February 2010 - Mg-rast - mailman3.cels.anl.gov

Re: [mg-rast] Upload file size and error message
by dsouza＠mcs.anl.gov 26 Feb '10

26 Feb '10

Dominique, The files you uploaded are gzipped only, not tarred and gzipped. Since the file name has a .tgz extension, the system is attempting to untar it and failing. If you rename your file with a '.gz' extension and go through the upload again you should have no problem. ----- "Dominique Chaput" <dlch(a)ceh.ac.uk> wrote: > From: "Dominique Chaput" <dlch(a)ceh.ac.uk> > To: mg-rast(a)mcs.anl.gov > Sent: Friday, February 26, 2010 11:16:24 AM GMT -06:00 US/Canada Central > Subject: [mg-rast] Upload file size and error message > > Hi, > > I have a 340 Mb fasta file from 454 pyrosequencing, which I’ve > compressed to 100 Mb with tar gzip. Is this still too large to upload > into MG-RAST? When I tried, I received the following error message: > > Error unpacking uploaded tarfile: Error closing tar pipe: $?=512 $!= > at > /vol/mg-rast-prod/Frontend-FIGdisk/dist/releases/dev/common/lib/MGRAST/WebPage/UploadMetagenome.pm > line 680. > > Please let me know if I need to modify my file before trying again. > > Best wishes, > Dominique Chaput > > -- > This message (and any attachments) is for the recipient only. NERC > is subject to the Freedom of Information Act 2000 and the contents > of this email and any reply you make may be disclosed by NERC unless > it is exempt from release under the Act. Any material supplied to > NERC may be stored in an electronic records management system. -- Regards, Mark D'Souza -- for the MG-RAST team mg-rast(a)mcs.anl.gov http://metagenomics.anl.gov/

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Upload file size and error message
by Chaput, Dominique 26 Feb '10

26 Feb '10

Hi, I have a 340 Mb fasta file from 454 pyrosequencing, which I've compressed to 100 Mb with tar gzip. Is this still too large to upload into MG-RAST? When I tried, I received the following error message: Error unpacking uploaded tarfile: Error closing tar pipe: $?=512 $!= at /vol/mg-rast-prod/Frontend-FIGdisk/dist/releases/dev/common/lib/MGRAST/WebPage/UploadMetagenome.pm line 680. Please let me know if I need to modify my file before trying again. Best wishes, Dominique Chaput -- This message (and any attachments) is for the recipient only. NERC is subject to the Freedom of Information Act 2000 and the contents of this email and any reply you make may be disclosed by NERC unless it is exempt from release under the Act. Any material supplied to NERC may be stored in an electronic records management system.

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Fwd: Export table bug
by vgomez＠msu.edu 26 Feb '10

26 Feb '10

* * * Hi Mark, Thanks for the update, downloading the sequences for a particular subsystems is great and useful. But our work demand downloading the complete tables (i.e. functional role assignments). Therefore I need to apologize for my last e-mail regarding the tables. We mistakenly mention the sequences but we were referring to the export tables, which right now are still limit to display the first 10,000. Both tools will be a plus for our research and others. Thanks for the last response and again apologize for any inconvenience Vicente Gomez-Alvarez, Ph.D. ----- Forwarded message from vgomez(a)msu.edu ----- Date: Mon, 22 Feb 2010 11:18:20 -0500 From: vgomez(a)msu.edu Subject: Export table bug To: "mg-rast(a)mcs.anl.gov" <mg-rast(a)mcs.anl.gov> Dear MG-RAST, Hi, recently when I looked for a specific subsytem (e.g./Membrane Transport/) in one of my job 4443324.3 It said it found 21,183 sequences matching these criteria. However only show 10,000 in the table's page and therefore I can only download 10,000 of these sequences. Months ago I can see all the sequences that match with that particular subsystem and downloaded at one time. If there a limited now for viewing your matches (i.e. 10,000)? And why now you can not filter by subsystems (e.g. subsystems1, susbsystems3, etc)? For our work we need to download all the matches with their respectevily information. If there any way to download all of them at the same time. Before we select one subsystem and downloaded all matches (28 subsystems) individulally. Of course now is not possible wuith the 10,000 limitatuion. This situation ocurr with all my projects. Thanks for any comments or solution Vicente Gomez-Alvarez ----- End forwarded message -----

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(Job 6432 , ID ) . is now publicly available.
by mg-rast＠mcs.anl.gov 25 Feb '10

25 Feb '10

Christopher Schadt (WebServerBackend::User=HASH(0x1bfa6590)) has made the genome public. Link provided: http://mg-rast.mcs.anl.gov/mg-rast/FIG/linkin.cgi?metagenome=.

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(Job 6411 , ID 4446533.3) . is now publicly available.
by mg-rast＠mcs.anl.gov 25 Feb '10

25 Feb '10

Christopher Schadt (WebServerBackend::User=HASH(0xeb62680)) has made the genome public. Link provided: http://mg-rast.mcs.anl.gov/mg-rast/FIG/linkin.cgi?metagenome=4446533.3.

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(Job 6411 , ID 4446533.3) . is now publicly available.
by mg-rast＠mcs.anl.gov 25 Feb '10

25 Feb '10

Christopher Schadt (WebServerBackend::User=HASH(0x1d9d5530)) has made the genome public. Link provided: http://mg-rast.mcs.anl.gov/mg-rast/FIG/linkin.cgi?metagenome=4446533.3.

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Re: [mg-rast] Jobs 6411 and 6410
by Schadt, Christopher Warren 25 Feb '10

25 Feb '10

Please disregard the email below. I see that I missed that option at the upload stage. :( CHRIS ---------------------------------------------------------- CHRISTOPHER W. SCHADT, Ph.D. Staff Scientist & Group Leader, Oak Ridge National Laboratory Adjunct Professor, University of Tennessee EMAIL: schadtcw(a)ornl.gov WEB: http://www.ornl.gov/~cys/MMEmain.html PHONE: 865.576.3982 FAX: 865.576.8646 SECRETARY: Karen Popham; 865.574.7375; pophamkl(a)ornl.gov ---------------------------------------------------------- "We know more about the movement of celestial bodies than about the soil underfoot." - Leonardo Da Vinci, circa 1510 On 2/25/10 6:52 PM, "Schadt, Christopher Warren (cys)" <schadtcw(a)ornl.gov> wrote: Thanks so much for your help and reply. Im watching it progress as we speak and learning more about the program browsing other data sets! One think I learned is that the preprocessing step removes identical sequences. Is it possible to disable this option? It is important for amplicon sequencing (rRNA and other targeted, as opposed to shotgun methods) to either leave these in or reaccount for it somehow in the phylogenetic composition charts/tables. This will allow me to use the data to assess relative abundance, and therefore relative importance, of different taxa in the samples. CHRIS ---------------------------------------------------------- CHRISTOPHER W. SCHADT, Ph.D. Staff Scientist & Group Leader, Oak Ridge National Laboratory Adjunct Professor, University of Tennessee EMAIL: schadtcw(a)ornl.gov WEB: http://www.ornl.gov/~cys/MMEmain.html PHONE: 865.576.3982 FAX: 865.576.8646 SECRETARY: Karen Popham; 865.574.7375; pophamkl(a)ornl.gov ---------------------------------------------------------- "We know more about the movement of celestial bodies than about the soil underfoot." - Leonardo Da Vinci, circa 1510 On 2/25/10 1:21 PM, "Mark D'Souza" <dsouza(a)mcs.anl.gov> wrote: Chris, We had a glitch in our system and some processing steps were not going through correctly. This has now been fixed and your jobs should proceed normally. Thanks for letting us know about the problem Regards, Mark D'Souza -- for the MG-RAST team mg-rast(a)mcs.anl.gov http://metagenomics.anl.gov/ On Feb 25, 2010, at 4:44 AM, Schadt, Christopher Warren wrote: > > A couple of questions, with the caveat that I'm using MJ RAST for the first time so maybe the following is typical. If so, sorry for the newbie questions. > > I uploaded these jobs on Tuesday afternoon. For some reason I cant see the detailed status of 6411 and get the message "An error has occured: Sorry, but you are lacking the rights required for this page". > > When I look at the details page for 6410 I see that it says it has uploaded (but doesn't show the seq# or length). > > Is it typical that this is as far as it gets after 2days? Is it perhaps due to the fact these are not shotgun data but 454 amplicon amplification targeted at fungal LSU rRNA. These data sets are between 4000 & 12000 sequences that have already been QCd on RDP. > > I was hoping to use your tools to quickly classify the sequences using the phylogenetic interface to the SILVA LSU databases on your system. > > Thanks so much for the tools! > CHRIS > > > ---------------------------------------------------------- > CHRISTOPHER W. SCHADT, Ph.D. > Staff Scientist & Group Leader, Oak Ridge National Laboratory > Adjunct Professor, University of Tennessee > EMAIL: schadtcw(a)ornl.gov > WEB: http://www.ornl.gov/~cys/MMEmain.html > PHONE: 865.576.3982 FAX: 865.576.8646 > SECRETARY: Karen Popham; 865.574.7375; pophamkl(a)ornl.gov > ---------------------------------------------------------- > "We know more about the movement of celestial bodies than about the soil > underfoot." - Leonardo Da Vinci, circa 1510 >

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(Job 6410 , ID 4446534.3) . is now publicly available.
by mg-rast＠mcs.anl.gov 25 Feb '10

25 Feb '10

Christopher Schadt (WebServerBackend::User=HASH(0x32c67e0)) has made the genome public. Link provided: http://mg-rast.mcs.anl.gov/mg-rast/FIG/linkin.cgi?metagenome=4446534.3.

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(Job 6410 , ID 4446534.3) . is now publicly available.
by mg-rast＠mcs.anl.gov 25 Feb '10

25 Feb '10

Christopher Schadt (WebServerBackend::User=HASH(0x173bf680)) has made the genome public. Link provided: http://mg-rast.mcs.anl.gov/mg-rast/FIG/linkin.cgi?metagenome=4446534.3.

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Re: [mg-rast] Jobs 6411 and 6410
by Mark D'Souza 25 Feb '10

25 Feb '10

Chris, We had a glitch in our system and some processing steps were not going through correctly. This has now been fixed and your jobs should proceed normally. Thanks for letting us know about the problem Regards, Mark D'Souza -- for the MG-RAST team mg-rast(a)mcs.anl.gov http://metagenomics.anl.gov/ On Feb 25, 2010, at 4:44 AM, Schadt, Christopher Warren wrote: > > A couple of questions, with the caveat that I'm using MJ RAST for the first time so maybe the following is typical. If so, sorry for the newbie questions. > > I uploaded these jobs on Tuesday afternoon. For some reason I cant see the detailed status of 6411 and get the message "An error has occured: Sorry, but you are lacking the rights required for this page". > > When I look at the details page for 6410 I see that it says it has uploaded (but doesn't show the seq# or length). > > Is it typical that this is as far as it gets after 2days? Is it perhaps due to the fact these are not shotgun data but 454 amplicon amplification targeted at fungal LSU rRNA. These data sets are between 4000 & 12000 sequences that have already been QCd on RDP. > > I was hoping to use your tools to quickly classify the sequences using the phylogenetic interface to the SILVA LSU databases on your system. > > Thanks so much for the tools! > CHRIS > > > ---------------------------------------------------------- > CHRISTOPHER W. SCHADT, Ph.D. > Staff Scientist & Group Leader, Oak Ridge National Laboratory > Adjunct Professor, University of Tennessee > EMAIL: schadtcw(a)ornl.gov > WEB: http://www.ornl.gov/~cys/MMEmain.html > PHONE: 865.576.3982 FAX: 865.576.8646 > SECRETARY: Karen Popham; 865.574.7375; pophamkl(a)ornl.gov > ---------------------------------------------------------- > "We know more about the movement of celestial bodies than about the soil > underfoot." - Leonardo Da Vinci, circa 1510 >

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