Map with BWA for Illumina is hung

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How to analyze the Encode RNA-seq...

Casey,Richard

30 Apr 2013 30 Apr '13

9:36 a.m.

Hi, when we try using Map with BWA for Illumina on the public server, it never starts running and sits in a queued state forever. We have jobs that have been queued for more than 5 days. Any ideas on why these jobs never start? ------------------------------------------- Richard Casey, PhD CSU 970-492-4127 970-980-5975 richard.casey@colostate.edu<mailto:richard.casey@colostate.edu>

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Jennifer Jackson

1 May 1 May

1:25 p.m.

Hello Richard, The public Main Galaxy server is very busy right now. I didn't find an account associated with this email address. If you would like to send me your account email (a direct reply would be fine) - I can check the queue. Best, Jen Galaxy team On 4/30/13 7:36 AM, Casey,Richard wrote:

...

Hi, when we try using Map with BWA for Illumina on the public server, it never starts running and sits in a queued state forever. We have jobs that have been queued for more than 5 days. Any ideas on why these jobs never start?

-------------------------------------------

Richard Casey, PhD

CSU

970-492-4127

970-980-5975

richard.casey@colostate.edu <mailto:richard.casey@colostate.edu>

___________________________________________________________ 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:

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To manage your subscriptions to this and other Galaxy lists, please use the interface at:

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-- Jennifer Hillman-Jackson Galaxy Support and Training http://galaxyproject.org

Casey,Richard

1:51 p.m.

Hi Jennifer, It looks like it finally ran yesterday. I guess the server was just very busy. ------------------------------------------- Richard Casey, PhD CSU 970-492-4127 970-980-5975 richard.casey@colostate.edu<mailto:richard.casey@colostate.edu> From: Jennifer Jackson [mailto:jen@bx.psu.edu] Sent: Wednesday, May 01, 2013 12:25 PM To: Casey,Richard Cc: galaxy-user@lists.bx.psu.edu Subject: Re: [galaxy-user] Map with BWA for Illumina is hung Hello Richard, The public Main Galaxy server is very busy right now. I didn't find an account associated with this email address. If you would like to send me your account email (a direct reply would be fine) - I can check the queue. Best, Jen Galaxy team On 4/30/13 7:36 AM, Casey,Richard wrote: Hi, when we try using Map with BWA for Illumina on the public server, it never starts running and sits in a queued state forever. We have jobs that have been queued for more than 5 days. Any ideas on why these jobs never start? ------------------------------------------- Richard Casey, PhD CSU 970-492-4127 970-980-5975 richard.casey@colostate.edu<mailto:richard.casey@colostate.edu> ___________________________________________________________ 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/ -- Jennifer Hillman-Jackson Galaxy Support and Training http://galaxyproject.org

Noa Sher

12 May 12 May

1:46 p.m.

Alfredo Hidalgo Miranda

2:35 p.m.

Claro que si! Por que no habria de hacerlo?? Te dijeron algo?? Alfredo Hidalgo Miranda, Ph.D. Head of the Cancer Genomics Laboratory National Institute of Genomic Medicine, Mexico Tel. +52 (55) 53501974, 75 ahidalgo@inmegen.gob.mx ----- Mensaje original ----- De: Noa Sher <noa.sher@gmail.com> Para: galaxy-user@lists.bx.psu.edu Enviado: Sun, 12 May 2013 13:46:05 -0500 (CDT) Asunto: Re: [galaxy-user] Map with BWA for Illumina is hung <html> <head> <style>body p { margin-bottom: 0cm; margin-top: 0pt; } </style> </head> <body style="direction: ltr;"> Was this ever resolved? I am in the same situation for 3 days now. I tried to rerun as well - stays marked grey forever.<br> THanks<br> Noa<br> <br> <div class="moz-cite-prefix">On 30/04/2013 17:36, Casey,Richard wrote:<br> </div> <blockquote cite="mid:199D272F308D2549A861D7ABAAC5197D27C5E2D9@ex12.colostate.edu"> <style></style> <div class="WordSection1"> <p class="MsoNormal">Hi, when we try using Map with BWA for Illumina on the public server, it never starts running and sits in a queued state forever. We have jobs that have been queued for more than 5 days. Any ideas on why these jobs never start? </p> <p class="MsoNormal"> </p> <p class="MsoNormal"> </p> <p class="MsoNormal">-------------------------------------------</p> <p class="MsoNormal">Richard Casey, PhD</p> <p class="MsoNormal">CSU</p> <p class="MsoNormal">970-492-4127</p> <p class="MsoNormal">970-980-5975</p> <p class="MsoNormal"><a href="mailto:richard.casey@colostate.edu" target="_blank">richard.casey@colostate.edu</a></p> <p class="MsoNormal"> </p> </div> <br> <fieldset class="mimeAttachmentHeader"></fieldset> <br> <pre>___________________________________________________________ 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: <a class="moz-txt-link-freetext" href="http://lists.bx.psu.edu/listinfo/galaxy-dev" target="_blank">http://lists.bx.psu.edu/listinfo/galaxy-dev</a> To manage your subscriptions to this and other Galaxy lists, please use the interface at: <a class="moz-txt-link-freetext" href="http://lists.bx.psu.edu/" target="_blank">http://lists.bx.psu.edu/</a> To search Galaxy mailing lists use the unified search at: <a class="moz-txt-link-freetext" href="http://galaxyproject.org/search/mailinglists/" target="_blank">http://galaxyproject.org/search/mailinglists/</a></pre> </blockquote> <br> </body> </html>

Jennifer Jackson

13 May 13 May

10:02 a.m.

Hi Noa, Casey did reply that the job ran, the queue was just full, resulting in a wait time. Another user who had an issue with workflows last week also replied that the processing ran. These don't always get posted back to the list, sorry about that, we generally leave it up to the sender to post replies like that about specific issues. In your case, the re-running may be contributing to the extended wait. The server is busy, but when you re-run jobs, this causes the new job to be added back to the end of the queue. Your original job that was waiting loses it's place in line and there is a certain amount of processing to exit the job, which can start to delay your other jobs if these are numerous enough. If you continue to do this, the wait could be significantly extended. The best strategy is to leave queued, waiting jobs alone to run. When a processing window opens, you want your jobs there and available to execute. If for some reason a job fails, one re-run is recommended. If problems persist, please send in a bug report and we can provide feedback about your exact situation. Hopefully this helps to explain how to best run jobs during peak usage times, Best, Jen Galaxy team On 5/12/13 11:46 AM, Noa Sher wrote:

...

Was this ever resolved? I am in the same situation for 3 days now. I tried to rerun as well - stays marked grey forever. THanks Noa

-- Jennifer Hillman-Jackson Galaxy Support and Training http://galaxyproject.org

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participants (4)

Alfredo Hidalgo Miranda
Casey,Richard
Jennifer Jackson
Noa Sher