[mira_talk] Re: Run MIRA in Galaxy....
- From: Peter Cock <p.j.a.cock@xxxxxxxxxxxxxx>
- To: mira_talk@xxxxxxxxxxxxx
- Date: Mon, 19 Dec 2011 10:16:33 +0000
On Mon, Dec 19, 2011 at 8:32 AM, Bastien Chevreux <bach@xxxxxxxxxxxx> wrote:
> On Dec 19, 2011, at 7:56 , Manju Rawat wrote:
>>
>> Ya this problem is related to MIRA..But I am not able to find the prblm...
>> I tried this in terminal.... and the it stoped before the complete execution
>> by giving following error..
>>
>> Analysing hstat files:
>> [0%] ....|.Segmentation fault.
>>
>
> A seg fault? That should never be. ! Can I get the full log please? And if
> this reproducible, eventually the data?
>
> B.
The segmentation fault is probably a MIRA problem.
However, the prior "uname: write error: Broken pipe"
might be something to do with Galaxy though.
Are you finding these problems to be reproducible?
I hope you've got a small 454 dataset so this is quick
to test.
i.e. If you repeat the task in Galaxy, does it consistently
fail the same way, and if you try to run a failed command
directly from the command line terminal (copy and paste
what Galaxy tried), does that work?
I did see the "uname: write error: Broken pipe" on my
machine, but it doesn't seem to be consistent.
I have not seen the "Missing .wig output file" issue,
which is a message from my wrapper, which treats
this as an error condition (so the history in Galaxy
will go red). In this case the MIRA log should help
explain what went wrong.
Regards,
Peter
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