Unable to reproduce the same FunDi results with the same command and the same seed

[novigit]

IQTREE version:

IQ-TREE multicore version 2.2.5 COVID-edition for Linux 64-bit built Sep 15 2023

Command line:

TAXA="xd-EG_Diplonema_sp,xd-EG_Bodo_saltans,am-AM_Dictyostelium_discoideum,di-CH_Micromonas_commoda,am-AM_Echinamoeba_exudans,di-CH_Dunaliella_salina,di-AL_Neospora_caninum,xd-HL_Acrasis_kona,am-FU_Catenaria_anguillulae,xd-EG_Rhabdomonas_costata,di-CH_Chlamydomonas_reinhardtii,di-PL_Selaginella_moellendorffii,xd-HL_Naegleria_lovaniensis,di-CH_Volvox_carteri,di-PL_Phalaenopsis_equestris,di-PL_Chara_braunii,am-FU_Ustilago_maydis,xm-PX_Paratrimastix_eleionoma,di-RP_Rhodosorus_marinus,xd-EG_Trypanosoma_sp,di-ST_Aplanochytrium_sp,xm-PX_Streblomastix_strix,di-PL_Oryza_brachyantha,xd-EG_Leptomonas_pyrrhocoris,di-AL_Amphidinium_massartii,di-ST_Ochromonas_sp,am-AM_Polysphondylium_pallidum,am-FU_Mortierella_elongata,am-AM_Cavostelium_apophysatum,am-FU_Aspergillus_aculeatus,xd-EG_Lacrimia_lanifica,xm-FR_Giardia_muris,di-RZ_Lotharella_sp,xm-PX_Paratrimastix_pyriformis,di-RP_Rhodella_sp,xd-JA_Andalucia_godoyi,di-CH_Monoraphidium_neglectum,xm-PB_Trichomonas_tenax,am-AM_Vermamoeba_vermiformis,am-FU_Allomyces_macrogynus,xd-EG_Hemistasia_phaeocysticola,xd-HL_Pharyngomonas_kirbyi,xd-EG_Leishmania_braziliensis,am-HO_Priapulus_caudatus,di-AL_Tetrahymena_thermophila,xm-PX_Trimastix_marina,xm-PB_Trichomitus_batrachorum,di-PL_Klebsormidium_nitens,di-RP_Gracilariopsis_chorda,am-AM_Dictyostelium_purpureum,di-RP_Porphyra_umbilicalis,am-FU_Aspergillus_nidulans,xd-HL_Percolomonas_cosmoAE1,xd-EG_Rhynchopus_humris,di-AL_Perkinsus_marinus,am-HO_Trichoplax_adhaerens,di-PL_Amborella_trichopoda,xd-HL_Naegleria_gruberi,di-ST_Phytophthora_sp,am-HO_Exaiptasia_pallida,xd-EG_Distigma_spP2,di-RZ_Partenskyella_glossopodia,am-FU_Rhizoclosmatium_globosum,xm-PB_Tritrichomonas_foetus,di-RZ_Bigelowiella_natans,xm-PB_Dientamoeba_fragilis,xm-FR_Carpediemonas_membranifera,di-CH_Bathycoccus_prasinos,di-ST_Ectocarpus_siliculosus,di-RP_Chondrus_crispus,xd-HL_Willaertia_magna,di-PL_Setaria_italica,xm-FR_Chilomastix_sp,xd-EG_Neobodo_designis,xd-EG_Ploeotia_vitrea,am-FU_Batrachochytrium_dendrobatidis,am-AM_Cryptodifflugia_operculata,di-CH_Coccomyxa_subellipsoidea,am-HO_Nematostella_vectensis,am-FU_Moniliophthora_roreri,xd-EG_Artemidia_motanka,xd-JA_Stygiella_incarcerata,am-FU_Gonapodya_prolifera,di-CH_Micractinium_conductrix,di-AL_Scrippsiella_Hangoei,xm-PB_Histomonas_meleagridis,am-HO_Monosiga_brevicollis,xm-PB_Trichomonas_gallinae,di-RZ_Plasmodiophora_brassicae,di-PL_Dioscorea_cayenensis,am-HO_Acanthoecalike_sp,am-HO_Danio_rerio,am-HO_Branchiostoma_floridae,di-CH_Auxenochlorella_protothecoides,xm-FR_Retortamonas_caviae,di-AL_Paramecium_tetraurelia,am-AM_Clastostelium_recurvatum,am-HO_Apis_mellifera,di-AL_Vitrella_brassicaformis,di-AL_Stentor_coeruleus,am-HO_Capsaspora_owczarzaki,am-HO_Hydra_vulgaris,di-AL_Polarella_glacialis,di-AL_Besnoitia_besnoiti,xd-HL_Percolomonas_cosmoWS,di-ST_Fistulifera_solaris,di-AL_Hammondia_hammondi,di-ST_Nannochloropsis_gaditana,di-AL_Toxoplasma_gondii,di-CH_Chlorella_variabilis,xd-EG_Eutreptiella_gymnastica,xd-EG_Namystynia_karyoxenos,di-AL_Stylonychia_lemnae,xm-FR_Dysnectes_brevis,am-FU_Spizellomyces_punctatus,am-HO_Stegodyphus_mimosarum,xd-JA_Seculamonas_ecuadoriensis,am-HO_Salpingoeca_rosetta,xm-FR_Kipferlia_bialata,di-AL_Togula_jolla,am-AM_Filamoeba_nolandi,di-ST_Aphanomyces_astaci,di-CH_Edaphochlamys_debaryana,am-AM_Copromyxa_protea,xd-EG_Sulcionema_specki,di-RZ_Chlorarachnion_reptans,xm-PB_Pentatrichomonas_hominis,di-PL_Ananas_comosus,am-FU_Laccaria_bicolor,am-FU_Rhizophagus_irregularis,di-PL_Triticum_urartu,xd-EG_Rhynchopus_euleeides,di-ST_Albugo_candida,di-RP_Porphyridium_purpureum,di-ST_Schizochytrium_aggregatum,di-ST_Thalassiosira_pseudonana,di-AL_Chromera_velia,am-AM_Acytostelium_subglobosum,xm-PX_Monocercomonoides_sp,xd-HL_Naegleria_fowleri,xd-EG_Strigomonas_culicis,xm-FR_Carpediemonas_likeNY0171,di-PL_Physcomitrella_patens,di-PL_Marchantia_polymorpha,am-AM_Protostelium_nocturnum"

iqtree2 -s supermatrix_loci_183.fasta -te c60.treefile -seed 137888 -m LG+fundi_C10+G4 -mdef re-optimized-model.nexus -a 0.6250003068091398 --fundi $TAXA,estimate --prefix supermatrix_loci_183.fullTree.C10.out/fundi_full_tree -nt 20 -prec 10 --quiet

The model fundi_C10 is specified in the re-optimized-model.nexus file, which states the per-class frequencies and weights.

I ran this exact run twice, and it gave me two markedly different results with regards to FunDi results:

Run1:

NOTE: 51844 MB RAM (50 GB) is required!
Estimate model parameters (epsilon = 0.010)
1. Initial log-likelihood: -6590864.099
2. Current log-likelihood: -6589798.467
3. Current log-likelihood: -6589429.568
4. Current log-likelihood: -6589373.746
5. Current log-likelihood: -6589364.260
6. Current log-likelihood: -6589362.464
7. Current log-likelihood: -6589362.104
8. Current log-likelihood: -6589362.030
Optimal log-likelihood: -6589362.018
Mixture weights: 0.099 0.308 0.067 0.040 0.097 0.089 0.096 0.029 0.097 0.078
Gamma shape alpha: 0.625
Parameters optimization took 8 rounds (503.782 sec)
Wrote distance file to...
BEST SCORE FOUND : -6589362.018
Optimizing FunDi model...
rho = 0.000
Central branch length: 1.593
Optimizing FunDi model parameters...
WARNING: Numerical underflow for non-rev lh-branch Noname
Best FunDi parameter rho: 0.494
Best FunDi central branch length: 0.450
FunDi log-likelihood: -6492752.884
Time taken to optimize FunDi model: 4.158 sec
Total tree length: 90.597

Run2:

NOTE: 51844 MB RAM (50 GB) is required!
Estimate model parameters (epsilon = 0.010)
1. Initial log-likelihood: -6590864.099
2. Current log-likelihood: -6589798.467
3. Current log-likelihood: -6589429.568
4. Current log-likelihood: -6589373.746
5. Current log-likelihood: -6589364.260
6. Current log-likelihood: -6589362.464
7. Current log-likelihood: -6589362.104
8. Current log-likelihood: -6589362.030
Optimal log-likelihood: -6589362.018
Mixture weights: 0.099 0.308 0.067 0.040 0.097 0.089 0.096 0.029 0.097 0.078
Gamma shape alpha: 0.625
Parameters optimization took 8 rounds (358.080 sec)
Wrote distance file to...
BEST SCORE FOUND : -6589362.018
Optimizing FunDi model...
rho = 0.000
Central branch length: 1.593
Optimizing FunDi model parameters...
WARNING: Numerical underflow for non-rev lh-branch Noname
Best FunDi parameter rho: 0.491
Best FunDi central branch length: 2.627
FunDi log-likelihood: -6495746.928
Time taken to optimize FunDi model: 2.660 sec
Total tree length: 92.774

Note that these FunDi results are different, particularly the inferred central branch length and log likelihood:

Run1:

Best FunDi parameter rho: 0.494
Best FunDi central branch length: 0.450
FunDi log-likelihood: -6492752.884

Run2:

Best FunDi parameter rho: 0.491
Best FunDi central branch length: 2.627
FunDi log-likelihood: -6495746.928

The only difference between these runs is that they were run on different nodes of the same cluster.

Run1:

Host:    perun17 (AVX2, FMA3, 755 GB RAM)
Command: iqtree2 -s supermatrix_loci_183.fasta -te c60.treefile -m LG+fundi_C10+G4 ....
Seed:    137888 (Using SPRNG - Scalable Parallel Random Number Generator)
Time:    Wed Dec  4 15:22:23 2024
Kernel:  AVX+FMA - 40 threads (64 CPU cores detected)

Run2:

Host:    perun23 (AVX2, FMA3, 2003 GB RAM)
Command: iqtree2 -s supermatrix_loci_183.fasta -te c60.treefile -m LG+fundi_C10+G4 ....
Seed:    137888 (Using SPRNG - Scalable Parallel Random Number Generator)
Time:    Tue Nov 26 11:12:53 2024
Kernel:  AVX+FMA - 20 threads (256 CPU cores detected)

I suspect that perhaps the starting seed ensures reproducibility up to optimization of the "normal" tree inference, but then when FunDi optimization starts, some other random element causes two different runs to diverge?

Also, there is the numerical underflow warning, could that be related somehow?

[bqminh]

We're currently still testing the FunDi model implementation with Andrew Roger's group. I can't really guarantee it works in all cases at the moment... I will update here once we make some progress.