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 06:46:46 as follows:

raxml-ng --msa /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/P16885/2_msa/P16885_trimmed_msa.fasta --data-type AA --model LG4X --prefix /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/P16885/3_mltree/P16885 --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/P16885/2_msa/P16885_trimmed_msa.fasta
[00:00:00] Loaded alignment with 1001 taxa and 647 sites

WARNING: Sequences tr_M3XQR0_M3XQR0_MUSPF_9669 and tr_A0A2Y9KGU7_A0A2Y9KGU7_ENHLU_391180 are exactly identical!
WARNING: Sequences tr_G3QXU1_G3QXU1_GORGO_9595 and tr_H2QKD0_H2QKD0_PANTR_9598 are exactly identical!
WARNING: Sequences tr_G3QXU1_G3QXU1_GORGO_9595 and sp_P19174_PLCG1_HUMAN_9606 are exactly identical!
WARNING: Sequences tr_H2PBD1_H2PBD1_PONAB_9601 and tr_A0A2I3RKF6_A0A2I3RKF6_PANTR_9598 are exactly identical!
WARNING: Sequences tr_H2PBD1_H2PBD1_PONAB_9601 and sp_Q9UPR0_PLCL2_HUMAN_9606 are exactly identical!
WARNING: Sequences tr_H2PBD1_H2PBD1_PONAB_9601 and tr_A0A096MUM1_A0A096MUM1_PAPAN_9555 are exactly identical!
WARNING: Sequences tr_H2PBD1_H2PBD1_PONAB_9601 and tr_A0A0D9RC42_A0A0D9RC42_CHLSB_60711 are exactly identical!
WARNING: Sequences tr_H2PBD1_H2PBD1_PONAB_9601 and tr_A0A2K5L983_A0A2K5L983_CERAT_9531 are exactly identical!
WARNING: Sequences tr_H2PBD1_H2PBD1_PONAB_9601 and tr_A0A2K5XAK8_A0A2K5XAK8_MANLE_9568 are exactly identical!
WARNING: Sequences tr_H2PBD1_H2PBD1_PONAB_9601 and tr_A0A2R8ZE07_A0A2R8ZE07_PANPA_9597 are exactly identical!
WARNING: Sequences tr_A0A2I3RV12_A0A2I3RV12_PANTR_9598 and tr_A0A2R9C5Q7_A0A2R9C5Q7_PANPA_9597 are exactly identical!
WARNING: Sequences tr_A0A2I3SHP7_A0A2I3SHP7_PANTR_9598 and tr_A0A2R9BVU6_A0A2R9BVU6_PANPA_9597 are exactly identical!
WARNING: Sequences tr_A0A2I3SPP9_A0A2I3SPP9_PANTR_9598 and tr_A0A2R8ZFE7_A0A2R8ZFE7_PANPA_9597 are exactly identical!
WARNING: Sequences tr_A0A158Q0F3_A0A158Q0F3_BRUMA_6279 and tr_A0A0N4T397_A0A0N4T397_BRUPA_6280 are exactly identical!
WARNING: Sequences tr_F7GU01_F7GU01_MACMU_9544 and tr_A0A2K5KQ11_A0A2K5KQ11_CERAT_9531 are exactly identical!
WARNING: Sequences tr_F7GVF8_F7GVF8_MACMU_9544 and tr_G7NY20_G7NY20_MACFA_9541 are exactly identical!
WARNING: Sequences tr_F7GVF8_F7GVF8_MACMU_9544 and tr_A0A2K6CKD4_A0A2K6CKD4_MACNE_9545 are exactly identical!
WARNING: Sequences tr_F7H663_F7H663_MACMU_9544 and tr_A0A2K5NYC9_A0A2K5NYC9_CERAT_9531 are exactly identical!
WARNING: Sequences tr_F7H663_F7H663_MACMU_9544 and tr_A0A2K6DLY9_A0A2K6DLY9_MACNE_9545 are exactly identical!
WARNING: Sequences tr_H0YY72_H0YY72_TAEGU_59729 and tr_A0A218VEW1_A0A218VEW1_9PASE_299123 are exactly identical!
WARNING: Sequences tr_A0A1B8Y9Z8_A0A1B8Y9Z8_XENTR_8364 and tr_F6V4E2_F6V4E2_XENTR_8364 are exactly identical!
WARNING: Sequences tr_F1SRY6_F1SRY6_PIG_9823 and sp_Q8SPR7_PLCD4_PIG_9823 are exactly identical!
WARNING: Sequences tr_G7NYL0_G7NYL0_MACFA_9541 and tr_A0A2I3MCP9_A0A2I3MCP9_PAPAN_9555 are exactly identical!
WARNING: Sequences tr_A0A015JTD1_A0A015JTD1_9GLOM_1432141 and tr_A0A2H5R1Y1_A0A2H5R1Y1_RHIID_747089 are exactly identical!
WARNING: Sequences tr_A0A096NXD8_A0A096NXD8_PAPAN_9555 and tr_A0A2K5MB06_A0A2K5MB06_CERAT_9531 are exactly identical!
WARNING: Sequences tr_A0A096NXD8_A0A096NXD8_PAPAN_9555 and tr_A0A2K6DV46_A0A2K6DV46_MACNE_9545 are exactly identical!
WARNING: Sequences tr_A0A096NXD8_A0A096NXD8_PAPAN_9555 and tr_A0A2K5ZLL6_A0A2K5ZLL6_MANLE_9568 are exactly identical!
WARNING: Sequences tr_A0A096P654_A0A096P654_PAPAN_9555 and tr_A0A2K5M3Q0_A0A2K5M3Q0_CERAT_9531 are exactly identical!
WARNING: Sequences tr_A0A0V0X5Y1_A0A0V0X5Y1_9BILA_92179 and tr_A0A0V1KSP8_A0A0V1KSP8_9BILA_6335 are exactly identical!
WARNING: Sequences tr_A0A226N4Q4_A0A226N4Q4_CALSU_9009 and tr_A0A226P5M8_A0A226P5M8_COLVI_9014 are exactly identical!
WARNING: Sequences tr_A0A226N6P1_A0A226N6P1_CALSU_9009 and tr_A0A226P129_A0A226P129_COLVI_9014 are exactly identical!
WARNING: Sequences tr_A0A2D0QW08_A0A2D0QW08_ICTPU_7998 and tr_A0A2D0QWC6_A0A2D0QWC6_ICTPU_7998 are exactly identical!
WARNING: Sequences tr_A0A2D0QW08_A0A2D0QW08_ICTPU_7998 and tr_A0A2D0QXY5_A0A2D0QXY5_ICTPU_7998 are exactly identical!
WARNING: Sequences tr_A0A2D0QW08_A0A2D0QW08_ICTPU_7998 and tr_A0A2D0QYM5_A0A2D0QYM5_ICTPU_7998 are exactly identical!
WARNING: Sequences tr_A0A2D0SJ10_A0A2D0SJ10_ICTPU_7998 and tr_W5U851_W5U851_ICTPU_7998 are exactly identical!
WARNING: Sequences tr_A0A2D0T8X6_A0A2D0T8X6_ICTPU_7998 and tr_A0A2D0T8Z5_A0A2D0T8Z5_ICTPU_7998 are exactly identical!
WARNING: Sequences tr_A0A2K5M3I3_A0A2K5M3I3_CERAT_9531 and tr_A0A2K6AJD5_A0A2K6AJD5_MANLE_9568 are exactly identical!
WARNING: Sequences tr_A0A2U4B9U1_A0A2U4B9U1_TURTR_9739 and tr_A0A2U4B9W9_A0A2U4B9W9_TURTR_9739 are exactly identical!
WARNING: Duplicate sequences found: 38

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/P16885/3_mltree/P16885.raxml.reduced.phy

Alignment comprises 1 partitions and 647 patterns

Partition 0: noname
Model: LG4X+R4
Alignment sites / patterns: 647 / 647
Gaps: 7.06 %
Invariant sites: 0.00 %


NOTE: Binary MSA file created: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/P16885/3_mltree/P16885.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 / 162 / 12960
[00:00:00] Data distribution: max. searches per worker: 10

Starting ML tree search with 20 distinct starting trees

[00:00:00 -1074827.219308] Initial branch length optimization
[00:00:10 -905445.076639] Model parameter optimization (eps = 10.000000)
[00:00:52 -903582.395107] AUTODETECT spr round 1 (radius: 5)
[00:03:34 -551257.788308] AUTODETECT spr round 2 (radius: 10)
[00:06:18 -373279.036973] AUTODETECT spr round 3 (radius: 15)
[00:09:14 -320201.797590] AUTODETECT spr round 4 (radius: 20)
[00:12:49 -279643.561710] AUTODETECT spr round 5 (radius: 25)
[00:16:36 -276346.416280] SPR radius for FAST iterations: 25 (autodetect)
[00:16:36 -276346.416280] Model parameter optimization (eps = 3.000000)
[00:16:56 -276208.906200] FAST spr round 1 (radius: 25)
[00:19:53 -237043.229739] FAST spr round 2 (radius: 25)
[00:22:07 -235670.813561] FAST spr round 3 (radius: 25)
[00:24:14 -235582.552092] FAST spr round 4 (radius: 25)
[00:26:13 -235555.995124] FAST spr round 5 (radius: 25)
[00:28:09 -235555.854660] FAST spr round 6 (radius: 25)
[00:29:59 -235555.853891] Model parameter optimization (eps = 1.000000)
[00:30:18 -235550.378474] SLOW spr round 1 (radius: 5)
[00:32:51 -235484.458667] SLOW spr round 2 (radius: 5)
[00:35:20 -235473.694475] SLOW spr round 3 (radius: 5)
[00:37:43 -235473.693489] SLOW spr round 4 (radius: 10)
[00:40:09 -235472.009428] SLOW spr round 5 (radius: 5)
[00:43:05 -235472.008791] SLOW spr round 6 (radius: 10)
[00:45:48 -235472.008230] SLOW spr round 7 (radius: 15)
[00:49:18 -235472.007691] SLOW spr round 8 (radius: 20)
[00:54:58 -235472.007171] SLOW spr round 9 (radius: 25)
[01:01:19] [worker #1] ML tree search #2, logLikelihood: -235489.914762
[01:01:33 -235472.006666] Model parameter optimization (eps = 0.100000)

[01:01:46] [worker #0] ML tree search #1, logLikelihood: -235471.789813

[01:01:46 -1086141.024699] Initial branch length optimization
[01:01:53 -924683.218688] Model parameter optimization (eps = 10.000000)
[01:03:21 -922460.811263] AUTODETECT spr round 1 (radius: 5)
[01:06:11 -553094.907565] AUTODETECT spr round 2 (radius: 10)
[01:09:02 -402183.519381] AUTODETECT spr round 3 (radius: 15)
[01:12:08 -333447.511801] AUTODETECT spr round 4 (radius: 20)
[01:15:24 -300046.920724] AUTODETECT spr round 5 (radius: 25)
[01:19:13 -278379.405641] SPR radius for FAST iterations: 25 (autodetect)
[01:19:13 -278379.405641] Model parameter optimization (eps = 3.000000)
[01:19:37 -278250.976580] FAST spr round 1 (radius: 25)
[01:22:43 -237303.217904] FAST spr round 2 (radius: 25)
[01:25:13 -235641.284677] FAST spr round 3 (radius: 25)
[01:27:23 -235570.882603] FAST spr round 4 (radius: 25)
[01:29:25 -235564.495655] FAST spr round 5 (radius: 25)
[01:31:18 -235564.483845] Model parameter optimization (eps = 1.000000)
[01:31:32 -235562.484313] SLOW spr round 1 (radius: 5)
[01:34:03 -235489.432156] SLOW spr round 2 (radius: 5)
[01:36:36 -235480.663648] SLOW spr round 3 (radius: 5)
[01:38:57 -235480.663426] SLOW spr round 4 (radius: 10)
[01:41:25 -235478.627999] SLOW spr round 5 (radius: 5)
[01:44:25 -235466.342216] SLOW spr round 6 (radius: 5)
[01:47:05 -235464.299782] SLOW spr round 7 (radius: 5)
[01:49:38 -235459.002776] SLOW spr round 8 (radius: 5)
[01:52:00 -235459.002756] SLOW spr round 9 (radius: 10)
[01:54:28 -235459.002740] SLOW spr round 10 (radius: 15)
[01:58:14 -235459.002728] SLOW spr round 11 (radius: 20)
[02:04:05 -235459.002718] SLOW spr round 12 (radius: 25)
[02:11:09 -235459.002710] Model parameter optimization (eps = 0.100000)

[02:11:20] [worker #0] ML tree search #3, logLikelihood: -235458.595457

[02:11:20 -1078035.124620] Initial branch length optimization
[02:11:28 -916172.713871] Model parameter optimization (eps = 10.000000)
[02:12:12 -914311.394349] AUTODETECT spr round 1 (radius: 5)
[02:14:56 -546156.705148] AUTODETECT spr round 2 (radius: 10)
[02:17:42 -393380.382820] AUTODETECT spr round 3 (radius: 15)
[02:19:38] [worker #1] ML tree search #4, logLikelihood: -235468.986637
[02:20:42 -336859.472493] AUTODETECT spr round 4 (radius: 20)
[02:24:02 -285456.824701] AUTODETECT spr round 5 (radius: 25)
[02:27:35 -274926.233980] SPR radius for FAST iterations: 25 (autodetect)
[02:27:35 -274926.233980] Model parameter optimization (eps = 3.000000)
[02:27:57 -274798.505542] FAST spr round 1 (radius: 25)
[02:31:01 -237487.078878] FAST spr round 2 (radius: 25)
[02:33:19 -235641.157539] FAST spr round 3 (radius: 25)
[02:35:17 -235547.920380] FAST spr round 4 (radius: 25)
[02:37:05 -235540.611992] FAST spr round 5 (radius: 25)
[02:38:48 -235536.393510] FAST spr round 6 (radius: 25)
[02:40:26 -235536.393032] Model parameter optimization (eps = 1.000000)
[02:40:38 -235533.750942] SLOW spr round 1 (radius: 5)
[02:42:54 -235482.345715] SLOW spr round 2 (radius: 5)
[02:45:06 -235479.435579] SLOW spr round 3 (radius: 5)
[02:47:14 -235479.434827] SLOW spr round 4 (radius: 10)
[02:49:23 -235479.434130] SLOW spr round 5 (radius: 15)
[02:52:43 -235479.433467] SLOW spr round 6 (radius: 20)
[02:57:38 -235479.432835] SLOW spr round 7 (radius: 25)
[03:03:38 -235479.432227] Model parameter optimization (eps = 0.100000)

[03:03:47] [worker #0] ML tree search #5, logLikelihood: -235479.294038

[03:03:48 -1078855.899150] Initial branch length optimization
[03:03:56 -917956.534445] Model parameter optimization (eps = 10.000000)
[03:04:29 -915931.408996] AUTODETECT spr round 1 (radius: 5)
[03:06:52 -558660.560130] AUTODETECT spr round 2 (radius: 10)
[03:09:20 -400674.244455] AUTODETECT spr round 3 (radius: 15)
[03:12:02 -314218.394424] AUTODETECT spr round 4 (radius: 20)
[03:15:15 -270643.457767] AUTODETECT spr round 5 (radius: 25)
[03:18:32 -266522.858397] SPR radius for FAST iterations: 25 (autodetect)
[03:18:32 -266522.858397] Model parameter optimization (eps = 3.000000)
[03:18:51 -266415.882868] FAST spr round 1 (radius: 25)
[03:21:34 -237036.195515] FAST spr round 2 (radius: 25)
[03:23:50 -235665.192830] FAST spr round 3 (radius: 25)
[03:25:45 -235555.969899] FAST spr round 4 (radius: 25)
[03:26:49] [worker #1] ML tree search #6, logLikelihood: -235461.963051
[03:27:29 -235549.966330] FAST spr round 5 (radius: 25)
[03:29:10 -235549.965185] Model parameter optimization (eps = 1.000000)
[03:29:19 -235549.289146] SLOW spr round 1 (radius: 5)
[03:31:36 -235473.350211] SLOW spr round 2 (radius: 5)
[03:33:52 -235460.703042] SLOW spr round 3 (radius: 5)
[03:36:01 -235458.111331] SLOW spr round 4 (radius: 5)
[03:38:09 -235458.093839] SLOW spr round 5 (radius: 10)
[03:40:21 -235457.811512] SLOW spr round 6 (radius: 5)
[03:43:02 -235453.691071] SLOW spr round 7 (radius: 5)
[03:45:24 -235453.690880] SLOW spr round 8 (radius: 10)
[03:47:42 -235453.520367] SLOW spr round 9 (radius: 5)
[03:50:23 -235453.237766] SLOW spr round 10 (radius: 5)
[03:52:45 -235453.236968] SLOW spr round 11 (radius: 10)
[03:55:03 -235453.236897] SLOW spr round 12 (radius: 15)
[03:58:17 -235453.236871] SLOW spr round 13 (radius: 20)
[04:03:20 -235453.236852] SLOW spr round 14 (radius: 25)
[04:09:20 -235453.236837] Model parameter optimization (eps = 0.100000)

[04:09:30] [worker #0] ML tree search #7, logLikelihood: -235452.943602

[04:09:30 -1073736.011468] Initial branch length optimization
[04:09:38 -909357.403597] Model parameter optimization (eps = 10.000000)
[04:10:10 -907463.915179] AUTODETECT spr round 1 (radius: 5)
[04:12:32 -531820.708233] AUTODETECT spr round 2 (radius: 10)
[04:15:01 -389792.316050] AUTODETECT spr round 3 (radius: 15)
[04:17:38 -328915.792377] AUTODETECT spr round 4 (radius: 20)
[04:20:28 -294111.961336] AUTODETECT spr round 5 (radius: 25)
[04:24:16 -278517.844155] SPR radius for FAST iterations: 25 (autodetect)
[04:24:16 -278517.844155] Model parameter optimization (eps = 3.000000)
[04:24:21] [worker #1] ML tree search #8, logLikelihood: -235457.015658
[04:24:36 -278265.917137] FAST spr round 1 (radius: 25)
[04:27:26 -237862.787139] FAST spr round 2 (radius: 25)
[04:29:41 -235736.581363] FAST spr round 3 (radius: 25)
[04:31:40 -235582.996682] FAST spr round 4 (radius: 25)
[04:33:27 -235568.362735] FAST spr round 5 (radius: 25)
[04:35:08 -235561.478662] FAST spr round 6 (radius: 25)
[04:36:47 -235561.475209] Model parameter optimization (eps = 1.000000)
[04:37:00 -235558.670016] SLOW spr round 1 (radius: 5)
[04:39:16 -235497.274539] SLOW spr round 2 (radius: 5)
[04:41:31 -235481.670430] SLOW spr round 3 (radius: 5)
[04:43:42 -235477.498435] SLOW spr round 4 (radius: 5)
[04:45:50 -235477.497147] SLOW spr round 5 (radius: 10)
[04:48:01 -235473.451926] SLOW spr round 6 (radius: 5)
[04:50:40 -235473.450646] SLOW spr round 7 (radius: 10)
[04:53:02 -235473.450429] SLOW spr round 8 (radius: 15)
[04:56:08 -235473.450298] SLOW spr round 9 (radius: 20)
[05:01:08 -235473.450213] SLOW spr round 10 (radius: 25)
[05:06:52 -235473.450155] Model parameter optimization (eps = 0.100000)

[05:07:00] [worker #0] ML tree search #9, logLikelihood: -235473.239498

[05:07:00 -1072698.652596] Initial branch length optimization
[05:07:10 -908599.344765] Model parameter optimization (eps = 10.000000)
[05:07:53 -906693.662629] AUTODETECT spr round 1 (radius: 5)
[05:10:17 -549736.312711] AUTODETECT spr round 2 (radius: 10)
[05:12:48 -393232.222528] AUTODETECT spr round 3 (radius: 15)
[05:14:40] [worker #1] ML tree search #10, logLikelihood: -235461.424420
[05:15:23 -339370.961142] AUTODETECT spr round 4 (radius: 20)
[05:18:17 -322625.368763] AUTODETECT spr round 5 (radius: 25)
[05:21:48 -282861.734326] SPR radius for FAST iterations: 25 (autodetect)
[05:21:48 -282861.734326] Model parameter optimization (eps = 3.000000)
[05:22:11 -282667.587944] FAST spr round 1 (radius: 25)
[05:24:59 -238881.378203] FAST spr round 2 (radius: 25)
[05:27:13 -235777.198594] FAST spr round 3 (radius: 25)
[05:29:09 -235510.062343] FAST spr round 4 (radius: 25)
[05:30:54 -235499.702947] FAST spr round 5 (radius: 25)
[05:32:36 -235498.354149] FAST spr round 6 (radius: 25)
[05:34:16 -235498.353011] Model parameter optimization (eps = 1.000000)
[05:34:31 -235493.371250] SLOW spr round 1 (radius: 5)
[05:36:47 -235471.775146] SLOW spr round 2 (radius: 5)
[05:38:56 -235471.647794] SLOW spr round 3 (radius: 5)
[05:41:04 -235471.647216] SLOW spr round 4 (radius: 10)
[05:43:13 -235471.109012] SLOW spr round 5 (radius: 5)
[05:45:51 -235471.107099] SLOW spr round 6 (radius: 10)
[05:48:15 -235471.106629] SLOW spr round 7 (radius: 15)
[05:51:24 -235471.106203] SLOW spr round 8 (radius: 20)
[05:56:30 -235471.105783] SLOW spr round 9 (radius: 25)
[06:02:28 -235471.105363] Model parameter optimization (eps = 0.100000)

[06:02:38] [worker #0] ML tree search #11, logLikelihood: -235470.959032

[06:02:38 -1074815.029092] Initial branch length optimization
[06:02:43 -912673.881629] Model parameter optimization (eps = 10.000000)
[06:03:28 -910706.645609] AUTODETECT spr round 1 (radius: 5)
[06:05:56 -560131.671462] AUTODETECT spr round 2 (radius: 10)
[06:08:28 -387802.712946] AUTODETECT spr round 3 (radius: 15)
[06:11:05 -317396.573051] AUTODETECT spr round 4 (radius: 20)
[06:13:08] [worker #1] ML tree search #12, logLikelihood: -235455.219609
[06:14:14 -281172.621192] AUTODETECT spr round 5 (radius: 25)
[06:17:41 -269618.032179] SPR radius for FAST iterations: 25 (autodetect)
[06:17:41 -269618.032179] Model parameter optimization (eps = 3.000000)
[06:17:59 -269461.093995] FAST spr round 1 (radius: 25)
[06:20:41 -236853.257043] FAST spr round 2 (radius: 25)
[06:22:53 -235667.745461] FAST spr round 3 (radius: 25)
[06:24:50 -235542.513451] FAST spr round 4 (radius: 25)
[06:26:38 -235535.190606] FAST spr round 5 (radius: 25)
[06:28:18 -235535.190004] Model parameter optimization (eps = 1.000000)
[06:28:30 -235532.156663] SLOW spr round 1 (radius: 5)
[06:30:47 -235473.854626] SLOW spr round 2 (radius: 5)
[06:33:01 -235457.714640] SLOW spr round 3 (radius: 5)
[06:35:10 -235457.713257] SLOW spr round 4 (radius: 10)
[06:37:20 -235455.044497] SLOW spr round 5 (radius: 5)
[06:40:04 -235452.709413] SLOW spr round 6 (radius: 5)
[06:42:25 -235452.708893] SLOW spr round 7 (radius: 10)
[06:44:42 -235452.708476] SLOW spr round 8 (radius: 15)
[06:47:54 -235452.708141] SLOW spr round 9 (radius: 20)
[06:52:48 -235452.707872] SLOW spr round 10 (radius: 25)
[06:58:47 -235452.707654] Model parameter optimization (eps = 0.100000)

[06:58:52] [worker #0] ML tree search #13, logLikelihood: -235452.647141

[06:58:52 -1085011.599170] Initial branch length optimization
[06:58:59 -920551.602311] Model parameter optimization (eps = 10.000000)
[06:59:31 -918579.785692] AUTODETECT spr round 1 (radius: 5)
[07:01:58 -554855.746316] AUTODETECT spr round 2 (radius: 10)
[07:04:29 -386480.034735] AUTODETECT spr round 3 (radius: 15)
[07:07:09 -322992.953209] AUTODETECT spr round 4 (radius: 20)
[07:08:00] [worker #1] ML tree search #14, logLikelihood: -235459.920783
[07:10:16 -277437.058745] AUTODETECT spr round 5 (radius: 25)
[07:13:43 -273267.928788] SPR radius for FAST iterations: 25 (autodetect)
[07:13:43 -273267.928788] Model parameter optimization (eps = 3.000000)
[07:14:09 -273088.705414] FAST spr round 1 (radius: 25)
[07:17:07 -238022.467337] FAST spr round 2 (radius: 25)
[07:19:21 -235685.401723] FAST spr round 3 (radius: 25)
[07:21:24 -235555.439052] FAST spr round 4 (radius: 25)
[07:23:22 -235546.329969] FAST spr round 5 (radius: 25)
[07:25:14 -235546.329182] Model parameter optimization (eps = 1.000000)
[07:25:29 -235539.619363] SLOW spr round 1 (radius: 5)
[07:28:02 -235475.434848] SLOW spr round 2 (radius: 5)
[07:30:32 -235469.729727] SLOW spr round 3 (radius: 5)
[07:32:55 -235469.099548] SLOW spr round 4 (radius: 5)
[07:35:17 -235469.099105] SLOW spr round 5 (radius: 10)
[07:37:42 -235467.159013] SLOW spr round 6 (radius: 5)
[07:40:24 -235463.128282] SLOW spr round 7 (radius: 5)
[07:42:46 -235463.127834] SLOW spr round 8 (radius: 10)
[07:45:00 -235463.127387] SLOW spr round 9 (radius: 15)
[07:48:15 -235463.126939] SLOW spr round 10 (radius: 20)
[07:53:16 -235463.126492] SLOW spr round 11 (radius: 25)
[07:59:19 -235463.126045] Model parameter optimization (eps = 0.100000)

[07:59:26] [worker #0] ML tree search #15, logLikelihood: -235463.030191

[07:59:26 -1082491.081470] Initial branch length optimization
[07:59:34 -918934.852153] Model parameter optimization (eps = 10.000000)
[08:00:09 -917140.089843] AUTODETECT spr round 1 (radius: 5)
[08:02:37 -546873.356132] AUTODETECT spr round 2 (radius: 10)
[08:05:04 -382090.857625] AUTODETECT spr round 3 (radius: 15)
[08:06:29] [worker #1] ML tree search #16, logLikelihood: -235451.941998
[08:07:40 -325665.948990] AUTODETECT spr round 4 (radius: 20)
[08:10:48 -274441.116878] AUTODETECT spr round 5 (radius: 25)
[08:14:12 -272427.478234] SPR radius for FAST iterations: 25 (autodetect)
[08:14:12 -272427.478234] Model parameter optimization (eps = 3.000000)
[08:14:33 -272312.041661] FAST spr round 1 (radius: 25)
[08:17:22 -237296.085120] FAST spr round 2 (radius: 25)
[08:19:38 -235609.609985] FAST spr round 3 (radius: 25)
[08:21:42 -235533.412714] FAST spr round 4 (radius: 25)
[08:23:28 -235523.353917] FAST spr round 5 (radius: 25)
[08:25:09 -235523.342181] Model parameter optimization (eps = 1.000000)
[08:25:21 -235520.392089] SLOW spr round 1 (radius: 5)
[08:27:41 -235462.744116] SLOW spr round 2 (radius: 5)
[08:29:54 -235460.431667] SLOW spr round 3 (radius: 5)
[08:32:08 -235453.070372] SLOW spr round 4 (radius: 5)
[08:34:19 -235450.339902] SLOW spr round 5 (radius: 5)
[08:36:26 -235450.339372] SLOW spr round 6 (radius: 10)
[08:38:35 -235447.015667] SLOW spr round 7 (radius: 5)
[08:41:14 -235447.015633] SLOW spr round 8 (radius: 10)
[08:43:39 -235445.334627] SLOW spr round 9 (radius: 5)
[08:46:14 -235445.334563] SLOW spr round 10 (radius: 10)
[08:48:35 -235445.334549] SLOW spr round 11 (radius: 15)
[08:51:44 -235445.334537] SLOW spr round 12 (radius: 20)
[08:56:44 -235445.334528] SLOW spr round 13 (radius: 25)
[09:02:33 -235445.334520] Model parameter optimization (eps = 0.100000)

[09:02:38] [worker #0] ML tree search #17, logLikelihood: -235445.305915

[09:02:38 -1081725.581757] Initial branch length optimization
[09:02:47 -917290.574940] Model parameter optimization (eps = 10.000000)
[09:03:35 -915328.236829] AUTODETECT spr round 1 (radius: 5)
[09:06:01 -537997.652689] AUTODETECT spr round 2 (radius: 10)
[09:08:27 -364042.589075] AUTODETECT spr round 3 (radius: 15)
[09:09:38] [worker #1] ML tree search #18, logLikelihood: -235465.695904
[09:11:08 -282129.379638] AUTODETECT spr round 4 (radius: 20)
[09:14:25 -264470.236901] AUTODETECT spr round 5 (radius: 25)
[09:18:43 -263218.901056] SPR radius for FAST iterations: 25 (autodetect)
[09:18:43 -263218.901056] Model parameter optimization (eps = 3.000000)
[09:19:04 -263077.962331] FAST spr round 1 (radius: 25)
[09:21:49 -237142.445384] FAST spr round 2 (radius: 25)
[09:23:57 -235708.992407] FAST spr round 3 (radius: 25)
[09:25:56 -235606.704672] FAST spr round 4 (radius: 25)
[09:27:44 -235597.643877] FAST spr round 5 (radius: 25)
[09:29:25 -235596.260028] FAST spr round 6 (radius: 25)
[09:31:06 -235593.409639] FAST spr round 7 (radius: 25)
[09:32:44 -235593.408862] Model parameter optimization (eps = 1.000000)
[09:32:54 -235592.047621] SLOW spr round 1 (radius: 5)
[09:35:10 -235502.323988] SLOW spr round 2 (radius: 5)
[09:37:21 -235476.698548] SLOW spr round 3 (radius: 5)
[09:39:29 -235476.391237] SLOW spr round 4 (radius: 5)
[09:41:34 -235476.390231] SLOW spr round 5 (radius: 10)
[09:43:41 -235476.170734] SLOW spr round 6 (radius: 5)
[09:46:20 -235475.272051] SLOW spr round 7 (radius: 5)
[09:48:41 -235475.271717] SLOW spr round 8 (radius: 10)
[09:50:56 -235475.271610] SLOW spr round 9 (radius: 15)
[09:54:12 -235475.271561] SLOW spr round 10 (radius: 20)
[09:59:19 -235475.271534] SLOW spr round 11 (radius: 25)
[10:05:23 -235475.271517] Model parameter optimization (eps = 0.100000)

[10:05:30] [worker #0] ML tree search #19, logLikelihood: -235474.976317

[10:14:48] [worker #1] ML tree search #20, logLikelihood: -235468.975146

Optimized model parameters:

   Partition 0: noname
   Rate heterogeneity: FREE (4 cats, mean),  weights&rates: (0.178379,0.333438) (0.224563,0.485427) (0.349327,0.980817) (0.247731,1.973456) 
   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: -235445.305915

AIC score: 474900.611830 / AICc score: 8518960.611830 / BIC score: 483867.666150
Free parameters (model + branch lengths): 2005

WARNING: Number of free parameters (K=2005) is larger than alignment size (n=647).
         This might lead to overfitting and compromise tree inference results!


WARNING: Best ML tree contains 122 near-zero branches!

Best ML tree with collapsed near-zero branches saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/P16885/3_mltree/P16885.raxml.bestTreeCollapsed
Best ML tree saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/P16885/3_mltree/P16885.raxml.bestTree
All ML trees saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/P16885/3_mltree/P16885.raxml.mlTrees
Optimized model saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/P16885/3_mltree/P16885.raxml.bestModel

Execution log saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/P16885/3_mltree/P16885.raxml.log

Analysis started: 02-Jul-2021 06:46:46 / finished: 02-Jul-2021 17:01:35

Elapsed time: 36888.932 seconds

Consumed energy: 3265.666 Wh (= 16 km in an electric car, or 82 km with an e-scooter!)