May 2011 - Mg-rast - mailman3.cels.anl.gov

Re: [mg-rast] Evalue cut off problem
by Jack Gilbert 02 May '11

02 May '11

Sorry dude, Still doing it. Quit and restarted firefox, still there - see attached. Not a biggie, but just a small glitch. J On Mon, May 2, 2011 at 12:52 PM, Jared Wilkening <jared.wilkening(a)gmail.com>wrote: > Could you restart your browser and see if happens again. I can't reproduce. > > Jared > > On Mon, May 2, 2011 at 12:38 PM, Jack Gilbert <gilbertjack(a)gmail.com> > wrote: > > firefox > > > > See attached > > > > On Mon, May 2, 2011 at 12:35 PM, Jared Wilkening < > jared.wilkening(a)gmail.com> > > wrote: > >> > >> Which browser are you using? > >> > >> I just tried the live site with both firefox and chrome and it worked > >> fine. > >> > >> Jared > >> > >> On Mon, May 2, 2011 at 12:30 PM, Jack Gilbert <gilbertjack(a)gmail.com> > >> wrote: > >> > FYI, > >> > > >> > When I type in the evalue cut off in the analysis section it lists it > >> > always > >> > 1e-0 no matter what cutoff I enter. > >> > > >> > J > >> > > >> > -- > >> > Dr. Jack A. Gilbert B.Sc. Ph.D. > >> > Argonne National Laboratory > >> > Bldg. 202, Biosciences > >> > Room B373 > >> > 9700 South Cass Avenue > >> > Argonne, IL, 60430 > >> > Tel: +1 630 252-7489 > >> > Cell: +1 630 915 2383 > >> > Email: gilbertjack(a)gmail.com > >> > Twitter: @gilbertjacka > >> > > >> > > > > > > > > > -- > > Dr. Jack A. Gilbert B.Sc. Ph.D. > > Argonne National Laboratory > > Bldg. 202, Biosciences > > Room B373 > > 9700 South Cass Avenue > > Argonne, IL, 60430 > > Tel: +1 630 252-7489 > > Cell: +1 630 915 2383 > > Email: gilbertjack(a)gmail.com > > Twitter: @gilbertjacka > > > > > -- Dr. Jack A. Gilbert B.Sc. Ph.D. Argonne National Laboratory Bldg. 202, Biosciences Room B373 9700 South Cass Avenue Argonne, IL, 60430 Tel: +1 630 252-7489 Cell: +1 630 915 2383 Email: gilbertjack(a)gmail.com Twitter: @gilbertjacka

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Re: [mg-rast] Evalue cut off problem
by Jared Wilkening 02 May '11

02 May '11

Could you restart your browser and see if happens again. I can't reproduce. Jared On Mon, May 2, 2011 at 12:38 PM, Jack Gilbert <gilbertjack(a)gmail.com> wrote: > firefox > > See attached > > On Mon, May 2, 2011 at 12:35 PM, Jared Wilkening <jared.wilkening(a)gmail.com> > wrote: >> >> Which browser are you using? >> >> I just tried the live site with both firefox and chrome and it worked >> fine. >> >> Jared >> >> On Mon, May 2, 2011 at 12:30 PM, Jack Gilbert <gilbertjack(a)gmail.com> >> wrote: >> > FYI, >> > >> > When I type in the evalue cut off in the analysis section it lists it >> > always >> > 1e-0 no matter what cutoff I enter. >> > >> > J >> > >> > -- >> > Dr. Jack A. Gilbert B.Sc. Ph.D. >> > Argonne National Laboratory >> > Bldg. 202, Biosciences >> > Room B373 >> > 9700 South Cass Avenue >> > Argonne, IL, 60430 >> > Tel: +1 630 252-7489 >> > Cell: +1 630 915 2383 >> > Email: gilbertjack(a)gmail.com >> > Twitter: @gilbertjacka >> > >> > > > > > -- > Dr. Jack A. Gilbert B.Sc. Ph.D. > Argonne National Laboratory > Bldg. 202, Biosciences > Room B373 > 9700 South Cass Avenue > Argonne, IL, 60430 > Tel: +1 630 252-7489 > Cell: +1 630 915 2383 > Email: gilbertjack(a)gmail.com > Twitter: @gilbertjacka > >

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Re: [mg-rast] Evalue cut off problem
by Jack Gilbert 02 May '11

02 May '11

firefox See attached On Mon, May 2, 2011 at 12:35 PM, Jared Wilkening <jared.wilkening(a)gmail.com>wrote: > Which browser are you using? > > I just tried the live site with both firefox and chrome and it worked fine. > > Jared > > On Mon, May 2, 2011 at 12:30 PM, Jack Gilbert <gilbertjack(a)gmail.com> > wrote: > > FYI, > > > > When I type in the evalue cut off in the analysis section it lists it > always > > 1e-0 no matter what cutoff I enter. > > > > J > > > > -- > > Dr. Jack A. Gilbert B.Sc. Ph.D. > > Argonne National Laboratory > > Bldg. 202, Biosciences > > Room B373 > > 9700 South Cass Avenue > > Argonne, IL, 60430 > > Tel: +1 630 252-7489 > > Cell: +1 630 915 2383 > > Email: gilbertjack(a)gmail.com > > Twitter: @gilbertjacka > > > > > -- Dr. Jack A. Gilbert B.Sc. Ph.D. Argonne National Laboratory Bldg. 202, Biosciences Room B373 9700 South Cass Avenue Argonne, IL, 60430 Tel: +1 630 252-7489 Cell: +1 630 915 2383 Email: gilbertjack(a)gmail.com Twitter: @gilbertjacka

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Re: [mg-rast] Evalue cut off problem
by Jared Wilkening 02 May '11

02 May '11

Which browser are you using? I just tried the live site with both firefox and chrome and it worked fine. Jared On Mon, May 2, 2011 at 12:30 PM, Jack Gilbert <gilbertjack(a)gmail.com> wrote: > FYI, > > When I type in the evalue cut off in the analysis section it lists it always > 1e-0 no matter what cutoff I enter. > > J > > -- > Dr. Jack A. Gilbert B.Sc. Ph.D. > Argonne National Laboratory > Bldg. 202, Biosciences > Room B373 > 9700 South Cass Avenue > Argonne, IL, 60430 > Tel: +1 630 252-7489 > Cell: +1 630 915 2383 > Email: gilbertjack(a)gmail.com > Twitter: @gilbertjacka > >

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Evalue cut off problem
by Jack Gilbert 02 May '11

02 May '11

FYI, When I type in the evalue cut off in the analysis section it lists it always 1e-0 no matter what cutoff I enter. J -- Dr. Jack A. Gilbert B.Sc. Ph.D. Argonne National Laboratory Bldg. 202, Biosciences Room B373 9700 South Cass Avenue Argonne, IL, 60430 Tel: +1 630 252-7489 Cell: +1 630 915 2383 Email: gilbertjack(a)gmail.com Twitter: @gilbertjacka

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Re: [mg-rast] version 2
by Mark D'Souza 02 May '11

02 May '11

Great, let us know if you see behavior like this again, the v2 machine is old and a bit flakey. Mark ----- Original Message ----- > From: "liz dinsdale" <elizabeth_dinsdale(a)hotmail.com> > To: dsouza(a)mcs.anl.gov > Sent: Monday, May 2, 2011 11:18:57 AM > Subject: RE: [mg-rast] version 2 > HI Mark > > Ya it is working again! > > thanks > > Liz > > Elizabeth Dinsdale, PhD > Assistant Professor > Biology Department > San Diego State University > 5500 Campanile Dr > San Diego 92182 > California > > > > > > Date: Mon, 2 May 2011 11:16:04 -0500 > > From: dsouza(a)mcs.anl.gov > > To: elizabeth_dinsdale(a)hotmail.com > > CC: mg-rast(a)mcs.anl.gov > > Subject: Re: [mg-rast] version 2 > > > > Liz, the site is back up, let us know if you are still having > > trouble with it. > > > > Mark > > > > ----- Original Message ----- > > > From: "Mark D'Souza" <dsouza(a)mcs.anl.gov> > > > To: "liz dinsdale" <elizabeth_dinsdale(a)hotmail.com> > > > Cc: "MG- Rast" <mg-rast(a)mcs.anl.gov> > > > Sent: Monday, May 2, 2011 11:12:02 AM > > > Subject: Re: [mg-rast] version 2 > > > Hi, > > > > > > The machine is in a weird state, it is rebooting right now. > > > > > > Mark > > > > > > ----- Original Message ----- > > > > From: "liz dinsdale" <elizabeth_dinsdale(a)hotmail.com> > > > > To: dsouza(a)mcs.anl.gov > > > > Sent: Monday, May 2, 2011 10:58:43 AM > > > > Subject: RE: [mg-rast] version 2 > > > > Hi Mark > > > > > > > > this occurs at the log in stage, so for private metagenomes > > > > > > > > I actually can't even get the first page to load now! > > > > > > > > Liz > > > > > > > > Elizabeth Dinsdale, PhD > > > > Assistant Professor > > > > Biology Department > > > > San Diego State University > > > > 5500 Campanile Dr > > > > San Diego 92182 > > > > California > > > > > > > > > > > > > > > > > > > > > Date: Mon, 2 May 2011 10:55:23 -0500 > > > > > From: dsouza(a)mcs.anl.gov > > > > > To: elizabeth_dinsdale(a)hotmail.com > > > > > CC: mg-rast(a)mcs.anl.gov > > > > > Subject: Re: [mg-rast] version 2 > > > > > > > > > > Hi, > > > > > > > > > > Were you looking at a public job? The private jobs are working > > > > > fine, > > > > > which is why I had not seen the problem. We will see what is > > > > > going > > > > > on. > > > > > > > > > > Mark > > > > > > > > > > ----- Original Message ----- > > > > > > From: "liz dinsdale" <elizabeth_dinsdale(a)hotmail.com> > > > > > > To: dsouza(a)mcs.anl.gov > > > > > > Sent: Monday, May 2, 2011 10:48:39 AM > > > > > > Subject: RE: [mg-rast] version 2 > > > > > > The page you are looking for is temporarily unavailable. > > > > > > Please > > > > > > try > > > > > > again later. > > > > > > > > > > > > Website Administrator > > > > > > > > > > > > Something has triggered an error on your website. This is > > > > > > the > > > > > > default > > > > > > error page for nginx that is distributed with EPEL. It is > > > > > > located > > > > > > /usr/share/nginx/html/50x.html > > > > > > You should customize this error page for your own site or > > > > > > edit > > > > > > the > > > > > > error_page directive in the nginx configuration file > > > > > > /etc/nginx/nginx.conf . > > > > > > > > > > > > [ Powered by nginx ][ Powered by Fedora EPEL ] > > > > > > > > > > > > Hi Mark > > > > > > > > > > > > I have been trying the site - as have several students since > > > > > > Friday - > > > > > > from various internet connections and it has not worked > > > > > > > > > > > > thanks for you quick response > > > > > > > > > > > > Liz > > > > > > > > > > > > Elizabeth Dinsdale, PhD > > > > > > Assistant Professor > > > > > > Biology Department > > > > > > San Diego State University > > > > > > 5500 Campanile Dr > > > > > > San Diego 92182 > > > > > > California > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > Date: Mon, 2 May 2011 10:01:59 -0500 > > > > > > > From: dsouza(a)mcs.anl.gov > > > > > > > To: elizabeth_dinsdale(a)hotmail.com > > > > > > > CC: mg-rast(a)mcs.anl.gov > > > > > > > Subject: Re: [mg-rast] version 2 > > > > > > > > > > > > > > Hi, > > > > > > > > > > > > > > I do not have any problem accessing the v2 site, though > > > > > > > the > > > > > > > error > > > > > > > log does show timeouts occurring, please let us know what > > > > > > > you > > > > > > > are > > > > > > > seeing, screen shot if possible and browser information. > > > > > > > > > > > > > > I will keep looking into this ... > > > > > > > > > > > > > > Mark > > > > > > > > > > > > > > > > > > > > > ----- Original Message ----- > > > > > > > > From: "elizabeth dinsdale" > > > > > > > > <elizabeth_dinsdale(a)hotmail.com> > > > > > > > > To: mg-rast(a)mcs.anl.gov > > > > > > > > Sent: Monday, May 2, 2011 9:29:20 AM > > > > > > > > Subject: [mg-rast] version 2 > > > > > > > > HI > > > > > > > > > > > > > > > > Version 2 of mg-rast has stalled again! > > > > > > > > > > > > > > > > Is it possible to have the link checked - i teach an > > > > > > > > undergraduate > > > > > > > > class with this platform today at 1pm and it would be > > > > > > > > great > > > > > > > > if > > > > > > > > it > > > > > > > > was > > > > > > > > working by then > > > > > > > > > > > > > > > > thanks > > > > > > > > > > > > > > > > Liz

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Re: [mg-rast] version 2
by Mark D'Souza 02 May '11

02 May '11

Liz, the site is back up, let us know if you are still having trouble with it. Mark ----- Original Message ----- > From: "Mark D'Souza" <dsouza(a)mcs.anl.gov> > To: "liz dinsdale" <elizabeth_dinsdale(a)hotmail.com> > Cc: "MG- Rast" <mg-rast(a)mcs.anl.gov> > Sent: Monday, May 2, 2011 11:12:02 AM > Subject: Re: [mg-rast] version 2 > Hi, > > The machine is in a weird state, it is rebooting right now. > > Mark > > ----- Original Message ----- > > From: "liz dinsdale" <elizabeth_dinsdale(a)hotmail.com> > > To: dsouza(a)mcs.anl.gov > > Sent: Monday, May 2, 2011 10:58:43 AM > > Subject: RE: [mg-rast] version 2 > > Hi Mark > > > > this occurs at the log in stage, so for private metagenomes > > > > I actually can't even get the first page to load now! > > > > Liz > > > > Elizabeth Dinsdale, PhD > > Assistant Professor > > Biology Department > > San Diego State University > > 5500 Campanile Dr > > San Diego 92182 > > California > > > > > > > > > > > Date: Mon, 2 May 2011 10:55:23 -0500 > > > From: dsouza(a)mcs.anl.gov > > > To: elizabeth_dinsdale(a)hotmail.com > > > CC: mg-rast(a)mcs.anl.gov > > > Subject: Re: [mg-rast] version 2 > > > > > > Hi, > > > > > > Were you looking at a public job? The private jobs are working > > > fine, > > > which is why I had not seen the problem. We will see what is going > > > on. > > > > > > Mark > > > > > > ----- Original Message ----- > > > > From: "liz dinsdale" <elizabeth_dinsdale(a)hotmail.com> > > > > To: dsouza(a)mcs.anl.gov > > > > Sent: Monday, May 2, 2011 10:48:39 AM > > > > Subject: RE: [mg-rast] version 2 > > > > The page you are looking for is temporarily unavailable. Please > > > > try > > > > again later. > > > > > > > > Website Administrator > > > > > > > > Something has triggered an error on your website. This is the > > > > default > > > > error page for nginx that is distributed with EPEL. It is > > > > located > > > > /usr/share/nginx/html/50x.html > > > > You should customize this error page for your own site or edit > > > > the > > > > error_page directive in the nginx configuration file > > > > /etc/nginx/nginx.conf . > > > > > > > > [ Powered by nginx ][ Powered by Fedora EPEL ] > > > > > > > > Hi Mark > > > > > > > > I have been trying the site - as have several students since > > > > Friday - > > > > from various internet connections and it has not worked > > > > > > > > thanks for you quick response > > > > > > > > Liz > > > > > > > > Elizabeth Dinsdale, PhD > > > > Assistant Professor > > > > Biology Department > > > > San Diego State University > > > > 5500 Campanile Dr > > > > San Diego 92182 > > > > California > > > > > > > > > > > > > > > > > > > > > Date: Mon, 2 May 2011 10:01:59 -0500 > > > > > From: dsouza(a)mcs.anl.gov > > > > > To: elizabeth_dinsdale(a)hotmail.com > > > > > CC: mg-rast(a)mcs.anl.gov > > > > > Subject: Re: [mg-rast] version 2 > > > > > > > > > > Hi, > > > > > > > > > > I do not have any problem accessing the v2 site, though the > > > > > error > > > > > log does show timeouts occurring, please let us know what you > > > > > are > > > > > seeing, screen shot if possible and browser information. > > > > > > > > > > I will keep looking into this ... > > > > > > > > > > Mark > > > > > > > > > > > > > > > ----- Original Message ----- > > > > > > From: "elizabeth dinsdale" <elizabeth_dinsdale(a)hotmail.com> > > > > > > To: mg-rast(a)mcs.anl.gov > > > > > > Sent: Monday, May 2, 2011 9:29:20 AM > > > > > > Subject: [mg-rast] version 2 > > > > > > HI > > > > > > > > > > > > Version 2 of mg-rast has stalled again! > > > > > > > > > > > > Is it possible to have the link checked - i teach an > > > > > > undergraduate > > > > > > class with this platform today at 1pm and it would be great > > > > > > if > > > > > > it > > > > > > was > > > > > > working by then > > > > > > > > > > > > thanks > > > > > > > > > > > > Liz

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Re: [mg-rast] version 2
by Mark D'Souza 02 May '11

02 May '11

Hi, The machine is in a weird state, it is rebooting right now. Mark ----- Original Message ----- > From: "liz dinsdale" <elizabeth_dinsdale(a)hotmail.com> > To: dsouza(a)mcs.anl.gov > Sent: Monday, May 2, 2011 10:58:43 AM > Subject: RE: [mg-rast] version 2 > Hi Mark > > this occurs at the log in stage, so for private metagenomes > > I actually can't even get the first page to load now! > > Liz > > Elizabeth Dinsdale, PhD > Assistant Professor > Biology Department > San Diego State University > 5500 Campanile Dr > San Diego 92182 > California > > > > > > Date: Mon, 2 May 2011 10:55:23 -0500 > > From: dsouza(a)mcs.anl.gov > > To: elizabeth_dinsdale(a)hotmail.com > > CC: mg-rast(a)mcs.anl.gov > > Subject: Re: [mg-rast] version 2 > > > > Hi, > > > > Were you looking at a public job? The private jobs are working fine, > > which is why I had not seen the problem. We will see what is going > > on. > > > > Mark > > > > ----- Original Message ----- > > > From: "liz dinsdale" <elizabeth_dinsdale(a)hotmail.com> > > > To: dsouza(a)mcs.anl.gov > > > Sent: Monday, May 2, 2011 10:48:39 AM > > > Subject: RE: [mg-rast] version 2 > > > The page you are looking for is temporarily unavailable. Please > > > try > > > again later. > > > > > > Website Administrator > > > > > > Something has triggered an error on your website. This is the > > > default > > > error page for nginx that is distributed with EPEL. It is located > > > /usr/share/nginx/html/50x.html > > > You should customize this error page for your own site or edit the > > > error_page directive in the nginx configuration file > > > /etc/nginx/nginx.conf . > > > > > > [ Powered by nginx ][ Powered by Fedora EPEL ] > > > > > > Hi Mark > > > > > > I have been trying the site - as have several students since > > > Friday - > > > from various internet connections and it has not worked > > > > > > thanks for you quick response > > > > > > Liz > > > > > > Elizabeth Dinsdale, PhD > > > Assistant Professor > > > Biology Department > > > San Diego State University > > > 5500 Campanile Dr > > > San Diego 92182 > > > California > > > > > > > > > > > > > > > > Date: Mon, 2 May 2011 10:01:59 -0500 > > > > From: dsouza(a)mcs.anl.gov > > > > To: elizabeth_dinsdale(a)hotmail.com > > > > CC: mg-rast(a)mcs.anl.gov > > > > Subject: Re: [mg-rast] version 2 > > > > > > > > Hi, > > > > > > > > I do not have any problem accessing the v2 site, though the > > > > error > > > > log does show timeouts occurring, please let us know what you > > > > are > > > > seeing, screen shot if possible and browser information. > > > > > > > > I will keep looking into this ... > > > > > > > > Mark > > > > > > > > > > > > ----- Original Message ----- > > > > > From: "elizabeth dinsdale" <elizabeth_dinsdale(a)hotmail.com> > > > > > To: mg-rast(a)mcs.anl.gov > > > > > Sent: Monday, May 2, 2011 9:29:20 AM > > > > > Subject: [mg-rast] version 2 > > > > > HI > > > > > > > > > > Version 2 of mg-rast has stalled again! > > > > > > > > > > Is it possible to have the link checked - i teach an > > > > > undergraduate > > > > > class with this platform today at 1pm and it would be great if > > > > > it > > > > > was > > > > > working by then > > > > > > > > > > thanks > > > > > > > > > > Liz

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Re: [mg-rast] FYI: your mg-rast v2 site is down.
by Mark D'Souza 02 May '11

02 May '11

Thanks Gary, We are looking into it. Mark ----- Original Message ----- > From: "Gary Xie" <xie(a)lanl.gov> > To: "Mark D'Souza" <dsouza(a)mcs.anl.gov> > Cc: mg-rast(a)mcs.anl.gov > Sent: Monday, May 2, 2011 10:43:24 AM > Subject: FYI: your mg-rast v2 site is down. > http://press.mcs.anl.gov/mg-rast/2011/03/18/mg-rast-v2-is-still-available/ > > > Network Error (tcp_error) > > A communication error occurred: "" The Web Server may be down, too > busy, or experiencing other problems preventing it from responding to > requests. You may wish to try again at a later time. > For assistance, contact your network support team.

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Re: [mg-rast] version 2
by Mark D'Souza 02 May '11

02 May '11

Hi, Were you looking at a public job? The private jobs are working fine, which is why I had not seen the problem. We will see what is going on. Mark ----- Original Message ----- > From: "liz dinsdale" <elizabeth_dinsdale(a)hotmail.com> > To: dsouza(a)mcs.anl.gov > Sent: Monday, May 2, 2011 10:48:39 AM > Subject: RE: [mg-rast] version 2 > The page you are looking for is temporarily unavailable. Please try > again later. > > Website Administrator > > Something has triggered an error on your website. This is the default > error page for nginx that is distributed with EPEL. It is located > /usr/share/nginx/html/50x.html > You should customize this error page for your own site or edit the > error_page directive in the nginx configuration file > /etc/nginx/nginx.conf . > > [ Powered by nginx ][ Powered by Fedora EPEL ] > > Hi Mark > > I have been trying the site - as have several students since Friday - > from various internet connections and it has not worked > > thanks for you quick response > > Liz > > Elizabeth Dinsdale, PhD > Assistant Professor > Biology Department > San Diego State University > 5500 Campanile Dr > San Diego 92182 > California > > > > > > Date: Mon, 2 May 2011 10:01:59 -0500 > > From: dsouza(a)mcs.anl.gov > > To: elizabeth_dinsdale(a)hotmail.com > > CC: mg-rast(a)mcs.anl.gov > > Subject: Re: [mg-rast] version 2 > > > > Hi, > > > > I do not have any problem accessing the v2 site, though the error > > log does show timeouts occurring, please let us know what you are > > seeing, screen shot if possible and browser information. > > > > I will keep looking into this ... > > > > Mark > > > > > > ----- Original Message ----- > > > From: "elizabeth dinsdale" <elizabeth_dinsdale(a)hotmail.com> > > > To: mg-rast(a)mcs.anl.gov > > > Sent: Monday, May 2, 2011 9:29:20 AM > > > Subject: [mg-rast] version 2 > > > HI > > > > > > Version 2 of mg-rast has stalled again! > > > > > > Is it possible to have the link checked - i teach an undergraduate > > > class with this platform today at 1pm and it would be great if it > > > was > > > working by then > > > > > > thanks > > > > > > Liz

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