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 01-Jul-2021 06:28:57 as follows: raxml-ng --msa /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q9HC97/2_msa/Q9HC97_trimmed_msa.fasta --data-type AA --model LG4X --prefix /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q9HC97/3_mltree/Q9HC97 --seed 2 --threads 6 --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 (6 threads), thread pinning: OFF [00:00:00] Reading alignment from file: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q9HC97/2_msa/Q9HC97_trimmed_msa.fasta [00:00:00] Loaded alignment with 869 taxa and 410 sites WARNING: Sequences sp_Q8BLG2_LPAR4_MOUSE_10090 and tr_D3ZHA3_D3ZHA3_RAT_10116 are exactly identical! WARNING: Sequences tr_A0A2I3FQU8_A0A2I3FQU8_NOMLE_61853 and tr_A0A2I2YZ13_A0A2I2YZ13_GORGO_9595 are exactly identical! WARNING: Sequences tr_A0A2I3FQU8_A0A2I3FQU8_NOMLE_61853 and tr_K7D4M0_K7D4M0_PANTR_9598 are exactly identical! WARNING: Sequences tr_A0A2I3FQU8_A0A2I3FQU8_NOMLE_61853 and sp_P46093_GPR4_HUMAN_9606 are exactly identical! WARNING: Sequences tr_A0A2I3FQU8_A0A2I3FQU8_NOMLE_61853 and tr_A0A2R8Z9Z0_A0A2R8Z9Z0_PANPA_9597 are exactly identical! WARNING: Sequences tr_G1SBK7_G1SBK7_NOMLE_61853 and tr_H2PW41_H2PW41_PONAB_9601 are exactly identical! WARNING: Sequences tr_G3ICW4_G3ICW4_CRIGR_10029 and tr_A0A3Q0CDJ3_A0A3Q0CDJ3_MESAU_10036 are exactly identical! WARNING: Sequences tr_G3ICW4_G3ICW4_CRIGR_10029 and tr_D5MRP4_D5MRP4_MESAU_10036 are exactly identical! WARNING: Sequences tr_G3R4Y1_G3R4Y1_GORGO_9595 and tr_H2R9N3_H2R9N3_PANTR_9598 are exactly identical! WARNING: Sequences tr_G3RRG1_G3RRG1_GORGO_9595 and tr_K7B3P4_K7B3P4_PANTR_9598 are exactly identical! WARNING: Sequences tr_G3RRG1_G3RRG1_GORGO_9595 and sp_P43657_LPAR6_HUMAN_9606 are exactly identical! WARNING: Sequences tr_G3RRG1_G3RRG1_GORGO_9595 and tr_A0A2R8ZD42_A0A2R8ZD42_PANPA_9597 are exactly identical! WARNING: Sequences tr_E2RIH0_E2RIH0_CANLF_9615 and tr_M3X0L1_M3X0L1_FELCA_9685 are exactly identical! WARNING: Sequences tr_A0A2J8PZJ2_A0A2J8PZJ2_PANTR_9598 and tr_A0A2R8ZPM2_A0A2R8ZPM2_PANPA_9597 are exactly identical! WARNING: Sequences tr_G2HJ56_G2HJ56_PANTR_9598 and tr_A0A2R8ZEB9_A0A2R8ZEB9_PANPA_9597 are exactly identical! WARNING: Sequences tr_H2RGA1_H2RGA1_PANTR_9598 and tr_A0A2R8ZEH5_A0A2R8ZEH5_PANPA_9597 are exactly identical! WARNING: Sequences tr_A0A1D5QR05_A0A1D5QR05_MACMU_9544 and tr_G7PJ85_G7PJ85_MACFA_9541 are exactly identical! WARNING: Sequences tr_F6R9Y2_F6R9Y2_MACMU_9544 and tr_G7PXX4_G7PXX4_MACFA_9541 are exactly identical! WARNING: Sequences tr_F6R9Y2_F6R9Y2_MACMU_9544 and tr_A0A0A0MVS8_A0A0A0MVS8_PAPAN_9555 are exactly identical! WARNING: Sequences tr_F6R9Y2_F6R9Y2_MACMU_9544 and tr_A0A0D9SE33_A0A0D9SE33_CHLSB_60711 are exactly identical! WARNING: Sequences tr_F6R9Y2_F6R9Y2_MACMU_9544 and tr_A0A2K5KTY5_A0A2K5KTY5_CERAT_9531 are exactly identical! WARNING: Sequences tr_F6R9Y2_F6R9Y2_MACMU_9544 and tr_A0A2K6AN93_A0A2K6AN93_MACNE_9545 are exactly identical! WARNING: Sequences tr_F6R9Y2_F6R9Y2_MACMU_9544 and tr_A0A2K5XCE6_A0A2K5XCE6_MANLE_9568 are exactly identical! WARNING: Sequences tr_F7B7B1_F7B7B1_MACMU_9544 and tr_G7Q339_G7Q339_MACFA_9541 are exactly identical! WARNING: Sequences tr_F7B7B1_F7B7B1_MACMU_9544 and tr_A0A0D9SAL6_A0A0D9SAL6_CHLSB_60711 are exactly identical! WARNING: Sequences tr_F7B7B1_F7B7B1_MACMU_9544 and tr_A0A2K5NV18_A0A2K5NV18_CERAT_9531 are exactly identical! WARNING: Sequences tr_F7B7B1_F7B7B1_MACMU_9544 and tr_A0A2K6B3U1_A0A2K6B3U1_MACNE_9545 are exactly identical! WARNING: Sequences tr_F7B7B1_F7B7B1_MACMU_9544 and tr_A0A2K5XRV2_A0A2K5XRV2_MANLE_9568 are exactly identical! WARNING: Sequences tr_G7N948_G7N948_MACMU_9544 and tr_G7PK96_G7PK96_MACFA_9541 are exactly identical! WARNING: Sequences tr_G7N948_G7N948_MACMU_9544 and tr_A0A2K6AUB6_A0A2K6AUB6_MACNE_9545 are exactly identical! WARNING: Sequences tr_A0A096ML30_A0A096ML30_PAPAN_9555 and tr_A0A2K5L152_A0A2K5L152_CERAT_9531 are exactly identical! WARNING: Sequences tr_A0A096ML30_A0A096ML30_PAPAN_9555 and tr_A0A2K5XEI4_A0A2K5XEI4_MANLE_9568 are exactly identical! WARNING: Sequences tr_A0A096N579_A0A096N579_PAPAN_9555 and tr_A0A2K5KS60_A0A2K5KS60_CERAT_9531 are exactly identical! WARNING: Sequences tr_A0A096NCQ0_A0A096NCQ0_PAPAN_9555 and tr_A0A2K5KP97_A0A2K5KP97_CERAT_9531 are exactly identical! WARNING: Sequences tr_A0A0D9SCZ3_A0A0D9SCZ3_CHLSB_60711 and tr_A0A2K5KKW9_A0A2K5KKW9_CERAT_9531 are exactly identical! WARNING: Sequences tr_A0A151NDX2_A0A151NDX2_ALLMI_8496 and tr_A0A1U7RCF9_A0A1U7RCF9_ALLSI_38654 are exactly identical! WARNING: Sequences tr_A0A087RIW6_A0A087RIW6_APTFO_9233 and tr_A0A091WEA5_A0A091WEA5_OPIHO_30419 are exactly identical! WARNING: Sequences tr_A0A093HEZ5_A0A093HEZ5_STRCA_441894 and tr_A0A099ZX19_A0A099ZX19_TINGU_94827 are exactly identical! WARNING: Sequences tr_A0A2U3V3Q4_A0A2U3V3Q4_TURTR_9739 and tr_A0A2Y9FHD8_A0A2Y9FHD8_PHYCD_9755 are exactly identical! WARNING: Sequences tr_A0A2U3V3Q4_A0A2U3V3Q4_TURTR_9739 and tr_A0A384APZ3_A0A384APZ3_BALAS_310752 are exactly identical! WARNING: Duplicate sequences found: 40 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/Q9HC97/3_mltree/Q9HC97.raxml.reduced.phy Alignment comprises 1 partitions and 410 patterns Partition 0: noname Model: LG4X+R4 Alignment sites / patterns: 410 / 410 Gaps: 21.67 % Invariant sites: 0.24 % NOTE: Binary MSA file created: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q9HC97/3_mltree/Q9HC97.raxml.rba Parallelization scheme autoconfig: 3 worker(s) x 2 thread(s) Parallel reduction/worker buffer size: 1 KB / 0 KB [00:00:00] Generating 20 random starting tree(s) with 869 taxa [00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 205 / 16400 [00:00:00] Data distribution: max. searches per worker: 7 Starting ML tree search with 20 distinct starting trees [00:00:00 -661402.679069] Initial branch length optimization [00:00:07 -558879.174462] Model parameter optimization (eps = 10.000000) [00:01:11 -553489.494792] AUTODETECT spr round 1 (radius: 5) [00:03:51 -385213.748953] AUTODETECT spr round 2 (radius: 10) [00:06:51 -277661.692821] AUTODETECT spr round 3 (radius: 15) [00:10:08 -210356.463311] AUTODETECT spr round 4 (radius: 20) [00:13:59 -197599.363805] AUTODETECT spr round 5 (radius: 25) [00:20:17 -195200.801296] SPR radius for FAST iterations: 25 (autodetect) [00:20:17 -195200.801296] Model parameter optimization (eps = 3.000000) [00:20:47 -194325.299064] FAST spr round 1 (radius: 25) [00:23:30 -173643.339079] FAST spr round 2 (radius: 25) [00:25:37 -172465.929138] FAST spr round 3 (radius: 25) [00:27:36 -172359.087977] FAST spr round 4 (radius: 25) [00:29:27 -172345.523600] FAST spr round 5 (radius: 25) [00:31:11 -172334.176270] FAST spr round 6 (radius: 25) [00:32:49 -172332.777695] FAST spr round 7 (radius: 25) [00:34:27 -172332.777157] Model parameter optimization (eps = 1.000000) [00:34:48 -172327.498326] SLOW spr round 1 (radius: 5) [00:37:12 -172288.867927] SLOW spr round 2 (radius: 5) [00:39:35 -172280.982060] SLOW spr round 3 (radius: 5) [00:41:55 -172274.906632] SLOW spr round 4 (radius: 5) [00:44:08 -172274.906489] SLOW spr round 5 (radius: 10) [00:46:30 -172270.482219] SLOW spr round 6 (radius: 5) [00:49:27 -172270.482196] SLOW spr round 7 (radius: 10) [00:52:03 -172269.183581] SLOW spr round 8 (radius: 5) [00:54:57 -172269.173370] SLOW spr round 9 (radius: 10) [00:57:31 -172269.150307] SLOW spr round 10 (radius: 15) [01:01:36 -172269.150306] SLOW spr round 11 (radius: 20) [01:10:04 -172269.150305] SLOW spr round 12 (radius: 25) [01:13:31] [worker #1] ML tree search #2, logLikelihood: -172264.036797 [01:19:34 -172269.150305] Model parameter optimization (eps = 0.100000) [01:19:51] [worker #0] ML tree search #1, logLikelihood: -172266.415634 [01:19:52 -663692.702472] Initial branch length optimization [01:20:01 -559226.216157] Model parameter optimization (eps = 10.000000) [01:21:15 -554859.226737] AUTODETECT spr round 1 (radius: 5) [01:21:43] [worker #2] ML tree search #3, logLikelihood: -172255.156663 [01:23:55 -400394.646192] AUTODETECT spr round 2 (radius: 10) [01:26:57 -280174.507172] AUTODETECT spr round 3 (radius: 15) [01:30:27 -225661.688650] AUTODETECT spr round 4 (radius: 20) [01:34:27 -211957.983476] AUTODETECT spr round 5 (radius: 25) [01:39:06 -204106.773254] SPR radius for FAST iterations: 25 (autodetect) [01:39:06 -204106.773254] Model parameter optimization (eps = 3.000000) [01:39:31 -203680.235265] FAST spr round 1 (radius: 25) [01:42:18 -173411.806511] FAST spr round 2 (radius: 25) [01:44:17 -172442.075447] FAST spr round 3 (radius: 25) [01:46:11 -172347.812440] FAST spr round 4 (radius: 25) [01:47:57 -172336.582536] FAST spr round 5 (radius: 25) [01:49:36 -172336.581795] Model parameter optimization (eps = 1.000000) [01:49:53 -172327.880608] SLOW spr round 1 (radius: 5) [01:52:19 -172279.414491] SLOW spr round 2 (radius: 5) [01:54:42 -172269.163058] SLOW spr round 3 (radius: 5) [01:57:02 -172267.133806] SLOW spr round 4 (radius: 5) [01:59:16 -172267.133627] SLOW spr round 5 (radius: 10) [02:01:38 -172265.227193] SLOW spr round 6 (radius: 5) [02:04:37 -172265.222608] SLOW spr round 7 (radius: 10) [02:07:14 -172264.908738] SLOW spr round 8 (radius: 5) [02:10:06 -172264.908733] SLOW spr round 9 (radius: 10) [02:12:42 -172264.908733] SLOW spr round 10 (radius: 15) [02:16:41 -172264.908732] SLOW spr round 11 (radius: 20) [02:22:05] [worker #1] ML tree search #5, logLikelihood: -172264.947726 [02:25:04 -172264.908732] SLOW spr round 12 (radius: 25) [02:34:44 -172264.908732] Model parameter optimization (eps = 0.100000) [02:34:56] [worker #0] ML tree search #4, logLikelihood: -172264.795612 [02:34:56 -660704.497326] Initial branch length optimization [02:35:04 -558988.158994] Model parameter optimization (eps = 10.000000) [02:36:21 -554131.477565] AUTODETECT spr round 1 (radius: 5) [02:36:57] [worker #2] ML tree search #6, logLikelihood: -172260.567672 [02:39:01 -380582.837824] AUTODETECT spr round 2 (radius: 10) [02:41:58 -269957.667906] AUTODETECT spr round 3 (radius: 15) [02:45:17 -214599.098176] AUTODETECT spr round 4 (radius: 20) [02:48:53 -198680.794365] AUTODETECT spr round 5 (radius: 25) [02:53:44 -196999.978351] SPR radius for FAST iterations: 25 (autodetect) [02:53:44 -196999.978351] Model parameter optimization (eps = 3.000000) [02:54:17 -196030.574653] FAST spr round 1 (radius: 25) [02:57:16 -173318.756560] FAST spr round 2 (radius: 25) [02:59:27 -172394.406073] FAST spr round 3 (radius: 25) [03:01:24 -172314.618000] FAST spr round 4 (radius: 25) [03:03:11 -172306.431830] FAST spr round 5 (radius: 25) [03:04:51 -172306.431765] Model parameter optimization (eps = 1.000000) [03:05:07 -172302.402240] SLOW spr round 1 (radius: 5) [03:07:39 -172266.806678] SLOW spr round 2 (radius: 5) [03:10:03 -172262.981789] SLOW spr round 3 (radius: 5) [03:12:19 -172262.981312] SLOW spr round 4 (radius: 10) [03:14:42 -172259.920977] SLOW spr round 5 (radius: 5) [03:17:40 -172259.920935] SLOW spr round 6 (radius: 10) [03:20:19 -172259.900743] SLOW spr round 7 (radius: 15) [03:24:18 -172259.900734] SLOW spr round 8 (radius: 20) [03:32:48 -172259.900727] SLOW spr round 9 (radius: 25) [03:42:20 -172259.900720] Model parameter optimization (eps = 0.100000) [03:42:26] [worker #0] ML tree search #7, logLikelihood: -172259.821016 [03:42:27 -665890.118480] Initial branch length optimization [03:42:35 -562815.840210] Model parameter optimization (eps = 10.000000) [03:43:37] [worker #1] ML tree search #8, logLikelihood: -172262.687684 [03:43:54 -557844.408569] AUTODETECT spr round 1 (radius: 5) [03:46:32 -383296.975478] AUTODETECT spr round 2 (radius: 10) [03:49:22 -268703.304819] AUTODETECT spr round 3 (radius: 15) [03:51:31] [worker #2] ML tree search #9, logLikelihood: -172243.566374 [03:52:42 -207672.021278] AUTODETECT spr round 4 (radius: 20) [03:57:02 -193631.668071] AUTODETECT spr round 5 (radius: 25) [04:03:23 -193460.513920] SPR radius for FAST iterations: 25 (autodetect) [04:03:23 -193460.513920] Model parameter optimization (eps = 3.000000) [04:03:52 -193065.595570] FAST spr round 1 (radius: 25) [04:06:48 -173112.079785] FAST spr round 2 (radius: 25) [04:09:05 -172440.364651] FAST spr round 3 (radius: 25) [04:11:11 -172363.069559] FAST spr round 4 (radius: 25) [04:13:00 -172330.690604] FAST spr round 5 (radius: 25) [04:14:42 -172330.690476] Model parameter optimization (eps = 1.000000) [04:14:59 -172328.248504] SLOW spr round 1 (radius: 5) [04:17:27 -172292.403880] SLOW spr round 2 (radius: 5) [04:19:53 -172289.357658] SLOW spr round 3 (radius: 5) [04:22:09 -172289.357427] SLOW spr round 4 (radius: 10) [04:24:34 -172288.870563] SLOW spr round 5 (radius: 5) [04:27:38 -172282.830219] SLOW spr round 6 (radius: 5) [04:30:11 -172282.829948] SLOW spr round 7 (radius: 10) [04:32:41 -172282.576554] SLOW spr round 8 (radius: 5) [04:35:36 -172282.576526] SLOW spr round 9 (radius: 10) [04:38:14 -172282.576519] SLOW spr round 10 (radius: 15) [04:42:12 -172282.523463] SLOW spr round 11 (radius: 20) [04:50:32 -172282.523456] SLOW spr round 12 (radius: 25) [04:59:58 -172282.523450] Model parameter optimization (eps = 0.100000) [05:00:04] [worker #0] ML tree search #10, logLikelihood: -172282.462729 [05:00:04 -660604.415350] Initial branch length optimization [05:00:12 -557176.517697] Model parameter optimization (eps = 10.000000) [05:01:31 -552663.324579] AUTODETECT spr round 1 (radius: 5) [05:02:37] [worker #2] ML tree search #12, logLikelihood: -172263.792322 [05:04:08 -395047.085984] AUTODETECT spr round 2 (radius: 10) [05:07:00 -273119.942808] AUTODETECT spr round 3 (radius: 15) [05:10:22 -218550.883108] AUTODETECT spr round 4 (radius: 20) [05:13:53] [worker #1] ML tree search #11, logLikelihood: -172264.202289 [05:15:16 -198375.379120] AUTODETECT spr round 5 (radius: 25) [05:20:55 -197492.680518] SPR radius for FAST iterations: 25 (autodetect) [05:20:55 -197492.680518] Model parameter optimization (eps = 3.000000) [05:21:19 -197095.563700] FAST spr round 1 (radius: 25) [05:24:15 -173454.317695] FAST spr round 2 (radius: 25) [05:26:26 -172415.075987] FAST spr round 3 (radius: 25) [05:28:20 -172342.823040] FAST spr round 4 (radius: 25) [05:30:02 -172342.822076] Model parameter optimization (eps = 1.000000) [05:30:21 -172332.370735] SLOW spr round 1 (radius: 5) [05:32:52 -172280.803311] SLOW spr round 2 (radius: 5) [05:35:17 -172273.309644] SLOW spr round 3 (radius: 5) [05:37:37 -172272.150267] SLOW spr round 4 (radius: 5) [05:39:51 -172272.150092] SLOW spr round 5 (radius: 10) [05:42:13 -172269.865566] SLOW spr round 6 (radius: 5) [05:45:10 -172267.656639] SLOW spr round 7 (radius: 5) [05:47:42 -172267.656582] SLOW spr round 8 (radius: 10) [05:50:08 -172267.629148] SLOW spr round 9 (radius: 15) [05:54:13 -172267.629141] SLOW spr round 10 (radius: 20) [06:02:30 -172267.629136] SLOW spr round 11 (radius: 25) [06:10:37] [worker #2] ML tree search #15, logLikelihood: -172261.701264 [06:12:03 -172267.629131] Model parameter optimization (eps = 0.100000) [06:12:10] [worker #0] ML tree search #13, logLikelihood: -172267.568004 [06:12:10 -666950.265748] Initial branch length optimization [06:12:19 -562425.046888] Model parameter optimization (eps = 10.000000) [06:13:14 -557443.857768] AUTODETECT spr round 1 (radius: 5) [06:15:49 -390787.633600] AUTODETECT spr round 2 (radius: 10) [06:18:44 -261607.973107] AUTODETECT spr round 3 (radius: 15) [06:20:58] [worker #1] ML tree search #14, logLikelihood: -172262.408551 [06:21:55 -217718.874910] AUTODETECT spr round 4 (radius: 20) [06:26:11 -199133.045263] AUTODETECT spr round 5 (radius: 25) [06:31:30 -195909.328430] SPR radius for FAST iterations: 25 (autodetect) [06:31:30 -195909.328430] Model parameter optimization (eps = 3.000000) [06:31:56 -195687.245550] FAST spr round 1 (radius: 25) [06:34:59 -174339.448176] FAST spr round 2 (radius: 25) [06:37:12 -172590.723373] FAST spr round 3 (radius: 25) [06:39:15 -172371.290794] FAST spr round 4 (radius: 25) [06:41:02 -172364.030746] FAST spr round 5 (radius: 25) [06:42:42 -172364.030537] Model parameter optimization (eps = 1.000000) [06:43:02 -172358.507083] SLOW spr round 1 (radius: 5) [06:45:36 -172278.837475] SLOW spr round 2 (radius: 5) [06:48:00 -172273.246950] SLOW spr round 3 (radius: 5) [06:50:17 -172273.245868] SLOW spr round 4 (radius: 10) [06:52:42 -172270.037300] SLOW spr round 5 (radius: 5) [06:55:43 -172270.026161] SLOW spr round 6 (radius: 10) [06:58:21 -172268.201251] SLOW spr round 7 (radius: 5) [07:01:14 -172268.201154] SLOW spr round 8 (radius: 10) [07:03:49 -172268.133978] SLOW spr round 9 (radius: 15) [07:07:48 -172268.133914] SLOW spr round 10 (radius: 20) [07:15:57 -172268.133913] SLOW spr round 11 (radius: 25) [07:25:19 -172268.133913] Model parameter optimization (eps = 0.100000) [07:25:25] [worker #0] ML tree search #16, logLikelihood: -172268.093405 [07:25:25 -660856.661051] Initial branch length optimization [07:25:35 -555452.064225] Model parameter optimization (eps = 10.000000) [07:27:01 -550899.086127] AUTODETECT spr round 1 (radius: 5) [07:27:25] [worker #2] ML tree search #18, logLikelihood: -172258.508438 [07:29:37 -389242.965367] AUTODETECT spr round 2 (radius: 10) [07:32:24 -284193.366035] AUTODETECT spr round 3 (radius: 15) [07:34:24] [worker #1] ML tree search #17, logLikelihood: -172264.294905 [07:35:33 -233724.272076] AUTODETECT spr round 4 (radius: 20) [07:39:06 -203992.018940] AUTODETECT spr round 5 (radius: 25) [07:44:17 -201604.682160] SPR radius for FAST iterations: 25 (autodetect) [07:44:17 -201604.682160] Model parameter optimization (eps = 3.000000) [07:44:47 -201089.861036] FAST spr round 1 (radius: 25) [07:47:52 -173453.968747] FAST spr round 2 (radius: 25) [07:50:11 -172494.991737] FAST spr round 3 (radius: 25) [07:52:17 -172324.810606] FAST spr round 4 (radius: 25) [07:54:01 -172320.077183] FAST spr round 5 (radius: 25) [07:55:41 -172318.914902] FAST spr round 6 (radius: 25) [07:57:19 -172318.914898] Model parameter optimization (eps = 1.000000) [07:57:33 -172314.176573] SLOW spr round 1 (radius: 5) [08:00:03 -172262.092082] SLOW spr round 2 (radius: 5) [08:02:28 -172260.763258] SLOW spr round 3 (radius: 5) [08:04:49 -172258.744754] SLOW spr round 4 (radius: 5) [08:07:04 -172258.744731] SLOW spr round 5 (radius: 10) [08:09:30 -172253.795235] SLOW spr round 6 (radius: 5) [08:12:28 -172253.795215] SLOW spr round 7 (radius: 10) [08:15:04 -172253.795214] SLOW spr round 8 (radius: 15) [08:18:59 -172253.795214] SLOW spr round 9 (radius: 20) [08:27:24 -172253.795214] SLOW spr round 10 (radius: 25) [08:35:40] [worker #1] ML tree search #20, logLikelihood: -172262.085791 [08:36:20 -172253.795213] Model parameter optimization (eps = 0.100000) [08:36:25] [worker #0] ML tree search #19, logLikelihood: -172253.746913 Optimized model parameters: Partition 0: noname Rate heterogeneity: FREE (4 cats, mean), weights&rates: (0.156414,0.417363) (0.154452,0.627300) (0.331650,0.741472) (0.357484,1.655798) 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: -172243.566374 AIC score: 347969.132748 / AICc score: 6413613.132748 / BIC score: 354961.262363 Free parameters (model + branch lengths): 1741 WARNING: Number of free parameters (K=1741) is larger than alignment size (n=410). 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/Q9HC97/3_mltree/Q9HC97.raxml.bestTree All ML trees saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q9HC97/3_mltree/Q9HC97.raxml.mlTrees Optimized model saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q9HC97/3_mltree/Q9HC97.raxml.bestModel Execution log saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q9HC97/3_mltree/Q9HC97.raxml.log Analysis started: 01-Jul-2021 06:28:57 / finished: 01-Jul-2021 15:05:23 Elapsed time: 30986.038 seconds Consumed energy: 2973.365 Wh (= 15 km in an electric car, or 74 km with an e-scooter!)