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 6140 CPU @ 2.30GHz, 36 cores, 251 GB RAM

RAxML-NG was called at 12-Jul-2021 14:04:52 as follows:

raxml-ng --msa /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q8NFF2/2_msa/Q8NFF2_trimmed_msa.fasta --data-type AA --model LG4X --prefix /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q8NFF2/3_mltree/Q8NFF2 --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: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q8NFF2/2_msa/Q8NFF2_trimmed_msa.fasta
[00:00:00] Loaded alignment with 1001 taxa and 757 sites

WARNING: Sequences tr_A0A1L1RQA3_A0A1L1RQA3_CHICK_9031 and sp_Q9IAL7_NCKX2_CHICK_9031 are exactly identical!
WARNING: Sequences tr_G3RK82_G3RK82_GORGO_9595 and sp_Q9UI40_NCKX2_HUMAN_9606 are exactly identical!
WARNING: Sequences tr_A0A1D5QCC5_A0A1D5QCC5_MACMU_9544 and tr_A0A2K5M903_A0A2K5M903_CERAT_9531 are exactly identical!
WARNING: Sequences tr_A0A1D5QCC5_A0A1D5QCC5_MACMU_9544 and tr_A0A2K6BCU4_A0A2K6BCU4_MACNE_9545 are exactly identical!
WARNING: Sequences tr_A0A096NJE3_A0A096NJE3_PAPAN_9555 and tr_A0A2K5Y8P9_A0A2K5Y8P9_MANLE_9568 are exactly identical!
WARNING: Sequences tr_A0A096P1G5_A0A096P1G5_PAPAN_9555 and tr_A0A2K6BVJ5_A0A2K6BVJ5_MACNE_9545 are exactly identical!
WARNING: Sequences tr_A0A096P1G5_A0A096P1G5_PAPAN_9555 and tr_A0A2K6A243_A0A2K6A243_MANLE_9568 are exactly identical!
WARNING: Duplicate sequences found: 7

NOTE: Reduced alignment (with duplicates and gap-only sites/taxa removed) 
NOTE: was saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q8NFF2/3_mltree/Q8NFF2.raxml.reduced.phy

Alignment comprises 1 partitions and 757 patterns

Partition 0: noname
Model: LG4X+R4
Alignment sites / patterns: 757 / 757
Gaps: 34.52 %
Invariant sites: 0.00 %


NOTE: Binary MSA file created: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q8NFF2/3_mltree/Q8NFF2.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 / 190 / 15200
[00:00:00] Data distribution: max. searches per worker: 10

Starting ML tree search with 20 distinct starting trees

[00:00:00 -922557.889395] Initial branch length optimization
[00:00:07 -778248.520021] Model parameter optimization (eps = 10.000000)
[00:01:05 -776878.043370] AUTODETECT spr round 1 (radius: 5)
[00:04:21 -542419.638402] AUTODETECT spr round 2 (radius: 10)
[00:07:57 -413952.354314] AUTODETECT spr round 3 (radius: 15)
[00:12:06 -359265.562037] AUTODETECT spr round 4 (radius: 20)
[00:17:22 -331836.881972] AUTODETECT spr round 5 (radius: 25)
[00:22:59 -327492.018024] SPR radius for FAST iterations: 25 (autodetect)
[00:22:59 -327492.018024] Model parameter optimization (eps = 3.000000)
[00:23:40 -327284.511451] FAST spr round 1 (radius: 25)
[00:28:22 -292123.471106] FAST spr round 2 (radius: 25)
[00:31:43 -290937.795317] FAST spr round 3 (radius: 25)
[00:34:35 -290817.729535] FAST spr round 4 (radius: 25)
[00:37:04 -290814.617673] FAST spr round 5 (radius: 25)
[00:39:22 -290814.616201] Model parameter optimization (eps = 1.000000)
[00:39:39 -290809.816322] SLOW spr round 1 (radius: 5)
[00:42:49 -290769.012718] SLOW spr round 2 (radius: 5)
[00:45:51 -290758.242024] SLOW spr round 3 (radius: 5)
[00:48:41 -290758.241591] SLOW spr round 4 (radius: 10)
[00:51:42 -290755.880369] SLOW spr round 5 (radius: 5)
[00:55:26 -290755.880000] SLOW spr round 6 (radius: 10)
[00:58:47 -290755.879839] SLOW spr round 7 (radius: 15)
[01:03:43 -290755.879686] SLOW spr round 8 (radius: 20)
[01:12:22 -290755.879533] SLOW spr round 9 (radius: 25)
[01:23:16 -290755.879380] Model parameter optimization (eps = 0.100000)

[01:23:31] [worker #0] ML tree search #1, logLikelihood: -290755.402863

[01:23:32 -917767.661447] Initial branch length optimization
[01:23:38 -776090.825846] Model parameter optimization (eps = 10.000000)
[01:24:31 -774717.755599] AUTODETECT spr round 1 (radius: 5)
[01:27:40 -551037.356895] AUTODETECT spr round 2 (radius: 10)
[01:28:28] [worker #1] ML tree search #2, logLikelihood: -290748.501259
[01:31:15 -432315.966222] AUTODETECT spr round 3 (radius: 15)
[01:35:45 -371348.690695] AUTODETECT spr round 4 (radius: 20)
[01:40:08 -340648.946854] AUTODETECT spr round 5 (radius: 25)
[01:45:09 -328259.753324] SPR radius for FAST iterations: 25 (autodetect)
[01:45:09 -328259.753324] Model parameter optimization (eps = 3.000000)
[01:45:54 -328122.372327] FAST spr round 1 (radius: 25)
[01:50:30 -292442.729436] FAST spr round 2 (radius: 25)
[01:53:35 -290956.721842] FAST spr round 3 (radius: 25)
[01:56:15 -290873.846504] FAST spr round 4 (radius: 25)
[01:58:38 -290853.674523] FAST spr round 5 (radius: 25)
[02:00:51 -290853.674270] Model parameter optimization (eps = 1.000000)
[02:01:13 -290848.773088] SLOW spr round 1 (radius: 5)
[02:04:24 -290782.201383] SLOW spr round 2 (radius: 5)
[02:07:26 -290772.342841] SLOW spr round 3 (radius: 5)
[02:10:20 -290768.769038] SLOW spr round 4 (radius: 5)
[02:13:09 -290768.768841] SLOW spr round 5 (radius: 10)
[02:16:03 -290768.768695] SLOW spr round 6 (radius: 15)
[02:21:26 -290768.768557] SLOW spr round 7 (radius: 20)
[02:29:32 -290768.768420] SLOW spr round 8 (radius: 25)
[02:40:25 -290768.768283] Model parameter optimization (eps = 0.100000)

[02:40:39] [worker #0] ML tree search #3, logLikelihood: -290767.421140

[02:40:39 -924566.313769] Initial branch length optimization
[02:40:46 -781662.555088] Model parameter optimization (eps = 10.000000)
[02:41:41 -780370.370067] AUTODETECT spr round 1 (radius: 5)
[02:44:46 -546923.056984] AUTODETECT spr round 2 (radius: 10)
[02:48:21 -417083.620707] AUTODETECT spr round 3 (radius: 15)
[02:52:15 -365978.617285] AUTODETECT spr round 4 (radius: 20)
[02:54:18] [worker #1] ML tree search #4, logLikelihood: -290766.595326
[02:57:32 -331036.019170] AUTODETECT spr round 5 (radius: 25)
[03:03:36 -325017.704796] SPR radius for FAST iterations: 25 (autodetect)
[03:03:36 -325017.704796] Model parameter optimization (eps = 3.000000)
[03:04:13 -324890.677027] FAST spr round 1 (radius: 25)
[03:09:05 -291962.730054] FAST spr round 2 (radius: 25)
[03:12:28 -290917.386832] FAST spr round 3 (radius: 25)
[03:15:22 -290816.632291] FAST spr round 4 (radius: 25)
[03:17:45 -290810.854808] FAST spr round 5 (radius: 25)

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 6140 CPU @ 2.30GHz, 36 cores, 251 GB RAM

RAxML-NG was called at 14-Jul-2021 15:54:02 as follows:

raxml-ng --msa /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q8NFF2/2_msa/Q8NFF2_trimmed_msa.fasta --data-type AA --model LG4X --prefix /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q8NFF2/3_mltree/Q8NFF2 --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

WARNING: The model you specified on the command line (LG4X) will be ignored 
         since the binary MSA file already contains a model definition.
         If you want to change the model, please re-run RAxML-NG 
         with the original PHYLIP/FASTA alignment and --redo option.

[00:00:00] Loading binary alignment from file: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q8NFF2/3_mltree/Q8NFF2.raxml.rba
[00:00:00] Alignment comprises 1001 taxa, 1 partitions and 757 patterns

Partition 0: noname
Model: LG4X+R4
Alignment sites / patterns: 757 / 757
Gaps: 34.52 %
Invariant sites: 0.00 %


Parallelization scheme autoconfig: 2 worker(s) x 4 thread(s)

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

[00:00:00] NOTE: Resuming execution from checkpoint (logLH: -290810.85, ML trees: 4, bootstraps: 0)
[00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 190 / 15200
[00:00:00] Data distribution: max. searches per worker: 8

ERROR: CPU core oversubscription detected! RAxML-NG will terminate now to avoid wasting resources.
NOTE:  Details: https://github.com/amkozlov/raxml-ng/wiki/Parallelization#core-oversubscription
NOTE:  You can use '--force perf_threads' to disable this check, but ONLY if you are 200% sure this is a false alarm!


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 6140 CPU @ 2.30GHz, 36 cores, 251 GB RAM

RAxML-NG was called at 24-Jul-2021 20:58:08 as follows:

raxml-ng --msa /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q8NFF2/2_msa/Q8NFF2_trimmed_msa.fasta --data-type AA --model LG4X --prefix /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q8NFF2/3_mltree/Q8NFF2 --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

WARNING: The model you specified on the command line (LG4X) will be ignored 
         since the binary MSA file already contains a model definition.
         If you want to change the model, please re-run RAxML-NG 
         with the original PHYLIP/FASTA alignment and --redo option.

[00:00:00] Loading binary alignment from file: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q8NFF2/3_mltree/Q8NFF2.raxml.rba
[00:00:00] Alignment comprises 1001 taxa, 1 partitions and 757 patterns

Partition 0: noname
Model: LG4X+R4
Alignment sites / patterns: 757 / 757
Gaps: 34.52 %
Invariant sites: 0.00 %


Parallelization scheme autoconfig: 2 worker(s) x 4 thread(s)

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

[00:00:00] NOTE: Resuming execution from checkpoint (logLH: -290810.85, ML trees: 4, bootstraps: 0)
[00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 190 / 15200
[00:00:00] Data distribution: max. searches per worker: 8

Starting ML tree search with 20 distinct starting trees

[00:00:00 -290810.854808] SPR radius for FAST iterations: 25 (autodetect)
[00:00:00 -290810.854808] FAST spr round 5 (radius: 25)
[00:02:22 -290804.028915] FAST spr round 6 (radius: 25)
[00:04:32 -290804.028582] Model parameter optimization (eps = 1.000000)
[00:04:52 -290795.613852] SLOW spr round 1 (radius: 5)
[00:08:05 -290755.951780] SLOW spr round 2 (radius: 5)
[00:11:05 -290749.232628] SLOW spr round 3 (radius: 5)
[00:13:58 -290748.079060] SLOW spr round 4 (radius: 5)
[00:16:47 -290748.077797] SLOW spr round 5 (radius: 10)
[00:19:42 -290748.077630] SLOW spr round 6 (radius: 15)
[00:25:03 -290748.077492] SLOW spr round 7 (radius: 20)
[00:33:10 -290748.077356] SLOW spr round 8 (radius: 25)
[00:44:06 -290748.077220] Model parameter optimization (eps = 0.100000)

[00:44:20] [worker #0] ML tree search #5, logLikelihood: -290747.934121

[00:44:20 -923567.715867] Initial branch length optimization
[00:44:27 -780365.570636] Model parameter optimization (eps = 10.000000)
[00:45:43 -779195.593054] AUTODETECT spr round 1 (radius: 5)
[00:48:54 -556167.295170] AUTODETECT spr round 2 (radius: 10)
[00:52:40 -430283.767953] AUTODETECT spr round 3 (radius: 15)
[00:56:57 -378606.003798] AUTODETECT spr round 4 (radius: 20)
[01:01:25 -353244.527788] AUTODETECT spr round 5 (radius: 25)
[01:04:36] [worker #1] ML tree search #6, logLikelihood: -290759.645218
[01:06:49 -330476.739773] SPR radius for FAST iterations: 25 (autodetect)
[01:06:49 -330476.739773] Model parameter optimization (eps = 3.000000)
[01:07:24 -330162.647796] FAST spr round 1 (radius: 25)
[01:12:10 -292509.077525] FAST spr round 2 (radius: 25)
[01:15:37 -290907.897930] FAST spr round 3 (radius: 25)
[01:18:29 -290833.051883] FAST spr round 4 (radius: 25)
[01:21:00 -290817.579580] FAST spr round 5 (radius: 25)
[01:23:19 -290817.579159] Model parameter optimization (eps = 1.000000)
[01:23:36 -290813.863976] SLOW spr round 1 (radius: 5)
[01:26:54 -290752.281043] SLOW spr round 2 (radius: 5)
[01:29:59 -290743.376823] SLOW spr round 3 (radius: 5)
[01:32:55 -290740.584245] SLOW spr round 4 (radius: 5)
[01:35:48 -290740.583512] SLOW spr round 5 (radius: 10)
[01:38:55 -290740.583335] SLOW spr round 6 (radius: 15)
[01:44:29 -290740.583185] SLOW spr round 7 (radius: 20)
[01:52:46 -290740.583038] SLOW spr round 8 (radius: 25)
[02:03:46 -290740.582891] Model parameter optimization (eps = 0.100000)

[02:04:07] [worker #0] ML tree search #7, logLikelihood: -290738.703895

[02:04:07 -920640.211940] Initial branch length optimization
[02:04:13 -775536.063131] Model parameter optimization (eps = 10.000000)
[02:05:31 -774130.279220] AUTODETECT spr round 1 (radius: 5)
[02:08:41 -548832.203444] AUTODETECT spr round 2 (radius: 10)
[02:12:26 -399023.185738] AUTODETECT spr round 3 (radius: 15)
[02:16:48 -345826.305189] AUTODETECT spr round 4 (radius: 20)
[02:21:53 -326263.863487] AUTODETECT spr round 5 (radius: 25)
[02:27:14 -322035.650747] SPR radius for FAST iterations: 25 (autodetect)
[02:27:14 -322035.650747] Model parameter optimization (eps = 3.000000)
[02:27:47 -321972.944739] FAST spr round 1 (radius: 25)
[02:31:18] [worker #1] ML tree search #8, logLikelihood: -290743.844551
[02:32:32 -292503.170351] FAST spr round 2 (radius: 25)
[02:36:01 -290951.916568] FAST spr round 3 (radius: 25)
[02:38:55 -290848.942244] FAST spr round 4 (radius: 25)
[02:41:25 -290848.794258] FAST spr round 5 (radius: 25)
[02:43:47 -290848.793945] Model parameter optimization (eps = 1.000000)
[02:44:14 -290833.111694] SLOW spr round 1 (radius: 5)
[02:47:36 -290757.260063] SLOW spr round 2 (radius: 5)
[02:50:50 -290737.319155] SLOW spr round 3 (radius: 5)
[02:53:54 -290732.506817] SLOW spr round 4 (radius: 5)
[02:56:56 -290732.506425] SLOW spr round 5 (radius: 10)
[03:00:01 -290732.506269] SLOW spr round 6 (radius: 15)
[03:05:31 -290732.506118] SLOW spr round 7 (radius: 20)
[03:13:48 -290732.505967] SLOW spr round 8 (radius: 25)
[03:24:54 -290732.505816] Model parameter optimization (eps = 0.100000)

[03:25:13] [worker #0] ML tree search #9, logLikelihood: -290732.068361

[03:25:13 -918598.909743] Initial branch length optimization
[03:25:21 -774050.219364] Model parameter optimization (eps = 10.000000)
[03:26:19 -772790.602972] AUTODETECT spr round 1 (radius: 5)
[03:29:32 -563529.380100] AUTODETECT spr round 2 (radius: 10)
[03:33:14 -423378.511044] AUTODETECT spr round 3 (radius: 15)
[03:37:37 -363010.769073] AUTODETECT spr round 4 (radius: 20)
[03:42:39 -335827.191555] AUTODETECT spr round 5 (radius: 25)
[03:48:48 -327126.148653] SPR radius for FAST iterations: 25 (autodetect)
[03:48:48 -327126.148653] Model parameter optimization (eps = 3.000000)
[03:49:26 -326922.039181] FAST spr round 1 (radius: 25)
[03:54:21 -291915.067964] FAST spr round 2 (radius: 25)
[03:54:57] [worker #1] ML tree search #10, logLikelihood: -290766.863256
[03:57:50 -290891.143049] FAST spr round 3 (radius: 25)
[04:00:48 -290828.872247] FAST spr round 4 (radius: 25)
[04:03:21 -290818.889700] FAST spr round 5 (radius: 25)
[04:05:45 -290818.889549] Model parameter optimization (eps = 1.000000)
[04:06:13 -290810.874930] SLOW spr round 1 (radius: 5)
[04:09:39 -290754.333266] SLOW spr round 2 (radius: 5)
[04:12:49 -290750.858180] SLOW spr round 3 (radius: 5)
[04:15:50 -290750.048711] SLOW spr round 4 (radius: 5)
[04:18:50 -290750.047431] SLOW spr round 5 (radius: 10)
[04:21:56 -290747.791871] SLOW spr round 6 (radius: 5)
[04:25:42 -290747.791492] SLOW spr round 7 (radius: 10)
[04:29:08 -290747.791362] SLOW spr round 8 (radius: 15)
[04:34:11 -290747.791241] SLOW spr round 9 (radius: 20)
[04:42:42 -290747.791121] SLOW spr round 10 (radius: 25)
[04:53:34 -290747.791000] Model parameter optimization (eps = 0.100000)

[04:53:49] [worker #0] ML tree search #11, logLikelihood: -290746.470319

[04:53:49 -926093.891488] Initial branch length optimization
[04:53:56 -783733.792641] Model parameter optimization (eps = 10.000000)
[04:54:58 -782437.103587] AUTODETECT spr round 1 (radius: 5)
[04:58:16 -546615.816708] AUTODETECT spr round 2 (radius: 10)
[05:01:49 -429775.935490] AUTODETECT spr round 3 (radius: 15)
[05:06:12 -354655.849851] AUTODETECT spr round 4 (radius: 20)
[05:10:32 -329170.422535] AUTODETECT spr round 5 (radius: 25)
[05:15:51 -326413.936329] SPR radius for FAST iterations: 25 (autodetect)
[05:15:51 -326413.936329] Model parameter optimization (eps = 3.000000)
[05:16:27 -326279.560281] FAST spr round 1 (radius: 25)
[05:20:52] [worker #1] ML tree search #12, logLikelihood: -290742.901212
[05:21:06 -292237.995758] FAST spr round 2 (radius: 25)
[05:24:35 -290977.744812] FAST spr round 3 (radius: 25)
[05:27:33 -290871.621101] FAST spr round 4 (radius: 25)
[05:30:06 -290855.332654] FAST spr round 5 (radius: 25)
[05:32:23 -290852.718608] FAST spr round 6 (radius: 25)
[05:34:41 -290850.354328] FAST spr round 7 (radius: 25)
[05:36:52 -290850.353988] Model parameter optimization (eps = 1.000000)
[05:37:14 -290843.236105] SLOW spr round 1 (radius: 5)
[05:40:24 -290776.608016] SLOW spr round 2 (radius: 5)
[05:43:26 -290749.413131] SLOW spr round 3 (radius: 5)
[05:46:20 -290748.835103] SLOW spr round 4 (radius: 5)
[05:49:14 -290748.834710] SLOW spr round 5 (radius: 10)
[05:52:23 -290747.774946] SLOW spr round 6 (radius: 5)
[05:56:14 -290747.774791] SLOW spr round 7 (radius: 10)
[05:59:47 -290747.774667] SLOW spr round 8 (radius: 15)
[06:04:53 -290747.774543] SLOW spr round 9 (radius: 20)
[06:13:27 -290747.774419] SLOW spr round 10 (radius: 25)
[06:24:15 -290747.774295] Model parameter optimization (eps = 0.100000)

[06:24:34] [worker #0] ML tree search #13, logLikelihood: -290747.365181

[06:24:34 -923546.565120] Initial branch length optimization
[06:24:41 -779331.454288] Model parameter optimization (eps = 10.000000)
[06:25:52 -778008.411060] AUTODETECT spr round 1 (radius: 5)
[06:29:09 -548952.439002] AUTODETECT spr round 2 (radius: 10)
[06:32:52 -427940.795472] AUTODETECT spr round 3 (radius: 15)
[06:37:00 -349916.906731] AUTODETECT spr round 4 (radius: 20)
[06:41:14 -343283.271090] AUTODETECT spr round 5 (radius: 25)
[06:46:13 -329947.082888] SPR radius for FAST iterations: 25 (autodetect)
[06:46:13 -329947.082888] Model parameter optimization (eps = 3.000000)
[06:46:48 -329818.458513] FAST spr round 1 (radius: 25)
[06:51:30 -292995.251783] FAST spr round 2 (radius: 25)
[06:54:46 -290902.448795] FAST spr round 3 (radius: 25)
[06:57:12] [worker #1] ML tree search #14, logLikelihood: -290745.326870
[06:57:35 -290791.861840] FAST spr round 4 (radius: 25)
[07:00:02 -290787.069702] FAST spr round 5 (radius: 25)
[07:02:26 -290787.069158] Model parameter optimization (eps = 1.000000)
[07:02:51 -290783.871064] SLOW spr round 1 (radius: 5)
[07:06:15 -290735.030543] SLOW spr round 2 (radius: 5)
[07:09:26 -290729.680420] SLOW spr round 3 (radius: 5)
[07:12:30 -290729.680104] SLOW spr round 4 (radius: 10)
[07:15:38 -290728.622874] SLOW spr round 5 (radius: 5)
[07:19:26 -290728.622688] SLOW spr round 6 (radius: 10)
[07:23:00 -290728.015952] SLOW spr round 7 (radius: 5)
[07:26:52 -290726.902211] SLOW spr round 8 (radius: 5)
[07:30:11 -290726.901752] SLOW spr round 9 (radius: 10)
[07:33:27 -290726.318751] SLOW spr round 10 (radius: 5)
[07:37:15 -290726.317688] SLOW spr round 11 (radius: 10)
[07:40:39 -290726.317526] SLOW spr round 12 (radius: 15)
[07:45:37 -290726.317380] SLOW spr round 13 (radius: 20)
[07:53:53 -290726.317234] SLOW spr round 14 (radius: 25)
[08:04:51 -290726.317088] Model parameter optimization (eps = 0.100000)

[08:05:08] [worker #0] ML tree search #15, logLikelihood: -290726.132173

[08:05:08 -921743.956320] Initial branch length optimization
[08:05:14 -778703.039225] Model parameter optimization (eps = 10.000000)
[08:06:33 -777202.446303] AUTODETECT spr round 1 (radius: 5)
[08:09:44 -539787.729143] AUTODETECT spr round 2 (radius: 10)
[08:13:22 -422594.418791] AUTODETECT spr round 3 (radius: 15)
[08:18:02 -357115.241763] AUTODETECT spr round 4 (radius: 20)
[08:23:08 -333634.948859] AUTODETECT spr round 5 (radius: 25)
[08:23:13] [worker #1] ML tree search #16, logLikelihood: -290754.926784
[08:28:14 -329558.246094] SPR radius for FAST iterations: 25 (autodetect)
[08:28:14 -329558.246094] Model parameter optimization (eps = 3.000000)
[08:28:47 -329418.055781] FAST spr round 1 (radius: 25)
[08:33:28 -292395.684328] FAST spr round 2 (radius: 25)
[08:36:45 -290921.235520] FAST spr round 3 (radius: 25)
[08:39:31 -290817.845476] FAST spr round 4 (radius: 25)
[08:41:55 -290814.668279] FAST spr round 5 (radius: 25)
[08:44:12 -290814.667858] Model parameter optimization (eps = 1.000000)
[08:44:32 -290809.590573] SLOW spr round 1 (radius: 5)
[08:47:47 -290767.960196] SLOW spr round 2 (radius: 5)
[08:50:55 -290759.178574] SLOW spr round 3 (radius: 5)
[08:53:59 -290755.675013] SLOW spr round 4 (radius: 5)
[08:57:03 -290755.674729] SLOW spr round 5 (radius: 10)
[09:00:13 -290751.880077] SLOW spr round 6 (radius: 5)
[09:04:10 -290747.450469] SLOW spr round 7 (radius: 5)
[09:07:36 -290747.221944] SLOW spr round 8 (radius: 5)
[09:10:47 -290747.221629] SLOW spr round 9 (radius: 10)
[09:13:59 -290745.831187] SLOW spr round 10 (radius: 5)
[09:17:51 -290744.313978] SLOW spr round 11 (radius: 5)
[09:21:16 -290743.424504] SLOW spr round 12 (radius: 5)
[09:24:25 -290743.422910] SLOW spr round 13 (radius: 10)
[09:27:31 -290743.422582] SLOW spr round 14 (radius: 15)
[09:33:05 -290743.422405] SLOW spr round 15 (radius: 20)
[09:41:27 -290743.422248] SLOW spr round 16 (radius: 25)
[09:51:54] [worker #1] ML tree search #18, logLikelihood: -290745.227950
[09:52:37 -290743.422094] Model parameter optimization (eps = 0.100000)

[09:52:45] [worker #0] ML tree search #17, logLikelihood: -290743.363552

[09:52:45 -916373.751747] Initial branch length optimization
[09:52:53 -772629.686013] Model parameter optimization (eps = 10.000000)
[09:54:07 -771353.179230] AUTODETECT spr round 1 (radius: 5)
[09:57:28 -555259.567048] AUTODETECT spr round 2 (radius: 10)
[10:01:23 -413922.759256] AUTODETECT spr round 3 (radius: 15)
[10:06:11 -360088.565829] AUTODETECT spr round 4 (radius: 20)
[10:11:16 -330695.572734] AUTODETECT spr round 5 (radius: 25)
[10:16:31 -325961.830545] SPR radius for FAST iterations: 25 (autodetect)
[10:16:31 -325961.830545] Model parameter optimization (eps = 3.000000)
[10:17:06 -325881.141174] FAST spr round 1 (radius: 25)
[10:22:06 -292448.596334] FAST spr round 2 (radius: 25)
[10:25:36 -290994.951623] FAST spr round 3 (radius: 25)
[10:28:40 -290865.226582] FAST spr round 4 (radius: 25)
[10:31:12 -290863.528169] FAST spr round 5 (radius: 25)
[10:33:33 -290863.527406] Model parameter optimization (eps = 1.000000)
[10:34:01 -290853.341033] SLOW spr round 1 (radius: 5)
[10:37:22 -290789.636991] SLOW spr round 2 (radius: 5)
[10:40:29 -290777.936895] SLOW spr round 3 (radius: 5)
[10:43:24 -290777.928807] SLOW spr round 4 (radius: 10)
[10:46:26 -290775.832482] SLOW spr round 5 (radius: 5)
[10:50:10 -290774.381386] SLOW spr round 6 (radius: 5)
[10:53:24 -290773.039345] SLOW spr round 7 (radius: 5)
[10:56:23 -290773.037334] SLOW spr round 8 (radius: 10)
[10:59:24 -290773.037046] SLOW spr round 9 (radius: 15)
[11:04:48 -290773.036893] SLOW spr round 10 (radius: 20)
[11:11:54] [worker #1] ML tree search #20, logLikelihood: -290739.948062
[11:13:11 -290773.036754] SLOW spr round 11 (radius: 25)
[11:24:05 -290773.036618] Model parameter optimization (eps = 0.100000)

[11:24:16] [worker #0] ML tree search #19, logLikelihood: -290772.927472


Optimized model parameters:

   Partition 0: noname
   Rate heterogeneity: FREE (4 cats, mean),  weights&rates: (0.195231,0.283836) (0.155690,0.475968) (0.309137,0.858459) (0.339942,1.780013) 
   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: -290726.132173

AIC score: 585462.264346 / AICc score: 8629522.264346 / BIC score: 594744.137669
Free parameters (model + branch lengths): 2005

WARNING: Number of free parameters (K=2005) is larger than alignment size (n=757).
         This might lead to overfitting and compromise tree inference results!


WARNING: Best ML tree contains 51 near-zero branches!

Best ML tree with collapsed near-zero branches saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q8NFF2/3_mltree/Q8NFF2.raxml.bestTreeCollapsed
Best ML tree saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q8NFF2/3_mltree/Q8NFF2.raxml.bestTree
All ML trees saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q8NFF2/3_mltree/Q8NFF2.raxml.mlTrees
Optimized model saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q8NFF2/3_mltree/Q8NFF2.raxml.bestModel

Execution log saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q8NFF2/3_mltree/Q8NFF2.raxml.log

Analysis started: 24-Jul-2021 20:58:08 / finished: 25-Jul-2021 08:22:25

Elapsed time: 41056.814 seconds (this run) / 52922.350 seconds (total with restarts)