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 On Sat, Jul 4, 2015 at 2:32 PM, Dooley, Damion <damion.doo...@bccdc.ca> wrote: > Makeblastdb can spit out warning notices when a higher count of N ambiguous > nucleotides occurs in the first row of fasta data, but goes ahead and > completes the blast database. > > "Error: (1431.1) FASTA-Reader: Warning: FASTA-Reader: First data line in seq > is about 45% ambiguous nucleotides (shouldn't be over 40%)" > > At moment the NCBI Blast+ wrappers > (toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_makeblastdb/0.1.01) > are saying "yup those are errors", but i think they should be downgraded to > just Notices? If the tool is part of a workflow it fails - on db's like RDP > RNA this is quite a nuisance. > > Anyone else run into the same thing? > > d. > > Also see: > > http://www.acgt.me/blog/2014/5/15/fun-with-an-error-message-from-ncbi-blast > > Hsiao lab, BC Public Health Microbiology & Reference Laboratory, BC Centre > for Disease Control > 655 West 12th Avenue, Vancouver, British Columbia, V5Z 4R4 Canada > ___________________________________________________________ > Please keep all replies on the list by using "reply all" > in your mail client. To manage your subscriptions to this > and other Galaxy lists, please use the interface at: > https://lists.galaxyproject.org/ > > To search Galaxy mailing lists use the unified search at: > http://galaxyproject.org/search/mailinglists/ ___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
