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POSQL beginner - Why does my MySQL Join-query use no index / work so slow?
 

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  1. POSQL beginner - Why does my MySQL Join-query use no index / work so slow?
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    <p>I got the following problem with my MySQL 5.5 DB - i am pretty new to this so it might be very obvious whats wrong but i just cant seem to get it:</p> <p>Two tables:</p> <hr> <p>Table1</p> <pre><code>CREATE TABLE `sequence_matches` ( `Sample_ID` INT(6) NOT NULL, `Sequence_Match_ID` INT(8) NOT NULL, `Start` INT(6) NULL DEFAULT NULL, `End` INT(6) NULL DEFAULT NULL, `Coverage` DOUBLE(5,2) NULL DEFAULT NULL, `Frag_String` VARCHAR(255) NULL DEFAULT NULL, `rms_mass_error_prod` DOUBLE(10,4) NULL DEFAULT NULL, `rms_rt_error_prod` DOUBLE(10,4) NULL DEFAULT NULL, PRIMARY KEY (`Sample_ID`, `Sequence_Match_ID`) ) </code></pre> <hr> <p>and </p> <hr> <p>Table 2</p> <pre><code>CREATE TABLE `peptide_identifications` ( `Sample_ID` INT(6) NOT NULL, `Peptide_identification_ID` INT(8) NOT NULL, `Mass_error` DOUBLE(10,4) NULL DEFAULT NULL, `Mass_error_ppm` DOUBLE(10,4) NULL DEFAULT NULL, `Score` DOUBLE(10,4) NULL DEFAULT NULL, `Type` VARCHAR(45) NULL DEFAULT NULL, `global_pept_ID` INT(8) NOT NULL, PRIMARY KEY (`Sample_ID`, `Peptide_identification_ID`), INDEX `Index` (`global_pept_ID`) ) </code></pre> <hr> <p>each of them contains ~15 million rows. </p> <p>Now, i want all those rows from <code>Table2</code> where <code>global_pept_id = 27443</code> and then use the <code>peptide_identification_id</code> of those, to query all information from <code>Table1</code> where <code>peptide_identification_id = sequence_match_id</code>.</p> <p>I tried the following statement:</p> <pre><code>SELECT * from sequence_matches JOIN ( SELECT peptide_identification_id FROM peptide_identifications WHERE global_pept_id = 27443 ) as tmp_pept ON sequence_match_id = peptide_identification_id; </code></pre> <p>Here the Explain for that query:</p> <p><a href="https://i.stack.imgur.com/QV3ER.jpg" rel="nofollow noreferrer"><img src="https://i.stack.imgur.com/QV3ERm.jpg" alt="http://i.stack.imgur.com/QV3ER.jpg"></a> (click to enlarge)</p> <p>Now this query is very, very slow (i actually never finished it, stopepd it after ~10min) and i can imagine it's because there is no Index used for the second table although both ID's are primary key and thus they should be indexed right?</p> <p>The results for the inner select require ~3 sek and return ~3k rows if performed alone. So the i think the problem is making 3000 * 15mio compares cause every row is checked in Table2.</p> <p>But how do i fix this?</p> <p>any help appreciated -voiD</p>
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