Here is the verbose output (including some post-sha1 output showing error):
[--- output start ---] C:\Inetpub\tpp-bin>mzWiff.exe --verbose --mzXML "\data\ProjectX \ProjectX 11March2009_1.wiff" Started: Mon Mar 16 00:06:25 2009 INFO: AnalystQS 2.0 (2000004) detected. Using v2.0 interface. INFO: Analyst QS Version 2.0 is installed. INFO: C:\data\ProjectX\ProjectX 11March2009_1.wiff is created with Analyst QS 2.0 INFO: It has an associated scan file with extension .wiff.scan INFO: Associated scan file located. INFO: 2 sample(s) recorded. INFO: Sample#1(...ES-7) INFO: Sample#2(...ES-7) Started: Sample#1: Mon Mar 16 00:06:25 2009 INFO: Found Manufacturer tag "AB Sciex Instruments" in file. INFO: Found Model tag "QSTAR Elite" in file. INFO: Found Serial Number tag "AP11440710" in file. INFO: Found Hardware Version tag "M401402 B4T0301 M3L1415 B3T0300" in file. WARNING: Sample#1 Failed to get number of periods. INFO: Allocated 0 scan slot(s) via full sweep. (got computer name: HAL) Calculating sha1-sum of C:\data\ProjectX\ProjectX 11March2009_1.wiff --done (sha1):62ddd02e21ed0916ebdfb9c05445623de4921a6c Calculating sha1-sum of mzXML --done (mzXML sha1):3605f993436b7620d3ff9dcad875392d65f344df Ended: Sample#1: Mon Mar 16 00:06:26 2009 Elapsed: Sample#1: 1 sec Started: Sample#2: Mon Mar 16 00:06:26 2009 INFO: Found Manufacturer tag "AB Sciex Instruments" in file. INFO: Found Model tag "QSTAR Elite" in file. INFO: Found Serial Number tag "AP00000000" in file. INFO: Found Hardware Version tag "0000000 0000000 0000000 0000000" in file. INFO: Period#0, has 4 experiment(s) recorded. INFO: Experiment#0: Scan(TOF MS1/+), 19579/19579 INFO: Experiment#1: Scan(TOF MS2/+), 1864/19579 INFO: Experiment#2: Scan(TOF MS2/+), 237/19579 INFO: Experiment#3: Scan(TOF MS2/+), 43/19579 INFO: Allocated 21723 scan slot(s) via full sweep. INFO: Using Precursor info from DDEEX data stream. (got computer name: HAL) Calculating sha1-sum of C:\data\ProjectX\ProjectX 11March2009_1.wiff --done (sha1):62ddd02e21ed0916ebdfb9c05445623de4921a6c .........100/21723 .........200/21723 [snip] .........11400/21723 .........11500/21723 ......... ERROR: COM error 80004005 while processing sample#2 INFO: error message: Unspecified error Ended: Sample#2: Mon Mar 16 00:13:42 2009 Elapsed: Sample#2: 7 min 16 sec Ended: Mon Mar 16 00:13:42 2009 Elapsed: 7 min 17 sec [--- output end ---] On Mar 16, 5:46 pm, Natalie Tasman <[email protected]> wrote: > http://groups.google.com/group/spctools-discuss/web/how-to-upload-fil... > > > > On Mon, Mar 16, 2009 at 2:43 PM, Moe <[email protected]> wrote: > > > Thanks for the VC tips. Where can I upload the BSA file? > > > Moyez > > > On Mar 16, 5:25 pm, Natalie Tasman <[email protected]> wrote: > >> Hi Moyez, > > >> Of course we have our own files to test, but yes, please upload your > >> file, as we've never observed the behavior you're reporting. > > >> And also please rerun your conversions with the "-v" (verbose) option > >> and copy and paste the output up to the "sha-1" calculation. > > >> You're welcome to rebuild and debug the converter on your own. Just > >> open the TPP.sln file and build the mzWiff project from there. Note > >> you'll also need the "win_lib" project to be checked out at the same > >> level as the TPP code for boost, zlib, etc. > > >> -Natalie > > >> On Mon, Mar 16, 2009 at 2:07 PM, Moe <[email protected]> wrote: > > >> > Hi Natalie, > > >> > The leak is apparent in QStar WIFF files of any size. For a 30 minute > >> > BSA QC run (25 MB file size), peak memory usage reached 314 MB (to > >> > produce ~195 MB mzXML output), which doesn't seem reasonable. Do you > >> > have your own data files that you can debug with? If not, I can upload > >> > the BSA run to your FTP site (need the details). > > >> > The data I'm trying to analyze consists of 2 hour runs at about 500 MB > >> > each. mzWiff crashes about halfway through a data file, leaving a 1.3 > >> > GB (incomplete) mzXML file which ends at an elution time of about 60 > >> > minutes (when memory reaches slightly > 2 GB). > > >> > I have tried older releases of the executable up to 4.0.0 and all > >> > behave the same. I am considering recompiling a 64-bit executable, or > >> > trying to locate the leak. I'll check out the code from SourceForge, > >> > but if you have additional instructions for setting up the VC project, > >> > please let me know. > > >> > Thanks, > >> > Moyez > > >> > On Mar 16, 1:41 pm, Natalie Tasman <[email protected]> wrote: > >> >> Hello Moyez, > > >> >> Thank you for the detailed bug report. I haven't heard of issues with > >> >> mzWiff. Thanks for the MSVC hint-- I'm pretty sure this is not turned > >> >> on yet, but actually probably shouldn't be necessary. I agree with > >> >> you that that much memory usage sounds like a memory leak. The > >> >> converters are designed to process data scan-by-scan with a relatively > >> >> low memory overhead. > > >> >> If you can upload a sample file we can take a look and see if we can > >> >> replicate behavior and then fix it. > > >> >> Thanks, > > >> >> Natalie > > >> >> On Mon, Mar 16, 2009 at 9:11 AM, Moe <[email protected]> wrote: > > >> >> > I'm trying to convert Analyst QStar Elite data acquired with Analyst > >> >> > QS 2.0, with mzWiff version 4.2.0(build Feb 19 2009 09:48:08), on > >> >> > Windows XP Pro SP3 and Windows Server 2003 R2 x64 Standard SP2. > > >> >> > There appears to be a memory leak causing process memory to accumulate > >> >> > to > 2GB, shortly after which the program crashes with error: > > >> >> > ERROR: COM error 80004005 while processing sample#2 > >> >> > INFO: error message: Unspecified error > > >> >> > This happens both on 32-bit XP and 64-bit Server 2003, both systems > >> >> > have > 4GB physical memory. The per-process addressable limit for a > >> >> > 32- > >> >> > bit process is 2GB unless compiled with the /LARGEADDRESSAWARE Visual > >> >> > C > >> >> > ++ linker flag. > > >> >> > Is anyone aware of this problem? Is this in fact a leak that can be > >> >> > avoided? > > >> >> > Thanks, > >> >> > Moyez- Hide quoted text - > > >> >> - Show quoted text -- Hide quoted text - > > >> - Show quoted text -- Hide quoted text - > > - Show quoted text - --~--~---------~--~----~------------~-------~--~----~ You received this message because you are subscribed to the Google Groups "spctools-discuss" group. To post to this group, send email to [email protected] To unsubscribe from this group, send email to [email protected] For more options, visit this group at http://groups.google.com/group/spctools-discuss?hl=en -~----------~----~----~----~------~----~------~--~---
