[maker-devel] MAKER / RepeatRunner configuration issue

[Carson Holt]

I can't reproduce your issue, so it is probably something about your system
or environment.

1. Is you /tmp directory full (or whatever you have $TMPDIR environmental
variable is set to). Use 'df -h /tmp' to check.
2. Are you running in a directory on an NFS drive?  Is it true NFS or is it
something like FUSE.
3. Is your current working directory full.
4. 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.
5. Is your default /tmp directory in fact locally mounted (some clusters set
this to in memory scratch).
6. Even though you already checked, humor me and run this exact command -->
/Volumes/Qnap/external/Linux_x86_64/ncbi-blast/bin/blastx -version
--Carson


From:  Dave Messina <online at davemessina.com>
Date:  Monday, May 5, 2014 at 12:05 PM
To:  Carson Holt <carsonhh at gmail.com>
Cc:  <maker-devel at yandell-lab.org>
Subject:  Re: [maker-devel] MAKER / RepeatRunner configuration issue

Thanks for your quick reply, Carson.

I'm using BLAST+ version 2.2.28, and even after upgrading from MAKER 2.31 to
2.31.3, unfortunately I'm still seeing the same issue.

I've uploaded a new tarball containing the latest (failed) output on the dpp
sample data.

Any thoughts you have on how to resolve this would be great.


Thanks!
Dave




On Mon, May 5, 2014 at 11:53 AM, Carson Holt <carsonhh at gmail.com> wrote:
> Use BLAST+ version 2.2.28.  Also Make sure you are not using an old version of
> MAKER (2.31.3 is current).
> 
> ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/2.2.28/
> 
> --Carson
> 
> 
> From:  Dave Messina <online at davemessina.com>
> Date:  Monday, May 5, 2014 at 10:48 AM
> To:  <maker-devel at yandell-lab.org>
> Subject:  [maker-devel] MAKER / RepeatRunner configuration issue
> 
> Hi,
> 
> Even with the sample data, I'm getting a "Sequence contains no data" error
> from blastx during the RepeatRunner phase.
> 
> I've uploaded a tarball with my run on the dpp sample data to the MAKER File
> Upload site (filename maker_test.tgz).
> 
> Could you please take a look and give me your thoughts?
> 
> 
> Thanks!
> Dave
> 
> 
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