[mira_talk] Re: Error: while assembling Illumina paired end reads
- From: John Nash <john.he.nash@xxxxxxxxx>
- To: mira_talk@xxxxxxxxxxxxx
- Date: Mon, 18 Apr 2011 19:42:49 -0400
On 2011-04-18, at 5:32 PM, Sravya Tamma wrote:
>
> Hi,
>
> I am trying to assemble Illumina paired end reads of one of the Helicobacter
> pylori genome. I have prepared the fastq file of paired end reads
> (Hpy_in_solexa.fq) and placed it in bin/my_project folder.
>
> But when i run the following command:
> /mira3.2.1.13/bin/my_project$ mira --project=Hpy
> --job=denovo,genome,accurate,solexa SOLEXA_SETTINGS -GE:tismin=100;tismax=300
> >&log_assembly.txt
>
> it gives me the following error in the log_assembly.txt file.
>
> "Could not stat the newly created directory 'Hpy_assembly'.: Value too large
> for defined data type
> Creating directory Hpy_assembly ...
> Fatal error (may be due to problems of the input data or parameters):
>
> "Could not make sure that a needed directory exists, aborting MIRA."
>
> ->Thrown: void Assembly::ensureStandardDirectories(bool purge)
> ->Caught: main
>
> Aborting process, probably due to error in the input data or parametrisation."
>
> Could you please let me know where am i doing wrong?
Sounds to me like a permissions problem. If the path attributions are to be
taken literally from the error message, mira seems to be installed off root
(/mira3.2.1.13/bin/my_project), and the assembly folder seems to be hooked onto
the installation folder. Unless it's Windows, that would cause problems in most
systems.
Could the original poster please let us know if it's Un*x, Mac, Windows or
whatever, and whether he/she has admin privileges. Also where your home
directory is.
J
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