Hello!!
I'm trying to de novo assembly a set of mRNA sequences of a fasta (.fa)
file, there's no quality file on these sequences.
Per the assembly manaual the input file is a .fa file, the --noqualities
and -CL:pec=false parameters are stated in the manifest file as well as a
default_qual=30.
When assemblying the system is stil requesting a quality file for the fasta
file.
I'm using Mira 4.9.5_2 version (the defaul version of BioLinux 8)
############################
My manifest file is as follows...
################################
# First part: defining some basic things
project = Cqd_assembly
job = est,denovo,accurate
parameters = COMMON_SETTINGS -GENERAL:number_of_threads=2 \
-OUTPUT:output_result_caf=no
parameters= TEXT_SETTINGS -ALIGN:min_relative_score=40 \
-ASSEMBLY:minimum_read_length=50\
--noqualities\
--noclipping=all\
-CL:pec=false
# The second part
readgroup = RNAs_from_Cqd
data = /cqd-dir/Cqd-mRNAs.fa
default_qual=30
technology = text
#########################################
Here's the error I'm getting...
##########################################
********************************************************************************
* FASTA quality file expected to exist, but no quality filename given???
Refer *
* to
*
*
http://mira-assembler.sourceforge.net/docs/DefinitiveGuideToMIRA.html#sect_ref_manifest_readgroups*
* on how to load FASTA data without corresponding quality files.
####################################3
Please advise.
THANKS =)
