Hi Njuguna,
I'm able to reproduce the peculiarly slow gzip compression in the mzXML writer. It does not occur in the mzML writer though. After a short investigation, I was
unable to pinpoint any particular bottleneck. At some point I'll profile it to figure out where the time is going, but I don't have time for it In the near
future. In the meantime you could use mzML.gz if you all the applications you intend to use (i.e. TPP or pwiz) support it.
Thanks,
-Matt
On 11/30/2010 11:10 AM, Brian Pratt wrote:
Forwarding to proteowizard support list, asTPP uses the official pwiz
msconvert binary instead of building its own...
On Tue, Nov 30, 2010 at 4:55 AM, Njuguna<[email protected]> wrote:
We have been running msconvert to convert our raw files to mzXML
format and then latter on compressing the files using gzip.
We would like to simplify the conversion process by using only 1 tool
and 1 command to do so. However when we downloaded the latest windows
version (2.1.2393 ) from sourceforge and ran it with and without the
compression option we got very different time frames. With 130 Mb raw
files these were converted to plain mzXML files (without the
compression option) in an average 8 minutes then using gzip they were
zipped in an average 3 minutes (Total time an average of 11 minutes).
When they are converted with the compression option they take 38 to 40
minutes to convert. Why is this? I thought it should take less time
when running them with the -g option.
I am using an Amazon Windows 2003 server Small Instance. The
proteowizard version is 2.1.2393 artifact is pwiz-bin-windows-x86-vc90-
release-2_1_2393.tar.bz2 that is 21.57 Mb in size checked in on 26
November 2010.
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