[E::hts_idx_push] Region 536872557..536872641 cannot be stored in a bai index. Try using a csi index with min_shift = 14, n_lvls >= 6
Error: Error processing one or more read files. Check warnings().
In addition: Warning messages:
1: In mclapply(arglist, fn, ..., mc.preschedule = TRUE, mc.allow.recursive = TRUE) :
  all scheduled cores encountered errors in user code
2:   file: bam/JW_1.uniq.sort.rmdup.1A.bam 



# include your problematic code here with any corresponding output 
# please also include the results of running the following in an R session 

dbObj <- dba(sampleSheet=samples)
dbObj <- dba.count(dbObj, bUseSummarizeOverlaps=TRUE)

I use the hg38 genome for diffbind is OK, while wheat genome is so big, how can use diffbind to analyze the wheat project?

That error doesn't come from DiffBind, but instead it comes from samtools/htslib.

You may be able to index your files using a csi index, but I am not sure that it will then work with DiffBind, as IIRC Rsamtools requires a bai index.