$re = '/((?=\w+)[\w|-]+.fa)/m';
$str = 'chr5fa 153584000fa 15359999fas9 D160||||73_orphan_reads|||.fa;709[F18|R11] unkn 1 unkn 2509
chr7 153764000 153775999 D16073_orphan_reads.fa;710[F9fa|R21fa],14892_orphan_reads.fa;229[F19|R16] unkn 1 unkn 2510
chr3 127848000 127871999 B15971_orphan_reads.fa;172[F35|R6],D16157-14_orphan_reads.fa;183[F6|R13],14892_orphan_reads.fa;229[F19|R16],USP19283_orphan_reads.fa;336[F10|R6],D15927-14_orphan_reads.fa;176[F11|R10],1007,1007 46 1007 1658
(...)';
preg_match_all($re, $str, $matches, PREG_SET_ORDER, 0);
// Print the entire match result
var_dump($matches);
Please keep in mind that these code samples are automatically generated and are not guaranteed to work. If you find any syntax errors, feel free to submit a bug report. For a full regex reference for PHP, please visit: http://php.net/manual/en/ref.pcre.php