I tried what you suggested still it didn't work.. :( Here is the new logfile with changes: http://dl.dropbox.com/u/10010521/logfile Kindly help ! Thanks, Jyotsna On Thu, Oct 6, 2011 at 5:11 PM, jyotsna guleria <jyotsna.guleria@xxxxxxxxx>wrote: > Thanks so much !! > > So, you suggest I should not use -SK:nrr=10 for 4k reads? > Can you suggest a range to use this option? e.g can I use it if I have 10k > reads or more? > > For your question: any special reason you switch of proposed end clipping? > (-CL:pec=no) > > We had a discussion about it long back where I mentioned that for some > reason if I turn ON this option of clipping I get more debris...don't know > why but it did happen and from then I have been assembling reads with same > command and never had any trouble so far...! > > > > Many thanks for the help! > > Jyotsna > > > On Thu, Oct 6, 2011 at 4:58 PM, Bastien Chevreux <bach@xxxxxxxxxxxx>wrote: > >> ** >> >> On Thursday 06 October 2011 18:07:28 jyotsna guleria wrote: >> >> > Can someone please help me in understanding what is going wrong by >> looking >> >> > at the logfile uploaded at : >> >> > All of my reads are going into debris list, I am not able to understand >> >> > why.... >> >> >> >> 1. wrong command line. Do not write >> >> mira --project=... --job=... [some options] --highlyrepetitive ... >> >> but >> >> mira --project=... --job=... --highlyrepetitive [other options] ... >> >> >> "--highlyrepetitive" is a position dependend parameter, look that up in >> the documentation. >> >> >> >> 2. any special reason you switch of proposed end clipping? (-CL:pec=no) >> >> >> 3. -SK:nrr=10 might be one cause for your problem. Almost every read has >> some >> >> kind of probelamtic stretch, see the log line: >> >> >> "Writing read repeat info to: >> >> JCV345MDA_assembly/JCV345MDA_d_info/JCV345MDA_info_readrepeats.lst ... >> >> 3289 sequences with 8201 masked stretches." >> >> Such a tiny project with 4k reads does not need that. >> >> 4. Only 1/3 of the reads is finally used in the assembly. See log lines >> >> Building new contig 1 >> >> Localtime: Thu Oct 6 16:23:12 2011 >> >> Unused reads: 1514 >> >> The rest did not have any kind of overlaps. See again -SK:nrr >> >> B. >> > >