[galaxy-dev] Can't save BAM file from Galaxy
liisa.koski at dnalandmarks.ca
Tue Mar 22 12:47:22 EDT 2011
Thanks Nate! I set 'debug = False'and now I have no problem downloading my
Nate Coraor <nate at bx.psu.edu>
Liisa Koski <liisa.koski at dnalandmarks.ca>
galaxy-dev at bx.psu.edu
Re: [galaxy-dev] Can't save BAM file from Galaxy
Liisa Koski wrote:
> 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
> on the save icon my Galaxy instance crashes with the following error.
> 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?
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
> Thanks in advance for any help,
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