February 2011 - Mg-rast - mailman3.cels.anl.gov

Re: [mg-rast] Quality scores question
by William Trimble 09 Feb '11

09 Feb '11

While applying quality filtering is essential for assembly and SNP detection, similarity searching for automated annotation is more tolerant of sequencing errors. The errors do introduce noise, and will reduce the significance of some of the hits, but the increased number of comparisons (in this case) we suspect outweighs their reduced quality. If corrupt data still has similarity to the database, at worst it will by chance match a related sequence. The version 2 pipeline doesn't do anything with the quality scores. Our users sometimes upload raw, unfiltered data and sometimes apply quality filters to their data before submitting. You are welcome to do the same if it's important for your application that the individual reads that MG-RAST tries to align have a certain quality. William Trimble MG-RAST team Argonne National Laboratory On Tue, Feb 8, 2011 at 4:38 PM, Powell Phd, Amy Jo <ajpowel(a)sandia.gov> wrote: > Hi Folker, > > Thanks very much chatting today. It was really helpful. > > I wanted to ask why you think a ‘quality scores’ filter (for Illumina seqs) > isn’t very useful/helpful? Our filter is tuned to 30. > > I would like to pass your opinion/advice along to my team. Regards, AJP > > > Amy J. Powell, Ph.D. > > Sandia National Laboratories > Department of Bioenergy & Defense Technology > 1515 Eubank Blvd., SE > Albuquerque, NM 87123 > USA > > Telephone: (505)284-8050 > Fax: (505)284-1323 > > "We are all agreed that your theory is crazy. My own feeling is that it is > not crazy enough." > > Niels Bohr, Nobel Prize winner in Physics > > >

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Re: [mg-rast] 6 day jobs
by Mark D'Souza 09 Feb '11

09 Feb '11

Hi Iddo, The jobs should be done within a week. Regards, Mark ----- Original Message ----- > From: "Iddo Friedberg" <idoerg(a)gmail.com> > To: mg-rast(a)mcs.anl.gov > Sent: Wednesday, February 9, 2011 10:11:26 AM > Subject: [mg-rast] 6 day jobs > Hi, > > > The following jobs were submitted 6 days ago, and have been in this > status ever since. What is the current time frame for job conclusion > on MG-RAST? > > > Thanks, > > > Iddo > > > > 14070 Friedberg, Iddo 4454467.3 PoolB sample 12 97934417 2011-02-03 > view details > 14069 Friedberg, Iddo 4454465.3 PoolB sample 11 73326429 2011-02-03 > view details > 14068 Friedberg, Iddo 4454466.3 PoolB sample 10 94170371 2011-02-03 > view details > 14067 Friedberg, Iddo 4454464.3 PoolB sample 10 110751265 2011-02-03 > view details > 14066 Friedberg, Iddo 4454462.3 PoolA sample 6 99459083 2011-02-03 > view details > 14065 Friedberg, Iddo 4454463.3 PoolA sample 5 88665968 2011-02-03 > view details > 14064 Friedberg, Iddo 4454461.3 PoolA Sample 4 86541269 2011-02-03 > view details > 14063 Friedberg, Iddo 4454460.3 PoolA sample 3 53061240 2011-02-03 > view details > 14062 Friedberg, Iddo 4454459.3 PoolA sample 2 126395516 2011-02-03 > view details > 14061 Friedberg, Iddo 4454458.3 PoolA Sample 1 38858938 2011-02-03 > view details > -- > Iddo Friedberg > http://iddo-friedberg.net/contact.html

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6 day jobs
by Iddo Friedberg 09 Feb '11

09 Feb '11

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Your MG-RAST job (14164, Stromatolite)
by Mark D'Souza 09 Feb '11

09 Feb '11

Hi, The job you submitted to MG-RAST has failed as the sequence file contains non-sequence characters -- the first sequence contains a '2': >1 AGAGT... ... CAAAG...2 AATT ... Please remove all non-sequence characters and resubmit to the MG-RAST server.

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Re: [mg-rast] Beta-user pa55wd request for MG-RAST
by Powell Phd, Amy Jo 08 Feb '11

08 Feb '11

On 2/8/11 3:54 PM, "Mark D'Souza" <dsouza(a)mcs.anl.gov> wrote: Hi Amy, You can log on to the MG-RAST beta site with your current MG-RAST username and password, there is a second username/password controlling access to the beta site: username: beta password: tester **Hi Mark & Folker, Thanks for the access. We are in the process of finalizing some steps in the data processing pipeline right now, so data sets you submit will not be processed completely. If you could hold off on the submission for a little while we will let you know as soon as it becomes fully functional. **Can you give me an approx timeline for when the system will become fully functional? I am keen to get these data uploaded & analyzed. If helpful to you, I can convert my fastq (unassembled) seq files to fasta....would this obviate the need for MG Rast-based data processing steps? In their current state, these data are already partially curated/pre-processed. Thanks for any guidance you cold provide. Regards, AJP Regards, Mark ----- Original Message ----- > From: "Powell Phd, Amy Jo" <ajpowel(a)sandia.gov> > To: mg-rast(a)mcs.anl.gov, "Folker Meyer" <folker.meyer(a)gmail.com> > Sent: Tuesday, February 8, 2011 4:27:55 PM > Subject: [mg-rast] Beta-user pa55wd request for MG-RAST > Hi Folker, Mark, et al., > > Thanks so much for letting me help you with the new version of MG > Rast-very exciting. > > Per Folker's instructions, I went to this site to become a beta > tester: > > http://test.metagenomics.anl.gov/ > > I would like to request a password, so that I can upload a couple of > (fastq unassembled) sequence files into the MG Rast beta system for > analyses. > > Would you please send the password for these purposes ASAP? > > Please do not hesitate to contact me if you have further questions > about my data, planned analyses &/or if I, or my colleagues can help > in any way with MG Rast development. Regards, AJP > > > > > Amy J. Powell, Ph.D. > > Sandia National Laboratories > Department of Bioenergy & Defense Technology > 1515 Eubank Blvd., SE > Albuquerque, NM 87123 > USA > > Telephone: (505)284-8050 > Fax: (505)284-1323 > > "We are all agreed that your theory is crazy. My own feeling is that > it is not crazy enough." > > Niels Bohr, Nobel Prize winner in Physics Amy J. Powell, Ph.D. Sandia National Laboratories Department of Bioenergy & Defense Technology 1515 Eubank Blvd., SE Albuquerque, NM 87123 USA Telephone: (505)284-8050 Fax: (505)284-1323 "We are all agreed that your theory is crazy. My own feeling is that it is not crazy enough." Niels Bohr, Nobel Prize winner in Physics

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Fwd: Job 14157 failed?
by Mark D'Souza 08 Feb '11

08 Feb '11

----- Forwarded Message ----- > From: "Michelle L. Cilia" <mlc68(a)cornell.edu> > To: "Mark D'Souza" <dsouza(a)mcs.anl.gov> > Sent: Tuesday, February 8, 2011 4:48:17 PM > Subject: RE: [mg-rast] Job 14157 failed? > Hi Mark, > Ok. I'll give that a shot and resubmit it. Thanks for your help. > > > Michelle Cilia > Research Molecular Biologist > USDA-ARS > Functional and Comparative Proteomics Center > Robert W. Holley Center for Agriculture and Health > Ithaca, NY 14850 > (607) 255-4596 > ________________________________________ > From: Mark D'Souza [dsouza(a)mcs.anl.gov] > Sent: Tuesday, February 08, 2011 5:36 PM > To: Michelle L. Cilia > Cc: mg-rast(a)mcs.anl.gov > Subject: Re: [mg-rast] Job 14157 failed? > > Hi, > > I believe the problem is the short sequences, the 'length=0' sequences > confuses our FASTA parser as it expects every sequence identifier line > to be followed by a sequence, editing these out and resubmitting > should fix things. > > ----- Original Message ----- > > From: "Michelle L. Cilia" <mlc68(a)cornell.edu> > > To: mg-rast(a)mcs.anl.gov > > Sent: Tuesday, February 8, 2011 4:20:57 PM > > Subject: [mg-rast] Job 14157 failed? > > Hello there, > > I am a USDA-ARS employee in Ithaca, NY. Dave Schneider recommended > > to > > me to use MG-RAST to analyze our 454 transcriptome data. > > Our job number is 14157, and the status update indicates there was > > an > > error processing the file. > > Can someone help me figure out what the problem is and how to fix > > it? > > I can make the original, uncompressed *.fna file available on our > > FTP > > site if there was a problem with the compression, its only about > > 50MB. > > Please let me know how to proceed. We are anxiously awaiting our > > results! > > Thank you for your time and assistance, > > Michelle > > > > > > > > Michelle Cilia > > Research Molecular Biologist > > USDA-ARS > > Functional and Comparative Proteomics Center > > Robert W. Holley Center for Agriculture and Health > > Ithaca, NY 14850 > > (607) 255-4596 > > -- > 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] Beta-user pa55wd request for MG-RAST
by Mark D'Souza 08 Feb '11

08 Feb '11

Hi Amy, You can log on to the MG-RAST beta site with your current MG-RAST username and password, there is a second username/password controlling access to the beta site: username: beta password: tester We are in the process of finalizing some steps in the data processing pipeline right now, so data sets you submit will not be processed completely. If you could hold off on the submission for a little while we will let you know as soon as it becomes fully functional. Regards, Mark ----- Original Message ----- > From: "Powell Phd, Amy Jo" <ajpowel(a)sandia.gov> > To: mg-rast(a)mcs.anl.gov, "Folker Meyer" <folker.meyer(a)gmail.com> > Sent: Tuesday, February 8, 2011 4:27:55 PM > Subject: [mg-rast] Beta-user pa55wd request for MG-RAST > Hi Folker, Mark, et al., > > Thanks so much for letting me help you with the new version of MG > Rast-very exciting. > > Per Folker’s instructions, I went to this site to become a beta > tester: > > http://test.metagenomics.anl.gov/ > > I would like to request a password, so that I can upload a couple of > (fastq unassembled) sequence files into the MG Rast beta system for > analyses. > > Would you please send the password for these purposes ASAP? > > Please do not hesitate to contact me if you have further questions > about my data, planned analyses &/or if I, or my colleagues can help > in any way with MG Rast development. Regards, AJP > > > > > Amy J. Powell, Ph.D. > > Sandia National Laboratories > Department of Bioenergy & Defense Technology > 1515 Eubank Blvd., SE > Albuquerque, NM 87123 > USA > > Telephone: (505)284-8050 > Fax: (505)284-1323 > > "We are all agreed that your theory is crazy. My own feeling is that > it is not crazy enough." > > Niels Bohr, Nobel Prize winner in Physics

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Quality scores question
by Powell Phd, Amy Jo 08 Feb '11

08 Feb '11

Hi Folker, Thanks very much chatting today. It was really helpful. I wanted to ask why you think a 'quality scores' filter (for Illumina seqs) isn't very useful/helpful? Our filter is tuned to 30. I would like to pass your opinion/advice along to my team. Regards, AJP Amy J. Powell, Ph.D. Sandia National Laboratories Department of Bioenergy & Defense Technology 1515 Eubank Blvd., SE Albuquerque, NM 87123 USA Telephone: (505)284-8050 Fax: (505)284-1323 "We are all agreed that your theory is crazy. My own feeling is that it is not crazy enough." Niels Bohr, Nobel Prize winner in Physics

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Re: [mg-rast] Job 14157 failed?
by Mark D'Souza 08 Feb '11

08 Feb '11

Hi, I believe the problem is the short sequences, the 'length=0' sequences confuses our FASTA parser as it expects every sequence identifier line to be followed by a sequence, editing these out and resubmitting should fix things. ----- Original Message ----- > From: "Michelle L. Cilia" <mlc68(a)cornell.edu> > To: mg-rast(a)mcs.anl.gov > Sent: Tuesday, February 8, 2011 4:20:57 PM > Subject: [mg-rast] Job 14157 failed? > Hello there, > I am a USDA-ARS employee in Ithaca, NY. Dave Schneider recommended to > me to use MG-RAST to analyze our 454 transcriptome data. > Our job number is 14157, and the status update indicates there was an > error processing the file. > Can someone help me figure out what the problem is and how to fix it? > I can make the original, uncompressed *.fna file available on our FTP > site if there was a problem with the compression, its only about 50MB. > Please let me know how to proceed. We are anxiously awaiting our > results! > Thank you for your time and assistance, > Michelle > > > > Michelle Cilia > Research Molecular Biologist > USDA-ARS > Functional and Comparative Proteomics Center > Robert W. Holley Center for Agriculture and Health > Ithaca, NY 14850 > (607) 255-4596 -- 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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Beta-user pa55wd request for MG-RAST
by Powell Phd, Amy Jo 08 Feb '11

08 Feb '11

Hi Folker, Mark, et al., Thanks so much for letting me help you with the new version of MG Rast-very exciting. Per Folker's instructions, I went to this site to become a beta tester: http://test.metagenomics.anl.gov/ I would like to request a password, so that I can upload a couple of (fastq unassembled) sequence files into the MG Rast beta system for analyses. Would you please send the password for these purposes ASAP? Please do not hesitate to contact me if you have further questions about my data, planned analyses &/or if I, or my colleagues can help in any way with MG Rast development. Regards, AJP Amy J. Powell, Ph.D. Sandia National Laboratories Department of Bioenergy & Defense Technology 1515 Eubank Blvd., SE Albuquerque, NM 87123 USA Telephone: (505)284-8050 Fax: (505)284-1323 "We are all agreed that your theory is crazy. My own feeling is that it is not crazy enough." Niels Bohr, Nobel Prize winner in Physics

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