R package DiffBind -- Error: No sites have activity greater than minMaxval

Question

[alexmondaini]

When running dba.count() on my dba object:

samples <- dba(sampleSheet = "../samplesheet.csv",peakFormat = "bed",scoreCol = 5)

ep_293T_siNeg_R1  ep_293T_siNeg   1 bed
ep_293T_siNeg_R2  ep_293T_siNeg   2 bed
ep_293T_siFUS_R1  ep_293T_siFUS   1 bed
ep_293T_siFUS_R2  ep_293T_siFUS   2 bed

I get the following error:

samples <- dba.count(samples)

Computing summits...
Sample: shard-0/execution/10249_sample1.bam125 
Sample: shard-1/execution/10249_sample2.bam125 
Sample: shard-2/execution/10249_sample3.bam125 
Sample: shard-3/execution/10249_sample4.bam125 
Sample: shard-4/execution/10249_sample5.bam125 
Sample: shard-5/execution/10249_sample6.bam125 
Sample: shard-6/execution/10249_sample7.bam125 
Sample: shard-7/execution/10249_sample8.bam125 
Re-centering peaks...
Sample: shard-0/execution/10249_sample1.bam125 
Reads will be counted as Paired-end.
Sample: shard-1/execution/10249_sample2.bam125 
Reads will be counted as Paired-end.
Sample: shard-2/execution/10249_sample3.bam125 
Reads will be counted as Paired-end.
Sample: shard-3/execution/10249_sample4.bam125 
Reads will be counted as Paired-end.
Sample: shard-4/execution/10249_sample5.bam125 
Reads will be counted as Paired-end.
Sample: shard-5/execution/10249_sample6.bam125 
Reads will be counted as Paired-end.
Sample: shard-6/execution/10249_sample7.bam125 
Reads will be counted as Paired-end.
Sample: shard-7/execution/10249_sample8.bam125 
Reads will be counted as Paired-end.
Error: No sites have activity greater than minMaxval
In addition: Warning message:
Parallel execution unavailable: executing serially. 

What am I getting wrong here ? Thanks

P.S: from github the error stems from this section : https://github.com/aeron15/DiffBind/blob/master/R/counts.R#L579 but I'm not familiar with what those lines mean.

Answer 1

[Shilong]

You can try using dba.count(dbaObject, bUseSummarizeOverlaps=FALSE) to solve this.

I met the same problem with yours and I use this way to solve this problem. But I don't know the reason.

[alexmondaini]

You're right, it worked for me too to set bUseSummarizeOverlaps=FALSE thanks a lot.