OK, I think I figured it out: it seems to be the result of the /tmp
directory being filled up (which only had 8G of space), so no more files
were allowed to be created there.
The program subsequently crashes because it can't find files in that /tmp
directory that should have been there.
This makes sense, because probably what happened during the decrease of
memory just before the crash is that a lot of that memory was written to
files in /tmp ?
Anyway, the solution is to specify a different tmp directory (in this case
/var/tmp) where more space is available, by using the following command:
env TMPDIR=/var/tmp/ /usr/local/bin/mauve_2.3.1/linux-x64/progressiveMauve
--output=pmout.xmfa *.fna
I hope this was it, at least it's still running now...
Bas
On Wed, Dec 19, 2012 at 9:58 AM, Bas E. Dutilh <[email protected]> wrote:
> On 2010-12-09 00:53 an email was sent to this mailinglist about a Bad file
> descriptor error, and I now have the same error. As there was no answer in
> 2010, I am asking if maybe now anyone knows how to resolve this?
>
> ==============================
> Writing guide tree to /tmp/guide_tree13605.000
> reading tree...
> initializing alignment tree...
> Constructing seed occurrence lists for repeat detection
> terminate called after throwing an instance of 'std::ios_base::failure'
> what(): failed opening file: Bad file descriptor
> Aborted
> ==============================
>
> I ran the following command (64bit version of progressiveMauve):
> /usr/local/bin/mauve_2.3.1/linux-x64/progressiveMauve --output=pmout.xmfa
> *.fna
>
> There were 234 genomes (in contigs) as input (*.fna).
> Interestingly, when I ran the same command a second time, I got an error
> round about the same point in the program (Constructing seed occurrence
> lists for repeat detection) but with a different error message:
>
> ==============================
> Writing guide tree to /tmp/guide_tree32051.000
> reading tree...
> initializing alignment tree...
> Constructing seed occurrence lists for repeat detection
> terminate called after throwing an instance of 'std::ios_base::failure'
> what(): failed mapping file: Invalid argument
> Aborted
> ==============================
>
> Below are the last few lines from the top for this process, showing that
> the memory is probably not the issue (?) because just a few minutes before
> the crash the memory usage was decreased:
> 32051 dutilh 20 0 40.7g 39g 3.6g R 100 15.6 2595:49
> progressiveMauv
> 32051 dutilh 20 0 40.7g 39g 3.6g R 100 15.6 2596:49
> progressiveMauv
> 32051 dutilh 20 0 40.7g 39g 3.6g R 100 15.6 2597:49
> progressiveMauv
> 32051 dutilh 20 0 14.2g 12g 3.6g R 99 5.1 2598:49
> progressiveMauv
> 32051 dutilh 20 0 14.8g 12g 3.6g R 100 5.1 2599:49
> progressiveMauv
>
> Any help or tips would be greatly appreciated! Merry Xmas, Bas
>
>
--
Dr. Bas E. Dutilh
CMBI | NCMLS | Radboud University Medical Centre
http://www.cmbi.ru.nl/~dutilh
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