Hi Abria,
   I don't think the error is about about your drive space, it is about your 
RAM memory.

Try to watch with 'ps' command in a loop how much memory your mauve instance 
takes just before the repeatable crash.


Also, consider recompiling mauve and using a different BOOST library version 
and enable extra debug symbols to be retained in the resulting binary.


You could be hitting an internal limits of enforced by your parent shell. Read 
'man bash' on you system and make sure you raised your limits:

        ulimit [-HSTabcdefilmnpqrstuvx [limit]]
               Provides  control over the resources available to the shell and 
to processes started by it, on systems that allow such con‐
               trol.  The -H and -S options specify that the hard or soft limit 
is set for the given resource.  A  hard  limit  cannot  be
               increased  by  a non-root user once it is set; a soft limit may 
be increased up to the value of the hard limit.  If neither
               -H nor -S is specified, both the soft and hard limits are set.  
The value of limit can be a number in  the  unit  specified
               for the resource or one of the special values hard, soft, or 
unlimited, which stand for the current hard limit, the current
               soft limit, and no limit, respectively.  If limit is omitted, 
the current value of  the  soft  limit  of  the  resource  is
               printed,  unless  the  -H  option  is given.  When more than one 
resource is specified, the limit name and unit are printed
               before the value.  Other options are interpreted as follows:
               -a     All current limits are reported
               -b     The maximum socket buffer size
               -c     The maximum size of core files created
               -d     The maximum size of a process's data segment
               -e     The maximum scheduling priority ("nice")
               -f     The maximum size of files written by the shell and its 
children
               -i     The maximum number of pending signals
               -l     The maximum size that may be locked into memory
               -m     The maximum resident set size (many systems do not honor 
this limit)
               -n     The maximum number of open file descriptors (most systems 
do not allow this value to be set)
               -p     The pipe size in 512-byte blocks (this may not be set)
               -q     The maximum number of bytes in POSIX message queues
               -r     The maximum real-time scheduling priority
               -s     The maximum stack size
               -t     The maximum amount of cpu time in seconds
               -u     The maximum number of processes available to a single user
               -v     The maximum amount of virtual memory available to the 
shell and, on some systems, to its children
               -x     The maximum number of file locks
               -T     The maximum number of threads

               If limit is given, and the -a option is not used, limit is the 
new value of the specified resource.  If no option is given,
               then  -f  is  assumed.   Values  are  in 1024-byte increments, 
except for -t, which is in seconds; -p, which is in units of
               512-byte blocks; and -T, -b, -n, and -u, which are unscaled 
values.  The return status is 0 unless  an  invalid  option  or
               argument is supplied, or an error occurs while setting a new 
limit.

$ ulimit -l unlimited
$ ulimit -m unlimited
$ ulimit -s unlimited

Finally, as it seems you did not receive your coredump file, execute also teh 
following from the parent Bourne shell:

$ ulimit -c unlimited

This will help you getting a filename called core with crashed instance of 
mauve.


After the crash resolve the core file:

$ gdb/home/Analysis_Tools/mauve_snapshot_2015-02-13/linux-x64/progressiveMauve

On the gdb commandline '(gdb)' type 3 commands:

(gdb) where
(gdb) bt full
(gdb) quit

Martin

Abria Magee wrote:
> 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 Magee*
> abria2...@sbcglobal.net <mailto:abria2...@sbcglobal.net>
>
>
> :
>
>> *From:* Aaron Darling <aaron.darl...@uts.edu.au 
>> <mailto:aaron.darl...@uts.edu.au>>
>> *Date:* July 7, 2015 at 8:14:35 PM CDT
>> *To:* mauve-users@lists.sourceforge.net 
>> <mailto: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!


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