Dear Praveen,I would show this output to your system administrator and ask his advice about where to run your job. If that is not an option, then follow suggestion #3 and accept the performance degradation.
Regards, Bob Raj Kumar, Praveen Kumar Mr. wrote:
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
begin:vcard fn:Robert Bruccoleri n:Bruccoleri;Robert org:Audacious Energy, LLC and Congenomics, LLC adr:;;60 Gates Farm Road;Glastonbury;CT;06033;USA email;internet:bruc@xxxxxxx title:President tel;home:860 633 6655 tel;cell:609 902 8419 version:2.1 end:vcard