Bastien Chevreux a écrit :
On Donnerstag 17 Dezember 2009 Laurent Manchon wrote:--Hi, i have made assembly on 454 reads (~600 000 reads) using mira 2.9.43 and with this command line: bin/mira -project=planaire -fasta=planaire.fa -job=denovo,est,normal,454 -notraceinfo -GENERAL:kcim=yes,not=3 -SK:rt=4 -CO:fnicpst=yes,rodirs=10,asir=yes -CL:cpat=no,pec=no,pvlc=no,qc=no,bsqc=no,mbc=no,emlc=yes,mlcr=0,smlc=0,emrc =yes,mrcr=0,smrc=0 -AL:bip=5,bmin=10,mrs=90:egp=yes:egpl=reject_codongaps:megpp=100,mo=60 -AS:mrl=30,bdq=30 -SK:mnr=yes,rt=8,mmhr=6 and i obtain 53867 contigs but some contigs (~18163) are only built using one sequence, why ? So, i don't understand... I thought that contigs established(constituted) by a single sequence was singulets and had to appear in debrislists, don't you ?The default for this command line is to still save tagged singlets: Save tagged singlets in project (stsip) : [san] yes [454] yesso I suppose those reads were tagged in earlier passes. If not, please confirm the current version has the same behaviour and tell, this would be a bug.Regards, Bastien
okay by adding parameter -OUT:sssip=no the singlets are not saved in the assembly result.
so the command line syntax is (v2.9.43):bin/mira -project=planaire -fasta=planaire.fa -job=denovo,est,normal,454 -OUT:sssip=no -notraceinfo -GENERAL:kcim=yes,not=3 -SK:rt=4 -CO:fnicpst=yes,rodirs=10,asir=yes,mr=no -CL:cpat=no,pec=no,pvlc=no,qc=no,bsqc=no,mbc=no,emlc=yes,mlcr=0,smlc=0,emrc=yes,mrcr=0,smrc=0 -AL:bip=5,bmin=10,mrs=90:egp=yes:egpl=reject_codongaps:megpp=100,mo=60 -AS:mrl=30,bdq=30 -SK:mnr=yes,rt=8,mmhr=6
