RAxML-NG v. 1.0.2 released on 22.02.2021 by The Exelixis Lab. Developed by: Alexey M. Kozlov and Alexandros Stamatakis. Contributors: Diego Darriba, Tomas Flouri, Benoit Morel, Sarah Lutteropp, Ben Bettisworth. Latest version: https://github.com/amkozlov/raxml-ng Questions/problems/suggestions? Please visit: https://groups.google.com/forum/#!forum/raxml System: Intel(R) Xeon(R) Gold 6148 CPU @ 2.40GHz, 40 cores, 376 GB RAM RAxML-NG was called at 06-Jul-2021 05:11:30 as follows: raxml-ng --msa /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q92785/2_msa/Q92785_trimmed_msa.fasta --data-type AA --model LG4X --prefix /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q92785/3_mltree/Q92785 --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/Q92785/2_msa/Q92785_trimmed_msa.fasta [00:00:00] Loaded alignment with 1001 taxa and 350 sites WARNING: Sequences tr_F1NT94_F1NT94_CHICK_9031 and tr_G1MW59_G1MW59_MELGA_9103 are exactly identical! WARNING: Sequences tr_M3XW45_M3XW45_MUSPF_9669 and tr_A0A1U7U312_A0A1U7U312_TARSY_1868482 are exactly identical! WARNING: Sequences tr_M3XW45_M3XW45_MUSPF_9669 and tr_A0A2Y9J329_A0A2Y9J329_ENHLU_391180 are exactly identical! WARNING: Sequences tr_M3Y325_M3Y325_MUSPF_9669 and tr_A0A2U3YJI9_A0A2U3YJI9_LEPWE_9713 are exactly identical! WARNING: Sequences tr_M3YKN8_M3YKN8_MUSPF_9669 and tr_A0A2I3GFB6_A0A2I3GFB6_NOMLE_61853 are exactly identical! WARNING: Sequences tr_M3YKN8_M3YKN8_MUSPF_9669 and tr_A0A2I2YF53_A0A2I2YF53_GORGO_9595 are exactly identical! WARNING: Sequences tr_M3YKN8_M3YKN8_MUSPF_9669 and tr_Q5NVQ5_Q5NVQ5_PONAB_9601 are exactly identical! WARNING: Sequences tr_M3YKN8_M3YKN8_MUSPF_9669 and tr_F1PXH9_F1PXH9_CANLF_9615 are exactly identical! WARNING: Sequences tr_M3YKN8_M3YKN8_MUSPF_9669 and tr_H2Q428_H2Q428_PANTR_9598 are exactly identical! WARNING: Sequences tr_M3YKN8_M3YKN8_MUSPF_9669 and tr_A0A1D5QM80_A0A1D5QM80_MACMU_9544 are exactly identical! WARNING: Sequences tr_M3YKN8_M3YKN8_MUSPF_9669 and tr_F1RRH9_F1RRH9_PIG_9823 are exactly identical! WARNING: Sequences tr_M3YKN8_M3YKN8_MUSPF_9669 and tr_M3X7E3_M3X7E3_FELCA_9685 are exactly identical! WARNING: Sequences tr_M3YKN8_M3YKN8_MUSPF_9669 and tr_A0A2K5P1K1_A0A2K5P1K1_CERAT_9531 are exactly identical! WARNING: Sequences tr_M3YKN8_M3YKN8_MUSPF_9669 and tr_A0A2K6C232_A0A2K6C232_MACNE_9545 are exactly identical! WARNING: Sequences tr_M3YKN8_M3YKN8_MUSPF_9669 and tr_A0A2R9CH18_A0A2R9CH18_PANPA_9597 are exactly identical! WARNING: Sequences tr_M3YKN8_M3YKN8_MUSPF_9669 and tr_A0A2U3VGU8_A0A2U3VGU8_ODORO_9708 are exactly identical! WARNING: Sequences tr_M3YKN8_M3YKN8_MUSPF_9669 and tr_A0A2U3Y0D0_A0A2U3Y0D0_LEPWE_9713 are exactly identical! WARNING: Sequences tr_M3YKN8_M3YKN8_MUSPF_9669 and tr_A0A2Y9JPK7_A0A2Y9JPK7_ENHLU_391180 are exactly identical! WARNING: Sequences tr_M3Z2C3_M3Z2C3_MUSPF_9669 and tr_H2NYN0_H2NYN0_PONAB_9601 are exactly identical! WARNING: Sequences tr_M3Z2C3_M3Z2C3_MUSPF_9669 and tr_A0A2I3RZX7_A0A2I3RZX7_PANTR_9598 are exactly identical! WARNING: Sequences tr_M3Z2C3_M3Z2C3_MUSPF_9669 and tr_H0XUW5_H0XUW5_OTOGA_30611 are exactly identical! WARNING: Sequences tr_M3Z2C3_M3Z2C3_MUSPF_9669 and tr_A0A287A0B2_A0A287A0B2_PIG_9823 are exactly identical! WARNING: Sequences tr_M3Z2C3_M3Z2C3_MUSPF_9669 and tr_G1LVL2_G1LVL2_AILME_9646 are exactly identical! WARNING: Sequences tr_M3Z2C3_M3Z2C3_MUSPF_9669 and tr_A0A337SDV6_A0A337SDV6_FELCA_9685 are exactly identical! WARNING: Sequences tr_M3Z2C3_M3Z2C3_MUSPF_9669 and tr_A0A0A0MV96_A0A0A0MV96_PAPAN_9555 are exactly identical! WARNING: Sequences tr_M3Z2C3_M3Z2C3_MUSPF_9669 and tr_A0A0D9QVT6_A0A0D9QVT6_CHLSB_60711 are exactly identical! WARNING: Sequences tr_M3Z2C3_M3Z2C3_MUSPF_9669 and tr_A0A1S3AFY0_A0A1S3AFY0_ERIEU_9365 are exactly identical! WARNING: Sequences tr_M3Z2C3_M3Z2C3_MUSPF_9669 and tr_A0A2K5NGN1_A0A2K5NGN1_CERAT_9531 are exactly identical! WARNING: Sequences tr_M3Z2C3_M3Z2C3_MUSPF_9669 and tr_A0A2K6DUM2_A0A2K6DUM2_MACNE_9545 are exactly identical! WARNING: Sequences tr_M3Z2C3_M3Z2C3_MUSPF_9669 and tr_A0A2U3VN25_A0A2U3VN25_ODORO_9708 are exactly identical! WARNING: Sequences tr_M3Z2C3_M3Z2C3_MUSPF_9669 and tr_A0A2U3Z3B9_A0A2U3Z3B9_LEPWE_9713 are exactly identical! WARNING: Sequences tr_M3Z2C3_M3Z2C3_MUSPF_9669 and tr_A0A2Y9L6H4_A0A2Y9L6H4_ENHLU_391180 are exactly identical! WARNING: Sequences tr_M3Z2C3_M3Z2C3_MUSPF_9669 and tr_A0A383ZY98_A0A383ZY98_BALAS_310752 are exactly identical! WARNING: Sequences tr_Q9VYA9_Q9VYA9_DROME_7227 and tr_B4IG43_B4IG43_DROSE_7238 are exactly identical! WARNING: Sequences tr_Q9VYA9_Q9VYA9_DROME_7227 and tr_A0A1W4VTV2_A0A1W4VTV2_DROFC_30025 are exactly identical! WARNING: Sequences tr_A0A2I3HSG9_A0A2I3HSG9_NOMLE_61853 and tr_G3SB55_G3SB55_GORGO_9595 are exactly identical! WARNING: Sequences tr_A0A2I3HSG9_A0A2I3HSG9_NOMLE_61853 and tr_A0A2J8PJ86_A0A2J8PJ86_PANTR_9598 are exactly identical! WARNING: Sequences tr_A0A2I3HSG9_A0A2I3HSG9_NOMLE_61853 and tr_A0A1D5R0Q0_A0A1D5R0Q0_MACMU_9544 are exactly identical! WARNING: Sequences tr_A0A2I3HSG9_A0A2I3HSG9_NOMLE_61853 and tr_A0A2R8PHK6_A0A2R8PHK6_CALJA_9483 are exactly identical! WARNING: Sequences tr_A0A2I3HSG9_A0A2I3HSG9_NOMLE_61853 and tr_A0A2I3MKJ4_A0A2I3MKJ4_PAPAN_9555 are exactly identical! WARNING: Sequences tr_A0A2I3HSG9_A0A2I3HSG9_NOMLE_61853 and tr_A0A2K5KNT2_A0A2K5KNT2_CERAT_9531 are exactly identical! WARNING: Sequences tr_A0A2I3HSG9_A0A2I3HSG9_NOMLE_61853 and tr_A0A2K6BNC7_A0A2K6BNC7_MACNE_9545 are exactly identical! WARNING: Sequences tr_A0A2I3HSG9_A0A2I3HSG9_NOMLE_61853 and tr_A0A2K5ZCM6_A0A2K5ZCM6_MANLE_9568 are exactly identical! WARNING: Sequences tr_G1RQI0_G1RQI0_NOMLE_61853 and tr_G3S8U6_G3S8U6_GORGO_9595 are exactly identical! WARNING: Sequences tr_G1RQI0_G1RQI0_NOMLE_61853 and tr_A0A2J8TNS6_A0A2J8TNS6_PONAB_9601 are exactly identical! WARNING: Sequences tr_G1RQI0_G1RQI0_NOMLE_61853 and tr_H2QW31_H2QW31_PANTR_9598 are exactly identical! WARNING: Sequences tr_G1RQI0_G1RQI0_NOMLE_61853 and sp_Q92794_KAT6A_HUMAN_9606 are exactly identical! WARNING: Sequences tr_G1RQI0_G1RQI0_NOMLE_61853 and tr_A0A2R8ZBH1_A0A2R8ZBH1_PANPA_9597 are exactly identical! WARNING: Sequences tr_G3R085_G3R085_GORGO_9595 and tr_H2Q248_H2Q248_PANTR_9598 are exactly identical! WARNING: Sequences tr_G3R085_G3R085_GORGO_9595 and sp_Q8WYB5_KAT6B_HUMAN_9606 are exactly identical! WARNING: Sequences tr_G3R085_G3R085_GORGO_9595 and tr_A0A2R8ZD29_A0A2R8ZD29_PANPA_9597 are exactly identical! WARNING: Sequences tr_H2NAI1_H2NAI1_PONAB_9601 and tr_F7E3A7_F7E3A7_MACMU_9544 are exactly identical! WARNING: Sequences tr_H2NAI1_H2NAI1_PONAB_9601 and tr_F7HQQ5_F7HQQ5_CALJA_9483 are exactly identical! WARNING: Sequences tr_H2NAI1_H2NAI1_PONAB_9601 and tr_G7PEZ6_G7PEZ6_MACFA_9541 are exactly identical! WARNING: Sequences tr_H2NAI1_H2NAI1_PONAB_9601 and tr_A0A096P4J9_A0A096P4J9_PAPAN_9555 are exactly identical! WARNING: Sequences tr_H2NAI1_H2NAI1_PONAB_9601 and tr_A0A0D9R9L9_A0A0D9R9L9_CHLSB_60711 are exactly identical! WARNING: Sequences tr_H2NAI1_H2NAI1_PONAB_9601 and tr_A0A2K5LVU6_A0A2K5LVU6_CERAT_9531 are exactly identical! WARNING: Sequences tr_H2NAI1_H2NAI1_PONAB_9601 and tr_A0A2K5YPU8_A0A2K5YPU8_MANLE_9568 are exactly identical! WARNING: Sequences tr_Q293H0_Q293H0_DROPS_46245 and tr_B4GBI7_B4GBI7_DROPE_7234 are exactly identical! WARNING: Sequences tr_Q29FM2_Q29FM2_DROPS_46245 and tr_B4HA22_B4HA22_DROPE_7234 are exactly identical! WARNING: Sequences tr_E2R922_E2R922_CANLF_9615 and tr_G1LFV0_G1LFV0_AILME_9646 are exactly identical! WARNING: Sequences tr_E2R922_E2R922_CANLF_9615 and tr_A0A337SD10_A0A337SD10_FELCA_9685 are exactly identical! WARNING: Sequences tr_E2R922_E2R922_CANLF_9615 and tr_A0A2Y9J0K1_A0A2Y9J0K1_ENHLU_391180 are exactly identical! WARNING: Sequences tr_E2R922_E2R922_CANLF_9615 and tr_A0A384DCL6_A0A384DCL6_URSMA_29073 are exactly identical! WARNING: Sequences tr_A0A2I3SHM1_A0A2I3SHM1_PANTR_9598 and tr_A0A2R9BEX6_A0A2R9BEX6_PANPA_9597 are exactly identical! WARNING: Sequences tr_H2QU23_H2QU23_PANTR_9598 and sp_Q8WUB8_PHF10_HUMAN_9606 are exactly identical! WARNING: Sequences tr_F6W581_F6W581_MONDO_13616 and tr_G3W6G6_G3W6G6_SARHA_9305 are exactly identical! WARNING: Sequences tr_F6RD05_F6RD05_HORSE_9796 and tr_A0A2U3WES6_A0A2U3WES6_ODORO_9708 are exactly identical! WARNING: Sequences tr_F6SJG9_F6SJG9_HORSE_9796 and sp_Q92784_DPF3_HUMAN_9606 are exactly identical! WARNING: Sequences tr_F6SJG9_F6SJG9_HORSE_9796 and tr_A0A287B1K9_A0A287B1K9_PIG_9823 are exactly identical! WARNING: Sequences tr_F6SJG9_F6SJG9_HORSE_9796 and tr_A0A2R9BH70_A0A2R9BH70_PANPA_9597 are exactly identical! WARNING: Sequences tr_F6WJQ4_F6WJQ4_HORSE_9796 and sp_Q92785_REQU_HUMAN_9606 are exactly identical! WARNING: Sequences tr_F6WJQ4_F6WJQ4_HORSE_9796 and tr_G7PPI4_G7PPI4_MACFA_9541 are exactly identical! WARNING: Sequences tr_W5PY56_W5PY56_SHEEP_9940 and tr_A6QQS0_A6QQS0_BOVIN_9913 are exactly identical! WARNING: Sequences tr_M3ZKK0_M3ZKK0_XIPMA_8083 and tr_A0A087XTV1_A0A087XTV1_POEFO_48698 are exactly identical! WARNING: Sequences tr_A0A087ZP93_A0A087ZP93_APIME_7460 and tr_A0A2A3EU25_A0A2A3EU25_APICC_94128 are exactly identical! WARNING: Sequences tr_A0A158NGY7_A0A158NGY7_ATTCE_12957 and tr_A0A195DX06_A0A195DX06_9HYME_471704 are exactly identical! WARNING: Sequences tr_A0A158NGY7_A0A158NGY7_ATTCE_12957 and tr_A0A195B6J9_A0A195B6J9_9HYME_520822 are exactly identical! WARNING: Sequences tr_A0A158NSD9_A0A158NSD9_ATTCE_12957 and tr_F4W5M5_F4W5M5_ACREC_103372 are exactly identical! WARNING: Sequences tr_A0A287DF98_A0A287DF98_ICTTR_43179 and tr_A0A286XIP0_A0A286XIP0_CAVPO_10141 are exactly identical! WARNING: Sequences tr_A0A287DF98_A0A287DF98_ICTTR_43179 and tr_A0A091DBF8_A0A091DBF8_FUKDA_885580 are exactly identical! WARNING: Sequences tr_F6XFX0_F6XFX0_MACMU_9544 and tr_A0A2Y9P8C0_A0A2Y9P8C0_DELLE_9749 are exactly identical! WARNING: Sequences tr_F7FSM6_F7FSM6_MACMU_9544 and tr_A0A096N3T6_A0A096N3T6_PAPAN_9555 are exactly identical! WARNING: Sequences tr_F7FSM6_F7FSM6_MACMU_9544 and tr_A0A2K5LXN3_A0A2K5LXN3_CERAT_9531 are exactly identical! WARNING: Sequences tr_F7FSM6_F7FSM6_MACMU_9544 and tr_A0A2K6DIR2_A0A2K6DIR2_MACNE_9545 are exactly identical! WARNING: Sequences tr_F7FSM6_F7FSM6_MACMU_9544 and tr_A0A2K5XJM6_A0A2K5XJM6_MANLE_9568 are exactly identical! WARNING: Sequences tr_F4NTH8_F4NTH8_BATDJ_684364 and tr_A0A177W8W3_A0A177W8W3_BATDE_403673 are exactly identical! WARNING: Sequences tr_H0Z4T5_H0Z4T5_TAEGU_59729 and tr_A0A218UJD2_A0A218UJD2_9PASE_299123 are exactly identical! WARNING: Sequences tr_A0A2R8PC97_A0A2R8PC97_CALJA_9483 and tr_A0A2Y9THR0_A0A2Y9THR0_PHYCD_9755 are exactly identical! WARNING: Sequences tr_B4M388_B4M388_DROVI_7244 and tr_A0A0Q9WXD1_A0A0Q9WXD1_DROMO_7230 are exactly identical! WARNING: Sequences tr_B3RUC0_B3RUC0_TRIAD_10228 and tr_A0A369SGM6_A0A369SGM6_9METZ_287889 are exactly identical! WARNING: Sequences tr_U3JWW5_U3JWW5_FICAL_59894 and tr_A0A093SEX2_A0A093SEX2_9PASS_328815 are exactly identical! WARNING: Sequences tr_A0A0A1NRP0_A0A0A1NRP0_9FUNG_58291 and tr_A0A367K2P4_A0A367K2P4_9FUNG_86630 are exactly identical! WARNING: Sequences tr_A0A151MSW9_A0A151MSW9_ALLMI_8496 and tr_A0A1U7RE23_A0A1U7RE23_ALLSI_38654 are exactly identical! WARNING: Sequences tr_A0A091ULP8_A0A091ULP8_NIPNI_128390 and tr_A0A087R6T8_A0A087R6T8_APTFO_9233 are exactly identical! WARNING: Sequences tr_A0A2I0LJJ9_A0A2I0LJJ9_COLLI_8932 and tr_A0A1V4KHE3_A0A1V4KHE3_PATFA_372326 are exactly identical! WARNING: Sequences tr_A0A0V1N4D9_A0A0V1N4D9_9BILA_268474 and tr_A0A0V1H7A3_A0A0V1H7A3_9BILA_268475 are exactly identical! WARNING: Sequences tr_A0A0V1PBS6_A0A0V1PBS6_9BILA_92180 and tr_A0A0V0TYR8_A0A0V0TYR8_9BILA_144512 are exactly identical! WARNING: Sequences tr_A0A1S3Q7I8_A0A1S3Q7I8_SALSA_8030 and tr_A0A060W9T9_A0A060W9T9_ONCMY_8022 are exactly identical! WARNING: Sequences tr_A0A226N536_A0A226N536_CALSU_9009 and tr_A0A226NUG8_A0A226NUG8_COLVI_9014 are exactly identical! WARNING: Sequences tr_A0A2D0PLV7_A0A2D0PLV7_ICTPU_7998 and tr_A0A2D0PLW2_A0A2D0PLW2_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0PLV7_A0A2D0PLV7_ICTPU_7998 and tr_A0A2D0PNI8_A0A2D0PNI8_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0Q9U2_A0A2D0Q9U2_ICTPU_7998 and tr_A0A2D0QBI3_A0A2D0QBI3_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0Q9V0_A0A2D0Q9V0_ICTPU_7998 and tr_A0A2D0QCF6_A0A2D0QCF6_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2U4A710_A0A2U4A710_TURTR_9739 and tr_A0A2Y9MYQ4_A0A2Y9MYQ4_DELLE_9749 are exactly identical! WARNING: Sequences tr_A0A2U4A710_A0A2U4A710_TURTR_9739 and tr_A0A384A487_A0A384A487_BALAS_310752 are exactly identical! WARNING: Sequences tr_A0A2U4BEE6_A0A2U4BEE6_TURTR_9739 and tr_A0A2Y9PLI7_A0A2Y9PLI7_DELLE_9749 are exactly identical! WARNING: Sequences tr_A0A2U4BEE6_A0A2U4BEE6_TURTR_9739 and tr_A0A2Y9TE41_A0A2Y9TE41_PHYCD_9755 are exactly identical! WARNING: Sequences tr_A0A2U4BEE6_A0A2U4BEE6_TURTR_9739 and tr_A0A383YUS0_A0A383YUS0_BALAS_310752 are exactly identical! WARNING: Duplicate sequences found: 109 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/Q92785/3_mltree/Q92785.raxml.reduced.phy Alignment comprises 1 partitions and 350 patterns Partition 0: noname Model: LG4X+R4 Alignment sites / patterns: 350 / 350 Gaps: 26.37 % Invariant sites: 0.00 % NOTE: Binary MSA file created: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q92785/3_mltree/Q92785.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 / 350 / 28000 [00:00:00] Data distribution: max. searches per worker: 4 Starting ML tree search with 20 distinct starting trees [00:00:00 -511760.790948] Initial branch length optimization [00:00:11 -417280.501930] Model parameter optimization (eps = 10.000000) [00:02:04 -416188.094962] AUTODETECT spr round 1 (radius: 5) [00:06:48 -281095.527726] AUTODETECT spr round 2 (radius: 10) [00:11:44 -208091.530990] AUTODETECT spr round 3 (radius: 15) [00:17:09 -171309.538507] AUTODETECT spr round 4 (radius: 20) [00:23:30 -152447.418669] AUTODETECT spr round 5 (radius: 25) [00:31:42 -147535.717163] SPR radius for FAST iterations: 25 (autodetect) [00:31:42 -147535.717163] Model parameter optimization (eps = 3.000000) [00:32:35 -147436.323096] FAST spr round 1 (radius: 25) [00:38:45 -126954.375958] FAST spr round 2 (radius: 25) [00:43:12 -125787.328810] FAST spr round 3 (radius: 25) [00:47:08 -125688.795523] FAST spr round 4 (radius: 25) [00:50:36 -125667.302779] FAST spr round 5 (radius: 25) [00:53:41 -125656.794258] FAST spr round 6 (radius: 25) [00:56:40 -125656.793544] Model parameter optimization (eps = 1.000000) [00:57:02 -125654.032268] SLOW spr round 1 (radius: 5) [01:01:11 -125625.401037] SLOW spr round 2 (radius: 5) [01:05:17 -125624.740491] SLOW spr round 3 (radius: 5) [01:09:19 -125624.739891] SLOW spr round 4 (radius: 10) [01:13:25 -125622.572348] SLOW spr round 5 (radius: 5) [01:18:31 -125622.159058] SLOW spr round 6 (radius: 5) [01:23:00 -125622.158333] SLOW spr round 7 (radius: 10) [01:27:17 -125622.158284] SLOW spr round 8 (radius: 15) [01:34:56 -125617.795901] SLOW spr round 9 (radius: 5) [01:40:08 -125617.795778] SLOW spr round 10 (radius: 10) [01:45:09 -125617.795745] SLOW spr round 11 (radius: 15) [01:52:15 -125617.795739] SLOW spr round 12 (radius: 20) [01:56:18] [worker #1] ML tree search #2, logLikelihood: -125611.860078 [02:03:37 -125617.795728] SLOW spr round 13 (radius: 25) [02:05:58] [worker #3] ML tree search #4, logLikelihood: -125598.194734 [02:19:03 -125617.795725] Model parameter optimization (eps = 0.100000) [02:19:14] [worker #0] ML tree search #1, logLikelihood: -125617.776471 [02:19:14 -508755.620943] Initial branch length optimization [02:19:25 -415590.647232] Model parameter optimization (eps = 10.000000) [02:21:57 -414392.814934] AUTODETECT spr round 1 (radius: 5) [02:26:33 -287780.057693] AUTODETECT spr round 2 (radius: 10) [02:31:35] [worker #2] ML tree search #3, logLikelihood: -125606.217764 [02:31:36 -212090.296557] AUTODETECT spr round 3 (radius: 15) [02:37:01 -168478.873767] AUTODETECT spr round 4 (radius: 20) [02:44:18 -154206.659519] AUTODETECT spr round 5 (radius: 25) [02:53:20] [worker #4] ML tree search #5, logLikelihood: -125598.781793 [02:53:28 -146088.431021] SPR radius for FAST iterations: 25 (autodetect) [02:53:28 -146088.431021] Model parameter optimization (eps = 3.000000) [02:54:18 -145994.110171] FAST spr round 1 (radius: 25) [03:00:20 -126676.881216] FAST spr round 2 (radius: 25) [03:04:35 -125758.230176] FAST spr round 3 (radius: 25) [03:08:21 -125672.632963] FAST spr round 4 (radius: 25) [03:11:42 -125659.154139] FAST spr round 5 (radius: 25) [03:14:48 -125656.154328] FAST spr round 6 (radius: 25) [03:17:45 -125656.152990] Model parameter optimization (eps = 1.000000) [03:18:16 -125650.191835] SLOW spr round 1 (radius: 5) [03:22:18 -125613.087437] SLOW spr round 2 (radius: 5) [03:26:20 -125601.819645] SLOW spr round 3 (radius: 5) [03:30:23 -125596.278809] SLOW spr round 4 (radius: 5) [03:34:22 -125596.278236] SLOW spr round 5 (radius: 10) [03:38:29 -125595.374993] SLOW spr round 6 (radius: 5) [03:43:35 -125595.072909] SLOW spr round 7 (radius: 5) [03:48:03 -125595.072791] SLOW spr round 8 (radius: 10) [03:52:19 -125595.072742] SLOW spr round 9 (radius: 15) [03:53:02] [worker #3] ML tree search #9, logLikelihood: -125576.017332 [03:56:33] [worker #1] ML tree search #7, logLikelihood: -125631.743017 [03:59:52 -125594.395529] SLOW spr round 10 (radius: 5) [04:05:06 -125594.395158] SLOW spr round 11 (radius: 10) [04:10:05 -125594.395137] SLOW spr round 12 (radius: 15) [04:17:03 -125594.395123] SLOW spr round 13 (radius: 20) [04:28:27 -125594.395113] SLOW spr round 14 (radius: 25) [04:44:10 -125594.395048] Model parameter optimization (eps = 0.100000) [04:44:39] [worker #0] ML tree search #6, logLikelihood: -125592.545375 [04:44:39 -507829.563100] Initial branch length optimization [04:44:49 -411909.815625] Model parameter optimization (eps = 10.000000) [04:46:51 -410770.014440] AUTODETECT spr round 1 (radius: 5) [04:47:27] [worker #2] ML tree search #8, logLikelihood: -125606.953032 [04:51:31 -280359.477868] AUTODETECT spr round 2 (radius: 10) [04:56:22 -206606.219275] AUTODETECT spr round 3 (radius: 15) [05:01:58 -160779.304027] AUTODETECT spr round 4 (radius: 20) [05:08:16 -149666.786625] AUTODETECT spr round 5 (radius: 25) [05:15:20 -144871.327171] SPR radius for FAST iterations: 25 (autodetect) [05:15:20 -144871.327171] Model parameter optimization (eps = 3.000000) [05:15:59 -144811.064221] FAST spr round 1 (radius: 25) [05:16:13] [worker #4] ML tree search #10, logLikelihood: -125580.288775 [05:22:01 -126879.295191] FAST spr round 2 (radius: 25) [05:26:50 -126035.294267] FAST spr round 3 (radius: 25) [05:31:04 -125771.257630] FAST spr round 4 (radius: 25) [05:34:44 -125704.526128] FAST spr round 5 (radius: 25) [05:37:56 -125698.624422] FAST spr round 6 (radius: 25) [05:41:01 -125693.091473] FAST spr round 7 (radius: 25) [05:44:01 -125693.089307] Model parameter optimization (eps = 1.000000) [05:44:29 -125690.384545] SLOW spr round 1 (radius: 5) [05:48:45 -125656.054937] SLOW spr round 2 (radius: 5) [05:53:06 -125651.322396] SLOW spr round 3 (radius: 5) [05:57:16 -125647.939535] SLOW spr round 4 (radius: 5) [06:01:17 -125647.776659] SLOW spr round 5 (radius: 5) [06:02:00] [worker #1] ML tree search #12, logLikelihood: -125564.846875 [06:05:15 -125647.776120] SLOW spr round 6 (radius: 10) [06:09:23 -125646.874202] SLOW spr round 7 (radius: 5) [06:14:31 -125646.874028] SLOW spr round 8 (radius: 10) [06:18:55] [worker #3] ML tree search #14, logLikelihood: -125596.095528 [06:19:13 -125646.873965] SLOW spr round 9 (radius: 15) [06:25:55 -125646.873910] SLOW spr round 10 (radius: 20) [06:36:31 -125646.873859] SLOW spr round 11 (radius: 25) [06:49:56 -125646.873811] Model parameter optimization (eps = 0.100000) [06:50:29] [worker #0] ML tree search #11, logLikelihood: -125646.519922 [06:50:29 -509201.589810] Initial branch length optimization [06:50:37 -412048.349922] Model parameter optimization (eps = 10.000000) [06:51:01] [worker #2] ML tree search #13, logLikelihood: -125692.544545 [06:52:09 -410942.282574] AUTODETECT spr round 1 (radius: 5) [06:56:30 -278551.942108] AUTODETECT spr round 2 (radius: 10) [07:01:20 -208699.654039] AUTODETECT spr round 3 (radius: 15) [07:07:03 -180312.600673] AUTODETECT spr round 4 (radius: 20) [07:12:14] [worker #4] ML tree search #15, logLikelihood: -125625.331909 [07:13:31 -159519.230549] AUTODETECT spr round 5 (radius: 25) [07:20:28 -149628.293199] SPR radius for FAST iterations: 25 (autodetect) [07:20:28 -149628.293199] Model parameter optimization (eps = 3.000000) [07:21:10 -149556.103225] FAST spr round 1 (radius: 25) [07:27:29 -127113.255909] FAST spr round 2 (radius: 25) [07:32:09 -125780.672189] FAST spr round 3 (radius: 25) [07:35:55 -125657.241644] FAST spr round 4 (radius: 25) [07:39:19 -125621.095152] FAST spr round 5 (radius: 25) [07:42:20 -125619.510708] FAST spr round 6 (radius: 25) [07:45:16 -125619.143708] FAST spr round 7 (radius: 25) [07:48:08 -125619.142293] Model parameter optimization (eps = 1.000000) [07:48:29 -125617.397626] SLOW spr round 1 (radius: 5) [07:52:29 -125603.619097] SLOW spr round 2 (radius: 5) [07:56:30 -125601.034318] SLOW spr round 3 (radius: 5) [08:00:30 -125600.498665] SLOW spr round 4 (radius: 5) [08:04:22 -125600.498606] SLOW spr round 5 (radius: 10) [08:06:06] [worker #1] ML tree search #17, logLikelihood: -125607.616533 [08:08:28 -125599.813819] SLOW spr round 6 (radius: 5) [08:13:33 -125599.812356] SLOW spr round 7 (radius: 10) [08:18:13 -125599.812184] SLOW spr round 8 (radius: 15) [08:18:34] [worker #3] ML tree search #19, logLikelihood: -125617.925614 [08:24:58 -125599.607415] SLOW spr round 9 (radius: 5) [08:30:10 -125599.607351] SLOW spr round 10 (radius: 10) [08:35:07 -125599.607319] SLOW spr round 11 (radius: 15) [08:41:46 -125599.607314] SLOW spr round 12 (radius: 20) [08:53:12 -125599.607310] SLOW spr round 13 (radius: 25) [09:08:26 -125599.607305] Model parameter optimization (eps = 0.100000) [09:08:32] [worker #0] ML tree search #16, logLikelihood: -125599.605991 [09:13:13] [worker #2] ML tree search #18, logLikelihood: -125611.563249 [09:28:49] [worker #4] ML tree search #20, logLikelihood: -125605.045213 Optimized model parameters: Partition 0: noname Rate heterogeneity: FREE (4 cats, mean), weights&rates: (0.109655,0.359312) (0.067333,1.115360) (0.356696,0.701522) (0.466315,1.362315) 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: -125564.846875 AIC score: 255139.693750 / AICc score: 8299199.693750 / BIC score: 262874.849724 Free parameters (model + branch lengths): 2005 WARNING: Number of free parameters (K=2005) is larger than alignment size (n=350). This might lead to overfitting and compromise tree inference results! WARNING: Best ML tree contains 213 near-zero branches! Best ML tree with collapsed near-zero branches saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q92785/3_mltree/Q92785.raxml.bestTreeCollapsed Best ML tree saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q92785/3_mltree/Q92785.raxml.bestTree All ML trees saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q92785/3_mltree/Q92785.raxml.mlTrees Optimized model saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q92785/3_mltree/Q92785.raxml.bestModel Execution log saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q92785/3_mltree/Q92785.raxml.log Analysis started: 06-Jul-2021 05:11:30 / finished: 06-Jul-2021 14:40:19 Elapsed time: 34129.418 seconds Consumed energy: 3069.754 Wh (= 15 km in an electric car, or 77 km with an e-scooter!)