RAxML-NG v. 1.0.2 released on 22.02.2021 by The Exelixis Lab.
Developed by: Alexey M. Kozlov and Alexandros Stamatakis.
Contributors: Diego Darriba, Tomas Flouri, Benoit Morel, Sarah Lutteropp, Ben Bettisworth.
Latest version: https://github.com/amkozlov/raxml-ng
Questions/problems/suggestions? Please visit: https://groups.google.com/forum/#!forum/raxml

System: Intel(R) Xeon(R) Gold 6148 CPU @ 2.40GHz, 40 cores, 376 GB RAM

RAxML-NG was called at 01-Jul-2021 04:55:24 as follows:

raxml-ng --msa /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/O95630/2_msa/O95630_trimmed_msa.fasta --data-type AA --model LG4X --prefix /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/O95630/3_mltree/O95630 --seed 2 --threads 8 --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 (8 threads), thread pinning: OFF

[00:00:00] Reading alignment from file: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/O95630/2_msa/O95630_trimmed_msa.fasta
[00:00:00] Loaded alignment with 1001 taxa and 675 sites

WARNING: Sequences tr_J3K3U5_J3K3U5_COCIM_246410 and tr_A0A0J6YGL4_A0A0J6YGL4_COCIT_404692 are exactly identical!
WARNING: Sequences tr_B8MZZ2_B8MZZ2_ASPFN_332952 and tr_Q2UQ45_Q2UQ45_ASPOR_510516 are exactly identical!
WARNING: Sequences tr_F9FAK0_F9FAK0_FUSOF_660025 and tr_X0CG05_X0CG05_FUSOX_1089458 are exactly identical!
WARNING: Sequences tr_F9FAK0_F9FAK0_FUSOF_660025 and tr_A0A2H3GMW5_A0A2H3GMW5_FUSOX_327505 are exactly identical!
WARNING: Sequences sp_Q96FJ0_STALP_HUMAN_9606 and tr_A0A2R8ZNB1_A0A2R8ZNB1_PANPA_9597 are exactly identical!
WARNING: Sequences tr_A0A0E0FL92_A0A0E0FL92_ORYNI_4536 and tr_B8A7G8_B8A7G8_ORYSI_39946 are exactly identical!
WARNING: Sequences tr_F6XZX0_F6XZX0_MACMU_9544 and tr_G7PMI1_G7PMI1_MACFA_9541 are exactly identical!
WARNING: Sequences tr_F6XZX0_F6XZX0_MACMU_9544 and tr_A0A0D9RSK0_A0A0D9RSK0_CHLSB_60711 are exactly identical!
WARNING: Sequences tr_F6XZX0_F6XZX0_MACMU_9544 and tr_A0A2K5N8N8_A0A2K5N8N8_CERAT_9531 are exactly identical!
WARNING: Sequences tr_F6XZX0_F6XZX0_MACMU_9544 and tr_A0A2K6E7T4_A0A2K6E7T4_MACNE_9545 are exactly identical!
WARNING: Sequences tr_G7XBP6_G7XBP6_ASPKW_1033177 and tr_A0A146FDE5_A0A146FDE5_9EURO_1069201 are exactly identical!
WARNING: Sequences tr_G2XPF9_G2XPF9_BOTF4_999810 and tr_M7UIV8_M7UIV8_BOTF1_1290391 are exactly identical!
WARNING: Sequences tr_G7PDH7_G7PDH7_MACFA_9541 and tr_A0A2I3LL18_A0A2I3LL18_PAPAN_9555 are exactly identical!
WARNING: Sequences tr_G7PDH7_G7PDH7_MACFA_9541 and tr_A0A2K6CQH9_A0A2K6CQH9_MACNE_9545 are exactly identical!
WARNING: Sequences tr_V2WZI5_V2WZI5_MONRO_1381753 and tr_A0A0W0FGJ0_A0A0W0FGJ0_9AGAR_221103 are exactly identical!
WARNING: Sequences tr_A0A015ITA2_A0A015ITA2_9GLOM_1432141 and tr_A0A2H5TBQ6_A0A2H5TBQ6_RHIID_747089 are exactly identical!
WARNING: Sequences tr_A0A044T8X7_A0A044T8X7_ONCVO_6282 and tr_A0A182EFC0_A0A182EFC0_ONCOC_42157 are exactly identical!
WARNING: Sequences tr_A0A0D3EP84_A0A0D3EP84_9ORYZ_65489 and tr_A0A0D9Y954_A0A0D9Y954_9ORYZ_40148 are exactly identical!
WARNING: Sequences tr_A0A0D3ES43_A0A0D3ES43_9ORYZ_65489 and tr_A0A0D9YCR3_A0A0D9YCR3_9ORYZ_40148 are exactly identical!
WARNING: Sequences tr_A0A067DUV2_A0A067DUV2_CITSI_2711 and tr_A0A2H5PLZ0_A0A2H5PLZ0_CITUN_55188 are exactly identical!
WARNING: Sequences tr_A0A067H4C2_A0A067H4C2_CITSI_2711 and tr_V4SUT8_V4SUT8_9ROSI_85681 are exactly identical!
WARNING: Sequences tr_A0A078HHU8_A0A078HHU8_BRANA_3708 and tr_A0A0D3C945_A0A0D3C945_BRAOL_109376 are exactly identical!
WARNING: Sequences tr_A0A078HUZ9_A0A078HUZ9_BRANA_3708 and tr_A0A0D3CPB0_A0A0D3CPB0_BRAOL_109376 are exactly identical!
WARNING: Sequences tr_A0A151P0C0_A0A151P0C0_ALLMI_8496 and tr_A0A3Q0H3H4_A0A3Q0H3H4_ALLSI_38654 are exactly identical!
WARNING: Sequences tr_A0A091EAT3_A0A091EAT3_CORBR_85066 and tr_A0A091JFF4_A0A091JFF4_EGRGA_188379 are exactly identical!
WARNING: Sequences tr_A0A091EAT3_A0A091EAT3_CORBR_85066 and tr_A0A091W9M0_A0A091W9M0_OPIHO_30419 are exactly identical!
WARNING: Sequences tr_A0A091EAT3_A0A091EAT3_CORBR_85066 and tr_A0A0A0AT54_A0A0A0AT54_CHAVO_50402 are exactly identical!
WARNING: Sequences tr_A0A164NSZ6_A0A164NSZ6_9HOMO_1314777 and tr_A0A165YYU6_A0A165YYU6_9HOMO_1314776 are exactly identical!
WARNING: Sequences tr_A0A2D0S9R2_A0A2D0S9R2_ICTPU_7998 and tr_A0A2D0S9R3_A0A2D0S9R3_ICTPU_7998 are exactly identical!
WARNING: Duplicate sequences found: 29

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/O95630/3_mltree/O95630.raxml.reduced.phy

Alignment comprises 1 partitions and 675 patterns

Partition 0: noname
Model: LG4X+R4
Alignment sites / patterns: 675 / 675
Gaps: 37.48 %
Invariant sites: 0.00 %


NOTE: Binary MSA file created: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/O95630/3_mltree/O95630.raxml.rba

Parallelization scheme autoconfig: 2 worker(s) x 4 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 / 169 / 13520
[00:00:00] Data distribution: max. searches per worker: 10

Starting ML tree search with 20 distinct starting trees

[00:00:00 -875815.381382] Initial branch length optimization
[00:00:08 -762187.844885] Model parameter optimization (eps = 10.000000)
[00:00:53 -760975.252131] AUTODETECT spr round 1 (radius: 5)
[00:03:39 -563667.787025] AUTODETECT spr round 2 (radius: 10)
[00:06:45 -403048.813307] AUTODETECT spr round 3 (radius: 15)
[00:10:12 -344066.247619] AUTODETECT spr round 4 (radius: 20)
[00:13:54 -331159.589262] AUTODETECT spr round 5 (radius: 25)
[00:18:06 -327763.329017] SPR radius for FAST iterations: 25 (autodetect)
[00:18:06 -327763.329017] Model parameter optimization (eps = 3.000000)
[00:18:30 -327615.114492] FAST spr round 1 (radius: 25)
[00:22:32 -297072.084236] FAST spr round 2 (radius: 25)
[00:25:29 -295977.530559] FAST spr round 3 (radius: 25)
[00:27:57 -295927.807247] FAST spr round 4 (radius: 25)
[00:30:06 -295912.814859] FAST spr round 5 (radius: 25)
[00:32:11 -295912.814377] Model parameter optimization (eps = 1.000000)
[00:32:20 -295912.277157] SLOW spr round 1 (radius: 5)
[00:35:18 -295837.951473] SLOW spr round 2 (radius: 5)
[00:37:59 -295837.147902] SLOW spr round 3 (radius: 5)
[00:40:36 -295837.147184] SLOW spr round 4 (radius: 10)
[00:43:19 -295835.992381] SLOW spr round 5 (radius: 5)
[00:46:37 -295824.240435] SLOW spr round 6 (radius: 5)
[00:49:34 -295813.504346] SLOW spr round 7 (radius: 5)
[00:52:15 -295813.504198] SLOW spr round 8 (radius: 10)
[00:54:55 -295813.504191] SLOW spr round 9 (radius: 15)
[00:59:40 -295813.504190] SLOW spr round 10 (radius: 20)
[01:06:31 -295813.504190] SLOW spr round 11 (radius: 25)
[01:09:46] [worker #1] ML tree search #2, logLikelihood: -295802.419986
[01:15:43 -295813.504190] Model parameter optimization (eps = 0.100000)

[01:15:55] [worker #0] ML tree search #1, logLikelihood: -295812.782559

[01:15:55 -875954.874972] Initial branch length optimization
[01:16:01 -761228.286770] Model parameter optimization (eps = 10.000000)
[01:16:38 -760121.182606] AUTODETECT spr round 1 (radius: 5)
[01:19:23 -552740.484205] AUTODETECT spr round 2 (radius: 10)
[01:22:34 -402671.073587] AUTODETECT spr round 3 (radius: 15)
[01:25:36 -345978.591836] AUTODETECT spr round 4 (radius: 20)
[01:28:50 -327368.572700] AUTODETECT spr round 5 (radius: 25)
[01:32:56 -325650.791755] SPR radius for FAST iterations: 25 (autodetect)
[01:32:56 -325650.791755] Model parameter optimization (eps = 3.000000)
[01:33:18 -325483.009099] FAST spr round 1 (radius: 25)
[01:37:37 -297337.246064] FAST spr round 2 (radius: 25)
[01:40:57 -296079.467978] FAST spr round 3 (radius: 25)
[01:43:43 -295917.056013] FAST spr round 4 (radius: 25)
[01:46:06 -295903.666932] FAST spr round 5 (radius: 25)
[01:48:22 -295902.256014] FAST spr round 6 (radius: 25)
[01:50:35 -295902.255961] Model parameter optimization (eps = 1.000000)
[01:50:56 -295894.383123] SLOW spr round 1 (radius: 5)
[01:54:06 -295832.264964] SLOW spr round 2 (radius: 5)
[01:57:04 -295825.247817] SLOW spr round 3 (radius: 5)
[01:59:54 -295825.247675] SLOW spr round 4 (radius: 10)
[02:02:53 -295824.362363] SLOW spr round 5 (radius: 5)
[02:06:22 -295824.225130] SLOW spr round 6 (radius: 5)
[02:09:26 -295824.225104] SLOW spr round 7 (radius: 10)
[02:12:24 -295824.225091] SLOW spr round 8 (radius: 15)
[02:17:19 -295824.225079] SLOW spr round 9 (radius: 20)
[02:24:15 -295824.225066] SLOW spr round 10 (radius: 25)
[02:26:44] [worker #1] ML tree search #4, logLikelihood: -295809.361480
[02:33:19 -295824.225053] Model parameter optimization (eps = 0.100000)

[02:33:33] [worker #0] ML tree search #3, logLikelihood: -295824.182220

[02:33:33 -874965.239946] Initial branch length optimization
[02:33:41 -762759.701783] Model parameter optimization (eps = 10.000000)
[02:34:30 -761284.770001] AUTODETECT spr round 1 (radius: 5)
[02:37:31 -565983.862616] AUTODETECT spr round 2 (radius: 10)
[02:40:54 -436388.390554] AUTODETECT spr round 3 (radius: 15)
[02:44:41 -363669.511735] AUTODETECT spr round 4 (radius: 20)
[02:48:28 -343208.128058] AUTODETECT spr round 5 (radius: 25)
[02:52:38 -340131.063252] SPR radius for FAST iterations: 25 (autodetect)
[02:52:38 -340131.063252] Model parameter optimization (eps = 3.000000)
[02:53:06 -339959.002937] FAST spr round 1 (radius: 25)
[02:57:34 -297253.480644] FAST spr round 2 (radius: 25)
[03:00:55 -296047.741328] FAST spr round 3 (radius: 25)
[03:03:49 -295915.824274] FAST spr round 4 (radius: 25)
[03:06:14 -295899.649985] FAST spr round 5 (radius: 25)
[03:08:27 -295896.770235] FAST spr round 6 (radius: 25)
[03:10:35 -295896.769850] Model parameter optimization (eps = 1.000000)
[03:10:55 -295894.221747] SLOW spr round 1 (radius: 5)
[03:14:04 -295818.640861] SLOW spr round 2 (radius: 5)
[03:17:00 -295814.452050] SLOW spr round 3 (radius: 5)
[03:19:53 -295814.374793] SLOW spr round 4 (radius: 10)
[03:22:47 -295813.452416] SLOW spr round 5 (radius: 5)
[03:26:16 -295813.452340] SLOW spr round 6 (radius: 10)
[03:29:35 -295813.398611] SLOW spr round 7 (radius: 15)
[03:34:23 -295813.398599] SLOW spr round 8 (radius: 20)
[03:41:49 -295813.398599] SLOW spr round 9 (radius: 25)
[03:46:18] [worker #1] ML tree search #6, logLikelihood: -295813.316515
[03:51:25 -295813.398599] Model parameter optimization (eps = 0.100000)

[03:51:39] [worker #0] ML tree search #5, logLikelihood: -295812.427604

[03:51:39 -877629.913396] Initial branch length optimization
[03:51:45 -765675.629746] Model parameter optimization (eps = 10.000000)
[03:52:36 -764375.765862] AUTODETECT spr round 1 (radius: 5)
[03:55:34 -562699.448088] AUTODETECT spr round 2 (radius: 10)
[03:58:54 -432464.991229] AUTODETECT spr round 3 (radius: 15)
[04:02:34 -376430.759480] AUTODETECT spr round 4 (radius: 20)
[04:06:44 -357937.315432] AUTODETECT spr round 5 (radius: 25)
[04:12:12 -344270.211926] SPR radius for FAST iterations: 25 (autodetect)
[04:12:12 -344270.211926] Model parameter optimization (eps = 3.000000)
[04:12:43 -344120.323972] FAST spr round 1 (radius: 25)
[04:17:19 -298135.749975] FAST spr round 2 (radius: 25)
[04:20:43 -295990.635137] FAST spr round 3 (radius: 25)
[04:23:30 -295916.827233] FAST spr round 4 (radius: 25)
[04:25:53 -295903.115134] FAST spr round 5 (radius: 25)
[04:28:08 -295903.114425] Model parameter optimization (eps = 1.000000)
[04:28:29 -295901.320453] SLOW spr round 1 (radius: 5)
[04:31:37 -295818.882840] SLOW spr round 2 (radius: 5)
[04:34:39 -295807.338811] SLOW spr round 3 (radius: 5)
[04:37:34 -295804.713241] SLOW spr round 4 (radius: 5)
[04:40:23 -295804.389067] SLOW spr round 5 (radius: 5)
[04:43:10 -295804.389001] SLOW spr round 6 (radius: 10)
[04:46:00 -295802.676429] SLOW spr round 7 (radius: 5)
[04:49:26 -295802.676420] SLOW spr round 8 (radius: 10)
[04:52:43 -295802.676420] SLOW spr round 9 (radius: 15)
[04:57:34 -295802.676420] SLOW spr round 10 (radius: 20)
[04:59:48] [worker #1] ML tree search #8, logLikelihood: -295806.736021
[05:05:08 -295802.676420] SLOW spr round 11 (radius: 25)
[05:14:50 -295802.676420] Model parameter optimization (eps = 0.100000)

[05:14:57] [worker #0] ML tree search #7, logLikelihood: -295802.614091

[05:14:57 -875975.732401] Initial branch length optimization
[05:15:03 -760621.177894] Model parameter optimization (eps = 10.000000)
[05:15:51 -759269.110342] AUTODETECT spr round 1 (radius: 5)
[05:18:54 -562406.229231] AUTODETECT spr round 2 (radius: 10)
[05:22:19 -428600.276987] AUTODETECT spr round 3 (radius: 15)
[05:26:00 -386411.145399] AUTODETECT spr round 4 (radius: 20)
[05:30:37 -349149.501485] AUTODETECT spr round 5 (radius: 25)
[05:35:33 -342164.002496] SPR radius for FAST iterations: 25 (autodetect)
[05:35:33 -342164.002496] Model parameter optimization (eps = 3.000000)
[05:36:00 -341950.355826] FAST spr round 1 (radius: 25)
[05:40:30 -297382.928341] FAST spr round 2 (radius: 25)
[05:43:46 -296045.171865] FAST spr round 3 (radius: 25)
[05:46:32 -295945.668936] FAST spr round 4 (radius: 25)
[05:49:02 -295904.851193] FAST spr round 5 (radius: 25)
[05:51:19 -295892.286476] FAST spr round 6 (radius: 25)
[05:53:32 -295892.283520] Model parameter optimization (eps = 1.000000)
[05:53:53 -295890.622598] SLOW spr round 1 (radius: 5)
[05:57:00 -295822.628631] SLOW spr round 2 (radius: 5)
[06:00:00 -295805.327466] SLOW spr round 3 (radius: 5)
[06:02:49 -295804.787531] SLOW spr round 4 (radius: 5)
[06:05:35 -295804.787100] SLOW spr round 5 (radius: 10)
[06:08:27 -295804.786938] SLOW spr round 6 (radius: 15)
[06:13:38 -295804.786876] SLOW spr round 7 (radius: 20)
[06:14:01] [worker #1] ML tree search #10, logLikelihood: -295816.909962
[06:20:56 -295804.786853] SLOW spr round 8 (radius: 25)
[06:30:21 -295804.786844] Model parameter optimization (eps = 0.100000)

[06:30:32] [worker #0] ML tree search #9, logLikelihood: -295804.652904

[06:30:32 -878085.827899] Initial branch length optimization
[06:30:37 -764182.922961] Model parameter optimization (eps = 10.000000)
[06:31:22 -762843.163987] AUTODETECT spr round 1 (radius: 5)
[06:34:19 -560891.290870] AUTODETECT spr round 2 (radius: 10)
[06:37:43 -424401.063007] AUTODETECT spr round 3 (radius: 15)
[06:41:14 -367592.472754] AUTODETECT spr round 4 (radius: 20)
[06:45:10 -337329.882709] AUTODETECT spr round 5 (radius: 25)
[06:50:20 -336606.557105] SPR radius for FAST iterations: 25 (autodetect)
[06:50:20 -336606.557105] Model parameter optimization (eps = 3.000000)
[06:50:48 -336360.295493] FAST spr round 1 (radius: 25)
[06:55:23 -297625.434304] FAST spr round 2 (radius: 25)
[06:58:43 -296029.184089] FAST spr round 3 (radius: 25)
[07:01:34 -295932.493332] FAST spr round 4 (radius: 25)
[07:03:58 -295903.271559] FAST spr round 5 (radius: 25)
[07:06:11 -295895.690982] FAST spr round 6 (radius: 25)
[07:08:19 -295895.690449] Model parameter optimization (eps = 1.000000)
[07:08:37 -295893.741459] SLOW spr round 1 (radius: 5)
[07:11:43 -295811.808663] SLOW spr round 2 (radius: 5)
[07:14:37 -295806.355718] SLOW spr round 3 (radius: 5)
[07:17:24 -295805.536444] SLOW spr round 4 (radius: 5)
[07:20:09 -295805.534767] SLOW spr round 5 (radius: 10)
[07:23:01 -295802.779841] SLOW spr round 6 (radius: 5)
[07:26:26 -295802.778720] SLOW spr round 7 (radius: 10)
[07:26:34] [worker #1] ML tree search #12, logLikelihood: -295851.053470
[07:29:43 -295802.778620] SLOW spr round 8 (radius: 15)
[07:34:33 -295802.778608] SLOW spr round 9 (radius: 20)
[07:42:23 -295802.778607] SLOW spr round 10 (radius: 25)
[07:52:26 -295802.778606] Model parameter optimization (eps = 0.100000)

[07:52:36] [worker #0] ML tree search #11, logLikelihood: -295802.377299

[07:52:36 -877257.013462] Initial branch length optimization
[07:52:44 -763650.403481] Model parameter optimization (eps = 10.000000)
[07:53:38 -762497.507816] AUTODETECT spr round 1 (radius: 5)
[07:56:39 -559991.883914] AUTODETECT spr round 2 (radius: 10)
[08:00:06 -410850.166671] AUTODETECT spr round 3 (radius: 15)
[08:03:42 -358886.185102] AUTODETECT spr round 4 (radius: 20)
[08:08:07 -331974.879382] AUTODETECT spr round 5 (radius: 25)
[08:13:34 -331002.053841] SPR radius for FAST iterations: 25 (autodetect)
[08:13:34 -331002.053841] Model parameter optimization (eps = 3.000000)
[08:14:06 -330805.748870] FAST spr round 1 (radius: 25)
[08:18:20 -297072.924795] FAST spr round 2 (radius: 25)
[08:21:28 -296060.245009] FAST spr round 3 (radius: 25)
[08:24:07 -295943.743005] FAST spr round 4 (radius: 25)
[08:26:29 -295926.899503] FAST spr round 5 (radius: 25)
[08:28:41 -295926.899298] Model parameter optimization (eps = 1.000000)
[08:29:05 -295925.336207] SLOW spr round 1 (radius: 5)
[08:32:11 -295811.789918] SLOW spr round 2 (radius: 5)
[08:35:09 -295801.269714] SLOW spr round 3 (radius: 5)
[08:37:59 -295797.895077] SLOW spr round 4 (radius: 5)
[08:40:47 -295794.688311] SLOW spr round 5 (radius: 5)
[08:43:32 -295794.688268] SLOW spr round 6 (radius: 10)
[08:43:49] [worker #1] ML tree search #14, logLikelihood: -295815.440112
[08:46:24 -295794.688260] SLOW spr round 7 (radius: 15)
[08:51:43 -295794.688253] SLOW spr round 8 (radius: 20)
[08:59:13 -295794.688245] SLOW spr round 9 (radius: 25)
[09:09:04 -295794.688237] Model parameter optimization (eps = 0.100000)

[09:09:23] [worker #0] ML tree search #13, logLikelihood: -295793.016977

[09:09:23 -869488.931386] Initial branch length optimization
[09:09:28 -758645.741774] Model parameter optimization (eps = 10.000000)
[09:10:33 -757268.295644] AUTODETECT spr round 1 (radius: 5)
[09:13:23 -543077.007004] AUTODETECT spr round 2 (radius: 10)
[09:16:51 -399491.503956] AUTODETECT spr round 3 (radius: 15)
[09:20:41 -350464.606588] AUTODETECT spr round 4 (radius: 20)
[09:24:41 -331572.244461] AUTODETECT spr round 5 (radius: 25)
[09:29:30 -328597.132637] SPR radius for FAST iterations: 25 (autodetect)
[09:29:30 -328597.132637] Model parameter optimization (eps = 3.000000)
[09:30:05 -328470.893881] FAST spr round 1 (radius: 25)
[09:34:22 -297086.384052] FAST spr round 2 (radius: 25)
[09:37:37 -296062.344605] FAST spr round 3 (radius: 25)
[09:40:26 -295934.613588] FAST spr round 4 (radius: 25)
[09:42:47 -295929.923359] FAST spr round 5 (radius: 25)
[09:44:58 -295929.921966] Model parameter optimization (eps = 1.000000)
[09:45:07 -295929.550479] SLOW spr round 1 (radius: 5)
[09:48:17 -295838.053213] SLOW spr round 2 (radius: 5)
[09:51:19 -295814.431841] SLOW spr round 3 (radius: 5)
[09:53:26] [worker #1] ML tree search #16, logLikelihood: -295807.256860
[09:54:06 -295814.318317] SLOW spr round 4 (radius: 5)
[09:56:52 -295814.315255] SLOW spr round 5 (radius: 10)
[09:59:40 -295806.390334] SLOW spr round 6 (radius: 5)
[10:03:05 -295805.568242] SLOW spr round 7 (radius: 5)
[10:05:53 -295805.568026] SLOW spr round 8 (radius: 10)
[10:08:34 -295805.568017] SLOW spr round 9 (radius: 15)
[10:12:36 -295805.568010] SLOW spr round 10 (radius: 20)
[10:18:17 -295805.568002] SLOW spr round 11 (radius: 25)
[10:25:54 -295805.567995] Model parameter optimization (eps = 0.100000)

[10:26:06] [worker #0] ML tree search #15, logLikelihood: -295804.706971

[10:26:06 -877329.904639] Initial branch length optimization
[10:26:11 -762414.722690] Model parameter optimization (eps = 10.000000)
[10:26:56 -761271.167619] AUTODETECT spr round 1 (radius: 5)
[10:29:20 -567414.092574] AUTODETECT spr round 2 (radius: 10)
[10:32:07 -412993.173119] AUTODETECT spr round 3 (radius: 15)
[10:35:16 -349434.913450] AUTODETECT spr round 4 (radius: 20)
[10:38:32 -330921.664147] AUTODETECT spr round 5 (radius: 25)
[10:43:10 -329297.163641] SPR radius for FAST iterations: 25 (autodetect)
[10:43:10 -329297.163641] Model parameter optimization (eps = 3.000000)
[10:43:32 -329078.599697] FAST spr round 1 (radius: 25)
[10:48:03 -297170.290030] FAST spr round 2 (radius: 25)
[10:51:11 -295969.931902] FAST spr round 3 (radius: 25)
[10:53:45 -295911.923428] FAST spr round 4 (radius: 25)
[10:55:38] [worker #1] ML tree search #18, logLikelihood: -295799.145736
[10:55:56 -295900.130688] FAST spr round 5 (radius: 25)
[10:58:11 -295898.675587] FAST spr round 6 (radius: 25)
[11:00:13 -295898.675497] Model parameter optimization (eps = 1.000000)
[11:00:47 -295895.051300] SLOW spr round 1 (radius: 5)
[11:04:05 -295823.562257] SLOW spr round 2 (radius: 5)
[11:07:02 -295816.340904] SLOW spr round 3 (radius: 5)
[11:09:51 -295812.591114] SLOW spr round 4 (radius: 5)
[11:12:27 -295812.589256] SLOW spr round 5 (radius: 10)
[11:15:22 -295812.588593] SLOW spr round 6 (radius: 15)
[11:20:42 -295812.588354] SLOW spr round 7 (radius: 20)
[11:27:53 -295812.588269] SLOW spr round 8 (radius: 25)
[11:37:53 -295812.588238] Model parameter optimization (eps = 0.100000)

[11:38:13] [worker #0] ML tree search #17, logLikelihood: -295810.330538

[11:38:13 -871328.386267] Initial branch length optimization
[11:38:20 -756785.769668] Model parameter optimization (eps = 10.000000)
[11:39:16 -755620.213027] AUTODETECT spr round 1 (radius: 5)
[11:42:15 -553605.728542] AUTODETECT spr round 2 (radius: 10)
[11:45:08 -420283.140291] AUTODETECT spr round 3 (radius: 15)
[11:48:45 -358797.847186] AUTODETECT spr round 4 (radius: 20)
[11:52:36 -335220.185912] AUTODETECT spr round 5 (radius: 25)
[11:56:59 -331857.590730] SPR radius for FAST iterations: 25 (autodetect)
[11:56:59 -331857.590730] Model parameter optimization (eps = 3.000000)
[11:57:35 -331696.251362] FAST spr round 1 (radius: 25)
[12:02:04 -297570.499137] FAST spr round 2 (radius: 25)
[12:05:19 -296075.007417] FAST spr round 3 (radius: 25)
[12:06:43] [worker #1] ML tree search #20, logLikelihood: -295809.442499
[12:08:07 -295955.681766] FAST spr round 4 (radius: 25)
[12:10:39 -295941.078859] FAST spr round 5 (radius: 25)
[12:12:53 -295941.077907] Model parameter optimization (eps = 1.000000)
[12:13:16 -295937.747822] SLOW spr round 1 (radius: 5)
[12:16:24 -295838.080484] SLOW spr round 2 (radius: 5)
[12:19:24 -295814.690667] SLOW spr round 3 (radius: 5)
[12:22:16 -295812.662825] SLOW spr round 4 (radius: 5)
[12:25:05 -295812.027773] SLOW spr round 5 (radius: 5)
[12:27:58 -295812.027749] SLOW spr round 6 (radius: 10)
[12:30:53 -295807.936322] SLOW spr round 7 (radius: 5)
[12:35:04 -295807.934760] SLOW spr round 8 (radius: 10)
[12:38:19 -295807.934557] SLOW spr round 9 (radius: 15)
[12:43:04 -295807.934524] SLOW spr round 10 (radius: 20)
[12:50:42 -295807.934518] SLOW spr round 11 (radius: 25)
[13:00:34 -295807.934517] Model parameter optimization (eps = 0.100000)

[13:00:47] [worker #0] ML tree search #19, logLikelihood: -295807.310540


Optimized model parameters:

   Partition 0: noname
   Rate heterogeneity: FREE (4 cats, mean),  weights&rates: (0.087464,0.172555) (0.106802,0.211784) (0.236370,0.616707) (0.569364,1.434087) 
   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: -295793.016977

AIC score: 595596.033955 / AICc score: 8639656.033955 / BIC score: 604648.032900
Free parameters (model + branch lengths): 2005

WARNING: Number of free parameters (K=2005) is larger than alignment size (n=675).
         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/O95630/3_mltree/O95630.raxml.bestTree
All ML trees saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/O95630/3_mltree/O95630.raxml.mlTrees
Optimized model saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/O95630/3_mltree/O95630.raxml.bestModel

Execution log saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/O95630/3_mltree/O95630.raxml.log

Analysis started: 01-Jul-2021 04:55:24 / finished: 01-Jul-2021 17:56:12

Elapsed time: 46847.875 seconds

Consumed energy: 4422.080 Wh (= 22 km in an electric car, or 111 km with an e-scooter!)