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

Re: [mg-rast] problem with "share jobs"
by Mark DSouza 31 Aug '11

31 Aug '11

Hi, This is actually a problem on our side, there is some weirdness in the database that is preventing the page from displaying correctly. I will get back to you when it is fixed. Mark ----- Original Message ----- > From: "Sheri Simmons" <ssimmons(a)mbl.edu> > To: "Mark DSouza" <dsouza(a)mcs.anl.gov> > Sent: Wednesday, August 31, 2011 11:32:06 AM > Subject: Re: [mg-rast] problem with "share jobs" > The problem must be with something in my browser configuration then. > Here's the URL of a share job attempt that failed for me: > http://metagenomics.anl.gov/metagenomics.cgi?page=JobShare&metagenome=44684… > I am running Firefox 6.0.1 and the latest version of Adobe Flash if > that helps. > > The job ids to delete are: > 4466400.3 > 4466414.3 > 4466415.3 > 4467614.3 > 4467626.3 > 4467627.3 > 4467661.3 > 4467662.3 > 4467664.3 > 4467671.3 > 4467674.3 > 4467675.3 > 4467676.3 > 4467677.3 > 4467678.3 > 4467683.3 > 4467684.3 > 4468427.3 > > Thanks again for your help. > > Sheri > > On 8/31/2011 12:11 PM, Mark DSouza wrote: > > Hi, > > That is very odd, I just opened the page using your account and did > not have any trouble. Can you send me the URL which opens the page, I > can check through the logs and find out what is going on. > > It is not possible to delete private jobs right now, though I hope we > will have it in the next release. Let me have the MG-RAST job IDs and > I can delete them for you. > > Regards, > Mark > > ----- Original Message ----- > > From: "Sheri Simmons" <ssimmons(a)mbl.edu> To: "Mark DSouza" > <dsouza(a)mcs.anl.gov> Sent: Wednesday, August 31, 2011 10:24:22 AM > Subject: Re: [mg-rast] problem with "share jobs" > Hi, thanks for your quick reply. The "share a job" page is still not > displaying for me, though I am able to use other analysis features. > One other quick question- is it possible to delete private jobs? I > have some metagenomes on the site that I later discovered to have some > pre-processing issues so I'd like to take them down to avoid any > future confusion. > > Sheri > > On 8/31/2011 11:13 AM, Mark DSouza wrote: > > Hi, > > I am not able to reproduce this problem, we did have a server downtime > earlier today which may have been responsible if you hit the server > before it went down and it was wedged. Could you check if the page is > still not displaying. The suggestion for sharing multiple metagenomes > is a good one, we have a number of operations which work on single > metagenomes which which would make sense to extend to multiple > metagenomes. > > -- > Sheri Simmons > Assistant Scientist, Bay Paul Center | Marine Biological Laboratory > Woods Hole, MA 02543 > (508) 289-7177 http://www.simmonslab.org > > -- > Sheri Simmons > Assistant Scientist, Bay Paul Center | Marine Biological Laboratory > Woods Hole, MA 02543 > (508) 289-7177 > http://www.simmonslab.org

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Re: [mg-rast] Yor MG-RAST uploads
by Mark DSouza 31 Aug '11

31 Aug '11

No problem, we will take a look at the three jobs with processing errors and get them fixed. Regards, Mark ----- Original Message ----- > From: "Nicolás Rascovan" <nicorascovan(a)soilgene.net> > Cc: "mg-rast" <mg-rast(a)mcs.anl.gov> > Sent: Wednesday, August 31, 2011 2:12:38 PM > Subject: Re: [mg-rast] Yor MG-RAST uploads > I´m sorry, I found it. It was on next page.... > > > El 31 de agosto de 2011 16:09, Nicolás Rascovan < > nicorascovan(a)soilgene.net > escribió: > > > I have a question about job 4471485.3 . It is not shown either on the > In Progress tab or the Available for Analysis tab. Is there any > problem with that dataset? Was it deleted or something? Jobs > 4471464.3, 4471463.3 and 4471461.3 are still giving error (they change > from step they were this morning though...) > > > Thanks, > > > Nicolas. > > > > > > > El 31 de agosto de 2011 09:12, Nicolás Rascovan < > nicorascovan(a)soilgene.net > escribió: > > > > > > > Hi, > > > I´ve uploaded some metagenomes and it seems that there was a problem > during the processing of some of them. The IDs of the ones that gave > error is: > > > 4471485.3 > 4471484.3 > 4471464.3 > 4471463.3 > 4471461.3 > > > I hope you can solve this error, > > > Thanks, > > > Nicolas Rascovan

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Re: [mg-rast] Export figures
by Mark DSouza 31 Aug '11

31 Aug '11

Hi, Sorry about that, it appears to be a bug in the system. The latest version of FireFox is the test bed in which we expect everything to work, in this case we will have to make some changes. Thanks for bringing it to our attention. -- Regards, Mark D'Souza -- for the MG-RAST team mg-rast(a)mcs.anl.gov http://metagenomics.anl.gov/ If you need to respond to this email please address it to the mailing-list mg-rast(a)mcs.anl.gov ----- Original Message ----- > From: "Antje Gittel" <Antje.Gittel(a)bio.uib.no> > To: mg-rast(a)mcs.anl.gov > Sent: Wednesday, August 31, 2011 2:48:26 PM > Subject: [mg-rast] Export figures > Dear MG-Rast team, > > I was trying to export a PCoA figure a couple of times, but using the > "static mode" results in disappearance of the figure and disables > right-click/save routine. > > Could you let me know how to solve that problem and make the figure > exportable? > > Best regards, > Antje Gittel > > > > ----- > Antje Gittel (PhD) > Department of Biology/Centre for Geobiology > University of Bergen > Thormøhlensgate 53A/B > 5006 Bergen > Norway > > ----- > Contact: > office +47 5558 4715 > mobil +47 96878182 > for calls from Germany +49 441 3096923 > > ----- > http://www.uib.no/persons/Antje.Gittel > http://genetics-ecology.univie.ac.at/gittel.html > > > CryoCARB project: > http://www.univie.ac.at/cryocarb/ > > Private homepage: > https://sites.google.com/site/antjegittel/home

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Re: [mg-rast] Export figures
by Mark DSouza 31 Aug '11

31 Aug '11

I just tested it, this is a real bug. Tobi, I think that earlier the savable image was shifted to the bottom of the page when the button was pressed and people were not seeing it. Now it disappears from the page completely, could you look into this? Thanks, Mark ----- Original Message ----- > From: "Folker Meyer" <folker(a)anl.gov> > To: "MG- Rast" <mg-rast(a)mcs.anl.gov> > Sent: Wednesday, August 31, 2011 2:55:27 PM > Subject: Re: [mg-rast] Export figures > Mark: > > do another video for exporting figures and include screenshots on the > mac (apple shift 4) btw :) > > Folker > > On Aug 31, 2011, at 2:48 PM, Antje Gittel wrote: > > > Dear MG-Rast team, > > > > I was trying to export a PCoA figure a couple of times, but using > > the "static mode" results in disappearance of the figure and > > disables right-click/save routine. > > > > Could you let me know how to solve that problem and make the figure > > exportable? > > > > Best regards, > > Antje Gittel > > > > > > > > ----- > > Antje Gittel (PhD) > > Department of Biology/Centre for Geobiology > > University of Bergen > > Thormøhlensgate 53A/B > > 5006 Bergen > > Norway > > > > ----- > > Contact: > > office +47 5558 4715 > > mobil +47 96878182 > > for calls from Germany +49 441 3096923 > > > > ----- > > http://www.uib.no/persons/Antje.Gittel > > http://genetics-ecology.univie.ac.at/gittel.html > > > > > > CryoCARB project: > > http://www.univie.ac.at/cryocarb/ > > > > Private homepage: > > https://sites.google.com/site/antjegittel/home

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Re: [mg-rast] Export figures
by Folker Meyer 31 Aug '11

31 Aug '11

Mark: do another video for exporting figures and include screenshots on the mac (apple shift 4) btw :) Folker On Aug 31, 2011, at 2:48 PM, Antje Gittel wrote: > Dear MG-Rast team, > > I was trying to export a PCoA figure a couple of times, but using the "static mode" results in disappearance of the figure and disables right-click/save routine. > > Could you let me know how to solve that problem and make the figure exportable? > > Best regards, > Antje Gittel > > > > ----- > Antje Gittel (PhD) > Department of Biology/Centre for Geobiology > University of Bergen > Thormøhlensgate 53A/B > 5006 Bergen > Norway > > ----- > Contact: > office +47 5558 4715 > mobil +47 96878182 > for calls from Germany +49 441 3096923 > > ----- > http://www.uib.no/persons/Antje.Gittel > http://genetics-ecology.univie.ac.at/gittel.html > > > CryoCARB project: > http://www.univie.ac.at/cryocarb/ > > Private homepage: > https://sites.google.com/site/antjegittel/home

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Export figures
by Antje Gittel 31 Aug '11

31 Aug '11

Dear MG-Rast team, I was trying to export a PCoA figure a couple of times, but using the "static mode" results in disappearance of the figure and disables right-click/save routine. Could you let me know how to solve that problem and make the figure exportable? Best regards, Antje Gittel ----- Antje Gittel (PhD) Department of Biology/Centre for Geobiology University of Bergen Thormøhlensgate 53A/B 5006 Bergen Norway ----- Contact: office +47 5558 4715 mobil +47 96878182 for calls from Germany +49 441 3096923 ----- http://www.uib.no/persons/Antje.Gittel http://genetics-ecology.univie.ac.at/gittel.html CryoCARB project: http://www.univie.ac.at/cryocarb/ Private homepage: https://sites.google.com/site/antjegittel/home

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Re: [mg-rast] Yor MG-RAST uploads
by Nicolás Rascovan 31 Aug '11

31 Aug '11

I´m sorry, I found it. It was on next page.... El 31 de agosto de 2011 16:09, Nicolás Rascovan <nicorascovan(a)soilgene.net>escribió: > I have a question about job 4471485.3 . It is not shown either on the In > Progress tab or the Available for Analysis tab. Is there any problem with > that dataset? Was it deleted or something? Jobs 4471464.3, 4471463.3 > and 4471461.3 are still giving error (they change from step they were this > morning though...) > > Thanks, > > Nicolas. > > > > El 31 de agosto de 2011 09:12, Nicolás Rascovan <nicorascovan(a)soilgene.net > > escribió: > > Hi, >> >> I´ve uploaded some metagenomes and it seems that there was a problem >> during the processing of some of them. The IDs of the ones that gave error >> is: >> >> 4471485.3 >> 4471484.3 >> 4471464.3 >> 4471463.3 >> 4471461.3 >> >> I hope you can solve this error, >> >> Thanks, >> >> Nicolas Rascovan >> > >

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Re: [mg-rast] Yor MG-RAST uploads
by Nicolás Rascovan 31 Aug '11

31 Aug '11

I have a question about job 4471485.3 . It is not shown either on the In Progress tab or the Available for Analysis tab. Is there any problem with that dataset? Was it deleted or something? Jobs 4471464.3, 4471463.3 and 4471461.3 are still giving error (they change from step they were this morning though...) Thanks, Nicolas. El 31 de agosto de 2011 09:12, Nicolás Rascovan <nicorascovan(a)soilgene.net>escribió: > Hi, > > I´ve uploaded some metagenomes and it seems that there was a problem during > the processing of some of them. The IDs of the ones that gave error is: > > 4471485.3 > 4471484.3 > 4471464.3 > 4471463.3 > 4471461.3 > > I hope you can solve this error, > > Thanks, > > Nicolas Rascovan >

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Re: [mg-rast] problem with "share jobs"
by Mark DSouza 31 Aug '11

31 Aug '11

Hi, That is very odd, I just opened the page using your account and did not have any trouble. Can you send me the URL which opens the page, I can check through the logs and find out what is going on. It is not possible to delete private jobs right now, though I hope we will have it in the next release. Let me have the MG-RAST job IDs and I can delete them for you. Regards, Mark ----- Original Message ----- > From: "Sheri Simmons" <ssimmons(a)mbl.edu> > To: "Mark DSouza" <dsouza(a)mcs.anl.gov> > Sent: Wednesday, August 31, 2011 10:24:22 AM > Subject: Re: [mg-rast] problem with "share jobs" > Hi, thanks for your quick reply. The "share a job" page is still not > displaying for me, though I am able to use other analysis features. > One other quick question- is it possible to delete private jobs? I > have some metagenomes on the site that I later discovered to have some > pre-processing issues so I'd like to take them down to avoid any > future confusion. > > Sheri > > On 8/31/2011 11:13 AM, Mark DSouza wrote: > > Hi, > > I am not able to reproduce this problem, we did have a server downtime > earlier today which may have been responsible if you hit the server > before it went down and it was wedged. Could you check if the page is > still not displaying. The suggestion for sharing multiple metagenomes > is a good one, we have a number of operations which work on single > metagenomes which which would make sense to extend to multiple > metagenomes. > > -- > Sheri Simmons > Assistant Scientist, Bay Paul Center | Marine Biological Laboratory > Woods Hole, MA 02543 > (508) 289-7177 > http://www.simmonslab.org

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Re: [mg-rast] A quick question
by Mark D'Souza 31 Aug '11

31 Aug '11

Sorry, forgot to attach this image. Mark On Aug 31, 2011, at 10:45 AM, Mark D'Souza wrote: > Hi, > > Ah, I understand, the problem is that you have not reached the stage where the workbench is available. After selecting the features with the checkboxes you need to click on the 'to workbench' button in the header row of the table which will move the selected features to the workbench. When the tab tab header 'Workbench (0 features)' is updated with the number of features moved you can click on the tab heading and work on the selected features only. This new workbench tab will have the download link where you can retrieve the sequences for the reads with the selected features. > > Regards, > Mark > > > > On Aug 31, 2011, at 8:31 AM, fancy-yf wrote: > >> Hi, Mark >> >> I tried to find the link of 'download metagenome dna FASTA annotated by' in the workbench tab , unfortunately, I really could not find that! >> Will you please check it and direct me specificly how to do it? Attached is my interface on the worbench. >> Regards, >> >> Fancy >> >> >> <Catch1.jpg> >> >> >> >> >> 2011-08-31 >> fancy-yf >> 发件人： Mark DSouza >> 发送时间： 2011-08-31 00:54:38 >> 收件人： fancy-yf >> 抄送： MG- Rast >> 主题： Re: [mg-rast] A quick question >> Hi, >> Once you have selected your features to the workbench the workbench tab will have a link 'download metagenome dna FASTA annotated by' where you can select a dabase source and download the sequence data. >> The md5s do refer to protein sequences, these are clickable and will display all the annotations from the databases used to create the m5nr non-redundant protein database. >> Regards, >> Mark >> ----- Original Message ----- >>> From: "fancy-yf" <fancy-yf(a)163.com> >>> To: "Mark DSouza" <dsouza(a)mcs.anl.gov> >>> Sent: Tuesday, August 30, 2011 7:20:59 AM >>> Subject: Re: Re: [mg-rast] A quick question >>> Hello, Mark >>> >>> Do you mean the column of md5s?Is it refer to the protein sequences? >>> Actually, I can't find other specific column in the workbench on >>> downloading fasta-formatted sequences. >>> Would you mind tell me how to find that? >>> >>> Thanks! >>> >>> >>> 2011-08-30 >>> >>> fancy-yf >>> >>> 发件人： Mark DSouza >>> 发送时间： 2011-08-22 23:18:49 >>> 收件人： fancy-yf >>> 抄送： mg-rast >>> 主题： Re: [mg-rast] A quick question >>> >>> >>> Hi, >>> >>> The workbench enables download of individual sequences, select the >>> rows for the function under the 'to workbench column'. The workbench >>> is then accessed through the 'Workbench tab' where you can download >>> fasta formatted metagenomic sequence data for the selected sequences. >>> >>> -- >>> Regards, >>> Mark D'Souza >>> -- for the MG-RAST team >>> >>> mg-rast(a)mcs.anl.gov >>> http://metagenomics.anl.gov/ >>> >>> If you need to respond to this email please address it to the >>> mailing-list mg-rast(a)mcs.anl.gov >>> >>> >>> ----- Original Message ----- >>>> From: "fancy-yf" <fancy-yf(a)163.com> >>>> To: "mg-rast" <mg-rast(a)mcs.anl.gov> >>>> Sent: Sunday, August 21, 2011 9:15:45 PM >>>> Subject: [mg-rast] A quick question >>>> Hello, >>>> >>>> Here I have a question and might need your help. For the MG-RAST >>>> annotation result of my metagenomic data downloaded from MG-RAST >>>> server (as attached). Here I want to find the exact sequence of >>>> specific object in function column (eg. Alanine racemase (EC >>>> 5.1.1.1) >>>> ). How could I get that sequence? >>>> >>>> Hope for your replies! >>>> >>>> fancy >>>> >>>> >>>> 2011-08-22 >>>> >>>> fancy-yf >

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