Hi Bastien, I just got this error message: A file named 'addReaderror_REPLAY_do_not_delete.log' has been written to the working directory. Please send it to the author to get that bug fixed! Internal logic/programming/debugging error (*sigh* this should not have happened). Please file a bug report on http://sourceforge.net/apps/trac/mira-assembler/ "WARNING/ERROR: contig did not put refid into affected reads. Please file a bug report to https://sourceforge.net/apps/trac/mira-assembler/ and please send a mail to mira_talk@xxxxxxxxxxxxx " ->Thrown: void Contig::addRead(vector<Align> & aligncache, const AlignedDualSeqFacts * initialadsf, int32 refid, int32 newid, int32 direction_frnid, errorstatus_t & errstat) ->Caught: void Contig::addRead(vector<Align> & aligncache, const AlignedDualSeqFacts * initialadsf, int32 refid, int32 newid, int32 direction_frnid, errorstatus_t & errstat) Aborting process, probably due to an internal error. --- It occurred during Pass 1 / 5 The assembly was the following: I reference mapped a small eukaryote genome(10 megabase) to a closely related genome. I then grabbed the unmapped reads from the paired 454 reads and the unpaired 454 reads to separate read files, and performed a de novo assembly from these unmapped reads, of which there were 1890039 (248877164 bases) before all the clipping routines started. I'll send you the addReaderror_REPLAY_do_not_delete.log file back channel, and I'll not delete the working directory yet, in case you need more. Is it worth re-trying with 3.9.4 or even 3.4? cheers, John -- 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