[khmer] normalize-by-median.py - IOError: [Errno 30] Read-only file system:
Efraim Rodrigues
efraimnaassom at gmail.com
Thu Jul 3 10:01:21 PDT 2014
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
>
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