Thermo Tribrid data are not parsed #78
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Could you please describe the issue you are encountering and provide information related to the questions posed above? |
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I tried to parse metrics from Thermo Tribrid data, the process seemed to proceed in Windows command prompt view, but no files were written. I used the GUI.
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From: Christopher Hughes ***@***.***>
Sent: Monday, October 17, 2022 3:34:06 PM
To: kevinkovalchik/RawTools ***@***.***>
Cc: Ross, Mark M (mmr6q) ***@***.***>; Author ***@***.***>
Subject: Re: [kevinkovalchik/RawTools] Thermo Tribrid data are not parsed (Issue #78)
Could you please describe the issue you are encountering and provide information related to the questions posed above?
—
Reply to this email directly, view it on GitHub<#78 (comment)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/A3VBU43MULC4J4R4YOYAER3WDWS25ANCNFSM6AAAAAARHDR34Q>.
You are receiving this because you authored the thread.Message ID: ***@***.***>
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Hi, In order to help you I need some more information so I can try to re-create the bug and hopefully solve it. Can you please answer these questions: Provide details about the raw file you are trying to process (e.g. Is it DDA? MS2 or SPS-MS3)? Provide details of what commands you have input into the GUI (e.g. which options did you select, which did you not? screenshot here might help). Does it appear like the command finishes? If there are no files written, it is likely hitting an error. I know in the GUI this can be hard to catch, but there should be a 'rawtools_log.txt' file that gets written into the RawTools directory. Can you please provide me with what is in this file? Thank you, |
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Chris,
Thank you for your reply.
The raw file was acquired using a SPS-MS3 method.
Below first is the GUI parameters I used. Yesterday, the process seems to run to completion as viewed in the Windows Command Prompt window, but no files were written to the specified folder.
Below second is the output from running the program from the Command Prompt.
This process yielded the attached text file.
Mark
***@***.***
Output from using the Command Prompt:
C:\RawTools-2.0.7\RawTools-2.0.7>rawtools parse -f JM5072_HCT_Cys_TMT4-1.raw -x
Processing: C:\RawTools-2.0.7\RawTools-2.0.7\JM5072_HCT_Cys_TMT4-1.raw
Determing MS analysis order... Done!
Extracting scan indices: 99%
Unhandled Exception: System.AggregateException: One or more errors occurred. ---> System.NullReferenceException: Object reference not set to an instance of an object.
at RawTools.Algorithms.ExtractData.Extract.<>c__DisplayClass0_0.<ScanIndicesPrecursorsDependents>b__1(IEnumerable`1 batch) in C:\Users\chughes\Documents\bccrc\softwareRepository\RawTools\rawtoolsDev\RawTools\Algorithms\Extraction\ExtractData.cs:line 135
at System.Threading.Tasks.Parallel.<>c__DisplayClass42_0`2.<PartitionerForEachWorker>b__1()
at System.Threading.Tasks.Task.InnerInvokeWithArg(Task childTask)
at System.Threading.Tasks.Task.<>c__DisplayClass176_0.<ExecuteSelfReplicating>b__0(Object <p0>)
--- End of inner exception stack trace ---
at System.Threading.Tasks.Task.ThrowIfExceptional(Boolean includeTaskCanceledExceptions)
at System.Threading.Tasks.Task.Wait(Int32 millisecondsTimeout, CancellationToken cancellationToken)
at System.Threading.Tasks.Parallel.PartitionerForEachWorker[TSource,TLocal](Partitioner`1 source, ParallelOptions parallelOptions, Action`1 simpleBody, Action`2 bodyWithState, Action`3 bodyWithStateAndIndex, Func`4 bodyWithStateAndLocal, Func`5 bodyWithEverything, Func`1 localInit, Action`1 localFinally)
at System.Threading.Tasks.Parallel.ForEachWorker[TSource,TLocal](IEnumerable`1 source, ParallelOptions parallelOptions, Action`1 body, Action`2 bodyWithState, Action`3 bodyWithStateAndIndex, Func`4 bodyWithStateAndLocal, Func`5 bodyWithEverything, Func`1 localInit, Action`1 localFinally)
at System.Threading.Tasks.Parallel.ForEach[TSource](IEnumerable`1 source, ParallelOptions parallelOptions, Action`1 body)
at RawTools.Algorithms.ExtractData.Extract.ScanIndicesPrecursorsDependents(IRawFileThreadManager rawFileAccessor, Int32 MaxProcesses) in C:\Users\chughes\Documents\bccrc\softwareRepository\RawTools\rawtoolsDev\RawTools\Algorithms\Extraction\ExtractData.cs:line 177
at RawTools.WorkFlows.WorkFlowsDDA.UniversalDDA(IRawFileThreadManager rawFileThreadManager, WorkflowParameters parameters, QcDataCollection qcDataCollection) in C:\Users\chughes\Documents\bccrc\softwareRepository\RawTools\rawtoolsDev\RawTools\WorkFlows\DDA.cs:line 71
at RawTools.Program.Run(Dictionary`2 opts) in C:\Users\chughes\Documents\bccrc\softwareRepository\RawTools\rawtoolsDev\RawTools\Program.cs:line 243
at RawTools.Program.Main(String[] args) in C:\Users\chughes\Documents\bccrc\softwareRepository\RawTools\rawtoolsDev\RawTools\Program.cs:line 73
From: Christopher Hughes ***@***.***>
Sent: Monday, October 17, 2022 4:56 PM
To: kevinkovalchik/RawTools ***@***.***>
Cc: Ross, Mark M (mmr6q) ***@***.***>; Author ***@***.***>
Subject: Re: [kevinkovalchik/RawTools] Thermo Tribrid data are not parsed (Issue #78)
Hi,
In order to help you I need some more information so I can try to re-create the bug and hopefully solve it. Can you please answer these questions:
Provide details about the raw file you are trying to process (e.g. Is it DDA? MS2 or SPS-MS3)?
Provide details of what commands you have input into the GUI (e.g. which options did you select, which did you not? screenshot here might help).
Does it appear like the command finishes? If there are no files written, it is likely hitting an error. I know in the GUI this can be hard to catch, but there should be a 'rawtools_log.txt' file that gets written into the RawTools directory. Can you please provide me with what is in this file?
Thank you,
Chris
—
Reply to this email directly, view it on GitHub<#78 (comment)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/A3VBU444MCBHHDDXPTGZHVLWDW4MXANCNFSM6AAAAAARHDR34Q>.
You are receiving this because you authored the thread.Message ID: ***@***.******@***.***>>
2022-05-04 19:55:02.227 -07:00 [INF] Program started with arguments: -f C:\Users\chughes\Documents\bccrc\softwareRepository\RawTools\raw-test-file\200fm_BSA_100_FS_01_220409050657.raw -xic 500,10
2022-05-04 19:55:02.642 -07:00 [INF] Files to be processed, provided as list: C:\Users\chughes\Documents\bccrc\softwareRepository\RawTools\raw-test-file\200fm_BSA_100_FS_01_220409050657.raw
2022-05-04 19:55:02.670 -07:00 [INF] Extracting scan indices
2022-05-04 19:55:02.845 -07:00 [INF] Extracting method/instrument information
2022-05-04 19:55:03.086 -07:00 [INF] Extracting trailer extras
2022-05-04 19:55:03.103 -07:00 [INF] Extracting precursor masses
2022-05-04 19:55:03.113 -07:00 [INF] Extracting retention times
2022-05-04 20:00:45.293 -07:00 [INF] Program started with arguments: -f C:\Users\chughes\Documents\bccrc\softwareRepository\RawTools\raw-test-file\200fm_BSA_100_FS_01_220409050657.raw -xic 500,10
2022-05-04 20:00:45.405 -07:00 [INF] Files to be processed, provided as list: C:\Users\chughes\Documents\bccrc\softwareRepository\RawTools\raw-test-file\200fm_BSA_100_FS_01_220409050657.raw
2022-05-04 20:00:45.433 -07:00 [INF] Extracting scan indices
2022-05-04 20:00:45.605 -07:00 [INF] Extracting method/instrument information
2022-05-04 20:00:45.838 -07:00 [INF] Extracting trailer extras
2022-05-04 20:00:45.852 -07:00 [INF] Extracting precursor masses
2022-05-04 20:00:45.862 -07:00 [INF] Extracting retention times
2022-05-05 13:03:56.704 -07:00 [INF] Program started with arguments: -f C:\Users\chughes\Documents\bccrc\softwareRepository\RawTools\raw-test-file\200fm_BSA_100_FS_01_220409050657.raw - -faimsMgf
2022-05-05 13:03:57.071 -07:00 [INF] Files to be processed, provided as list: C:\Users\chughes\Documents\bccrc\softwareRepository\RawTools\raw-test-file\200fm_BSA_100_FS_01_220409050657.raw
2022-05-05 13:03:57.098 -07:00 [INF] Extracting scan indices
2022-05-05 13:03:57.269 -07:00 [INF] Extracting method/instrument information
2022-05-05 13:03:57.509 -07:00 [INF] Extracting trailer extras
2022-05-05 13:03:57.523 -07:00 [INF] Extracting precursor masses
2022-05-05 13:03:57.532 -07:00 [INF] Extracting retention times
2022-10-14 09:51:30.527 -04:00 [INF] Program started with arguments:
2022-10-14 09:54:34.579 -04:00 [INF] Program started with arguments: -f C:\Xcalibur\data\RawTools-2.0.7\JM5072_HCT_Cys_TMT4-1.raw -x -chro 1TB
2022-10-14 09:54:34.970 -04:00 [INF] Files to be processed, provided as list: C:\Xcalibur\data\RawTools-2.0.7\JM5072_HCT_Cys_TMT4-1.raw
2022-10-14 09:54:35.022 -04:00 [INF] Extracting scan indices
2022-10-14 10:19:08.895 -04:00 [INF] Program started with arguments: -d C:\Xcalibur\data\RawTools-2.0.7 -px -o -q -r TMT16 -chro 12TB -qc
2022-10-14 10:19:08.960 -04:00 [INF] Appears to be a new QC directory. New QC data collection created.
2022-10-14 10:19:08.973 -04:00 [INF] Raw files in QC queue: ["C:\\Xcalibur\\data\\RawTools-2.0.7\\JM5072_HCT_Cys_TMT4-1.raw"]
2022-10-14 10:19:09.033 -04:00 [INF] Files to be processed, provided as directory: C:\Xcalibur\data\RawTools-2.0.7\JM5072_HCT_Cys_TMT4-1.raw
2022-10-14 10:19:09.067 -04:00 [INF] Extracting scan indices
2022-10-14 13:52:28.648 -04:00 [INF] Program started with arguments: -f C:\Xcalibur\data\RawTools-2.0.7\JM5072_HCT_Cys_TMT4-1.raw -x
2022-10-14 13:52:28.780 -04:00 [INF] Files to be processed, provided as list: C:\Xcalibur\data\RawTools-2.0.7\JM5072_HCT_Cys_TMT4-1.raw
2022-10-14 13:52:28.813 -04:00 [INF] Extracting scan indices
2022-10-17 10:04:02.461 -04:00 [INF] Program started with arguments: -f C:\Xcalibur\data\RawTools-2.0.7\20220824_KY_DPQE_HeLa_KYK2_01.raw -x
2022-10-17 10:04:02.608 -04:00 [INF] Files to be processed, provided as list: C:\Xcalibur\data\RawTools-2.0.7\20220824_KY_DPQE_HeLa_KYK2_01.raw
2022-10-17 10:04:02.645 -04:00 [INF] Extracting scan indices
2022-10-17 10:04:06.397 -04:00 [INF] Extracting scan events
2022-10-17 10:04:06.406 -04:00 [INF] Extracting method/instrument information
2022-10-17 10:04:08.904 -04:00 [INF] Extracting trailer extras
2022-10-17 10:04:09.057 -04:00 [INF] Extracting precursor masses
2022-10-17 10:04:09.088 -04:00 [INF] Extracting retention times
2022-10-17 10:12:14.998 -04:00 [INF] Program started with arguments: -d C:\Xcalibur\data\RawTools-2.0.7 -px -q -r TMT6 -chro 12TB
2022-10-17 10:12:15.193 -04:00 [INF] Files to be processed, provided as directory: C:\Xcalibur\data\RawTools-2.0.7\20220824_KY_DPQE_HeLa_KYK2_01.raw ***@***.***_e_MS1c_KYK1_BR1.raw C:\Xcalibur\data\RawTools-2.0.7\JM5072_HCT_Cys_TMT4-1.raw
2022-10-17 10:12:15.213 -04:00 [INF] Extracting scan indices
2022-10-17 10:12:18.814 -04:00 [INF] Extracting scan events
2022-10-17 10:12:18.836 -04:00 [INF] Extracting method/instrument information
2022-10-17 10:12:21.036 -04:00 [INF] Extracting trailer extras
2022-10-17 10:12:21.120 -04:00 [INF] Extracting precursor masses
2022-10-17 10:12:21.166 -04:00 [INF] Extracting retention times
2022-10-17 10:12:39.701 -04:00 [INF] Extracting scan indices
2022-10-17 10:12:42.741 -04:00 [INF] Extracting scan events
2022-10-17 10:12:42.757 -04:00 [INF] Extracting method/instrument information
2022-10-17 10:12:45.065 -04:00 [INF] Extracting trailer extras
2022-10-17 10:12:45.182 -04:00 [INF] Extracting precursor masses
2022-10-17 10:12:45.207 -04:00 [INF] Extracting retention times
2022-10-17 10:13:01.961 -04:00 [INF] Extracting scan indices
2022-10-18 10:02:00.142 -04:00 [INF] Program started with arguments: -f C:\Xcalibur\data\RawTools-2.0.7\JM5072_HCT_Cys_TMT4-1.raw -x
2022-10-18 10:02:00.318 -04:00 [INF] Files to be processed, provided as list: C:\Xcalibur\data\RawTools-2.0.7\JM5072_HCT_Cys_TMT4-1.raw
2022-10-18 10:02:00.368 -04:00 [INF] Extracting scan indices
2022-10-18 10:10:08.040 -04:00 [INF] Program started with arguments: -d C:\Xcalibur\data\RawTools-2.0.7\RawTools-2.0.7 -x
2022-10-18 10:10:08.107 -04:00 [INF] Files to be processed, provided as directory:
2022-10-18 10:10:27.217 -04:00 [INF] Program started with arguments: -f C:\Xcalibur\data\RawTools-2.0.7\JM5072_HCT_Cys_TMT4-1.raw -x
2022-10-18 10:10:27.346 -04:00 [INF] Files to be processed, provided as list: C:\Xcalibur\data\RawTools-2.0.7\JM5072_HCT_Cys_TMT4-1.raw
2022-10-18 10:10:27.373 -04:00 [INF] Extracting scan indices
2022-10-18 10:21:47.450 -04:00 [INF] Program started with arguments: -d C:\Xcalibur\data\RawTools-2.0.7\RawTools-2.0.7 -x
2022-10-18 10:21:47.511 -04:00 [INF] Files to be processed, provided as directory:
2022-10-18 10:26:04.930 -04:00 [INF] Program started with arguments: parse -f JM5072_HCT_Cys_TMT4-1.raw -x
2022-10-18 10:26:05.031 -04:00 [INF] Files to be processed, provided as list: C:\RawTools-2.0.7\RawTools-2.0.7\JM5072_HCT_Cys_TMT4-1.raw
2022-10-18 10:26:05.072 -04:00 [INF] Extracting scan indices
2022-10-18 10:36:26.457 -04:00 [INF] Program started with arguments: -f C:\RawTools-2.0.7\RawTools-2.0.7\JM5072_HCT_Cys_TMT4-1.raw -x
2022-10-18 10:36:26.578 -04:00 [INF] Files to be processed, provided as list: C:\RawTools-2.0.7\RawTools-2.0.7\JM5072_HCT_Cys_TMT4-1.raw
2022-10-18 10:36:26.621 -04:00 [INF] Extracting scan indices
2022-10-18 10:44:53.677 -04:00 [INF] Program started with arguments: -f C:\RawTools-2.0.7\RawTools-2.0.7\JM5072_HCT_Cys_TMT4-1.raw -x
2022-10-18 10:44:53.812 -04:00 [INF] Files to be processed, provided as list: C:\RawTools-2.0.7\RawTools-2.0.7\JM5072_HCT_Cys_TMT4-1.raw
2022-10-18 10:44:53.856 -04:00 [INF] Extracting scan indices
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I did not finish the message…today using the GUI with the parameters shown below resulted in the program stopping (crashing) at the first step, extracting indices.
From: Ross, Mark M (mmr6q)
Sent: Tuesday, October 18, 2022 10:50 AM
To: kevinkovalchik/RawTools ***@***.***>
Subject: RE: [kevinkovalchik/RawTools] Thermo Tribrid data are not parsed (Issue #78)
Chris,
Thank you for your reply.
The raw file was acquired using a SPS-MS3 method.
Below first is the GUI parameters I used. Yesterday, the process seems to run to completion as viewed in the Windows Command Prompt window, but no files were written to the specified folder.
Below second is the output from running the program from the Command Prompt.
This process yielded the attached text file.
Mark
***@***.***
Output from using the Command Prompt:
C:\RawTools-2.0.7\RawTools-2.0.7>rawtools parse -f JM5072_HCT_Cys_TMT4-1.raw -x
Processing: C:\RawTools-2.0.7\RawTools-2.0.7\JM5072_HCT_Cys_TMT4-1.raw
Determing MS analysis order... Done!
Extracting scan indices: 99%
Unhandled Exception: System.AggregateException: One or more errors occurred. ---> System.NullReferenceException: Object reference not set to an instance of an object.
at RawTools.Algorithms.ExtractData.Extract.<>c__DisplayClass0_0.<ScanIndicesPrecursorsDependents>b__1(IEnumerable`1 batch) in C:\Users\chughes\Documents\bccrc\softwareRepository\RawTools\rawtoolsDev\RawTools\Algorithms\Extraction\ExtractData.cs:line 135
at System.Threading.Tasks.Parallel.<>c__DisplayClass42_0`2.<PartitionerForEachWorker>b__1()
at System.Threading.Tasks.Task.InnerInvokeWithArg(Task childTask)
at System.Threading.Tasks.Task.<>c__DisplayClass176_0.<ExecuteSelfReplicating>b__0(Object <p0>)
--- End of inner exception stack trace ---
at System.Threading.Tasks.Task.ThrowIfExceptional(Boolean includeTaskCanceledExceptions)
at System.Threading.Tasks.Task.Wait(Int32 millisecondsTimeout, CancellationToken cancellationToken)
at System.Threading.Tasks.Parallel.PartitionerForEachWorker[TSource,TLocal](Partitioner`1 source, ParallelOptions parallelOptions, Action`1 simpleBody, Action`2 bodyWithState, Action`3 bodyWithStateAndIndex, Func`4 bodyWithStateAndLocal, Func`5 bodyWithEverything, Func`1 localInit, Action`1 localFinally)
at System.Threading.Tasks.Parallel.ForEachWorker[TSource,TLocal](IEnumerable`1 source, ParallelOptions parallelOptions, Action`1 body, Action`2 bodyWithState, Action`3 bodyWithStateAndIndex, Func`4 bodyWithStateAndLocal, Func`5 bodyWithEverything, Func`1 localInit, Action`1 localFinally)
at System.Threading.Tasks.Parallel.ForEach[TSource](IEnumerable`1 source, ParallelOptions parallelOptions, Action`1 body)
at RawTools.Algorithms.ExtractData.Extract.ScanIndicesPrecursorsDependents(IRawFileThreadManager rawFileAccessor, Int32 MaxProcesses) in C:\Users\chughes\Documents\bccrc\softwareRepository\RawTools\rawtoolsDev\RawTools\Algorithms\Extraction\ExtractData.cs:line 177
at RawTools.WorkFlows.WorkFlowsDDA.UniversalDDA(IRawFileThreadManager rawFileThreadManager, WorkflowParameters parameters, QcDataCollection qcDataCollection) in C:\Users\chughes\Documents\bccrc\softwareRepository\RawTools\rawtoolsDev\RawTools\WorkFlows\DDA.cs:line 71
at RawTools.Program.Run(Dictionary`2 opts) in C:\Users\chughes\Documents\bccrc\softwareRepository\RawTools\rawtoolsDev\RawTools\Program.cs:line 243
at RawTools.Program.Main(String[] args) in C:\Users\chughes\Documents\bccrc\softwareRepository\RawTools\rawtoolsDev\RawTools\Program.cs:line 73
From: Christopher Hughes ***@***.******@***.***>>
Sent: Monday, October 17, 2022 4:56 PM
To: kevinkovalchik/RawTools ***@***.******@***.***>>
Cc: Ross, Mark M (mmr6q) ***@***.******@***.***>>; Author ***@***.******@***.***>>
Subject: Re: [kevinkovalchik/RawTools] Thermo Tribrid data are not parsed (Issue #78)
Hi,
In order to help you I need some more information so I can try to re-create the bug and hopefully solve it. Can you please answer these questions:
Provide details about the raw file you are trying to process (e.g. Is it DDA? MS2 or SPS-MS3)?
Provide details of what commands you have input into the GUI (e.g. which options did you select, which did you not? screenshot here might help).
Does it appear like the command finishes? If there are no files written, it is likely hitting an error. I know in the GUI this can be hard to catch, but there should be a 'rawtools_log.txt' file that gets written into the RawTools directory. Can you please provide me with what is in this file?
Thank you,
Chris
—
Reply to this email directly, view it on GitHub<#78 (comment)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/A3VBU444MCBHHDDXPTGZHVLWDW4MXANCNFSM6AAAAAARHDR34Q>.
You are receiving this because you authored the thread.Message ID: ***@***.******@***.***>>
|
|
So, it looks like QC works but maybe parse doesn't? If you run this one file that is giving an error in the GUI, it will fail. If you run another file, also MS3, with the same parameters does it succeed? I think this is an issue related to orphan scans that I actually recently pushed a solution for (https://github.com/kevinkovalchik/RawTools/tree/branchVersion204), but I haven't incorporated it into a release yet. If you go into your raw file in XCalibur or something, is the last scan in the file an MS2 scan that doesn't have a matched MS3? |
|
I analyzed another SPS-MS3 raw file using the GUI with Parse and Metrics checked, and text file was written. The last scan of that raw file is an MS1 spectrum. The text file reported 0 MS2 scans and many MS1 and MS3 scans.
Thank you.
Mark
From: Christopher Hughes ***@***.***>
Sent: Tuesday, October 18, 2022 1:53 PM
To: kevinkovalchik/RawTools ***@***.***>
Cc: Ross, Mark M (mmr6q) ***@***.***>; Author ***@***.***>
Subject: Re: [kevinkovalchik/RawTools] Thermo Tribrid data are not parsed (Issue #78)
So, it looks like QC works but maybe parse doesn't? If you run this one file that is giving an error in the GUI, it will fail. If you run another file, also MS3, with the same parameters does it succeed?
I think this is an issue related to orphan scans that I actually recently pushed a solution for (https://github.com/kevinkovalchik/RawTools/tree/branchVersion204), but I haven't incorporated it into a release yet. If you go into your raw file in XCalibur or something, is the last scan in the file an MS2 scan that doesn't have a matched MS3?
—
Reply to this email directly, view it on GitHub<#78 (comment)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/A3VBU446GTFEQ5DDGNJH4ZTWD3PXHANCNFSM6AAAAAARHDR34Q>.
You are receiving this because you authored the thread.Message ID: ***@***.******@***.***>>
|
|
That is good, so it is an issue with that one specific file then. The MS2 scans being zero is a bug I know about and will be fixed in the next release, it does not impact the actual processing. Just to clarify, the last scan of the raw file that is failing is an MS1 scan? |
|
A raw file that failed during RawTools parsing has an MS2 spectrum as the last scan.
Mark
From: Christopher Hughes ***@***.***>
Sent: Tuesday, October 18, 2022 4:03 PM
To: kevinkovalchik/RawTools ***@***.***>
Cc: Ross, Mark M (mmr6q) ***@***.***>; Author ***@***.***>
Subject: Re: [kevinkovalchik/RawTools] Thermo Tribrid data are not parsed (Issue #78)
That is good, so it is an issue with that one specific file then. The MS2 scans being zero is a bug I know about and will be fixed in the next release, it does not impact the actual processing.
Just to clarify, the last scan of the raw file that is failing is an MS1 scan?
—
Reply to this email directly, view it on GitHub<#78 (comment)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/A3VBU42EDTHNVY5JNJDDCMTWD366NANCNFSM6AAAAAARHDR34Q>.
You are receiving this because you authored the thread.Message ID: ***@***.***>
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Describe the bug
Briefly describe what you were trying to do and what went wrong. Be general, there is room for specifics below.
Description of raw file
Provide details about the raw file you are trying to process. e.g. Is it DDA? MS2 or SPS-MS3? How long was the run and how big is the file?
Command line arguments
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Command line output
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Screenshots
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Desktop & RawTools information:
Additional context
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