On Oct 13, 2011, at 16:56 , John Nash wrote: > *sigh* I just got the following message from convert_project... and from > mira when I tried using the same CAF file (which came from a de novo > assembly) in a mapping assembly: > > Fatal error (may be due to problems of the input data or parameters): > > "Duplicate readname in CAF file: HWI-ST813_B0202ABXX:2:1108:6120:28342#0/" > > ->Thrown: Read & CAF::createCafRead() > ->Caught: Error while creating CAF-Object. > > > True enough, a grep of the fastq file from my sequencing provider showed that > the sequence was duplicated in the results. The assembly took two days on a > 64 cpu computer and I really do not want to do it again. Is there any way to > remove the offending entry from the CAF file? Oh f*ck! (sorry) Normally MIRA should have could that on loading already!? Which version ... and what parameters did you use? Back to your problem: if it is just one read, then chances are good one can fix that. Easiest way is to edit the MAF file, because there all data needed is together in one blob. Have a look at http://mira-assembler.sourceforge.net/docs/DefinitiveGuideToMIRA.html#sect2_contigs In the small example there, deleting the read U13a05e07.t1 is done by deleting everything from RD U13a05e07.t1 up to and including the next line with AT That should do the trick. Make sure to delete only one copy of that read or else you might end up with a illegal contig if the coverage drops to zero. B. PS: Sorry for the inconvenience. -- 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