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 02-Jul-2021 02:21:19 as follows: raxml-ng --msa /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/P30038/2_msa/P30038_trimmed_msa.fasta --data-type AA --model LG4X --prefix /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/P30038/3_mltree/P30038 --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/P30038/2_msa/P30038_trimmed_msa.fasta [00:00:00] Loaded alignment with 1001 taxa and 534 sites WARNING: Sequences tr_A0A0E1RWZ4_A0A0E1RWZ4_COCIM_246410 and tr_A0A0J7B2T2_A0A0J7B2T2_COCIT_404692 are exactly identical! WARNING: Sequences tr_B6QB17_B6QB17_TALMQ_441960 and tr_A0A093UVB4_A0A093UVB4_TALMA_1077442 are exactly identical! WARNING: Sequences tr_B8NP70_B8NP70_ASPFN_332952 and tr_Q2UN07_Q2UN07_ASPOR_510516 are exactly identical! WARNING: Sequences tr_F9FQM3_F9FQM3_FUSOF_660025 and tr_A0A0D2X8P0_A0A0D2X8P0_FUSO4_426428 are exactly identical! WARNING: Sequences tr_F9FQM3_F9FQM3_FUSOF_660025 and tr_N4TT09_N4TT09_FUSC1_1229664 are exactly identical! WARNING: Sequences tr_F9FQM3_F9FQM3_FUSOF_660025 and tr_X0CFF6_X0CFF6_FUSOX_1089458 are exactly identical! WARNING: Sequences tr_F9FQM3_F9FQM3_FUSOF_660025 and tr_A0A2H3STU9_A0A2H3STU9_FUSOX_5507 are exactly identical! WARNING: Sequences tr_F9FQM3_F9FQM3_FUSOF_660025 and tr_A0A2H3HUB0_A0A2H3HUB0_FUSOX_327505 are exactly identical! WARNING: Sequences tr_F9FTM0_F9FTM0_FUSOF_660025 and tr_N4UJG1_N4UJG1_FUSC1_1229664 are exactly identical! WARNING: Sequences tr_F9FTM0_F9FTM0_FUSOF_660025 and tr_X0BYA3_X0BYA3_FUSOX_1089458 are exactly identical! WARNING: Sequences tr_F9FTM0_F9FTM0_FUSOF_660025 and tr_A0A2H3SIW2_A0A2H3SIW2_FUSOX_5507 are exactly identical! WARNING: Sequences tr_F9FTM0_F9FTM0_FUSOF_660025 and tr_A0A2H3G6B6_A0A2H3G6B6_FUSOX_327505 are exactly identical! WARNING: Sequences tr_C6HEZ8_C6HEZ8_AJECH_544712 and tr_F0UN88_F0UN88_AJEC8_544711 are exactly identical! WARNING: Sequences tr_J5K4S2_J5K4S2_BEAB2_655819 and tr_A0A2N6P121_A0A2N6P121_BEABA_176275 are exactly identical! WARNING: Sequences tr_A0A0J9Y7J2_A0A0J9Y7J2_BRUMA_6279 and tr_A0A0R3QLA3_A0A0R3QLA3_9BILA_42155 are exactly identical! WARNING: Sequences tr_A2QC50_A2QC50_ASPNC_425011 and tr_A0A319ASJ8_A0A319ASJ8_9EURO_1450533 are exactly identical! WARNING: Sequences tr_A2QNB0_A2QNB0_ASPNC_425011 and tr_G3XYQ8_G3XYQ8_ASPNA_380704 are exactly identical! WARNING: Sequences tr_A2QNB0_A2QNB0_ASPNC_425011 and tr_A0A319AYY5_A0A319AYY5_9EURO_1450533 are exactly identical! WARNING: Sequences tr_A2QWR5_A2QWR5_ASPNC_425011 and tr_G3YD59_G3YD59_ASPNA_380704 are exactly identical! WARNING: Sequences tr_A2QWR5_A2QWR5_ASPNC_425011 and tr_A0A319AFZ5_A0A319AFZ5_9EURO_1450533 are exactly identical! WARNING: Sequences tr_G7X9Z4_G7X9Z4_ASPKW_1033177 and tr_A0A146F9A7_A0A146F9A7_9EURO_1069201 are exactly identical! WARNING: Sequences tr_G7XF54_G7XF54_ASPKW_1033177 and tr_A0A100IDU6_A0A100IDU6_ASPNG_5061 are exactly identical! WARNING: Sequences tr_G7XF54_G7XF54_ASPKW_1033177 and tr_A0A146F0T3_A0A146F0T3_9EURO_1069201 are exactly identical! WARNING: Sequences tr_G7XF54_G7XF54_ASPKW_1033177 and tr_A0A1L9MY83_A0A1L9MY83_ASPTU_767770 are exactly identical! WARNING: Sequences tr_G7XL12_G7XL12_ASPKW_1033177 and tr_A0A146EXQ3_A0A146EXQ3_9EURO_1069201 are exactly identical! WARNING: Sequences tr_F9WYJ2_F9WYJ2_ZYMTI_336722 and tr_A0A1X7RHA3_A0A1X7RHA3_ZYMTR_1276538 are exactly identical! WARNING: Sequences tr_F2SZD4_F2SZD4_TRIRC_559305 and tr_A0A178F3X5_A0A178F3X5_TRIRU_5551 are exactly identical! WARNING: Sequences tr_F2Q593_F2Q593_TRIEC_559882 and tr_A0A059J012_A0A059J012_9EURO_1215338 are exactly identical! WARNING: Sequences tr_U5HJ93_U5HJ93_USTV1_683840 and tr_A0A2X0M9R4_A0A2X0M9R4_9BASI_796604 are exactly identical! WARNING: Sequences tr_A0A0L0T9C6_A0A0L0T9C6_ALLMA_578462 and tr_A0A0L0TBL5_A0A0L0TBL5_ALLMA_578462 are exactly identical! WARNING: Sequences tr_A0A0V1NIR6_A0A0V1NIR6_9BILA_92180 and tr_A0A0V0TH63_A0A0V0TH63_9BILA_144512 are exactly identical! WARNING: Sequences tr_A0A124BXH6_A0A124BXH6_ASPNG_5061 and tr_A0A1L9N1M9_A0A1L9N1M9_ASPTU_767770 are exactly identical! WARNING: Sequences tr_A0A124BXH6_A0A124BXH6_ASPNG_5061 and tr_A0A317WEC1_A0A317WEC1_9EURO_1448314 are exactly identical! WARNING: Duplicate sequences found: 33 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/P30038/3_mltree/P30038.raxml.reduced.phy Alignment comprises 1 partitions and 533 patterns Partition 0: noname Model: LG4X+R4 Alignment sites / patterns: 534 / 533 Gaps: 0.99 % Invariant sites: 1.31 % NOTE: Binary MSA file created: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/P30038/3_mltree/P30038.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 / 267 / 21360 [00:00:00] Data distribution: max. searches per worker: 7 Starting ML tree search with 20 distinct starting trees [00:00:00 -768138.041710] Initial branch length optimization [00:00:08 -665848.330139] Model parameter optimization (eps = 10.000000) [00:01:02 -664752.219809] AUTODETECT spr round 1 (radius: 5) [00:05:00 -483772.376114] AUTODETECT spr round 2 (radius: 10) [00:09:37 -350439.436045] AUTODETECT spr round 3 (radius: 15) [00:15:03 -299222.092684] AUTODETECT spr round 4 (radius: 20) [00:21:39 -277750.114713] AUTODETECT spr round 5 (radius: 25) [00:29:25 -274297.678592] SPR radius for FAST iterations: 25 (autodetect) [00:29:25 -274297.678592] Model parameter optimization (eps = 3.000000) [00:29:51 -274224.777321] FAST spr round 1 (radius: 25) [00:34:38 -237464.360310] FAST spr round 2 (radius: 25) [00:37:58 -235605.460867] FAST spr round 3 (radius: 25) [00:40:52 -235561.970159] FAST spr round 4 (radius: 25) [00:43:21 -235558.924801] FAST spr round 5 (radius: 25) [00:45:44 -235558.924785] Model parameter optimization (eps = 1.000000) [00:46:05 -235551.990513] SLOW spr round 1 (radius: 5) [00:49:56 -235477.951737] SLOW spr round 2 (radius: 5) [00:53:30 -235467.198806] SLOW spr round 3 (radius: 5) [00:56:53 -235465.199826] SLOW spr round 4 (radius: 5) [01:00:10 -235465.199813] SLOW spr round 5 (radius: 10) [01:03:38 -235463.951549] SLOW spr round 6 (radius: 5) [01:08:07 -235461.939970] SLOW spr round 7 (radius: 5) [01:11:57 -235461.938941] SLOW spr round 8 (radius: 10) [01:15:32 -235461.938930] SLOW spr round 9 (radius: 15) [01:21:53 -235461.938930] SLOW spr round 10 (radius: 20) [01:26:13] [worker #2] ML tree search #3, logLikelihood: -235451.127943 [01:31:44 -235461.938930] SLOW spr round 11 (radius: 25) [01:44:00 -235461.938930] Model parameter optimization (eps = 0.100000) [01:44:13] [worker #0] ML tree search #1, logLikelihood: -235461.664272 [01:44:14 -766856.832416] Initial branch length optimization [01:44:20 -665870.313109] Model parameter optimization (eps = 10.000000) [01:45:14 -664767.856892] AUTODETECT spr round 1 (radius: 5) [01:49:13 -496278.472721] AUTODETECT spr round 2 (radius: 10) [01:49:44] [worker #1] ML tree search #2, logLikelihood: -235433.815390 [01:54:08 -365630.907995] AUTODETECT spr round 3 (radius: 15) [01:59:33 -317109.910348] AUTODETECT spr round 4 (radius: 20) [02:05:39 -289220.450206] AUTODETECT spr round 5 (radius: 25) [02:12:39 -278453.769903] SPR radius for FAST iterations: 25 (autodetect) [02:12:39 -278453.769903] Model parameter optimization (eps = 3.000000) [02:13:08 -278384.221531] FAST spr round 1 (radius: 25) [02:18:07 -238367.516789] FAST spr round 2 (radius: 25) [02:21:30 -235808.762682] FAST spr round 3 (radius: 25) [02:24:26 -235580.685186] FAST spr round 4 (radius: 25) [02:26:56 -235574.969747] FAST spr round 5 (radius: 25) [02:29:19 -235574.969746] Model parameter optimization (eps = 1.000000) [02:29:29 -235574.705376] SLOW spr round 1 (radius: 5) [02:33:25 -235470.581926] SLOW spr round 2 (radius: 5) [02:37:10 -235451.125296] SLOW spr round 3 (radius: 5) [02:40:34 -235447.853625] SLOW spr round 4 (radius: 5) [02:43:51 -235447.853615] SLOW spr round 5 (radius: 10) [02:47:13 -235442.000107] SLOW spr round 6 (radius: 5) [02:51:41 -235439.114915] SLOW spr round 7 (radius: 5) [02:55:29 -235439.114910] SLOW spr round 8 (radius: 10) [02:58:57 -235439.114910] SLOW spr round 9 (radius: 15) [02:59:43] [worker #2] ML tree search #6, logLikelihood: -235444.780301 [03:05:03 -235439.114910] SLOW spr round 10 (radius: 20) [03:14:48 -235439.114910] SLOW spr round 11 (radius: 25) [03:16:57] [worker #1] ML tree search #5, logLikelihood: -235436.377137 [03:27:00 -235439.114910] Model parameter optimization (eps = 0.100000) [03:27:07] [worker #0] ML tree search #4, logLikelihood: -235439.049382 [03:27:07 -768236.395094] Initial branch length optimization [03:27:14 -666724.332948] Model parameter optimization (eps = 10.000000) [03:28:04 -665614.608070] AUTODETECT spr round 1 (radius: 5) [03:31:56 -488139.800941] AUTODETECT spr round 2 (radius: 10) [03:36:37 -348904.029690] AUTODETECT spr round 3 (radius: 15) [03:41:50 -300592.321262] AUTODETECT spr round 4 (radius: 20) [03:47:16 -283343.952930] AUTODETECT spr round 5 (radius: 25) [03:54:23 -277261.836397] SPR radius for FAST iterations: 25 (autodetect) [03:54:23 -277261.836397] Model parameter optimization (eps = 3.000000) [03:54:32 -277260.255859] FAST spr round 1 (radius: 25) [03:59:26 -237131.691546] FAST spr round 2 (radius: 25) [04:02:50 -235693.959432] FAST spr round 3 (radius: 25) [04:05:54 -235607.924313] FAST spr round 4 (radius: 25) [04:08:21 -235600.763871] FAST spr round 5 (radius: 25) [04:10:42 -235600.763824] Model parameter optimization (eps = 1.000000) [04:11:05 -235547.363134] SLOW spr round 1 (radius: 5) [04:14:53 -235465.627852] SLOW spr round 2 (radius: 5) [04:18:27 -235463.459863] SLOW spr round 3 (radius: 5) [04:21:47 -235463.459752] SLOW spr round 4 (radius: 10) [04:25:10 -235459.855676] SLOW spr round 5 (radius: 5) [04:29:38 -235458.099309] SLOW spr round 6 (radius: 5) [04:30:30] [worker #2] ML tree search #9, logLikelihood: -235433.255880 [04:33:28 -235458.099267] SLOW spr round 7 (radius: 10) [04:36:55 -235458.099267] SLOW spr round 8 (radius: 15) [04:43:10 -235457.770536] SLOW spr round 9 (radius: 5) [04:47:49 -235457.767862] SLOW spr round 10 (radius: 10) [04:51:52 -235457.767581] SLOW spr round 11 (radius: 15) [04:52:45] [worker #1] ML tree search #8, logLikelihood: -235447.076068 [04:57:44 -235457.767550] SLOW spr round 12 (radius: 20) [05:07:52 -235457.767547] SLOW spr round 13 (radius: 25) [05:20:26 -235457.767546] Model parameter optimization (eps = 0.100000) [05:20:41] [worker #0] ML tree search #7, logLikelihood: -235456.791378 [05:20:41 -767359.575172] Initial branch length optimization [05:20:48 -667692.117183] Model parameter optimization (eps = 10.000000) [05:21:53 -666534.527658] AUTODETECT spr round 1 (radius: 5) [05:25:51 -497263.987670] AUTODETECT spr round 2 (radius: 10) [05:30:43 -364537.372916] AUTODETECT spr round 3 (radius: 15) [05:35:47 -292851.946584] AUTODETECT spr round 4 (radius: 20) [05:41:39 -267951.332100] AUTODETECT spr round 5 (radius: 25) [05:49:19 -264779.750316] SPR radius for FAST iterations: 25 (autodetect) [05:49:19 -264779.750316] Model parameter optimization (eps = 3.000000) [05:49:53 -264713.421408] FAST spr round 1 (radius: 25) [05:54:22 -237148.733286] FAST spr round 2 (radius: 25) [05:57:44 -235609.470674] FAST spr round 3 (radius: 25) [06:00:40 -235544.971885] FAST spr round 4 (radius: 25) [06:03:10 -235538.863429] FAST spr round 5 (radius: 25) [06:05:34 -235537.306535] FAST spr round 6 (radius: 25) [06:07:57 -235529.277677] FAST spr round 7 (radius: 25) [06:10:15 -235529.277666] Model parameter optimization (eps = 1.000000) [06:10:27 -235526.571784] SLOW spr round 1 (radius: 5) [06:14:10 -235439.959625] SLOW spr round 2 (radius: 5) [06:16:13] [worker #2] ML tree search #12, logLikelihood: -235443.995805 [06:17:40 -235432.152369] SLOW spr round 3 (radius: 5) [06:18:50] [worker #1] ML tree search #11, logLikelihood: -235433.273916 [06:21:00 -235432.152292] SLOW spr round 4 (radius: 10) [06:24:25 -235427.032139] SLOW spr round 5 (radius: 5) [06:28:54 -235427.032125] SLOW spr round 6 (radius: 10) [06:32:45 -235427.032125] SLOW spr round 7 (radius: 15) [06:38:47 -235427.032125] SLOW spr round 8 (radius: 20) [06:48:51 -235427.032125] SLOW spr round 9 (radius: 25) [07:00:57 -235427.032125] Model parameter optimization (eps = 0.100000) [07:01:03] [worker #0] ML tree search #10, logLikelihood: -235427.019703 [07:01:03 -771016.801338] Initial branch length optimization [07:01:10 -666894.988591] Model parameter optimization (eps = 10.000000) [07:01:59 -665744.244594] AUTODETECT spr round 1 (radius: 5) [07:05:52 -488816.440093] AUTODETECT spr round 2 (radius: 10) [07:10:26 -349624.344998] AUTODETECT spr round 3 (radius: 15) [07:15:31 -293061.360308] AUTODETECT spr round 4 (radius: 20) [07:21:04 -276103.809414] AUTODETECT spr round 5 (radius: 25) [07:27:13 -272929.019101] SPR radius for FAST iterations: 25 (autodetect) [07:27:13 -272929.019101] Model parameter optimization (eps = 3.000000) [07:27:42 -272761.396519] FAST spr round 1 (radius: 25) [07:32:13 -237583.948592] FAST spr round 2 (radius: 25) [07:35:31 -235646.544304] FAST spr round 3 (radius: 25) [07:38:21 -235530.455917] FAST spr round 4 (radius: 25) [07:40:50 -235527.242498] FAST spr round 5 (radius: 25) [07:43:11 -235527.242491] Model parameter optimization (eps = 1.000000) [07:43:30 -235516.951224] SLOW spr round 1 (radius: 5) [07:47:18 -235442.491617] SLOW spr round 2 (radius: 5) [07:50:49 -235434.173444] SLOW spr round 3 (radius: 5) [07:52:22] [worker #1] ML tree search #14, logLikelihood: -235458.397550 [07:54:08 -235434.173357] SLOW spr round 4 (radius: 10) [07:56:03] [worker #2] ML tree search #15, logLikelihood: -235453.989548 [07:57:34 -235434.173350] SLOW spr round 5 (radius: 15) [08:03:59 -235434.173350] SLOW spr round 6 (radius: 20) [08:13:31 -235434.173350] SLOW spr round 7 (radius: 25) [08:25:49 -235434.173350] Model parameter optimization (eps = 0.100000) [08:25:56] [worker #0] ML tree search #13, logLikelihood: -235434.114430 [08:25:57 -764034.282176] Initial branch length optimization [08:26:02 -662708.699002] Model parameter optimization (eps = 10.000000) [08:26:52 -661572.772048] AUTODETECT spr round 1 (radius: 5) [08:30:48 -487622.198170] AUTODETECT spr round 2 (radius: 10) [08:35:43 -352687.020919] AUTODETECT spr round 3 (radius: 15) [08:41:06 -290458.041201] AUTODETECT spr round 4 (radius: 20) [08:47:06 -266338.633488] AUTODETECT spr round 5 (radius: 25) [08:54:05 -264032.848243] SPR radius for FAST iterations: 25 (autodetect) [08:54:05 -264032.848243] Model parameter optimization (eps = 3.000000) [08:54:33 -263961.203830] FAST spr round 1 (radius: 25) [08:59:11 -236912.121760] FAST spr round 2 (radius: 25) [09:02:32 -235644.260324] FAST spr round 3 (radius: 25) [09:05:26 -235539.344109] FAST spr round 4 (radius: 25) [09:08:06 -235530.948632] FAST spr round 5 (radius: 25) [09:10:28 -235530.948631] Model parameter optimization (eps = 1.000000) [09:10:49 -235529.202951] SLOW spr round 1 (radius: 5) [09:14:47 -235470.388798] SLOW spr round 2 (radius: 5) [09:18:20 -235457.057612] SLOW spr round 3 (radius: 5) [09:21:41 -235455.312982] SLOW spr round 4 (radius: 5) [09:22:48] [worker #2] ML tree search #18, logLikelihood: -235438.910859 [09:24:59 -235455.312941] SLOW spr round 5 (radius: 10) [09:27:07] [worker #1] ML tree search #17, logLikelihood: -235445.201622 [09:28:21 -235452.497423] SLOW spr round 6 (radius: 5) [09:32:45 -235452.497416] SLOW spr round 7 (radius: 10) [09:36:31 -235452.497416] SLOW spr round 8 (radius: 15) [09:42:16 -235452.497416] SLOW spr round 9 (radius: 20) [09:52:01 -235452.497416] SLOW spr round 10 (radius: 25) [10:03:47 -235452.497416] Model parameter optimization (eps = 0.100000) [10:04:00] [worker #0] ML tree search #16, logLikelihood: -235452.270762 [10:04:00 -766028.237220] Initial branch length optimization [10:04:07 -665016.202256] Model parameter optimization (eps = 10.000000) [10:04:54 -663902.121287] AUTODETECT spr round 1 (radius: 5) [10:08:53 -487450.016893] AUTODETECT spr round 2 (radius: 10) [10:13:33 -377216.123876] AUTODETECT spr round 3 (radius: 15) [10:19:30 -307640.169672] AUTODETECT spr round 4 (radius: 20) [10:25:55 -282678.478075] AUTODETECT spr round 5 (radius: 25) [10:32:23 -275507.706791] SPR radius for FAST iterations: 25 (autodetect) [10:32:23 -275507.706791] Model parameter optimization (eps = 3.000000) [10:32:49 -275433.889144] FAST spr round 1 (radius: 25) [10:37:38 -236899.141353] FAST spr round 2 (radius: 25) [10:41:06 -235679.569754] FAST spr round 3 (radius: 25) [10:44:10 -235536.755299] FAST spr round 4 (radius: 25) [10:46:42 -235515.203057] FAST spr round 5 (radius: 25) [10:49:02 -235515.203030] Model parameter optimization (eps = 1.000000) [10:49:19 -235513.223671] SLOW spr round 1 (radius: 5) [10:53:09 -235449.206147] SLOW spr round 2 (radius: 5) [10:56:44 -235438.151278] SLOW spr round 3 (radius: 5) [11:00:11 -235433.510550] SLOW spr round 4 (radius: 5) [11:03:29 -235433.510495] SLOW spr round 5 (radius: 10) [11:04:19] [worker #1] ML tree search #20, logLikelihood: -235433.533527 [11:06:51 -235433.510494] SLOW spr round 6 (radius: 15) [11:13:20 -235430.695531] SLOW spr round 7 (radius: 5) [11:18:01 -235428.226971] SLOW spr round 8 (radius: 5) [11:21:58 -235428.226962] SLOW spr round 9 (radius: 10) [11:25:30 -235428.226962] SLOW spr round 10 (radius: 15) [11:31:38 -235428.226962] SLOW spr round 11 (radius: 20) [11:41:31 -235428.226962] SLOW spr round 12 (radius: 25) [11:52:21 -235428.226962] Model parameter optimization (eps = 0.100000) [11:52:32] [worker #0] ML tree search #19, logLikelihood: -235428.106750 Optimized model parameters: Partition 0: noname Rate heterogeneity: FREE (4 cats, mean), weights&rates: (0.228477,0.285627) (0.340719,0.499686) (0.222161,1.055977) (0.208644,2.539696) 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: -235427.019703 AIC score: 474864.039405 / AICc score: 8518924.039405 / BIC score: 483446.233062 Free parameters (model + branch lengths): 2005 WARNING: Number of free parameters (K=2005) is larger than alignment size (n=534). This might lead to overfitting and compromise tree inference results! WARNING: Best ML tree contains 47 near-zero branches! Best ML tree with collapsed near-zero branches saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/P30038/3_mltree/P30038.raxml.bestTreeCollapsed Best ML tree saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/P30038/3_mltree/P30038.raxml.bestTree All ML trees saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/P30038/3_mltree/P30038.raxml.mlTrees Optimized model saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/P30038/3_mltree/P30038.raxml.bestModel Execution log saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/P30038/3_mltree/P30038.raxml.log Analysis started: 02-Jul-2021 02:21:19 / finished: 02-Jul-2021 14:13:52 Elapsed time: 42752.897 seconds Consumed energy: 3057.768 Wh (= 15 km in an electric car, or 76 km with an e-scooter!)