galaxy-user February 2014

galaxy-user@lists.galaxyproject.org

39 participants
46 discussions

Re: [galaxy-user] Galaxy job is waiting to run forever
by Martin Čech 17 Feb '14

17 Feb '14

Martina: it seems that the server you are downloading from has troubles communicating with Galaxy. This is probably FTP issue that we cannot control. The workaround is to download it yourself to your computer from the site and then upload it to Galaxy directly. Let me know how it goes regards Martin, Galaxy team On Mon, Feb 17, 2014 at 3:12 PM, Martina Kracikova < martina_kracikova(a)yahoo.co.uk> wrote: > Hi Martin, > > Unfortunately, this job also isn't running (I'm attaching a screen shot of > the job queue). I also got a new error message saying that Galaxy couldn't > be reached (I'm attaching that too), perhaps that's the problem? Thank you, > > Martina > > > On Monday, February 17, 2014 2:32 PM, Martin Čech <marten(a)bx.psu.edu> > wrote: > Hi Martina, > > this is the actual URL of the file: > ftp://ftp.ddbj.nig.ac.jp/ddbj_database/dra/fastq/SRA046/SRA046351/SRX099052/SRR349685.fastq.bz2 > > The URL that you were using is the link to the folder, not the file (you > can tell e.g. by the suffix of the file - my link has it, yours does not). > > Please try the new link and let me know if you encounter any problems. > Goodluck. > > thank you for using Galaxy! > > Martin, Galaxy team > > > On Mon, Feb 17, 2014 at 2:23 PM, Martina Kracikova < > martina_kracikova(a)yahoo.co.uk> wrote: > > Hi Martin, > > Yes, I used usegalaxy.org. I uploaded the data from "Get Data", "Upload > File" and then pasted this link and selected FASTQ as file format: > ftp://ftp.ddbj.nig.ac.jp/ddbj_database/dra/fastq/SRA046/SRA046351/SRX099052 It > should be 337MB. > > The job was running for over 20 hours and never finished, so I eventually > deleted it. Now I can't run any other jobs, not even a small job from the > Galaxy 101 tutorial (Sort on data 4 has been waiting to run for over 2 > hours now), which on my colleague's computer took less than a minute to > finish. This makes me think it's something specific to my account. Thanks > for your help! > > Martina > > > On Monday, February 17, 2014 1:36 PM, Martin Čech <marten(a)bx.psu.edu> > wrote: > Hello Martina, > > how did you try to upload it and on what server? I assume it was > usegalaxy.org but please confirm. DId you use the upload button on the > main page or *Get Data / Upload File* from the tool menu? How big is the > file? > > thanks > > Martin, Galaxy team > > > > On Mon, Feb 17, 2014 at 11:37 AM, Martina Kracikova < > martina_kracikova(a)yahoo.co.uk> wrote: > > Hello, > > I tried to upload some fasq data but the jobs never started running and I > waited over 20 hours. I deleted them but now even very small jobs in the > Galaxy 101 tutorial never start running. My colleague tried to execute the > same job in the tutorial and it finished in less than a minute, so is this > something to do with my account? I'm a registered user and am only using > 8.4MB and am only trying to run 1 job. I would appreciate any help. Thank > you! > > ___________________________________________________________ > 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/ > > To search Galaxy mailing lists use the unified search at: > > http://galaxyproject.org/search/mailinglists/ > > > > > > > >

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Re: [galaxy-user] Galaxy job is waiting to run forever
by Martin Čech 17 Feb '14

17 Feb '14

Hi Martina, this is the actual URL of the file: ftp://ftp.ddbj.nig.ac.jp/ddbj_database/dra/fastq/SRA046/SRA046351/SRX099052/SRR349685.fastq.bz2 The URL that you were using is the link to the folder, not the file (you can tell e.g. by the suffix of the file - my link has it, yours does not). Please try the new link and let me know if you encounter any problems. Goodluck. thank you for using Galaxy! Martin, Galaxy team On Mon, Feb 17, 2014 at 2:23 PM, Martina Kracikova < martina_kracikova(a)yahoo.co.uk> wrote: > Hi Martin, > > Yes, I used usegalaxy.org. I uploaded the data from "Get Data", "Upload > File" and then pasted this link and selected FASTQ as file format: > ftp://ftp.ddbj.nig.ac.jp/ddbj_database/dra/fastq/SRA046/SRA046351/SRX099052 It > should be 337MB. > > The job was running for over 20 hours and never finished, so I eventually > deleted it. Now I can't run any other jobs, not even a small job from the > Galaxy 101 tutorial (Sort on data 4 has been waiting to run for over 2 > hours now), which on my colleague's computer took less than a minute to > finish. This makes me think it's something specific to my account. Thanks > for your help! > > Martina > > > On Monday, February 17, 2014 1:36 PM, Martin Čech <marten(a)bx.psu.edu> > wrote: > Hello Martina, > > how did you try to upload it and on what server? I assume it was > usegalaxy.org but please confirm. DId you use the upload button on the > main page or *Get Data / Upload File* from the tool menu? How big is the > file? > > thanks > > Martin, Galaxy team > > > > On Mon, Feb 17, 2014 at 11:37 AM, Martina Kracikova < > martina_kracikova(a)yahoo.co.uk> wrote: > > Hello, > > I tried to upload some fasq data but the jobs never started running and I > waited over 20 hours. I deleted them but now even very small jobs in the > Galaxy 101 tutorial never start running. My colleague tried to execute the > same job in the tutorial and it finished in less than a minute, so is this > something to do with my account? I'm a registered user and am only using > 8.4MB and am only trying to run 1 job. I would appreciate any help. Thank > you! > > ___________________________________________________________ > 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/ > > To search Galaxy mailing lists use the unified search at: > > http://galaxyproject.org/search/mailinglists/ > > > > >

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Galaxy job is waiting to run forever
by Martina Kracikova 17 Feb '14

17 Feb '14

Hello, I tried to upload some fasq data but the jobs never started running and I waited over 20 hours. I deleted them but now even very small jobs in the Galaxy 101 tutorial never start running. My colleague tried to execute the same job in the tutorial and it finished in less than a minute, so is this something to do with my account? I'm a registered user and am only using 8.4MB and am only trying to run 1 job. I would appreciate any help. Thank you!

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Same RNAseq samples give different FPKM values when run against different samples
by Elwood Linney 17 Feb '14

17 Feb '14

Hello, I am sure this has come up before and maybe I missed the answer. If in using cuffdiff I run a sample 1(3 repeats) vs a sample 2 and then run the same sample 1(3 repeats) against a sample 3 or a sample 4, I get different value for fpkm from sample 1 each time. Is there something going wrong here or is there something in the program that causes this difference? I have seen this with online Galaxy and with the instance I have on my Mac Pro el linney Duke University

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FTP Error
by Andres Lavore 15 Feb '14

15 Feb '14

Hello, I'm trying to upload a data set through FileZilla (url:usegalaxy.org, user........ and pass.........), but an error appear: Error: Failed to retrieve directory listing Error: Disconnected from serverr: ECONNABORTED - Connection aborted Could someone help me to send the data using the FileZilla program? thanks

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How can I get back a permanently deleted history?
by Enklaar, Thorsten 14 Feb '14

14 Feb '14

Dear All, I'm working on Main and just deleted my history with all actual datasets and analyses instead of purging the deleted datasets. Is there a way to get it back? Is there a kind of backup? There were more than 1000 datasets in the history, a lot of workflows produced datasets that were further analysed and had to be purged to save diskplace. Then I unfortunatly clicked on delete permanently instead of purge deleted... Thanks, Thorsten

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Bisulfite seq
by Mathew Bunj 14 Feb '14

14 Feb '14

Do we have any tool which can be used for analyzing and QC check for bisulfite sequencing. I have FASTq files. Thanks Mathew

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Re: [galaxy-user] galaxy-user Digest, Vol 91, Issue 21
by Gang Wang 13 Feb '14

13 Feb '14

Hi, I just notice that NGS FASTQ Trimmer<https://usegalaxy.org/tool_runner?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2F…>by column can't detect the fastq file I loaded. Anyone knows why. thanks a lot. On Fri, Jan 24, 2014 at 11:00 AM, <galaxy-user-request(a)lists.bx.psu.edu>wrote: > Send galaxy-user mailing list submissions to > galaxy-user(a)lists.bx.psu.edu > > To subscribe or unsubscribe via the World Wide Web, visit > http://lists.bx.psu.edu/listinfo/galaxy-user > or, via email, send a message with subject or body 'help' to > galaxy-user-request(a)lists.bx.psu.edu > > You can reach the person managing the list at > galaxy-user-owner(a)lists.bx.psu.edu > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of galaxy-user digest..." > > > HEY! This is important! If you reply to a thread in a digest, please > 1. Change the subject of your response from "Galaxy-user Digest Vol ..." > to the original subject for the thread. > 2. Strip out everything else in the digest that is not part of the thread > you are responding to. > > Why? > 1. This will keep the subject meaningful. People will have some idea from > the subject line if they should read it or not. > 2. Not doing this greatly increases the number of emails that match search > queries, but that aren't actually informative. > > Today's Topics: > > 1. Re: Creating a Trackster visualisation from a reference in > your history (Jeremy Goecks) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Thu, 23 Jan 2014 15:49:44 -0500 > From: Jeremy Goecks <jgoecks(a)email.gwu.edu> > To: graham etherington (TSL) > <graham.etherington(a)sainsbury-laboratory.ac.uk> > Cc: galaxy-user(a)lists.bx.psu.edu > Subject: Re: [galaxy-user] Creating a Trackster visualisation from a > reference in your history > Message-ID: <C3382F38-D243-4979-B6A7-BA13EF161EE5(a)email.gwu.edu> > Content-Type: text/plain; charset="windows-1252" > > > Is it possible to create a custom build and use it to view a SAM file > without adding the .len and .2bit files in to the Galaxy file system as an > administrator? > > Yes, it definitely is. > > > If so, what am I doing wrong? > > > This is a Galaxy bug which has been fixed in this commit: > > > https://bitbucket.org/galaxy/galaxy-central/commits/117fef56513fc563dd23151… > > We have a release coming up, so this fix will be included in the release > and will make it to our public server soon. In the meantime, note that you > can use the genome fasta file rather than the len file to create a custom > build and everything should work. > > Thanks, > J. > >

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cuffmerge
by Janice Patterson 12 Feb '14

12 Feb '14

I am analyzing RNA-seq data and I ran Cufflinks with the genes.gtf as a reference annotation guide, with bias correction using the genome.fa as a reference. When I subsequently attempt to run cuffmerge on my assembled transcript files, however, I get the following errors, and cuffmerge fails. Error: duplicate GFF ID 'CUFF.1.1' encountered! [FAILED] Error: could not execute gtf_to_sam I am using the same genes.gtf file I used for cufflinks. It is the genes.gtf file attained from the Data Libraries provided by galaxy. I ran Cufflinks on the same data set without bias correction (and therefore a genome.fa file was unnecessary) and no multi-read correct, and subsequent cuffmerge with the same genes.gtf file provided ran just fine. Why did turning on bias correction and providing cufflinks with a fasta reference file making cuffmerge fail? Thanks. Janice Patterson

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Error running the Picard tool?
by Dottorini, Tania 12 Feb '14

12 Feb '14

Hi, I am trying to determine the mean inner distance between mate pairs, but encountered odd results. Briefly, to calculate the mean inner distance I mapped PE data with 2x100bp read length with Bowtie against the reference transcriptome, and used the Picard InsertSize Metrics to calculate the Mean insert size. I then, subtracted the combined insert size (2*100) from the Mean insert size value, thus obtaining the mean inner distance between mate pairs. In all the cases studied, 4 samples and 4 controls, I have always obtained negative mean inner distance between mate pairs values. In addition, in some cases I had the following error running the Picard Tool: "Unable to find expected pdf file /galaxy/main/jobdir/006/471/.…../InsertSizeHist.pdf …This always happens if single ended data was provided to this tool" But in all cases I can confirm I provided paired-end NGS data. For same of the runs that gave me this failure log, I rerun them again but mapping to the genome instead of the transcriptome, and in this case it did work but always giving me negative distance values. I would like to know if this is the correct procedure to be followed or if there are other approaches I can use to find these distance values and if I can eventually use such negative distance values in Tophat Thank you for your help Tania

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galaxy-user February 2014