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Question: Question: How to redirect MIRA temporary file to non-NFS mounted location ?

Priya Singh
197 days ago

Question: How to redirect MIRA temporary file to non-NFS mounted location ?

I run MIRA on my dataset and got the following error. I have /tmp directory mounted on non-NFS protocol. I wanted to use it for temporary location. How to do that? Sorry, M new to MIRA.

WARNING WARNING WARNING!

It looks like the directory MIRA uses for temporary files
/home/user/MIRA/mira_4.0.2_linux-gnu_x86_64_static//Test_Asbly_d_tmp_MJYclL
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.

Answers
0

I think it should be fairly easy. May I have your manifest file please...

Here it is 

# Example for a manifest describing a de-novo assembly with
# paired-end Illumina

# First part: defining some basic things
# In this example, we just give a name to the assembly
# and tell MIRA it should assemble a genome de-novo in accurate mode
# As special parameter, we want to use 4 threads in parallel (where possible) ==> TRY?

project = test_Asbly
job = genome,denovo,accurate
parameters = -NW:cac=warn

# The second part defines the sequencing data MIRA should load and assemble
# The data is logically divided into "readgroups": this reflects the
# ... that read sequences ...

# defining the paired-end Illumina reads, fixing all needed pair information
readgroup = PairedEndIlluminaReads
data = /home/user/MIRA/test.R1.fastq /home/user/MIRA/test.R2.fastq
technology = solexa
template_size = 400 600
segment_placement = ---> <---
segment_naming = solexa
rename_prefix = HISEQ578:1035: lane1

Priya Singh 197 days ago

You need to provide /tmp location at

parameters = -NW:cac=warn -NW:cnfs=warn -DI:trt=/tmp

Abhinav 197 days ago