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

[Ed Gray]

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
Date: Tue, 27 May 2014 09:31:48 +0100
To: 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> 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
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;port=5306] as a locator:
DBI connect('database=drosophila_melanogaster_core_75_546;host=ensembldb.ensembl.org;port=5306','anonymous',...) failed: Can't connect to MySQL server on '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 InformationAddress: A2/162, Renmin South Road, Taicang, 215400, Jiangsu Province, P.R.ChinaPhone:（+86）512-82782588_______________________________________________
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