2024-02-23 03:17:37 INFO::Writing function arguments to log file
2024-02-23 03:17:37 DEBUG::Function arguments
2024-02-23 03:17:37 DEBUG::Input data file: D:/R-4.2.3/library/Maaslin2/extdata/HMP2_taxonomy.tsv
2024-02-23 03:17:37 DEBUG::Input metadata file: D:/R-4.2.3/library/Maaslin2/extdata/HMP2_metadata.tsv
2024-02-23 03:17:37 DEBUG::Output folder: demo-output
2024-02-23 03:17:37 DEBUG::Min Abundance: 0.000000
2024-02-23 03:17:37 DEBUG::Min Prevalence: 0.100000
2024-02-23 03:17:37 DEBUG::Normalization: TSS
2024-02-23 03:17:37 DEBUG::Transform: LOG
2024-02-23 03:17:37 DEBUG::Analysis method: LM
2024-02-23 03:17:37 DEBUG::Max significance: 0.250000
2024-02-23 03:17:37 DEBUG::Random effects: site,subject
2024-02-23 03:17:37 DEBUG::Fixed effects: dysbiosisnonIBD,dysbiosisUC,dysbiosisCD,antibiotics,age
2024-02-23 03:17:37 DEBUG::Correction method: BH
2024-02-23 03:17:37 DEBUG::Standardize: FALSE
2024-02-23 03:17:37 DEBUG::Cores: 1
2024-02-23 03:17:37 INFO::Verifying options selected are valid
2024-02-23 03:17:37 INFO::Determining format of input files
2024-02-23 03:17:37 INFO::Input format is data samples as rows and metadata samples as rows
2024-02-23 03:17:37 DEBUG::A total of 1595 samples were found in both the data and metadata
2024-02-23 03:17:37 DEBUG::Reordering data/metadata to use same sample ordering
2024-02-23 03:17:37 INFO::Formula for random effects: expr ~ (1 | site) + (1 | subject)
2024-02-23 03:17:37 INFO::Formula for fixed effects: expr ~  dysbiosisnonIBD + dysbiosisUC + dysbiosisCD + antibiotics + age
2024-02-23 03:17:37 INFO::Filter data based on min abundance and min prevalence
2024-02-23 03:17:37 INFO::Total samples in data: 1595
2024-02-23 03:17:37 INFO::Min samples required with min abundance for a feature not to be filtered: 159.500000
2024-02-23 03:17:37 INFO::Total filtered features: 0
2024-02-23 03:17:37 INFO::Filtered feature names from abundance and prevalence filtering:
2024-02-23 03:17:37 INFO::Total filtered features with variance filtering: 0
2024-02-23 03:17:37 INFO::Filtered feature names from variance filtering:
2024-02-23 03:17:37 INFO::Running selected normalization method: TSS
2024-02-23 03:17:37 INFO::Bypass z-score application to metadata
2024-02-23 03:17:37 INFO::Running selected transform method: LOG
2024-02-23 03:17:37 INFO::Running selected analysis method: LM
2024-02-23 03:17:37 INFO::Fitting model to feature number 1, Bifidobacterium.adolescentis
2024-02-23 03:17:37 WARNING::Fitting problem for feature 1 returning NA
2024-02-23 03:17:37 INFO::Fitting model to feature number 2, Bifidobacterium.bifidum
2024-02-23 03:17:37 WARNING::Fitting problem for feature 2 returning NA
2024-02-23 03:17:37 INFO::Fitting model to feature number 3, Bifidobacterium.longum
2024-02-23 03:17:37 WARNING::Fitting problem for feature 3 returning NA
2024-02-23 03:17:37 INFO::Fitting model to feature number 4, Bifidobacterium.pseudocatenulatum
2024-02-23 03:17:37 WARNING::Fitting problem for feature 4 returning NA
2024-02-23 03:17:37 INFO::Fitting model to feature number 5, Collinsella.aerofaciens
2024-02-23 03:17:38 WARNING::Fitting problem for feature 5 returning NA
2024-02-23 03:17:38 INFO::Fitting model to feature number 6, Bacteroides.caccae
2024-02-23 03:17:38 WARNING::Fitting problem for feature 6 returning NA
2024-02-23 03:17:38 INFO::Fitting model to feature number 7, Bacteroides.cellulosilyticus
2024-02-23 03:17:38 WARNING::Fitting problem for feature 7 returning NA
2024-02-23 03:17:38 INFO::Fitting model to feature number 8, Bacteroides.dorei
2024-02-23 03:17:38 WARNING::Fitting problem for feature 8 returning NA
2024-02-23 03:17:38 INFO::Fitting model to feature number 9, Bacteroides.eggerthii
2024-02-23 03:17:38 WARNING::Fitting problem for feature 9 returning NA
2024-02-23 03:17:38 INFO::Fitting model to feature number 10, Bacteroides.faecis
2024-02-23 03:17:38 WARNING::Fitting problem for feature 10 returning NA
2024-02-23 03:17:38 INFO::Fitting model to feature number 11, Bacteroides.finegoldii
2024-02-23 03:17:38 WARNING::Fitting problem for feature 11 returning NA
2024-02-23 03:17:38 INFO::Fitting model to feature number 12, Bacteroides.fragilis
2024-02-23 03:17:38 WARNING::Fitting problem for feature 12 returning NA
2024-02-23 03:17:38 INFO::Fitting model to feature number 13, Bacteroides.intestinalis
2024-02-23 03:17:38 WARNING::Fitting problem for feature 13 returning NA
2024-02-23 03:17:38 INFO::Fitting model to feature number 14, Bacteroides.massiliensis
2024-02-23 03:17:38 WARNING::Fitting problem for feature 14 returning NA
2024-02-23 03:17:38 INFO::Fitting model to feature number 15, Bacteroides.ovatus
2024-02-23 03:17:38 WARNING::Fitting problem for feature 15 returning NA
2024-02-23 03:17:38 INFO::Fitting model to feature number 16, Bacteroides.salyersiae
2024-02-23 03:17:38 WARNING::Fitting problem for feature 16 returning NA
2024-02-23 03:17:38 INFO::Fitting model to feature number 17, Bacteroides.stercoris
2024-02-23 03:17:38 WARNING::Fitting problem for feature 17 returning NA
2024-02-23 03:17:38 INFO::Fitting model to feature number 18, Bacteroides.thetaiotaomicron
2024-02-23 03:17:38 WARNING::Fitting problem for feature 18 returning NA
2024-02-23 03:17:38 INFO::Fitting model to feature number 19, Bacteroides.uniformis
2024-02-23 03:17:38 WARNING::Fitting problem for feature 19 returning NA
2024-02-23 03:17:38 INFO::Fitting model to feature number 20, Bacteroides.vulgatus
2024-02-23 03:17:38 WARNING::Fitting problem for feature 20 returning NA
2024-02-23 03:17:38 INFO::Fitting model to feature number 21, Bacteroides.xylanisolvens
2024-02-23 03:17:38 WARNING::Fitting problem for feature 21 returning NA
2024-02-23 03:17:38 INFO::Fitting model to feature number 22, Bacteroidales.bacterium.ph8
2024-02-23 03:17:38 WARNING::Fitting problem for feature 22 returning NA
2024-02-23 03:17:38 INFO::Fitting model to feature number 23, Barnesiella.intestinihominis
2024-02-23 03:17:38 WARNING::Fitting problem for feature 23 returning NA
2024-02-23 03:17:38 INFO::Fitting model to feature number 24, Coprobacter.fastidiosus
2024-02-23 03:17:38 WARNING::Fitting problem for feature 24 returning NA
2024-02-23 03:17:38 INFO::Fitting model to feature number 25, Odoribacter.splanchnicus
2024-02-23 03:17:38 WARNING::Fitting problem for feature 25 returning NA
2024-02-23 03:17:38 INFO::Fitting model to feature number 26, Parabacteroides.distasonis
2024-02-23 03:17:38 WARNING::Fitting problem for feature 26 returning NA
2024-02-23 03:17:38 INFO::Fitting model to feature number 27, Parabacteroides.goldsteinii
2024-02-23 03:17:38 WARNING::Fitting problem for feature 27 returning NA
2024-02-23 03:17:38 INFO::Fitting model to feature number 28, Parabacteroides.merdae
2024-02-23 03:17:38 WARNING::Fitting problem for feature 28 returning NA
2024-02-23 03:17:38 INFO::Fitting model to feature number 29, Parabacteroides.unclassified
2024-02-23 03:17:38 WARNING::Fitting problem for feature 29 returning NA
2024-02-23 03:17:38 INFO::Fitting model to feature number 30, Paraprevotella.clara
2024-02-23 03:17:38 WARNING::Fitting problem for feature 30 returning NA
2024-02-23 03:17:38 INFO::Fitting model to feature number 31, Paraprevotella.unclassified
2024-02-23 03:17:39 WARNING::Fitting problem for feature 31 returning NA
2024-02-23 03:17:39 INFO::Fitting model to feature number 32, Prevotella.copri
2024-02-23 03:17:39 WARNING::Fitting problem for feature 32 returning NA
2024-02-23 03:17:39 INFO::Fitting model to feature number 33, Alistipes.finegoldii
2024-02-23 03:17:39 WARNING::Fitting problem for feature 33 returning NA
2024-02-23 03:17:39 INFO::Fitting model to feature number 34, Alistipes.onderdonkii
2024-02-23 03:17:39 WARNING::Fitting problem for feature 34 returning NA
2024-02-23 03:17:39 INFO::Fitting model to feature number 35, Alistipes.putredinis
2024-02-23 03:17:39 WARNING::Fitting problem for feature 35 returning NA
2024-02-23 03:17:39 INFO::Fitting model to feature number 36, Alistipes.shahii
2024-02-23 03:17:39 WARNING::Fitting problem for feature 36 returning NA
2024-02-23 03:17:39 INFO::Fitting model to feature number 37, Alistipes.unclassified
2024-02-23 03:17:39 WARNING::Fitting problem for feature 37 returning NA
2024-02-23 03:17:39 INFO::Fitting model to feature number 38, Streptococcus.salivarius
2024-02-23 03:17:39 WARNING::Fitting problem for feature 38 returning NA
2024-02-23 03:17:39 INFO::Fitting model to feature number 39, Clostridium.bolteae
2024-02-23 03:17:39 WARNING::Fitting problem for feature 39 returning NA
2024-02-23 03:17:39 INFO::Fitting model to feature number 40, Clostridium.citroniae
2024-02-23 03:17:39 WARNING::Fitting problem for feature 40 returning NA
2024-02-23 03:17:39 INFO::Fitting model to feature number 41, Clostridium.clostridioforme
2024-02-23 03:17:39 WARNING::Fitting problem for feature 41 returning NA
2024-02-23 03:17:39 INFO::Fitting model to feature number 42, Clostridium.hathewayi
2024-02-23 03:17:39 WARNING::Fitting problem for feature 42 returning NA
2024-02-23 03:17:39 INFO::Fitting model to feature number 43, Clostridium.leptum
2024-02-23 03:17:39 WARNING::Fitting problem for feature 43 returning NA
2024-02-23 03:17:39 INFO::Fitting model to feature number 44, Clostridium.nexile
2024-02-23 03:17:39 WARNING::Fitting problem for feature 44 returning NA
2024-02-23 03:17:39 INFO::Fitting model to feature number 45, Clostridium.symbiosum
2024-02-23 03:17:39 WARNING::Fitting problem for feature 45 returning NA
2024-02-23 03:17:39 INFO::Fitting model to feature number 46, Flavonifractor.plautii
2024-02-23 03:17:39 WARNING::Fitting problem for feature 46 returning NA
2024-02-23 03:17:39 INFO::Fitting model to feature number 47, Eubacterium.eligens
2024-02-23 03:17:39 WARNING::Fitting problem for feature 47 returning NA
2024-02-23 03:17:39 INFO::Fitting model to feature number 48, Eubacterium.hallii
2024-02-23 03:17:39 WARNING::Fitting problem for feature 48 returning NA
2024-02-23 03:17:39 INFO::Fitting model to feature number 49, Eubacterium.rectale
2024-02-23 03:17:39 WARNING::Fitting problem for feature 49 returning NA
2024-02-23 03:17:39 INFO::Fitting model to feature number 50, Eubacterium.siraeum
2024-02-23 03:17:39 WARNING::Fitting problem for feature 50 returning NA
2024-02-23 03:17:39 INFO::Fitting model to feature number 51, Eubacterium.sp.3.1.31
2024-02-23 03:17:39 WARNING::Fitting problem for feature 51 returning NA
2024-02-23 03:17:39 INFO::Fitting model to feature number 52, Eubacterium.ventriosum
2024-02-23 03:17:39 WARNING::Fitting problem for feature 52 returning NA
2024-02-23 03:17:39 INFO::Fitting model to feature number 53, Ruminococcus.gnavus
2024-02-23 03:17:39 WARNING::Fitting problem for feature 53 returning NA
2024-02-23 03:17:39 INFO::Fitting model to feature number 54, Ruminococcus.obeum
2024-02-23 03:17:39 WARNING::Fitting problem for feature 54 returning NA
2024-02-23 03:17:39 INFO::Fitting model to feature number 55, Ruminococcus.torques
2024-02-23 03:17:39 WARNING::Fitting problem for feature 55 returning NA
2024-02-23 03:17:39 INFO::Fitting model to feature number 56, Coprococcus.comes
2024-02-23 03:17:39 WARNING::Fitting problem for feature 56 returning NA
2024-02-23 03:17:39 INFO::Fitting model to feature number 57, Dorea.longicatena
2024-02-23 03:17:39 WARNING::Fitting problem for feature 57 returning NA
2024-02-23 03:17:39 INFO::Fitting model to feature number 58, Lachnospiraceae.bacterium.1.1.57FAA
2024-02-23 03:17:39 WARNING::Fitting problem for feature 58 returning NA
2024-02-23 03:17:39 INFO::Fitting model to feature number 59, Lachnospiraceae.bacterium.3.1.46FAA
2024-02-23 03:17:39 WARNING::Fitting problem for feature 59 returning NA
2024-02-23 03:17:39 INFO::Fitting model to feature number 60, Roseburia.hominis
2024-02-23 03:17:39 WARNING::Fitting problem for feature 60 returning NA
2024-02-23 03:17:39 INFO::Fitting model to feature number 61, Roseburia.intestinalis
2024-02-23 03:17:39 WARNING::Fitting problem for feature 61 returning NA
2024-02-23 03:17:39 INFO::Fitting model to feature number 62, Roseburia.inulinivorans
2024-02-23 03:17:39 WARNING::Fitting problem for feature 62 returning NA
2024-02-23 03:17:39 INFO::Fitting model to feature number 63, Roseburia.unclassified
2024-02-23 03:17:39 WARNING::Fitting problem for feature 63 returning NA
2024-02-23 03:17:39 INFO::Fitting model to feature number 64, Oscillibacter.unclassified
2024-02-23 03:17:39 WARNING::Fitting problem for feature 64 returning NA
2024-02-23 03:17:39 INFO::Fitting model to feature number 65, Peptostreptococcaceae.noname.unclassified
2024-02-23 03:17:39 WARNING::Fitting problem for feature 65 returning NA
2024-02-23 03:17:39 INFO::Fitting model to feature number 66, Faecalibacterium.prausnitzii
2024-02-23 03:17:39 WARNING::Fitting problem for feature 66 returning NA
2024-02-23 03:17:39 INFO::Fitting model to feature number 67, Ruminococcus.bromii
2024-02-23 03:17:39 WARNING::Fitting problem for feature 67 returning NA
2024-02-23 03:17:39 INFO::Fitting model to feature number 68, Ruminococcus.callidus
2024-02-23 03:17:40 WARNING::Fitting problem for feature 68 returning NA
2024-02-23 03:17:40 INFO::Fitting model to feature number 69, Ruminococcus.lactaris
2024-02-23 03:17:40 WARNING::Fitting problem for feature 69 returning NA
2024-02-23 03:17:40 INFO::Fitting model to feature number 70, Subdoligranulum.unclassified
2024-02-23 03:17:40 WARNING::Fitting problem for feature 70 returning NA
2024-02-23 03:17:40 INFO::Fitting model to feature number 71, Coprobacillus.unclassified
2024-02-23 03:17:40 WARNING::Fitting problem for feature 71 returning NA
2024-02-23 03:17:40 INFO::Fitting model to feature number 72, Acidaminococcus.unclassified
2024-02-23 03:17:40 WARNING::Fitting problem for feature 72 returning NA
2024-02-23 03:17:40 INFO::Fitting model to feature number 73, Dialister.invisus
2024-02-23 03:17:40 WARNING::Fitting problem for feature 73 returning NA
2024-02-23 03:17:40 INFO::Fitting model to feature number 74, Veillonella.atypica
2024-02-23 03:17:40 WARNING::Fitting problem for feature 74 returning NA
2024-02-23 03:17:40 INFO::Fitting model to feature number 75, Veillonella.dispar
2024-02-23 03:17:40 WARNING::Fitting problem for feature 75 returning NA
2024-02-23 03:17:40 INFO::Fitting model to feature number 76, Veillonella.parvula
2024-02-23 03:17:40 WARNING::Fitting problem for feature 76 returning NA
2024-02-23 03:17:40 INFO::Fitting model to feature number 77, Veillonella.unclassified
2024-02-23 03:17:40 WARNING::Fitting problem for feature 77 returning NA
2024-02-23 03:17:40 INFO::Fitting model to feature number 78, Burkholderiales.bacterium.1.1.47
2024-02-23 03:17:40 WARNING::Fitting problem for feature 78 returning NA
2024-02-23 03:17:40 INFO::Fitting model to feature number 79, Parasutterella.excrementihominis
2024-02-23 03:17:40 WARNING::Fitting problem for feature 79 returning NA
2024-02-23 03:17:40 INFO::Fitting model to feature number 80, Sutterella.wadsworthensis
2024-02-23 03:17:40 WARNING::Fitting problem for feature 80 returning NA
2024-02-23 03:17:40 INFO::Fitting model to feature number 81, Bilophila.unclassified
2024-02-23 03:17:40 WARNING::Fitting problem for feature 81 returning NA
2024-02-23 03:17:40 INFO::Fitting model to feature number 82, Escherichia.coli
2024-02-23 03:17:40 WARNING::Fitting problem for feature 82 returning NA
2024-02-23 03:17:40 INFO::Fitting model to feature number 83, Escherichia.unclassified
2024-02-23 03:17:40 WARNING::Fitting problem for feature 83 returning NA
2024-02-23 03:17:40 INFO::Fitting model to feature number 84, Klebsiella.pneumoniae
2024-02-23 03:17:40 WARNING::Fitting problem for feature 84 returning NA
2024-02-23 03:17:40 INFO::Fitting model to feature number 85, Haemophilus.parainfluenzae
2024-02-23 03:17:40 WARNING::Fitting problem for feature 85 returning NA
2024-02-23 03:17:40 INFO::Fitting model to feature number 86, Akkermansia.muciniphila
2024-02-23 03:17:40 WARNING::Fitting problem for feature 86 returning NA
2024-02-23 03:17:40 INFO::Fitting model to feature number 87, C2likevirus.unclassified
2024-02-23 03:17:40 WARNING::Fitting problem for feature 87 returning NA
2024-02-23 03:17:40 INFO::Counting total values for each feature
2024-02-23 03:17:40 INFO::Writing residuals to file demo-output/residuals.rds
2024-02-23 03:17:40 INFO::Writing fitted values to file demo-output/fitted.rds
2024-02-23 03:17:40 INFO::Writing extracted random effects to file demo-output/ranef.rds
2024-02-23 03:17:40 INFO::Writing all results to file (ordered by increasing q-values): demo-output/all_results.tsv
2024-02-23 03:17:40 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): demo-output/significant_results.tsv
2024-02-23 03:17:40 INFO::Writing heatmap of significant results to file: demo-output/heatmap.pdf
2024-02-23 03:17:40 INFO::Writing association plots (one for each significant association) to output folder: demo-output