this does not work for the life of me, and I cannot figure out why. I have included the first few rows of the tables I am using. Any help would be appreciated.

background genes table:

geneID  05A_Day 05A_Night   05B_Day 05B_Night   05C_Day 05C_Night
Mpyr-NLJ1B.v3.hap1.scaffold1.g290530    20.05568525 53.86420316 56.49455967 28.41990016 48.78295061 37.9769104
Mpyr-NLJ1B.v3.hap1.scaffold1.g290540    47.31084726 81.7249979  20.54347624 64.67977278 0   77.80635302
Mpyr-NLJ1B.v3.hap1.scaffold1.g290550    281.2938418 212.1135173 169.483679  438.0584611 272.1575139 206.557342
Mpyr-NLJ1B.v3.hap1.scaffold1.g290560    110.563393  70.95215727 35.95108343 59.45312448 35.94533203 100.0367396
Mpyr-NLJ1B.v3.hap1.scaffold1.g290570    33.42614208 51.63533958 102.7173812 50.95982098 2.567523717 69.46995806
Mpyr-NLJ1B.v3.hap1.scaffold1.g290580    540.4750051 383.7360129 847.418395  368.15204   349.1832254 285.2899611

interesting genes table

geneID  baseMean    logFC   lfcSE   stat    pvalue  adj.P.Val
Mpyr-NLJ1B.v3.hap1.scaffold1.g290550    243.9175367 0.001196208 0.176017136 0.006795974 0.994577639 0.998036968
Mpyr-NLJ1B.v3.hap1.scaffold1.g290560    108.715009  -0.284412885    0.20512363  -1.386543741    0.165580933 0.455729319
Mpyr-NLJ1B.v3.hap1.scaffold1.g290580    327.5049888 -0.082834566    0.167084009 -0.495765971    0.620059536 0.836427073
Mpyr-NLJ1B.v3.hap1.scaffold1.g290590    68.88003752 -0.085763374    0.204751831 -0.418864991    0.675314804 0.865074287
Mpyr-NLJ1B.v3.hap1.scaffold1.g290600    193.7374652 0.0812508   0.179763836 0.451986347 0.651278818 0.852783145
Mpyr-NLJ1B.v3.hap1.scaffold1.g290620    287.2999812 -0.108514385    0.138438937 -0.783842948    0.43313227  0.72177919...

term2name table

term    name
GO:0000001  mitochondrion inheritance
GO:0000002  mitochondrial genome maintenance
GO:0000006  high-affinity zinc transmembrane transporter activity
GO:0000007  low-affinity zinc ion transmembrane transporter activity
GO:0000009  alpha-1,6-mannosyltransferase activity
GO:0000010  heptaprenyl diphosphate synthase activity
GO:0000011  vacuole inheritance
GO:0000012  single strand break repair....

term2gene table

gene    term
Mpyr-NLJ1B.v3.hap1.ctg1.g000070 GO:0003676
Mpyr-NLJ1B.v3.hap1.ctg1.g000070 GO:0005524
Mpyr-NLJ1B.v3.hap1.ctg10.g000100    GO:0006457
Mpyr-NLJ1B.v3.hap1.ctg10.g000100    GO:0051082
Mpyr-NLJ1B.v3.hap1.ctg10.g000100    GO:0140662
Mpyr-NLJ1B.v3.hap1.ctg10.g000100    GO:0005524
Mpyr-NLJ1B.v3.hap1.ctg10.g000110    GO:0009228...

# perform ORA
background_genes <- read_tsv("normalized_counts.tsv") %>%
    dplyr::select("geneID") %>%
    unlist() %>%
    as.vector()

# read the gene list of interest
interesting_set <- read_tsv("interesting-diffexpr-results-day-night-only.tsv") %>%
    dplyr::filter(abs(logFC) >= 0.5 & adj.P.Val <= 0.05) %>%
    dplyr::select("geneID") %>%
    unlist() %>%
    as.vector()

# 3) quick overlap check
message("Genes in common: ", sum(interesting_set %in% background_genes), " of ", length(interesting_set))
# perform ORA
term2gene <- read_tsv("term2gene_GO.tsv")
term2name <- read_tsv("term2name_GO.tsv")


enrichment <- enricher(interesting_set,
                       TERM2GENE = term2gene,
                       TERM2NAME = term2name,
                       universe = background_genes)

if (nrow(enrichment@result) == 0) {
  warning("No enriched terms found.  Check your overlap and your term2gene IDs.")
} else {
  head(enrichment@result)
}

sessionInfo( )

Your gene IDs are things like this: Mpyr-NLJ1B.v3.hap1.scaffold1.g290550, and the genes in your term2gene table are things like this: Mpyr-NLJ1B.v3.hap1.ctg1.g000070. Is there any overlap between the IDs in your interesting/background gene tables and the term2gene table?