Hi, When I run DiffBind3 on my datasets (5GB-8GB for each sample bam file), it needs very large memory but still produce errors. I find a post but without any solution. DiffBind:all samples have 0 counts for all genes. I am not sure it is caused by my data. Thanks for any suggestions.

tf_dba <- dba(sampleSheet=fs,minOverlap=1,# If peak is at least exising in one peak file
              config=data.frame(AnalysisMethod=DBA_DESEQ2,th=0.05,
                                DataType=DBA_DATA_GRANGES, RunParallel=FALSE,
                                minQCth=-1, fragmentSize=200,
                                bCorPlot=FALSE, reportInit="DBA",
                                bUsePval=FALSE, design=TRUE,
                                doBlacklist=F, doGreylist=F),
              bRemoveM=F, bRemoveRandom=F
              )

#tf_dba$config$singleEnd=FALSE

tf_dba <- dba.count(tf_dba,summits=FALSE,  filter = 0, minCount=0,
                    bRemoveDuplicates=TRUE, bLog=TRUE)

GM12890_H3K36me3_1 Homo H3K36me3 GM12890 GM12890 1 bed GM12890_H3K36me3_1.2 Homo H3K36me3 GM12890 GM12890 3 bed GM12891_H3K36me3_1 Homo H3K36me3 GM12891 GM12891 1 bed GM12891_H3K36me3_2 Homo H3K36me3 GM12891 GM12891 2 bed Reads will be counted as Paired-end. Sample: GM12890_H3K36me3_1.nodup.bam200 Sample: GM12890_H3K36me3_1.2.nodup.bam200 Sample: GM12891_H3K36me3_1.nodup.bam200 Sample: GM12891_H3K36me3_2.nodup.bam200 Sample: GM12890_Input_1.nodup.bam200 Sample: GM12891_Input_1.nodup.bam200 Error in DESeqDataSet(se, design = design, ignoreRank) : all samples have 0 counts for all genes. check the counting script. Calls: dba.count ... suppressMessages -> withCallingHandlers -> <Anonymous> -> DESeqDataSet Execution halted