On Oct 30, 2011, at 3:10 , vladimir mashanov wrote: > The input file: > @HWUSI-EAS1676_0036_FC:6:1:10274:1044#0/1 And there lies your problem: the full name of the read is HWUSI-EAS1676_0036_FC:6:1:10274:1044#0/1 whereas in your name file you had: HWUSI-EAS1676_0036_FC:6:1:10274:1044#0 Note the missing /1 (and probably also /2) in the read names of your name file. B. -- You have received this mail because you are subscribed to the mira_talk mailing list. For information on how to subscribe or unsubscribe, please visit http://www.chevreux.org/mira_mailinglists.html