April 2012 - galaxy-user - lists.galaxyproject.org

bwa/bowtie not running
by Furey, Terry 27 Apr '12

27 Apr '12

Hi- I'm having trouble getting bwa to run on the main server. It seems stuck in the "waiting to run" state. I have tried changing the assembly to align to, and have tried re-running a previous workflow that ran fine a couple weeks ago. I even tried running bowtie, and that seems stuck. Is something wrong with the NGS server? Other NGS jobs (FastQC, filters, grooomer) seem to be fine. Thanks, Terry

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Cufflinks jobs in queue
by Scroggins, Sheena 27 Apr '12

27 Apr '12

Hi, My cufflinks jobs sat in the queued state for 12+ hours so I restarted them this morning. They've been in the queued state now for about 2-3 hours. Any idea why? Here's a link to my history: https://main.g2.bx.psu.edu/u/sheenams/h/clone-of-s1jaf13mir-active-items-on… Thanks Sheena __________________________________________________ Sheena Scroggins Post Masters Research Associate-Bioinformatics Pacific Northwest National Laboratory

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Chicken reference genome
by Nicholas Beckloff 27 Apr '12

27 Apr '12

Dear Galaxy, I noticed upon uploading a FASTQ file that the ICGSC version of the 2011 November Chicken genome is available. Why is this not available for use with the tools? Also, is this available for download? -- Nicholas Beckloff, PhD Genomics Core Laboratory Director Department of Genetics and Genome Sciences Case Western Reserve University 2109 Adelbert Road BRB 646 Cleveland, OH 44106 phone: 216-368-2791 fax: 216-368-3432 http://genomics.case.edu email: nmb64(a)case.edu

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bowtie stuck for past day
by Eirini Trompouki 27 Apr '12

27 Apr '12

Hi, I started a series of bowtie runs yesterday but nothing has happened. i tried rerunning them but still nothing. is anyone else having this problem? et -- Eirini Trompouki,Ph.D. Karp Family Research Labs (Karp 7)RB07005F Zon lab 1 Blackfan Circle Boston MA 02115 USA

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long time waiting to run tophat jobs
by Matthew McCormack 27 Apr '12

27 Apr '12

I have had some tophat jpbs waiting to run for over 20 hrs. Have I done something wrong ? I have never had to wait anything near this time previously, although I have never run tophat before. Matthew The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.

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Jobs in queue
by 杨继文 27 Apr '12

27 Apr '12

I have similar problems. My tophat job was sent 6 hours ago. Now the job is still waiting to be run. Jiwen Hi, My cufflinks jobs sat in the queued state for 12+ hours so I restarted them this morning. They've been in the queued state now for about 2-3 hours. Any idea why? Here's a link to my history: https://main.g2.bx.psu.edu/u/sheenams/h/clone-of-s1jaf13mir-active-items-on… Thanks Sheena

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please help rmdupl
by Teresita Diaz De Ståhl 27 Apr '12

27 Apr '12

Hello I wonder if it is possible to rmdupl using galaxy on the free public server. I uploaded the bam files via ftp (main.g2.bx.psu.edu) but they are not visible in my public interface, I can only see the fastq uploaded files. I would very much appreciate some suggestion how to remove PCR duplicates from my bam files Thanks Teresita Teresita Díaz de Ståhl, Department of Oncology-Pathology Cancer Center Karolinska, CCK R8:04 Karolinska Institutet SE-171 76 Stockholm, Sweden +46-8-517 721 35 (office) E-mail: Teresita.Diaz.de.Stahl(a)ki.se<mailto:Teresita.Diaz.de.Stahl@ki.se>

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Cuffmerge - "Use Sequence" option.
by Mohammad Heydarian 26 Apr '12

26 Apr '12

Hi, Can anyone shed light on what the "use sequence" parameter (Y/N) in Cuffmerge is doing? The Cuffflinks manual says: -s/--ref-sequence <seq_dir>/<seq_fasta> This argument should point to the genomic DNA sequences for the reference. When "no" is chosen for the "use sequence" option I still get genomic coordinates for each entry. Also, when "no" is chosen, I get less entries than when "yes" is chosen. Any insight would be greatly appreciated. Have a great day. Cheers, Mo Heydarian

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MegaBLAST output
by Sarah Hicks 26 Apr '12

26 Apr '12

I am having trouble finding information on the MegaBLAST output columns. What is each column for? I can't seem to figure this out by comparing info in the columns to NCBI directly because the GI#'s don't match with the correct entry on NCBI. I've seen that others have posted about that problem, so I'm also waiting on details on that question, but for now, I'd just like to know what to make of the output... best, Sarah

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Re: [galaxy-user] Arabidopsis thaliana genome
by Jennifer Jackson 26 Apr '12

26 Apr '12

Hi Franziska, Both species are available for NGS mapping tools (excluding megablast, which is not intended to host individual genomes on the public instance). To locate these, including /A. thaliana/, type in 'Arab' into the "Select a reference genome:" box to perform a search. Perhaps default sort order of the builds list when viewed by scrolling is what made it appear that only /A. lyrata/ was available (it is the first in the list and has a different legacy name structure)? Many people use the main public instance to do NGS mapping every day. There are significant resources dedicated to this service, but there are usage quotas, limits on job size (72 hr job runtime limit), and delays during peak usage times (we are experiencing one right now). Your needs will determine the best type of Galaxy instance for your purposes. This wiki has details about Galaxy options: http://wiki.g2.bx.psu.edu/Big%20Picture/Choices Hopefully this helps, Jen Galaxy team On 4/25/12 2:02 PM, Franziska Turck wrote: > Dear Jennifer, > > actually I wanted it for NGS mapping and it wasn`t in the drop down > menue although Arabidopsis lyrata was. Is NGS mapping with GALAXY even > realistic or does it take too much cpu time on the cluster. > > Best, > Franziska > > ----- Original Message ----- > From: Jennifer Jackson <jen(a)bx.psu.edu> > Date: Wednesday, April 25, 2012 22:46 > Subject: Re: [galaxy-user] Arabidopsis thaliana genome > To: Franziska Turck <turck(a)mpipz.mpg.de> > Cc: galaxy-user(a)bx.psu.edu > > > Hello Franziska, > > > > TAIR9 and TAIR10 are available for most tools, with the notable > > exception of the new 'NGS: GATK Tools (beta)' tool set. Is this > > where > > you wanted to have the genomes added? For now, only one genome > > is > > available while in beta and using the custom reference genome > > feature > > for other genomes is the current option. > > > > Our plans are to add genomes to the GATK tool set and fill in > > genomes > > for other tools in the near term. I can make sure that the > > Arabidopsis > > genome is included. Normally, we would put as a priority the > > most > > current build, which would be TAIR10. Are other builds of > > interest? > > Links and other information would be great. The source we have > > used in > > the past is (below), please send additions/corrections, help is > > always > > appreciated! The core input is a fasta version of the genome, > > with > > additional related data such as Mitochrondrial, Chloroplast, > > Plasmid, > > etc. as appropriate. > > ftp://ftp.arabidopsis.org/home/tair/Sequences/whole_chromosomes/ > > > > Until this is completed, here are instructions for using a > > custom > > reference genome (available with most tools): > > http://wiki.g2.bx.psu.edu/Support#Custom_reference_genome > > > > Best, > > > > Jen > > Galaxy team > > > > On 4/25/12 8:06 AM, Franziska Turck wrote: > > > Dear Galaxy team! > > > > > > Could you put the Arabidopsis thaliana genome in the drop down list? > > > What kind of data would you need for that, I can help find all > > the links > > > from TAIR > > > > > > Best, > > > Franziska > > > > > > Dr. Franziska Turck > > > Max Planck Institute for Plant Breeding Research > > > Department Plant Developmental Biology > > > Group Transcription Control by Chromatin Structure > > > > > > Carl von Linné Weg 10 > > > 50829 Köln > > > Germany > > > > > > Tel: +49 221 5062 246 > > > Fax:+49 221 5062 207 > > > > > > > > > ___________________________________________________________ > > > The Galaxy User list should be used for the discussion of > > > Galaxy analysis and other features on the public server > > > at usegalaxy.org. Please keep all replies on the list by > > > using "reply all" in your mail client. For discussion of > > > local Galaxy instances and the Galaxy source code, please > > > use the Galaxy Development list: > > > > > > http://lists.bx.psu.edu/listinfo/galaxy-dev > > > > > > To manage your subscriptions to this and other Galaxy lists, > > > please use the interface at: > > > > > > http://lists.bx.psu.edu/ > > > > -- > > Jennifer Jackson > > http://galaxyproject.org > > Dr. Franziska Turck > Max Planck Institute for Plant Breeding Research > Department Plant Developmental Biology > Group Transcription Control by Chromatin Structure > > Carl von Linné Weg 10 > 50829 Köln > Germany > > Tel: +49 221 5062 246 > Fax:+49 221 5062 207 -- Jennifer Jackson http://galaxyproject.org

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