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 23-Jun-2021 15:23:17 as follows: raxml-ng --msa /cta/users/eakkoyun/WORKFOLDER/PROD/run_040621/phylogeny-snakemake/results/O60706/2_msa/O60706_trimmed_msa.fasta --data-type AA --model LG4X --prefix /cta/users/eakkoyun/WORKFOLDER/PROD/run_040621/phylogeny-snakemake/results/O60706/3_mltree/O60706 --seed 2 --threads 8 --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 (8 threads), thread pinning: OFF [00:00:00] Reading alignment from file: /cta/users/eakkoyun/WORKFOLDER/PROD/run_040621/phylogeny-snakemake/results/O60706/2_msa/O60706_trimmed_msa.fasta [00:00:00] Loaded alignment with 1001 taxa and 1409 sites WARNING: Sequences tr_A0A179UYT6_A0A179UYT6_BLAGS_559298 and tr_C5GY12_C5GY12_AJEDR_559297 are exactly identical! WARNING: Sequences tr_A0A2I3S6S2_A0A2I3S6S2_PANTR_9598 and sp_O60706_ABCC9_HUMAN_9606 are exactly identical! WARNING: Sequences tr_A0A2I3S6S2_A0A2I3S6S2_PANTR_9598 and tr_A0A2R9AZ23_A0A2R9AZ23_PANPA_9597 are exactly identical! WARNING: Sequences tr_H2R5J8_H2R5J8_PANTR_9598 and tr_A0A2R8ZS53_A0A2R8ZS53_PANPA_9597 are exactly identical! WARNING: Sequences tr_F9G4Z3_F9G4Z3_FUSOF_660025 and tr_N4UPB2_N4UPB2_FUSC1_1229664 are exactly identical! WARNING: Sequences tr_F9G4Z3_F9G4Z3_FUSOF_660025 and tr_A0A2H3U217_A0A2H3U217_FUSOX_5507 are exactly identical! WARNING: Sequences tr_F4P102_F4P102_BATDJ_684364 and tr_A0A177WDX7_A0A177WDX7_BATDE_403673 are exactly identical! WARNING: Sequences tr_W2PWQ0_W2PWQ0_PHYPN_761204 and tr_W2KR63_W2KR63_PHYPR_4792 are exactly identical! WARNING: Sequences tr_A0A015KCR6_A0A015KCR6_9GLOM_1432141 and tr_A0A2H5SSS0_A0A2H5SSS0_RHIID_747089 are exactly identical! WARNING: Sequences tr_A0A078F8D8_A0A078F8D8_BRANA_3708 and tr_A0A0D3CEV4_A0A0D3CEV4_BRAOL_109376 are exactly identical! WARNING: Sequences tr_A0A078FGE1_A0A078FGE1_BRANA_3708 and tr_A0A0D3BJ45_A0A0D3BJ45_BRAOL_109376 are exactly identical! WARNING: Sequences tr_A0A0F8V4S6_A0A0F8V4S6_9EURO_308745 and tr_A0A2T5LU50_A0A2T5LU50_9EURO_1392256 are exactly identical! WARNING: Sequences tr_A0A1S3XZQ2_A0A1S3XZQ2_TOBAC_4097 and tr_A0A1U7X257_A0A1U7X257_NICSY_4096 are exactly identical! WARNING: Sequences tr_A0A2D0T5R3_A0A2D0T5R3_ICTPU_7998 and tr_A0A2D0T5Y8_A0A2D0T5Y8_ICTPU_7998 are exactly identical! WARNING: Duplicate sequences found: 14 NOTE: Reduced alignment (with duplicates and gap-only sites/taxa removed) NOTE: was saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_040621/phylogeny-snakemake/results/O60706/3_mltree/O60706.raxml.reduced.phy Alignment comprises 1 partitions and 1409 patterns Partition 0: noname Model: LG4X+R4 Alignment sites / patterns: 1409 / 1409 Gaps: 5.47 % Invariant sites: 0.64 % NOTE: Binary MSA file created: /cta/users/eakkoyun/WORKFOLDER/PROD/run_040621/phylogeny-snakemake/results/O60706/3_mltree/O60706.raxml.rba Parallelization scheme autoconfig: 1 worker(s) x 8 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 / 177 / 14160 [00:00:00] Data distribution: max. searches per worker: 20 Starting ML tree search with 20 distinct starting trees [00:00:00 -2470365.284122] Initial branch length optimization [00:00:07 -2105292.269249] Model parameter optimization (eps = 10.000000) [00:00:48 -2100903.752452] AUTODETECT spr round 1 (radius: 5) [00:03:55 -1491457.411246] AUTODETECT spr round 2 (radius: 10) [00:07:27 -1089606.910363] AUTODETECT spr round 3 (radius: 15) [00:11:13 -906777.331288] AUTODETECT spr round 4 (radius: 20) [00:15:32 -852920.531714] AUTODETECT spr round 5 (radius: 25) [00:20:50 -842671.158923] SPR radius for FAST iterations: 25 (autodetect) [00:20:50 -842671.158923] Model parameter optimization (eps = 3.000000) [00:21:19 -842382.409441] FAST spr round 1 (radius: 25) [00:25:43 -757730.355095] FAST spr round 2 (radius: 25) [00:28:48 -755147.153228] FAST spr round 3 (radius: 25) [00:31:19 -754946.778116] FAST spr round 4 (radius: 25) [00:33:37 -754932.797744] FAST spr round 5 (radius: 25) [00:35:49 -754922.885226] FAST spr round 6 (radius: 25) [00:37:53 -754922.885201] Model parameter optimization (eps = 1.000000) [00:38:14 -754909.583483] SLOW spr round 1 (radius: 5) [00:41:24 -754846.507266] SLOW spr round 2 (radius: 5) [00:44:15 -754841.342709] SLOW spr round 3 (radius: 5) [00:47:01 -754841.342685] SLOW spr round 4 (radius: 10) [00:49:55 -754841.342666] SLOW spr round 5 (radius: 15) [00:55:21 -754841.342647] SLOW spr round 6 (radius: 20) [01:04:22 -754841.342627] SLOW spr round 7 (radius: 25) [01:15:47 -754841.342608] Model parameter optimization (eps = 0.100000) [01:15:58] ML tree search #1, logLikelihood: -754841.221181 [01:15:58 -2481990.035137] Initial branch length optimization [01:16:04 -2109662.581483] Model parameter optimization (eps = 10.000000) [01:16:54 -2105670.026585] AUTODETECT spr round 1 (radius: 5) [01:20:03 -1508415.878207] AUTODETECT spr round 2 (radius: 10) [01:23:37 -1113667.815091] AUTODETECT spr round 3 (radius: 15) [01:27:19 -911543.417827] AUTODETECT spr round 4 (radius: 20) [01:31:17 -857224.585130] AUTODETECT spr round 5 (radius: 25) [01:36:38 -843260.597023] SPR radius for FAST iterations: 25 (autodetect) [01:36:38 -843260.597023] Model parameter optimization (eps = 3.000000) [01:36:45 -843258.660944] FAST spr round 1 (radius: 25) [01:41:07 -759211.882779] FAST spr round 2 (radius: 25) [01:44:16 -755502.616923] FAST spr round 3 (radius: 25) [01:46:57 -755357.260486] FAST spr round 4 (radius: 25) [01:49:10 -755357.260271] Model parameter optimization (eps = 1.000000) [01:49:30 -755052.374656] SLOW spr round 1 (radius: 5) [01:52:49 -754862.007750] SLOW spr round 2 (radius: 5) [01:55:49 -754854.507110] SLOW spr round 3 (radius: 5) [01:58:38 -754852.921870] SLOW spr round 4 (radius: 5) [02:01:25 -754852.921843] SLOW spr round 5 (radius: 10) [02:04:21 -754851.544529] SLOW spr round 6 (radius: 5) [02:08:02 -754849.897443] SLOW spr round 7 (radius: 5) [02:11:13 -754849.897423] SLOW spr round 8 (radius: 10) [02:14:18 -754849.897403] SLOW spr round 9 (radius: 15) [02:19:30 -754849.897383] SLOW spr round 10 (radius: 20) [02:28:43 -754849.897363] SLOW spr round 11 (radius: 25) [02:40:02 -754849.897343] Model parameter optimization (eps = 0.100000) [02:40:11] ML tree search #2, logLikelihood: -754849.467132 [02:40:11 -2491550.795015] Initial branch length optimization [02:40:17 -2121721.668746] Model parameter optimization (eps = 10.000000) [02:41:01 -2117470.955637] AUTODETECT spr round 1 (radius: 5) [02:44:09 -1517841.840154] AUTODETECT spr round 2 (radius: 10) [02:47:43 -1088267.126316] AUTODETECT spr round 3 (radius: 15) [02:51:29 -926860.632977] AUTODETECT spr round 4 (radius: 20) [02:56:04 -854057.330584] AUTODETECT spr round 5 (radius: 25) [03:01:22 -846708.142395] SPR radius for FAST iterations: 25 (autodetect) [03:01:22 -846708.142395] Model parameter optimization (eps = 3.000000) [03:01:46 -846371.183098] FAST spr round 1 (radius: 25) [03:05:45 -757670.232928] FAST spr round 2 (radius: 25) [03:08:41 -755264.992473] FAST spr round 3 (radius: 25) [03:11:15 -755072.422814] FAST spr round 4 (radius: 25) [03:13:29 -755056.550739] FAST spr round 5 (radius: 25) [03:15:36 -755056.550696] Model parameter optimization (eps = 1.000000) [03:15:56 -755029.099928] SLOW spr round 1 (radius: 5) [03:19:04 -754847.708117] SLOW spr round 2 (radius: 5) [03:21:55 -754846.155370] SLOW spr round 3 (radius: 5) [03:24:42 -754846.155370] SLOW spr round 4 (radius: 10) [03:27:40 -754832.802456] SLOW spr round 5 (radius: 5) [03:31:22 -754824.592951] SLOW spr round 6 (radius: 5) [03:34:34 -754823.534694] SLOW spr round 7 (radius: 5) [03:37:32 -754823.534550] SLOW spr round 8 (radius: 10) [03:40:31 -754823.534549] SLOW spr round 9 (radius: 15) [03:45:54 -754823.534549] SLOW spr round 10 (radius: 20) [03:55:19 -754823.534549] SLOW spr round 11 (radius: 25) [04:06:52 -754823.534549] Model parameter optimization (eps = 0.100000) [04:07:11] ML tree search #3, logLikelihood: -754821.108054 [04:07:11 -2468346.740259] Initial branch length optimization [04:07:20 -2091645.998093] Model parameter optimization (eps = 10.000000) [04:08:05 -2087566.199468] AUTODETECT spr round 1 (radius: 5) [04:11:14 -1504625.157587] AUTODETECT spr round 2 (radius: 10) [04:14:49 -1106664.480085] AUTODETECT spr round 3 (radius: 15) [04:18:54 -910127.523848] AUTODETECT spr round 4 (radius: 20) [04:24:00 -861897.862507] AUTODETECT spr round 5 (radius: 25) [04:30:02 -855942.241164] SPR radius for FAST iterations: 25 (autodetect) [04:30:02 -855942.241164] Model parameter optimization (eps = 3.000000) [04:30:32 -855572.592885] FAST spr round 1 (radius: 25) [04:34:59 -758422.842909] FAST spr round 2 (radius: 25) [04:38:11 -755353.035402] FAST spr round 3 (radius: 25) [04:40:53 -754994.492186] FAST spr round 4 (radius: 25) [04:43:05 -754991.227769] FAST spr round 5 (radius: 25) [04:45:13 -754991.227763] Model parameter optimization (eps = 1.000000) [04:45:18 -754991.205222] SLOW spr round 1 (radius: 5) [04:48:32 -754875.495378] SLOW spr round 2 (radius: 5) [04:51:24 -754867.791230] SLOW spr round 3 (radius: 5) [04:54:11 -754867.791071] SLOW spr round 4 (radius: 10) [04:57:05 -754867.626463] SLOW spr round 5 (radius: 5) [05:00:48 -754863.558694] SLOW spr round 6 (radius: 5) [05:03:59 -754863.558266] SLOW spr round 7 (radius: 10) [05:07:01 -754863.558266] SLOW spr round 8 (radius: 15) [05:12:10 -754863.558266] SLOW spr round 9 (radius: 20) [05:21:27 -754863.558266] SLOW spr round 10 (radius: 25) [05:32:40 -754863.558266] Model parameter optimization (eps = 0.100000) [05:33:00] ML tree search #4, logLikelihood: -754835.051025 [05:33:01 -2476923.273098] Initial branch length optimization [05:33:08 -2102842.349067] Model parameter optimization (eps = 10.000000) [05:33:56 -2098604.741003] AUTODETECT spr round 1 (radius: 5) [05:37:05 -1509461.857687] AUTODETECT spr round 2 (radius: 10) [05:40:35 -1104465.392640] AUTODETECT spr round 3 (radius: 15) [05:44:14 -935322.104402] AUTODETECT spr round 4 (radius: 20) [05:49:10 -853656.843225] AUTODETECT spr round 5 (radius: 25) [05:54:45 -847887.845456] SPR radius for FAST iterations: 25 (autodetect) [05:54:45 -847887.845456] Model parameter optimization (eps = 3.000000) [05:55:09 -847547.602321] FAST spr round 1 (radius: 25) [05:59:27 -758518.531502] FAST spr round 2 (radius: 25) [06:02:32 -755247.542405] FAST spr round 3 (radius: 25) [06:05:16 -755001.242739] FAST spr round 4 (radius: 25) [06:07:35 -754969.262852] FAST spr round 5 (radius: 25) [06:09:45 -754963.211217] FAST spr round 6 (radius: 25) [06:11:50 -754963.211204] Model parameter optimization (eps = 1.000000) [06:12:08 -754950.591193] SLOW spr round 1 (radius: 5) [06:15:18 -754831.164377] SLOW spr round 2 (radius: 5) [06:18:10 -754826.688378] SLOW spr round 3 (radius: 5) [06:20:57 -754826.688331] SLOW spr round 4 (radius: 10) [06:23:52 -754826.151410] SLOW spr round 5 (radius: 5) [06:27:37 -754823.084535] SLOW spr round 6 (radius: 5) [06:30:49 -754823.084451] SLOW spr round 7 (radius: 10) [06:33:53 -754823.084451] SLOW spr round 8 (radius: 15) [06:39:04 -754823.084451] SLOW spr round 9 (radius: 20) [06:48:19 -754823.084451] SLOW spr round 10 (radius: 25) [06:59:42 -754823.084450] Model parameter optimization (eps = 0.100000) [06:59:54] ML tree search #5, logLikelihood: -754822.717287 [06:59:54 -2484970.653521] Initial branch length optimization [07:00:02 -2114493.558160] Model parameter optimization (eps = 10.000000) [07:00:49 -2109842.800946] AUTODETECT spr round 1 (radius: 5) [07:03:57 -1517396.806510] AUTODETECT spr round 2 (radius: 10) [07:07:32 -1087625.378806] AUTODETECT spr round 3 (radius: 15) [07:11:20 -895189.467748] AUTODETECT spr round 4 (radius: 20) [07:15:51 -855072.674600] AUTODETECT spr round 5 (radius: 25) [07:21:28 -848125.418589] SPR radius for FAST iterations: 25 (autodetect) [07:21:28 -848125.418589] Model parameter optimization (eps = 3.000000) [07:21:52 -847818.458634] FAST spr round 1 (radius: 25) [07:26:17 -759689.186814] FAST spr round 2 (radius: 25) [07:29:27 -755337.013670] FAST spr round 3 (radius: 25) [07:32:11 -755119.865924] FAST spr round 4 (radius: 25) [07:34:26 -755107.984774] FAST spr round 5 (radius: 25) [07:36:35 -755107.984730] Model parameter optimization (eps = 1.000000) [07:36:58 -755073.819515] SLOW spr round 1 (radius: 5) [07:40:17 -754856.415307] SLOW spr round 2 (radius: 5) [07:43:12 -754848.743730] SLOW spr round 3 (radius: 5) [07:46:00 -754848.743510] SLOW spr round 4 (radius: 10) [07:48:57 -754848.743509] SLOW spr round 5 (radius: 15) [07:54:21 -754848.743509] SLOW spr round 6 (radius: 20) [08:03:16 -754848.743509] SLOW spr round 7 (radius: 25) [08:14:36 -754848.743509] Model parameter optimization (eps = 0.100000) [08:14:49] ML tree search #6, logLikelihood: -754848.207162 [08:14:49 -2471614.457255] Initial branch length optimization [08:14:55 -2108249.858010] Model parameter optimization (eps = 10.000000) [08:15:47 -2103679.510638] AUTODETECT spr round 1 (radius: 5) [08:18:53 -1519936.220042] AUTODETECT spr round 2 (radius: 10) [08:22:26 -1073831.039496] AUTODETECT spr round 3 (radius: 15) [08:26:12 -910832.148751] AUTODETECT spr round 4 (radius: 20) [08:31:04 -863965.182523] AUTODETECT spr round 5 (radius: 25) [08:36:15 -849652.585393] SPR radius for FAST iterations: 25 (autodetect) [08:36:15 -849652.585393] Model parameter optimization (eps = 3.000000) [08:36:41 -849275.602162] FAST spr round 1 (radius: 25) [08:40:47 -758375.353205] FAST spr round 2 (radius: 25) [08:43:52 -755143.681891] FAST spr round 3 (radius: 25) [08:46:32 -755028.421592] FAST spr round 4 (radius: 25) [08:48:49 -755004.178911] FAST spr round 5 (radius: 25) [08:50:58 -755004.178884] Model parameter optimization (eps = 1.000000) [08:51:07 -755003.267474] SLOW spr round 1 (radius: 5) [08:54:21 -754856.330503] SLOW spr round 2 (radius: 5) [08:57:22 -754838.303716] SLOW spr round 3 (radius: 5) [09:00:11 -754838.303527] SLOW spr round 4 (radius: 10) [09:03:08 -754837.704997] SLOW spr round 5 (radius: 5) [09:06:52 -754834.547915] SLOW spr round 6 (radius: 5) [09:10:05 -754834.547913] SLOW spr round 7 (radius: 10) [09:13:10 -754834.547913] SLOW spr round 8 (radius: 15) [09:18:25 -754834.547912] SLOW spr round 9 (radius: 20) [09:27:49 -754834.547912] SLOW spr round 10 (radius: 25) [09:39:27 -754834.547912] Model parameter optimization (eps = 0.100000) [09:39:40] ML tree search #7, logLikelihood: -754834.244182 [09:39:40 -2471188.554454] Initial branch length optimization [09:39:46 -2094352.160339] Model parameter optimization (eps = 10.000000) [09:40:31 -2090212.727604] AUTODETECT spr round 1 (radius: 5) [09:43:38 -1536654.372010] AUTODETECT spr round 2 (radius: 10) [09:47:12 -1146007.394225] AUTODETECT spr round 3 (radius: 15) [09:51:23 -933021.852073] AUTODETECT spr round 4 (radius: 20) [09:55:59 -854413.163364] AUTODETECT spr round 5 (radius: 25) [10:01:10 -849034.518738] SPR radius for FAST iterations: 25 (autodetect) [10:01:10 -849034.518738] Model parameter optimization (eps = 3.000000) [10:01:39 -848737.877217] FAST spr round 1 (radius: 25) [10:05:51 -759085.991215] FAST spr round 2 (radius: 25) [10:08:58 -755284.806986] FAST spr round 3 (radius: 25) [10:11:36 -755071.960425] FAST spr round 4 (radius: 25) [10:13:57 -755054.677706] FAST spr round 5 (radius: 25) [10:16:05 -755054.677660] Model parameter optimization (eps = 1.000000) [10:16:26 -755031.683599] SLOW spr round 1 (radius: 5) [10:19:41 -754870.024015] SLOW spr round 2 (radius: 5) [10:22:37 -754866.008935] SLOW spr round 3 (radius: 5) [10:25:26 -754866.008904] SLOW spr round 4 (radius: 10) [10:28:24 -754866.008904] SLOW spr round 5 (radius: 15) [10:33:49 -754866.008904] SLOW spr round 6 (radius: 20) [10:42:50 -754866.008903] SLOW spr round 7 (radius: 25) [10:54:08 -754866.008903] Model parameter optimization (eps = 0.100000) [10:54:20] ML tree search #8, logLikelihood: -754865.277051 [10:54:20 -2475047.876016] Initial branch length optimization [10:54:28 -2106113.771912] Model parameter optimization (eps = 10.000000) [10:55:20 -2101754.826012] AUTODETECT spr round 1 (radius: 5) [10:58:27 -1524810.521411] AUTODETECT spr round 2 (radius: 10) [11:02:00 -1123279.654147] AUTODETECT spr round 3 (radius: 15) [11:05:51 -933956.605620] AUTODETECT spr round 4 (radius: 20) [11:10:33 -850633.803487] AUTODETECT spr round 5 (radius: 25) [11:15:47 -847696.304691] SPR radius for FAST iterations: 25 (autodetect) [11:15:47 -847696.304691] Model parameter optimization (eps = 3.000000) [11:16:16 -847399.224105] FAST spr round 1 (radius: 25) [11:20:21 -758789.182922] FAST spr round 2 (radius: 25) [11:23:25 -755294.903908] FAST spr round 3 (radius: 25) [11:26:06 -755107.001949] FAST spr round 4 (radius: 25) [11:28:31 -755052.701971] FAST spr round 5 (radius: 25) [11:30:45 -755039.086307] FAST spr round 6 (radius: 25) [11:32:56 -755033.937490] FAST spr round 7 (radius: 25) [11:35:01 -755033.937469] Model parameter optimization (eps = 1.000000) [11:35:23 -755001.347588] SLOW spr round 1 (radius: 5) [11:38:28 -754839.541275] SLOW spr round 2 (radius: 5) [11:41:20 -754828.386254] SLOW spr round 3 (radius: 5) [11:44:08 -754828.386212] SLOW spr round 4 (radius: 10) [11:47:06 -754828.386211] SLOW spr round 5 (radius: 15) [11:52:32 -754828.386211] SLOW spr round 6 (radius: 20) [12:01:36 -754828.386211] SLOW spr round 7 (radius: 25) [12:13:03 -754828.386211] Model parameter optimization (eps = 0.100000) [12:13:16] ML tree search #9, logLikelihood: -754827.766496 [12:13:16 -2466227.750685] Initial branch length optimization [12:13:22 -2091655.026231] Model parameter optimization (eps = 10.000000) [12:14:09 -2087649.875505] AUTODETECT spr round 1 (radius: 5) [12:17:17 -1527816.863127] AUTODETECT spr round 2 (radius: 10) [12:20:53 -1187377.559573] AUTODETECT spr round 3 (radius: 15) [12:25:02 -970782.096813] AUTODETECT spr round 4 (radius: 20) [12:29:33 -871925.399182] AUTODETECT spr round 5 (radius: 25) [12:34:00 -863456.690132] SPR radius for FAST iterations: 25 (autodetect) [12:34:01 -863456.690132] Model parameter optimization (eps = 3.000000) [12:34:37 -863180.283721] FAST spr round 1 (radius: 25) [12:38:46 -758536.615677] FAST spr round 2 (radius: 25) [12:41:53 -755244.090717] FAST spr round 3 (radius: 25) [12:44:31 -755076.548608] FAST spr round 4 (radius: 25) [12:46:45 -755069.747688] FAST spr round 5 (radius: 25) [12:48:53 -755069.747600] Model parameter optimization (eps = 1.000000) [12:49:12 -755043.714773] SLOW spr round 1 (radius: 5) [12:52:17 -754876.190406] SLOW spr round 2 (radius: 5) [12:55:13 -754869.990848] SLOW spr round 3 (radius: 5) [12:58:01 -754869.990453] SLOW spr round 4 (radius: 10) [13:00:58 -754849.429177] SLOW spr round 5 (radius: 5) [13:04:39 -754849.428814] SLOW spr round 6 (radius: 10) [13:08:00 -754849.428787] SLOW spr round 7 (radius: 15) [13:13:02 -754849.428768] SLOW spr round 8 (radius: 20) [13:22:50 -754849.428748] SLOW spr round 9 (radius: 25) [13:34:24 -754849.428729] Model parameter optimization (eps = 0.100000) [13:34:37] ML tree search #10, logLikelihood: -754848.756352 [13:34:37 -2484077.135203] Initial branch length optimization [13:34:43 -2113078.817289] Model parameter optimization (eps = 10.000000) [13:35:29 -2108854.463001] AUTODETECT spr round 1 (radius: 5) [13:38:37 -1548436.195658] AUTODETECT spr round 2 (radius: 10) [13:42:11 -1107121.336195] AUTODETECT spr round 3 (radius: 15) [13:46:11 -900810.933453] AUTODETECT spr round 4 (radius: 20) [13:51:03 -856069.145384] AUTODETECT spr round 5 (radius: 25) [13:56:46 -841116.447454] SPR radius for FAST iterations: 25 (autodetect) [13:56:46 -841116.447454] Model parameter optimization (eps = 3.000000) [13:56:53 -841114.341250] FAST spr round 1 (radius: 25) [14:01:17 -759012.099947] FAST spr round 2 (radius: 25) [14:04:33 -755679.015965] FAST spr round 3 (radius: 25) [14:07:13 -755419.853802] FAST spr round 4 (radius: 25) [14:09:35 -755385.084866] FAST spr round 5 (radius: 25) [14:11:47 -755375.625944] FAST spr round 6 (radius: 25) [14:13:53 -755375.625869] Model parameter optimization (eps = 1.000000) [14:14:16 -755006.881564] SLOW spr round 1 (radius: 5) [14:17:25 -754841.267673] SLOW spr round 2 (radius: 5) [14:20:18 -754832.812816] SLOW spr round 3 (radius: 5) [14:23:05 -754832.812797] SLOW spr round 4 (radius: 10) [14:26:04 -754832.812797] SLOW spr round 5 (radius: 15) [14:31:32 -754832.812797] SLOW spr round 6 (radius: 20) [14:40:53 -754832.812797] SLOW spr round 7 (radius: 25) [14:52:31 -754832.812796] Model parameter optimization (eps = 0.100000) [14:52:46] ML tree search #11, logLikelihood: -754832.469597 [14:52:46 -2474284.331150] Initial branch length optimization [14:52:52 -2103010.931801] Model parameter optimization (eps = 10.000000) [14:53:57 -2099014.151569] AUTODETECT spr round 1 (radius: 5) [14:57:05 -1500710.604392] AUTODETECT spr round 2 (radius: 10) [15:00:37 -1108654.145465] AUTODETECT spr round 3 (radius: 15) [15:04:27 -898368.497935] AUTODETECT spr round 4 (radius: 20) [15:09:21 -838348.244638] AUTODETECT spr round 5 (radius: 25) [15:15:32 -837686.092550] SPR radius for FAST iterations: 25 (autodetect) [15:15:32 -837686.092550] Model parameter optimization (eps = 3.000000) [15:15:55 -837354.911696] FAST spr round 1 (radius: 25) [15:19:55 -757396.988355] FAST spr round 2 (radius: 25) [15:22:59 -755204.881368] FAST spr round 3 (radius: 25) [15:25:38 -754984.030891] FAST spr round 4 (radius: 25) [15:27:57 -754962.746695] FAST spr round 5 (radius: 25) [15:30:05 -754962.448249] FAST spr round 6 (radius: 25) [15:32:10 -754962.448228] Model parameter optimization (eps = 1.000000) [15:32:35 -754959.835051] SLOW spr round 1 (radius: 5) [15:35:43 -754832.700637] SLOW spr round 2 (radius: 5) [15:38:37 -754822.795872] SLOW spr round 3 (radius: 5) [15:41:27 -754820.703086] SLOW spr round 4 (radius: 5) [15:44:14 -754820.703075] SLOW spr round 5 (radius: 10) [15:47:12 -754819.326336] SLOW spr round 6 (radius: 5) [15:50:53 -754817.675615] SLOW spr round 7 (radius: 5) [15:54:06 -754817.675614] SLOW spr round 8 (radius: 10) [15:57:12 -754817.675614] SLOW spr round 9 (radius: 15) [16:02:25 -754817.675614] SLOW spr round 10 (radius: 20) [16:11:52 -754817.675614] SLOW spr round 11 (radius: 25) [16:23:32 -754817.675614] Model parameter optimization (eps = 0.100000) [16:23:43] ML tree search #12, logLikelihood: -754817.443290 [16:23:43 -2478255.942551] Initial branch length optimization [16:23:49 -2111232.420577] Model parameter optimization (eps = 10.000000) [16:24:40 -2106999.491917] AUTODETECT spr round 1 (radius: 5) [16:27:50 -1538881.590644] AUTODETECT spr round 2 (radius: 10) [16:31:25 -1119733.394906] AUTODETECT spr round 3 (radius: 15) [16:35:13 -928179.327386] AUTODETECT spr round 4 (radius: 20) [16:40:08 -847961.047658] AUTODETECT spr round 5 (radius: 25) [16:45:04 -837681.374091] SPR radius for FAST iterations: 25 (autodetect) [16:45:04 -837681.374091] Model parameter optimization (eps = 3.000000) [16:45:29 -837367.124873] FAST spr round 1 (radius: 25) [16:49:47 -758707.786129] FAST spr round 2 (radius: 25) [16:52:51 -755159.794958] FAST spr round 3 (radius: 25) [16:55:34 -755001.702172] FAST spr round 4 (radius: 25) [16:57:55 -754977.631953] FAST spr round 5 (radius: 25) [17:00:03 -754977.631928] Model parameter optimization (eps = 1.000000) [17:00:28 -754974.441585] SLOW spr round 1 (radius: 5) [17:03:45 -754813.538210] SLOW spr round 2 (radius: 5) [17:06:40 -754811.536441] SLOW spr round 3 (radius: 5) [17:09:28 -754811.536438] SLOW spr round 4 (radius: 10) [17:12:28 -754811.536438] SLOW spr round 5 (radius: 15) [17:17:59 -754811.536437] SLOW spr round 6 (radius: 20) [17:27:10 -754811.536437] SLOW spr round 7 (radius: 25) [17:38:44 -754811.536437] Model parameter optimization (eps = 0.100000) [17:38:56] ML tree search #13, logLikelihood: -754810.801816 [17:38:56 -2489521.790538] Initial branch length optimization [17:39:03 -2117105.041185] Model parameter optimization (eps = 10.000000) [17:39:38 -2112828.193255] AUTODETECT spr round 1 (radius: 5) [17:42:46 -1525755.133326] AUTODETECT spr round 2 (radius: 10) [17:46:22 -1148722.010088] AUTODETECT spr round 3 (radius: 15) [17:50:31 -918085.139358] AUTODETECT spr round 4 (radius: 20) [17:55:53 -861945.701502] AUTODETECT spr round 5 (radius: 25) [18:02:08 -860131.234270] SPR radius for FAST iterations: 25 (autodetect) [18:02:08 -860131.234270] Model parameter optimization (eps = 3.000000) [18:02:14 -860130.045746] FAST spr round 1 (radius: 25) [18:06:31 -759169.714512] FAST spr round 2 (radius: 25) [18:09:35 -755802.741910] FAST spr round 3 (radius: 25) [18:12:20 -755397.898389] FAST spr round 4 (radius: 25) [18:14:39 -755377.089161] FAST spr round 5 (radius: 25) [18:16:49 -755376.668994] FAST spr round 6 (radius: 25) [18:18:55 -755376.668974] Model parameter optimization (eps = 1.000000) [18:19:18 -755061.122676] SLOW spr round 1 (radius: 5) [18:22:28 -754852.787749] SLOW spr round 2 (radius: 5) [18:25:21 -754851.032893] SLOW spr round 3 (radius: 5) [18:28:08 -754851.032867] SLOW spr round 4 (radius: 10) [18:31:06 -754851.032866] SLOW spr round 5 (radius: 15) [18:36:37 -754851.032866] SLOW spr round 6 (radius: 20) [18:45:50 -754851.032866] SLOW spr round 7 (radius: 25) [18:57:16 -754851.032866] Model parameter optimization (eps = 0.100000) [18:57:27] ML tree search #14, logLikelihood: -754850.464388 [18:57:27 -2476451.939760] Initial branch length optimization [18:57:34 -2101669.397003] Model parameter optimization (eps = 10.000000) [18:58:37 -2097570.024450] AUTODETECT spr round 1 (radius: 5) [19:01:44 -1539186.579413] AUTODETECT spr round 2 (radius: 10) [19:05:20 -1110395.300394] AUTODETECT spr round 3 (radius: 15) [19:09:09 -917688.301844] AUTODETECT spr round 4 (radius: 20) [19:14:01 -869586.325937] AUTODETECT spr round 5 (radius: 25) [19:19:04 -853297.090580] SPR radius for FAST iterations: 25 (autodetect) [19:19:04 -853297.090580] Model parameter optimization (eps = 3.000000) [19:19:38 -852940.280300] FAST spr round 1 (radius: 25) [19:23:55 -758817.294883] FAST spr round 2 (radius: 25) [19:27:04 -755326.146548] FAST spr round 3 (radius: 25) [19:29:49 -755125.623275] FAST spr round 4 (radius: 25) [19:32:18 -755036.710453] FAST spr round 5 (radius: 25) [19:34:30 -755020.299324] FAST spr round 6 (radius: 25) [19:36:39 -755004.772478] FAST spr round 7 (radius: 25) [19:38:44 -755004.772444] Model parameter optimization (eps = 1.000000) [19:38:53 -755003.883572] SLOW spr round 1 (radius: 5) [19:42:06 -754849.881468] SLOW spr round 2 (radius: 5) [19:44:59 -754845.528644] SLOW spr round 3 (radius: 5) [19:47:47 -754845.528561] SLOW spr round 4 (radius: 10) [19:50:48 -754845.528542] SLOW spr round 5 (radius: 15) [19:56:15 -754845.528522] SLOW spr round 6 (radius: 20) [20:05:36 -754845.528503] SLOW spr round 7 (radius: 25) [20:17:12 -754845.528483] Model parameter optimization (eps = 0.100000) [20:17:24] ML tree search #15, logLikelihood: -754844.690977 [20:17:24 -2481821.312309] Initial branch length optimization [20:17:30 -2110800.540664] Model parameter optimization (eps = 10.000000) [20:18:05 -2106628.400378] AUTODETECT spr round 1 (radius: 5) [20:21:14 -1522391.897894] AUTODETECT spr round 2 (radius: 10) [20:24:52 -1097944.204231] AUTODETECT spr round 3 (radius: 15) [20:28:44 -902665.057284] AUTODETECT spr round 4 (radius: 20) [20:33:18 -871693.377097] AUTODETECT spr round 5 (radius: 25) 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 24-Jun-2021 21:04:03 as follows: raxml-ng --msa /cta/users/eakkoyun/WORKFOLDER/PROD/run_040621/phylogeny-snakemake/results/O60706/2_msa/O60706_trimmed_msa.fasta --data-type AA --model LG4X --prefix /cta/users/eakkoyun/WORKFOLDER/PROD/run_040621/phylogeny-snakemake/results/O60706/3_mltree/O60706 --seed 2 --threads 8 --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 (8 threads), thread pinning: OFF WARNING: The model you specified on the command line (LG4X) will be ignored since the binary MSA file already contains a model definition. If you want to change the model, please re-run RAxML-NG with the original PHYLIP/FASTA alignment and --redo option. [00:00:00] Loading binary alignment from file: /cta/users/eakkoyun/WORKFOLDER/PROD/run_040621/phylogeny-snakemake/results/O60706/3_mltree/O60706.raxml.rba [00:00:00] Alignment comprises 1001 taxa, 1 partitions and 1409 patterns Partition 0: noname Model: LG4X+R4 Alignment sites / patterns: 1409 / 1409 Gaps: 5.47 % Invariant sites: 0.64 % Parallelization scheme autoconfig: 1 worker(s) x 8 thread(s) Parallel reduction/worker buffer size: 1 KB / 0 KB [00:00:00] NOTE: Resuming execution from checkpoint (logLH: -871693.38, ML trees: 15, bootstraps: 0) [00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 177 / 14160 [00:00:00] Data distribution: max. searches per worker: 5 Starting ML tree search with 20 distinct starting trees [00:00:00 -871693.377097] AUTODETECT spr round 5 (radius: 25) [00:05:08 -867257.628329] SPR radius for FAST iterations: 25 (autodetect) [00:05:08 -867257.628329] Model parameter optimization (eps = 3.000000) [00:05:32 -866930.354877] FAST spr round 1 (radius: 25) [00:09:37 -762922.904238] FAST spr round 2 (radius: 25) [00:12:44 -755447.952464] FAST spr round 3 (radius: 25) [00:15:20 -755068.621417] FAST spr round 4 (radius: 25) [00:17:39 -755009.891018] FAST spr round 5 (radius: 25) [00:19:51 -755007.535975] FAST spr round 6 (radius: 25) [00:21:57 -755007.535875] Model parameter optimization (eps = 1.000000) [00:22:18 -754970.341951] SLOW spr round 1 (radius: 5) [00:25:21 -754851.183414] SLOW spr round 2 (radius: 5) [00:28:13 -754846.334976] SLOW spr round 3 (radius: 5) [00:31:00 -754846.334964] SLOW spr round 4 (radius: 10) [00:33:57 -754846.334964] SLOW spr round 5 (radius: 15) [00:39:22 -754846.334964] SLOW spr round 6 (radius: 20) [00:48:36 -754846.334963] SLOW spr round 7 (radius: 25) [01:00:04 -754846.334963] Model parameter optimization (eps = 0.100000) [01:00:12] ML tree search #16, logLikelihood: -754846.265814 [01:00:13 -2475102.437432] Initial branch length optimization [01:00:20 -2108973.293544] Model parameter optimization (eps = 10.000000) [01:00:56 -2104771.073427] AUTODETECT spr round 1 (radius: 5) [01:04:03 -1535100.979927] AUTODETECT spr round 2 (radius: 10) [01:07:36 -1144090.544749] AUTODETECT spr round 3 (radius: 15) [01:11:35 -905672.329514] AUTODETECT spr round 4 (radius: 20) [01:16:32 -849763.748105] AUTODETECT spr round 5 (radius: 25) [01:22:11 -845869.187488] SPR radius for FAST iterations: 25 (autodetect) [01:22:11 -845869.187488] Model parameter optimization (eps = 3.000000) [01:22:40 -845571.816746] FAST spr round 1 (radius: 25) [01:27:00 -758866.373523] FAST spr round 2 (radius: 25) [01:30:02 -755218.746705] FAST spr round 3 (radius: 25) [01:32:42 -755098.821402] FAST spr round 4 (radius: 25) [01:35:03 -755064.168556] FAST spr round 5 (radius: 25) [01:37:15 -755054.609068] FAST spr round 6 (radius: 25) [01:39:20 -755054.609037] Model parameter optimization (eps = 1.000000) [01:39:26 -755054.090507] SLOW spr round 1 (radius: 5) [01:42:36 -754887.356377] SLOW spr round 2 (radius: 5) [01:45:28 -754884.283430] SLOW spr round 3 (radius: 5) [01:48:17 -754883.335132] SLOW spr round 4 (radius: 5) [01:51:02 -754883.335132] SLOW spr round 5 (radius: 10) [01:53:58 -754881.990513] SLOW spr round 6 (radius: 5) [01:57:38 -754880.445049] SLOW spr round 7 (radius: 5) [02:00:49 -754880.445049] SLOW spr round 8 (radius: 10) [02:03:53 -754880.445049] SLOW spr round 9 (radius: 15) [02:09:01 -754880.445049] SLOW spr round 10 (radius: 20) [02:18:04 -754880.445049] SLOW spr round 11 (radius: 25) [02:29:10 -754880.445049] Model parameter optimization (eps = 0.100000) [02:29:32] ML tree search #17, logLikelihood: -754841.248057 [02:29:32 -2474832.067211] Initial branch length optimization [02:29:38 -2110987.283378] Model parameter optimization (eps = 10.000000) [02:30:29 -2106548.410423] AUTODETECT spr round 1 (radius: 5) [02:33:35 -1513941.594035] AUTODETECT spr round 2 (radius: 10) [02:37:10 -1091036.944945] AUTODETECT spr round 3 (radius: 15) [02:41:08 -901686.094925] AUTODETECT spr round 4 (radius: 20) [02:45:32 -866909.553093] AUTODETECT spr round 5 (radius: 25) [02:51:22 -856718.126593] SPR radius for FAST iterations: 25 (autodetect) [02:51:22 -856718.126593] Model parameter optimization (eps = 3.000000) [02:51:56 -856341.334161] FAST spr round 1 (radius: 25) [02:56:25 -757446.205692] FAST spr round 2 (radius: 25) [02:59:36 -755124.947174] FAST spr round 3 (radius: 25) [03:02:13 -754990.286763] FAST spr round 4 (radius: 25) [03:04:27 -754980.183139] FAST spr round 5 (radius: 25) [03:06:35 -754977.730663] FAST spr round 6 (radius: 25) [03:08:41 -754977.730639] Model parameter optimization (eps = 1.000000) [03:08:58 -754971.638569] SLOW spr round 1 (radius: 5) [03:12:03 -754842.860375] SLOW spr round 2 (radius: 5) [03:14:53 -754841.354520] SLOW spr round 3 (radius: 5) [03:17:39 -754841.354516] SLOW spr round 4 (radius: 10) [03:20:40 -754831.388044] SLOW spr round 5 (radius: 5) [03:24:22 -754830.086078] SLOW spr round 6 (radius: 5) [03:27:33 -754830.086075] SLOW spr round 7 (radius: 10) [03:30:38 -754830.086075] SLOW spr round 8 (radius: 15) [03:35:53 -754830.086074] SLOW spr round 9 (radius: 20) [03:45:14 -754830.086074] SLOW spr round 10 (radius: 25) [03:56:43 -754830.086074] Model parameter optimization (eps = 0.100000) [03:56:57] ML tree search #18, logLikelihood: -754829.427919 [03:56:58 -2477697.525422] Initial branch length optimization [03:57:04 -2107187.295531] Model parameter optimization (eps = 10.000000) [03:58:00 -2103039.757008] AUTODETECT spr round 1 (radius: 5) [04:01:08 -1543838.690373] AUTODETECT spr round 2 (radius: 10) [04:04:47 -1105085.952470] AUTODETECT spr round 3 (radius: 15) [04:08:42 -921352.897848] AUTODETECT spr round 4 (radius: 20) [04:13:33 -836958.823552] AUTODETECT spr round 5 (radius: 25) [04:18:52 -834061.499152] SPR radius for FAST iterations: 25 (autodetect) [04:18:52 -834061.499152] Model parameter optimization (eps = 3.000000) [04:19:24 -833674.923226] FAST spr round 1 (radius: 25) [04:23:33 -758456.023732] FAST spr round 2 (radius: 25) [04:26:34 -755162.708933] FAST spr round 3 (radius: 25) [04:29:09 -755109.741039] FAST spr round 4 (radius: 25) [04:31:24 -755102.032676] FAST spr round 5 (radius: 25) [04:33:31 -755102.032661] Model parameter optimization (eps = 1.000000) [04:33:37 -755101.993063] SLOW spr round 1 (radius: 5) [04:36:52 -754890.368238] SLOW spr round 2 (radius: 5) [04:39:53 -754869.416124] SLOW spr round 3 (radius: 5) [04:42:42 -754868.329391] SLOW spr round 4 (radius: 5) [04:45:28 -754868.329327] SLOW spr round 5 (radius: 10) [04:48:26 -754868.329326] SLOW spr round 6 (radius: 15) [04:53:51 -754868.329325] SLOW spr round 7 (radius: 20) [05:02:47 -754868.329325] SLOW spr round 8 (radius: 25) [05:14:06 -754868.329325] Model parameter optimization (eps = 0.100000) [05:14:25] ML tree search #19, logLikelihood: -754847.041456 [05:14:25 -2474242.366899] Initial branch length optimization [05:14:33 -2104961.163739] Model parameter optimization (eps = 10.000000) [05:15:12 -2100587.712267] AUTODETECT spr round 1 (radius: 5) [05:18:17 -1480061.727450] AUTODETECT spr round 2 (radius: 10) [05:21:51 -1072747.645607] AUTODETECT spr round 3 (radius: 15) [05:25:39 -902801.016281] AUTODETECT spr round 4 (radius: 20) [05:30:08 -844421.280340] AUTODETECT spr round 5 (radius: 25) [05:36:02 -840576.442750] SPR radius for FAST iterations: 25 (autodetect) [05:36:02 -840576.442750] Model parameter optimization (eps = 3.000000) [05:36:37 -840287.942019] FAST spr round 1 (radius: 25) [05:40:43 -758247.372711] FAST spr round 2 (radius: 25) [05:43:53 -755232.458723] FAST spr round 3 (radius: 25) [05:46:34 -755037.296871] FAST spr round 4 (radius: 25) [05:48:53 -755019.135780] FAST spr round 5 (radius: 25) [05:51:02 -755019.132726] Model parameter optimization (eps = 1.000000) [05:51:17 -755015.520788] SLOW spr round 1 (radius: 5) [05:54:23 -754825.322719] SLOW spr round 2 (radius: 5) [05:57:15 -754823.458741] SLOW spr round 3 (radius: 5) [06:00:02 -754823.458739] SLOW spr round 4 (radius: 10) [06:02:58 -754823.458739] SLOW spr round 5 (radius: 15) [06:08:24 -754823.458739] SLOW spr round 6 (radius: 20) [06:17:34 -754823.458738] SLOW spr round 7 (radius: 25) [06:29:02 -754823.458738] Model parameter optimization (eps = 0.100000) [06:29:15] ML tree search #20, logLikelihood: -754823.339303 Optimized model parameters: Partition 0: noname Rate heterogeneity: FREE (4 cats, mean), weights&rates: (0.188540,0.340974) (0.288030,0.443626) (0.356296,1.206903) (0.167134,2.261185) 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: -754810.801816 AIC score: 1513631.603631 / AICc score: 9557691.603631 / BIC score: 1524159.127832 Free parameters (model + branch lengths): 2005 WARNING: Number of free parameters (K=2005) is larger than alignment size (n=1409). This might lead to overfitting and compromise tree inference results! WARNING: Best ML tree contains 37 near-zero branches! Best ML tree with collapsed near-zero branches saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_040621/phylogeny-snakemake/results/O60706/3_mltree/O60706.raxml.bestTreeCollapsed Best ML tree saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_040621/phylogeny-snakemake/results/O60706/3_mltree/O60706.raxml.bestTree All ML trees saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_040621/phylogeny-snakemake/results/O60706/3_mltree/O60706.raxml.mlTrees Optimized model saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_040621/phylogeny-snakemake/results/O60706/3_mltree/O60706.raxml.bestModel Execution log saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_040621/phylogeny-snakemake/results/O60706/3_mltree/O60706.raxml.log Analysis started: 24-Jun-2021 21:04:03 / finished: 25-Jun-2021 03:33:18 Elapsed time: 23355.573 seconds (this run) / 97353.620 seconds (total with restarts)