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

MG-RAST fasta output
by Lex Nederbragt 28 Nov '08

28 Nov '08

Hi, I am using MG-RAST for annotating my metagenome and find it very useful. However, I have a question about data export/download. I found that I could download the entire dataset as a Genbank file, which gives me all reads and with annotations where applicable (i.e. where one was assigned). I guess these are the same annotations as the results displayed for Metabolic profile, Dataset SEED, default parameters? However, I would very much like to download the entire dataset as well with the /phylogenetic/ placement of each read. This would allow me to make a comparison between the two profiles. So far, the only way I can see to achieve this would be to click on a phylum, download all reads as fasta, and repeat for the next phylum. This would be a lot of work so I was hoping there would be an easier way to do this. Regards, Lex Nederbragt -- P Save a tree...please don't print this e-mail unless you really need to Lex Nederbragt Postdoctoral fellow University of Oslo, Dept. of Biology Center for Ecological and Evolutionary Synthesis (CEES) P.O. Box 1066 Blindern 0316 Oslo, Norway Ph. +47 22844132 Fax. +47 22854001 Email lex.nederbragt(a)bio.uio.no Internet http://folk.uio.no/alexajo www.cees.uio.no/utsp

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by Bill statser 27 Nov '08

27 Nov '08

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Re: [mg-rast] is there any hope for job 1556?
by Alex Rodriguez 27 Nov '08

27 Nov '08

I ran the two fasta files in the job directory through the metagene tool: bio-macpro-1:~> ll /vol/mg-rast-prod/jobs/1568/raw/ total 131752 -rw-rw-rw- 1 mgrastprod metag48 67380725 2008-10-29 04:19 4441676.3.fa.unformatted -rw-rw-rw- 1 mgrastprod metag48 67380725 2008-11-20 15:01 4441816.3.fa.unformatted Total of 68 sequences. and they produced two new files at: bio-macpro-1:~> ll /home/arodri7/44* -rw-rw-rw- 1 arodri7 seed-users 58148728 2008-11-27 09:13 /home/ arodri7/4441676.3.fa.metagene -rw-rw-rw- 1 arodri7 seed-users 58148728 2008-11-27 09:17 /home/ arodri7/4441816.3.fa.metagene These have 117164 sequences. The original files were broken down into the different starts the metagene tool suggested. Can we just take the files I produces and submit them through the pipeline? The metagene pipeline is not fully functional yet on the mg-rast-test server, so if we submit it to the test server it will not work right. Alex On Nov 27, 2008, at 7:59 AM, Folker Meyer wrote: > This is not a good candidate for the current pipeline. We might > consider rejecting it or we could ask Alex to test his new metagene > driven ORF calling? On the Cmd Line? > > Folker > On Nov 27, 2008, at 12:48 AM, Mark D'Souza wrote: > >> I ran the steps from the command line -- preprocess, sims etc. >> >> I had not looked into 1568 before, it is ~66MB, with 34 contigs. >> >> Any suggestions on how to deal with this. >> >> The sims are churning away, and have eaten up a lot of time on the >> cluster. >> >> Mark >> >> qstat: >> 523482 0.57410 ms_1568 mgrastprod r 11/20/2008 15:11:05 >> compute.q@bio-intel-compute-1. >> 523482 0.57410 ms_1568 mgrastprod Rr 11/24/2008 10:43:20 >> compute.q@bio-intel-compute-1. >> 523482 0.57410 ms_1568 mgrastprod r 11/20/2008 15:13:50 >> compute.q@bio-intel-compute-10 >> 523482 0.57410 ms_1568 mgrastprod r 11/20/2008 15:14:05 >> compute.q@bio-intel-compute-13 >> 523482 0.57410 ms_1568 mgrastprod Rr 11/25/2008 12:11:20 >> compute.q@bio-intel-compute-2. >> 523482 0.57410 ms_1568 mgrastprod r 11/20/2008 15:15:20 >> compute.q@bio-intel-compute-2. >> 523482 0.57410 ms_1568 mgrastprod r 11/20/2008 15:13:50 >> compute.q@bio-intel-compute-3. >> 523482 0.57410 ms_1568 mgrastprod r 11/20/2008 15:14:50 >> compute.q@bio-intel-compute-3. >> 523482 0.57410 ms_1568 mgrastprod Rr 11/25/2008 12:11:20 >> compute.q@bio-intel-compute-5. >> 523482 0.57410 ms_1568 mgrastprod r 11/20/2008 15:15:05 >> compute.q@bio-intel-compute-6. >> 523482 0.57410 ms_1568 mgrastprod r 11/20/2008 15:14:20 >> compute.q@bio-intel-compute-9. >> >> >> >> On Wed, 26 Nov 2008, Rob Edwards wrote: >> >>> What was the fix for this? There are other jobs that are in a >>> seemingly similar state (e.g. 1568). >>> >>> Rob >>> >>> >>> On Nov 19, 2008, at 11:26 AM, Ken Dewar, Dr. wrote: >>> >>>> Thank you Mark >>>> Ken >>>> -----Original Message----- >>>> From: Mark D'Souza [mailto:[email protected]] >>>> Sent: November 19, 2008 1:38 PM >>>> To: Ken Dewar, Dr. >>>> Cc: mg-rast(a)mcs.anl.gov >>>> Subject: Re: [mg-rast] is there any hope for job 1556? >>>> Hi Ken, >>>> I am looking into what went wrong with your job, it does not seem >>>> to be >>>> a >>>> problem that you can fix. I will get back to you when I have more >>>> information. >>>> Regards, >>>> Mark D'Souza >>>> On Wed, 19 Nov 2008, Ken Dewar, Dr. wrote: >>>>> Is there anything I could do at my end to help? >>>>> Thanks >>>>> Ken >>> >

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When can I expect job1608 to be finnished
by Knut Rrudi 27 Nov '08

27 Nov '08

Best, Knut user KnutRudi ---------------------------------------------------------------------- Knut Rudi, Professor Molecular Genetics, Dr. Scient, Hedmark University College, Holsetgt. 22, 2318 HAMAR, phone: +47 62517853, homepage: privat.hihm.no/knutru/RudiLab -----------------------------------------------------------------------

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Re: [mg-rast] is there any hope for job 1556?
by Folker Meyer 27 Nov '08

27 Nov '08

This is not a good candidate for the current pipeline. We might consider rejecting it or we could ask Alex to test his new metagene driven ORF calling? On the Cmd Line? Folker On Nov 27, 2008, at 12:48 AM, Mark D'Souza wrote: > I ran the steps from the command line -- preprocess, sims etc. > > I had not looked into 1568 before, it is ~66MB, with 34 contigs. > > Any suggestions on how to deal with this. > > The sims are churning away, and have eaten up a lot of time on the > cluster. > > Mark > > qstat: > 523482 0.57410 ms_1568 mgrastprod r 11/20/2008 15:11:05 > compute.q@bio-intel-compute-1. > 523482 0.57410 ms_1568 mgrastprod Rr 11/24/2008 10:43:20 > compute.q@bio-intel-compute-1. > 523482 0.57410 ms_1568 mgrastprod r 11/20/2008 15:13:50 > compute.q@bio-intel-compute-10 > 523482 0.57410 ms_1568 mgrastprod r 11/20/2008 15:14:05 > compute.q@bio-intel-compute-13 > 523482 0.57410 ms_1568 mgrastprod Rr 11/25/2008 12:11:20 > compute.q@bio-intel-compute-2. > 523482 0.57410 ms_1568 mgrastprod r 11/20/2008 15:15:20 > compute.q@bio-intel-compute-2. > 523482 0.57410 ms_1568 mgrastprod r 11/20/2008 15:13:50 > compute.q@bio-intel-compute-3. > 523482 0.57410 ms_1568 mgrastprod r 11/20/2008 15:14:50 > compute.q@bio-intel-compute-3. > 523482 0.57410 ms_1568 mgrastprod Rr 11/25/2008 12:11:20 > compute.q@bio-intel-compute-5. > 523482 0.57410 ms_1568 mgrastprod r 11/20/2008 15:15:05 > compute.q@bio-intel-compute-6. > 523482 0.57410 ms_1568 mgrastprod r 11/20/2008 15:14:20 > compute.q@bio-intel-compute-9. > > > > On Wed, 26 Nov 2008, Rob Edwards wrote: > >> What was the fix for this? There are other jobs that are in a >> seemingly similar state (e.g. 1568). >> >> Rob >> >> >> On Nov 19, 2008, at 11:26 AM, Ken Dewar, Dr. wrote: >> >>> Thank you Mark >>> Ken >>> -----Original Message----- >>> From: Mark D'Souza [mailto:[email protected]] >>> Sent: November 19, 2008 1:38 PM >>> To: Ken Dewar, Dr. >>> Cc: mg-rast(a)mcs.anl.gov >>> Subject: Re: [mg-rast] is there any hope for job 1556? >>> Hi Ken, >>> I am looking into what went wrong with your job, it does not seem >>> to be >>> a >>> problem that you can fix. I will get back to you when I have more >>> information. >>> Regards, >>> Mark D'Souza >>> On Wed, 19 Nov 2008, Ken Dewar, Dr. wrote: >>>> Is there anything I could do at my end to help? >>>> Thanks >>>> Ken >>

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Re: [mg-rast] is there any hope for job 1556?
by Mark D'Souza 27 Nov '08

27 Nov '08

I ran the steps from the command line -- preprocess, sims etc. I had not looked into 1568 before, it is ~66MB, with 34 contigs. Any suggestions on how to deal with this. The sims are churning away, and have eaten up a lot of time on the cluster. Mark qstat: 523482 0.57410 ms_1568 mgrastprod r 11/20/2008 15:11:05 compute.q@bio-intel-compute-1. 523482 0.57410 ms_1568 mgrastprod Rr 11/24/2008 10:43:20 compute.q@bio-intel-compute-1. 523482 0.57410 ms_1568 mgrastprod r 11/20/2008 15:13:50 compute.q@bio-intel-compute-10 523482 0.57410 ms_1568 mgrastprod r 11/20/2008 15:14:05 compute.q@bio-intel-compute-13 523482 0.57410 ms_1568 mgrastprod Rr 11/25/2008 12:11:20 compute.q@bio-intel-compute-2. 523482 0.57410 ms_1568 mgrastprod r 11/20/2008 15:15:20 compute.q@bio-intel-compute-2. 523482 0.57410 ms_1568 mgrastprod r 11/20/2008 15:13:50 compute.q@bio-intel-compute-3. 523482 0.57410 ms_1568 mgrastprod r 11/20/2008 15:14:50 compute.q@bio-intel-compute-3. 523482 0.57410 ms_1568 mgrastprod Rr 11/25/2008 12:11:20 compute.q@bio-intel-compute-5. 523482 0.57410 ms_1568 mgrastprod r 11/20/2008 15:15:05 compute.q@bio-intel-compute-6. 523482 0.57410 ms_1568 mgrastprod r 11/20/2008 15:14:20 compute.q@bio-intel-compute-9. On Wed, 26 Nov 2008, Rob Edwards wrote: > What was the fix for this? There are other jobs that are in a seemingly > similar state (e.g. 1568). > > Rob > > > On Nov 19, 2008, at 11:26 AM, Ken Dewar, Dr. wrote: > >> Thank you Mark >> >> Ken >> >> -----Original Message----- >> From: Mark D'Souza [mailto:[email protected]] >> Sent: November 19, 2008 1:38 PM >> To: Ken Dewar, Dr. >> Cc: mg-rast(a)mcs.anl.gov >> Subject: Re: [mg-rast] is there any hope for job 1556? >> >> Hi Ken, >> >> I am looking into what went wrong with your job, it does not seem to be >> a >> problem that you can fix. I will get back to you when I have more >> information. >> >> Regards, >> Mark D'Souza >> >> >> On Wed, 19 Nov 2008, Ken Dewar, Dr. wrote: >> >>> Is there anything I could do at my end to help? >>> >>> >>> >>> Thanks >>> >>> >>> >>> Ken >>> >>> >>> >>> >>> >>> >

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Re: [mg-rast] (no subject)
by Mark D'Souza 27 Nov '08

27 Nov '08

This is odd, 1564 failed twice, and I restarted it twice, the second time it went through. 1565 did have to be restarted, but then it did not fail a second time. The sims seem to have been calculated but not loaded (or a small fraction got loaded). We need to rerun this job, how is this done? Thanks, Mark On Wed, 26 Nov 2008, Amee Manges, Dr. wrote: > > Hello folks at MG_RAST. > > I was looking at the results for these two jobs. I needed to get the phylogenetic results for these data. Job #1564 appeared to work but #1565 did not. Could you re-run 1565 or let me know why the RDP phylogenetic results do not appear. > > 1565 Manges, Amee 4441827.3 Intest_16S_3024 12361775 2008-10-27 <http://metagenomics.nmpdr.org/metagenomics.cgi?page=JobDetails&job=1565> > [ view details <http://metagenomics.nmpdr.org/metagenomics.cgi?page=JobDetails&job=1565> ] > 1564 Manges, Amee 4441860.3 Intest_16S_3046 12780692 2008-10-27 <http://metagenomics.nmpdr.org/metagenomics.cgi?page=JobDetails&job=1564> > [ view details <http://metagenomics.nmpdr.org/metagenomics.cgi?page=JobDetails&job=1564> ] > > Thanks a bunch. > > Amee > > Amee Manges, MPH, PhD > Epidemiology, Biostatistics & Occupational Health > 1020 Pine Avenue West, 36B > McGill University > Montreal, QC H3A 1A2 > > phone 514 398 3267 > fax 514 398 4503 > website http://www.medicine.mcgill.ca/epidemiology/manges/ >

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Re: [mg-rast] (no subject)
by Mark D'Souza 27 Nov '08

27 Nov '08

Hi Amee, Let me check and see what went wrong, I will get back to you. Regards, Mark D'Souza -- for the MG-RAST team mg-rast(a)mcs.anl.gov http://metagenomics.nmpdr.org/ On Wed, 26 Nov 2008, Amee Manges, Dr. wrote: > > Hello folks at MG_RAST. > > I was looking at the results for these two jobs. I needed to get the phylogenetic results for these data. Job #1564 appeared to work but #1565 did not. Could you re-run 1565 or let me know why the RDP phylogenetic results do not appear. > > 1565 Manges, Amee 4441827.3 Intest_16S_3024 12361775 2008-10-27 <http://metagenomics.nmpdr.org/metagenomics.cgi?page=JobDetails&job=1565> > [ view details <http://metagenomics.nmpdr.org/metagenomics.cgi?page=JobDetails&job=1565> ] > 1564 Manges, Amee 4441860.3 Intest_16S_3046 12780692 2008-10-27 <http://metagenomics.nmpdr.org/metagenomics.cgi?page=JobDetails&job=1564> > [ view details <http://metagenomics.nmpdr.org/metagenomics.cgi?page=JobDetails&job=1564> ] > > Thanks a bunch. > > Amee > > Amee Manges, MPH, PhD > Epidemiology, Biostatistics & Occupational Health > 1020 Pine Avenue West, 36B > McGill University > Montreal, QC H3A 1A2 > > phone 514 398 3267 > fax 514 398 4503 > website http://www.medicine.mcgill.ca/epidemiology/manges/ >

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Re: [mg-rast] new users requests
by Mark D'Souza 26 Nov '08

26 Nov '08

Almost a hundred since the 7th. Mark On Wed, 26 Nov 2008, Folker Meyer wrote: > Hi all, > > how many new users did we get since the meeting in San Diego? > > It seems there are a lot coming in. It is also clear to me we should > advertise NMPDR on the front page more directly and also RAST. > > I have lost user management ability and can only see pending users requests > (of which there are a lot). > > Folker

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by Bill statser 26 Nov '08

26 Nov '08

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