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. >