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

[Efraim Rodrigues]

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
>
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