<html><head><meta http-equiv="content-type" content="text/html; charset=utf-8"></head><body style="overflow-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;">Hi Timothé,<div><br></div><div>Thanks for your email.</div><div><br></div><div>There appears to be networking maintenance work on some Ensembl-related services today, which may have had an impact here. This work is only scheduled for this afternoon; please could you check your script again tomorrow and let us know if it’s still causing issues?</div><div><br></div><div>Thanks very much and best wishes,</div><div>Natalie</div><div><br><div>
<meta charset="UTF-8"><div dir="auto" style="caret-color: rgb(0, 0, 0); color: rgb(0, 0, 0); letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none; word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;"><div dir="auto" style="caret-color: rgb(0, 0, 0); color: rgb(0, 0, 0); letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none; word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;"><b>Natalie Willhöft</b><br>Ensembl Infrastructure Team<br>EMBL-EBI <br>nwillhoft@ebi.ac.uk</div></div>
</div>
<div><br><blockquote type="cite"><div>On 4 Jun 2024, at 15:06, Timothé van Meter <timothe.vm@posteo.net> wrote:</div><br class="Apple-interchange-newline"><div><div>Hello,<br><br><br>I am using a perl script to access programmatically the ensembl database for the mouse's genome. This script which was previously working for a while without any warnings is now not functioning anymore with the following error message:<br><br>"<br>DBI connect('host=ensembldb.ensembl.org;port=3306','anonymous',...) failed: Can't connect to MySQL server on 'ensembldb.ensembl.org:3306' (110) at /home/timothe/src/ensembl/modules/Bio/EnsEMBL/Registry.pm line 1771.<br><br>-------------------- EXCEPTION --------------------<br>MSG: Cannot connect to the Ensembl MySQL server at ensembldb.ensembl.org:3306; check your settings & DBI error message: Can't connect to MySQL server on 'ensembldb.ensembl.org:3306' (110)<br>STACK Bio::EnsEMBL::Registry::load_registry_from_db /home/timothe/src/ensembl/modules/Bio/EnsEMBL/Registry.pm:1771<br>STACK toplevel get.associated.genes.pl:31<br>Date (localtime) = Tue Jun 4 15:41:31 2024<br>Ensembl API version = 110<br>---------------------------------------------------<br>"<br><br>I copied the entire script I am using, get.associated.genes.pl, at the end of this email.<br><br>Below I am reporting the output of the recommended commands for debugging the Ensembl API hoping they might be useful.<br><br>calling ping -c 5 in the terminal returns the following:<br>PING hl-ensembl-databases.ebi.ac.uk (193.62.192.245) 56(84) bytes of data.<br><br>--- hl-ensembl-databases.ebi.ac.uk ping statistics ---<br>5 packets transmitted, 0 received, 100% packet loss, time 4084ms<br><br><br>Below the output of the perl ping_ensembl.pl script advised on the "Debugging Ensembl API Connections" webpage:<br><br>-------------------- EXCEPTION --------------------<br>MSG: Cannot connect to the Ensembl MySQL server at ensembldb.ensembl.org:3306; check your settings & DBI error message: Can't connect to MySQL server on 'ensembldb.ensembl.org:3306' (110)<br>STACK Bio::EnsEMBL::Registry::load_registry_from_db /home/timothe/src/ensembl/modules/Bio/EnsEMBL/Registry.pm:1771<br>STACK (eval) ping_ensembl.pl:122<br>STACK toplevel ping_ensembl.pl:113<br>Date (localtime) = Tue Jun 4 11:52:08 2024<br>Ensembl API version = 110<br>---------------------------------------------------<br><br><br>The output of the "perl -V" command is written at the end of the message.<br><br>The output of the "perl -MDBI -e 'warn $DBI::VERSION'" command: 1.643 at -e line 1.<br><br>The output of the "perl -MDBD::mysql -e 'warn $DBD::mysql::VERSION'" command: 5.003 at -e line 1.<br><br>I am available to answer any questions that might further help solve this problem. Thank you in advance for your consideration.<br><br><br>Best regards,<br>Timothé van Meter<br><br><br><br><br># ---------------------------------------------------------------------<br>Contents of the script get.associated.genes.pl<br># ---------------------------------------------------------------------<br>#!/usr/bin/perl<br><br>use strict;<br>use warnings;<br>use Data::Dumper;<br>use Bio::EnsEMBL::Registry;<br>use Bio::Tools::Run::Ensembl;<br>use Try::Tiny;<br>use Term::ProgressBar;<br><br># my $filename = '/data/blasting/out.awk';<br>my $filename = $ARGV[0];<br>my $extension = 4000;<br><br># # Name of the output file with enhancers<br>my $output = 'test.genes.associated';<br><br>my $registry = "Bio::EnsEMBL::Registry";<br>$registry->load_registry_from_db(<br> -HOST => 'ensembldb.ensembl.org',<br> -USER => 'anonymous',<br> # -PORT => '3306'<br> # -PORT => '5306'<br> -VERBOSE => 1<br> );<br><br>sub parsePromoters {<br> my ($filename) = @_;<br> my @promoters;<br> open(FH, '<', $filename) or die $!;<br> while(<FH>){<br> chomp;<br> push @promoters, [ split(/ /, $_) ];<br> }<br> close(FH);<br> return @promoters;<br>}<br><br><br>my $slice_adaptor = $registry->get_adaptor( "Mouse", 'Core', 'Slice' );<br># # my $slice = $slice_adaptor->fetch_by_region( 'chromosome', '10', 3700000, 3830000 );<br>my @genes;<br><br># # OPEN THE OUTPUT FILE AND PRINT THE<br># # RESULTS DIRECTLY IN IT<br>open(FH, '>', $output) or die $!;<br><br>my $i = 0;<br><br>my @testGenes;<br><br># LOOP OVER ALL GENES LOADED FROM FILE<br>for $i (0 .. $#promoters) {<br> print "$promoters[$i][0]\n";<br> # if( exists( $hash{$gene} )) {<br> # my $slice;<br> my $start = $promoters[$i][3] - $extension;<br> my $end = $promoters[$i][4] + $extension;<br> try {<br><br> print "region = ", $promoters[$i][2], " : ", $start, " - ", $end, "\n";<br><br> my $slice = $slice_adaptor->fetch_by_region( 'chromosome', $promoters[$i][2], $start, $end );<br> # my $slice = $slice_adaptor->fetch_by_region( 'chromosome', '10', 3770000, 3790000 );<br> foreach my $gene ( @{ $slice->get_all_Genes() } ) {<br> print "Gene ID: ", $gene->stable_id, "\n";<br> # print "Gene Name: ", $gene->display_id, "\n";<br> push @testGenes, [ $promoters[$i][0], $gene->stable_id, $gene->seq_region_start(), $gene->seq_region_end() ];<br> }<br><br> # print "@{ $slice->get_all_Genes() }\n";<br><br> # push @genes, @templist;<br><br> # print "$genes[0][0]\n";<br><br> # print FH "\n>", $genes[0], "\n";<br><br> } catch {<br> next;<br> }<br> # } else {<br> # next;<br> # }<br> # $progress_bar->update($i);<br> # $i++;<br>}<br>print "\n---------------\n";<br><br># foreach my gene (@testGenes) {<br># print $gene[0]," ",$gene[1]," ",$gene[2],"\n";<br># }<br>for my $i (0 .. $#testGenes) {<br> # print FH $testGenes[$i][0]," ",$testGenes[$i][1]," ",$testGenes[$i][2],"\n";<br> print FH $testGenes[$i][0]," ",$testGenes[$i][1],"\n";<br>}<br># # CLOSE STREAM TO OUTPUT FILE<br>close(FH);<br><br>print "DONE!\n\n";<br># ---------------------------------------------------------------------<br># ---------------------------------------------------------------------<br><br><br># ---------------------------------------------------------------------<br>Output of perl -V<br># ---------------------------------------------------------------------<br>Summary of my perl5 (revision 5 version 34 subversion 0) configuration:<br><br> Platform:<br> osname=linux<br> osvers=4.19.0<br> archname=x86_64-linux-gnu-thread-multi<br> uname='linux localhost 4.19.0 #1 smp debian 4.19.0 x86_64 gnulinux '<br> config_args='-Dmksymlinks -Dusethreads -Duselargefiles -Dcc=x86_64-linux-gnu-gcc -Dcpp=x86_64-linux-gnu-cpp -Dld=x86_64-linux-gnu-gcc -Dccflags=-DDEBIAN -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/dummy/build/dir=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Dldflags= -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -flto=auto -Wl,-z,relro -Dlddlflags=-shared -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -flto=auto -Wl,-z,relro -Dcccdlflags=-fPIC -Darchname=x86_64-linux-gnu -Dprefix=/usr -Dprivlib=/usr/share/perl/5.34 -Darchlib=/usr/lib/x86_64-linux-gnu/perl/5.34 -Dvendorprefix=/usr -Dvendorlib=/usr/share/perl5 -Dvendorarch=/usr/lib/x86_64-linux-gnu/perl5/5.34 -Dsiteprefix=/usr/local -Dsitelib=/usr/local/share/perl/5.34.0 -Dsitearch=/usr/local/lib/x86_64-linux-gnu/perl/5.34.0 -Dman1dir=/usr/share/man/man1 -Dman3dir=/usr/share/man/man3 -Dsiteman1dir=/usr/local/man/man1 -Dsiteman3dir=/usr/local/man/man3 -Duse64bitint -Dman1ext=1 -Dman3ext=3perl -Dpager=/usr/bin/sensible-pager -Uafs -Ud_csh -Ud_ualarm -Uusesfio -Uusenm -Ui_libutil -Ui_xlocale -Uversiononly -DDEBUGGING=-g -Doptimize=-O2 -dEs -Duseshrplib -Dlibperl=libperl.so.5.34.0'<br> hint=recommended<br> useposix=true<br> d_sigaction=define<br> useithreads=define<br> usemultiplicity=define<br> use64bitint=define<br> use64bitall=define<br> uselongdouble=undef<br> usemymalloc=n<br> default_inc_excludes_dot=define<br> Compiler:<br> cc='x86_64-linux-gnu-gcc'<br> ccflags ='-D_REENTRANT -D_GNU_SOURCE -DDEBIAN -fwrapv -fno-strict-aliasing -pipe -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64'<br> optimize='-O2 -g'<br> cppflags='-D_REENTRANT -D_GNU_SOURCE -DDEBIAN -fwrapv -fno-strict-aliasing -pipe -I/usr/local/include'<br> ccversion=''<br> gccversion='11.4.0'<br> gccosandvers=''<br> intsize=4<br> longsize=8<br> ptrsize=8<br> doublesize=8<br> byteorder=12345678<br> doublekind=3<br> d_longlong=define<br> longlongsize=8<br> d_longdbl=define<br> longdblsize=16<br> longdblkind=3<br> ivtype='long'<br> ivsize=8<br> nvtype='double'<br> nvsize=8<br> Off_t='off_t'<br> lseeksize=8<br> alignbytes=8<br> prototype=define<br> Linker and Libraries:<br> ld='x86_64-linux-gnu-gcc'<br> ldflags =' -fstack-protector-strong -L/usr/local/lib'<br> libpth=/usr/local/lib /usr/lib/x86_64-linux-gnu /usr/lib /lib/x86_64-linux-gnu /lib<br> libs=-lgdbm -lgdbm_compat -ldb -ldl -lm -lpthread -lc -lcrypt<br> perllibs=-ldl -lm -lpthread -lc -lcrypt<br> libc=/lib/x86_64-linux-gnu/libc.so.6<br> so=so<br> useshrplib=true<br> libperl=libperl.so.5.34<br> gnulibc_version='2.35'<br> Dynamic Linking:<br> dlsrc=dl_dlopen.xs<br> dlext=so<br> d_dlsymun=undef<br> ccdlflags='-Wl,-E'<br> cccdlflags='-fPIC'<br> lddlflags='-shared -L/usr/local/lib -fstack-protector-strong'<br><br><br>Characteristics of this binary (from libperl):<br> Compile-time options:<br> HAS_TIMES<br> MULTIPLICITY<br> PERLIO_LAYERS<br> PERL_COPY_ON_WRITE<br> PERL_DONT_CREATE_GVSV<br> PERL_IMPLICIT_CONTEXT<br> PERL_MALLOC_WRAP<br> PERL_OP_PARENT<br> PERL_PRESERVE_IVUV<br> USE_64_BIT_ALL<br> USE_64_BIT_INT<br> USE_ITHREADS<br> USE_LARGE_FILES<br> USE_LOCALE<br> USE_LOCALE_COLLATE<br> USE_LOCALE_CTYPE<br> USE_LOCALE_NUMERIC<br> USE_LOCALE_TIME<br> USE_PERLIO<br> USE_PERL_ATOF<br> USE_REENTRANT_API<br> USE_THREAD_SAFE_LOCALE<br> Locally applied patches:<br> DEBPKG:debian/cpan_definstalldirs - Provide a sensible INSTALLDIRS default for modules installed from CPAN.<br> DEBPKG:debian/db_file_ver - https://bugs.debian.org/340047 Remove overly restrictive DB_File version check.<br> DEBPKG:debian/doc_info - Replace generic man(1) instructions with Debian-specific information.<br> DEBPKG:debian/enc2xs_inc - https://bugs.debian.org/290336 Tweak enc2xs to follow symlinks and ignore missing @INC directories.<br> DEBPKG:debian/errno_ver - https://bugs.debian.org/343351 Remove Errno version check due to upgrade problems with long-running processes.<br> DEBPKG:debian/libperl_embed_doc - https://bugs.debian.org/186778 Note that libperl-dev package is required for embedded linking<br> DEBPKG:fixes/respect_umask - Respect umask during installation<br> DEBPKG:debian/writable_site_dirs - Set umask approproately for site install directories<br> DEBPKG:debian/extutils_set_libperl_path - EU:MM: set location of libperl.a under /usr/lib<br> DEBPKG:debian/no_packlist_perllocal - Don't install .packlist or perllocal.pod for perl or vendor<br> DEBPKG:debian/fakeroot - Postpone LD_LIBRARY_PATH evaluation to the binary targets.<br> DEBPKG:debian/instmodsh_doc - Debian policy doesn't install .packlist files for core or vendor.<br> DEBPKG:debian/ld_run_path - Remove standard libs from LD_RUN_PATH as per Debian policy.<br> DEBPKG:debian/libnet_config_path - Set location of libnet.cfg to /etc/perl/Net as /usr may not be writable.<br> DEBPKG:debian/perlivp - https://bugs.debian.org/510895 Make perlivp skip include directories in /usr/local<br> DEBPKG:debian/squelch-locale-warnings - https://bugs.debian.org/508764 Squelch locale warnings in Debian package maintainer scripts<br> DEBPKG:debian/patchlevel - https://bugs.debian.org/567489 List packaged patches for 5.34.0-3ubuntu1.3 in patchlevel.h<br> DEBPKG:fixes/document_makemaker_ccflags - https://bugs.debian.org/628522 [rt.cpan.org #68613] Document that CCFLAGS should include $Config{ccflags}<br> DEBPKG:debian/find_html2text - https://bugs.debian.org/640479 Configure CPAN::Distribution with correct name of html2text<br> DEBPKG:debian/perl5db-x-terminal-emulator.patch - https://bugs.debian.org/668490 Invoke x-terminal-emulator rather than xterm in perl5db.pl<br> DEBPKG:debian/cpan-missing-site-dirs - https://bugs.debian.org/688842 Fix CPAN::FirstTime defaults with nonexisting site dirs if a parent is writable<br> DEBPKG:fixes/memoize_storable_nstore - [rt.cpan.org #77790] https://bugs.debian.org/587650 Memoize::Storable: respect 'nstore' option not respected<br> DEBPKG:debian/makemaker-pasthru - https://bugs.debian.org/758471 Pass LD settings through to subdirectories<br> DEBPKG:debian/makemaker-manext - https://bugs.debian.org/247370 Make EU::MakeMaker honour MANnEXT settings in generated manpage headers<br> DEBPKG:debian/kfreebsd-softupdates - https://bugs.debian.org/796798 Work around Debian Bug#796798<br> DEBPKG:fixes/memoize-pod - [rt.cpan.org #89441] Fix POD errors in Memoize<br> DEBPKG:debian/hurd-softupdates - https://bugs.debian.org/822735 Fix t/op/stat.t failures on hurd<br> DEBPKG:fixes/math_complex_doc_great_circle - https://bugs.debian.org/697567 [rt.cpan.org #114104] Math::Trig: clarify definition of great_circle_midpoint<br> DEBPKG:fixes/math_complex_doc_see_also - https://bugs.debian.org/697568 [rt.cpan.org #114105] Math::Trig: add missing SEE ALSO<br> DEBPKG:fixes/math_complex_doc_angle_units - https://bugs.debian.org/731505 [rt.cpan.org #114106] Math::Trig: document angle units<br> DEBPKG:fixes/cpan_web_link - https://bugs.debian.org/367291 CPAN: Add link to main CPAN web site<br> DEBPKG:debian/hppa_op_optimize_workaround - https://bugs.debian.org/838613 Temporarily lower the optimization of op.c on hppa due to gcc-6 problems<br> DEBPKG:debian/installman-utf8 - https://bugs.debian.org/840211 Generate man pages with UTF-8 characters<br> DEBPKG:debian/hppa_opmini_optimize_workaround - https://bugs.debian.org/869122 Lower the optimization level of opmini.c on hppa<br> DEBPKG:debian/sh4_op_optimize_workaround - https://bugs.debian.org/869373 Also lower the optimization level of op.c and opmini.c on sh4<br> DEBPKG:debian/perldoc-pager - https://bugs.debian.org/870340 [rt.cpan.org #120229] Fix perldoc terminal escapes when sensible-pager is less<br> DEBPKG:debian/prune_libs - https://bugs.debian.org/128355 Prune the list of libraries wanted to what we actually need.<br> DEBPKG:debian/mod_paths - Tweak @INC ordering for Debian<br> DEBPKG:debian/deprecate-with-apt - https://bugs.debian.org/747628 Point users to Debian packages of deprecated core modules<br> DEBPKG:debian/disable-stack-check - https://bugs.debian.org/902779 [GH #16607] Disable debugperl stack extension checks for binary compatibility with perl<br> DEBPKG:debian/perlbug-editor - https://bugs.debian.org/922609 Use "editor" as the default perlbug editor, as per Debian policy<br> DEBPKG:debian/eu-mm-perl-base - https://bugs.debian.org/962138 Suppress an ExtUtils::MakeMaker warning about our non-default @INC<br> DEBPKG:fixes/io_socket_ip_ipv6 - Disable getaddrinfo(3) AI_ADDRCONFIG for localhost and IPv4 numeric addresses<br> DEBPKG:debian/usrmerge-lib64 - https://bugs.debian.org/914128 Configure / libpth.U: Do not adjust glibpth when /usr/lib64 is present.<br> DEBPKG:debian/usrmerge-realpath - https://bugs.debian.org/914128 Configure / libpth.U: use realpath --no-symlinks on Debian<br> DEBPKG:debian/configure-regen - https://bugs.debian.org/762638 Regenerate Configure et al. after probe unit changes<br> DEBPKG:fixes/x32-io-msg-skip - https://bugs.debian.org/922609 Skip io/msg.t on x32 due to broken System V message queues<br> DEBPKG:fixes/encode-CVE-2021-36770 - mitigate @INC pollution when loading ConfigLocal<br> DEBPKG:fixes/gdbm-1.20 - https://bugs.debian.org/993514 [GH #18915] Fix GDBM_File to compile with version 1.20 and earlier<br> DEBPKG:disable-libperl-tests -<br> DEBPKG:CVE-2020-16156-1.patch - [PATCH] bugfix: signature verification type CANNOT_VERIFY was not recognized<br> DEBPKG:CVE-2020-16156-2.patch - [PATCH] Add two new failure modes based on cpan_path<br> DEBPKG:CVE-2020-16156-3.patch - [PATCH] use gpg --verify --output ... to disentangle data and signature<br> DEBPKG:CVE-2020-16156-4.patch - [PATCH] replacing die with mydie in three spots<br> DEBPKG:CVE-2020-16156-5.patch - [PATCH] disambiguate the call to gpg --output by adding --verify<br> DEBPKG:CVE-2020-16156-6.patch - [PATCH] s/gpg/$gpg/ in system, add quotes where needed<br> DEBPKG:CVE-2020-16156-7.patch - [PATCH] s,/dev/null,$devnull,<br> DEBPKG:CVE-2023-31484.patch - [PATCH] Add verify_SSL=>1 to HTTP::Tiny to verify https server identity<br> DEBPKG:CVE-2023-47038.patch - [PATCH 1/2] Fix read/write past buffer end: perl-security#140<br> DEBPKG:CVE-2022-48522.patch - [PATCH] Don't try to Sv[PI]V() on an undef index SV in find_uninit_var()<br> Built under linux<br> Compiled at Nov 23 2023 14:56:46<br> %ENV:<br>PERL5LIB="/home/timothe/perl5/lib/perl5::/home/timothe/src/bioperl-1.6.924:/home/timothe/src/ensembl/modules:/home/timothe/src/ensembl-compara/modules:/home/timothe/src/ensembl-variation/modules:/home/timothe/src/ensembl-funcgen/modules"<br> PERL_LOCAL_LIB_ROOT="/home/timothe/perl5"<br> PERL_MB_OPT="--install_base "/home/timothe/perl5""<br> PERL_MM_OPT="INSTALL_BASE=/home/timothe/perl5"<br> @INC:<br>/home/timothe/perl5/lib/perl5/5.34.0/x86_64-linux-gnu-thread-multi<br> /home/timothe/perl5/lib/perl5/5.34.0<br> /home/timothe/perl5/lib/perl5/x86_64-linux-gnu-thread-multi<br> /home/timothe/perl5/lib/perl5<br> /home/timothe/src/bioperl-1.6.924<br> /home/timothe/src/ensembl/modules<br> /home/timothe/src/ensembl-compara/modules<br> /home/timothe/src/ensembl-variation/modules<br> /home/timothe/src/ensembl-funcgen/modules<br> /etc/perl<br> /usr/local/lib/x86_64-linux-gnu/perl/5.34.0<br> /usr/local/share/perl/5.34.0<br> /usr/lib/x86_64-linux-gnu/perl5/5.34<br> /usr/share/perl5<br> /usr/lib/x86_64-linux-gnu/perl-base<br> /usr/lib/x86_64-linux-gnu/perl/5.34<br> /usr/share/perl/5.34<br> /usr/local/lib/site_perl<br># ---------------------------------------------------------------------<br># ---------------------------------------------------------------------<br><br><br>_______________________________________________<br>Dev mailing list Dev@ensembl.org<br>Posting guidelines and subscribe/unsubscribe info: https://lists.ensembl.org/mailman/listinfo/dev_ensembl.org<br>Ensembl Blog: http://www.ensembl.info/<br></div></div></blockquote></div><br></div></body></html>