Hi, I am using Diffbind and get the following message:
[1] "en_US.UTF-8" Fatal error: An undefined error occured, please check your intput carefully and contact your administrator. Loading required package: GenomicRanges Loading required package: methods Loading required package: stats4 Loading required pack
Any tips?
Hello,
This error message comes out when there is a problem with the inputs. The current version of Diffbind does not have any known issues, so you do not need to consider a server-side problem if working at https://usegalaxy.org.
The important part of the error message can be seen after clicking on the bug icon (but you don't need to send this in since I've already looked at your history). This warning message can indicate that there is a mixup in the inputs.
Warning message:
No sites above threshold
Error in pv.getPlotData(DBA, attributes = attributes, contrast = contrast, :
Unable to plot -- no sites within threshold
Calls: dba.plotHeatmap -> pv.getPlotData
The given names of the inputs also seem to indicate that there might be a mixup between the BAM/BED pairs for some samples. But these are custom names, so you'll need to trace back through prior steps to find out which are the proper file pairs to use and/or if an earlier job/step didn't actually use the intended input data.
I didn't notice any obvious data content issues, but just for reference I'll give you the link to the support FAQs that help address those in case any are a factor once you dig into the problem: https://galaxyproject.org/support/#troubleshooting
Hope that helps! Jen, Galaxy team
Hi Jen, The BAM/BED pairings are correct, and I think the issue may be due to the lack of Database/Build specifications. I updated the BAM files to include the build (hg19), but I was unable to do the same for the BED files (galaxy would not let me save the changes when I tried to Edit Attributes):
Here's what I'd like to do: 1. add Database/Build info: “Human Feb. 2009 (GRCh37/hg19)(hg19)” 2. Change Name/Identifier column from “4” to “unspecified” (since these BEDs do not have this info) 3. confirm that score is in column “4”
Any hints/suggestions? (I'm desperate!) -melissa
Update: Double check the format of the BED datasets and correct to match specification as needed. Then the datatype/database can be assigned through Edit Attributes.