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

Fwd: [mgrastdev] Fwd: 1 problem
by Andreas Wilke 01 Sep '11

01 Sep '11

Begin forwarded message: > From: Mark DSouza <dsouza(a)mcs.anl.gov> > Subject: [mgrastdev] Fwd: 1 problem > Date: August 31, 2011 4:40:27 PM CDT > To: mg-rast dev <mgrastdev(a)mcs.anl.gov> > > Not sure who this belongs to ... > > This is for the recruitment plot, I checked and the evalue can be changed in the dropdown, but clicking the OK button has no effect. > The displayed text for the abundance scale does change with the OK button, but the resulting circle map does not. > > Mark > > > ----- Forwarded Message ----- >> From: "Peter Noble" <panoble(a)washington.edu> >> To: "Mark DSouza" <dsouza(a)mcs.anl.gov> >> Sent: Tuesday, August 30, 2011 4:37:16 PM >> Subject: Re: 1 problem >> Hi Mark, >> >> I see that the recruitment plot now allows private datasets =) (yes i >> am using firefox) >> >> However, there is now a problem with setting the e-value.... it >> reports *none* but I tried to set it to 10-5... I clicked the ok >> button but no response. >> >> I hope this helps. >> >> Peter >> >> >> On Aug 30, 2011, at 11:44 AM, Mark DSouza wrote: >> >>> Hi, >>> >>> And thanks, glad to hear the system is useful to you. >>> >>> The recruitment plot should work for all datasets, including private >>> ones. Please send us the MG-RAST ID for the dataset and a >>> description of the failure mode, with screenshots if possible and we >>> will look into it. You can also examine the data analysis through >>> the organism hierarchical classification tools (table, barchart, >>> heatmap, tree) to determine dominant species through the abundance >>> counts. >>> >>> We will be adding a delete function in the next release, till then >>> if you send me the MG-RAST IDs for the datasets to be deleted I can >>> do this 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: panoble(a)washington.edu >>>> To: mg-rast(a)mcs.anl.gov >>>> Sent: Tuesday, August 30, 2011 10:15:02 AM >>>> Subject: [mg-rast] 2 problems >>>> Hi, >>>> >>>> 1) I want to do a recruitment plot of a certain bacterial species >>>> and >>>> my private data sets but mg-rast will only let me use public data >>>> sets.... why? How can I test to see if I have a dominant known >>>> species >>>> in my 454 samples, as my analyses show? >>>> >>>> 2) There appears to be function to delete files. I put a couple >>>> test >>>> files on your site to see how your web site works. However, they >>>> are >>>> now useless. How do I get rid of them.... I looked for delete >>>> functions but could not find. >>>> >>>> Lastly, nice programs.... I am having fun playing with my data. >>>> >>>> Peter > _______________________________________________ > mgrastdev mailing list > mgrastdev(a)mcs.anl.gov > https://lists.mcs.anl.gov/mailman/listinfo/mgrastdev Andreas Wilke Argonne National Laboratory Mathematics and Computer Science Division Bldg. 240 , 4F8 9700 South Cass Avenue Argonne, IL 60439 (630) 252-3190 (phone) (630) 252-5986.(fax)

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Re: [mg-rast] problems with MG-RAST
by Mark DSouza 01 Sep '11

01 Sep '11

Hi, I reset the upload page so that the three older tabs are not displayed. The jobs are not being created for a couple of reasons. A number of the sequence files you submitted have alignment information in them (the '-' characters) which should be rejected by the system as they are not handled correctly, you would need to remove these characters in your sequence files. The version 3 of MG-RAST is specifically designed to handle large numbers of short metagenomic reads and the analysis for small (less than a Mbp) sequence files is quite poor. The jobs you have submitted recently are smaller than this and we are not finding any sequence matches in the database. I am sorry I could not be of more help, for a small number of sequences MG-RAST is probably not the correct tool for your analysis and the results from submitting to the NCBI BLAST server may be more useful. -- 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: "Marcio Costa" <costam(a)uoguelph.ca> > To: mg-rast(a)mcs.anl.gov > Sent: Thursday, September 1, 2011 11:06:30 AM > Subject: [mg-rast] problems with MG-RAST > Dear sir/madam, > > I've been trying for the last few days to upload files in the server, > but after the processing is completed, the job does not appear on my > list of jobs available for analysis. In addition, on my upload page, I > have three tabs from older jobs that are incomplete, but stay > permanently there. I registered as costamc. > > Thanks you, > > Marcio Costa.

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problems with MG-RAST
by Marcio Costa 01 Sep '11

01 Sep '11

Dear sir/madam, I've been trying for the last few days to upload files in the server, but after the processing is completed, the job does not appear on my list of jobs available for analysis. In addition, on my upload page, I have three tabs from older jobs that are incomplete, but stay permanently there. I registered as costamc. Thanks you, Marcio Costa.

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Re: [mg-rast] A quick question
by Mark DSouza 01 Sep '11

01 Sep '11

Hi, You could select all the 8000 function features in one step though the interface is not really designed for this. A better way would be to go to the download page where you can get the annotations + clustering + sequence files. The annotated, Sims (650.superblat.expand.protein) file contains functional annotations along with the metagenomic read ID or cluster ID assigned by MG-RAST. The cluster IDs can be mapped back to read IDs using the aa90, Cluster (550.cluster.aa90.mapping) file. The blog page http://blog.metagenomics.anl.gov/howto/downloads/ has more details. Regards, Mark ----- Original Message ----- > From: "fancy-yf" <fancy-yf(a)163.com> > To: "Mark D'Souza" <dsouza(a)mcs.anl.gov> > Sent: Thursday, September 1, 2011 10:05:26 AM > Subject: Re: Re: [mg-rast] A quick question > Hi, Mark > > I find it! Thanks very much for your detailed direction. I really > appreciate your patience and excellent professionalism. > > And another question is could I select all the features in one step, > as I want to download all the sequences affiliated to nearly 8000 > function features. How I can get that result? > > Thanks! > > Fang > > > > 2011-09-01 > > fancy-yf > > 发件人： Mark D'Souza > 发送时间： 2011-08-31 23:46:03 > 收件人： fancy-yf > 抄送： mg-rast > 主题： Re: [mg-rast] A quick question > > > Hi, > > Ah, I understand, the problem is that you have not reached the stage > where the workbench is available. After selecting the features with > the checkboxes you need to click on the 'to workbench' button in the > header row of the table which will move the selected features to the > workbench. When the tab tab header 'Workbench (0 features)' is updated > with the number of features moved you can click on the tab heading and > work on the selected features only. This new workbench tab will have > the download link where you can retrieve the sequences for the reads > with the selected features. > > Regards, > Mark > > > > On Aug 31, 2011, at 8:31 AM, fancy-yf wrote: > > > Hi, Mark > > > > I tried to find the link of 'download metagenome dna FASTA annotated > > by' in the workbench tab , unfortunately, I really could not find > > that! > > Will you please check it and direct me specificly how to do it? > > Attached is my interface on the worbench. > > Regards, > > > > Fancy > > > > > > <Catch1.jpg> > > > > > > > > > > 2011-08-31 > > fancy-yf > > 发件人： Mark DSouza > > 发送时间： 2011-08-31 00:54:38 > > 收件人： fancy-yf > > 抄送： MG- Rast > > 主题： Re: [mg-rast] A quick question > > Hi, > > Once you have selected your features to the workbench the workbench > > tab will have a link 'download metagenome dna FASTA annotated by' > > where you can select a dabase source and download the sequence data. > > The md5s do refer to protein sequences, these are clickable and will > > display all the annotations from the databases used to create the > > m5nr non-redundant protein database. > > Regards, > > Mark > > ----- Original Message ----- > > > From: "fancy-yf" <fancy-yf(a)163.com> > > > To: "Mark DSouza" <dsouza(a)mcs.anl.gov> > > > Sent: Tuesday, August 30, 2011 7:20:59 AM > > > Subject: Re: Re: [mg-rast] A quick question > > > Hello, Mark > > > > > > Do you mean the column of md5s?Is it refer to the protein > > > sequences? > > > Actually, I can't find other specific column in the workbench on > > > downloading fasta-formatted sequences. > > > Would you mind tell me how to find that? > > > > > > Thanks! > > > > > > > > > 2011-08-30 > > > > > > fancy-yf > > > > > > 发件人： Mark DSouza > > > 发送时间： 2011-08-22 23:18:49 > > > 收件人： fancy-yf > > > 抄送： mg-rast > > > 主题： Re: [mg-rast] A quick question > > > > > > > > > Hi, > > > > > > The workbench enables download of individual sequences, select the > > > rows for the function under the 'to workbench column'. The > > > workbench > > > is then accessed through the 'Workbench tab' where you can > > > download > > > fasta formatted metagenomic sequence data for the selected > > > sequences. > > > > > > -- > > > 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: "fancy-yf" <fancy-yf(a)163.com> > > > > To: "mg-rast" <mg-rast(a)mcs.anl.gov> > > > > Sent: Sunday, August 21, 2011 9:15:45 PM > > > > Subject: [mg-rast] A quick question > > > > Hello, > > > > > > > > Here I have a question and might need your help. For the MG-RAST > > > > annotation result of my metagenomic data downloaded from MG-RAST > > > > server (as attached). Here I want to find the exact sequence of > > > > specific object in function column (eg. Alanine racemase (EC > > > > 5.1.1.1) > > > > ). How could I get that sequence? > > > > > > > > Hope for your replies! > > > > > > > > fancy > > > > > > > > > > > > 2011-08-22 > > > > > > > > fancy-yf > > .

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Re: [mg-rast] problem with "share jobs"
by Mark DSouza 01 Sep '11

01 Sep '11

Hi, This problem has been fixed, the share page displays correctly. There =is= a 'share multiple metagenomes' on the share page which opens a drop down where you can select multiple metagenomes which I had not seen before, my earlier email about this was wrong. Regards, Mark ----- Original Message ----- > From: "Mark DSouza" <dsouza(a)mcs.anl.gov> > To: "Sheri Simmons" <ssimmons(a)mbl.edu> > Cc: "MG- Rast" <mg-rast(a)mcs.anl.gov> > Sent: Wednesday, August 31, 2011 5:04:23 PM > Subject: Re: [mg-rast] problem with "share jobs" > Hi, > > This is actually a problem on our side, there is some weirdness in the > database that is preventing the page from displaying correctly. I will > get back to you when it is fixed. > > Mark > > ----- Original Message ----- > > From: "Sheri Simmons" <ssimmons(a)mbl.edu> > > To: "Mark DSouza" <dsouza(a)mcs.anl.gov> > > Sent: Wednesday, August 31, 2011 11:32:06 AM > > Subject: Re: [mg-rast] problem with "share jobs" > > The problem must be with something in my browser configuration then. > > Here's the URL of a share job attempt that failed for me: > > http://metagenomics.anl.gov/metagenomics.cgi?page=JobShare&metagenome=44684… > > I am running Firefox 6.0.1 and the latest version of Adobe Flash if > > that helps. > > > > The job ids to delete are: > > 4466400.3 > > 4466414.3 > > 4466415.3 > > 4467614.3 > > 4467626.3 > > 4467627.3 > > 4467661.3 > > 4467662.3 > > 4467664.3 > > 4467671.3 > > 4467674.3 > > 4467675.3 > > 4467676.3 > > 4467677.3 > > 4467678.3 > > 4467683.3 > > 4467684.3 > > 4468427.3 > > > > Thanks again for your help. > > > > Sheri > > > > On 8/31/2011 12:11 PM, Mark DSouza wrote: > > > > Hi, > > > > That is very odd, I just opened the page using your account and did > > not have any trouble. Can you send me the URL which opens the page, > > I > > can check through the logs and find out what is going on. > > > > It is not possible to delete private jobs right now, though I hope > > we > > will have it in the next release. Let me have the MG-RAST job IDs > > and > > I can delete them for you. > > > > Regards, > > Mark > > > > ----- Original Message ----- > > > > From: "Sheri Simmons" <ssimmons(a)mbl.edu> To: "Mark DSouza" > > <dsouza(a)mcs.anl.gov> Sent: Wednesday, August 31, 2011 10:24:22 AM > > Subject: Re: [mg-rast] problem with "share jobs" > > Hi, thanks for your quick reply. The "share a job" page is still not > > displaying for me, though I am able to use other analysis features. > > One other quick question- is it possible to delete private jobs? I > > have some metagenomes on the site that I later discovered to have > > some > > pre-processing issues so I'd like to take them down to avoid any > > future confusion. > > > > Sheri > > > > On 8/31/2011 11:13 AM, Mark DSouza wrote: > > > > Hi, > > > > I am not able to reproduce this problem, we did have a server > > downtime > > earlier today which may have been responsible if you hit the server > > before it went down and it was wedged. Could you check if the page > > is > > still not displaying. The suggestion for sharing multiple > > metagenomes > > is a good one, we have a number of operations which work on single > > metagenomes which which would make sense to extend to multiple > > metagenomes. > > > > -- > > Sheri Simmons > > Assistant Scientist, Bay Paul Center | Marine Biological Laboratory > > Woods Hole, MA 02543 > > (508) 289-7177 http://www.simmonslab.org > > > > -- > > Sheri Simmons > > Assistant Scientist, Bay Paul Center | Marine Biological Laboratory > > Woods Hole, MA 02543 > > (508) 289-7177 > > http://www.simmonslab.org

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Re: [mg-rast] HeatMap analysis?
by Tobias Paczian 01 Sep '11

01 Sep '11

This is the same problem as with the incorrect coloring of the PCA. Kevin, should I correct this on the perl side or is this an easy thing to change in the r? Cheers Tobi On Aug 26, 2011, at 5:41 PM, Rick White wrote: > Hello Mark, > I have noticed that the scale bar isn't included with the image. > Also, the order of the samples doesn't in the order that you select. > > For example > I pick samples > A , B , C > > The analysis moves them all around in a different order. Would it > be possible to make the output in the order you select like the > barchart? > > Thanks > Rick > > -- > Richard Allen White III M.S. > PhD Student - Suttle Lab > Department of Microbiology & Immunology > The University of British Columbia > Vancouver, BC, Canada > V6T 1Z4 > ph.(604) 827-5715 > cell. ***My new number is 604-440-5150*** > http://www.ocgy.ubc.ca/~suttle/ > > For Shipping: > Richard Allen White III & Amy Chan > Suttle Lab > UBC-Botany/zoology/micro > 1316-6270 University Blvd. > Vancouver, BC > V6T 1Z4 > 1.604.827.5715 >

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Re: [mg-rast] Export figures
by Tobias Paczian 01 Sep '11

01 Sep '11

This is a known feature failure in Firefox 4. I have not yet found a solution. It is on the list already :) Cheers Tobi On Aug 31, 2011, at 3:32 PM, Mark DSouza wrote: > I just tested it, this is a real bug. > > Tobi, I think that earlier the savable image was shifted to the > bottom of the page when the button was pressed and people were not > seeing it. Now it disappears from the page completely, could you > look into this? > > Thanks, > Mark > > > ----- Original Message ----- >> From: "Folker Meyer" <folker(a)anl.gov> >> To: "MG- Rast" <mg-rast(a)mcs.anl.gov> >> Sent: Wednesday, August 31, 2011 2:55:27 PM >> Subject: Re: [mg-rast] Export figures >> Mark: >> >> do another video for exporting figures and include screenshots on the >> mac (apple shift 4) btw :) >> >> Folker >> >> On Aug 31, 2011, at 2:48 PM, Antje Gittel wrote: >> >>> Dear MG-Rast team, >>> >>> I was trying to export a PCoA figure a couple of times, but using >>> the "static mode" results in disappearance of the figure and >>> disables right-click/save routine. >>> >>> Could you let me know how to solve that problem and make the figure >>> exportable? >>> >>> Best regards, >>> Antje Gittel >>> >>> >>> >>> ----- >>> Antje Gittel (PhD) >>> Department of Biology/Centre for Geobiology >>> University of Bergen >>> Thormøhlensgate 53A/B >>> 5006 Bergen >>> Norway >>> >>> ----- >>> Contact: >>> office +47 5558 4715 >>> mobil +47 96878182 >>> for calls from Germany +49 441 3096923 >>> >>> ----- >>> http://www.uib.no/persons/Antje.Gittel >>> http://genetics-ecology.univie.ac.at/gittel.html >>> >>> >>> CryoCARB project: >>> http://www.univie.ac.at/cryocarb/ >>> >>> Private homepage: >>> https://sites.google.com/site/antjegittel/home

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Fwd: MGRAST Processing
by Andreas Wilke 31 Aug '11

31 Aug '11

Begin forwarded message: > From: "Owens, Sarah" <Sarah.Owens(a)anl.gov> > Subject: MGRAST Processing > Date: August 31, 2011 1:44:43 PM CDT > To: Andreas Wilke <wilke(a)mcs.anl.gov> > > Hi Andreas, > > I just received an email from a collaborator inquiring about the fashion in which MGRAST processes sequence files. They are requesting a protocol/manual sort of thing regarding how the sequences (quality check, etc.) have been treated. > > Do you have anything like this or could you just give me a quick overview? I should probably know this anyway... > > Thanks! > Sarah > > -- > Sarah Owens > Laboratory Manager & Technician, Gilbert Lab > Argonne National Laboratory > 9700 S. Cass Avenue, Bldg. 202 Rm. B369 > Lemont, IL 60439 > Sarah.Owens(a)anl.gov > 630.252.2101 > Andreas Wilke Argonne National Laboratory Mathematics and Computer Science Division Bldg. 240 , 4F8 9700 South Cass Avenue Argonne, IL 60439 (630) 252-3190 (phone) (630) 252-5986.(fax)

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Paired-end Illumina sequencing reads
by edmund_ling＠hotmail.com 31 Aug '11

31 Aug '11

Hi, Does MG-RAST support paired-end read data from Illumina? If so, in what format should we submit the paired-read data, e.g. interleaved read1, read2; separate read1 and read2 files etc.? Thank you. Kind regards, Edmund

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Re: [mg-rast] problem with "share jobs"
by Mark DSouza 31 Aug '11

31 Aug '11

Hi, This is actually a problem on our side, there is some weirdness in the database that is preventing the page from displaying correctly. I will get back to you when it is fixed. Mark ----- Original Message ----- > From: "Sheri Simmons" <ssimmons(a)mbl.edu> > To: "Mark DSouza" <dsouza(a)mcs.anl.gov> > Sent: Wednesday, August 31, 2011 11:32:06 AM > Subject: Re: [mg-rast] problem with "share jobs" > The problem must be with something in my browser configuration then. > Here's the URL of a share job attempt that failed for me: > http://metagenomics.anl.gov/metagenomics.cgi?page=JobShare&metagenome=44684… > I am running Firefox 6.0.1 and the latest version of Adobe Flash if > that helps. > > The job ids to delete are: > 4466400.3 > 4466414.3 > 4466415.3 > 4467614.3 > 4467626.3 > 4467627.3 > 4467661.3 > 4467662.3 > 4467664.3 > 4467671.3 > 4467674.3 > 4467675.3 > 4467676.3 > 4467677.3 > 4467678.3 > 4467683.3 > 4467684.3 > 4468427.3 > > Thanks again for your help. > > Sheri > > On 8/31/2011 12:11 PM, Mark DSouza wrote: > > Hi, > > That is very odd, I just opened the page using your account and did > not have any trouble. Can you send me the URL which opens the page, I > can check through the logs and find out what is going on. > > It is not possible to delete private jobs right now, though I hope we > will have it in the next release. Let me have the MG-RAST job IDs and > I can delete them for you. > > Regards, > Mark > > ----- Original Message ----- > > From: "Sheri Simmons" <ssimmons(a)mbl.edu> To: "Mark DSouza" > <dsouza(a)mcs.anl.gov> Sent: Wednesday, August 31, 2011 10:24:22 AM > Subject: Re: [mg-rast] problem with "share jobs" > Hi, thanks for your quick reply. The "share a job" page is still not > displaying for me, though I am able to use other analysis features. > One other quick question- is it possible to delete private jobs? I > have some metagenomes on the site that I later discovered to have some > pre-processing issues so I'd like to take them down to avoid any > future confusion. > > Sheri > > On 8/31/2011 11:13 AM, Mark DSouza wrote: > > Hi, > > I am not able to reproduce this problem, we did have a server downtime > earlier today which may have been responsible if you hit the server > before it went down and it was wedged. Could you check if the page is > still not displaying. The suggestion for sharing multiple metagenomes > is a good one, we have a number of operations which work on single > metagenomes which which would make sense to extend to multiple > metagenomes. > > -- > Sheri Simmons > Assistant Scientist, Bay Paul Center | Marine Biological Laboratory > Woods Hole, MA 02543 > (508) 289-7177 http://www.simmonslab.org > > -- > Sheri Simmons > Assistant Scientist, Bay Paul Center | Marine Biological Laboratory > Woods Hole, MA 02543 > (508) 289-7177 > http://www.simmonslab.org

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