[mira_talk] Re: (no subject)
- From: Bastien Chevreux <bach@xxxxxxxxxxxx>
- To: mira_talk@xxxxxxxxxxxxx
- Date: Mon, 29 Aug 2016 08:42:46 -0400
On 29 Aug 2016, at 6:09 , Rhiannon Mondav <rhiannon.mondav@xxxxxxxxx> wrote:
[…]
I am a little bit at loss here with this error report, because there are
several things I scratch my head.
on an assembly (mapping) of small genome ~1M bacteria with x10 to x20
coverage on Mira 4.0.2. Process got to 'ATG PREDICTIONS' before timing out on
my cluster job.
This is the first thing. I regularly use MIRA for mapping against bacteria. I
don’t know by the exact times by heart, but a 4M bacterium with ~80x coverage
is done in less than 30 minutes (8 cores).
You have a 1M bacterium which times out at 20x max??? This is *very* strange.
I attempted to utilise the fabulous resume function. The log file got to
'File / directory output names: ..... Wiggle:
P4710_101_mapd2_AAA028-C07_out.wig' when Mira issued the following error:
I thought I’d blocked resume in mapping mode as there are oddities in this case
I haven’t had the time to iron out. Maybe I did that only later though.
[…|
Deleting old directory
P4710_101_mapd2_AAA028-C07_assembly/P4710_101_mapd2_AAA028-C07_d_results ...
done.
Creating directory
P4710_101_mapd2_AAA028-C07_assembly/P4710_101_mapd2_AAA028-C07_d_results ...
done.
A 'standard' exception occured (that's NOT normal):
boost::filesystem::create_symlink: File exists:
"/scratch//P4710_101_mapd2_AAA028-C07_d_tmp_Nu6X7Z",
"P4710_101_mapd2_AAA028-C07_assembly/P4710_101_mapd2_AAA028-C07_d_tmp”
This is another thing which “should not happen” under normal circumstances. The
only times I got reports about this was indeed when people ran on some weird
NFS or other network based file systems. Is that the case for you?
Could you please share the manifest file you used?
B.
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