Create index for multiple WHERE EXISTS subqueries
3
I have to find an efficient way to write a very specific query for an application that I'm developing.
The idea is the following: Find all the genetic markers for which there exists at least one plant line per species for which the genotype value is "1".
So I've got, say, 3 plant species: "species_1", "species_2" and "species_3".
I've got these tables: accessions (plant lines), markers (the genetic markers), genotypes (the genotype; one per marker, accession and dataset), datasets (to subdivide genotype values into datasets) and taxonomies (the plant species).
I've come up with this query:
SELECT
markers.*, 1 AS "species_1",
1 AS "species_2",
1 AS "species_3"
FROM
markers
LEFT JOIN genotypes g ON g.marker_id = markers.id
WHERE
g.dataset_id = 3
AND EXISTS (
SELECT
1
FROM
genotypes
LEFT JOIN accession ON genotypes.accession_id = accession.id
LEFT JOIN taxonomies ON taxonomies.id = accession.taxonomy_id
WHERE
genotypes.marker_id = markers.id
AND genotypes.a = 1
AND taxonomies.genus = "genus1"
AND taxonomies.species = "species1"
)
AND EXISTS (
SELECT
1
FROM
genotypes
LEFT JOIN accession ON genotypes.accession_id = accession.id
LEFT JOIN taxonomies ON taxonomies.id = accession.taxonomy_id
WHERE
genotypes.marker_id = markers.id
AND genotypes.a = 1
AND taxonomies.genus = "genus2"
AND taxonomies.species = "species2"
)
AND EXISTS (
SELECT
1
FROM
genotypes
LEFT JOIN accession ON genotypes.accession_id = accession.id
LEFT JOIN taxonomies ON taxonomies.id = accession.taxonomy_id
WHERE
genotypes.marker_id = markers.id
AND genotypes.a = 1
AND taxonomies.genus = "genus3"
AND taxonomies.species = "species3"
)
NOTE: If you're wondering about the SELECT 1 AS bits, this is only because I also run the query for 0 and NOT EXISTS. So this is only one example query.
It returns the correct result, but is quite slow on a genotypes table with roughtly 2 million rows.
I've had a look at EXPLAIN of the query and tried to generate indices so that each sub-query has an index to use. The index that did improve performance was on genotypes.marker_id, genotypes.dataset_id, genotypes.a.
However, the query takes around 7-8 seconds to return the result and I think it could run faster if only I can figure out which other index to use or how to restructure the query.
Does anyone have any suggestions as to how to improve performance?
EDIT:
CREATE TABLE `genotypes` (
`id` BIGINT (20) NOT NULL AUTO_INCREMENT,
`marker_id` INT (11) NOT NULL,
`dataset_id` INT (11) NOT NULL,
`accession_id` INT (11) NOT NULL,
`a` VARCHAR (3) DEFAULT NULL,
PRIMARY KEY (`id`),
KEY `marker_id` (`marker_id`) USING BTREE,
KEY `dataset_id` (`dataset_id`) USING BTREE,
KEY `accession_id` (`accession_id`) USING BTREE,
KEY `genotypes_marker_dataset_allele1` (
`marker_id`,
`dataset_id`,
`a`
) USING BTREE,
KEY `genotypes_marker_allele1` (`marker_id`, `a`) USING BTREE,
CONSTRAINT `genotypes_ibfk_1` FOREIGN KEY (`marker_id`) REFERENCES `markers` (`id`) ON DELETE CASCADE ON UPDATE CASCADE,
CONSTRAINT `genotypes_ibfk_2` FOREIGN KEY (`dataset_id`) REFERENCES `datasets` (`id`) ON DELETE CASCADE ON UPDATE CASCADE,
CONSTRAINT `genotypes_ibfk_3` FOREIGN KEY (`accession_id`) REFERENCES `accessions` (`id`) ON DELETE CASCADE ON UPDATE CASCADE
) ENGINE = INNODB AUTO_INCREMENT = 2007206 DEFAULT CHARSET = latin1
CREATE TABLE `markers` (
`id` INT (11) NOT NULL AUTO_INCREMENT,
`marker_name` VARCHAR (45) DEFAULT NULL,
PRIMARY KEY (`id`)
) ENGINE = INNODB AUTO_INCREMENT = 8665 DEFAULT CHARSET = latin1
CREATE TABLE `accessions` (
`id` INT (11) NOT NULL AUTO_INCREMENT,
`name` VARCHAR (255) NOT NULL,
`taxonomy_id` INT (11) DEFAULT NULL,
PRIMARY KEY (`id`),
KEY `taxonomy_id` (`taxonomy_id`) USING BTREE,
CONSTRAINT `accessions_ibfk_3` FOREIGN KEY (`taxonomy_id`) REFERENCES `taxonomies` (`id`) ON DELETE NO ACTION ON UPDATE CASCADE,
) ENGINE = INNODB AUTO_INCREMENT = 2304 DEFAULT CHARSET = latin1
CREATE TABLE `taxonomies` (
`id` INT (11) NOT NULL AUTO_INCREMENT,
`genus` VARCHAR (255) NOT NULL DEFAULT '',
`species` VARCHAR (255) NOT NULL DEFAULT '',
PRIMARY KEY (`id`),
KEY `taxonomies_genus` (`genus`) USING BTREE,
KEY `taxonomies_species` (`species`) USING BTREE,
KEY `taxonomies_genus_species` (`genus`, `species`) USING BTREE
) ENGINE = INNODB AUTO_INCREMENT = 103 DEFAULT CHARSET = latin1
id select_type table type possible_keys key key_len ref rows Extra
1 PRIMARY markers ALL PRIMARY 8803 Using where; Using temporary
1 PRIMARY g ref marker_id,dataset_id,genotypes_marker_dataset_allele1,genotypes_marker_allele1 genotypes_marker_dataset_allele1 8 markers.id,const 104 Using index; Distinct
6 DEPENDENT SUBQUERY taxonomies ref PRIMARY,taxonomies_genus,taxonomies_species,taxonomies_genus_species taxonomies_species 257 const 1 Using index condition; Using where
6 DEPENDENT SUBQUERY genotypes ref marker_id,accession_id,genotypes_marker_dataset_allele1,genotypes_marker_allele1 marker_id 4 markers.id 115 Using where
6 DEPENDENT SUBQUERY accessions eq_ref PRIMARY,taxonomy_id PRIMARY 4 genotypes.accession_id 1 Using where
5 DEPENDENT SUBQUERY taxonomies ref PRIMARY,taxonomies_genus,taxonomies_species,taxonomies_genus_species taxonomies_species 257 const 1 Using index condition; Using where
5 DEPENDENT SUBQUERY genotypes ref marker_id,accession_id,genotypes_marker_dataset_allele1,genotypes_marker_allele1 marker_id 4 markers.id 115 Using where
5 DEPENDENT SUBQUERY accessions eq_ref PRIMARY,taxonomy_id PRIMARY 4 genotypes.accession_id 1 Using where
4 DEPENDENT SUBQUERY taxonomies ref PRIMARY,taxonomies_genus,taxonomies_species,taxonomies_genus_species taxonomies_species 257 const 1 Using index condition; Using where
4 DEPENDENT SUBQUERY genotypes ref marker_id,accession_id,genotypes_marker_dataset_allele1,genotypes_marker_allele1 marker_id 4 markers.id 115 Using where
4 DEPENDENT SUBQUERY accessions eq_ref PRIMARY,taxonomy_id PRIMARY 4 genotypes.accession_id 1 Using where
3 DEPENDENT SUBQUERY taxonomies ref PRIMARY,taxonomies_genus,taxonomies_species,taxonomies_genus_species taxonomies_species 257 const 1 Using index condition; Using where
3 DEPENDENT SUBQUERY genotypes ref marker_id,accession_id,genotypes_marker_dataset_allele1,genotypes_marker_allele1 marker_id 4 markers.id 115 Using where
3 DEPENDENT SUBQUERY accessions eq_ref PRIMARY,taxonomy_id PRIMARY 4 genotypes.accession_id 1 Using where
2 DEPENDENT SUBQUERY taxonomies ref PRIMARY,taxonomies_genus,taxonomies_species,taxonomies_genus_species taxonomies_species 257 const 1 Using index condition; Using where
2 DEPENDENT SUBQUERY genotypes ref marker_id,accession_id,genotypes_marker_dataset_allele1,genotypes_marker_allele1 marker_id 4 markers.id 115 Using where
2 DEPENDENT SUBQUERY accessions eq_ref PRIMARY,taxonomy_id PRIMARY 4 genotypes.accession_id 1 Using where
mysql index query-performance subquery
asked Jun 8 '16 at 9:00
BazBaz
105119
bumped to the homepage by Community♦ 15 mins ago
This question has answers that may be good or bad; the system has marked it active so that they can be reviewed.
|
show 2 more comments
3
I have to find an efficient way to write a very specific query for an application that I'm developing.
The idea is the following: Find all the genetic markers for which there exists at least one plant line per species for which the genotype value is "1".
So I've got, say, 3 plant species: "species_1", "species_2" and "species_3".
I've got these tables: accessions (plant lines), markers (the genetic markers), genotypes (the genotype; one per marker, accession and dataset), datasets (to subdivide genotype values into datasets) and taxonomies (the plant species).
I've come up with this query:
SELECT
markers.*, 1 AS "species_1",
1 AS "species_2",
1 AS "species_3"
FROM
markers
LEFT JOIN genotypes g ON g.marker_id = markers.id
WHERE
g.dataset_id = 3
AND EXISTS (
SELECT
1
FROM
genotypes
LEFT JOIN accession ON genotypes.accession_id = accession.id
LEFT JOIN taxonomies ON taxonomies.id = accession.taxonomy_id
WHERE
genotypes.marker_id = markers.id
AND genotypes.a = 1
AND taxonomies.genus = "genus1"
AND taxonomies.species = "species1"
)
AND EXISTS (
SELECT
1
FROM
genotypes
LEFT JOIN accession ON genotypes.accession_id = accession.id
LEFT JOIN taxonomies ON taxonomies.id = accession.taxonomy_id
WHERE
genotypes.marker_id = markers.id
AND genotypes.a = 1
AND taxonomies.genus = "genus2"
AND taxonomies.species = "species2"
)
AND EXISTS (
SELECT
1
FROM
genotypes
LEFT JOIN accession ON genotypes.accession_id = accession.id
LEFT JOIN taxonomies ON taxonomies.id = accession.taxonomy_id
WHERE
genotypes.marker_id = markers.id
AND genotypes.a = 1
AND taxonomies.genus = "genus3"
AND taxonomies.species = "species3"
)
NOTE: If you're wondering about the SELECT 1 AS bits, this is only because I also run the query for 0 and NOT EXISTS. So this is only one example query.
It returns the correct result, but is quite slow on a genotypes table with roughtly 2 million rows.
I've had a look at EXPLAIN of the query and tried to generate indices so that each sub-query has an index to use. The index that did improve performance was on genotypes.marker_id, genotypes.dataset_id, genotypes.a.
However, the query takes around 7-8 seconds to return the result and I think it could run faster if only I can figure out which other index to use or how to restructure the query.
Does anyone have any suggestions as to how to improve performance?
EDIT:
CREATE TABLE `genotypes` (
`id` BIGINT (20) NOT NULL AUTO_INCREMENT,
`marker_id` INT (11) NOT NULL,
`dataset_id` INT (11) NOT NULL,
`accession_id` INT (11) NOT NULL,
`a` VARCHAR (3) DEFAULT NULL,
PRIMARY KEY (`id`),
KEY `marker_id` (`marker_id`) USING BTREE,
KEY `dataset_id` (`dataset_id`) USING BTREE,
KEY `accession_id` (`accession_id`) USING BTREE,
KEY `genotypes_marker_dataset_allele1` (
`marker_id`,
`dataset_id`,
`a`
) USING BTREE,
KEY `genotypes_marker_allele1` (`marker_id`, `a`) USING BTREE,
CONSTRAINT `genotypes_ibfk_1` FOREIGN KEY (`marker_id`) REFERENCES `markers` (`id`) ON DELETE CASCADE ON UPDATE CASCADE,
CONSTRAINT `genotypes_ibfk_2` FOREIGN KEY (`dataset_id`) REFERENCES `datasets` (`id`) ON DELETE CASCADE ON UPDATE CASCADE,
CONSTRAINT `genotypes_ibfk_3` FOREIGN KEY (`accession_id`) REFERENCES `accessions` (`id`) ON DELETE CASCADE ON UPDATE CASCADE
) ENGINE = INNODB AUTO_INCREMENT = 2007206 DEFAULT CHARSET = latin1
CREATE TABLE `markers` (
`id` INT (11) NOT NULL AUTO_INCREMENT,
`marker_name` VARCHAR (45) DEFAULT NULL,
PRIMARY KEY (`id`)
) ENGINE = INNODB AUTO_INCREMENT = 8665 DEFAULT CHARSET = latin1
CREATE TABLE `accessions` (
`id` INT (11) NOT NULL AUTO_INCREMENT,
`name` VARCHAR (255) NOT NULL,
`taxonomy_id` INT (11) DEFAULT NULL,
PRIMARY KEY (`id`),
KEY `taxonomy_id` (`taxonomy_id`) USING BTREE,
CONSTRAINT `accessions_ibfk_3` FOREIGN KEY (`taxonomy_id`) REFERENCES `taxonomies` (`id`) ON DELETE NO ACTION ON UPDATE CASCADE,
) ENGINE = INNODB AUTO_INCREMENT = 2304 DEFAULT CHARSET = latin1
CREATE TABLE `taxonomies` (
`id` INT (11) NOT NULL AUTO_INCREMENT,
`genus` VARCHAR (255) NOT NULL DEFAULT '',
`species` VARCHAR (255) NOT NULL DEFAULT '',
PRIMARY KEY (`id`),
KEY `taxonomies_genus` (`genus`) USING BTREE,
KEY `taxonomies_species` (`species`) USING BTREE,
KEY `taxonomies_genus_species` (`genus`, `species`) USING BTREE
) ENGINE = INNODB AUTO_INCREMENT = 103 DEFAULT CHARSET = latin1
id select_type table type possible_keys key key_len ref rows Extra
1 PRIMARY markers ALL PRIMARY 8803 Using where; Using temporary
1 PRIMARY g ref marker_id,dataset_id,genotypes_marker_dataset_allele1,genotypes_marker_allele1 genotypes_marker_dataset_allele1 8 markers.id,const 104 Using index; Distinct
6 DEPENDENT SUBQUERY taxonomies ref PRIMARY,taxonomies_genus,taxonomies_species,taxonomies_genus_species taxonomies_species 257 const 1 Using index condition; Using where
6 DEPENDENT SUBQUERY genotypes ref marker_id,accession_id,genotypes_marker_dataset_allele1,genotypes_marker_allele1 marker_id 4 markers.id 115 Using where
6 DEPENDENT SUBQUERY accessions eq_ref PRIMARY,taxonomy_id PRIMARY 4 genotypes.accession_id 1 Using where
5 DEPENDENT SUBQUERY taxonomies ref PRIMARY,taxonomies_genus,taxonomies_species,taxonomies_genus_species taxonomies_species 257 const 1 Using index condition; Using where
5 DEPENDENT SUBQUERY genotypes ref marker_id,accession_id,genotypes_marker_dataset_allele1,genotypes_marker_allele1 marker_id 4 markers.id 115 Using where
5 DEPENDENT SUBQUERY accessions eq_ref PRIMARY,taxonomy_id PRIMARY 4 genotypes.accession_id 1 Using where
4 DEPENDENT SUBQUERY taxonomies ref PRIMARY,taxonomies_genus,taxonomies_species,taxonomies_genus_species taxonomies_species 257 const 1 Using index condition; Using where
4 DEPENDENT SUBQUERY genotypes ref marker_id,accession_id,genotypes_marker_dataset_allele1,genotypes_marker_allele1 marker_id 4 markers.id 115 Using where
4 DEPENDENT SUBQUERY accessions eq_ref PRIMARY,taxonomy_id PRIMARY 4 genotypes.accession_id 1 Using where
3 DEPENDENT SUBQUERY taxonomies ref PRIMARY,taxonomies_genus,taxonomies_species,taxonomies_genus_species taxonomies_species 257 const 1 Using index condition; Using where
3 DEPENDENT SUBQUERY genotypes ref marker_id,accession_id,genotypes_marker_dataset_allele1,genotypes_marker_allele1 marker_id 4 markers.id 115 Using where
3 DEPENDENT SUBQUERY accessions eq_ref PRIMARY,taxonomy_id PRIMARY 4 genotypes.accession_id 1 Using where
2 DEPENDENT SUBQUERY taxonomies ref PRIMARY,taxonomies_genus,taxonomies_species,taxonomies_genus_species taxonomies_species 257 const 1 Using index condition; Using where
2 DEPENDENT SUBQUERY genotypes ref marker_id,accession_id,genotypes_marker_dataset_allele1,genotypes_marker_allele1 marker_id 4 markers.id 115 Using where
2 DEPENDENT SUBQUERY accessions eq_ref PRIMARY,taxonomy_id PRIMARY 4 genotypes.accession_id 1 Using where
mysql index query-performance subquery
asked Jun 8 '16 at 9:00
BazBaz
105119
bumped to the homepage by Community♦ 15 mins ago
This question has answers that may be good or bad; the system has marked it active so that they can be reviewed.
Show us the execution plan and theSHOW CREATE TABLE table_name;output for all the 4 tables.
– ypercubeᵀᴹ
Jun 8 '16 at 9:16
@ypercubeᵀᴹ I've added the create statements. What do you mean by execution plan?
– Baz
Jun 8 '16 at 9:29
The EXPLAIN output of the query.
– ypercubeᵀᴹ
Jun 8 '16 at 9:30
@ypercubeᵀᴹ Ok, I've added that as well.
– Baz
Jun 8 '16 at 10:13
2
I'd try an index on(a, marker_id, accession_id)and on(a, accession_id, marker_id). And since thatais a varchar, use string literals, not numbers:where a = '1'. If the stored values are only numbers, then convert it from varchar to an appropriate number type (tinyiny, smallint).
– ypercubeᵀᴹ
Jun 8 '16 at 10:31
|
show 2 more comments
3
3
3
I have to find an efficient way to write a very specific query for an application that I'm developing.
The idea is the following: Find all the genetic markers for which there exists at least one plant line per species for which the genotype value is "1".
So I've got, say, 3 plant species: "species_1", "species_2" and "species_3".
I've got these tables: accessions (plant lines), markers (the genetic markers), genotypes (the genotype; one per marker, accession and dataset), datasets (to subdivide genotype values into datasets) and taxonomies (the plant species).
I've come up with this query:
SELECT
markers.*, 1 AS "species_1",
1 AS "species_2",
1 AS "species_3"
FROM
markers
LEFT JOIN genotypes g ON g.marker_id = markers.id
WHERE
g.dataset_id = 3
AND EXISTS (
SELECT
1
FROM
genotypes
LEFT JOIN accession ON genotypes.accession_id = accession.id
LEFT JOIN taxonomies ON taxonomies.id = accession.taxonomy_id
WHERE
genotypes.marker_id = markers.id
AND genotypes.a = 1
AND taxonomies.genus = "genus1"
AND taxonomies.species = "species1"
)
AND EXISTS (
SELECT
1
FROM
genotypes
LEFT JOIN accession ON genotypes.accession_id = accession.id
LEFT JOIN taxonomies ON taxonomies.id = accession.taxonomy_id
WHERE
genotypes.marker_id = markers.id
AND genotypes.a = 1
AND taxonomies.genus = "genus2"
AND taxonomies.species = "species2"
)
AND EXISTS (
SELECT
1
FROM
genotypes
LEFT JOIN accession ON genotypes.accession_id = accession.id
LEFT JOIN taxonomies ON taxonomies.id = accession.taxonomy_id
WHERE
genotypes.marker_id = markers.id
AND genotypes.a = 1
AND taxonomies.genus = "genus3"
AND taxonomies.species = "species3"
)
NOTE: If you're wondering about the SELECT 1 AS bits, this is only because I also run the query for 0 and NOT EXISTS. So this is only one example query.
It returns the correct result, but is quite slow on a genotypes table with roughtly 2 million rows.
I've had a look at EXPLAIN of the query and tried to generate indices so that each sub-query has an index to use. The index that did improve performance was on genotypes.marker_id, genotypes.dataset_id, genotypes.a.
However, the query takes around 7-8 seconds to return the result and I think it could run faster if only I can figure out which other index to use or how to restructure the query.
Does anyone have any suggestions as to how to improve performance?
EDIT:
CREATE TABLE `genotypes` (
`id` BIGINT (20) NOT NULL AUTO_INCREMENT,
`marker_id` INT (11) NOT NULL,
`dataset_id` INT (11) NOT NULL,
`accession_id` INT (11) NOT NULL,
`a` VARCHAR (3) DEFAULT NULL,
PRIMARY KEY (`id`),
KEY `marker_id` (`marker_id`) USING BTREE,
KEY `dataset_id` (`dataset_id`) USING BTREE,
KEY `accession_id` (`accession_id`) USING BTREE,
KEY `genotypes_marker_dataset_allele1` (
`marker_id`,
`dataset_id`,
`a`
) USING BTREE,
KEY `genotypes_marker_allele1` (`marker_id`, `a`) USING BTREE,
CONSTRAINT `genotypes_ibfk_1` FOREIGN KEY (`marker_id`) REFERENCES `markers` (`id`) ON DELETE CASCADE ON UPDATE CASCADE,
CONSTRAINT `genotypes_ibfk_2` FOREIGN KEY (`dataset_id`) REFERENCES `datasets` (`id`) ON DELETE CASCADE ON UPDATE CASCADE,
CONSTRAINT `genotypes_ibfk_3` FOREIGN KEY (`accession_id`) REFERENCES `accessions` (`id`) ON DELETE CASCADE ON UPDATE CASCADE
) ENGINE = INNODB AUTO_INCREMENT = 2007206 DEFAULT CHARSET = latin1
CREATE TABLE `markers` (
`id` INT (11) NOT NULL AUTO_INCREMENT,
`marker_name` VARCHAR (45) DEFAULT NULL,
PRIMARY KEY (`id`)
) ENGINE = INNODB AUTO_INCREMENT = 8665 DEFAULT CHARSET = latin1
CREATE TABLE `accessions` (
`id` INT (11) NOT NULL AUTO_INCREMENT,
`name` VARCHAR (255) NOT NULL,
`taxonomy_id` INT (11) DEFAULT NULL,
PRIMARY KEY (`id`),
KEY `taxonomy_id` (`taxonomy_id`) USING BTREE,
CONSTRAINT `accessions_ibfk_3` FOREIGN KEY (`taxonomy_id`) REFERENCES `taxonomies` (`id`) ON DELETE NO ACTION ON UPDATE CASCADE,
) ENGINE = INNODB AUTO_INCREMENT = 2304 DEFAULT CHARSET = latin1
CREATE TABLE `taxonomies` (
`id` INT (11) NOT NULL AUTO_INCREMENT,
`genus` VARCHAR (255) NOT NULL DEFAULT '',
`species` VARCHAR (255) NOT NULL DEFAULT '',
PRIMARY KEY (`id`),
KEY `taxonomies_genus` (`genus`) USING BTREE,
KEY `taxonomies_species` (`species`) USING BTREE,
KEY `taxonomies_genus_species` (`genus`, `species`) USING BTREE
) ENGINE = INNODB AUTO_INCREMENT = 103 DEFAULT CHARSET = latin1
id select_type table type possible_keys key key_len ref rows Extra
1 PRIMARY markers ALL PRIMARY 8803 Using where; Using temporary
1 PRIMARY g ref marker_id,dataset_id,genotypes_marker_dataset_allele1,genotypes_marker_allele1 genotypes_marker_dataset_allele1 8 markers.id,const 104 Using index; Distinct
6 DEPENDENT SUBQUERY taxonomies ref PRIMARY,taxonomies_genus,taxonomies_species,taxonomies_genus_species taxonomies_species 257 const 1 Using index condition; Using where
6 DEPENDENT SUBQUERY genotypes ref marker_id,accession_id,genotypes_marker_dataset_allele1,genotypes_marker_allele1 marker_id 4 markers.id 115 Using where
6 DEPENDENT SUBQUERY accessions eq_ref PRIMARY,taxonomy_id PRIMARY 4 genotypes.accession_id 1 Using where
5 DEPENDENT SUBQUERY taxonomies ref PRIMARY,taxonomies_genus,taxonomies_species,taxonomies_genus_species taxonomies_species 257 const 1 Using index condition; Using where
5 DEPENDENT SUBQUERY genotypes ref marker_id,accession_id,genotypes_marker_dataset_allele1,genotypes_marker_allele1 marker_id 4 markers.id 115 Using where
5 DEPENDENT SUBQUERY accessions eq_ref PRIMARY,taxonomy_id PRIMARY 4 genotypes.accession_id 1 Using where
4 DEPENDENT SUBQUERY taxonomies ref PRIMARY,taxonomies_genus,taxonomies_species,taxonomies_genus_species taxonomies_species 257 const 1 Using index condition; Using where
4 DEPENDENT SUBQUERY genotypes ref marker_id,accession_id,genotypes_marker_dataset_allele1,genotypes_marker_allele1 marker_id 4 markers.id 115 Using where
4 DEPENDENT SUBQUERY accessions eq_ref PRIMARY,taxonomy_id PRIMARY 4 genotypes.accession_id 1 Using where
3 DEPENDENT SUBQUERY taxonomies ref PRIMARY,taxonomies_genus,taxonomies_species,taxonomies_genus_species taxonomies_species 257 const 1 Using index condition; Using where
3 DEPENDENT SUBQUERY genotypes ref marker_id,accession_id,genotypes_marker_dataset_allele1,genotypes_marker_allele1 marker_id 4 markers.id 115 Using where
3 DEPENDENT SUBQUERY accessions eq_ref PRIMARY,taxonomy_id PRIMARY 4 genotypes.accession_id 1 Using where
2 DEPENDENT SUBQUERY taxonomies ref PRIMARY,taxonomies_genus,taxonomies_species,taxonomies_genus_species taxonomies_species 257 const 1 Using index condition; Using where
2 DEPENDENT SUBQUERY genotypes ref marker_id,accession_id,genotypes_marker_dataset_allele1,genotypes_marker_allele1 marker_id 4 markers.id 115 Using where
2 DEPENDENT SUBQUERY accessions eq_ref PRIMARY,taxonomy_id PRIMARY 4 genotypes.accession_id 1 Using where
mysql index query-performance subquery
asked Jun 8 '16 at 9:00
BazBaz
105119
I have to find an efficient way to write a very specific query for an application that I'm developing.
The idea is the following: Find all the genetic markers for which there exists at least one plant line per species for which the genotype value is "1".
So I've got, say, 3 plant species: "species_1", "species_2" and "species_3".
I've got these tables: accessions (plant lines), markers (the genetic markers), genotypes (the genotype; one per marker, accession and dataset), datasets (to subdivide genotype values into datasets) and taxonomies (the plant species).
I've come up with this query:
SELECT
markers.*, 1 AS "species_1",
1 AS "species_2",
1 AS "species_3"
FROM
markers
LEFT JOIN genotypes g ON g.marker_id = markers.id
WHERE
g.dataset_id = 3
AND EXISTS (
SELECT
1
FROM
genotypes
LEFT JOIN accession ON genotypes.accession_id = accession.id
LEFT JOIN taxonomies ON taxonomies.id = accession.taxonomy_id
WHERE
genotypes.marker_id = markers.id
AND genotypes.a = 1
AND taxonomies.genus = "genus1"
AND taxonomies.species = "species1"
)
AND EXISTS (
SELECT
1
FROM
genotypes
LEFT JOIN accession ON genotypes.accession_id = accession.id
LEFT JOIN taxonomies ON taxonomies.id = accession.taxonomy_id
WHERE
genotypes.marker_id = markers.id
AND genotypes.a = 1
AND taxonomies.genus = "genus2"
AND taxonomies.species = "species2"
)
AND EXISTS (
SELECT
1
FROM
genotypes
LEFT JOIN accession ON genotypes.accession_id = accession.id
LEFT JOIN taxonomies ON taxonomies.id = accession.taxonomy_id
WHERE
genotypes.marker_id = markers.id
AND genotypes.a = 1
AND taxonomies.genus = "genus3"
AND taxonomies.species = "species3"
)
NOTE: If you're wondering about the SELECT 1 AS bits, this is only because I also run the query for 0 and NOT EXISTS. So this is only one example query.
It returns the correct result, but is quite slow on a genotypes table with roughtly 2 million rows.
I've had a look at EXPLAIN of the query and tried to generate indices so that each sub-query has an index to use. The index that did improve performance was on genotypes.marker_id, genotypes.dataset_id, genotypes.a.
However, the query takes around 7-8 seconds to return the result and I think it could run faster if only I can figure out which other index to use or how to restructure the query.
Does anyone have any suggestions as to how to improve performance?
EDIT:
CREATE TABLE `genotypes` (
`id` BIGINT (20) NOT NULL AUTO_INCREMENT,
`marker_id` INT (11) NOT NULL,
`dataset_id` INT (11) NOT NULL,
`accession_id` INT (11) NOT NULL,
`a` VARCHAR (3) DEFAULT NULL,
PRIMARY KEY (`id`),
KEY `marker_id` (`marker_id`) USING BTREE,
KEY `dataset_id` (`dataset_id`) USING BTREE,
KEY `accession_id` (`accession_id`) USING BTREE,
KEY `genotypes_marker_dataset_allele1` (
`marker_id`,
`dataset_id`,
`a`
) USING BTREE,
KEY `genotypes_marker_allele1` (`marker_id`, `a`) USING BTREE,
CONSTRAINT `genotypes_ibfk_1` FOREIGN KEY (`marker_id`) REFERENCES `markers` (`id`) ON DELETE CASCADE ON UPDATE CASCADE,
CONSTRAINT `genotypes_ibfk_2` FOREIGN KEY (`dataset_id`) REFERENCES `datasets` (`id`) ON DELETE CASCADE ON UPDATE CASCADE,
CONSTRAINT `genotypes_ibfk_3` FOREIGN KEY (`accession_id`) REFERENCES `accessions` (`id`) ON DELETE CASCADE ON UPDATE CASCADE
) ENGINE = INNODB AUTO_INCREMENT = 2007206 DEFAULT CHARSET = latin1
CREATE TABLE `markers` (
`id` INT (11) NOT NULL AUTO_INCREMENT,
`marker_name` VARCHAR (45) DEFAULT NULL,
PRIMARY KEY (`id`)
) ENGINE = INNODB AUTO_INCREMENT = 8665 DEFAULT CHARSET = latin1
CREATE TABLE `accessions` (
`id` INT (11) NOT NULL AUTO_INCREMENT,
`name` VARCHAR (255) NOT NULL,
`taxonomy_id` INT (11) DEFAULT NULL,
PRIMARY KEY (`id`),
KEY `taxonomy_id` (`taxonomy_id`) USING BTREE,
CONSTRAINT `accessions_ibfk_3` FOREIGN KEY (`taxonomy_id`) REFERENCES `taxonomies` (`id`) ON DELETE NO ACTION ON UPDATE CASCADE,
) ENGINE = INNODB AUTO_INCREMENT = 2304 DEFAULT CHARSET = latin1
CREATE TABLE `taxonomies` (
`id` INT (11) NOT NULL AUTO_INCREMENT,
`genus` VARCHAR (255) NOT NULL DEFAULT '',
`species` VARCHAR (255) NOT NULL DEFAULT '',
PRIMARY KEY (`id`),
KEY `taxonomies_genus` (`genus`) USING BTREE,
KEY `taxonomies_species` (`species`) USING BTREE,
KEY `taxonomies_genus_species` (`genus`, `species`) USING BTREE
) ENGINE = INNODB AUTO_INCREMENT = 103 DEFAULT CHARSET = latin1
id select_type table type possible_keys key key_len ref rows Extra
1 PRIMARY markers ALL PRIMARY 8803 Using where; Using temporary
1 PRIMARY g ref marker_id,dataset_id,genotypes_marker_dataset_allele1,genotypes_marker_allele1 genotypes_marker_dataset_allele1 8 markers.id,const 104 Using index; Distinct
6 DEPENDENT SUBQUERY taxonomies ref PRIMARY,taxonomies_genus,taxonomies_species,taxonomies_genus_species taxonomies_species 257 const 1 Using index condition; Using where
6 DEPENDENT SUBQUERY genotypes ref marker_id,accession_id,genotypes_marker_dataset_allele1,genotypes_marker_allele1 marker_id 4 markers.id 115 Using where
6 DEPENDENT SUBQUERY accessions eq_ref PRIMARY,taxonomy_id PRIMARY 4 genotypes.accession_id 1 Using where
5 DEPENDENT SUBQUERY taxonomies ref PRIMARY,taxonomies_genus,taxonomies_species,taxonomies_genus_species taxonomies_species 257 const 1 Using index condition; Using where
5 DEPENDENT SUBQUERY genotypes ref marker_id,accession_id,genotypes_marker_dataset_allele1,genotypes_marker_allele1 marker_id 4 markers.id 115 Using where
5 DEPENDENT SUBQUERY accessions eq_ref PRIMARY,taxonomy_id PRIMARY 4 genotypes.accession_id 1 Using where
4 DEPENDENT SUBQUERY taxonomies ref PRIMARY,taxonomies_genus,taxonomies_species,taxonomies_genus_species taxonomies_species 257 const 1 Using index condition; Using where
4 DEPENDENT SUBQUERY genotypes ref marker_id,accession_id,genotypes_marker_dataset_allele1,genotypes_marker_allele1 marker_id 4 markers.id 115 Using where
4 DEPENDENT SUBQUERY accessions eq_ref PRIMARY,taxonomy_id PRIMARY 4 genotypes.accession_id 1 Using where
3 DEPENDENT SUBQUERY taxonomies ref PRIMARY,taxonomies_genus,taxonomies_species,taxonomies_genus_species taxonomies_species 257 const 1 Using index condition; Using where
3 DEPENDENT SUBQUERY genotypes ref marker_id,accession_id,genotypes_marker_dataset_allele1,genotypes_marker_allele1 marker_id 4 markers.id 115 Using where
3 DEPENDENT SUBQUERY accessions eq_ref PRIMARY,taxonomy_id PRIMARY 4 genotypes.accession_id 1 Using where
2 DEPENDENT SUBQUERY taxonomies ref PRIMARY,taxonomies_genus,taxonomies_species,taxonomies_genus_species taxonomies_species 257 const 1 Using index condition; Using where
2 DEPENDENT SUBQUERY genotypes ref marker_id,accession_id,genotypes_marker_dataset_allele1,genotypes_marker_allele1 marker_id 4 markers.id 115 Using where
2 DEPENDENT SUBQUERY accessions eq_ref PRIMARY,taxonomy_id PRIMARY 4 genotypes.accession_id 1 Using where
mysql index query-performance subquery
mysql index query-performance subquery
asked Jun 8 '16 at 9:00
BazBaz
105119
asked Jun 8 '16 at 9:00
BazBaz
105119
edited Jun 8 '16 at 10:13
Baz
asked Jun 8 '16 at 9:00
BazBaz
105119
asked Jun 8 '16 at 9:00
BazBaz
105119
asked Jun 8 '16 at 9:00
BazBaz
105119
105119
bumped to the homepage by Community♦ 15 mins ago
This question has answers that may be good or bad; the system has marked it active so that they can be reviewed.
bumped to the homepage by Community♦ 15 mins ago
This question has answers that may be good or bad; the system has marked it active so that they can be reviewed.
Show us the execution plan and theSHOW CREATE TABLE table_name;output for all the 4 tables.
– ypercubeᵀᴹ
Jun 8 '16 at 9:16
@ypercubeᵀᴹ I've added the create statements. What do you mean by execution plan?
– Baz
Jun 8 '16 at 9:29
The EXPLAIN output of the query.
– ypercubeᵀᴹ
Jun 8 '16 at 9:30
@ypercubeᵀᴹ Ok, I've added that as well.
– Baz
Jun 8 '16 at 10:13
2
I'd try an index on(a, marker_id, accession_id)and on(a, accession_id, marker_id). And since thatais a varchar, use string literals, not numbers:where a = '1'. If the stored values are only numbers, then convert it from varchar to an appropriate number type (tinyiny, smallint).
– ypercubeᵀᴹ
Jun 8 '16 at 10:31
|
show 2 more comments
Show us the execution plan and theSHOW CREATE TABLE table_name;output for all the 4 tables.
– ypercubeᵀᴹ
Jun 8 '16 at 9:16
@ypercubeᵀᴹ I've added the create statements. What do you mean by execution plan?
– Baz
Jun 8 '16 at 9:29
The EXPLAIN output of the query.
– ypercubeᵀᴹ
Jun 8 '16 at 9:30
@ypercubeᵀᴹ Ok, I've added that as well.
– Baz
Jun 8 '16 at 10:13
2
I'd try an index on(a, marker_id, accession_id)and on(a, accession_id, marker_id). And since thatais a varchar, use string literals, not numbers:where a = '1'. If the stored values are only numbers, then convert it from varchar to an appropriate number type (tinyiny, smallint).
– ypercubeᵀᴹ
Jun 8 '16 at 10:31
Show us the execution plan and the
SHOW CREATE TABLE table_name; output for all the 4 tables.– ypercubeᵀᴹ
Jun 8 '16 at 9:16
Show us the execution plan and the
SHOW CREATE TABLE table_name; output for all the 4 tables.– ypercubeᵀᴹ
Jun 8 '16 at 9:16
@ypercubeᵀᴹ I've added the create statements. What do you mean by execution plan?
– Baz
Jun 8 '16 at 9:29
@ypercubeᵀᴹ I've added the create statements. What do you mean by execution plan?
– Baz
Jun 8 '16 at 9:29
The EXPLAIN output of the query.
– ypercubeᵀᴹ
Jun 8 '16 at 9:30
The EXPLAIN output of the query.
– ypercubeᵀᴹ
Jun 8 '16 at 9:30
@ypercubeᵀᴹ Ok, I've added that as well.
– Baz
Jun 8 '16 at 10:13
@ypercubeᵀᴹ Ok, I've added that as well.
– Baz
Jun 8 '16 at 10:13
2
2
I'd try an index on
(a, marker_id, accession_id) and on (a, accession_id, marker_id). And since that a is a varchar, use string literals, not numbers: where a = '1'. If the stored values are only numbers, then convert it from varchar to an appropriate number type (tinyiny, smallint).– ypercubeᵀᴹ
Jun 8 '16 at 10:31
I'd try an index on
(a, marker_id, accession_id) and on (a, accession_id, marker_id). And since that a is a varchar, use string literals, not numbers: where a = '1'. If the stored values are only numbers, then convert it from varchar to an appropriate number type (tinyiny, smallint).– ypercubeᵀᴹ
Jun 8 '16 at 10:31
|
show 2 more comments
1 Answer
1
active
oldest
votes
0
g.dataset_id = 3 is killing the left
try this
FROM markers
JOIN genotypes g
ON g.marker_id = markers.id
AND g.dataset_id = 3
The where is killing the left joins in the exists so you can drop that
This may give you better performance
and exists
( SELECT 1
FROM genotypes
join accession
ON genotypes.accession_id = accession.id
AND genotypes.a = 1
AND genotypes.marker_id = markers.id
join taxonomies
ON taxonomies.id = accession.taxonomy_id
AND taxonomies.genus = "genus1"
AND taxonomies.species = "species1"
)
and exists
( SELECT 1
FROM genotypes
join accession
ON genotypes.accession_id = accession.id
AND genotypes.a = 1
AND genotypes.marker_id = markers.id
join taxonomies
ON taxonomies.id = accession.taxonomy_id
AND taxonomies.genus = "genus2"
AND taxonomies.species = "species2"
)
and exists
( SELECT 1
FROM genotypes
join accession
ON genotypes.accession_id = accession.id
AND genotypes.a = 1
AND genotypes.marker_id = markers.id
join taxonomies
ON taxonomies.id = accession.taxonomy_id
AND taxonomies.genus = "genus3"
AND taxonomies.species = "species3"
)
ypercube is correct you cannot combine all 3
This would mean that had to be equal on the same accession.taxonomy_id
SELECT 1
FROM genotypes
join accession
ON genotypes.accession_id = accession.id
AND genotypes.a = 1
AND genotypes.marker_id = markers.id
join taxonomies as t1
ON t1.id = accession.taxonomy_id
AND t1.genus = "genus1"
AND t1.species = "species1"
join taxonomies as t2
ON t2.id = accession.taxonomy_id
AND t2.genus = "genus2"
AND t2.species = "species2"
join taxonomies as t3
ON t3.id = accession.taxonomy_id
AND t3.genus = "genus3"
AND t3.species = "species3"
answered Jun 8 '16 at 10:38
paparazzopaparazzo
4,6141230
@ypercubeᵀᴹ what is different?
– paparazzo
Jun 8 '16 at 10:41
@ypercubeᵀᴹ I will take another look at it
– paparazzo
Jun 8 '16 at 11:01
add a comment |
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1 Answer
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1 Answer
1
active
oldest
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active
oldest
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active
oldest
votes
0
g.dataset_id = 3 is killing the left
try this
FROM markers
JOIN genotypes g
ON g.marker_id = markers.id
AND g.dataset_id = 3
The where is killing the left joins in the exists so you can drop that
This may give you better performance
and exists
( SELECT 1
FROM genotypes
join accession
ON genotypes.accession_id = accession.id
AND genotypes.a = 1
AND genotypes.marker_id = markers.id
join taxonomies
ON taxonomies.id = accession.taxonomy_id
AND taxonomies.genus = "genus1"
AND taxonomies.species = "species1"
)
and exists
( SELECT 1
FROM genotypes
join accession
ON genotypes.accession_id = accession.id
AND genotypes.a = 1
AND genotypes.marker_id = markers.id
join taxonomies
ON taxonomies.id = accession.taxonomy_id
AND taxonomies.genus = "genus2"
AND taxonomies.species = "species2"
)
and exists
( SELECT 1
FROM genotypes
join accession
ON genotypes.accession_id = accession.id
AND genotypes.a = 1
AND genotypes.marker_id = markers.id
join taxonomies
ON taxonomies.id = accession.taxonomy_id
AND taxonomies.genus = "genus3"
AND taxonomies.species = "species3"
)
ypercube is correct you cannot combine all 3
This would mean that had to be equal on the same accession.taxonomy_id
SELECT 1
FROM genotypes
join accession
ON genotypes.accession_id = accession.id
AND genotypes.a = 1
AND genotypes.marker_id = markers.id
join taxonomies as t1
ON t1.id = accession.taxonomy_id
AND t1.genus = "genus1"
AND t1.species = "species1"
join taxonomies as t2
ON t2.id = accession.taxonomy_id
AND t2.genus = "genus2"
AND t2.species = "species2"
join taxonomies as t3
ON t3.id = accession.taxonomy_id
AND t3.genus = "genus3"
AND t3.species = "species3"
answered Jun 8 '16 at 10:38
paparazzopaparazzo
4,6141230
@ypercubeᵀᴹ what is different?
– paparazzo
Jun 8 '16 at 10:41
@ypercubeᵀᴹ I will take another look at it
– paparazzo
Jun 8 '16 at 11:01
add a comment |
0
g.dataset_id = 3 is killing the left
try this
FROM markers
JOIN genotypes g
ON g.marker_id = markers.id
AND g.dataset_id = 3
The where is killing the left joins in the exists so you can drop that
This may give you better performance
and exists
( SELECT 1
FROM genotypes
join accession
ON genotypes.accession_id = accession.id
AND genotypes.a = 1
AND genotypes.marker_id = markers.id
join taxonomies
ON taxonomies.id = accession.taxonomy_id
AND taxonomies.genus = "genus1"
AND taxonomies.species = "species1"
)
and exists
( SELECT 1
FROM genotypes
join accession
ON genotypes.accession_id = accession.id
AND genotypes.a = 1
AND genotypes.marker_id = markers.id
join taxonomies
ON taxonomies.id = accession.taxonomy_id
AND taxonomies.genus = "genus2"
AND taxonomies.species = "species2"
)
and exists
( SELECT 1
FROM genotypes
join accession
ON genotypes.accession_id = accession.id
AND genotypes.a = 1
AND genotypes.marker_id = markers.id
join taxonomies
ON taxonomies.id = accession.taxonomy_id
AND taxonomies.genus = "genus3"
AND taxonomies.species = "species3"
)
ypercube is correct you cannot combine all 3
This would mean that had to be equal on the same accession.taxonomy_id
SELECT 1
FROM genotypes
join accession
ON genotypes.accession_id = accession.id
AND genotypes.a = 1
AND genotypes.marker_id = markers.id
join taxonomies as t1
ON t1.id = accession.taxonomy_id
AND t1.genus = "genus1"
AND t1.species = "species1"
join taxonomies as t2
ON t2.id = accession.taxonomy_id
AND t2.genus = "genus2"
AND t2.species = "species2"
join taxonomies as t3
ON t3.id = accession.taxonomy_id
AND t3.genus = "genus3"
AND t3.species = "species3"
answered Jun 8 '16 at 10:38
paparazzopaparazzo
4,6141230
@ypercubeᵀᴹ what is different?
– paparazzo
Jun 8 '16 at 10:41
@ypercubeᵀᴹ I will take another look at it
– paparazzo
Jun 8 '16 at 11:01
add a comment |
0
0
0
g.dataset_id = 3 is killing the left
try this
FROM markers
JOIN genotypes g
ON g.marker_id = markers.id
AND g.dataset_id = 3
The where is killing the left joins in the exists so you can drop that
This may give you better performance
and exists
( SELECT 1
FROM genotypes
join accession
ON genotypes.accession_id = accession.id
AND genotypes.a = 1
AND genotypes.marker_id = markers.id
join taxonomies
ON taxonomies.id = accession.taxonomy_id
AND taxonomies.genus = "genus1"
AND taxonomies.species = "species1"
)
and exists
( SELECT 1
FROM genotypes
join accession
ON genotypes.accession_id = accession.id
AND genotypes.a = 1
AND genotypes.marker_id = markers.id
join taxonomies
ON taxonomies.id = accession.taxonomy_id
AND taxonomies.genus = "genus2"
AND taxonomies.species = "species2"
)
and exists
( SELECT 1
FROM genotypes
join accession
ON genotypes.accession_id = accession.id
AND genotypes.a = 1
AND genotypes.marker_id = markers.id
join taxonomies
ON taxonomies.id = accession.taxonomy_id
AND taxonomies.genus = "genus3"
AND taxonomies.species = "species3"
)
ypercube is correct you cannot combine all 3
This would mean that had to be equal on the same accession.taxonomy_id
SELECT 1
FROM genotypes
join accession
ON genotypes.accession_id = accession.id
AND genotypes.a = 1
AND genotypes.marker_id = markers.id
join taxonomies as t1
ON t1.id = accession.taxonomy_id
AND t1.genus = "genus1"
AND t1.species = "species1"
join taxonomies as t2
ON t2.id = accession.taxonomy_id
AND t2.genus = "genus2"
AND t2.species = "species2"
join taxonomies as t3
ON t3.id = accession.taxonomy_id
AND t3.genus = "genus3"
AND t3.species = "species3"
answered Jun 8 '16 at 10:38
paparazzopaparazzo
4,6141230
g.dataset_id = 3 is killing the left
try this
FROM markers
JOIN genotypes g
ON g.marker_id = markers.id
AND g.dataset_id = 3
The where is killing the left joins in the exists so you can drop that
This may give you better performance
and exists
( SELECT 1
FROM genotypes
join accession
ON genotypes.accession_id = accession.id
AND genotypes.a = 1
AND genotypes.marker_id = markers.id
join taxonomies
ON taxonomies.id = accession.taxonomy_id
AND taxonomies.genus = "genus1"
AND taxonomies.species = "species1"
)
and exists
( SELECT 1
FROM genotypes
join accession
ON genotypes.accession_id = accession.id
AND genotypes.a = 1
AND genotypes.marker_id = markers.id
join taxonomies
ON taxonomies.id = accession.taxonomy_id
AND taxonomies.genus = "genus2"
AND taxonomies.species = "species2"
)
and exists
( SELECT 1
FROM genotypes
join accession
ON genotypes.accession_id = accession.id
AND genotypes.a = 1
AND genotypes.marker_id = markers.id
join taxonomies
ON taxonomies.id = accession.taxonomy_id
AND taxonomies.genus = "genus3"
AND taxonomies.species = "species3"
)
ypercube is correct you cannot combine all 3
This would mean that had to be equal on the same accession.taxonomy_id
SELECT 1
FROM genotypes
join accession
ON genotypes.accession_id = accession.id
AND genotypes.a = 1
AND genotypes.marker_id = markers.id
join taxonomies as t1
ON t1.id = accession.taxonomy_id
AND t1.genus = "genus1"
AND t1.species = "species1"
join taxonomies as t2
ON t2.id = accession.taxonomy_id
AND t2.genus = "genus2"
AND t2.species = "species2"
join taxonomies as t3
ON t3.id = accession.taxonomy_id
AND t3.genus = "genus3"
AND t3.species = "species3"
answered Jun 8 '16 at 10:38
paparazzopaparazzo
4,6141230
edited Jun 8 '16 at 12:27
answered Jun 8 '16 at 10:38
paparazzopaparazzo
4,6141230
answered Jun 8 '16 at 10:38
paparazzopaparazzo
4,6141230
answered Jun 8 '16 at 10:38
paparazzopaparazzo
4,6141230
4,6141230
@ypercubeᵀᴹ what is different?
– paparazzo
Jun 8 '16 at 10:41
@ypercubeᵀᴹ I will take another look at it
– paparazzo
Jun 8 '16 at 11:01
add a comment |
@ypercubeᵀᴹ what is different?
– paparazzo
Jun 8 '16 at 10:41
@ypercubeᵀᴹ I will take another look at it
– paparazzo
Jun 8 '16 at 11:01
@ypercubeᵀᴹ what is different?
– paparazzo
Jun 8 '16 at 10:41
@ypercubeᵀᴹ what is different?
– paparazzo
Jun 8 '16 at 10:41
@ypercubeᵀᴹ I will take another look at it
– paparazzo
Jun 8 '16 at 11:01
@ypercubeᵀᴹ I will take another look at it
– paparazzo
Jun 8 '16 at 11:01
add a comment |
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Show us the execution plan and the
SHOW CREATE TABLE table_name;output for all the 4 tables.– ypercubeᵀᴹ
Jun 8 '16 at 9:16
@ypercubeᵀᴹ I've added the create statements. What do you mean by execution plan?
– Baz
Jun 8 '16 at 9:29
The EXPLAIN output of the query.
– ypercubeᵀᴹ
Jun 8 '16 at 9:30
@ypercubeᵀᴹ Ok, I've added that as well.
– Baz
Jun 8 '16 at 10:13
2
I'd try an index on
(a, marker_id, accession_id)and on(a, accession_id, marker_id). And since thatais a varchar, use string literals, not numbers:where a = '1'. If the stored values are only numbers, then convert it from varchar to an appropriate number type (tinyiny, smallint).– ypercubeᵀᴹ
Jun 8 '16 at 10:31