[mira_talk] Re: Problem with installation, even with GCC version 4.8.1, its asking for updated version of GCC

  • From: Andrej Benjak <abenjak@xxxxxxxxx>
  • To: mira_talk@xxxxxxxxxxxxx
  • Date: Mon, 22 Aug 2016 10:27:27 +0200

Option 1: You should remove the 'autopairing' in the readgroup=DataIlluminaForUnPaired.

Option2: MIRA should handle singles in a paired dataset. Just include the singles.fq in the DataIlluminaForPairedEnd and remove the DataIlluminaForUnPaired section (and see what happens, but I think it should work)


Andrej


On 22/08/16 09:51, Hukum rawal wrote:

I recived this error:

Checking pairs of readgroup 1 (named: 'DataIlluminaForPairedEnd'): found 218024046
Checking pairs of readgroup 2 (named: 'DataIlluminaForUnPaired'):  found 0
WARNING: in the above readgroup, no read is paired although the manifest says there should be pairs. This is fishy!

for the following manifest.conf file:

project=trans_MIRA
job=est,denovo,accurate

#readgroup with paired data as G_left.fq and G_right.fq

readgroup=DataIlluminaForPairedEnd
rename_prefix = SNL139:68:C7C53ACXX: G_
technology=solexa
autopairing
data=fastq::G_left.fq fastq::G_right.fq

#readgroup with un-paired data as G_singles.fq

readgroup=DataIlluminaForUnPaired
rename_prefix = SNL139:68:C7C53ACXX: G_
technology=solexa
autopairing
data=fastq::G_singles.fq


How to deal with this input data which has both paired and unpaired data?

On Fri, Aug 19, 2016 at 5:53 PM, Hukum rawal <hukam.rawal@xxxxxxxxx <mailto:hukam.rawal@xxxxxxxxx>> wrote:

    Yes its common. MIRA must understand .fq.
    Meanwhile assembly with sample data completed well with MIRA
    Now I am running it with real data.
    Thank you for support.

    On Fri, Aug 19, 2016 at 5:38 PM, Bastien Chevreux
    <bach@xxxxxxxxxxxx <mailto:bach@xxxxxxxxxxxx>> wrote:

        On 19 Aug 2016, at 5:12 , Peter Cock (Redacted sender
        "p.j.a.cock" for DMARC) <dmarc-noreply@xxxxxxxxxxxxx
        <mailto:dmarc-noreply@xxxxxxxxxxxxx>> wrote:
        > I think the problem might be MIRA not recognising the .fq
        extension,
        > the manual only mentions .fastq
        > […]
        > (Is this right Bastien? Using .fq is fairly common)

        MIRA indeed does not know the .fq extension. Is it really
        common? It’s the first time I encounter it "in the wild.”

        B.


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-- Hukam C. Rawal




--
Hukam C. Rawal

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