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<p style="margin-top:0;margin-bottom:0">Hello Simon,</p>
<p style="margin-top:0;margin-bottom:0"><br>
</p>
<p style="margin-top:0;margin-bottom:0">Thanks you very much for the solution, indeed it solves the problem! </p>
<p style="margin-top:0;margin-bottom:0">I tried to decrease the timeout to 10 and it seems to be enough.</p>
<p style="margin-top:0;margin-bottom:0"><br>
</p>
<p style="margin-top:0;margin-bottom:0">I was also getting the same problem with R 3.4.4 and R 3.3.1 so </p>
<p style="margin-top:0;margin-bottom:0">I don't really know why it's taking longer to connect!</p>
<p style="margin-top:0;margin-bottom:0"><br>
</p>
<p style="margin-top:0;margin-bottom:0">Thanks very much for your very quick answer I really appreciate it!</p>
<p style="margin-top:0;margin-bottom:0"><br>
</p>
<p style="margin-top:0;margin-bottom:0">All the best,</p>
<p style="margin-top:0;margin-bottom:0"><br>
</p>
<p style="margin-top:0;margin-bottom:0">David</p>
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<div id="divRplyFwdMsg" dir="ltr"><font face="Calibri, sans-serif" style="font-size:11pt" color="#000000"><b>From:</b> Seqinr-forum <seqinr-forum-bounces@lists.r-forge.r-project.org> on behalf of Simon Penel <simon.penel@univ-lyon1.fr><br>
<b>Sent:</b> Thursday, March 7, 2019 11:12:39 PM<br>
<b>To:</b> seqinr-forum@lists.r-forge.r-project.org<br>
<b>Subject:</b> Re: [Seqinr-forum] Problem to get sequences from GenBank using query function</font>
<div> </div>
</div>
<div class="BodyFragment"><font size="2"><span style="font-size:11pt;">
<div class="PlainText">Hello David,<br>
<br>
I was able to reproduce the error you get.<br>
<br>
it seems that the problem occurs since R 3.5.1. but this has to be checked.<br>
<br>
It suspect that the problem is due to response time, wich seems quite <br>
long now,<br>
<br>
As a temporary solution, you may increase the minimum response time <br>
before the socket stops waiting.<br>
<br>
I was able to get rid off the problem using the following commands (be <br>
aware of the new usage of the query function : list names should be the <br>
same for result and in the query):<br>
<br>
<br>
choosebank("genbank",timeout=20)<br>
ee<-query("ee","sp=Pterois antennata")<br>
<br>
<br>
<br>
The verbose version gives<br>
<br>
ee<-query("ee","sp=Pterois antennata",verbose=T)<br>
I'm checking the arguments...<br>
... and everything is OK up to now.<br>
I'm checking the status of the socket connection...<br>
... and everything is OK up to now.<br>
I'm sending query to server...<br>
... answer from server is: code=0&lrank=2&count=44&type=SQ&locus=T<br>
I'm trying to analyse answer from server...<br>
... and everything is OK up to now.<br>
... and the rank of the resulting list is: 2 .<br>
... and there are 44 elements in the list.<br>
... and the elements in the list are of type SQ .<br>
... and there are only parent sequences in the list.<br>
I'm trying to get the infos about the elements of the list...<br>
... and I have received 44 lines as expected.<br>
><br>
<br>
<br>
<br>
<br>
My session info is<br>
<br>
R version 3.5.2 (2018-12-20)<br>
Platform: x86_64-pc-linux-gnu (64-bit)<br>
Running under: Ubuntu 16.04.5 LTS<br>
<br>
Matrix products: default<br>
BLAS: /usr/lib/libblas/libblas.so.3.6.0<br>
LAPACK: /usr/lib/lapack/liblapack.so.3.6.0<br>
<br>
locale:<br>
[1] LC_CTYPE=fr_FR.UTF-8 LC_NUMERIC=C<br>
[3] LC_TIME=fr_FR.UTF-8 LC_COLLATE=fr_FR.UTF-8<br>
[5] LC_MONETARY=fr_FR.UTF-8 LC_MESSAGES=fr_FR.UTF-8<br>
[7] LC_PAPER=fr_FR.UTF-8 LC_NAME=C<br>
[9] LC_ADDRESS=C LC_TELEPHONE=C<br>
[11] LC_MEASUREMENT=fr_FR.UTF-8 LC_IDENTIFICATION=C<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] MASS_7.3-51.1 compiler_3.5.2 ade4_1.7-13<br>
<br>
<br>
I hope this helps, at least for the moment<br>
<br>
All the best<br>
<br>
Simon<br>
<br>
<br>
.Le 07/03/2019 à 05:45, Eme, David a écrit :<br>
><br>
> Dear seqinr users,<br>
><br>
><br>
> I'm trying to extract DNA sequences from GenBank using the "query" <br>
> function from seqinr (I used to use it a lot a year ago and it was <br>
> working well), but I got an erratic behaviour from the function <br>
> reporting an error message for a large number of species which have <br>
> DNA sequences that I was able to get using the same function a year <br>
> ago (sequences that can also be found through the NCBI web platform).<br>
><br>
><br>
> Here an example with a problematic species (Pterois antennata, <br>
> taxonomic ID = 185882) in the following web page <br>
> <a href="https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=185882">https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=185882</a> we
<br>
> can see the presence of 44 sequences in the Nucleotides database <br>
> (sequences that I could get a year ago, using the same code).<br>
><br>
> Taxonomy Browser <br>
> <<a href="https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=185882">https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=185882</a>><br>
> <a href="http://www.ncbi.nlm.nih.gov">www.ncbi.nlm.nih.gov</a><br>
> THE NCBI Taxonomy database allows browsing of the taxonomy tree, which <br>
> contains a classification of organisms.<br>
><br>
> Below the code I have used (I have tried on different computers but <br>
> I'm getting the same results).<br>
><br>
><br>
> library(seqinr)<br>
><br>
> choosebank("genbank")<br>
><br>
> ee = seqinr::query("sp=Pterois antennata")<br>
><br>
> # the first time I got the following error message<br>
><br>
> Error in readLines(socket, n = nelem, ok = FALSE) :<br>
> too few lines read in readLines<br>
><br>
> # but trying again the same query I got the following error message:<br>
><br>
> ee = seqinr::query("sp=Pterois antennata")<br>
><br>
> Error in seqinr::query("sp=Pterois antennata") :<br>
> invalid request:"FJ584021"<br>
><br>
> # I also tried using the NCBI taxid<br>
><br>
> ee = seqinr::query("tid=185882")<br>
> Error in seqinr::query("tid=185882") : invalid request:"FJ584022"<br>
><br>
><br>
><br>
> Interestingly the accession number reported in the error message for <br>
> instance "FJ584022" is a DNA sequences belonging to the species of <br>
> interest "Pterois antennata"<br>
><br>
><br>
> I don't really understand the problem considering that the function <br>
> works for other species.<br>
><br>
><br>
> I'm about to finalize a revision of a manuscript using this function <br>
> as part of a new R package, and I would be really glad if you can find <br>
> a solution to this problem!!!<br>
><br>
><br>
> Thanks you very much in advance for your help greatly appreciated!<br>
><br>
><br>
> David Eme<br>
><br>
><br>
> PS: for information my sessionInfo() for the two computers i tried <br>
> with are reported below.<br>
><br>
> sessionInfo()<br>
> R version 3.4.4 (2018-03-15)<br>
> Platform: x86_64-pc-linux-gnu (64-bit)<br>
> Running under: Ubuntu 14.04.5 LTS<br>
><br>
> Matrix products: default<br>
> BLAS: /usr/lib/libblas/libblas.so.3.0<br>
> LAPACK: /usr/lib/lapack/liblapack.so.3.0<br>
><br>
> locale:<br>
> [1] LC_CTYPE=en_NZ.UTF-8 LC_NUMERIC=C<br>
> [3] LC_TIME=en_NZ.UTF-8 LC_COLLATE=en_NZ.UTF-8<br>
> [5] LC_MONETARY=en_NZ.UTF-8 LC_MESSAGES=en_NZ.UTF-8<br>
> [7] LC_PAPER=en_NZ.UTF-8 LC_NAME=C<br>
> [9] LC_ADDRESS=C LC_TELEPHONE=C<br>
> [11] LC_MEASUREMENT=en_NZ.UTF-8 LC_IDENTIFICATION=C<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 regPhylo_1.0.1<br>
><br>
> loaded via a namespace (and not attached):<br>
> [1] MASS_7.3-44 compiler_3.4.4 tools_3.4.4 ade4_1.7-13<br>
><br>
><br>
> sessionInfo()<br>
> R version 3.5.2 (2018-12-20)<br>
> Platform: x86_64-w64-mingw32/x64 (64-bit)<br>
> Running under: Windows 10 x64 (build 17134)<br>
><br>
> Matrix products: default<br>
><br>
> locale:<br>
> [1] LC_COLLATE=English_New Zealand.1252 LC_CTYPE=English_New <br>
> Zealand.1252 LC_MONETARY=English_New Zealand.1252<br>
> [4] LC_NUMERIC=C LC_TIME=English_New Zealand.1252<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] MASS_7.3-51.1 compiler_3.5.2 ade4_1.7-13<br>
><br>
><br>
><br>
><br>
><br>
><br>
><br>
><br>
><br>
><br>
> _______________________________________________<br>
> Seqinr-forum mailing list<br>
> Seqinr-forum@lists.r-forge.r-project.org<br>
> <a href="https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/seqinr-forum">
https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/seqinr-forum</a><br>
<br>
<br>
-- <br>
Simon Penel ^(;,;)^<br>
Laboratoire de Biometrie et Biologie Evolutive<br>
Bat 711 - CNRS UMR 5558<br>
43 bd du 11 novembre 1918 69622 Villeurbanne Cedex<br>
Tel: 04 72 43 29 04 Fax: 04 72 43 13 88<br>
<a href="http://lbbe.univ-lyon1.fr/-Penel-Simon-.html?lang=fr">http://lbbe.univ-lyon1.fr/-Penel-Simon-.html?lang=fr</a><br>
<br>
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