[mira_talk] Re: Help
- From: "Raj Kumar, Praveen Kumar Mr." <rajkump@xxxxxxxxxx>
- To: "mira_talk@xxxxxxxxxxxxx" <mira_talk@xxxxxxxxxxxxx>
- Date: Fri, 6 Aug 2010 12:09:57 -0400
Dear Bastien,
Could you please reply to the following email.
Thank you,
Praveen
________________________________________
From: mira_talk-bounce@xxxxxxxxxxxxx [mira_talk-bounce@xxxxxxxxxxxxx] On Behalf
Of Robert Bruccoleri [bruc@xxxxxxxxxxxxxxxxxxxxx]
Sent: Thursday, August 05, 2010 5:43 PM
To: mira_talk@xxxxxxxxxxxxx
Subject: [mira_talk] Re: Help
Dear Praveen,
I have no idea what's wrong -- perhaps Bastien or someone else will
comment.
You might want to look at the source code to see just what it's
doing there.
Regards,
Bob
Raj Kumar, Praveen Kumar Mr. wrote:
> 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
>
>
>
>
>
>
>
>
>
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