Yann Dumont writes:
> Just one point, as I read your answer : the GI number mentioned in my
> message is from the query file, not from the subject file. It is just
> a precision, since the work-around will still work.
It looks like this behavior occurs only when explicitly using
-parse_deflines
Just one point, as I read your answer : the GI number mentioned in my
message is from the query file, not from the subject file. It is just
a precision, since the work-around will still work.
You are very welcome, since I only do troubleshooting and you may do
the hardest part of the debugging !
> Is there any way to by-pass this ? Telling blast to write sequence in
> the ASN file systematically ? Is it a expected behaviour ?
AFAICT, blastx and the like have no such option at present, but I expect
it would be relatively straightforward to implement one. Also, it might
be possible to run
Okay, I come with new stuff.
I realised that the bug happens only when I used fasta from NCBI, so I
was assuming blast_formatter downloads unuseful stuff from NCBI before
performing the formatting.
Actually formatter's behaviour seems correct. The problems comes from
the ASN.1 file I use for quer
Thanks for clarifying.
It sounds like the formatter is retrieving actual data, not just
speculatively setting up a connection, so enabling offline operation
won't be as easy as I'd hoped.
Yann Dumont writes:
> Well, you may not have assumed so... I run this command in another tab of
> my consol
Well, you may not have assumed so... I run this command in another tab of
my console (echo of the variable returned nothing, I was kind of suspicion
there).
Now I have done it correctly (echo returns no), but it doesn't change the
result : I still have the warnings and the empty result file.
If i
Yes, that's what I meant, assuming you proceeded to run blast_formatter
from the same shell session. I'll take a closer look when I get a chance.
-- Aaron
Yann Dumont writes:
> I am not sure I have done what you asked correctly. I am not very familiar
> with environnement variables. I just run
I am not sure I have done what you asked correctly. I am not very familiar
with environnement variables. I just run
$ export NCBI_CONFIG__GENBANK__PREOPEN=no
without rebooting, and it did not change anything.
2015-07-15 16:57 GMT+02:00 Aaron M. Ucko :
> Yann Dumont writes:
>
> > I am currently
Yann Dumont writes:
> I am currently have some connection issues, so I realized that blast_formatter
> failled when internet connection is off.
I'm sorry to hear that. Does the environment setting
NCBI_CONFIG__GENBANK__PREOPEN=no
help?
--
Aaron M. Ucko, KB1CJC (amu at alum.mit.edu, ucko at
Package: ncbi-blast+
Version: 2.2.30-4
Severity: important
Dear Maintainer,
I am currently have some connection issues, so I realized that blast_formatter
failled when internet connection is off.
This is what I obtain :
Error: (311.22) SOCK#1000[?]: [SOCK::Connect] Failed
SOCK_gethostbyname("w
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