Question: (Closed) cummeRbund SQLite database error from Galaxy main CuffDiff tool
gravatar for nevil
3.2 years ago by
United States
nevil20 wrote:

I'm trying to create an SQLite database to download and use with cummeRbund by using the "Create SQLite database" option with Cuffdiff on the main Galaxy instance. However, when this option is selected, the run "fails" though all the other tabular output files seem to still be generated (SQLite db file is empty). Normally, when I have run the same data through Cuffdiff, but do not select the SQLite option it works perfectly.

I'm using two replicates (so for samples total) and a refseq gtf annotation file. I have also tried using both output from Cuffmerge and Cuffcompare as my input for Cuffdiff, but the result is the same.

Any ideas what is happening?

rna-seq cufflinks galaxy R • 1.7k views
ADD COMMENTlink modified 3 months ago by Jennifer Hillman Jackson25k • written 3.2 years ago by nevil20


Would you be able to share a history with We can confirm inputs and if this is a true bug, get it ticketed for a correction. Please include a link to this question in the comments and be sure that all inputs/outputs from the sample errors are left undeleted.

Thanks, Jen, Galaxy team

ADD REPLYlink written 3.2 years ago by Jennifer Hillman Jackson25k


I'm having an issue with cuffdiff output- everything's in tabular format. How do I manipulate to use it in cummerbund? Please help.

Thanks, Vaish

ADD REPLYlink written 2.2 years ago by vaisharaghu0

I am also having the similar problem as Vaisharaghu has posted.Please help as soon as possible.

ADD REPLYlink written 7 months ago by adoorprabha0

I am also having this same problem. I've duplicated the run and when I run the data to generate SQLite for cummeRbund it errors but when I disable that function with all else the same, it works perfectly.

ADD REPLYlink written 3 months ago by sdbaney10

Hello nevil!

Questions similar to yours can already be found at:

We have closed your question to allow us to keep similar content in the same thread.

If you disagree with this please tell us why in a reply below. We'll be happy to talk about it.


ADD REPLYlink written 3 months ago by Jennifer Hillman Jackson25k
gravatar for Jennifer Hillman Jackson
3 months ago by
United States
Jennifer Hillman Jackson25k wrote:


The earlier tool version had this corrected but the newer version regressed and now has the same problem.

In short, the most current version of the tool will fail when the option for SQLite output is selected. Either avoid that option or use the earlier tool version.

Post with details and issue ticket link:

Thanks! Jen, Galaxy team

ADD COMMENTlink written 3 months ago by Jennifer Hillman Jackson25k
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