Hi David, I am also using orbitrap and the biggest collection of files I have used is 220 !
I have a Win7 64 bit system with 8GB RAM and I have set the Heap Size to 4GB One thing is that I don't convert to mzML I read the .RAW files directly which can be done if you install the Thermo MS Filereader software or Xcalibur. Unfortunately the XML formats are very wasteful in terms of space. It's a shame someone hasn't invented a compressed format. One tricky issue is that Excalibur is not available in 64 bit version just yet I seem to recall using regsvr32.exe to register Xrawfile.dll but be aware of the following: http://support.microsoft.com/kb/282747 >When you attempt to run Regsvr32.exe to register a 32-bit dynamic-link library >(DLL) on a 64-bit version of Windows, you receive the following error message: >Filename.dll is not an executable file and no registration helper is >registered for this file type. > >This behavior occurs because the Regsvr32.exe file in the System32 folder is a >64-bit version. When you run Regsvr32 to register a DLL, you are using the >64->bit version by default. > >To resolve this issue, run Regsvr32.exe from the %SystemRoot%\Syswow64 folder. >For example, type the following commands to register the DLL: >cd \windows\syswow64 >regsvr32 c:\filename.dll Another workaround is to install Xcalibur on your 32 bit PC, load the data as .RAW then save the mzMine project and transfer to your 64bit PC where you will be able to open the project. Hope this helps, Mark -- ----------------------------------------- Mark Earll Research Leader - Metabolomics Analytical Sciences (Office 102/65) Syngenta Jealott's Hill International Research Centre Bracknell Berkshire RG42 6EY United Kingdom Direct +44 1344 414316 mark.ea...@syngenta.com www.syngenta.com -----Original Message----- From: mzmine-devel-requ...@lists.sourceforge.net [mailto:mzmine-devel-requ...@lists.sourceforge.net] Sent: 21 December 2011 01:32 To: mzmine-devel@lists.sourceforge.net Subject: Mzmine-devel Digest, Vol 43, Issue 8 Send Mzmine-devel mailing list submissions to mzmine-devel@lists.sourceforge.net To subscribe or unsubscribe via the World Wide Web, visit https://lists.sourceforge.net/lists/listinfo/mzmine-devel or, via email, send a message with subject or body 'help' to mzmine-devel-requ...@lists.sourceforge.net You can reach the person managing the list at mzmine-devel-ow...@lists.sourceforge.net When replying, please edit your Subject line so it is more specific than "Re: Contents of Mzmine-devel digest..." Today's Topics: 1. [ mzmine-Bugs-3459191 ] Poor performance rendering many chromatograms at once (SourceForge.net) 2. Re: Please help with mzMine error (Tomas Pluskal) 3. Process MS files by MZmine (a.ma...@studenti.unisa.it) 4. outofmemoryerror: gc overhead (Martin Wagner) 5. Re: outofmemoryerror: gc overhead (Tomas Pluskal) ---------------------------------------------------------------------- Message: 1 Date: Tue, 13 Dec 2011 18:10:10 -0800 From: SourceForge.net <nore...@sourceforge.net> Subject: [Mzmine-devel] [ mzmine-Bugs-3459191 ] Poor performance rendering many chromatograms at once To: SourceForge.net <nore...@sourceforge.net> Message-ID: <mailman.104625.1324431101.26619.mzmine-de...@lists.sourceforge.net> Content-Type: text/plain; charset=UTF-8 Bugs item #3459191, was opened at 2011-12-13 18:10 Message generated for change (Tracker Item Submitted) made by cpudney You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=744692&aid=3459191&group_id=139835 Please note that this message will contain a full copy of the comment thread, including the initial issue submission, for this request, not just the latest update. Category: Visualizers Group: None Status: Open Resolution: None Priority: 5 Private: No Submitted By: Chris Pudney (cpudney) Assigned to: Nobody/Anonymous (nobody) Summary: Poor performance rendering many chromatograms at once Initial Comment: If the user selects many (10+) raw data files and plots a TIC of them then performance can be quite poor (particularly for raw data files with many data points). The problem seems to be that the TICDataSet generates a refresh event every 100ms with the result being that when multiple TICs are plotted MZmine spends most of its time redrawing the chromatograms and little time generating the data set. The fix is to remove this periodic refresh and simply refresh only when each TICDataSet completes calculating its values. ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=744692&aid=3459191&group_id=139835 ------------------------------ Message: 2 Date: Wed, 14 Dec 2011 12:34:50 +0900 From: Tomas Pluskal <plus...@oist.jp> Subject: Re: [Mzmine-devel] Please help with mzMine error To: Developer discussion <mzmine-devel@lists.sourceforge.net> Cc: David Lyon <david.l...@univie.ac.at> Message-ID: <e85684c8-67d3-4193-843b-72e14cc47...@oist.jp> Content-Type: text/plain; charset="iso-8859-1" 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>------------------------------------------------------------------------------ >> All the data continuously generated in your IT infrastructure >> contains a definitive record of customers, application performance, >> security threats, fraudulent activity, and more. Splunk takes this >> data and makes sense of it. IT sense. And common sense. >> http://p.sf.net/sfu/splunk-novd2d_______________________________________________ >> Mzmine-devel mailing list >> Mzmine-devel@lists.sourceforge.net >> https://lists.sourceforge.net/lists/listinfo/mzmine-devel > > =============================================== > 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 > > ------------------------------------------------------------------------------ > Cloud Services Checklist: Pricing and Packaging Optimization > This white paper is intended to serve as a reference, checklist and point of > discussion for anyone considering optimizing the pricing and packaging model > of a cloud services business. Read Now! > http://www.accelacomm.com/jaw/sfnl/114/51491232/_______________________________________________ > Mzmine-devel mailing list > Mzmine-devel@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/mzmine-devel =============================================== 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 -------------- next part -------------- An HTML attachment was scrubbed... ------------------------------ Message: 3 Date: Fri, 16 Dec 2011 11:10:03 +0100 (CET) From: a.ma...@studenti.unisa.it Subject: [Mzmine-devel] Process MS files by MZmine To: "MZMINE-DEVEL@LISTS.SOURCEFORGE.NET" <MZMINE-DEVEL@LISTS.SOURCEFORGE.NET> Message-ID: <385578484.560.1324030203118.JavaMail.bearun@pda02> Content-Type: text/plain; charset=UTF-8 Dear MZmine team, I've 8 MS spectra (ESI/(LIT)MS-Thermo) to compare and each file contains both MS and MSn experiments. I'm interested in processing and comparing only fullMS spectra by MZmine. At first I've applied the data set filter (crop filter) to define RT range for each spectra (different form each spectra). Then I've centroided all spectra, applied the Chromatogram builder and the Chromatogram deconvolution (Baseline cut off) to obtain my MZmine peak list. My question is about the peak list alignment (Join aligner): what about the parameters for retention time? Just because I'm processing MS spectra (so RT is not the main parameter)I've tried with a RT tolerance value very high (10 and) and a RT weight very low (0.5) but I'm not sure.. Infact My final peak aligned list excludes some important m/z values present in all my MS spectra.. Could you please help me? Kind regards Angela Angela Mari, PhD student Department of Pharmaceutical and Biomedical Science University of Salerno Via Ponte Don Melillo, 84084 e-mail: a.ma...@studenti.unisa.it mobile phone: 3491523102 office: +39 089969394 ------------------------------ Message: 4 Date: Tue, 20 Dec 2011 13:06:24 +0100 From: Martin Wagner <wag...@bio.uni-frankfurt.de> Subject: [Mzmine-devel] outofmemoryerror: gc overhead To: mzmine-devel@lists.sourceforge.net Message-ID: <65dab488-3fa3-468f-a4ac-ad4477e14...@bio.uni-frankfurt.de> Content-Type: text/plain; charset=us-ascii Hej MZmine team, It appears I am having a similar problem like David Lyon (posted on 2011-12-14). I have run some environmental samples on an LTQ Velos in full scan, data-dependent MSn and PDA. The size of the raw files is circa 180 MB in the negative mode and 40 MB in positive ionization. I am working with MZmine 2.4 on an octacore server with 16 GB RAM running Ubuntu (64Bit). My heap size is 14 GB. Processing of the data according to the workflow works fine until the RAM gets full. The fuller it is the slower the processing. This appears when I run the mass detection (exact mass) even with only 16 samples. Chromatogram detection is even worse. It takes app. 6 h computation with the local minimum algorithm. Sometimes the computer manages the calculation (when I wait long enough), sometimes it produces an "outofmemoryerror: gc overhead" error. I have tried the following without any improvement: - calculate on a Windows 7 machine and on MacOS X - calculate with MZmine 2.3 - increase noise level during mass detection - crop the PDA and MSn data from the raw files (files don't get really smaller) - convert to mzXML (files get much smaller, from 180 MB to 30 MB, but same problem) I did similar calculations with similar samples in MZmine 2.2 and never experienced problems. Now I'm running out of ideas. It appears to be a problem with the JavaVM rather than with MZmine but I don't know how to solve that. Thanks for your help & all the best from snowy Germany! Martin ------------------------------ Message: 5 Date: Wed, 21 Dec 2011 10:31:16 +0900 From: Tomas Pluskal <plus...@oist.jp> Subject: Re: [Mzmine-devel] outofmemoryerror: gc overhead To: Developer discussion <mzmine-devel@lists.sourceforge.net> Cc: David Lyon <david.l...@univie.ac.at>, Martin Wagner <wag...@bio.uni-frankfurt.de> Message-ID: <de43cf4f-c001-4944-b6ea-4edf334c9...@oist.jp> Content-Type: text/plain; charset="us-ascii" Hi Martin, David, If the error is reproducible, I would like to take a look at it in detail. But I will need your cooperation. Could you prepare a ZIP archive of your raw files, and send it to me e.g. via rapidshare.com, dropbox.com or some other sharing website? Also, please include the exact settings in your startMZmine script, and the exact steps and parameters you used for processing. Thanks a lot! Tomas On Dec 20, 2011, at 9:06 PM, Martin Wagner wrote: > Hej MZmine team, > > It appears I am having a similar problem like David Lyon (posted on > 2011-12-14). > > I have run some environmental samples on an LTQ Velos in full scan, > data-dependent MSn and PDA. The size of the raw files is circa 180 MB in the > negative mode and 40 MB in positive ionization. > > I am working with MZmine 2.4 on an octacore server with 16 GB RAM running > Ubuntu (64Bit). My heap size is 14 GB. Processing of the data according to > the workflow works fine until the RAM gets full. The fuller it is the slower > the processing. This appears when I run the mass detection (exact mass) even > with only 16 samples. Chromatogram detection is even worse. It takes app. 6 h > computation with the local minimum algorithm. Sometimes the computer manages > the calculation (when I wait long enough), sometimes it produces an > "outofmemoryerror: gc overhead" error. > > I have tried the following without any improvement: > - calculate on a Windows 7 machine and on MacOS X > - calculate with MZmine 2.3 > - increase noise level during mass detection > - crop the PDA and MSn data from the raw files (files don't get really > smaller) > - convert to mzXML (files get much smaller, from 180 MB to 30 MB, but same > problem) > > I did similar calculations with similar samples in MZmine 2.2 and never > experienced problems. Now I'm running out of ideas. It appears to be a > problem with the JavaVM rather than with MZmine but I don't know how to solve > that. > > Thanks for your help & all the best from snowy Germany! > > Martin > > > ------------------------------------------------------------------------------ > Write once. Port to many. > Get the SDK and tools to simplify cross-platform app development. Create > new or port existing apps to sell to consumers worldwide. Explore the > Intel AppUpSM program developer opportunity. appdeveloper.intel.com/join > http://p.sf.net/sfu/intel-appdev > _______________________________________________ > Mzmine-devel mailing list > Mzmine-devel@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/mzmine-devel > =============================================== 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 -------------- next part -------------- An HTML attachment was scrubbed... ------------------------------ ------------------------------------------------------------------------------ Write once. Port to many. Get the SDK and tools to simplify cross-platform app development. Create new or port existing apps to sell to consumers worldwide. Explore the Intel AppUpSM program developer opportunity. appdeveloper.intel.com/join http://p.sf.net/sfu/intel-appdev ------------------------------ _______________________________________________ Mzmine-devel mailing list Mzmine-devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/mzmine-devel End of Mzmine-devel Digest, Vol 43, Issue 8 ******************************************* This message may contain confidential information. If you are not the designated recipient, please notify the sender immediately, and delete the original and any copies. Any use of the message by you is prohibited. ------------------------------------------------------------------------------ Write once. Port to many. Get the SDK and tools to simplify cross-platform app development. Create new or port existing apps to sell to consumers worldwide. Explore the Intel AppUpSM program developer opportunity. appdeveloper.intel.com/join http://p.sf.net/sfu/intel-appdev _______________________________________________ Mzmine-devel mailing list Mzmine-devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/mzmine-devel
