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

Special request
by Gustavo B. Gregoracci 29 Jan '11

29 Jan '11

Hello there, I'm the MG Rast user "montedeletras". I'm currently analysing a couple of metagenomes and I'm using the Stamp software to perform the statistical analysis. The thing is, I have some samples which are replicates and I wanted to add their number of hits so to compare different points, since they are pretty similar anyway and Stamp can only compare two metagenomes at a time. I can export the tables but there are subsystems/organisms missing in one of the replicates which could present a problem for our merging of tables. Is it possible for you guys to export for me some complete tables? We think that if we had full tables for the metagenomes with zero values for the absent members we could merge the tables for the replicates way more easily, and then exclude the ones that are both zeroed. The metagenomes I need are the ones filed in my private account: Name Job ID Juliana_RL3 12982 4453375.3 Juliana_RL4 12983 4453376.3 Juliana_RL6 12986 4453379.3 Juliana_RL6 12987 4453380.3 Juliana_RL7 12988 4453381.3 JulianaRL8 13286 4453712.3 And since I'm already bothering you guys with this, perhaps it would be interesting if we had the option to see the full tables in the site as well, with zero numbers for the absent hits. That would simplify cases such as mine in the future and I guess wouldn't be costly for you guys. Thanks very much in advance, Best regards, Gustavo Gustavo Bueno Gregoracci -- MSc., Dr. in Microbiology (Genetics and Molecular Biology) Email: gustavo_biomed(a)yahoo.com -- Pos doc Student Laboratório de Microbiologia (Prof. Fabiano Thompson) Centro de Ciências de Saúde - Instituto de Biologia - UFRJ Tel: +55 (21) 2562-6567

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Re: [mg-rast] Your MG-RAST jobs (13384, 13415)
by Powell Phd, Amy Jo 28 Jan '11

28 Jan '11

Hi Mark, Thanks very much for getting in touch about this. Yes, please do delete 13384. This job was launched when I was still trying to figure things out on MG Rast. On a different, but related MG Rast note, we are interested in implementing MG Rast on our systems here at Sandia. Is there a downloadable MG RAST that we could put on our local servers? Any help you could provide in this realm would be greatly appreciated! Regards, AJP On 1/28/11 11:55 AM, "Mark D'Souza" <dsouza(a)mcs.anl.gov> wrote: Hi, The two jobs 13384 and 13415 appear to be identical and are both named 'SA01_WBC_PE_2', probably the sequence file got uploaded twice by mistake. To conserve our compute resources I will let 13415 complete and put a hold on the processing of 13384 and delete it in two days if I do not hear from 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 Amy J. Powell, Ph.D. Sandia National Laboratories Department of Bioenergy & Defense Technology 1515 Eubank Blvd., SE Albuquerque, NM 87123 USA Telephone: (505)284-8050 Fax: (505)284-1323 "We are all agreed that your theory is crazy. My own feeling is that it is not crazy enough." Niels Bohr, Nobel Prize winner in Physics

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Re: [mg-rast] Your MG-RAST jobs (13829, 13831 and 13830, 13832)
by Mark D'Souza 28 Jan '11

28 Jan '11

Hi Steven, No problem. To delete a job, click on the 'view details' link on the page listing all your jobs, the next page has a 'delete this job' option in the drop down green menu bar. Mark ----- Original Message ----- > From: "Steven Quistad" <steven.quistad(a)gmail.com> > To: "Mark D'Souza" <dsouza(a)mcs.anl.gov> > Sent: Friday, January 28, 2011 12:55:40 PM > Subject: Re: Your MG-RAST jobs (13829, 13831 and 13830, 13832) > Hi Mark, > Sorry about that, I realized that right after I uploaded the > metagenomes are looked for a way to stop the processing. Is there a > way to stop a job once its submitted? Thanks > Steven > On Jan 28, 2011, at 9:50 AM, Mark D'Souza wrote: > > > Hi, > > > > The two jobs 13829 (SharkSkinMaldenVir2009) and 13831 > > (CoralCaroline9Vir2009NotAsem) appear to be identical, probably the > > sequence file got uploaded twice by mistake. To conserve our > > computing resourves, I will let 13829 complete and put a hold on the > > processing of 13831 and delete it in two days if I do not hear from > > you. > > > > The same is true for 13830 (CoralCaroline12Vir2009) and 13832 > > (CoralCaroline12Vir2009NotAssemb), I will hold 13832. > > > > Let us know if you need job names switched around. > > > > -- > > 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 (13384, 13415)
by Mark D'Souza 28 Jan '11

28 Jan '11

Hi, The two jobs 13384 and 13415 appear to be identical and are both named 'SA01_WBC_PE_2', probably the sequence file got uploaded twice by mistake. To conserve our compute resources I will let 13415 complete and put a hold on the processing of 13384 and delete it in two days if I do not hear from 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

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Your MG-RAST jobs (13409, 13467)
by Mark D'Souza 28 Jan '11

28 Jan '11

Hi, The two jobs 13409 (827026821) and 13467 (Blobs2) appear to be identical, probably the sequence file got uploaded twice by mistake. To conserve our compute resources I will let 13409 complete and put a hold on the processing of 13467 and delete it in two days if I do not hear from 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

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Your MG-RAST jobs (13876, 13877)
by Mark D'Souza 28 Jan '11

28 Jan '11

Hi, The two jobs 13876 and 13877 appear to be identical and are both named 'Kaziranga', probably the sequence file got uploaded twice by mistake. To conserve our compute resources I will let 13876 complete and put a hold on the processing of 13877 and delete it in two days if I do not hear from 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

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Your MG-RAST jobs (13829, 13831 and 13830, 13832)
by Mark D'Souza 28 Jan '11

28 Jan '11

Hi, The two jobs 13829 (SharkSkinMaldenVir2009) and 13831 (CoralCaroline9Vir2009NotAsem) appear to be identical, probably the sequence file got uploaded twice by mistake. To conserve our computing resourves, I will let 13829 complete and put a hold on the processing of 13831 and delete it in two days if I do not hear from you. The same is true for 13830 (CoralCaroline12Vir2009) and 13832 (CoralCaroline12Vir2009NotAssemb), I will hold 13832. Let us know if you need job names switched around. -- 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 (13842, 13843)
by Mark D'Souza 28 Jan '11

28 Jan '11

Hi, The two jobs 13842 and 13843 appear to be identical and are both named 'NRC-B', probably the sequence file got uploaded twice by mistake. I will let 13842 complete and put a hold on the processing of 13843 and delete it in two days if I do not hear from 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

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Your MG-RAST job (13910)
by Mark D'Souza 28 Jan '11

28 Jan '11

Hi, As you probably already know, the MG-RAST job (13910, cladeIA_454reads2) was created from a '._' (._GBZF.GSIO.fna) file which Mac OS X includes with a tar file and does not contain sequence data. I am going to delete it as it an artifact of the system. -- 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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Dereplicator doesn't do nice things to SSU
by William Trimble 27 Jan '11

27 Jan '11

Attached find graphs of some gross properties of a few thousand datasets in MG-rast private. Bottom line: the v3 dereplicator will take out most sequences from SSU datasets Many of the (probably SSU) datasets have large fracitons of the sequences that hit the protein database. w

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