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 6140 CPU @ 2.30GHz, 36 cores, 251 GB RAM RAxML-NG was called at 18-Jul-2021 01:00:00 as follows: raxml-ng --msa /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q9NYB5/2_msa/Q9NYB5_trimmed_msa.fasta --data-type AA --model LG4X --prefix /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q9NYB5/3_mltree/Q9NYB5 --seed 2 --threads 7 --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 (7 threads), thread pinning: OFF [00:00:00] Reading alignment from file: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q9NYB5/2_msa/Q9NYB5_trimmed_msa.fasta [00:00:00] Loaded alignment with 950 taxa and 577 sites WARNING: Sequences tr_A0A2I2Z0F8_A0A2I2Z0F8_GORGO_9595 and tr_A0A2R9CP22_A0A2R9CP22_PANPA_9597 are exactly identical! WARNING: Sequences tr_H2RFP8_H2RFP8_PANTR_9598 and sp_Q9UIG8_SO3A1_HUMAN_9606 are exactly identical! WARNING: Sequences tr_F6UHF6_F6UHF6_MACMU_9544 and tr_A0A2K6B8M8_A0A2K6B8M8_MACNE_9545 are exactly identical! WARNING: Sequences tr_F7E5T7_F7E5T7_MACMU_9544 and tr_A0A2K6DUV0_A0A2K6DUV0_MACNE_9545 are exactly identical! WARNING: Sequences tr_F7F9F8_F7F9F8_MACMU_9544 and tr_G7NXY6_G7NXY6_MACFA_9541 are exactly identical! WARNING: Sequences tr_F7HBN9_F7HBN9_MACMU_9544 and tr_G7PK01_G7PK01_MACFA_9541 are exactly identical! WARNING: Sequences tr_F7HBN9_F7HBN9_MACMU_9544 and tr_A0A096NPQ2_A0A096NPQ2_PAPAN_9555 are exactly identical! WARNING: Sequences tr_F7HBN9_F7HBN9_MACMU_9544 and tr_A0A2K6AWP4_A0A2K6AWP4_MACNE_9545 are exactly identical! WARNING: Sequences tr_F7HBN9_F7HBN9_MACMU_9544 and tr_A0A2K5ZDC6_A0A2K5ZDC6_MANLE_9568 are exactly identical! WARNING: Sequences tr_A0A096NNB5_A0A096NNB5_PAPAN_9555 and tr_A0A2K5MUR2_A0A2K5MUR2_CERAT_9531 are exactly identical! WARNING: Sequences tr_A0A096NNB5_A0A096NNB5_PAPAN_9555 and tr_A0A2K6CAN6_A0A2K6CAN6_MACNE_9545 are exactly identical! WARNING: Sequences tr_A0A091IWX4_A0A091IWX4_EGRGA_188379 and tr_A0A087QWW1_A0A087QWW1_APTFO_9233 are exactly identical! WARNING: Sequences tr_A0A091IWX4_A0A091IWX4_EGRGA_188379 and tr_A0A091WDZ9_A0A091WDZ9_OPIHO_30419 are exactly identical! WARNING: Sequences tr_A0A091IWX4_A0A091IWX4_EGRGA_188379 and tr_A0A099ZWQ1_A0A099ZWQ1_CHAVO_50402 are exactly identical! WARNING: Sequences tr_A0A091GI79_A0A091GI79_9AVES_55661 and tr_A0A091GMU0_A0A091GMU0_9AVES_55661 are exactly identical! WARNING: Sequences tr_A0A151XD33_A0A151XD33_9HYME_64791 and tr_A0A195FFK7_A0A195FFK7_9HYME_34720 are exactly identical! WARNING: Sequences tr_A0A2U4C7C8_A0A2U4C7C8_TURTR_9739 and tr_A0A2Y9QGV4_A0A2Y9QGV4_DELLE_9749 are exactly identical! WARNING: Duplicate sequences found: 17 NOTE: Reduced alignment (with duplicates and gap-only sites/taxa removed) NOTE: was saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q9NYB5/3_mltree/Q9NYB5.raxml.reduced.phy Alignment comprises 1 partitions and 577 patterns Partition 0: noname Model: LG4X+R4 Alignment sites / patterns: 577 / 577 Gaps: 16.03 % Invariant sites: 0.17 % NOTE: Binary MSA file created: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q9NYB5/3_mltree/Q9NYB5.raxml.rba Parallelization scheme autoconfig: 1 worker(s) x 7 thread(s) Parallel reduction/worker buffer size: 1 KB / 0 KB [00:00:00] Generating 20 random starting tree(s) with 950 taxa [00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 83 / 6640 [00:00:00] Data distribution: max. searches per worker: 20 Starting ML tree search with 20 distinct starting trees [00:00:00 -892877.741091] Initial branch length optimization [00:00:05 -751506.251884] Model parameter optimization (eps = 10.000000) [00:00:40 -748634.617178] AUTODETECT spr round 1 (radius: 5) [00:02:20 -466064.522736] AUTODETECT spr round 2 (radius: 10) [00:04:10 -315036.891480] AUTODETECT spr round 3 (radius: 15) [00:06:22 -273884.225467] AUTODETECT spr round 4 (radius: 20) [00:08:40 -253412.563939] AUTODETECT spr round 5 (radius: 25) [00:11:30 -246032.522542] SPR radius for FAST iterations: 25 (autodetect) [00:11:30 -246032.522542] Model parameter optimization (eps = 3.000000) [00:11:46 -245492.109730] FAST spr round 1 (radius: 25) [00:14:02 -213091.752089] FAST spr round 2 (radius: 25) [00:15:47 -211446.392692] FAST spr round 3 (radius: 25) [00:17:22 -211377.210134] FAST spr round 4 (radius: 25) [00:18:52 -211358.117512] FAST spr round 5 (radius: 25) [00:20:18 -211353.003277] FAST spr round 6 (radius: 25) [00:21:40 -211353.002638] Model parameter optimization (eps = 1.000000) [00:21:54 -211345.845523] SLOW spr round 1 (radius: 5) [00:23:40 -211286.276583] SLOW spr round 2 (radius: 5) [00:25:25 -211285.308954] SLOW spr round 3 (radius: 5) [00:27:07 -211285.307648] SLOW spr round 4 (radius: 10) [00:28:54 -211268.554243] SLOW spr round 5 (radius: 5) [00:30:59 -211268.225610] SLOW spr round 6 (radius: 5) [00:32:52 -211268.225550] SLOW spr round 7 (radius: 10) [00:34:42 -211268.225533] SLOW spr round 8 (radius: 15) [00:37:23 -211268.225526] SLOW spr round 9 (radius: 20) [00:41:29 -211268.225522] SLOW spr round 10 (radius: 25) [00:46:54 -211268.225521] Model parameter optimization (eps = 0.100000) [00:47:07] ML tree search #1, logLikelihood: -211267.463991 [00:47:07 -897220.525440] Initial branch length optimization [00:47:12 -757805.075501] Model parameter optimization (eps = 10.000000) [00:47:43 -754795.764399] AUTODETECT spr round 1 (radius: 5) [00:49:25 -463980.538830] AUTODETECT spr round 2 (radius: 10) [00:51:19 -300505.251306] AUTODETECT spr round 3 (radius: 15) [00:53:31 -249321.037502] AUTODETECT spr round 4 (radius: 20) [00:55:46 -236900.054754] AUTODETECT spr round 5 (radius: 25) [00:58:28 -236316.345687] SPR radius for FAST iterations: 25 (autodetect) [00:58:28 -236316.345687] Model parameter optimization (eps = 3.000000) [00:58:47 -235785.605808] FAST spr round 1 (radius: 25) [01:01:02 -212366.644617] FAST spr round 2 (radius: 25) [01:02:54 -211401.136934] FAST spr round 3 (radius: 25) [01:04:30 -211343.743404] FAST spr round 4 (radius: 25) [01:06:01 -211334.915694] FAST spr round 5 (radius: 25) [01:07:26 -211331.634109] FAST spr round 6 (radius: 25) [01:08:49 -211331.633483] Model parameter optimization (eps = 1.000000) [01:09:02 -211326.184034] SLOW spr round 1 (radius: 5) [01:10:51 -211281.757807] SLOW spr round 2 (radius: 5) [01:12:38 -211268.999776] SLOW spr round 3 (radius: 5) [01:14:22 -211264.954063] SLOW spr round 4 (radius: 5) [01:16:04 -211264.953891] SLOW spr round 5 (radius: 10) [01:17:51 -211263.165604] SLOW spr round 6 (radius: 5) [01:19:59 -211253.933830] SLOW spr round 7 (radius: 5) [01:21:55 -211250.338451] SLOW spr round 8 (radius: 5) [01:23:41 -211250.338053] SLOW spr round 9 (radius: 10) [01:25:29 -211249.951414] SLOW spr round 10 (radius: 5) [01:27:34 -211249.951411] SLOW spr round 11 (radius: 10) [01:29:30 -211249.583737] SLOW spr round 12 (radius: 5) [01:31:32 -211249.583650] SLOW spr round 13 (radius: 10) [01:33:26 -211249.583626] SLOW spr round 14 (radius: 15) [01:36:10 -211249.583618] SLOW spr round 15 (radius: 20) [01:40:32 -211249.583616] SLOW spr round 16 (radius: 25) [01:46:15 -211249.583615] Model parameter optimization (eps = 0.100000) [01:46:27] ML tree search #2, logLikelihood: -211248.991047 [01:46:27 -891127.494436] Initial branch length optimization [01:46:33 -752386.060940] Model parameter optimization (eps = 10.000000) [01:47:05 -749580.269301] AUTODETECT spr round 1 (radius: 5) [01:48:47 -470952.832661] AUTODETECT spr round 2 (radius: 10) [01:50:46 -324335.174521] AUTODETECT spr round 3 (radius: 15) [01:53:00 -263228.667727] AUTODETECT spr round 4 (radius: 20) [01:55:16 -244996.912225] AUTODETECT spr round 5 (radius: 25) [01:58:07 -242166.373452] SPR radius for FAST iterations: 25 (autodetect) [01:58:07 -242166.373452] Model parameter optimization (eps = 3.000000) [01:58:24 -241588.154127] FAST spr round 1 (radius: 25) [02:00:30 -213241.091099] FAST spr round 2 (radius: 25) [02:02:14 -211479.586616] FAST spr round 3 (radius: 25) [02:03:51 -211352.575314] FAST spr round 4 (radius: 25) [02:05:23 -211330.859431] FAST spr round 5 (radius: 25) [02:06:47 -211330.498325] FAST spr round 6 (radius: 25) [02:08:11 -211330.496616] Model parameter optimization (eps = 1.000000) [02:08:25 -211322.163812] SLOW spr round 1 (radius: 5) [02:10:11 -211270.848543] SLOW spr round 2 (radius: 5) [02:11:56 -211265.398984] SLOW spr round 3 (radius: 5) [02:13:38 -211265.398624] SLOW spr round 4 (radius: 10) [02:15:25 -211261.522716] SLOW spr round 5 (radius: 5) [02:17:32 -211256.599006] SLOW spr round 6 (radius: 5) [02:19:26 -211255.612938] SLOW spr round 7 (radius: 5) [02:21:13 -211255.612734] SLOW spr round 8 (radius: 10) [02:23:01 -211255.612727] SLOW spr round 9 (radius: 15) [02:25:47 -211255.612722] SLOW spr round 10 (radius: 20) [02:30:02 -211255.612717] SLOW spr round 11 (radius: 25) [02:35:38 -211255.612712] Model parameter optimization (eps = 0.100000) [02:35:45] ML tree search #3, logLikelihood: -211255.501026 [02:35:45 -890456.894354] Initial branch length optimization [02:35:49 -747995.836869] Model parameter optimization (eps = 10.000000) [02:36:18 -745101.293667] AUTODETECT spr round 1 (radius: 5) [02:38:01 -458319.452341] AUTODETECT spr round 2 (radius: 10) [02:39:51 -309945.073205] AUTODETECT spr round 3 (radius: 15) [02:41:57 -241929.944684] AUTODETECT spr round 4 (radius: 20) [02:44:15 -233310.889747] AUTODETECT spr round 5 (radius: 25) [02:46:54 -232305.986768] SPR radius for FAST iterations: 25 (autodetect) [02:46:54 -232305.986768] Model parameter optimization (eps = 3.000000) [02:47:17 -231833.815596] FAST spr round 1 (radius: 25) [02:49:29 -212218.980887] FAST spr round 2 (radius: 25) [02:51:15 -211458.759618] FAST spr round 3 (radius: 25) [02:52:53 -211348.315236] FAST spr round 4 (radius: 25) [02:54:23 -211331.099718] FAST spr round 5 (radius: 25) [02:55:49 -211327.623558] FAST spr round 6 (radius: 25) [02:57:12 -211327.622082] Model parameter optimization (eps = 1.000000) [02:57:26 -211320.174657] SLOW spr round 1 (radius: 5) [02:59:15 -211267.787658] SLOW spr round 2 (radius: 5) [03:00:59 -211264.802678] SLOW spr round 3 (radius: 5) [03:02:41 -211264.801685] SLOW spr round 4 (radius: 10) [03:04:29 -211261.783232] SLOW spr round 5 (radius: 5) [03:06:36 -211261.241388] SLOW spr round 6 (radius: 5) [03:08:30 -211261.152731] SLOW spr round 7 (radius: 10) [03:10:21 -211259.408389] SLOW spr round 8 (radius: 5) [03:12:25 -211259.407953] SLOW spr round 9 (radius: 10) [03:14:21 -211259.407819] SLOW spr round 10 (radius: 15) [03:17:02 -211259.407761] SLOW spr round 11 (radius: 20) [03:21:25 -211259.407734] SLOW spr round 12 (radius: 25) [03:27:06 -211259.407722] Model parameter optimization (eps = 0.100000) [03:27:12] ML tree search #4, logLikelihood: -211259.332848 [03:27:12 -898875.529627] Initial branch length optimization [03:27:16 -758577.711065] Model parameter optimization (eps = 10.000000) [03:27:50 -755569.970049] AUTODETECT spr round 1 (radius: 5) [03:29:33 -463282.063497] AUTODETECT spr round 2 (radius: 10) [03:31:24 -321754.330759] AUTODETECT spr round 3 (radius: 15) [03:33:41 -249075.683809] AUTODETECT spr round 4 (radius: 20) [03:35:50 -237791.752875] AUTODETECT spr round 5 (radius: 25) [03:38:18 -237552.622711] SPR radius for FAST iterations: 25 (autodetect) [03:38:18 -237552.622711] Model parameter optimization (eps = 3.000000) [03:38:40 -237049.984349] FAST spr round 1 (radius: 25) [03:40:51 -212221.537565] FAST spr round 2 (radius: 25) [03:42:40 -211443.695973] FAST spr round 3 (radius: 25) [03:44:17 -211386.151769] FAST spr round 4 (radius: 25) [03:45:46 -211380.358694] FAST spr round 5 (radius: 25) [03:47:11 -211380.357197] Model parameter optimization (eps = 1.000000) [03:47:23 -211373.224291] SLOW spr round 1 (radius: 5) [03:49:14 -211294.060454] SLOW spr round 2 (radius: 5) [03:51:00 -211275.831062] SLOW spr round 3 (radius: 5) [03:52:44 -211274.224439] SLOW spr round 4 (radius: 5) [03:54:26 -211274.221028] SLOW spr round 5 (radius: 10) [03:56:15 -211272.424294] SLOW spr round 6 (radius: 5) [03:58:20 -211272.423556] SLOW spr round 7 (radius: 10) [04:00:19 -211269.286735] SLOW spr round 8 (radius: 5) [04:02:23 -211269.156780] SLOW spr round 9 (radius: 5) [04:04:14 -211269.156471] SLOW spr round 10 (radius: 10) [04:06:04 -211269.156469] SLOW spr round 11 (radius: 15) [04:08:51 -211268.275520] SLOW spr round 12 (radius: 5) [04:11:02 -211268.272070] SLOW spr round 13 (radius: 10) [04:13:03 -211268.271900] SLOW spr round 14 (radius: 15) [04:15:43 -211268.271888] SLOW spr round 15 (radius: 20) [04:20:12 -211268.271886] SLOW spr round 16 (radius: 25) [04:26:01 -211268.271886] Model parameter optimization (eps = 0.100000) [04:26:07] ML tree search #5, logLikelihood: -211268.183092 [04:26:07 -893339.460676] Initial branch length optimization [04:26:12 -757410.755714] Model parameter optimization (eps = 10.000000) [04:26:39 -754331.008162] AUTODETECT spr round 1 (radius: 5) [04:28:21 -465425.823007] AUTODETECT spr round 2 (radius: 10) [04:30:15 -313209.657907] AUTODETECT spr round 3 (radius: 15) [04:32:30 -264702.305086] AUTODETECT spr round 4 (radius: 20) [04:34:54 -241515.299443] AUTODETECT spr round 5 (radius: 25) [04:37:25 -236199.772157] SPR radius for FAST iterations: 25 (autodetect) [04:37:25 -236199.772157] Model parameter optimization (eps = 3.000000) [04:37:44 -235680.077420] FAST spr round 1 (radius: 25) [04:39:52 -212535.076416] FAST spr round 2 (radius: 25) [04:41:43 -211517.637872] FAST spr round 3 (radius: 25) [04:43:23 -211362.482442] FAST spr round 4 (radius: 25) [04:44:52 -211355.079523] FAST spr round 5 (radius: 25) [04:46:18 -211355.076152] Model parameter optimization (eps = 1.000000) [04:46:33 -211350.117482] SLOW spr round 1 (radius: 5) [04:48:26 -211302.107510] SLOW spr round 2 (radius: 5) [04:50:17 -211294.525073] SLOW spr round 3 (radius: 5) [04:52:01 -211294.363358] SLOW spr round 4 (radius: 5) [04:53:42 -211294.363031] SLOW spr round 5 (radius: 10) [04:55:31 -211289.732487] SLOW spr round 6 (radius: 5) [04:57:37 -211289.731306] SLOW spr round 7 (radius: 10) [04:59:35 -211289.730948] SLOW spr round 8 (radius: 15) [05:02:18 -211287.771504] SLOW spr round 9 (radius: 5) [05:04:31 -211281.372395] SLOW spr round 10 (radius: 5) [05:06:35 -211281.372353] SLOW spr round 11 (radius: 10) [05:08:36 -211281.372348] SLOW spr round 12 (radius: 15) [05:11:34 -211281.372344] SLOW spr round 13 (radius: 20) [05:16:27 -211278.106943] SLOW spr round 14 (radius: 5) [05:18:52 -211278.106754] SLOW spr round 15 (radius: 10) [05:21:05 -211278.106739] SLOW spr round 16 (radius: 15) [05:24:00 -211278.106732] SLOW spr round 17 (radius: 20) [05:28:53 -211278.106728] SLOW spr round 18 (radius: 25) [05:35:19 -211277.604997] SLOW spr round 19 (radius: 5) [05:37:43 -211277.546082] SLOW spr round 20 (radius: 10) [05:39:55 -211277.545764] SLOW spr round 21 (radius: 15) [05:42:46 -211276.443857] SLOW spr round 22 (radius: 5) [05:45:06 -211276.440139] SLOW spr round 23 (radius: 10) [05:47:15 -211276.438759] SLOW spr round 24 (radius: 15) [05:50:09 -211276.438268] SLOW spr round 25 (radius: 20) [05:55:01 -211276.438091] SLOW spr round 26 (radius: 25) [06:01:25 -211276.438024] Model parameter optimization (eps = 0.100000) [06:01:34] ML tree search #6, logLikelihood: -211276.244724 [06:01:35 -893006.807075] Initial branch length optimization [06:01:40 -752923.004741] Model parameter optimization (eps = 10.000000) [06:02:14 -750048.854562] AUTODETECT spr round 1 (radius: 5) [06:03:58 -474352.887602] AUTODETECT spr round 2 (radius: 10) [06:05:55 -319374.133406] AUTODETECT spr round 3 (radius: 15) [06:08:08 -268074.131589] AUTODETECT spr round 4 (radius: 20) [06:10:15 -244467.135289] AUTODETECT spr round 5 (radius: 25) [06:12:42 -242265.478674] SPR radius for FAST iterations: 25 (autodetect) [06:12:42 -242265.478674] Model parameter optimization (eps = 3.000000) [06:13:02 -241748.950365] FAST spr round 1 (radius: 25) [06:15:19 -212596.197767] FAST spr round 2 (radius: 25) [06:17:10 -211448.578197] FAST spr round 3 (radius: 25) [06:18:49 -211358.359315] FAST spr round 4 (radius: 25) [06:20:20 -211335.438918] FAST spr round 5 (radius: 25) [06:21:46 -211332.724967] FAST spr round 6 (radius: 25) [06:23:10 -211332.724584] Model parameter optimization (eps = 1.000000) [06:23:23 -211324.084225] SLOW spr round 1 (radius: 5) [06:25:12 -211277.884890] SLOW spr round 2 (radius: 5) [06:27:02 -211277.303006] SLOW spr round 3 (radius: 5) [06:28:48 -211277.300701] SLOW spr round 4 (radius: 10) [06:30:38 -211275.137632] SLOW spr round 5 (radius: 5) [06:32:51 -211275.131225] SLOW spr round 6 (radius: 10) [06:34:52 -211275.131125] SLOW spr round 7 (radius: 15) [06:37:29 -211275.131072] SLOW spr round 8 (radius: 20) [06:41:37 -211275.131035] SLOW spr round 9 (radius: 25) [06:47:03 -211275.131005] Model parameter optimization (eps = 0.100000) [06:47:08] ML tree search #7, logLikelihood: -211275.060757 [06:47:08 -897308.827511] Initial branch length optimization [06:47:11 -754312.780671] Model parameter optimization (eps = 10.000000) [06:47:50 -751416.500189] AUTODETECT spr round 1 (radius: 5) [06:49:31 -466556.524260] AUTODETECT spr round 2 (radius: 10) [06:51:25 -311279.146105] AUTODETECT spr round 3 (radius: 15) [06:53:35 -255078.712180] AUTODETECT spr round 4 (radius: 20) [06:55:40 -243569.359138] AUTODETECT spr round 5 (radius: 25) [06:58:31 -235644.566264] SPR radius for FAST iterations: 25 (autodetect) [06:58:31 -235644.566264] Model parameter optimization (eps = 3.000000) [06:58:50 -235150.064796] FAST spr round 1 (radius: 25) [07:01:00 -212506.541604] FAST spr round 2 (radius: 25) [07:02:51 -211463.402515] FAST spr round 3 (radius: 25) [07:04:28 -211377.926283] FAST spr round 4 (radius: 25) [07:05:57 -211366.520728] FAST spr round 5 (radius: 25) [07:07:22 -211358.816727] FAST spr round 6 (radius: 25) [07:08:46 -211353.900020] FAST spr round 7 (radius: 25) [07:10:09 -211353.899853] Model parameter optimization (eps = 1.000000) [07:10:22 -211349.088026] SLOW spr round 1 (radius: 5) [07:12:10 -211296.341530] SLOW spr round 2 (radius: 5) [07:13:55 -211287.254620] SLOW spr round 3 (radius: 5) [07:15:38 -211284.457375] SLOW spr round 4 (radius: 5) [07:17:19 -211284.457334] SLOW spr round 5 (radius: 10) [07:19:05 -211280.988968] SLOW spr round 6 (radius: 5) [07:21:11 -211276.571445] SLOW spr round 7 (radius: 5) [07:23:02 -211276.571405] SLOW spr round 8 (radius: 10) [07:24:51 -211276.571390] SLOW spr round 9 (radius: 15) [07:27:30 -211276.571384] SLOW spr round 10 (radius: 20) [07:31:35 -211276.571382] SLOW spr round 11 (radius: 25) [07:37:03 -211276.571381] Model parameter optimization (eps = 0.100000) [07:37:14] ML tree search #8, logLikelihood: -211276.344454 [07:37:14 -896961.664041] Initial branch length optimization [07:37:18 -756317.221541] Model parameter optimization (eps = 10.000000) [07:37:53 -753414.308431] AUTODETECT spr round 1 (radius: 5) [07:39:35 -477002.014621] AUTODETECT spr round 2 (radius: 10) [07:41:32 -318339.404237] AUTODETECT spr round 3 (radius: 15) [07:43:27 -265383.629218] AUTODETECT spr round 4 (radius: 20) [07:45:33 -252361.662978] AUTODETECT spr round 5 (radius: 25) [07:47:58 -243543.944720] SPR radius for FAST iterations: 25 (autodetect) [07:47:58 -243543.944720] Model parameter optimization (eps = 3.000000) [07:48:16 -242895.455454] FAST spr round 1 (radius: 25) [07:50:25 -213074.015209] FAST spr round 2 (radius: 25) [07:52:12 -211461.545785] FAST spr round 3 (radius: 25) [07:53:50 -211393.944770] FAST spr round 4 (radius: 25) [07:55:18 -211388.826495] FAST spr round 5 (radius: 25) [07:56:42 -211387.123825] FAST spr round 6 (radius: 25) [07:58:04 -211387.122234] Model parameter optimization (eps = 1.000000) [07:58:17 -211382.510958] SLOW spr round 1 (radius: 5) [08:00:04 -211308.681383] SLOW spr round 2 (radius: 5) [08:01:49 -211290.838966] SLOW spr round 3 (radius: 5) [08:03:32 -211290.679917] SLOW spr round 4 (radius: 5) [08:05:13 -211290.679843] SLOW spr round 5 (radius: 10) [08:07:00 -211289.964223] SLOW spr round 6 (radius: 5) [08:09:05 -211289.960073] SLOW spr round 7 (radius: 10) [08:11:01 -211289.958824] SLOW spr round 8 (radius: 15) [08:13:39 -211283.024597] SLOW spr round 9 (radius: 5) [08:15:50 -211283.024323] SLOW spr round 10 (radius: 10) [08:17:51 -211283.024279] SLOW spr round 11 (radius: 15) [08:20:26 -211283.024257] SLOW spr round 12 (radius: 20) [08:24:54 -211283.024242] SLOW spr round 13 (radius: 25) [08:30:46 -211283.024228] Model parameter optimization (eps = 0.100000) [08:30:56] ML tree search #9, logLikelihood: -211282.800961 [08:30:56 -892022.421628] Initial branch length optimization [08:31:04 -750752.739548] Model parameter optimization (eps = 10.000000) [08:31:39 -748164.844877] AUTODETECT spr round 1 (radius: 5) [08:33:20 -465072.235870] AUTODETECT spr round 2 (radius: 10) [08:35:21 -311700.796071] AUTODETECT spr round 3 (radius: 15) [08:37:31 -261917.206379] AUTODETECT spr round 4 (radius: 20) [08:39:50 -253679.733907] AUTODETECT spr round 5 (radius: 25) [08:42:43 -241816.611219] SPR radius for FAST iterations: 25 (autodetect) [08:42:43 -241816.611219] Model parameter optimization (eps = 3.000000) [08:43:04 -241315.395530] FAST spr round 1 (radius: 25) [08:45:09 -213424.845825] FAST spr round 2 (radius: 25) [08:46:51 -211554.292789] FAST spr round 3 (radius: 25) [08:48:26 -211355.802735] FAST spr round 4 (radius: 25) [08:49:53 -211350.414139] FAST spr round 5 (radius: 25) [08:51:18 -211347.850405] FAST spr round 6 (radius: 25) [08:52:41 -211347.849234] Model parameter optimization (eps = 1.000000) [08:52:56 -211341.611624] SLOW spr round 1 (radius: 5) [08:54:41 -211309.472429] SLOW spr round 2 (radius: 5) [08:56:27 -211303.473692] SLOW spr round 3 (radius: 5) [08:58:08 -211303.306238] SLOW spr round 4 (radius: 5) [08:59:50 -211303.306227] SLOW spr round 5 (radius: 10) [09:01:37 -211296.885599] SLOW spr round 6 (radius: 5) [09:03:41 -211293.854663] SLOW spr round 7 (radius: 5) [09:05:33 -211293.853518] SLOW spr round 8 (radius: 10) [09:07:22 -211293.693140] SLOW spr round 9 (radius: 5) [09:09:24 -211293.653466] SLOW spr round 10 (radius: 10) [09:11:19 -211293.652560] SLOW spr round 11 (radius: 15) [09:13:54 -211293.652276] SLOW spr round 12 (radius: 20) [09:18:01 -211293.652187] SLOW spr round 13 (radius: 25) [09:23:30 -211293.652159] Model parameter optimization (eps = 0.100000) [09:23:40] ML tree search #10, logLikelihood: -211293.528792 [09:23:40 -895029.753613] Initial branch length optimization [09:23:44 -755091.553722] Model parameter optimization (eps = 10.000000) [09:24:09 -752224.084219] AUTODETECT spr round 1 (radius: 5) [09:25:51 -472023.329618] AUTODETECT spr round 2 (radius: 10) [09:27:47 -325302.422640] AUTODETECT spr round 3 (radius: 15) [09:29:49 -273584.057645] AUTODETECT spr round 4 (radius: 20) [09:31:56 -253043.232994] AUTODETECT spr round 5 (radius: 25) [09:35:00 -242275.351598] SPR radius for FAST iterations: 25 (autodetect) [09:35:01 -242275.351598] Model parameter optimization (eps = 3.000000) [09:35:18 -241722.033953] FAST spr round 1 (radius: 25) [09:37:34 -212749.478484] FAST spr round 2 (radius: 25) [09:39:21 -211450.526688] FAST spr round 3 (radius: 25) [09:41:02 -211378.112664] FAST spr round 4 (radius: 25) [09:42:31 -211370.193235] FAST spr round 5 (radius: 25) [09:43:55 -211370.177424] Model parameter optimization (eps = 1.000000) [09:44:07 -211367.296303] SLOW spr round 1 (radius: 5) [09:45:58 -211303.104981] SLOW spr round 2 (radius: 5) [09:47:46 -211292.026102] SLOW spr round 3 (radius: 5) [09:49:30 -211291.444751] SLOW spr round 4 (radius: 5) [09:51:12 -211291.444618] SLOW spr round 5 (radius: 10) [09:53:00 -211281.603325] SLOW spr round 6 (radius: 5) [09:55:06 -211274.410056] SLOW spr round 7 (radius: 5) [09:56:58 -211274.409735] SLOW spr round 8 (radius: 10) [09:58:47 -211274.409670] SLOW spr round 9 (radius: 15) [10:01:32 -211274.409632] SLOW spr round 10 (radius: 20) [10:05:52 -211274.409602] SLOW spr round 11 (radius: 25) [10:11:38 -211274.409574] Model parameter optimization (eps = 0.100000) [10:11:43] ML tree search #11, logLikelihood: -211274.333282 [10:11:43 -891307.930160] Initial branch length optimization [10:11:48 -754332.939235] Model parameter optimization (eps = 10.000000) [10:12:14 -751392.250121] AUTODETECT spr round 1 (radius: 5) [10:13:55 -462668.380111] AUTODETECT spr round 2 (radius: 10) [10:15:52 -310719.663722] AUTODETECT spr round 3 (radius: 15) [10:18:06 -257970.929423] AUTODETECT spr round 4 (radius: 20) [10:20:21 -248193.163488] AUTODETECT spr round 5 (radius: 25) [10:23:00 -240037.121164] SPR radius for FAST iterations: 25 (autodetect) [10:23:00 -240037.121164] Model parameter optimization (eps = 3.000000) [10:23:16 -239425.890563] FAST spr round 1 (radius: 25) [10:25:23 -212461.305251] FAST spr round 2 (radius: 25) [10:27:10 -211481.156289] FAST spr round 3 (radius: 25) [10:28:51 -211368.456626] FAST spr round 4 (radius: 25) [10:30:21 -211358.005169] FAST spr round 5 (radius: 25) [10:31:45 -211355.914380] FAST spr round 6 (radius: 25) [10:33:08 -211355.914237] Model parameter optimization (eps = 1.000000) [10:33:21 -211348.853310] SLOW spr round 1 (radius: 5) [10:35:08 -211291.134041] SLOW spr round 2 (radius: 5) [10:36:56 -211283.134198] SLOW spr round 3 (radius: 5) [10:38:39 -211280.793767] SLOW spr round 4 (radius: 5) [10:40:21 -211280.757743] SLOW spr round 5 (radius: 10) [10:42:08 -211279.861438] SLOW spr round 6 (radius: 5) [10:44:11 -211279.853029] SLOW spr round 7 (radius: 10) [10:46:06 -211279.852401] SLOW spr round 8 (radius: 15) [10:48:43 -211279.852351] SLOW spr round 9 (radius: 20) [10:52:56 -211279.852346] SLOW spr round 10 (radius: 25) [10:58:34 -211279.852346] Model parameter optimization (eps = 0.100000) [10:58:38] ML tree search #12, logLikelihood: -211279.791992 [10:58:38 -891928.072376] Initial branch length optimization [10:58:42 -754577.581626] Model parameter optimization (eps = 10.000000) [10:59:11 -751619.064125] AUTODETECT spr round 1 (radius: 5) [11:00:52 -478643.406151] AUTODETECT spr round 2 (radius: 10) [11:02:51 -311805.172955] AUTODETECT spr round 3 (radius: 15) [11:04:58 -255135.648152] AUTODETECT spr round 4 (radius: 20) [11:07:12 -244496.951360] AUTODETECT spr round 5 (radius: 25) [11:09:45 -238461.612306] SPR radius for FAST iterations: 25 (autodetect) [11:09:45 -238461.612306] Model parameter optimization (eps = 3.000000) [11:10:04 -237969.792795] FAST spr round 1 (radius: 25) [11:12:16 -212654.645540] FAST spr round 2 (radius: 25) [11:14:05 -211444.022109] FAST spr round 3 (radius: 25) [11:15:43 -211366.213525] FAST spr round 4 (radius: 25) [11:17:10 -211358.316484] FAST spr round 5 (radius: 25) [11:18:34 -211357.308140] FAST spr round 6 (radius: 25) [11:19:56 -211357.307916] Model parameter optimization (eps = 1.000000) [11:20:10 -211352.936635] SLOW spr round 1 (radius: 5) [11:21:59 -211284.884383] SLOW spr round 2 (radius: 5) [11:23:43 -211282.206825] SLOW spr round 3 (radius: 5) [11:25:25 -211282.204966] SLOW spr round 4 (radius: 10) [11:27:08 -211281.055071] SLOW spr round 5 (radius: 5) [11:29:12 -211281.054833] SLOW spr round 6 (radius: 10) [11:31:06 -211281.054759] SLOW spr round 7 (radius: 15) [11:33:41 -211281.054727] SLOW spr round 8 (radius: 20) [11:38:01 -211280.268326] SLOW spr round 9 (radius: 5) [11:40:13 -211278.530695] SLOW spr round 10 (radius: 5) [11:42:10 -211278.529704] SLOW spr round 11 (radius: 10) [11:44:02 -211276.508749] SLOW spr round 12 (radius: 5) [11:46:04 -211276.505370] SLOW spr round 13 (radius: 10) [11:47:59 -211276.505171] SLOW spr round 14 (radius: 15) [11:50:36 -211275.755458] SLOW spr round 15 (radius: 5) [11:52:47 -211275.755369] SLOW spr round 16 (radius: 10) [11:54:47 -211275.755365] SLOW spr round 17 (radius: 15) [11:57:22 -211275.755363] SLOW spr round 18 (radius: 20) [12:01:43 -211275.755362] SLOW spr round 19 (radius: 25) [12:07:29 -211275.755362] Model parameter optimization (eps = 0.100000) [12:07:40] ML tree search #13, logLikelihood: -211275.200279 [12:07:40 -900547.505590] Initial branch length optimization [12:07:45 -760499.689772] Model parameter optimization (eps = 10.000000) [12:08:18 -757608.231344] AUTODETECT spr round 1 (radius: 5) [12:10:00 -458426.101374] AUTODETECT spr round 2 (radius: 10) [12:11:54 -315158.411622] AUTODETECT spr round 3 (radius: 15) [12:14:08 -276997.480540] AUTODETECT spr round 4 (radius: 20) [12:16:35 -247640.379428] AUTODETECT spr round 5 (radius: 25) [12:19:04 -241952.604685] SPR radius for FAST iterations: 25 (autodetect) [12:19:04 -241952.604685] Model parameter optimization (eps = 3.000000) [12:19:24 -241446.364849] FAST spr round 1 (radius: 25) [12:21:34 -212577.143021] FAST spr round 2 (radius: 25) [12:23:24 -211422.872422] FAST spr round 3 (radius: 25) [12:25:02 -211324.325703] FAST spr round 4 (radius: 25) [12:26:30 -211322.874381] FAST spr round 5 (radius: 25) [12:27:55 -211322.872773] Model parameter optimization (eps = 1.000000) [12:28:13 -211310.057556] SLOW spr round 1 (radius: 5) [12:30:04 -211260.683533] SLOW spr round 2 (radius: 5) [12:31:51 -211255.940254] SLOW spr round 3 (radius: 5) [12:33:35 -211255.917514] SLOW spr round 4 (radius: 10) [12:35:23 -211253.374595] SLOW spr round 5 (radius: 5) [12:37:29 -211253.338263] SLOW spr round 6 (radius: 10) [12:39:27 -211252.802676] SLOW spr round 7 (radius: 5) [12:41:30 -211252.777115] SLOW spr round 8 (radius: 10) [12:43:26 -211252.775067] SLOW spr round 9 (radius: 15) [12:46:03 -211252.774406] SLOW spr round 10 (radius: 20) [12:50:09 -211252.774188] SLOW spr round 11 (radius: 25) [12:55:28 -211252.774114] Model parameter optimization (eps = 0.100000) [12:55:38] ML tree search #14, logLikelihood: -211252.456090 [12:55:38 -899877.776947] Initial branch length optimization [12:55:45 -756433.676200] Model parameter optimization (eps = 10.000000) [12:56:31 -753541.665636] AUTODETECT spr round 1 (radius: 5) [12:58:15 -472470.456895] AUTODETECT spr round 2 (radius: 10) [13:00:10 -350690.555785] AUTODETECT spr round 3 (radius: 15) [13:02:09 -285729.188767] AUTODETECT spr round 4 (radius: 20) [13:04:24 -270967.308710] AUTODETECT spr round 5 (radius: 25) [13:06:49 -251098.202707] SPR radius for FAST iterations: 25 (autodetect) [13:06:49 -251098.202707] Model parameter optimization (eps = 3.000000) [13:07:08 -250619.961529] FAST spr round 1 (radius: 25) [13:09:20 -213462.751666] FAST spr round 2 (radius: 25) [13:11:12 -211526.877365] FAST spr round 3 (radius: 25) [13:12:52 -211393.404397] FAST spr round 4 (radius: 25) [13:14:24 -211346.744629] FAST spr round 5 (radius: 25) [13:15:47 -211346.440745] FAST spr round 6 (radius: 25) [13:17:10 -211346.440426] Model parameter optimization (eps = 1.000000) [13:17:24 -211331.248217] SLOW spr round 1 (radius: 5) [13:19:10 -211299.317477] SLOW spr round 2 (radius: 5) [13:20:56 -211290.174048] SLOW spr round 3 (radius: 5) [13:22:37 -211288.164953] SLOW spr round 4 (radius: 5) [13:24:19 -211288.164829] SLOW spr round 5 (radius: 10) [13:26:08 -211271.914635] SLOW spr round 6 (radius: 5) [13:28:15 -211271.913533] SLOW spr round 7 (radius: 10) [13:30:12 -211271.913397] SLOW spr round 8 (radius: 15) [13:32:54 -211271.536510] SLOW spr round 9 (radius: 5) [13:35:06 -211271.535686] SLOW spr round 10 (radius: 10) [13:37:08 -211271.535467] SLOW spr round 11 (radius: 15) [13:39:49 -211271.535358] SLOW spr round 12 (radius: 20) [13:44:23 -211271.535332] SLOW spr round 13 (radius: 25) [13:50:22 -211271.535322] Model parameter optimization (eps = 0.100000) [13:50:33] ML tree search #15, logLikelihood: -211270.954616 [13:50:33 -897433.321503] Initial branch length optimization [13:50:37 -753390.788038] Model parameter optimization (eps = 10.000000) [13:51:07 -750399.385038] AUTODETECT spr round 1 (radius: 5) [13:52:50 -472224.915157] AUTODETECT spr round 2 (radius: 10) [13:54:49 -318773.197531] AUTODETECT spr round 3 (radius: 15) [13:57:11 -255801.444681] AUTODETECT spr round 4 (radius: 20) [13:59:21 -238776.463712] AUTODETECT spr round 5 (radius: 25) [14:02:01 -237051.654355] SPR radius for FAST iterations: 25 (autodetect) [14:02:01 -237051.654355] Model parameter optimization (eps = 3.000000) [14:02:22 -236508.245916] FAST spr round 1 (radius: 25) [14:04:31 -212462.579147] FAST spr round 2 (radius: 25) [14:06:21 -211503.429796] FAST spr round 3 (radius: 25) [14:08:03 -211361.480078] FAST spr round 4 (radius: 25) [14:09:32 -211351.497751] FAST spr round 5 (radius: 25) [14:10:58 -211349.084545] FAST spr round 6 (radius: 25) [14:12:22 -211349.084427] Model parameter optimization (eps = 1.000000) [14:12:38 -211344.789755] SLOW spr round 1 (radius: 5) [14:14:25 -211290.116969] SLOW spr round 2 (radius: 5) [14:16:12 -211269.853912] SLOW spr round 3 (radius: 5) [14:17:59 -211260.236588] SLOW spr round 4 (radius: 5) [14:19:42 -211260.236454] SLOW spr round 5 (radius: 10) [14:21:30 -211258.337864] SLOW spr round 6 (radius: 5) [14:23:37 -211257.803841] SLOW spr round 7 (radius: 5) [14:25:30 -211257.801227] SLOW spr round 8 (radius: 10) [14:27:24 -211248.547353] SLOW spr round 9 (radius: 5) [14:29:29 -211247.808106] SLOW spr round 10 (radius: 5) [14:31:22 -211247.805195] SLOW spr round 11 (radius: 10) [14:33:14 -211247.424732] SLOW spr round 12 (radius: 5) [14:35:19 -211247.424335] SLOW spr round 13 (radius: 10) [14:37:15 -211247.049560] SLOW spr round 14 (radius: 5) [14:39:19 -211247.048204] SLOW spr round 15 (radius: 10) [14:41:15 -211247.048000] SLOW spr round 16 (radius: 15) [14:43:53 -211246.054656] SLOW spr round 17 (radius: 5) [14:46:05 -211245.947136] SLOW spr round 18 (radius: 5) [14:48:02 -211245.946589] SLOW spr round 19 (radius: 10) [14:49:54 -211245.946372] SLOW spr round 20 (radius: 15) [14:52:34 -211245.946288] SLOW spr round 21 (radius: 20) [14:56:37 -211245.946255] SLOW spr round 22 (radius: 25) [15:01:57 -211245.946243] Model parameter optimization (eps = 0.100000) [15:02:10] ML tree search #16, logLikelihood: -211245.624155 [15:02:10 -898750.303746] Initial branch length optimization [15:02:14 -756835.822347] Model parameter optimization (eps = 10.000000) [15:02:42 -753906.050736] AUTODETECT spr round 1 (radius: 5) [15:04:25 -472684.227390] AUTODETECT spr round 2 (radius: 10) [15:06:17 -317805.381878] AUTODETECT spr round 3 (radius: 15) [15:08:20 -261713.637252] AUTODETECT spr round 4 (radius: 20) [15:10:32 -240599.179652] AUTODETECT spr round 5 (radius: 25) [15:13:08 -239308.711377] SPR radius for FAST iterations: 25 (autodetect) [15:13:08 -239308.711377] Model parameter optimization (eps = 3.000000) [15:13:27 -238794.723862] FAST spr round 1 (radius: 25) [15:15:46 -212683.246693] FAST spr round 2 (radius: 25) [15:17:36 -211434.802183] FAST spr round 3 (radius: 25) [15:19:11 -211326.763682] FAST spr round 4 (radius: 25) [15:20:40 -211317.963633] FAST spr round 5 (radius: 25) [15:22:06 -211309.749212] FAST spr round 6 (radius: 25) [15:23:30 -211309.748580] Model parameter optimization (eps = 1.000000) [15:23:43 -211305.749267] SLOW spr round 1 (radius: 5) [15:25:31 -211255.456502] SLOW spr round 2 (radius: 5) [15:27:18 -211244.286075] SLOW spr round 3 (radius: 5) [15:29:01 -211244.174124] SLOW spr round 4 (radius: 5) [15:30:43 -211244.174017] SLOW spr round 5 (radius: 10) [15:32:31 -211244.173991] SLOW spr round 6 (radius: 15) [15:35:20 -211244.173974] SLOW spr round 7 (radius: 20) [15:39:39 -211244.173959] SLOW spr round 8 (radius: 25) [15:45:24 -211244.173944] Model parameter optimization (eps = 0.100000) [15:45:31] ML tree search #17, logLikelihood: -211244.050559 [15:45:31 -896892.340761] Initial branch length optimization [15:45:36 -755170.158488] Model parameter optimization (eps = 10.000000) [15:46:03 -752216.659662] AUTODETECT spr round 1 (radius: 5) [15:47:46 -483960.289362] AUTODETECT spr round 2 (radius: 10) [15:49:36 -319441.319742] AUTODETECT spr round 3 (radius: 15) [15:51:39 -260719.110843] AUTODETECT spr round 4 (radius: 20) [15:53:59 -239521.187300] AUTODETECT spr round 5 (radius: 25) [15:56:51 -237293.924923] SPR radius for FAST iterations: 25 (autodetect) [15:56:51 -237293.924923] Model parameter optimization (eps = 3.000000) [15:57:10 -236820.840889] FAST spr round 1 (radius: 25) [15:59:16 -212795.408268] FAST spr round 2 (radius: 25) [16:01:06 -211481.215672] FAST spr round 3 (radius: 25) [16:02:43 -211385.246553] FAST spr round 4 (radius: 25) [16:04:13 -211370.522780] FAST spr round 5 (radius: 25) [16:05:38 -211370.473408] Model parameter optimization (eps = 1.000000) [16:05:53 -211361.214492] SLOW spr round 1 (radius: 5) [16:07:42 -211303.399678] SLOW spr round 2 (radius: 5) [16:09:30 -211284.374142] SLOW spr round 3 (radius: 5) [16:11:17 -211281.792331] SLOW spr round 4 (radius: 5) [16:13:01 -211281.790686] SLOW spr round 5 (radius: 10) [16:14:48 -211281.405235] SLOW spr round 6 (radius: 5) [16:16:56 -211269.746827] SLOW spr round 7 (radius: 5) [16:18:50 -211266.346918] SLOW spr round 8 (radius: 5) [16:20:38 -211266.346814] SLOW spr round 9 (radius: 10) [16:22:26 -211266.346780] SLOW spr round 10 (radius: 15) [16:25:07 -211266.253384] SLOW spr round 11 (radius: 20) [16:29:10 -211266.249809] SLOW spr round 12 (radius: 25) [16:34:32 -211266.248781] Model parameter optimization (eps = 0.100000) [16:34:44] ML tree search #18, logLikelihood: -211265.904074 [16:34:44 -897773.133147] Initial branch length optimization [16:34:48 -755691.876605] Model parameter optimization (eps = 10.000000) [16:35:18 -752755.718196] AUTODETECT spr round 1 (radius: 5) [16:36:59 -477194.541698] AUTODETECT spr round 2 (radius: 10) [16:38:54 -336667.446195] AUTODETECT spr round 3 (radius: 15) [16:40:57 -278146.685356] AUTODETECT spr round 4 (radius: 20) [16:43:14 -249805.181448] AUTODETECT spr round 5 (radius: 25) [16:45:51 -242221.332930] SPR radius for FAST iterations: 25 (autodetect) [16:45:51 -242221.332930] Model parameter optimization (eps = 3.000000) [16:46:08 -241675.164049] FAST spr round 1 (radius: 25) [16:48:15 -212626.889159] FAST spr round 2 (radius: 25) [16:50:01 -211469.808790] FAST spr round 3 (radius: 25) [16:51:40 -211374.151560] FAST spr round 4 (radius: 25) [16:53:08 -211358.466311] FAST spr round 5 (radius: 25) [16:54:31 -211358.464156] Model parameter optimization (eps = 1.000000) [16:54:44 -211350.549305] SLOW spr round 1 (radius: 5) [16:56:30 -211285.826436] SLOW spr round 2 (radius: 5) [16:58:15 -211284.566285] SLOW spr round 3 (radius: 5) [16:59:58 -211283.575851] SLOW spr round 4 (radius: 5) [17:01:39 -211283.574177] SLOW spr round 5 (radius: 10) [17:03:27 -211273.230132] SLOW spr round 6 (radius: 5) [17:05:32 -211272.739606] SLOW spr round 7 (radius: 5) [17:07:23 -211272.737531] SLOW spr round 8 (radius: 10) [17:09:12 -211272.736989] SLOW spr round 9 (radius: 15) [17:11:55 -211272.340390] SLOW spr round 10 (radius: 5) [17:14:05 -211272.340269] SLOW spr round 11 (radius: 10) [17:16:05 -211272.340243] SLOW spr round 12 (radius: 15) [17:18:41 -211272.340233] SLOW spr round 13 (radius: 20) [17:23:07 -211272.340228] SLOW spr round 14 (radius: 25) [17:28:55 -211272.340226] Model parameter optimization (eps = 0.100000) [17:29:04] ML tree search #19, logLikelihood: -211272.158721 [17:29:04 -896102.523784] Initial branch length optimization [17:29:08 -756115.522128] Model parameter optimization (eps = 10.000000) [17:29:40 -753260.648546] AUTODETECT spr round 1 (radius: 5) [17:31:22 -480283.022808] AUTODETECT spr round 2 (radius: 10) [17:33:17 -323751.884739] AUTODETECT spr round 3 (radius: 15) [17:35:10 -268785.311778] AUTODETECT spr round 4 (radius: 20) [17:37:20 -242277.759796] AUTODETECT spr round 5 (radius: 25) [17:39:52 -237286.149911] SPR radius for FAST iterations: 25 (autodetect) [17:39:52 -237286.149911] Model parameter optimization (eps = 3.000000) [17:40:08 -236828.010996] FAST spr round 1 (radius: 25) [17:42:17 -212563.929548] FAST spr round 2 (radius: 25) [17:44:05 -211380.273227] FAST spr round 3 (radius: 25) [17:45:43 -211321.505614] FAST spr round 4 (radius: 25) [17:47:14 -211314.555659] FAST spr round 5 (radius: 25) [17:48:40 -211314.554082] Model parameter optimization (eps = 1.000000) [17:48:50 -211313.403677] SLOW spr round 1 (radius: 5) [17:50:39 -211274.106416] SLOW spr round 2 (radius: 5) [17:52:27 -211270.248280] SLOW spr round 3 (radius: 5) [17:54:10 -211270.213392] SLOW spr round 4 (radius: 10) [17:55:58 -211270.211243] SLOW spr round 5 (radius: 15) [17:58:41 -211270.210533] SLOW spr round 6 (radius: 20) [18:02:42 -211269.830079] SLOW spr round 7 (radius: 5) [18:04:56 -211269.829944] SLOW spr round 8 (radius: 10) [18:07:00 -211269.829905] SLOW spr round 9 (radius: 15) [18:09:36 -211269.829890] SLOW spr round 10 (radius: 20) [18:13:40 -211269.829884] SLOW spr round 11 (radius: 25) [18:18:57 -211269.829881] Model parameter optimization (eps = 0.100000) [18:19:07] ML tree search #20, logLikelihood: -211269.670001 Optimized model parameters: Partition 0: noname Rate heterogeneity: FREE (4 cats, mean), weights&rates: (0.211050,0.468287) (0.292090,0.558578) (0.330974,1.089301) (0.165887,2.275546) 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: -211244.050559 AIC score: 426294.101118 / AICc score: 7672918.101118 / BIC score: 434587.074952 Free parameters (model + branch lengths): 1903 WARNING: Number of free parameters (K=1903) is larger than alignment size (n=577). This might lead to overfitting and compromise tree inference results! Best ML tree saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q9NYB5/3_mltree/Q9NYB5.raxml.bestTree All ML trees saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q9NYB5/3_mltree/Q9NYB5.raxml.mlTrees Optimized model saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q9NYB5/3_mltree/Q9NYB5.raxml.bestModel Execution log saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q9NYB5/3_mltree/Q9NYB5.raxml.log Analysis started: 18-Jul-2021 01:00:00 / finished: 18-Jul-2021 19:19:07 Elapsed time: 65947.313 seconds