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kevinkovalchik / RawTools

RawTools is an open-source and freely available package designed to perform scan data parsing and quantification, and quality control analysis of Thermo Orbitrap raw mass spectrometer files from data-dependent acquisition experiments.
Apache License 2.0
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System.MissingMethodException: Method 'Array.Empty' not found #50

Open eltonjrv opened 4 years ago

eltonjrv commented 4 years ago

Describe the bug Trying to run Rawtools for quality control analysis along with a database search on TMT10 raw data which has an empty channel.

Description of raw file MS2 - TMT10.

Command line arguments $ mono /usr/local/RawTools/RawTools.exe -d . -qc gluc-qc_Btau_trembl -db ../Btaurus-uniprot-trembl.fasta -fmods 57.0214@C -vmods 15.9949@M -N 1000 -X /usr/local/RawTools/tandem-linux-15-12-15-2/bin/

Command line output Processing: /run/media/elton/TOSHIBA EXT/TMTrawData/glucose/./130619_Fraction_1.raw

Determing MS analysis order... Done! Extracting scan indices: 100%
Checking for orphaned scans: 100%

================ Scan indexing report ================

Total scans in file: 62959

Scans linked: 62959

Orphan scans:

None!

All scans accounted for!

======================================================

Extracting reaction events: 100%
Extracting scan data: 100%
Extracting trailer extras: 100%
Extracting precursor masses: 100%
Extracting retention times: 100%
Analyzing precursor peaks: 100%

Calculating meta data

MS1 isolation interference

MS2 scan cycle density

Ion injection time

Duty cycle

Intensity distribution

Summed intensities

Calculating metrics

Unhandled Exception: System.MissingMethodException: Method 'Array.Empty' not found. at RawTools.QC.Search.WriteSearchMGF (RawTools.WorkFlows.WorkflowParameters parameters, RawTools.Data.Collections.CentroidStreamCollection centroids, RawTools.Data.Collections.SegmentScanCollection segments, RawTools.Data.Collections.RetentionTimeCollection retentionTimes, RawTools.Data.Collections.PrecursorMassCollection precursorMasses, RawTools.Data.Collections.PrecursorScanCollection precursorScans, RawTools.Data.Collections.TrailerExtraCollection trailerExtras, RawTools.Data.Containers.MethodDataContainer methodData, RawTools.Data.Containers.ScanIndex index, System.String rawFileName, Boolean fixedScans) <0x4062dcb0 + 0x000d7> in :0 at RawTools.WorkFlows.WorkFlowsDDA.UniversalDDA (IRawFileThreadManager rawFileThreadManager, RawTools.WorkFlows.WorkflowParameters parameters, RawTools.QC.QcDataCollection qcDataCollection) <0x405a7000 + 0x0099b> in :0 at RawTools.Program.Run (System.Collections.Generic.Dictionary2 opts) <0x40569650 + 0x00cb7> in <filename unknown>:0 at RawTools.Program.Main (System.String[] args) <0x404e3e30 + 0x0021f> in <filename unknown>:0 [ERROR] FATAL UNHANDLED EXCEPTION: System.MissingMethodException: Method 'Array.Empty' not found. at RawTools.QC.Search.WriteSearchMGF (RawTools.WorkFlows.WorkflowParameters parameters, RawTools.Data.Collections.CentroidStreamCollection centroids, RawTools.Data.Collections.SegmentScanCollection segments, RawTools.Data.Collections.RetentionTimeCollection retentionTimes, RawTools.Data.Collections.PrecursorMassCollection precursorMasses, RawTools.Data.Collections.PrecursorScanCollection precursorScans, RawTools.Data.Collections.TrailerExtraCollection trailerExtras, RawTools.Data.Containers.MethodDataContainer methodData, RawTools.Data.Containers.ScanIndex index, System.String rawFileName, Boolean fixedScans) <0x4062dcb0 + 0x000d7> in <filename unknown>:0 at RawTools.WorkFlows.WorkFlowsDDA.UniversalDDA (IRawFileThreadManager rawFileThreadManager, RawTools.WorkFlows.WorkflowParameters parameters, RawTools.QC.QcDataCollection qcDataCollection) <0x405a7000 + 0x0099b> in <filename unknown>:0 at RawTools.Program.Run (System.Collections.Generic.Dictionary2 opts) <0x40569650 + 0x00cb7> in :0 at RawTools.Program.Main (System.String[] args) <0x404e3e30 + 0x0021f> in :0 

[Paste output here, between the triple quotes]

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kevinkovalchik commented 4 years ago

Thanks for reporting this. RawTools has been on the back burner for a while, but with all that is happening now work has slowed down and I might have some time to get to some of the open issues.

Best, Kevin

On Mon, Apr 6, 2020 at 9:46 AM Elton Vasconcelos notifications@github.com wrote:

Describe the bug Trying to run Rawtools for quality control analysis along with a database search on TMT10 raw data which has an empty channel.

Description of raw file MS2 - TMT10.

Command line arguments $ mono /usr/local/RawTools/RawTools.exe -d . -qc gluc-qc_Btau_trembl -db ../Btaurus-uniprot-trembl.fasta -fmods 57.0214@C -vmods 15.9949@M -N 1000 -X /usr/local/RawTools/tandem-linux-15-12-15-2/bin/

Command line output Processing: /run/media/elton/TOSHIBA EXT/TMTrawData/glucose/./130619_Fraction_1.raw

Determing MS analysis order... Done! Extracting scan indices: 100% Checking for orphaned scans: 100%

================ Scan indexing report ================

Total scans in file: 62959

Scans linked: 62959

Orphan scans:

None!

All scans accounted for!

======================================================

Extracting reaction events: 100% Extracting scan data: 100% Extracting trailer extras: 100% Extracting precursor masses: 100% Extracting retention times: 100% Analyzing precursor peaks: 100%

Calculating meta data

MS1 isolation interference

MS2 scan cycle density

Ion injection time

Duty cycle

Intensity distribution

Summed intensities

Calculating metrics

Unhandled Exception: System.MissingMethodException: Method 'Array.Empty' not found. at RawTools.QC.Search.WriteSearchMGF (RawTools.WorkFlows.WorkflowParameters parameters, RawTools.Data.Collections.CentroidStreamCollection centroids, RawTools.Data.Collections.SegmentScanCollection segments, RawTools.Data.Collections.RetentionTimeCollection retentionTimes, RawTools.Data.Collections.PrecursorMassCollection precursorMasses, RawTools.Data.Collections.PrecursorScanCollection precursorScans, RawTools.Data.Collections.TrailerExtraCollection trailerExtras, RawTools.Data.Containers.MethodDataContainer methodData, RawTools.Data.Containers.ScanIndex index, System.String rawFileName, Boolean fixedScans) <0x4062dcb0 + 0x000d7> in :0 at RawTools.WorkFlows.WorkFlowsDDA.UniversalDDA (IRawFileThreadManager rawFileThreadManager, RawTools.WorkFlows.WorkflowParameters parameters, RawTools.QC.QcDataCollection qcDataCollection) <0x405a7000 + 0x0099b> in :0 at RawTools.Program.Run (System.Collections.Generic.Dictionary2 opts) <0x40569650 + 0x00cb7> in :0 at RawTools.Program.Main (System.String[] args) <0x404e3e30 + 0x0021f> in :0 [ERROR] FATAL UNHANDLED EXCEPTION: System.MissingMethodException: Method 'Array.Empty' not found. at RawTools.QC.Search.WriteSearchMGF (RawTools.WorkFlows.WorkflowParameters parameters, RawTools.Data.Collections.CentroidStreamCollection centroids, RawTools.Data.Collections.SegmentScanCollection segments, RawTools.Data.Collections.RetentionTimeCollection retentionTimes, RawTools.Data.Collections.PrecursorMassCollection precursorMasses, RawTools.Data.Collections.PrecursorScanCollection precursorScans, RawTools.Data.Collections.TrailerExtraCollection trailerExtras, RawTools.Data.Containers.MethodDataContainer methodData, RawTools.Data.Containers.ScanIndex index, System.String rawFileName, Boolean fixedScans) <0x4062dcb0 + 0x000d7> in :0 at RawTools.WorkFlows.WorkFlowsDDA.UniversalDDA (IRawFileThreadManager rawFileThreadManager, RawTools.WorkFlows.WorkflowParameters parameters, RawTools.QC.QcDataCollection qcDataCollection) <0x405a7000 + 0x0099b> in

:0 at RawTools.Program.Run (System.Collections.Generic.Dictionary2 opts) <0x40569650 + 0x00cb7> in :0 at RawTools.Program.Main (System.String[] args) <0x404e3e30 + 0x0021f> in :0 [Paste output here, between the triple quotes] *Screenshots* If applicable, add screenshots to help explain your problem. *Desktop & RawTools information:* - OS: [e.g. iOS] - RawTools version: [e.g. 1.3.3] *Additional context* Add any other context about the problem here. — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub , or unsubscribe .
chrishuges commented 4 years ago

I can take a look at this as well. Can you try updating to the latest version of the software and trying this command again?

Thanks, Chris

eltonjrv commented 4 years ago

I'm already using the latest 2.0.2 one. Is there any other suggestion? Thank, though.

chrishuges commented 4 years ago

Yes, my mistake. I misread the version.

If you process this raw file without a search, just in the regular raw tools pipeline, including mgf creation and quant, does it work without error?

eltonjrv commented 4 years ago

Yes, the regular "RawTools for quantification" command work well on the same data.

chrishuges commented 4 years ago

I can't seem to reproduce this error on my own system (CentOS7, RawTools 2.0.2) using a command essentially the same as yours (relative paths, same input flags) and a DDA TMT file (MS2 TMT, or MS3 TMT).

Is it at all possible to share the raw file giving you an issue so I can test it on my system to help track down where the issue might be?

eltonjrv commented 4 years ago

Thanks for your prompt attention on that, Chirs! I don't think the PI owner of that data would allow such thing. Sorry! Did you get on my initial message that it is a TMT 10-plex lacking one channel (we only have 9 samples). Could that be the reason of this issue?

chrishuges commented 4 years ago

Yes, the TMT empty channel should make no difference. The test runs I did on my system also had empty channels, just to make sure.

Is there anything else you can tell me about the method used to acquire the data? Instrument, acquisition method, sample complexity? Any details you can give would be helpful.

Having the raw data would help a lot. Just to say, in case this helps, but I have no way of telling anything about the data from just the raw file. Without knowing the TMT sample assignments, what the sample is, or where it is from, it is impossible for me to do anything of use with these data beyond testing it with our tool.

kevinkovalchik commented 4 years ago

Do you know what version of dotnet or mono you are using? The missing array.empty method sounds familiar to me, but I don't recall what the context was... Anyway, I'll have a look at the code on Monday.

On Sat, Apr 18, 2020, 1:18 PM Christopher Hughes, notifications@github.com wrote:

Yes, the TMT empty channel should make no difference. The test runs I did on my system also had empty channels, just to make sure.

Is there anything else you can tell me about the method used to acquire the data? Instrument, acquisition method, sample complexity? Any details you can give would be helpful.

Having the raw data would help a lot. Just to say, in case this helps, but I have no way of telling anything about the data from just the raw file. Without knowing the TMT sample assignments, what the sample is, or where it is from, it is impossible for me to do anything of use with these data beyond testing it with our tool.

— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/kevinkovalchik/RawTools/issues/50#issuecomment-615906676, or unsubscribe https://github.com/notifications/unsubscribe-auth/AD2PTUG4OUN6EQNVVMJMXTLRNHOH7ANCNFSM4MCJH4DQ .

kevinkovalchik commented 4 years ago

This could possibly be an issue with an old version of Mono. Is it possible to update and try with the new version?

eltonjrv commented 4 years ago

Hey guys, Thanks again for your attention and sorry for being out for a while! I've been working on my Windows partition in the past two days due to some particular collaborations' requirements. Once I reboot my laptop on my Fedora partition, I'll tell you which mono version I'm using. Kevin might be right regarding an outdated mono version, since I also have an outdated Fedora one. JFYI: I already circumvented this situation two weeks ago by running Comet on all mgf files, and then writing a PERL script to match scans from Comet results to the ones from your RawTools -q output. But I'm sure it will definitely be cool to compare those results with your "QC with database search" tool, which I'm aware uses X!Tandem as the search engine.