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

Fwd: Information
by Mark D'Souza 28 Feb '11

28 Feb '11

forgot to copy this to the mg-rast list. M. ----- Forwarded Message ----- > From: "Mark D'Souza" <dsouza(a)mcs.anl.gov> > To: "Valeria Lentini" <vlentini(a)unime.it> > Sent: Monday, February 28, 2011 11:11:18 AM > Subject: Re: [mg-rast] Information > Hi Valeria, > > The file size is not a problem, it could take some weeks to complete > the analysis of this sequence data which is over 3 Gbp. > > We keep your sequence data private so that only you can login and view > the analysis. The jobs are tied to your registered user account so > that when you log in to the system you can view them but no other > users can view them. At a later date if you wish to make a data set > public for anyone to see you can do this through the website, but > until then you are the only one who can view these jobs. > > > ----- Original Message ----- > > From: "Valeria Lentini" <vlentini(a)unime.it> > > To: "Mark D'Souza" <dsouza(a)mcs.anl.gov> > > Sent: Monday, February 28, 2011 2:53:54 AM > > Subject: Re: [mg-rast] Information > > Hi, > > I uploaded my data on MG-RAST, all the files are larger than 30 MB > > (about 250 MB).Is this a problem? > > > > Furthermore, I prefer that my data remain private until publication. > > What is the procedure about this?I have some guarantee? > > > > Valeria Lentini > > -- > 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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Your MG-RAST jobs (14883, 14884, 14885, 14888, 14889, 14891)
by Mark D'Souza 28 Feb '11

28 Feb '11

Hi, A couple of the jobs you submitted to MG-RAST (14889, 14891) have failed as the sequence files contain header lines with sequence identifiers which are not followed by a sequence. The jobs 14883, 14884, 14885, 14888, 14889 and 14891 contain complete genomes and can not be analyzed by MG-RAST. The system was designed to analyze large numbers of short reads from a metagenomic sample and the analysis for complete genomes with large contigs is quite meaningless. You may want to submit these jobs to the sister site RAST (http://rast.nmpdr.org/) here at Argonne National Laboratory which is specifically designed to analyze complete prokaryotic genomes, you are already registered for this service as the login username and password you use for MG-RAST will work for RAST too. -- 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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Your MG-RAST jobs (14796, 14797, 14798)
by Mark D'Souza 28 Feb '11

28 Feb '11

Hi, The jobs you submitted to MG-RAST (Dog1DefiniteChemera, Dog1NotChimera, Dog1NotClassified) have failed as the uploaded sequence files are all zero-size. It is not clear whether this is a problem that occurred during the upload process or if the files on your end are zero-size before upload. In either case, you will need to resubmit these data sets. -- 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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Fwd: About job 14802
by Mark D'Souza 28 Feb '11

28 Feb '11

----- Forwarded Message ----- > From: "Shan Wei" <vsbanry(a)gmail.com> > To: "Mark D'Souza" <dsouza(a)mcs.anl.gov> > Sent: Monday, February 28, 2011 9:54:07 AM > Subject: Re: [mg-rast] About job 14802 > Hi, Mark, > Thank you for identifying this error for me. I appreciate that. > > > Regards, > Shan Wei (Vivian) > > > On Mon, Feb 28, 2011 at 10:09 AM, Mark D'Souza < dsouza(a)mcs.anl.gov > > wrote: > > > Hi, > > The job failed because the sequence data contains non-sequence > characters -- the last two sequences contain a '~'. If you remove > these two characters and resubmit you should be OK. > > > > > ----- Original Message ----- > > From: "Shan Wei" < vsbanry(a)gmail.com > > > To: mg-rast(a)mcs.anl.gov > > Sent: Sunday, February 27, 2011 5:00:38 PM > > Subject: [mg-rast] About job 14802 > > Dear MG-RAST staff, > > My job 14802 uploaded at 2011-02-25 failed with an error. But I > > don't > > have to right to check out what the problem is. Will you be able to > > help me to identify that error? Thank you for you attention. > > > > > > Regards, > > Shan Wei (Vivian) > > -- > 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] About job 14802
by Mark D'Souza 28 Feb '11

28 Feb '11

Hi, The job failed because the sequence data contains non-sequence characters -- the last two sequences contain a '~'. If you remove these two characters and resubmit you should be OK. ----- Original Message ----- > From: "Shan Wei" <vsbanry(a)gmail.com> > To: mg-rast(a)mcs.anl.gov > Sent: Sunday, February 27, 2011 5:00:38 PM > Subject: [mg-rast] About job 14802 > Dear MG-RAST staff, > My job 14802 uploaded at 2011-02-25 failed with an error. But I don't > have to right to check out what the problem is. Will you be able to > help me to identify that error? Thank you for you attention. > > > Regards, > Shan Wei (Vivian) -- 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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About job 14802
by Shan Wei 27 Feb '11

27 Feb '11

Dear MG-RAST staff, My job 14802 uploaded at 2011-02-25 failed with an error. But I don't have to right to check out what the problem is. Will you be able to help me to identify that error? Thank you for you attention. Regards, Shan Wei (Vivian)

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(Job 830 , ID 4440973.3) . is now publicly available.
by mg-rast＠mcs.anl.gov 25 Feb '11

25 Feb '11

Jennifer Biddle (WebServerBackend::User=HASH(0x1fdee110)) has made the genome public. Link provided: http://mg-rast.mcs.anl.gov/mg-rast/FIG/linkin.cgi?metagenome=4440973.3.

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(Job 818 , ID 4440961.3) . is now publicly available.
by mg-rast＠mcs.anl.gov 25 Feb '11

25 Feb '11

Jennifer Biddle (WebServerBackend::User=HASH(0x6fa0200)) has made the genome public. Link provided: http://mg-rast.mcs.anl.gov/mg-rast/FIG/linkin.cgi?metagenome=4440961.3.

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(Job 818 , ID 4440961.3) . is now publicly available.
by mg-rast＠mcs.anl.gov 25 Feb '11

25 Feb '11

Jennifer Biddle (WebServerBackend::User=HASH(0x168c4100)) has made the genome public. Link provided: http://mg-rast.mcs.anl.gov/mg-rast/FIG/linkin.cgi?metagenome=4440961.3.

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(Job 817 , ID 4440960.3) . is now publicly available.
by mg-rast＠mcs.anl.gov 25 Feb '11

25 Feb '11

Jennifer Biddle (WebServerBackend::User=HASH(0x10b47250)) has made the genome public. Link provided: http://mg-rast.mcs.anl.gov/mg-rast/FIG/linkin.cgi?metagenome=4440960.3.

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