Hi David,
You have 30 files of 250 MB, that is ~ 8BG of data.. I think 4 GB of RAM should
be enough to process that.
Of course, it depends on your parameter settings - e.g. if you set the noise
level too low, it will generate too many noise peaks and you may run out of
memory.
Using centroided files would reduce the memory usage significantly.
Tomas
On Dec 9, 2011, at 8:58 PM, David Lyon wrote:
> Dear Tomas,
>
> Yes I've adapted the Heap Size (tried it with 2, 3, and 4 GB) on Win7 64bit.
> I've only got 4GB.
>
> I've got Orbitrap data:
> original Raw files: ca. 250mb
> mzXML converted with MassMatrix file converter --> centroided ca. 550mb
> (I've initially used the centroided mzXML files, but Mass Detection gave
> error message, therefore I switched to profile data.)
>
> mzXML converted with MassMatrix file converter ca. 550mb
> mzXML converted with Proteowizard file converter ca. 300mb
>
> I've tried all of them. Always same result.
>
> Thank you for your support!!
>
> Best regards,
> David
>
>
>
>
>
>
>
>
>
>
>
>
> Am 03.12.2011 04:54 schrieb "Tomas Pluskal" <plus...@oist.jp>:
> Hi David,
>
> Did you edit the HEAP_SIZE parameter in the startMZmine script?
>
> How big are your files?
>
> Tomas
>
>
> On Nov 24, 2011, at 1:11 AM, David Lyon wrote:
>
>> Dear humans,
>>
>> I'm a PhD student at the University of Vienna, Austria. Trying to evaluate
>> untargeted LC/MS metabolomics data acquired with the Orbitrap.
>> I've been playing around with mzMine for some time now, but have not been
>> able to resolve this problem. I've used 32bit Win7 and 64bit Win7 (on two
>> different PCs) as well as MacOSX. Evaluating only single files is not a
>> problem, but I want to evaluate 30 files together (one experiment -->
>> alignment etc.)
>> I've attached the error message in a .ppt.
>> I've directly imported 30 raw files (Thermo), cropped them, did baseline
>> correction (including remove original data files), and then mass detection
>> (exact mass).
>> --> here the error occurs. The first files are processed and then the
>> program gets slower and produces the error message.
>> I've set the Heap size to 4GB (all I got on Win7 64bit) also tried 1, 2 and
>> 3GB.
>> Tried 4, 5, 6, 8 GB on another PC. Same problem a bit later (meaning it
>> processed more files but still broke down). I tried processing only 3 files
>> then saving the project, closing mzMine, opening again, loading the project
>> and processing the next 3 files, and so on. After about 15 files the same
>> problem occured.
>> (I've changed the preferences to only use one CPU, this didn't help either.)
>>
>> Please help.
>>
>> Thank you for your effort and time!!!
>>
>> Best regards from Vienna,
>> David
>>
>>
>>
>>
>>
>> --
>> Mag. David Lyon (MOSYS)
>> UZA 1, Ebene 1, Spange 3, Raum 1313
>> Althanstrasse 14
>> 1090 Vienna
>> Austria
>> +431427757702
>> david.l...@univie.ac.at
>> <ErrorMessageMZMINE.pptx>------------------------------------------------------------------------------
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> ===============================================
> Tomas Pluskal
> G0 Cell Unit, Okinawa Institute of Science and Technology Graduate University
> 1919-1 Tancha, Onna-son, Okinawa 904-0495, Japan
> TEL: +81-98-966-8684
>
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===============================================
Tomas Pluskal
G0 Cell Unit, Okinawa Institute of Science and Technology Graduate University
1919-1 Tancha, Onna-son, Okinawa 904-0495, Japan
TEL: +81-98-966-8684
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