Question: DiffBind problem on Galaxy
0
gravatar for melissa_hancock
11 weeks ago by
melissa_hancock0 wrote:

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?

galaxy chip-seq • 121 views
ADD COMMENTlink modified 11 weeks ago • written 11 weeks ago by melissa_hancock0
0
gravatar for Jennifer Hillman Jackson
11 weeks ago by
United States
Jennifer Hillman Jackson23k wrote:

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

ADD COMMENTlink modified 11 weeks ago • written 11 weeks ago by Jennifer Hillman Jackson23k
0
gravatar for melissa_hancock
11 weeks ago by
melissa_hancock0 wrote:

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

ADD COMMENTlink modified 11 weeks ago • written 11 weeks ago by melissa_hancock0
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