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

Your MG-RAST job (10548, KB-1_JGI_fake)
by dsouza＠mcs.anl.gov 31 Aug '10

31 Aug '10

Hi, You are right, this is a fake job, it gets created from the dot-underscore file (._KB1_all_reads.fas) created by Mac OSX, I deleted the job. -- 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 (10521, 10522)
by dsouza＠mcs.anl.gov 30 Aug '10

30 Aug '10

Hi, The jobs you submitted to MG-RAST (10521, 10522) appear to be for complete bacterial genomes. MG-RAST is designed to analyze large numbers of short reads from a metagenomic sample and takes an incredibly long time for jobs like this and the results are quite useless. With this in mind I will halt the processing of these two jobs to avoid wasting compute cycles. You should submit these two genomes to the sister site RAST (http://rast.nmpdr.org/) which is explicitly designed to annotate complete and near-complete prokaryotic genomes. -- 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] questions MG RAST
by dsouza＠mcs.anl.gov 30 Aug '10

30 Aug '10

Hi, The files for these jobs have the same FASTA formatting errors as the previous job (which has now been deleted) with sequence ID lines which do not start on new lines. 10500 has: ...gt>contig00019ct... and ...ac>contig00057aa... and 10502 has: ...ca>contig00001gg... Perhaps the software that writes the files is creating this error. Regards, Mark ----- lservin(a)lcg.unam.mx wrote: > From: lservin(a)lcg.unam.mx > To: mg-rast(a)mcs.anl.gov > Sent: Sunday, August 29, 2010 6:00:41 PM GMT -06:00 US/Canada Central > Subject: [mg-rast] questions MG RAST > > Hello, > > I´m the user Luis Servin. Thanks for telling me what was the problem > with > the file from job 10489 > "Contigs_All_methods_map_Arch1_CAP3_contigs_singlets". I would like > to > know if there´s a way to delete only that job from my jobs overview > page. > > Also, I just submitted more jobs but two of them (jobs 10500 > "Arch1_CAP3" > and job 10502 "Arch2_CAP3") also say failed with an error. I don´t > know > what the problems is, can you help me? > > Thanks, your system is helping me a lot! > > Luis E. Servin

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Re: [mg-rast] less classified sequences with more number of submitted sequences
by Folker Meyer 30 Aug '10

30 Aug '10

Dear hiroko The reads are probably too short. Have you tried assembly? Best Folker -- Sent from mobile device On Aug 30, 2010, at 3:55 AM, Hiroko Iwanaga <hirokoiw(a)kais.kyoto-u.ac.jp> wrote: Dear Sir/Madam Hello. I tried to use the MG-RAST server with my random shotgun metagenome data obtained by Illumina GAII (average sequence length 50bp). First I tried with a subset (200,000 reads) of all the reads and got 197 classified reads in metabolic analysis. Next I tried with the all reads (10,552,476 reads) and got just 43classified reads. What's wrong with the all reads? Is it too many reads to analyze? I would appreciate any suggestions and advices. Thank you in advance. Hiroko ----------------------------- Hiroko Iwanaga (Sc.D.) Laboratory of Plant Genetics Graduate School of Agriculture Kyoto University Kitashirakawaoiwake-cho, Sakyo-ku, Kyoto 606-8502, Japan Tel:+81-(0)75-753-6145 Fax:+81-(0)75-753-6486 e-mail: hirokoiw(a)kais.kyoto-u.ac.jp -----------------------------

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October 4-6 registration
by Emmanuel Prestat 30 Aug '10

30 Aug '10

Hi, I would like to participate to this workshop and asked for that in precedent messages. Can you confirm that there will be some place for me in this tutorial ? (I will also be in Argonne at the october 6-8 workshop). Do I need to register something, to have the right to enter the campus (as I am a french citizen...) ? Best regards, Emmanuel Prestat ---------------------------------------- Emmanuel Prestat, PhD Ecole Centrale de Lyon UMR CNRS 5005, Laboratoire Ampère "Environmental Microbial Genomics" Group 36 avenue Guy de Collongue 69134 Ecully Cedex France Tel: +33 4 72 18 61 18 Fax: +33 4 78 43 37 17 emmanuel.prestat(a)ec-lyon.fr www.GenomEnviron.org

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less classified sequences with more number of submitted sequences
by Hiroko Iwanaga 30 Aug '10

30 Aug '10

Dear Sir/Madam Hello. I tried to use the MG-RAST server with my random shotgun metagenome data obtained by Illumina GAII (average sequence length 50bp). First I tried with a subset (200,000 reads) of all the reads and got 197 classified reads in metabolic analysis. Next I tried with the all reads (10,552,476 reads) and got just 43 classified reads. What's wrong with the all reads? Is it too many reads to analyze? I would appreciate any suggestions and advices. Thank you in advance. Hiroko ----------------------------- Hiroko Iwanaga (Sc.D.) Laboratory of Plant Genetics Graduate School of Agriculture Kyoto University Kitashirakawaoiwake-cho, Sakyo-ku, Kyoto 606-8502, Japan Tel:+81-(0)75-753-6145 Fax:+81-(0)75-753-6486 e-mail: hirokoiw(a)kais.kyoto-u.ac.jp -----------------------------

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questions MG RAST
by lservin＠lcg.unam.mx 29 Aug '10

29 Aug '10

Hello, Iï¿½m the user Luis Servin. Thanks for telling me what was the problem with the file from job 10489 "Contigs_All_methods_map_Arch1_CAP3_contigs_singlets". I would like to know if thereï¿½s a way to delete only that job from my jobs overview page. Also, I just submitted more jobs but two of them (jobs 10500 "Arch1_CAP3" and job 10502 "Arch2_CAP3") also say failed with an error. I donï¿½t know what the problems is, can you help me? Thanks, your system is helping me a lot! Luis E. Servin

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Your MG-RASTR jobs (10489, Contigs_All_methods_map_Arch1_CAP3_contigs_singlets)
by dsouza＠mcs.anl.gov 27 Aug '10

27 Aug '10

Hi, The job you submitted to MG-RAST has failed as the sequence file does not conform to the FASTA standard, the sequences following NODE_838_length_448_cov_18.482143 and NODE_862_length_75_cov_21.533333 are missing line breaks, e.g. >NODE_838_length_448_cov_18.482143 aacggt...gctgcagt>contig00019ctctc... Please check that your sequence file has not been corrupted, edit it to make it conform to the FASTA standard and resubmit to the MG-RAST server. -- 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 (10481, 250 Miles From Panama)
by dsouza＠mcs.anl.gov 27 Aug '10

27 Aug '10

Hi, The job you submitted to MG-RAST had failed as the upload process did not complete correctly. I restarted the job and it should proceed normally, it is not clear why this occurred. Your earlier submissions to the MG-RAST server had failed as the .tgz files were gzipped without being tarred. -- 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] my job
by Karimpour-Fard, Anis 27 Aug '10

27 Aug '10

thanks Mark, when will you update? can I get the list of your current genome and the list of the genome you will have in your updated version? thanks, Anis ________________________________________ From: dsouza(a)mcs.anl.gov [dsouza(a)mcs.anl.gov] Sent: Friday, August 27, 2010 7:42 AM To: Karimpour-Fard, Anis Cc: mg-rast(a)mcs.anl.gov; Mark D'Souza Subject: Re: my job Hi, I did not find this genome in the SEED database which is used by MG-RAST for phylogenetic and metabolic analysis. The next version of MG-RAST due soon will use a much more comprehensive coverage of available protein databases. Regards, Mark ----- "Anis Karimpour-Fard" <Anis.Karimpour-Fard(a)ucdenver.edu> wrote: > From: "Anis Karimpour-Fard" <Anis.Karimpour-Fard(a)ucdenver.edu> > To: "Mark D'Souza" <dsouza(a)mcs.anl.gov> > Cc: mg-rast(a)mcs.anl.gov > Sent: Thursday, August 26, 2010 6:31:36 PM GMT -06:00 US/Canada Central > Subject: RE: my job > > Hi, my result does not show any similarity to Phaeodactylum > tricornutum genome. I used local blast and blast my contigs against > Phaeodactylum tricornutum genome and there are several hits. > > Is there any reason that they are missing from the result from the > MG-RAST? > > Thanks, > Anis > ________________________________________ > From: Mark D'Souza [dsouza(a)mcs.anl.gov] > Sent: Monday, August 23, 2010 12:27 PM > To: Karimpour-Fard, Anis > Cc: Karimpour-Fard, Anis; dsouza(a)mcs.anl.gov > Subject: Re: my job > > Hi, > > Your job should be completed within a day or two, it got queued for > similarity computation with over 20Gbp sequence data which took some > time to process. > > ----- "Anis Karimpour-Fard" <Anis.Karimpour-Fard(a)ucdenver.edu> wrote: > > > From: "Anis Karimpour-Fard" <Anis.Karimpour-Fard(a)ucdenver.edu> > > To: "Anis Karimpour-Fard" <Anis.Karimpour-Fard(a)ucdenver.edu>, > dsouza(a)mcs.anl.gov > > Sent: Tuesday, August 17, 2010 6:14:08 PM GMT -06:00 US/Canada > Central > > Subject: my job > > > > Hi, my job has been running since last week. could you please let > me > > know when it will be ready? > > > > thanks, > > Anis > > -- > 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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