[mira_talk] Re: Assembling with no quality file. System requesting quality file even when indicated the contrary.
- From: Bastien Chevreux <bach@xxxxxxxxxxxx>
- To: mira_talk@xxxxxxxxxxxxx
- Date: Tue, 6 Oct 2015 10:18:47 -0400 (EDT)
On October 6, 2015 at 12:40 AM Patricia Carvajal
<patriciacarvajal.mxli@xxxxxxxxx> wrote:
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.
[...]
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.
There is a last security fence of MIRA (which is described in a somewhat hidden
manner in the manual) trying to prevent you from doing something foolish or
going on when not all data is present: a FASTA file with the postfix ".fasta"
(or".fa") is expected to have a quality file present (named ".fasta.qual" or
".fa.qual").
This check is not performed when reading FASTA files with a ".fna" postfix or if
you force MIRA to treat a .fasta file as .fna file, the latter can be done by
this:
data = fna::/cqd-dir/Cqd-mRNAs.fa
Regarding assembling without quality values, my usual warnings still apply:
simply don't do it. The longer version of this:
http://mira-assembler.sourceforge.net/docs/DefinitiveGuideToMIRA.html#sect_ref_never_without_quality_values
B.
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