[ensembl-dev] "Too many concurrent connections" errors when using get_all_Alleles()
andrew126 at mac.com
andrew126 at mac.com
Wed Jul 6 20:50:55 BST 2016
Hi,
I'm using API 84 on 64-bit Ubuntu.
uname -a
Linux ubuntu1404-64-ak 4.2.0-27-generic #32~14.04.1-Ubuntu SMP Fri Jan 22 15:32:26 UTC 2016 x86_64 x86_64 x86_64 GNU/Linux
The below script reliably generates errors because of the number of concurrent connections. If get_all_Alleles() is not called, then no errors are experienced. I think other similar calls also generate these errors, but this is a simple example to get started.
Posted below the script is an example of the error messages encountered.
Is there a way to accomplish the same goal (summary of all alleles for each variant) without generating such errors?
Please let me know if any other information would be useful.
Thanks for any help,
Andrew
use strict;
$|=1;
use IPC::Run;
use Bio::EnsEMBL::Registry;
use Bio::EnsEMBL::ApiVersion;
printf( "The API version used is %s\n", software_version() );
my $registry = 'Bio::EnsEMBL::Registry';
$registry->load_all();
$registry->set_reconnect_when_lost();
$registry->load_registry_from_db(
-host => 'useastdb.ensembl.org',
-user => 'anonymous'
);
my $gene_adaptor = $registry->get_adaptor('homo_sapiens','core','gene');
my $slice_adaptor = $registry->get_adaptor('homo_sapiens','core','slice');
my $slice = $slice_adaptor->fetch_by_region( 'chromosome', "4", 139000000, 139100000);
print "Variation:\n";
my $vf_adaptor = $registry->get_adaptor( 'human', 'variation', 'variationfeature' );
$vf_adaptor->db->use_vcf(1);
my $vars = $vf_adaptor->fetch_all_by_Slice($slice);
foreach my $vf (@{$vars}){
print "\t".$vf->variation_name(),"\n";
print "\t".$vf->allele_string(),"\n";
print "\tChromosome: ".$slice->seq_region_name."\n";
print "\tStart-End: ".$vf->seq_region_start."-".$vf->seq_region_end."\n";
print "\tConsequences: ".join(",",@{$vf->consequence_type()}),"\n";
if (1==1) {
my $alleles = $vf->variation->get_all_Alleles();
foreach my $allele (@{$alleles}) {
next unless (defined $allele->population);
my $allele_string = $allele->allele;
my $frequency = $allele->frequency || 'NA';
my $population_name = $allele->population->name;
printf("\tAllele %s has frequency: %s in population %s.\n", $allele_string, $frequency, $population_name);
}
}
print "\n";
}
andrew at ubuntu1404-64-ak:~/gte$ perl tryit_crash.pl > tic.out &
[2] 3059
andrew at ubuntu1404-64-ak:~/gte$ UNIVERSAL->import is deprecated and will be removed in a future perl at /home/andrew/gte/src/bioperl-live/Bio/Tree/TreeFunctionsI.pm line 94.
Subroutine Tabix::tabix_open redefined at /home/andrew/gte/src/lib/perl/5.18.2/Tabix.pm line 17.
Subroutine Tabix::tabix_close redefined at /home/andrew/gte/src/lib/perl/5.18.2/Tabix.pm line 17.
Subroutine Tabix::tabix_query redefined at /home/andrew/gte/src/lib/perl/5.18.2/Tabix.pm line 17.
Subroutine Tabix::tabix_read redefined at /home/andrew/gte/src/lib/perl/5.18.2/Tabix.pm line 17.
Subroutine Tabix::tabix_getnames redefined at /home/andrew/gte/src/lib/perl/5.18.2/Tabix.pm line 17.
Subroutine TabixIterator::tabix_iter_free redefined at /home/andrew/gte/src/lib/perl/5.18.2/Tabix.pm line 17.
[kftp_connect_file] 530 You may not have more than 15 concurrent connections at any time.
[main] fail to open the data file.
[kftp_connect_file] 530 You may not have more than 15 concurrent connections at any time.
*** buffer overflow detected ***: perl terminated
======= Backtrace: =========
/lib/x86_64-linux-gnu/libc.so.6(+0x7338f)[0x7f7fcd13138f]
/lib/x86_64-linux-gnu/libc.so.6(__fortify_fail+0x5c)[0x7f7fcd1c8c9c]
/lib/x86_64-linux-gnu/libc.so.6(+0x109b60)[0x7f7fcd1c7b60]
/lib/x86_64-linux-gnu/libc.so.6(+0x10abe7)[0x7f7fcd1c8be7]
/home/andrew/gte/src/lib/perl/5.18.2/auto/Tabix/Tabix.so(+0xaebd)[0x7f7fc8011ebd]
/home/andrew/gte/src/lib/perl/5.18.2/auto/Tabix/Tabix.so(+0xb0aa)[0x7f7fc80120aa]
/home/andrew/gte/src/lib/perl/5.18.2/auto/Tabix/Tabix.so(knet_read+0xb8)[0x7f7fc8012c18]
/home/andrew/gte/src/lib/perl/5.18.2/auto/Tabix/Tabix.so(bgzf_read_block+0x165)[0x7f7fc8010c25]
/home/andrew/gte/src/lib/perl/5.18.2/auto/Tabix/Tabix.so(bgzf_getline+0x37)[0x7f7fc8011cc7]
/home/andrew/gte/src/lib/perl/5.18.2/auto/Tabix/Tabix.so(ti_iter_read+0xd2)[0x7f7fc8010172]
/home/andrew/gte/src/lib/perl/5.18.2/auto/Tabix/Tabix.so(+0x3368)[0x7f7fc800a368]
/usr/lib/libperl.so.5.18(Perl_pp_entersub+0x596)[0x7f7fcd53c866]
/usr/lib/libperl.so.5.18(Perl_runops_standard+0x16)[0x7f7fcd534e86]
/usr/lib/libperl.so.5.18(perl_run+0x254)[0x7f7fcd4cd714]
perl(main+0x149)[0x400dd9]
/lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xf5)[0x7f7fcd0dfec5]
perl[0x400e11]
======= Memory map: ========
00400000-00402000 r-xp 00000000 fc:00 133596 /usr/bin/perl
00601000-00602000 r--p 00001000 fc:00 133596 /usr/bin/perl
00602000-00603000 rw-p 00002000 fc:00 133596 /usr/bin/perl
01805000-061dc000 rw-p 00000000 00:00 0 [heap]
7f7fc4000000-7f7fc4021000 rw-p 00000000 00:00 0
7f7fc4021000-7f7fc8000000 ---p 00000000 00:00 0
7f7fc8007000-7f7fc8015000 r-xp 00000000 fc:00 532847 /home/andrew/gte/src/lib/perl/5.18.2/auto/Tabix/Tabix.so
7f7fc8015000-7f7fc8214000 ---p 0000e000 fc:00 532847 /home/andrew/gte/src/lib/perl/5.18.2/auto/Tabix/Tabix.so
7f7fc8214000-7f7fc8215000 r--p 0000d000 fc:00 532847 /home/andrew/gte/src/lib/perl/5.18.2/auto/Tabix/Tabix.so
7f7fc8215000-7f7fc8216000 rw-p 0000e000 fc:00 532847 /home/andrew/gte/src/lib/perl/5.18.2/auto/Tabix/Tabix.so
7f7fc8216000-7f7fc822b000 r-xp 00000000 fc:00 260284 /usr/lib/perl/5.18.2/auto/Storable/Storable.so
7f7fc822b000-7f7fc842a000 ---p 00015000 fc:00 260284 /usr/lib/perl/5.18.2/auto/Storable/Storable.so
7f7fc842a000-7f7fc842b000 r--p 00014000 fc:00 260284 /usr/lib/perl/5.18.2/auto/Storable/Storable.so
7f7fc842b000-7f7fc842c000 rw-p 00015000 fc:00 260284 /usr/lib/perl/5.18.2/auto/Storable/Storable.so
7f7fc842c000-7f7fc842e000 r-xp 00000000 fc:00 260313 /usr/lib/perl/5.18.2/auto/attributes/attributes.so
7f7fc842e000-7f7fc862d000 ---p 00002000 fc:00 260313 /usr/lib/perl/5.18.2/auto/attributes/attributes.so
7f7fc862d000-7f7fc862e000 r--p 00001000 fc:00 260313 /usr/lib/perl/5.18.2/auto/attributes/attributes.so
7f7fc862e000-7f7fc862f000 rw-p 00002000 fc:00 260313 /usr/lib/perl/5.18.2/auto/attributes/attributes.so
7f7fc862f000-7f7fc863d000 r-xp 00000000 fc:00 311765 /usr/lib/perl5/auto/JSON/XS/XS.so
7f7fc863d000-7f7fc883c000 ---p 0000e000 fc:00 311765 /usr/lib/perl5/auto/JSON/XS/XS.so
7f7fc883c000-7f7fc883d000 r--p 0000d000 fc:00 311765 /usr/lib/perl5/auto/JSON/XS/XS.so
7f7fc883d000-7f7fc883e000 rw-p 0000e000 fc:00 311765 /usr/lib/perl5/auto/JSON/XS/XS.so
7f7fc883e000-7f7fc884c000 r-xp 00000000 fc:00 260173 /usr/lib/perl/5.18.2/auto/Compress/Raw/Zlib/Zlib.so
7f7fc884c000-7f7fc8a4b000 ---p 0000e000 fc:00 260173 /usr/lib/perl/5.18.2/auto/Compress/Raw/Zlib/Zlib.so
7f7fc8a4b000-7f7fc8a4c000 r--p 0000d000 fc:00 260173 /usr/lib/perl/5.18.2/auto/Compress/Raw/Zlib/Zlib.so
7f7fc8a4c000-7f7fc8a4d000 rw-p 0000e000 fc:00 260173 /usr/lib/perl/5.18.2/auto/Compress/Raw/Zlib/Zlib.so
7f7fc8a4d000-7f7fc8a53000 r-xp 00000000 fc:00 260228 /usr/lib/perl/5.18.2/auto/File/Glob/Glob.so
7f7fc8a53000-7f7fc8c52000 ---p 00006000 fc:00 260228 /usr/lib/perl/5.18.2/auto/File/Glob/Glob.so
7f7fc8c52000-7f7fc8c53000 r--p 00005000 fc:00 260228 /usr/lib/perl/5.18.2/auto/File/Glob/Glob.so
7f7fc8c53000-7f7fc8c54000 rw-p 00006000 fc:00 260228 /usr/lib/perl/5.18.2/auto/File/Glob/Glob.so
7f7fc8c54000-7f7fc8c5c000 r-xp 00000000 fc:00 260282 /usr/lib/perl/5.18.2/auto/Socket/Socket.so
7f7fc8c5c000-7f7fc8e5c000 ---p 00008000 fc:00 260282 /usr/lib/perl/5.18.2/auto/Socket/Socket.so
7f7fc8e5c000-7f7fc8e5e000 r--p 00008000 fc:00 260282 /usr/lib/perl/5.18.2/auto/Socket/Socket.so
7f7fc8e5e000-7f7fc8e5f000 rw-p 0000a000 fc:00 260282 /usr/lib/perl/5.18.2/auto/Socket/Socket.so
7f7fc8e5f000-7f7fc8e63000 r-xp 00000000 fc:00 260192 /usr/lib/perl/5.18.2/auto/Digest/MD5/MD5.so
7f7fc8e63000-7f7fc9062000 ---p 00004000 fc:00 260192 /usr/lib/perl/5.18.2/auto/Digest/MD5/MD5.so
7f7fc9062000-7f7fc9063000 r--p 00003000 fc:00 260192 /usr/lib/perl/5.18.2/auto/Digest/MD5/MD5.so
7f7fc9063000-7f7fc9064000 rw-p 00004000 fc:00 260192 /usr/lib/perl/5.18.2/auto/Digest/MD5/MD5.so
7f7fc9064000-7f7fc9066000 r-xp 00000000 fc:00 260176 /usr/lib/perl/5.18.2/auto/Cwd/Cwd.so
7f7fc9066000-7f7fc9265000 ---p 00002000 fc:00 260176 /usr/lib/perl/5.18.2/auto/Cwd/Cwd.so
7f7fc9265000-7f7fc9266000 r--p 00001000 fc:00 260176 /usr/lib/perl/5.18.2/auto/Cwd/Cwd.so
7f7fc9266000-7f7fc9267000 rw-p 00002000 fc:00 260176 /usr/lib/perl/5.18.2/auto/Cwd/Cwd.so
7f7fc9267000-7f7fc927e000 r-xp 00000000 fc:00 395859 /lib/x86_64-linux-gnu/libresolv-2.19.so
7f7fc927e000-7f7fc947e000 ---p 00017000 fc:00 395859 /lib/x86_64-linux-gnu/libresolv-2.19.so
7f7fc947e000-7f7fc947f000 r--p 00017000 fc:00 395859 /lib/x86_64-linux-gnu/libresolv-2.19.so
7f7fc947f000-7f7fc9480000 rw-p 00018000 fc:00 395859 /lib/x86_64-linux-gnu/libresolv-2.19.so
7f7fc9480000-7f7fc9482000 rw-p 00000000 00:00 0
7f7fc9482000-7f7fc9487000 r-xp 00000000 fc:00 395806 /lib/x86_64-linux-gnu/libnss_dns-2.19.so
7f7fc9487000-7f7fc9686000 ---p 00005000 fc:00 395806 /lib/x86_64-linux-gnu/libnss_dns-2.19.so
7f7fc9686000-7f7fc9687000 r--p 00004000 fc:00 395806 /lib/x86_64-linux-gnu/libnss_dns-2.19.so
7f7fc9687000-7f7fc9688000 rw-p 00005000 fc:00 395806 /lib/x86_64-linux-gnu/libnss_dns-2.19.so
7f7fc9688000-7f7fc968a000 r-xp 00000000 fc:00 395814 /lib/x86_64-linux-gnu/libnss_mdns4_minimal.so.2
7f7fc968a000-7f7fc9889000 ---p 00002000 fc:00 395814 /lib/x86_64-linux-gnu/libnss_mdns4_minimal.so.2
7f7fc9889000-7f7fc988a000 r--p 00001000 fc:00 395814 /lib/x86_64-linux-gnu/libnss_mdns4_minimal.so.2
7f7fc988a000-7f7fc988b000 rw-p 00002000 fc:00 395814 /lib/x86_64-linux-gnu/libnss_mdns4_minimal.so.2
7f7fc988b000-7f7fc9896000 r-xp 00000000 fc:00 395808 /lib/x86_64-linux-gnu/libnss_files-2.19.so
7f7fc9896000-7f7fc9a95000 ---p 0000b000 fc:00 395808 /lib/x86_64-linux-gnu/libnss_files-2.19.so
7f7fc9a95000-7f7fc9a96000 r--p 0000a000 fc:00 395808 /lib/x86_64-linux-gnu/libnss_files-2.19.so
7f7fc9a96000-7f7fc9a97000 rw-p 0000b000 fc:00 395808 /lib/x86_64-linux-gnu/libnss_files-2.19.so
7f7fc9a97000-7f7fc9aad000 r-xp 00000000 fc:00 395760 /lib/x86_64-linux-gnu/libgcc_s.so.1
7f7fc9aad000-7f7fc9cac000 ---p 00016000 fc:00 395760 /lib/x86_64-linux-gnu/libgcc_s.so.1
7f7fc9cac000-7f7fc9cad000 rw-p 00015000 fc:00 395760 /lib/x86_64-linux-gnu/libgcc_s.so.1
7f7fc9cad000-7f7fc9cae000 ---p 00000000 00:00 0
7f7fc9cae000-7f7fca4ae000 rw-p 00000000 00:00 0
7f7fca4ae000-7f7fca4c6000 r-xp 00000000 fc:00 395896 /lib/x86_64-linux-gnu/libz.so.1.2.8
7f7fca4c6000-7f7fca6c5000 ---p 00018000 fc:00 395896 /lib/x86_64-linux-gnu/libz.so.1.2.8
7f7fca6c5000-7f7fca6c6000 r--p 00017000 fc:00 395896 /lib/x86_64-linux-gnu/libz.so.1.2.8
7f7fca6c6000-7f7fca6c7000 rw-p 00018000 fc:00 395896 /lib/x86_64-linux-gnu/libz.so.1.2.8
7f7fca6c7000-7f7fca977000 r-xp 00000000 fc:00 183788 /usr/lib/x86_64-linux-gnu/libmysqlclient.so.18.0.0
7f7fca977000-7f7fcab77000 ---p 002b0000 fc:00 183788 /usr/lib/x86_64-linux-gnu/libmysqlclient.so.18.0.0
7f7fcab77000-7f7fcab7c000 r--p 002b0000 fc:00 183788 /usr/lib/x86_64-linux-gnu/libmysqlclient.so.18.0.0
7f7fcab7c000-7f7fcabfa000 rw-p 002b5000 fc:00 183788 /usr/lib/x86_64-linux-gnu/libmysqlclient.so.18.0.0
7f7fcabfa000-7f7fcabff000 rw-p 00000000 00:00 0
7f7fcabff000-7f7fcac19000 r-xp 00000000 fc:00 183957 /usr/lib/perl5/auto/DBD/mysql/mysql.so
7f7fcac19000-7f7fcae19000 ---p 0001a000 fc:00 183957 /usr/lib/perl5/auto/DBD/mysql/mysql.so
7f7fcae19000-7f7fcae1b000 r--p 0001a000 fc:00 183957 /usr/lib/perl5/auto/DBD/mysql/mysql.so
7f7fcae1b000-7f7fcae1c000 rw-p 0001c000 fc:00 183957 /usr/lib/perl5/auto/DBD/mysql/mysql.so
7f7fcae1c000-7f7fcae24000 r-xp 00000000 fc:00 260182 /usr/lib/perl/5.18.2/auto/Data/Dumper/Dumper.so
7f7fcae24000-7f7fcb023000 ---p 00008000 fc:00 260182 /usr/lib/perl/5.18.2/auto/Data/Dumper/Dumper.so
7f7fcb023000-7f7fcb024000 r--p 00007000 fc:00 260182 /usr/lib/perl/5.18.2/auto/Data/Dumper/Dumper.so
7f7fcb024000-7f7fcb025000 rw-p 00008000 fc:00 260182 /usr/lib/perl/5.18.2/auto/Data/Dumper/Dumper.so
7f7fcb025000-7f7fcb02c000 r-xp 00000000 fc:00 395861 /lib/x86_64-linux-gnu/librt-2.19.so
7f7fcb02c000-7f7fcb22b000 ---p 00007000 fc:00 395861 /lib/x86_64-linux-gnu/librt-2.19.so
7f7fcb22b000-7f7fcb22c000 r--p 00006000 fc:00 395861 /lib/x86_64-linux-gnu/librt-2.19.so
7f7fcb22c000-7f7fcb22d000 rw-p 00007000 fc:00 395861 /lib/x86_64-linux-gnu/librt-2.19.so
7f7fcb22d000-7f7fcb232000 r-xp 00000000 fc:00 260301 /usr/lib/perl/5.18.2/auto/Time/HiRes/HiRes.so
7f7fcb232000-7f7fcb431000 ---p 00005000 fc:00 260301 /usr/lib/perl/5.18.2/auto/Time/HiRes/HiRes.so
7f7fcb431000-7f7fcb432000 r--p 00004000 fc:00 260301 /usr/lib/perl/5.18.2/auto/Time/HiRes/HiRes.so
7f7fcb432000-7f7fcb433000 rw-p 00005000 fc:00 260301 /usr/lib/perl/5.18.2/auto/Time/HiRes/HiRes.so
7f7fcb433000-7f7fcb435000 r-xp 00000000 fc:00 260297 /usr/lib/perl/5.18.2/auto/Tie/Hash/NamedCapture/NamedCapture.so
7f7fcb435000-7f7fcb634000 ---p 00002000 fc:00 260297 /usr/lib/perl/5.18.2/auto/Tie/Hash/NamedCapture/NamedCapture.so
7f7fcb634000-7f7fcb635000 r--p 00001000 fc:00 260297 /usr/lib/perl/5.18.2/auto/Tie/Hash/NamedCapture/NamedCapture.so
7f7fcb635000-7f7fcb636000 rw-p 00002000 fc:00 260297 /usr/lib/perl/5.18.2/auto/Tie/Hash/NamedCapture/NamedCapture.so
7f7fcb636000-7f7fcb63b000 r-xp 00000000 fc:00 260251 /usr/lib/perl/5.18.2/auto/List/Util/Util.so
7f7fcb63b000-7f7fcb83b000 ---p 00005000 fc:00 260251 /usr/lib/perl/5.18.2/auto/List/Util/Util.so
7f7fcb83b000-7f7fcb83c000 r--p 00005000 fc:00 260251 /usr/lib/perl/5.18.2/auto/List/Util/Util.so
7f7fcb83c000-7f7fcb83d000 rw-p 00006000 fc:00 260251 /usr/lib/perl/5.18.2/auto/List/Util/Util.so
7f7fcb83d000-7f7fcb85b000 r-xp 00000000 fc:00 183894 /usr/lib/perl5/auto/DBI/DBI.so
7f7fcb85b000-7f7fcba5a000 ---p 0001e000 fc:00 183894 /usr/lib/perl5/auto/DBI/DBI.so
7f7fcba5a000-7f7fcba5b000 r--p 0001d000 fc:00 183894 /usr/lib/perl5/auto/DBI/DBI.so
7f7fcba5b000-7f7fcba5c000 rw-p 0001e000 fc:00 183894 /usr/lib/perl5/auto/DBI/DBI.so
7f7fcba5c000-7f7fcba60000 r-xp 00000000 fc:00 260245 /usr/lib/perl/5.18.2/auto/IO/IO.so
7f7fcba60000-7f7fcbc5f000 ---p 00004000 fc:00 260245 /usr/lib/perl/5.18.2/auto/IO/IO.so
7f7fcbc5f000-7f7fcbc60000 r--p 00003000 fc:00 260245 /usr/lib/perl/5.18.2/auto/IO/IO.so
7f7fcbc60000-7f7fcbc61000 rw-p 00004000 fc:00 260245 /usr/lib/perl/5.18.2/auto/IO/IO.so
7f7fcbc61000-7f7fcbc73000 r-xp 00000000 fc:00 260266 /usr/lib/perl/5.18.2/auto/POSIX/POSIX.so
7f7fcbc73000-7f7fcbe72000 ---p 00012000 fc:00 260266 /usr/lib/perl/5.18.2/auto/POSIX/POSIX.so
7f7fcbe72000-7f7fcbe75000 r--p 00011000 fc:00 260266 /usr/lib/perl/5.18.2/auto/POSIX/POSIX.so
7f7fcbe75000-7f7fcbe76000 rw-p 00014000 fc:00 260266 /usr/lib/perl/5.18.2/auto/POSIX/POSIX.so
7f7fcbe76000-7f7fcbe79000 r-xp 00000000 fc:00 260222 /usr/lib/perl/5.18.2/auto/Fcntl/Fcntl.so
7f7fcbe79000-7f7fcc079000 ---p 00003000 fc:00 260222 /usr/lib/perl/5.18.2/auto/Fcntl/Fcntl.so
7f7fcc079000-7f7fcc07a000 r--p 00003000 fc:00 260222 /usr/lib/perl/5.18.2/auto/Fcntl/Fcntl.so
7f7fcc07a000-7f7fcc07b000 rw-p 00004000 fc:00 260222 /usr/lib/perl/5.18.2/auto/Fcntl/Fcntl.so
7f7fcc07b000-7f7fcc75d000 r--p 00000000 fc:00 140924 /usr/lib/locale/locale-archive
7f7fcc75d000-7f7fcc766000 r-xp 00000000 fc:00 395743 /lib/x86_64-linux-gnu/libcrypt-2.19.so
7f7fcc766000-7f7fcc966000 ---p 00009000 fc:00 395743 /lib/x86_64-linux-gnu/libcrypt-2.19.so
7f7fcc966000-7f7fcc967000 r--p 00009000 fc:00 395743 /lib/x86_64-linux-gnu/libcrypt-2.19.so
7f7fcc967000-7f7fcc968000 rw-p 0000a000 fc:00 395743 /lib/x86_64-linux-gnu/libcrypt-2.19.so
[2]+ Aborted (core dumped) perl tryit_crash.pl > tic.out
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