[ensembl-dev] beekeeper fails in EPO_pt1 update_genome_db_locator

[Matthieu Muffato]

Hi Lel,

Can you check the content of the meta (or pipeline_wide_parameters) 
table in the database ? I think init_pipeline may have stored 
"additional_core_db_urls" as "HASH(0xbda308)" in the database instead of 
the actual content.

Matthieu
PS: Which version of eHive are you using ?

On 10/09/14 14:47, Lel Eory wrote:
> Dear Compara-team,
>
> Can you please help me with the following:
> I try to test-run a the EPO pipeline for the 3 high-coverage Ensembl
> birds, but beekeeper fails.
> I have changed the config file
> Bio::EnsEMBL::Compara::PipeConfig::EPO_pt1_conf and init_pipeline runs
> OK. Also beekeeper runs fine on the first few steps, but then it fails
> in the "update_genome_db_locator" step.
>
> The error message I got is the following:
> ~~~~~~~~~~~~~~~~~~~
> Worker 18 [ update_genome_db_locator(7) ] Job 14 : died in status
> 'FETCH_INPUT' for the following reason: Can't use string
> ("HASH(0xbda308)") as a HASH ref while "strict refs" in use at
> /groups2/avian_genomes/software/src/ensembl/ensgit/ensembl-compara/modules/Bio/EnsEMBL/Compara/Production/EPOanchors/UpdateGenomeDBLocator.pm
> line 75.
> ~~~~~~~~~~~~~~~~~~~
>
> The offending line refers to the 'additional_core_db_urls'  section from
> my EPO_pt1_conf copied below.
> I have set up the config file to pick the species from
> ensembldb.ensembl.org specifying this with the 'main_core_dbs'. Do I
> need to set-up a section for each of the species I want to run the EPO
> pipeline for, or are the connections picked-up by the code? I have also
> specified the 'additional_core_db_urls' with my local install of the
> ensembl birds, just in case, but the error still occurs...
>
> The relevant lines from my EPO_pt1_conf are:
> ~~~~~~~~~~~~~~~~~~~
> 106         'main_core_dbs' => [
> 107           {
> 108             -user => 'anonymous',
> 109             -port => 5306,
> 110             -host => 'ensembldb.ensembl.org',
> 111             -driver => 'mysql',
> 112             -pass => '',
> 113             -dbname => '',
> 114             -db_version => $self->o('core_db_version'),
> 115           },
> 116         ],
> 117         # any additional core dbs
> 118         'additional_core_db_urls' => {
> 119                 'gallus_gallus' =>
> 'mysql://USER:PASS@HOST:3306/gallus_gallus_core_75',
> 120                 'taeniopygia_guttata' =>
> 'mysql://USER:PASS@HOST:3306/taeniopygia_guttata_core_75',
> 121                 'meleagris_gallopavo' =>
> 'mysql://USER:PASS@HOST:3306/meleagris_gallopavo_core_75',
> 122         },
>
> ~~~~~~~~~~~~~~~~~~~
>
> What modifications do I need to do to avoid the error?
>
> Thank you.
>
> Best wishes,
> Lel
>

-- 
Matthieu Muffato, Ph.D.
Ensembl Compara Project Leader
European Bioinformatics Institute (EMBL-EBI)
European Molecular Biology Laboratory
Wellcome Trust Genome Campus, Hinxton
Cambridge, CB10 1SD, United Kingdom
Room  A3-145
Phone + 44 (0) 1223 49 4631
Fax   + 44 (0) 1223 49 4468