Hi Rosie, apologies for the late reply, I am catching up on email and
think the answer may be useful for others even if you have moved on
from this work.
First, the --scratch-path options control use of temporary storage when
building sorted seed lists (sslist index files) for very large genomes
where a single genome's index will not fit into RAM. In your case it
will not have an effect because S. aureus genomes are fairly small. I
would suggest running without those options and if it still exits with
signal 11 (segmentation fault), it is possible that you need a machine
with more RAM. The total amount of disk space required should not be
more than a 10-20 GB for 100 genomes of the size of S. aureus. That
said, progressiveMauve's compute time grows at least cubically in the
sequence count, so you may find that it is too slow to align more than
50 or so genomes at once.
Best,
-Aaron
On Fri, 2016-08-05 at 09:18 +1000, Rosemarie Sadsad wrote:
> Dear users,
>
> I am trying to use progressiveMauve on 96 samples of S. aureus. I am
> running this via command line on the university HPC and have
> specified alternative scratch paths to allow more temporary storage
> space. It stores (Storing raw sequence at ..) and loads (Sequence
> loaded successfully..) only a subset of the samples and I receive the
> error:
>
> Caught signal 11
> Cleaning up and exiting!
>
> Does anyone have any ideas on how to overcome this?
>
> Thank you for your help.
>
> Rosie
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--
Aaron E. Darling, Ph.D.
Associate Professor, ithree institute
University of Technology Sydney
Australia
http://darlinglab.org
twitter: @koadman
UTS CRICOS Provider Code: 00099F
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