January 2009 - Mg-rast - mailman3.cels.anl.gov

Job 2298 Not Progressing
by Harry J. Tripp 31 Jan '09

31 Jan '09

Hello, I submitted job 2298 yesterday with three other jobs. The three other jobs finished, but 2298 never made it past similarity checking. Jim Tripp

1 0

Re: [mg-rast] Server Question
by Folker Meyer 30 Jan '09

30 Jan '09

Hi Ben, looking at your data it looks to me as if they are not a collection of very small fragments (what we optimized MG-RAST for) but rather complete or semi-complete genomes. Maybe you can try our RAST server for complete genomes it is probably better suited. It is at http://rast.nmpdr.org Best, Folker On Jan 30, 2009, at 5:43 PM, Ben Tully wrote: > To Whom It May Concern: > > My account login is btully, and I have a question about assignments > through MG-RAST. I submitted several genomes, Prokaryotic_Cren > (4441247.3), N. maritimus (4441246.3) & GOM (4441157.3) from project > Gulf_of_Maine. Why do these metagenomes have 0% assignments to SEED > subsystems, and how can I remedy such situations in the future? > > Thanks you for your time > > Ben Tully > > -- > University of Southern California > Graduate Student > Marine Environmental Biology Department

1 0

Re: [mg-rast] Server Question
by Jared Wilkening 30 Jan '09

30 Jan '09

Hmm, seems like this guy might not know what he's submitting. Prokaryotic_Cren (4441247.3) Total no. of sequences 609 Total sequence size 4,111,169 N. maritimus (4441246.3) Total no. of sequences 1 Total sequence size 1,645,259 GOM (4441157.3) Total no. of sequences 117,673 Total sequence size 430,034,892 I'm not quite sure how to politely tell him this. Could someone give it a try? Jared On Fri, Jan 30, 2009 at 5:43 PM, Ben Tully <tully.bj(a)gmail.com> wrote: > To Whom It May Concern: > > My account login is btully, and I have a question about assignments through > MG-RAST. I submitted several genomes, Prokaryotic_Cren (4441247.3), N. > maritimus (4441246.3) & GOM (4441157.3) from project Gulf_of_Maine. Why do > these metagenomes have 0% assignments to SEED subsystems, and how can I > remedy such situations in the future? > > Thanks you for your time > > Ben Tully > > -- > University of Southern California > Graduate Student > Marine Environmental Biology Department >

1 0

Server Question
by Ben Tully 30 Jan '09

30 Jan '09

To Whom It May Concern: My account login is btully, and I have a question about assignments through MG-RAST. I submitted several genomes, Prokaryotic_Cren (4441247.3), N. maritimus (4441246.3) & GOM (4441157.3) from project Gulf_of_Maine. Why do these metagenomes have 0% assignments to SEED subsystems, and how can I remedy such situations in the future? Thanks you for your time Ben Tully -- University of Southern California Graduate Student Marine Environmental Biology Department

1 0

error message metagenomics view MG-RAST
by Hilary G. Morrison 30 Jan '09

30 Jan '09

Can't locate object method "new" via package "WebPage::FeatureList" at /vol/mg-rast-prod/FIGdisk/dist/releases/mgrast_2008_1110/common/lib/ WebApplication/WebApplication.pm line 1310. referring page:http://metagenomics.nmpdr.org/metagenomics.cgi?page=Kegg&organism=4442… EC 2.3.2.2 Mozilla/5.0 (Macintosh; U; Intel Mac OS X 10.5; en-US; rv:1.9.0.5) Gecko/2008120121 Firefox/3.0.5 Hilary G. Morrison, Ph.D. Associate Research Scientist Josephine Bay Paul Center Marine Biological Laboratory 7 MBL Street Woods Hole, MA 02543-1015 508-289-7339 508-457-4727 (fax) morrison(a)mbl.edu https://jbpc.mbl.edu/labs-morrison.html www.giardiadb.org/giardiadb/

1 0

Re: [mg-rast] server up
by Jared Wilkening 29 Jan '09

29 Jan '09

Done On Thu, Jan 29, 2009 at 4:31 PM, Robert Olson <olson(a)mcs.anl.gov> wrote: > I've swtiched the proxy to point over at the live server again. > > someone will need to pull the maintenance message from it. >

1 0

server up
by Robert Olson 29 Jan '09

29 Jan '09

I've swtiched the proxy to point over at the live server again. someone will need to pull the maintenance message from it.

1 0

Re: [mg-rast] Scheduling down time for mg-rast
by Robert Olson 29 Jan '09

29 Jan '09

cool, and it looks liek the cname change has made it into place. let me know when it is back and I'll fix the redirect back to the live server. --bob On Thu, 29 Jan 2009, Jared Wilkening wrote: > Fixed it mostly by configuring my cgi_url to use a path on bioseed. Not > perfect but acceptable. > > Jared > > On Thu, Jan 29, 2009 at 9:13 AM, Robert Olson <olson(a)mcs.anl.gov> wrote: > >> I have the redirect in place on the proxy server for the downtime message; >> Jared, you will need to change the cgi_url or absolute_url (depending how >> you've got it configured) to use the metagenomics.nmpdr.org base URL >> instead of biologin-4, since biologin-4 is not directly accessible from the >> outside; otherwise there are errors on loading the images and css sheets. >> >> --bob >> >> >> On Wed, 28 Jan 2009, Jared Wilkening wrote: >> >> Bob, >>> >>> I have one of my sandboxes setup with a MG-RAST downtime message. Here >>> is the link. >>> >>> http://biologin-4.mcs.anl.gov/~jared/mgrast/metagenomics.cgi<http://biologin-4.mcs.anl.gov/%7Ejared/mgrast/metagenomics.cgi> >>> >>> Jared >>> >>> On Wed, Jan 28, 2009 at 3:38 PM, Jared Wilkening >>> <jared.wilkening(a)gmail.com> wrote: >>> >>>> We can put the warning up at anytime. Doing so today would likely be >>>> social behavior. If you have suggestions for the content I'll put it >>>> up or I can just write it. >>>> >>>> During the actual downtime of the mg-rast we need redirect the site >>>> some other FIGdisk in order for it to be displayed. I don't have an >>>> opinion of how would be best/easiest to do that. I think Bob would >>>> have to comment. >>>> >>>> Jared >>>> >>>> On Wed, Jan 28, 2009 at 3:26 PM, Folker Meyer >>>> <folker.meyer(a)googlemail.com> wrote: >>>> >>>>> Bill: >>>>> >>>>> please sync with Jared on the downtime. We need to put up a notice to >>>>> users >>>>> and some warning up front >>>>> >>>>> Folker >>>>> >>>>> Begin forwarded message: >>>>> >>>>> From: William Mihalo <wmihalo(a)ci.uchicago.edu> >>>>>> Date: January 28, 2009 3:15:53 PM CST >>>>>> To: Folker Meyer <folker(a)mcs.anl.gov>, Robert Olson <olson(a)mcs.anl.gov >>>>>>> >>>>>> Subject: Scheduling down time for mg-rast >>>>>> >>>>>> Is it OK to go ahead and start draining the mg-rast queues? I would >>>>>> like >>>>>> to do the upgrade/storage move tomorrow. The disk check on mg-rast will >>>>>> take >>>>>> at least 3 hours to complete. The system update and installation of the >>>>>> 3ware driver in the new kernel will take about 30 minutes. >>>>>> >>>>>> Once all of this completes and I see the external RAID enclosure, I'll >>>>>> start work on wiping out the contents of the external RAID system and >>>>>> install a single GPFS volume on it. >>>>>> >>>>>> Bill >>>>>> >>>>> >>>>> >>>>> >>>> >>> >

1 0

Re: [mg-rast] Scheduling down time for mg-rast
by Jared Wilkening 29 Jan '09

29 Jan '09

Fixed it mostly by configuring my cgi_url to use a path on bioseed. Not perfect but acceptable. Jared On Thu, Jan 29, 2009 at 9:13 AM, Robert Olson <olson(a)mcs.anl.gov> wrote: > I have the redirect in place on the proxy server for the downtime message; > Jared, you will need to change the cgi_url or absolute_url (depending how > you've got it configured) to use the metagenomics.nmpdr.org base URL > instead of biologin-4, since biologin-4 is not directly accessible from the > outside; otherwise there are errors on loading the images and css sheets. > > --bob > > > On Wed, 28 Jan 2009, Jared Wilkening wrote: > > Bob, >> >> I have one of my sandboxes setup with a MG-RAST downtime message. Here >> is the link. >> >> http://biologin-4.mcs.anl.gov/~jared/mgrast/metagenomics.cgi<http://biologin-4.mcs.anl.gov/%7Ejared/mgrast/metagenomics.cgi> >> >> Jared >> >> On Wed, Jan 28, 2009 at 3:38 PM, Jared Wilkening >> <jared.wilkening(a)gmail.com> wrote: >> >>> We can put the warning up at anytime. Doing so today would likely be >>> social behavior. If you have suggestions for the content I'll put it >>> up or I can just write it. >>> >>> During the actual downtime of the mg-rast we need redirect the site >>> some other FIGdisk in order for it to be displayed. I don't have an >>> opinion of how would be best/easiest to do that. I think Bob would >>> have to comment. >>> >>> Jared >>> >>> On Wed, Jan 28, 2009 at 3:26 PM, Folker Meyer >>> <folker.meyer(a)googlemail.com> wrote: >>> >>>> Bill: >>>> >>>> please sync with Jared on the downtime. We need to put up a notice to >>>> users >>>> and some warning up front >>>> >>>> Folker >>>> >>>> Begin forwarded message: >>>> >>>> From: William Mihalo <wmihalo(a)ci.uchicago.edu> >>>>> Date: January 28, 2009 3:15:53 PM CST >>>>> To: Folker Meyer <folker(a)mcs.anl.gov>, Robert Olson <olson(a)mcs.anl.gov >>>>> > >>>>> Subject: Scheduling down time for mg-rast >>>>> >>>>> Is it OK to go ahead and start draining the mg-rast queues? I would >>>>> like >>>>> to do the upgrade/storage move tomorrow. The disk check on mg-rast will >>>>> take >>>>> at least 3 hours to complete. The system update and installation of the >>>>> 3ware driver in the new kernel will take about 30 minutes. >>>>> >>>>> Once all of this completes and I see the external RAID enclosure, I'll >>>>> start work on wiping out the contents of the external RAID system and >>>>> install a single GPFS volume on it. >>>>> >>>>> Bill >>>>> >>>> >>>> >>>> >>> >>

1 0

Re: [mg-rast] Scheduling down time for mg-rast
by Robert Olson 29 Jan '09

29 Jan '09

I have the redirect in place on the proxy server for the downtime message; Jared, you will need to change the cgi_url or absolute_url (depending how you've got it configured) to use the metagenomics.nmpdr.org base URL instead of biologin-4, since biologin-4 is not directly accessible from the outside; otherwise there are errors on loading the images and css sheets. --bob On Wed, 28 Jan 2009, Jared Wilkening wrote: > Bob, > > I have one of my sandboxes setup with a MG-RAST downtime message. Here > is the link. > > http://biologin-4.mcs.anl.gov/~jared/mgrast/metagenomics.cgi > > Jared > > On Wed, Jan 28, 2009 at 3:38 PM, Jared Wilkening > <jared.wilkening(a)gmail.com> wrote: >> We can put the warning up at anytime. Doing so today would likely be >> social behavior. If you have suggestions for the content I'll put it >> up or I can just write it. >> >> During the actual downtime of the mg-rast we need redirect the site >> some other FIGdisk in order for it to be displayed. I don't have an >> opinion of how would be best/easiest to do that. I think Bob would >> have to comment. >> >> Jared >> >> On Wed, Jan 28, 2009 at 3:26 PM, Folker Meyer >> <folker.meyer(a)googlemail.com> wrote: >>> Bill: >>> >>> please sync with Jared on the downtime. We need to put up a notice to users >>> and some warning up front >>> >>> Folker >>> >>> Begin forwarded message: >>> >>>> From: William Mihalo <wmihalo(a)ci.uchicago.edu> >>>> Date: January 28, 2009 3:15:53 PM CST >>>> To: Folker Meyer <folker(a)mcs.anl.gov>, Robert Olson <olson(a)mcs.anl.gov> >>>> Subject: Scheduling down time for mg-rast >>>> >>>> Is it OK to go ahead and start draining the mg-rast queues? I would like >>>> to do the upgrade/storage move tomorrow. The disk check on mg-rast will take >>>> at least 3 hours to complete. The system update and installation of the >>>> 3ware driver in the new kernel will take about 30 minutes. >>>> >>>> Once all of this completes and I see the external RAID enclosure, I'll >>>> start work on wiping out the contents of the external RAID system and >>>> install a single GPFS volume on it. >>>> >>>> Bill >>> >>> >> >

1 0