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Sometimes BLAST+ warning messages treated as errors #40
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This problem was fixed in BLAST+ 2.2.30, so I am closing this issue for now. |
Reopening: Similar issue reported on galaxy-dev list http://dev.list.galaxyproject.org/Cosmetic-Makeblastdb-error-promulgated-through-wrapper-tc4667485.html by Damion Dooley (@ddooley), and blogged about by Keith Bradnam (@kbradnam) here: http://www.acgt.me/blog/2014/5/15/fun-with-an-error-message-from-ncbi-blast
Again, this looks like a warning which the NCBI BLAST suite is wrongly labelling as an error. |
I emailed the NCBI about this on 2014-05-14 and had the following reply:
|
Thanks Keith. Hopefully they'll fix this in the next BLAST+ release, but I'm open to adjusting our regex so these |
As noted on galaxy board,
provides a workaround until NCBI downgrades the Error:. The regex line has to be constrained with a carrot because otherwise it matches the too-generic first line of error report. I can set myself up to do a pull request on this if desired. Will have to wait a few weeks as I have other things on the go though, incl. conference and holiday. ciao, Damion |
Thanks Damion - I'm also on the road (currently at the Galaxy conference GCC2015 in Norwich), but adjusting the regex should be fine. Thanks! |
I've just hit the following problem with BLAST+ 2.2.29 writing these warning messages to stderr which (sadly) start with
Error:
and so match our regex:Currently in
ncbi_macros.xml
we have:I will report this to the NCBI, see http://blastedbio.blogspot.co.uk/2014/04/error-1431-fasta-reader-ignoring-modifiers.html for details. However, perhaps as a short term workaround the
Error:
regex could be relaxed ifWarning:
also appears in the same line?The text was updated successfully, but these errors were encountered: