[ensembl-dev] EFG Array Mapping Slow Queries

[Oliver, Gavin]

Can anyone experienced with the EFG/Array Mapping environment take a
look at the below sample of my mysql sloq query log and tell me whether
it seems normal?

 

These are generated at the RunTranscriptXrefs stage.

 

Thanks in advance, 

 

Gavin

 

# Time: 100916 10:18:51

# User at Host: pipeline[pipeline] @ localhost []

# Query_time: 34.386525  Lock_time: 0.000231 Rows_sent: 23
Rows_examined: 13635438

SET timestamp=1284628731;

SELECT  pf.probe_feature_id, pf.seq_region_id, pf.seq_region_start,
pf.seq_region_end, pf.seq_region_strand, pf.probe_id, pf.analysis_id,
pf.mismatches, pf.cigar_line, p.name, p.probe_set_id

FROM  (probe_feature pf, probe p, array_chip ac) 

 WHERE  ac.array_id IN (56,52,54,55,53,58,57) and
ac.array_chip_id=p.array_chip_id  AND pf.seq_region_id = 581 AND
pf.seq_region_start <= 40600181 AND pf.seq_region_end >= 40598166 AND
pf.seq_region_start >= 39437730  AND

       pf.probe_id = p.probe_id 

 GROUP by pf.probe_feature_id  ORDER BY pf.seq_region_id,
pf.seq_region_start, pf.probe_feature_id;

 

 

# Time: 100916 10:19:26

# User at Host: pipeline[pipeline] @ localhost []

# Query_time: 34.402924  Lock_time: 0.000100 Rows_sent: 0
Rows_examined: 13635392

SET timestamp=1284628766;

SELECT  pf.probe_feature_id, pf.seq_region_id, pf.seq_region_start,
pf.seq_region_end, pf.seq_region_strand, pf.probe_id, pf.analysis_id,
pf.mismatches, pf.cigar_line, p.name, p.probe_set_id

FROM  (probe_feature pf, probe p, array_chip ac) 

 WHERE  ac.array_id IN (56,52,54,55,53,58,57) and
ac.array_chip_id=p.array_chip_id  AND pf.seq_region_id = 581 AND
pf.seq_region_start <= 40728924 AND pf.seq_region_end >= 40727284 AND
pf.seq_region_start >= 39566848  AND

       pf.probe_id = p.probe_id 

 GROUP by pf.probe_feature_id  ORDER BY pf.seq_region_id,
pf.seq_region_start, pf.probe_feature_id;

 

 

# Time: 100916 10:20:00

# User at Host: pipeline[pipeline] @ localhost []

# Query_time: 34.280024  Lock_time: 0.000166 Rows_sent: 0
Rows_examined: 13635392

SET timestamp=1284628800;

SELECT  pf.probe_feature_id, pf.seq_region_id, pf.seq_region_start,
pf.seq_region_end, pf.seq_region_strand, pf.probe_id, pf.analysis_id,
pf.mismatches, pf.cigar_line, p.name, p.probe_set_id

FROM  (probe_feature pf, probe p, array_chip ac) 

 WHERE  ac.array_id IN (56,52,54,55,53,58,57) and
ac.array_chip_id=p.array_chip_id  AND pf.seq_region_id = 581 AND
pf.seq_region_start <= 40750237 AND pf.seq_region_end >= 40747718 AND
pf.seq_region_start >= 39587282  AND

       pf.probe_id = p.probe_id 

 GROUP by pf.probe_feature_id  ORDER BY pf.seq_region_id,
pf.seq_region_start, pf.probe_feature_id;

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