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

Re: [mg-rast] Blast against whole database
by dsouza＠mcs.anl.gov 30 Sep '10

30 Sep '10

Hi, I am afraid this is not possible to do because of the computation time required. The public MG-RAST jobs have around 30 Gbp of sequence data which is available at ftp://ftp.theseed.org/metagenomes/contigs/ through anonymous ftp. Running this on a single personal computer is not really feasible, you should consider running against a small subset of these metagenomes. -- 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 ----- ggpozo(a)us.es wrote: > From: ggpozo(a)us.es > To: mg-rast(a)mcs.anl.gov > Sent: Monday, September 27, 2010 6:06:04 AM GMT -06:00 US/Canada Central > Subject: [mg-rast] Blast against whole database > > Dear Sir, > > I am a registered user of MG-RAST. I would greatly appreciate any help > you can give me. I want to do a blast seach with a nucleotide sequence > against all 522 metagenomes of MG-RAST. Is it possible? In the MG-Rast > server I can select one metagenome and do the blast search with it, > but it can not be selected more than one genome. If it is not possible > to do it, I can download the 522 metagenomes and do the search myself, > I have blast programs installed in my personal computer. Is it > possible to download all metagenomes? > > Do you know if there is any other way to do a blast search against the > whole database? > > > Thank you very much. > > Gabriel Gutiérrez > Departamento de Genética > Universidad de Sevilla

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Your MG-RAST job (11071, coral_pedra)
by Mark D'Souza 29 Sep '10

29 Sep '10

Hi, The job you submitted to MG-RAST (11071, coral_pedra) has failed as the sequence file contains alignment information (the '-' characters) which are not accepted by the MG-RAST fasta parser. Please edit your sequence file to remove these characters 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/ If you need to respond to this email please address it to the mailing-list mg-rast(a)mcs.anl.gov

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Re: [mg-rast] question on jobID 4451335.3
by dsouza＠mcs.anl.gov 29 Sep '10

29 Sep '10

Hi, I expect your first job will take between 4 days to a week, the other 3 jobs may take up to two weeks. This is just a rough estimate as it is being run on the fusion machine here at Argonne and a lot depends on the load from other users. We currently have over 8Gb of sequence data in the queue for similarity computation. Regards, Mark ----- "Yuri Galachyants" <yuragal(a)gmail.com> wrote: > From: "Yuri Galachyants" <yuragal(a)gmail.com> > To: "Mark D'Souza" <dsouza(a)mcs.anl.gov> > Cc: mg-rast(a)mcs.anl.gov > Sent: Tuesday, September 28, 2010 9:29:15 PM GMT -06:00 US/Canada Central > Subject: Re: [mg-rast] question on jobID 4451335.3 > > Hi, Mark! > > Thanks for reply. Could you tell are there estimates of the job > execution time and current MG-RAST queue load? > > Best regards, Yuri. > > > On Wed, Sep 29, 2010 at 5:01 AM, Mark D'Souza <dsouza(a)mcs.anl.gov> > wrote: > > Hi Yuri, > > > > There is no problem with the job, it is queued for similarity > computation which takes longer than any of the other steps. > > > > Go ahead and submit the 80 Mb files, the 30 MB size limit was for > uncompressed data, and was only mentioned because some users were > having trouble uploading large files. > > > > ----- "Yuri Galachyants" <yuragal(a)gmail.com> wrote: > > > >> From: "Yuri Galachyants" <yuragal(a)gmail.com> > >> To: mg-rast(a)mcs.anl.gov > >> Sent: Tuesday, September 28, 2010 7:42:59 AM GMT -06:00 US/Canada > Central > >> Subject: [mg-rast] question on jobID 4451335.3 > >> > >> Hello, > >> > >> My name is Yuri and I just registered on MG-RAST web-server with > >> login > >> "yuragal". I have a couple of questions on the test job I started > >> recently. > >> > >> First, it seems that job 4451335.3 hangs on the stage of > "Similarity > >> processing setup". I believe that after successful finishing of > the > >> one stage the icon and status of the next stage should change. But > it > >> does not happen. Could you please consult if there is a problem? > >> > >> Second, I have a couple of metagenomic datasets consisting from > 454 > >> shotgun reads. These datasets are quite large in terms of size > (~80Mb > >> of compressed fasta file each). So I can not upload and analyze > these > >> data as single projects. Of course, there is an option to split > data > >> into chunks and analyze it separately. However, it will require to > >> download and merge annotation results manually. Could you suggest > >> whether merging of data available before/after data processing > within > >> MG-RAST pipeline or could you help me in uploading files that > exceed > >> 30Mb limit? > >> > >> > >> Best regards, Yuri. > > > > -- > > 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 > >

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Your MG-RAST jobs (11041, 11054)
by Mark D'Souza 29 Sep '10

29 Sep '10

Hi, The jobs you submitted to MG-RAST (11041, 11054) have failed and can not be processed. The problem is the sequence file is not correctly FASTA formatted as the sequence lines contain non-sequence data: >gi|257091663|ref|NC_013194.1|_1001-2001_gc_0.5260 CandidatusAccumulibacterphosphatiscladeIIAstr.UW-1,completegenomeGAGTTTTTTTTCGTTTTCAATGCCTT... Please edit your sequence file to remove this text 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/ If you need to respond to this email please address it to the mailing-list mg-rast(a)mcs.anl.gov

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Your MG-RAST job (11040, Bthai ChI)
by dsouza＠mcs.anl.gov 29 Sep '10

29 Sep '10

Hi, The job you submitted to MG-RAST failed during the upload -- the uploaded file is zero-size. Please verify that your file is intact 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/ If you need to respond to this email please address it to the mailing-list mg-rast(a)mcs.anl.gov

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Re: [mg-rast] question on jobID 4451335.3
by Yuri Galachyants 28 Sep '10

28 Sep '10

Hi, Mark! Thanks for reply. Could you tell are there estimates of the job execution time and current MG-RAST queue load? Best regards, Yuri. On Wed, Sep 29, 2010 at 5:01 AM, Mark D'Souza <dsouza(a)mcs.anl.gov> wrote: > Hi Yuri, > > There is no problem with the job, it is queued for similarity computation which takes longer than any of the other steps. > > Go ahead and submit the 80 Mb files, the 30 MB size limit was for uncompressed data, and was only mentioned because some users were having trouble uploading large files. > > ----- "Yuri Galachyants" <yuragal(a)gmail.com> wrote: > >> From: "Yuri Galachyants" <yuragal(a)gmail.com> >> To: mg-rast(a)mcs.anl.gov >> Sent: Tuesday, September 28, 2010 7:42:59 AM GMT -06:00 US/Canada Central >> Subject: [mg-rast] question on jobID 4451335.3 >> >> Hello, >> >> My name is Yuri and I just registered on MG-RAST web-server with >> login >> "yuragal". I have a couple of questions on the test job I started >> recently. >> >> First, it seems that job 4451335.3 hangs on the stage of "Similarity >> processing setup". I believe that after successful finishing of the >> one stage the icon and status of the next stage should change. But it >> does not happen. Could you please consult if there is a problem? >> >> Second, I have a couple of metagenomic datasets consisting from 454 >> shotgun reads. These datasets are quite large in terms of size (~80Mb >> of compressed fasta file each). So I can not upload and analyze these >> data as single projects. Of course, there is an option to split data >> into chunks and analyze it separately. However, it will require to >> download and merge annotation results manually. Could you suggest >> whether merging of data available before/after data processing within >> MG-RAST pipeline or could you help me in uploading files that exceed >> 30Mb limit? >> >> >> Best regards, Yuri. > > -- > 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 >

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Re: [mg-rast] MG-RAST - account request approved
by 김택승 28 Sep '10

28 Sep '10

Dear. mg-rast staff Thank you for your accession Sincerely Taek-Seung Kim 2010/9/28 <mg-rast(a)mcs.anl.gov> > Dear Taek-Seung Kim, > > your account request for access to our web service MG-RAST has been > accepted. > > Your login is: byebus > Your password is: zhBuw/h3 > > We recommend to change the password immediately. To do so please go to our > web service http://metagenomics.nmpdr.org/ and change your password from > the account management. > > > -- > > This email was automatically generated by the MG-RAST web service. Do not > reply. >

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Your MG-RAST jobs (11015, 11016, 11017, 11031)
by dsouza＠mcs.anl.gov 28 Sep '10

28 Sep '10

Hi, I noticed that you have multiple failed 'sugarcane_Farm_soil' jobs. It is not clear what the problem is from the log files, but the file for each job is the same size, so I think the upload itself was not the issue. It looks the job failed while the optional information (altitude, time etc.) was being entered, could there be a problem with the formatting? special (non-alphanumeric) characters? The uploaded file for each job is B5_Chapman_RL9.fna, 126968048 bytes in size and has md5 9e83c9cb3f595e30921662b377935ebf. I restarted 11031 and it appears to be proceeding normally. Data you may have entered for habitat, lat-long and time has been lost. I will delete the other (11015-11017) 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

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Re: [mg-rast] question on jobID 4451335.3
by Mark D'Souza 28 Sep '10

28 Sep '10

Hi Yuri, There is no problem with the job, it is queued for similarity computation which takes longer than any of the other steps. Go ahead and submit the 80 Mb files, the 30 MB size limit was for uncompressed data, and was only mentioned because some users were having trouble uploading large files. ----- "Yuri Galachyants" <yuragal(a)gmail.com> wrote: > From: "Yuri Galachyants" <yuragal(a)gmail.com> > To: mg-rast(a)mcs.anl.gov > Sent: Tuesday, September 28, 2010 7:42:59 AM GMT -06:00 US/Canada Central > Subject: [mg-rast] question on jobID 4451335.3 > > Hello, > > My name is Yuri and I just registered on MG-RAST web-server with > login > "yuragal". I have a couple of questions on the test job I started > recently. > > First, it seems that job 4451335.3 hangs on the stage of "Similarity > processing setup". I believe that after successful finishing of the > one stage the icon and status of the next stage should change. But it > does not happen. Could you please consult if there is a problem? > > Second, I have a couple of metagenomic datasets consisting from 454 > shotgun reads. These datasets are quite large in terms of size (~80Mb > of compressed fasta file each). So I can not upload and analyze these > data as single projects. Of course, there is an option to split data > into chunks and analyze it separately. However, it will require to > download and merge annotation results manually. Could you suggest > whether merging of data available before/after data processing within > MG-RAST pipeline or could you help me in uploading files that exceed > 30Mb limit? > > > Best regards, Yuri. -- 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

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question on jobID 4451335.3
by Yuri Galachyants 28 Sep '10

28 Sep '10

Hello, My name is Yuri and I just registered on MG-RAST web-server with login "yuragal". I have a couple of questions on the test job I started recently. First, it seems that job 4451335.3 hangs on the stage of "Similarity processing setup". I believe that after successful finishing of the one stage the icon and status of the next stage should change. But it does not happen. Could you please consult if there is a problem? Second, I have a couple of metagenomic datasets consisting from 454 shotgun reads. These datasets are quite large in terms of size (~80Mb of compressed fasta file each). So I can not upload and analyze these data as single projects. Of course, there is an option to split data into chunks and analyze it separately. However, it will require to download and merge annotation results manually. Could you suggest whether merging of data available before/after data processing within MG-RAST pipeline or could you help me in uploading files that exceed 30Mb limit? Best regards, Yuri.

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