Details
-
Type: Bug
-
Status: Open
-
Priority: Critical
-
Resolution: Unresolved
-
Affects Version/s: 2.11.1
-
Fix Version/s: 2.11.1
-
Component/s: data retrieval services, variants
-
Labels:
Description
In 2.11.1
- retrieve the uniprot sequences found by the following query (gene:BACE2 OR gene:BACE1) AND reviewed:yes
These are
BACE1_HUMAN
BACE1_MOUSE
BACE1_RAT
BACE1_CAVPO
BACE1_BOVIN
BACE2_HUMAN
BACE2_MOUSE
BACE2_RAT
-- however, trying these on there own seem to not result in the bug happening...
- retrieve crossrefs to Ensembl (this takes a while)
Mouse over the CDS sequences - most will have a Species:Chromosome dbref, but one mouse or human sequence (so far in my testing) seem to only get the chromosome number, not the species.
I don't see this problem with a smaller number of sequences, suggesting there may be a race condition somewhere in the ensembl fetcher in the vicinity of the Locus construction code.
- retrieve the uniprot sequences found by the following query (gene:BACE2 OR gene:BACE1) AND reviewed:yes
These are
BACE1_HUMAN
BACE1_MOUSE
BACE1_RAT
BACE1_CAVPO
BACE1_BOVIN
BACE2_HUMAN
BACE2_MOUSE
BACE2_RAT
-- however, trying these on there own seem to not result in the bug happening...
- retrieve crossrefs to Ensembl (this takes a while)
Mouse over the CDS sequences - most will have a Species:Chromosome dbref, but one mouse or human sequence (so far in my testing) seem to only get the chromosome number, not the species.
I don't see this problem with a smaller number of sequences, suggesting there may be a race condition somewhere in the ensembl fetcher in the vicinity of the Locus construction code.