[mira_talk] Template segment not recognized.
- From: "hoshiga.f.aa" <hoshiga.f.aa@xxxxxxxxxxxxxx>
- To: "mira_talk" <mira_talk@xxxxxxxxxxxxx>
- Date: Thu, 05 Jun 2014 20:35:02 +0900 (JST)
Dear, All
I started to learn about MIRA. But I encountered a problem which I can't solve
by myself. So I need help.
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).
Version of MIRA was 4.0.2.
And this is the manifest file I used.
project = O104_H4_denovo
job = genome,denovo,draft
readgroup = O104_H4
data = ./SRR254209.fastq
technology = iontor
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. Read
at fault:
SRR254209.3
4 DNA template SRR254209 has more than two reads, template info not used. Read
at fault:
SRR254209.4
5 DNA template SRR254209 has more than two reads, template info not used. Read
at fault:
SRR254209.5
6 DNA template SRR254209 has more than two reads, template info not used. Read
at fault:
SRR254209.6
7 DNA template SRR254209 has more than two reads, template info not used. Read
at fault:
SRR254209.7
8 DNA template SRR254209 has more than two reads, template info not used. Read
at fault:
SRR254209.8
9 DNA template SRR254209 has more than two reads, template info not used. Read
at fault:
SRR254209.9
DNA template SRR254209_0, read SRR254209.20: template segment not recognised.
DNA template SRR254209_0, read SRR254209.10: template segment not recognised.
Reads SRR254209.20 and SRR254209.10 have the same template segments.
DNA template SRR254209_1, read SRR254209.21: template segment not recognised.
DNA template SRR254209_1, read SRR254209.11: template segment not recognised.
Reads SRR254209.21 and SRR254209.11 have the same template segments.
DNA template SRR254209_2, read SRR254209.22: template segment not recognised.
DNA template SRR254209_2, read SRR254209.12: template segment not recognised.
Reads SRR254209.22 and SRR254209.12 have the same template segments.
DNA template SRR254209_3, read SRR254209.23: template segment not recognised.
DNA template SRR254209_3, read SRR254209.13: template segment not recognised.
Reads SRR254209.23 and SRR254209.13 have the same template segments.
... (and hundreds of similar messages) ...
Fatal error (may be due to problems of the input data or parameters):
********************************************************************************
* 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.
Please give me some advice.
Best regards.
Hoshiga
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