Is your instance configured to set metadata externally ( on your
cluster nodes )? If not, in your universe_wsgi.ini file, add the
following to the [app:main] section:
set_metadata_externally = True
On Jan 6, 2010, at 5:13 PM, Assaf Gordon wrote:
Continuing the search for slowness in my local Galaxy server (see
The datatypes/sequence.py file is also scanning and parsing entire
files when creating a new FASTA/FASTQ file.
It's nice and fun and informative for small files, but with a 2.7GB
FASTA file - the python process stays at 100% CPU for a long long
time, causing everything else to be very slow.
The offending code is at sequence.py, method "set_meta", lines 30-39.
I think Illumina expects 25x coverage of the human genome in a
single run by the end of the year - this will roughly translates to
8 FASTQ files of more than 8GB each => FASTA files of 4GB each...
Galaxy will not be able to just casually scan these files.
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Greg Von Kuster
Galaxy Development Team