[ensembl-dev] error message compara API
nconte
nconte at ebi.ac.uk
Mon Feb 15 18:39:02 GMT 2016
Hi,
I am trying to link genomic blocks between mouse and human. The script
will start and then will stop and throw an error, I am not sure why
-------------------- EXCEPTION --------------------
MSG: [] should be a Bio::EnsEMBL::Slice object
STACK
Bio::EnsEMBL::Compara::DBSQL::GenomicAlignBlockAdaptor::fetch_all_by_MethodLinkSpeciesSet_Slice
/net/isilon5/ma/home/nconte/src/ensembl-compara/modules/Bio/EnsEMBL/Compara/DBSQL/Geno
micAlignBlockAdaptor.pm:526
STACK toplevel ./Ortho_mouse_human.pl:125
Date (localtime) = Mon Feb 15 17:31:12 2016
Ensembl API version = 83
---------------------------------------------------
This is the bit in the script where the error points at:
my $method_link_species_set_adaptor =
Bio::EnsEMBL::Registry->get_adaptor(
"Multi", "compara", "MethodLinkSpeciesSet");
my $methodLinkSpeciesSet = $method_link_species_set_adaptor->
fetch_by_method_link_type_species_set_name("EPO", "mammals");
my $mouse_slice_adaptor =
Bio::EnsEMBL::Registry->get_adaptor(
"$non_ref_name", "core", "Slice");
my $gab_adaptor = Bio::EnsEMBL::Registry->get_adaptor(
'Multi', 'compara', 'GenomicAlignBlock');
# this is where I create the mouse slice from a gene object
my $mouse_chromosome= $gene->seq_region_name;
my $mouse_start= $gene->seq_region_start;
my $mouse_end= $gene->seq_region_end;
my $mouse_slice = $mouse_slice_adaptor->fetch_by_region(
"chromosome", $mouse_chromosome, $mouse_start, $mouse_end);
my $all_genomic_align_blocks = $gab_adaptor->
fetch_all_by_MethodLinkSpeciesSet_Slice($methodLinkSpeciesSet,
$mouse_slice); #method to link genomics blocks between species
Then the script continues to get other type of features from the align
block. The error message point at the
fetch_all_by_MethodLinkSpeciesSet_Slice stating I should use
Bio::EnsEMBL::Slice object which I do, $mouse_slice is a slice object. I
am not sure if this is the reason why the scripts stops but this is the
only error message in the error file. This script was working on a
previous ensembl version (79).
the output file show this
Exited with exit code 255.
Resource usage summary:
CPU time : 267.21 sec.
Max Memory : 162 MB
Average Memory : 155.47 MB
Thanks for any tips.
Nathalie
More information about the Dev
mailing list