[mira_talk] Re: mira assembly error
- From: Bastien Chevreux <bach@xxxxxxxxxxxx>
- To: mira_talk@xxxxxxxxxxxxx
- Date: Tue, 24 Apr 2012 22:02:39 +0200
On Apr 24, 2012, at 21:25 , Chauhan, Archana wrote:
> I am trying to assemble my 454 upaired and the paired reads. I used the
> following command to direct the output to a directory “$TMPDIR”. This
> directory is guaranteed to use a local hard drive.
> “mira --project=HK44 --job=denovo,genome,accurate,454, -DI:$TMPDIR
> >&log_assembly”
>
> and got the following error:
I'm astonished the parameter parser didn't cry out loud, because the above
contains an error. What you want is
mira --project=HK44 --job=denovo,genome,accurate,454, -DI:trt=$TMPDIR
>&log_assembly
> I than ran the following command (not recomended) to make mira run:
> “mira --project=HK44 --job=denovo,genome,accurate,454, -MI:sonfs=no
> >&log_assembly”
>
> And I got the following error:
> "Could not open FASTQ file 'HK44_in.454.fastq'. Is it present? Is it
> readable? Did you want to load your data in another format?"
>
> My data files look ok . Below is the snapshots of my qual and fasta files:
Well, you provide FASTA and FASTA quality files, but MIRA wanted to load FASTQ.
This will clash.
Solution: use "-Q" in "sff_extract" to create FASTQ files.
B.
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