DiffBind: error with dba.count

blakeoft · 09-03-2014, 11:28 AM

Hello,

I've been using DiffBind to analyze some ATAC-seq peak data. Briefly, peaks in these datasets represent sites of open chromatin. DiffBind seems to do a very good job, but I've encountered an error in my most recent comparison. Here's the R code:

Code:

> library(DiffBind)
> diffpeaks <- dba(sampleSheet = "metadata.csv")
# suppressed output
> diffpeaks <- dba.count(diffpeaks)
# suppressed output
Error in if (sum(tokeep) < length(tokeep)) { : 
  missing value where TRUE/FALSE needed
In addition: Warning message:
In dba.multicore.init(DBA$config) :
  Parallel execution unavailable: executing serially.

I've bolded the actual error. I've looked through the dba.count() code, and I can't tell where the error is coming from. My best guess is that it's from the pv.count() function, but I can't seem to find anything about it anywhere. This is really a mystery to me (and I thought I knew what was going on in R too

)...

I’ve selected subsets of the metadata with varying sizes--sometimes it works, and sometimes I get the same error. This leads me to believe that it isn’t a memory issue.

Does anyone have any ideas about this?

Thanks for any help,

Blake

rory · 09-09-2014, 12:03 PM

It appears that DiffBind can't handle the "-" character (minus sign/hyphen) in the file names. Remove them and it should work!

Cheers-
Rory

lime gin · 09-22-2014, 12:27 PM

Hi Blake, just curious if this has been resolved. I'm getting the same exact error with my data; while I've pinpointed the exact subset where the error is coming from, my file names all have alphanumeric characters.

blakeoft · 09-22-2014, 12:36 PM

Unfortunately, I have not resolved the issue yet. I'm just curious, what kind of machine are you running DiffBind on? I've used it several times without error on a Unix based HPC. But ever since I've tried using it on my windows computer, I get this error. The HPC has been down for maintenance, so I haven't been able to see if running it there solves the problem. I'll post my results whenever the cluster is back up.

lime gin · 09-22-2014, 12:42 PM

Thanks for your response. I'm running it on my Windows computer through RStudio. We do have a Unix based HPC, but I've never tried running R there. I'll give it a shot and see how it goes.

lime gin · 09-23-2014, 12:02 PM

Update: I ran the same set of data on our Unix based HPC and it worked!

blakeoft · 09-23-2014, 12:05 PM

That's good to hear. I really don't have any sort of an idea of why DiffBind (specifically dba.count()) does not seem to work on Windows. I look forward to when I can use our HPC again! Thanks for the update.

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09-03-2014, 11:28 AM	#1
blakeoft Member Location: Connecticut Join Date: Oct 2013 Posts: 79	DiffBind: error with dba.count Hello, I've been using DiffBind to analyze some ATAC-seq peak data. Briefly, peaks in these datasets represent sites of open chromatin. DiffBind seems to do a very good job, but I've encountered an error in my most recent comparison. Here's the R code: Code: > library(DiffBind) > diffpeaks <- dba(sampleSheet = "metadata.csv") # suppressed output > diffpeaks <- dba.count(diffpeaks) # suppressed output Error in if (sum(tokeep) < length(tokeep)) { : missing value where TRUE/FALSE needed In addition: Warning message: In dba.multicore.init(DBA$config) : Parallel execution unavailable: executing serially. I've bolded the actual error. I've looked through the dba.count() code, and I can't tell where the error is coming from. My best guess is that it's from the pv.count() function, but I can't seem to find anything about it anywhere. This is really a mystery to me (and I thought I knew what was going on in R too )... I’ve selected subsets of the metadata with varying sizes--sometimes it works, and sometimes I get the same error. This leads me to believe that it isn’t a memory issue. Does anyone have any ideas about this? Thanks for any help, Blake

09-09-2014, 12:03 PM	#2
rory Member Location: Cambridge, UK Join Date: Aug 2008 Posts: 28	It appears that DiffBind can't handle the "-" character (minus sign/hyphen) in the file names. Remove them and it should work! Cheers- Rory

09-22-2014, 12:27 PM	#3
lime gin Junior Member Location: missoula, mt Join Date: Jul 2012 Posts: 3	Hi Blake, just curious if this has been resolved. I'm getting the same exact error with my data; while I've pinpointed the exact subset where the error is coming from, my file names all have alphanumeric characters.

09-22-2014, 12:36 PM	#4
blakeoft Member Location: Connecticut Join Date: Oct 2013 Posts: 79	Unfortunately, I have not resolved the issue yet. I'm just curious, what kind of machine are you running DiffBind on? I've used it several times without error on a Unix based HPC. But ever since I've tried using it on my windows computer, I get this error. The HPC has been down for maintenance, so I haven't been able to see if running it there solves the problem. I'll post my results whenever the cluster is back up.

09-22-2014, 12:42 PM	#5
lime gin Junior Member Location: missoula, mt Join Date: Jul 2012 Posts: 3	Thanks for your response. I'm running it on my Windows computer through RStudio. We do have a Unix based HPC, but I've never tried running R there. I'll give it a shot and see how it goes.

09-23-2014, 12:02 PM	#6
lime gin Junior Member Location: missoula, mt Join Date: Jul 2012 Posts: 3	Update: I ran the same set of data on our Unix based HPC and it worked!

09-23-2014, 12:05 PM	#7
blakeoft Member Location: Connecticut Join Date: Oct 2013 Posts: 79	That's good to hear. I really don't have any sort of an idea of why DiffBind (specifically dba.count()) does not seem to work on Windows. I look forward to when I can use our HPC again! Thanks for the update.