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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>
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From: annelyle@ebi.ac.uk<BR>Date: Tue, 27 May 2014 09:31:48 +0100<BR>To: dev@ensembl.org<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></DIV></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>
<DIV>And I have no idea for the second error, about panic: sv_setpvn.</DIV></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>-- <BR>
<DIV><FONT size=1 face="verdana, sans-serif">Gang Chen</FONT></DIV>
<DIV><FONT size=1 face="verdana, sans-serif">TILSI</FONT></DIV>
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