[mira_talk] Re: duplicate read names not allowed ?
- From: Laurent MANCHON <lmanchon@xxxxxxxxxxxxxx>
- To: mira_talk@xxxxxxxxxxxxx
- Date: Tue, 18 Sep 2012 12:06:57 +0200
Le 18/09/2012 11:46, Peter Cock a écrit :
On Tue, Sep 18, 2012 at 10:16 AM, Laurent MANCHON
<lmanchon@xxxxxxxxxxxxxx> wrote:
Le 18/09/2012 10:25, Peter Cock a écrit :
Add the /1 and /2 without a space in front of them.
Peter
...
nothing change, i have the same error message.
head GAMMA-1.solexa.fastq
/1@D61655M1:276:D10YJACXX:8:1101:1456:1955
...
Apologies - on re-reading my English was ambiguous,
although it should have been obvious that isn't a valid
FASTQ file as the identifier line must start with '@'.
As Jason pointed out, what I meant was your read
should start:
@D61655M1:276:D10YJACXX:8:1101:1456:1955/1
etc
Peter
yes, it works now,
there are so many standard fastq, so I thought Mira was able to
recognize / 2 or / 1 with or without a space before.
but it's strange, i have 36M reads in each file and only subsets of them
are loaded by Mira:
Pushing back filename: "GAMMA-1.solexa.fastq"
look at ext: .fastq
Loading GAMMA-1.solexa.fastq type fastq
Localtime: Tue Sep 18 12:00:33 2012
Loading data from FASTQ file: GAMMA-1.solexa.fastq
(sorry, no progress indicator for that, possible only with zlib >=1.34)
Done.
Loaded 2241 reads, Localtime: Tue Sep 18 12:00:33 2012
Looking at FASTQ type ... guessing FASTQ-33 (Sanger)
Running quality values adaptation ... done.
Pushing back filename: "GAMMA-2.solexa.fastq"
look at ext: .fastq
Loading GAMMA-2.solexa.fastq type fastq
Localtime: Tue Sep 18 12:00:33 2012
Loading data from FASTQ file: GAMMA-2.solexa.fastq
(sorry, no progress indicator for that, possible only with zlib >=1.34)
Done.
Loaded 6923 reads, Localtime: Tue Sep 18 12:00:34 2012
Looking at FASTQ type ... guessing FASTQ-33 (Sanger)
Running quality values adaptation ... done.
Checking reads for trace data (loading qualities if needed):
[0%] ....|.... [10%] ....|.... [20%] ....|.... [30%] ....|.... [40%]
....|.... [50%] ....|.... [60%] ....|.... [70%] ....|.... [80%]
....|.... [90%] ....|.... [100%]
No SCF data present in any read, automatic contig editing for Sanger
data is now switched off.
9164 reads with valid data for assembly.
Localtime: Tue Sep 18 12:00:34 2012
Generated 6923 unique template ids for 9164 valid reads.
TODO: Like Readpool: strain x has y reads
Have read pool with 9164 reads.
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