Dear Mr.Chevreux, Thank you for your reply, although i try to set the -AS:mrpc=1 , i do get "unrecognized string or unexpected character", it is because of parsing parameters i guess, but i can not see the problem.. what to do? Visam From: bach@xxxxxxxxxxxx To: mira_talk@xxxxxxxxxxxxx Subject: [mira_talk] Re: singlets fasta file.. Date: Mon, 21 Mar 2011 20:22:16 +0100 On Monday 21 March 2011 11:21:06 Visam Gültekin wrote: > In some earlier posts, getting singlets as fasta file had been discussed. MIRA does never output a separate FASTA file with singlets. It however may add singlets to regular result FASTA files. > Although i followed the recommendation, i can see no fasta file for > singlets.Hhere is the command i used.. mira -project=project_p_run4 -fasta > -job=denovo,genome,accurate,454 -highlyrepetitive -GE:not=8 -AS:sep=1 > -SK:not=8 -SK:bph=18 -SK:mchr=4096 454_SETTINGS -ED:ace=1 -OUT:sssip=on > -OUT:stsip=on so i can not see any information about singlets, else of txt > files. i guess i miss a big notch Yep. You may or may not have missed the following note in the description of the -OUT:sssip and -OUT:stsip parameters: Note Note that a value larger 1 of the [-AS:mrpc] parameter will disable the function of this parameter. (see http://mira-assembler.sourceforge.net/docs/DefinitiveGuideToMIRA.html#sect_ref_output_out) As the command line you use takes the default parameter for -AS:mrpc (look at the MIRA output log in the top section where all used parameters are listed), MIRA won't write singlets to the result files. Simply set -AS:mrpc accordingly. B. PS: trust me: in a 454 genome denovo assembly, you do not want to have singklets in your regular results. You have been warned :-)