[mira_talk] Re: Mixed case Roche 454 data and -CL:lowercase_clip
- From: Peter <peter@xxxxxxxxxxxxxxxxxxxxx>
- To: mira_talk@xxxxxxxxxxxxx
- Date: Mon, 23 Nov 2009 12:04:33 +0000
On Sun, Nov 22, 2009 at 9:00 AM, Bastien Chevreux <bach@xxxxxxxxxxxx> wrote:
>
> On Mittwoch 18 November 2009 Peter wrote:
>> For the record, that assembly finished, and seems to give results broadly
>> similar to those earlier using FASTA+QUAL+XML version of the same 454
>> reads, in about the same run time. However, the contigs do differ.
>
> Try running with -GE:nop=1, then the should be identical in both cases.
>
Hi Bastien,
Could you clarify here - I can't get that to work, e.g.
mira -job=denovo,genome,accurate,454 454_SETTINGS -CL:lowercase_clip
-fastq=phage.fastq -LR:mxti=no -GE:nop=1 > mira.log
mira -job=denovo,genome,accurate,454 454_SETTINGS
-CL:lowercase_clip=yes -fastq=phage.fastq -LR:mxti=no -GE:nop=1 >
mira.log
mira -GE:nop=1 -job=denovo,genome,accurate,454 454_SETTINGS
-CL:lowercase_clip=yes -fastq=phage.fastq -LR:mxti=no > mira.log
all give:
========================= Parameter parsing error(s) ==========================
* Parameter section: '-GE'
* unrecognised string or unexpected character: nop
* Parameter section: '-GE'
* unrecognised string or unexpected character: 1
===============================================================================
Abort trap
Thanks,
Peter
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