[maker-devel] MAKER / RepeatRunner configuration issue

[Mark Yandell]

you are the Man, Carson.

--mark




________________________________________
From: maker-devel [maker-devel-bounces at yandell-lab.org] on behalf of Carson Holt [carsonhh at gmail.com]
Sent: Monday, May 05, 2014 4:34 PM
To: Dave Messina
Cc: maker-devel at yandell-lab.org
Subject: Re: [maker-devel] MAKER / RepeatRunner configuration issue

After logging in I found the issue.  You have a broken BioPerl build.  Specifically Bio::DB::Fasta.  Quite some time ago, there was a download direct from the BioPerl website that was broken and I think you may have that broken version. Just update to the current CPAN version.  I was able to run fine when I forced MAKER to use a path I made for the the newer version of BioPerl.  You can delete my credentials now.

Thanks,
Carson

From: Carson Holt <carsonhh at gmail.com<mailto:carsonhh at gmail.com>>
Date: Monday, May 5, 2014 at 2:00 PM
To: Dave Messina <online at davemessina.com<mailto:online at davemessina.com>>
Cc: <maker-devel at yandell-lab.org<mailto:maker-devel at yandell-lab.org>>
Subject: Re: [maker-devel] MAKER / RepeatRunner configuration issue

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<mailto:online at davemessina.com>>
Date: Monday, May 5, 2014 at 1:53 PM
To: Carson Holt <carsonhh at gmail.com<mailto:carsonhh at gmail.com>>
Cc: <maker-devel at yandell-lab.org<mailto: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<mailto: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