[mira_talk] Re: Template segment not recognized.
- From: Bastien Chevreux <bach@xxxxxxxxxxxx>
- To: mira_talk@xxxxxxxxxxxxx
- Date: Thu, 5 Jun 2014 14:48:38 +0200 (CEST)
> On June 5, 2014 at 1:35 PM "hoshiga.f.aa" <hoshiga.f.aa@xxxxxxxxxxxxxx> wrote:
> I tried to assemble the data of IonTorrent whole genome sequencing of E.coli
> O104:H4 str.LB226692 obtained from SRA by MIRA.
> SRA file was converted to fastq by SRA Toolkit(fastq-dump).
> [...]
> And I got following error message.
>
>
> DNA template SRR254209, read SRR254209.2: template segment not recognised.
> DNA template SRR254209, read SRR254209.1: template segment not recognised.
> Reads SRR254209.2 and SRR254209.1 have the same template segments.
> 3 DNA template SRR254209 has more than two reads, template info not used.
> [...]
> ********************************************************************************
> * Problems found with the template data, see output log for more info. This *
> * points some serious problem either with read naming (like unrecognised read
> *
> * naming scheme) or broken template information, please fix your input files!
> *
> * Or switch off this warning with -NW:ctp=no (but you'll do this at own risk!)
> *
> ********************************************************************************
>
> I couldn't understand what this messages means and what is going on.
>
> When I used MIRA to assemble NGS data of phage genome obtained from our lab
> previously, MIRA worked totally fine.
> So I think input data may be problematic, but I can't fix it.
The problem indeed is the read naming as enforced by the SRA: it does not adhere
to any other naming scheme. I think you may have a way out by using the "-F"
("--origfmt") of fastq-dump from the SRA toolkit.
Hope that helps,
Bastien
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