[khmer] normalize-by-median.py - IOError: [Errno 30] Read-only file system:

[C. Titus Brown]

Hi Efraim,

then I have no ideas left!  My only suggestion would be to try running
khmer in a directory on a different file system.

Michael, any thoughts?

cheers,
--titus

On Thu, Jul 03, 2014 at 12:01:21PM -0500, Efraim Rodrigues wrote:
> No. I'm running it in developer mode.
> 
> 
> On Thu, Jul 3, 2014 at 9:42 AM, C. Titus Brown <ctb at msu.edu> wrote:
> 
> > OK, very weird :).  Are you using virtualbox, by any chance?
> >
> > https://github.com/pypa/virtualenv/issues/209
> >
> > cheers,
> > --titus
> >
> > On Wed, Jul 02, 2014 at 04:36:02PM -0500, Efraim Rodrigues wrote:
> > > Hi, Titus.
> > >
> > > Yes, I have the privileges to write. The instruction 'touch' worked, but
> > I
> > > still have the error.
> > >
> > > Regards,
> > >
> > >
> > > On Wed, Jul 2, 2014 at 12:53 PM, C. Titus Brown <ctb at msu.edu> wrote:
> > >
> > > > Hi Efraim,
> > > >
> > > > looks to me like the directory you're running normalize-by-median.py in
> > > > is mounted read-only -- could be incompatibility, could be just mounted
> > > > that way.  Try doing 'touch jjj' to see if you have write privileges;
> > > > if that works then something strange is going on :).
> > > >
> > > > One likely confusion here is that most of our scripts write output
> > files
> > > > into
> > > > the current working directory.  That's intentional design but not
> > > > particularly standard...
> > > >
> > > > Let us know how it goes!
> > > >
> > > > cheers,
> > > > --titus
> > > >
> > > > On Wed, Jul 02, 2014 at 11:41:00AM -0500, Efraim Rodrigues wrote:
> > > > > Greetings Ramakrishnan,
> > > > >
> > > > > Thank you for quick reply.
> > > > >
> > > > > This is the output for 'uname -a', 2.6.32-431.11.2.el6.x86_64 #1 SMP
> > Tue
> > > > > Mar 25 11:15:18 CDT 2014 x86_64 x86_64 x86_64 GNU/Linux
> > > > >
> > > > > My output for 'mount' is "type nfs
> > > > > (rw,nfsvers=3,rsize=32678,wsize=32678,noacl,sloppy)".
> > > > >
> > > > > Thank you!
> > > > >
> > > > >
> > > > > On Wed, Jul 2, 2014 at 11:28 AM, Ramakrishnan Srinivasan <
> > ramrs at nyu.edu>
> > > > > wrote:
> > > > >
> > > > > > Hello Efraim,
> > > > > >
> > > > > > Thank you for using khmer. This looks like an error owing to
> > > > incompatible
> > > > > > file system formats.
> > > > > >
> > > > > > This might happen if we tried writing to an incompatible file
> > system
> > > > (say,
> > > > > > NTFS) from certain versions of Linux. Any information on the exact
> > > > Linux
> > > > > > distro+version you're running and the filesystem format of the
> > > > partition
> > > > > > you are writing to would help.
> > > > > >
> > > > > > Could you maybe give us the output of the following commands:
> > > > > > `uname -a`
> > > > > > `mount`
> > > > > >
> > > > > > Thank you!
> > > > > >
> > > > > >
> > > > > >
> > > > > > --
> > > > > > Ram
> > > > > >
> > > > > >
> > > > > > On Wed, Jul 2, 2014 at 12:13 PM, Efraim Rodrigues <
> > > > efraimnaassom at gmail.com
> > > > > > > wrote:
> > > > > >
> > > > > >> Greetings,
> > > > > >>
> > > > > >> Before running normalize-by-median.py, I ran interleave-reads.py
> > which
> > > > > >> generated a 'se' file. Then, it looks like the
> > normalize-by-median.py
> > > > > >> requires special rights to work on this output file from
> > > > > >> interleave-reads.py and even though I have already set all
> > possible
> > > > rights,
> > > > > >> it is still returning the error  IOError: [Errno 30] Read-only
> > file
> > > > system:
> > > > > >>
> > > > > >> I looked it up on github issues and khmer.readthedocs.org/ but I
> > > > could
> > > > > >> not find anything related to it. Thus, has anyone faced this
> > problem
> > > > before?
> > > > > >>
> > > > > >> Regards,
> > > > > >> Efraim Rodrigues.
> > > > > >>
> > > > > >> _______________________________________________
> > > > > >> khmer mailing list
> > > > > >> khmer at lists.idyll.org
> > > > > >> http://lists.idyll.org/listinfo/khmer
> > > > > >>
> > > > > >>
> > > > > >
> > > >
> > > > > _______________________________________________
> > > > > khmer mailing list
> > > > > khmer at lists.idyll.org
> > > > > http://lists.idyll.org/listinfo/khmer
> > > >
> > > >
> > > > --
> > > > C. Titus Brown, ctb at msu.edu
> > > >
> >
> > --
> > C. Titus Brown, ctb at msu.edu
> >

-- 
C. Titus Brown, ctb at msu.edu