2023-05-16 19:07:47 INFO::Writing function arguments to log file 2023-05-16 19:07:47 DEBUG::Function arguments 2023-05-16 19:07:47 DEBUG::Output folder: MaAsLin2/MaAsLin2_Bacteria_SpeciesPost_Op 2023-05-16 19:07:47 DEBUG::Min Abundance: 0.000000 2023-05-16 19:07:47 DEBUG::Min Prevalence: 0.100000 2023-05-16 19:07:47 DEBUG::Normalization: TSS 2023-05-16 19:07:47 DEBUG::Transform: LOG 2023-05-16 19:07:47 DEBUG::Analysis method: LM 2023-05-16 19:07:47 DEBUG::Max significance: 0.250000 2023-05-16 19:07:47 DEBUG::Random effects: 2023-05-16 19:07:47 DEBUG::Fixed effects: nutrient1,nutrient2,nutrient3,nutrient4,nutrient5,nutrient6,nutrient7,nutrient8,nutrient9,nutrient10,nutrient11,nutrient12,nutrient13,nutrient14,nutrient15,nutrient16,nutrient17,nutrient18,nutrient19,nutrient20,nutrient21,nutrient22 2023-05-16 19:07:47 DEBUG::Correction method: BH 2023-05-16 19:07:47 DEBUG::Standardize: TRUE 2023-05-16 19:07:47 DEBUG::Cores: 1 2023-05-16 19:07:47 INFO::Verifying options selected are valid 2023-05-16 19:07:47 INFO::Determining format of input files 2023-05-16 19:07:47 INFO::Input format is data samples as rows and metadata samples as rows 2023-05-16 19:07:47 DEBUG::The following samples were found to have metadata but no features. They will be removed. OBE001_Baseline_Only_CP04053,OBE002_Baseline_CP04053,OBE004_Baseline_CP04053,OBE005_Baseline_CP04053,OBE006_Baseline_CP04053,OBE008_Baseline_CP04053,OBE009_Baseline_CP04053,OBE011_Baseline_Only_CP04053,OBE013_Baseline_CP04053,OBE014_Baseline_CP04053,OBE015_Baseline_CP04053,OBE016_Baseline_CP04053,OBE019_Baseline_CP04053,OBE020_Baseline_CP04053,OBE021_Baseline_CP04053,OBE023_Baseline_CP04053,OBE024_Baseline_CP04053,OBE025_Baseline_CP04053,OBE026_Baseline_CP04053,OBE027_Baseline_Only_CP04053,OBE028_Baseline_CP04053,OBE029_Baseline_CP04053,OBE030_Baseline_Only_CP04053,OBE031_Baseline_CP04053,OBE032_Baseline_CP04053,OBE033_Baseline_CP04053,OBE034_Baseline_CP04053,OBE036_Baseline_only_CP04053,OBE037_Baseline_CP04053 2023-05-16 19:07:47 DEBUG::A total of 18 samples were found in both the data and metadata 2023-05-16 19:07:47 DEBUG::Reordering data/metadata to use same sample ordering 2023-05-16 19:07:47 INFO::Formula for fixed effects: expr ~ nutrient1 + nutrient2 + nutrient3 + nutrient4 + nutrient5 + nutrient6 + nutrient7 + nutrient8 + nutrient9 + nutrient10 + nutrient11 + nutrient12 + nutrient13 + nutrient14 + nutrient15 + nutrient16 + nutrient17 + nutrient18 + nutrient19 + nutrient20 + nutrient21 + nutrient22 2023-05-16 19:07:47 INFO::Filter data based on min abundance and min prevalence 2023-05-16 19:07:47 INFO::Total samples in data: 18 2023-05-16 19:07:47 INFO::Min samples required with min abundance for a feature not to be filtered: 1.800000 2023-05-16 19:07:47 INFO::Total filtered features: 204 2023-05-16 19:07:47 INFO::Filtered feature names from abundance and prevalence filtering: Acetivibrio_ethanolgignens, Acidaminococcus_provencensis, Acidaminococcus_timonensis, Acidipropionibacterium_acidipropionici, Acinetobacter_baumannii, Agathobaculum_desmolans, Alistipes_inops, Alistipes_provencensis, Alloscardovia_omnicolens, Alloscardovia_u_s, Anaerococcus_lactolyticus, Anaerococcus_prevotii, Anaerococcus_vaginimassiliensis, Anaerococcus_u_s, Anaeromassilibacillus_senegalensis, Anaerostipes_rhamnosivorans, Anaerotruncus_rubiinfantis, Angelakisella_massiliensis, Atopobium_deltae, Bacteroides_acidifaciens, Bacteroides_caecimuri, Bacteroides_stercorirosoris, Bacteroides_timonensis, Bifidobacterium_angulatum, Bifidobacterium_animalis, Bifidobacterium_merycicum, Bifidobacterium_minimum, Bifidobacterium_moukalabense, Bifidobacterium_pullorum, Blautia_marasmi, Bulleidia_extructa, Butyricicoccus_pullicaecorum, Butyricimonas_faecalis, Butyricimonas_synergistica, Campylobacter_ureolyticus, Christensenella_u_s, Citrobacter_braakii, Citrobacter_farmeri, Citrobacter_freundii, Citrobacter_koseri, Citrobacter_u_s, Cloacibacillus_evryensis, Clostridium_paraputrificum, Clostridium_porci, Coprobacter_fastidiosus, Coprococcus_eutactus, Corynebacterium_argentoratense, Corynebacterium_durum, Corynebacterium_matruchotii, Dellaglioa_algida, Desulfovibrio_desulfuricans, Desulfovibrio_legallii, Desulfovibrio_porci, Desulfovibrio_u_s, Dialister_hominis, Dialister_massiliensis, Dialister_pneumosintes, Dysgonomonas_capnocytophagoides, Enorma_massiliensis, Enterobacter_cloacae_complex, Enterobacter_hormaechei, Enterobacter_kobei, Enterobacter_roggenkampii, Enterococcus_avium, Enterococcus_casseliflavus, Enteroscipio_rubneri, Eubacterium_limosum, Eubacterium_maltosivorans, Fenollaria_timonensis, Finegoldia_magna, Finegoldia_u_s, Fusobacterium_mortiferum, Fusobacterium_nucleatum, Fusobacterium_ulcerans, Gabonibacter_massiliensis, Gardnerella_vaginalis, Gardnerella_u_s, Gemella_haemolysans, Granulicatella_adiacens, Granulicatella_u_s, Haemophilus_influenzae, Hafnia_alvei, Holdemania_u_s, Kingella_oralis, Klebsiella_aerogenes, Klebsiella_oxytoca, Kluyvera_ascorbata, Lachnoanaerobaculum_orale, Lachnoclostridium_phocaeense, Lacrimispora_saccharolytica, Lacticaseibacillus_casei, Lacticaseibacillus_paracasei, Lactiplantibacillus_plantarum, Lactobacillaceae_u_s, Lactobacillus_acidophilus, Lactobacillus_casei_group, Lactobacillus_delbrueckii, Lactobacillus_helveticus, Lactobacillus_iners, Lactococcus_piscium, Lactococcus_raffinolactis, Laribacter_hongkongensis, Leuconostoc_citreum, Leuconostoc_garlicum, Leuconostoc_gelidum, Leuconostoc_lactis, Leuconostoc_mesenteroides, Leuconostoc_u_s, Limosilactobacillus_oris, Limosilactobacillus_reuteri, Longibaculum_u_s, Longicatena_caecimuris, Marvinbryantia_formatexigens, Massilicoli_timonensis, Massilimicrobiota_timonensis, Mediterranea_massiliensis, Megamonas_hypermegale, Megamonas_u_s, Megasphaera_elsdenii, Megasphaera_hexanoica, Megasphaera_micronuciformis, Methanosphaera_stadtmanae, Mitsuokella_jalaludinii, Mitsuokella_multacida, Mogibacterium_timidum, Mogibacterium_u_s, Morganella_morganii, Morganella_u_s, Muricomes_intestini, Olsenella_profusa, Oribacterium_sinus, Oscillibacter_ruminantium, Oxalobacter_formigenes, Paeniclostridium_sordellii, Parabacteroides_goldsteinii, Parabacteroides_johnsonii, Parabacteroides_timonensis, Paraeggerthella_hongkongensis, Parvimonas_u_s, Peptococcus_niger, Peptoniphilaceae_u_s, Peptoniphilus_coxii, Peptoniphilus_grossensis, Peptoniphilus_harei, Peptoniphilus_u_s, Peptostreptococcus_anaerobius, Phocaeicola_barnesiae, Phocaeicola_coprophilus, Porphyromonas_asaccharolytica, Porphyromonas_bennonis, Prevotella_bergensis, Prevotella_colorans, Prevotella_corporis, Prevotella_denticola, Prevotella_disiens, Prevotella_histicola, Prevotella_lascolaii, Propionibacterium_freudenreichii, Propionibacterium_u_s, Pseudoflavonifractor_capillosus, Pseudopropionibacterium_propionicum, Pyramidobacter_porci, Pyramidobacter_u_s, Raoultibacter_massiliensis, Romboutsia_ilealis, Rothia_mucilaginosa, Ruminococcus_gauvreauii, Sanguibacteroides_justesenii, Scardovia_u_s, Schaalia_turicensis, Selenomonas_noxia, Slackia_piriformis, Slackia_u_s, Sneathia_amnii, Sodaliphilus_pleomorphus, Solobacterium_moorei, Staphylococcus_aureus, Staphylococcus_u_s, Streptococcus_alactolyticus, Streptococcus_equinus, Streptococcus_gallolyticus, Streptococcus_infantarius, Streptococcus_intermedius, Streptococcus_koreensis, Streptococcus_lutetiensis, Streptococcus_massiliensis, Streptococcus_pasteurianus, Streptococcus_sobrinus, Streptococcus_timonensis, Sutterella_faecalis, Sutterella_u_s, TM7_phylum_sp_oral_taxon_352, Tannerella_u_s, Tidjanibacter_massiliensis, Traorella_massiliensis, Varibaculum_cambriense, Veillonella_tobetsuensis, Weissella_cibaria, Weissella_confusa, Clostridium_methoxybenzovorans, Clostridium_saccharogumia, Eubacterium_nodatum, Eubacterium_saphenum, Eubacterium_sulci 2023-05-16 19:07:47 INFO::Total filtered features with variance filtering: 0 2023-05-16 19:07:47 INFO::Filtered feature names from variance filtering: 2023-05-16 19:07:47 INFO::Running selected normalization method: TSS 2023-05-16 19:07:47 INFO::Applying z-score to standardize continuous metadata 2023-05-16 19:07:47 INFO::Running selected transform method: LOG 2023-05-16 19:07:47 INFO::Running selected analysis method: LM 2023-05-16 19:07:47 INFO::Fitting model to feature number 1, Absiella_u_s 2023-05-16 19:07:47 INFO::Fitting model to feature number 2, Acidaminococcus_fermentans 2023-05-16 19:07:47 INFO::Fitting model to feature number 3, Acidaminococcus_intestini 2023-05-16 19:07:47 INFO::Fitting model to feature number 4, Acidaminococcus_u_s 2023-05-16 19:07:47 INFO::Fitting model to feature number 5, Actinobaculum_u_s 2023-05-16 19:07:47 INFO::Fitting model to feature number 6, Actinomyces_bouchesdurhonensis 2023-05-16 19:07:47 INFO::Fitting model to feature number 7, Actinomyces_dentalis 2023-05-16 19:07:47 INFO::Fitting model to feature number 8, Actinomyces_gerencseriae 2023-05-16 19:07:47 INFO::Fitting model to feature number 9, Actinomyces_graevenitzii 2023-05-16 19:07:47 INFO::Fitting model to feature number 10, Actinomyces_israelii 2023-05-16 19:07:47 INFO::Fitting model to feature number 11, Actinomyces_johnsonii 2023-05-16 19:07:47 INFO::Fitting model to feature number 12, Actinomyces_massiliensis 2023-05-16 19:07:47 INFO::Fitting model to feature number 13, Actinomyces_naeslundii 2023-05-16 19:07:47 INFO::Fitting model to feature number 14, Actinomyces_oris 2023-05-16 19:07:47 INFO::Fitting model to feature number 15, Actinomyces_viscosus 2023-05-16 19:07:47 INFO::Fitting model to feature number 16, Actinomyces_u_s 2023-05-16 19:07:47 INFO::Fitting model to feature number 17, Adlercreutzia_equolifaciens 2023-05-16 19:07:47 INFO::Fitting model to feature number 18, Agathobaculum_butyriciproducens 2023-05-16 19:07:47 INFO::Fitting model to feature number 19, Akkermansia_muciniphila 2023-05-16 19:07:47 INFO::Fitting model to feature number 20, Akkermansia_u_s 2023-05-16 19:07:47 INFO::Fitting model to feature number 21, Alcanivorax_profundi 2023-05-16 19:07:47 INFO::Fitting model to feature number 22, Alistipes_communis 2023-05-16 19:07:47 INFO::Fitting model to feature number 23, Alistipes_dispar 2023-05-16 19:07:47 INFO::Fitting model to feature number 24, Alistipes_finegoldii 2023-05-16 19:07:47 INFO::Fitting model to feature number 25, Alistipes_ihumii 2023-05-16 19:07:47 INFO::Fitting model to feature number 26, Alistipes_indistinctus 2023-05-16 19:07:47 INFO::Fitting model to feature number 27, Alistipes_onderdonkii 2023-05-16 19:07:47 INFO::Fitting model to feature number 28, Alistipes_putredinis 2023-05-16 19:07:47 INFO::Fitting model to feature number 29, Alistipes_senegalensis 2023-05-16 19:07:47 INFO::Fitting model to feature number 30, Alistipes_shahii 2023-05-16 19:07:47 INFO::Fitting model to feature number 31, Alistipes_timonensis 2023-05-16 19:07:47 INFO::Fitting model to feature number 32, Alistipes_u_s 2023-05-16 19:07:47 INFO::Fitting model to feature number 33, Allisonella_histaminiformans 2023-05-16 19:07:47 INFO::Fitting model to feature number 34, Amedibacillus_dolichus 2023-05-16 19:07:47 INFO::Fitting model to feature number 35, Anaerobutyricum_hallii 2023-05-16 19:07:47 INFO::Fitting model to feature number 36, Anaerobutyricum_soehngenii 2023-05-16 19:07:47 INFO::Fitting model to feature number 37, Anaerofustis_stercorihominis 2023-05-16 19:07:47 INFO::Fitting model to feature number 38, Anaeromassilibacillus_u_s 2023-05-16 19:07:47 INFO::Fitting model to feature number 39, Anaerostipes_caccae 2023-05-16 19:07:47 INFO::Fitting model to feature number 40, Anaerostipes_hadrus 2023-05-16 19:07:47 INFO::Fitting model to feature number 41, Anaerostipes_u_s 2023-05-16 19:07:47 INFO::Fitting model to feature number 42, Anaerotignum_faecicola 2023-05-16 19:07:47 INFO::Fitting model to feature number 43, Anaerotignum_lactatifermentans 2023-05-16 19:07:47 INFO::Fitting model to feature number 44, Anaerotruncus_colihominis 2023-05-16 19:07:47 INFO::Fitting model to feature number 45, Anaerotruncus_massiliensis 2023-05-16 19:07:47 INFO::Fitting model to feature number 46, Anaerotruncus_u_s 2023-05-16 19:07:47 INFO::Fitting model to feature number 47, Atopobium_u_s 2023-05-16 19:07:47 INFO::Fitting model to feature number 48, Bacteria_u_s 2023-05-16 19:07:47 INFO::Fitting model to feature number 49, Bacteroidales_u_s 2023-05-16 19:07:47 INFO::Fitting model to feature number 50, Bacteroides_caccae 2023-05-16 19:07:47 INFO::Fitting model to feature number 51, Bacteroides_caecimuris 2023-05-16 19:07:47 INFO::Fitting model to feature number 52, Bacteroides_cellulosilyticus 2023-05-16 19:07:47 INFO::Fitting model to feature number 53, Bacteroides_clarus 2023-05-16 19:07:47 INFO::Fitting model to feature number 54, Bacteroides_eggerthii 2023-05-16 19:07:47 INFO::Fitting model to feature number 55, Bacteroides_faecis 2023-05-16 19:07:47 INFO::Fitting model to feature number 56, Bacteroides_finegoldii 2023-05-16 19:07:47 INFO::Fitting model to feature number 57, Bacteroides_fragilis 2023-05-16 19:07:47 INFO::Fitting model to feature number 58, Bacteroides_intestinalis 2023-05-16 19:07:47 INFO::Fitting model to feature number 59, Bacteroides_nordii 2023-05-16 19:07:47 INFO::Fitting model to feature number 60, Bacteroides_ovatus 2023-05-16 19:07:47 INFO::Fitting model to feature number 61, Bacteroides_rodentium 2023-05-16 19:07:47 INFO::Fitting model to feature number 62, Bacteroides_salyersiae 2023-05-16 19:07:47 INFO::Fitting model to feature number 63, Bacteroides_stercoris 2023-05-16 19:07:47 INFO::Fitting model to feature number 64, Bacteroides_thetaiotaomicron 2023-05-16 19:07:47 INFO::Fitting model to feature number 65, Bacteroides_uniformis 2023-05-16 19:07:47 INFO::Fitting model to feature number 66, Bacteroides_xylanisolvens 2023-05-16 19:07:47 INFO::Fitting model to feature number 67, Bacteroides_u_s 2023-05-16 19:07:47 INFO::Fitting model to feature number 68, Bariatricus_massiliensis 2023-05-16 19:07:47 INFO::Fitting model to feature number 69, Barnesiella_intestinihominis 2023-05-16 19:07:47 INFO::Fitting model to feature number 70, Bifidobacterium_adolescentis 2023-05-16 19:07:47 INFO::Fitting model to feature number 71, Bifidobacterium_bifidum 2023-05-16 19:07:47 INFO::Fitting model to feature number 72, Bifidobacterium_breve 2023-05-16 19:07:47 INFO::Fitting model to feature number 73, Bifidobacterium_catenulatum 2023-05-16 19:07:47 INFO::Fitting model to feature number 74, Bifidobacterium_dentium 2023-05-16 19:07:47 INFO::Fitting model to feature number 75, Bifidobacterium_longum 2023-05-16 19:07:47 INFO::Fitting model to feature number 76, Bifidobacterium_pseudocatenulatum 2023-05-16 19:07:47 INFO::Fitting model to feature number 77, Bifidobacterium_ruminantium 2023-05-16 19:07:47 INFO::Fitting model to feature number 78, Bifidobacterium_scardovii 2023-05-16 19:07:47 INFO::Fitting model to feature number 79, Bifidobacterium_u_s 2023-05-16 19:07:47 INFO::Fitting model to feature number 80, Bilophila_wadsworthia 2023-05-16 19:07:47 INFO::Fitting model to feature number 81, Bilophila_u_s 2023-05-16 19:07:47 INFO::Fitting model to feature number 82, Bittarella_massiliensis 2023-05-16 19:07:47 INFO::Fitting model to feature number 83, Blautia_argi 2023-05-16 19:07:47 INFO::Fitting model to feature number 84, Blautia_coccoides 2023-05-16 19:07:47 INFO::Fitting model to feature number 85, Blautia_faecicola 2023-05-16 19:07:47 INFO::Fitting model to feature number 86, Blautia_hominis 2023-05-16 19:07:47 INFO::Fitting model to feature number 87, Blautia_hydrogenotrophica 2023-05-16 19:07:47 INFO::Fitting model to feature number 88, Blautia_luti 2023-05-16 19:07:47 INFO::Fitting model to feature number 89, Blautia_massiliensis 2023-05-16 19:07:47 INFO::Fitting model to feature number 90, Blautia_obeum 2023-05-16 19:07:47 INFO::Fitting model to feature number 91, Blautia_producta 2023-05-16 19:07:47 INFO::Fitting model to feature number 92, Blautia_wexlerae 2023-05-16 19:07:47 INFO::Fitting model to feature number 93, Blautia_u_s 2023-05-16 19:07:47 INFO::Fitting model to feature number 94, Burkholderiales_u_s 2023-05-16 19:07:47 INFO::Fitting model to feature number 95, Butyricicoccus_u_s 2023-05-16 19:07:47 INFO::Fitting model to feature number 96, Butyricimonas_virosa 2023-05-16 19:07:47 INFO::Fitting model to feature number 97, Butyricimonas_u_s 2023-05-16 19:07:47 INFO::Fitting model to feature number 98, Campylobacter_coli 2023-05-16 19:07:47 INFO::Fitting model to feature number 99, Catabacter_hongkongensis 2023-05-16 19:07:47 INFO::Fitting model to feature number 100, Catenibacterium_mitsuokai 2023-05-16 19:07:47 INFO::Fitting model to feature number 101, Catenibacterium_u_s 2023-05-16 19:07:47 INFO::Fitting model to feature number 102, Chitinophaga_silvisoli 2023-05-16 19:07:47 INFO::Fitting model to feature number 103, Christensenella_minuta 2023-05-16 19:07:47 INFO::Fitting model to feature number 104, Clostridia_u_s 2023-05-16 19:07:47 INFO::Fitting model to feature number 105, Clostridiaceae_u_s 2023-05-16 19:07:47 INFO::Fitting model to feature number 106, Clostridiales_u_s 2023-05-16 19:07:47 INFO::Fitting model to feature number 107, Clostridioides_difficile 2023-05-16 19:07:47 INFO::Fitting model to feature number 108, Clostridium_fessum 2023-05-16 19:07:47 INFO::Fitting model to feature number 109, Clostridium_perfringens 2023-05-16 19:07:47 INFO::Fitting model to feature number 110, Clostridium_phoceensis 2023-05-16 19:07:47 INFO::Fitting model to feature number 111, Clostridium_saudiense 2023-05-16 19:07:47 INFO::Fitting model to feature number 112, Clostridium_u_s 2023-05-16 19:07:47 INFO::Fitting model to feature number 113, Collinsella_aerofaciens 2023-05-16 19:07:47 INFO::Fitting model to feature number 114, Collinsella_bouchesdurhonensis 2023-05-16 19:07:47 INFO::Fitting model to feature number 115, Collinsella_intestinalis 2023-05-16 19:07:47 INFO::Fitting model to feature number 116, Collinsella_stercoris 2023-05-16 19:07:47 INFO::Fitting model to feature number 117, Collinsella_u_s 2023-05-16 19:07:47 INFO::Fitting model to feature number 118, Coprobacillus_cateniformis 2023-05-16 19:07:47 INFO::Fitting model to feature number 119, Coprobacillus_u_s 2023-05-16 19:07:47 INFO::Fitting model to feature number 120, Coprobacter_secundus 2023-05-16 19:07:47 INFO::Fitting model to feature number 121, Coprococcus_catus 2023-05-16 19:07:47 INFO::Fitting model to feature number 122, Coprococcus_comes 2023-05-16 19:07:47 INFO::Fitting model to feature number 123, Coprococcus_u_s 2023-05-16 19:07:47 INFO::Fitting model to feature number 124, Cryptobacterium_curtum 2023-05-16 19:07:47 INFO::Fitting model to feature number 125, Dakarella_massiliensis 2023-05-16 19:07:47 INFO::Fitting model to feature number 126, Desulfotomaculum_u_s 2023-05-16 19:07:47 INFO::Fitting model to feature number 127, Desulfovibrio_piger 2023-05-16 19:07:47 INFO::Fitting model to feature number 128, Dialister_invisus 2023-05-16 19:07:47 INFO::Fitting model to feature number 129, Dielma_fastidiosa 2023-05-16 19:07:47 INFO::Fitting model to feature number 130, Dorea_formicigenerans 2023-05-16 19:07:47 INFO::Fitting model to feature number 131, Dorea_longicatena 2023-05-16 19:07:47 INFO::Fitting model to feature number 132, Dorea_u_s 2023-05-16 19:07:47 INFO::Fitting model to feature number 133, Drancourtella_massiliensis 2023-05-16 19:07:47 INFO::Fitting model to feature number 134, Dysosmobacter_welbionis 2023-05-16 19:07:47 INFO::Fitting model to feature number 135, Eggerthella_lenta 2023-05-16 19:07:47 INFO::Fitting model to feature number 136, Eggerthella_u_s 2023-05-16 19:07:47 INFO::Fitting model to feature number 137, Eisenbergiella_tayi 2023-05-16 19:07:47 INFO::Fitting model to feature number 138, Eisenbergiella_u_s 2023-05-16 19:07:47 INFO::Fitting model to feature number 139, Emergencia_timonensis 2023-05-16 19:07:47 INFO::Fitting model to feature number 140, Enterobacter_u_s 2023-05-16 19:07:47 INFO::Fitting model to feature number 141, Enterobacteriaceae_u_s 2023-05-16 19:07:47 INFO::Fitting model to feature number 142, Enterocloster_aldensis 2023-05-16 19:07:47 INFO::Fitting model to feature number 143, Enterocloster_asparagiformis 2023-05-16 19:07:47 INFO::Fitting model to feature number 144, Enterocloster_bolteae 2023-05-16 19:07:47 INFO::Fitting model to feature number 145, Enterocloster_citroniae 2023-05-16 19:07:47 INFO::Fitting model to feature number 146, Enterocloster_clostridioformis 2023-05-16 19:07:47 INFO::Fitting model to feature number 147, Enterococcus_faecalis 2023-05-16 19:07:47 INFO::Fitting model to feature number 148, Enterococcus_faecium 2023-05-16 19:07:47 INFO::Fitting model to feature number 149, Enterococcus_hirae 2023-05-16 19:07:47 INFO::Fitting model to feature number 150, Enterococcus_u_s 2023-05-16 19:07:47 INFO::Fitting model to feature number 151, Erysipelatoclostridium_ramosum 2023-05-16 19:07:47 INFO::Fitting model to feature number 152, Erysipelotrichaceae_u_s 2023-05-16 19:07:47 INFO::Fitting model to feature number 153, Escherichia_coli 2023-05-16 19:07:47 INFO::Fitting model to feature number 154, Escherichia_u_s 2023-05-16 19:07:47 INFO::Fitting model to feature number 155, Eubacterium_callanderi 2023-05-16 19:07:47 INFO::Fitting model to feature number 156, Eubacterium_ramulus 2023-05-16 19:07:47 INFO::Fitting model to feature number 157, Eubacterium_ventriosum 2023-05-16 19:07:47 INFO::Fitting model to feature number 158, Eubacterium_u_s 2023-05-16 19:07:47 INFO::Fitting model to feature number 159, Evtepia_gabavorous 2023-05-16 19:07:47 INFO::Fitting model to feature number 160, Faecalibacterium_prausnitzii 2023-05-16 19:07:47 INFO::Fitting model to feature number 161, Faecalibacterium_u_s 2023-05-16 19:07:47 INFO::Fitting model to feature number 162, Faecalimonas_umbilicata 2023-05-16 19:07:47 INFO::Fitting model to feature number 163, Faecalitalea_cylindroides 2023-05-16 19:07:47 INFO::Fitting model to feature number 164, Firmicutes_u_s 2023-05-16 19:07:47 INFO::Fitting model to feature number 165, Flavonifractor_plautii 2023-05-16 19:07:47 INFO::Fitting model to feature number 166, Flavonifractor_u_s 2023-05-16 19:07:47 INFO::Fitting model to feature number 167, Flintibacter_u_s 2023-05-16 19:07:47 INFO::Fitting model to feature number 168, Fusobacterium_u_s 2023-05-16 19:07:47 INFO::Fitting model to feature number 169, Gabonia_massiliensis 2023-05-16 19:07:47 INFO::Fitting model to feature number 170, Gemella_sanguinis 2023-05-16 19:07:47 INFO::Fitting model to feature number 171, Gemmiger_formicilis 2023-05-16 19:07:47 INFO::Fitting model to feature number 172, Gordonibacter_pamelaeae 2023-05-16 19:07:47 INFO::Fitting model to feature number 173, Gordonibacter_u_s 2023-05-16 19:07:47 INFO::Fitting model to feature number 174, Haemophilus_parainfluenzae 2023-05-16 19:07:47 INFO::Fitting model to feature number 175, Haemophilus_u_s 2023-05-16 19:07:47 INFO::Fitting model to feature number 176, Hafnia_paralvei 2023-05-16 19:07:47 INFO::Fitting model to feature number 177, Harryflintia_acetispora 2023-05-16 19:07:47 INFO::Fitting model to feature number 178, Holdemanella_biformis 2023-05-16 19:07:47 INFO::Fitting model to feature number 179, Holdemania_filiformis 2023-05-16 19:07:47 INFO::Fitting model to feature number 180, Holdemania_massiliensis 2023-05-16 19:07:47 INFO::Fitting model to feature number 181, Hungatella_effluvii 2023-05-16 19:07:47 INFO::Fitting model to feature number 182, Hungatella_hathewayi 2023-05-16 19:07:47 INFO::Fitting model to feature number 183, Hungatella_u_s 2023-05-16 19:07:47 INFO::Fitting model to feature number 184, Intestinibacter_bartlettii 2023-05-16 19:07:47 INFO::Fitting model to feature number 185, Intestinimonas_butyriciproducens 2023-05-16 19:07:47 INFO::Fitting model to feature number 186, Intestinimonas_massiliensis 2023-05-16 19:07:47 INFO::Fitting model to feature number 187, Intestinimonas_timonensis 2023-05-16 19:07:47 INFO::Fitting model to feature number 188, Klebsiella_michiganensis 2023-05-16 19:07:47 INFO::Fitting model to feature number 189, Klebsiella_pneumoniae 2023-05-16 19:07:47 INFO::Fitting model to feature number 190, Klebsiella_variicola 2023-05-16 19:07:47 INFO::Fitting model to feature number 191, Klebsiella_u_s 2023-05-16 19:07:47 INFO::Fitting model to feature number 192, Lachnoclostridium_edouardi 2023-05-16 19:07:47 INFO::Fitting model to feature number 193, Lachnoclostridium_pacaense 2023-05-16 19:07:47 INFO::Fitting model to feature number 194, Lachnoclostridium_u_s 2023-05-16 19:07:47 INFO::Fitting model to feature number 195, Lachnospira_eligens 2023-05-16 19:07:47 INFO::Fitting model to feature number 196, Lachnospira_pectinoschiza 2023-05-16 19:07:47 INFO::Fitting model to feature number 197, Lachnospiraceae_u_s 2023-05-16 19:07:47 INFO::Fitting model to feature number 198, Lachnotalea_u_s 2023-05-16 19:07:47 INFO::Fitting model to feature number 199, Lacticaseibacillus_rhamnosus 2023-05-16 19:07:47 INFO::Fitting model to feature number 200, Lactobacillus_gasseri 2023-05-16 19:07:47 INFO::Fitting model to feature number 201, Lactobacillus_paragasseri 2023-05-16 19:07:47 INFO::Fitting model to feature number 202, Lactobacillus_rogosae 2023-05-16 19:07:47 INFO::Fitting model to feature number 203, Lactobacillus_u_s 2023-05-16 19:07:47 INFO::Fitting model to feature number 204, Lactococcus_lactis 2023-05-16 19:07:47 INFO::Fitting model to feature number 205, Lancefieldella_parvula 2023-05-16 19:07:47 INFO::Fitting model to feature number 206, Latilactobacillus_curvatus 2023-05-16 19:07:47 INFO::Fitting model to feature number 207, Lawsonibacter_asaccharolyticus 2023-05-16 19:07:47 INFO::Fitting model to feature number 208, Levyella_massiliensis 2023-05-16 19:07:47 INFO::Fitting model to feature number 209, Ligilactobacillus_animalis 2023-05-16 19:07:47 INFO::Fitting model to feature number 210, Ligilactobacillus_salivarius 2023-05-16 19:07:47 INFO::Fitting model to feature number 211, Limosilactobacillus_fermentum 2023-05-16 19:07:47 INFO::Fitting model to feature number 212, Limosilactobacillus_vaginalis 2023-05-16 19:07:47 INFO::Fitting model to feature number 213, Longibaculum_muris 2023-05-16 19:07:47 INFO::Fitting model to feature number 214, Massilimaliae_massiliensis 2023-05-16 19:07:47 INFO::Fitting model to feature number 215, Massilimaliae_timonensis 2023-05-16 19:07:47 INFO::Fitting model to feature number 216, Massilimicrobiota_u_s 2023-05-16 19:07:47 INFO::Fitting model to feature number 217, Massilioclostridium_coli 2023-05-16 19:07:47 INFO::Fitting model to feature number 218, Massilistercora_timonensis 2023-05-16 19:07:47 INFO::Fitting model to feature number 219, Mediterraneibacter_butyricigenes 2023-05-16 19:07:47 INFO::Fitting model to feature number 220, Mediterraneibacter_faecis 2023-05-16 19:07:47 INFO::Fitting model to feature number 221, Mediterraneibacter_massiliensis 2023-05-16 19:07:47 INFO::Fitting model to feature number 222, Megasphaera_massiliensis 2023-05-16 19:07:47 INFO::Fitting model to feature number 223, Megasphaera_u_s 2023-05-16 19:07:47 INFO::Fitting model to feature number 224, Merdimonas_faecis 2023-05-16 19:07:47 INFO::Fitting model to feature number 225, Metaprevotella_massiliensis 2023-05-16 19:07:47 INFO::Fitting model to feature number 226, Methanobrevibacter_smithii 2023-05-16 19:07:47 INFO::Fitting model to feature number 227, Mogibacterium_diversum 2023-05-16 19:07:47 INFO::Fitting model to feature number 228, Murimonas_intestini 2023-05-16 19:07:47 INFO::Fitting model to feature number 229, Negativibacillus_massiliensis 2023-05-16 19:07:47 INFO::Fitting model to feature number 230, Neglecta_timonensis 2023-05-16 19:07:47 INFO::Fitting model to feature number 231, Neobittarella_massiliensis 2023-05-16 19:07:47 INFO::Fitting model to feature number 232, Odoribacter_laneus 2023-05-16 19:07:47 INFO::Fitting model to feature number 233, Odoribacter_splanchnicus 2023-05-16 19:07:47 INFO::Fitting model to feature number 234, Odoribacter_u_s 2023-05-16 19:07:47 INFO::Fitting model to feature number 235, Oliverpabstia_intestinalis 2023-05-16 19:07:47 INFO::Fitting model to feature number 236, Olsenella_uli 2023-05-16 19:07:47 INFO::Fitting model to feature number 237, Olsenella_u_s 2023-05-16 19:07:47 INFO::Fitting model to feature number 238, Oscillibacter_u_s 2023-05-16 19:07:47 INFO::Fitting model to feature number 239, Oscillospiraceae_u_s 2023-05-16 19:07:47 INFO::Fitting model to feature number 240, Parabacteroides_distasonis 2023-05-16 19:07:47 INFO::Fitting model to feature number 241, Parabacteroides_massiliensis 2023-05-16 19:07:47 INFO::Fitting model to feature number 242, Parabacteroides_merdae 2023-05-16 19:07:47 INFO::Fitting model to feature number 243, Parabacteroides_u_s 2023-05-16 19:07:47 INFO::Fitting model to feature number 244, Paraprevotella_clara 2023-05-16 19:07:47 INFO::Fitting model to feature number 245, Paraprevotella_xylaniphila 2023-05-16 19:07:47 INFO::Fitting model to feature number 246, Parasutterella_excrementihominis 2023-05-16 19:07:47 INFO::Fitting model to feature number 247, Parolsenella_catena 2023-05-16 19:07:47 INFO::Fitting model to feature number 248, Pediococcus_acidilactici 2023-05-16 19:07:47 INFO::Fitting model to feature number 249, Peptoniphilus_lacrimalis 2023-05-16 19:07:47 INFO::Fitting model to feature number 250, Peptostreptococcus_stomatis 2023-05-16 19:07:47 INFO::Fitting model to feature number 251, Phascolarctobacterium_faecium 2023-05-16 19:07:47 INFO::Fitting model to feature number 252, Phascolarctobacterium_succinatutens 2023-05-16 19:07:47 INFO::Fitting model to feature number 253, Phocaeicola_coprocola 2023-05-16 19:07:47 INFO::Fitting model to feature number 254, Phocaeicola_dorei 2023-05-16 19:07:47 INFO::Fitting model to feature number 255, Phocaeicola_massiliensis 2023-05-16 19:07:47 INFO::Fitting model to feature number 256, Phocaeicola_plebeius 2023-05-16 19:07:47 INFO::Fitting model to feature number 257, Phocaeicola_sartorii 2023-05-16 19:07:47 INFO::Fitting model to feature number 258, Phocaeicola_vulgatus 2023-05-16 19:07:47 INFO::Fitting model to feature number 259, Phocea_massiliensis 2023-05-16 19:07:47 INFO::Fitting model to feature number 260, Porphyromonas_uenonis 2023-05-16 19:07:47 INFO::Fitting model to feature number 261, Porphyromonas_u_s 2023-05-16 19:07:47 INFO::Fitting model to feature number 262, Prevotella_bivia 2023-05-16 19:07:47 INFO::Fitting model to feature number 263, Prevotella_copri 2023-05-16 19:07:47 INFO::Fitting model to feature number 264, Prevotella_hominis 2023-05-16 19:07:47 INFO::Fitting model to feature number 265, Prevotella_marseillensis 2023-05-16 19:07:47 INFO::Fitting model to feature number 266, Prevotella_pectinovora 2023-05-16 19:07:47 INFO::Fitting model to feature number 267, Prevotella_stercorea 2023-05-16 19:07:47 INFO::Fitting model to feature number 268, Prevotella_timonensis 2023-05-16 19:07:47 INFO::Fitting model to feature number 269, Prevotella_u_s 2023-05-16 19:07:47 INFO::Fitting model to feature number 270, Prevotellamassilia_timonensis 2023-05-16 19:07:47 INFO::Fitting model to feature number 271, Propionibacterium_acidifaciens 2023-05-16 19:07:47 INFO::Fitting model to feature number 272, Proteus_mirabilis 2023-05-16 19:07:47 INFO::Fitting model to feature number 273, Proteus_u_s 2023-05-16 19:07:47 INFO::Fitting model to feature number 274, Provencibacterium_massiliense 2023-05-16 19:07:47 INFO::Fitting model to feature number 275, Pseudoflavonifractor_u_s 2023-05-16 19:07:47 INFO::Fitting model to feature number 276, Pseudoruminococcus_massiliensis 2023-05-16 19:07:47 INFO::Fitting model to feature number 277, Pyramidobacter_piscolens 2023-05-16 19:07:47 INFO::Fitting model to feature number 278, Raoultibacter_timonensis 2023-05-16 19:07:47 INFO::Fitting model to feature number 279, Romboutsia_timonensis 2023-05-16 19:07:47 INFO::Fitting model to feature number 280, Roseburia_faecis 2023-05-16 19:07:47 INFO::Fitting model to feature number 281, Roseburia_hominis 2023-05-16 19:07:47 INFO::Fitting model to feature number 282, Roseburia_intestinalis 2023-05-16 19:07:47 INFO::Fitting model to feature number 283, Roseburia_inulinivorans 2023-05-16 19:07:47 INFO::Fitting model to feature number 284, Roseburia_u_s 2023-05-16 19:07:47 INFO::Fitting model to feature number 285, Rothia_dentocariosa 2023-05-16 19:07:47 INFO::Fitting model to feature number 286, Rothia_u_s 2023-05-16 19:07:47 INFO::Fitting model to feature number 287, Ruminococcaceae_u_s 2023-05-16 19:07:47 INFO::Fitting model to feature number 288, Ruminococcus_bicirculans 2023-05-16 19:07:47 INFO::Fitting model to feature number 289, Ruminococcus_bromii 2023-05-16 19:07:47 INFO::Fitting model to feature number 290, Ruminococcus_callidus 2023-05-16 19:07:47 INFO::Fitting model to feature number 291, Ruminococcus_u_s 2023-05-16 19:07:47 INFO::Fitting model to feature number 292, Ruthenibacterium_lactatiformans 2023-05-16 19:07:47 INFO::Fitting model to feature number 293, Scardovia_wiggsiae 2023-05-16 19:07:47 INFO::Fitting model to feature number 294, Schaalia_odontolytica 2023-05-16 19:07:47 INFO::Fitting model to feature number 295, Sellimonas_intestinalis 2023-05-16 19:07:47 INFO::Fitting model to feature number 296, Senegalimassilia_anaerobia 2023-05-16 19:07:47 INFO::Fitting model to feature number 297, Slackia_isoflavoniconvertens 2023-05-16 19:07:47 INFO::Fitting model to feature number 298, Streptococcus_agalactiae 2023-05-16 19:07:47 INFO::Fitting model to feature number 299, Streptococcus_anginosus 2023-05-16 19:07:47 INFO::Fitting model to feature number 300, Streptococcus_australis 2023-05-16 19:07:47 INFO::Fitting model to feature number 301, Streptococcus_constellatus 2023-05-16 19:07:47 INFO::Fitting model to feature number 302, Streptococcus_gordonii 2023-05-16 19:07:47 INFO::Fitting model to feature number 303, Streptococcus_halitosis 2023-05-16 19:07:47 INFO::Fitting model to feature number 304, Streptococcus_infantis 2023-05-16 19:07:47 INFO::Fitting model to feature number 305, Streptococcus_milleri 2023-05-16 19:07:47 INFO::Fitting model to feature number 306, Streptococcus_mitis 2023-05-16 19:07:47 INFO::Fitting model to feature number 307, Streptococcus_mutans 2023-05-16 19:07:47 INFO::Fitting model to feature number 308, Streptococcus_oralis 2023-05-16 19:07:47 INFO::Fitting model to feature number 309, Streptococcus_parasanguinis 2023-05-16 19:07:47 INFO::Fitting model to feature number 310, Streptococcus_periodonticum 2023-05-16 19:07:47 INFO::Fitting model to feature number 311, Streptococcus_peroris 2023-05-16 19:07:47 INFO::Fitting model to feature number 312, Streptococcus_rubneri 2023-05-16 19:07:47 INFO::Fitting model to feature number 313, Streptococcus_salivarius 2023-05-16 19:07:47 INFO::Fitting model to feature number 314, Streptococcus_sanguinis 2023-05-16 19:07:47 INFO::Fitting model to feature number 315, Streptococcus_suis 2023-05-16 19:07:47 INFO::Fitting model to feature number 316, Streptococcus_thermophilus 2023-05-16 19:07:47 INFO::Fitting model to feature number 317, Streptococcus_vestibularis 2023-05-16 19:07:47 INFO::Fitting model to feature number 318, Streptococcus_viridans 2023-05-16 19:07:47 INFO::Fitting model to feature number 319, Streptococcus_xiaochunlingii 2023-05-16 19:07:47 INFO::Fitting model to feature number 320, Streptococcus_u_s 2023-05-16 19:07:47 INFO::Fitting model to feature number 321, Subdoligranulum_variabile 2023-05-16 19:07:47 INFO::Fitting model to feature number 322, Subdoligranulum_u_s 2023-05-16 19:07:47 INFO::Fitting model to feature number 323, Sutterella_wadsworthensis 2023-05-16 19:07:48 INFO::Fitting model to feature number 324, Synergistes_u_s 2023-05-16 19:07:48 INFO::Fitting model to feature number 325, Turicibacter_sanguinis 2023-05-16 19:07:48 INFO::Fitting model to feature number 326, Turicibacter_u_s 2023-05-16 19:07:48 INFO::Fitting model to feature number 327, Tyzzerella_nexilis 2023-05-16 19:07:48 INFO::Fitting model to feature number 328, Veillonella_atypica 2023-05-16 19:07:48 INFO::Fitting model to feature number 329, Veillonella_dispar 2023-05-16 19:07:48 INFO::Fitting model to feature number 330, Veillonella_infantium 2023-05-16 19:07:48 INFO::Fitting model to feature number 331, Veillonella_parvula 2023-05-16 19:07:48 INFO::Fitting model to feature number 332, Veillonella_u_s 2023-05-16 19:07:48 INFO::Fitting model to feature number 333, Velocimicrobium_porci 2023-05-16 19:07:48 INFO::Fitting model to feature number 334, Victivallales_u_s 2023-05-16 19:07:48 INFO::Fitting model to feature number 335, Victivallis_lenta 2023-05-16 19:07:48 INFO::Fitting model to feature number 336, Victivallis_vadensis 2023-05-16 19:07:48 INFO::Fitting model to feature number 337, Waltera_intestinalis 2023-05-16 19:07:48 INFO::Fitting model to feature number 338, Clostridium_hylemonae 2023-05-16 19:07:48 INFO::Fitting model to feature number 339, Clostridium_innocuum 2023-05-16 19:07:48 INFO::Fitting model to feature number 340, Clostridium_scindens 2023-05-16 19:07:48 INFO::Fitting model to feature number 341, Clostridium_spiroforme 2023-05-16 19:07:48 INFO::Fitting model to feature number 342, Clostridium_symbiosum 2023-05-16 19:07:48 INFO::Fitting model to feature number 343, Eubacterium_brachy 2023-05-16 19:07:48 INFO::Fitting model to feature number 344, Ruminococcus_gnavus 2023-05-16 19:07:48 INFO::Fitting model to feature number 345, Ruminococcus_lactaris 2023-05-16 19:07:48 INFO::Fitting model to feature number 346, Ruminococcus_torques 2023-05-16 19:07:48 INFO::Counting total values for each feature 2023-05-16 19:07:48 INFO::Writing residuals to file MaAsLin2/MaAsLin2_Bacteria_SpeciesPost_Op/residuals.rds 2023-05-16 19:07:48 INFO::Writing fitted values to file MaAsLin2/MaAsLin2_Bacteria_SpeciesPost_Op/fitted.rds 2023-05-16 19:07:48 INFO::Writing all results to file (ordered by increasing q-values): MaAsLin2/MaAsLin2_Bacteria_SpeciesPost_Op/all_results.tsv 2023-05-16 19:07:48 INFO::Writing the significant results (those which are less than or equal to the threshold of 0.250000 ) to file (ordered by increasing q-values): MaAsLin2/MaAsLin2_Bacteria_SpeciesPost_Op/significant_results.tsv 2023-05-16 19:07:48 INFO::Writing heatmap of significant results to file: MaAsLin2/MaAsLin2_Bacteria_SpeciesPost_Op/heatmap.pdf 2023-05-16 19:07:48 INFO::Writing association plots (one for each significant association) to output folder: MaAsLin2/MaAsLin2_Bacteria_SpeciesPost_Op