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

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

RAxML-NG was called at 01-Jul-2021 01:12:33 as follows:

raxml-ng --msa /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q75V66/2_msa/Q75V66_trimmed_msa.fasta --data-type AA --model LG4X --prefix /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q75V66/3_mltree/Q75V66 --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/Q75V66/2_msa/Q75V66_trimmed_msa.fasta
[00:00:00] Loaded alignment with 1001 taxa and 695 sites

WARNING: Sequences tr_F1NVE6_F1NVE6_CHICK_9031 and tr_G1NGP1_G1NGP1_MELGA_9103 are exactly identical!
WARNING: Sequences sp_Q8C5H1_ANO4_MOUSE_10090 and tr_A0A3Q0CNK9_A0A3Q0CNK9_MESAU_10036 are exactly identical!
WARNING: Sequences tr_M3YI34_M3YI34_MUSPF_9669 and tr_G1LCW5_G1LCW5_AILME_9646 are exactly identical!
WARNING: Sequences tr_M3YI34_M3YI34_MUSPF_9669 and tr_A0A2U3X3X6_A0A2U3X3X6_ODORO_9708 are exactly identical!
WARNING: Sequences tr_M3YI34_M3YI34_MUSPF_9669 and tr_A0A384BSB0_A0A384BSB0_URSMA_29073 are exactly identical!
WARNING: Sequences tr_M3YJL9_M3YJL9_MUSPF_9669 and tr_E2RI51_E2RI51_CANLF_9615 are exactly identical!
WARNING: Sequences tr_M3YJL9_M3YJL9_MUSPF_9669 and tr_A0A2Y9IS00_A0A2Y9IS00_ENHLU_391180 are exactly identical!
WARNING: Sequences tr_G3RKI2_G3RKI2_GORGO_9595 and tr_H2Q3B1_H2Q3B1_PANTR_9598 are exactly identical!
WARNING: Sequences tr_G3RKI2_G3RKI2_GORGO_9595 and sp_Q75V66_ANO5_HUMAN_9606 are exactly identical!
WARNING: Sequences tr_G3RKI2_G3RKI2_GORGO_9595 and tr_A0A2R9AG47_A0A2R9AG47_PANPA_9597 are exactly identical!
WARNING: Sequences tr_G3S0E2_G3S0E2_GORGO_9595 and tr_A0A2I3SL13_A0A2I3SL13_PANTR_9598 are exactly identical!
WARNING: Sequences tr_G3S0E2_G3S0E2_GORGO_9595 and tr_A0A2R8ZKA7_A0A2R8ZKA7_PANPA_9597 are exactly identical!
WARNING: Sequences tr_Q2M0Y5_Q2M0Y5_DROPS_46245 and tr_B4GQY0_B4GQY0_DROPE_7234 are exactly identical!
WARNING: Sequences tr_A0A2I3RK99_A0A2I3RK99_PANTR_9598 and tr_A0A2R9BIY8_A0A2R9BIY8_PANPA_9597 are exactly identical!
WARNING: Sequences tr_A0A2I3SMX8_A0A2I3SMX8_PANTR_9598 and sp_Q9BYT9_ANO3_HUMAN_9606 are exactly identical!
WARNING: Sequences tr_A0A2I3SMX8_A0A2I3SMX8_PANTR_9598 and tr_A0A2R9B3M4_A0A2R9B3M4_PANPA_9597 are exactly identical!
WARNING: Sequences tr_A0A2I3SV02_A0A2I3SV02_PANTR_9598 and tr_A0A2R9A8K2_A0A2R9A8K2_PANPA_9597 are exactly identical!
WARNING: Sequences tr_F7FL71_F7FL71_MONDO_13616 and tr_G3WNA6_G3WNA6_SARHA_9305 are exactly identical!
WARNING: Sequences tr_W5PXP8_W5PXP8_SHEEP_9940 and sp_A6QLE6_ANO4_BOVIN_9913 are exactly identical!
WARNING: Sequences tr_A0A158NR82_A0A158NR82_ATTCE_12957 and tr_A0A195BFB9_A0A195BFB9_9HYME_520822 are exactly identical!
WARNING: Sequences tr_F6RSE7_F6RSE7_MACMU_9544 and tr_G7PQI8_G7PQI8_MACFA_9541 are exactly identical!
WARNING: Sequences tr_F6RSE7_F6RSE7_MACMU_9544 and tr_A0A2I3N385_A0A2I3N385_PAPAN_9555 are exactly identical!
WARNING: Sequences tr_F6RSE7_F6RSE7_MACMU_9544 and tr_A0A0D9QYS3_A0A0D9QYS3_CHLSB_60711 are exactly identical!
WARNING: Sequences tr_F6RSE7_F6RSE7_MACMU_9544 and tr_A0A2K5L9N5_A0A2K5L9N5_CERAT_9531 are exactly identical!
WARNING: Sequences tr_F6RSE7_F6RSE7_MACMU_9544 and tr_A0A2K5Z059_A0A2K5Z059_MANLE_9568 are exactly identical!
WARNING: Sequences tr_F7B4Z3_F7B4Z3_MACMU_9544 and tr_A0A096NYE7_A0A096NYE7_PAPAN_9555 are exactly identical!
WARNING: Sequences tr_F7B4Z3_F7B4Z3_MACMU_9544 and tr_A0A2K5LE66_A0A2K5LE66_CERAT_9531 are exactly identical!
WARNING: Sequences tr_F7B4Z3_F7B4Z3_MACMU_9544 and tr_A0A2K6APC1_A0A2K6APC1_MACNE_9545 are exactly identical!
WARNING: Sequences tr_F7B4Z3_F7B4Z3_MACMU_9544 and tr_A0A2K5XZW2_A0A2K5XZW2_MANLE_9568 are exactly identical!
WARNING: Sequences tr_F7GVV8_F7GVV8_MACMU_9544 and tr_G7PHN1_G7PHN1_MACFA_9541 are exactly identical!
WARNING: Sequences tr_F7HQS3_F7HQS3_MACMU_9544 and tr_A0A2K6DFS5_A0A2K6DFS5_MACNE_9545 are exactly identical!
WARNING: Sequences tr_G7PJA5_G7PJA5_MACFA_9541 and tr_A0A2I3LU78_A0A2I3LU78_PAPAN_9555 are exactly identical!
WARNING: Sequences tr_G7PJA5_G7PJA5_MACFA_9541 and tr_A0A0D9S198_A0A0D9S198_CHLSB_60711 are exactly identical!
WARNING: Sequences tr_G7PJA5_G7PJA5_MACFA_9541 and tr_A0A2K6AEU5_A0A2K6AEU5_MANLE_9568 are exactly identical!
WARNING: Sequences tr_R0LBR7_R0LBR7_ANAPL_8839 and tr_A0A091V072_A0A091V072_NIPNI_128390 are exactly identical!
WARNING: Sequences tr_R0LBR7_R0LBR7_ANAPL_8839 and tr_A0A087QJG5_A0A087QJG5_APTFO_9233 are exactly identical!
WARNING: Sequences tr_R0LBR7_R0LBR7_ANAPL_8839 and tr_A0A091WHE9_A0A091WHE9_OPIHO_30419 are exactly identical!
WARNING: Sequences tr_R0LBR7_R0LBR7_ANAPL_8839 and tr_A0A099ZYZ8_A0A099ZYZ8_CHAVO_50402 are exactly identical!
WARNING: Sequences tr_A0A0D9QYP9_A0A0D9QYP9_CHLSB_60711 and tr_A0A2K5N629_A0A2K5N629_CERAT_9531 are exactly identical!
WARNING: Sequences tr_A0A151MBM6_A0A151MBM6_ALLMI_8496 and tr_A0A3Q0GCJ2_A0A3Q0GCJ2_ALLSI_38654 are exactly identical!
WARNING: Sequences tr_A0A091FJ48_A0A091FJ48_CORBR_85066 and tr_A0A093S4Q4_A0A093S4Q4_9PASS_328815 are exactly identical!
WARNING: Sequences tr_A0A091W9N5_A0A091W9N5_OPIHO_30419 and tr_A0A0A0AJG0_A0A0A0AJG0_CHAVO_50402 are exactly identical!
WARNING: Sequences tr_A0A0A0AIM3_A0A0A0AIM3_CHAVO_50402 and tr_A0A093GLV9_A0A093GLV9_DRYPU_118200 are exactly identical!
WARNING: Sequences tr_A0A0V1CP90_A0A0V1CP90_TRIBR_45882 and tr_A0A0V0UX40_A0A0V0UX40_9BILA_181606 are exactly identical!
WARNING: Sequences tr_A0A0V1CQJ3_A0A0V1CQJ3_TRIBR_45882 and tr_A0A0V0VBL3_A0A0V0VBL3_9BILA_181606 are exactly identical!
WARNING: Sequences tr_A0A0V1CQJ3_A0A0V1CQJ3_TRIBR_45882 and tr_A0A0V0TJD0_A0A0V0TJD0_9BILA_144512 are exactly identical!
WARNING: Sequences tr_A0A0V0X718_A0A0V0X718_9BILA_92179 and tr_A0A0V1L4A4_A0A0V1L4A4_9BILA_6335 are exactly identical!
WARNING: Sequences tr_A0A0V1NL49_A0A0V1NL49_9BILA_92180 and tr_A0A0V0UIN4_A0A0V0UIN4_9BILA_144512 are exactly identical!
WARNING: Sequences tr_A0A0V1P5M0_A0A0V1P5M0_9BILA_92180 and tr_A0A0V0U4W6_A0A0V0U4W6_9BILA_144512 are exactly identical!
WARNING: Sequences tr_A0A2D0SFF9_A0A2D0SFF9_ICTPU_7998 and tr_A0A2D0SFG5_A0A2D0SFG5_ICTPU_7998 are exactly identical!
WARNING: Sequences tr_A0A2D0SFF9_A0A2D0SFF9_ICTPU_7998 and tr_A0A2D0SFH4_A0A2D0SFH4_ICTPU_7998 are exactly identical!
WARNING: Sequences tr_A0A2D0SFF9_A0A2D0SFF9_ICTPU_7998 and tr_A0A2D0SGT3_A0A2D0SGT3_ICTPU_7998 are exactly identical!
WARNING: Sequences tr_A0A2K5N7E2_A0A2K5N7E2_CERAT_9531 and tr_A0A2K6CM90_A0A2K6CM90_MACNE_9545 are exactly identical!
WARNING: Sequences tr_A0A2U4CEH8_A0A2U4CEH8_TURTR_9739 and tr_A0A2Y9PAM5_A0A2Y9PAM5_DELLE_9749 are exactly identical!
WARNING: Sequences tr_A0A2U4CEH8_A0A2U4CEH8_TURTR_9739 and tr_A0A2Y9SGC7_A0A2Y9SGC7_PHYCD_9755 are exactly identical!
WARNING: Sequences tr_A0A2U3ZK93_A0A2U3ZK93_ODORO_9708 and tr_A0A384DAH7_A0A384DAH7_URSMA_29073 are exactly identical!
WARNING: Sequences tr_A0A2Y9QDP6_A0A2Y9QDP6_DELLE_9749 and tr_A0A383YT25_A0A383YT25_BALAS_310752 are exactly identical!
WARNING: Duplicate sequences found: 57

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/Q75V66/3_mltree/Q75V66.raxml.reduced.phy

Alignment comprises 1 partitions and 695 patterns

Partition 0: noname
Model: LG4X+R4
Alignment sites / patterns: 695 / 695
Gaps: 4.61 %
Invariant sites: 0.00 %


NOTE: Binary MSA file created: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q75V66/3_mltree/Q75V66.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 / 174 / 13920
[00:00:00] Data distribution: max. searches per worker: 10

Starting ML tree search with 20 distinct starting trees

[00:00:00 -1117447.186050] Initial branch length optimization
[00:00:06 -936840.233822] Model parameter optimization (eps = 10.000000)
[00:01:21 -935346.233314] AUTODETECT spr round 1 (radius: 5)
[00:04:09 -607317.407584] AUTODETECT spr round 2 (radius: 10)
[00:07:19 -435220.758315] AUTODETECT spr round 3 (radius: 15)
[00:10:55 -328586.830839] AUTODETECT spr round 4 (radius: 20)
[00:15:12 -296990.058929] AUTODETECT spr round 5 (radius: 25)
[00:19:23 -290990.833166] SPR radius for FAST iterations: 25 (autodetect)
[00:19:23 -290990.833166] Model parameter optimization (eps = 3.000000)
[00:19:49 -290611.416485] FAST spr round 1 (radius: 25)
[00:22:47 -254765.846804] FAST spr round 2 (radius: 25)
[00:25:10 -253374.519294] FAST spr round 3 (radius: 25)
[00:27:21 -253204.962200] FAST spr round 4 (radius: 25)
[00:29:19 -253176.204883] FAST spr round 5 (radius: 25)
[00:31:08 -253160.881189] FAST spr round 6 (radius: 25)
[00:32:54 -253160.881138] Model parameter optimization (eps = 1.000000)
[00:33:10 -253140.734373] SLOW spr round 1 (radius: 5)
[00:35:41 -253076.663999] SLOW spr round 2 (radius: 5)
[00:38:10 -253054.625624] SLOW spr round 3 (radius: 5)
[00:40:28 -253054.625593] SLOW spr round 4 (radius: 10)
[00:42:48 -253054.023675] SLOW spr round 5 (radius: 5)
[00:45:43 -253054.023671] SLOW spr round 6 (radius: 10)
[00:48:19 -253054.023671] SLOW spr round 7 (radius: 15)
[00:51:31 -253054.023671] SLOW spr round 8 (radius: 20)
[00:57:14 -253054.023671] SLOW spr round 9 (radius: 25)
[01:03:27] [worker #1] ML tree search #2, logLikelihood: -253055.022767
[01:05:07 -253054.023671] Model parameter optimization (eps = 0.100000)

[01:05:19] [worker #0] ML tree search #1, logLikelihood: -253053.231975

[01:05:20 -1113154.599161] Initial branch length optimization
[01:05:25 -935499.941438] Model parameter optimization (eps = 10.000000)
[01:05:59 -934011.977464] AUTODETECT spr round 1 (radius: 5)
[01:08:24 -607348.358748] AUTODETECT spr round 2 (radius: 10)
[01:11:09 -463008.368772] AUTODETECT spr round 3 (radius: 15)
[01:14:14 -360372.448467] AUTODETECT spr round 4 (radius: 20)
[01:17:39 -309758.149991] AUTODETECT spr round 5 (radius: 25)
[01:21:47 -295747.728150] SPR radius for FAST iterations: 25 (autodetect)
[01:21:47 -295747.728150] Model parameter optimization (eps = 3.000000)
[01:22:09 -295418.221125] FAST spr round 1 (radius: 25)
[01:24:42 -256777.573223] FAST spr round 2 (radius: 25)
[01:26:42 -253715.657844] FAST spr round 3 (radius: 25)
[01:28:33 -253150.783383] FAST spr round 4 (radius: 25)
[01:30:21 -253111.689212] FAST spr round 5 (radius: 25)
[01:32:00 -253108.177164] FAST spr round 6 (radius: 25)
[01:33:37 -253108.177129] Model parameter optimization (eps = 1.000000)
[01:33:52 -253101.459532] SLOW spr round 1 (radius: 5)
[01:36:06 -253061.490619] SLOW spr round 2 (radius: 5)
[01:38:15 -253057.934775] SLOW spr round 3 (radius: 5)
[01:40:22 -253057.934735] SLOW spr round 4 (radius: 10)
[01:42:30 -253056.192914] SLOW spr round 5 (radius: 5)
[01:45:09 -253056.192912] SLOW spr round 6 (radius: 10)
[01:47:31 -253056.192912] SLOW spr round 7 (radius: 15)
[01:50:47 -253056.192911] SLOW spr round 8 (radius: 20)
[01:56:43 -253056.192911] SLOW spr round 9 (radius: 25)
[02:04:58 -253056.192911] Model parameter optimization (eps = 0.100000)

[02:05:07] [worker #0] ML tree search #3, logLikelihood: -253056.090729

[02:05:07 -1113034.063084] Initial branch length optimization
[02:05:12 -936145.393334] Model parameter optimization (eps = 10.000000)
[02:05:43 -934568.589643] AUTODETECT spr round 1 (radius: 5)
[02:06:05] [worker #1] ML tree search #4, logLikelihood: -253054.800829
[02:08:04 -605826.256236] AUTODETECT spr round 2 (radius: 10)
[02:10:45 -422351.787335] AUTODETECT spr round 3 (radius: 15)
[02:13:49 -338565.879387] AUTODETECT spr round 4 (radius: 20)
[02:17:27 -324109.712615] AUTODETECT spr round 5 (radius: 25)
[02:21:51 -297515.504702] SPR radius for FAST iterations: 25 (autodetect)
[02:21:51 -297515.504702] Model parameter optimization (eps = 3.000000)
[02:22:19 -297119.750745] FAST spr round 1 (radius: 25)
[02:25:16 -254876.643969] FAST spr round 2 (radius: 25)
[02:27:30 -253218.329425] FAST spr round 3 (radius: 25)
[02:29:35 -253158.114595] FAST spr round 4 (radius: 25)
[02:31:34 -253143.914488] FAST spr round 5 (radius: 25)
[02:33:26 -253141.442635] FAST spr round 6 (radius: 25)
[02:35:17 -253141.442579] Model parameter optimization (eps = 1.000000)
[02:35:33 -253135.887218] SLOW spr round 1 (radius: 5)
[02:38:02 -253061.848476] SLOW spr round 2 (radius: 5)
[02:40:29 -253056.474809] SLOW spr round 3 (radius: 5)
[02:42:52 -253056.468636] SLOW spr round 4 (radius: 10)
[02:45:15 -253056.468635] SLOW spr round 5 (radius: 15)
[02:49:09 -253056.468635] SLOW spr round 6 (radius: 20)
[02:55:43 -253056.468635] SLOW spr round 7 (radius: 25)
[03:05:12 -253056.468635] Model parameter optimization (eps = 0.100000)

[03:05:25] [worker #0] ML tree search #5, logLikelihood: -253056.070396

[03:05:25 -1117947.524468] Initial branch length optimization
[03:05:30 -939544.774573] Model parameter optimization (eps = 10.000000)
[03:06:10 -938163.944698] AUTODETECT spr round 1 (radius: 5)
[03:08:54 -596617.200515] AUTODETECT spr round 2 (radius: 10)
[03:11:55 -411718.398186] AUTODETECT spr round 3 (radius: 15)
[03:12:07] [worker #1] ML tree search #6, logLikelihood: -253050.086054
[03:15:09 -338754.036164] AUTODETECT spr round 4 (radius: 20)
[03:19:20 -304482.401306] AUTODETECT spr round 5 (radius: 25)
[03:23:57 -298933.420316] SPR radius for FAST iterations: 25 (autodetect)
[03:23:57 -298933.420316] Model parameter optimization (eps = 3.000000)
[03:24:21 -298519.149732] FAST spr round 1 (radius: 25)
[03:27:24 -256212.410022] FAST spr round 2 (radius: 25)
[03:29:50 -253322.889461] FAST spr round 3 (radius: 25)
[03:32:07 -253132.323389] FAST spr round 4 (radius: 25)
[03:34:02 -253122.703659] FAST spr round 5 (radius: 25)
[03:35:52 -253122.703572] Model parameter optimization (eps = 1.000000)
[03:36:05 -253121.089165] SLOW spr round 1 (radius: 5)
[03:38:36 -253062.896684] SLOW spr round 2 (radius: 5)
[03:41:04 -253058.049874] SLOW spr round 3 (radius: 5)
[03:43:27 -253056.161863] SLOW spr round 4 (radius: 5)
[03:45:49 -253055.970848] SLOW spr round 5 (radius: 5)
[03:48:11 -253055.970800] SLOW spr round 6 (radius: 10)
[03:50:35 -253054.924538] SLOW spr round 7 (radius: 5)
[03:53:34 -253051.866590] SLOW spr round 8 (radius: 5)
[03:56:12 -253051.583548] SLOW spr round 9 (radius: 5)
[03:58:39 -253051.583524] SLOW spr round 10 (radius: 10)
[04:01:02 -253051.583523] SLOW spr round 11 (radius: 15)
[04:04:52 -253051.583523] SLOW spr round 12 (radius: 20)
[04:11:29 -253051.583523] SLOW spr round 13 (radius: 25)
[04:13:14] [worker #1] ML tree search #8, logLikelihood: -253062.490783
[04:20:56 -253051.583522] Model parameter optimization (eps = 0.100000)

[04:21:01] [worker #0] ML tree search #7, logLikelihood: -253051.514009

[04:21:01 -1107509.165797] Initial branch length optimization
[04:21:08 -931386.489618] Model parameter optimization (eps = 10.000000)
[04:21:53 -929930.846560] AUTODETECT spr round 1 (radius: 5)
[04:24:39 -612053.487678] AUTODETECT spr round 2 (radius: 10)
[04:27:53 -420147.843633] AUTODETECT spr round 3 (radius: 15)
[04:30:55 -357879.393673] AUTODETECT spr round 4 (radius: 20)
[04:34:23 -316159.745521] AUTODETECT spr round 5 (radius: 25)
[04:38:16 -290250.375154] SPR radius for FAST iterations: 25 (autodetect)
[04:38:16 -290250.375154] Model parameter optimization (eps = 3.000000)
[04:38:41 -289833.982140] FAST spr round 1 (radius: 25)
[04:41:36 -255120.787258] FAST spr round 2 (radius: 25)
[04:43:59 -253195.761632] FAST spr round 3 (radius: 25)
[04:46:02 -253120.834219] FAST spr round 4 (radius: 25)
[04:47:58 -253112.391497] FAST spr round 5 (radius: 25)
[04:49:49 -253111.016343] FAST spr round 6 (radius: 25)
[04:51:39 -253111.016341] Model parameter optimization (eps = 1.000000)
[04:51:54 -253107.631615] SLOW spr round 1 (radius: 5)
[04:54:27 -253064.840270] SLOW spr round 2 (radius: 5)
[04:56:54 -253057.868488] SLOW spr round 3 (radius: 5)
[04:59:15 -253057.708955] SLOW spr round 4 (radius: 5)
[05:01:35 -253057.708950] SLOW spr round 5 (radius: 10)
[05:03:56 -253056.697807] SLOW spr round 6 (radius: 5)
[05:06:54 -253056.697805] SLOW spr round 7 (radius: 10)
[05:09:32 -253056.697804] SLOW spr round 8 (radius: 15)
[05:12:34] [worker #1] ML tree search #10, logLikelihood: -253068.993256
[05:13:11 -253056.697804] SLOW spr round 9 (radius: 20)
[05:19:57 -253056.697804] SLOW spr round 10 (radius: 25)
[05:29:01 -253056.697804] Model parameter optimization (eps = 0.100000)

[05:29:07] [worker #0] ML tree search #9, logLikelihood: -253056.646972

[05:29:07 -1121860.757646] Initial branch length optimization
[05:29:14 -943100.497092] Model parameter optimization (eps = 10.000000)
[05:29:56 -941547.015715] AUTODETECT spr round 1 (radius: 5)
[05:32:46 -617905.827715] AUTODETECT spr round 2 (radius: 10)
[05:35:54 -429828.656807] AUTODETECT spr round 3 (radius: 15)
[05:39:20 -348276.962075] AUTODETECT spr round 4 (radius: 20)
[05:43:09 -327515.700251] AUTODETECT spr round 5 (radius: 25)
[05:48:50 -315231.447890] SPR radius for FAST iterations: 25 (autodetect)
[05:48:50 -315231.447890] Model parameter optimization (eps = 3.000000)
[05:49:13 -314834.288946] FAST spr round 1 (radius: 25)
[05:52:13 -261074.254575] FAST spr round 2 (radius: 25)
[05:54:30 -255447.883083] FAST spr round 3 (radius: 25)
[05:56:33 -253242.096779] FAST spr round 4 (radius: 25)
[05:58:36 -253142.511250] FAST spr round 5 (radius: 25)
[06:00:25 -253142.511238] Model parameter optimization (eps = 1.000000)
[06:00:42 -253124.070254] SLOW spr round 1 (radius: 5)
[06:03:11 -253060.302388] SLOW spr round 2 (radius: 5)
[06:05:39 -253048.222367] SLOW spr round 3 (radius: 5)
[06:08:05 -253044.381044] SLOW spr round 4 (radius: 5)
[06:10:26 -253044.380988] SLOW spr round 5 (radius: 10)
[06:12:48 -253044.021278] SLOW spr round 6 (radius: 5)
[06:15:45 -253043.710531] SLOW spr round 7 (radius: 5)
[06:18:21 -253043.710523] SLOW spr round 8 (radius: 10)
[06:20:47 -253043.710523] SLOW spr round 9 (radius: 15)
[06:23:57] [worker #1] ML tree search #12, logLikelihood: -253060.775155
[06:24:35 -253042.948189] SLOW spr round 10 (radius: 5)
[06:27:45 -253042.948164] SLOW spr round 11 (radius: 10)
[06:30:36 -253042.948159] SLOW spr round 12 (radius: 15)
[06:34:19 -253042.948159] SLOW spr round 13 (radius: 20)
[06:41:15 -253042.948159] SLOW spr round 14 (radius: 25)
[06:50:40 -253042.948159] Model parameter optimization (eps = 0.100000)

[06:50:46] [worker #0] ML tree search #11, logLikelihood: -253042.871553

[06:50:46 -1112210.491661] Initial branch length optimization
[06:50:54 -936319.337476] Model parameter optimization (eps = 10.000000)
[06:51:35 -934847.242273] AUTODETECT spr round 1 (radius: 5)
[06:54:25 -594687.646434] AUTODETECT spr round 2 (radius: 10)
[06:57:32 -418527.419123] AUTODETECT spr round 3 (radius: 15)
[07:00:38 -350321.304017] AUTODETECT spr round 4 (radius: 20)
[07:04:25 -302784.121059] AUTODETECT spr round 5 (radius: 25)
[07:09:00 -296796.718628] SPR radius for FAST iterations: 25 (autodetect)
[07:09:00 -296796.718628] Model parameter optimization (eps = 3.000000)
[07:09:29 -296376.985355] FAST spr round 1 (radius: 25)
[07:12:34 -254464.532560] FAST spr round 2 (radius: 25)
[07:14:57 -253277.182513] FAST spr round 3 (radius: 25)
[07:17:08 -253143.642271] FAST spr round 4 (radius: 25)
[07:19:01 -253137.970092] FAST spr round 5 (radius: 25)
[07:20:49 -253137.970086] Model parameter optimization (eps = 1.000000)
[07:21:04 -253134.369247] SLOW spr round 1 (radius: 5)
[07:23:37 -253066.396582] SLOW spr round 2 (radius: 5)
[07:26:09 -253054.971447] SLOW spr round 3 (radius: 5)
[07:28:33 -253051.944934] SLOW spr round 4 (radius: 5)
[07:30:52 -253051.944932] SLOW spr round 5 (radius: 10)
[07:33:13 -253050.227035] SLOW spr round 6 (radius: 5)
[07:34:03] [worker #1] ML tree search #14, logLikelihood: -253070.181306
[07:36:11 -253050.227024] SLOW spr round 7 (radius: 10)
[07:38:51 -253050.227024] SLOW spr round 8 (radius: 15)
[07:42:32 -253050.227024] SLOW spr round 9 (radius: 20)
[07:49:16 -253050.227023] SLOW spr round 10 (radius: 25)
[07:58:31 -253050.227023] Model parameter optimization (eps = 0.100000)

[07:58:49] [worker #0] ML tree search #13, logLikelihood: -253049.346540

[07:58:49 -1119254.220488] Initial branch length optimization
[07:58:56 -934832.566239] Model parameter optimization (eps = 10.000000)
[07:59:35 -933453.370566] AUTODETECT spr round 1 (radius: 5)
[08:02:25 -609628.526599] AUTODETECT spr round 2 (radius: 10)
[08:05:35 -451272.161411] AUTODETECT spr round 3 (radius: 15)
[08:09:03 -383287.316011] AUTODETECT spr round 4 (radius: 20)
[08:13:03 -314281.092658] AUTODETECT spr round 5 (radius: 25)
[08:17:37 -305199.235575] SPR radius for FAST iterations: 25 (autodetect)
[08:17:37 -305199.235575] Model parameter optimization (eps = 3.000000)
[08:18:01 -304779.734464] FAST spr round 1 (radius: 25)
[08:21:04 -255378.245176] FAST spr round 2 (radius: 25)
[08:23:24 -253269.257395] FAST spr round 3 (radius: 25)
[08:25:30 -253110.004815] FAST spr round 4 (radius: 25)
[08:27:25 -253102.623026] FAST spr round 5 (radius: 25)
[08:29:13 -253102.622918] Model parameter optimization (eps = 1.000000)
[08:29:28 -253095.396010] SLOW spr round 1 (radius: 5)
[08:31:58 -253048.480640] SLOW spr round 2 (radius: 5)
[08:34:24 -253045.523461] SLOW spr round 3 (radius: 5)
[08:36:46 -253045.319147] SLOW spr round 4 (radius: 5)
[08:39:05 -253045.318955] SLOW spr round 5 (radius: 10)
[08:41:26 -253044.716333] SLOW spr round 6 (radius: 5)
[08:43:18] [worker #1] ML tree search #16, logLikelihood: -253044.448152
[08:44:23 -253044.716324] SLOW spr round 7 (radius: 10)
[08:47:02 -253044.716323] SLOW spr round 8 (radius: 15)
[08:50:43 -253044.716323] SLOW spr round 9 (radius: 20)
[08:57:31 -253044.716322] SLOW spr round 10 (radius: 25)
[09:06:54 -253044.716321] Model parameter optimization (eps = 0.100000)

[09:06:59] [worker #0] ML tree search #15, logLikelihood: -253044.707210

[09:06:59 -1111265.678903] Initial branch length optimization
[09:07:05 -935960.845790] Model parameter optimization (eps = 10.000000)
[09:07:46 -934450.620995] AUTODETECT spr round 1 (radius: 5)
[09:10:38 -600463.898036] AUTODETECT spr round 2 (radius: 10)
[09:13:50 -398747.135175] AUTODETECT spr round 3 (radius: 15)
[09:16:58 -313071.517214] AUTODETECT spr round 4 (radius: 20)
[09:20:25 -295523.589136] AUTODETECT spr round 5 (radius: 25)
[09:24:10 -291039.110039] SPR radius for FAST iterations: 25 (autodetect)
[09:24:10 -291039.110039] Model parameter optimization (eps = 3.000000)
[09:24:34 -290637.501374] FAST spr round 1 (radius: 25)
[09:27:30 -254410.008036] FAST spr round 2 (radius: 25)
[09:29:47 -253246.269290] FAST spr round 3 (radius: 25)
[09:31:52 -253161.440186] FAST spr round 4 (radius: 25)
[09:33:46 -253123.868074] FAST spr round 5 (radius: 25)
[09:35:34 -253123.868020] Model parameter optimization (eps = 1.000000)
[09:35:52 -253119.375483] SLOW spr round 1 (radius: 5)
[09:38:20 -253058.597999] SLOW spr round 2 (radius: 5)
[09:40:44 -253057.496211] SLOW spr round 3 (radius: 5)
[09:43:03 -253057.496170] SLOW spr round 4 (radius: 10)
[09:45:22 -253057.489867] SLOW spr round 5 (radius: 15)
[09:49:12 -253057.077577] SLOW spr round 6 (radius: 5)
[09:52:07] [worker #1] ML tree search #18, logLikelihood: -253054.571828
[09:52:14 -253057.077575] SLOW spr round 7 (radius: 10)
[09:54:58 -253057.077575] SLOW spr round 8 (radius: 15)
[09:58:35 -253057.077575] SLOW spr round 9 (radius: 20)
[10:05:19 -253057.077575] SLOW spr round 10 (radius: 25)
[10:14:29 -253057.077574] Model parameter optimization (eps = 0.100000)

[10:14:36] [worker #0] ML tree search #17, logLikelihood: -253056.983623

[10:14:36 -1116347.718736] Initial branch length optimization
[10:14:46 -930790.584243] Model parameter optimization (eps = 10.000000)
[10:15:26 -929301.835036] AUTODETECT spr round 1 (radius: 5)
[10:18:15 -602559.297305] AUTODETECT spr round 2 (radius: 10)
[10:21:19 -415041.227466] AUTODETECT spr round 3 (radius: 15)
[10:24:32 -341575.811949] AUTODETECT spr round 4 (radius: 20)
[10:28:34 -303506.499731] AUTODETECT spr round 5 (radius: 25)
[10:33:18 -294226.168245] SPR radius for FAST iterations: 25 (autodetect)
[10:33:18 -294226.168245] Model parameter optimization (eps = 3.000000)
[10:33:45 -293903.226643] FAST spr round 1 (radius: 25)
[10:36:47 -254871.212454] FAST spr round 2 (radius: 25)
[10:39:13 -253385.289201] FAST spr round 3 (radius: 25)
[10:41:21 -253194.598874] FAST spr round 4 (radius: 25)
[10:43:25 -253134.933287] FAST spr round 5 (radius: 25)
[10:45:17 -253125.968912] FAST spr round 6 (radius: 25)
[10:47:04 -253125.968877] Model parameter optimization (eps = 1.000000)
[10:47:19 -253121.910616] SLOW spr round 1 (radius: 5)
[10:49:51 -253063.443042] SLOW spr round 2 (radius: 5)
[10:52:17 -253051.984914] SLOW spr round 3 (radius: 5)
[10:54:39 -253046.010403] SLOW spr round 4 (radius: 5)
[10:56:58 -253046.005862] SLOW spr round 5 (radius: 10)
[10:59:17 -253045.593547] SLOW spr round 6 (radius: 5)
[11:02:11 -253045.593544] SLOW spr round 7 (radius: 10)
[11:04:47 -253045.593543] SLOW spr round 8 (radius: 15)
[11:08:03] [worker #1] ML tree search #20, logLikelihood: -253059.630391
[11:08:27 -253045.593542] SLOW spr round 9 (radius: 20)
[11:15:05 -253045.593541] SLOW spr round 10 (radius: 25)
[11:24:15 -253045.593541] Model parameter optimization (eps = 0.100000)

[11:24:26] [worker #0] ML tree search #19, logLikelihood: -253045.071164


Optimized model parameters:

   Partition 0: noname
   Rate heterogeneity: FREE (4 cats, mean),  weights&rates: (0.255898,0.466607) (0.244485,0.769313) (0.352768,1.020501) (0.146849,2.264301) 
   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: -253042.871553

AIC score: 510095.743107 / AICc score: 8554155.743107 / BIC score: 519206.286357
Free parameters (model + branch lengths): 2005

WARNING: Number of free parameters (K=2005) is larger than alignment size (n=695).
         This might lead to overfitting and compromise tree inference results!


WARNING: Best ML tree contains 136 near-zero branches!

Best ML tree with collapsed near-zero branches saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q75V66/3_mltree/Q75V66.raxml.bestTreeCollapsed
Best ML tree saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q75V66/3_mltree/Q75V66.raxml.bestTree
All ML trees saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q75V66/3_mltree/Q75V66.raxml.mlTrees
Optimized model saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q75V66/3_mltree/Q75V66.raxml.bestModel

Execution log saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q75V66/3_mltree/Q75V66.raxml.log

Analysis started: 01-Jul-2021 01:12:33 / finished: 01-Jul-2021 12:37:00

Elapsed time: 41067.009 seconds

Consumed energy: 3784.128 Wh (= 19 km in an electric car, or 95 km with an e-scooter!)