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

Re: [mg-rast] MG-RAST - account request approved
by Mark D'Souza 30 Nov '10

30 Nov '10

Hi, The best thing would be to request a new password at http://metagenomics.anl.gov/metagenomics.cgi?page=RequestNewPassword your email address is stored as 'H_Vrionis(a)yahoo.ca'. We have not had any problems with the passwords but resetting it should fix whatever went wrong. ----- Original Message ----- > From: "Helen Vrionis" <h_vrionis(a)yahoo.ca> > To: "Mark D'Souza" <dsouza(a)mcs.anl.gov> > Sent: Tuesday, November 30, 2010 1:13:31 PM > Subject: Re: [mg-rast] MG-RAST - account request approved > Hi Mark - yes - actually to avoid problems I always go back and cut > and paste the password from the original email (period included!!!) > Thanks, > Helen > > > > From: Mark D'Souza <dsouza(a)mcs.anl.gov> > To: Helen Vrionis <h_vrionis(a)yahoo.ca> > Cc: mg-rast(a)mcs.anl.gov > Sent: Tue, November 30, 2010 12:47:54 PM > Subject: Re: [mg-rast] MG-RAST - account request approved > > Hi, > > Are you adding the period at the end of the password? That was the > problem the last time. > > Mark > > ----- Original Message ----- > > From: "Helen Vrionis" < h_vrionis(a)yahoo.ca > > > To: mg-rast(a)mcs.anl.gov > > Sent: Tuesday, November 30, 2010 11:43:06 AM > > Subject: Re: [mg-rast] MG-RAST - account request approved > > Hello, > > I am using the below info but suddenly cannot seem to log into my > > account. Please advise! > > thank you! > > > > > > H. > > > > > > > > > > > > From: " mg-rast(a)mcs.anl.gov " < mg-rast(a)mcs.anl.gov > > > To: H_Vrionis(a)yahoo.ca > > Sent: Mon, June 21, 2010 11:47:53 AM > > Subject: MG-RAST - account request approved > > > > Dear Helen Vrionis, > > > > your account request for access to our web service MG-RAST has been > > accepted. > > > > Your login is: rouge > > Your password is: 13pt7Z0. > > > > We recommend to change the password immediately. To do so please go > > to > > our web service http://metagenomics.nmpdr.org/ and change your > > password from the account management. > > > > > > -- > > > > This email was automatically generated by the MG-RAST web service. > > Do > > not reply.

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Re: [mg-rast] Compare metagenomes
by Mark D'Souza 30 Nov '10

30 Nov '10

Hi, I think you are coming up against the limits of what the system can handle, I was able to get a heat map for 40 metagenomes but at 50 I got the blank screen. I will look into it and check what can be done. ----- Original Message ----- > From: "David Walsh" <dwal(a)alcor.concordia.ca> > To: mg-rast(a)mcs.anl.gov > Sent: Tuesday, November 30, 2010 10:16:39 AM > Subject: [mg-rast] Compare metagenomes > Hello, > I am attempting to generate a heatmap of ~40 metagenomes using the > "Compare metagenomes" function and when I click "Re-compute results", > I come up with a blank screen. Is there a limit on the number of > metagenomesthat can be compared at the website? Thanks. > > David Walsh > Assistant Professor > Concordia University > Department of Biology > 7141 Sherbrooke St West > Room SP437.09 > Montreal, Quebec H4B 1R6 > Canada > > T: 514-848-2424 (ext 3477) > F: 514-848-2881 > dwal(a)alcor.concordia.ca -- 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

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Re: [mg-rast] MG-RAST - account request approved
by Mark D'Souza 30 Nov '10

30 Nov '10

Hi, Are you adding the period at the end of the password? That was the problem the last time. Mark ----- Original Message ----- > From: "Helen Vrionis" <h_vrionis(a)yahoo.ca> > To: mg-rast(a)mcs.anl.gov > Sent: Tuesday, November 30, 2010 11:43:06 AM > Subject: Re: [mg-rast] MG-RAST - account request approved > Hello, > I am using the below info but suddenly cannot seem to log into my > account. Please advise! > thank you! > > > H. > > > > > > From: "mg-rast(a)mcs.anl.gov" <mg-rast(a)mcs.anl.gov> > To: H_Vrionis(a)yahoo.ca > Sent: Mon, June 21, 2010 11:47:53 AM > Subject: MG-RAST - account request approved > > Dear Helen Vrionis, > > your account request for access to our web service MG-RAST has been > accepted. > > Your login is: rouge > Your password is: 13pt7Z0. > > We recommend to change the password immediately. To do so please go to > our web service http://metagenomics.nmpdr.org/ and change your > password from the account management. > > > -- > > This email was automatically generated by the MG-RAST web service. Do > not reply.

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Re: [mg-rast] MG-RAST - account request approved
by Helen Vrionis 30 Nov '10

30 Nov '10

Hello, I am using the below info but suddenly cannot seem to log into my account. Please advise! thank you! H. ________________________________ From: "mg-rast(a)mcs.anl.gov" <mg-rast(a)mcs.anl.gov> To: H_Vrionis(a)yahoo.ca Sent: Mon, June 21, 2010 11:47:53 AM Subject: MG-RAST - account request approved Dear Helen Vrionis, your account request for access to our web service MG-RAST has been accepted. Your login is: rouge Your password is: 13pt7Z0. We recommend to change the password immediately. To do so please go to our web service http://metagenomics.nmpdr.org/ and change your password from the account management. -- This email was automatically generated by the MG-RAST web service. Do not reply.

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Your MG-RAST job (12738, FOS62_09)
by Mark D'Souza 30 Nov '10

30 Nov '10

Hi, The job you submitted to MG-RAST (12738, FOS62_09) has failed as the sequence file does not conform to the FASTA standard due to a line which contains both the sequence identifier as well as the sequence: >FOS624.CPF_O16 (662)CGACGATTCTTTCATCGACCGGTGCGGGGTGCCC... Please check that your sequence file has not been corrupted and fix this before resubmitting to the MG-RAST server if you have not already done so. -- 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

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Compare metagenomes
by David Walsh 30 Nov '10

30 Nov '10

Hello, I am attempting to generate a heatmap of ~40 metagenomes using the "Compare metagenomes" function and when I click "Re-compute results", I come up with a blank screen. Is there a limit on the number of metagenomesthat can be compared at the website? Thanks. David Walsh Assistant Professor Concordia University Department of Biology 7141 Sherbrooke St West Room SP437.09 Montreal, Quebec H4B 1R6 Canada T: 514-848-2424 (ext 3477) F: 514-848-2881 dwal(a)alcor.concordia.ca

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Re: [mg-rast] Correlating SEED taxonomic and functional assignments
by Folker Meyer 29 Nov '10

29 Nov '10

Dear Lisa: version 3.0 will include that feature. We hope to release the beta this week. Best, Folker On Nov 29, 2010, at 4:24 PM, Durso, Lisa wrote: > Dear MG-RAST, > > I was wondering if there is a feature that would allow me to see both the SEED taxonomic assignment, and the gene assignment for each sequence? I would like to look at a specific category of functional genes, and figure out with which taxa they are likely associated. > > The data is available indirectly through the SEED phylogentic assignment page, but requires clicking on each taxon to get the assignment list. So I would need to click on each taxa, download the assignment, then go back and do the whole procedure for the next taxa. Do you know of an easier way to get at this kind of information? > > Thanks for your help, > Lisa Durso > > > > Lisa Durso, Ph.D. > Research Microbiologist > > Agroecosystem Management Research Unit > Room 121 Keim Hall > UNL-East Campus > Lincoln, NE 68583-0938 > > Phone: 402-472-9622 > Fax: 402-437-5712 > > lisa.durso(a)ars.usda.gov > >

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Re: [mg-rast] Your MG-RAST jobs (12653, 12654, 12655)
by Mark D'Souza 29 Nov '10

29 Nov '10

Great! A small job like this should get done within a day. Mark ----- Original Message ----- > From: "archana jeeva" <archieniv(a)gmail.com> > To: "Mark D'Souza" <dsouza(a)mcs.anl.gov> > Sent: Monday, November 29, 2010 4:24:31 PM > Subject: Re: Your MG-RAST jobs (12653, 12654, 12655) > It got uploaded!! Thanks a million!! When will it get done? > > Archana > > > > On Tue, Nov 30, 2010 at 3:38 AM, archana jeeva < archieniv(a)gmail.com > > wrote: > > > I'm not a computer person , so I don't know how to change the file or > modify it !! If I send the file now via e-mail to you will you be able > to upload it? > > Archana > > > > > > On Tue, Nov 30, 2010 at 3:28 AM, Mark D'Souza < dsouza(a)mcs.anl.gov > > wrote: > > > Getting a blank page indicates an error occurred. What data are you > entering in the forms? One of the error messages states 'Malformed > UTF-8 character', try entering the job details using only ASCII > characters. > > > Mark > > ----- Original Message ----- > > From: "archana jeeva" < archieniv(a)gmail.com > > > To: "Mark D'Souza" < dsouza(a)mcs.anl.gov > > > > > > Sent: Monday, November 29, 2010 3:04:01 PM > > Subject: Re: Your MG-RAST jobs (12653, 12654, 12655) > > Well, after I upload the fna file , fill in all the details and > > click > > the finish upload button , MG RAST just opens a new window which is > > blank . But the job then turns up on the manage uploaded metagenomes > > when I return to MG RAST home and check it over there. But I'm not > > able to view any of the details of the job over there except for job > > # > > 12730, which is why I thought maybe that one worked. I don't have > > access to another machine right now. Will try from another machine > > in > > an hour or two. Do you have any idea why I'm having these problems? > > > > Archana > > > > > > On Tue, Nov 30, 2010 at 2:26 AM, Mark D'Souza < dsouza(a)mcs.anl.gov > > > wrote: > > > > > > No, none of the latest batch (12729-12732) came through OK. The > > sequence file seems to be consistent -- 499578 bytes, md5 is > > 0b31066a7cea114031706507b535eb78. Maybe something further down the > > line is breaking things, does the submission go all the way to the > > last step where the job number (e.g. 12730) is displayed? > > > > > > Mark > > > > ----- Original Message ----- > > > From: "archana jeeva" < archieniv(a)gmail.com > > > > To: "Mark D'Souza" < dsouza(a)mcs.anl.gov > > > > > > > > > > Sent: Monday, November 29, 2010 2:43:08 PM > > > Subject: Re: Your MG-RAST jobs (12653, 12654, 12655) > > > Has job #12730 been uploaded? I can't seem to access the rest. For > > > the > > > time being, I just need this metagenome to be annotated. Please > > > let > > > me > > > know if #12730 has been uploaded. > > > > > > Thanks, > > > Archana > > > > > > On Tue, Nov 30, 2010 at 12:23 AM, archana jeeva < > > > archieniv(a)gmail.com > > > > wrote: > > > > > > > > > I thought the last one I did was ok. Will try from another machine > > > . > > > > > > Archana > > > > > > > > > > > > > > > > > > On Tue, Nov 30, 2010 at 12:22 AM, Mark D'Souza < > > > dsouza(a)mcs.anl.gov > > > > > > > wrote: > > > > > > > > > Hmm, all four of the recent submissions are incomplete, something > > > is > > > going wrong during the upload and the complete information > > > required > > > to > > > process the jobs is not being stored. Not sure what the problem > > > is, > > > could you try from another machine/browser. > > > > > > Regards, > > > Mark > > > > > > > > > > > > > > > > > > ----- Original Message ----- > > > > From: "archana jeeva" < archieniv(a)gmail.com > > > > > To: "Mark D'Souza" < dsouza(a)mcs.anl.gov > > > > > Sent: Monday, November 29, 2010 12:33:01 PM > > > > Subject: Re: Your MG-RAST jobs (12653, 12654, 12655) > > > > I have uploaded my metagenome again!! Kindly let me know if the > > > > upload > > > > process was completed. I did not face any problems. > > > > > > > > Thanks > > > > Archana > > > > > > > > > > > > On Mon, Nov 29, 2010 at 11:05 PM, Mark D'Souza < > > > > dsouza(a)mcs.anl.gov > > > > > > > > > wrote: > > > > > > > > > > > > Hi, > > > > > > > > The jobs you submitted to MG-RAST have failed as the upload > > > > process > > > > was not completed and can not be processed. Please resubmit > > > > these > > > > jobs > > > > to the MG-RAST server, completing all 3 steps of the process and > > > > let > > > > us know if you encounter any problems. > > > > > > > > -- > > > > 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

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Correlating SEED taxonomic and functional assignments
by Durso, Lisa 29 Nov '10

29 Nov '10

Dear MG-RAST, I was wondering if there is a feature that would allow me to see both the SEED taxonomic assignment, and the gene assignment for each sequence? I would like to look at a specific category of functional genes, and figure out with which taxa they are likely associated. The data is available indirectly through the SEED phylogentic assignment page, but requires clicking on each taxon to get the assignment list. So I would need to click on each taxa, download the assignment, then go back and do the whole procedure for the next taxa. Do you know of an easier way to get at this kind of information? Thanks for your help, Lisa Durso Lisa Durso, Ph.D. Research Microbiologist Agroecosystem Management Research Unit Room 121 Keim Hall UNL-East Campus Lincoln, NE 68583-0938 Phone: 402-472-9622 Fax: 402-437-5712 lisa.durso(a)ars.usda.gov

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Re: [mg-rast] Your MG-RAST jobs (12653, 12654, 12655)
by Mark D'Souza 29 Nov '10

29 Nov '10

ah, no, I am not suggesting changing the file, the uploaded file looks fine. If this is the problem then the non-ASCII character is being entered by you manually through the webpage when you enter the job details (latitude, etc.). Mark ----- Original Message ----- > From: "archana jeeva" <archieniv(a)gmail.com> > To: "Mark D'Souza" <dsouza(a)mcs.anl.gov> > Sent: Monday, November 29, 2010 4:08:58 PM > Subject: Re: Your MG-RAST jobs (12653, 12654, 12655) > I'm not a computer person , so I don't know how to change the file or > modify it !! If I send the file now via e-mail to you will you be able > to upload it? > > Archana > > > On Tue, Nov 30, 2010 at 3:28 AM, Mark D'Souza < dsouza(a)mcs.anl.gov > > wrote: > > > Getting a blank page indicates an error occurred. What data are you > entering in the forms? One of the error messages states 'Malformed > UTF-8 character', try entering the job details using only ASCII > characters. > > > Mark > > ----- Original Message ----- > > From: "archana jeeva" < archieniv(a)gmail.com > > > To: "Mark D'Souza" < dsouza(a)mcs.anl.gov > > > > > > Sent: Monday, November 29, 2010 3:04:01 PM > > Subject: Re: Your MG-RAST jobs (12653, 12654, 12655) > > Well, after I upload the fna file , fill in all the details and > > click > > the finish upload button , MG RAST just opens a new window which is > > blank . But the job then turns up on the manage uploaded metagenomes > > when I return to MG RAST home and check it over there. But I'm not > > able to view any of the details of the job over there except for job > > # > > 12730, which is why I thought maybe that one worked. I don't have > > access to another machine right now. Will try from another machine > > in > > an hour or two. Do you have any idea why I'm having these problems? > > > > Archana > > > > > > On Tue, Nov 30, 2010 at 2:26 AM, Mark D'Souza < dsouza(a)mcs.anl.gov > > > wrote: > > > > > > No, none of the latest batch (12729-12732) came through OK. The > > sequence file seems to be consistent -- 499578 bytes, md5 is > > 0b31066a7cea114031706507b535eb78. Maybe something further down the > > line is breaking things, does the submission go all the way to the > > last step where the job number (e.g. 12730) is displayed? > > > > > > Mark > > > > ----- Original Message ----- > > > From: "archana jeeva" < archieniv(a)gmail.com > > > > To: "Mark D'Souza" < dsouza(a)mcs.anl.gov > > > > > > > > > > Sent: Monday, November 29, 2010 2:43:08 PM > > > Subject: Re: Your MG-RAST jobs (12653, 12654, 12655) > > > Has job #12730 been uploaded? I can't seem to access the rest. For > > > the > > > time being, I just need this metagenome to be annotated. Please > > > let > > > me > > > know if #12730 has been uploaded. > > > > > > Thanks, > > > Archana > > > > > > On Tue, Nov 30, 2010 at 12:23 AM, archana jeeva < > > > archieniv(a)gmail.com > > > > wrote: > > > > > > > > > I thought the last one I did was ok. Will try from another machine > > > . > > > > > > Archana > > > > > > > > > > > > > > > > > > On Tue, Nov 30, 2010 at 12:22 AM, Mark D'Souza < > > > dsouza(a)mcs.anl.gov > > > > > > > wrote: > > > > > > > > > Hmm, all four of the recent submissions are incomplete, something > > > is > > > going wrong during the upload and the complete information > > > required > > > to > > > process the jobs is not being stored. Not sure what the problem > > > is, > > > could you try from another machine/browser. > > > > > > Regards, > > > Mark > > > > > > > > > > > > > > > > > > ----- Original Message ----- > > > > From: "archana jeeva" < archieniv(a)gmail.com > > > > > To: "Mark D'Souza" < dsouza(a)mcs.anl.gov > > > > > Sent: Monday, November 29, 2010 12:33:01 PM > > > > Subject: Re: Your MG-RAST jobs (12653, 12654, 12655) > > > > I have uploaded my metagenome again!! Kindly let me know if the > > > > upload > > > > process was completed. I did not face any problems. > > > > > > > > Thanks > > > > Archana > > > > > > > > > > > > On Mon, Nov 29, 2010 at 11:05 PM, Mark D'Souza < > > > > dsouza(a)mcs.anl.gov > > > > > > > > > wrote: > > > > > > > > > > > > Hi, > > > > > > > > The jobs you submitted to MG-RAST have failed as the upload > > > > process > > > > was not completed and can not be processed. Please resubmit > > > > these > > > > jobs > > > > to the MG-RAST server, completing all 3 steps of the process and > > > > let > > > > us know if you encounter any problems. > > > > > > > > -- > > > > 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

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