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System.MissingMethodException: Method 'Array.Empty' not found #50
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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 ***@***.***> 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 ***@***.*** -vmods ***@***.*** -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]
*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.
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|
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, |
I'm already using the latest 2.0.2 one. |
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? |
Yes, the regular "RawTools for quantification" command work well on the same data. |
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? |
Thanks for your prompt attention on that, Chirs! |
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. |
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, ***@***.***> 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.
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This could possibly be an issue with an old version of Mono. Is it possible to update and try with the new version? |
Hey guys, |
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.Dictionary
2 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.Dictionary
2 opts) <0x40569650 + 0x00cb7> in :0at RawTools.Program.Main (System.String[] args) <0x404e3e30 + 0x0021f> in :0
Screenshots
If applicable, add screenshots to help explain your problem.
Desktop & RawTools information:
Additional context
Add any other context about the problem here.
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