File.php

<?php

// ...

class File
{
    /**
     * @Id
     * @GeneratedValue
     * @Column(type="bigint")
     *
     * @var int
     */
    private $id;

    /**
     * @ManyToMany(targetEntity="Tag")
     * @JoinTable(name="file_tags",
     *     joinColumns={@JoinColumn(name="file_id", referencedColumnName="id")},
     *     inverseJoinColumns={@JoinColumn(name="tag_id", referencedColumnName="id")}
     * )
     *
     * @var Collection
     */
    private $tags;
    
    //..
}

MyController.php

<?php

// ...

Class MyController
{
    public function myAction()
    {
        // ...
        $this->getDoctrine()
            ->getRepository('MyBundle:File')
            ->findByTags($tag);
            
        // Throws: Undefined index: joinColumns in vendor/doctrine/orm/lib/Doctrine/ORM/Persisters/BasicEntityPersister.php line 1495
    }
}

Tag.php

<?php

// ...
class Tag
{
    
    /**
     * @Id
     * @GeneratedValue
     * @Column(type="bigint")
     *
     * @var int
     */
    private $id;
    //..
}