Can't save BAM file from Galaxy
Hello, I have a local instance of galaxy and after successfully running an NGS analysis I am trying to save my BAM file to my local machine. When I click on the save icon my Galaxy instance crashes with the following error. This also happens when I try to save the SAM file. It does not happen when I try to save a txt file. python: ./Modules/cStringIO.c:419: O_cwrite: Assertion `oself->pos + l < 2147483647' failed. ./run.sh: line 48: 19187 Aborted python ./scripts/paster.py serve universe_wsgi.ini $@ Something to do with base positions? Thanks in advance for any help, Liisa
Liisa Koski wrote:
Hello, I have a local instance of galaxy and after successfully running an NGS analysis I am trying to save my BAM file to my local machine. When I click on the save icon my Galaxy instance crashes with the following error. This also happens when I try to save the SAM file. It does not happen when I try to save a txt file.
python: ./Modules/cStringIO.c:419: O_cwrite: Assertion `oself->pos + l < 2147483647' failed. ./run.sh: line 48: 19187 Aborted python ./scripts/paster.py serve universe_wsgi.ini $@
Something to do with base positions?
Hi Liisa, I'm not completely certain, but it may just be the debugging modules that are enabled by default trying to load the entire bam/sam file into memory before sending it. Try restarting your Galaxy server after setting 'debug = False' in universe_wsgi.ini and see if this makes a difference. --nate
Thanks in advance for any help, Liisa
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Thanks Nate! I set 'debug = False'and now I have no problem downloading my BAM/SAM files. Cheers, Liisa From: Nate Coraor <nate@bx.psu.edu> To: Liisa Koski <liisa.koski@dnalandmarks.ca> Cc: galaxy-dev@bx.psu.edu Date: 2011-03-22 12:06 Subject: Re: [galaxy-dev] Can't save BAM file from Galaxy Liisa Koski wrote:
Hello, I have a local instance of galaxy and after successfully running an NGS analysis I am trying to save my BAM file to my local machine. When I click on the save icon my Galaxy instance crashes with the following error. This also happens when I try to save the SAM file. It does not happen when I try to save a txt file.
python: ./Modules/cStringIO.c:419: O_cwrite: Assertion `oself->pos + l <
2147483647' failed. ./run.sh: line 48: 19187 Aborted python ./scripts/paster.py serve universe_wsgi.ini $@
Something to do with base positions?
Hi Liisa, I'm not completely certain, but it may just be the debugging modules that are enabled by default trying to load the entire bam/sam file into memory before sending it. Try restarting your Galaxy server after setting 'debug = False' in universe_wsgi.ini and see if this makes a difference. --nate
Thanks in advance for any help, Liisa
___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at:
On 3/22/11 12:06 PM, Nate Coraor wrote:
Liisa Koski wrote:
Hello, I have a local instance of galaxy and after successfully running an NGS analysis I am trying to save my BAM file to my local machine. When I click on the save icon my Galaxy instance crashes with the following error. This also happens when I try to save the SAM file. It does not happen when I try to save a txt file.
python: ./Modules/cStringIO.c:419: O_cwrite: Assertion `oself->pos + l< 2147483647' failed. ./run.sh: line 48: 19187 Aborted python ./scripts/paster.py serve universe_wsgi.ini $@
Something to do with base positions?
Hi Liisa,
I'm not completely certain, but it may just be the debugging modules that are enabled by default trying to load the entire bam/sam file into memory before sending it. Try restarting your Galaxy server after setting 'debug = False' in universe_wsgi.ini and see if this makes a difference.
--nate
Thanks in advance for any help, Liisa
Nate - Is there a way to get the pbs job scripts to still get saved with debugging turned off? I'm running into this same problem but still prefer to have the job scripts kept in case something goes wrong. Ryan
Ryan Golhar wrote:
Nate - Is there a way to get the pbs job scripts to still get saved with debugging turned off? I'm running into this same problem but still prefer to have the job scripts kept in case something goes wrong.
Not without modifying the call to cleanup() in the job runner (lib/galaxy/jobs/__init__.py). It'd be a simple change, though.
Ryan
+1 Nate Coraor wrote, On 03/31/2011 12:34 PM:
Ryan Golhar wrote:
Nate - Is there a way to get the pbs job scripts to still get saved with debugging turned off?
Not without modifying the call to cleanup() in the job runner (lib/galaxy/jobs/__init__.py). It'd be a simple change, though.
It would be beneficial if instead of one generic "debug=true" there would be separate debug statement in the INI for each module or feature. Just a thought, -gordon
Assaf Gordon wrote:
+1
Nate Coraor wrote, On 03/31/2011 12:34 PM:
Ryan Golhar wrote:
Nate - Is there a way to get the pbs job scripts to still get saved with debugging turned off?
Not without modifying the call to cleanup() in the job runner (lib/galaxy/jobs/__init__.py). It'd be a simple change, though.
It would be beneficial if instead of one generic "debug=true" there would be separate debug statement in the INI for each module or feature.
I go back and forth on this stuff, since we also run the risk of having so many options in the config file that it begins to become unmanageable. If this would be a useful one to break out it can certainly be done. --nate
Just a thought, -gordon ___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at:
participants (4)
-
Assaf Gordon -
Liisa Koski -
Nate Coraor -
Ryan Golhar