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<div>I¡¯ve hit that one before with MySQL running out of file handles. See: <a href="http://stackoverflow.com/questions/11390213/1016-cant-open-file-database-name-sql-38f-36aa-frm-errno-24">http://stackoverflow.com/questions/11390213/1016-cant-open-file-database-name-sql-38f-36aa-frm-errno-24</a>.
You can usually set the server variable open-files-limit (IIRC, by default in many configs, it¡¯s set low). </div>
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<div>All the best</div>
<div>Stuart</div>
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<div>On May 27, 2014, at 10:22 AM, Ed Gray <<a href="mailto:gray_ed@hotmail.com">gray_ed@hotmail.com</a>> wrote:</div>
<br class="Apple-interchange-newline">
<blockquote type="cite">
<div class="hmmessage" style="font-size: 12pt; font-family: Calibri; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px;">
<div dir="ltr"> <br>
strange error:<br>
<br>
here is what I did:<br>
<br>
my @homs = @{$gene->get_all_homologous_Genes};<br>
<br>
DBD::mysql::st execute failed: Can't open file: './ensembl_compara_75/member.frm' (errno: 24) at /usr/local/share/perl/5.12.4/ensembl-compara/modules/Bio/EnsEMBL/Compara/DBSQL/BaseAdaptor.pm line 168.<br>
-------------------- EXCEPTION --------------------<br>
MSG: Detected an error whilst executing SQL 'SELECT m.member_id, m.source_name, m.stable_id, m.version, m.taxon_id, m.genome_db_id, m.description, m.chr_name, m.chr_start, m.chr_end, m.chr_strand, m.sequence_id, m.gene_member_id, m.canonical_member_id, m.display_label,
hm.cigar_line, hm.perc_cov, hm.perc_id, hm.perc_pos FROM (member m, homology_member hm) WHERE hm.homology_id = ? AND m.member_id = hm.peptide_member_id ': DBD::mysql::st execute failed: Can't open file: './ensembl_compara_75/member.frm' (errno: 24) at /usr/local/share/perl/5.12.4/ensembl-compara/modules/Bio/EnsEMBL/Compara/DBSQL/BaseAdaptor.pm
line 168.<br>
STACK Bio::EnsEMBL::Compara::DBSQL::BaseAdaptor::generic_fetch /usr/local/share/perl/5.12.4/ensembl-compara/modules/Bio/EnsEMBL/Compara/DBSQL/BaseAdaptor.pm:169<br>
STACK Bio::EnsEMBL::Compara::DBSQL::AlignedMemberAdaptor::fetch_all_by_Homology /usr/local/share/perl/5.12.4/ensembl-compara/modules/Bio/EnsEMBL/Compara/DBSQL/AlignedMemberAdaptor.pm:120<br>
STACK Bio::EnsEMBL::Compara::DBSQL::AlignedMemberAdaptor::fetch_all_by_AlignedMemberSet /usr/local/share/perl/5.12.4/ensembl-compara/modules/Bio/EnsEMBL/Compara/DBSQL/AlignedMemberAdaptor.pm:88<br>
STACK Bio::EnsEMBL::Compara::MemberSet::get_all_Members /usr/local/share/perl/5.12.4/ensembl-compara/modules/Bio/EnsEMBL/Compara/MemberSet.pm:443<br>
STACK Bio::EnsEMBL::Compara::MemberSet::get_all_GeneMembers /usr/local/share/perl/5.12.4/ensembl-compara/modules/Bio/EnsEMBL/Compara/MemberSet.pm:489<br>
STACK Bio::EnsEMBL::Gene::get_all_homologous_Genes /usr/local/share/perl/5.12.4/ensembl/modules/Bio/EnsEMBL/Gene.pm:857<br>
STACK main::process_homologs newget_gene_info.pl:423<br>
STACK toplevel newget_gene_info.pl:292<br>
Date (localtime) = Tue May 27 12:46:41 2014<br>
Ensembl API version = 75<br>
---------------------------------------------------<br>
<br>
<br>
<div>
<hr id="stopSpelling">
From:<span class="Apple-converted-space"> </span><a href="mailto:annelyle@ebi.ac.uk">annelyle@ebi.ac.uk</a><br>
Date: Tue, 27 May 2014 09:31:48 +0100<br>
To:<span class="Apple-converted-space"> </span><a href="mailto:dev@ensembl.org">dev@ensembl.org</a><br>
Subject: Re: [ensembl-dev] DB connection and panic: sv_setpvn error<br>
<br>
<br>
<div>
<div>On 26 May 2014, at 07:59, ³Â¸Ú <<a href="mailto:danielchen06@gmail.com">danielchen06@gmail.com</a>> wrote:</div>
<br class="ecxApple-interchange-newline">
<blockquote>
<div dir="ltr">Hi All
<div><br>
</div>
<div>Our mirror has database connection and sv_setpvn errors (version 75). The public-plugins/mirror/conf/ini-files/DEFAULTS.ini has been changed, but it doesn't work. The DB connection is not our real DB IP, user name and password.</div>
<div><br>
</div>
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</blockquote>
<div><br>
</div>
<div>Did you remove config.packed after making changes to DEFAULTS.ini (e.g. using ctrl_scripts/restart_server -r)?</div>
<div><br>
</div>
<br>
<blockquote>
<div dir="ltr">And I have no idea for the second error, about panic: sv_setpvn.</div>
</blockquote>
<div><br>
</div>
<div>Sorry, I have no idea either - hopefully someone from the Software (API) team will have insight into that one.</div>
<div><br>
</div>
<div>
<div>Cheers</div>
<div><br>
</div>
<div>Anne</div>
<div><br>
</div>
</div>
<br>
<blockquote>
<div dir="ltr">
<div><br>
</div>
<div>The error massage:</div>
<div><br>
</div>
<div>First:</div>
<div><br>
</div>
<div>
<div> Executing perl startup file</div>
<div> Retrieving conf from /usr/local/Ensembl/ensembl-webcode/conf/config.packed</div>
<div>:: Auto-selecting build 546 core DB as:<span style="white-space: pre;"> </span>
anonymous@drosophila_melanogaster_core_75_546:<a href="http://ensembldb.ensembl.org:5306/" target="_blank">ensembldb.ensembl.org:5306</a></div>
<div>Could not connect to database drosophila_melanogaster_core_75_546 as user anonymous using [DBI:mysql:database=drosophila_melanogaster_core_75_546;host=<a href="http://ensembldb.ensembl.org/" target="_blank">ensembldb.ensembl.org</a>;port=5306] as a locator:</div>
<div>DBI connect('database=drosophila_melanogaster_core_75_546;host=<a href="http://ensembldb.ensembl.org/" target="_blank">ensembldb.ensembl.org</a>;port=5306','anonymous',...) failed: Can't connect to MySQL server on '<a href="http://ensembldb.ensembl.org/" target="_blank">ensembldb.ensembl.org</a>'
(111) at /usr/local/Ensembl/ensembl/modules/Bio/EnsEMBL/DBSQL/DBConnection.pm line 262.</div>
<div>Syntax error on line 152 of /usr/local/Ensembl/ensembl-webcode/conf/httpd.conf:<br>
</div>
<div><br>
</div>
<div>Second:</div>
<div><br>
</div>
<div>panic: sv_setpvn called with negative strlen -1 at /usr/local/Ensembl/ensembl/modules/Bio/EnsEMBL/Utils/Exception.pm line 420.\n</div>
</div>
<div>
<div><br>
</div>
<div><br>
</div>
<div>Best regards</div>
<div><br>
</div>
--<span class="Apple-converted-space"> </span><br>
<div><font size="1" face="verdana, sans-serif">Gang Chen</font></div>
<div><font size="1" face="verdana, sans-serif">TILSI</font></div>
<div><font size="1" face="verdana, sans-serif"><span style="background-color: rgb(255, 255, 255);">Taicang Institute For Life Science Information</span><br style="background-color: rgb(255, 255, 255);">
<span style="background-color: rgb(255, 255, 255);">Address: A2/162, Renmin South Road, Taicang, 215400, Jiangsu Province, P.R.China</span><br style="background-color: rgb(255, 255, 255);">
<span style="background-color: rgb(255, 255, 255);">Phone:£¨+86£©512-82782588</span></font></div>
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