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

how to 'unshare' datasets
by Cheryl Kuske 11 Feb '11

11 Feb '11

Hi MG RAST, Is there a way to 'unshare' datasets with other accounts. If so, would you please help guide me to the correct website window? Thank you, Cheryl Cheryl Kuske, Ph.D. Bioscience Division Los Alamos National Laboratory kuske(a)lanl.gov

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Your MG-RAST job (14271, Human Gut and 14272, ec)
by Mark D'Souza 11 Feb '11

11 Feb '11

Hi, The job you submitted to MG-RAST has failed as the sequence file contains a line with non-sequence characters just after the sequence identifier line. Please note that MG-RAST version 2.0 is designed to analyse short reads in a metagenomic sample and since your sequence files contain a single long sequence the analysis will be extremely poor, you would be better off using BLAST at the NCBI site. -- 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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Out of Office: MG-RAST job completed
by Gardy, Jennifer 11 Feb '11

11 Feb '11

I will be out of the office at a workshop on Thursday, February 10 and my response time to emails will be somewhat delayed.

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Re: [mg-rast] Removal of Metagenomes?
by Mark D'Souza 10 Feb '11

10 Feb '11

Hi Steven, You can do this through the website -- click on the 'view details' link for the job and the next page has a 'delete this job' option in the dropdown from the green menu bar. ----- Original Message ----- > From: "Steven Quistad" <steven.quistad(a)gmail.com> > To: mg-rast(a)mcs.anl.gov > Sent: Thursday, February 10, 2011 4:35:57 PM > Subject: [mg-rast] Removal of Metagenomes? > Hello, > The following metagenomes were incorrectly uploaded, could they be > removed? I don't want to take up uneccesary space on the server. > Thanks > Steven > > > 13830 Quistad, Steven 4454223.3 CoralCaroline12Vir2009 23789034 > 2011-01-25 > view details > 13829 Quistad, Steven 4454222.3 SharkSkinMaldenVir2009 17735614 > 2011-01-25 > view details > -- > Steven Douglass Quistad > Joint-Doctoral Program Student > San Diego State University > University of California San Diego > San Diego, CA 92192 -- 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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Removal of Metagenomes?
by Steven Quistad 10 Feb '11

10 Feb '11

Hello, The following metagenomes were incorrectly uploaded, could they be removed? I don't want to take up uneccesary space on the server. Thanks Steven 13830Quistad, Steven4454223.3CoralCaroline12Vir2009237890342011-01-25<http://metagenomics.nmpdr.org/metagenomics.cgi?page=JobDetails&job=13830> *view details*<http://metagenomics.nmpdr.org/metagenomics.cgi?page=JobDetails&job=13830> 13829Quistad, Steven4454222.3SharkSkinMaldenVir2009177356142011-01-25<http://metagenomics.nmpdr.org/metagenomics.cgi?page=JobDetails&job=13829> *view details*<http://metagenomics.nmpdr.org/metagenomics.cgi?page=JobDetails&job=13829> -- Steven Douglass Quistad Joint-Doctoral Program Student San Diego State University University of California San Diego San Diego, CA 92192

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Re: [mg-rast] Job #13908
by Mark D'Souza 10 Feb '11

10 Feb '11

Hi Tom, You are welcome. The tasks completed in a short time and the number of RNA (well, Silva SSU) hits is low so everything seems to be in order, it should complete within an hour or so. Regards, Mark ----- Original Message ----- > From: "Tom Turner (JIC)" <Tom.Turner(a)bbsrc.ac.uk> > To: "Mark D'Souza" <dsouza(a)mcs.anl.gov> > Sent: Thursday, February 10, 2011 10:27:06 AM > Subject: RE: [mg-rast] Job #13908 > Hi Mark, > > Thanks for the quick response. > > If it helps, the file should not contain any rRNA reads. I've stripped > them out in silico. So there shouldn't be any, or only very few, hits > to these rRNA databases. > > Tom > > -----Original Message----- > From: Mark D'Souza [mailto:[email protected]] > Sent: 10 February 2011 16:22 > To: Tom Turner (JIC) > Cc: mg-rast(a)mcs.anl.gov > Subject: Re: [mg-rast] Job #13908 > > Hi, > > The similarity computation for your job had got into a strange state > where the BLAST against greengenes, Silva LSU and Silva SSU had failed > without any warning. Given that your jobs is labeled RNA this may mean > something. I restarted the failed tasks and will keep an eye on them. > If all goes well the job should complete within a day, let me know if > it does not. Sorry for the delay. > > > ----- Original Message ----- > > From: "Tom Turner (JIC)" <Tom.Turner(a)bbsrc.ac.uk> > > To: mg-rast(a)mcs.anl.gov > > Sent: Thursday, February 10, 2011 5:36:40 AM > > Subject: [mg-rast] Job #13908 > > Hi, > > > > > > > > I uploaded a data file to MG-RAST on 28/01/11 and have not yet > > received the notification that the job is complete. I noticed that > > on > > the Jobs Overview page that the “similarity final check has not been > > started”. I realise this is quite a large data set, but I just > > wondered if any progress was being made on the job, or whether it > > had > > stalled somewhere for whatever reason. > > > > > > > > The job number is 13908. > > > > > > > > I look forward to hearing from you. > > > > > > > > Thanks, > > > > Tom Turner > > > > > > > > Tom Turner > > > > PhD Student > > > > Molecular Microbiology > > > > John Innes Centre > > -- > 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] Job #13908
by Mark D'Souza 10 Feb '11

10 Feb '11

Hi, The similarity computation for your job had got into a strange state where the BLAST against greengenes, Silva LSU and Silva SSU had failed without any warning. Given that your jobs is labeled RNA this may mean something. I restarted the failed tasks and will keep an eye on them. If all goes well the job should complete within a day, let me know if it does not. Sorry for the delay. ----- Original Message ----- > From: "Tom Turner (JIC)" <Tom.Turner(a)bbsrc.ac.uk> > To: mg-rast(a)mcs.anl.gov > Sent: Thursday, February 10, 2011 5:36:40 AM > Subject: [mg-rast] Job #13908 > Hi, > > > > I uploaded a data file to MG-RAST on 28/01/11 and have not yet > received the notification that the job is complete. I noticed that on > the Jobs Overview page that the “similarity final check has not been > started”. I realise this is quite a large data set, but I just > wondered if any progress was being made on the job, or whether it had > stalled somewhere for whatever reason. > > > > The job number is 13908. > > > > I look forward to hearing from you. > > > > Thanks, > > Tom Turner > > > > Tom Turner > > PhD Student > > Molecular Microbiology > > John Innes Centre -- 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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Job #13908
by Tom Turner (JIC) 10 Feb '11

10 Feb '11

Hi, I uploaded a data file to MG-RAST on 28/01/11 and have not yet received the notification that the job is complete. I noticed that on the Jobs Overview page that the "similarity final check has not been started". I realise this is quite a large data set, but I just wondered if any progress was being made on the job, or whether it had stalled somewhere for whatever reason. The job number is 13908. I look forward to hearing from you. Thanks, Tom Turner Tom Turner PhD Student Molecular Microbiology John Innes Centre

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Fwd: Job 14157 failed?
by Mark D'Souza 09 Feb '11

09 Feb '11

----- Forwarded Message ----- > From: "Michelle L. Cilia" <mlc68(a)cornell.edu> > To: "Mark D'Souza" <dsouza(a)mcs.anl.gov> > Cc: "James I Vanee" <jiv2(a)cornell.edu> > Sent: Wednesday, February 9, 2011 12:10:53 PM > Subject: RE: [mg-rast] Job 14157 failed? > Outstanding. Thanks for the update! > > Michelle Cilia > Research Molecular Biologist > USDA-ARS > Functional and Comparative Proteomics Center > Robert W. Holley Center for Agriculture and Health > Ithaca, NY 14850 > (607) 255-4596 > ________________________________________ > From: Mark D'Souza [dsouza(a)mcs.anl.gov] > Sent: Wednesday, February 09, 2011 1:08 PM > To: Michelle L. Cilia > Subject: Re: [mg-rast] Job 14157 failed? > > Hi Michelle, > > The job is queued for similarity computation behind earlier jobs, it > should be done some time next week. > > Regards, > Mark

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Re: [mg-rast] 6 day jobs
by Mark D'Souza 09 Feb '11

09 Feb '11

Hi Iddo, That would be one week from today, depending on machine availability. Sorry, these last few months have been really busy. Mark ----- Original Message ----- > From: "Iddo Friedberg" <idoerg(a)gmail.com> > To: "Mark D'Souza" <dsouza(a)mcs.anl.gov> > Sent: Wednesday, February 9, 2011 12:13:45 PM > Subject: Re: [mg-rast] 6 day jobs > Hi Mark, > > Just to clarify: within a week from now or a week from submission? > > Thanks, > > ./I > > > On Wed, Feb 9, 2011 at 11:59 AM, Mark D'Souza < dsouza(a)mcs.anl.gov > > wrote: > > > Hi Iddo, > > The jobs should be done within a week. > > Regards, > Mark > > > > > > ----- Original Message ----- > > From: "Iddo Friedberg" < idoerg(a)gmail.com > > > To: mg-rast(a)mcs.anl.gov > > Sent: Wednesday, February 9, 2011 10:11:26 AM > > Subject: [mg-rast] 6 day jobs > > Hi, > > > > > > The following jobs were submitted 6 days ago, and have been in this > > status ever since. What is the current time frame for job conclusion > > on MG-RAST? > > > > > > Thanks, > > > > > > Iddo > > > > > > > > 14070 Friedberg, Iddo 4454467.3 PoolB sample 12 97934417 2011-02-03 > > view details > > 14069 Friedberg, Iddo 4454465.3 PoolB sample 11 73326429 2011-02-03 > > view details > > 14068 Friedberg, Iddo 4454466.3 PoolB sample 10 94170371 2011-02-03 > > view details > > 14067 Friedberg, Iddo 4454464.3 PoolB sample 10 110751265 2011-02-03 > > view details > > 14066 Friedberg, Iddo 4454462.3 PoolA sample 6 99459083 2011-02-03 > > view details > > 14065 Friedberg, Iddo 4454463.3 PoolA sample 5 88665968 2011-02-03 > > view details > > 14064 Friedberg, Iddo 4454461.3 PoolA Sample 4 86541269 2011-02-03 > > view details > > 14063 Friedberg, Iddo 4454460.3 PoolA sample 3 53061240 2011-02-03 > > view details > > 14062 Friedberg, Iddo 4454459.3 PoolA sample 2 126395516 2011-02-03 > > view details > > 14061 Friedberg, Iddo 4454458.3 PoolA Sample 1 38858938 2011-02-03 > > view details > > -- > > Iddo Friedberg > > http://iddo-friedberg.net/contact.html > > > > -- > Iddo Friedberg > http://iddo-friedberg.net/contact.html

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