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 01-Jul-2021 16:23:21 as follows: raxml-ng --msa /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q9Y4C8/2_msa/Q9Y4C8_trimmed_msa.fasta --data-type AA --model LG4X --prefix /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q9Y4C8/3_mltree/Q9Y4C8 --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/Q9Y4C8/2_msa/Q9Y4C8_trimmed_msa.fasta [00:00:00] Loaded alignment with 1001 taxa and 725 sites WARNING: Sequences tr_A0A0E1RYR7_A0A0E1RYR7_COCIM_246410 and tr_A0A0J6YBK5_A0A0J6YBK5_COCIT_404692 are exactly identical! WARNING: Sequences tr_J3KEH1_J3KEH1_COCIM_246410 and tr_A0A0J7B5C5_A0A0J7B5C5_COCIT_404692 are exactly identical! WARNING: Sequences tr_B6QKH1_B6QKH1_TALMQ_441960 and tr_A0A093UTC8_A0A093UTC8_TALMA_1077442 are exactly identical! WARNING: Sequences tr_B8N198_B8N198_ASPFN_332952 and tr_A0A1S9DM78_A0A1S9DM78_ASPOZ_5062 are exactly identical! WARNING: Sequences tr_A0A179V1T5_A0A179V1T5_BLAGS_559298 and tr_C5GCS6_C5GCS6_AJEDR_559297 are exactly identical! WARNING: Sequences tr_C6HAM9_C6HAM9_AJECH_544712 and tr_F0UHT6_F0UHT6_AJEC8_544711 are exactly identical! WARNING: Sequences tr_A2Q8B7_A2Q8B7_ASPNC_425011 and tr_G3XRU7_G3XRU7_ASPNA_380704 are exactly identical! WARNING: Sequences tr_G7XPD5_G7XPD5_ASPKW_1033177 and tr_A0A146FQ08_A0A146FQ08_9EURO_1069201 are exactly identical! WARNING: Sequences tr_M7Z861_M7Z861_TRIUA_4572 and tr_A0A3B6B4H2_A0A3B6B4H2_WHEAT_4565 are exactly identical! WARNING: Sequences tr_W2QYX5_W2QYX5_PHYPN_761204 and tr_A0A0W8CHL8_A0A0W8CHL8_PHYNI_4790 are exactly identical! WARNING: Sequences tr_W2QYX5_W2QYX5_PHYPN_761204 and tr_W2I9G2_W2I9G2_PHYPR_4792 are exactly identical! WARNING: Sequences tr_A0A015NA92_A0A015NA92_9GLOM_1432141 and tr_A0A2H5S2H7_A0A2H5S2H7_RHIID_747089 are exactly identical! WARNING: Sequences tr_A0A094E963_A0A094E963_9PEZI_1420912 and tr_A0A1B8G7W2_A0A1B8G7W2_9PEZI_342668 are exactly identical! WARNING: Sequences tr_X0CX91_X0CX91_FUSOX_1089458 and tr_A0A2H3TC16_A0A2H3TC16_FUSOX_5507 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_300621/phylogeny-snakemake/results/Q9Y4C8/3_mltree/Q9Y4C8.raxml.reduced.phy Alignment comprises 1 partitions and 725 patterns Partition 0: noname Model: LG4X+R4 Alignment sites / patterns: 725 / 725 Gaps: 14.03 % Invariant sites: 0.00 % NOTE: Binary MSA file created: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q9Y4C8/3_mltree/Q9Y4C8.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 1001 taxa [00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 104 / 8320 [00:00:00] Data distribution: max. searches per worker: 20 Starting ML tree search with 20 distinct starting trees [00:00:00 -1157366.585626] Initial branch length optimization [00:00:04 -1003687.038789] Model parameter optimization (eps = 10.000000) [00:00:37 -999994.596784] AUTODETECT spr round 1 (radius: 5) [00:02:52 -762254.582277] AUTODETECT spr round 2 (radius: 10) [00:05:27 -590471.765194] AUTODETECT spr round 3 (radius: 15) [00:08:16 -536511.653919] AUTODETECT spr round 4 (radius: 20) [00:11:23 -497537.707272] AUTODETECT spr round 5 (radius: 25) [00:15:15 -496299.675803] SPR radius for FAST iterations: 25 (autodetect) [00:15:15 -496299.675803] Model parameter optimization (eps = 3.000000) [00:15:33 -496238.426457] FAST spr round 1 (radius: 25) [00:19:19 -436940.812599] FAST spr round 2 (radius: 25) [00:22:04 -435296.769903] FAST spr round 3 (radius: 25) [00:24:28 -435124.812949] FAST spr round 4 (radius: 25) [00:26:26 -435122.215781] FAST spr round 5 (radius: 25) [00:28:19 -435121.089480] FAST spr round 6 (radius: 25) [00:30:09 -435121.087339] Model parameter optimization (eps = 1.000000) [00:30:21 -435118.278113] SLOW spr round 1 (radius: 5) [00:33:07 -435020.409320] SLOW spr round 2 (radius: 5) [00:35:38 -435016.169025] SLOW spr round 3 (radius: 5) [00:38:06 -435015.935218] SLOW spr round 4 (radius: 5) [00:40:33 -435015.935075] SLOW spr round 5 (radius: 10) [00:43:09 -435010.893273] SLOW spr round 6 (radius: 5) [00:46:09 -435010.892861] SLOW spr round 7 (radius: 10) [00:49:00 -435010.892853] SLOW spr round 8 (radius: 15) [00:53:04 -435010.892853] SLOW spr round 9 (radius: 20) [00:59:24 -435010.892852] SLOW spr round 10 (radius: 25) [01:07:40 -435010.892852] Model parameter optimization (eps = 0.100000) [01:07:45] ML tree search #1, logLikelihood: -435010.823563 [01:07:46 -1166189.490721] Initial branch length optimization [01:07:49 -1007372.395501] Model parameter optimization (eps = 10.000000) [01:08:42 -1003617.292600] AUTODETECT spr round 1 (radius: 5) [01:10:57 -775590.259299] AUTODETECT spr round 2 (radius: 10) [01:13:35 -600150.021552] AUTODETECT spr round 3 (radius: 15) [01:16:22 -518694.216671] AUTODETECT spr round 4 (radius: 20) [01:19:57 -489034.411469] AUTODETECT spr round 5 (radius: 25) [01:24:07 -485019.486301] SPR radius for FAST iterations: 25 (autodetect) [01:24:07 -485019.486301] Model parameter optimization (eps = 3.000000) [01:24:25 -484920.740648] FAST spr round 1 (radius: 25) [01:28:12 -436637.714655] FAST spr round 2 (radius: 25) [01:30:56 -435272.340519] FAST spr round 3 (radius: 25) [01:33:19 -435161.285198] FAST spr round 4 (radius: 25) [01:35:21 -435140.727574] FAST spr round 5 (radius: 25) [01:37:15 -435134.398668] FAST spr round 6 (radius: 25) [01:39:05 -435134.398635] Model parameter optimization (eps = 1.000000) [01:39:20 -435129.878543] SLOW spr round 1 (radius: 5) [01:42:00 -435062.938913] SLOW spr round 2 (radius: 5) [01:44:37 -435045.671248] SLOW spr round 3 (radius: 5) [01:47:09 -435040.486178] SLOW spr round 4 (radius: 5) [01:49:36 -435040.484989] SLOW spr round 5 (radius: 10) [01:52:14 -435027.205007] SLOW spr round 6 (radius: 5) [01:55:20 -435021.399225] SLOW spr round 7 (radius: 5) [01:58:03 -435020.358048] SLOW spr round 8 (radius: 5) [02:00:37 -435020.357604] SLOW spr round 9 (radius: 10) [02:03:15 -435016.702099] SLOW spr round 10 (radius: 5) [02:06:17 -435016.208485] SLOW spr round 11 (radius: 5) [02:08:59 -435016.208451] SLOW spr round 12 (radius: 10) [02:11:38 -435016.208441] SLOW spr round 13 (radius: 15) [02:15:56 -435016.208436] SLOW spr round 14 (radius: 20) [02:22:34 -435016.208433] SLOW spr round 15 (radius: 25) [02:31:23 -435016.208431] Model parameter optimization (eps = 0.100000) [02:31:35] ML tree search #2, logLikelihood: -435015.364008 [02:31:35 -1162448.247580] Initial branch length optimization [02:31:40 -1006841.302526] Model parameter optimization (eps = 10.000000) [02:32:20 -1003129.275622] AUTODETECT spr round 1 (radius: 5) [02:34:34 -778492.433291] AUTODETECT spr round 2 (radius: 10) [02:37:10 -598343.864271] AUTODETECT spr round 3 (radius: 15) [02:39:56 -523376.414347] AUTODETECT spr round 4 (radius: 20) [02:43:01 -491214.549398] AUTODETECT spr round 5 (radius: 25) [02:46:29 -487901.503921] SPR radius for FAST iterations: 25 (autodetect) [02:46:29 -487901.503921] Model parameter optimization (eps = 3.000000) [02:46:38 -487897.755032] FAST spr round 1 (radius: 25) [02:50:13 -437167.694793] FAST spr round 2 (radius: 25) [02:52:57 -435372.028358] FAST spr round 3 (radius: 25) [02:55:13 -435257.771914] FAST spr round 4 (radius: 25) [02:57:14 -435209.603135] FAST spr round 5 (radius: 25) [02:59:07 -435207.432825] FAST spr round 6 (radius: 25) [03:00:59 -435207.432525] Model parameter optimization (eps = 1.000000) [03:01:17 -435180.783213] SLOW spr round 1 (radius: 5) [03:04:01 -435034.990849] SLOW spr round 2 (radius: 5) [03:06:42 -435001.010030] SLOW spr round 3 (radius: 5) [03:09:15 -434996.085575] SLOW spr round 4 (radius: 5) [03:11:47 -434993.828905] SLOW spr round 5 (radius: 5) [03:14:15 -434993.826550] SLOW spr round 6 (radius: 10) [03:16:52 -434987.906985] SLOW spr round 7 (radius: 5) [03:19:59 -434987.796899] SLOW spr round 8 (radius: 5) [03:22:45 -434987.794422] SLOW spr round 9 (radius: 10) [03:25:26 -434987.793686] SLOW spr round 10 (radius: 15) [03:29:50 -434987.793470] SLOW spr round 11 (radius: 20) [03:36:26 -434987.793407] SLOW spr round 12 (radius: 25) [03:45:08 -434986.872194] SLOW spr round 13 (radius: 5) [03:48:28 -434986.871859] SLOW spr round 14 (radius: 10) [03:51:39 -434986.505876] SLOW spr round 15 (radius: 5) [03:54:40 -434986.505770] SLOW spr round 16 (radius: 10) [03:57:31 -434986.505767] SLOW spr round 17 (radius: 15) [04:01:47 -434986.505767] SLOW spr round 18 (radius: 20) [04:11:08 -434986.505767] SLOW spr round 19 (radius: 25) [04:23:53 -434986.505767] Model parameter optimization (eps = 0.100000) [04:24:21] ML tree search #3, logLikelihood: -434983.775634 [04:24:21 -1162478.289108] Initial branch length optimization [04:24:26 -1006774.095077] Model parameter optimization (eps = 10.000000) [04:25:01 -1002963.899574] AUTODETECT spr round 1 (radius: 5) [04:28:46 -772861.390979] AUTODETECT spr round 2 (radius: 10) [04:32:53 -593387.450112] AUTODETECT spr round 3 (radius: 15) [04:37:22 -516208.707551] AUTODETECT spr round 4 (radius: 20) [04:42:04 -492393.532657] AUTODETECT spr round 5 (radius: 25) [04:47:50 -487591.636022] SPR radius for FAST iterations: 25 (autodetect) [04:47:50 -487591.636022] Model parameter optimization (eps = 3.000000) [04:48:14 -487525.418736] FAST spr round 1 (radius: 25) [04:53:40 -437210.922015] FAST spr round 2 (radius: 25) [04:57:35 -435218.927662] FAST spr round 3 (radius: 25) [05:00:52 -435165.340416] FAST spr round 4 (radius: 25) [05:03:28 -435154.366265] FAST spr round 5 (radius: 25) [05:06:07 -435151.385603] FAST spr round 6 (radius: 25) [05:08:33 -435151.385281] Model parameter optimization (eps = 1.000000) [05:08:42 -435150.814093] SLOW spr round 1 (radius: 5) [05:12:20 -435060.582275] SLOW spr round 2 (radius: 5) [05:16:01 -435050.478397] SLOW spr round 3 (radius: 5) [05:19:29 -435042.096200] SLOW spr round 4 (radius: 5) [05:22:41 -435042.095234] SLOW spr round 5 (radius: 10) [05:26:37 -435033.867286] SLOW spr round 6 (radius: 5) [05:30:47 -435032.833466] SLOW spr round 7 (radius: 5) [05:34:46 -435032.833398] SLOW spr round 8 (radius: 10) [05:38:30 -435032.676664] SLOW spr round 9 (radius: 5) [05:42:56 -435029.460692] SLOW spr round 10 (radius: 5) [05:46:53 -435029.460490] SLOW spr round 11 (radius: 10) [05:50:43 -435029.460463] SLOW spr round 12 (radius: 15) [05:57:13 -435029.460437] SLOW spr round 13 (radius: 20) [06:07:29 -435029.460411] SLOW spr round 14 (radius: 25) [06:21:27 -435029.460385] Model parameter optimization (eps = 0.100000) [06:21:39] ML tree search #4, logLikelihood: -435028.930501 [06:21:39 -1164697.733363] Initial branch length optimization [06:21:56 -1011479.006287] Model parameter optimization (eps = 10.000000) [06:22:39 -1007742.077929] AUTODETECT spr round 1 (radius: 5) [06:26:12 -775686.128232] AUTODETECT spr round 2 (radius: 10) [06:30:35 -599633.007822] AUTODETECT spr round 3 (radius: 15) [06:34:48 -533628.646193] AUTODETECT spr round 4 (radius: 20) [06:39:42 -484594.382108] AUTODETECT spr round 5 (radius: 25) [06:44:52 -479979.020514] SPR radius for FAST iterations: 25 (autodetect) [06:44:52 -479979.020514] Model parameter optimization (eps = 3.000000) [06:45:14 -479909.201197] FAST spr round 1 (radius: 25) [06:50:29 -437269.848200] FAST spr round 2 (radius: 25) [06:53:58 -435344.351144] FAST spr round 3 (radius: 25) [06:57:11 -435219.976069] FAST spr round 4 (radius: 25) [07:00:01 -435150.629370] FAST spr round 5 (radius: 25) [07:02:24 -435148.314262] FAST spr round 6 (radius: 25) [07:04:49 -435147.234412] FAST spr round 7 (radius: 25) [07:07:20 -435147.234359] Model parameter optimization (eps = 1.000000) [07:07:37 -435146.046454] SLOW spr round 1 (radius: 5) [07:11:27 -435041.995875] SLOW spr round 2 (radius: 5) [07:14:51 -435032.378263] SLOW spr round 3 (radius: 5) [07:18:15 -435027.859296] SLOW spr round 4 (radius: 5) [07:21:41 -435027.847594] SLOW spr round 5 (radius: 10) [07:25:16 -435019.267183] SLOW spr round 6 (radius: 5) [07:29:33 -435014.311670] SLOW spr round 7 (radius: 5) [07:33:01 -435014.311330] SLOW spr round 8 (radius: 10) [07:36:41 -435014.311289] SLOW spr round 9 (radius: 15) [07:42:39 -435014.311279] SLOW spr round 10 (radius: 20) [07:52:18 -435014.311276] SLOW spr round 11 (radius: 25) [08:05:47 -435011.585980] SLOW spr round 12 (radius: 5) [08:10:16 -435011.585859] SLOW spr round 13 (radius: 10) [08:14:48 -435011.585857] SLOW spr round 14 (radius: 15) [08:20:39 -435011.585857] SLOW spr round 15 (radius: 20) [08:31:17 -435011.585857] SLOW spr round 16 (radius: 25) [08:45:32 -435011.585857] Model parameter optimization (eps = 0.100000) [08:45:46] ML tree search #5, logLikelihood: -435010.651725 [08:45:46 -1163938.328998] Initial branch length optimization [08:45:51 -1008337.707867] Model parameter optimization (eps = 10.000000) [08:46:33 -1004545.889553] AUTODETECT spr round 1 (radius: 5) [08:50:33 -773073.969762] AUTODETECT spr round 2 (radius: 10) [08:54:41 -576205.171582] AUTODETECT spr round 3 (radius: 15) [08:58:55 -494559.100879] AUTODETECT spr round 4 (radius: 20) [09:03:17 -482446.012376] AUTODETECT spr round 5 (radius: 25) [09:08:46 -480464.132331] SPR radius for FAST iterations: 25 (autodetect) [09:08:46 -480464.132331] Model parameter optimization (eps = 3.000000) [09:09:09 -480391.901757] FAST spr round 1 (radius: 25) [09:15:04 -436421.995766] FAST spr round 2 (radius: 25) [09:19:12 -435287.103343] FAST spr round 3 (radius: 25) [09:22:47 -435175.443429] FAST spr round 4 (radius: 25) [09:25:39 -435160.570724] FAST spr round 5 (radius: 25) [09:28:32 -435153.585128] FAST spr round 6 (radius: 25) [09:30:56 -435153.585020] Model parameter optimization (eps = 1.000000) [09:31:01 -435153.529098] SLOW spr round 1 (radius: 5) [09:34:53 -435054.637325] SLOW spr round 2 (radius: 5) [09:38:32 -435043.145485] SLOW spr round 3 (radius: 5) [09:42:01 -435042.412318] SLOW spr round 4 (radius: 5) [09:45:26 -435042.412288] SLOW spr round 5 (radius: 10) [09:49:13 -435039.531880] SLOW spr round 6 (radius: 5) [09:53:17 -435039.531561] SLOW spr round 7 (radius: 10) [09:57:07 -435039.531535] SLOW spr round 8 (radius: 15) [10:03:14 -435039.531533] SLOW spr round 9 (radius: 20) [10:13:14 -435039.531533] SLOW spr round 10 (radius: 25) [10:26:18 -435039.531533] Model parameter optimization (eps = 0.100000) [10:26:24] ML tree search #6, logLikelihood: -435039.522207 [10:26:24 -1162201.925584] Initial branch length optimization [10:26:36 -1004544.667078] Model parameter optimization (eps = 10.000000) [10:27:10 -1000967.064770] AUTODETECT spr round 1 (radius: 5) [10:30:47 -759418.051799] AUTODETECT spr round 2 (radius: 10) [10:35:00 -580569.816767] AUTODETECT spr round 3 (radius: 15) [10:39:11 -533218.174708] AUTODETECT spr round 4 (radius: 20) [10:43:41 -491729.763210] AUTODETECT spr round 5 (radius: 25) [10:49:16 -481270.378903] SPR radius for FAST iterations: 25 (autodetect) [10:49:16 -481270.378903] Model parameter optimization (eps = 3.000000) [10:49:43 -481225.384550] FAST spr round 1 (radius: 25) [10:53:21 -436898.640514] FAST spr round 2 (radius: 25) [10:56:12 -435291.541632] FAST spr round 3 (radius: 25) [10:58:42 -435177.921782] FAST spr round 4 (radius: 25) [11:00:52 -435167.980336] FAST spr round 5 (radius: 25) [11:02:59 -435161.782059] FAST spr round 6 (radius: 25) [11:05:01 -435161.781533] Model parameter optimization (eps = 1.000000) [11:05:17 -435153.817734] SLOW spr round 1 (radius: 5) [11:08:15 -435017.684209] SLOW spr round 2 (radius: 5) [11:11:06 -435010.578417] SLOW spr round 3 (radius: 5) [11:13:50 -435009.346622] SLOW spr round 4 (radius: 5) [11:16:31 -435009.335072] SLOW spr round 5 (radius: 10) [11:19:18 -435002.636182] SLOW spr round 6 (radius: 5) [11:22:36 -435002.625243] SLOW spr round 7 (radius: 10) [11:25:42 -435002.625202] SLOW spr round 8 (radius: 15) [11:30:10 -435002.625196] SLOW spr round 9 (radius: 20) [11:37:21 -435002.625195] SLOW spr round 10 (radius: 25) [11:46:41 -435001.061862] SLOW spr round 11 (radius: 5) [11:50:13 -435001.061506] SLOW spr round 12 (radius: 10) [11:53:38 -435001.061496] SLOW spr round 13 (radius: 15) [11:58:01 -435001.061496] SLOW spr round 14 (radius: 20) [12:05:13 -435001.061496] SLOW spr round 15 (radius: 25) [12:14:31 -435001.061496] Model parameter optimization (eps = 0.100000) [12:14:44] ML tree search #7, logLikelihood: -435000.413025 [12:14:45 -1167767.978314] Initial branch length optimization [12:14:48 -1010045.445165] Model parameter optimization (eps = 10.000000) [12:15:22 -1006266.128857] AUTODETECT spr round 1 (radius: 5) [12:17:51 -772655.666483] AUTODETECT spr round 2 (radius: 10) [12:20:41 -591581.942993] AUTODETECT spr round 3 (radius: 15) [12:23:43 -512520.719576] AUTODETECT spr round 4 (radius: 20) [12:27:19 -488801.472119] AUTODETECT spr round 5 (radius: 25) [12:31:11 -486477.440664] SPR radius for FAST iterations: 25 (autodetect) [12:31:11 -486477.440664] Model parameter optimization (eps = 3.000000) [12:31:38 -486436.120684] FAST spr round 1 (radius: 25) [12:35:37 -436912.385631] FAST spr round 2 (radius: 25) [12:38:29 -435304.745428] FAST spr round 3 (radius: 25) [12:41:01 -435171.525104] FAST spr round 4 (radius: 25) [12:43:15 -435162.459954] FAST spr round 5 (radius: 25) [12:45:17 -435158.618157] FAST spr round 6 (radius: 25) [12:47:17 -435158.617511] Model parameter optimization (eps = 1.000000) [12:47:22 -435158.556775] SLOW spr round 1 (radius: 5) [12:50:17 -435043.976837] SLOW spr round 2 (radius: 5) [12:53:07 -435010.878939] SLOW spr round 3 (radius: 5) [12:55:46 -435010.878798] SLOW spr round 4 (radius: 10) [12:58:31 -435009.790352] SLOW spr round 5 (radius: 5) [13:01:44 -435009.790005] SLOW spr round 6 (radius: 10) [13:04:46 -435009.789997] SLOW spr round 7 (radius: 15) [13:09:01 -435009.789997] SLOW spr round 8 (radius: 20) [13:15:28 -435009.789997] SLOW spr round 9 (radius: 25) [13:23:43 -435009.789997] Model parameter optimization (eps = 0.100000) [13:23:47] ML tree search #8, logLikelihood: -435009.787746 [13:23:47 -1163674.383525] Initial branch length optimization [13:23:51 -1006537.379538] Model parameter optimization (eps = 10.000000) [13:24:20 -1002907.039342] AUTODETECT spr round 1 (radius: 5) [13:26:46 -768859.770713] AUTODETECT spr round 2 (radius: 10) [13:29:36 -608797.946087] AUTODETECT spr round 3 (radius: 15) [13:32:34 -517311.387644] AUTODETECT spr round 4 (radius: 20) [13:36:02 -488388.509595] AUTODETECT spr round 5 (radius: 25) [13:40:17 -480711.420634] SPR radius for FAST iterations: 25 (autodetect) [13:40:17 -480711.420634] Model parameter optimization (eps = 3.000000) [13:40:44 -480676.185886] FAST spr round 1 (radius: 25) [13:44:38 -436675.140846] FAST spr round 2 (radius: 25) [13:47:31 -435328.207007] FAST spr round 3 (radius: 25) [13:50:04 -435236.781836] FAST spr round 4 (radius: 25) [13:52:22 -435169.055924] FAST spr round 5 (radius: 25) [13:54:36 -435157.145279] FAST spr round 6 (radius: 25) [13:56:40 -435157.145206] Model parameter optimization (eps = 1.000000) [13:57:04 -435152.289250] SLOW spr round 1 (radius: 5) [14:00:00 -435032.351646] SLOW spr round 2 (radius: 5) [14:02:47 -435030.319386] SLOW spr round 3 (radius: 5) [14:05:30 -435030.319324] SLOW spr round 4 (radius: 10) [14:08:21 -435024.901651] SLOW spr round 5 (radius: 5) [14:11:40 -435011.706076] SLOW spr round 6 (radius: 5) [14:14:36 -435011.392478] SLOW spr round 7 (radius: 5) [14:17:23 -435011.392429] SLOW spr round 8 (radius: 10) [14:20:14 -435005.537123] SLOW spr round 9 (radius: 5) [14:23:30 -435005.536780] SLOW spr round 10 (radius: 10) [14:26:36 -435005.536756] SLOW spr round 11 (radius: 15) [14:31:00 -435005.536744] SLOW spr round 12 (radius: 20) [14:37:56 -435005.536739] SLOW spr round 13 (radius: 25) [14:46:50 -435005.536736] Model parameter optimization (eps = 0.100000) [14:46:55] ML tree search #9, logLikelihood: -435005.487018 [14:46:56 -1162846.112035] Initial branch length optimization [14:47:00 -1007019.971343] Model parameter optimization (eps = 10.000000) [14:47:35 -1003311.683447] AUTODETECT spr round 1 (radius: 5) [14:50:03 -776132.618797] AUTODETECT spr round 2 (radius: 10) [14:52:53 -586819.906875] AUTODETECT spr round 3 (radius: 15) [14:55:54 -494185.017734] AUTODETECT spr round 4 (radius: 20) [14:59:03 -483519.707005] AUTODETECT spr round 5 (radius: 25) [15:02:58 -479995.256479] SPR radius for FAST iterations: 25 (autodetect) [15:02:58 -479995.256479] Model parameter optimization (eps = 3.000000) [15:03:21 -479955.094511] FAST spr round 1 (radius: 25) [15:07:14 -436695.442091] FAST spr round 2 (radius: 25) [15:10:12 -435263.264159] FAST spr round 3 (radius: 25) [15:12:47 -435177.526858] FAST spr round 4 (radius: 25) [15:15:00 -435167.415245] FAST spr round 5 (radius: 25) [15:17:06 -435167.414401] Model parameter optimization (eps = 1.000000) [15:17:17 -435164.657002] SLOW spr round 1 (radius: 5) [15:20:17 -435032.733872] SLOW spr round 2 (radius: 5) [15:23:03 -435027.615120] SLOW spr round 3 (radius: 5) [15:25:45 -435026.303423] SLOW spr round 4 (radius: 5) [15:28:25 -435026.303331] SLOW spr round 5 (radius: 10) [15:31:16 -435019.237337] SLOW spr round 6 (radius: 5) [15:34:34 -435010.351952] SLOW spr round 7 (radius: 5) [15:37:30 -435009.282828] SLOW spr round 8 (radius: 5) [15:40:21 -434998.832002] SLOW spr round 9 (radius: 5) [15:43:04 -434997.966927] SLOW spr round 10 (radius: 5) [15:45:45 -434994.483115] SLOW spr round 11 (radius: 5) [15:48:24 -434994.482608] SLOW spr round 12 (radius: 10) [15:51:11 -434994.252146] SLOW spr round 13 (radius: 5) [15:54:27 -434994.252046] SLOW spr round 14 (radius: 10) [15:57:34 -434994.252041] SLOW spr round 15 (radius: 15) [16:02:01 -434994.252040] SLOW spr round 16 (radius: 20) [16:09:19 -434994.252040] SLOW spr round 17 (radius: 25) [16:18:47 -434994.252040] Model parameter optimization (eps = 0.100000) [16:18:57] ML tree search #10, logLikelihood: -434993.956598 [16:18:57 -1161069.589074] Initial branch length optimization [16:19:01 -1002843.323240] Model parameter optimization (eps = 10.000000) [16:19:50 -999300.285207] AUTODETECT spr round 1 (radius: 5) [16:22:18 -774381.211291] AUTODETECT spr round 2 (radius: 10) [16:25:07 -605691.844895] AUTODETECT spr round 3 (radius: 15) [16:28:14 -516419.537647] AUTODETECT spr round 4 (radius: 20) [16:31:39 -487527.442290] AUTODETECT spr round 5 (radius: 25) [16:35:35 -483415.855004] SPR radius for FAST iterations: 25 (autodetect) [16:35:35 -483415.855004] Model parameter optimization (eps = 3.000000) [16:35:45 -483411.939600] FAST spr round 1 (radius: 25) [16:39:32 -436673.724221] FAST spr round 2 (radius: 25) [16:42:28 -435299.882969] FAST spr round 3 (radius: 25) [16:44:57 -435160.274263] FAST spr round 4 (radius: 25) [16:47:06 -435140.031173] FAST spr round 5 (radius: 25) [16:49:09 -435130.935330] FAST spr round 6 (radius: 25) [16:51:08 -435130.935136] Model parameter optimization (eps = 1.000000) [16:51:25 -435101.012761] SLOW spr round 1 (radius: 5) [16:54:16 -435031.577321] SLOW spr round 2 (radius: 5) [16:57:01 -435019.180895] SLOW spr round 3 (radius: 5) [16:59:39 -435019.063841] SLOW spr round 4 (radius: 5) [17:02:15 -435019.062767] SLOW spr round 5 (radius: 10) [17:05:03 -435004.276710] SLOW spr round 6 (radius: 5) [17:08:19 -434995.226304] SLOW spr round 7 (radius: 5) [17:11:12 -434994.302682] SLOW spr round 8 (radius: 5) [17:13:55 -434994.280762] SLOW spr round 9 (radius: 10) [17:16:43 -434992.092814] SLOW spr round 10 (radius: 5) [17:19:54 -434992.091344] SLOW spr round 11 (radius: 10) [17:22:57 -434992.089999] SLOW spr round 12 (radius: 15) [17:27:17 -434992.088657] SLOW spr round 13 (radius: 20) [17:34:05 -434992.087399] SLOW spr round 14 (radius: 25) [17:42:53 -434992.087026] Model parameter optimization (eps = 0.100000) [17:43:05] ML tree search #11, logLikelihood: -434991.985975 [17:43:05 -1166918.028252] Initial branch length optimization [17:43:09 -1008532.645101] Model parameter optimization (eps = 10.000000) [17:43:46 -1004920.977396] AUTODETECT spr round 1 (radius: 5) [17:46:15 -779026.986584] AUTODETECT spr round 2 (radius: 10) [17:49:02 -590845.727884] AUTODETECT spr round 3 (radius: 15) [17:51:59 -526423.911463] AUTODETECT spr round 4 (radius: 20) [17:55:34 -495145.833722] AUTODETECT spr round 5 (radius: 25) [17:59:26 -486733.706934] SPR radius for FAST iterations: 25 (autodetect) [17:59:26 -486733.706934] Model parameter optimization (eps = 3.000000) [17:59:35 -486729.970503] FAST spr round 1 (radius: 25) [18:03:17 -437173.291573] FAST spr round 2 (radius: 25) [18:06:18 -435359.766171] FAST spr round 3 (radius: 25) [18:08:50 -435226.546820] FAST spr round 4 (radius: 25) [18:11:05 -435202.120852] FAST spr round 5 (radius: 25) [18:13:09 -435200.144293] FAST spr round 6 (radius: 25) [18:15:11 -435200.013593] FAST spr round 7 (radius: 25) [18:17:12 -435200.000921] Model parameter optimization (eps = 1.000000) [18:17:16 -435199.991451] SLOW spr round 1 (radius: 5) [18:20:08 -435090.277726] SLOW spr round 2 (radius: 5) [18:22:58 -435068.047344] SLOW spr round 3 (radius: 5) [18:25:38 -435067.709645] SLOW spr round 4 (radius: 5) [18:28:17 -435067.709516] SLOW spr round 5 (radius: 10) [18:31:03 -435064.098289] SLOW spr round 6 (radius: 5) [18:34:17 -435063.468380] SLOW spr round 7 (radius: 5) [18:37:10 -435063.467354] SLOW spr round 8 (radius: 10) [18:40:03 -435062.693145] SLOW spr round 9 (radius: 5) [18:43:17 -435061.709404] SLOW spr round 10 (radius: 5) [18:46:09 -435061.709393] SLOW spr round 11 (radius: 10) [18:49:00 -435061.709391] SLOW spr round 12 (radius: 15) [18:53:29 -435061.709390] SLOW spr round 13 (radius: 20) [19:00:28 -435061.709389] SLOW spr round 14 (radius: 25) [19:09:25 -435061.235179] SLOW spr round 15 (radius: 5) [19:12:52 -435059.694814] SLOW spr round 16 (radius: 5) [19:15:49 -435059.694742] SLOW spr round 17 (radius: 10) [19:18:39 -435059.694741] SLOW spr round 18 (radius: 15) [19:23:01 -435059.694741] SLOW spr round 19 (radius: 20) [19:29:58 -435059.694741] SLOW spr round 20 (radius: 25) [19:38:44 -435059.694741] Model parameter optimization (eps = 0.100000) [19:38:51] ML tree search #12, logLikelihood: -435059.670211 [19:38:51 -1167960.052760] Initial branch length optimization [19:38:55 -1008898.323143] Model parameter optimization (eps = 10.000000) [19:39:48 -1005221.859162] AUTODETECT spr round 1 (radius: 5) [19:42:22 -779970.784691] AUTODETECT spr round 2 (radius: 10) [19:45:10 -611196.628319] AUTODETECT spr round 3 (radius: 15) [19:48:17 -525227.049913] AUTODETECT spr round 4 (radius: 20) [19:51:46 -490459.099767] AUTODETECT spr round 5 (radius: 25) [19:55:40 -487325.966736] SPR radius for FAST iterations: 25 (autodetect) [19:55:40 -487325.966736] Model parameter optimization (eps = 3.000000) [19:56:01 -487258.653992] FAST spr round 1 (radius: 25) [19:59:52 -437449.413384] FAST spr round 2 (radius: 25) [20:02:46 -435325.038229] FAST spr round 3 (radius: 25) [20:05:20 -435192.867669] FAST spr round 4 (radius: 25) [20:07:37 -435175.990291] FAST spr round 5 (radius: 25) [20:09:41 -435175.990285] Model parameter optimization (eps = 1.000000) [20:09:56 -435174.009949] SLOW spr round 1 (radius: 5) [20:12:56 -435024.892477] SLOW spr round 2 (radius: 5) [20:15:46 -435011.256371] SLOW spr round 3 (radius: 5) [20:18:25 -435011.229517] SLOW spr round 4 (radius: 10) [20:21:15 -435007.297771] SLOW spr round 5 (radius: 5) [20:24:33 -435005.250813] SLOW spr round 6 (radius: 5) [20:27:29 -435005.250523] SLOW spr round 7 (radius: 10) [20:30:27 -435005.250475] SLOW spr round 8 (radius: 15) [20:35:07 -435005.250466] SLOW spr round 9 (radius: 20) [20:42:07 -435005.250463] SLOW spr round 10 (radius: 25) [20:51:24 -435004.995933] SLOW spr round 11 (radius: 5) [20:54:57 -435003.084170] SLOW spr round 12 (radius: 5) [20:58:04 -435003.084115] SLOW spr round 13 (radius: 10) [21:01:05 -435003.084114] SLOW spr round 14 (radius: 15) [21:05:41 -435003.084114] SLOW spr round 15 (radius: 20) [21:12:40 -435003.084114] SLOW spr round 16 (radius: 25) [21:21:55 -435003.084114] Model parameter optimization (eps = 0.100000) [21:22:04] ML tree search #13, logLikelihood: -435002.713398 [21:22:04 -1166508.194770] Initial branch length optimization [21:22:08 -1009620.251302] Model parameter optimization (eps = 10.000000) [21:22:43 -1005928.955082] AUTODETECT spr round 1 (radius: 5) [21:25:12 -769294.919597] AUTODETECT spr round 2 (radius: 10) [21:28:03 -597439.501921] AUTODETECT spr round 3 (radius: 15) [21:31:05 -513365.651003] AUTODETECT spr round 4 (radius: 20) [21:34:43 -482435.364591] AUTODETECT spr round 5 (radius: 25) [21:38:47 -475678.059596] SPR radius for FAST iterations: 25 (autodetect) [21:38:47 -475678.059596] Model parameter optimization (eps = 3.000000) [21:38:56 -475674.544154] FAST spr round 1 (radius: 25) [21:42:49 -436567.973963] FAST spr round 2 (radius: 25) [21:45:52 -435389.011349] FAST spr round 3 (radius: 25) [21:48:33 -435312.226767] FAST spr round 4 (radius: 25) [21:51:00 -435273.935956] FAST spr round 5 (radius: 25) [21:53:09 -435273.817088] FAST spr round 6 (radius: 25) [21:55:17 -435272.750260] FAST spr round 7 (radius: 25) [21:57:21 -435272.742685] Model parameter optimization (eps = 1.000000) [21:57:26 -435272.638884] SLOW spr round 1 (radius: 5) [22:00:26 -435143.421159] SLOW spr round 2 (radius: 5) [22:03:19 -435110.477432] SLOW spr round 3 (radius: 5) [22:06:05 -435105.673642] SLOW spr round 4 (radius: 5) [22:08:47 -435105.672754] SLOW spr round 5 (radius: 10) [22:11:38 -435102.708118] SLOW spr round 6 (radius: 5) [22:14:56 -435102.707430] SLOW spr round 7 (radius: 10) [22:18:04 -435102.707034] SLOW spr round 8 (radius: 15) [22:25:32 -435102.706709] SLOW spr round 9 (radius: 20) [22:35:03 -435102.706440] SLOW spr round 10 (radius: 25) [22:43:37 -435101.518392] SLOW spr round 11 (radius: 5) [22:46:57 -435101.517869] SLOW spr round 12 (radius: 10) [22:50:12 -435101.517733] SLOW spr round 13 (radius: 15) [22:54:33 -435101.517623] SLOW spr round 14 (radius: 20) [23:01:24 -435101.517531] SLOW spr round 15 (radius: 25) [23:09:53 -435101.517454] Model parameter optimization (eps = 0.100000) [23:09:59] ML tree search #14, logLikelihood: -435101.479489 [23:09:59 -1164981.431517] Initial branch length optimization [23:10:03 -1008247.957593] Model parameter optimization (eps = 10.000000) [23:10:30 -1004548.774857] AUTODETECT spr round 1 (radius: 5) [23:12:49 -770586.115028] AUTODETECT spr round 2 (radius: 10) [23:15:35 -606978.505528] AUTODETECT spr round 3 (radius: 15) [23:18:36 -525903.607238] AUTODETECT spr round 4 (radius: 20) [23:22:04 -495635.196153] AUTODETECT spr round 5 (radius: 25) [23:25:59 -485792.337651] SPR radius for FAST iterations: 25 (autodetect) [23:25:59 -485792.337651] Model parameter optimization (eps = 3.000000) [23:26:07 -485789.192678] FAST spr round 1 (radius: 25) [23:29:45 -437024.723418] FAST spr round 2 (radius: 25) [23:32:34 -435380.509620] FAST spr round 3 (radius: 25) [23:34:51 -435204.539474] FAST spr round 4 (radius: 25) [23:37:08 -435173.102994] FAST spr round 5 (radius: 25) [23:39:12 -435165.908125] FAST spr round 6 (radius: 25) [23:41:14 -435164.776446] FAST spr round 7 (radius: 25) [23:43:12 -435164.776443] Model parameter optimization (eps = 1.000000) [23:43:31 -435136.665775] SLOW spr round 1 (radius: 5) [23:46:25 -435022.074910] SLOW spr round 2 (radius: 5) [23:49:07 -435010.618363] SLOW spr round 3 (radius: 5) [23:51:42 -435010.616566] SLOW spr round 4 (radius: 10) [23:54:20 -435010.615699] SLOW spr round 5 (radius: 15) [23:58:44 -435010.615159] SLOW spr round 6 (radius: 20) [24:05:19 -435010.614794] SLOW spr round 7 (radius: 25) [24:14:01 -435009.117714] SLOW spr round 8 (radius: 5) [24:17:23 -435009.116769] SLOW spr round 9 (radius: 10) [24:20:33 -435008.719405] SLOW spr round 10 (radius: 5) [24:23:34 -435008.719196] SLOW spr round 11 (radius: 10) [24:26:35 -435008.719104] SLOW spr round 12 (radius: 15) [24:30:53 -435008.719030] SLOW spr round 13 (radius: 20) [24:37:35 -435008.718969] SLOW spr round 14 (radius: 25) [24:46:12 -435008.718918] Model parameter optimization (eps = 0.100000) [24:46:24] ML tree search #15, logLikelihood: -435008.450766 [24:46:24 -1164889.058077] Initial branch length optimization [24:46:28 -1006583.753160] Model parameter optimization (eps = 10.000000) [24:46:55 -1002871.823494] AUTODETECT spr round 1 (radius: 5) [24:49:21 -776141.234757] AUTODETECT spr round 2 (radius: 10) [24:52:06 -608270.051323] AUTODETECT spr round 3 (radius: 15) [24:55:15 -513021.683220] AUTODETECT spr round 4 (radius: 20) [24:58:51 -493475.038469] AUTODETECT spr round 5 (radius: 25) [25:02:58 -488859.408267] SPR radius for FAST iterations: 25 (autodetect) [25:02:58 -488859.408267] Model parameter optimization (eps = 3.000000) [25:03:07 -488855.306108] FAST spr round 1 (radius: 25) [25:06:58 -436834.283503] FAST spr round 2 (radius: 25) [25:09:45 -435320.454245] FAST spr round 3 (radius: 25) [25:12:10 -435198.419451] FAST spr round 4 (radius: 25) [25:14:24 -435181.363328] FAST spr round 5 (radius: 25) [25:16:29 -435177.591572] FAST spr round 6 (radius: 25) [25:18:32 -435174.311402] FAST spr round 7 (radius: 25) [25:20:29 -435174.311333] Model parameter optimization (eps = 1.000000) [25:20:49 -435139.696166] SLOW spr round 1 (radius: 5) [25:23:38 -435028.878297] SLOW spr round 2 (radius: 5) [25:26:19 -435022.763818] SLOW spr round 3 (radius: 5) [25:28:58 -435017.851510] SLOW spr round 4 (radius: 5) [25:31:30 -435017.839861] SLOW spr round 5 (radius: 10) [25:34:09 -435012.941883] SLOW spr round 6 (radius: 5) [25:37:24 -435000.052437] SLOW spr round 7 (radius: 5) [25:40:19 -435000.048725] SLOW spr round 8 (radius: 10) [25:43:11 -434997.128826] SLOW spr round 9 (radius: 5) [25:46:25 -434995.355186] SLOW spr round 10 (radius: 5) [25:49:15 -434995.353985] SLOW spr round 11 (radius: 10) [25:52:01 -434995.353914] SLOW spr round 12 (radius: 15) [25:56:25 -434995.353898] SLOW spr round 13 (radius: 20) [26:03:08 -434995.353890] SLOW spr round 14 (radius: 25) [26:11:55 -434993.651479] SLOW spr round 15 (radius: 5) [26:15:20 -434993.651059] SLOW spr round 16 (radius: 10) [26:18:38 -434993.651045] SLOW spr round 17 (radius: 15) [26:22:48 -434993.651044] SLOW spr round 18 (radius: 20) [26:29:41 -434993.651044] SLOW spr round 19 (radius: 25) [26:38:25 -434993.651044] Model parameter optimization (eps = 0.100000) [26:38:35] ML tree search #16, logLikelihood: -434993.481832 [26:38:35 -1161071.938692] Initial branch length optimization [26:38:39 -1006276.204390] Model parameter optimization (eps = 10.000000) [26:39:26 -1002511.902890] AUTODETECT spr round 1 (radius: 5) [26:41:48 -767648.872832] AUTODETECT spr round 2 (radius: 10) [26:44:30 -587216.094641] AUTODETECT spr round 3 (radius: 15) [26:47:28 -499262.812110] AUTODETECT spr round 4 (radius: 20) [26:51:00 -480321.103895] AUTODETECT spr round 5 (radius: 25) [27:07:12 -477221.919330] SPR radius for FAST iterations: 25 (autodetect) [27:07:12 -477221.919330] Model parameter optimization (eps = 3.000000) [27:07:21 -477217.208892] FAST spr round 1 (radius: 25) [27:10:59 -436756.017341] FAST spr round 2 (radius: 25) [27:13:49 -435360.475595] FAST spr round 3 (radius: 25) [27:16:24 -435243.619904] FAST spr round 4 (radius: 25) [27:18:43 -435200.400393] FAST spr round 5 (radius: 25) [27:20:52 -435196.749323] FAST spr round 6 (radius: 25) [27:22:57 -435196.749197] Model parameter optimization (eps = 1.000000) [27:23:16 -435143.245640] SLOW spr round 1 (radius: 5) [27:26:13 -435043.916993] SLOW spr round 2 (radius: 5) [27:29:00 -435034.862278] SLOW spr round 3 (radius: 5) [27:31:46 -435029.865241] SLOW spr round 4 (radius: 5) [27:34:28 -435028.135108] SLOW spr round 5 (radius: 5) [27:37:10 -435028.134937] SLOW spr round 6 (radius: 10) [27:40:01 -435020.762025] SLOW spr round 7 (radius: 5) [27:43:23 -435014.488936] SLOW spr round 8 (radius: 5) [27:46:21 -435005.390038] SLOW spr round 9 (radius: 5) [27:49:09 -435004.333280] SLOW spr round 10 (radius: 5) [27:51:54 -435004.332954] SLOW spr round 11 (radius: 10) [27:54:43 -435004.306629] SLOW spr round 12 (radius: 15) [27:59:21 -435004.302600] SLOW spr round 13 (radius: 20) [28:06:09 -435004.301462] SLOW spr round 14 (radius: 25) [28:15:22 -435001.359270] SLOW spr round 15 (radius: 5) [28:18:56 -435000.220835] SLOW spr round 16 (radius: 5) [28:22:01 -435000.220743] SLOW spr round 17 (radius: 10) [28:25:02 -434996.373640] SLOW spr round 18 (radius: 5) [28:28:20 -434989.263252] SLOW spr round 19 (radius: 5) [28:31:19 -434988.617452] SLOW spr round 20 (radius: 5) [28:34:07 -434988.617396] SLOW spr round 21 (radius: 10) [28:36:59 -434988.617395] SLOW spr round 22 (radius: 15) [28:41:38 -434988.617394] SLOW spr round 23 (radius: 20) [28:48:29 -434988.617394] SLOW spr round 24 (radius: 25) [28:57:29 -434988.617394] Model parameter optimization (eps = 0.100000) [28:57:38] ML tree search #17, logLikelihood: -434988.106790 [28:57:39 -1168236.178267] Initial branch length optimization [28:57:42 -1009350.146938] Model parameter optimization (eps = 10.000000) [28:58:14 -1005524.309293] AUTODETECT spr round 1 (radius: 5) [29:00:41 -770333.756892] AUTODETECT spr round 2 (radius: 10) [29:03:25 -583001.385919] AUTODETECT spr round 3 (radius: 15) [29:06:17 -492246.143884] AUTODETECT spr round 4 (radius: 20) [29:09:29 -474020.072835] AUTODETECT spr round 5 (radius: 25) [29:13:01 -473024.449514] SPR radius for FAST iterations: 25 (autodetect) [29:13:01 -473024.449514] Model parameter optimization (eps = 3.000000) [29:13:11 -473019.645935] FAST spr round 1 (radius: 25) [29:16:50 -436697.268801] FAST spr round 2 (radius: 25) [29:19:41 -435314.943000] FAST spr round 3 (radius: 25) [29:22:05 -435216.645350] FAST spr round 4 (radius: 25) [29:24:11 -435214.718987] FAST spr round 5 (radius: 25) [29:26:11 -435213.625250] FAST spr round 6 (radius: 25) [29:28:09 -435213.625198] Model parameter optimization (eps = 1.000000) [29:28:14 -435213.583762] SLOW spr round 1 (radius: 5) [29:31:13 -435087.571660] SLOW spr round 2 (radius: 5) [29:33:57 -435076.989030] SLOW spr round 3 (radius: 5) [29:36:38 -435076.646927] SLOW spr round 4 (radius: 5) [29:39:17 -435076.646887] SLOW spr round 5 (radius: 10) [29:42:01 -435076.646885] SLOW spr round 6 (radius: 15) [29:46:39 -435076.024631] SLOW spr round 7 (radius: 5) [29:50:02 -435075.998141] SLOW spr round 8 (radius: 10) [29:53:14 -435075.995935] SLOW spr round 9 (radius: 15) [29:57:34 -435075.994242] SLOW spr round 10 (radius: 20) [30:04:30 -435073.978911] SLOW spr round 11 (radius: 5) [30:07:52 -435073.886256] SLOW spr round 12 (radius: 10) [30:11:07 -435073.886181] SLOW spr round 13 (radius: 15) [30:15:20 -435073.886180] SLOW spr round 14 (radius: 20) [30:22:13 -435073.886180] SLOW spr round 15 (radius: 25) [30:31:00 -435073.886180] Model parameter optimization (eps = 0.100000) [30:31:04] ML tree search #18, logLikelihood: -435073.867047 [30:31:04 -1159667.328894] Initial branch length optimization [30:31:08 -1005146.381122] Model parameter optimization (eps = 10.000000) [30:31:44 -1001388.874238] AUTODETECT spr round 1 (radius: 5) [30:34:12 -769002.711214] AUTODETECT spr round 2 (radius: 10) [30:37:01 -584493.875779] AUTODETECT spr round 3 (radius: 15) [30:40:05 -517121.800469] AUTODETECT spr round 4 (radius: 20) [30:43:38 -485732.427720] AUTODETECT spr round 5 (radius: 25) [30:47:40 -479575.098152] SPR radius for FAST iterations: 25 (autodetect) [30:47:40 -479575.098152] Model parameter optimization (eps = 3.000000) [30:47:49 -479570.721209] FAST spr round 1 (radius: 25) [30:51:41 -437012.387633] FAST spr round 2 (radius: 25) [30:54:34 -435322.797325] FAST spr round 3 (radius: 25) [30:57:06 -435204.195526] FAST spr round 4 (radius: 25) [30:59:16 -435189.163349] FAST spr round 5 (radius: 25) [31:01:21 -435186.787347] FAST spr round 6 (radius: 25) [31:03:23 -435186.787126] Model parameter optimization (eps = 1.000000) [31:03:44 -435158.483957] SLOW spr round 1 (radius: 5) [31:06:42 -435022.097959] SLOW spr round 2 (radius: 5) [31:09:31 -435013.168840] SLOW spr round 3 (radius: 5) [31:12:10 -435012.558515] SLOW spr round 4 (radius: 5) [31:14:47 -435012.557522] SLOW spr round 5 (radius: 10) [31:17:35 -435004.392899] SLOW spr round 6 (radius: 5) [31:20:54 -434998.190993] SLOW spr round 7 (radius: 5) [31:23:44 -434998.190945] SLOW spr round 8 (radius: 10) [31:26:34 -434998.190938] SLOW spr round 9 (radius: 15) [31:31:06 -434998.090476] SLOW spr round 10 (radius: 5) [31:34:25 -434998.090410] SLOW spr round 11 (radius: 10) [31:37:35 -434998.090410] SLOW spr round 12 (radius: 15) [31:41:58 -434998.090410] SLOW spr round 13 (radius: 20) [31:49:15 -434998.090410] SLOW spr round 14 (radius: 25) [31:58:35 -434998.090410] Model parameter optimization (eps = 0.100000) [31:58:46] ML tree search #19, logLikelihood: -434997.637363 [31:58:47 -1164213.334613] Initial branch length optimization [31:58:50 -1005730.812931] Model parameter optimization (eps = 10.000000) [31:59:32 -1001973.524536] AUTODETECT spr round 1 (radius: 5) [32:01:56 -775170.627929] AUTODETECT spr round 2 (radius: 10) [32:04:41 -592903.791701] AUTODETECT spr round 3 (radius: 15) [32:07:40 -505445.763167] AUTODETECT spr round 4 (radius: 20) [32:11:12 -492321.707479] AUTODETECT spr round 5 (radius: 25) [32:15:18 -485159.879444] SPR radius for FAST iterations: 25 (autodetect) [32:15:18 -485159.879444] Model parameter optimization (eps = 3.000000) [32:15:38 -485092.953460] FAST spr round 1 (radius: 25) [32:19:23 -437393.843167] FAST spr round 2 (radius: 25) [32:22:15 -435318.592153] FAST spr round 3 (radius: 25) [32:24:49 -435162.092211] FAST spr round 4 (radius: 25) [32:26:58 -435151.542657] FAST spr round 5 (radius: 25) [32:28:59 -435150.727482] FAST spr round 6 (radius: 25) [32:30:59 -435150.727210] Model parameter optimization (eps = 1.000000) [32:31:13 -435140.231211] SLOW spr round 1 (radius: 5) [32:34:08 -435022.972214] SLOW spr round 2 (radius: 5) [32:36:52 -435011.953961] SLOW spr round 3 (radius: 5) [32:39:27 -435011.942142] SLOW spr round 4 (radius: 10) [32:42:13 -435002.819618] SLOW spr round 5 (radius: 5) [32:45:26 -434996.468479] SLOW spr round 6 (radius: 5) [32:48:18 -434995.894873] SLOW spr round 7 (radius: 5) [32:51:02 -434995.894737] SLOW spr round 8 (radius: 10) [32:53:52 -434995.894730] SLOW spr round 9 (radius: 15) [32:58:40 -434995.415645] SLOW spr round 10 (radius: 5) [33:02:03 -434995.414839] SLOW spr round 11 (radius: 10) [33:05:23 -434995.414212] SLOW spr round 12 (radius: 15) [33:09:54 -434995.413694] SLOW spr round 13 (radius: 20) [33:17:19 -434995.413264] SLOW spr round 14 (radius: 25) [33:26:57 -434995.338352] Model parameter optimization (eps = 0.100000) [33:27:10] ML tree search #20, logLikelihood: -434995.161062 Optimized model parameters: Partition 0: noname Rate heterogeneity: FREE (4 cats, mean), weights&rates: (0.146090,0.232057) (0.197882,0.328819) (0.283310,0.727541) (0.372718,1.864444) 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: -434983.775634 AIC score: 873977.551267 / AICc score: 8918037.551267 / BIC score: 883172.825435 Free parameters (model + branch lengths): 2005 WARNING: Number of free parameters (K=2005) is larger than alignment size (n=725). 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/Q9Y4C8/3_mltree/Q9Y4C8.raxml.bestTree All ML trees saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q9Y4C8/3_mltree/Q9Y4C8.raxml.mlTrees Optimized model saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q9Y4C8/3_mltree/Q9Y4C8.raxml.bestModel Execution log saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q9Y4C8/3_mltree/Q9Y4C8.raxml.log Analysis started: 01-Jul-2021 16:23:21 / finished: 03-Jul-2021 01:50:31 Elapsed time: 120430.628 seconds