Re: [galaxy-user] Galaxy job is waiting to run forever
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_kracik...@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 > 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_kracik...@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 > 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_kracik...@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/ > > > > > > > > ___ 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/
Re: [galaxy-user] Galaxy job is waiting to run forever
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_kracik...@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 > 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_kracik...@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/ > > > > > ___ 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/
Re: [galaxy-user] Galaxy job is waiting to run forever
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_kracik...@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/ > ___ 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/
