December 2008 - Mg-rast - mailman3.cels.anl.gov

FW: Internal Server Error
by Durso, Lisa 31 Dec '08

31 Dec '08

Hi Rob, I just realized that this e-mail did not make it to you. I'll send this version, and try one without the giant attachment. I am on my way out of town, but will touch base with you again on Monday. Thanks for your help. Lisa Lisa M. Durso, Ph.D. U.S. Meat Animal Research Center PO Box 166, State Spur 18D Clay Center, Nebraska 68933 Phone (402) 762-4359 Fax: (402) 762-4375 Email: lisa.durso(a)ars.usda.gov ________________________________ From: Durso, Lisa Sent: Wednesday, December 31, 2008 2:55 PM To: 'MG- Rast' Subject: RE: [mg-rast] Internal Server Error Hi Rob, It is immediately after upload. Well, to be more precise it is about 20 seconds after I try to upload, but before I get any new screen. I have only tried the two files so far. It usually takes me a while before I figure out how things are supposed to run. I've attached the file that I was trying to upload. Can you see if you are able to upload it from your location? In the past I have had problems trying to use a web interface from my government computer - something about the firewall settings and the many layers of computer administration in our agency. I was unable to submit data to one of the LBL computers through their Greengenes web pages. This data is from our first "metagenomic" 454 run - only two sections of a 16-section chip. Of course there is also the possibility that I do not have the files in the correct format. For example, I am guessing that the changes I made to the file extension were ok, but I don't really know. I changed the file extension from *.tar.gzip to *.tgz. Thanks for your quick response. Lisa Lisa M. Durso, Ph.D. U.S. Meat Animal Research Center PO Box 166, State Spur 18D Clay Center, Nebraska 68933 Phone (402) 762-4359 Fax: (402) 762-4375 Email: lisa.durso(a)ars.usda.gov ________________________________ From: Rob Edwards [mailto:[email protected]] Sent: Wednesday, December 31, 2008 2:28 PM To: Durso, Lisa Cc: mg-rast(a)mcs.anl.gov Subject: Re: [mg-rast] Internal Server Error Hi Lisa I just tested the upload and it is working fine. Where does the error occur? Is it immediately after upload, or does it get to the next page? Rob On Dec 31, 2008, at 11:26 AM, Durso, Lisa wrote: Dear Server Administrator, I am writing again at the request of the error pop up box. Time of error: approximately 1:22 pm CST December 31, 2008 Anything I might have done: This time I tried just uploading the *fasta file directly. I'll wait on trying again so that I don't have to keep sending these e-mails. Kind Regards, Lisa Durso Lisa M. Durso, Ph.D. U.S. Meat Animal Research Center PO Box 166, State Spur 18D Clay Center, Nebraska 68933 Phone (402) 762-4359 Fax: (402) 762-4375 Email: lisa.durso(a)ars.usda.gov

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Re: [mg-rast] Internal Server Error
by Rob Edwards 31 Dec '08

31 Dec '08

Hi Lisa I just tested the upload and it is working fine. Where does the error occur? Is it immediately after upload, or does it get to the next page? Rob On Dec 31, 2008, at 11:26 AM, Durso, Lisa wrote: > Dear Server Administrator, > > I am writing again at the request of the error pop up box. > > Time of error: approximately 1:22 pm CST December 31, 2008 > > Anything I might have done: This time I tried just uploading the > *fasta file directly. > > I’ll wait on trying again so that I don’t have to keep sending these > e-mails. > > Kind Regards, > Lisa Durso > > > > Lisa M. Durso, Ph.D. > U.S. Meat Animal Research Center > PO Box 166, State Spur 18D > Clay Center, Nebraska 68933 > > Phone (402) 762-4359 > Fax: (402) 762-4375 > Email: lisa.durso(a)ars.usda.gov > >

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Internal Server Error
by Durso, Lisa 31 Dec '08

31 Dec '08

Dear Server Administrator, I am writing again at the request of the error pop up box. Time of error: approximately 1:22 pm CST December 31, 2008 Anything I might have done: This time I tried just uploading the *fasta file directly. I'll wait on trying again so that I don't have to keep sending these e-mails. Kind Regards, Lisa Durso Lisa M. Durso, Ph.D. U.S. Meat Animal Research Center PO Box 166, State Spur 18D Clay Center, Nebraska 68933 Phone (402) 762-4359 Fax: (402) 762-4375 Email: lisa.durso(a)ars.usda.gov

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Internal Server Error
by Durso, Lisa 31 Dec '08

31 Dec '08

Dear Server Administrator, I am writing this e-mail at the request of a pop up error message. Time of error: approximately 1:05 pm CST, December 31, 2008 Anything I might have done to cause the error: This is my first attempt at uploading a file. I have two files, one *.qual, and one *.fasta. I tar-ed these, then gziped them, then dragged the whole thing onto my desktop and changed the file extension from *.tar.gzip to *.tgz. Then I uploaded the file via the web browser. I am not familiar with the pop up error message box - is this something that I can ignore in the future? Or do I need to e-mail you each time I get an error message? Kind Regards, Lisa Durso Lisa M. Durso, Ph.D. U.S. Meat Animal Research Center PO Box 166, State Spur 18D Clay Center, Nebraska 68933 Phone (402) 762-4359 Fax: (402) 762-4375 Email: lisa.durso(a)ars.usda.gov

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Re: [mg-rast] annotation
by Mark D'Souza 29 Dec '08

29 Dec '08

Hi Lynn, There is a genbank format download available from the Job Details page (click on 'View Details') which contains all the annotations. We are adding new download options for tab-separated text files of the annotations, but this is not in production yet. Regards, Mark D'Souza -- for the MG-RAST team mg-rast(a)mcs.anl.gov http://metagenomics.nmpdr.org/ On Mon, 22 Dec 2008, Lynn Williamson wrote: > How do I access the annotation results for job 2001, ID 4442092.3? > Thank you, > lynn williamson >

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annotated data
by Lynn Williamson 29 Dec '08

29 Dec '08

I have completed job 4442092.3. How do I view my results? I would like to download my data into an excel file. How do I do this? The only download format available is GenBank. lynn williamson llw(a)bact.wisc.edu

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Job 2038
by Regina Lamendella 23 Dec '08

23 Dec '08

Hello, I submitted a pig fecal metagenome for processing through the MG-RAST server, as job 2038. It has been processing for almost 48 hours and I was inquiring as to whether the job is still being processed on your end. It looks like it has made it through the similarity processing and I was wondering if everything is still ok with the job. Thanks for your time in this matter. Regina Lamendella Contractor to US EPA (513)-569-7243 M.S. Environmental Science Department of Civil and Environmental Engineering University of Cincinnati (513)-556-3798 _________________________________________________________________ It’s the same Hotmail®. If by “same” you mean up to 70% faster. http://windowslive.com/online/hotmail?ocid=TXT_TAGLM_WL_hotmail_acq_broad1_…

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Free hits counter Stats
by Bill statser 23 Dec '08

23 Dec '08

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annotation
by Lynn Williamson 22 Dec '08

22 Dec '08

How do I access the annotation results for job 2001, ID 4442092.3? Thank you, lynn williamson

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Re: [mg-rast] downloads
by Elizabeth M. Glass 22 Dec '08

22 Dec '08

It looks great Mark ----- Original Message ----- From: Mark D'Souza <dsouza(a)mcs.anl.gov> To: Leslie McNeil <lkmcneil(a)ncsa.uiuc.edu> Cc: mg-rast <mg-rast(a)mcs.anl.gov> Sent: Mon, 22 Dec 2008 15:06:04 -0600 (CST) Subject: Re: [mg-rast] downloads Hi, I have this working in my sandbox: http://bioseed.mcs.anl.gov/~dsouza/FIG/metagenomics.cgi on the JobDetails page. The drop-down select now has: Genbank export -- gbk file DNA sequence (MG-RAST) -- contigs file (used by mgrast for processing) DNA sequence (submitted) -- uploaded file from raw directory DNA sequence quality -- uploaded quality file AA locations -- peg tbl file AA sequence -- peg fasta file AA function -- assigned_functions file AA subsystems -- subsystems bindings file Only the text on the left gets displayed, so we want it to be be self-evident what it points to. Suggestions? Each option is offered only if the file is present and can be unambiguously identified. If I don't hear from anyone I will drop this into CVS and it will go in with the next update. I do worry about downloads of files which are many 10s or 100s of MB in size. Will deal with it when it becomes an issue. Mark On Mon, 22 Dec 2008, Mark D'Souza wrote: > Leslie, > > The one download that all jobs should have is the genbank file. > > There are some others which are being created, and could be made downloadable > -- contigs, subsystem bindings, Features -- peg tbl (peg locations), peg > fasta, peg assigned functions. > > Any others? > > If I don't hear from anyone I will add these to the download options. > > Does anyone know which IDs are used in the contigs file? V1 seem to have > mapped IDs, and V2 seem to have original (as submitted) IDs. > > Mark > > > On Sun, 21 Dec 2008, Leslie McNeil wrote: > >> Hello, >> >> I have been looking at various completed jobs while making a tutorial. >> Different jobs have different available download formats. Which do I list >> in a tutorial document? >> >> thanks, leslie >> >> >> Leslie Klis McNeil >> lkmcneil(a)ncsa.uiuc.edu >> 217-244-0597 >> >

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