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

Re: [mg-rast] problem with recruitment plot
by dsouza＠mcs.anl.gov 31 Mar '10

31 Mar '10

Hi Paul, I was not able to reproduce this problem. Are you changing the filter options (cutoffs)? If the cutoffs eliminate the two hits you would get this 'no fragments found' message. Other than that, unless we were having database issues you should not see this. Please try again and let us know if still does not work for you. Thanks, Mark D'Souza -- for the MG-RAST team mg-rast(a)mcs.anl.gov http://metagenomics.anl.gov/ ----- "Paul Cantalupo" <pcantalupo(a)gmail.com> wrote: > From: "Paul Cantalupo" <pcantalupo(a)gmail.com> > To: mg-rast(a)mcs.anl.gov > Sent: Wednesday, March 31, 2010 3:59:42 PM GMT -06:00 US/Canada Central > Subject: [mg-rast] problem with recruitment plot > > Hello, > > I'm trying to analyze my Barcelona2 (4446713.3) data set on MG-RAST. > When I go to the recruitment plot and select "Bordetella phage > BIP-1", > I get the error "No fragments found for ()." I'm seen this error for > other reference genomes during my analysis and have even seen it when > analyzing other people's metagenomic datasets on MG-RAST. Any ideas > as > to what is wrong? > > Thank you for your help and time, > > Paul > > > Paul Cantalupo > Research Specialist/Systems Programmer > 559 Crawford Hall > Department of Biological Sciences > University of Pittsburgh > Pittsburgh, PA 15260 > Work: 412-624-4687 > Fax: 412-624-4759

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problem with recruitment plot
by Paul Cantalupo 31 Mar '10

31 Mar '10

Hello, I'm trying to analyze my Barcelona2 (4446713.3) data set on MG-RAST. When I go to the recruitment plot and select "Bordetella phage BIP-1", I get the error "No fragments found for ()." I'm seen this error for other reference genomes during my analysis and have even seen it when analyzing other people's metagenomic datasets on MG-RAST. Any ideas as to what is wrong? Thank you for your help and time, Paul Paul Cantalupo Research Specialist/Systems Programmer 559 Crawford Hall Department of Biological Sciences University of Pittsburgh Pittsburgh, PA 15260 Work: 412-624-4687 Fax: 412-624-4759

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Your MG-RAST job (7110)
by Mark D'Souza 31 Mar '10

31 Mar '10

Hi, The job you submitted to MG-RAST (7110) cannot be processed as it consists of amino acid sequences and MG-RAST is designed to analyse nucleotide sequences only. -- Regards, Mark D'Souza -- for the MG-RAST team mg-rast(a)mcs.anl.gov http://metagenomics.anl.gov/

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Your MG-RAST jobs (7108,7109)
by Mark D'Souza 31 Mar '10

31 Mar '10

Hi, The jobs you submitted to MG-RAST (7108, 7109) cannot be processed as they consist of amino acid sequences and MG-RAST is designed to handle nucleotide sequences only. -- Regards, Mark D'Souza -- for the MG-RAST team mg-rast(a)mcs.anl.gov http://metagenomics.anl.gov/

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Your MG-RAST jobs (7028, 7029)
by dsouza＠mcs.anl.gov 29 Mar '10

29 Mar '10

Hi, The jobs you recently submitted to MG-RAST (7028, 7029) cannot be processed as they contain what appears to be a bacterial genome sequence in a single contig. MG-RAST is designed to analyse metagenomic sequence data in short reads and will not produce meaningful results for a bacterial genome. I would strongly advise you to submit this genome to RAST at http://rast.nmpdr.org/rast.cgi. The username and password you use for MG-RAST will work for RAST too. RAST is the sister application to MG-RAST and is designed specifically to analyze single genomes and is the perfect match for this task. -- Regards, Mark D'Souza -- for the MG-RAST team mg-rast(a)mcs.anl.gov http://metagenomics.anl.gov/

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Different status of ""SEED organism directory creation" for completed jobs
by Xiaoqing Rong 28 Mar '10

28 Mar '10

In the "Job Details" page of my job 6817, there is "SEED organism directory creation has been successfully completed", but for the jobs 6818, 6819, 6820 and 6821, it's shown as "SEED organism directory creation has not yet started". May I know why that could happen? Thanks a lot! RONG, Xiaoqing Graduate Student Department of Plant Pathology The Ohio State University / OARDC

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Your MG-RAST jobs (7033, 7038)
by dsouza＠mcs.anl.gov 25 Mar '10

25 Mar '10

Hi, The jobs you submitted to MG-RAST (7033, Evry and 7038, Nogent) have both failed as the sequence file names did not have an extension, e.g. '.fasta'. These jobs cannot be processed further as the upload step did not complete correctly, please rename the sequence files and resubmit them to the MG_RAST Server. -- Regards, Mark D'Souza -- for the MG-RAST team mg-rast(a)mcs.anl.gov http://metagenomics.anl.gov/

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Your MG-RAST job (6983)
by Mark D'Souza 25 Mar '10

25 Mar '10

Hi, The job you submitted to MG-RAST (6983, High Andean Forest Soil) has failed as the upload did not complete normally and the job cannot be processed. Please resubmit this job going through all three steps of the upload process and let us know if you have any problems. -- Regards, Mark D'Souza -- for the MG-RAST team mg-rast(a)mcs.anl.gov http://metagenomics.anl.gov/

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Your MG-RAST jobs (6479, 6480, 6481)
by dsouza＠mcs.anl.gov 25 Mar '10

25 Mar '10

Hi, The jobs you submitted to MG-RAST: 6479, GS87 6480, GS88 6481, GS89 cannot be processed as all the sequences are improperly labeled -- every sequence has the ID 'Noname'. Please modify your sequence files 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/

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technical question
by Sun,Yijun 25 Mar '10

25 Mar '10

Dear sir: I submitted a metagenomics data (~600K reads) to MG-rast. I would like to download the annotation information of all reads, but not sure how to do it. I explored the system and found that I can only downloaded the first 10000 entries by clicking "export table". Could you please show me how to download all of the information? Thanks. Best, ---- Yijun Sun, Ph.D. University of Florida URL: plaza.ufl.edu/sunyijun Email: sunyijun(a)biotech.ufl.edu

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