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
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