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

MG-RAST upload of 16S pyrosequencing reads through QIIME
by Marcus Claesson 29 Jul '11

29 Jul '11

Dear List, Is it currently possible to upload fasta files of (barcode/primer-stripped) 16S pyrosequencing reads to my existing MG-RAST account using this script: http://qiime.sourceforge.net/scripts/submit_to_mgrast.html?highlight=submit… I have just generated an authorisation key but don't have the Project ID. How can I find that? Many thanks, Marcus

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Re: [mg-rast] Fwd: Submission to MG-RAST
by Omry Koren 29 Jul '11

29 Jul '11

Hi Mark, Thanks for all the previous help. At the moment I have one file stuck at finalizing for a long time, is there something I can do? Thanks Omry On Tue, Jul 5, 2011 at 9:57 AM, Omry Koren <korenomry(a)gmail.com> wrote: > Hi Mark, > A few of my files are stuck with an error. Is there anything I should do? > Thank you very much for all your help and time, > Omry > > > On Wed, Jun 29, 2011 at 12:50 PM, Mark DSouza <dsouza(a)mcs.anl.gov> wrote: > >> Hi Omry, >> >> There is no way to delete jobs from the web interface right now, we will >> be adding this in the future. In the meantime I can delete the jobs, is this >> the correct list? >> 25749 4466152.3 1234 >> 25892 4466295.3 1264 >> 25853 4466256.3 2264 >> 25747 4466150.3 2264 >> 25687 4466090.3 2195 >> >> We will check the job 1303 (25745, 4466148.3) which is showing an error. >> >> Regards, >> Mark >> >> >> ----- Original Message ----- >> > From: "Omry Koren" <korenomry(a)gmail.com> >> > To: mg-rast(a)mcs.anl.gov >> > Sent: Wednesday, June 29, 2011 10:36:21 AM >> > Subject: [mg-rast] Fwd: Submission to MG-RAST >> > ---------- Forwarded message ---------- >> > From: Omry Koren < korenomry(a)gmail.com > >> > Date: Tue, Jun 21, 2011 at 12:18 PM >> > Subject: Re: Submission to MG-RAST >> > To: Mark DSouza < dsouza(a)mcs.anl.gov > >> > >> > Hi Mark, >> > I went over all of the files and I have a few questions: >> > 1. How do I delete files? I have a few duplicates (1234,1264, and >> > 2195) and I would also like to delete both 2264 since the sequencing >> > center just notified me that they are very bad quality. >> > 2. A few files are showing errors, anything I can do? >> > >> > >> > >> > >> > Thank you very much for your time, >> > Omry >> > >> > >> > >> > >> > >> > On Mon, Jun 13, 2011 at 8:24 PM, Omry Koren < korenomry(a)gmail.com > >> > wrote: >> > >> > >> > I am really sorry about that, I thought some of the files were >> > corrupted. This is my first time using MG-RAST and I will contact you >> > next time I run into trouble. >> > Thank you and sorry again, >> > Omry >> > >> > >> > >> > >> > >> > On Mon, Jun 13, 2011 at 5:32 PM, Mark DSouza < dsouza(a)mcs.anl.gov > >> > wrote: >> > >> > >> > Hi, >> > >> > I am still seeing multiple uploads for the same file, 2195 was >> > uploaded four times, including once today, 2264 has been uploaded >> > thrice, including once today, 1234 and 1264 were uploaded twice with >> > an upload of 1264 today. Check if a dataset is already running before >> > uploading it and contact us if a job is not progressing, we can fix >> > things on our side. Creating duplicate jobs loads our compute machines >> > unnecessarily and affects the processing times for all our users. >> > These datasets are each multiple Gbp in size and will not get >> > completed in a day, if you are patient and work with us the jobs will >> > get processed. >> > >> > >> > Regards, >> > Mark >> > >> > >> > >> > ----- Original Message ----- >> > > From: "Omry Koren" < korenomry(a)gmail.com > >> > > To: "Mark DSouza" < dsouza(a)mcs.anl.gov > >> > >> > >> > >> > > Sent: Friday, June 10, 2011 5:09:17 PM >> > > Subject: Re: Submission to MG-RAST >> > > okay, thank you very much >> > > >> > > >> > > On Fri, Jun 10, 2011 at 6:06 PM, Mark DSouza < dsouza(a)mcs.anl.gov > >> > > wrote: >> > > >> > > >> > > Hi, >> > > >> > > No problem. I deleted the duplicated jobs. I also noticed that the >> > > upload for 2342 seems to be truncated, please compare the file size >> > > from the upload page against your local file, you probably need to >> > > redo the upload for this job. >> > > >> > > Regards, >> > > Mark >> > > >> > > >> > > >> > > >> > > >> > > ----- Original Message ----- >> > > > From: "Omry Koren" < korenomry(a)gmail.com > >> > > > To: "Mark DSouza" < dsouza(a)mcs.anl.gov > >> > > > Sent: Friday, June 10, 2011 3:26:17 PM >> > > > Subject: Re: Submission to MG-RAST >> > > > Hi, >> > > > Yes those are duplicates and can be deleted, thank you. >> > > > Besides what I am uploading now I only have one more file to >> > > > upload >> > > > so >> > > > will save the ftp option for next time. >> > > > Thank you very much >> > > > Omry >> > > > >> > > > >> > > > On Fri, Jun 10, 2011 at 4:24 PM, Mark DSouza < dsouza(a)mcs.anl.gov >> > > > > >> > > > wrote: >> > > > >> > > > >> > > > Hi, >> > > > >> > > > It appears that you are uploading a large amount of sequence data >> > > > to >> > > > MG-RAST. While this is not a problem, it would make the process >> > > > easier >> > > > for both of us if we coordinate these uploads. If you have more >> > > > data >> > > > to submit we can create an ftp site where you can dump your data >> > > > files >> > > > and we can then use the files to complete the submission. >> > > > >> > > > From the jobs which have been created the files 2195.txt and >> > > > 2264.txt >> > > > have been uploaded multiple times and seem to be running multiple >> > > > jobs. If you can confirm that these are identical datasets I will >> > > > delete the duplicated jobs. >> > > > >> > > > Please let us know about the ftp option, this will make the upload >> > > > process easier for you as well as help us in balancing the load on >> > > > our >> > > > machines and avoid duplicating jobs. >> > > > >> > > > -- >> > > > 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 >> > > > >> > > > >> > > > >> > > > -- >> > > > Omry Koren, Ph.D. >> > > > Postdoctoral Associate >> > > > Department of Microbiology >> > > > 467 Biotechnology building >> > > > Cornell University >> > > > Ithaca, NY 14853 >> > > > Email: ok46(a)cornell.edu >> > > >> > > >> > > >> > > -- >> > > Omry Koren, Ph.D. >> > > Postdoctoral Associate >> > > Department of Microbiology >> > > 467 Biotechnology building >> > > Cornell University >> > > Ithaca, NY 14853 >> > > Email: ok46(a)cornell.edu >> > >> > >> > >> > -- >> > >> > Omry Koren, Ph.D. >> > Postdoctoral Associate >> > Department of Microbiology >> > 467 Biotechnology building >> > Cornell University >> > Ithaca, NY 14853 >> > Email: ok46(a)cornell.edu >> > >> > >> > >> > >> > -- >> > >> > Omry Koren, Ph.D. >> > Postdoctoral Associate >> > Department of Microbiology >> > 467 Biotechnology building >> > Cornell University >> > Ithaca, NY 14853 >> > Email: ok46(a)cornell.edu >> > >> > >> > >> > >> > -- >> > Omry Koren, Ph.D. >> > Postdoctoral Associate >> > Department of Microbiology >> > 467 Biotechnology building >> > Cornell University >> > Ithaca, NY 14853 >> > Email: ok46(a)cornell.edu >> > > > > -- > Omry Koren, Ph.D. > Postdoctoral Associate > Department of Microbiology > 467 Biotechnology building > Cornell University > Ithaca, NY 14853 > Email: ok46(a)cornell.edu > > -- Omry Koren, Ph.D. Postdoctoral Associate Department of Microbiology 467 Biotechnology building Cornell University Ithaca, NY 14853 Email: ok46(a)cornell.edu

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Re: [mg-rast] Fwd: Re: Analysis question
by William Trimble 29 Jul '11

29 Jul '11

Those jobs were rerun and completed. The main symptom, abundance counts that well exceeded the number of reads, seems to have been resolved. Please let us know if you find anything else that doesn't make sense. William Trimble --for the MG-RAST team On Thu, Jul 28, 2011 at 3:15 PM, <legatzki(a)email.arizona.edu> wrote: > Hi, > I'm wondering if you got a chance to look at the data set together with a > colleague (see below) to check if the data set seems ok now. > Thanks, > > Antje > > -- > Antje Legatzki > Dept Soil Water and Environmental Science > Shantz Bldg. Rm 429 > University of Arizona > Tucson, AZ 85721 > 520-621-9759 > > > Quoting Mark DSouza <dsouza(a)mcs.anl.gov>: > >> Hi, >> >> It does look like the steps which had to be rerun have completed, I am >> verifying this with a colleague and will get back to you as soon as I have >> confirmation. >> >> Regards, >> Mark >> >> ----- Original Message ----- >>> >>> From: legatzki(a)email.arizona.edu >>> To: mg-rast(a)mcs.anl.gov >>> Cc: dsouza(a)mcs.anl.gov >>> Sent: Thursday, July 21, 2011 10:45:09 AM >>> Subject: Re: [mg-rast] Fwd: Re: Analysis question >>> Hi Analysis team, >>> please see below. I wanted to ask what the status of this is. >>> I checked my data set and it seems that you solved the problem since >>> the numbers >>> for Speleothem B went down. But I wanted to confirm with you. >>> >>> Thanks, >>> Antje >>> >>> >>> Quoting Mark D'Souza <dsouza(a)mcs.anl.gov>: >>> >>> > Hi, >>> > >>> > Your explanation was clear, I had mis-read your earlier email. >>> > >>> > The numbers for SpeleothemB do seem unusual, we are rerunning one of >>> > the pipeline stages which may be responsible, I will get back to you >>> > when this is done. >>> > >>> > Regards, >>> > Mark >>> > >>> > >>> > >>> > On Jul 11, 2011, at 11:34 AM, legatzki(a)email.arizona.edu wrote: >>> > >>> >> Hi Analysis team, >>> >> thanks for your fast response. >>> >> The MG-Rast ID's for the three samples are: >>> >> 4466357.3 (Speleothem A); 4466359.3 (Wet Rock); 4466556.3 >>> >> (Speleothem B) >>> >> 4466556.3 (Speleothem B) is the sample I NAMED IN MY FIRST EMAIL >>> >> SAMPLE A. >>> >> >>> >> The number of counts for sample A were significantly higher. >>> >> For example when I compared the three samples in the organisms >>> >> classification >>> >> mode using the SEED database (max. e-value cutoff: 1e-5, min. >>> >> identity cutoff: >>> >> 50%, min. alignment cutoff: 50, raw data) than I got for the >>> >> bacteria bar >>> >> (barchart graph): >>> >> >>> >> MG-RAST ID 4466556.3 - 2,454,565 counts >>> >> MG-RAST ID 4466359.3 - 488,597 counts >>> >> MG RAST ID 4466556.3 - 447,833 counts. For the other categories >>> >> (unassigned, >>> >> Archaea...) the counts of MG-RAST ID 4466556.3 were also much >>> >> higher >>> >> compared >>> >> to the other two samples. >>> >> When I chose another database to compare it looked similar. For >>> >> example when I >>> >> chose Swiss Prot (same settings like before fore SEED), than I got >>> >> for >>> >> bacteria: >>> >> MG-RAST ID 4466556.3 - 567,335 counts >>> >> MG-RAST ID 4466359.3 - 81,623 counts >>> >> MG-RAST ID 4466357.3 - 71,885 counts. >>> >> >>> >> Please let me know, if you have any questions regarding my >>> >> explanation. >>> >> >>> >> Regards, >>> >> >>> >> Antje >>> >> >>> >> -- >>> >> Antje Legatzki >>> >> Dept Soil Water and Environmental Science >>> >> Shantz Bldg. Rm 429 >>> >> University of Arizona >>> >> Tucson, AZ 85721 >>> >> 520-621-9759 >>> >> > > >

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Re: [mg-rast] Doubt about MG-Rast annotation
by Gustavo B. Gregoracci 28 Jul '11

28 Jul '11

Hello there Mark, Sorry to insist, but we are hanging on these questions to proceed with our analysis. If they are gonna take you too much of your time, please, redirect us to a reference or someone that can spare some time for these answers. I'll repeat the example and the questions for easy reference: Let's use an example, like the metagenome I sent you. We used the Subsytems database and separated Photosynthesis with 209 of abundance and 66 unique proteins in the group. We sent it to the Workbench to look into the taxonomic profile (Genbank). 1. It stored all the 209 hits from the abundance in the workbench, right? But in the Genbank it identified only 150, 101 as Eukaryota and 49 as Bacteria, which is shown in the workbench abundance column. Is this reasoning right? This loss is the result of the conversion between databases? 2. Each one of these 209 sequences is re-annotated in the Genbank, but can each sequence generate more than one annotation? Cause we got for bacteria an abundance of 245 and for eukarya an abundance of 403, from the 209 sequences selected in the workbench. 3. Similarly, if we got 150 proteins recognized in the workbench abundance from the 209 hits (see question 1), how do they turn into 97 unique proteins for bacteria and 163 unique proteins for eukarya? Again, I thank you for the time and patience, Looking forward to hear from you, 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 >________________________________ >From: Gustavo B. Gregoracci <gustavo_biomed(a)yahoo.com> >To: Mark DSouza <dsouza(a)mcs.anl.gov> >Cc: Louisi Oliveira <louisioliveira(a)gmail.com>; MG- Rast <mg-rast(a)mcs.anl.gov> >Sent: Wednesday, July 20, 2011 5:53 PM >Subject: Re: Doubt about MG-Rast annotation > > >Hi there, > > >Thanks for the help so far. We cleared some important questions but there are new ones. > > > >Let's use an example, like the metagenome I sent you. We used the Subsytems database and separated Photosynthesis with 209 of abundance and 66 unique proteins in the group. We sent it to the Workbench to look into the taxonomic profile (Genbank). > > >1. It stored all the 209 hits from the abundance in the workbench, right? But in the Genbank it identified only 150, 101 as Eukaryota and 49 as Bacteria, which is shown in the workbench abundance column. Is this reasoning right? This is the conversion between databases? > > > >2. Each one of these 209 sequences is re-annotated in the Genbank, but can each sequence generate more than one annotation? Cause we got for bacteria an abundance of 245 and for eukarya an abundance of 403, from the 209 sequences selected in the workbench. > > >3. Similarly, if we got 150 proteins recognized in the workbench abundance from the 209 hits (see question 1), how do they turn into 97 unique proteins for bacteria and 163 unique proteins for eukarya? > > >Sorry to trouble you again, but we really need to clarify these questions to continue with our analyses. We also will be spreading this information among our colleagues. > >Thanks again! >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 > > >>________________________________ >>From: Mark DSouza <dsouza(a)mcs.anl.gov> >>To: Gustavo B. Gregoracci <gustavo_biomed(a)yahoo.com> >>Cc: MG- Rast <mg-rast(a)mcs.anl.gov>; Louisi Oliveira <louisioliveira(a)gmail.com> >>Sent: Wednesday, July 20, 2011 2:44 PM >>Subject: Re: Doubt about MG-Rast annotation >> >>Hi, >> >>> The "# proteins" field gives me the number of unique sequences which matched the genbank database ... >> >>No, this is not accurate, the '# proteins' field gives the number of unique sequences within the selected grouping so if you group by phylum you will get unique sequences within the phylum. >> >>> ... the "abundance" is the total number of matches including repeated matches to the "# proteins" proteins. Is that so? >> >>Yes, this is correct. >> >>> When I send these to the workbench the "# proteins" is sent; and this subset is re-annotated with Subsystems, for example. The "#proteins" falls since not all of the original set annotated with Genbank will be recognized here, right? >> >>That is right, there may be sequences in GenBank which are not present in the SEED Subsystems database and vice versa. >> >>> But the abundance may increase because more repeats can be found in the larger database? >> >>When moving to a database with a larger number of sequences, the abundance will be expected to increase because of the greater chance of finding a match. >> >>> And what the "workbench abundance" means? >>The workbench abundance is the count of the reads in the metagenomic sample with hits against the protein sequences (from database A, e.g. Subsystems) selected in the workbench which were found in the database B (e.g. GenBank). In this example database A is used to select the proteins placed in the workbench and database B is used to create the organism classification, using the proteins from the workbench. >> >>Regards, >>Mark >> >> >>----- Original Message ----- >>> From: "Gustavo B. Gregoracci" <gustavo_biomed(a)yahoo.com> >>> To: "Mark DSouza" <dsouza(a)mcs.anl.gov> >>> Cc: "MG- Rast" <mg-rast(a)mcs.anl.gov>, "Louisi Oliveira" <louisioliveira(a)gmail.com> >>> Sent: Tuesday, July 19, 2011 8:46:22 PM >>> Subject: Re: Doubt about MG-Rast annotation >>> Hi there! >>> >>> >>> I'm not sure I got it right. Let's see... I annotated the metagenome >>> through Genbank, for example. The "# proteins" field gives me the >>> number of unique sequences which matched the genbank database and the >>> "abundance" is the total number of matches including repeated matches >>> to the "# proteins" proteins. Is that so? When I send these to the >>> workbench the "# proteins" is sent; and this subset is re-annotated >>> with Subsystems, for example. The "#proteins" falls since not all of >>> the original set annotated with Genbank will be recognized here, >>> right? But the abundance may increase because more repeats can be >>> found in the larger database? >>> >>> >>> >>> And what the "workbench abundance" means? >>> >>> >>> Sorry to bother you further, but I'm could not grasp the explanation >>> previously, >>> Thanks again for the help and patience, >>> >>> >>> 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 >>> >>> >>> >>> >>> >>> From: Mark DSouza <dsouza(a)mcs.anl.gov> >>> To: Gustavo B. Gregoracci <gustavo_biomed(a)yahoo.com> >>> Cc: MG- Rast <mg-rast(a)mcs.anl.gov>; Louisi Oliveira >>> <louisioliveira(a)gmail.com> >>> Sent: Monday, July 18, 2011 7:13 PM >>> Subject: Re: Doubt about MG-Rast annotation >>> >>> Hi, >>> >>> The number discrepancy arises from the use of different databases, the >>> original 209 hits is specific to the SEED subsystem, with 66 hits >>> against the proteins in these organisms. When you perform the organism >>> classification against GenBank, the number of hits is higher because >>> of the greater number of organisms in the GenBank database, and so >>> does the abundance counts. The workbench abundance column of the table >>> gives a better breakdown of the taxonomic counts as compared to the >>> 209 count. This is not very intuitive from the display and we are >>> looking into changing the table to make this more explicit. >>> >>> Regards, >>> Mark >>> >>> ----- Original Message ----- >>> > From: "Gustavo B. Gregoracci" < gustavo_biomed(a)yahoo.com > >>> > To: "Mark DSouza" < dsouza(a)mcs.anl.gov > >>> > Cc: "MG- Rast" < mg-rast(a)mcs.anl.gov >, "Louisi Oliveira" < >>> > louisioliveira(a)gmail.com > >>> > Sent: Monday, July 18, 2011 1:03:28 PM >>> > Subject: Re: Doubt about MG-Rast annotation >>> > Hi there Mark, >>> > >>> > >>> > Thanks for the reply. So, the metagenome ID is 4465448.3 and its >>> > called Forno. The glitch has actually happened in others as well, >>> > and >>> > I'm only using this one as an example. >>> > >>> > >>> > I re-checked the numbers and they still don't add. I'm working with >>> > Genbank (e-5) for organism classification, and subsystems (e-5) for >>> > functional classification, for that matter. >>> > >>> > >>> > I have 209 hits in this entire metagenome for photosynthesis. If I >>> > check the number of photosynthesis hits among the bacterial hits I >>> > get >>> > 140, while the same for eukaryotic gives me 142 hits. That puzzled >>> > me. >>> > When I do the opposite, and check the taxonomic composition of just >>> > the 209 photosynthesis hits the numbers are even more weirder. I get >>> > 245 hits for bacteria and 403 for eukaryotes! >>> > >>> > >>> > Thanks again for the help, >>> > I'm available for any further explanations necessary, >>> > >>> > >>> > 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 >>> > >>> > >>> > >>> > >>> > >>> > From: Mark DSouza < dsouza(a)mcs.anl.gov > >>> > To: Gustavo B. Gregoracci < gustavo_biomed(a)yahoo.com > >>> > Cc: MG- Rast < mg-rast(a)mcs.anl.gov > >>> > Sent: Monday, July 18, 2011 1:33 PM >>> > Subject: Re: Doubt about MG-Rast annotation >>> > >>> > Hi, >>> > >>> > Can you please send us the MG-RAST ID for the dataset where you >>> > observed this, we will check into it for 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 >>> > >>> > >>> > ----- Original Message ----- >>> > > From: "Gustavo B. Gregoracci" < gustavo_biomed(a)yahoo.com > >>> > > To: "Mark D'Souza" < dsouza(a)mcs.anl.gov > >>> > > Sent: Saturday, July 16, 2011 10:05:14 AM >>> > > Subject: Doubt about MG-Rast annotation >>> > > Hello there Mark, >>> > > >>> > > >>> > > >>> > > As I was analyzing some metagenomes, I ran into a recurrent >>> > > problem. >>> > > I >>> > > was trying to cross information from taxonomic and functional >>> > > annotation, and discovered some inconsistencies. I could not >>> > > figure >>> > > those out so I’m writing you in the hope that you can help me, >>> > > since >>> > > this will affect my analysis. >>> > > >>> > > >>> > > You see… I wanted to understand the contribution of different >>> > > phylogenetic groups to a given subsystem. So I got the total >>> > > number >>> > > of >>> > > sequences for the photosynthesis subsystem, for example, which was >>> > > 209 >>> > > hits. Then I went into taxonomy and separated all entries >>> > > identified >>> > > as eukaryotes, sending them to the workbench. I changed again to >>> > > functional and checked the total number of eukaryotic hits to >>> > > photosynthesis, which was 163. So far so good, but I decided to >>> > > perform the same analysis regarding prokaryotes. Sent all >>> > > prokaryotic >>> > > entries to the workbench and changed to functional to see their >>> > > contribution to photosynthesis as well. I got 174 hits! >>> > > >>> > > >>> > > >>> > > How is this possible? If my whole metagenome has 209 hits to a >>> > > subsystem, how can I have 163 eukaryotic hits within it and 174 >>> > > prokaryotic hits to the same subsystem? Can sequences be annotated >>> > > as >>> > > both eukaryotic and prokaryotic? Cause I was interpreting these >>> > > categories as mutually exclusive… >>> > > >>> > > >>> > > Thanks in advance for the help, >>> > > Looking forward to hear from you, >>> > > >>> > > >>> > > 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] Fwd: Re: Analysis question
by legatzki＠email.arizona.edu 28 Jul '11

28 Jul '11

Hi, I'm wondering if you got a chance to look at the data set together with a colleague (see below) to check if the data set seems ok now. Thanks, Antje -- Antje Legatzki Dept Soil Water and Environmental Science Shantz Bldg. Rm 429 University of Arizona Tucson, AZ 85721 520-621-9759 Quoting Mark DSouza <dsouza(a)mcs.anl.gov>: > Hi, > > It does look like the steps which had to be rerun have completed, I > am verifying this with a colleague and will get back to you as soon > as I have confirmation. > > Regards, > Mark > > ----- Original Message ----- >> From: legatzki(a)email.arizona.edu >> To: mg-rast(a)mcs.anl.gov >> Cc: dsouza(a)mcs.anl.gov >> Sent: Thursday, July 21, 2011 10:45:09 AM >> Subject: Re: [mg-rast] Fwd: Re: Analysis question >> Hi Analysis team, >> please see below. I wanted to ask what the status of this is. >> I checked my data set and it seems that you solved the problem since >> the numbers >> for Speleothem B went down. But I wanted to confirm with you. >> >> Thanks, >> Antje >> >> >> Quoting Mark D'Souza <dsouza(a)mcs.anl.gov>: >> >> > Hi, >> > >> > Your explanation was clear, I had mis-read your earlier email. >> > >> > The numbers for SpeleothemB do seem unusual, we are rerunning one of >> > the pipeline stages which may be responsible, I will get back to you >> > when this is done. >> > >> > Regards, >> > Mark >> > >> > >> > >> > On Jul 11, 2011, at 11:34 AM, legatzki(a)email.arizona.edu wrote: >> > >> >> Hi Analysis team, >> >> thanks for your fast response. >> >> The MG-Rast ID's for the three samples are: >> >> 4466357.3 (Speleothem A); 4466359.3 (Wet Rock); 4466556.3 >> >> (Speleothem B) >> >> 4466556.3 (Speleothem B) is the sample I NAMED IN MY FIRST EMAIL >> >> SAMPLE A. >> >> >> >> The number of counts for sample A were significantly higher. >> >> For example when I compared the three samples in the organisms >> >> classification >> >> mode using the SEED database (max. e-value cutoff: 1e-5, min. >> >> identity cutoff: >> >> 50%, min. alignment cutoff: 50, raw data) than I got for the >> >> bacteria bar >> >> (barchart graph): >> >> >> >> MG-RAST ID 4466556.3 - 2,454,565 counts >> >> MG-RAST ID 4466359.3 - 488,597 counts >> >> MG RAST ID 4466556.3 - 447,833 counts. For the other categories >> >> (unassigned, >> >> Archaea...) the counts of MG-RAST ID 4466556.3 were also much >> >> higher >> >> compared >> >> to the other two samples. >> >> When I chose another database to compare it looked similar. For >> >> example when I >> >> chose Swiss Prot (same settings like before fore SEED), than I got >> >> for >> >> bacteria: >> >> MG-RAST ID 4466556.3 - 567,335 counts >> >> MG-RAST ID 4466359.3 - 81,623 counts >> >> MG-RAST ID 4466357.3 - 71,885 counts. >> >> >> >> Please let me know, if you have any questions regarding my >> >> explanation. >> >> >> >> Regards, >> >> >> >> Antje >> >> >> >> -- >> >> Antje Legatzki >> >> Dept Soil Water and Environmental Science >> >> Shantz Bldg. Rm 429 >> >> University of Arizona >> >> Tucson, AZ 85721 >> >> 520-621-9759 >> >>

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Re: [mg-rast] Your MG-RAST jobs (28672..28687)
by Mark DSouza 27 Jul '11

27 Jul '11

Hi Thanks for your response, I will check into the QIIME submission process. When I used your account to login to the MG-RAST site the 'add' button opened the file selection box as required. Are you using FireFox? We try to have the site work on other browsers but some parts work best on FireFox. -- 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 ----- Original Message ----- > From: "Vanessa Coats" <vanessa.coats(a)maine.edu> > To: "Mark DSouza" <dsouza(a)mcs.anl.gov>, mg-rast(a)mcs.anl.gov > Sent: Tuesday, July 26, 2011 6:46:04 PM > Subject: Re: Your MG-RAST jobs (28672..28687) > Hi, > I've been using the QIIME pipeline (python based) for my data analysis > and I came across the QIIME documentation with commands to upload a > fasta file directly to MG-RAST. I received a log of error messages so > I'm not surprised it didn't work. I'm unsure of what the actual > problem was during the upload process (error messages just said there > was an error and the upload was unable to complete... no error codes > or anything). For more info see: > http://qiime.org/scripts/submit_to_mgrast.html > > I have successfully uploaded files to the MG-RAST server (v2) in the > past but I've not been able to upload anything since the switch to > version 3.0. I work on a mac and I've enabled the Java applet > necessary to upload files directly but it doesn't work. I click "add" > and nothing happens... > Any suggestions? > > Thanks, > Vanessa > > > > On Tue, Jul 26, 2011 at 1:16 PM, Mark DSouza < dsouza(a)mcs.anl.gov > > wrote: > > > > > Hi, > > I am afraid the jobs you created yesterday (28672..28687) did not get > created cleanly and can not be processed, you will need to upload them > again. > > To prevent the same problem occurring again, could you let us know how > whether you used the website page to upload the files for these jobs. > If not, please let us know how the upload was performed? We have seen > something like this occur before and would like to fix our site so > that it does not occur again. You will probably need to modify your > upload method till we sort this out. > > Please reply to the 'mg-rast(a)mcs.anl.gov ' address so that it reaches > the entire team and this can get attended to quickly. > > -- > Thanks, > 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 > > > > -- > Vanessa Coats > PhD Student, Rumpho Lab > Dept. of Molecular and Biomedical Sciences > 5735 Hitchner Hall, rm 300 > University of Maine > Orono, ME, 04469 > (207) 581-2799

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Query re use of recruitment plot analysis function
by William Trimble 27 Jul '11

27 Jul '11

---------- Forwarded message ---------- From: William Trimble <wltrimbl(a)gmail.com> Date: Wed, Jul 27, 2011 at 10:07 PM Subject: Re: [mg-rast] Query re use of recruitment plot analysis function To: Katherine Wright <katherine.wright(a)colorado.edu>, mgrast(a)mcs.anl.gov Thanks for using MG-RAST. The contigs on the recruitment plot page are contigs in the reference genome. This terminology is used since some of the reference genomes are drafts. At present, MG-RAST does not do assembly of submitted sequences, though this is something we'd like to include in the future. What you can download are translations of the protiens in your sequences. William Trimble --for the MG-RAST team On Wed, Jul 27, 2011 at 10:00 PM, Katherine Wright <katherine.wright(a)colorado.edu> wrote: > Dear MG-RAST team, > > I am using the analysis tools to look at the results of the analysis of my metagenome (which is private, not part of the public database). > > In the recruitment plot section I can see the results of aligning metagenome sequences against different reference genomes. I can download the table that gives the summary of the results of this, which is extremely useful, but in the table I see a reference to a contig (which I assume is a contig that MG-RAST has produced from my metagenome sequences, and which aligns with the reference genome). I would like to be able to download the sequence of that contig, but I can't find out how to do it. > > I've looked at the online help, but couldn't figure it out, so I'd be grateful for instructions! > > Many thanks, > > Katherine >

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Query re use of recruitment plot analysis function
by Katherine Wright 27 Jul '11

27 Jul '11

Dear MG-RAST team, I am using the analysis tools to look at the results of the analysis of my metagenome (which is private, not part of the public database). In the recruitment plot section I can see the results of aligning metagenome sequences against different reference genomes. I can download the table that gives the summary of the results of this, which is extremely useful, but in the table I see a reference to a contig (which I assume is a contig that MG-RAST has produced from my metagenome sequences, and which aligns with the reference genome). I would like to be able to download the sequence of that contig, but I can't find out how to do it. I've looked at the online help, but couldn't figure it out, so I'd be grateful for instructions! Many thanks, Katherine

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Re: [mg-rast] Any way to upload genbank genomes for KEGG comparison?
by Tobias Paczian 27 Jul '11

27 Jul '11

If the Genbank file has EC numbers, it should not be a problem. Cheers Tobi On Jul 26, 2011, at 12:07 PM, Mark DSouza wrote: > Tobi, > > Would it be possible to allow the user to do this (see user email > below)? > > Maybe upload a file with the relevant information and create the > comparison to a metagenome for them? Or just have the KEGG data > downloadable so that they can do this themselves. > > Mark > > ----- Forwarded Message ----- >> From: "Stephen Mondo" <sjm284(a)cornell.edu> >> To: mg-rast(a)mcs.anl.gov >> Sent: Tuesday, July 26, 2011 10:55:32 AM >> Subject: [mg-rast] Any way to upload genbank genomes for KEGG >> comparison? >> Dear MG-RAST, I have uploaded my data and am interested in seeing how >> my KEGG pathways overlap with a particular genome which is deposited >> in Genbank (ie data A = my metagenome, data B = Genbank genome). Is >> this feature available? If not, where should I look to find such a >> comparison? >> >> Thanks a lot, >> Stephen

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Re: [mg-rast] Your MG-RAST jobs (28672..28687)
by Vanessa Coats 26 Jul '11

26 Jul '11

Hi, I've been using the QIIME pipeline (python based) for my data analysis and I came across the QIIME documentation with commands to upload a fasta file directly to MG-RAST. I received a log of error messages so I'm not surprised it didn't work. I'm unsure of what the actual problem was during the upload process (error messages just said there was an error and the upload was unable to complete... no error codes or anything). For more info see: http://qiime.org/scripts/submit_to_mgrast.html I have successfully uploaded files to the MG-RAST server (v2) in the past but I've not been able to upload anything since the switch to version 3.0. I work on a mac and I've enabled the Java applet necessary to upload files directly but it doesn't work. I click "add" and nothing happens... Any suggestions? Thanks, Vanessa On Tue, Jul 26, 2011 at 1:16 PM, Mark DSouza <dsouza(a)mcs.anl.gov> wrote: > ** ** > Hi, > > I am afraid the jobs you created yesterday (28672..28687) did not get > created cleanly and can not be processed, you will need to upload them > again. > > To prevent the same problem occurring again, could you let us know how > whether you used the website page to upload the files for these jobs. If > not, please let us know how the upload was performed? We have seen something > like this occur before and would like to fix our site so that it does not > occur again. You will probably need to modify your upload method till we > sort this out. > > Please reply to the 'mg-rast(a)mcs.anl.gov' address so that it reaches the > entire team and this can get attended to quickly. > > -- > Thanks, > 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 > > -- Vanessa Coats PhD Student, Rumpho Lab Dept. of Molecular and Biomedical Sciences 5735 Hitchner Hall, rm 300 University of Maine Orono, ME, 04469 (207) 581-2799

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