[ensembl-dev] error message compara API

nconte nconte at ebi.ac.uk
Mon Feb 15 18:39:02 GMT 2016

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 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 =
       "Multi", "compara", "MethodLinkSpeciesSet");
my $methodLinkSpeciesSet = $method_link_species_set_adaptor->
	fetch_by_method_link_type_species_set_name("EPO", "mammals");
my $mouse_slice_adaptor =
       "$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->
$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.

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