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

Re: MG-RAST data job number 956 genome 4441094.3 - ENvironmental_enrichment
by Mark D'Souza 31 Jul '08

31 Jul '08

Hi Stuart, I will leave some of your questions to be answered by people on the mg-rast list. It does look like something is not right with the data you downloaded, the people who wrote the genbank file code would know better. I don't think a resubmission should be necessary, if there is something wrong we can fix it, and if our file format is incorrect we can change that. There is no size limit on the data you submit, if we have a problem processing it we will contact you. Regards, Mark D'Souza -- for the MG-RAST team http://metagenomics.nmpdr.org/ On Thu, 31 Jul 2008 Stuart.Denman(a)csiro.au wrote: > Hi Mark > > I have a few questions regarding the results from our data that we sent > to your server (job # 956 genome 4441094.3 - ENvironmental_enrichment). > > I have downloaded the annotated genbank file for the genome annotation, > when I open the file I can only count 136982 sequences compared to > 465226 called after preprocessing. From the other data that we have sent > up and got back we normally get the same number of sequences in the > annotated file as that which appears in the job details summary for the > number of sequences after preprocessing. Is this what you would normally > expect? > > We normally download the genbank file and use this for some of our > analysis here. Can we get a hold of the complete annotation or do we > need to resend the data (this took 30 days to calculate)? It would > appear if we use the seed viewer to view the annotated genome all the > sequence fragments are there we just don't get them all when we download > the file. > > Also for this data set the server seems to time out when we request to > view the features table is this due to the file size? > > Thanks for any help with this. Do you have a size limit on the data set > that could be submitted? > > Regards > > Stuart > > > > > > > > > > > > Stuart Denman > > CSIRO Livestock Industries > 306 Carmody Rd, St Lucia QLD 4067, Australia > Ph: +61-7-3214 2273 Fax: +61-7-3214 2900 > > Stuart.Denman(a)csiro.au > > > > > >

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mg-rast email
by Mark D'Souza 31 Jul '08

31 Jul '08

Hi, Just a reminder, I will be away tomorrow and the next week. Can someone take over responding to mg-rast email. Mark

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Re: [mg-rast] Fwd: MG-RAST registration
by Folker Meyer 31 Jul '08

31 Jul '08

I know! And I believe Mark's answer was both rapid and helpful. good Job. Folker On Jul 31, 2008, at 4:22 PM, Rob Edwards wrote: > FYI Kayo is the administrator for CAMERA. > > > On Jul 31, 2008, at 1:43 PM, Folker Meyer wrote: > >> can somebody help her? >> >> Folker >> >> Begin forwarded message: >> >>> From: "kayo arima" <karima(a)ucsd.edu> >>> Date: July 31, 2008 3:26:01 PM CDT >>> To: "Folker Meyer" <folker(a)mcs.anl.gov> >>> Subject: Fwd: MG-RAST registration >>> >>> Hi Falker, >>> I hope you are all well. >>> I attended SEED/RAST demo at ISMB2008 and was very interested in >>> using MG-RAST. However, somehow I did not find how to obtain my >>> user name and password. Will you help me or will you let me know >>> whom I should contact? >>> >>> Thank you so much! >>> Kayo >>> >>> ---------- Forwarded message ---------- >>> From: kayo arima <karima(a)ucsd.edu> >>> Date: Wed, Jul 30, 2008 at 3:01 PM >>> Subject: MG-RAST registration >>> To: info(a)theseed.org >>> >>> >>> Hi, >>> I registered MG-RAST but could not find how to get my username and >>> password. >>> Will you help me? >>> Thank you. >>> Kayo >>> >>> -- >>> Kayo Arima, PhD. >>> University of California, San Diego >>> California Institute for Telecommunication and Information >>> Technology >>> 9500 Gilman Dr. La Jolla, CA 92093-0440 >>> Office: 858-822-4649 >>> Fax: 858-822-5033 >>> >>> >>> >>> -- >>> Kayo Arima, PhD. >>> University of California, San Diego >>> California Institute for Telecommunication and Information >>> Technology >>> 9500 Gilman Dr. La Jolla, CA 92093-0440 >>> Office: 858-822-4649 >>> Fax: 858-822-5033 >> >> >> ______________________________________________________________________ >> This email has been scanned by the MessageLabs Email Security System. >> For more information please visit http://www.messagelabs.com/email >> ______________________________________________________________________ >

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Re: [mg-rast] Fwd: MG-RAST registration
by Rob Edwards 31 Jul '08

31 Jul '08

FYI Kayo is the administrator for CAMERA. On Jul 31, 2008, at 1:43 PM, Folker Meyer wrote: > can somebody help her? > > Folker > > Begin forwarded message: > >> From: "kayo arima" <karima(a)ucsd.edu> >> Date: July 31, 2008 3:26:01 PM CDT >> To: "Folker Meyer" <folker(a)mcs.anl.gov> >> Subject: Fwd: MG-RAST registration >> >> Hi Falker, >> I hope you are all well. >> I attended SEED/RAST demo at ISMB2008 and was very interested in >> using MG-RAST. However, somehow I did not find how to obtain my >> user name and password. Will you help me or will you let me know >> whom I should contact? >> >> Thank you so much! >> Kayo >> >> ---------- Forwarded message ---------- >> From: kayo arima <karima(a)ucsd.edu> >> Date: Wed, Jul 30, 2008 at 3:01 PM >> Subject: MG-RAST registration >> To: info(a)theseed.org >> >> >> Hi, >> I registered MG-RAST but could not find how to get my username and >> password. >> Will you help me? >> Thank you. >> Kayo >> >> -- >> Kayo Arima, PhD. >> University of California, San Diego >> California Institute for Telecommunication and Information Technology >> 9500 Gilman Dr. La Jolla, CA 92093-0440 >> Office: 858-822-4649 >> Fax: 858-822-5033 >> >> >> >> -- >> Kayo Arima, PhD. >> University of California, San Diego >> California Institute for Telecommunication and Information Technology >> 9500 Gilman Dr. La Jolla, CA 92093-0440 >> Office: 858-822-4649 >> Fax: 858-822-5033 > > > ______________________________________________________________________ > This email has been scanned by the MessageLabs Email Security System. > For more information please visit http://www.messagelabs.com/email > ______________________________________________________________________

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Re: [mg-rast] Fwd: MG-RAST registration
by Mark D'Souza 31 Jul '08

31 Jul '08

Hi Kayo, If you go to: http://metagenomics.nmpdr.org/rast.cgi?page=Login&action=forgot_password and enter your login/username (karima) and email address, your password will be reset and sent to you by email. Mark On Thu, 31 Jul 2008, Folker Meyer wrote: > can somebody help her? > > Folker > > Begin forwarded message: > > > From: "kayo arima" <karima(a)ucsd.edu> > > Date: July 31, 2008 3:26:01 PM CDT > > To: "Folker Meyer" <folker(a)mcs.anl.gov> > > Subject: Fwd: MG-RAST registration > > > > Hi Falker, > > I hope you are all well. > > I attended SEED/RAST demo at ISMB2008 and was very interested in > > using MG-RAST. However, somehow I did not find how to obtain my user > > name and password. Will you help me or will you let me know whom I > > should contact? > > > > Thank you so much! > > Kayo > > > > ---------- Forwarded message ---------- > > From: kayo arima <karima(a)ucsd.edu> > > Date: Wed, Jul 30, 2008 at 3:01 PM > > Subject: MG-RAST registration > > To: info(a)theseed.org > > > > > > Hi, > > I registered MG-RAST but could not find how to get my username and > > password. > > Will you help me? > > Thank you. > > Kayo > > > > -- > > Kayo Arima, PhD. > > University of California, San Diego > > California Institute for Telecommunication and Information Technology > > 9500 Gilman Dr. La Jolla, CA 92093-0440 > > Office: 858-822-4649 > > Fax: 858-822-5033 > > > > > > > > -- > > Kayo Arima, PhD. > > University of California, San Diego > > California Institute for Telecommunication and Information Technology > > 9500 Gilman Dr. La Jolla, CA 92093-0440 > > Office: 858-822-4649 > > Fax: 858-822-5033 > >

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Fwd: MG-RAST registration
by Folker Meyer 31 Jul '08

31 Jul '08

can somebody help her? Folker Begin forwarded message: > From: "kayo arima" <karima(a)ucsd.edu> > Date: July 31, 2008 3:26:01 PM CDT > To: "Folker Meyer" <folker(a)mcs.anl.gov> > Subject: Fwd: MG-RAST registration > > Hi Falker, > I hope you are all well. > I attended SEED/RAST demo at ISMB2008 and was very interested in > using MG-RAST. However, somehow I did not find how to obtain my user > name and password. Will you help me or will you let me know whom I > should contact? > > Thank you so much! > Kayo > > ---------- Forwarded message ---------- > From: kayo arima <karima(a)ucsd.edu> > Date: Wed, Jul 30, 2008 at 3:01 PM > Subject: MG-RAST registration > To: info(a)theseed.org > > > Hi, > I registered MG-RAST but could not find how to get my username and > password. > Will you help me? > Thank you. > Kayo > > -- > Kayo Arima, PhD. > University of California, San Diego > California Institute for Telecommunication and Information Technology > 9500 Gilman Dr. La Jolla, CA 92093-0440 > Office: 858-822-4649 > Fax: 858-822-5033 > > > > -- > Kayo Arima, PhD. > University of California, San Diego > California Institute for Telecommunication and Information Technology > 9500 Gilman Dr. La Jolla, CA 92093-0440 > Office: 858-822-4649 > Fax: 858-822-5033

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Re: metagenomics
by Brian Palenik 31 Jul '08

31 Jul '08

Developers! Is there an expected update coming up. I am hoping one of our genomes Synechococcus CC9311 will make it into the database soon. As far as I can tell the current update is May 16, 2008? Thanks, Brian Palenik On Jun 9, 2008, at 10:40 AM, Rob Edwards wrote: > Hey Brian > > No problems on the email - we have an email list mg- > rast(a)mcs.anl.gov that you can use to contact all the developers. > > That's very weird, for some reason we only got the CC9311 genome a > short while ago. It is being processed and should appear in the > SEED shortly. > > Sorry about that, > > Rob > > > > On Jun 9, 2008, at 9:46 AM, Brian Palenik wrote: > >> Hi Rob, >> >> I am checking out the metagenomics website and just got some >> results back. >> One puzzle is that our metagenome shows hits to several of our >> isolate genomes that were done by JGI (eg WH8102, CC9902, CC9605) >> but not the one done by TIGR called CC9311. We know through our >> own analyses that we should see 30,000 or so hits. Is CC9311 not >> in the Seed database? Not sure you are the right person to ask but >> if you could forward the message to the right person that would be >> great. >> Best wishes, >> Brian >> >> >> >> NC_008319 >> Links >> Synechococcus sp. CC9311, complete genome >> DNA; circular; Length: 2,606,748 nt >> Replicon Type: chromosome >> Created: 2006/09/05 >> >> Synechococcus(67661) >> Synechococcus elongatus PCC 6301.(136) >> Synechococcus elongatus PCC 7942.(246) >> Synechococcus sp. CC9605.(7660) >> Synechococcus sp. CC9902.(32478) >> Synechococcus sp. PCC 7002.(1) >> Synechococcus sp. RS9917.(8450) >> Synechococcus sp. WH 5701.(2444) >> Synechococcus sp. WH 7805.(12239) >> Synechococcus sp. WH 8102.(4007) >

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Re: [mg-rast] why are there only 27 public metagenomes?
by Rob Edwards 31 Jul '08

31 Jul '08

Right now on v.2.0 for me it says Jobs you have access to : You currently have access to 175 public jobs. But there are only ca. 20 or so listed in the table Rob On Jul 31, 2008, at 8:24 AM, Folker Meyer wrote: > there was something else wrong > > dunno why, but somebody did something to make them appear > > we really need some SOPs for making things work without any magic > happening. > > Folker > > > On Jul 31, 2008, at 10:23 AM, Rob Edwards wrote: > >> The difference between 177 and 145 maybe because not all those >> marked PUBLIC are finished processing. >> >> for i in $(ls */PUBLIC | cut -d '/' -f 1); do if [ -e $i/DONE ]; >> then echo $i; fi; done | wc -l >> 150 >> >> >> also note ... >> for i in $(ls */PUBLIC | cut -d '/' -f 1); do if [ -e $i/DELETE ]; >> then echo $i; fi; done | wc -l >> 6 >> >> >> Rob >> >> >> On Jul 30, 2008, at 9:25 PM, Andreas Wilke wrote: >> >>> Hi Mark, >>> >>> this is weird. There are 177 jobs with the public file in /vol/mg- >>> rast-prod/jobs/ >>> >>> find . -name PUBLIC |wc -l >>> 177 >>> >>> but only 27 are displayed as public at http://mg-rast.mcs.anl.gov/mg-rast/FIG/metagenomics.cgi >>> >>> There must be an additional mechanism to determine whether a >>> genome is public or not. >>> >>> I have added some genomes to the public scope, now there are 145, >>> but still not 177. >>> >>> Let's meet tomorrow to figure this out. >>> >>> >>> Andreas >>> >>> >>> On Jul 30, 2008, at 9:11 PM, Folker Meyer wrote: >>> >>>> Hi, >>>> >>>> after I informed the reviewers that we have >100 public >>>> metagenomes in MG-RAST v2 it is quite embarrassing to have 27 >>>> >>>> Can we please fix this? >>>> >>>> Folker >>>> >>> >>> >>> >>> ------------------------------------------------------ >>> Andreas Wilke >>> Argonne National Laboratory >>> Mathematics and Computer Science Division >>> Bldg. 221, Room A147 >>> 9700 South Cass Avenue >>> Argonne, IL 60439 >>> (630) 252-3190 (phone) >>> (630) 252-5986.(fax) >>> ------------------------------------------------------- >>> >>> >>> >>> >>> ______________________________________________________________________ >>> This email has been scanned by the MessageLabs Email Security >>> System. >>> For more information please visit http://www.messagelabs.com/email >>> ______________________________________________________________________ >> >

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Re: [mg-rast] why are there only 27 public metagenomes?
by Folker Meyer 31 Jul '08

31 Jul '08

there was something else wrong dunno why, but somebody did something to make them appear we really need some SOPs for making things work without any magic happening. Folker On Jul 31, 2008, at 10:23 AM, Rob Edwards wrote: > The difference between 177 and 145 maybe because not all those > marked PUBLIC are finished processing. > > for i in $(ls */PUBLIC | cut -d '/' -f 1); do if [ -e $i/DONE ]; > then echo $i; fi; done | wc -l > 150 > > > also note ... > for i in $(ls */PUBLIC | cut -d '/' -f 1); do if [ -e $i/DELETE ]; > then echo $i; fi; done | wc -l > 6 > > > Rob > > > On Jul 30, 2008, at 9:25 PM, Andreas Wilke wrote: > >> Hi Mark, >> >> this is weird. There are 177 jobs with the public file in /vol/mg- >> rast-prod/jobs/ >> >> find . -name PUBLIC |wc -l >> 177 >> >> but only 27 are displayed as public at http://mg-rast.mcs.anl.gov/mg-rast/FIG/metagenomics.cgi >> >> There must be an additional mechanism to determine whether a genome >> is public or not. >> >> I have added some genomes to the public scope, now there are 145, >> but still not 177. >> >> Let's meet tomorrow to figure this out. >> >> >> Andreas >> >> >> On Jul 30, 2008, at 9:11 PM, Folker Meyer wrote: >> >>> Hi, >>> >>> after I informed the reviewers that we have >100 public >>> metagenomes in MG-RAST v2 it is quite embarrassing to have 27 >>> >>> Can we please fix this? >>> >>> Folker >>> >> >> >> >> ------------------------------------------------------ >> Andreas Wilke >> Argonne National Laboratory >> Mathematics and Computer Science Division >> Bldg. 221, Room A147 >> 9700 South Cass Avenue >> Argonne, IL 60439 >> (630) 252-3190 (phone) >> (630) 252-5986.(fax) >> ------------------------------------------------------- >> >> >> >> >> ______________________________________________________________________ >> This email has been scanned by the MessageLabs Email Security System. >> For more information please visit http://www.messagelabs.com/email >> ______________________________________________________________________ >

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Re: [mg-rast] why are there only 27 public metagenomes?
by Rob Edwards 31 Jul '08

31 Jul '08

The difference between 177 and 145 maybe because not all those marked PUBLIC are finished processing. for i in $(ls */PUBLIC | cut -d '/' -f 1); do if [ -e $i/DONE ]; then echo $i; fi; done | wc -l 150 also note ... for i in $(ls */PUBLIC | cut -d '/' -f 1); do if [ -e $i/DELETE ]; then echo $i; fi; done | wc -l 6 Rob On Jul 30, 2008, at 9:25 PM, Andreas Wilke wrote: > Hi Mark, > > this is weird. There are 177 jobs with the public file in /vol/mg- > rast-prod/jobs/ > > find . -name PUBLIC |wc -l > 177 > > but only 27 are displayed as public at http://mg-rast.mcs.anl.gov/mg-rast/FIG/metagenomics.cgi > > There must be an additional mechanism to determine whether a genome > is public or not. > > I have added some genomes to the public scope, now there are 145, > but still not 177. > > Let's meet tomorrow to figure this out. > > > Andreas > > > On Jul 30, 2008, at 9:11 PM, Folker Meyer wrote: > >> Hi, >> >> after I informed the reviewers that we have >100 public metagenomes >> in MG-RAST v2 it is quite embarrassing to have 27 >> >> Can we please fix this? >> >> Folker >> > > > > ------------------------------------------------------ > Andreas Wilke > Argonne National Laboratory > Mathematics and Computer Science Division > Bldg. 221, Room A147 > 9700 South Cass Avenue > Argonne, IL 60439 > (630) 252-3190 (phone) > (630) 252-5986.(fax) > ------------------------------------------------------- > > > > > ______________________________________________________________________ > This email has been scanned by the MessageLabs Email Security System. > For more information please visit http://www.messagelabs.com/email > ______________________________________________________________________

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