[galaxy-dev] Can't save BAM file from Galaxy

Nate Coraor nate at bx.psu.edu
Tue Mar 22 12:06:48 EDT 2011


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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