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

Re: [mg-rast] Hello -question about sequence files for MG-RAST
by William Trimble 30 Jun '11

30 Jun '11

Thanks for your interest in MG-RAST. If your sequences contain ribosomal sequences, MG-RAST can identify and annotate those sequences with only 36 bp. The protein annotation part of the pipeline, however, does not work for sequences shorter than 70bp. If have shotgun data and want protein function annotation, you will need to assemble the sequences first, with something like SOAP, velvet, or euler-sr. William Trimble -for the MG-RAST team On Thu, Jun 30, 2011 at 5:03 PM, Luis Eduardo Servín <lservin(a)lcg.unam.mx> wrote: > Hello I am a user of MG-RAST, I would like to know if I can submit raw > solexa sequences in fasta format but that are 36 bp long and the total > sequence is about 2.5 Gb. > Thanks a lot! >

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Hello -question about sequence files for MG-RAST
by Luis Eduardo Servín 30 Jun '11

30 Jun '11

Hello I am a user of MG-RAST, I would like to know if I can submit raw solexa sequences in fasta format but that are 36 bp long and the total sequence is about 2.5 Gb. Thanks a lot!

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Fwd: problem login in and seeing the data
by cimcime bayındırlı 30 Jun '11

30 Jun '11

Hi thank you very much for your replay I am not quite sure which form you were talking about, but I just cant see any forms in the terms of servise page.. is there name for that form please? or a quick link? I was looking around the web site and found the registary request fo rthe existing account form, which could be the one you were talking about probably, but then since I think I dont know my login name anymore it really doesnt work for me :\ can you please let me know where can I learn my login name or how can I reset it please? thank you very much Cansu ---------- Forwarded message ---------- From: Mark D'Souza <dsouza(a)mcs.anl.gov> Date: 30 June 2011 22:05 Subject: Re: [mg-rast] problem login in and seeing the data To: eftelia(a)gmail.com Cc: mg-rast(a)mcs.anl.gov Hi, When you first log in to the V3 system you will see a 'Terms of Service' page with some text and a form that you are required to fill in. I think in this case since you have not filled in the form but went directly to the metagenome page the system would not display the analysis. Please try logging in to the system from the front page, agree to the terms of service and then go on to viewing the metagenome page. If that does not work let us know. 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 On Jun 30, 2011, at 11:03 AM, eftelia(a)gmail.com wrote: > Hiya, > I have two problems, if you could help, that would be great!! > > first is that, I was trying to login to my account but I cant.. > tried to reset my password but couldn't do that either > probably i mis-remember my login ID..?? > is there way to reset both of them?? > > secondly; > I have been granted access to 18 different sequenced data by supervisor (Jack Gilbert) on MGRAST. > however, when i click to the link, the following message appears: > "An error has occured: > > Unable to retrieve the job for metagenome '4465513.3'. > > To continue please go back to the start page." > > do you know why this could be happening? > or can you please help me on how to get access to all these data sets please?? > > thank you very much > Cansu Bayindirli

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Fwd: id 4467103.3
by Mark D'Souza 30 Jun '11

30 Jun '11

Travis, please check this job, Thanks, Mark Begin forwarded message: > From: Rodrigo Mendes <rrmendess(a)gmail.com> > Date: June 30, 2011 6:17:36 AM CDT > To: mg-rast(a)mcs.anl.gov > Subject: [mg-rast] id 4467103.3 > > Hi Guys, could you please check the job detailed below? I uploaded this with more 5 other metagenomes 3 days ago, but only this one is not available for analysis. > > job 26700, > id 4467103.3, name > Sr_2, status > > Loading Database : completed > > Thanks > Rodrigo > > > -- > Rodrigo Mendes > >

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Re: [mg-rast] id 4467103.3
by Mark D'Souza 30 Jun '11

30 Jun '11

Hi, Sorry about that, we will take a look and get it moving. 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 On Jun 30, 2011, at 6:17 AM, Rodrigo Mendes wrote: > Hi Guys, could you please check the job detailed below? I uploaded this with more 5 other metagenomes 3 days ago, but only this one is not available for analysis. > > job 26700, > id 4467103.3, name > Sr_2, status > > Loading Database : completed > > Thanks > Rodrigo > > > -- > Rodrigo Mendes > >

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Re: [mg-rast] problem login in and seeing the data
by Mark D'Souza 30 Jun '11

30 Jun '11

Hi, When you first log in to the V3 system you will see a 'Terms of Service' page with some text and a form that you are required to fill in. I think in this case since you have not filled in the form but went directly to the metagenome page the system would not display the analysis. Please try logging in to the system from the front page, agree to the terms of service and then go on to viewing the metagenome page. If that does not work let us know. 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 On Jun 30, 2011, at 11:03 AM, eftelia(a)gmail.com wrote: > Hiya, > I have two problems, if you could help, that would be great!! > > first is that, I was trying to login to my account but I cant.. > tried to reset my password but couldn't do that either > probably i mis-remember my login ID..?? > is there way to reset both of them?? > > secondly; > I have been granted access to 18 different sequenced data by supervisor (Jack Gilbert) on MGRAST. > however, when i click to the link, the following message appears: > "An error has occured: > > Unable to retrieve the job for metagenome '4465513.3'. > > To continue please go back to the start page." > > do you know why this could be happening? > or can you please help me on how to get access to all these data sets please?? > > thank you very much > Cansu Bayindirli

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Re: [mg-rast] problem to upload file
by Mark DSouza 30 Jun '11

30 Jun '11

Hi, The problem is with line 1495 which contains the end of a sequence followed by a sequence header line which does not begin on a new line: 1495 TTGGATCCCG>PL02_16S_BT_C11_.b_05.ab1 CHROMAT_FILE: PL02_16S_BT_C11_.b_05.ab1 PL02_16S_BT_C11_.b_05.ab1.phd.4 01:52:35 2011 Since it does not conform to the FASTA standard our system was unable to read it. If you edit your sequence file to add the new line and resubmit the file should be processed OK, let us know if the processing does not complete within an hour. Regards, Mark ----- Original Message ----- > From: "Mark DSouza" <dsouza(a)mcs.anl.gov> > To: "Rodrigo Pereira" <rodrigo(a)bioinfo.com.br> > Cc: mg-rast(a)mcs.anl.gov > Sent: Thursday, June 30, 2011 3:21:30 PM > Subject: Re: [mg-rast] problem to upload file > Hi, > > Definitely sounds like something went wrong, I will take a look and > get back to you. > > -- > 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: "Rodrigo Pereira" <rodrigo(a)bioinfo.com.br> > > To: mg-rast(a)mcs.anl.gov > > Sent: Thursday, June 30, 2011 3:18:51 PM > > Subject: [mg-rast] problem to upload file > > Hello, > > I have a problem to upload a small file. Same weeks ago i uploaded 3 > > files, but the fourth file don´t work. This fali has only 192 > > sequences... The message showed in the "upload status" page is: > > "processing uploaded file .." but other 3 files (that has the > > similar > > sizes) were processed in a few minutes, and the last file is running > > by weeks and never end... > > Someone could help me? > > > > Thanks by attention > > > > -- > > Prof. Dr. Rodrigo Matheus Pereira > > Faculdade de Ciências Biológicas e Ambientais - FCBA > > Universidade Federal da Grande Dourados - UFGD > > Rodovia Dourados-Itahum, km 12 > > CEP:79804-970 Caixa-Postal: 533 > > Dourados - MS - Brasil

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Re: [mg-rast] problem to upload file
by Mark DSouza 30 Jun '11

30 Jun '11

Hi, Definitely sounds like something went wrong, I will take a look and get back to you. -- 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: "Rodrigo Pereira" <rodrigo(a)bioinfo.com.br> > To: mg-rast(a)mcs.anl.gov > Sent: Thursday, June 30, 2011 3:18:51 PM > Subject: [mg-rast] problem to upload file > Hello, > I have a problem to upload a small file. Same weeks ago i uploaded 3 > files, but the fourth file don´t work. This fali has only 192 > sequences... The message showed in the "upload status" page is: > "processing uploaded file .." but other 3 files (that has the similar > sizes) were processed in a few minutes, and the last file is running > by weeks and never end... > Someone could help me? > > Thanks by attention > > -- > Prof. Dr. Rodrigo Matheus Pereira > Faculdade de Ciências Biológicas e Ambientais - FCBA > Universidade Federal da Grande Dourados - UFGD > Rodovia Dourados-Itahum, km 12 > CEP:79804-970 Caixa-Postal: 533 > Dourados - MS - Brasil

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problem to upload file
by Rodrigo Pereira 30 Jun '11

30 Jun '11

Hello, I have a problem to upload a small file. Same weeks ago i uploaded 3 files, but the fourth file don´t work. This fali has only 192 sequences... The message showed in the "upload status" page is: "processing uploaded file .." but other 3 files (that has the similar sizes) were processed in a few minutes, and the last file is running by weeks and never end... Someone could help me? Thanks by attention -- Prof. Dr. Rodrigo Matheus Pereira Faculdade de Ciências Biológicas e Ambientais - FCBA Universidade Federal da Grande Dourados - UFGD Rodovia Dourados-Itahum, km 12 CEP:79804-970 Caixa-Postal: 533 Dourados - MS - Brasil

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problem login in and seeing the data
by eftelia＠gmail.com 30 Jun '11

30 Jun '11

Hiya, I have two problems, if you could help, that would be great!! first is that, I was trying to login to my account but I cant.. tried to reset my password but couldn't do that either probably i mis-remember my login ID..?? is there way to reset both of them?? secondly; I have been granted access to 18 different sequenced data by supervisor (Jack Gilbert) on MGRAST. however, when i click to the link, the following message appears: "An error has occured: Unable to retrieve the job for metagenome '4465513.3'. To continue please go back to the start page." do you know why this could be happening? or can you please help me on how to get access to all these data sets please?? thank you very much Cansu Bayindirli

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