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...
# 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?
# 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
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 2755 days ago
You need to provide /tmp location at
— Abhi 2755 days ago