I ran into this error running cuffdiff. I had a hard time debugging
this user error, so I though it would be nice to share the solution.
This was in a local instance, but I don't see why it wouldn't happen
in Galaxy Main under the same circumstances.

Tool execution generated the following error message:
Error running cuffdiff. Error: cannot open reference GTF file

The tool produced the following additional output:
cuffdiff v1.3.0 ()
cuffdiff --no-update-check -q -p 4 -c 1000 --FDR 0.050000 -N -b

The problem ended being the use of "Perform Bias Correction"(-b) and a
GTF file with no "Database/Build" associated. Looking at cuffdiff
wrapper I found, if a FASTA reference is not selected from the
history, the FASTA reference of the GTF file associated build is used.
If there is not build association, your cuffdiff run will fail with
this not so helpful error.

My feeling is, cuffdiff should check for a non-dashed string after
'-b' and complain if is absents, but this doesn't happen currently.

Kind regards,
The Galaxy User list should be used for the discussion of
Galaxy analysis and other features on the public server
at usegalaxy.org.  Please keep all replies on the list by
using "reply all" in your mail client.  For discussion of
local Galaxy instances and the Galaxy source code, please
use the Galaxy Development list:


To manage your subscriptions to this and other Galaxy lists,
please use the interface at:


Reply via email to