Hello Nate

Is it galaxy or samtools consuming the memory when this happens?

I believe it's samtools. I asked our sysadmin to add 1GB swap :-)

Is debug = False set in universe_wsgi.ini?

No. If I set it to false, I get the same error as Michael described in http://gmod.827538.n3.nabble.com/Possible-Bug-tt969896.html#a969896

regards,,

Isabelle

-- Isabelle Phan, DPhil Seattle Biomedical Research Institute +1(206)256 7113 ________________________________________ From: Nate Coraor [nate@bx.psu.edu] Sent: Monday, August 30, 2010 10:47 AM To: Isabelle Phan Cc: 'galaxy-dev@lists.bx.psu.edu' Subject: Re: [galaxy-dev] swap issue

Isabelle Phan wrote:

Hello,

I am running galaxy, using a postgres backend.

The galaxy server systematically gets killed whenever I try uploading a bam file. The samtools process is still running. This is the end of the log:

2010-08-26 18:08:11,371 INFO sqlalchemy.engine.threadlocal.TLEngine.0x...4610 {'param_1': 8} sqlalchemy.engine.threadlocal.TLEngine.0x...4610 INFO 2010-08-26 18:08:11,371 {'param_1': 8} 2010-08-26 18:08:11,378 INFO sqlalchemy.pool.QueuePool.0x...4ed0 Connection <connection object at 0x567bf30; dsn: 'dbname=galaxy host=/var closed: 0> being returned to pool sqlalchemy.pool.QueuePool.0x...4ed0 INFO 2010-08-26 18:08:11,378 Connection <connection object at 0x567bf30; dsn: 'dbname=galaxy host=/var closed: 0> being returned to pool 10.1.20.44 - - [26/Aug/2010:18:08:06 -0700] "POST /root/history_item_updates HTTP/1.1" 200 - "http://galaxy:8080/history" "Mozilla/5.0 (X1 (x86_64); en-US; rv:1.9.2.8) Gecko/20100722 Firefox/3.6.8" Killed

I have the following options set in universe_wsgi.ini:

database_engine_option_server_side_cursors = True database_engine_option_strategy = threadlocal

It seems to be running out of swap. I monitored memory usage with 'top' and galaxy died when available swap hit 0k free.

I am not superuser on the machine where galaxy is running and I have no other server available. Is there something I could do to prevent galaxy from dying?

Hi Isabelle,

Is it galaxy or samtools consuming the memory when this happens?

Is debug = False set in universe_wsgi.ini?

Thanks, --nate

Thanks,

Isabelle

-- Isabelle Phan, DPhil Seattle Biomedical Research Institute +1(206)256 7113

---

galaxy-dev mailing list galaxy-dev@lists.bx.psu.edu http://lists.bx.psu.edu/listinfo/galaxy-dev

Hello Isabelle,

There is nothing in the Tool Shed yet for this particular tool, but there are some other assembly tools. And you could keep an eye out for new additions.

http://community.g2.bx.psu.edu/

Browse by category -> Assembly

Best,

Jen Galaxy team

On 2/8/11 3:25 PM, Isabelle Phan wrote:

Hello,

Has anybody written a mosaik reference-alignment/assembly tool for galaxy that they would be willing to share?

Thanks,

Isabelle

Isabelle Phan, DPhil Seattle Biomedical Research Institute +1(206)256 7113

---

galaxy-dev mailing list galaxy-dev@lists.bx.psu.edu http://lists.bx.psu.edu/listinfo/galaxy-dev