I have an output file containing upregulated genes from a non model organism ordered by adjusted p-value.

geneID
Rp.chr4.1864
Rp.chr1.1957
Rp.chr4.2000
Rp.chrX.1597
Rp.chr4.1782
Rp.chr4.1865

and a second file containing the same gene IDs as well as their best hits from different databases

geneID  Nr  Nt  SwissProt   KOG eggNOG  Interpro    GO  KEGG
Rp.chr1.0001    protein BUD31 homolog   PREDICTED: Megachile rotundata protein BUD31 homolog (LOC100880403), transcript variant X3, mRNA    Protein BUD31 homolog   KOG3404: G10 protein/predicted nuclear transcription regulator  G10 protein IPR001748: G10 protein; IPR018230: BUD31/G10-related, conserved site    GO:0000398: mRNA splicing, via spliceosome; GO:0005634: nucleus; GO:0010467: gene expression    K12873: BUD31,G10;bud site selection protein 31
Rp.chr1.0002    putative ATP synthase subunit f, mitochondrial  Riptortus pedestris mRNA for conserved hypothetical protein, complete cds, sequence id: Rped-0111   Putative ATP synthase subunit f, mitochondrial  KOG4092: Mitochondrial F1F0-ATP synthase, subunit f Mitochondrial F1F0-ATP synthase, subunit f  IPR019344: Mitochondrial F1-F0 ATP synthase subunit F, predicted    GO:0000276: mitochondrial proton-transporting ATP synthase complex, coupling factor F(o); GO:0005622: intracellular; GO:0005623: cell; GO:0005737: cytoplasm; GO:0005739: mitochondrion; GO:0005740: mitochondrial envelope; GO:0005743: mitochondrial inner membrane; GO:0005753: mitochondrial proton-transporting ATP synthase complex; GO:1902600: proton transmembrane transport   K02130: ATPeF0F,ATP5J2;F-type H+-transporting ATPase subunit f
Rp.chr1.0003    hypothetical protein EVAR_64278_1   PREDICTED: Bombyx mandarina uncharacterized LOC114246253 (LOC114246253), transcript variant X2, mRNA    -   -   DNA helicase activity   -   -   -
Rp.chr1.0005    Retrovirus-related Pol polyprotein from type-1 retrotransposable element R1 2   -   -   -   Reverse transcriptase (RNA-dependent DNA polymerase)    IPR000477: Reverse transcriptase domain -   -
Rp.chr1.0006    -   -   -   -   -   IPR005135: Endonuclease/exonuclease/phosphatase; IPR036691: Endonuclease/exonuclease/phosphatase superfamily    -   -
Rp.chr1.0007    piggyBac transposable element-derived protein 4-like; hypothetical protein AGLY_017479  -   -   -   DDE superfamily endonuclease    IPR029526: PiggyBac transposable element-derived protein    -   -
Rp.chr1.0008    hypothetical protein GE061_11589    -   -   -       -   -   -

I want a command which selects all upregulated genes from file1 and outputs the annotation from file2 next to the correct geneID e.g.:

geneID  Nr  Nt  SwissProt   KOG eggNOG  Interpro    GO  KEGG
Rp.chr4.1864    hexamerin   Riptortus clavatus mRNA for cyanoprotein alpha subunit precursor, complete cds  -   -   Hemocyanin, all-alpha domain    IPR000896: Hemocyanin/hexamerin middle domain; IPR005203: Hemocyanin, C-terminal; IPR005204: Hemocyanin, N-terminal; IPR008922: Uncharacterised domain, di-copper centre; IPR013788: Hemocyanin/hexamerin; IPR014756: Immunoglobulin E-set; IPR036697: Hemocyanin, N-terminal domain superfamily; IPR037020: Hemocyanin, C-terminal domain superfamily  -   -
Rp.chr1.1957    cuticle protein 7-like  -   Cuticle protein 19  -   pupal cuticle protein   IPR000618: Insect cuticle protein   GO:0005576: extracellular region; GO:0007275: multicellular organism development; GO:0008010: structural constituent of chitin-based larval cuticle; GO:0031012: extracellular matrix; GO:0040003: chitin-based cuticle development -
Rp.chr4.2000    prophenoloxidase    PREDICTED: Acyrthosiphon pisum phenoloxidase 1 (LOC100160034), mRNA Hemocyanin F chain; Phenoloxidase 1 -   Common central domain of tyrosinase IPR000896: Hemocyanin/hexamerin middle domain; IPR002227: Tyrosinase copper-binding domain; IPR005203: Hemocyanin, C-terminal; IPR005204: Hemocyanin, N-terminal; IPR008922: Uncharacterised domain, di-copper centre; IPR013788: Hemocyanin/hexamerin; IPR014756: Immunoglobulin E-set; IPR036697: Hemocyanin, N-terminal domain superfamily; IPR037020: Hemocyanin, C-terminal domain superfamily GO:0004503: monophenol monooxygenase activity; GO:0005576: extracellular region; GO:0005615: extracellular space; GO:0006583: melanin biosynthetic process from tyrosine; GO:0035011: melanotic encapsulation of foreign target; GO:0036263: L-DOPA monooxygenase activity; GO:0036264: dopamine monooxygenase activity; GO:0042417: dopamine metabolic process; GO:0050830: defense response to Gram-positive bacterium; GO:0050832: defense response to fungus; GO:0055114: oxidation-reduction process   -
Rp.chrX.1597    chitooligosaccharidolytic beta-N-acetylglucosaminidase isoform X1   Riptortus pedestris mRNA for beta-hexosaminidase, partial cds, sequence id: Rped-0394, expressed in midgut  Probable beta-hexosaminidase fdl; Chitooligosaccharidolytic beta-N-acetylglucosaminidase    KOG2499: Beta-N-acetylhexosaminidase    beta-acetyl hexosaminidase like IPR015883: Glycoside hydrolase family 20, catalytic domain; IPR017853: Glycoside hydrolase superfamily; IPR025705: Beta-hexosaminidase; IPR029018: Beta-hexosaminidase-like, domain 2; IPR029019: Beta-hexosaminidase, eukaryotic type, N-terminal  GO:0005623: cell; GO:0005886: plasma membrane; GO:0005975: carbohydrate metabolic process; GO:0006032: chitin catabolic process; GO:0006491: N-glycan processing; GO:0006517: protein deglycosylation; GO:0016063: rhodopsin biosynthetic process; GO:0016231: beta-N-acetylglucosaminidase activity; GO:0048069: eye pigmentation; GO:0071944: cell periphery  K12373: HEXA_B;hexosaminidase [EC:3.2.1.52]
Rp.chr4.1782    hypothetical protein GE061_16316    -   -   -       -   -   -
Rp.chr4.1865    hexamerin   Riptortus clavatus mRNA for cyanoprotein beta subunit precursor, complete cds   -   -   Hemocyanin, all-alpha domain    IPR000896: Hemocyanin/hexamerin middle domain; IPR005203: Hemocyanin, C-terminal; IPR005204: Hemocyanin, N-terminal; IPR008922: Uncharacterised domain, di-copper centre; IPR013788: Hemocyanin/hexamerin; IPR014756: Immunoglobulin E-set; IPR036697: Hemocyanin, N-terminal domain superfamily; IPR037020: Hemocyanin, C-terminal domain superfamily  -   -

I've tried several options in WSL and R such as join, awk, grep or somethings like:

comm -1 -3 <(sort gene_list.csv) <(sort upregulated_genes.csv) > upreg_genes.csv

or

df1<- read.csv("gene_list.csv")
df2<- read.csv("upregulated_genes.csv")

exporttab <- merge(x=df1, y=df2, by.x='geneID', by.y='gene_list', fill=-9999)

write.csv(exporttab, "known_genes.csv", row.names=FALSE)

However I can't get anything to work and am out of options online. Please help

This is just a general R question that you should be able to easily answer by using Google. Or you could ask on stackoverflow or biostars, or R-help, which are more general forums than this (which is intended for Bioconductor-specific questions).

But anyway, it's a simple matter of matching.

> tomatch <- data.frame(ID = LETTERS)
> matchable <- data.frame(ID = sample(LETTERS, 26), prot = paste0("protein", 1:26))
> matchable
   ID      prot
1   E  protein1
2   A  protein2
3   F  protein3
4   O  protein4
5   U  protein5
6   V  protein6
7   M  protein7
8   K  protein8
9   S  protein9
10  I protein10
11  P protein11
12  G protein12
13  Z protein13
14  L protein14
15  W protein15
16  J protein16
17  N protein17
18  B protein18
19  Y protein19
20  D protein20
21  X protein21
22  Q protein22
23  C protein23
24  H protein24
25  T protein25
26  R protein26
> matched <- data.frame(ID = tomatch[,1], prot = matchable[match(tomatch[,1], matchable[,1]),2])
> matched
   ID      prot
1   A  protein2
2   B protein18
3   C protein23
4   D protein20
5   E  protein1
6   F  protein3
7   G protein12
8   H protein24
9   I protein10
10  J protein16
11  K  protein8
12  L protein14
13  M  protein7
14  N protein17
15  O  protein4
16  P protein11
17  Q protein22
18  R protein26
19  S  protein9
20  T protein25
21  U  protein5
22  V  protein6
23  W protein15
24  X protein21
25  Y protein19
26  Z protein13

You could use merge in this case as well, but then you may need to use match to reorder, so I mostly use match directly.