April 2008 - Mg-rast - mailman3.cels.anl.gov

Re: mg-rast Who is user jwilkening1
by Robert Olson 30 Apr '08

30 Apr '08

oh, I needed to edit USER on those jobs to match his new login. On Apr 30, 2008, at 5:06 PM, Andreas Wilke wrote: > I tried to sync the jobs for mg-rast-test but it failed with: > > bash-3.1$ rast_sync > [SYNC] Syncing /vol/mg-rast-test/jobs > [SYNC] Error during job sync: Unable to find user in database: > jwilkening1 > [SYNC] Update failed on job 607. > [SYNC] Updated 10 in the job directory. > bash-3.1$ cd 607/ > bash-3.1$ less USER > jwilkening1 > > Jared,is this your login? > > Andreas > ------------------------------------------------------ > Andreas Wilke > Argonne National Laboratory > Mathematics and Computer Science Division > Bldg. 221, Room A147 > 9700 South Cass Avenue > Argonne, IL 60439 > (630) 252-3190 (phone) > (630) 252-5986.(fax) > ------------------------------------------------------- > > > > --Apple-Mail-6--642253404--

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mg-rast Who is user jwilkening1
by Andreas Wilke 30 Apr '08

30 Apr '08

I tried to sync the jobs for mg-rast-test but it failed with: bash-3.1$ rast_sync [SYNC] Syncing /vol/mg-rast-test/jobs [SYNC] Error during job sync: Unable to find user in database: jwilkening1 [SYNC] Update failed on job 607. [SYNC] Updated 10 in the job directory. bash-3.1$ cd 607/ bash-3.1$ less USER jwilkening1 Jared,is this your login? Andreas ------------------------------------------------------ Andreas Wilke Argonne National Laboratory Mathematics and Computer Science Division Bldg. 221, Room A147 9700 South Cass Avenue Argonne, IL 60439 (630) 252-3190 (phone) (630) 252-5986.(fax) -------------------------------------------------------

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Re: mg-rast test server now using postgres db's
by Rob Edwards 30 Apr '08

30 Apr '08

Logged in as redwards. You currently have no jobs How sad :( Rob On Wed, Apr 30, 2008 at 2:09 PM, Robert Olson <olson(a)mcs.anl.gov> wrote: > http://mg-rast.mcs.anl.gov/mg-rast-test/FIG/rast.cgi > > > > ______________________________________________________________________ > This email has been scanned by the MessageLabs Email Security System. > For more information please visit http://www.messagelabs.com/email > ______________________________________________________________________ >

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mg-rast test server now using postgres db's
by Robert Olson 30 Apr '08

30 Apr '08

http://mg-rast.mcs.anl.gov/mg-rast-test/FIG/rast.cgi

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Re: mg-rast q on the recruitment plot
by Jared Wilkening 29 Apr '08

29 Apr '08

Odd, I will look into it tomorrow. Jared On Tue, Apr 29, 2008 at 6:36 PM, Folker Meyer <folker.meyer(a)googlemail.com> wrote: > Hi all, > > is Jared on this list? > > If not put him on please... > > Folker > On Apr 29, 2008, at 4:59 PM, Robert Olson wrote: > > I was trying out the recruitement plot using the mgrast2 data under my > > sandbox at http://mg-rast/olson/FIG/metagenomics.cgi. metagenome > > MG_Soybean_Field_Sample (4440698.3). I chose Magnetospirillum magneticum > > AMB-1 (342108.5) as the reference genome since it was the bacteria with the > > most hits according to SEED taxonomy. > > > > The recruitment plot tells me "No fragments found for Magnetospirillum > > magneticum AMB-1 (342108.5)". > > > > --bob > > > > >

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Re: mg-rast q on the recruitment plot
by Folker Meyer 29 Apr '08

29 Apr '08

Hi all, is Jared on this list? If not put him on please... Folker On Apr 29, 2008, at 4:59 PM, Robert Olson wrote: > I was trying out the recruitement plot using the mgrast2 data under > my sandbox at http://mg-rast/olson/FIG/metagenomics.cgi. metagenome > MG_Soybean_Field_Sample (4440698.3). I chose Magnetospirillum > magneticum AMB-1 (342108.5) as the reference genome since it was the > bacteria with the most hits according to SEED taxonomy. > > The recruitment plot tells me "No fragments found for > Magnetospirillum magneticum AMB-1 (342108.5)". > > --bob >

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Fwd: mg-rast current test version
by Folker Meyer 29 Apr '08

29 Apr '08

all: did we manage to look at this? Is this still the preferred place for testing? What about the new postgres backend? Is this in place here? Do we have a beta-version? FOlker Begin forwarded message: > From: Daniel Paarmann <paarmann(a)mcs.anl.gov> > Date: April 18, 2008 3:47:08 PM CDT > To: mg-rast(a)mcs.anl.gov > Subject: mg-rast current test version > > Here's a link to the current snapshot of the development code for > MGRAST frontend: > > http://mg-rast.mcs.anl.gov/mg-rast-test/FIG/rast.cgi > ( this is the RAST part of it ) > > http://mg-rast.mcs.anl.gov/mg-rast-test/FIG/metagenomics.cgi > ( MG-SeedViewer part ) > > > A few jobs have already been loaded into that database, ranging from > small to very large ones. > > Feedback is appreciated, > > Daniel >

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mg-rast q on the recruitment plot
by Robert Olson 29 Apr '08

29 Apr '08

I was trying out the recruitement plot using the mgrast2 data under my sandbox at http://mg-rast/olson/FIG/metagenomics.cgi. metagenome MG_Soybean_Field_Sample (4440698.3). I chose Magnetospirillum magneticum AMB-1 (342108.5) as the reference genome since it was the bacteria with the most hits according to SEED taxonomy. The recruitment plot tells me "No fragments found for Magnetospirillum magneticum AMB-1 (342108.5)". --bob

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login form wrong on new mg-rast
by Robert Olson 29 Apr '08

29 Apr '08

In safari anyway it appears below the green bar: --bob

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mg-rast we'll have some cleanup to do
by Robert Olson 25 Apr '08

25 Apr '08

There's a bunch of stuff running on the cluster; I need to shut down the scheduler and will be shutting down the nodes before too long. we may have to restart the things that are currently running; if we're lucky the scheduler will restart them for us. worst case we just restart the running jobs. --bob

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