PeakPicking Vendor files & empty scan #635
Comments
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If the scan looks blank in QualBrowser it's a safe bet the file is corrupt. Once that scan is accessed things go wonky. Try running a convert job with an index filter that includes everything EXCEPT that scan. There very well may be other corrupt scans too so you may need to exclude a range of scans. For example if you have 500 scans and scan 124 is corrupt, use filters: edit: fixed off by one error |
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Thanks for your reply! It is not that this scan and the following scans are very important, but it would be nice if msconvert could skip scans that generate an error during conversion and continue with other scans (if it is manageable). |
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I've found out that if I add --filter "defaultArrayLength 1-" after --filter "peakPicking vendor", msconvert skips the corrupt scan and exits normally. So, this works now: |
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If the vendor API mishandles the corrupt scan and messes up the process memory, everything that happens afterward is what's called "undefined behavior". It may look like everything is fine, but things may silently be corrupted. It's better to do the index filter as I said. It doesn't need to be the first filter. It can come after peakPicking. |
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If I put index fileter after --filter "peakPicking vendor" like: msconvert creates the same error as in [1]
However, I am satisfied with the solution I've posted before. Thanks! |
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The indices are 0 based and scan numbers are 1 based, so index 29315 is scan 29316. :) Sorry I didn't make that clear before (and the ranges are inclusive on both ends). Doh. I see I got it wrong in my reply! I was even trying to pay attention to that too... |
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Sorry, my mistake too, --filter "peakPicking vendor" --filter "index 0-29314,29316-" works! Thanks for your helping! |
Dear Developers,
thank you very much for your amazing job. I have some problems running msconvert using windows command line, I hope you can help me and point out what I am doing wrong.
I have a thermo .raw file acquired on Thermo Fusion Lumos instrument. It containts MS2 and SPS-MS3 spectra in profile mode and the goal is to convert it to .mgf file format.
I am using Windows 10 command line and ProteoWizard release: 3.0.19248 (37b2e98)
Build date: Sep 5 2019 21:34:03
gives an error message while writing the output file:
The output file is created, however only scans up to 29315 are returned, the further scans are missing. The command line freezes and does not return the prompt back.
However, the first scan reported looks normal:
The scan=29316 looks empty when I check it in Thermo Xcalibur browser. I am not sure why it was created and not filtered out.
it runs through without an issue, the output file is created, but the result is rather strange:
First, there are flanking 0 ions around each centroided peak, second, the ions above ~160 m/z are missing or reporterd as 0
The troublesome scan 29316 and all scans after it are reported:
msconvert test_file.raw --mgf --filter "peakPicking cwt" --filter "titleMaker <RunId>.<ScanNumber>.<ScanNumber>.<ChargeState>"creates and output very similar to the one from GUI, but with fewer 0 reported, so the output is much smaller in size.
--filter "zeroSamples removeExtra"So far I feel myself lost and cannot explain the different output I get from gui and cmd and how I can proceed further. Am I missing something when running msconvert in command line? I would appreciate any help!
Thank you very much in advance,
Ivan
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