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From: Henry H. N. L. <ke...@us...> - 2011-01-18 03:45:43
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Dear Matt/Darren, This is Henry Lam, formerly of ISB. I have been using msconvert to convert Thermo RAW files to mzXML/mzML, but recently I ran into some RAW files that are very big (over 2 GB). I don't know if that's the reason or not (smaller files from the same dataset were converted normally), but msconvert gives a cryptic error: processing file: 25ulV_110112104522.RAW (... a minute or two passes...) [SHA1Calculator] Error hashing file ./25ulV_110112104522.RAW Error processing file 25ulV_110112104522.RAW I used all default parameters. The version was 1.6.1386 (2009-10-06). Could you help sort this out? Thanks for your help in advance. Henry -- Henry H. N. Lam Assistant Professor Department of Chemical and Biomolecular Engineering Hong Kong University of Science and Technology Phone: 2358-7133 Fax: 2358-0054 Email: ke...@us... |
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From: Franka G. P. <gar...@to...> - 2012-11-14 11:31:59
Attachments:
error mgf file creation.txt
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Dear Sir or madam, please find attached the error message I received using msconvert and was asked to report to you. An mgf file was created. Can this file be trusted? Yours sincerely Franka García Prado -- Dr. Franka GARCÍA PRADO TOPLAB Gesellschaft für angewandte Biotechnologie mbH Fraunhoferstr. 18a D-82152 Martinsried +49 89 8565 1284 Amtsgericht München HRB 105017 Geschäftsführerin: Dr. Elfriede Müller ISO 9001:2008 zertifiziert Diese E-Mail kann vertrauliche und / oder rechtlich geschützte Informationen enthalten. Wenn Sie nicht der richtige Adressat sind oder diese E-Mail irrtümlich erhalten haben, informieren Sie bitte sofort den Absender und vernichten Sie diese E-Mail. Das unerlaubte Kopieren sowie die unbefugte Weitergabe dieser E-Mail ist nicht gestattet. -------------------------------------------------------------------- This e-mail may contain confidential and / or privileged information. If you are not the intended recipient (or have received this e-mail in error) please notify the sender immediately and destroy this e-mail. Any unauthorized copying, disclosure or distribution of the material in this e-mail is strictly forbidden. |
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From: Matt C. <mat...@gm...> - 2012-11-14 16:34:59
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Hi Franka, No, the file seems to be corrupt. Can you open the file in QualBrowser? If so you can send the file to me and I'll find out if it's truly corrupt or else what the problem is. Thanks for reporting, -Matt On 11/14/2012 5:31 AM, Franka Garcia Prado wrote: > Dear Sir or madam, > > please find attached the error message I received using msconvert and was asked to report to you. > > An mgf file was created. Can this file be trusted? > > Yours sincerely > Franka García Prado |
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From: Christopher H. <chr...@em...> - 2013-11-11 11:06:49
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Hi, I am having an error with msconvert. I am feeding it the following command: msconvert -f <path to txt file with list of files to convert> --mgf --merge --filter “MS2Deisotope” --filter “mzWindow [133,5000]” --filter “peakPicking true 2-“ -o <output directory> I have 10 files listed in my input file. It will read the first 3 correctly, then give errors for all of the files after this. The error is: Error reading file <path to file>: [ThermoRawFile] [RawFile::actor] Unable to open file <path to file> This is not a problem with the file itself, or the path. The path it gives is correct, and the file is there. If I remove the first three files from the list of 10, it will again process the first three (4,5,6 in the original that gave errors) correctly, then give errors for the rest. If I just give it three files alone, it will process them correctly and give me the output I expect using the same command as above. Any ideas? Thanks, Chris |
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From: Brian P. <bs...@pr...> - 2013-11-13 14:25:58
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If I had to guess (and I do have to guess, without seeing the data) I'd say it's running out of memory or some other resource. Are these large files? Brian On Mon, Nov 11, 2013 at 2:45 AM, Christopher Hughes < chr...@em...> wrote: > Hi, > > I am having an error with msconvert. I am feeding it the following > command: > > msconvert -f <path to txt file with list of files to convert> --mgf > --merge --filter “MS2Deisotope” --filter “mzWindow [133,5000]” --filter > “peakPicking true 2-“ -o <output directory> > > I have 10 files listed in my input file. It will read the first 3 > correctly, then give errors for all of the files after this. The error is: > > Error reading file <path to file>: [ThermoRawFile] [RawFile::actor] Unable > to open file <path to file> > > This is not a problem with the file itself, or the path. The path it gives > is correct, and the file is there. If I remove the first three files from > the list of 10, it will again process the first three (4,5,6 in the > original that gave errors) correctly, then give errors for the rest. If I > just give it three files alone, it will process them correctly and give me > the output I expect using the same command as above. > > Any ideas? > > Thanks, > Chris > > > > ------------------------------------------------------------------------------ > November Webinars for C, C++, Fortran Developers > Accelerate application performance with scalable programming models. > Explore > techniques for threading, error checking, porting, and tuning. Get the most > from the latest Intel processors and coprocessors. See abstracts and > register > http://pubads.g.doubleclick.net/gampad/clk?id=60136231&iu=/4140/ostg.clktrk > _______________________________________________ > proteowizard-support mailing list > pro...@li... > https://lists.sourceforge.net/lists/listinfo/proteowizard-support > |
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From: Brian P. <bs...@pr...> - 2013-11-13 16:03:23
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Excellent! Brian On Wed, Nov 13, 2013 at 6:45 AM, Christopher Hughes < chr...@em...> wrote: > Hi Brian, > > Good guess! The files are approx. 1.5 gigabytes each. I was running in the > 32-bit version of msconvert. I switched to the 64-bit version and all is > fine now. > > Thanks, > Chris > > > On 13 Nov 2013, at 15:25, Brian Pratt <bs...@pr...> wrote: > > If I had to guess (and I do have to guess, without seeing the data) I'd > say it's running out of memory or some other resource. Are these large > files? > > Brian > > > On Mon, Nov 11, 2013 at 2:45 AM, Christopher Hughes < > chr...@em...> wrote: > >> Hi, >> >> I am having an error with msconvert. I am feeding it the following >> command: >> >> msconvert -f <path to txt file with list of files to convert> --mgf >> --merge --filter “MS2Deisotope” --filter “mzWindow [133,5000]” --filter >> “peakPicking true 2-“ -o <output directory> >> >> I have 10 files listed in my input file. It will read the first 3 >> correctly, then give errors for all of the files after this. The error is: >> >> Error reading file <path to file>: [ThermoRawFile] [RawFile::actor] >> Unable to open file <path to file> >> >> This is not a problem with the file itself, or the path. The path it >> gives is correct, and the file is there. If I remove the first three files >> from the list of 10, it will again process the first three (4,5,6 in the >> original that gave errors) correctly, then give errors for the rest. If I >> just give it three files alone, it will process them correctly and give me >> the output I expect using the same command as above. >> >> Any ideas? >> >> Thanks, >> Chris >> >> >> >> ------------------------------------------------------------------------------ >> November Webinars for C, C++, Fortran Developers >> Accelerate application performance with scalable programming models. >> Explore >> techniques for threading, error checking, porting, and tuning. Get the >> most >> from the latest Intel processors and coprocessors. See abstracts and >> register >> >> http://pubads.g.doubleclick.net/gampad/clk?id=60136231&iu=/4140/ostg.clktrk >> _______________________________________________ >> proteowizard-support mailing list >> pro...@li... >> https://lists.sourceforge.net/lists/listinfo/proteowizard-support >> > > > |
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From: Phil R. <phi...@gm...> - 2014-07-29 18:03:31
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Hi, I’m currently trying to convert some .wiff files to mzXML and am encountering the following error: Starting… Opening file… Failed - System.Exception [WiffFileImp::getSampleCount] External component has thrown an exception. at pwiz.CLI.msdata.ReaderList.read(String fliename, MSDataList results) Any idea what this means or how I can fix the problem? mzWiff isn’t working either... Best, Phil --------------------- Bioinformatician Manuel Llinás Lab, PSU Cell Phone: +1(631) 561 8704 http://methodicallyadventurous.com Sent with Sparrow (http://www.sparrowmailapp.com/?sig) |
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From: Brian P. <bs...@pr...> - 2014-07-29 18:13:34
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That sounds a lot like a corrupted file - are you able to open it with any other software? On Tue, Jul 29, 2014 at 11:03 AM, Phil Ross <phi...@gm...> wrote: > Hi, > > I’m currently trying to convert some .wiff files to mzXML and am > encountering the following error: > > *Starting…* > *Opening file…* > *Failed - System.Exception [WiffFileImp::getSampleCount] External > component has thrown an exception.* > * at pwiz.CLI.msdata.ReaderList.read(String fliename, MSDataList results)* > > Any idea what this means or how I can fix the problem? mzWiff isn’t > working either... > > Best, > Phil > > --------------------- > Bioinformatician > Manuel Llinás Lab, PSU > Cell Phone: +1(631) 561 8704 > http://methodicallyadventurous.com > Sent with Sparrow <http://www.sparrowmailapp.com/?sig> > > > > ------------------------------------------------------------------------------ > Infragistics Professional > Build stunning WinForms apps today! > Reboot your WinForms applications with our WinForms controls. > Build a bridge from your legacy apps to the future. > > http://pubads.g.doubleclick.net/gampad/clk?id=153845071&iu=/4140/ostg.clktrk > _______________________________________________ > proteowizard-support mailing list > pro...@li... > https://lists.sourceforge.net/lists/listinfo/proteowizard-support > > |
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From: Lauzikaite, E. <e.l...@im...> - 2017-05-17 14:25:18
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Hello, I was running msconvert on virtual Win10, when an error occurred and processing stopped. 8 command lines were running at the same time, all stopped at approximately the same time. Input was Waters raw files. The syntax: msconvert –f ‘path\to\filelist.txt’ --outdir ‘path\to\folder’ --outfile ‘filename’ --zlib -v The error message: processing file: X:\MS\PLASMA\LPOS.PRO\Data\final_data\AIRWAVE_LPOS_ToF05_P71W47_LTR.raw writing output file: W:\mzML\airwave1\SLPOS\ AIRWAVE_LPOS_ToF05_P71W47_LTR.mzML [SpectrumWorkerThreads::work] error in thread: Scan Read Error Then, after a while, the output changed to: processing file: X:\MS\PLASMA\LPOS.PRO\Data\final_data\AIRWAVE_LPOS_ToF05_P71W47_LTR.raw [msconvert] Caught unknown exception. Please report this error to su...@pr.... Attach the command output and this version information in your report: ProteoWizard release: 3.0.10765 (2017-4-20) ProteoWizard MSData: 3.0.10765 (2017-4-20) ProteoWizard Analysis: 3.0.10730 (2017-4-10) Build date: Apr 20 2017 09:42:48 The files look alright when opened with ‘SeeMS’ and this error hasn’t occurred before. What should I change in my approach? Thank you so much in advance. Regards, Elzbieta --- Elzbieta Lauzikaite PhD student Imperial College London Section of Computational and Systems Medicine SAF Building, Exhibition Road London, SW7 2AZ Email: e.l...@im... |Phone: +44 (0)77 9470 0505 |
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From: Chambers, M. <mat...@gm...> - 2017-05-17 14:31:04
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Hi Elzbieta, Does the error only happen on that file and at about the same scan? Might be a corrupt file. -Matt On 5/17/2017 9:24 AM, Lauzikaite, Elzbieta wrote: > > Hello, > > I was running msconvert on virtual Win10, when an error occurred and processing stopped. 8 command lines were running at the same time, > all stopped at approximately the same time. Input was Waters raw files. > > The syntax: > > msconvert –f ‘path\to\filelist.txt’ --outdir ‘path\to\folder’ --outfile ‘filename’ --zlib -v > > The error message: > > processing file: X:\MS\PLASMA\LPOS.PRO\Data\final_data\AIRWAVE_LPOS_ToF05_P71W47_LTR.raw > > writing output file: W:\mzML\airwave1\SLPOS\ AIRWAVE_LPOS_ToF05_P71W47_LTR.mzML > > [SpectrumWorkerThreads::work] error in thread: Scan Read Error > > Then, after a while, the output changed to: > > processing file: X:\MS\PLASMA\LPOS.PRO\Data\final_data\AIRWAVE_LPOS_ToF05_P71W47_LTR.raw > > [msconvert] Caught unknown exception. > > Please report this error to su...@pr.... > > Attach the command output and this version information in your report: > > ProteoWizard release: 3.0.10765 (2017-4-20) > > ProteoWizard MSData: 3.0.10765 (2017-4-20) > > ProteoWizard Analysis: 3.0.10730 (2017-4-10) > > Build date: Apr 20 2017 09:42:48 > > The files look alright when opened with ‘SeeMS’ and this error hasn’t occurred before. What should I change in my approach? > > Thank you so much in advance. > > Regards, > > Elzbieta > > --- > > Elzbieta Lauzikaite > > PhD student > > Imperial College London > > Section of Computational and Systems Medicine > > SAF Building, Exhibition Road > > London, SW7 2AZ > > Email: e.l...@im... |Phone: +44 (0)77 9470 0505 > > > > ------------------------------------------------------------------------------ > Check out the vibrant tech community on one of the world's most > engaging tech sites, Slashdot.org! http://sdm.link/slashdot > > > _______________________________________________ > proteowizard-support mailing list > pro...@li... > https://lists.sourceforge.net/lists/listinfo/proteowizard-support |
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From: Lauzikaite, E. <e.l...@im...> - 2017-05-17 14:46:29
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Hi Matt, Thanks for your reply. No, it happens for multiple files - different files were being processed in different command windows and all processes stopped with the same error on different files. Thank you, Elzbieta On 17 May 2017, at 15:30, Chambers, Matthew <mat...@gm...<mailto:mat...@gm...>> wrote: Hi Elzbieta, Does the error only happen on that file and at about the same scan? Might be a corrupt file. -Matt On 5/17/2017 9:24 AM, Lauzikaite, Elzbieta wrote: Hello, I was running msconvert on virtual Win10, when an error occurred and processing stopped. 8 command lines were running at the same time, all stopped at approximately the same time. Input was Waters raw files. The syntax: msconvert –f ‘path\to\filelist.txt’ --outdir ‘path\to\folder’ --outfile ‘filename’ --zlib -v The error message: processing file: X:\MS\PLASMA\LPOS.PRO\Data\final_data\AIRWAVE_LPOS_ToF05_P71W47_LTR.raw writing output file: W:\mzML\airwave1\SLPOS\ AIRWAVE_LPOS_ToF05_P71W47_LTR.mzML [SpectrumWorkerThreads::work] error in thread: Scan Read Error Then, after a while, the output changed to: processing file: X:\MS\PLASMA\LPOS.PRO\Data\final_data\AIRWAVE_LPOS_ToF05_P71W47_LTR.raw [msconvert] Caught unknown exception. Please report this error to su...@pr...<mailto:su...@pr...>. Attach the command output and this version information in your report: ProteoWizard release: 3.0.10765 (2017-4-20) ProteoWizard MSData: 3.0.10765 (2017-4-20) ProteoWizard Analysis: 3.0.10730 (2017-4-10) Build date: Apr 20 2017 09:42:48 The files look alright when opened with ‘SeeMS’ and this error hasn’t occurred before. What should I change in my approach? Thank you so much in advance. Regards, Elzbieta --- Elzbieta Lauzikaite PhD student Imperial College London Section of Computational and Systems Medicine SAF Building, Exhibition Road London, SW7 2AZ Email: e.l...@im...<mailto:e.l...@im...> |Phone: +44 (0)77 9470 0505 ------------------------------------------------------------------------------ Check out the vibrant tech community on one of the world's most engaging tech sites, Slashdot.org<http://Slashdot.org>! http://sdm.link/slashdot _______________________________________________ proteowizard-support mailing list pro...@li...<mailto:pro...@li...> https://lists.sourceforge.net/lists/listinfo/proteowizard-support |
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From: Chambers, M. <mat...@gm...> - 2017-05-17 14:50:51
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An obvious thing to try would be rerunning the commands one at a time. :) It would be very strange for different processes to interfere with each other, but it's possible they do something odd in their DLL. It could also be a hiccup with your VM IO I suppose. -Matt On 5/17/2017 9:46 AM, Lauzikaite, Elzbieta wrote: > Hi Matt, > > Thanks for your reply. No, it happens for multiple files - different files were being processed in different command windows and all > processes stopped with the same error on different files. > > Thank you, > > Elzbieta > > On 17 May 2017, at 15:30, Chambers, Matthew <mat...@gm... <mailto:mat...@gm...>> wrote: > >> Hi Elzbieta, >> >> Does the error only happen on that file and at about the same scan? Might be a corrupt file. >> >> -Matt >> >> >> On 5/17/2017 9:24 AM, Lauzikaite, Elzbieta wrote: >>> >>> Hello, >>> >>> I was running msconvert on virtual Win10, when an error occurred and processing stopped. 8 command lines were running at the same time, >>> all stopped at approximately the same time. Input was Waters raw files. >>> >>> The syntax: >>> >>> msconvert –f ‘path\to\filelist.txt’ --outdir ‘path\to\folder’ --outfile ‘filename’ --zlib -v >>> >>> The error message: >>> >>> processing file: X:\MS\PLASMA\LPOS.PRO\Data\final_data\AIRWAVE_LPOS_ToF05_P71W47_LTR.raw >>> >>> writing output file: W:\mzML\airwave1\SLPOS\ AIRWAVE_LPOS_ToF05_P71W47_LTR.mzML >>> >>> [SpectrumWorkerThreads::work] error in thread: Scan Read Error >>> >>> Then, after a while, the output changed to: >>> >>> processing file: X:\MS\PLASMA\LPOS.PRO\Data\final_data\AIRWAVE_LPOS_ToF05_P71W47_LTR.raw >>> >>> [msconvert] Caught unknown exception. >>> >>> Please report this error to su...@pr.... >>> >>> Attach the command output and this version information in your report: >>> >>> ProteoWizard release: 3.0.10765 (2017-4-20) >>> >>> ProteoWizard MSData: 3.0.10765 (2017-4-20) >>> >>> ProteoWizard Analysis: 3.0.10730 (2017-4-10) >>> >>> Build date: Apr 20 2017 09:42:48 >>> >>> The files look alright when opened with ‘SeeMS’ and this error hasn’t occurred before. What should I change in my approach? >>> >>> Thank you so much in advance. >>> >>> Regards, >>> >>> Elzbieta >>> >>> --- >>> >>> Elzbieta Lauzikaite >>> >>> PhD student >>> >>> Imperial College London >>> >>> Section of Computational and Systems Medicine >>> >>> SAF Building, Exhibition Road >>> >>> London, SW7 2AZ >>> >>> Email: e.l...@im... |Phone: +44 (0)77 9470 0505 >>> >>> >>> >>> ------------------------------------------------------------------------------ >>> Check out the vibrant tech community on one of the world's most >>> engaging tech sites,Slashdot.org <http://Slashdot.org>!http://sdm.link/slashdot >>> >>> >>> _______________________________________________ >>> proteowizard-support mailing list >>> pro...@li... >>> https://lists.sourceforge.net/lists/listinfo/proteowizard-support >> |
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From: Lauzikaite, E. <e.l...@im...> - 2017-05-17 17:10:26
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Will try that. Thank you for such a quick response. Elzbieta From: Chambers, Matthew [mailto:mat...@gm...] Sent: 17 May 2017 15:52 To: Lauzikaite, Elzbieta <e.l...@im...> Cc: su...@pr... Subject: Re: [proteowizard-support] msconvert error An obvious thing to try would be rerunning the commands one at a time. :) It would be very strange for different processes to interfere with each other, but it's possible they do something odd in their DLL. It could also be a hiccup with your VM IO I suppose. -Matt On 5/17/2017 9:46 AM, Lauzikaite, Elzbieta wrote: Hi Matt, Thanks for your reply. No, it happens for multiple files - different files were being processed in different command windows and all processes stopped with the same error on different files. Thank you, Elzbieta On 17 May 2017, at 15:30, Chambers, Matthew <mat...@gm...<mailto:mat...@gm...>> wrote: Hi Elzbieta, Does the error only happen on that file and at about the same scan? Might be a corrupt file. -Matt On 5/17/2017 9:24 AM, Lauzikaite, Elzbieta wrote: Hello, I was running msconvert on virtual Win10, when an error occurred and processing stopped. 8 command lines were running at the same time, all stopped at approximately the same time. Input was Waters raw files. The syntax: msconvert –f ‘path\to\filelist.txt’ --outdir ‘path\to\folder’ --outfile ‘filename’ --zlib -v The error message: processing file: X:\MS\PLASMA\LPOS.PRO\Data\final_data\AIRWAVE_LPOS_ToF05_P71W47_LTR.raw writing output file: W:\mzML\airwave1\SLPOS\ AIRWAVE_LPOS_ToF05_P71W47_LTR.mzML [SpectrumWorkerThreads::work] error in thread: Scan Read Error Then, after a while, the output changed to: processing file: X:\MS\PLASMA\LPOS.PRO\Data\final_data\AIRWAVE_LPOS_ToF05_P71W47_LTR.raw [msconvert] Caught unknown exception. Please report this error to su...@pr...<mailto:su...@pr...>. Attach the command output and this version information in your report: ProteoWizard release: 3.0.10765 (2017-4-20) ProteoWizard MSData: 3.0.10765 (2017-4-20) ProteoWizard Analysis: 3.0.10730 (2017-4-10) Build date: Apr 20 2017 09:42:48 The files look alright when opened with ‘SeeMS’ and this error hasn’t occurred before. What should I change in my approach? Thank you so much in advance. Regards, Elzbieta --- Elzbieta Lauzikaite PhD student Imperial College London Section of Computational and Systems Medicine SAF Building, Exhibition Road London, SW7 2AZ Email: e.l...@im...<mailto:e.l...@im...> |Phone: +44 (0)77 9470 0505 ------------------------------------------------------------------------------ Check out the vibrant tech community on one of the world's most engaging tech sites, Slashdot.org<http://Slashdot.org>! http://sdm.link/slashdot _______________________________________________ proteowizard-support mailing list pro...@li...<mailto:pro...@li...> https://lists.sourceforge.net/lists/listinfo/proteowizard-support |
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From: Lauzikaite, E. <e.l...@im...> - 2017-05-18 10:27:29
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Hi Matt, I was trying to run one process at a time, but after ~30 files the process stopped with the same error. The file is not corrupted and was successfully converted to mzML with a new process window. Perhaps you would know why processes keep stopping like that and whether I can change anything? I have ~19k files to converted, so optimising the system would be very useful :) Thank you, Elzbieta From: "Lauzikaite, Elzbieta" <e.l...@im...> Date: Wednesday, 17 May 2017 at 18:10 To: "Chambers, Matthew" <mat...@gm...> Cc: "su...@pr..." <su...@pr...> Subject: RE: [proteowizard-support] msconvert error Will try that. Thank you for such a quick response. Elzbieta From: Chambers, Matthew [mailto:mat...@gm...] Sent: 17 May 2017 15:52 To: Lauzikaite, Elzbieta <e.l...@im...> Cc: su...@pr... Subject: Re: [proteowizard-support] msconvert error An obvious thing to try would be rerunning the commands one at a time. :) It would be very strange for different processes to interfere with each other, but it's possible they do something odd in their DLL. It could also be a hiccup with your VM IO I suppose. -Matt On 5/17/2017 9:46 AM, Lauzikaite, Elzbieta wrote: Hi Matt, Thanks for your reply. No, it happens for multiple files - different files were being processed in different command windows and all processes stopped with the same error on different files. Thank you, Elzbieta On 17 May 2017, at 15:30, Chambers, Matthew <mat...@gm...<mailto:mat...@gm...>> wrote: Hi Elzbieta, Does the error only happen on that file and at about the same scan? Might be a corrupt file. -Matt On 5/17/2017 9:24 AM, Lauzikaite, Elzbieta wrote: Hello, I was running msconvert on virtual Win10, when an error occurred and processing stopped. 8 command lines were running at the same time, all stopped at approximately the same time. Input was Waters raw files. The syntax: msconvert –f ‘path\to\filelist.txt’ --outdir ‘path\to\folder’ --outfile ‘filename’ --zlib -v The error message: processing file: X:\MS\PLASMA\LPOS.PRO\Data\final_data\AIRWAVE_LPOS_ToF05_P71W47_LTR.raw writing output file: W:\mzML\airwave1\SLPOS\ AIRWAVE_LPOS_ToF05_P71W47_LTR.mzML [SpectrumWorkerThreads::work] error in thread: Scan Read Error Then, after a while, the output changed to: processing file: X:\MS\PLASMA\LPOS.PRO\Data\final_data\AIRWAVE_LPOS_ToF05_P71W47_LTR.raw [msconvert] Caught unknown exception. Please report this error to su...@pr...<mailto:su...@pr...>. Attach the command output and this version information in your report: ProteoWizard release: 3.0.10765 (2017-4-20) ProteoWizard MSData: 3.0.10765 (2017-4-20) ProteoWizard Analysis: 3.0.10730 (2017-4-10) Build date: Apr 20 2017 09:42:48 The files look alright when opened with ‘SeeMS’ and this error hasn’t occurred before. What should I change in my approach? Thank you so much in advance. Regards, Elzbieta --- Elzbieta Lauzikaite PhD student Imperial College London Section of Computational and Systems Medicine SAF Building, Exhibition Road London, SW7 2AZ Email: e.l...@im...<mailto:e.l...@im...> |Phone: +44 (0)77 9470 0505 ------------------------------------------------------------------------------ Check out the vibrant tech community on one of the world's most engaging tech sites, Slashdot.org<http://Slashdot.org>! http://sdm.link/slashdot _______________________________________________ proteowizard-support mailing list pro...@li...<mailto:pro...@li...> https://lists.sourceforge.net/lists/listinfo/proteowizard-support |
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From: Chambers, M. <mat...@gm...> - 2017-05-18 14:14:39
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Wow, that's a lot of files! It does sound like some non-deterministic problem with your VM's file system. Try to find a naked metal Windows computer to avoid the VM overhead and whatever IO issue you're seeing. Alternatively, you could try a different hypervisor, or tweaking settings, but I have no idea what to recommend there. Sorry. -Matt On 5/18/2017 5:27 AM, Lauzikaite, Elzbieta wrote: > > Hi Matt, > > I was trying to run one process at a time, but after ~30 files the process stopped with the same error. The file is not corrupted and was > successfully converted to mzML with a new process window. > > Perhaps you would know why processes keep stopping like that and whether I can change anything? I have ~19k files to converted, so > optimising the system would be very useful :) > > Thank you, > > Elzbieta > > *From: *"Lauzikaite, Elzbieta" <e.l...@im...> > *Date: *Wednesday, 17 May 2017 at 18:10 > *To: *"Chambers, Matthew" <mat...@gm...> > *Cc: *"su...@pr..." <su...@pr...> > *Subject: *RE: [proteowizard-support] msconvert error > > Will try that. Thank you for such a quick response. > > Elzbieta > > *From:*Chambers, Matthew [mailto:mat...@gm...] > *Sent:* 17 May 2017 15:52 > *To:* Lauzikaite, Elzbieta <e.l...@im...> > *Cc:* su...@pr... > *Subject:* Re: [proteowizard-support] msconvert error > > An obvious thing to try would be rerunning the commands one at a time. :) It would be very strange for different processes to interfere > with each other, but it's possible they do something odd in their DLL. It could also be a hiccup with your VM IO I suppose. > > -Matt > > > On 5/17/2017 9:46 AM, Lauzikaite, Elzbieta wrote: > > Hi Matt, > > Thanks for your reply. No, it happens for multiple files - different files were being processed in different command windows and all > processes stopped with the same error on different files. > > Thank you, > > Elzbieta > > > On 17 May 2017, at 15:30, Chambers, Matthew <mat...@gm... <mailto:mat...@gm...>> wrote: > > Hi Elzbieta, > > Does the error only happen on that file and at about the same scan? Might be a corrupt file. > > -Matt > > > On 5/17/2017 9:24 AM, Lauzikaite, Elzbieta wrote: > > Hello, > > I was running msconvert on virtual Win10, when an error occurred and processing stopped. 8 command lines were running at the > same time, all stopped at approximately the same time. Input was Waters raw files. > > The syntax: > > msconvert –f ‘path\to\filelist.txt’ --outdir ‘path\to\folder’ --outfile ‘filename’ --zlib -v > > The error message: > > processing file: X:\MS\PLASMA\LPOS.PRO\Data\final_data\AIRWAVE_LPOS_ToF05_P71W47_LTR.raw > > writing output file: W:\mzML\airwave1\SLPOS\ AIRWAVE_LPOS_ToF05_P71W47_LTR.mzML > > [SpectrumWorkerThreads::work] error in thread: Scan Read Error > > Then, after a while, the output changed to: > > processing file: X:\MS\PLASMA\LPOS.PRO\Data\final_data\AIRWAVE_LPOS_ToF05_P71W47_LTR.raw > > [msconvert] Caught unknown exception. > > Please report this error to su...@pr... <mailto:su...@pr...>. > > Attach the command output and this version information in your report: > > ProteoWizard release: 3.0.10765 (2017-4-20) > > ProteoWizard MSData: 3.0.10765 (2017-4-20) > > ProteoWizard Analysis: 3.0.10730 (2017-4-10) > > Build date: Apr 20 2017 09:42:48 > > The files look alright when opened with ‘SeeMS’ and this error hasn’t occurred before. What should I change in my approach? > > Thank you so much in advance. > > Regards, > > Elzbieta > > --- > > Elzbieta Lauzikaite > > PhD student > > Imperial College London > > Section of Computational and Systems Medicine > > SAF Building, Exhibition Road > > London, SW7 2AZ > > Email: e.l...@im... <mailto:e.l...@im...> |Phone: +44 (0)77 9470 0505 > > > > > > ------------------------------------------------------------------------------ > > Check out the vibrant tech community on one of the world's most > > engaging tech sites,Slashdot.org <http://Slashdot.org>!http://sdm.link/slashdot > > > > > > _______________________________________________ > > proteowizard-support mailing list > > pro...@li... <mailto:pro...@li...> > > https://lists.sourceforge.net/lists/listinfo/proteowizard-support > |
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From: Lauzikaite, E. <e.l...@im...> - 2017-05-28 19:09:38
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Hi Matt, Just to let you know, the error was indeed unrelated to msconvert itself, but rather to slightly disrupted network connection between the remote file storage and the VM. I have sorted this by using a “copy-to-local/process/copy-to-remote” approach, preventing files getting interrupted while loading onto RAM. Thank you for your help, Elzbieta From: Chambers, Matthew [mailto:mat...@gm...] Sent: 18 May 2017 15:16 To: Lauzikaite, Elzbieta <e.l...@im...> Cc: su...@pr... Subject: Re: [proteowizard-support] msconvert error Wow, that's a lot of files! It does sound like some non-deterministic problem with your VM's file system. Try to find a naked metal Windows computer to avoid the VM overhead and whatever IO issue you're seeing. Alternatively, you could try a different hypervisor, or tweaking settings, but I have no idea what to recommend there. Sorry. -Matt On 5/18/2017 5:27 AM, Lauzikaite, Elzbieta wrote: Hi Matt, I was trying to run one process at a time, but after ~30 files the process stopped with the same error. The file is not corrupted and was successfully converted to mzML with a new process window. Perhaps you would know why processes keep stopping like that and whether I can change anything? I have ~19k files to converted, so optimising the system would be very useful :) Thank you, Elzbieta From: "Lauzikaite, Elzbieta" <e.l...@im...><mailto:e.l...@im...> Date: Wednesday, 17 May 2017 at 18:10 To: "Chambers, Matthew" <mat...@gm...><mailto:mat...@gm...> Cc: "su...@pr..."<mailto:su...@pr...> <su...@pr...><mailto:su...@pr...> Subject: RE: [proteowizard-support] msconvert error Will try that. Thank you for such a quick response. Elzbieta From: Chambers, Matthew [mailto:mat...@gm...] Sent: 17 May 2017 15:52 To: Lauzikaite, Elzbieta <e.l...@im...><mailto:e.l...@im...> Cc: su...@pr...<mailto:su...@pr...> Subject: Re: [proteowizard-support] msconvert error An obvious thing to try would be rerunning the commands one at a time. :) It would be very strange for different processes to interfere with each other, but it's possible they do something odd in their DLL. It could also be a hiccup with your VM IO I suppose. -Matt On 5/17/2017 9:46 AM, Lauzikaite, Elzbieta wrote: Hi Matt, Thanks for your reply. No, it happens for multiple files - different files were being processed in different command windows and all processes stopped with the same error on different files. Thank you, Elzbieta On 17 May 2017, at 15:30, Chambers, Matthew <mat...@gm...<mailto:mat...@gm...>> wrote: Hi Elzbieta, Does the error only happen on that file and at about the same scan? Might be a corrupt file. -Matt On 5/17/2017 9:24 AM, Lauzikaite, Elzbieta wrote: Hello, I was running msconvert on virtual Win10, when an error occurred and processing stopped. 8 command lines were running at the same time, all stopped at approximately the same time. Input was Waters raw files. The syntax: msconvert –f ‘path\to\filelist.txt’ --outdir ‘path\to\folder’ --outfile ‘filename’ --zlib -v The error message: processing file: X:\MS\PLASMA\LPOS.PRO\Data\final_data\AIRWAVE_LPOS_ToF05_P71W47_LTR.raw writing output file: W:\mzML\airwave1\SLPOS\ AIRWAVE_LPOS_ToF05_P71W47_LTR.mzML [SpectrumWorkerThreads::work] error in thread: Scan Read Error Then, after a while, the output changed to: processing file: X:\MS\PLASMA\LPOS.PRO\Data\final_data\AIRWAVE_LPOS_ToF05_P71W47_LTR.raw [msconvert] Caught unknown exception. Please report this error to su...@pr...<mailto:su...@pr...>. Attach the command output and this version information in your report: ProteoWizard release: 3.0.10765 (2017-4-20) ProteoWizard MSData: 3.0.10765 (2017-4-20) ProteoWizard Analysis: 3.0.10730 (2017-4-10) Build date: Apr 20 2017 09:42:48 The files look alright when opened with ‘SeeMS’ and this error hasn’t occurred before. What should I change in my approach? Thank you so much in advance. Regards, Elzbieta --- Elzbieta Lauzikaite PhD student Imperial College London Section of Computational and Systems Medicine SAF Building, Exhibition Road London, SW7 2AZ Email: e.l...@im...<mailto:e.l...@im...> |Phone: +44 (0)77 9470 0505 ------------------------------------------------------------------------------ Check out the vibrant tech community on one of the world's most engaging tech sites, Slashdot.org<http://Slashdot.org>! http://sdm.link/slashdot _______________________________________________ proteowizard-support mailing list pro...@li...<mailto:pro...@li...> https://lists.sourceforge.net/lists/listinfo/proteowizard-support |
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From: Cristina López-H. <n12...@uc...> - 2018-10-10 15:09:47
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Hello, I am Cristina and I have problems with the MSe .RAW (Waters files) conversion to .mzXML I tried this: Also, I tried the program in windows but I have problems also. I would know if there is a tutorial or which is the mistake. Sorry, because I have not high level in informatics. Thanks you very much, Cristina |
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From: Chambers, M. <mat...@gm...> - 2018-10-10 16:44:21
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Hi Cristina, Two problems: 1. You need to update your pwiz version and try again. 2. You must use the Windows version to convert vendor files, possibly via Wine/Docker (https://hub.docker.com/r/chambm/pwiz-skyline-i-agree-to-the-vendor-licenses) Hope this helps, -Matt On 10/10/2018 11:09 AM, Cristina López-Hidalgo wrote: > > Hello, > > I am Cristina and I have problems with the MSe .RAW (Waters files) conversion to .mzXML > > I tried this: > > Also, I tried the program in windows but I have problems also. > > I would know if there is a tutorial or which is the mistake. > > Sorry, because I have not high level in informatics. > > Thanks you very much, > > Cristina > > > > > > _______________________________________________ > proteowizard-support mailing list > pro...@li... > https://lists.sourceforge.net/lists/listinfo/proteowizard-support |
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From: Matthew S. <MJ...@st...> - 2018-10-30 17:12:25
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Please find the command and error message below.
The file I was wanting to convert to mzml is Waters raw data.
λ msconvert "20180621 DELYAN IC50 PLATES.raw" --64 --filter "peakPicking true 1-" --filter "scanTime [600, 660]"
format: mzML
m/z: Compression-None, 64-bit
intensity: Compression-None, 64-bit
rt: Compression-None, 64-bit
ByteOrder_LittleEndian
indexed="true"
outputPath: .
extension: .mzML
contactFilename:
runIndexSet:
spectrum list filters:
peakPicking true 1-
scanTime [600, 660]
chromatogram list filters:
filenames:
20180621 DELYAN IC50 PLATES.raw
processing file: 20180621 DELYAN IC50 PLATES.raw
writing output file: .\20180621 DELYAN IC50 PLATES.mzML
[msconvert] Caught unknown exception.
ProteoWizard release: 3.0.18294 (6c5e69c23)
Build date: Oct 21 2018 00:26:44
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From: Chambers, M. <mat...@gm...> - 2018-10-30 17:18:00
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Hi Matt S, Do you also get the error without the peak picking and scan time filters? -Matt C On 10/30/2018 1:12 PM, Matthew Smith wrote: > Please find the command and error message below. > The file I was wanting to convert to mzml is Waters raw data. > > > λ msconvert "20180621 DELYAN IC50 PLATES.raw" --64 --filter "peakPicking true 1-" --filter "scanTime [600, 660]" > > format: mzML > m/z: Compression-None, 64-bit > intensity: Compression-None, 64-bit > rt: Compression-None, 64-bit > ByteOrder_LittleEndian > indexed="true" > outputPath: . > extension: .mzML > contactFilename: > runIndexSet: > > spectrum list filters: > peakPicking true 1- > scanTime [600, 660] > > chromatogram list filters: > > filenames: > 20180621 DELYAN IC50 PLATES.raw > > processing file: 20180621 DELYAN IC50 PLATES.raw > writing output file: .\20180621 DELYAN IC50 PLATES.mzML > [msconvert] Caught unknown exception. > > > ProteoWizard release: 3.0.18294 (6c5e69c23) > Build date: Oct 21 2018 00:26:44 |
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From: Khawla S. <kha...@ul...> - 2020-06-08 13:57:38
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<html>
<head>
<meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1">
<style type="text/css" style="display:none"><!--P{margin-top:0;margin-bottom:0;}
p { margin-bottom: 0.25cm; line-height: 115% }--></style>
</head>
<body dir="ltr" style="font-size:12pt;color:#000000;background-color:#FFFFFF;font-family:Calibri,Arial,Helvetica,sans-serif;">
<style type="text/css">
p { margin-bottom: 0.25cm; line-height: 115% }</style>
<p><font face="Times New Roman, Times, serif">Hi,</font></p>
<p><a name="ms-rterangepaste-start"></a><font face="Times New Roman, Times, serif">I am a PhD student at Laval University. I am a regular user of your msconvert tool, I usually use it on windows but I want to use it for the first time with the docker version
of linux.</font></p>
<p><font face="Times New Roman, Times, serif">I want to convert my raw files (Waters raw) into mzXML.
</font></p>
<p><font face="Times New Roman, Times, serif">My files are in « raw » directory. I am using this command :</font></p>
<p><span style="font-family: "Times New Roman", Times, serif;">-bash-4.2$ docker run -it --rm -v /Nextcloud/files/me/DataMass/Bacteria/raw/msconvertdocker:/data chambm/pwiz-skyline-i-agree-to-the-vendor-licenses wine msconvert Nextcloud/files/me/DataMass/Bacteria/raw/*.raw
–mzXML</span></p>
<p><br>
</p>
<p><span style="font-family: "Times New Roman", Times, serif;">It fonds the files, but I am getting this error :</span></p>
<p><span style="font-family: "Times New Roman", Times, serif;">[msconvert] no files found matching "Nextcloud/files/me/DataMass/Bacteria/raw/20160701_BACTERIES_SOUCHE_1.raw"</span></p>
<p><span style="font-family: "Times New Roman", Times, serif;">[msconvert] no files found matching "Nextcloud/files/me/DataMass/Bacteria/raw/20160701_BACTERIES_SOUCHE_2.raw"</span></p>
<p><span style="font-family: "Times New Roman", Times, serif;">[msconvert] no files found matching "Nextcloud/files/me/DataMass/Bacteria/raw/20160701_BACTERIES_SOUCHE_3.raw"</span></p>
<p><span style="font-family: "Times New Roman", Times, serif;">[msconvert] no files found matching "Nextcloud/files/me/DataMass/Bacteria/raw/20160701_BACTERIES_SOUCHE_4.raw"</span></p>
<p><span style="font-family: "Times New Roman", Times, serif;">[msconvert] no files found matching "Nextcloud/files/me/DataMass/Bacteria/raw/20160701_BACTERIES_SOUCHE_7.raw"</span></p>
<p><span style="font-family: "Times New Roman", Times, serif;">[msconvert] No files specified.</span></p>
<p><span style="font-family: "Times New Roman", Times, serif;"><br>
</span></p>
<p><span style="font-family: "Times New Roman", Times, serif;">Bests,<br>
</span></p>
<p><span style="font-family: "Times New Roman", Times, serif;">Khawla<br>
</span></p>
</body>
</html>
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From: Brian P. <bs...@pr...> - 2020-06-08 15:57:46
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Perhaps you need a leading / on " Nextcloud/files/me/DataMass/Bacteria/raw/*.raw" ? On Mon, Jun 8, 2020 at 6:57 AM Khawla Seddiki <kha...@ul...> wrote: > Hi, > > I am a PhD student at Laval University. I am a regular user of your > msconvert tool, I usually use it on windows but I want to use it for the > first time with the docker version of linux. > > I want to convert my raw files (Waters raw) into mzXML. > > My files are in « raw » directory. I am using this command : > > -bash-4.2$ docker run -it --rm -v > /Nextcloud/files/me/DataMass/Bacteria/raw/msconvertdocker:/data > chambm/pwiz-skyline-i-agree-to-the-vendor-licenses wine msconvert > Nextcloud/files/me/DataMass/Bacteria/raw/*.raw –mzXML > > > It fonds the files, but I am getting this error : > > [msconvert] no files found matching > "Nextcloud/files/me/DataMass/Bacteria/raw/20160701_BACTERIES_SOUCHE_1.raw" > > [msconvert] no files found matching > "Nextcloud/files/me/DataMass/Bacteria/raw/20160701_BACTERIES_SOUCHE_2.raw" > > [msconvert] no files found matching > "Nextcloud/files/me/DataMass/Bacteria/raw/20160701_BACTERIES_SOUCHE_3.raw" > > [msconvert] no files found matching > "Nextcloud/files/me/DataMass/Bacteria/raw/20160701_BACTERIES_SOUCHE_4.raw" > > [msconvert] no files found matching > "Nextcloud/files/me/DataMass/Bacteria/raw/20160701_BACTERIES_SOUCHE_7.raw" > > [msconvert] No files specified. > > > Bests, > > Khawla > _______________________________________________ > proteowizard-support mailing list > pro...@li... > https://lists.sourceforge.net/lists/listinfo/proteowizard-support > |
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From: Chambers, M. <mat...@gm...> - 2020-06-08 18:23:22
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Hi Khawla, In the volume mount: /Nextcloud/files/me/DataMass/Bacteria/raw/msconvertdocker:/data /Nextcloud... is the host-side path, /data is the docker-side path. So your docker command should use the /data path. docker run -it --rm -v /Nextcloud/files/me/DataMass/Bacteria/raw/msconvertdocker:/data chambm/pwiz-skyline-i-agree-to-the-vendor-licenses wine msconvert /data/*.raw -o /data –mzXML Hope this helps, -Matt On 6/8/2020 9:57 AM, Khawla Seddiki wrote: > > Hi, > > I am a PhD student at Laval University. I am a regular user of your msconvert tool, I usually use it on windows but I want to use it for > the first time with the docker version of linux. > > I want to convert my raw files (Waters raw) into mzXML. > > My files are in « raw » directory. I am using this command : > > -bash-4.2$ docker run -it --rm -v /Nextcloud/files/me/DataMass/Bacteria/raw/msconvertdocker:/data > chambm/pwiz-skyline-i-agree-to-the-vendor-licenses wine msconvert Nextcloud/files/me/DataMass/Bacteria/raw/*.raw –mzXML > > > It fonds the files, but I am getting this error : > > [msconvert] no files found matching "Nextcloud/files/me/DataMass/Bacteria/raw/20160701_BACTERIES_SOUCHE_1.raw" > > [msconvert] no files found matching "Nextcloud/files/me/DataMass/Bacteria/raw/20160701_BACTERIES_SOUCHE_2.raw" > > [msconvert] no files found matching "Nextcloud/files/me/DataMass/Bacteria/raw/20160701_BACTERIES_SOUCHE_3.raw" > > [msconvert] no files found matching "Nextcloud/files/me/DataMass/Bacteria/raw/20160701_BACTERIES_SOUCHE_4.raw" > > [msconvert] no files found matching "Nextcloud/files/me/DataMass/Bacteria/raw/20160701_BACTERIES_SOUCHE_7.raw" > > [msconvert] No files specified. > > > Bests, > > Khawla > > > > _______________________________________________ > proteowizard-support mailing list > pro...@li... > https://lists.sourceforge.net/lists/listinfo/proteowizard-support |
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From: Matthew C. <mat...@gm...> - 2011-01-18 15:55:04
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I doubt it'll fix this issue, but just in case, try this conversion using the latest version of ProteoWizard. At the very least, it'll give a much better conversion of Thermo data, e.g. isolation windows parsed from the instrument method. -Matt On 1/17/2011 9:45 PM, Henry H. N. Lam wrote: > Dear Matt/Darren, > > This is Henry Lam, formerly of ISB. I have been using msconvert to convert Thermo RAW files to > mzXML/mzML, but recently I ran into some RAW files that are very big (over 2 GB). I don't know if > that's the reason or not (smaller files from the same dataset were converted normally), but > msconvert gives a cryptic error: > > processing file: 25ulV_110112104522.RAW > > (... a minute or two passes...) > > [SHA1Calculator] Error hashing file ./25ulV_110112104522.RAW > Error processing file 25ulV_110112104522.RAW > > I used all default parameters. The version was 1.6.1386 (2009-10-06). > > Could you help sort this out? Thanks for your help in advance. > > Henry |
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From: Matthew C. <mat...@gm...> - 2011-01-18 17:17:44
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Upon further testing, I'm fairly certain the new version WILL fix the problem. There was an update to the sha1 code which added support f or large file lengths. -Matt On 1/17/2011 9:45 PM, Henry H. N. Lam wrote: > Dear Matt/Darren, > > This is Henry Lam, formerly of ISB. I have been using msconvert to convert Thermo RAW files to > mzXML/mzML, but recently I ran into some RAW files that are very big (over 2 GB). I don't know if > that's the reason or not (smaller files from the same dataset were converted normally), but > msconvert gives a cryptic error: > > processing file: 25ulV_110112104522.RAW > > (... a minute or two passes...) > > [SHA1Calculator] Error hashing file ./25ulV_110112104522.RAW > Error processing file 25ulV_110112104522.RAW > > I used all default parameters. The version was 1.6.1386 (2009-10-06). > > Could you help sort this out? Thanks for your help in advance. > > Henry |
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