Hi All, I'm getting this error "*Job output not returned from cluster*"
galaxy.jobs.runners.drmaa DEBUG 2011-07-26 17:00:59,552 (4915/17234) state change: job is queued and active galaxy.jobs.runners.drmaa DEBUG 2011-07-26 17:01:03,552 (4915/17234) state change: job is running 139.80.26.223 - - [26/Jul/2011:17:01:03 +1300] "POST /galaxy/root/history_item_updates HTTP/1.1" 200 - " http://bioanalysis.otago.ac.nz/galaxy/history" "Mozilla/5.0 (X11; U; Linux x86_64; en-US) AppleWebKit/534.16 (KHTML, like Gecko) Chrome/10.0.648.205 Safari/534.16" galaxy.jobs.runners.drmaa DEBUG 2011-07-26 17:01:04,632 (4915/17234) state change: job finished, but failed galaxy.jobs.runners.drmaa DEBUG 2011-07-26 17:01:04,632 Job output not returned from cluster galaxy.jobs DEBUG 2011-07-26 17:01:04,762 job 4915 ended
I tried changing permission in __init__.py as mentioned in http://www.mail-archive.com/galaxy-dev@lists.bx.psu.edu/msg01613.html
but no luck.
I saw Erick has the same problem, and looks like he got a fix as mentioned http://gmod.827538.n3.nabble.com/Job-output-not-returned-from-cluster-td8795...
but no detail of what should be done.
Thanks in advance.
With Regards, ---------------- Ambarish Biswas, University of Otago Department of Biochemistry, Dunedin, New Zealand, Tel: +64(22)0855647 Fax: +64(0)3 479 7866
Those changes to permission in __init__.py are only necessary of running the job as the actual logged in user and not as the galaxy user. There are additional changes that are needed to get actual user name integration to work with SGE.
From: galaxy-dev-bounces@lists.bx.psu.edu [mailto:galaxy-dev-bounces@lists.bx.psu.edu] On Behalf Of ambarish biswas Sent: Monday, July 25, 2011 11:12 PM To: galaxy-dev@lists.bx.psu.edu" Subject: [galaxy-dev] galaxy sge Job output not returned from cluster
Hi All, I'm getting this error "Job output not returned from cluster"
galaxy.jobs.runners.drmaa DEBUG 2011-07-26 17:00:59,552 (4915/17234) state change: job is queued and active galaxy.jobs.runners.drmaa DEBUG 2011-07-26 17:01:03,552 (4915/17234) state change: job is running 139.80.26.223 - - [26/Jul/2011:17:01:03 +1300] "POST /galaxy/root/history_item_updates HTTP/1.1" 200 - "http://bioanalysis.otago.ac.nz/galaxy/history" "Mozilla/5.0 (X11; U; Linux x86_64; en-US) AppleWebKit/534.16 (KHTML, like Gecko) Chrome/10.0.648.205 Safari/534.16" galaxy.jobs.runners.drmaa DEBUG 2011-07-26 17:01:04,632 (4915/17234) state change: job finished, but failed galaxy.jobs.runners.drmaa DEBUG 2011-07-26 17:01:04,632 Job output not returned from cluster galaxy.jobshttp://galaxy.jobs DEBUG 2011-07-26 17:01:04,762 job 4915 ended
I tried changing permission in __init__.py as mentioned in http://www.mail-archive.com/galaxy-dev@lists.bx.psu.edu/msg01613.html
but no luck.
I saw Erick has the same problem, and looks like he got a fix as mentioned http://gmod.827538.n3.nabble.com/Job-output-not-returned-from-cluster-td8795...
but no detail of what should be done.
Thanks in advance.
With Regards, ---------------- Ambarish Biswas, University of Otago Department of Biochemistry, Dunedin, New Zealand, Tel: +64(22)0855647 Fax: +64(0)3 479 7866
Thanks Chrony, but do u know a fix, for this problem. Like what configuration change I should make and where?
With Regards, ---------------- Ambarish Biswas, University of Otago Department of Biochemistry, Dunedin, New Zealand, Tel: +64(22)0855647 Fax: +64(0)3 479 7866
On Wed, Jul 27, 2011 at 4:24 AM, Chorny, Ilya ichorny@illumina.com wrote:
Those changes to permission in __init__.py are only necessary of running the job as the actual logged in user and not as the galaxy user. There are additional changes that are needed to get actual user name integration to work with SGE. ** **
*From:* galaxy-dev-bounces@lists.bx.psu.edu [mailto: galaxy-dev-bounces@lists.bx.psu.edu] *On Behalf Of *ambarish biswas *Sent:* Monday, July 25, 2011 11:12 PM *To:* galaxy-dev@lists.bx.psu.edu" *Subject:* [galaxy-dev] galaxy sge Job output not returned from cluster***
Hi All,****
I'm getting this error "*Job output not returned from cluster*"*
galaxy.jobs.runners.drmaa DEBUG 2011-07-26 17:00:59,552 (4915/17234) state change: job is queued and active****
galaxy.jobs.runners.drmaa DEBUG 2011-07-26 17:01:03,552 (4915/17234) state change: job is running****
139.80.26.223 - - [26/Jul/2011:17:01:03 +1300] "POST /galaxy/root/history_item_updates HTTP/1.1" 200 - " http://bioanalysis.otago.ac.nz/galaxy/history" "Mozilla/5.0 (X11; U; Linux x86_64; en-US) AppleWebKit/534.16 (KHTML, like Gecko) Chrome/10.0.648.205 Safari/534.16"****
galaxy.jobs.runners.drmaa DEBUG 2011-07-26 17:01:04,632 (4915/17234) state change: job finished, but failed****
galaxy.jobs.runners.drmaa DEBUG 2011-07-26 17:01:04,632 Job output not returned from cluster****
galaxy.jobs DEBUG 2011-07-26 17:01:04,762 job 4915 ended****
I tried changing permission in __init__.py as mentioned in****
http://www.mail-archive.com/galaxy-dev@lists.bx.psu.edu/msg01613.html
but no luck.****
I saw Erick has the same problem, and looks like he got a fix as mentioned
http://gmod.827538.n3.nabble.com/Job-output-not-returned-from-cluster-td8795...
but no detail of what should be done.****
Thanks in advance.****
With Regards,
Ambarish Biswas, University of Otago Department of Biochemistry, Dunedin, New Zealand, Tel: +64(22)0855647 Fax: +64(0)3 479 7866****
galaxy-dev@lists.galaxyproject.org
-
ambarish biswas -
Chorny, Ilya