Hi,
I am querying a Postgresql 8.3 database table that has approximately 22 million records. The (explain analyze) query is listed below:
gdr_gbrowse_live=> explain analyze SELECT f.id,f.object,f.typeid,f.seqid,f.start,f.end,f.strand FROM feature as f, name as n WHERE (n.id=f.id AND lower(n.name) LIKE 'Scaffold:scaffold_163:1000..1199%' AND n.display_name>0);
QUERY PLAN
------------------------------------------------------------------------------------------------------------------------------------------------
Nested Loop (cost=0.01..5899.93 rows=734 width=884) (actual time=0.033..0.033 rows=0 loops=1)
-> Index Scan using name_name_lower_pattern_ops_idx on name n (cost=0.01..9.53 rows=734 width=4) (actual time=0.032..0.032 rows=0 loops=1)
Index Cond: ((lower((name)::text) ~>=~ 'Scaffold:scaffold'::text) AND (lower((name)::text) ~<~ 'Scaffold:scaffole'::text))
Filter: ((display_name > 0) AND (lower((name)::text) ~~ 'Scaffold:scaffold_163:1000..1199%'::text))
-> Index Scan using feature_pkey on feature f (cost=0.00..8.01 rows=1 width=884) (never executed)
Index Cond: (f.id = n.id)
Total runtime: 0.119 ms
(7 rows)
I can see I am hitting an index using an index that I created using the varchar_pattern_ops setting. This is very fast and performs like I would expect. However, when my application, GBrowse, access the database, I see in my slow query log this:
2010-03-29 09:34:38.083 PDT,"gdr_gbrowse_live","gdr_gbrowse_live",11649,"10.0.0.235:59043",4bb0399d.2d81,8,"SELECT",2010-03-28 22:24:45 PDT,4/118607,0,LOG,00000,"duration: 21467.467 ms execute dbdpg_p25965_9: SELECT f.id,f.object,f.typeid,f.seqid,f.start,f.end,f.strand
FROM feature as f, name as n
WHERE (n.id=f.id AND lower(n.name) LIKE $1)
","parameters: $1 = 'Scaffold:scaffold\_163:1000..1199%'",,,,,,,
GBrowse is a perl based application. Looking at the duration for this query is around 21 seconds. That is a bit long. Does anyone have any ideas why the query duration is so different?
Randall Svancara
Systems Administrator/DBA/Developer
Main Bioinformatics Laboratory
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