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