Hi Aaron,I made sure I had read and write access to the tmp directory. I also
made sure that there was plenty of room (storage). I tried your redirection and
was unsuccessful, I got the same error message. Any other suggestions would be
greatly appreciated. Thanks! Abria mageeabria2...@sbcglobal.net
:
From: Aaron Darling <aaron.darl...@uts.edu.au>
Date: July 7, 2015 at 8:14:35 PM CDT
To: mauve-users@lists.sourceforge.net
Subject: Re: [Mauve-users] Linux Error- for StripsubsetLCBs
Hi Abria, see below...
On Tue, 2015-07-07 at 17:00 +0000, Abria Magee wrote:
I ran mauve on windows to generate an alignment of about 20 genomes. I
used that alignment on the Linux machine to stripSubsetLCBs. I
received the following error:
Storing raw sequence at /tmp/rawseq7173.000
terminate called after throwing an instance of
'boost::exception_detail::clone_impl<boost::exception_detail::error_info_injector<std::ios_base::failure>
>'
what(): failed mapping file: Cannot allocate memory
Aborted (core dumped)
I ran the following command:
/home/Analysis_Tools/mauve_snapshot_2015-02-13/linux-x64/progressi
veMauve /home/ahaynes/MRPAClonalFrame/stripSubsetLCBs
/home/ahaynes/MRPAClonalFrame/MRPA_Alignment_mauve
/home/ahaynes/MRPAClonalFrame/MRPA_Alignment_mauve.bbcols core_alignmen
t.xmfa 500
Could you help me get this working please? Thanks!
The software is trying to store temporary files in the system's /tmp
directory. Can you check that the directory is writeable and the disk
partition is not full? Note that you should be able to redirect the
temporary storage used by the mauve command-line software by setting the
TMPDIR environment variable, e.g. in bash:
mkdir $HOME/tmp
export TMPDIR=$HOME/tmp
Best,
-Aaron
--
Aaron E. Darling, Ph.D.
Associate Professor, ithree institute
University of Technology Sydney
Australia
http://darlinglab.org
twitter: @koadman
UTS CRICOS Provider Code: 00099F
DISCLAIMER: This email message and any accompanying attachments may contain
confidential information.
If you are not the intended recipient, do not read, use, disseminate,
distribute or copy this message or
attachments. If you have received this message in error, please notify the
sender immediately and delete
this message. Any views expressed in this message are those of the individual
sender, except where the
sender expressly, and with authority, states them to be the views of the
University of Technology Sydney.
Before opening any attachments, please check them for viruses and defects.
Think. Green. Do.
Please consider the environment before printing this email.
------------------------------------------------------------------------------
Don't Limit Your Business. Reach for the Cloud.
GigeNET's Cloud Solutions provide you with the tools and support that
you need to offload your IT needs and focus on growing your business.
Configured For All Businesses. Start Your Cloud Today.
https://www.gigenetcloud.com/
_______________________________________________
Mauve-users mailing list
Mauve-users@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/mauve-users
------------------------------------------------------------------------------
Don't Limit Your Business. Reach for the Cloud.
GigeNET's Cloud Solutions provide you with the tools and support that
you need to offload your IT needs and focus on growing your business.
Configured For All Businesses. Start Your Cloud Today.
https://www.gigenetcloud.com/
_______________________________________________
Mauve-users mailing list
Mauve-users@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/mauve-users
