Mira Error

[robelb4]

Hello all,

I'm using Mira assembler for the illumina pe reads. I followed all the procedure for the denovo assembly but I'm getting an error (please see the some part of the log file ).

What would be the other problem if I ignore to redirect the tmp file from NFS mount?

After I fix the read naming according to the /1/2 illumina scheme it append /1 and /2 just after the @WHI and followed by the rest of the description, but is it correct or it has to be the end of the description?

Thanks
Robel

####################################################
Creating directory robtest_assembly ... done.
Creating directory robtest_assembly/robtest_d_tmp ... done.
Creating directory robtest_assembly/robtest_d_results ... done.
Creating directory robtest_assembly/robtest_d_info ... done.
Creating directory robtest_assembly/robtest_d_chkpt ... done.






WARNING WARNING WARNING!

It looks like the tmp directory 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) POSSIBLE: put the whole project somewhere else and restart MIRA.
3) ABSOLUTELY NOT RECOMMENDED AT ALL: use "-MI:sonfs=no" 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.

####################################################

[sklages]

Concerning the NFS stuff: it will dramatically slow down assembly as there is a lot
temp data written during assembly. You can choose between 1), 2) and 3) ...

For the fastq stuff you should have look at the relevant part of the docs.

You should post to the mira_talk mailing list to get more specific answers.

hth, Sven

[robelb4]

Thanks a lot sklages,

My problem was the the input file and got fix it, but the NFS issue you're right it may slower the process but still working

Robel

[metheuse]

Hi robelb4, could you tell me how to fix the problem? I was running mira-3.9 and got the same error. Thanks.

[sklages]

Hi robelb4, could you tell me how to fix the problem? I was running mira-3.9 and got the same error. Thanks.

Have you read the above postings?

"Concerning the NFS stuff: it will dramatically slow down assembly as there is a lot
temp data written during assembly. You can choose between 1), 2) and 3) ...
[..]
You should post to the mira_talk mailing list to get more specific answers."

Assuming it is really the same error.

hth,
Sven