MIRA controlled termination

[Bobbie Shaban]

Hi,

I am trying out MITObim but I am receiving an error regarding the MIRA execution.

I have used MIRA on numerous occasions and know it dislikes being run on an NFS, we have inifiniband links a high speed scratch disk, so I don't mind so much.

the command I use is

../MITObim_1.8.pl -sample testpool -ref M5 -readpool M5.merged.fastq --quick M5_mtgenome_partial10K.fa -end 100

Which is fine for the most part but I receive the following error with mira. I understand it's an NFS disk (essentially) but I don't really mind. Normally I would add -NW:cnfs=warn to the manifest file, but it doesn't look like you can add that when using MITObim?

Is there any way to continue this without the need of using local disk or creating a ramdisk?

Thanks for your help,
Bobbie

 WARNING WARNING WARNING!

 It looks like the directory MIRA uses for temporary files
     testpool-M5_assembly/testpool-M5_d_tmp
 is on a NFS (Network File System) 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:trt to redirect the tmp directory somewhere else on a
    local disk or even SSD.
 2) ALSO POSSIBLE: put the whole project somewhere else on your file system.
 3) ABSOLUTELY NOT RECOMMENDED AT ALL: use "-NW:cnfs=warn" to tell MIRA not
    to stop when it finds the tmp directory on NFS.

 If you do not know what NFS is and which directory to use in "-DI:trt", ask
 your local system administrator to guide you.


 Fatal error (may be due to problems of the input data or parameters):

 *******************************************************************************                                                                                                                                                             *
 * Tmp directory is on a NFS mount ... but we don't want that.                                                                                                                                                                               *
 *******************************************************************************                                                                                                                                                             *
 ->Thrown: void Assembly::checkForNFSMountOnTmpDir()
 ->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.
 Subscribing / unsubscribing to mira talk, see: http://www.freelists.org/list/mi                                                                                                                                                             ra_talk

 CWD: /scratch/CAGRF9846/mitobin/example/iteration0
 Thank you for noticing that this is *NOT* a crash, but a
 controlled program stop.
 Failure, wrapped MIRA process aborted.

[Chris H]

Hi Bobbie,

Sorry for the delay - I have added a new option `--NFS_warn_only` in MITObim for you, which is adding '-NW:cnfs=warn' to the manifest file, so it should run through. Just pull the latest version from Github or use the latest Docker image. 

Alternatively you can redirect your temp directory via `--redirect` to a non-NFS directory. 

Hope that helps!

cheers,
Christoph

[Bobbie Shaban]

Hi Christoph, thanks for that!!

Is there a way to manually add mira parameters? MIRA is able to be run (in parts I think ) multithreaded. I would like to add  -GE:not=0 to make use of available resources.

Thanks for your help!

[Christoph Hahn]

Hello,

MIRA runs using `-GE:not=0` per default, so it should make use of all available resources automatically (in the parts of the assembly process that can be multithreaded).

cheers,
Christoph

is the default so MIRA will automatically use

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[Bobbie Shaban]

ok, thanks!

Thanks for your help.

Bobbie.

[Nathan Ricks]

How do we exactly use this option? I've tried the following input "MITObim_1.8.pl -start 1 -end 10 -sample testpool -ref Salpinus_mt_genome -readpool reads.fastq -maf initial-mapping-testpool-to-Salpinus-mt_assembly/initial-mapping-testpool-to-Salpinus-mt_d_results/initial-mapping-testpool-to-Salpinus-mt_out.maf --NFS_warn_only &> log"

Yet it still returns the message warning against running on NFS

[Chris H]

Hi,

This problem should be fixed now - Just pull the latest MITObim Github version and retry. Sorry for the inconvenience!

cheers,
Christoph