RAxML-NG v. 1.0.2 released on 22.02.2021 by The Exelixis Lab. Developed by: Alexey M. Kozlov and Alexandros Stamatakis. Contributors: Diego Darriba, Tomas Flouri, Benoit Morel, Sarah Lutteropp, Ben Bettisworth. Latest version: https://github.com/amkozlov/raxml-ng Questions/problems/suggestions? Please visit: https://groups.google.com/forum/#!forum/raxml System: Intel(R) Xeon(R) Gold 6148 CPU @ 2.40GHz, 40 cores, 376 GB RAM RAxML-NG was called at 30-Jun-2021 18:11:08 as follows: raxml-ng --msa /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q9H2B4/2_msa/Q9H2B4_trimmed_msa.fasta --data-type AA --model LG4X --prefix /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q9H2B4/3_mltree/Q9H2B4 --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: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q9H2B4/2_msa/Q9H2B4_trimmed_msa.fasta [00:00:00] Loaded alignment with 975 taxa and 670 sites WARNING: Sequences tr_B4QPC8_B4QPC8_DROSI_7240 and tr_B4HLC4_B4HLC4_DROSE_7238 are exactly identical! WARNING: Sequences tr_A0A2J8JU76_A0A2J8JU76_PANTR_9598 and tr_A0A2R9CKT3_A0A2R9CKT3_PANPA_9597 are exactly identical! WARNING: Sequences tr_A0A1D5Q707_A0A1D5Q707_MACMU_9544 and tr_G7P1Y9_G7P1Y9_MACFA_9541 are exactly identical! WARNING: Sequences tr_A0A1D5Q707_A0A1D5Q707_MACMU_9544 and tr_A0A2K5P5T0_A0A2K5P5T0_CERAT_9531 are exactly identical! WARNING: Sequences tr_A0A1D5Q707_A0A1D5Q707_MACMU_9544 and tr_A0A2K6D7N3_A0A2K6D7N3_MACNE_9545 are exactly identical! WARNING: Sequences tr_A0A1D5Q707_A0A1D5Q707_MACMU_9544 and tr_A0A2K5Z1Q6_A0A2K5Z1Q6_MANLE_9568 are exactly identical! WARNING: Sequences tr_F6TNJ1_F6TNJ1_MACMU_9544 and tr_G7P8N8_G7P8N8_MACFA_9541 are exactly identical! WARNING: Sequences tr_F6TNJ1_F6TNJ1_MACMU_9544 and tr_A0A2K6B952_A0A2K6B952_MACNE_9545 are exactly identical! WARNING: Sequences tr_F7GEW8_F7GEW8_MACMU_9544 and tr_A0A2K6DXH2_A0A2K6DXH2_MACNE_9545 are exactly identical! WARNING: Sequences tr_A0A0E0CWL3_A0A0E0CWL3_9ORYZ_40149 and tr_Q10QI2_Q10QI2_ORYSJ_39947 are exactly identical! WARNING: Sequences tr_A0A096N7V2_A0A096N7V2_PAPAN_9555 and tr_A0A2K6E1B5_A0A2K6E1B5_MACNE_9545 are exactly identical! WARNING: Sequences tr_A0A0V0RX22_A0A0V0RX22_9BILA_6336 and tr_A0A0V1CSF5_A0A0V1CSF5_TRIBR_45882 are exactly identical! WARNING: Sequences tr_A0A0V0RX22_A0A0V0RX22_9BILA_6336 and tr_A0A0V0WZC1_A0A0V0WZC1_9BILA_92179 are exactly identical! WARNING: Sequences tr_A0A0V0RX22_A0A0V0RX22_9BILA_6336 and tr_A0A0V1L7B2_A0A0V1L7B2_9BILA_6335 are exactly identical! WARNING: Sequences tr_A0A0V0RX22_A0A0V0RX22_9BILA_6336 and tr_A0A0V1P2S2_A0A0V1P2S2_9BILA_92180 are exactly identical! WARNING: Sequences tr_A0A0V0RX22_A0A0V0RX22_9BILA_6336 and tr_A0A0V0U0C3_A0A0V0U0C3_9BILA_144512 are exactly identical! WARNING: Sequences tr_A0A0V1MVZ4_A0A0V1MVZ4_9BILA_268474 and tr_A0A0V1I5Z4_A0A0V1I5Z4_9BILA_268475 are exactly identical! WARNING: Sequences tr_A0A226ME94_A0A226ME94_CALSU_9009 and tr_A0A226NBB5_A0A226NBB5_CALSU_9009 are exactly identical! WARNING: Duplicate sequences found: 18 NOTE: Reduced alignment (with duplicates and gap-only sites/taxa removed) NOTE: was saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q9H2B4/3_mltree/Q9H2B4.raxml.reduced.phy Alignment comprises 1 partitions and 670 patterns Partition 0: noname Model: LG4X+R4 Alignment sites / patterns: 670 / 670 Gaps: 13.17 % Invariant sites: 0.00 % NOTE: Binary MSA file created: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q9H2B4/3_mltree/Q9H2B4.raxml.rba Parallelization scheme autoconfig: 2 worker(s) x 4 thread(s) Parallel reduction/worker buffer size: 1 KB / 0 KB [00:00:00] Generating 20 random starting tree(s) with 975 taxa [00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 168 / 13440 [00:00:00] Data distribution: max. searches per worker: 10 Starting ML tree search with 20 distinct starting trees [00:00:00 -1111555.364804] Initial branch length optimization [00:00:06 -952777.412794] Model parameter optimization (eps = 10.000000) [00:01:01 -946663.136818] AUTODETECT spr round 1 (radius: 5) [00:03:47 -664241.748544] AUTODETECT spr round 2 (radius: 10) [00:06:53 -462334.339830] AUTODETECT spr round 3 (radius: 15) [00:10:03 -388816.522335] AUTODETECT spr round 4 (radius: 20) [00:14:20 -373392.368963] AUTODETECT spr round 5 (radius: 25) [00:19:20 -368381.774985] SPR radius for FAST iterations: 25 (autodetect) [00:19:20 -368381.774985] Model parameter optimization (eps = 3.000000) [00:19:44 -368224.407913] FAST spr round 1 (radius: 25) [00:23:29 -331636.201257] FAST spr round 2 (radius: 25) [00:26:20 -330033.448879] FAST spr round 3 (radius: 25) [00:28:52 -329857.813801] FAST spr round 4 (radius: 25) [00:31:01 -329854.585016] FAST spr round 5 (radius: 25) [00:33:06 -329853.699385] FAST spr round 6 (radius: 25) [00:35:08 -329853.699241] Model parameter optimization (eps = 1.000000) [00:35:24 -329847.928269] SLOW spr round 1 (radius: 5) [00:38:05 -329805.173361] SLOW spr round 2 (radius: 5) [00:40:47 -329789.907492] SLOW spr round 3 (radius: 5) [00:43:23 -329783.316508] SLOW spr round 4 (radius: 5) [00:45:54 -329783.314271] SLOW spr round 5 (radius: 10) [00:48:42 -329782.958871] SLOW spr round 6 (radius: 5) [00:51:51 -329780.850681] SLOW spr round 7 (radius: 5) [00:54:39 -329780.334406] SLOW spr round 8 (radius: 5) [00:57:18 -329780.334260] SLOW spr round 9 (radius: 10) [01:00:08 -329780.334256] SLOW spr round 10 (radius: 15) [01:05:26 -329780.334254] SLOW spr round 11 (radius: 20) [01:14:25 -329780.334253] SLOW spr round 12 (radius: 25) [01:22:04] [worker #1] ML tree search #2, logLikelihood: -329766.004588 [01:25:19 -329780.334252] Model parameter optimization (eps = 0.100000) [01:25:25] [worker #0] ML tree search #1, logLikelihood: -329780.315051 [01:25:25 -1104934.800528] Initial branch length optimization [01:25:32 -945296.218756] Model parameter optimization (eps = 10.000000) [01:26:32 -939474.879583] AUTODETECT spr round 1 (radius: 5) [01:29:17 -653206.405557] AUTODETECT spr round 2 (radius: 10) [01:32:16 -472791.230329] AUTODETECT spr round 3 (radius: 15) [01:35:27 -392002.119694] AUTODETECT spr round 4 (radius: 20) [01:40:26 -370872.212626] AUTODETECT spr round 5 (radius: 25) [01:46:20 -369684.179567] SPR radius for FAST iterations: 25 (autodetect) [01:46:20 -369684.179567] Model parameter optimization (eps = 3.000000) [01:46:43 -369551.112812] FAST spr round 1 (radius: 25) [01:50:33 -331328.967597] FAST spr round 2 (radius: 25) [01:53:34 -329978.754958] FAST spr round 3 (radius: 25) [01:56:12 -329890.790831] FAST spr round 4 (radius: 25) [01:58:30 -329874.472509] FAST spr round 5 (radius: 25) [02:00:35 -329874.454760] Model parameter optimization (eps = 1.000000) [02:00:53 -329871.594103] SLOW spr round 1 (radius: 5) [02:03:45 -329794.081191] SLOW spr round 2 (radius: 5) [02:06:30 -329783.464551] SLOW spr round 3 (radius: 5) [02:09:05 -329783.464270] SLOW spr round 4 (radius: 10) [02:11:54 -329778.923903] SLOW spr round 5 (radius: 5) [02:15:04 -329778.922489] SLOW spr round 6 (radius: 10) [02:18:15 -329778.922219] SLOW spr round 7 (radius: 15) [02:23:07 -329778.922143] SLOW spr round 8 (radius: 20) [02:32:20 -329778.922119] SLOW spr round 9 (radius: 25) [02:43:43 -329778.922111] Model parameter optimization (eps = 0.100000) [02:43:54] [worker #0] ML tree search #3, logLikelihood: -329778.816492 [02:43:54 -1107954.566042] Initial branch length optimization [02:44:00 -950094.602533] Model parameter optimization (eps = 10.000000) [02:44:36 -944182.417946] AUTODETECT spr round 1 (radius: 5) [02:47:18 -658150.422969] AUTODETECT spr round 2 (radius: 10) [02:50:15 -469186.704478] AUTODETECT spr round 3 (radius: 15) [02:53:26 -391624.610992] AUTODETECT spr round 4 (radius: 20) [02:57:06 -371041.331461] AUTODETECT spr round 5 (radius: 25) [03:01:37 -366123.883758] SPR radius for FAST iterations: 25 (autodetect) [03:01:37 -366123.883758] Model parameter optimization (eps = 3.000000) [03:02:00 -366003.341241] FAST spr round 1 (radius: 25) [03:02:51] [worker #1] ML tree search #4, logLikelihood: -329770.056415 [03:05:48 -331532.019677] FAST spr round 2 (radius: 25) [03:08:30 -329965.236436] FAST spr round 3 (radius: 25) [03:10:56 -329874.564548] FAST spr round 4 (radius: 25) [03:13:07 -329861.385266] FAST spr round 5 (radius: 25) [03:15:11 -329861.383995] Model parameter optimization (eps = 1.000000) [03:15:19 -329861.027291] SLOW spr round 1 (radius: 5) [03:18:09 -329801.335490] SLOW spr round 2 (radius: 5) [03:20:53 -329791.315641] SLOW spr round 3 (radius: 5) [03:23:30 -329791.315412] SLOW spr round 4 (radius: 10) [03:26:19 -329789.348194] SLOW spr round 5 (radius: 5) [03:29:34 -329787.877732] SLOW spr round 6 (radius: 5) [03:32:28 -329786.531685] SLOW spr round 7 (radius: 5) [03:35:13 -329786.531430] SLOW spr round 8 (radius: 10) [03:38:04 -329786.531427] SLOW spr round 9 (radius: 15) [03:43:08 -329786.531427] SLOW spr round 10 (radius: 20) [03:51:46 -329786.531427] SLOW spr round 11 (radius: 25) [04:02:31 -329786.531427] Model parameter optimization (eps = 0.100000) [04:02:36] [worker #0] ML tree search #5, logLikelihood: -329786.470442 [04:02:37 -1107342.981275] Initial branch length optimization [04:02:44 -950480.345774] Model parameter optimization (eps = 10.000000) [04:03:36 -944517.429448] AUTODETECT spr round 1 (radius: 5) [04:06:19 -659376.659185] AUTODETECT spr round 2 (radius: 10) [04:09:16 -484456.823276] AUTODETECT spr round 3 (radius: 15) [04:12:34 -412054.940129] AUTODETECT spr round 4 (radius: 20) [04:16:09 -381764.021462] AUTODETECT spr round 5 (radius: 25) [04:19:18] [worker #1] ML tree search #6, logLikelihood: -329801.352461 [04:21:16 -372004.558846] SPR radius for FAST iterations: 25 (autodetect) [04:21:16 -372004.558846] Model parameter optimization (eps = 3.000000) [04:21:23 -372001.820116] FAST spr round 1 (radius: 25) [04:25:10 -332089.863685] FAST spr round 2 (radius: 25) [04:28:02 -330095.773423] FAST spr round 3 (radius: 25) [04:30:32 -329965.835785] FAST spr round 4 (radius: 25) [04:32:46 -329948.707863] FAST spr round 5 (radius: 25) [04:34:49 -329947.667836] FAST spr round 6 (radius: 25) [04:36:47 -329947.667736] Model parameter optimization (eps = 1.000000) [04:37:12 -329835.529866] SLOW spr round 1 (radius: 5) [04:39:55 -329778.643500] SLOW spr round 2 (radius: 5) [04:42:31 -329773.908245] SLOW spr round 3 (radius: 5) [04:45:01 -329773.907331] SLOW spr round 4 (radius: 10) [04:47:52 -329771.549072] SLOW spr round 5 (radius: 5) [04:51:05 -329771.479366] SLOW spr round 6 (radius: 10) [04:54:22 -329771.479362] SLOW spr round 7 (radius: 15) [04:59:19 -329771.479360] SLOW spr round 8 (radius: 20) [05:08:20 -329771.479359] SLOW spr round 9 (radius: 25) [05:19:30 -329771.479358] Model parameter optimization (eps = 0.100000) [05:19:36] [worker #0] ML tree search #7, logLikelihood: -329771.401863 [05:19:36 -1111839.578456] Initial branch length optimization [05:19:43 -952045.499021] Model parameter optimization (eps = 10.000000) [05:20:26 -946090.786786] AUTODETECT spr round 1 (radius: 5) [05:23:06 -665704.809771] AUTODETECT spr round 2 (radius: 10) [05:26:06 -481926.980608] AUTODETECT spr round 3 (radius: 15) [05:29:21 -417370.437764] AUTODETECT spr round 4 (radius: 20) [05:33:10 -386790.852555] AUTODETECT spr round 5 (radius: 25) [05:38:14 -379203.411666] SPR radius for FAST iterations: 25 (autodetect) [05:38:14 -379203.411666] Model parameter optimization (eps = 3.000000) [05:38:30 -379067.597361] FAST spr round 1 (radius: 25) [05:42:32 -331785.429710] FAST spr round 2 (radius: 25) [05:44:11] [worker #1] ML tree search #8, logLikelihood: -329780.673513 [05:45:34 -330058.586946] FAST spr round 3 (radius: 25) [05:48:14 -329903.083658] FAST spr round 4 (radius: 25) [05:50:29 -329876.338338] FAST spr round 5 (radius: 25) [05:52:33 -329876.338149] Model parameter optimization (eps = 1.000000) [05:52:43 -329875.532176] SLOW spr round 1 (radius: 5) [05:55:29 -329801.332071] SLOW spr round 2 (radius: 5) [05:58:14 -329791.730599] SLOW spr round 3 (radius: 5) [06:00:50 -329789.358680] SLOW spr round 4 (radius: 5) [06:03:23 -329789.355711] SLOW spr round 5 (radius: 10) [06:06:13 -329786.502082] SLOW spr round 6 (radius: 5) [06:09:23 -329786.490492] SLOW spr round 7 (radius: 10) [06:12:34 -329786.487503] SLOW spr round 8 (radius: 15) [06:17:28 -329786.486416] SLOW spr round 9 (radius: 20) [06:26:39 -329786.485973] SLOW spr round 10 (radius: 25) [06:37:48 -329786.485770] Model parameter optimization (eps = 0.100000) [06:38:06] [worker #0] ML tree search #9, logLikelihood: -329786.034766 [06:38:06 -1108779.776324] Initial branch length optimization [06:38:14 -949577.925602] Model parameter optimization (eps = 10.000000) [06:38:58 -943456.129099] AUTODETECT spr round 1 (radius: 5) [06:41:41 -653981.064407] AUTODETECT spr round 2 (radius: 10) [06:44:40 -474510.411236] AUTODETECT spr round 3 (radius: 15) [06:47:54 -418864.161153] AUTODETECT spr round 4 (radius: 20) [06:51:26] [worker #1] ML tree search #10, logLikelihood: -329771.628878 [06:51:56 -375313.155468] AUTODETECT spr round 5 (radius: 25) [06:57:01 -372237.076100] SPR radius for FAST iterations: 25 (autodetect) [06:57:01 -372237.076100] Model parameter optimization (eps = 3.000000) [06:57:23 -372102.074112] FAST spr round 1 (radius: 25) [07:01:14 -332338.787254] FAST spr round 2 (radius: 25) [07:04:15 -329984.147505] FAST spr round 3 (radius: 25) [07:06:43 -329857.042568] FAST spr round 4 (radius: 25) [07:08:52 -329839.935169] FAST spr round 5 (radius: 25) [07:10:56 -329830.667935] FAST spr round 6 (radius: 25) [07:12:53 -329828.155712] FAST spr round 7 (radius: 25) [07:14:47 -329828.155601] Model parameter optimization (eps = 1.000000) [07:15:04 -329823.497513] SLOW spr round 1 (radius: 5) [07:17:54 -329781.979435] SLOW spr round 2 (radius: 5) [07:20:34 -329772.934550] SLOW spr round 3 (radius: 5) [07:23:10 -329772.048823] SLOW spr round 4 (radius: 5) [07:25:43 -329772.048713] SLOW spr round 5 (radius: 10) [07:28:33 -329770.553190] SLOW spr round 6 (radius: 5) [07:31:47 -329769.482279] SLOW spr round 7 (radius: 5) [07:34:47 -329764.997007] SLOW spr round 8 (radius: 5) [07:37:28 -329764.449579] SLOW spr round 9 (radius: 5) [07:40:03 -329764.449339] SLOW spr round 10 (radius: 10) [07:42:53 -329764.449270] SLOW spr round 11 (radius: 15) [07:48:12 -329764.449226] SLOW spr round 12 (radius: 20) [07:57:05 -329764.449194] SLOW spr round 13 (radius: 25) [08:08:25 -329764.449169] Model parameter optimization (eps = 0.100000) [08:08:31] [worker #0] ML tree search #11, logLikelihood: -329764.380151 [08:08:31 -1116144.760018] Initial branch length optimization [08:08:37 -954754.826420] Model parameter optimization (eps = 10.000000) [08:09:12 -948522.429355] AUTODETECT spr round 1 (radius: 5) [08:11:51 -655006.390671] AUTODETECT spr round 2 (radius: 10) [08:12:36] [worker #1] ML tree search #12, logLikelihood: -329782.571993 [08:14:50 -469960.916317] AUTODETECT spr round 3 (radius: 15) [08:18:01 -385347.333426] AUTODETECT spr round 4 (radius: 20) [08:22:05 -367033.382388] AUTODETECT spr round 5 (radius: 25) [08:27:59 -365424.387852] SPR radius for FAST iterations: 25 (autodetect) [08:27:59 -365424.387852] Model parameter optimization (eps = 3.000000) [08:28:21 -365318.106890] FAST spr round 1 (radius: 25) [08:32:11 -331156.175597] FAST spr round 2 (radius: 25) [08:35:00 -329978.323674] FAST spr round 3 (radius: 25) [08:37:29 -329874.166434] FAST spr round 4 (radius: 25) [08:39:40 -329868.177748] FAST spr round 5 (radius: 25) [08:41:44 -329862.769725] FAST spr round 6 (radius: 25) [08:43:45 -329862.768302] Model parameter optimization (eps = 1.000000) [08:44:03 -329859.845186] SLOW spr round 1 (radius: 5) [08:46:52 -329794.187433] SLOW spr round 2 (radius: 5) [08:49:33 -329781.259624] SLOW spr round 3 (radius: 5) [08:52:04 -329781.259571] SLOW spr round 4 (radius: 10) [08:54:52 -329781.259567] SLOW spr round 5 (radius: 15) [09:00:25 -329781.259566] SLOW spr round 6 (radius: 20) [09:09:53 -329781.259566] SLOW spr round 7 (radius: 25) [09:21:30 -329781.259565] Model parameter optimization (eps = 0.100000) [09:21:44] [worker #0] ML tree search #13, logLikelihood: -329780.555189 [09:21:44 -1115644.613102] Initial branch length optimization [09:21:51 -955117.540674] Model parameter optimization (eps = 10.000000) [09:22:35 -949058.365873] AUTODETECT spr round 1 (radius: 5) [09:25:17 -671013.605481] AUTODETECT spr round 2 (radius: 10) [09:27:05] [worker #1] ML tree search #14, logLikelihood: -329798.014277 [09:28:18 -457699.200365] AUTODETECT spr round 3 (radius: 15) [09:31:31 -383803.961322] AUTODETECT spr round 4 (radius: 20) [09:35:23 -367112.288813] AUTODETECT spr round 5 (radius: 25) [09:40:13 -365177.563220] SPR radius for FAST iterations: 25 (autodetect) [09:40:13 -365177.563220] Model parameter optimization (eps = 3.000000) [09:40:33 -365092.419704] FAST spr round 1 (radius: 25) [09:44:21 -331574.043715] FAST spr round 2 (radius: 25) [09:47:23 -330210.028273] FAST spr round 3 (radius: 25) [09:49:54 -329966.671196] FAST spr round 4 (radius: 25) [09:52:08 -329931.931763] FAST spr round 5 (radius: 25) [09:54:11 -329917.437514] FAST spr round 6 (radius: 25) [09:56:09 -329916.943924] FAST spr round 7 (radius: 25) [09:58:05 -329913.353657] FAST spr round 8 (radius: 25) [10:00:00 -329913.352020] Model parameter optimization (eps = 1.000000) [10:00:05 -329912.536003] SLOW spr round 1 (radius: 5) [10:02:42 -329833.851451] SLOW spr round 2 (radius: 5) [10:05:23 -329825.844644] SLOW spr round 3 (radius: 5) [10:07:56 -329825.844219] SLOW spr round 4 (radius: 10) [10:10:44 -329817.628602] SLOW spr round 5 (radius: 5) [10:14:00 -329801.282235] SLOW spr round 6 (radius: 5) [10:16:49 -329799.966977] SLOW spr round 7 (radius: 5) [10:19:26 -329799.966594] SLOW spr round 8 (radius: 10) [10:22:15 -329799.966540] SLOW spr round 9 (radius: 15) [10:27:26 -329799.966531] SLOW spr round 10 (radius: 20) [10:34:37] [worker #1] ML tree search #16, logLikelihood: -329771.675324 [10:36:25 -329799.966529] SLOW spr round 11 (radius: 25) [10:48:09 -329799.966528] Model parameter optimization (eps = 0.100000) [10:48:25] [worker #0] ML tree search #15, logLikelihood: -329794.283913 [10:48:25 -1111501.198115] Initial branch length optimization [10:48:31 -953363.918891] Model parameter optimization (eps = 10.000000) [10:49:15 -947469.780495] AUTODETECT spr round 1 (radius: 5) [10:52:01 -671926.328530] AUTODETECT spr round 2 (radius: 10) [10:55:07 -459812.950822] AUTODETECT spr round 3 (radius: 15) [10:58:23 -395188.452833] AUTODETECT spr round 4 (radius: 20) [11:02:08 -374757.863925] AUTODETECT spr round 5 (radius: 25) [11:06:48 -366531.867051] SPR radius for FAST iterations: 25 (autodetect) [11:06:48 -366531.867051] Model parameter optimization (eps = 3.000000) [11:07:14 -366383.116520] FAST spr round 1 (radius: 25) [11:11:10 -331138.918614] FAST spr round 2 (radius: 25) [11:14:05 -330033.758556] FAST spr round 3 (radius: 25) [11:16:43 -329890.683681] FAST spr round 4 (radius: 25) [11:18:52 -329885.665165] FAST spr round 5 (radius: 25) [11:20:53 -329881.111986] FAST spr round 6 (radius: 25) [11:22:51 -329879.747024] FAST spr round 7 (radius: 25) [11:24:46 -329879.746905] Model parameter optimization (eps = 1.000000) [11:25:02 -329876.234945] SLOW spr round 1 (radius: 5) [11:27:46 -329812.233009] SLOW spr round 2 (radius: 5) [11:30:24 -329797.707512] SLOW spr round 3 (radius: 5) [11:32:56 -329792.651141] SLOW spr round 4 (radius: 5) [11:35:28 -329791.618279] SLOW spr round 5 (radius: 5) [11:37:59 -329791.617791] SLOW spr round 6 (radius: 10) [11:40:46 -329791.373417] SLOW spr round 7 (radius: 5) [11:42:48] [worker #1] ML tree search #18, logLikelihood: -329771.734718 [11:43:56 -329791.371610] SLOW spr round 8 (radius: 10) [11:47:11 -329791.371364] SLOW spr round 9 (radius: 15) [11:52:05 -329791.371238] SLOW spr round 10 (radius: 20) [12:01:02 -329791.371153] SLOW spr round 11 (radius: 25) [12:12:23 -329791.371096] Model parameter optimization (eps = 0.100000) [12:12:38] [worker #0] ML tree search #17, logLikelihood: -329790.824863 [12:12:38 -1107547.526061] Initial branch length optimization [12:12:43 -948306.795828] Model parameter optimization (eps = 10.000000) [12:13:31 -942528.134645] AUTODETECT spr round 1 (radius: 5) [12:16:16 -672171.913210] AUTODETECT spr round 2 (radius: 10) [12:19:13 -485214.218361] AUTODETECT spr round 3 (radius: 15) [12:22:21 -392268.625905] AUTODETECT spr round 4 (radius: 20) [12:26:17 -369578.534055] AUTODETECT spr round 5 (radius: 25) [12:31:11 -367829.148670] SPR radius for FAST iterations: 25 (autodetect) [12:31:11 -367829.148670] Model parameter optimization (eps = 3.000000) [12:31:39 -367695.973546] FAST spr round 1 (radius: 25) [12:35:25 -331313.546140] FAST spr round 2 (radius: 25) [12:38:18 -329995.882058] FAST spr round 3 (radius: 25) [12:40:51 -329870.848350] FAST spr round 4 (radius: 25) [12:43:02 -329859.262579] FAST spr round 5 (radius: 25) [12:45:04 -329859.262528] Model parameter optimization (eps = 1.000000) [12:45:11 -329858.641939] SLOW spr round 1 (radius: 5) [12:47:58 -329795.330861] SLOW spr round 2 (radius: 5) [12:50:38 -329785.813049] SLOW spr round 3 (radius: 5) [12:53:09 -329785.812773] SLOW spr round 4 (radius: 10) [12:54:42] [worker #1] ML tree search #20, logLikelihood: -329765.263767 [12:55:54 -329784.846541] SLOW spr round 5 (radius: 5) [12:59:00 -329783.175228] SLOW spr round 6 (radius: 5) [13:01:45 -329782.846830] SLOW spr round 7 (radius: 5) [13:04:20 -329782.432917] SLOW spr round 8 (radius: 5) [13:06:49 -329782.432767] SLOW spr round 9 (radius: 10) [13:09:33 -329782.432722] SLOW spr round 10 (radius: 15) [13:14:46 -329782.432696] SLOW spr round 11 (radius: 20) [13:23:47 -329782.432677] SLOW spr round 12 (radius: 25) [13:34:51 -329782.432663] Model parameter optimization (eps = 0.100000) [13:35:01] [worker #0] ML tree search #19, logLikelihood: -329782.269641 Optimized model parameters: Partition 0: noname Rate heterogeneity: FREE (4 cats, mean), weights&rates: (0.240320,0.481598) (0.264046,0.608824) (0.272907,0.946670) (0.222727,2.088442) 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: -329764.380151 AIC score: 663434.760302 / AICc score: 8295758.760302 / BIC score: 672237.473674 Free parameters (model + branch lengths): 1953 WARNING: Number of free parameters (K=1953) is larger than alignment size (n=670). This might lead to overfitting and compromise tree inference results! Best ML tree saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q9H2B4/3_mltree/Q9H2B4.raxml.bestTree All ML trees saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q9H2B4/3_mltree/Q9H2B4.raxml.mlTrees Optimized model saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q9H2B4/3_mltree/Q9H2B4.raxml.bestModel Execution log saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q9H2B4/3_mltree/Q9H2B4.raxml.log Analysis started: 30-Jun-2021 18:11:08 / finished: 01-Jul-2021 07:46:09 Elapsed time: 48901.504 seconds Consumed energy: 4570.653 Wh (= 23 km in an electric car, or 114 km with an e-scooter!)