGA_9103 are exactly identical! WARNING: Sequences tr_P87373_P87373_CHICK_9031 and tr_U3JGJ4_U3JGJ4_FICAL_59894 are exactly identical! WARNING: Sequences tr_P87373_P87373_CHICK_9031 and tr_A0A091J5V0_A0A091J5V0_EGRGA_188379 are exactly identical! WARNING: Sequences tr_P87373_P87373_CHICK_9031 and tr_A0A091VXT6_A0A091VXT6_NIPNI_128390 are exactly identical! WARNING: Sequences tr_P87373_P87373_CHICK_9031 and tr_A0A087R301_A0A087R301_APTFO_9233 are exactly identical! WARNING: Sequences tr_P87373_P87373_CHICK_9031 and tr_A0A093HXR7_A0A093HXR7_STRCA_441894 are exactly identical! WARNING: Sequences tr_P87373_P87373_CHICK_9031 and tr_A0A091I476_A0A091I476_CALAN_9244 are exactly identical! WARNING: Sequences sp_P23359_BMP7_MOUSE_10090 and tr_G3V6W8_G3V6W8_RAT_10116 are exactly identical! WARNING: Sequences tr_M3Y272_M3Y272_MUSPF_9669 and tr_W5QIU1_W5QIU1_SHEEP_9940 are exactly identical! WARNING: Sequences tr_M3Y272_M3Y272_MUSPF_9669 and tr_A7LJT9_A7LJT9_PIG_9823 are exactly identical! WARNING: Sequences tr_M3Y272_M3Y272_MUSPF_9669 and tr_D2HCK9_D2HCK9_AILME_9646 are exactly identical! WARNING: Sequences tr_M3Y272_M3Y272_MUSPF_9669 and sp_Q2KJH1_BMP4_BOVIN_9913 are exactly identical! WARNING: Sequences tr_M3Y272_M3Y272_MUSPF_9669 and tr_A0A2U3Z034_A0A2U3Z034_LEPWE_9713 are exactly identical! WARNING: Sequences tr_M3Y272_M3Y272_MUSPF_9669 and tr_A0A384CYI9_A0A384CYI9_URSMA_29073 are exactly identical! WARNING: Sequences tr_M3Z276_M3Z276_MUSPF_9669 and tr_G1P2I8_G1P2I8_MYOLU_59463 are exactly identical! WARNING: Sequences tr_G1QSM4_G1QSM4_NOMLE_61853 and tr_H2QT84_H2QT84_PANTR_9598 are exactly identical! WARNING: Sequences tr_G1QSM4_G1QSM4_NOMLE_61853 and sp_P22003_BMP5_HUMAN_9606 are exactly identical! WARNING: Sequences tr_G1QSM4_G1QSM4_NOMLE_61853 and tr_F7H4M7_F7H4M7_MACMU_9544 are exactly identical! WARNING: Sequences tr_G1QSM4_G1QSM4_NOMLE_61853 and tr_G7P2W6_G7P2W6_MACFA_9541 are exactly identical! WARNING: Sequences tr_G1QSM4_G1QSM4_NOMLE_61853 and tr_A0A2K5MWP5_A0A2K5MWP5_CERAT_9531 are exactly identical! WARNING: Sequences tr_G1QSM4_G1QSM4_NOMLE_61853 and tr_A0A2K6C242_A0A2K6C242_MACNE_9545 are exactly identical! WARNING: Sequences tr_G1QSM4_G1QSM4_NOMLE_61853 and tr_A0A2K5XQZ9_A0A2K5XQZ9_MANLE_9568 are exactly identical! WARNING: Sequences tr_G1QSM4_G1QSM4_NOMLE_61853 and tr_A0A2R8Z8H0_A0A2R8Z8H0_PANPA_9597 are exactly identical! WARNING: Sequences tr_G3RG26_G3RG26_GORGO_9595 and tr_H2Q8B9_H2Q8B9_PANTR_9598 are exactly identical! WARNING: Sequences tr_G3RG26_G3RG26_GORGO_9595 and sp_P12644_BMP4_HUMAN_9606 are exactly identical! WARNING: Sequences tr_G3RG26_G3RG26_GORGO_9595 and tr_F7ACJ7_F7ACJ7_MACMU_9544 are exactly identical! WARNING: Sequences tr_G3RG26_G3RG26_GORGO_9595 and tr_G8F272_G8F272_MACFA_9541 are exactly identical! WARNING: Sequences tr_G3RG26_G3RG26_GORGO_9595 and tr_B0CM38_B0CM38_PAPAN_9555 are exactly identical! WARNING: Sequences tr_G3RG26_G3RG26_GORGO_9595 and tr_A0A0D9RQR1_A0A0D9RQR1_CHLSB_60711 are exactly identical! WARNING: Sequences tr_G3RG26_G3RG26_GORGO_9595 and tr_A0A2K5NPX8_A0A2K5NPX8_CERAT_9531 are exactly identical! WARNING: Sequences tr_G3RG26_G3RG26_GORGO_9595 and tr_A0A2K6CR04_A0A2K6CR04_MACNE_9545 are exactly identical! WARNING: Sequences tr_G3RG26_G3RG26_GORGO_9595 and tr_A0A2K6AGA5_A0A2K6AGA5_MANLE_9568 are exactly identical! WARNING: Sequences tr_G3RZN8_G3RZN8_GORGO_9595 and tr_A0A0D9RM38_A0A0D9RM38_CHLSB_60711 are exactly identical! WARNING: Sequences tr_A0A2J8VJ76_A0A2J8VJ76_PONAB_9601 and tr_B0CM78_B0CM78_PAPAN_9555 are exactly identical! WARNING: Sequences tr_A0A2J8VJ76_A0A2J8VJ76_PONAB_9601 and tr_A0A0D9RDH1_A0A0D9RDH1_CHLSB_60711 are exactly identical! WARNING: Sequences tr_A0A2J8VJ76_A0A2J8VJ76_PONAB_9601 and tr_A0A2K5NAV9_A0A2K5NAV9_CERAT_9531 are exactly identical! WARNING: Sequences tr_A0A2J8VJ76_A0A2J8VJ76_PONAB_9601 and tr_A0A2K6BCE3_A0A2K6BCE3_MACNE_9545 are exactly identical! WARNING: Sequences tr_A0A2J8VJ76_A0A2J8VJ76_PONAB_9601 and tr_A0A2K5Z7Q6_A0A2K5Z7Q6_MANLE_9568 are exactly identical! WARNING: Sequences tr_G1NA46_G1NA46_MELGA_9103 and tr_A0A093HWJ3_A0A093HWJ3_STRCA_441894 are exactly identical! WARNING: Sequences tr_E2RNJ0_E2RNJ0_CANLF_9615 and tr_G3TG31_G3TG31_LOXAF_9785 are exactly identical! WARNING: Sequences tr_E2RNJ0_E2RNJ0_CANLF_9615 and tr_A0A1U7UVW7_A0A1U7UVW7_TARSY_1868482 are exactly identical! WARNING: Sequences tr_E2RNJ0_E2RNJ0_CANLF_9615 and tr_A0A2Y9RTD5_A0A2Y9RTD5_TRIMA_127582 are exactly identical! WARNING: Sequences tr_J9P401_J9P401_CANLF_9615 and tr_A0A2U3Z3S1_A0A2U3Z3S1_LEPWE_9713 are exactly identical! WARNING: Sequences tr_J9P6P0_J9P6P0_CANLF_9615 and tr_H2QKM7_H2QKM7_PANTR_9598 are exactly identical! WARNING: Sequences tr_J9P6P0_J9P6P0_CANLF_9615 and sp_P18075_BMP7_HUMAN_9606 are exactly identical! WARNING: Sequences tr_J9P6P0_J9P6P0_CANLF_9615 and tr_A0A096NNJ3_A0A096NNJ3_PAPAN_9555 are exactly identical! WARNING: Sequences tr_J9P6P0_J9P6P0_CANLF_9615 and tr_A0A0D9RSE9_A0A0D9RSE9_CHLSB_60711 are exactly identical! WARNING: Sequences tr_J9P6P0_J9P6P0_CANLF_9615 and tr_A0A2K5KKN9_A0A2K5KKN9_CERAT_9531 are exactly identical! WARNING: Sequences tr_J9P6P0_J9P6P0_CANLF_9615 and tr_A0A2R9AT21_A0A2R9AT21_PANPA_9597 are exactly identical! WARNING: Sequences tr_J9P6P0_J9P6P0_CANLF_9615 and tr_A0A2Y9IPN4_A0A2Y9IPN4_ENHLU_391180 are exactly identical! WARNING: Sequences tr_B0XHY0_B0XHY0_CULQU_7176 and tr_B0XHY1_B0XHY1_CULQU_7176 are exactly identical! WARNING: Sequences tr_M3ZUZ0_M3ZUZ0_XIPMA_8083 and tr_A0A087XTC9_A0A087XTC9_POEFO_48698 are exactly identical! WARNING: Sequences tr_A0A088AQN8_A0A088AQN8_APIME_7460 and tr_A0A2A3EIB7_A0A2A3EIB7_APICC_94128 are exactly identical! WARNING: Sequences tr_A0A158P1S4_A0A158P1S4_ATTCE_12957 and tr_A0A195BSU4_A0A195BSU4_9HYME_520822 are exactly identical! WARNING: Sequences sp_P12643_BMP2_HUMAN_9606 and tr_A0A2R9ABN7_A0A2R9ABN7_PANPA_9597 are exactly identical! WARNING: Sequences tr_H0ZRG8_H0ZRG8_TAEGU_59729 and tr_A0A226P9Y7_A0A226P9Y7_COLVI_9014 are exactly identical! WARNING: Sequences tr_D2HR91_D2HR91_AILME_9646 and tr_A0A384D3I4_A0A384D3I4_URSMA_29073 are exactly identical! WARNING: Sequences tr_G7PGY1_G7PGY1_MACFA_9541 and tr_A0A2I3MVB6_A0A2I3MVB6_PAPAN_9555 are exactly identical! WARNING: Sequences tr_G7PGY1_G7PGY1_MACFA_9541 and tr_A0A2K6CS17_A0A2K6CS17_MACNE_9545 are exactly identical! WARNING: Sequences tr_A0A096MMW8_A0A096MMW8_PAPAN_9555 and tr_A0A2K5MTU4_A0A2K5MTU4_CERAT_9531 are exactly identical! WARNING: Sequences tr_A0A096NKT8_A0A096NKT8_PAPAN_9555 and tr_A0A2K5N9E7_A0A2K5N9E7_CERAT_9531 are exactly identical! WARNING: Sequences tr_A0A096NKT8_A0A096NKT8_PAPAN_9555 and tr_A0A2K6CHI7_A0A2K6CHI7_MACNE_9545 are exactly identical! WARNING: Sequences tr_A0A158PRG5_A0A158PRG5_BRUPA_6280 and tr_A0A0R3QMY1_A0A0R3QMY1_9BILA_42155 are exactly identical! WARNING: Sequences tr_A0A091EVJ8_A0A091EVJ8_CORBR_85066 and tr_A0A093PMM9_A0A093PMM9_9PASS_328815 are exactly identical! WARNING: Sequences tr_A0A091EVJ8_A0A091EVJ8_CORBR_85066 and tr_A0A0A0B527_A0A0A0B527_CHAVO_50402 are exactly identical! WARNING: Sequences tr_A0A091IZH0_A0A091IZH0_EGRGA_188379 and tr_A0A091VR03_A0A091VR03_NIPNI_128390 are exactly identical! WARNING: Sequences tr_A0A091K3C9_A0A091K3C9_EGRGA_188379 and tr_A0A091UPQ9_A0A091UPQ9_NIPNI_128390 are exactly identical! WARNING: Sequences tr_A0A091K3C9_A0A091K3C9_EGRGA_188379 and tr_A0A087R890_A0A087R890_APTFO_9233 are exactly identical! WARNING: Sequences tr_A0A091K3C9_A0A091K3C9_EGRGA_188379 and tr_A0A091W8G1_A0A091W8G1_OPIHO_30419 are exactly identical! WARNING: Sequences tr_A0A091K3C9_A0A091K3C9_EGRGA_188379 and tr_A0A0A0AKS8_A0A0A0AKS8_CHAVO_50402 are exactly identical! WARNING: Sequences tr_A0A091K3C9_A0A091K3C9_EGRGA_188379 and tr_A0A091IBT1_A0A091IBT1_CALAN_9244 are exactly identical! WARNING: Sequences tr_A0A0A0AKP2_A0A0A0AKP2_CHAVO_50402 and tr_A0A091HVH4_A0A091HVH4_CALAN_9244 are exactly identical! WARNING: Sequences tr_A0A2I0MU94_A0A2I0MU94_COLLI_8932 and tr_A0A1V4JML8_A0A1V4JML8_PATFA_372326 are exactly identical! WARNING: Sequences tr_A0A0V1CT11_A0A0V1CT11_TRIBR_45882 and tr_A0A0V0WSR4_A0A0V0WSR4_9BILA_92179 are exactly identical! WARNING: Sequences tr_A0A0V1CT11_A0A0V1CT11_TRIBR_45882 and tr_A0A0V0VIT9_A0A0V0VIT9_9BILA_181606 are exactly identical! WARNING: Sequences tr_A0A0V1CT11_A0A0V1CT11_TRIBR_45882 and tr_A0A0V1LAN0_A0A0V1LAN0_9BILA_6335 are exactly identical! WARNING: Sequences tr_A0A0V1CT11_A0A0V1CT11_TRIBR_45882 and tr_A0A0V1PEF8_A0A0V1PEF8_9BILA_92180 are exactly identical! WARNING: Sequences tr_A0A0V1CT11_A0A0V1CT11_TRIBR_45882 and tr_A0A0V0U9I7_A0A0V0U9I7_9BILA_144512 are exactly identical! WARNING: Sequences tr_A0A0V1D703_A0A0V1D703_TRIBR_45882 and tr_A0A0V1LLW5_A0A0V1LLW5_9BILA_6335 are exactly identical! WARNING: Sequences tr_A0A0V1D703_A0A0V1D703_TRIBR_45882 and tr_A0A0V0UFH5_A0A0V0UFH5_9BILA_144512 are exactly identical! WARNING: Sequences tr_A0A0V1AC85_A0A0V1AC85_9BILA_990121 and tr_A0A0V1P764_A0A0V1P764_9BILA_92180 are exactly identical! WARNING: Sequences tr_A0A0V1MPH6_A0A0V1MPH6_9BILA_268474 and tr_A0A0V1H5A1_A0A0V1H5A1_9BILA_268475 are exactly identical! WARNING: Sequences tr_A0A226MWB1_A0A226MWB1_CALSU_9009 and tr_A0A226PGR7_A0A226PGR7_COLVI_9014 are exactly identical! WARNING: Sequences tr_A0A226NDT4_A0A226NDT4_CALSU_9009 and tr_A0A226PL26_A0A226PL26_COLVI_9014 are exactly identical! WARNING: Sequences tr_A0A2U4B164_A0A2U4B164_TURTR_9739 and tr_A0A2U4B1M1_A0A2U4B1M1_TURTR_9739 are exactly identical! WARNING: Sequences tr_A0A2U4B164_A0A2U4B164_TURTR_9739 and tr_A0A2Y9NT83_A0A2Y9NT83_DELLE_9749 are exactly identical! WARNING: Sequences tr_A0A2U4B164_A0A2U4B164_TURTR_9739 and tr_A0A2Y9SH31_A0A2Y9SH31_PHYCD_9755 are exactly identical! WARNING: Sequences tr_A0A2U4B164_A0A2U4B164_TURTR_9739 and tr_A0A384AIG3_A0A384AIG3_BALAS_310752 are exactly identical! WARNING: Sequences tr_A0A2U4BV21_A0A2U4BV21_TURTR_9739 and tr_A0A2Y9LYV6_A0A2Y9LYV6_DELLE_9749 are exactly identical! WARNING: Sequences tr_A0A2U4BV21_A0A2U4BV21_TURTR_9739 and tr_A0A2Y9EJA8_A0A2Y9EJA8_PHYCD_9755 are exactly identical! WARNING: Sequences tr_A0A2U3VEP0_A0A2U3VEP0_ODORO_9708 and tr_A0A2U3YTC5_A0A2U3YTC5_LEPWE_9713 are exactly identical! WARNING: Sequences tr_A0A2U3W3B7_A0A2U3W3B7_ODORO_9708 and tr_A0A2U3X9N1_A0A2U3X9N1_LEPWE_9713 are exactly identical! WARNING: Sequences tr_A0A2Y9NAH8_A0A2Y9NAH8_DELLE_9749 and tr_A0A2Y9EIT4_A0A2Y9EIT4_PHYCD_9755 are exactly identical! WARNING: Sequences tr_A0A2Y9QCJ3_A0A2Y9QCJ3_DELLE_9749 and tr_A0A2Y9T1E2_A0A2Y9T1E2_PHYCD_9755 are exactly identical! WARNING: Duplicate sequences found: 98 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/Q7Z5Y6/3_mltree/Q7Z5Y6.raxml.reduced.phy Alignment comprises 1 partitions and 293 patterns Partition 0: noname Model: LG4X+R4 Alignment sites / patterns: 293 / 293 Gaps: 10.69 % Invariant sites: 0.34 % NOTE: Binary MSA file created: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q7Z5Y6/3_mltree/Q7Z5Y6.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 / 293 / 23440 [00:00:00] Data distribution: max. searches per worker: 4 Starting ML tree search with 20 distinct starting trees [00:00:00 -438800.403425] Initial branch length optimization [00:00:07 -353507.614894] Model parameter optimization (eps = 10.000000) [00:00:56 -353001.434636] AUTODETECT spr round 1 (radius: 5) [00:04:57 -235564.846385] AUTODETECT spr round 2 (radius: 10) [00:09:24 -169790.906440] AUTODETECT spr round 3 (radius: 15) [00:14:02 -137016.607809] AUTODETECT spr round 4 (radius: 20) [00:19:32 -120458.833531] AUTODETECT spr round 5 (radius: 25) [00:24:46 -113904.171505] SPR radius for FAST iterations: 25 (autodetect) [00:24:46 -113904.171505] Model parameter optimization (eps = 3.000000) [00:25:25 -113679.941448] FAST spr round 1 (radius: 25) [00:29:19 -95909.956934] FAST spr round 2 (radius: 25) [00:32:23 -94771.722257] FAST spr round 3 (radius: 25) [00:35:07 -94615.943518] FAST spr round 4 (radius: 25) [00:37:34 -94592.501716] FAST spr round 5 (radius: 25) [00:39:51 -94591.670038] FAST spr round 6 (radius: 25) [00:42:04 -94591.657943] Model parameter optimization (eps = 1.000000) [00:42:27 -94583.514273] SLOW spr round 1 (radius: 5) [00:45:30 -94557.177383] SLOW spr round 2 (radius: 5) [00:48:40 -94553.288293] SLOW spr round 3 (radius: 5) [00:52:08 -94553.285476] SLOW spr round 4 (radius: 10) [00:55:46 -94551.214081] SLOW spr round 5 (radius: 5) [01:00:10 -94551.213907] SLOW spr round 6 (radius: 10) [01:04:13 -94551.213883] SLOW spr round 7 (radius: 15) [01:09:21 -94551.213860] SLOW spr round 8 (radius: 20) [01:17:43 -94551.213838] SLOW spr round 9 (radius: 25) [01:25:31] [worker #2] ML tree search #3, logLikelihood: -94544.786263 [01:28:24 -94551.213817] Model parameter optimization (eps = 0.100000) [01:28:37] [worker #0] ML tree search #1, logLikelihood: -94551.062532 [01:28:38 -438774.961252] Initial branch length optimization [01:28:44 -352837.975198] Model parameter optimization (eps = 10.000000) [01:29:44 -352392.722487] AUTODETECT spr round 1 (radius: 5) [01:31:41] [worker #1] ML tree search #2, logLikelihood: -94546.083695 [01:34:01 -233411.851378] AUTODETECT spr round 2 (radius: 10) [01:34:14] [worker #5] ML tree search #6, logLikelihood: -94532.305561 [01:36:57] [worker #4] ML tree search #5, logLikelihood: -94540.654042 [01:38:51 -171460.887407] AUTODETECT spr round 3 (radius: 15) [01:43:47 -138687.490142] AUTODETECT spr round 4 (radius: 20) [01:47:56] [worker #3] ML tree search #4, logLikelihood: -94607.553585 [01:49:15 -120481.449812] AUTODETECT spr round 5 (radius: 25) [01:55:40 -112208.817259] SPR radius for FAST iterations: 25 (autodetect) [01:55:40 -112208.817259] Model parameter optimization (eps = 3.000000) [01:56:18 -111987.562692] FAST spr round 1 (radius: 25) [02:01:07 -95445.148510] FAST spr round 2 (radius: 25) [02:04:39 -94627.758818] FAST spr round 3 (radius: 25) [02:07:48 -94596.657007] FAST spr round 4 (radius: 25) [02:10:39 -94592.120996] FAST spr round 5 (radius: 25) [02:13:21 -94592.119325] Model parameter optimization (eps = 1.000000) [02:13:46 -94583.981292] SLOW spr round 1 (radius: 5) [02:17:23 -94554.452424] SLOW spr round 2 (radius: 5) [02:20:52 -94552.331387] SLOW spr round 3 (radius: 5) [02:24:14 -94552.329772] SLOW spr round 4 (radius: 10) [02:27:48 -94549.075367] SLOW spr round 5 (radius: 5) [02:32:08 -94548.785712] SLOW spr round 6 (radius: 5) [02:35:58 -94548.785670] SLOW spr round 7 (radius: 10) [02:39:43 -94548.785638] SLOW spr round 8 (radius: 15) [02:45:22 -94545.585828] SLOW spr round 9 (radius: 5) [02:50:04 -94545.581008] SLOW spr round 10 (radius: 10) [02:54:21 -94545.580504] SLOW spr round 11 (radius: 15) [02:59:48 -94545.580157] SLOW spr round 12 (radius: 20) [03:08:56 -94545.579915] SLOW spr round 13 (radius: 25) [03:10:03] [worker #4] ML tree search #11, logLikelihood: -94544.192452 [03:19:35] [worker #1] ML tree search #8, logLikelihood: -94537.701739 [03:20:27 -94545.579745] Model parameter optimization (eps = 0.100000) [03:20:41] [worker #0] ML tree search #7, logLikelihood: -94545.421614 [03:20:41 -438330.384854] Initial branch length optimization [03:20:48 -352869.809413] Model parameter optimization (eps = 10.000000) [03:21:55 -352406.366533] AUTODETECT spr round 1 (radius: 5) [03:24:07] [worker #5] ML tree search #12, logLikelihood: -94536.673787 [03:24:33] [worker #3] ML tree search #10, logLikelihood: -94537.919083 [03:24:56] [worker #2] ML tree search #9, logLikelihood: -94533.239079 [03:26:22 -236301.901829] AUTODETECT spr round 2 (radius: 10) [03:31:08 -175938.990620] AUTODETECT spr round 3 (radius: 15) [03:36:09 -137051.358396] AUTODETECT spr round 4 (radius: 20) [03:41:59 -120968.069255] AUTODETECT spr round 5 (radius: 25) [03:50:15 -113174.390131] SPR radius for FAST iterations: 25 (autodetect) [03:50:15 -113174.390131] Model parameter optimization (eps = 3.000000) [03:50:50 -112935.909963] FAST spr round 1 (radius: 25) [03:55:31 -95170.548981] FAST spr round 2 (radius: 25) [03:58:57 -94691.425712] FAST spr round 3 (radius: 25) [04:02:08 -94621.091049] FAST spr round 4 (radius: 25) [04:05:05 -94609.223633] FAST spr round 5 (radius: 25) [04:07:45 -94609.223352] Model parameter optimization (eps = 1.000000) [04:08:10 -94586.193355] SLOW spr round 1 (radius: 5) [04:11:48 -94560.964254] SLOW spr round 2 (radius: 5) [04:15:25 -94551.535557] SLOW spr round 3 (radius: 5) [04:18:58 -94551.534814] SLOW spr round 4 (radius: 10) [04:22:29 -94550.960671] SLOW spr round 5 (radius: 5) [04:26:52 -94550.960127] SLOW spr round 6 (radius: 10) [04:30:47 -94550.960046] SLOW spr round 7 (radius: 15) [04:35:50 -94549.399947] SLOW spr round 8 (radius: 5) [04:40:21 -94549.399838] SLOW spr round 9 (radius: 10) [04:44:31 -94549.399787] SLOW spr round 10 (radius: 15) [04:49:29 -94549.399740] SLOW spr round 11 (radius: 20) [04:56:36] [worker #4] ML tree search #17, logLikelihood: -94539.333758 [04:57:38 -94549.399696] SLOW spr round 12 (radius: 25) [05:00:20] [worker #2] ML tree search #15, logLikelihood: -94548.003485 [05:04:01] [worker #1] ML tree search #14, logLikelihood: -94529.290909 [05:04:07] [worker #5] ML tree search #18, logLikelihood: -94534.933376 [05:07:43 -94549.399655] Model parameter optimization (eps = 0.100000) [05:07:58] [worker #0] ML tree search #13, logLikelihood: -94549.050935 [05:07:58 -438571.731786] Initial branch length optimization [05:08:05 -353648.911432] Model parameter optimization (eps = 10.000000) [05:09:02 -353143.309139] AUTODETECT spr round 1 (radius: 5) [05:11:58] [worker #3] ML tree search #16, logLikelihood: -94565.907398 [05:13:20 -230950.775442] AUTODETECT spr round 2 (radius: 10) [05:18:06 -174766.863670] AUTODETECT spr round 3 (radius: 15) [05:23:05 -141078.008669] AUTODETECT spr round 4 (radius: 20) [05:28:37 -122362.694293] AUTODETECT spr round 5 (radius: 25) [05:35:23 -114581.594993] SPR radius for FAST iterations: 25 (autodetect) [05:35:23 -114581.594993] Model parameter optimization (eps = 3.000000) [05:36:10 -114306.828565] FAST spr round 1 (radius: 25) [05:41:26 -96075.032876] FAST spr round 2 (radius: 25) [05:44:48 -94724.613853] FAST spr round 3 (radius: 25) [05:47:44 -94630.927361] FAST spr round 4 (radius: 25) [05:50:34 -94615.037465] FAST spr round 5 (radius: 25) [05:53:10 -94614.212105] FAST spr round 6 (radius: 25) [05:55:41 -94614.211975] Model parameter optimization (eps = 1.000000) [05:56:03 -94611.394283] SLOW spr round 1 (radius: 5) [05:59:48 -94578.076811] SLOW spr round 2 (radius: 5) [06:03:17 -94570.580108] SLOW spr round 3 (radius: 5) [06:06:34 -94570.577010] SLOW spr round 4 (radius: 10) [06:10:02 -94563.453567] SLOW spr round 5 (radius: 5) [06:14:19 -94563.251300] SLOW spr round 6 (radius: 5) [06:18:05 -94563.249496] SLOW spr round 7 (radius: 10) [06:21:40 -94560.758433] SLOW spr round 8 (radius: 5) [06:25:56 -94555.239339] SLOW spr round 9 (radius: 5) [06:29:40 -94552.425705] SLOW spr round 10 (radius: 5) [06:33:08 -94552.425339] SLOW spr round 11 (radius: 10) [06:34:09] [worker #1] ML tree search #20, logLikelihood: -94542.261018 [06:36:33 -94552.425279] SLOW spr round 12 (radius: 15) [06:44:47 -94549.721446] SLOW spr round 13 (radius: 5) [06:51:45 -94549.721422] SLOW spr round 14 (radius: 10) [06:58:10 -94549.721406] SLOW spr round 15 (radius: 15) [07:05:57 -94549.721394] SLOW spr round 16 (radius: 20) [07:18:34 -94549.721384] SLOW spr round 17 (radius: 25) [07:34:19 -94549.721376] Model parameter optimization (eps = 0.100000) [07:34:42] [worker #0] ML tree search #19, logLikelihood: -94549.662454 Optimized model parameters: Partition 0: noname Rate heterogeneity: FREE (4 cats, mean), weights&rates: (0.206008,0.275837) (0.130260,0.641937) (0.367005,0.801947) (0.296727,1.904907) 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: -94529.290909 AIC score: 193068.581818 / AICc score: 8237128.581818 / BIC score: 200447.327899 Free parameters (model + branch lengths): 2005 WARNING: Number of free parameters (K=2005) is larger than alignment size (n=293). 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/Q7Z5Y6/3_mltree/Q7Z5Y6.raxml.bestTree All ML trees saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q7Z5Y6/3_mltree/Q7Z5Y6.raxml.mlTrees Optimized model saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q7Z5Y6/3_mltree/Q7Z5Y6.raxml.bestModel Execution log saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q7Z5Y6/3_mltree/Q7Z5Y6.raxml.log Analysis started: 05-Jul-2021 20:20:48 / finished: 06-Jul-2021 03:55:31 Elapsed time: 27283.176 seconds Consumed energy: 2487.941 Wh (= 12 km in an electric car, or 62 km with an e-scooter!)