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<p>Hi Jean,<br>
</p>
<p><br>
</p>
<p>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
<span lang="en-US"><font size="2" face="Calibri,sans-serif" style="font-family:Calibri,sans-serif,serif,"EmojiFont""><span style="font-size:11pt">R=Nature/460/352</span></font></span> did not work either. Look forward for your further update.
<br>
</p>
<p><br>
</p>
<p>Thank you and best regards,</p>
<p>Ran Wei<br>
</p>
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<div id="x_divRplyFwdMsg" dir="ltr"><font face="Calibri, sans-serif" color="#000000" style="font-size:11pt"><b>From:</b> Jean Lobry <jean.lobry@univ-lyon1.fr><br>
<b>Sent:</b> Monday, August 7, 2017 7:01:03 PM<br>
<b>To:</b> Ran Wei<br>
<b>Cc:</b> seqinr-forum@lists.r-forge.r-project.org; PENEL SIMON<br>
<b>Subject:</b> Re: [Seqinr-forum] Seqinr</font>
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<div class="PlainText">Hi Ran,<br>
<br>
now I'm able to reproduce the issue. There is an<br>
entry for ACC "NC_001477" as visible here:<br>
<br>
<a href="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">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</a><br>
<br>
But it clearly doesn't work here:<br>
<br>
> library(seqinr)<br>
> where.is.this.acc("NC_001477")<br>
Looking for available databases<br>
Looking for sequence with accession number NC_001477 in the following <br>
ACNUC databases:<br>
[1] "genbank" "embl" "emblwgs" "swissprot" <br>
<br>
[5] "ensembl" "hogenom" "hogenomdna" <br>
"hovergendna"<br>
[9] "hovergen" "hogenom5" "hogenom5dna" "hogenom4" <br>
<br>
[13] "hogenom4dna" "homolens" "homolensdna" "hobacnucl"<br>
[17] "hobacprot" "phever2" "phever2dna" "refseq"<br>
[21] "greviews" "bacterial" "archaeal" "protozoan"<br>
[25] "ensprotists" "ensfungi" "ensmetazoa" "ensplants"<br>
[29] "ensemblbacteria" "mito" "polymorphix" "emglib"<br>
[33] "refseqViruses" "ribodb" "taxodb"<br>
<br>
Trying to open bank with name --->genbank<--- ...... and opening was OK.<br>
==> Trying to find sequence NC_001477 in bank genbank ...... not found here.<br>
<br>
Trying to open bank with name --->embl<--- ...... and opening was OK.<br>
==> Trying to find sequence NC_001477 in bank embl ...... not found here.<br>
<br>
Trying to open bank with name --->emblwgs<--- ...Error in <br>
acnucopen(bank, socket) :<br>
Database with name -->emblwgs<-- is not known by server.<br>
<br>
... opening not OK, skipping this bank.<br>
<br>
Trying to open bank with name --->swissprot<--- ...... and opening was OK.<br>
==> Trying to find sequence NC_001477 in bank swissprot ...... not found <br>
here.<br>
<br>
Trying to open bank with name --->ensembl<--- ...Error in <br>
acnucopen(bank, socket) :<br>
Database with name -->ensembl<-- is not known by server.<br>
<br>
... opening not OK, skipping this bank.<br>
<br>
Trying to open bank with name --->hogenom<--- ...... and opening was OK.<br>
==> Trying to find sequence NC_001477 in bank hogenom ...... not found here.<br>
<br>
Trying to open bank with name --->hogenomdna<--- ...... and opening was OK.<br>
==> Trying to find sequence NC_001477 in bank hogenomdna ...... not <br>
found here.<br>
<br>
Trying to open bank with name --->hovergendna<--- ...Error in <br>
acnucopen(bank, socket) :<br>
Database with name -->hovergendna<-- is not known by server.<br>
<br>
... opening not OK, skipping this bank.<br>
<br>
Trying to open bank with name --->hovergen<--- ...Error in <br>
acnucopen(bank, socket) :<br>
Database with name -->hovergen<-- is not known by server.<br>
<br>
... opening not OK, skipping this bank.<br>
<br>
Trying to open bank with name --->hogenom5<--- ...Error in <br>
acnucopen(bank, socket) :<br>
Database with name -->hogenom5<-- is not known by server.<br>
<br>
... opening not OK, skipping this bank.<br>
<br>
Trying to open bank with name --->hogenom5dna<--- ...Error in <br>
acnucopen(bank, socket) :<br>
Database with name -->hogenom5dna<-- is not known by server.<br>
<br>
... opening not OK, skipping this bank.<br>
<br>
Trying to open bank with name --->hogenom4<--- ...Error in <br>
acnucopen(bank, socket) :<br>
Database with name -->hogenom4<-- is not known by server.<br>
<br>
... opening not OK, skipping this bank.<br>
<br>
Trying to open bank with name --->hogenom4dna<--- ...Error in <br>
acnucopen(bank, socket) :<br>
Database with name -->hogenom4dna<-- is not known by server.<br>
<br>
... opening not OK, skipping this bank.<br>
<br>
Trying to open bank with name --->homolens<--- ...Error in <br>
acnucopen(bank, socket) :<br>
Database with name -->homolens<-- is not known by server.<br>
<br>
... opening not OK, skipping this bank.<br>
<br>
Trying to open bank with name --->homolensdna<--- ...Error in <br>
acnucopen(bank, socket) :<br>
Database with name -->homolensdna<-- is not known by server.<br>
<br>
... opening not OK, skipping this bank.<br>
<br>
Trying to open bank with name --->hobacnucl<--- ...Error in <br>
acnucopen(bank, socket) :<br>
Database with name -->hobacnucl<-- is not known by server.<br>
<br>
... opening not OK, skipping this bank.<br>
<br>
Trying to open bank with name --->hobacprot<--- ...Error in <br>
acnucopen(bank, socket) :<br>
Database with name -->hobacprot<-- is not known by server.<br>
<br>
... opening not OK, skipping this bank.<br>
<br>
Trying to open bank with name --->phever2<--- ...Error in <br>
acnucopen(bank, socket) :<br>
Database with name -->phever2<-- is not known by server.<br>
<br>
... opening not OK, skipping this bank.<br>
<br>
Trying to open bank with name --->phever2dna<--- ...Error in <br>
acnucopen(bank, socket) :<br>
Database with name -->phever2dna<-- is not known by server.<br>
<br>
... opening not OK, skipping this bank.<br>
<br>
Trying to open bank with name --->refseq<--- ...Error in acnucopen(bank, <br>
socket) :<br>
Database with name -->refseq<-- is not known by server.<br>
<br>
... opening not OK, skipping this bank.<br>
<br>
Trying to open bank with name --->greviews<--- ...Error in <br>
acnucopen(bank, socket) :<br>
Database with name -->greviews<-- is not known by server.<br>
<br>
... opening not OK, skipping this bank.<br>
<br>
Trying to open bank with name --->bacterial<--- ...Error in <br>
acnucopen(bank, socket) :<br>
Database with name -->bacterial<-- is not known by server.<br>
<br>
... opening not OK, skipping this bank.<br>
<br>
Trying to open bank with name --->archaeal<--- ...Error in <br>
acnucopen(bank, socket) :<br>
Database with name -->archaeal<-- is not known by server.<br>
<br>
... opening not OK, skipping this bank.<br>
<br>
Trying to open bank with name --->protozoan<--- ...Error in <br>
acnucopen(bank, socket) :<br>
Database with name -->protozoan<-- is not known by server.<br>
<br>
... opening not OK, skipping this bank.<br>
<br>
Trying to open bank with name --->ensprotists<--- ...Error in <br>
acnucopen(bank, socket) :<br>
Database with name -->ensprotists<-- is not known by server.<br>
<br>
... opening not OK, skipping this bank.<br>
<br>
Trying to open bank with name --->ensfungi<--- ...Error in <br>
acnucopen(bank, socket) :<br>
Database with name -->ensfungi<-- is not known by server.<br>
<br>
... opening not OK, skipping this bank.<br>
<br>
Trying to open bank with name --->ensmetazoa<--- ...Error in <br>
acnucopen(bank, socket) :<br>
Database with name -->ensmetazoa<-- is not known by server.<br>
<br>
... opening not OK, skipping this bank.<br>
<br>
Trying to open bank with name --->ensplants<--- ...Error in <br>
acnucopen(bank, socket) :<br>
Database with name -->ensplants<-- is not known by server.<br>
<br>
... opening not OK, skipping this bank.<br>
<br>
Trying to open bank with name --->ensemblbacteria<--- ...Error in <br>
acnucopen(bank, socket) :<br>
Database with name -->ensemblbacteria<-- is not known by server.<br>
<br>
... opening not OK, skipping this bank.<br>
<br>
Trying to open bank with name --->mito<--- ...Error in acnucopen(bank, <br>
socket) :<br>
Database with name -->mito<-- is not known by server.<br>
<br>
... opening not OK, skipping this bank.<br>
<br>
Trying to open bank with name --->polymorphix<--- ...Error in <br>
acnucopen(bank, socket) :<br>
Database with name -->polymorphix<-- is not known by server.<br>
<br>
... opening not OK, skipping this bank.<br>
<br>
Trying to open bank with name --->emglib<--- ...Error in acnucopen(bank, <br>
socket) :<br>
Database with name -->emglib<-- is not known by server.<br>
<br>
... opening not OK, skipping this bank.<br>
<br>
Trying to open bank with name --->refseqViruses<--- ...Error in <br>
acnucopen(bank, socket) :<br>
Database with name -->refseqViruses<-- is not known by server.<br>
<br>
... opening not OK, skipping this bank.<br>
<br>
Trying to open bank with name --->ribodb<--- ...Error in acnucopen(bank, <br>
socket) :<br>
Database with name -->ribodb<-- is not known by server.<br>
<br>
... opening not OK, skipping this bank.<br>
<br>
Trying to open bank with name --->taxodb<--- ...Error in acnucopen(bank, <br>
socket) :<br>
Database with name -->taxodb<-- is not known by server.<br>
<br>
... opening not OK, skipping this bank.<br>
<br>
<br>
Sequence with accesion number NC_001477 was not found in available <br>
databases.<br>
Are you sure this is an accession number and not a sequence name?<br>
><br>
<br>
Here is my sessionInfo()<br>
<br>
> sessionInfo()<br>
R version 3.4.1 (2017-06-30)<br>
Platform: x86_64-apple-darwin15.6.0 (64-bit)<br>
Running under: macOS Sierra 10.12.6<br>
<br>
Matrix products: default<br>
BLAS: <br>
/Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libRblas.0.dylib<br>
LAPACK: <br>
/Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libRlapack.dylib<br>
<br>
locale:<br>
[1] fr_FR.UTF-8/fr_FR.UTF-8/fr_FR.UTF-8/C/fr_FR.UTF-8/fr_FR.UTF-8<br>
<br>
attached base packages:<br>
[1] stats graphics grDevices utils datasets methods base<br>
<br>
other attached packages:<br>
[1] seqinr_3.4-5<br>
<br>
loaded via a namespace (and not attached):<br>
[1] compiler_3.4.1 ade4_1.7-6<br>
><br>
<br>
<br>
<br>
Given the number of databases that failed to open my best guess<br>
is a problem on the server side. Not sure however.<br>
<br>
We'll keep you in touch.<br>
<br>
Best,<br>
<br>
JLO<br>
<br>
Le 08/08/2017 à 00:15, Ran Wei a écrit :<br>
> Hi Jean,<br>
> <br>
> Thank you very much for your reply. Actually there was a typo in my <br>
> first email. The accession number should be "NC_001477" instead of <br>
> "NC001477". Sorry about that, but the problem did not change. Please let <br>
> me know once the problem get fixed.<br>
> <br>
> Thank you,<br>
> Ran Wei<br>
<br>
<br>
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