[ensembl-dev] './ensembl_compara_75/member.frm' (errno: 24)

Tue May 27 15:32:42 BST 2014

I’ve hit that one before with MySQL running out of file handles. See: http://stackoverflow.com/questions/11390213/1016-cant-open-file-database-name-sql-38f-36aa-frm-errno-24. You can usually set the server variable open-files-limit (IIRC, by default in many configs, it’s set low).

All the best
Stuart

On May 27, 2014, at 10:22 AM, Ed Gray <gray_ed at hotmail.com<mailto:gray_ed at hotmail.com>> wrote:

strange error:

here is what I did:

my @homs = @{$gene->get_all_homologous_Genes};

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.
-------------------- EXCEPTION --------------------
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.
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
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
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
STACK Bio::EnsEMBL::Compara::MemberSet::get_all_Members /usr/local/share/perl/5.12.4/ensembl-compara/modules/Bio/EnsEMBL/Compara/MemberSet.pm:443
STACK Bio::EnsEMBL::Compara::MemberSet::get_all_GeneMembers /usr/local/share/perl/5.12.4/ensembl-compara/modules/Bio/EnsEMBL/Compara/MemberSet.pm:489
STACK Bio::EnsEMBL::Gene::get_all_homologous_Genes /usr/local/share/perl/5.12.4/ensembl/modules/Bio/EnsEMBL/Gene.pm:857
STACK main::process_homologs newget_gene_info.pl:423
STACK toplevel newget_gene_info.pl:292
Date (localtime)    = Tue May 27 12:46:41 2014
Ensembl API version = 75
---------------------------------------------------

________________________________
From: annelyle at ebi.ac.uk<mailto:annelyle at ebi.ac.uk>
Date: Tue, 27 May 2014 09:31:48 +0100
To: dev at ensembl.org<mailto:dev at ensembl.org>
Subject: Re: [ensembl-dev] DB connection and panic: sv_setpvn error

On 26 May 2014, at 07:59, 陈岗 <danielchen06 at gmail.com<mailto:danielchen06 at gmail.com>> wrote:

Hi All

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.

Did you remove config.packed after making changes to DEFAULTS.ini (e.g. using ctrl_scripts/restart_server -r)?

And I have no idea for the second error, about panic: sv_setpvn.

Sorry, I have no idea either - hopefully someone from the Software (API) team will have insight into that one.

Cheers

Anne

The error massage:

First:

 Executing perl startup file
 Retrieving conf from /usr/local/Ensembl/ensembl-webcode/conf/config.packed
:: Auto-selecting build 546 core DB as: anonymous at drosophila_melanogaster_core_75_546:ensembldb.ensembl.org:5306<http://ensembldb.ensembl.org:5306/>
Could not connect to database drosophila_melanogaster_core_75_546 as user anonymous using [DBI:mysql:database=drosophila_melanogaster_core_75_546;host=ensembldb.ensembl.org<http://ensembldb.ensembl.org/>;port=5306] as a locator:
DBI connect('database=drosophila_melanogaster_core_75_546;host=ensembldb.ensembl.org<http://ensembldb.ensembl.org/>;port=5306','anonymous',...) failed: Can't connect to MySQL server on 'ensembldb.ensembl.org<http://ensembldb.ensembl.org/>' (111) at /usr/local/Ensembl/ensembl/modules/Bio/EnsEMBL/DBSQL/DBConnection.pm line 262.
Syntax error on line 152 of /usr/local/Ensembl/ensembl-webcode/conf/httpd.conf:

Second:

panic: sv_setpvn called with negative strlen -1 at /usr/local/Ensembl/ensembl/modules/Bio/EnsEMBL/Utils/Exception.pm line 420.\n

Best regards

--
Gang Chen
TILSI
Taicang Institute For Life Science Information
Address: A2/162, Renmin South Road, Taicang, 215400, Jiangsu Province, P.R.China
Phone:（+86）512-82782588
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