[Seqinr-forum] Seqinr

[Ran Wei]

Hi Jean,


Thank you for posting the original website for this sequence. I also tried "NC_001477.1" according to the website you sent me but still did not work. You may be right the problem is from server, since accession number like R=Nature/460/352 did not work either. Look forward for your further update.


Thank you and best regards,

Ran Wei

________________________________
From: Jean Lobry <jean.lobry at univ-lyon1.fr>
Sent: Monday, August 7, 2017 7:01:03 PM
To: Ran Wei
Cc: seqinr-forum at lists.r-forge.r-project.org; PENEL SIMON
Subject: Re: [Seqinr-forum] Seqinr

Hi Ran,

now I'm able to reproduce the issue. There is an
entry for ACC "NC_001477" as visible here:

https://na01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fnuccore%2FNC_001477&data=02%7C01%7Cweira%40njms.rutgers.edu%7Ceaf7b90429d446d18afb08d4dde82fb4%7Cb92d2b234d35447093ff69aca6632ffe%7C1%7C0%7C636377436693506163&sdata=hVZsxaaWZ2zC8JelsGT8SHhUF8BoDqngxS1jwcsg2BU%3D&reserved=0

But it clearly doesn't work here:

 > library(seqinr)
 > where.is.this.acc("NC_001477")
Looking for available databases
Looking for sequence with accession number NC_001477 in the following
ACNUC databases:
  [1] "genbank"         "embl"            "emblwgs"         "swissprot"

  [5] "ensembl"         "hogenom"         "hogenomdna"
"hovergendna"
  [9] "hovergen"        "hogenom5"        "hogenom5dna"     "hogenom4"

[13] "hogenom4dna"     "homolens"        "homolensdna"     "hobacnucl"
[17] "hobacprot"       "phever2"         "phever2dna"      "refseq"
[21] "greviews"        "bacterial"       "archaeal"        "protozoan"
[25] "ensprotists"     "ensfungi"        "ensmetazoa"      "ensplants"
[29] "ensemblbacteria" "mito"            "polymorphix"     "emglib"
[33] "refseqViruses"   "ribodb"          "taxodb"

Trying to open bank with name --->genbank<--- ...... and opening was OK.
==> Trying to find sequence NC_001477 in bank genbank ...... not found here.

Trying to open bank with name --->embl<--- ...... and opening was OK.
==> Trying to find sequence NC_001477 in bank embl ...... not found here.

Trying to open bank with name --->emblwgs<--- ...Error in
acnucopen(bank, socket) :
   Database with name -->emblwgs<-- is not known by server.

... opening not OK, skipping this bank.

Trying to open bank with name --->swissprot<--- ...... and opening was OK.
==> Trying to find sequence NC_001477 in bank swissprot ...... not found
here.

Trying to open bank with name --->ensembl<--- ...Error in
acnucopen(bank, socket) :
   Database with name -->ensembl<-- is not known by server.

... opening not OK, skipping this bank.

Trying to open bank with name --->hogenom<--- ...... and opening was OK.
==> Trying to find sequence NC_001477 in bank hogenom ...... not found here.

Trying to open bank with name --->hogenomdna<--- ...... and opening was OK.
==> Trying to find sequence NC_001477 in bank hogenomdna ...... not
found here.

Trying to open bank with name --->hovergendna<--- ...Error in
acnucopen(bank, socket) :
   Database with name -->hovergendna<-- is not known by server.

... opening not OK, skipping this bank.

Trying to open bank with name --->hovergen<--- ...Error in
acnucopen(bank, socket) :
   Database with name -->hovergen<-- is not known by server.

... opening not OK, skipping this bank.

Trying to open bank with name --->hogenom5<--- ...Error in
acnucopen(bank, socket) :
   Database with name -->hogenom5<-- is not known by server.

... opening not OK, skipping this bank.

Trying to open bank with name --->hogenom5dna<--- ...Error in
acnucopen(bank, socket) :
   Database with name -->hogenom5dna<-- is not known by server.

... opening not OK, skipping this bank.

Trying to open bank with name --->hogenom4<--- ...Error in
acnucopen(bank, socket) :
   Database with name -->hogenom4<-- is not known by server.

... opening not OK, skipping this bank.

Trying to open bank with name --->hogenom4dna<--- ...Error in
acnucopen(bank, socket) :
   Database with name -->hogenom4dna<-- is not known by server.

... opening not OK, skipping this bank.

Trying to open bank with name --->homolens<--- ...Error in
acnucopen(bank, socket) :
   Database with name -->homolens<-- is not known by server.

... opening not OK, skipping this bank.

Trying to open bank with name --->homolensdna<--- ...Error in
acnucopen(bank, socket) :
   Database with name -->homolensdna<-- is not known by server.

... opening not OK, skipping this bank.

Trying to open bank with name --->hobacnucl<--- ...Error in
acnucopen(bank, socket) :
   Database with name -->hobacnucl<-- is not known by server.

... opening not OK, skipping this bank.

Trying to open bank with name --->hobacprot<--- ...Error in
acnucopen(bank, socket) :
   Database with name -->hobacprot<-- is not known by server.

... opening not OK, skipping this bank.

Trying to open bank with name --->phever2<--- ...Error in
acnucopen(bank, socket) :
   Database with name -->phever2<-- is not known by server.

... opening not OK, skipping this bank.

Trying to open bank with name --->phever2dna<--- ...Error in
acnucopen(bank, socket) :
   Database with name -->phever2dna<-- is not known by server.

... opening not OK, skipping this bank.

Trying to open bank with name --->refseq<--- ...Error in acnucopen(bank,
socket) :
   Database with name -->refseq<-- is not known by server.

... opening not OK, skipping this bank.

Trying to open bank with name --->greviews<--- ...Error in
acnucopen(bank, socket) :
   Database with name -->greviews<-- is not known by server.

... opening not OK, skipping this bank.

Trying to open bank with name --->bacterial<--- ...Error in
acnucopen(bank, socket) :
   Database with name -->bacterial<-- is not known by server.

... opening not OK, skipping this bank.

Trying to open bank with name --->archaeal<--- ...Error in
acnucopen(bank, socket) :
   Database with name -->archaeal<-- is not known by server.

... opening not OK, skipping this bank.

Trying to open bank with name --->protozoan<--- ...Error in
acnucopen(bank, socket) :
   Database with name -->protozoan<-- is not known by server.

... opening not OK, skipping this bank.

Trying to open bank with name --->ensprotists<--- ...Error in
acnucopen(bank, socket) :
   Database with name -->ensprotists<-- is not known by server.

... opening not OK, skipping this bank.

Trying to open bank with name --->ensfungi<--- ...Error in
acnucopen(bank, socket) :
   Database with name -->ensfungi<-- is not known by server.

... opening not OK, skipping this bank.

Trying to open bank with name --->ensmetazoa<--- ...Error in
acnucopen(bank, socket) :
   Database with name -->ensmetazoa<-- is not known by server.

... opening not OK, skipping this bank.

Trying to open bank with name --->ensplants<--- ...Error in
acnucopen(bank, socket) :
   Database with name -->ensplants<-- is not known by server.

... opening not OK, skipping this bank.

Trying to open bank with name --->ensemblbacteria<--- ...Error in
acnucopen(bank, socket) :
   Database with name -->ensemblbacteria<-- is not known by server.

... opening not OK, skipping this bank.

Trying to open bank with name --->mito<--- ...Error in acnucopen(bank,
socket) :
   Database with name -->mito<-- is not known by server.

... opening not OK, skipping this bank.

Trying to open bank with name --->polymorphix<--- ...Error in
acnucopen(bank, socket) :
   Database with name -->polymorphix<-- is not known by server.

... opening not OK, skipping this bank.

Trying to open bank with name --->emglib<--- ...Error in acnucopen(bank,
socket) :
   Database with name -->emglib<-- is not known by server.

... opening not OK, skipping this bank.

Trying to open bank with name --->refseqViruses<--- ...Error in
acnucopen(bank, socket) :
   Database with name -->refseqViruses<-- is not known by server.

... opening not OK, skipping this bank.

Trying to open bank with name --->ribodb<--- ...Error in acnucopen(bank,
socket) :
   Database with name -->ribodb<-- is not known by server.

... opening not OK, skipping this bank.

Trying to open bank with name --->taxodb<--- ...Error in acnucopen(bank,
socket) :
   Database with name -->taxodb<-- is not known by server.

... opening not OK, skipping this bank.


Sequence with accesion number NC_001477 was not found in available
databases.
  Are you sure this is an accession number and not a sequence name?
 >

Here is my sessionInfo()

 > sessionInfo()
R version 3.4.1 (2017-06-30)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS Sierra 10.12.6

Matrix products: default
BLAS:
/Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libRblas.0.dylib
LAPACK:
/Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libRlapack.dylib

locale:
[1] fr_FR.UTF-8/fr_FR.UTF-8/fr_FR.UTF-8/C/fr_FR.UTF-8/fr_FR.UTF-8

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base

other attached packages:
[1] seqinr_3.4-5

loaded via a namespace (and not attached):
[1] compiler_3.4.1 ade4_1.7-6
 >



Given the number of databases that failed to open my best guess
is a problem on the server side. Not sure however.

We'll keep you in touch.

Best,

JLO

Le 08/08/2017 à 00:15, Ran Wei a écrit :
> Hi Jean,
>
> Thank you very much for your reply. Actually there was a typo in my
> first email. The accession number should be "NC_001477" instead of
> "NC001477". Sorry about that, but the problem did not change. Please let
> me know once the problem get fixed.
>
> Thank you,
> Ran Wei


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