<div dir="ltr">Hi, Titus.<div><br></div><div>Yes, I have the privileges to write. The instruction 'touch' worked, but I still have the error.</div><div><br></div><div>Regards,</div></div><div class="gmail_extra"><br>
<br><div class="gmail_quote">On Wed, Jul 2, 2014 at 12:53 PM, C. Titus Brown <span dir="ltr"><<a href="mailto:ctb@msu.edu" target="_blank">ctb@msu.edu</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Hi Efraim,<br>
<br>
looks to me like the directory you're running normalize-by-median.py in<br>
is mounted read-only -- could be incompatibility, could be just mounted<br>
that way. Try doing 'touch jjj' to see if you have write privileges;<br>
if that works then something strange is going on :).<br>
<br>
One likely confusion here is that most of our scripts write output files into<br>
the current working directory. That's intentional design but not<br>
particularly standard...<br>
<br>
Let us know how it goes!<br>
<br>
cheers,<br>
--titus<br>
<div class="HOEnZb"><div class="h5"><br>
On Wed, Jul 02, 2014 at 11:41:00AM -0500, Efraim Rodrigues wrote:<br>
> Greetings Ramakrishnan,<br>
><br>
> Thank you for quick reply.<br>
><br>
> This is the output for 'uname -a', 2.6.32-431.11.2.el6.x86_64 #1 SMP Tue<br>
> Mar 25 11:15:18 CDT 2014 x86_64 x86_64 x86_64 GNU/Linux<br>
><br>
> My output for 'mount' is "type nfs<br>
> (rw,nfsvers=3,rsize=32678,wsize=32678,noacl,sloppy)".<br>
><br>
> Thank you!<br>
><br>
><br>
> On Wed, Jul 2, 2014 at 11:28 AM, Ramakrishnan Srinivasan <<a href="mailto:ramrs@nyu.edu">ramrs@nyu.edu</a>><br>
> wrote:<br>
><br>
> > Hello Efraim,<br>
> ><br>
> > Thank you for using khmer. This looks like an error owing to incompatible<br>
> > file system formats.<br>
> ><br>
> > This might happen if we tried writing to an incompatible file system (say,<br>
> > NTFS) from certain versions of Linux. Any information on the exact Linux<br>
> > distro+version you're running and the filesystem format of the partition<br>
> > you are writing to would help.<br>
> ><br>
> > Could you maybe give us the output of the following commands:<br>
> > `uname -a`<br>
> > `mount`<br>
> ><br>
> > Thank you!<br>
> ><br>
> ><br>
> ><br>
> > --<br>
> > Ram<br>
> ><br>
> ><br>
> > On Wed, Jul 2, 2014 at 12:13 PM, Efraim Rodrigues <<a href="mailto:efraimnaassom@gmail.com">efraimnaassom@gmail.com</a><br>
> > > wrote:<br>
> ><br>
> >> Greetings,<br>
> >><br>
> >> Before running normalize-by-median.py, I ran interleave-reads.py which<br>
> >> generated a 'se' file. Then, it looks like the normalize-by-median.py<br>
> >> requires special rights to work on this output file from<br>
> >> interleave-reads.py and even though I have already set all possible rights,<br>
> >> it is still returning the error IOError: [Errno 30] Read-only file system:<br>
> >><br>
> >> I looked it up on github issues and <a href="http://khmer.readthedocs.org/" target="_blank">khmer.readthedocs.org/</a> but I could<br>
> >> not find anything related to it. Thus, has anyone faced this problem before?<br>
> >><br>
> >> Regards,<br>
> >> Efraim Rodrigues.<br>
> >><br>
> >> _______________________________________________<br>
> >> khmer mailing list<br>
> >> <a href="mailto:khmer@lists.idyll.org">khmer@lists.idyll.org</a><br>
> >> <a href="http://lists.idyll.org/listinfo/khmer" target="_blank">http://lists.idyll.org/listinfo/khmer</a><br>
> >><br>
> >><br>
> ><br>
<br>
> _______________________________________________<br>
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> <a href="mailto:khmer@lists.idyll.org">khmer@lists.idyll.org</a><br>
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<br>
<br>
</div></div><span class="HOEnZb"><font color="#888888">--<br>
C. Titus Brown, <a href="mailto:ctb@msu.edu">ctb@msu.edu</a><br>
</font></span></blockquote></div><br></div>