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

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

RAxML-NG was called at 03-Jul-2021 17:02:45 as follows:

raxml-ng --msa /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q96P09/2_msa/Q96P09_trimmed_msa.fasta --data-type AA --model LG4X --prefix /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q96P09/3_mltree/Q96P09 --seed 2 --threads 5 --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 (5 threads), thread pinning: OFF

[00:00:00] Reading alignment from file: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q96P09/2_msa/Q96P09_trimmed_msa.fasta
[00:00:00] Loaded alignment with 1001 taxa and 233 sites

WARNING: Sequences tr_B4QVT1_B4QVT1_DROSI_7240 and tr_Q9VEM2_Q9VEM2_DROME_7227 are exactly identical!
WARNING: Sequences tr_B4QVT1_B4QVT1_DROSI_7240 and tr_B4IBK6_B4IBK6_DROSE_7238 are exactly identical!
WARNING: Sequences tr_M3XQJ2_M3XQJ2_MUSPF_9669 and tr_A0A2Y9KM82_A0A2Y9KM82_ENHLU_391180 are exactly identical!
WARNING: Sequences tr_M3XSP4_M3XSP4_MUSPF_9669 and tr_A0A2Y9KUG4_A0A2Y9KUG4_ENHLU_391180 are exactly identical!
WARNING: Sequences tr_G3QNH3_G3QNH3_GORGO_9595 and tr_H2QCP1_H2QCP1_PANTR_9598 are exactly identical!
WARNING: Sequences tr_G3QNH3_G3QNH3_GORGO_9595 and sp_Q8WZ73_RFFL_HUMAN_9606 are exactly identical!
WARNING: Sequences tr_G3QNH3_G3QNH3_GORGO_9595 and tr_A0A2R9AAH6_A0A2R9AAH6_PANPA_9597 are exactly identical!
WARNING: Sequences tr_G3QZ38_G3QZ38_GORGO_9595 and tr_H2Q4M6_H2Q4M6_PANTR_9598 are exactly identical!
WARNING: Sequences tr_G3QZ38_G3QZ38_GORGO_9595 and sp_Q13490_BIRC2_HUMAN_9606 are exactly identical!
WARNING: Sequences tr_G3QZ38_G3QZ38_GORGO_9595 and tr_A0A2R8Z7Y7_A0A2R8Z7Y7_PANPA_9597 are exactly identical!
WARNING: Sequences tr_G3RB95_G3RB95_GORGO_9595 and tr_H2PHZ8_H2PHZ8_PONAB_9601 are exactly identical!
WARNING: Sequences tr_Q28XZ5_Q28XZ5_DROPS_46245 and tr_B4GGC2_B4GGC2_DROPE_7234 are exactly identical!
WARNING: Sequences tr_A0A2J8L0U1_A0A2J8L0U1_PANTR_9598 and tr_A0A2R9C0Y4_A0A2R9C0Y4_PANPA_9597 are exactly identical!
WARNING: Sequences tr_H2R0D4_H2R0D4_PANTR_9598 and sp_Q8WY64_MYLIP_HUMAN_9606 are exactly identical!
WARNING: Sequences tr_H2R0D4_H2R0D4_PANTR_9598 and tr_A0A2R8ZC89_A0A2R8ZC89_PANPA_9597 are exactly identical!
WARNING: Sequences tr_K7D8W8_K7D8W8_PANTR_9598 and tr_A0A2R9A858_A0A2R9A858_PANPA_9597 are exactly identical!
WARNING: Sequences tr_W5PYL3_W5PYL3_SHEEP_9940 and sp_Q5E9J6_RNF34_BOVIN_9913 are exactly identical!
WARNING: Sequences tr_A0A088A7X5_A0A088A7X5_APIME_7460 and tr_A0A2A3EQ87_A0A2A3EQ87_APICC_94128 are exactly identical!
WARNING: Sequences tr_A0A158NKP4_A0A158NKP4_ATTCE_12957 and tr_A0A151WRQ9_A0A151WRQ9_9HYME_64791 are exactly identical!
WARNING: Sequences tr_A0A158NKP4_A0A158NKP4_ATTCE_12957 and tr_A0A195DG35_A0A195DG35_9HYME_471704 are exactly identical!
WARNING: Sequences tr_A0A158NKP4_A0A158NKP4_ATTCE_12957 and tr_A0A195BLW9_A0A195BLW9_9HYME_520822 are exactly identical!
WARNING: Sequences tr_A0A158NKP4_A0A158NKP4_ATTCE_12957 and tr_A0A195CJV5_A0A195CJV5_9HYME_456900 are exactly identical!
WARNING: Sequences tr_A0A158NRR2_A0A158NRR2_ATTCE_12957 and tr_A0A195BQ09_A0A195BQ09_9HYME_520822 are exactly identical!
WARNING: Sequences tr_K1QAX5_K1QAX5_CRAGI_29159 and tr_K1R0E3_K1R0E3_CRAGI_29159 are exactly identical!
WARNING: Sequences tr_A0A1D5Q1U6_A0A1D5Q1U6_MACMU_9544 and tr_G7P7P1_G7P7P1_MACFA_9541 are exactly identical!
WARNING: Sequences tr_A0A1D5R358_A0A1D5R358_MACMU_9544 and tr_G7PU30_G7PU30_MACFA_9541 are exactly identical!
WARNING: Sequences tr_F7FEI6_F7FEI6_MACMU_9544 and tr_A0A0D9S1T4_A0A0D9S1T4_CHLSB_60711 are exactly identical!
WARNING: Sequences tr_F7HHH8_F7HHH8_MACMU_9544 and tr_A0A0D9RUQ1_A0A0D9RUQ1_CHLSB_60711 are exactly identical!
WARNING: Sequences tr_H9FTU3_H9FTU3_MACMU_9544 and tr_A0A096NAP9_A0A096NAP9_PAPAN_9555 are exactly identical!
WARNING: Sequences tr_H9FTU3_H9FTU3_MACMU_9544 and tr_A0A0D9S0F4_A0A0D9S0F4_CHLSB_60711 are exactly identical!
WARNING: Sequences tr_H9FTU3_H9FTU3_MACMU_9544 and tr_A0A2K5LDZ2_A0A2K5LDZ2_CERAT_9531 are exactly identical!
WARNING: Sequences tr_H0ZR83_H0ZR83_TAEGU_59729 and tr_A0A218VAB9_A0A218VAB9_9PASE_299123 are exactly identical!
WARNING: Sequences tr_X1WKE1_X1WKE1_ACYPI_7029 and tr_X1XJN5_X1XJN5_ACYPI_7029 are exactly identical!
WARNING: Sequences tr_X1WKE1_X1WKE1_ACYPI_7029 and tr_X1XP01_X1XP01_ACYPI_7029 are exactly identical!
WARNING: Sequences tr_X1WMK2_X1WMK2_ACYPI_7029 and tr_X1X011_X1X011_ACYPI_7029 are exactly identical!
WARNING: Sequences tr_X1WZI0_X1WZI0_ACYPI_7029 and tr_X1XGA4_X1XGA4_ACYPI_7029 are exactly identical!
WARNING: Sequences tr_D2HJ47_D2HJ47_AILME_9646 and tr_A0A384DMI6_A0A384DMI6_URSMA_29073 are exactly identical!
WARNING: Sequences tr_G7PNJ6_G7PNJ6_MACFA_9541 and tr_A0A096NYE4_A0A096NYE4_PAPAN_9555 are exactly identical!
WARNING: Sequences tr_G7PNJ6_G7PNJ6_MACFA_9541 and tr_A0A2K5L6K9_A0A2K5L6K9_CERAT_9531 are exactly identical!
WARNING: Sequences tr_G7PNJ6_G7PNJ6_MACFA_9541 and tr_A0A2K6DEC5_A0A2K6DEC5_MACNE_9545 are exactly identical!
WARNING: Sequences tr_G7PNJ6_G7PNJ6_MACFA_9541 and tr_A0A2K6A571_A0A2K6A571_MANLE_9568 are exactly identical!
WARNING: Sequences tr_T1JSF1_T1JSF1_TETUR_32264 and tr_T1K6L9_T1K6L9_TETUR_32264 are exactly identical!
WARNING: Sequences tr_T1K8X2_T1K8X2_TETUR_32264 and tr_T1KRM4_T1KRM4_TETUR_32264 are exactly identical!
WARNING: Sequences tr_A0A096MN99_A0A096MN99_PAPAN_9555 and tr_A0A2K5N5Q0_A0A2K5N5Q0_CERAT_9531 are exactly identical!
WARNING: Sequences tr_A0A096MN99_A0A096MN99_PAPAN_9555 and tr_A0A2K6CZT7_A0A2K6CZT7_MACNE_9545 are exactly identical!
WARNING: Sequences tr_A0A096MN99_A0A096MN99_PAPAN_9555 and tr_A0A2K5Z3X5_A0A2K5Z3X5_MANLE_9568 are exactly identical!
WARNING: Sequences tr_A0A096NL29_A0A096NL29_PAPAN_9555 and tr_A0A0D9R5F6_A0A0D9R5F6_CHLSB_60711 are exactly identical!
WARNING: Sequences tr_A0A096NL29_A0A096NL29_PAPAN_9555 and tr_A0A2K5NU78_A0A2K5NU78_CERAT_9531 are exactly identical!
WARNING: Sequences tr_A0A096NL29_A0A096NL29_PAPAN_9555 and tr_A0A2K6DG22_A0A2K6DG22_MACNE_9545 are exactly identical!
WARNING: Sequences tr_A0A096NL29_A0A096NL29_PAPAN_9555 and tr_A0A2K5XX19_A0A2K5XX19_MANLE_9568 are exactly identical!
WARNING: Sequences tr_A0A096P3V7_A0A096P3V7_PAPAN_9555 and tr_A0A0D9R1X3_A0A0D9R1X3_CHLSB_60711 are exactly identical!
WARNING: Sequences tr_A0A096P3V7_A0A096P3V7_PAPAN_9555 and tr_A0A2K6A2W5_A0A2K6A2W5_MANLE_9568 are exactly identical!
WARNING: Sequences tr_A0A151P7A2_A0A151P7A2_ALLMI_8496 and tr_A0A3Q0HET8_A0A3Q0HET8_ALLSI_38654 are exactly identical!
WARNING: Sequences tr_A0A2D0RIM1_A0A2D0RIM1_ICTPU_7998 and tr_A0A2D0RIN6_A0A2D0RIN6_ICTPU_7998 are exactly identical!
WARNING: Sequences tr_A0A2D0RIM7_A0A2D0RIM7_ICTPU_7998 and tr_A0A2D0RIN8_A0A2D0RIN8_ICTPU_7998 are exactly identical!
WARNING: Sequences tr_A0A2D0SXL8_A0A2D0SXL8_ICTPU_7998 and tr_Q804E2_Q804E2_ICTPU_7998 are exactly identical!
WARNING: Sequences tr_A0A2G8JJD4_A0A2G8JJD4_STIJA_307972 and tr_A0A2G8KVP2_A0A2G8KVP2_STIJA_307972 are exactly identical!
WARNING: Sequences tr_A0A2U3VXH3_A0A2U3VXH3_ODORO_9708 and tr_A0A2U3YG34_A0A2U3YG34_LEPWE_9713 are exactly identical!
WARNING: Sequences tr_A0A2U3X226_A0A2U3X226_ODORO_9708 and tr_A0A2U3Z1X8_A0A2U3Z1X8_LEPWE_9713 are exactly identical!
WARNING: Sequences tr_A0A2Y9FG71_A0A2Y9FG71_PHYCD_9755 and tr_A0A384AV53_A0A384AV53_BALAS_310752 are exactly identical!
WARNING: Duplicate sequences found: 60

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/Q96P09/3_mltree/Q96P09.raxml.reduced.phy

Alignment comprises 1 partitions and 233 patterns

Partition 0: noname
Model: LG4X+R4
Alignment sites / patterns: 233 / 233
Gaps: 21.62 %
Invariant sites: 0.00 %


NOTE: Binary MSA file created: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q96P09/3_mltree/Q96P09.raxml.rba

Parallelization scheme autoconfig: 5 worker(s) x 1 thread(s)

Parallel reduction/worker buffer size: 1 KB  / 0 KB

[00:00:00] Generating 20 random starting tree(s) with 1001 taxa
[00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 233 / 18640
[00:00:00] Data distribution: max. searches per worker: 4

Starting ML tree search with 20 distinct starting trees

[00:00:00 -401894.420437] Initial branch length optimization
[00:00:07 -332878.085017] Model parameter optimization (eps = 10.000000)
[00:01:24 -332056.316130] AUTODETECT spr round 1 (radius: 5)
[00:05:01 -263480.523560] AUTODETECT spr round 2 (radius: 10)
[00:09:08 -206374.600585] AUTODETECT spr round 3 (radius: 15)
[00:13:48 -165001.436977] AUTODETECT spr round 4 (radius: 20)
[00:19:15 -147557.810989] AUTODETECT spr round 5 (radius: 25)
[00:26:36 -141251.671276] SPR radius for FAST iterations: 25 (autodetect)
[00:26:36 -141251.671276] Model parameter optimization (eps = 3.000000)
[00:27:10 -141135.393777] FAST spr round 1 (radius: 25)
[00:32:58 -126034.366954] FAST spr round 2 (radius: 25)
[00:37:09 -125253.445557] FAST spr round 3 (radius: 25)
[00:40:32 -125161.345595] FAST spr round 4 (radius: 25)
[00:43:34 -125139.749484] FAST spr round 5 (radius: 25)
[00:46:19 -125127.806545] FAST spr round 6 (radius: 25)
[00:48:52 -125127.349821] FAST spr round 7 (radius: 25)
[00:51:19 -125127.348135] Model parameter optimization (eps = 1.000000)
[00:51:40 -125114.809537] SLOW spr round 1 (radius: 5)
[00:55:09 -125094.691989] SLOW spr round 2 (radius: 5)
[00:58:26 -125093.387131] SLOW spr round 3 (radius: 5)
[01:01:37 -125093.386657] SLOW spr round 4 (radius: 10)
[01:04:56 -125092.605867] SLOW spr round 5 (radius: 5)
[01:08:55 -125092.369290] SLOW spr round 6 (radius: 5)
[01:12:27 -125092.368087] SLOW spr round 7 (radius: 10)
[01:15:56 -125091.739470] SLOW spr round 8 (radius: 5)
[01:19:49 -125090.209217] SLOW spr round 9 (radius: 5)
[01:23:18 -125090.209217] SLOW spr round 10 (radius: 10)
[01:26:46 -125089.961286] SLOW spr round 11 (radius: 5)
[01:30:38 -125089.792047] SLOW spr round 12 (radius: 5)
[01:34:07 -125089.791863] SLOW spr round 13 (radius: 10)
[01:37:31 -125089.791855] SLOW spr round 14 (radius: 15)
[01:43:40 -125088.886303] SLOW spr round 15 (radius: 5)
[01:47:39 -125088.884928] SLOW spr round 16 (radius: 10)
[01:51:36 -125088.590394] SLOW spr round 17 (radius: 5)
[01:55:26 -125088.257037] SLOW spr round 18 (radius: 5)
[01:56:41] [worker #2] ML tree search #3, logLikelihood: -125052.805384
[01:58:52 -125088.255551] SLOW spr round 19 (radius: 10)
[02:02:15 -125088.255362] SLOW spr round 20 (radius: 15)
[02:08:38 -125086.525078] SLOW spr round 21 (radius: 5)
[02:12:48 -125079.468740] SLOW spr round 22 (radius: 5)
[02:16:28 -125078.155079] SLOW spr round 23 (radius: 5)
[02:19:49 -125078.154192] SLOW spr round 24 (radius: 10)
[02:23:09 -125078.154137] SLOW spr round 25 (radius: 15)
[02:29:43 -125078.154132] SLOW spr round 26 (radius: 20)
[02:33:16] [worker #3] ML tree search #4, logLikelihood: -125129.697891
[02:39:14 -125078.154132] SLOW spr round 27 (radius: 25)
[02:50:16] [worker #1] ML tree search #2, logLikelihood: -125094.678645
[02:51:05 -125078.154132] Model parameter optimization (eps = 0.100000)

[02:51:12] [worker #0] ML tree search #1, logLikelihood: -125078.133538

[02:51:12 -400266.479049] Initial branch length optimization
[02:51:19 -331907.363778] Model parameter optimization (eps = 10.000000)
[02:52:41 -331011.714783] AUTODETECT spr round 1 (radius: 5)
[02:56:19 -259213.608862] AUTODETECT spr round 2 (radius: 10)
[03:00:20 -200111.653845] AUTODETECT spr round 3 (radius: 15)
[03:04:36 -168133.072553] AUTODETECT spr round 4 (radius: 20)
[03:05:43] [worker #4] ML tree search #5, logLikelihood: -125059.413692
[03:09:33 -153868.532449] AUTODETECT spr round 5 (radius: 25)
[03:15:16 -147267.265314] SPR radius for FAST iterations: 25 (autodetect)
[03:15:16 -147267.265314] Model parameter optimization (eps = 3.000000)
[03:15:47 -147131.128798] FAST spr round 1 (radius: 25)
[03:21:53 -128148.180328] FAST spr round 2 (radius: 25)
[03:26:17 -125357.662861] FAST spr round 3 (radius: 25)
[03:29:43 -125197.907953] FAST spr round 4 (radius: 25)
[03:32:42 -125165.786193] FAST spr round 5 (radius: 25)
[03:35:26 -125156.183029] FAST spr round 6 (radius: 25)
[03:38:00 -125154.902174] FAST spr round 7 (radius: 25)
[03:40:29 -125154.901994] Model parameter optimization (eps = 1.000000)
[03:40:42 -125154.249495] SLOW spr round 1 (radius: 5)
[03:43:59 -125125.959204] SLOW spr round 2 (radius: 5)
[03:46:40 -125121.267882] SLOW spr round 3 (radius: 5)
[03:49:22 -125119.823933] SLOW spr round 4 (radius: 5)
[03:51:56 -125119.823729] SLOW spr round 5 (radius: 10)
[03:54:32 -125115.425261] SLOW spr round 6 (radius: 5)
[03:58:17 -125112.190266] SLOW spr round 7 (radius: 5)
[04:01:55 -125108.592873] SLOW spr round 8 (radius: 5)
[04:05:16 -125108.574964] SLOW spr round 9 (radius: 10)
[04:08:31 -125108.572025] SLOW spr round 10 (radius: 15)
[04:14:37 -125101.564283] SLOW spr round 11 (radius: 5)
[04:18:47 -125094.589673] SLOW spr round 12 (radius: 5)
[04:22:23 -125094.316928] SLOW spr round 13 (radius: 5)
[04:25:45 -125094.315243] SLOW spr round 14 (radius: 10)
[04:29:01 -125093.973916] SLOW spr round 15 (radius: 5)
[04:33:00 -125093.272952] SLOW spr round 16 (radius: 5)
[04:36:35 -125090.487463] SLOW spr round 17 (radius: 5)
[04:39:56 -125087.527862] SLOW spr round 18 (radius: 5)
[04:43:09 -125087.527484] SLOW spr round 19 (radius: 10)
[04:46:23 -125087.527462] SLOW spr round 20 (radius: 15)
[04:52:40 -125083.679660] SLOW spr round 21 (radius: 5)
[04:56:44 -125083.397284] SLOW spr round 22 (radius: 5)
[05:00:18 -125083.396427] SLOW spr round 23 (radius: 10)
[05:03:43 -125083.396344] SLOW spr round 24 (radius: 15)
[05:09:47 -125083.396320] SLOW spr round 25 (radius: 20)
[05:14:50] [worker #1] ML tree search #7, logLikelihood: -125077.603045
[05:18:18 -125083.040020] SLOW spr round 26 (radius: 5)
[05:22:28 -125078.901211] SLOW spr round 27 (radius: 5)
[05:26:07 -125078.900946] SLOW spr round 28 (radius: 10)
[05:29:35 -125078.900930] SLOW spr round 29 (radius: 15)
[05:35:35 -125078.900926] SLOW spr round 30 (radius: 20)
[05:44:10 -125078.900923] SLOW spr round 31 (radius: 25)
[05:49:28] [worker #2] ML tree search #8, logLikelihood: -125055.953135
[05:55:17 -125078.900921] Model parameter optimization (eps = 0.100000)

[05:55:27] [worker #0] ML tree search #6, logLikelihood: -125078.818920

[05:55:27 -400286.028632] Initial branch length optimization
[05:55:34 -329789.682701] Model parameter optimization (eps = 10.000000)
[05:56:47 -328869.210863] AUTODETECT spr round 1 (radius: 5)
[05:57:53] [worker #3] ML tree search #9, logLikelihood: -125056.711511
[06:00:25 -257332.357733] AUTODETECT spr round 2 (radius: 10)
[06:04:27 -195943.395447] AUTODETECT spr round 3 (radius: 15)
[06:07:33] [worker #4] ML tree search #10, logLikelihood: -125129.354373
[06:08:38 -166154.671237] AUTODETECT spr round 4 (radius: 20)
[06:13:39 -146341.159605] AUTODETECT spr round 5 (radius: 25)
[06:19:03 -141368.521587] SPR radius for FAST iterations: 25 (autodetect)
[06:19:03 -141368.521587] Model parameter optimization (eps = 3.000000)
[06:19:27 -141157.769438] FAST spr round 1 (radius: 25)
[06:24:24 -125999.045683] FAST spr round 2 (radius: 25)
[06:27:51 -125246.808430] FAST spr round 3 (radius: 25)
[06:30:38 -125143.265617] FAST spr round 4 (radius: 25)
[06:32:55 -125133.336098] FAST spr round 5 (radius: 25)
[06:35:01 -125131.673823] FAST spr round 6 (radius: 25)
[06:37:02 -125131.672648] Model parameter optimization (eps = 1.000000)
[06:37:18 -125123.497766] SLOW spr round 1 (radius: 5)
[06:40:05 -125096.877753] SLOW spr round 2 (radius: 5)
[06:42:46 -125089.536511] SLOW spr round 3 (radius: 5)
[06:45:20 -125088.455403] SLOW spr round 4 (radius: 5)
[06:47:52 -125088.453977] SLOW spr round 5 (radius: 10)
[06:50:29 -125086.572808] SLOW spr round 6 (radius: 5)
[06:53:40 -125085.017288] SLOW spr round 7 (radius: 5)
[06:56:30 -125083.653425] SLOW spr round 8 (radius: 5)
[06:59:09 -125083.653124] SLOW spr round 9 (radius: 10)
[07:01:47 -125083.252941] SLOW spr round 10 (radius: 5)
[07:04:55 -125083.252004] SLOW spr round 11 (radius: 10)
[07:07:59 -125082.616093] SLOW spr round 12 (radius: 5)
[07:11:05 -125081.150419] SLOW spr round 13 (radius: 5)
[07:13:52 -125081.150408] SLOW spr round 14 (radius: 10)
[07:16:35 -125080.969878] SLOW spr round 15 (radius: 5)
[07:19:43 -125079.691330] SLOW spr round 16 (radius: 5)
[07:22:32 -125079.691116] SLOW spr round 17 (radius: 10)
[07:25:16 -125077.547955] SLOW spr round 18 (radius: 5)
[07:28:27 -125072.952691] SLOW spr round 19 (radius: 5)
[07:31:16 -125072.397007] SLOW spr round 20 (radius: 5)
[07:32:15] [worker #1] ML tree search #12, logLikelihood: -125072.620889
[07:33:54 -125072.395906] SLOW spr round 21 (radius: 10)
[07:36:30 -125072.395874] SLOW spr round 22 (radius: 15)
[07:41:43 -125071.582625] SLOW spr round 23 (radius: 5)
[07:44:25] [worker #3] ML tree search #14, logLikelihood: -125038.715775
[07:45:00 -125071.582422] SLOW spr round 24 (radius: 10)
[07:48:08 -125071.582398] SLOW spr round 25 (radius: 15)
[07:52:55 -125071.582384] SLOW spr round 26 (radius: 20)
[08:00:33 -125071.036120] SLOW spr round 27 (radius: 5)
[08:03:59 -125071.035701] SLOW spr round 28 (radius: 10)
[08:07:24 -125068.854115] SLOW spr round 29 (radius: 5)
[08:07:34] [worker #2] ML tree search #13, logLikelihood: -125073.782551
[08:08:38] [worker #4] ML tree search #15, logLikelihood: -125068.136071
[08:10:31 -125068.849365] SLOW spr round 30 (radius: 10)
[08:13:26 -125068.848800] SLOW spr round 31 (radius: 15)
[08:18:18 -125068.848722] SLOW spr round 32 (radius: 20)
[08:25:47 -125068.848700] SLOW spr round 33 (radius: 25)
[08:34:51 -125068.848685] Model parameter optimization (eps = 0.100000)

[08:35:08] [worker #0] ML tree search #11, logLikelihood: -125068.101266

[08:35:08 -400020.542857] Initial branch length optimization
[08:35:13 -331435.457195] Model parameter optimization (eps = 10.000000)
[08:36:19 -330500.985524] AUTODETECT spr round 1 (radius: 5)
[08:39:14 -257424.677161] AUTODETECT spr round 2 (radius: 10)
[08:42:35 -200921.705403] AUTODETECT spr round 3 (radius: 15)
[08:46:29 -166581.740984] AUTODETECT spr round 4 (radius: 20)
[08:51:13 -143461.728540] AUTODETECT spr round 5 (radius: 25)
[08:56:31 -141074.168062] SPR radius for FAST iterations: 25 (autodetect)
[08:56:31 -141074.168062] Model parameter optimization (eps = 3.000000)
[08:56:57 -140967.843427] FAST spr round 1 (radius: 25)
[09:01:37 -126010.669302] FAST spr round 2 (radius: 25)
[09:04:55 -125234.298396] FAST spr round 3 (radius: 25)
[09:07:35 -125181.683659] FAST spr round 4 (radius: 25)
[09:09:56 -125174.708477] FAST spr round 5 (radius: 25)
[09:12:04 -125174.707297] Model parameter optimization (eps = 1.000000)
[09:12:24 -125165.233768] SLOW spr round 1 (radius: 5)
[09:15:14 -125129.211160] SLOW spr round 2 (radius: 5)
[09:17:59 -125123.471544] SLOW spr round 3 (radius: 5)
[09:20:37 -125123.389103] SLOW spr round 4 (radius: 10)
[09:23:18 -125122.794686] SLOW spr round 5 (radius: 5)
[09:26:28 -125122.794594] SLOW spr round 6 (radius: 10)
[09:29:35] [worker #2] ML tree search #18, logLikelihood: -125071.992247
[09:29:35 -125122.175323] SLOW spr round 7 (radius: 5)
[09:32:40 -125120.666172] SLOW spr round 8 (radius: 5)
[09:35:27 -125120.666149] SLOW spr round 9 (radius: 10)
[09:38:11 -125120.339854] SLOW spr round 10 (radius: 5)
[09:41:15 -125120.329629] SLOW spr round 11 (radius: 10)
[09:43:59] [worker #3] ML tree search #19, logLikelihood: -125054.042323
[09:44:15 -125120.329126] SLOW spr round 12 (radius: 15)
[09:49:16 -125114.967564] SLOW spr round 13 (radius: 5)
[09:53:20 -125113.296321] SLOW spr round 14 (radius: 5)
[09:56:54 -125113.296176] SLOW spr round 15 (radius: 10)
[10:00:22 -125113.296173] SLOW spr round 16 (radius: 15)
[10:06:38 -125110.747589] SLOW spr round 17 (radius: 5)
[10:10:43 -125107.503776] SLOW spr round 18 (radius: 5)
[10:14:17 -125107.044463] SLOW spr round 19 (radius: 5)
[10:17:38 -125107.044286] SLOW spr round 20 (radius: 10)
[10:19:13] [worker #1] ML tree search #17, logLikelihood: -125037.603315
[10:20:57 -125107.044277] SLOW spr round 21 (radius: 15)
[10:27:40 -125106.263030] SLOW spr round 22 (radius: 5)
[10:31:41 -125105.888243] SLOW spr round 23 (radius: 5)
[10:35:14 -125105.887694] SLOW spr round 24 (radius: 10)
[10:38:44 -125105.887668] SLOW spr round 25 (radius: 15)
[10:45:05 -125105.887667] SLOW spr round 26 (radius: 20)
[10:52:34] [worker #4] ML tree search #20, logLikelihood: -125039.613576
[10:54:26 -125105.887666] SLOW spr round 27 (radius: 25)
[11:06:04 -125105.887666] Model parameter optimization (eps = 0.100000)

[11:06:12] [worker #0] ML tree search #16, logLikelihood: -125105.861068


Optimized model parameters:

   Partition 0: noname
   Rate heterogeneity: FREE (4 cats, mean),  weights&rates: (0.085018,0.324329) (0.081406,0.538168) (0.378779,0.707084) (0.454797,1.452928) 
   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: -125037.603315

AIC score: 254085.206629 / AICc score: 8298145.206629 / BIC score: 261004.538729
Free parameters (model + branch lengths): 2005

WARNING: Number of free parameters (K=2005) is larger than alignment size (n=233).
         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/Q96P09/3_mltree/Q96P09.raxml.bestTree
All ML trees saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q96P09/3_mltree/Q96P09.raxml.mlTrees
Optimized model saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q96P09/3_mltree/Q96P09.raxml.bestModel

Execution log saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q96P09/3_mltree/Q96P09.raxml.log

Analysis started: 03-Jul-2021 17:02:45 / finished: 04-Jul-2021 04:08:58

Elapsed time: 39972.260 seconds

Consumed energy: 3548.475 Wh (= 18 km in an electric car, or 89 km with an e-scooter!)