Hi,
I think I found one clue to solve this problem, 2.1Gb size dependent error.
I show two .mzML files. One is 1.4Gb and another is 2.3Gb.
With msconvert, there showed no error massage converting RAW to .mzML.
But, in the .mzML files, I found the difference in the bottom of the files.
1.4Gb
<offset idRef="controllerType=0 controllerNumber=1
scan=15495">1462718886</offset>
<offset idRef="controllerType=0 controllerNumber=1
scan=15496">1462895483</offset>
<offset idRef="controllerType=0 controllerNumber=1
scan=15497">1463069686</offset>
<offset idRef="controllerType=0 controllerNumber=1
scan=15498">1463247105</offset>
<offset idRef="controllerType=0 controllerNumber=1
scan=15499">1463432984</offset>
<offset idRef="controllerType=0 controllerNumber=1
scan=15500">1463520004</offset>
<offset idRef="controllerType=0 controllerNumber=1
scan=15501">1463682273</offset>
<offset idRef="controllerType=0 controllerNumber=1
scan=15502">1463843496</offset>
<offset idRef="controllerType=0 controllerNumber=1
scan=15503">1464024646</offset>
<offset idRef="controllerType=0 controllerNumber=1
scan=15504">1464202965</offset>
<offset idRef="controllerType=0 controllerNumber=1
scan=15505">1464390944</offset>
<offset idRef="controllerType=0 controllerNumber=1
scan=15506">1464565471</offset>
<offset idRef="controllerType=0 controllerNumber=1
scan=15507">1464741868</offset>
<offset idRef="controllerType=0 controllerNumber=1
scan=15508">1464933972</offset>
<offset idRef="controllerType=0 controllerNumber=1
scan=15509">1465105199</offset>
<offset idRef="controllerType=0 controllerNumber=1
scan=15510">1465295838</offset>
<offset idRef="controllerType=0 controllerNumber=1
scan=15511">1465460914</offset>
<offset idRef="controllerType=0 controllerNumber=1
scan=15512">1465648845</offset>
<offset idRef="controllerType=0 controllerNumber=1
scan=15513">1465843291</offset>
</index>
<index name="chromatogram">
<offset idRef="TIC">1466027995</offset>
</index>
</indexList>
<indexListOffset>1466277417</indexListOffset>
<fileChecksum>6bc73b1976be549ebf7ce3b3349449562f196ad0</fileChecksum>
</indexedmzML>
2.4Gb
<offset idRef="controllerType=0 controllerNumber=1
scan=14594">2143047271</offset>
<offset idRef="controllerType=0 controllerNumber=1
scan=14595">2143768434</offset>
<offset idRef="controllerType=0 controllerNumber=1
scan=14596">2143781329</offset>
<offset idRef="controllerType=0 controllerNumber=1
scan=14597">2143788264</offset>
<offset idRef="controllerType=0 controllerNumber=1
scan=14598">2144723421</offset>
<offset idRef="controllerType=0 controllerNumber=1
scan=14599">2144736958</offset>
<offset idRef="controllerType=0 controllerNumber=1
scan=14600">2145638144</offset>
<offset idRef="controllerType=0 controllerNumber=1
scan=14601">2146566315</offset>
<offset idRef="controllerType=0 controllerNumber=1
scan=14602">7</offset>
<offset idRef="controllerType=0 controllerNumber=1
scan=14603">7</offset>
<offset idRef="controllerType=0 controllerNumber=1
scan=14604">7</offset>
<offset idRef="controllerType=0 controllerNumber=1
scan=14605">7</offset>
<offset idRef="controllerType=0 controllerNumber=1
scan=14606">7</offset>
<offset idRef="controllerType=0 controllerNumber=1
scan=14607">7</offset>
<offset idRef="controllerType=0 controllerNumber=1
scan=14608">7</offset>
<offset idRef="controllerType=0 controllerNumber=1
scan=14609">7</offset>
<offset idRef="controllerType=0 controllerNumber=1
scan=14610">7</offset>
...
<offset idRef="controllerType=0 controllerNumber=1
scan=14974">7</offset>
<offset idRef="controllerType=0 controllerNumber=1
scan=14975">7</offset>
<offset idRef="controllerType=0 controllerNumber=1
scan=14976">7</offset>
<offset idRef="controllerType=0 controllerNumber=1
scan=14977">7</offset>
<offset idRef="controllerType=0 controllerNumber=1
scan=14978">7</offset>
<offset idRef="controllerType=0 controllerNumber=1
scan=14979">7</offset>
<offset idRef="controllerType=0 controllerNumber=1
scan=14980">7</offset>
<offset idRef="controllerType=0 controllerNumber=1
scan=14981">7</offset>
<offset idRef="controllerType=0 controllerNumber=1
scan=14982">7</offset>
<offset idRef="controllerType=0 controllerNumber=1
scan=14983">7</offset>
<offset idRef="controllerType=0 controllerNumber=1
scan=14984">7</offset>
<offset idRef="controllerType=0 controllerNumber=1
scan=14985">7</offset>
<offset idRef="controllerType=0 controllerNumber=1
scan=14986">7</offset>
<offset idRef="controllerType=0 controllerNumber=1
scan=14987">7</offset>
<offset idRef="controllerType=0 controllerNumber=1
scan=14988">7</offset>
<offset idRef="controllerType=0 controllerNumber=1
scan=14989">7</offset>
<offset idRef="controllerType=0 controllerNumber=1
scan=14990">7</offset>
<offset idRef="controllerType=0 controllerNumber=1
scan=14991">7</offset>
<offset idRef="controllerType=0 controllerNumber=1
scan=14992">7</offset>
<offset idRef="controllerType=0 controllerNumber=1
scan=14993">7</offset>
<offset idRef="controllerType=0 controllerNumber=1
scan=14994">7</offset>
</index>
<index name="chromatogram">
<offset idRef="TIC">7</offset>
</index>
</indexList>
<indexListOffset>1</indexListOffset>
<fileChecksum>2a6f45bbbcf022f1e41bc6c0f410bc025d340be9</fileChecksum>
</indexedmzML>
What is the '7' means? I think the problem is in there.
However, I have no idea to understand this phenomenon. I need an advice.
Additionally, in the GUI version of TPP, RAW to .mzML converting show the
error in the files that is sized as 2.1Gb over with msconvert.
See below.
EXECUTING: c:\Inetpub\tpp-bin\msconvert
c:/Inetpub/wwwroot/ISB/data/HbrainCID/raw/20111226_Alz_S1S2_08.raw -v
--mzML -o c:/Inetpub/wwwroot/ISB/data/HbrainCID/raw
format: mzML
m/z: Compression-None, 64-bit
intensity: Compression-None, 32-bit
rt: Compression-None, 64-bit
ByteOrder_LittleEndian
indexed="true"
outputPath: c:/Inetpub/wwwroot/ISB/data/HbrainCID/raw
extension: .mzML
contactFilename:
filters:
filenames:
c:/Inetpub/wwwroot/ISB/data/HbrainCID/raw\20111226_Alz_S1S2_08.raw
processing file:
c:/Inetpub/wwwroot/ISB/data/HbrainCID/raw\20111226_Alz_S1S2_08.raw
writing output file:
c:/Inetpub/wwwroot/ISB/data/HbrainCID/raw\20111226_Alz_S1S2_08.mzML
1/14994
100/14994
200/14994
300/14994
400/14994
500/14994
600/14994
700/14994
....
11000/14994
11100/14994
11200/14994
11300/14994
11400/14994
11500/14994
11600/14994
11700/14994
11800/14994
11900/14994
12000/14994
[SpectrumWorkerThreads::work] error in thread:
[SpectrumList_Thermo::spectrum()] Error retrieving spectrum
"controllerType=0 controllerNumber=1 scan=12015": [ThermoRawFile]
[RawFileImpl::getMassList(), GetMassListFromScanNum()] Failed call to
XRawfile: The system cannot find the file specified.
[SpectrumWorkerThreads::work] error in thread:
[SpectrumList_Thermo::spectrum()] Error retrieving spectrum
"controllerType=0 controllerNumber=1 scan=12024": [ThermoRawFile]
[RawFileImpl::getMassList(), GetMassListFromScanNum()] Failed call to
XRawfile: The system cannot find the file specified
Any anvice will be welcome.
thx.
Heeyoun
2015년 3월 10일 화요일 오전 1시 36분 39초 UTC+9, Heeyoun Hwang 님의 말:
>
> Hi, All
>
> I have tried to search several RAW files with MASCOT and TPP.
> Most files were searched over to protein prophet with no problem.
> but, some .dat files were able to convert to .pep.xml files depends on the
> size of their .mzXML files over 2.1Gb.
> I got same result from the command line and web version (TPP v.4.7)
>
> Welcome to your any advice.
>
>
>
> Command 9 [Mon Mar 9 13:27:39 2015] [ Show / Hide ]
> *EXECUTING: cd c:/Inetpub/wwwroot/ISB/data/HBRAINetd&
> c:\Inetpub\tpp-bin\Mascot2XML
> c:/Inetpub/wwwroot/ISB/data/HBRAINetd/20111216_EPT_S1_S2_10_ETD.dat
> -Dc:/Inetpub/wwwroot/ISB/data/HBRAINetd/nextprot_release_20150101.fasta
> -Etrypsin *
>
> filepath: c:/Inetpub/wwwroot/ISB/data/HBRAINetd/, extn:
> 20111216_EPT_S1_S2_10_ETD
> A stored as 71.0371
> B stored as 114.535
> C stored as 160.031
> D stored as 115.027
> E stored as 129.043
> F stored as 147.068
> G stored as 57.0215
> H stored as 137.059
> I stored as 113.084
> J stored as 0
> K stored as 128.095
> L stored as 113.084
> M stored as 131.04
> N stored as 114.043
> O stored as 0
> P stored as 97.0528
> Q stored as 128.059
> R stored as 156.101
> S stored as 87.032
> T stored as 101.048
> U stored as 150.954
> V stored as 99.0684
> W stored as 186.079
>
>
>
> X stored as 111
> Y stored as 163.063
> Z stored as 128.551
> c stored as 17.0027
> n stored as 1.00783
> variable modification 1, delta mass 42.0106 for Acetyl (K):
> residues: K
> nterm: 0
> cterm: 0
> protterm: 0
>
> variable modification 2, delta mass 15.9949 for Oxidation (M):
> residues: M
> nterm: 0
> cterm: 0
> protterm: 0
>
> c:/Inetpub/wwwroot/ISB/data/HBRAINetd/20111216_EPT_S1_S2_10_ETD.mzXML(1) :
> error 4: Syntax error parsing XML.
>
>
> *Command FAILED*
> RETURN CODE:63744
>
>
> thanx and regards.
>
> Heeyoun Hwang.
>
--
You received this message because you are subscribed to the Google Groups
"spctools-discuss" group.
To unsubscribe from this group and stop receiving emails from it, send an email
to [email protected].
To post to this group, send email to [email protected].
Visit this group at http://groups.google.com/group/spctools-discuss.
For more options, visit https://groups.google.com/d/optout.
