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.