[ensembl-dev] EFG Environment v59 ImportArrays problem

[Oliver, Gavin]

Hi all, 

 

I am attempting the ImportArrays function and am having problems.  The
job seems to hang and when I check the error files I see the output at
the end of this mail.  The error being reported is at the last line in
the PROBES file but there is nothing wrong with this file.  I have used
it with previous versions of the mapping environment with no problems.
Has anyone got any ideas what is happening?

 

Best, 

 

Gavin

 

Running job 1

Module is ImportArrays

Input id is AFFY_UTR:genome

Analysis is Import_AFFY_UTR_Arrays

Files are
/cluster_progs/data/Ensembl/59/process_dirs/lsf_default_output_dir/Impor
t_AFFY_UTR_Arrays/5/AFFY_UTR:genome.Import_AFFY_UTR_Arrays.230.out
/cluster_progs/da

ta/Ensembl/59/process_dirs/lsf_default_output_dir/Import_AFFY_UTR_Arrays
/5/AFFY_UTR:genome.Import_AFFY_UTR_Arrays.230.err

NOTE: rollback_ArrayChips. Need to implement ExperimentlChip check, is
the problem that ExperimentalChips are registered before ArrayChips
imported? at /cluster_progs

/data/Ensembl/59/ensembl-functgenomics/modules//Bio/EnsEMBL/Funcgen/Util
s/Helper.pm line 1957, <PROBES> line 1.

DBD::mysql::st bind_param failed: Illegal parameter number at
/cluster_progs/data/Ensembl/59/ensembl-functgenomics/modules//Bio/EnsEMB
L/Funcgen/DBSQL/ProbeAdaptor.pm 

line 569, <PROBES> line 548.

WRITING: Lost the will to live Error

Job 1 failed: [

-------------------- EXCEPTION --------------------

MSG: Problems for ImportArrays writing output for AFFY_UTR:genome
[DBD::mysql::st bind_param failed: Illegal parameter number at
/cluster_progs/data/Ensembl/59/ensemb

l-functgenomics/modules//Bio/EnsEMBL/Funcgen/DBSQL/ProbeAdaptor.pm line
569, <PROBES> line 548.

]

STACK Bio::EnsEMBL::Pipeline::Job::run_module
/cluster_progs/data/Ensembl/59/ensembl-pipeline/modules//Bio/EnsEMBL/Pip
eline/Job.pm:662

STACK (eval)
/cluster_progs/data/Ensembl/59/ensembl-pipeline/modules//Bio/EnsEMBL/Pip
eline/runner.pl:219

STACK main::run_jobs_with_lsfcopy
/cluster_progs/data/Ensembl/59/ensembl-pipeline/modules//Bio/EnsEMBL/Pip
eline/runner.pl:218

STACK toplevel
/cluster_progs/data/Ensembl/59/ensembl-pipeline/modules//Bio/EnsEMBL/Pip
eline/runner.pl:128

---------------------------------------------------

]Finished job 1

 

 

 

Gavin Oliver, MSc

Team Leader Genomic Research

Almac

Diagnostics

Tel: +44 (0)28 38395792

Fax: +44 (0)28 38398676

Visit our website at: http://www.almacgroup.com
<http://www.almacgroup.com/> 

 


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