Sure I could probably step up to the plate on that one.  I haven't reported it 
to NCBI - it didn't twig that this was an exit code > 0 .  I'll sneak it into 
BOSC codefest maybe!

d.

Hsiao lab, BC Public Health Microbiology & Reference Laboratory, BC Centre for 
Disease Control
655 West 12th Avenue, Vancouver, British Columbia, V5Z 4R4 Canada
________________________________________
From: Peter Cock [p.j.a.c...@googlemail.com]
Sent: Saturday, July 04, 2015 8:11 AM
To: Dooley, Damion
Cc: galaxy-...@lists.bx.psu.edu
Subject: Re: [galaxy-dev] Cosmetic Makeblastdb error promulgated through wrapper

Hi Damion,

The NCBI have a bug here - if it is just a warning, it shouldn't
say "Error". We had something similar before:

Error: (1431.1) FASTA-Reader: Warning: FASTA-Reader: Ignoring FASTA
modifier(s) found because the input was not expected to have any.

In that case the NCBI fixed it, see
https://github.com/peterjc/galaxy_blast/issues/40

Did you (or Keith Bradnam) report this to the NCBI?

In the short term we can probably tweak the regex so that these
"Error: *: Warning: *" lines on stderr are not treated as errors?
Do you fancy working on this?

Peter
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