Plots but no intervals in DiffBind

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Hi @jennaj, thanks again for your reply! I’d forgotten that there is more to the logs… I’ve now looked at stdout, which looks the same as in a successful job. The stderr looks a bit different:

Warning message:
In Sys.setlocale("LC_MESSAGES", "en_US.UTF-8") :
  OS reports request to set locale to "en_US.UTF-8" cannot be honored
6h 6h  6hXDMSO  1 raw
6h 6h  6hXDMSO  1 raw
6h 6h  6hXDMSO  1 raw
6h 6h  6hXdTAG  1 raw
6h 6h  6hXdTAG  1 raw
6h 6h  6hXdTAG  1 raw
converting counts to integer mode
gene-wise dispersion estimates
mean-dispersion relationship
final dispersion estimates
Error in wilcox.test.default(toplot[[i]], toplot[[j]], paired = FALSE) : 
  not enough 'y' observations
Calls: dba.plotBox ... pv.plotBoxplot -> pvalMethod -> wilcox.test.default
Warning message:
In wilcox.test.default(toplot[[i]], toplot[[j]], paired = TRUE) :
  cannot compute exact p-value with zeroes

Whereas in a successful DiffBind it looks like this:

Warning message:
In Sys.setlocale("LC_MESSAGES", "en_US.UTF-8") :
  OS reports request to set locale to "en_US.UTF-8" cannot be honored
6h 6h  6hXBRGi  1 raw
6h 6h  6hXBRGi  1 raw
6h 6h  6hXBRGi  1 raw
6h 6h  6hXdTAG  1 raw
6h 6h  6hXdTAG  1 raw
6h 6h  6hXdTAG  1 raw
converting counts to integer mode
gene-wise dispersion estimates
mean-dispersion relationship
final dispersion estimates
Warning messages:
1: In wilcox.test.default(toplot[[i]], toplot[[j]], paired = TRUE) :
  cannot compute exact p-value with zeroes
2: In wilcox.test.default(toplot[[i]], toplot[[j]], paired = TRUE) :
  cannot compute exact p-value with zeroes
3: In wilcox.test.default(toplot[[i]], toplot[[j]], paired = TRUE) :
  cannot compute exact p-value with zeroes

Are there just some, but not enough, differentially accessible sites in my dataset to carry out the Wilcox test (“Error in wilcox.test.default(toplot[[i]], toplot[[j]], paired = FALSE) : not enough ‘y’ observations”)?

I found this post from someone who had a similar problem (Diffbind error: Not enough y observations). Someone suggested either changing the FDR threshold to 0.1, or using a different tool entirely (macs2 bdgdiff) to identify differential peaks in that particular experiment.

I’m sharing the history with you (https://usegalaxy.org/u/alexbis/h/6h-abde3-atac) in case it is helpful. If you look at an “unsuccessful” output (files 19-24) there is in fact something in file 20 (Plots). Compare to, for example, files 25-30 where the operation was successful. In the unsuccessful DiffBind operation, if I weren’t getting anything in Plots at all I’d just assume it’s a matter of no differentially accessible peaks present – but that’s not the case. (I deleted the .bam files from the history recently for space saving purposes, but happy to re-upload them if this further helps you help me.) Thanks again for your patience.