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<p>I have the same result with -4 option, but connection fail with
the -6 option.</p>
<p>Thanks,</p>
<p>Julien<br>
</p>
<pre class="moz-signature" cols="72">Julien Fumey, Ph.D.
<a class="moz-txt-link-abbreviated" href="mailto:julien.fumey@i2bc.paris-saclay.fr">julien.fumey@i2bc.paris-saclay.fr</a>
I2BC High Throughput Sequencing Platform
CNRS Gif Bat 26
Avenue de la Terrasse
91198 Gif-sur-Yvette
France
+33.(0)1.69.82.31.90
platform mail: <a class="moz-txt-link-abbreviated" href="mailto:sequencage-i2bc@i2bc.paris-saclay.fr">sequencage-i2bc@i2bc.paris-saclay.fr</a></pre>
<div class="moz-cite-prefix">Le 04/04/2017 à 17:23, Thomas Maurel a
écrit :<br>
</div>
<blockquote
cite="mid:647298C0-2697-45C3-8003-0B6274CBAE7E@ebi.ac.uk"
type="cite">
<meta http-equiv="Content-Type" content="text/html;
charset=windows-1252">
Dear Julien,
<div class=""><br class="">
</div>
<div class="">I am really sorry to hear that. We only blacklist
IPs for a very good reason. Usually an IP block would affect the
other computers as well and it wouldn’t just block BioMart.</div>
<div class="">Could you please try to run wget with option “-4”
and then with “-6” and let me know if that makes any difference?</div>
<div class=""><br class="">
</div>
<div class="">Thanks a lot,</div>
<div class="">Kind Regards,</div>
<div class="">Thomas<br class="">
<div>
<blockquote type="cite" class="">
<div class="">On 4 Apr 2017, at 16:10, Julien Fumey <<a
moz-do-not-send="true"
href="mailto:julien.fumey@i2bc.paris-saclay.fr" class="">julien.fumey@i2bc.paris-saclay.fr</a>>
wrote:</div>
<br class="Apple-interchange-newline">
<div class="">
<div bgcolor="#FFFFFF" text="#000000" class="">
<p class="">I'm quite sure I don't have any problem with
my proxy. There is no proxy in my institute and I
never configured one.</p>
<p class="">I tried a wget on the registry file with two
computers. I can get the file from any computer except
the one on which I have problem with biomart. <br
class="">
</p>
<p class="">But I'm connected to the server. And then
the server close the connection without sending any
data.</p>
<p class="">wget <a moz-do-not-send="true"
class="moz-txt-link-freetext"
href="http://www.ensembl.org/biomart/martservice?type=registry">http://www.ensembl.org/biomart/martservice?type=registry</a><br
class="">
--2017-04-04 16:56:37-- <a moz-do-not-send="true"
class="moz-txt-link-freetext"
href="http://www.ensembl.org/biomart/martservice?type=registry">http://www.ensembl.org/biomart/martservice?type=registry</a><br
class="">
Resolving <a moz-do-not-send="true"
class="moz-txt-link-abbreviated"
href="http://www.ensembl.org/">www.ensembl.org</a> (<a
moz-do-not-send="true"
class="moz-txt-link-abbreviated"
href="http://www.ensembl.org/">www.ensembl.org</a>)…
193.62.203.138, 193.62.203.137, 2001:630:206:4::137,
...<br class="">
Connection to <a moz-do-not-send="true"
class="moz-txt-link-abbreviated"
href="http://www.ensembl.org/">www.ensembl.org</a> (<a
moz-do-not-send="true"
class="moz-txt-link-abbreviated"
href="http://www.ensembl.org/">www.ensembl.org</a>)|193.62.203.138|:80…
connected.<br class="">
HTTP request sent, awaiting response… No data
received.<br class="">
Retrying.</p>
<p class="">Is it possible that this computer is
blacklisted from the mart server ?<br class="">
</p>
<p class="">Julien<br class="">
</p>
<pre class="moz-signature" cols="72">Julien Fumey, Ph.D.
<a moz-do-not-send="true" class="moz-txt-link-abbreviated" href="mailto:julien.fumey@i2bc.paris-saclay.fr">julien.fumey@i2bc.paris-saclay.fr</a>
I2BC High Throughput Sequencing Platform
CNRS Gif Bat 26
Avenue de la Terrasse
91198 Gif-sur-Yvette
France
+33.(0)1.69.82.31.90
platform mail: <a moz-do-not-send="true" class="moz-txt-link-abbreviated" href="mailto:sequencage-i2bc@i2bc.paris-saclay.fr">sequencage-i2bc@i2bc.paris-saclay.fr</a></pre>
<div class="moz-cite-prefix">Le 04/04/2017 à 15:28,
Thomas Maurel a écrit :<br class="">
</div>
<blockquote
cite="mid:A7DE1838-364F-4792-A6C9-915747B7BCC2@ebi.ac.uk"
type="cite" class=""> Dear Julien,
<div class=""><br class="">
</div>
<div class="">I am afraid that I can’t help you
further here as something seems to be wrong with the
proxy set up on your computer. </div>
<div class="">Hopefully someone from your IT
department will be able to help from here. </div>
<div class=""><br class="">
</div>
<div class="">Kind Regards,</div>
<div class="">Thomas<br class="">
<div class="">
<blockquote type="cite" class="">
<div class="">On 4 Apr 2017, at 14:19, Julien
Fumey <<a moz-do-not-send="true"
href="mailto:julien.fumey@i2bc.paris-saclay.fr"
class="">julien.fumey@i2bc.paris-saclay.fr</a>>
wrote:</div>
<br class="Apple-interchange-newline">
<div class="">
<div bgcolor="#FFFFFF" text="#000000" class="">
<p class="">Thanks Thomas,</p>
<p class="">I tried your command on my
computer and I get 500. I tried on another
computer and I get 200.</p>
<p class="">Then I checked the 'http_proxy'
and the 'https_proxy' env variables, and
they are the same on both computers.</p>
<p class="">Julien<br class="">
</p>
<pre class="moz-signature" cols="72">Julien Fumey, Ph.D.
<a moz-do-not-send="true" class="moz-txt-link-abbreviated" href="mailto:julien.fumey@i2bc.paris-saclay.fr">julien.fumey@i2bc.paris-saclay.fr</a>
I2BC High Throughput Sequencing Platform
CNRS Gif Bat 26
Avenue de la Terrasse
91198 Gif-sur-Yvette
France
+33.(0)1.69.82.31.90
platform mail: <a moz-do-not-send="true" class="moz-txt-link-abbreviated" href="mailto:sequencage-i2bc@i2bc.paris-saclay.fr">sequencage-i2bc@i2bc.paris-saclay.fr</a></pre>
<div class="moz-cite-prefix">Le 04/04/2017 à
14:29, Thomas Maurel a écrit :<br class="">
</div>
<blockquote
cite="mid:4BEB7407-6FA0-45EA-B8A3-1A2025CC8AF3@ebi.ac.uk"
type="cite" class=""> Dear Julien,
<div class=""><br class="">
</div>
<div class="">We think that you might have
a proxy that is getting in the way here.</div>
<div class="">If you run the following
command:</div>
<blockquote style="margin: 0 0 0 40px;
border: none; padding: 0px;" class="">
<div class="">perl -MLWP::UserAgent -e
'print
LWP::UserAgent->new()->get("<a
moz-do-not-send="true"
href="http://www.ensembl.org/biomart/martservice?type=registry"
class="">http://www.ensembl.org/biomart/martservice?type=registry</a>")->code()'</div>
</blockquote>
<div class="">You should get back “200”
which mean that all is working fine. If
you get back “500”, this mean that your
proxy setting might be wrong or
something is going on with your proxy
server. Usually the proxy url is set up
in the following variable “http_proxy”.</div>
<div class=""><br class="">
</div>
<div class="">Hope this helps,</div>
<div class="">Kind Regards,</div>
<div class="">Thomas<br class="">
<div class="">
<blockquote type="cite" class="">
<div class="">On 3 Apr 2017, at
15:58, Julien Fumey <<a
moz-do-not-send="true"
href="mailto:julien.fumey@i2bc.paris-saclay.fr"
class="">julien.fumey@i2bc.paris-saclay.fr</a>>
wrote:</div>
<br
class="Apple-interchange-newline">
<div class="">
<div bgcolor="#FFFFFF"
text="#000000" class="">
<p class="">Thanks Thomas for
your answer.</p>
<p class="">I already changed
"zfin_id" to "zfin_id_id" and
re-generate the cache to use
version 88. But I still get
the error when generating the
cache.</p>
<p class="">I previously had
this error with the cache
already generated when
querying version 87.</p>
<p class="">Best,</p>
<p class="">Julien<br class="">
</p>
<pre class="moz-signature" cols="72">Julien Fumey, Ph.D.
<a moz-do-not-send="true" class="moz-txt-link-abbreviated" href="mailto:julien.fumey@i2bc.paris-saclay.fr">julien.fumey@i2bc.paris-saclay.fr</a>
I2BC High Throughput Sequencing Platform
CNRS Gif Bat 26
Avenue de la Terrasse
91198 Gif-sur-Yvette
France
+33.(0)1.69.82.31.90
platform mail: <a moz-do-not-send="true" class="moz-txt-link-abbreviated" href="mailto:sequencage-i2bc@i2bc.paris-saclay.fr">sequencage-i2bc@i2bc.paris-saclay.fr</a></pre>
<div class="moz-cite-prefix">Le
03/04/2017 à 16:54, Thomas
Maurel a écrit :<br class="">
</div>
<blockquote
cite="mid:DDE0D70C-49E9-404C-B15F-5E2C4D64551A@ebi.ac.uk"
type="cite" class=""> Dear
Julien,
<div class=""><br class="">
</div>
<div class="">
<div class="">Please note
that we have moved to a
new system this release to
generate and populate the
ensembl marts
filters/attributes. As a
result, we have improved
the consistency of our
mart across the vertebrate
and other ensembl
divisions. The following
filters and attributes
names have changed and
will affect script using
the BiomaRt package.</div>
<div class="">Please find
the full list below or on
our FTP site: <a
moz-do-not-send="true"
href="ftp://ftp.ensembl.org/pub/release-88/release_88_biomart_changes.txt"
class="">ftp://ftp.ensembl.org/pub/release-88/release_88_biomart_changes.txt</a></div>
<div class=""><br class="">
</div>
<div class="">If you replace
“zfin_id” with
“zfin_id_id” in your
script, it should work
again.</div>
<div class="">
<div class="">
<div class="">Also
please make sure to
set the $action
variable from “cached”
to “clean”, your
script will then
re-generate the cache
using our newly
released 88 version.</div>
<div class=""><br
class="">
</div>
</div>
</div>
<div class="">Kind Regards,</div>
<div class="">Thomas</div>
</div>
<div class="">
<blockquote type="cite"
class="">
<div class="">On 3 Apr
2017, at 13:35, Julien
Fumey <<a
moz-do-not-send="true"
href="mailto:julien.fumey@i2bc.paris-saclay.fr" class="">julien.fumey@i2bc.paris-saclay.fr</a>>
wrote:</div>
<br
class="Apple-interchange-newline">
<div class="">
<div class="">Dear
ensembl team,<br
class="">
<br class="">
I'm trying to get data
from Zv10 using the
BioMart Perl API. When
I try to build the
registry, I obtain the
following error.<br
class="">
<br class="">
Problems with the web
server: 500 Server
closed connection
without sending any
data back. No datasets
available with given
parameters for
Location:
ENSEMBL_MART_ENSEMBL<br
class="">
<br class="">
Problems with the
retrieval of dataset
configuration<br
class="">
Please
check:<br class="">
that
your mart Registry
files contains correct
connection params,<br
class="">
that you
are using the correct
version on
XML::Simple,<br
class="">
that
BioMart databases
contain a populated
meta_conf tables and<br
class="">
that you
have set martUser
correctly if you are
running in restricted
data<br class="">
access
mode (populated
meta_conf__user__dm)<br
class="">
<br class="">
<br class="">
I copy paste the
registry from here : <a
moz-do-not-send="true"
href="http://www.ensembl.org/biomart/martservice?type=registry"
class="">http://www.ensembl.org/biomart/martservice?type=registry</a><br
class="">
<br class="">
Is there a problem
with the server ? Or
maybe I did something
wrong ?<br class="">
<br class="">
Cheers,<br class="">
<br class="">
-- <br class="">
Julien Fumey, Ph.D.<br
class="">
<a
moz-do-not-send="true"
href="mailto:julien.fumey@i2bc.paris-saclay.fr" class="">julien.fumey@i2bc.paris-saclay.fr</a><br
class="">
I2BC High Throughput
Sequencing Platform<br
class="">
CNRS Gif Bat 26<br
class="">
Avenue de la Terrasse<br
class="">
91198 Gif-sur-Yvette<br
class="">
France<br class="">
+33.(0)1.69.82.31.90<br
class="">
platform mail: <a
moz-do-not-send="true"
class="moz-txt-link-abbreviated"
href="mailto:sequencage-i2bc@i2bc.paris-saclay.fr">sequencage-i2bc@i2bc.paris-saclay.fr</a><br
class="">
<br class="">
_______________________________________________<br class="">
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</div>
</div>
</blockquote>
</div>
<br class="">
<div class="">
<div class="">
<div class=""
style="orphans: 2;
widows: 2;">--</div>
<div class=""
style="orphans: 2;
widows: 2;">Thomas
Maurel<br class="">
Bioinformatician -
Ensembl Production Team<br
class="">
European Bioinformatics
Institute (EMBL-EBI)<br
class="">
European Molecular
Biology Laboratory<br
class="">
Wellcome Trust Genome
Campus<br class="">
Hinxton<br class="">
Cambridge CB10 1SD<br
class="">
United Kingdom</div>
</div>
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<br class="">
<br class="">
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class="mimeAttachmentHeader"></fieldset>
<br class="">
<pre class="" wrap="">_______________________________________________
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</pre>
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<br class="">
<div class="">
<div class="">
<div class="" style="orphans: 2;
widows: 2;">--</div>
<div class="" style="orphans: 2;
widows: 2;">Thomas Maurel<br
class="">
Bioinformatician - Ensembl
Production Team<br class="">
European Bioinformatics Institute
(EMBL-EBI)<br class="">
European Molecular Biology
Laboratory<br class="">
Wellcome Trust Genome Campus<br
class="">
Hinxton<br class="">
Cambridge CB10 1SD<br class="">
United Kingdom</div>
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<br class="">
<div class="">
<div class="">
<div class="" style="orphans: 2; widows: 2;">--</div>
<div class="" style="orphans: 2; widows: 2;">Thomas
Maurel<br class="">
Bioinformatician - Ensembl Production Team<br
class="">
European Bioinformatics Institute (EMBL-EBI)<br
class="">
European Molecular Biology Laboratory<br
class="">
Wellcome Trust Genome Campus<br class="">
Hinxton<br class="">
Cambridge CB10 1SD<br class="">
United Kingdom</div>
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<br class="">
<pre class="" wrap="">_______________________________________________
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<br class="">
<div class="">
<div class="">
<div class="" style="orphans: 2; widows: 2;">--</div>
<div class="" style="orphans: 2; widows: 2;">Thomas Maurel<br
class="">
Bioinformatician - Ensembl Production Team<br class="">
European Bioinformatics Institute (EMBL-EBI)<br class="">
European Molecular Biology Laboratory<br class="">
Wellcome Trust Genome Campus<br class="">
Hinxton<br class="">
Cambridge CB10 1SD<br class="">
United Kingdom</div>
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