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 02-Jul-2021 17:18:41 as follows: raxml-ng --msa /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q92622/2_msa/Q92622_trimmed_msa.fasta --data-type AA --model LG4X --prefix /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q92622/3_mltree/Q92622 --seed 2 --threads 4 --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 (4 threads), thread pinning: OFF [00:00:00] Reading alignment from file: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q92622/2_msa/Q92622_trimmed_msa.fasta [00:00:00] Loaded alignment with 800 taxa and 200 sites WARNING: Sequences tr_A0A2R8QUA5_A0A2R8QUA5_DANRE_7955 and tr_F1R282_F1R282_DANRE_7955 are exactly identical! WARNING: Sequences tr_A0A1D5PL26_A0A1D5PL26_CHICK_9031 and tr_A0A226P6I5_A0A226P6I5_COLVI_9014 are exactly identical! WARNING: Sequences tr_E1BSU7_E1BSU7_CHICK_9031 and tr_G1N8A0_G1N8A0_MELGA_9103 are exactly identical! WARNING: Sequences sp_Q99J78_DEFI8_MOUSE_10090 and tr_G3GRQ0_G3GRQ0_CRIGR_10029 are exactly identical! WARNING: Sequences sp_Q99J78_DEFI8_MOUSE_10090 and tr_A0A1U7QIY6_A0A1U7QIY6_MESAU_10036 are exactly identical! WARNING: Sequences tr_A0A2I3GT98_A0A2I3GT98_NOMLE_61853 and tr_A0A1D5QHZ6_A0A1D5QHZ6_MACMU_9544 are exactly identical! WARNING: Sequences tr_A0A2I3GT98_A0A2I3GT98_NOMLE_61853 and tr_A0A096MWE9_A0A096MWE9_PAPAN_9555 are exactly identical! WARNING: Sequences tr_A0A2I3GT98_A0A2I3GT98_NOMLE_61853 and tr_A0A0D9S3A4_A0A0D9S3A4_CHLSB_60711 are exactly identical! WARNING: Sequences tr_A0A2I3GT98_A0A2I3GT98_NOMLE_61853 and tr_A0A2K5NUB6_A0A2K5NUB6_CERAT_9531 are exactly identical! WARNING: Sequences tr_A0A2I3GT98_A0A2I3GT98_NOMLE_61853 and tr_A0A2K6C383_A0A2K6C383_MACNE_9545 are exactly identical! WARNING: Sequences tr_A0A2I3GT98_A0A2I3GT98_NOMLE_61853 and tr_A0A2K5YN00_A0A2K5YN00_MANLE_9568 are exactly identical! WARNING: Sequences tr_G1R670_G1R670_NOMLE_61853 and tr_G3QFB7_G3QFB7_GORGO_9595 are exactly identical! WARNING: Sequences tr_G1R670_G1R670_NOMLE_61853 and tr_H2P8F6_H2P8F6_PONAB_9601 are exactly identical! WARNING: Sequences tr_G1R670_G1R670_NOMLE_61853 and sp_Q6ZWE6_PKHM3_HUMAN_9606 are exactly identical! WARNING: Sequences tr_G1R670_G1R670_NOMLE_61853 and tr_H9ERP5_H9ERP5_MACMU_9544 are exactly identical! WARNING: Sequences tr_G1R670_G1R670_NOMLE_61853 and tr_F7HYJ4_F7HYJ4_CALJA_9483 are exactly identical! WARNING: Sequences tr_G1R670_G1R670_NOMLE_61853 and tr_A0A096MWL7_A0A096MWL7_PAPAN_9555 are exactly identical! WARNING: Sequences tr_G1R670_G1R670_NOMLE_61853 and tr_A0A0D9RCH2_A0A0D9RCH2_CHLSB_60711 are exactly identical! WARNING: Sequences tr_G1R670_G1R670_NOMLE_61853 and tr_A0A2K5MJ72_A0A2K5MJ72_CERAT_9531 are exactly identical! WARNING: Sequences tr_G1R670_G1R670_NOMLE_61853 and tr_A0A2K6E4C5_A0A2K6E4C5_MACNE_9545 are exactly identical! WARNING: Sequences tr_G1R670_G1R670_NOMLE_61853 and tr_A0A2K5Y2R9_A0A2K5Y2R9_MANLE_9568 are exactly identical! WARNING: Sequences tr_G3HU57_G3HU57_CRIGR_10029 and tr_A0A1U8BPU9_A0A1U8BPU9_MESAU_10036 are exactly identical! WARNING: Sequences tr_G3ICE1_G3ICE1_CRIGR_10029 and sp_Q5PQS0_PKHM1_RAT_10116 are exactly identical! WARNING: Sequences tr_D8QPZ9_D8QPZ9_SELML_88036 and tr_D8SKH7_D8SKH7_SELML_88036 are exactly identical! WARNING: Sequences tr_G3R769_G3R769_GORGO_9595 and tr_H2NRV1_H2NRV1_PONAB_9601 are exactly identical! WARNING: Sequences tr_G3R769_G3R769_GORGO_9595 and tr_A0A2J8J014_A0A2J8J014_PANTR_9598 are exactly identical! WARNING: Sequences tr_G3R769_G3R769_GORGO_9595 and sp_Q6ZN54_DEFI8_HUMAN_9606 are exactly identical! WARNING: Sequences tr_G3R769_G3R769_GORGO_9595 and tr_A0A2R9A7H0_A0A2R9A7H0_PANPA_9597 are exactly identical! WARNING: Sequences tr_A0A2I3SVT5_A0A2I3SVT5_PANTR_9598 and tr_A0A2R9A7U2_A0A2R9A7U2_PANPA_9597 are exactly identical! WARNING: Sequences tr_A0A2J8ML35_A0A2J8ML35_PANTR_9598 and tr_A0A2R9A3C7_A0A2R9A3C7_PANPA_9597 are exactly identical! WARNING: Sequences tr_H2QD91_H2QD91_PANTR_9598 and tr_A0A2R9C6Q4_A0A2R9C6Q4_PANPA_9597 are exactly identical! WARNING: Sequences tr_H2R347_H2R347_PANTR_9598 and tr_A0A2R9BME4_A0A2R9BME4_PANPA_9597 are exactly identical! WARNING: Sequences tr_F7CTD5_F7CTD5_MONDO_13616 and tr_G3W4W2_G3W4W2_SARHA_9305 are exactly identical! WARNING: Sequences tr_A0A088A1K7_A0A088A1K7_APIME_7460 and tr_A0A2A3EHR7_A0A2A3EHR7_APICC_94128 are exactly identical! WARNING: Sequences tr_A0A088AGT9_A0A088AGT9_APIME_7460 and tr_A0A2A3EA75_A0A2A3EA75_APICC_94128 are exactly identical! WARNING: Sequences tr_A0A158NLR8_A0A158NLR8_ATTCE_12957 and tr_A0A151WN75_A0A151WN75_9HYME_64791 are exactly identical! WARNING: Sequences tr_A0A158NLR8_A0A158NLR8_ATTCE_12957 and tr_A0A195DTH1_A0A195DTH1_9HYME_471704 are exactly identical! WARNING: Sequences tr_A0A158NLR8_A0A158NLR8_ATTCE_12957 and tr_A0A195BLG3_A0A195BLG3_9HYME_520822 are exactly identical! WARNING: Sequences tr_A0A158NLR8_A0A158NLR8_ATTCE_12957 and tr_A0A195CCF2_A0A195CCF2_9HYME_456900 are exactly identical! WARNING: Sequences tr_A0A158NR07_A0A158NR07_ATTCE_12957 and tr_A0A195B0W3_A0A195B0W3_9HYME_520822 are exactly identical! WARNING: Sequences tr_A0A286XW53_A0A286XW53_CAVPO_10141 and tr_A0A091DIC5_A0A091DIC5_FUKDA_885580 are exactly identical! WARNING: Sequences tr_A0A0K0JAE6_A0A0K0JAE6_BRUMA_6279 and tr_A0A0R3QSS6_A0A0R3QSS6_9BILA_42155 are exactly identical! WARNING: Sequences tr_A0A0K0JQ01_A0A0K0JQ01_BRUMA_6279 and tr_A0A0N4TPR3_A0A0N4TPR3_BRUPA_6280 are exactly identical! WARNING: Sequences tr_A0A0K0JQ01_A0A0K0JQ01_BRUMA_6279 and tr_A0A0R3R601_A0A0R3R601_9BILA_42155 are exactly identical! WARNING: Sequences tr_F6UUH3_F6UUH3_MACMU_9544 and tr_A0A2K6C681_A0A2K6C681_MACNE_9545 are exactly identical! WARNING: Sequences tr_F7H478_F7H478_MACMU_9544 and tr_G8F3T1_G8F3T1_MACFA_9541 are exactly identical! WARNING: Sequences tr_F4WPF9_F4WPF9_ACREC_103372 and tr_A0A195EUC8_A0A195EUC8_9HYME_34720 are exactly identical! WARNING: Sequences tr_A8WLQ1_A8WLQ1_CAEBR_6238 and tr_A8XLN6_A8XLN6_CAEBR_6238 are exactly identical! WARNING: Sequences tr_G1LBM3_G1LBM3_AILME_9646 and tr_A0A2I2UV59_A0A2I2UV59_FELCA_9685 are exactly identical! WARNING: Sequences tr_G1LBM3_G1LBM3_AILME_9646 and tr_A0A384DHW5_A0A384DHW5_URSMA_29073 are exactly identical! WARNING: Sequences tr_M4EY71_M4EY71_BRARP_51351 and tr_M4EY72_M4EY72_BRARP_51351 are exactly identical! WARNING: Sequences tr_M4EY71_M4EY71_BRARP_51351 and tr_A0A0D3A937_A0A0D3A937_BRAOL_109376 are exactly identical! WARNING: Sequences tr_A0A044SCZ5_A0A044SCZ5_ONCVO_6282 and tr_A0A182EPD7_A0A182EPD7_ONCOC_42157 are exactly identical! WARNING: Sequences tr_A0A044UZ69_A0A044UZ69_ONCVO_6282 and tr_A0A182EER4_A0A182EER4_ONCOC_42157 are exactly identical! WARNING: Sequences tr_A0A096P668_A0A096P668_PAPAN_9555 and tr_A0A0D9QUN9_A0A0D9QUN9_CHLSB_60711 are exactly identical! WARNING: Sequences tr_A0A096P668_A0A096P668_PAPAN_9555 and tr_A0A2K5L510_A0A2K5L510_CERAT_9531 are exactly identical! WARNING: Sequences tr_A0A096P668_A0A096P668_PAPAN_9555 and tr_A0A2K6AF96_A0A2K6AF96_MANLE_9568 are exactly identical! WARNING: Sequences tr_A0A0D9R7Z7_A0A0D9R7Z7_CHLSB_60711 and tr_A0A2K5N5H2_A0A2K5N5H2_CERAT_9531 are exactly identical! WARNING: Sequences tr_A0A0D9R7Z7_A0A0D9R7Z7_CHLSB_60711 and tr_A0A2K6D833_A0A2K6D833_MACNE_9545 are exactly identical! WARNING: Sequences tr_A0A0D9R7Z7_A0A0D9R7Z7_CHLSB_60711 and tr_A0A2K5ZGJ9_A0A2K5ZGJ9_MANLE_9568 are exactly identical! WARNING: Sequences tr_A0A151N9J5_A0A151N9J5_ALLMI_8496 and tr_A0A1U7SC17_A0A1U7SC17_ALLSI_38654 are exactly identical! WARNING: Sequences tr_A0A091JJ67_A0A091JJ67_EGRGA_188379 and tr_A0A093SWQ5_A0A093SWQ5_9PASS_328815 are exactly identical! WARNING: Sequences tr_A0A091JJ67_A0A091JJ67_EGRGA_188379 and tr_A0A091UWM0_A0A091UWM0_NIPNI_128390 are exactly identical! WARNING: Sequences tr_A0A091JJ67_A0A091JJ67_EGRGA_188379 and tr_A0A0A0AV57_A0A0A0AV57_CHAVO_50402 are exactly identical! WARNING: Sequences tr_A0A091JJ67_A0A091JJ67_EGRGA_188379 and tr_A0A093GHI4_A0A093GHI4_DRYPU_118200 are exactly identical! WARNING: Sequences tr_A0A0V1D203_A0A0V1D203_TRIBR_45882 and tr_A0A0V1L5B5_A0A0V1L5B5_9BILA_6335 are exactly identical! WARNING: Sequences tr_A0A0V1D203_A0A0V1D203_TRIBR_45882 and tr_A0A0V0UEJ3_A0A0V0UEJ3_9BILA_144512 are exactly identical! WARNING: Sequences tr_A0A0V1D9P9_A0A0V1D9P9_TRIBR_45882 and tr_A0A0V0WDE5_A0A0V0WDE5_9BILA_92179 are exactly identical! WARNING: Sequences tr_A0A0V1D9P9_A0A0V1D9P9_TRIBR_45882 and tr_A0A0V0V2X1_A0A0V0V2X1_9BILA_181606 are exactly identical! WARNING: Sequences tr_A0A0V1D9P9_A0A0V1D9P9_TRIBR_45882 and tr_A0A0V1LR97_A0A0V1LR97_9BILA_6335 are exactly identical! WARNING: Sequences tr_A0A0V1D9P9_A0A0V1D9P9_TRIBR_45882 and tr_A0A0V1P1H3_A0A0V1P1H3_9BILA_92180 are exactly identical! WARNING: Sequences tr_A0A0V1D9P9_A0A0V1D9P9_TRIBR_45882 and tr_A0A0V0TTY9_A0A0V0TTY9_9BILA_144512 are exactly identical! WARNING: Sequences tr_A0A0V1DGE3_A0A0V1DGE3_TRIBR_45882 and tr_A0A0V0VSL4_A0A0V0VSL4_9BILA_181606 are exactly identical! WARNING: Sequences tr_A0A0V1DGE3_A0A0V1DGE3_TRIBR_45882 and tr_A0A0V1AF85_A0A0V1AF85_9BILA_990121 are exactly identical! WARNING: Sequences tr_A0A0V1DGE3_A0A0V1DGE3_TRIBR_45882 and tr_A0A0V1NMQ4_A0A0V1NMQ4_9BILA_92180 are exactly identical! WARNING: Sequences tr_A0A0V1DGE3_A0A0V1DGE3_TRIBR_45882 and tr_A0A0V1NMR6_A0A0V1NMR6_9BILA_92180 are exactly identical! WARNING: Sequences tr_A0A0V1DGE3_A0A0V1DGE3_TRIBR_45882 and tr_A0A0V0UAS1_A0A0V0UAS1_9BILA_144512 are exactly identical! WARNING: Sequences tr_A0A0V0X9E6_A0A0V0X9E6_9BILA_92179 and tr_A0A0V1LCF1_A0A0V1LCF1_9BILA_6335 are exactly identical! WARNING: Sequences tr_A0A0V0X9E6_A0A0V0X9E6_9BILA_92179 and tr_A0A0V1LD32_A0A0V1LD32_9BILA_6335 are exactly identical! WARNING: Sequences tr_A0A0V1MBN4_A0A0V1MBN4_9BILA_268474 and tr_A0A0V1H4I3_A0A0V1H4I3_9BILA_268475 are exactly identical! WARNING: Sequences tr_A0A1S3PU50_A0A1S3PU50_SALSA_8030 and tr_A0A060XPG5_A0A060XPG5_ONCMY_8022 are exactly identical! WARNING: Sequences tr_A0A0M4EEK2_A0A0M4EEK2_DROBS_30019 and tr_A0A0M4EM58_A0A0M4EM58_DROBS_30019 are exactly identical! WARNING: Sequences tr_A0A1I7TSH2_A0A1I7TSH2_9PELO_1561998 and tr_A0A1I7TSH4_A0A1I7TSH4_9PELO_1561998 are exactly identical! WARNING: Sequences tr_A0A1I7TSH2_A0A1I7TSH2_9PELO_1561998 and tr_A0A1I7TSH5_A0A1I7TSH5_9PELO_1561998 are exactly identical! WARNING: Sequences tr_A0A226NCT2_A0A226NCT2_CALSU_9009 and tr_A0A226PG04_A0A226PG04_COLVI_9014 are exactly identical! WARNING: Sequences tr_A0A2D0QTS3_A0A2D0QTS3_ICTPU_7998 and tr_W5UL27_W5UL27_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0RSF1_A0A2D0RSF1_ICTPU_7998 and tr_A0A2D0RSF3_A0A2D0RSF3_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0RSF1_A0A2D0RSF1_ICTPU_7998 and tr_A0A2D0RSF5_A0A2D0RSF5_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0RWN0_A0A2D0RWN0_ICTPU_7998 and tr_A0A2D0RY73_A0A2D0RY73_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2U4ABA9_A0A2U4ABA9_TURTR_9739 and tr_A0A2Y9MXI9_A0A2Y9MXI9_DELLE_9749 are exactly identical! WARNING: Sequences tr_A0A2U4ABA9_A0A2U4ABA9_TURTR_9739 and tr_A0A2Y9SNZ0_A0A2Y9SNZ0_PHYCD_9755 are exactly identical! WARNING: Sequences tr_A0A2U4BN06_A0A2U4BN06_TURTR_9739 and tr_A0A2Y9MQP3_A0A2Y9MQP3_DELLE_9749 are exactly identical! WARNING: Sequences tr_A0A2U4BN06_A0A2U4BN06_TURTR_9739 and tr_A0A2Y9EZ10_A0A2Y9EZ10_PHYCD_9755 are exactly identical! WARNING: Sequences tr_A0A2U3VBR2_A0A2U3VBR2_ODORO_9708 and tr_A0A2U3Y430_A0A2U3Y430_LEPWE_9713 are exactly identical! WARNING: Sequences tr_A0A2Y9SRI2_A0A2Y9SRI2_PHYCD_9755 and tr_A0A383ZBR8_A0A383ZBR8_BALAS_310752 are exactly identical! WARNING: Duplicate sequences found: 95 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/Q92622/3_mltree/Q92622.raxml.reduced.phy Alignment comprises 1 partitions and 200 patterns Partition 0: noname Model: LG4X+R4 Alignment sites / patterns: 200 / 200 Gaps: 4.41 % Invariant sites: 0.00 % NOTE: Binary MSA file created: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q92622/3_mltree/Q92622.raxml.rba Parallelization scheme autoconfig: 4 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 800 taxa [00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 200 / 16000 [00:00:00] Data distribution: max. searches per worker: 5 Starting ML tree search with 20 distinct starting trees [00:00:00 -299094.640992] Initial branch length optimization [00:00:03 -247183.070457] Model parameter optimization (eps = 10.000000) [00:00:27 -247110.021816] AUTODETECT spr round 1 (radius: 5) [00:02:21 -170446.146282] AUTODETECT spr round 2 (radius: 10) [00:04:19 -133316.141846] AUTODETECT spr round 3 (radius: 15) [00:06:29 -108779.566668] AUTODETECT spr round 4 (radius: 20) [00:09:00 -99884.452325] AUTODETECT spr round 5 (radius: 25) [00:11:28 -94866.303289] SPR radius for FAST iterations: 25 (autodetect) [00:11:28 -94866.303289] Model parameter optimization (eps = 3.000000) [00:11:47 -94752.333734] FAST spr round 1 (radius: 25) [00:13:54 -78476.688558] FAST spr round 2 (radius: 25) [00:15:33 -77192.256518] FAST spr round 3 (radius: 25) [00:17:02 -77100.308024] FAST spr round 4 (radius: 25) [00:18:22 -77080.787824] FAST spr round 5 (radius: 25) [00:19:35 -77079.296077] FAST spr round 6 (radius: 25) [00:20:47 -77079.296052] Model parameter optimization (eps = 1.000000) [00:21:00 -77068.548836] SLOW spr round 1 (radius: 5) [00:22:45 -77042.673748] SLOW spr round 2 (radius: 5) [00:24:26 -77036.065522] SLOW spr round 3 (radius: 5) [00:26:07 -77033.802741] SLOW spr round 4 (radius: 5) [00:27:43 -77033.802540] SLOW spr round 5 (radius: 10) [00:29:20 -77031.431865] SLOW spr round 6 (radius: 5) [00:31:22 -77031.431683] SLOW spr round 7 (radius: 10) [00:33:13 -77029.460012] SLOW spr round 8 (radius: 5) [00:35:12 -77029.459375] SLOW spr round 9 (radius: 10) [00:36:57 -77029.459352] SLOW spr round 10 (radius: 15) [00:39:25 -77028.965485] SLOW spr round 11 (radius: 5) [00:41:34 -77028.097970] SLOW spr round 12 (radius: 5) [00:43:31 -77020.635474] SLOW spr round 13 (radius: 5) [00:45:19 -77016.687121] SLOW spr round 14 (radius: 5) [00:46:59 -77016.524112] SLOW spr round 15 (radius: 5) [00:48:36 -77016.523586] SLOW spr round 16 (radius: 10) [00:50:13 -77016.285691] SLOW spr round 17 (radius: 5) [00:52:15 -77016.285297] SLOW spr round 18 (radius: 10) [00:53:15] [worker #2] ML tree search #3, logLikelihood: -77007.497151 [00:54:06 -77016.285284] SLOW spr round 19 (radius: 15) [00:56:32 -77016.285279] SLOW spr round 20 (radius: 20) [00:59:50 -77016.285277] SLOW spr round 21 (radius: 25) [01:01:46] [worker #1] ML tree search #2, logLikelihood: -77012.230117 [01:03:41 -77016.242239] Model parameter optimization (eps = 0.100000) [01:03:48] [worker #0] ML tree search #1, logLikelihood: -77016.071777 [01:03:48 -298190.897254] Initial branch length optimization [01:03:52 -244480.564443] Model parameter optimization (eps = 10.000000) [01:04:20 -244397.293790] AUTODETECT spr round 1 (radius: 5) [01:06:16 -168977.338962] AUTODETECT spr round 2 (radius: 10) [01:08:15 -129747.577379] AUTODETECT spr round 3 (radius: 15) [01:10:23 -112402.442617] AUTODETECT spr round 4 (radius: 20) [01:11:45] [worker #3] ML tree search #4, logLikelihood: -76996.188449 [01:12:59 -99424.453142] AUTODETECT spr round 5 (radius: 25) [01:15:55 -89997.643274] SPR radius for FAST iterations: 25 (autodetect) [01:15:55 -89997.643274] Model parameter optimization (eps = 3.000000) [01:16:15 -89923.891100] FAST spr round 1 (radius: 25) [01:18:27 -77671.615505] FAST spr round 2 (radius: 25) [01:20:09 -77115.148268] FAST spr round 3 (radius: 25) [01:21:42 -77052.551580] FAST spr round 4 (radius: 25) [01:23:01 -77045.470102] FAST spr round 5 (radius: 25) [01:24:15 -77044.405966] FAST spr round 6 (radius: 25) [01:25:28 -77044.405572] Model parameter optimization (eps = 1.000000) [01:25:40 -77040.441750] SLOW spr round 1 (radius: 5) [01:27:24 -77021.088416] SLOW spr round 2 (radius: 5) [01:29:06 -77018.331339] SLOW spr round 3 (radius: 5) [01:30:43 -77018.039658] SLOW spr round 4 (radius: 5) [01:32:21 -77017.137705] SLOW spr round 5 (radius: 5) [01:33:58 -77017.137322] SLOW spr round 6 (radius: 10) [01:35:35 -77015.920482] SLOW spr round 7 (radius: 5) [01:37:37 -77015.196342] SLOW spr round 8 (radius: 5) [01:39:25 -77015.195872] SLOW spr round 9 (radius: 10) [01:41:07 -77015.195506] SLOW spr round 10 (radius: 15) [01:43:40 -77015.195143] SLOW spr round 11 (radius: 20) [01:47:03 -77013.439815] SLOW spr round 12 (radius: 5) [01:49:11 -77013.439455] SLOW spr round 13 (radius: 10) [01:51:14 -77013.439098] SLOW spr round 14 (radius: 15) [01:53:43 -77013.438742] SLOW spr round 15 (radius: 20) [01:54:37] [worker #2] ML tree search #7, logLikelihood: -76999.864058 [01:57:10 -77013.438386] SLOW spr round 16 (radius: 25) [02:01:25 -77013.438030] Model parameter optimization (eps = 0.100000) [02:01:30] [worker #0] ML tree search #5, logLikelihood: -77013.413359 [02:01:30 -298273.642124] Initial branch length optimization [02:01:33 -245429.729303] Model parameter optimization (eps = 10.000000) [02:02:07 -245337.951551] AUTODETECT spr round 1 (radius: 5) [02:02:24] [worker #3] ML tree search #8, logLikelihood: -77026.578916 [02:02:55] [worker #1] ML tree search #6, logLikelihood: -77021.202711 [02:03:59 -167696.692571] AUTODETECT spr round 2 (radius: 10) [02:05:58 -126471.774962] AUTODETECT spr round 3 (radius: 15) [02:08:04 -106549.892518] AUTODETECT spr round 4 (radius: 20) [02:11:13 -92302.272240] AUTODETECT spr round 5 (radius: 25) [02:13:59 -89046.701012] SPR radius for FAST iterations: 25 (autodetect) [02:13:59 -89046.701012] Model parameter optimization (eps = 3.000000) [02:14:16 -88959.890692] FAST spr round 1 (radius: 25) [02:16:34 -77705.056097] FAST spr round 2 (radius: 25) [02:18:18 -77179.298191] FAST spr round 3 (radius: 25) [02:19:50 -77123.696082] FAST spr round 4 (radius: 25) [02:21:09 -77122.408508] FAST spr round 5 (radius: 25) [02:22:26 -77122.406617] Model parameter optimization (eps = 1.000000) [02:22:43 -77117.828487] SLOW spr round 1 (radius: 5) [02:24:34 -77085.236623] SLOW spr round 2 (radius: 5) [02:26:21 -77081.701128] SLOW spr round 3 (radius: 5) [02:28:01 -77081.442344] SLOW spr round 4 (radius: 5) [02:29:40 -77081.442192] SLOW spr round 5 (radius: 10) [02:31:22 -77074.294697] SLOW spr round 6 (radius: 5) [02:33:29 -77071.993973] SLOW spr round 7 (radius: 5) [02:35:20 -77071.993961] SLOW spr round 8 (radius: 10) [02:37:05 -77066.239138] SLOW spr round 9 (radius: 5) [02:39:08 -77066.238804] SLOW spr round 10 (radius: 10) [02:40:59 -77066.238787] SLOW spr round 11 (radius: 15) [02:43:28 -77064.811894] SLOW spr round 12 (radius: 5) [02:45:36 -77064.811891] SLOW spr round 13 (radius: 10) [02:47:34 -77064.811891] SLOW spr round 14 (radius: 15) [02:50:00 -77064.811890] SLOW spr round 15 (radius: 20) [02:53:31 -77062.837194] SLOW spr round 16 (radius: 5) [02:55:44 -77061.520437] SLOW spr round 17 (radius: 5) [02:57:39 -77061.520272] SLOW spr round 18 (radius: 10) [02:59:24 -77061.520271] SLOW spr round 19 (radius: 15) [02:59:26] [worker #3] ML tree search #12, logLikelihood: -77007.584367 [03:01:45] [worker #2] ML tree search #11, logLikelihood: -77001.662170 [03:01:57 -77048.597075] SLOW spr round 20 (radius: 5) [03:04:05 -77045.843740] SLOW spr round 21 (radius: 5) [03:05:58 -77045.842903] SLOW spr round 22 (radius: 10) [03:07:42 -77045.842804] SLOW spr round 23 (radius: 15) [03:10:13 -77045.842793] SLOW spr round 24 (radius: 20) [03:13:40 -77045.842791] SLOW spr round 25 (radius: 25) [03:17:51 -77045.233467] SLOW spr round 26 (radius: 5) [03:20:02 -77045.233037] SLOW spr round 27 (radius: 10) [03:21:16] [worker #1] ML tree search #10, logLikelihood: -77054.824934 [03:22:07 -77045.232638] SLOW spr round 28 (radius: 15) [03:24:31 -77045.232241] SLOW spr round 29 (radius: 20) [03:28:01 -77045.231844] SLOW spr round 30 (radius: 25) [03:32:10 -77045.231447] Model parameter optimization (eps = 0.100000) [03:32:18] [worker #0] ML tree search #9, logLikelihood: -77045.073209 [03:32:18 -301365.718865] Initial branch length optimization [03:32:22 -247124.304988] Model parameter optimization (eps = 10.000000) [03:32:46 -247041.835146] AUTODETECT spr round 1 (radius: 5) [03:34:39 -170607.807320] AUTODETECT spr round 2 (radius: 10) [03:36:41 -135266.826036] AUTODETECT spr round 3 (radius: 15) [03:38:52 -112055.249191] AUTODETECT spr round 4 (radius: 20) [03:41:33 -102063.214105] AUTODETECT spr round 5 (radius: 25) [03:44:13 -94716.489169] SPR radius for FAST iterations: 25 (autodetect) [03:44:13 -94716.489169] Model parameter optimization (eps = 3.000000) [03:44:31 -94618.882812] FAST spr round 1 (radius: 25) [03:46:43 -79492.352646] FAST spr round 2 (radius: 25) [03:48:25 -77297.580780] FAST spr round 3 (radius: 25) [03:49:51 -77073.577669] FAST spr round 4 (radius: 25) [03:51:13 -77055.855934] FAST spr round 5 (radius: 25) [03:52:28 -77053.481208] FAST spr round 6 (radius: 25) [03:53:43 -77052.233222] FAST spr round 7 (radius: 25) [03:54:56 -77052.232631] Model parameter optimization (eps = 1.000000) [03:55:09 -77044.187542] SLOW spr round 1 (radius: 5) [03:56:52 -77021.781047] SLOW spr round 2 (radius: 5) [03:58:32 -77019.248564] SLOW spr round 3 (radius: 5) [04:00:04] [worker #2] ML tree search #15, logLikelihood: -77005.808827 [04:00:10 -77019.248350] SLOW spr round 4 (radius: 10) [04:01:18] [worker #3] ML tree search #16, logLikelihood: -77022.031122 [04:01:46 -77019.248334] SLOW spr round 5 (radius: 15) [04:04:27 -77019.188935] SLOW spr round 6 (radius: 20) [04:07:53 -77019.188931] SLOW spr round 7 (radius: 25) [04:10:49] [worker #1] ML tree search #14, logLikelihood: -77000.222449 [04:12:32 -77019.188929] Model parameter optimization (eps = 0.100000) [04:12:37] [worker #0] ML tree search #13, logLikelihood: -77019.093468 [04:12:37 -302349.532869] Initial branch length optimization [04:12:42 -248890.519368] Model parameter optimization (eps = 10.000000) [04:13:23 -248790.847827] AUTODETECT spr round 1 (radius: 5) [04:15:32 -176173.225228] AUTODETECT spr round 2 (radius: 10) [04:17:48 -130774.435749] AUTODETECT spr round 3 (radius: 15) [04:20:16 -108153.948678] AUTODETECT spr round 4 (radius: 20) [04:23:29 -93194.584267] AUTODETECT spr round 5 (radius: 25) [04:26:25 -89585.460759] SPR radius for FAST iterations: 25 (autodetect) [04:26:25 -89585.460759] Model parameter optimization (eps = 3.000000) [04:26:46 -89494.274318] FAST spr round 1 (radius: 25) [04:29:11 -77817.798618] FAST spr round 2 (radius: 25) [04:31:03 -77110.740418] FAST spr round 3 (radius: 25) [04:32:44 -77065.561403] FAST spr round 4 (radius: 25) [04:34:11 -77064.530958] FAST spr round 5 (radius: 25) [04:35:33 -77064.530080] Model parameter optimization (eps = 1.000000) [04:35:49 -77058.252261] SLOW spr round 1 (radius: 5) [04:37:47 -77038.396347] SLOW spr round 2 (radius: 5) [04:39:40 -77023.329386] SLOW spr round 3 (radius: 5) [04:41:32 -77022.060302] SLOW spr round 4 (radius: 5) [04:43:19 -77022.059676] SLOW spr round 5 (radius: 10) [04:45:06 -77020.831855] SLOW spr round 6 (radius: 5) [04:47:23 -77020.107800] SLOW spr round 7 (radius: 5) [04:49:24 -77020.107380] SLOW spr round 8 (radius: 10) [04:49:25] [worker #2] ML tree search #19, logLikelihood: -77028.630718 [04:51:17 -77020.107060] SLOW spr round 9 (radius: 15) [04:54:05 -77020.106741] SLOW spr round 10 (radius: 20) [04:58:05 -77020.106422] SLOW spr round 11 (radius: 25) [05:03:01 -77020.106103] Model parameter optimization (eps = 0.100000) [05:03:11] [worker #0] ML tree search #17, logLikelihood: -77019.703152 [05:09:30] [worker #1] ML tree search #18, logLikelihood: -77008.502269 [05:12:21] [worker #3] ML tree search #20, logLikelihood: -77012.442912 Optimized model parameters: Partition 0: noname Rate heterogeneity: FREE (4 cats, mean), weights&rates: (0.189717,0.249447) (0.188886,0.493681) (0.373691,1.011783) (0.247707,1.943155) 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: -76996.188449 AIC score: 157198.376898 / AICc score: 5299622.376898 / BIC score: 162485.579637 Free parameters (model + branch lengths): 1603 WARNING: Number of free parameters (K=1603) is larger than alignment size (n=200). This might lead to overfitting and compromise tree inference results! WARNING: Best ML tree contains 167 near-zero branches! Best ML tree with collapsed near-zero branches saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q92622/3_mltree/Q92622.raxml.bestTreeCollapsed Best ML tree saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q92622/3_mltree/Q92622.raxml.bestTree All ML trees saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q92622/3_mltree/Q92622.raxml.mlTrees Optimized model saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q92622/3_mltree/Q92622.raxml.bestModel Execution log saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q92622/3_mltree/Q92622.raxml.log Analysis started: 02-Jul-2021 17:18:41 / finished: 02-Jul-2021 22:31:03 Elapsed time: 18741.846 seconds Consumed energy: 1196.642 Wh (= 6 km in an electric car, or 30 km with an e-scooter!)