[mira_talk] Re: 4 won't run!
- From: <Theo.Allnutt@xxxxxxxx>
- To: <mira_talk@xxxxxxxxxxxxx>
- Date: Wed, 9 Apr 2014 12:20:26 +0000
Hi,
ok, I think I fixed the file not opening problem, though don't know how. I put
eveything in the same folder and that seemed to work.
Then I got the dreaded NFS warning, which is wrong because I'm using a
VirtualBox Linux shared folder, not an NFS.
I fixed that with the suggested switch, but then got the error:
* MIRA found duplicate read names in your data (see log above for more info). *
* *
* This should never, never be! *
* *
* You may have loaded a file more than once in the manifest or *
* reads may be present multiple times across your input file(s). *
* Either way: fix that!
However, I ahve checked and none of the reads have the same name. There are
paired reads with same name then /1 or /2 appended (by sff_extract). Is this
the problem Has the required format changed since 3.xx?
Thanks.
-----Original Message-----
From: mira_talk-bounce@xxxxxxxxxxxxx [mailto:mira_talk-bounce@xxxxxxxxxxxxx] On
Behalf Of Bastien Chevreux
Sent: Wednesday, 9 April 2014 5:49 PM
To: mira_talk@xxxxxxxxxxxxx
Subject: [mira_talk] Re: 4 won't run!
> On April 9, 2014 at 9:05 AM Theo.Allnutt@xxxxxxxx wrote:
> Every time I run Mira 4, I get a file not found error:
> Looking for files named in data ...Data
> '/path/is/definitely/correct/paired1.fastq' was not found (neither as
> file nor as directory) or led to a read error.
> What could be wrong? Its driving me mad, have tried with several
> different files.
> [...]
> data = /path/is/definitely/correct/paired1.fastq
As first approximation, I would still guess there's a typo somewhere (I know, I
know, you checked).
If you type "ls " and then copy/paste (no typing, really mouse-only copy/paste)
the full path from the "data=" line of the manifest into your terminal and then
hit RETURN, does this work?
Should that work we'd have to move on to more esoteric explanations like "is
MIRA run as another user which might not have the same access permissions as
you" and similar things.
Hope that helps,
Bastien
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