I attempted the run DiffBind (v3.4.0) for my samples ( I have bam, control bam and peak files in the sample sheet). After running about 5 hrs, it returns the following error. Any idea what causing this?

dba_obj <- dba(sampleSheet=Sample)

dba_obj <- dba.count(dba_obj, bUseSummarizeOverlaps=TRUE)

Computing summits...
Re-centering peaks...
Reads will be counted as Paired-end.
Reads will be counted as Paired-end.
Reads will be counted as Paired-end.
...
Error in SummarizedExperiment(assays = SimpleList(counts = countData),  : 
  the rownames and colnames of the supplied assay(s) must be NULL or
  identical to those of the SummarizedExperiment object (or derivative)
  to construct
Calls: sourceWithProgress ... withCallingHandlers -> <Anonymous> -> SummarizedExperiment
In addition: There were 50 or more warnings (use warnings() to see the first 50)
Execution halted

Using minOverlap=1 in dba.count , it seems to work but that means I have to use all the peak set for the analysis

dba_obj <- dba.count(dba_obj, minOverlap=1 )

It would help to see the warnings!

Also, you can try running this with bParallel=FALSE so you can see the messages for each file. If there is an issue with all the files, you'll see it when processing the first one. If the issue relates to one or more specific files, you'll see which they are.

Let me know what you see!