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 26-Jul-2021 00:26:15 as follows: raxml-ng --msa /truba/home/emrah/WORKFOLDER/PROD/250721_run/phylogeny-snakemake/results/O00268/2_msa/O00268_trimmed_msa.fasta --data-type AA --model LG4X --prefix /truba/home/emrah/WORKFOLDER/PROD/250721_run/phylogeny-snakemake/results/O00268/3_mltree/O00268 --seed 2 --threads 3 --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 (3 threads), thread pinning: OFF [00:00:00] Reading alignment from file: /truba/home/emrah/WORKFOLDER/PROD/250721_run/phylogeny-snakemake/results/O00268/2_msa/O00268_trimmed_msa.fasta [00:00:00] Loaded alignment with 369 taxa and 143 sites WARNING: Sequences tr_E1BXA9_E1BXA9_CHICK_9031 and tr_G1N132_G1N132_MELGA_9103 are exactly identical! WARNING: Sequences tr_E9QAP7_E9QAP7_MOUSE_10090 and tr_G3GWS2_G3GWS2_CRIGR_10029 are exactly identical! WARNING: Sequences tr_E9QAP7_E9QAP7_MOUSE_10090 and tr_A0A0G2K849_A0A0G2K849_RAT_10116 are exactly identical! WARNING: Sequences tr_E9QAP7_E9QAP7_MOUSE_10090 and tr_I3MNJ6_I3MNJ6_ICTTR_43179 are exactly identical! WARNING: Sequences tr_E9QAP7_E9QAP7_MOUSE_10090 and tr_A0A286XPV1_A0A286XPV1_CAVPO_10141 are exactly identical! WARNING: Sequences tr_E9QAP7_E9QAP7_MOUSE_10090 and tr_A0A1U8C8D2_A0A1U8C8D2_MESAU_10036 are exactly identical! WARNING: Sequences tr_M3Y855_M3Y855_MUSPF_9669 and tr_A0A2Y9INQ0_A0A2Y9INQ0_ENHLU_391180 are exactly identical! WARNING: Sequences sp_P47825_TAF4_DROME_7227 and tr_B4HJ19_B4HJ19_DROSE_7238 are exactly identical! WARNING: Sequences tr_G1S0P8_G1S0P8_NOMLE_61853 and tr_G3QI76_G3QI76_GORGO_9595 are exactly identical! WARNING: Sequences tr_G1S0P8_G1S0P8_NOMLE_61853 and tr_K7EU11_K7EU11_PONAB_9601 are exactly identical! WARNING: Sequences tr_G1S0P8_G1S0P8_NOMLE_61853 and tr_H2QKQ0_H2QKQ0_PANTR_9598 are exactly identical! WARNING: Sequences tr_G1S0P8_G1S0P8_NOMLE_61853 and tr_H2REF4_H2REF4_PANTR_9598 are exactly identical! WARNING: Sequences tr_G1S0P8_G1S0P8_NOMLE_61853 and sp_O00268_TAF4_HUMAN_9606 are exactly identical! WARNING: Sequences tr_G1S0P8_G1S0P8_NOMLE_61853 and tr_F7E5W7_F7E5W7_MACMU_9544 are exactly identical! WARNING: Sequences tr_G1S0P8_G1S0P8_NOMLE_61853 and tr_G7PFQ8_G7PFQ8_MACFA_9541 are exactly identical! WARNING: Sequences tr_G1S0P8_G1S0P8_NOMLE_61853 and tr_A0A096NND7_A0A096NND7_PAPAN_9555 are exactly identical! WARNING: Sequences tr_G1S0P8_G1S0P8_NOMLE_61853 and tr_A0A0D9RT44_A0A0D9RT44_CHLSB_60711 are exactly identical! WARNING: Sequences tr_G1S0P8_G1S0P8_NOMLE_61853 and tr_A0A2K5KIM2_A0A2K5KIM2_CERAT_9531 are exactly identical! WARNING: Sequences tr_G1S0P8_G1S0P8_NOMLE_61853 and tr_A0A2K6CLB0_A0A2K6CLB0_MACNE_9545 are exactly identical! WARNING: Sequences tr_G1S0P8_G1S0P8_NOMLE_61853 and tr_A0A2K6A491_A0A2K6A491_MANLE_9568 are exactly identical! WARNING: Sequences tr_G1S0P8_G1S0P8_NOMLE_61853 and tr_A0A2R9A2B2_A0A2R9A2B2_PANPA_9597 are exactly identical! WARNING: Sequences tr_G3QN01_G3QN01_GORGO_9595 and tr_H2NW33_H2NW33_PONAB_9601 are exactly identical! WARNING: Sequences tr_G3QN01_G3QN01_GORGO_9595 and tr_K7CTG6_K7CTG6_PANTR_9598 are exactly identical! WARNING: Sequences tr_G3QN01_G3QN01_GORGO_9595 and sp_Q92750_TAF4B_HUMAN_9606 are exactly identical! WARNING: Sequences tr_G3QN01_G3QN01_GORGO_9595 and tr_A0A2R9ASN4_A0A2R9ASN4_PANPA_9597 are exactly identical! WARNING: Sequences tr_Q29EN4_Q29EN4_DROPS_46245 and tr_B4H298_B4H298_DROPE_7234 are exactly identical! WARNING: Sequences tr_F1PV33_F1PV33_CANLF_9615 and tr_W5PZS8_W5PZS8_SHEEP_9940 are exactly identical! WARNING: Sequences tr_F1PV33_F1PV33_CANLF_9615 and tr_F1MNR6_F1MNR6_BOVIN_9913 are exactly identical! WARNING: Sequences tr_F1PV33_F1PV33_CANLF_9615 and tr_A0A1S2ZJM7_A0A1S2ZJM7_ERIEU_9365 are exactly identical! WARNING: Sequences tr_F1PV33_F1PV33_CANLF_9615 and tr_A0A1U7TT24_A0A1U7TT24_TARSY_1868482 are exactly identical! WARNING: Sequences tr_F1PV33_F1PV33_CANLF_9615 and tr_A0A2U4C1Z9_A0A2U4C1Z9_TURTR_9739 are exactly identical! WARNING: Sequences tr_F1PV33_F1PV33_CANLF_9615 and tr_A0A2U3WMI7_A0A2U3WMI7_ODORO_9708 are exactly identical! WARNING: Sequences tr_F1PV33_F1PV33_CANLF_9615 and tr_A0A2U3YLT4_A0A2U3YLT4_LEPWE_9713 are exactly identical! WARNING: Sequences tr_F1PV33_F1PV33_CANLF_9615 and tr_A0A2Y9RYJ8_A0A2Y9RYJ8_TRIMA_127582 are exactly identical! WARNING: Sequences tr_F1PV33_F1PV33_CANLF_9615 and tr_A0A2Y9QCE1_A0A2Y9QCE1_DELLE_9749 are exactly identical! WARNING: Sequences tr_F1PV33_F1PV33_CANLF_9615 and tr_A0A2Y9T3X6_A0A2Y9T3X6_PHYCD_9755 are exactly identical! WARNING: Sequences tr_F1PV33_F1PV33_CANLF_9615 and tr_A0A384BV44_A0A384BV44_URSMA_29073 are exactly identical! WARNING: Sequences tr_F1PV33_F1PV33_CANLF_9615 and tr_A0A384AE00_A0A384AE00_BALAS_310752 are exactly identical! WARNING: Sequences tr_F7DMG1_F7DMG1_MONDO_13616 and tr_G3WTA9_G3WTA9_SARHA_9305 are exactly identical! WARNING: Sequences tr_A0A087ZUI5_A0A087ZUI5_APIME_7460 and tr_A0A0L7QZ55_A0A0L7QZ55_9HYME_597456 are exactly identical! WARNING: Sequences tr_A0A087ZUI5_A0A087ZUI5_APIME_7460 and tr_A0A154P933_A0A154P933_9HYME_178035 are exactly identical! WARNING: Sequences tr_A0A087ZUI5_A0A087ZUI5_APIME_7460 and tr_A0A2A3ELP6_A0A2A3ELP6_APICC_94128 are exactly identical! WARNING: Sequences tr_A0A158NFF5_A0A158NFF5_ATTCE_12957 and tr_A0A151XFT8_A0A151XFT8_9HYME_64791 are exactly identical! WARNING: Sequences tr_A0A158NFF5_A0A158NFF5_ATTCE_12957 and tr_A0A195DAJ2_A0A195DAJ2_9HYME_471704 are exactly identical! WARNING: Sequences tr_A0A158NFF5_A0A158NFF5_ATTCE_12957 and tr_A0A195BDH4_A0A195BDH4_9HYME_520822 are exactly identical! WARNING: Sequences tr_A0A158NFF5_A0A158NFF5_ATTCE_12957 and tr_A0A195FQ29_A0A195FQ29_9HYME_34720 are exactly identical! WARNING: Sequences tr_F7FQ60_F7FQ60_MACMU_9544 and tr_A0A2I3N7J4_A0A2I3N7J4_PAPAN_9555 are exactly identical! WARNING: Sequences tr_F7FQ60_F7FQ60_MACMU_9544 and tr_A0A0D9RYZ6_A0A0D9RYZ6_CHLSB_60711 are exactly identical! WARNING: Sequences tr_F7FQ60_F7FQ60_MACMU_9544 and tr_A0A2K5LZP3_A0A2K5LZP3_CERAT_9531 are exactly identical! WARNING: Sequences tr_F7FQ60_F7FQ60_MACMU_9544 and tr_A0A2K6BLI8_A0A2K6BLI8_MACNE_9545 are exactly identical! WARNING: Sequences tr_F7FQ60_F7FQ60_MACMU_9544 and tr_A0A2K5YAC2_A0A2K5YAC2_MANLE_9568 are exactly identical! WARNING: Sequences tr_E5S6M8_E5S6M8_TRISP_6334 and tr_A0A0V0V5N9_A0A0V0V5N9_9BILA_181606 are exactly identical! WARNING: Sequences tr_H0ZC31_H0ZC31_TAEGU_59729 and tr_U3K7T8_U3K7T8_FICAL_59894 are exactly identical! WARNING: Sequences tr_H0ZC31_H0ZC31_TAEGU_59729 and tr_A0A093PF44_A0A093PF44_9PASS_328815 are exactly identical! WARNING: Sequences tr_H0ZC31_H0ZC31_TAEGU_59729 and tr_A0A218V0G3_A0A218V0G3_9PASE_299123 are exactly identical! WARNING: Sequences tr_H0ZGV6_H0ZGV6_TAEGU_59729 and tr_A0A218UIR4_A0A218UIR4_9PASE_299123 are exactly identical! WARNING: Sequences tr_Q0IJ02_Q0IJ02_XENTR_8364 and tr_A0A1L8ELM3_A0A1L8ELM3_XENLA_8355 are exactly identical! WARNING: Sequences tr_G1M6J9_G1M6J9_AILME_9646 and tr_A0A2U3ZRS7_A0A2U3ZRS7_ODORO_9708 are exactly identical! WARNING: Sequences tr_G1M6J9_G1M6J9_AILME_9646 and tr_A0A2U3YPI8_A0A2U3YPI8_LEPWE_9713 are exactly identical! WARNING: Sequences tr_G1M6J9_G1M6J9_AILME_9646 and tr_A0A2Y9IRX3_A0A2Y9IRX3_ENHLU_391180 are exactly identical! WARNING: Sequences tr_U3IP04_U3IP04_ANAPL_8839 and tr_A0A091JPC9_A0A091JPC9_EGRGA_188379 are exactly identical! WARNING: Sequences tr_U3IP04_U3IP04_ANAPL_8839 and tr_A0A091V3Y1_A0A091V3Y1_NIPNI_128390 are exactly identical! WARNING: Sequences tr_A0A087Y8J6_A0A087Y8J6_POEFO_48698 and tr_A0A096LXV3_A0A096LXV3_POEFO_48698 are exactly identical! WARNING: Sequences tr_A0A151N785_A0A151N785_ALLMI_8496 and tr_A0A3Q0GZV2_A0A3Q0GZV2_ALLSI_38654 are exactly identical! WARNING: Sequences tr_A0A151NYQ4_A0A151NYQ4_ALLMI_8496 and tr_A0A3Q0GWR6_A0A3Q0GWR6_ALLSI_38654 are exactly identical! WARNING: Sequences tr_A0A091FGA0_A0A091FGA0_CORBR_85066 and tr_A0A0A0A8S5_A0A0A0A8S5_CHAVO_50402 are exactly identical! WARNING: Sequences tr_A0A2I0M5W2_A0A2I0M5W2_COLLI_8932 and tr_A0A1V4KK83_A0A1V4KK83_PATFA_372326 are exactly identical! WARNING: Sequences tr_A0A2I0M7W7_A0A2I0M7W7_COLLI_8932 and tr_A0A1V4K0F2_A0A1V4K0F2_PATFA_372326 are exactly identical! WARNING: Sequences tr_A0A0V0SDU9_A0A0V0SDU9_9BILA_6336 and tr_A0A0V1CZB0_A0A0V1CZB0_TRIBR_45882 are exactly identical! WARNING: Sequences tr_A0A0V0SDU9_A0A0V0SDU9_9BILA_6336 and tr_A0A0V1AFY0_A0A0V1AFY0_9BILA_990121 are exactly identical! WARNING: Sequences tr_A0A1S3KR18_A0A1S3KR18_SALSA_8030 and tr_A0A060WDG2_A0A060WDG2_ONCMY_8022 are exactly identical! WARNING: Sequences tr_A0A1S3LCY7_A0A1S3LCY7_SALSA_8030 and tr_A0A1S3QWD2_A0A1S3QWD2_SALSA_8030 are exactly identical! WARNING: Sequences tr_A0A1S3LCY7_A0A1S3LCY7_SALSA_8030 and tr_A0A1S3QWR5_A0A1S3QWR5_SALSA_8030 are exactly identical! WARNING: Sequences tr_A0A2I4BE30_A0A2I4BE30_9TELE_52670 and tr_A0A2I4DA73_A0A2I4DA73_9TELE_52670 are exactly identical! WARNING: Sequences tr_A0A2D0PIH7_A0A2D0PIH7_ICTPU_7998 and tr_A0A2D0PK11_A0A2D0PK11_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0RI60_A0A2D0RI60_ICTPU_7998 and tr_A0A2D0RJ95_A0A2D0RJ95_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2Y9SDM4_A0A2Y9SDM4_PHYCD_9755 and tr_A0A384BDV7_A0A384BDV7_BALAS_310752 are exactly identical! WARNING: Duplicate sequences found: 77 NOTE: Reduced alignment (with duplicates and gap-only sites/taxa removed) NOTE: was saved to: /truba/home/emrah/WORKFOLDER/PROD/250721_run/phylogeny-snakemake/results/O00268/3_mltree/O00268.raxml.reduced.phy Alignment comprises 1 partitions and 143 patterns Partition 0: noname Model: LG4X+R4 Alignment sites / patterns: 143 / 143 Gaps: 5.00 % Invariant sites: 0.00 % NOTE: Binary MSA file created: /truba/home/emrah/WORKFOLDER/PROD/250721_run/phylogeny-snakemake/results/O00268/3_mltree/O00268.raxml.rba Parallelization scheme autoconfig: 3 worker(s) x 1 thread(s) Parallel reduction/worker buffer size: 1 KB / 0 KB [00:00:00] Generating 20 random starting tree(s) with 369 taxa [00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 143 / 11440 [00:00:00] Data distribution: max. searches per worker: 7 Starting ML tree search with 20 distinct starting trees [00:00:00 -62867.087665] Initial branch length optimization [00:00:01 -51758.700557] Model parameter optimization (eps = 10.000000) [00:00:24 -51488.142490] AUTODETECT spr round 1 (radius: 5) [00:01:00 -33689.832350] AUTODETECT spr round 2 (radius: 10) [00:01:45 -25966.988066] AUTODETECT spr round 3 (radius: 15) [00:02:45 -21952.706070] AUTODETECT spr round 4 (radius: 20) [00:03:49 -21303.460810] AUTODETECT spr round 5 (radius: 25) [00:04:59 -21284.238757] SPR radius for FAST iterations: 25 (autodetect) [00:04:59 -21284.238757] Model parameter optimization (eps = 3.000000) [00:05:16 -21235.783067] FAST spr round 1 (radius: 25) [00:05:59 -18929.123790] FAST spr round 2 (radius: 25) [00:06:36 -18735.520164] FAST spr round 3 (radius: 25) [00:07:08 -18724.896073] FAST spr round 4 (radius: 25) [00:07:38 -18724.895923] Model parameter optimization (eps = 1.000000) [00:07:51 -18719.953489] SLOW spr round 1 (radius: 5) [00:08:36 -18718.128172] SLOW spr round 2 (radius: 5) [00:09:23 -18717.748582] SLOW spr round 3 (radius: 5) [00:10:08 -18717.748449] SLOW spr round 4 (radius: 10) [00:10:52 -18717.748354] SLOW spr round 5 (radius: 15) [00:12:03 -18715.572480] SLOW spr round 6 (radius: 5) [00:13:10 -18714.692110] SLOW spr round 7 (radius: 5) [00:14:05 -18714.628342] SLOW spr round 8 (radius: 10) [00:14:54 -18714.464473] SLOW spr round 9 (radius: 5) [00:15:52 -18714.462421] SLOW spr round 10 (radius: 10) [00:16:42 -18714.462179] SLOW spr round 11 (radius: 15) [00:17:50 -18714.462145] SLOW spr round 12 (radius: 20) [00:19:25 -18714.462135] SLOW spr round 13 (radius: 25) [00:20:23] [worker #1] ML tree search #2, logLikelihood: -18712.652790 [00:21:04 -18714.462128] Model parameter optimization (eps = 0.100000) [00:21:08] [worker #0] ML tree search #1, logLikelihood: -18714.379083 [00:21:08 -63398.329324] Initial branch length optimization [00:21:10 -52381.177708] Model parameter optimization (eps = 10.000000) [00:21:33 -52123.126383] AUTODETECT spr round 1 (radius: 5) [00:22:10 -32976.204848] AUTODETECT spr round 2 (radius: 10) [00:22:55 -27066.796537] AUTODETECT spr round 3 (radius: 15) [00:23:47 -25483.923129] AUTODETECT spr round 4 (radius: 20) [00:24:44] [worker #2] ML tree search #3, logLikelihood: -18711.521575 [00:24:47 -22816.431279] AUTODETECT spr round 5 (radius: 25) [00:25:46 -22197.670712] SPR radius for FAST iterations: 25 (autodetect) [00:25:46 -22197.670712] Model parameter optimization (eps = 3.000000) [00:26:03 -22152.223743] FAST spr round 1 (radius: 25) [00:26:55 -18993.075680] FAST spr round 2 (radius: 25) [00:27:34 -18766.285144] FAST spr round 3 (radius: 25) [00:28:09 -18749.379802] FAST spr round 4 (radius: 25) [00:28:38 -18749.357396] Model parameter optimization (eps = 1.000000) [00:28:56 -18733.017951] SLOW spr round 1 (radius: 5) [00:29:40 -18727.374558] SLOW spr round 2 (radius: 5) [00:30:26 -18727.372923] SLOW spr round 3 (radius: 10) [00:31:12 -18727.372059] SLOW spr round 4 (radius: 15) [00:32:26 -18725.627753] SLOW spr round 5 (radius: 5) [00:33:32 -18725.626304] SLOW spr round 6 (radius: 10) [00:34:31 -18724.761653] SLOW spr round 7 (radius: 5) [00:35:28 -18724.760521] SLOW spr round 8 (radius: 10) [00:36:21 -18724.759947] SLOW spr round 9 (radius: 15) [00:37:17] [worker #1] ML tree search #5, logLikelihood: -18721.680566 [00:37:33 -18724.759428] SLOW spr round 10 (radius: 20) [00:39:11 -18722.920621] SLOW spr round 11 (radius: 5) [00:40:18 -18722.919957] SLOW spr round 12 (radius: 10) [00:41:18 -18722.919561] SLOW spr round 13 (radius: 15) [00:42:29 -18722.919216] SLOW spr round 14 (radius: 20) [00:44:06 -18722.918904] SLOW spr round 15 (radius: 25) [00:45:51 -18718.438467] SLOW spr round 16 (radius: 5) [00:47:01 -18718.284252] SLOW spr round 17 (radius: 5) [00:47:40] [worker #2] ML tree search #6, logLikelihood: -18711.755610 [00:47:56 -18718.283874] SLOW spr round 18 (radius: 10) [00:48:47 -18718.283659] SLOW spr round 19 (radius: 15) [00:50:00 -18718.283467] SLOW spr round 20 (radius: 20) [00:51:38 -18718.283292] SLOW spr round 21 (radius: 25) [00:53:23 -18718.283131] Model parameter optimization (eps = 0.100000) [00:53:39] [worker #0] ML tree search #4, logLikelihood: -18712.671701 [00:53:39 -62805.674986] Initial branch length optimization [00:53:41 -51696.678488] Model parameter optimization (eps = 10.000000) [00:54:07 -51423.458105] AUTODETECT spr round 1 (radius: 5) [00:54:43 -33593.548674] AUTODETECT spr round 2 (radius: 10) [00:55:28 -25305.303195] AUTODETECT spr round 3 (radius: 15) [00:56:21 -21376.388869] AUTODETECT spr round 4 (radius: 20) [00:57:21 -20840.572899] AUTODETECT spr round 5 (radius: 25) [00:57:52] [worker #1] ML tree search #8, logLikelihood: -18707.930807 [00:58:33 -20647.578825] SPR radius for FAST iterations: 25 (autodetect) [00:58:33 -20647.578825] Model parameter optimization (eps = 3.000000) [00:58:50 -20592.823706] FAST spr round 1 (radius: 25) [00:59:38 -18817.368458] FAST spr round 2 (radius: 25) [01:00:19 -18738.392699] FAST spr round 3 (radius: 25) [01:00:50 -18733.604609] FAST spr round 4 (radius: 25) [01:01:19 -18733.602100] Model parameter optimization (eps = 1.000000) [01:01:29 -18729.455879] SLOW spr round 1 (radius: 5) [01:02:16 -18722.950120] SLOW spr round 2 (radius: 5) [01:03:01 -18722.949748] SLOW spr round 3 (radius: 10) [01:03:46 -18722.057052] SLOW spr round 4 (radius: 5) [01:04:48 -18721.524358] SLOW spr round 5 (radius: 5) [01:05:40 -18721.524293] SLOW spr round 6 (radius: 10) [01:06:26 -18721.524278] SLOW spr round 7 (radius: 15) [01:07:35 -18721.524270] SLOW spr round 8 (radius: 20) [01:08:30] [worker #2] ML tree search #9, logLikelihood: -18703.737952 [01:09:06 -18719.548473] SLOW spr round 9 (radius: 5) [01:10:14 -18719.503094] SLOW spr round 10 (radius: 10) [01:11:11 -18719.502507] SLOW spr round 11 (radius: 15) [01:12:18 -18719.502204] SLOW spr round 12 (radius: 20) [01:13:49 -18719.502047] SLOW spr round 13 (radius: 25) [01:15:29 -18719.501966] Model parameter optimization (eps = 0.100000) [01:15:39] [worker #0] ML tree search #7, logLikelihood: -18718.861905 [01:15:39 -62911.674229] Initial branch length optimization [01:15:41 -51112.796306] Model parameter optimization (eps = 10.000000) [01:16:08 -50885.119580] AUTODETECT spr round 1 (radius: 5) [01:16:46 -33867.877803] AUTODETECT spr round 2 (radius: 10) [01:17:28 -25120.802831] AUTODETECT spr round 3 (radius: 15) [01:18:29 -21236.873808] AUTODETECT spr round 4 (radius: 20) [01:18:38] [worker #1] ML tree search #11, logLikelihood: -18705.773325 [01:19:54 -20979.362653] AUTODETECT spr round 5 (radius: 25) [01:21:27 -20921.903877] SPR radius for FAST iterations: 25 (autodetect) [01:21:28 -20921.903877] Model parameter optimization (eps = 3.000000) [01:21:49 -20856.843443] FAST spr round 1 (radius: 25) [01:22:39 -18841.531304] FAST spr round 2 (radius: 25) [01:23:20 -18768.061169] FAST spr round 3 (radius: 25) [01:23:54 -18752.313658] FAST spr round 4 (radius: 25) [01:24:24 -18750.011129] FAST spr round 5 (radius: 25) [01:24:53 -18749.521613] FAST spr round 6 (radius: 25) [01:25:22 -18749.521569] Model parameter optimization (eps = 1.000000) [01:25:36 -18739.638413] SLOW spr round 1 (radius: 5) [01:26:22 -18730.696924] SLOW spr round 2 (radius: 5) [01:27:09 -18727.943374] SLOW spr round 3 (radius: 5) [01:27:56 -18727.339386] SLOW spr round 4 (radius: 5) [01:28:41 -18723.739471] SLOW spr round 5 (radius: 5) [01:29:24 -18723.739461] SLOW spr round 6 (radius: 10) [01:30:09 -18723.739461] SLOW spr round 7 (radius: 15) [01:31:25 -18723.739461] SLOW spr round 8 (radius: 20) [01:33:02 -18723.694143] SLOW spr round 9 (radius: 25) [01:34:47 -18719.612007] SLOW spr round 10 (radius: 5) [01:35:14] [worker #2] ML tree search #12, logLikelihood: -18712.159469 [01:35:57 -18718.227774] SLOW spr round 11 (radius: 5) [01:36:52 -18718.067117] SLOW spr round 12 (radius: 5) [01:37:41 -18718.067034] SLOW spr round 13 (radius: 10) [01:38:27 -18717.941718] SLOW spr round 14 (radius: 5) [01:39:25 -18717.941635] SLOW spr round 15 (radius: 10) [01:40:16 -18717.941601] SLOW spr round 16 (radius: 15) [01:41:28 -18717.941584] SLOW spr round 17 (radius: 20) [01:43:06 -18717.941575] SLOW spr round 18 (radius: 25) [01:44:49 -18717.896058] Model parameter optimization (eps = 0.100000) [01:44:59] [worker #0] ML tree search #10, logLikelihood: -18717.295482 [01:44:59 -62645.909783] Initial branch length optimization [01:45:01 -51406.297648] Model parameter optimization (eps = 10.000000) [01:45:24 -51154.870927] AUTODETECT spr round 1 (radius: 5) [01:46:00 -33752.256717] AUTODETECT spr round 2 (radius: 10) [01:46:47 -27225.971229] AUTODETECT spr round 3 (radius: 15) [01:47:43 -23948.685208] AUTODETECT spr round 4 (radius: 20) [01:48:49 -22403.656547] AUTODETECT spr round 5 (radius: 25) [01:50:06 -22270.981298] SPR radius for FAST iterations: 25 (autodetect) [01:50:06 -22270.981298] Model parameter optimization (eps = 3.000000) [01:50:22 -22217.209909] FAST spr round 1 (radius: 25) [01:50:57] [worker #1] ML tree search #14, logLikelihood: -18705.644828 [01:51:11 -18961.317476] FAST spr round 2 (radius: 25) [01:51:48 -18730.609171] FAST spr round 3 (radius: 25) [01:52:21 -18723.202582] FAST spr round 4 (radius: 25) [01:52:50 -18722.741872] FAST spr round 5 (radius: 25) [01:53:18 -18722.741745] Model parameter optimization (eps = 1.000000) [01:53:30 -18715.304628] SLOW spr round 1 (radius: 5) [01:54:14 -18709.621940] SLOW spr round 2 (radius: 5) [01:54:53] [worker #2] ML tree search #15, logLikelihood: -18712.208500 [01:55:01 -18708.297354] SLOW spr round 3 (radius: 5) [01:55:45 -18708.297157] SLOW spr round 4 (radius: 10) [01:56:30 -18707.925326] SLOW spr round 5 (radius: 5) [01:57:30 -18707.925312] SLOW spr round 6 (radius: 10) [01:58:23 -18707.925312] SLOW spr round 7 (radius: 15) [01:59:32 -18707.925312] SLOW spr round 8 (radius: 20) [02:01:06 -18707.010784] SLOW spr round 9 (radius: 5) [02:02:14 -18706.317685] SLOW spr round 10 (radius: 5) [02:03:09 -18706.316959] SLOW spr round 11 (radius: 10) [02:03:59 -18706.047738] SLOW spr round 12 (radius: 5) [02:04:56 -18706.047585] SLOW spr round 13 (radius: 10) [02:05:47 -18706.047503] SLOW spr round 14 (radius: 15) [02:06:59 -18705.823064] SLOW spr round 15 (radius: 5) [02:08:04 -18705.817495] SLOW spr round 16 (radius: 10) [02:08:29] [worker #1] ML tree search #17, logLikelihood: -18706.920107 [02:09:01 -18705.816871] SLOW spr round 17 (radius: 15) [02:10:11 -18705.816788] SLOW spr round 18 (radius: 20) [02:10:27] [worker #2] ML tree search #18, logLikelihood: -18708.653577 [02:11:47 -18705.816768] SLOW spr round 19 (radius: 25) [02:13:27 -18705.816760] Model parameter optimization (eps = 0.100000) [02:13:38] [worker #0] ML tree search #13, logLikelihood: -18704.815882 [02:13:38 -63130.327687] Initial branch length optimization [02:13:39 -51821.581940] Model parameter optimization (eps = 10.000000) [02:14:00 -51209.312641] AUTODETECT spr round 1 (radius: 5) [02:14:37 -34295.094671] AUTODETECT spr round 2 (radius: 10) [02:15:21 -26248.442539] AUTODETECT spr round 3 (radius: 15) [02:16:22 -21744.540101] AUTODETECT spr round 4 (radius: 20) [02:17:30 -20795.093495] AUTODETECT spr round 5 (radius: 25) [02:18:48 -20641.470676] SPR radius for FAST iterations: 25 (autodetect) [02:18:48 -20641.470676] Model parameter optimization (eps = 3.000000) [02:19:04 -20591.965185] FAST spr round 1 (radius: 25) [02:19:53 -18882.630221] FAST spr round 2 (radius: 25) [02:20:31 -18762.449696] FAST spr round 3 (radius: 25) [02:21:04 -18728.198353] FAST spr round 4 (radius: 25) [02:21:35 -18725.846627] FAST spr round 5 (radius: 25) [02:22:03 -18725.845997] Model parameter optimization (eps = 1.000000) [02:22:14 -18721.562760] SLOW spr round 1 (radius: 5) [02:23:00 -18718.278879] SLOW spr round 2 (radius: 5) [02:23:46 -18718.226948] SLOW spr round 3 (radius: 10) [02:24:28 -18718.226730] SLOW spr round 4 (radius: 15) [02:25:36 -18718.226561] SLOW spr round 5 (radius: 20) [02:27:05 -18717.412409] SLOW spr round 6 (radius: 5) [02:28:11 -18716.829228] SLOW spr round 7 (radius: 5) [02:28:27] [worker #1] ML tree search #20, logLikelihood: -18714.206114 [02:29:05 -18716.826799] SLOW spr round 8 (radius: 10) [02:29:51 -18716.825197] SLOW spr round 9 (radius: 15) [02:30:56 -18716.824088] SLOW spr round 10 (radius: 20) [02:32:25 -18716.823315] SLOW spr round 11 (radius: 25) [02:34:05 -18716.562057] SLOW spr round 12 (radius: 5) [02:35:11 -18716.561596] SLOW spr round 13 (radius: 10) [02:36:06 -18716.561310] SLOW spr round 14 (radius: 15) [02:37:10 -18716.561098] SLOW spr round 15 (radius: 20) [02:38:40 -18716.560934] SLOW spr round 16 (radius: 25) [02:40:20 -18716.560803] Model parameter optimization (eps = 0.100000) [02:40:28] [worker #0] ML tree search #16, logLikelihood: -18716.418177 [02:40:28 -63063.022448] Initial branch length optimization [02:40:29 -52247.317597] Model parameter optimization (eps = 10.000000) [02:40:54 -51974.587099] AUTODETECT spr round 1 (radius: 5) [02:41:30 -33676.074139] AUTODETECT spr round 2 (radius: 10) [02:42:14 -28132.019209] AUTODETECT spr round 3 (radius: 15) [02:43:10 -25329.530606] AUTODETECT spr round 4 (radius: 20) [02:44:27 -22389.848162] AUTODETECT spr round 5 (radius: 25) [02:45:37 -22206.244851] SPR radius for FAST iterations: 25 (autodetect) [02:45:37 -22206.244851] Model parameter optimization (eps = 3.000000) [02:45:53 -22139.199160] FAST spr round 1 (radius: 25) [02:46:43 -18901.698269] FAST spr round 2 (radius: 25) [02:47:23 -18773.136715] FAST spr round 3 (radius: 25) [02:48:00 -18733.099541] FAST spr round 4 (radius: 25) [02:48:30 -18732.166149] FAST spr round 5 (radius: 25) [02:48:58 -18732.165922] Model parameter optimization (eps = 1.000000) [02:49:10 -18727.103702] SLOW spr round 1 (radius: 5) [02:49:56 -18722.527678] SLOW spr round 2 (radius: 5) [02:50:40 -18722.449534] SLOW spr round 3 (radius: 10) [02:51:25 -18721.341365] SLOW spr round 4 (radius: 5) [02:52:26 -18720.587726] SLOW spr round 5 (radius: 5) [02:53:18 -18720.587636] SLOW spr round 6 (radius: 10) [02:54:05 -18720.587571] SLOW spr round 7 (radius: 15) [02:55:13 -18720.587519] SLOW spr round 8 (radius: 20) [02:56:41 -18718.679670] SLOW spr round 9 (radius: 5) [02:57:49 -18718.679031] SLOW spr round 10 (radius: 10) [02:58:47 -18718.678852] SLOW spr round 11 (radius: 15) [02:59:53 -18718.678757] SLOW spr round 12 (radius: 20) [03:01:22 -18718.678697] SLOW spr round 13 (radius: 25) [03:02:57 -18718.102867] SLOW spr round 14 (radius: 5) [03:04:05 -18718.096780] SLOW spr round 15 (radius: 10) [03:05:04 -18718.096301] SLOW spr round 16 (radius: 15) [03:06:13 -18717.775243] SLOW spr round 17 (radius: 5) [03:07:18 -18717.773452] SLOW spr round 18 (radius: 10) [03:08:14 -18717.773244] SLOW spr round 19 (radius: 15) [03:09:20 -18717.773217] SLOW spr round 20 (radius: 20) [03:10:53 -18717.773211] SLOW spr round 21 (radius: 25) [03:12:30 -18717.773207] Model parameter optimization (eps = 0.100000) [03:12:40] [worker #0] ML tree search #19, logLikelihood: -18716.969358 Optimized model parameters: Partition 0: noname Rate heterogeneity: FREE (4 cats, mean), weights&rates: (0.234479,0.478719) (0.208818,1.158146) (0.427684,0.819012) (0.129018,2.291379) 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: -18703.737952 AIC score: 38889.475904 / AICc score: 1138533.475904 / BIC score: 41084.943775 Free parameters (model + branch lengths): 741 WARNING: Number of free parameters (K=741) is larger than alignment size (n=143). This might lead to overfitting and compromise tree inference results! WARNING: Best ML tree contains 123 near-zero branches! Best ML tree with collapsed near-zero branches saved to: /truba/home/emrah/WORKFOLDER/PROD/250721_run/phylogeny-snakemake/results/O00268/3_mltree/O00268.raxml.bestTreeCollapsed Best ML tree saved to: /truba/home/emrah/WORKFOLDER/PROD/250721_run/phylogeny-snakemake/results/O00268/3_mltree/O00268.raxml.bestTree All ML trees saved to: /truba/home/emrah/WORKFOLDER/PROD/250721_run/phylogeny-snakemake/results/O00268/3_mltree/O00268.raxml.mlTrees Optimized model saved to: /truba/home/emrah/WORKFOLDER/PROD/250721_run/phylogeny-snakemake/results/O00268/3_mltree/O00268.raxml.bestModel Execution log saved to: /truba/home/emrah/WORKFOLDER/PROD/250721_run/phylogeny-snakemake/results/O00268/3_mltree/O00268.raxml.log Analysis started: 26-Jul-2021 00:26:15 / finished: 26-Jul-2021 03:38:55 Elapsed time: 11560.533 seconds Consumed energy: 471.190 Wh (= 2 km in an electric car, or 12 km with an e-scooter!)