<div dir="ltr">Hi everyone,<div><br></div><div>Actually, when I tried to install by running 'make test', it returned the following message: </div><div><br></div><blockquote style="margin:0 0 0 40px;border:none;padding:0px">
<div>pip2 install --user nose || pip2 install nose</div><div>/bin/sh: pip2: command not found</div><div>/bin/sh: pip2: command not found</div></blockquote><div><br></div><div>Even though we have python/2.7 installed, It looks like my system has python/2.6 as default. Hence, in order to install 'khmer', I followed these steps:</div>
<div><br></div>
<div><blockquote style="margin:0 0 0 40px;border:none;padding:0px"><div>module load python/2.7</div></blockquote><blockquote style="margin:0 0 0 40px;border:none;padding:0px"><div>python setup.py install --user</div></blockquote>
</div><div><br></div><div>Apparently, it worked to install it locally, however I'm not sure about any additional file or module.</div><div><br></div><div>Cheers,</div></div><div class="gmail_extra"><br><br><div class="gmail_quote">
On Fri, Jul 4, 2014 at 12:49 PM, Ramakrishnan Srinivasan <span dir="ltr"><<a href="mailto:ramrs@nyu.edu" target="_blank">ramrs@nyu.edu</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<p dir="ltr">Efraim, </p>
<p dir="ltr">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? </p>
<p dir="ltr">--<br>
Ram<br>
Sent from my Phone</p><div class="HOEnZb"><div class="h5">
<div class="gmail_quote">On Jul 4, 2014 11:14 AM, "C. Titus Brown" <<a href="mailto:ctb@msu.edu" target="_blank">ctb@msu.edu</a>> wrote:<br type="attribution"><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Hi Efraim,<br>
<br>
then I have no ideas left! My only suggestion would be to try running<br>
khmer in a directory on a different file system.<br>
<br>
Michael, any thoughts?<br>
<br>
cheers,<br>
--titus<br>
<br>
On Thu, Jul 03, 2014 at 12:01:21PM -0500, Efraim Rodrigues wrote:<br>
> No. I'm running it in developer mode.<br>
><br>
><br>
> On Thu, Jul 3, 2014 at 9:42 AM, C. Titus Brown <<a href="mailto:ctb@msu.edu" target="_blank">ctb@msu.edu</a>> wrote:<br>
><br>
> > OK, very weird :). Are you using virtualbox, by any chance?<br>
> ><br>
> > <a href="https://github.com/pypa/virtualenv/issues/209" target="_blank">https://github.com/pypa/virtualenv/issues/209</a><br>
> ><br>
> > cheers,<br>
> > --titus<br>
> ><br>
> > On Wed, Jul 02, 2014 at 04:36:02PM -0500, Efraim Rodrigues wrote:<br>
> > > Hi, Titus.<br>
> > ><br>
> > > Yes, I have the privileges to write. The instruction 'touch' worked, but<br>
> > I<br>
> > > still have the error.<br>
> > ><br>
> > > Regards,<br>
> > ><br>
> > ><br>
> > > On Wed, Jul 2, 2014 at 12:53 PM, C. Titus Brown <<a href="mailto:ctb@msu.edu" target="_blank">ctb@msu.edu</a>> wrote:<br>
> > ><br>
> > > > 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<br>
> > files<br>
> > > > 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>
> > > ><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<br>
> > 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 <<br>
> > <a href="mailto:ramrs@nyu.edu" target="_blank">ramrs@nyu.edu</a>><br>
> > > > > wrote:<br>
> > > > ><br>
> > > > > > Hello Efraim,<br>
> > > > > ><br>
> > > > > > Thank you for using khmer. This looks like an error owing to<br>
> > > > incompatible<br>
> > > > > > file system formats.<br>
> > > > > ><br>
> > > > > > This might happen if we tried writing to an incompatible file<br>
> > system<br>
> > > > (say,<br>
> > > > > > NTFS) from certain versions of Linux. Any information on the exact<br>
> > > > Linux<br>
> > > > > > distro+version you're running and the filesystem format of the<br>
> > > > 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 <<br>
> > > > <a href="mailto:efraimnaassom@gmail.com" target="_blank">efraimnaassom@gmail.com</a><br>
> > > > > > > wrote:<br>
> > > > > ><br>
> > > > > >> Greetings,<br>
> > > > > >><br>
> > > > > >> Before running normalize-by-median.py, I ran interleave-reads.py<br>
> > which<br>
> > > > > >> generated a 'se' file. Then, it looks like the<br>
> > 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<br>
> > possible<br>
> > > > rights,<br>
> > > > > >> it is still returning the error IOError: [Errno 30] Read-only<br>
> > file<br>
> > > > 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<br>
> > > > could<br>
> > > > > >> not find anything related to it. Thus, has anyone faced this<br>
> > problem<br>
> > > > before?<br>
> > > > > >><br>
> > > > > >> Regards,<br>
> > > > > >> Efraim Rodrigues.<br>
> > > > > >><br>
> > > > > >> _______________________________________________<br>
> > > > > >> khmer mailing list<br>
> > > > > >> <a href="mailto:khmer@lists.idyll.org" target="_blank">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>
> > > > > khmer mailing list<br>
> > > > > <a href="mailto:khmer@lists.idyll.org" target="_blank">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>
> > > > C. Titus Brown, <a href="mailto:ctb@msu.edu" target="_blank">ctb@msu.edu</a><br>
> > > ><br>
> ><br>
> > --<br>
> > C. Titus Brown, <a href="mailto:ctb@msu.edu" target="_blank">ctb@msu.edu</a><br>
> ><br>
<br>
--<br>
C. Titus Brown, <a href="mailto:ctb@msu.edu" target="_blank">ctb@msu.edu</a><br>
</blockquote></div>
</div></div></blockquote></div><br></div>