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

[Ramakrishnan Srinivasan]

Efraim,

Could we maybe run `make test` in the khmer root directory and check for
any failing tests for hints on what may be going on?

--
Ram
Sent from my Phone
On Jul 4, 2014 11:14 AM, "C. Titus Brown" <ctb at msu.edu> wrote:

> 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
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://lists.idyll.org/pipermail/khmer/attachments/20140704/2a4956c3/attachment.htm>