[maker-devel] MAKER / RepeatRunner configuration issue

[Carson Holt]

This is one of those things that I would have to have access to your system
since I can't duplicate it and it is only happening to you.

If you can swing a temporary ssh account, I can look at it.  But it's really
just a shot in the dark otherwise.

--Carson


From:  Dave Messina <online at davemessina.com>
Date:  Monday, May 5, 2014 at 1:53 PM
To:  Carson Holt <carsonhh at gmail.com>
Cc:  <maker-devel at yandell-lab.org>
Subject:  Re: [maker-devel] MAKER / RepeatRunner configuration issue

Hi Carson,

On Mon, May 5, 2014 at 2:44 PM, Carson Holt <carsonhh at gmail.com> wrote:
> df -h /Volumes/Qnap/projects/projectAnwar_SNGN0016AA-A

Filesystem    Type    Size  Used Avail Use% Mounted on
10.0.1.128:/projects
               nfs     13T  9.6T  3.1T  76% /Volumes/Qnap

That one is on NFS, although the second tarball I uploaded was done in the
/tmp dir, and that's on a local disk:

Filesystem    Type    Size  Used Avail Use% Mounted on
/dev/mapper/vg_d5-lv_root
              ext4     50G  8.9G   38G  19% /
> 1. Is you /tmp directory full (or whatever you have $TMPDIR environmental
> variable is set to). Use 'df -h /tmp' to check.

$ df -h /tmp
Filesystem    Type    Size  Used Avail Use% Mounted on
/dev/mapper/vg_d5-lv_root
              ext4     50G  8.9G   38G  19% /
 
> 1. Are you running in a directory on an NFS drive?  Is it true NFS or is it
> something like FUSE.
Same error on true NFS or on local disk.

 
> 1. Is your current working directory full.
No.

 
> 1. Are you setting TMP= in the control files to either an NFS mounted location
> or an in memory mounted location.  Same issue if you are setting the system's
> TMPDIR environmental variable to one of these.
I tried setting it to /tmp just to be sure (no difference).
 
> 1. Is your default /tmp directory in fact locally mounted (some clusters set
> this to in memory scratch).
Yes.
 
> 1. Even though you already checked, humor me and run this exact command -->
> /Volumes/Qnap/external/Linux_x86_64/ncbi-blast/bin/blastx -version

$ /Volumes/Qnap/external/Linux_x86_64/ncbi-blast/bin/blastx -version
blastx: 2.2.28+
Package: blast 2.2.28, build Mar 12 2013 16:52:31



Thanks so much for your help.

Best,
Dave






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