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

[C. Titus Brown]

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
> >>
> >>
> >

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