Comments (5)
Hi @animesh,
I think the issue with these files is that the m/z values are out of order. It looks like it is reading the data properly, but it expects a sorted list of m/z. Try applying a simple sort and see if that works. However, there is already a raw reader in the software, so you might not need to write your own. Thanks, MTM
from unidec.
Thanks @michaelmarty for such a quick response! I tried sorting the values and at least the display doesn't look so messy after
210112__solveig_AN0.raw.intensityThreshold1000.PPM10.errTolDecimalPlace3.Time20210128191052.MS.txt
but facing error
screenshot
console
c:\python37\lib\site-packages\PyInstaller\loader\pyimod03_importers.py:493: MatplotlibDeprecationWarning:
The MATPLOTLIBDATA environment variable was deprecated in Matplotlib 3.1 and will be removed in 3.3.
Required multiplierz data file unimod.sqlite not found! Creating it.
WARNING: No unimod.sqlite found in F:\UniDec_Windows_210118\UniDec_Windows (F:\UniDec_Windows_210118\UniDec_Windows\GUI_UniDec.exe)
UniDec Engine v.4.4.0
UniDec Path: F:\UniDec_Windows_210118\UniDec_Windows\UniDec.exe
Launching UniDec
UniDec Engine v.4.4.0
UniDec Path: F:\UniDec_Windows_210118\UniDec_Windows\UniDec.exe
Display Size (1920, 1200)
Opening: 210112__solveig_AN0.raw.intensityThreshold1000.PPM10.errTolDecimalPlace3.Time20210128191052.MS.txt
Opening File: F:\SK\210112__solveig_AN0.raw.intensityThreshold1000.PPM10.errTolDecimalPlace3.Time20210128191052.MS.txt
Header Length: 1
Loading Time: 14s
Plot 1: 0.19s
Linear False
Data Prep Time: 11s
F:\UniDec_Windows_210118\UniDec_Windows\scipy\optimize\minpack.py:829: OptimizeWarning: Covariance of the parameters could not be estimated
Automatic Peak Width: 0.00294
Plot 1: 0.23s
Data Prep Done. Time: 15s
infile = F:\SK\210112__solveig_AN0.raw.intensityThreshold1000.PPM10.errTolDecimalPlace3.Time20210128191052.MS_unidecfiles\210112__solveig_AN0.raw.intensityThreshold1000.PPM10.errTolDecimalPlace3.Time20210128191052.MS_input.dat
UniDec Run
Length of Data: 846412
Threshold: 2.165771 UniDec run 22s
UniDec Run Error: 3221225477
Error 3221225477
probably input [210112__solveig_AN0.raw.intensityThreshold1000.PPM10.errTolDecimalPlace3.Time20210128191052.MS.txt] is incorrect still/needs some more pre-proc?
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Hi @animesh,
Yep! The data import looks good. I am pretty sure the error is coming from the fact that your data is really large, and the computer is running out of memory in a critical part. I think you can fix this by setting the Peak FWHM to 0. I am planning to put in a test for this. Thanks, MTM
from unidec.
Wondering where is this FWHM setting in UniDec @michaelmarty ? BTW if i convert to mzML and then import i get a totally different picture
so it could just be issue of how i am presenting the ions in txt file, which is just essentially all the ions and its (sum)Intensity sorted on mz values, probably every scan has to go separately in txt file?
from unidec.
The FWHM is under the additional Deconvolution Parameters. Yeah, each scan will have a slightly different m/z value, so if you just flatten all the scans, it will give you crazy big data. We use a merge scan function to determine the average resolution and then sum the data to match that for mzML data. For Waters and Thermo data, we actually use the scan averaging built in their DLL files. Not sure how it works, though...
from unidec.
Related Issues (20)
- Bug in Cube Plots HOT 1
- v3.1.0 won't open HOT 1
- pdf generation resulted in fatal error if file name contain . HOT 2
- Import of mzML files for "Using MetaUniDec to Analyze Chromatograms" not working HOT 3
- m/z range HOT 6
- mzML files and Linux HOT 2
- Exporting Waterfall Plot from Meta UniDec 4.2 HOT 2
- Converting data recorded with bunching factor to txt HOT 7
- RNA or DNA deconvolution HOT 1
- Scale problem HOT 2
- Could not import data reader: unidectools HOT 1
- Suggestion for MetaUniDec to skip bad runs HOT 2
- error with opening .raw files HOT 5
- Error 3e+09 HOT 7
- Unable To Make TIC Selection HOT 2
- Unable to output the DScore for each deconvoluted mass HOT 2
- Error/bug appears using export_params() and autorun() on docker container HOT 6
- mzML files won't open - error HOT 1
- Use command line to process the entire process HOT 2
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