Cosmetic Makeblastdb error promulgated through wrapper
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
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.Dooley@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/
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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.cock@googlemail.com] Sent: Saturday, July 04, 2015 8:11 AM To: Dooley, Damion Cc: galaxy-dev@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
On Sat, Jul 4, 2015 at 5:09 PM, Dooley, Damion <Damion.Dooley@bccdc.ca> wrote:
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.
What is the error code? It might still be zero (which is fine for a warning only). I've reopened https://github.com/peterjc/galaxy_blast/issues/40 for any potential Galaxy wrapper work around, Peter
I'll check it out in more detail next week. Maybe exit code is actually 0. 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.cock@googlemail.com] Sent: Saturday, July 04, 2015 9:27 AM To: Dooley, Damion Cc: galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] Cosmetic Makeblastdb error promulgated through wrapper ... What is the error code? It might still be zero (which is fine for a warning only). I've reopened https://github.com/peterjc/galaxy_blast/issues/40 for any potential Galaxy wrapper work around, Peter
So it does return error code 0, thankfully. I've dropped the workaround on https://github.com/peterjc/galaxy_blast/issues/40 , and could do the pull request process in a few weeks. d. ... What is the error code? It might still be zero (which is fine for a warning only). I've reopened https://github.com/peterjc/galaxy_blast/issues/40 for any potential Galaxy wrapper work around, Peter
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Peter Cock