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) CPU E5-2690 v4 @ 2.60GHz, 28 cores, 251 GB RAM RAxML-NG was called at 03-Jun-2021 14:55:51 as follows: raxml-ng --msa /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q04656/2_msa/Q04656_trimmed_msa.fasta --data-type AA --model LG4X --prefix /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q04656/3_mltree/Q04656 --seed 2 --threads 9 --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 (9 threads), thread pinning: OFF [00:00:00] Reading alignment from file: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q04656/2_msa/Q04656_trimmed_msa.fasta [00:00:00] Loaded alignment with 1001 taxa and 862 sites WARNING: Sequences tr_J3KHC0_J3KHC0_COCIM_246410 and tr_A0A0J6Y1H6_A0A0J6Y1H6_COCIT_404692 are exactly identical! WARNING: Sequences tr_A0A179UD93_A0A179UD93_BLAGS_559298 and tr_C5GG88_C5GG88_AJEDR_559297 are exactly identical! WARNING: Sequences tr_K7CAA6_K7CAA6_PANTR_9598 and sp_Q04656_ATP7A_HUMAN_9606 are exactly identical! WARNING: Sequences tr_K7CAA6_K7CAA6_PANTR_9598 and tr_A0A2R9CJU6_A0A2R9CJU6_PANPA_9597 are exactly identical! WARNING: Sequences tr_B0WRZ5_B0WRZ5_CULQU_7176 and tr_B0XIQ4_B0XIQ4_CULQU_7176 are exactly identical! WARNING: Sequences tr_F9F4A0_F9F4A0_FUSOF_660025 and tr_N4UMC8_N4UMC8_FUSC1_1229664 are exactly identical! WARNING: Sequences tr_A0A158NHF2_A0A158NHF2_ATTCE_12957 and tr_A0A195AZD5_A0A195AZD5_9HYME_520822 are exactly identical! WARNING: Sequences tr_Q2UUF9_Q2UUF9_ASPOR_510516 and tr_A0A1S9D564_A0A1S9D564_ASPOZ_5062 are exactly identical! WARNING: Sequences tr_A0A0E0G3A4_A0A0E0G3A4_ORYNI_4536 and tr_B8ADR7_B8ADR7_ORYSI_39946 are exactly identical! WARNING: Sequences tr_A0A0E0G3A4_A0A0E0G3A4_ORYNI_4536 and tr_A0A0E0NB69_A0A0E0NB69_ORYRU_4529 are exactly identical! WARNING: Sequences tr_A0A0E0G3A4_A0A0E0G3A4_ORYNI_4536 and sp_Q6H7M3_HMA4_ORYSJ_39947 are exactly identical! WARNING: Sequences tr_A0A0E0H429_A0A0E0H429_ORYNI_4536 and tr_A2XWB0_A2XWB0_ORYSI_39946 are exactly identical! WARNING: Sequences tr_A0A0E0H429_A0A0E0H429_ORYNI_4536 and tr_A0A0E0PCG7_A0A0E0PCG7_ORYRU_4529 are exactly identical! WARNING: Sequences tr_A0A0E0H429_A0A0E0H429_ORYNI_4536 and tr_A0A0D9ZP08_A0A0D9ZP08_9ORYZ_40148 are exactly identical! WARNING: Sequences tr_A0A0E0H429_A0A0E0H429_ORYNI_4536 and sp_A3AWA4_HMA5_ORYSJ_39947 are exactly identical! WARNING: Sequences tr_A0A1D5Q7M3_A0A1D5Q7M3_MACMU_9544 and tr_A0A2K6A361_A0A2K6A361_MANLE_9568 are exactly identical! WARNING: Sequences tr_A0A1D5RHZ6_A0A1D5RHZ6_MACMU_9544 and tr_G7Q336_G7Q336_MACFA_9541 are exactly identical! WARNING: Sequences tr_A0A1D5RHZ6_A0A1D5RHZ6_MACMU_9544 and tr_A0A2K6AXX4_A0A2K6AXX4_MACNE_9545 are exactly identical! WARNING: Sequences tr_A0A2K1L6M2_A0A2K1L6M2_PHYPA_3218 and tr_A0A2K1L6P6_A0A2K1L6P6_PHYPA_3218 are exactly identical! WARNING: Sequences tr_I1PNR0_I1PNR0_ORYGL_4538 and tr_A0A0D3FYS3_A0A0D3FYS3_9ORYZ_65489 are exactly identical! WARNING: Sequences tr_G2YXH4_G2YXH4_BOTF4_999810 and tr_M7TRM6_M7TRM6_BOTF1_1290391 are exactly identical! WARNING: Sequences tr_V2XBC6_V2XBC6_MONRO_1381753 and tr_A0A0W0FZ55_A0A0W0FZ55_9AGAR_221103 are exactly identical! WARNING: Sequences tr_A0A044VA77_A0A044VA77_ONCVO_6282 and tr_A0A182E780_A0A182E780_ONCOC_42157 are exactly identical! WARNING: Sequences tr_A0A067FCX4_A0A067FCX4_CITSI_2711 and tr_A0A2H5P477_A0A2H5P477_CITUN_55188 are exactly identical! WARNING: Sequences tr_A0A078IK73_A0A078IK73_BRANA_3708 and tr_A0A0D3EAG3_A0A0D3EAG3_BRAOL_109376 are exactly identical! WARNING: Sequences tr_V4UCI6_V4UCI6_9ROSI_85681 and tr_A0A2H5P9M2_A0A2H5P9M2_CITUN_55188 are exactly identical! WARNING: Sequences tr_A0A0A1P9Y2_A0A0A1P9Y2_9FUNG_58291 and tr_A0A367KGL8_A0A367KGL8_9FUNG_86630 are exactly identical! WARNING: Sequences tr_A0A1S3ZDL9_A0A1S3ZDL9_TOBAC_4097 and tr_A0A1U7VWW7_A0A1U7VWW7_NICSY_4096 are exactly identical! WARNING: Sequences tr_A0A1L9NBR3_A0A1L9NBR3_ASPTU_767770 and tr_A0A317VVE1_A0A317VVE1_9EURO_1448314 are exactly identical! WARNING: Sequences tr_A0A251SP72_A0A251SP72_HELAN_4232 and tr_A0A251SPV7_A0A251SPV7_HELAN_4232 are exactly identical! WARNING: Sequences tr_A0A2G3A6B6_A0A2G3A6B6_CAPAN_4072 and tr_A0A2G3D3S9_A0A2G3D3S9_CAPCH_80379 are exactly identical! WARNING: Duplicate sequences found: 31 NOTE: Reduced alignment (with duplicates and gap-only sites/taxa removed) NOTE: was saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q04656/3_mltree/Q04656.raxml.reduced.phy Alignment comprises 1 partitions and 861 patterns Partition 0: noname Model: LG4X+R4 Alignment sites / patterns: 862 / 861 Gaps: 2.27 % Invariant sites: 1.86 % NOTE: Binary MSA file created: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q04656/3_mltree/Q04656.raxml.rba Parallelization scheme autoconfig: 3 worker(s) x 3 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 / 287 / 22960 [00:00:00] Data distribution: max. searches per worker: 7 Starting ML tree search with 20 distinct starting trees [00:00:00 -1351494.488234] Initial branch length optimization [00:00:12 -1162963.571093] Model parameter optimization (eps = 10.000000) [00:01:31 -1161305.472918] AUTODETECT spr round 1 (radius: 5) [00:06:20 -778443.427956] AUTODETECT spr round 2 (radius: 10) [00:11:30 -581169.148125] AUTODETECT spr round 3 (radius: 15) [00:16:58 -485964.046366] AUTODETECT spr round 4 (radius: 20) 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) CPU E5-2690 v4 @ 2.60GHz, 28 cores, 251 GB RAM RAxML-NG was called at 03-Jun-2021 15:19:29 as follows: raxml-ng --msa /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q04656/2_msa/Q04656_trimmed_msa.fasta --data-type AA --model LG4X --prefix /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q04656/3_mltree/Q04656 --seed 2 --threads 9 --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 (9 threads), thread pinning: OFF WARNING: The model you specified on the command line (LG4X) will be ignored since the binary MSA file already contains a model definition. If you want to change the model, please re-run RAxML-NG with the original PHYLIP/FASTA alignment and --redo option. [00:00:00] Loading binary alignment from file: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q04656/3_mltree/Q04656.raxml.rba [00:00:00] Alignment comprises 1001 taxa, 1 partitions and 861 patterns Partition 0: noname Model: LG4X+R4 Alignment sites / patterns: 862 / 861 Gaps: 2.27 % Invariant sites: 1.86 % Parallelization scheme autoconfig: 3 worker(s) x 3 thread(s) Parallel reduction/worker buffer size: 1 KB / 0 KB [00:00:00] NOTE: Resuming execution from checkpoint (logLH: -485964.05, ML trees: 0, bootstraps: 0) [00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 287 / 22960 [00:00:00] Data distribution: max. searches per worker: 7 ERROR: CPU core oversubscription detected! RAxML-NG will terminate now to avoid wasting resources. NOTE: Details: https://github.com/amkozlov/raxml-ng/wiki/Parallelization#core-oversubscription NOTE: You can use '--force perf_threads' to disable this check, but ONLY if you are 200% sure this is a false alarm! 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 6258R CPU @ 2.70GHz, 56 cores, 187 GB RAM RAxML-NG was called at 04-Jun-2021 03:53:17 as follows: raxml-ng --msa /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q04656/2_msa/Q04656_trimmed_msa.fasta --data-type AA --model LG4X --prefix /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q04656/3_mltree/Q04656 --seed 2 --threads 9 --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 (9 threads), thread pinning: OFF WARNING: The model you specified on the command line (LG4X) will be ignored since the binary MSA file already contains a model definition. If you want to change the model, please re-run RAxML-NG with the original PHYLIP/FASTA alignment and --redo option. [00:00:00] Loading binary alignment from file: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q04656/3_mltree/Q04656.raxml.rba [00:00:00] Alignment comprises 1001 taxa, 1 partitions and 861 patterns Partition 0: noname Model: LG4X+R4 Alignment sites / patterns: 862 / 861 Gaps: 2.27 % Invariant sites: 1.86 % Parallelization scheme autoconfig: 3 worker(s) x 3 thread(s) Parallel reduction/worker buffer size: 1 KB / 0 KB [00:00:00] NOTE: Resuming execution from checkpoint (logLH: -485964.05, ML trees: 0, bootstraps: 0) [00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 287 / 22960 [00:00:00] Data distribution: max. searches per worker: 7 Starting ML tree search with 20 distinct starting trees [00:00:00 -485964.046366] AUTODETECT spr round 4 (radius: 20) [00:05:46 -439035.934281] AUTODETECT spr round 5 (radius: 25) [00:12:36 -427256.531866] SPR radius for FAST iterations: 25 (autodetect) [00:12:36 -427256.531866] Model parameter optimization (eps = 3.000000) [00:12:51 -427246.051382] FAST spr round 1 (radius: 25) [00:17:48 -349667.827925] FAST spr round 2 (radius: 25) [00:21:28 -346327.017168] FAST spr round 3 (radius: 25) [00:24:42 -346216.526204] FAST spr round 4 (radius: 25) [00:27:19 -346215.200736] FAST spr round 5 (radius: 25) [00:29:53 -346215.200717] Model parameter optimization (eps = 1.000000) [00:30:19 -346057.724517] SLOW spr round 1 (radius: 5) [00:34:21 -345947.700568] SLOW spr round 2 (radius: 5) [00:38:10 -345937.409710] SLOW spr round 3 (radius: 5) [00:41:42 -345936.773210] SLOW spr round 4 (radius: 5) [00:45:08 -345936.773178] SLOW spr round 5 (radius: 10) [00:48:47 -345936.773178] SLOW spr round 6 (radius: 15) [00:54:46 -345936.773178] SLOW spr round 7 (radius: 20) [01:03:27 -345936.773178] SLOW spr round 8 (radius: 25) [01:13:48 -345936.773178] Model parameter optimization (eps = 0.100000) [01:14:00] [worker #0] ML tree search #1, logLikelihood: -345936.544663 [01:14:01 -1350558.759405] Initial branch length optimization [01:14:11 -1163495.104190] Model parameter optimization (eps = 10.000000) [01:15:21 -1161649.781154] AUTODETECT spr round 1 (radius: 5) [01:19:40 -786018.501479] AUTODETECT spr round 2 (radius: 10) [01:20:43] [worker #2] ML tree search #3, logLikelihood: -345940.493542 [01:24:24 -590626.224255] AUTODETECT spr round 3 (radius: 15) [01:29:26 -507574.170506] AUTODETECT spr round 4 (radius: 20) [01:34:52 -423608.492125] AUTODETECT spr round 5 (radius: 25) [01:40:29 -414903.111333] SPR radius for FAST iterations: 25 (autodetect) [01:40:29 -414903.111333] Model parameter optimization (eps = 3.000000) [01:41:01 -414654.060168] FAST spr round 1 (radius: 25) [01:45:35 -348389.261767] FAST spr round 2 (radius: 25) [01:48:55 -346186.596039] FAST spr round 3 (radius: 25) [01:50:06] [worker #1] ML tree search #2, logLikelihood: -345920.195478 [01:51:53 -346082.272425] FAST spr round 4 (radius: 25) [01:54:35 -346061.687778] FAST spr round 5 (radius: 25) [01:57:09 -346048.899046] FAST spr round 6 (radius: 25) [01:59:34 -346048.899027] Model parameter optimization (eps = 1.000000) [01:59:54 -346024.421415] SLOW spr round 1 (radius: 5) [02:03:47 -345924.820691] SLOW spr round 2 (radius: 5) [02:07:21 -345920.944525] SLOW spr round 3 (radius: 5) [02:10:47 -345920.944333] SLOW spr round 4 (radius: 10) [02:14:20 -345920.944333] SLOW spr round 5 (radius: 15) [02:20:15 -345920.944333] SLOW spr round 6 (radius: 20) [02:28:54 -345920.944333] SLOW spr round 7 (radius: 25) [02:39:08 -345920.944333] Model parameter optimization (eps = 0.100000) [02:39:16] [worker #0] ML tree search #4, logLikelihood: -345920.887996 [02:39:16 -1354464.319510] Initial branch length optimization [02:39:26 -1160952.999091] Model parameter optimization (eps = 10.000000) [02:40:25 -1159420.597968] AUTODETECT spr round 1 (radius: 5) [02:44:37 -771205.043407] AUTODETECT spr round 2 (radius: 10) [02:49:14 -548163.910131] AUTODETECT spr round 3 (radius: 15) [02:50:34] [worker #2] ML tree search #6, logLikelihood: -345931.219052 [02:54:25 -448624.641126] AUTODETECT spr round 4 (radius: 20) [02:59:45 -424240.819878] AUTODETECT spr round 5 (radius: 25) [03:06:13 -419576.982848] SPR radius for FAST iterations: 25 (autodetect) [03:06:13 -419576.982848] Model parameter optimization (eps = 3.000000) [03:06:26 -419572.732400] FAST spr round 1 (radius: 25) [03:11:22 -349798.565008] FAST spr round 2 (radius: 25) [03:14:45 -346307.700114] FAST spr round 3 (radius: 25) [03:17:42 -346226.866225] FAST spr round 4 (radius: 25) [03:20:16 -346220.415658] FAST spr round 5 (radius: 25) [03:22:41 -346220.415547] Model parameter optimization (eps = 1.000000) [03:23:05 -346008.492312] SLOW spr round 1 (radius: 5) [03:26:58 -345934.773936] SLOW spr round 2 (radius: 5) [03:30:30 -345932.528326] SLOW spr round 3 (radius: 5) [03:32:53] [worker #1] ML tree search #5, logLikelihood: -345936.605623 [03:33:57 -345931.896852] SLOW spr round 4 (radius: 5) [03:37:21 -345931.896821] SLOW spr round 5 (radius: 10) [03:40:56 -345931.896819] SLOW spr round 6 (radius: 15) [03:47:00 -345931.896819] SLOW spr round 7 (radius: 20) [03:56:04 -345931.896819] SLOW spr round 8 (radius: 25) [04:06:45 -345931.896819] Model parameter optimization (eps = 0.100000) [04:07:00] [worker #0] ML tree search #7, logLikelihood: -345931.636638 [04:07:00 -1360884.247454] Initial branch length optimization [04:07:14 -1168229.280424] Model parameter optimization (eps = 10.000000) [04:08:17 -1166758.107892] AUTODETECT spr round 1 (radius: 5) [04:12:29 -766911.436183] AUTODETECT spr round 2 (radius: 10) [04:17:05 -586378.968046] AUTODETECT spr round 3 (radius: 15) [04:21:53 -509614.296001] AUTODETECT spr round 4 (radius: 20) [04:27:24 -439648.776763] AUTODETECT spr round 5 (radius: 25) [04:33:09 -424237.305789] SPR radius for FAST iterations: 25 (autodetect) [04:33:09 -424237.305789] Model parameter optimization (eps = 3.000000) [04:33:39 -424036.804941] FAST spr round 1 (radius: 25) [04:35:14] [worker #2] ML tree search #9, logLikelihood: -345922.700510 [04:38:21 -348333.776788] FAST spr round 2 (radius: 25) [04:41:38 -346126.414098] FAST spr round 3 (radius: 25) [04:44:24 -346078.058682] FAST spr round 4 (radius: 25) [04:46:52 -346078.058601] Model parameter optimization (eps = 1.000000) [04:47:13 -346044.927217] SLOW spr round 1 (radius: 5) [04:51:06 -345944.725645] SLOW spr round 2 (radius: 5) [04:54:48 -345930.875986] SLOW spr round 3 (radius: 5) [04:58:15 -345927.239409] SLOW spr round 4 (radius: 5) [05:01:35 -345927.239256] SLOW spr round 5 (radius: 10) [05:02:04] [worker #1] ML tree search #8, logLikelihood: -345929.061006 [05:05:08 -345927.239243] SLOW spr round 6 (radius: 15) [05:11:00 -345927.239242] SLOW spr round 7 (radius: 20) [05:19:36 -345927.239242] SLOW spr round 8 (radius: 25) [05:29:56 -345927.239242] Model parameter optimization (eps = 0.100000) [05:30:08] [worker #0] ML tree search #10, logLikelihood: -345927.116746 [05:30:08 -1356909.146279] Initial branch length optimization [05:30:23 -1166860.657423] Model parameter optimization (eps = 10.000000) [05:31:27 -1165269.979289] AUTODETECT spr round 1 (radius: 5) [05:35:44 -759876.560977] AUTODETECT spr round 2 (radius: 10) [05:40:32 -554710.109871] AUTODETECT spr round 3 (radius: 15) [05:45:33 -431928.259921] AUTODETECT spr round 4 (radius: 20) [05:50:43 -400207.089082] AUTODETECT spr round 5 (radius: 25) [05:57:08 -398991.747363] SPR radius for FAST iterations: 25 (autodetect) [05:57:08 -398991.747363] Model parameter optimization (eps = 3.000000) [05:57:18] [worker #2] ML tree search #12, logLikelihood: -345926.567856 [05:57:34 -398811.576230] FAST spr round 1 (radius: 25) [06:01:52 -347742.018701] FAST spr round 2 (radius: 25) [06:05:13 -346209.231474] FAST spr round 3 (radius: 25) [06:08:16 -346096.291052] FAST spr round 4 (radius: 25) [06:11:02 -346049.729333] FAST spr round 5 (radius: 25) [06:13:33 -346044.552258] FAST spr round 6 (radius: 25) [06:16:00 -346036.472822] FAST spr round 7 (radius: 25) [06:18:23 -346036.472813] Model parameter optimization (eps = 1.000000) [06:18:44 -346024.921498] SLOW spr round 1 (radius: 5) [06:22:42 -345929.211502] SLOW spr round 2 (radius: 5) [06:26:18 -345926.236101] SLOW spr round 3 (radius: 5) [06:27:01] [worker #1] ML tree search #11, logLikelihood: -345926.308989 [06:29:45 -345926.235972] SLOW spr round 4 (radius: 10) [06:33:24 -345926.235971] SLOW spr round 5 (radius: 15) [06:39:35 -345926.235971] SLOW spr round 6 (radius: 20) [06:48:25 -345926.235971] SLOW spr round 7 (radius: 25) [06:58:55 -345926.235971] Model parameter optimization (eps = 0.100000) [06:59:04] [worker #0] ML tree search #13, logLikelihood: -345926.142800 [06:59:04 -1352764.204617] Initial branch length optimization [06:59:19 -1162788.273649] Model parameter optimization (eps = 10.000000) [07:00:16 -1160948.942197] AUTODETECT spr round 1 (radius: 5) [07:04:28 -757757.240000] AUTODETECT spr round 2 (radius: 10) [07:09:01 -520867.728124] AUTODETECT spr round 3 (radius: 15) [07:13:36 -450020.694926] AUTODETECT spr round 4 (radius: 20) [07:20:07 -414265.290411] AUTODETECT spr round 5 (radius: 25) [07:26:35] [worker #2] ML tree search #15, logLikelihood: -345924.486336 [07:28:55 -401994.171315] SPR radius for FAST iterations: 25 (autodetect) [07:28:55 -401994.171315] Model parameter optimization (eps = 3.000000) [07:29:07 -401986.201064] FAST spr round 1 (radius: 25) [07:33:52 -349235.753963] FAST spr round 2 (radius: 25) [07:37:23 -346353.254863] FAST spr round 3 (radius: 25) [07:40:32 -346242.767010] FAST spr round 4 (radius: 25) [07:43:05 -346242.766941] Model parameter optimization (eps = 1.000000) [07:43:31 -346047.757366] SLOW spr round 1 (radius: 5) [07:47:48 -345938.823767] SLOW spr round 2 (radius: 5) [07:51:32 -345928.503985] SLOW spr round 3 (radius: 5) [07:55:01 -345927.735096] SLOW spr round 4 (radius: 5) [07:55:31] [worker #1] ML tree search #14, logLikelihood: -345930.805836 [07:58:29 -345927.735087] SLOW spr round 5 (radius: 10) [08:02:08 -345927.581857] SLOW spr round 6 (radius: 5) [08:06:45 -345925.980439] SLOW spr round 7 (radius: 5) [08:10:42 -345925.980439] SLOW spr round 8 (radius: 10) [08:14:31 -345925.980439] SLOW spr round 9 (radius: 15) [08:20:21 -345925.980439] SLOW spr round 10 (radius: 20) [08:29:30 -345925.980439] SLOW spr round 11 (radius: 25) [08:40:13 -345925.980439] Model parameter optimization (eps = 0.100000) [08:40:24] [worker #0] ML tree search #16, logLikelihood: -345925.781130 [08:40:25 -1353537.907810] Initial branch length optimization [08:40:36 -1162731.065463] Model parameter optimization (eps = 10.000000) [08:41:51 -1161368.156329] AUTODETECT spr round 1 (radius: 5) [08:46:15 -762707.815957] AUTODETECT spr round 2 (radius: 10) [08:50:52 -554325.018464] AUTODETECT spr round 3 (radius: 15) [08:51:53] [worker #2] ML tree search #18, logLikelihood: -345923.968891 [08:55:43 -489813.239038] AUTODETECT spr round 4 (radius: 20) [09:01:05 -447818.094367] AUTODETECT spr round 5 (radius: 25) [09:07:13 -423464.684331] SPR radius for FAST iterations: 25 (autodetect) [09:07:13 -423464.684331] Model parameter optimization (eps = 3.000000) [09:07:42 -423333.856688] FAST spr round 1 (radius: 25) [09:12:16 -350393.658123] FAST spr round 2 (radius: 25) [09:15:37 -346282.576937] FAST spr round 3 (radius: 25) [09:18:41 -346044.142364] FAST spr round 4 (radius: 25) [09:21:14 -346019.462828] FAST spr round 5 (radius: 25) [09:23:04] [worker #1] ML tree search #17, logLikelihood: -345921.458958 [09:23:40 -346019.462800] Model parameter optimization (eps = 1.000000) [09:24:09 -346000.000729] SLOW spr round 1 (radius: 5) [09:28:09 -345933.178987] SLOW spr round 2 (radius: 5) [09:31:42 -345930.007714] SLOW spr round 3 (radius: 5) [09:35:10 -345922.059614] SLOW spr round 4 (radius: 5) [09:38:32 -345922.059599] SLOW spr round 5 (radius: 10) [09:42:06 -345922.059598] SLOW spr round 6 (radius: 15) [09:48:02 -345922.059598] SLOW spr round 7 (radius: 20) [09:56:40 -345922.059598] SLOW spr round 8 (radius: 25) [10:06:46 -345922.059598] Model parameter optimization (eps = 0.100000) [10:07:07] [worker #0] ML tree search #19, logLikelihood: -345921.860809 [11:07:34] [worker #1] ML tree search #20, logLikelihood: -345924.068275 Optimized model parameters: Partition 0: noname Rate heterogeneity: FREE (4 cats, mean), weights&rates: (0.253656,0.279833) (0.295374,0.439785) (0.319017,1.357206) (0.131953,2.774817) 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: -345920.195478 AIC score: 695850.390957 / AICc score: 8739910.390957 / BIC score: 705392.697774 Free parameters (model + branch lengths): 2005 WARNING: Number of free parameters (K=2005) is larger than alignment size (n=862). This might lead to overfitting and compromise tree inference results! WARNING: Best ML tree contains 33 near-zero branches! Best ML tree with collapsed near-zero branches saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q04656/3_mltree/Q04656.raxml.bestTreeCollapsed Best ML tree saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q04656/3_mltree/Q04656.raxml.bestTree All ML trees saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q04656/3_mltree/Q04656.raxml.mlTrees Optimized model saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q04656/3_mltree/Q04656.raxml.bestModel Execution log saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q04656/3_mltree/Q04656.raxml.log Analysis started: 04-Jun-2021 03:53:17 / finished: 04-Jun-2021 15:00:51 Elapsed time: 40054.890 seconds (this run) / 41073.450 seconds (total with restarts) Consumed energy: 3804.916 Wh (= 19 km in an electric car, or 95 km with an e-scooter!)