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 03-Jul-2021 07:53:03 as follows: raxml-ng --msa /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q9Y5H6/2_msa/Q9Y5H6_trimmed_msa.fasta --data-type AA --model LG4X --prefix /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q9Y5H6/3_mltree/Q9Y5H6 --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/Q9Y5H6/2_msa/Q9Y5H6_trimmed_msa.fasta [00:00:00] Loaded alignment with 1001 taxa and 403 sites WARNING: Sequences tr_A0A0J9YJK6_A0A0J9YJK6_DANRE_7955 and tr_A0A2R8Q015_A0A2R8Q015_DANRE_7955 are exactly identical! WARNING: Sequences tr_A0A0N4SUG2_A0A0N4SUG2_DANRE_7955 and tr_A0A2R8QMY8_A0A2R8QMY8_DANRE_7955 are exactly identical! WARNING: Sequences tr_A0A0R4I9U6_A0A0R4I9U6_DANRE_7955 and tr_A0A0R4IMS0_A0A0R4IMS0_DANRE_7955 are exactly identical! WARNING: Sequences tr_A0A286Y8Q2_A0A286Y8Q2_DANRE_7955 and tr_A0A2R8RIS9_A0A2R8RIS9_DANRE_7955 are exactly identical! WARNING: Sequences tr_A0A2R8QGH0_A0A2R8QGH0_DANRE_7955 and tr_A0A2R8RQG5_A0A2R8RQG5_DANRE_7955 are exactly identical! WARNING: Sequences tr_E9PXQ7_E9PXQ7_MOUSE_10090 and tr_A0A1U7QCW6_A0A1U7QCW6_MESAU_10036 are exactly identical! WARNING: Sequences tr_M3Z0Y2_M3Z0Y2_MUSPF_9669 and tr_F6UP12_F6UP12_CANLF_9615 are exactly identical! WARNING: Sequences tr_M3Z0Y2_M3Z0Y2_MUSPF_9669 and tr_M3WRR5_M3WRR5_FELCA_9685 are exactly identical! WARNING: Sequences tr_M3Z0Y2_M3Z0Y2_MUSPF_9669 and tr_A0A2U3ZGF8_A0A2U3ZGF8_ODORO_9708 are exactly identical! WARNING: Sequences tr_M3Z0Y2_M3Z0Y2_MUSPF_9669 and tr_A0A2U3X6Y0_A0A2U3X6Y0_LEPWE_9713 are exactly identical! WARNING: Sequences tr_M3Z0Y2_M3Z0Y2_MUSPF_9669 and tr_A0A2Y9JLK1_A0A2Y9JLK1_ENHLU_391180 are exactly identical! WARNING: Sequences tr_G3QEF9_G3QEF9_GORGO_9595 and tr_F7GRQ8_F7GRQ8_MACMU_9544 are exactly identical! WARNING: Sequences tr_G3QEF9_G3QEF9_GORGO_9595 and tr_G7P8H9_G7P8H9_MACFA_9541 are exactly identical! WARNING: Sequences tr_G3QEF9_G3QEF9_GORGO_9595 and tr_A0A096N740_A0A096N740_PAPAN_9555 are exactly identical! WARNING: Sequences tr_G3QEF9_G3QEF9_GORGO_9595 and tr_A0A2K6DA37_A0A2K6DA37_MACNE_9545 are exactly identical! WARNING: Sequences tr_G3QEF9_G3QEF9_GORGO_9595 and tr_A0A2K5XAY4_A0A2K5XAY4_MANLE_9568 are exactly identical! WARNING: Sequences tr_G3S7B8_G3S7B8_GORGO_9595 and tr_H2PEB5_H2PEB5_PONAB_9601 are exactly identical! WARNING: Sequences tr_G3S7B8_G3S7B8_GORGO_9595 and tr_H2QQ62_H2QQ62_PANTR_9598 are exactly identical! WARNING: Sequences tr_G3S7B8_G3S7B8_GORGO_9595 and sp_Q9P2E7_PCD10_HUMAN_9606 are exactly identical! WARNING: Sequences tr_G3S7B8_G3S7B8_GORGO_9595 and tr_F7HQ33_F7HQ33_MACMU_9544 are exactly identical! WARNING: Sequences tr_G3S7B8_G3S7B8_GORGO_9595 and tr_A0A2R8M9N1_A0A2R8M9N1_CALJA_9483 are exactly identical! WARNING: Sequences tr_G3S7B8_G3S7B8_GORGO_9595 and tr_A0A2I3N6E1_A0A2I3N6E1_PAPAN_9555 are exactly identical! WARNING: Sequences tr_G3S7B8_G3S7B8_GORGO_9595 and tr_A0A0D9S0V7_A0A0D9S0V7_CHLSB_60711 are exactly identical! WARNING: Sequences tr_G3S7B8_G3S7B8_GORGO_9595 and tr_A0A2K5P019_A0A2K5P019_CERAT_9531 are exactly identical! WARNING: Sequences tr_G3S7B8_G3S7B8_GORGO_9595 and tr_A0A2K6AT55_A0A2K6AT55_MACNE_9545 are exactly identical! WARNING: Sequences tr_G3S7B8_G3S7B8_GORGO_9595 and tr_A0A2K5XFB2_A0A2K5XFB2_MANLE_9568 are exactly identical! WARNING: Sequences tr_H2QRN1_H2QRN1_PANTR_9598 and sp_Q5DRE1_PCDC2_PANTR_9598 are exactly identical! WARNING: Sequences tr_H2QRN1_H2QRN1_PANTR_9598 and sp_Q9Y5I4_PCDC2_HUMAN_9606 are exactly identical! WARNING: Sequences tr_H2QRN1_H2QRN1_PANTR_9598 and tr_A0A2R8ZNN9_A0A2R8ZNN9_PANPA_9597 are exactly identical! WARNING: Sequences tr_H2RAR2_H2RAR2_PANTR_9598 and sp_Q5DRB6_PCDG4_PANTR_9598 are exactly identical! WARNING: Sequences sp_Q5DRA3_PCDGL_PANTR_9598 and sp_Q9Y5F7_PCDGL_HUMAN_9606 are exactly identical! WARNING: Sequences sp_Q5DRB9_PCDGC_PANTR_9598 and sp_O60330_PCDGC_HUMAN_9606 are exactly identical! WARNING: Sequences tr_I3KX74_I3KX74_ORENI_8128 and tr_I3KZV5_I3KZV5_ORENI_8128 are exactly identical! WARNING: Sequences tr_A0A3B5K0Q4_A0A3B5K0Q4_TAKRU_31033 and tr_A0A3B5KC27_A0A3B5KC27_TAKRU_31033 are exactly identical! WARNING: Sequences tr_A0A286Y4F6_A0A286Y4F6_CAVPO_10141 and tr_G5BK54_G5BK54_HETGA_10181 are exactly identical! WARNING: Sequences tr_G1LW53_G1LW53_AILME_9646 and tr_A0A384C654_A0A384C654_URSMA_29073 are exactly identical! WARNING: Sequences tr_F1N2W7_F1N2W7_BOVIN_9913 and tr_A0A383ZC11_A0A383ZC11_BALAS_310752 are exactly identical! WARNING: Sequences tr_A0A2I3MIB5_A0A2I3MIB5_PAPAN_9555 and tr_A0A2K6BF17_A0A2K6BF17_MACNE_9545 are exactly identical! WARNING: Sequences tr_A0A1S3LRQ0_A0A1S3LRQ0_SALSA_8030 and tr_A0A1S3QMG3_A0A1S3QMG3_SALSA_8030 are exactly identical! WARNING: Sequences tr_A0A1S3LRZ0_A0A1S3LRZ0_SALSA_8030 and tr_A0A1S3QMQ4_A0A1S3QMQ4_SALSA_8030 are exactly identical! WARNING: Sequences tr_A0A1S3QSW8_A0A1S3QSW8_SALSA_8030 and tr_A0A1S3RIP7_A0A1S3RIP7_SALSA_8030 are exactly identical! WARNING: Sequences tr_A0A1S3QSW8_A0A1S3QSW8_SALSA_8030 and tr_A0A1S3RJP7_A0A1S3RJP7_SALSA_8030 are exactly identical! WARNING: Sequences tr_A0A1S3RRM6_A0A1S3RRM6_SALSA_8030 and tr_A0A1S3RST3_A0A1S3RST3_SALSA_8030 are exactly identical! WARNING: Sequences tr_A0A1S3RT49_A0A1S3RT49_SALSA_8030 and tr_A0A1S3STD0_A0A1S3STD0_SALSA_8030 are exactly identical! WARNING: Sequences tr_A0A1S3RT49_A0A1S3RT49_SALSA_8030 and tr_A0A1S3SU83_A0A1S3SU83_SALSA_8030 are exactly identical! WARNING: Sequences tr_A0A2I4BFF1_A0A2I4BFF1_9TELE_52670 and tr_A0A2I4D630_A0A2I4D630_9TELE_52670 are exactly identical! WARNING: Sequences tr_A0A2D0RIS0_A0A2D0RIS0_ICTPU_7998 and tr_A0A2D0RIT1_A0A2D0RIT1_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0RIS0_A0A2D0RIS0_ICTPU_7998 and tr_A0A2D0RKH0_A0A2D0RKH0_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0SDP3_A0A2D0SDP3_ICTPU_7998 and tr_A0A2D0SDQ4_A0A2D0SDQ4_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0SDP3_A0A2D0SDP3_ICTPU_7998 and tr_A0A2D0SF21_A0A2D0SF21_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0SDP6_A0A2D0SDP6_ICTPU_7998 and tr_A0A2D0SEF2_A0A2D0SEF2_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2U4AGK7_A0A2U4AGK7_TURTR_9739 and tr_A0A2U4AGN1_A0A2U4AGN1_TURTR_9739 are exactly identical! WARNING: Sequences tr_A0A2U4AGM1_A0A2U4AGM1_TURTR_9739 and tr_A0A2U4AH39_A0A2U4AH39_TURTR_9739 are exactly identical! WARNING: Sequences tr_A0A2U4AH34_A0A2U4AH34_TURTR_9739 and tr_A0A2Y9MYT6_A0A2Y9MYT6_DELLE_9749 are exactly identical! WARNING: Duplicate sequences found: 54 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/Q9Y5H6/3_mltree/Q9Y5H6.raxml.reduced.phy Alignment comprises 1 partitions and 402 patterns Partition 0: noname Model: LG4X+R4 Alignment sites / patterns: 403 / 402 Gaps: 0.57 % Invariant sites: 4.22 % NOTE: Binary MSA file created: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q9Y5H6/3_mltree/Q9Y5H6.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 1001 taxa [00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 201 / 16080 [00:00:00] Data distribution: max. searches per worker: 7 Starting ML tree search with 20 distinct starting trees [00:00:00 -639097.637511] Initial branch length optimization [00:00:06 -563319.035589] Model parameter optimization (eps = 10.000000) [00:01:11 -561668.670434] AUTODETECT spr round 1 (radius: 5) [00:04:24 -436290.654421] AUTODETECT spr round 2 (radius: 10) [00:07:59 -310354.549495] AUTODETECT spr round 3 (radius: 15) [00:11:52 -258049.511939] AUTODETECT spr round 4 (radius: 20) [00:17:15 -244485.889354] AUTODETECT spr round 5 (radius: 25) [00:23:28 -243418.136744] SPR radius for FAST iterations: 25 (autodetect) [00:23:28 -243418.136744] Model parameter optimization (eps = 3.000000) [00:23:52 -243344.471249] FAST spr round 1 (radius: 25) [00:27:26 -214795.052098] FAST spr round 2 (radius: 25) [00:30:12 -213623.745315] FAST spr round 3 (radius: 25) [00:32:42 -213552.895642] FAST spr round 4 (radius: 25) [00:34:50 -213550.343808] FAST spr round 5 (radius: 25) [00:36:51 -213550.343768] Model parameter optimization (eps = 1.000000) [00:37:11 -213540.549084] SLOW spr round 1 (radius: 5) [00:40:17 -213443.528210] SLOW spr round 2 (radius: 5) [00:43:08 -213430.443049] SLOW spr round 3 (radius: 5) [00:45:52 -213429.548593] SLOW spr round 4 (radius: 5) [00:48:30 -213429.548589] SLOW spr round 5 (radius: 10) [00:51:15 -213429.548589] SLOW spr round 6 (radius: 15) [00:56:44 -213427.485325] SLOW spr round 7 (radius: 5) [01:00:32 -213418.503436] SLOW spr round 8 (radius: 5) [01:03:46 -213416.077716] SLOW spr round 9 (radius: 5) [01:06:36 -213416.077688] SLOW spr round 10 (radius: 10) [01:09:23 -213416.077686] SLOW spr round 11 (radius: 15) [01:14:56 -213416.077686] SLOW spr round 12 (radius: 20) [01:25:09] [worker #2] ML tree search #3, logLikelihood: -213460.040608 [01:25:40 -213416.077686] SLOW spr round 13 (radius: 25) [01:33:28] [worker #1] ML tree search #2, logLikelihood: -213392.021823 [01:40:00 -213416.077686] Model parameter optimization (eps = 0.100000) [01:40:14] [worker #0] ML tree search #1, logLikelihood: -213414.863910 [01:40:14 -640904.772370] Initial branch length optimization [01:40:21 -564065.864508] Model parameter optimization (eps = 10.000000) [01:41:18 -562426.999921] AUTODETECT spr round 1 (radius: 5) [01:44:37 -436879.471869] AUTODETECT spr round 2 (radius: 10) [01:48:19 -308190.176310] AUTODETECT spr round 3 (radius: 15) [01:52:32 -250000.637870] AUTODETECT spr round 4 (radius: 20) [01:58:08 -243248.354219] AUTODETECT spr round 5 (radius: 25) [02:04:47 -242387.053897] SPR radius for FAST iterations: 25 (autodetect) [02:04:47 -242387.053897] Model parameter optimization (eps = 3.000000) [02:05:18 -242272.464489] FAST spr round 1 (radius: 25) [02:08:58 -214534.705744] FAST spr round 2 (radius: 25) [02:11:44 -213610.623707] FAST spr round 3 (radius: 25) [02:14:08 -213519.826360] FAST spr round 4 (radius: 25) [02:16:18 -213506.346760] FAST spr round 5 (radius: 25) [02:18:23 -213504.188142] FAST spr round 6 (radius: 25) [02:20:24 -213504.187997] Model parameter optimization (eps = 1.000000) [02:20:41 -213494.629904] SLOW spr round 1 (radius: 5) [02:23:44 -213437.210574] SLOW spr round 2 (radius: 5) [02:26:34 -213425.022543] SLOW spr round 3 (radius: 5) [02:29:17 -213420.268591] SLOW spr round 4 (radius: 5) [02:31:58 -213414.868250] SLOW spr round 5 (radius: 5) [02:34:35 -213414.868246] SLOW spr round 6 (radius: 10) [02:37:19 -213414.868057] SLOW spr round 7 (radius: 15) [02:42:47 -213413.111772] SLOW spr round 8 (radius: 5) [02:46:32 -213404.604050] SLOW spr round 9 (radius: 5) [02:49:41 -213404.603992] SLOW spr round 10 (radius: 10) [02:49:56] [worker #2] ML tree search #6, logLikelihood: -213426.498368 [02:52:32 -213404.603992] SLOW spr round 11 (radius: 15) [02:54:05] [worker #1] ML tree search #5, logLikelihood: -213440.189554 [02:57:49 -213404.603992] SLOW spr round 12 (radius: 20) [03:08:20 -213404.603992] SLOW spr round 13 (radius: 25) [03:22:08 -213404.603992] Model parameter optimization (eps = 0.100000) [03:22:21] [worker #0] ML tree search #4, logLikelihood: -213403.499484 [03:22:21 -638063.563149] Initial branch length optimization [03:22:26 -561786.809191] Model parameter optimization (eps = 10.000000) [03:23:08 -560241.547865] AUTODETECT spr round 1 (radius: 5) [03:26:21 -434330.632963] AUTODETECT spr round 2 (radius: 10) [03:29:59 -310667.123839] AUTODETECT spr round 3 (radius: 15) [03:34:10 -250105.794111] AUTODETECT spr round 4 (radius: 20) [03:38:51 -241492.916443] AUTODETECT spr round 5 (radius: 25) [03:44:10 -241291.285429] SPR radius for FAST iterations: 25 (autodetect) [03:44:10 -241291.285429] Model parameter optimization (eps = 3.000000) [03:44:44 -241145.082594] FAST spr round 1 (radius: 25) [03:48:26 -214570.387416] FAST spr round 2 (radius: 25) [03:51:13 -213516.749127] FAST spr round 3 (radius: 25) [03:53:34 -213466.705912] FAST spr round 4 (radius: 25) [03:55:43 -213453.264185] FAST spr round 5 (radius: 25) [03:57:48 -213450.643488] FAST spr round 6 (radius: 25) [03:59:51 -213450.642694] Model parameter optimization (eps = 1.000000) [04:00:05 -213448.501147] SLOW spr round 1 (radius: 5) [04:03:06 -213409.084778] SLOW spr round 2 (radius: 5) [04:05:54 -213405.630633] SLOW spr round 3 (radius: 5) [04:08:20] [worker #2] ML tree search #9, logLikelihood: -213403.042777 [04:08:38 -213405.630483] SLOW spr round 4 (radius: 10) [04:11:25 -213405.630482] SLOW spr round 5 (radius: 15) [04:14:09] [worker #1] ML tree search #8, logLikelihood: -213444.182902 [04:17:02 -213402.091820] SLOW spr round 6 (radius: 5) [04:20:53 -213394.036166] SLOW spr round 7 (radius: 5) [04:24:07 -213394.036116] SLOW spr round 8 (radius: 10) [04:27:00 -213394.036116] SLOW spr round 9 (radius: 15) [04:32:25 -213394.036116] SLOW spr round 10 (radius: 20) [04:42:56 -213394.036116] SLOW spr round 11 (radius: 25) [04:57:07 -213394.036116] Model parameter optimization (eps = 0.100000) [04:57:17] [worker #0] ML tree search #7, logLikelihood: -213393.833284 [04:57:17 -637498.353711] Initial branch length optimization [04:57:22 -561797.722793] Model parameter optimization (eps = 10.000000) [04:58:08 -560366.698020] AUTODETECT spr round 1 (radius: 5) [05:01:25 -431911.391781] AUTODETECT spr round 2 (radius: 10) [05:05:02 -320373.541721] AUTODETECT spr round 3 (radius: 15) [05:09:00 -269864.416842] AUTODETECT spr round 4 (radius: 20) [05:14:56 -252457.671207] AUTODETECT spr round 5 (radius: 25) [05:22:22 -251146.540461] SPR radius for FAST iterations: 25 (autodetect) [05:22:22 -251146.540461] Model parameter optimization (eps = 3.000000) [05:22:58 -251041.224731] FAST spr round 1 (radius: 25) [05:26:55 -214745.487184] FAST spr round 2 (radius: 25) [05:29:36 -213575.474784] FAST spr round 3 (radius: 25) [05:32:06 -213512.762095] FAST spr round 4 (radius: 25) [05:32:46] [worker #2] ML tree search #12, logLikelihood: -213430.174976 [05:34:14 -213507.257356] FAST spr round 5 (radius: 25) [05:36:16 -213507.257326] Model parameter optimization (eps = 1.000000) [05:36:34 -213505.220259] SLOW spr round 1 (radius: 5) [05:39:42 -213443.818750] SLOW spr round 2 (radius: 5) [05:39:54] [worker #1] ML tree search #11, logLikelihood: -213429.977568 [05:42:40 -213424.772629] SLOW spr round 3 (radius: 5) [05:45:26 -213420.231888] SLOW spr round 4 (radius: 5) [05:48:16 -213414.736646] SLOW spr round 5 (radius: 5) [05:50:58 -213414.736643] SLOW spr round 6 (radius: 10) [05:53:49 -213412.511798] SLOW spr round 7 (radius: 5) [05:57:30 -213411.308142] SLOW spr round 8 (radius: 5) [06:00:38 -213411.308137] SLOW spr round 9 (radius: 10) [06:03:30 -213411.308137] SLOW spr round 10 (radius: 15) [06:09:00 -213411.308137] SLOW spr round 11 (radius: 20) [06:19:52 -213411.308137] SLOW spr round 12 (radius: 25) [06:34:11 -213411.308137] Model parameter optimization (eps = 0.100000) [06:34:21] [worker #0] ML tree search #10, logLikelihood: -213410.875655 [06:34:22 -637649.485428] Initial branch length optimization [06:34:27 -561380.361011] Model parameter optimization (eps = 10.000000) [06:35:22 -559856.784843] AUTODETECT spr round 1 (radius: 5) [06:38:34 -432433.058563] AUTODETECT spr round 2 (radius: 10) [06:42:12 -294109.892068] AUTODETECT spr round 3 (radius: 15) [06:46:23 -251885.004517] AUTODETECT spr round 4 (radius: 20) [06:51:24 -245733.541878] AUTODETECT spr round 5 (radius: 25) [06:53:17] [worker #2] ML tree search #15, logLikelihood: -213440.706976 [06:57:36 -245325.158753] SPR radius for FAST iterations: 25 (autodetect) [06:57:36 -245325.158753] Model parameter optimization (eps = 3.000000) [06:58:00 -245217.375359] FAST spr round 1 (radius: 25) [07:01:37 -214778.143540] FAST spr round 2 (radius: 25) [07:04:18 -213598.359489] FAST spr round 3 (radius: 25) [07:04:45] [worker #1] ML tree search #14, logLikelihood: -213409.293922 [07:06:43 -213493.079699] FAST spr round 4 (radius: 25) [07:09:01 -213468.326648] FAST spr round 5 (radius: 25) [07:11:03 -213466.752710] FAST spr round 6 (radius: 25) [07:13:04 -213466.752612] Model parameter optimization (eps = 1.000000) [07:13:22 -213461.551999] SLOW spr round 1 (radius: 5) [07:16:19 -213409.559452] SLOW spr round 2 (radius: 5) [07:19:13 -213407.905963] SLOW spr round 3 (radius: 5) [07:22:01 -213407.903521] SLOW spr round 4 (radius: 10) [07:24:50 -213407.903376] SLOW spr round 5 (radius: 15) [07:30:19 -213407.903368] SLOW spr round 6 (radius: 20) [07:40:45 -213407.903368] SLOW spr round 7 (radius: 25) [07:54:38 -213407.903368] Model parameter optimization (eps = 0.100000) [07:54:45] [worker #0] ML tree search #13, logLikelihood: -213407.850010 [07:54:46 -637652.291229] Initial branch length optimization [07:54:50 -562467.835996] Model parameter optimization (eps = 10.000000) [07:56:00 -560903.422109] AUTODETECT spr round 1 (radius: 5) [07:59:16 -439225.119395] AUTODETECT spr round 2 (radius: 10) [08:02:59 -296007.655512] AUTODETECT spr round 3 (radius: 15) [08:07:11 -247438.131800] AUTODETECT spr round 4 (radius: 20) [08:11:08] [worker #2] ML tree search #18, logLikelihood: -213434.086631 [08:12:34 -243639.221457] AUTODETECT spr round 5 (radius: 25) [08:18:26 -242798.814848] SPR radius for FAST iterations: 25 (autodetect) [08:18:26 -242798.814848] Model parameter optimization (eps = 3.000000) [08:18:50 -242705.862307] FAST spr round 1 (radius: 25) [08:22:23 -214578.994993] FAST spr round 2 (radius: 25) [08:25:05 -213558.927238] FAST spr round 3 (radius: 25) [08:27:31 -213522.138274] FAST spr round 4 (radius: 25) [08:29:37 -213510.631693] FAST spr round 5 (radius: 25) [08:31:02] [worker #1] ML tree search #17, logLikelihood: -213404.892966 [08:31:42 -213499.689094] FAST spr round 6 (radius: 25) [08:33:45 -213499.689080] Model parameter optimization (eps = 1.000000) [08:34:04 -213496.245460] SLOW spr round 1 (radius: 5) [08:37:01 -213429.180474] SLOW spr round 2 (radius: 5) [08:39:49 -213417.885827] SLOW spr round 3 (radius: 5) [08:42:30 -213417.885814] SLOW spr round 4 (radius: 10) [08:45:20 -213415.790179] SLOW spr round 5 (radius: 5) [08:48:57 -213415.175466] SLOW spr round 6 (radius: 5) [08:52:02 -213415.175465] SLOW spr round 7 (radius: 10) [08:54:53 -213415.175465] SLOW spr round 8 (radius: 15) [09:00:16 -213415.175465] SLOW spr round 9 (radius: 20) [09:11:01 -213415.175465] SLOW spr round 10 (radius: 25) [09:25:02 -213415.175465] Model parameter optimization (eps = 0.100000) [09:25:11] [worker #0] ML tree search #16, logLikelihood: -213415.092587 [09:25:11 -638969.994590] Initial branch length optimization [09:25:16 -563680.773664] Model parameter optimization (eps = 10.000000) [09:26:29 -562091.111821] AUTODETECT spr round 1 (radius: 5) [09:29:44 -428331.922384] AUTODETECT spr round 2 (radius: 10) [09:33:10 -307564.511955] AUTODETECT spr round 3 (radius: 15) [09:37:07 -249145.748625] AUTODETECT spr round 4 (radius: 20) [09:42:28 -242200.644915] AUTODETECT spr round 5 (radius: 25) [09:48:12 -241411.518306] SPR radius for FAST iterations: 25 (autodetect) [09:48:12 -241411.518306] Model parameter optimization (eps = 3.000000) [09:48:46 -241305.957803] FAST spr round 1 (radius: 25) [09:52:30 -214382.443332] FAST spr round 2 (radius: 25) [09:55:15 -213586.240370] FAST spr round 3 (radius: 25) [09:55:23] [worker #1] ML tree search #20, logLikelihood: -213403.678461 [09:57:50 -213495.268478] FAST spr round 4 (radius: 25) [09:59:58 -213488.489229] FAST spr round 5 (radius: 25) [10:02:00 -213485.247839] FAST spr round 6 (radius: 25) [10:04:01 -213485.247837] Model parameter optimization (eps = 1.000000) [10:04:17 -213478.149090] SLOW spr round 1 (radius: 5) [10:07:16 -213435.406500] SLOW spr round 2 (radius: 5) [10:10:04 -213427.822071] SLOW spr round 3 (radius: 5) [10:12:41 -213427.821642] SLOW spr round 4 (radius: 10) [10:15:26 -213427.821642] SLOW spr round 5 (radius: 15) [10:20:40 -213427.821642] SLOW spr round 6 (radius: 20) [10:30:48 -213427.821642] SLOW spr round 7 (radius: 25) [10:44:28 -213427.821642] Model parameter optimization (eps = 0.100000) [10:44:45] [worker #0] ML tree search #19, logLikelihood: -213427.622505 Optimized model parameters: Partition 0: noname Rate heterogeneity: FREE (4 cats, mean), weights&rates: (0.109481,0.325102) (0.301201,0.411669) (0.341165,0.986323) (0.248153,2.030653) 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: -213392.021823 AIC score: 430794.043647 / AICc score: 8474854.043647 / BIC score: 438811.911454 Free parameters (model + branch lengths): 2005 WARNING: Number of free parameters (K=2005) is larger than alignment size (n=403). 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/Q9Y5H6/3_mltree/Q9Y5H6.raxml.bestTree All ML trees saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q9Y5H6/3_mltree/Q9Y5H6.raxml.mlTrees Optimized model saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q9Y5H6/3_mltree/Q9Y5H6.raxml.bestModel Execution log saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q9Y5H6/3_mltree/Q9Y5H6.raxml.log Analysis started: 03-Jul-2021 07:53:03 / finished: 03-Jul-2021 18:37:48 Elapsed time: 38685.275 seconds Consumed energy: 3652.365 Wh (= 18 km in an electric car, or 91 km with an e-scooter!)