July 2009 - Mg-rast - mailman3.cels.anl.gov

Your MG-RAST jobs (4056, 4247, 4248)
by dsouza＠mcs.anl.gov 31 Jul '09

31 Jul '09

Hi, The sequence files for the jobs 4056, 4247 and 4248 are identical. This was probably unintentional, but it does add to our computationl load at a time when we have a large number of submissions and Gbp of sequence data to process with limited resources. To remove this redundancy I have deleted the two most recent jobs, the third job is queued for computation and should complete within a week. Regards, Mark D'Souza -- for the MG-RAST team mg-rast(a)mcs.anl.gov http://metagenomics.nmpdr.org/

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Re: [mg-rast] Uploaded data status
by Mark D'Souza 31 Jul '09

31 Jul '09

Hi Benli, I believe the problem you had is caused by the sequence file being within a directory in the .tgz file you submitted -- it contains: 454TrimmedReads.qual and cd-hitresult/extracted_clusters_unique.fa Please try creating a .tgz file containing two files as: 454TrimmedReads.qual extracted_clusters_unique.fa and resubmit to MG-RAST. I think there is a good chance that this will solve the problem. Regards, Mark D'Souza -- for the MG-RAST team mg-rast(a)mcs.anl.gov http://metagenomics.nmpdr.org/ ----- "Benli Chai" <chaibenl(a)msu.edu> wrote: > From: "Benli Chai" <chaibenl(a)msu.edu> > To: mg-rast(a)mcs.anl.gov > Sent: Friday, July 31, 2009 8:36:46 AM GMT -06:00 US/Canada Central > Subject: [mg-rast] Uploaded data status > > Dear help desk staff, > > I uploaded a dataset of about 500,000 sequences to my account. Right > > now, the size of file is 0, the annotation status bar are still in > grey color and the data creation date is: 0000-00-00. Would you check > > for me whether the data upload is all right? Thank you. > > > Benli

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Fwd: Uploaded data status
by dsouza＠mcs.anl.gov 31 Jul '09

31 Jul '09

Hi, Any ideas why these failed? He tried twice (4266, 4267) the two uploaded files are identical which seems to indicate that the upload was OK. Hmm, is it the directory 'cd-hitresult' in the tarball? I seem to recall the fasta file should not be in higher directories. The meta file has: /vol/mg-rast-prod/jobs/4266$ meta meta.xml get_all optional_info.altitude: 266 options.remove_duplicates: 0 source_fasta: /vol/mg-rast-prod/jobs/incoming/chaibenl_490fab2f4a7a5ba680c5f0b4403ff064_Wj59pdC.tgz.extract/cd-hitresult/extracted_clusters_unique.fa options.run_metagene: 0 project.description: 454 Titanium reads from switchgrass rhizosphere options.public: 0 source_file: extracted_clusters_unique.fa No upload.timestamp or status.uploaded, so it did not proceed to preprocess. Permissions seem fine. Mark ----- Forwarded Message ----- From: "Benli Chai" <chaibenl(a)msu.edu> To: mg-rast(a)mcs.anl.gov Sent: Friday, July 31, 2009 8:36:46 AM GMT -06:00 US/Canada Central Subject: [mg-rast] Uploaded data status Dear help desk staff, I uploaded a dataset of about 500,000 sequences to my account. Right now, the size of file is 0, the annotation status bar are still in grey color and the data creation date is: 0000-00-00. Would you check for me whether the data upload is all right? Thank you. Benli

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Uploaded data status
by Benli Chai 31 Jul '09

31 Jul '09

Dear help desk staff, I uploaded a dataset of about 500,000 sequences to my account. Right now, the size of file is 0, the annotation status bar are still in grey color and the data creation date is: 0000-00-00. Would you check for me whether the data upload is all right? Thank you. Benli

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Re: [mg-rast] BBC Show
by Mark D'Souza 30 Jul '09

30 Jul '09

OK, all done. Mark ----- gilbertjack(a)gmail.com wrote: > From: gilbertjack(a)gmail.com > To: dsouza(a)mcs.anl.gov > Sent: Thursday, July 30, 2009 1:46:42 AM GMT -06:00 US/Canada Central > Subject: Re: [mg-rast] BBC Show > > Cheers mark - very odd! > > Jack > ------Original Message------ > From: dsouza(a)mcs.anl.gov > Sender: dsouza(a)mcs.anl.gov > To: Jack Gilbert > Cc: mg-rast(a)mcs.anl.gov > Subject: Re: [mg-rast] BBC Show > Sent: 29 Jul 2009 23:50 > > Hi Jack, > > These are all done except 4210, GSeaD1 which is taking a lot of time > blasting against the 16s sequences. It is progressing, but very > slowly, at this rate it should get done in 4-6 hours. > > Mark > > > > ----- dsouza(a)mcs.anl.gov wrote: > > > From: dsouza(a)mcs.anl.gov > > To: "Jack Gilbert" <gilbertjack(a)gmail.com> > > Cc: mg-rast(a)mcs.anl.gov > > Sent: Wednesday, July 29, 2009 10:20:52 AM GMT -06:00 US/Canada > Central > > Subject: Re: [mg-rast] BBC Show > > > > Hi Jack, > > > > Your jobs are running right now. I am pretty sure the removal of > > sequences is based on sequence identity, sequences having the same > ID > > would cause the job to fail. > > > > Mark > > > > > > > > ----- "Jack Gilbert" <gilbertjack(a)gmail.com> wrote: > > > > > From: "Jack Gilbert" <gilbertjack(a)gmail.com> > > > To: mg-rast(a)mcs.anl.gov > > > Sent: Wednesday, July 29, 2009 9:22:28 AM GMT -06:00 US/Canada > > Central > > > Subject: [mg-rast] BBC Show > > > > > > One last time? > > > > > > I ran the bacterial V6 tag sequences through last time with the > > remove > > > duplicate sequences flag on! from each file approx 75% of the > > > sequences were deleted. > > > > > > This would make sense if the removal was based on identifying > these > > > tags at 100 % sequence identity, it would not if it based this > > removal > > > on the sequences having the exact same fasta title. > > > > > > I am re-uploading these sequences now, without the removal flag - > > any > > > chance you could push these though? > > > > > > Jack > > > > > > -- > > > Dr. Jack A. Gilbert B.Sc. Ph.D. > > > Molecular Ecologist > > > Plymouth Marine Laboratory, > > > Prospect Place, The Hoe, > > > Plymouth, PL1 3DH, UK. > > > Work Tel: +44 (0)1752 633 416 > > > Home Tel: +44 (0)1752 255 783 > > > Mobile Tel: +44 (0)7764 190 147 > > > Email: gilbertjack(a)gmail.com > > > Sent from my BlackBerry® wireless device

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Your MG-RAST jobs (4225, 4233, 4236)
by dsouza＠mcs.anl.gov 29 Jul '09

29 Jul '09

Hi, The jobs you submitted MG-RAST (4225, 4233, 4236) have failed as the sequences contain the contains the non-IUPAC compliant character '-'. Please edit your sequence files to replace or delete every occurrence of this character and resubmit the to MG-RAST. Regards, Mark D'Souza -- for the MG-RAST team mg-rast(a)mcs.anl.gov http://metagenomics.nmpdr.org/

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Re: [mg-rast] BBC Show
by dsouza＠mcs.anl.gov 29 Jul '09

29 Jul '09

Hi Jack, These are all done except 4210, GSeaD1 which is taking a lot of time blasting against the 16s sequences. It is progressing, but very slowly, at this rate it should get done in 4-6 hours. Mark ----- dsouza(a)mcs.anl.gov wrote: > From: dsouza(a)mcs.anl.gov > To: "Jack Gilbert" <gilbertjack(a)gmail.com> > Cc: mg-rast(a)mcs.anl.gov > Sent: Wednesday, July 29, 2009 10:20:52 AM GMT -06:00 US/Canada Central > Subject: Re: [mg-rast] BBC Show > > Hi Jack, > > Your jobs are running right now. I am pretty sure the removal of > sequences is based on sequence identity, sequences having the same ID > would cause the job to fail. > > Mark > > > > ----- "Jack Gilbert" <gilbertjack(a)gmail.com> wrote: > > > From: "Jack Gilbert" <gilbertjack(a)gmail.com> > > To: mg-rast(a)mcs.anl.gov > > Sent: Wednesday, July 29, 2009 9:22:28 AM GMT -06:00 US/Canada > Central > > Subject: [mg-rast] BBC Show > > > > One last time? > > > > I ran the bacterial V6 tag sequences through last time with the > remove > > duplicate sequences flag on! from each file approx 75% of the > > sequences were deleted. > > > > This would make sense if the removal was based on identifying these > > tags at 100 % sequence identity, it would not if it based this > removal > > on the sequences having the exact same fasta title. > > > > I am re-uploading these sequences now, without the removal flag - > any > > chance you could push these though? > > > > Jack > > > > -- > > Dr. Jack A. Gilbert B.Sc. Ph.D. > > Molecular Ecologist > > Plymouth Marine Laboratory, > > Prospect Place, The Hoe, > > Plymouth, PL1 3DH, UK. > > Work Tel: +44 (0)1752 633 416 > > Home Tel: +44 (0)1752 255 783 > > Mobile Tel: +44 (0)7764 190 147 > > Email: gilbertjack(a)gmail.com

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Your MG-RAST jobs (4167, 4168, 4181, 4196)
by dsouza＠mcs.anl.gov 29 Jul '09

29 Jul '09

Hi, The jobs you submitted to MG-RAST (4167, 4168, 4181, 4196) have failed due to the sequence file being formatted as 'rich text format'. You will need to open the file with an editor that can handle both RTF as well as plain text files, e.g. Notepad on a Windows system, and save the file as plain text which is required by the MG-RAST system. Regards, Mark D'Souza -- for the MG-RAST team mg-rast(a)mcs.anl.gov http://metagenomics.nmpdr.org/

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Your MG-RAST job (4176)
by Mark D'Souza 29 Jul '09

29 Jul '09

Hi, I'm afraid the job you submitted to MG-RAST (4176, Barcode 12 (GCTA)) has failed. The fasta file has zero size -- it must have not got uploaded correctly. Please resubmit this to the MG-RAST server. Regards, Mark D'Souza -- for the MG-RAST team mg-rast(a)mcs.anl.gov http://metagenomics.nmpdr.org/

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Re: [mg-rast] BBC Show
by dsouza＠mcs.anl.gov 29 Jul '09

29 Jul '09

Hi Jack, Your jobs are running right now. I am pretty sure the removal of sequences is based on sequence identity, sequences having the same ID would cause the job to fail. Mark ----- "Jack Gilbert" <gilbertjack(a)gmail.com> wrote: > From: "Jack Gilbert" <gilbertjack(a)gmail.com> > To: mg-rast(a)mcs.anl.gov > Sent: Wednesday, July 29, 2009 9:22:28 AM GMT -06:00 US/Canada Central > Subject: [mg-rast] BBC Show > > One last time? > > I ran the bacterial V6 tag sequences through last time with the remove > duplicate sequences flag on! from each file approx 75% of the > sequences were deleted. > > This would make sense if the removal was based on identifying these > tags at 100 % sequence identity, it would not if it based this removal > on the sequences having the exact same fasta title. > > I am re-uploading these sequences now, without the removal flag - any > chance you could push these though? > > Jack > > -- > Dr. Jack A. Gilbert B.Sc. Ph.D. > Molecular Ecologist > Plymouth Marine Laboratory, > Prospect Place, The Hoe, > Plymouth, PL1 3DH, UK. > Work Tel: +44 (0)1752 633 416 > Home Tel: +44 (0)1752 255 783 > Mobile Tel: +44 (0)7764 190 147 > Email: gilbertjack(a)gmail.com

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