[mira_talk] Re: Help
- From: "Raj Kumar, Praveen Kumar Mr." <rajkump@xxxxxxxxxx>
- To: "mira_talk@xxxxxxxxxxxxx" <mira_talk@xxxxxxxxxxxxx>
- Date: Thu, 5 Aug 2010 17:04:37 -0400
Dear Bob,
I followed suggestion #3 and 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 -MI:sonfs=false >& log_assembly.txt
************************************************************************
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: /shared/liangcres/Chlamy-ESTassmbly
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 11:58 PM
To: mira_talk@xxxxxxxxxxxxx
Subject: [mira_talk] Re: Help
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<mailto:mira_talk-bounce@xxxxxxxxxxxxx>
[mira_talk-bounce@xxxxxxxxxxxxx<mailto:mira_talk-bounce@xxxxxxxxxxxxx>] On
Behalf Of Robert Bruccoleri
[bruc@xxxxxxxxxxxxxxxxxxxxx<mailto:bruc@xxxxxxxxxxxxxxxxxxxxx>]
Sent: Wednesday, August 04, 2010 8:33 PM
To: mira_talk@xxxxxxxxxxxxx<mailto: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
Other related posts:
