Re: [proteowizard-developer] Failure in "GetScanHeaderInfoForScanNum" reading certain .RAW files

[Matthew C. <mat...@va...>]

Hi Nick,

That fix looks good. Unless a failed call sets the other parameters to 
insane values instead of 0, in which case those would need to be 
re-initialized as well.

Thanks,
Matt


Nick Shulman wrote:
> Hi, Matt,
>
> Here's the code change that I want to make to fix the problem reading
> certain .RAW files:
>     HRESULT hr = raw_->GetScanHeaderInfoForScanNum(scanNumber_,
>                                                   &packetCount_,
>                                                   &startTime_,
>                                                   &lowMass_,
>                                                   &highMass_,
>                                                   &totalIonCurrent_,
>                                                   &basePeakMZ_,
>                                                   &basePeakIntensity_,
>                                                   &channelCount_,
>                                                   &isUniformTime,
>                                                   &frequency_);
>     if (hr != 0)
>     {
>         checkResult(raw_->GetStartTime(&startTime_),
> "[ScanInfoImpl::initialize(), GetStartTime()]");
>     }
>
> If it looks good to you, I'll check it in.
> Thanks,
> -- Nick
>
> On Fri, Sep 25, 2009 at 7:42 AM, Matthew Chambers
> <mat...@va...> wrote:
>   
>>> Hi Nick,
>>>
>>> Sorry for getting back to you late, I was dealing with my own "Failed
>>> HRESULT returned from COM
>>> object: 6" error in GetMassListRangeForScanNum which was failing for no
>>> apparent reason on one file but working on another. It sounds like a similar
>>> case with GetScanHeaderInfo. However, the latter function is quite
>>> important. If it fails, we need to catch it with try/catch and initialize at
>>> least startTime_ from another function. It's a shame to lose the TIC/BPI
>>> metadata too. I will look into it.
>>>
>>> WRT the large file handling, I thought we had that licked. We definitely
>>> need that support.
>>>
>>> Thanks,
>>> Matt
>>>
>>>
>>> Nick Shulman wrote:
>>>       
>>>> OK.  I finally learned how to build proteowizard.
>>>> It looks like the right thing to do is to remove the "checkResult"
>>>> from around the call to "GetScanHeaderInfoForScanNum".
>>>> At least, when I do that, everything works great for me.
>>>>
>>>> By the way, I noticed that mzML files don't work if they're bigger
>>>> than 4GB.  The code that's supposed to seek to the end and find the
>>>> offset of the index doesn't work.
>>>> Do you think this 4GB limit is worth looking into?
>>>>
>>>> -- Nick
>>>>
>>>> On Tue, Sep 22, 2009 at 3:49 PM, Nick Shulman <ni...@la...> wrote:
>>>>
>>>>         
>>>>> Hi, Matt,
>>>>>
>>>>> I have some .RAW files which can't be read by the current version of
>>>>> proteowizard.
>>>>> If I go all the way back to pwiz 1.51 then I can successfully convert
>>>>> the files to mzML.  But, with the current version, I get this error:
>>>>> [ThermoRawFile] [ScanInfoImpl::initialize(),
>>>>> GetScanHeaderInfoForScanNum()] Failed HRESULT returned from COM
>>>>> object: 6
>>>>> Error processing file 20090724_HT3_0.RAW
>>>>>
>>>>> I have put one of the offending files at:
>>>>> msrc-data.mc.vanderbilt.edu:/home/data/data/genshare/Matt
>>>>> Chambers/20090724_HT3_0.RAW
>>>>>
>>>>> Do you want to take a look at this?
>>>>> Let me know if there's anything I can do to help.
>>>>> -- Nick
>>>>>
>>>>>
>>>>>