Dear Bob, Thank you very much for your reply. I still get the following error msg, cmd: mira --project=EAch --job=est,denovo,accurate,sanger,454 SANGER_SETTINGS -CL:qc=no 454_SETTINGS -LR:mxti=no -AL:mrs=95 -CO:rodirs=5 COMMON_SETTINGS -SK:mnr=yes:nrr=10 >& log_assembly.txt WARNING WARNING WARNING! It looks like the log directory is on a NFS mount. This will slow down MIRA *considerably* ... by about a factor of 10! If you don't want that, you have three possibilities: 1) RECOMMENDED! Use -DI:lrt to redirect the log directory somewhere else on a local disk or even SSD. 2) POSSIBLE: put the whole project somewhere else and restart MIRA. 3) ABSOLUTELY NOT RECOMMENDED AT ALL: use -MI:sonfs=false to tell MIRA not to stop when it finds the log directory on NFS. Fatal error (may be due to problems of the input data or parameters): "Log directory is on a NFS mount ... but we don't want that." ->Thrown: void Assembly::checkForNFSMountOnLogDir() ->Caught: main Aborting process, probably due to error in the input data or parametrisation. Please check the output log for more information. For help, please write a mail to the mira talk mailing list. CWD: /home/rajkump/EST-assembly-mira/ALL_comb_4assmbl Thank you for noticing that this is *NOT* a crash, but a controlled program stop. regards Praveen ___________________________________ From: mira_talk-bounce@xxxxxxxxxxxxx [mira_talk-bounce@xxxxxxxxxxxxx] On Behalf Of Robert Bruccoleri [bruc@xxxxxxxxxxxxxxxxxxxxx] Sent: Wednesday, August 04, 2010 8:33 PM To: mira_talk@xxxxxxxxxxxxx Subject: [mira_talk] Re: Help Dear Praveen, You need to remove the minus sign "-" in front of "COMMON_SETTINGS" --Bob Raj Kumar, Praveen Kumar Mr. wrote: > Hi all, > I use the following cmd for EST assembly, but I am getting the following > error msg. Please help me here. > > mira --project=EAch --job=est,denovo,accurate,sanger,454 SANGER_SETTINGS > -CL:qc=no 454_SETTINGS -LR:mxti=no -COMMON_SETTINGS -SK:mnr=yes:nrr=10 > -AL:mrs=95 -CO:rodirs=5 >& log_assembly.txt > > > * for a specific sequencing type (454_SETTINGS). > > * Parameter section: '-SK' > * Parameter 'nrr' can only be set as COMMON_SETTINGS, not individually > * for a specific sequencing type (454_SETTINGS). > > =============================================================================== > > Fatal error (may be due to problems of the input data or parameters): > > "Error while parsing parameters, sorry." > > ->Thrown: void MIRAParameters::parse(istream & is, vector<MIRAParameters> & > Pv, MIRAParameters * singlemp) > ->Caught: main > > > regards, > Praveen > -- You have received this mail because you are subscribed to the mira_talk mailing list. For information on how to subscribe or unsubscribe, please visit http://www.chevreux.org/mira_mailinglists.html