I don't know where to report this, because it is (1) not so much an error as
requesting a more informative fail message and (2) this is from a student's
galaxy history, so I don't have access to the bug icon from her shared history.
But the gist of the request is when running Emboss tools water and needle on
very large (300kb) sequences, the Galaxy fail message is segmentation fault.
I ran the same sequences on command line water and needle from EMBOSS
installation here at Baylor college of medicine, and the fail message was
"Died: Sequences too big. Try 'matcher' or 'super matcher'".
Matcher and Super matcher are also available to use in galaxy under emboss
tools, but most users will not know to try those. Is it possible to have the
emboss fail message be the galaxy fail message?
Thanks so much,
1. Where you are using Galaxy (Main<http://wiki.galaxyproject.org/Main>,
local, or cloud instance). MAIN
2. The date/time the bug was detected 3/18/13
3. Exact steps to reproduce the issue -- load 2 sequences about 300kb each
into needle and/or water EMBOSS tools
4. What troubleshooting steps (if any) you have tested out -- saw
segmentation fault error message from galaxy and tried running on command line
emboss installation. Fail message from command line emboss tools was helpful,
pointing user to matcher and super matcher programs that handle larger
5. IMPORTANT: If data is involved, leave all of the related datasets in the
analysis thread leading up to the bug in your history undeleteduntil we have
written you back. Use Options → Show Deleted Datasets and click dataset links
to undelete to recover error datasets before reporting a bug if necessary. THE
HISTORY IS HERE:
Dr. Deborah Ritter
Postdoctoral Associate, IRACDA Fellow
Human Genome Sequencing Center
Baylor College of Medicine
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