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atc3 / maxquant_linux_guide

A guide to running MaxQuant in Linux
http://atchen.me/research/2019/03/21/mq-linux.html
MIT License
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Another UNHANDLED EXCEPTION #3

Open doggygugu opened 4 years ago

doggygugu commented 4 years ago

I tried to run the following script, but getting errors too. $mono MaxQuant/bin/MaxQuantCmd.exe data/mqpar.xml Configuring

Unhandled Exception: System.Exception: Exception during execution of external process: 5406 at BaseLibS.Util.WorkDispatcher.ProcessSingleRunExternalProcess (System.Int32 taskIndex, System.Int32 threadIndex) [0x001a1] in <3fc1eb7cc45041de8ce7f41aa00f3311>:0 at BaseLibS.Util.WorkDispatcher.DoWork (System.Int32 taskIndex, System.Int32 threadIndex) [0x0001e] in <3fc1eb7cc45041de8ce7f41aa00f3311>:0 at BaseLibS.Util.WorkDispatcher.Work (System.Object threadIndex) [0x00054] in <3fc1eb7cc45041de8ce7f41aa00f3311>:0 at System.Threading.ThreadHelper.ThreadStart_Context (System.Object state) [0x00025] in :0 at System.Threading.ExecutionContext.RunInternal (System.Threading.ExecutionContext executionContext, System.Threading.ContextCallback callback, System.Object state, System.Boolean preserveSyncCtx) [0x00071] in :0 at System.Threading.ExecutionContext.Run (System.Threading.ExecutionContext executionContext, System.Threading.ContextCallback callback, System.Object state, System.Boolean preserveSyncCtx) [0x00000] in :0 at System.Threading.ExecutionContext.Run (System.Threading.ExecutionContext executionContext, System.Threading.ContextCallback callback, System.Object state) [0x0002b] in :0 at System.Threading.ThreadHelper.ThreadStart (System.Object obj) [0x0000f] in :0 [ERROR] FATAL UNHANDLED EXCEPTION: System.Exception: Exception during execution of external process: 5406 at BaseLibS.Util.WorkDispatcher.ProcessSingleRunExternalProcess (System.Int32 taskIndex, System.Int32 threadIndex) [0x001a1] in <3fc1eb7cc45041de8ce7f41aa00f3311>:0 at BaseLibS.Util.WorkDispatcher.DoWork (System.Int32 taskIndex, System.Int32 threadIndex) [0x0001e] in <3fc1eb7cc45041de8ce7f41aa00f3311>:0 at BaseLibS.Util.WorkDispatcher.Work (System.Object threadIndex) [0x00054] in <3fc1eb7cc45041de8ce7f41aa00f3311>:0 at System.Threading.ThreadHelper.ThreadStart_Context (System.Object state) [0x00025] in :0 at System.Threading.ExecutionContext.RunInternal (System.Threading.ExecutionContext executionContext, System.Threading.ContextCallback callback, System.Object state, System.Boolean preserveSyncCtx) [0x00071] in :0 at System.Threading.ExecutionContext.Run (System.Threading.ExecutionContext executionContext, System.Threading.ContextCallback callback, System.Object state, System.Boolean preserveSyncCtx) [0x00000] in :0 at System.Threading.ExecutionContext.Run (System.Threading.ExecutionContext executionContext, System.Threading.ContextCallback callback, System.Object state) [0x0002b] in :0 at System.Threading.ThreadHelper.ThreadStart (System.Object obj) [0x0000f] in :0

I already checked the combined/proc folder as you said before, but only found a '#runningTimes.txt'. This file is empty.

atc3 commented 4 years ago

Can you provide some more info? The mqpar.xml file and vendor raw data format would be helpful. Is this a linux specific problem, or does it also happen on the Windows MaxQuant as well?

doggygugu commented 4 years ago

mqpar.txt This is the mqpar.xml file. The raw data is a .raw format . They are LTQ-Orbitrap Velos Pro mass spectrometer data. This problem just happened in Linux. We ran it well in Windows. Thank you very much!

atc3 commented 4 years ago

The paths specified in the mqpar.xml file aren't valid unix paths. 

<fastaFilePath>home/yajie/reference/uniprot-proteome%3AUP000005640.fasta</fastaFilePath>

Unix paths need to begin with the root, /, so change the above to:

<fastaFilePath>/home/yajie/reference/uniprot-proteome%3AUP000005640.fasta</fastaFilePath>
<filePaths>
    <string>home\yajie\data\080516-PC-mice-MP-control-IMAC-1_160805212051.raw</string>
...

Unix paths are delimited by /, not \, so change the above to:

<filePaths>
    <string>/home/yajie/data/080516-PC-mice-MP-control-IMAC-1_160805212051.raw</string>
...

And do the same for all file paths in the file

doggygugu commented 4 years ago

`taogroup@taogroup-Precision-7920-Tower:~/yajie$ mono MaxQuant/bin/MaxQuantCmd.exe data/mqpar.xml Configuring Testing fasta files Testing raw files Feature detection

Unhandled Exception: System.Exception: Exception during execution of external process: 19014 at BaseLibS.Util.WorkDispatcher.ProcessSingleRunExternalProcess (System.Int32 taskIndex, System.Int32 threadIndex) [0x001a1] in <3fc1eb7cc45041de8ce7f41aa00f3311>:0 at BaseLibS.Util.WorkDispatcher.DoWork (System.Int32 taskIndex, System.Int32 threadIndex) [0x0001e] in <3fc1eb7cc45041de8ce7f41aa00f3311>:0 at BaseLibS.Util.WorkDispatcher.Work (System.Object threadIndex) [0x00054] in <3fc1eb7cc45041de8ce7f41aa00f3311>:0 at System.Threading.ThreadHelper.ThreadStart_Context (System.Object state) [0x00025] in :0 at System.Threading.ExecutionContext.RunInternal (System.Threading.ExecutionContext executionContext, System.Threading.ContextCallback callback, System.Object state, System.Boolean preserveSyncCtx) [0x00071] in :0 at System.Threading.ExecutionContext.Run (System.Threading.ExecutionContext executionContext, System.Threading.ContextCallback callback, System.Object state, System.Boolean preserveSyncCtx) [0x00000] in :0 at System.Threading.ExecutionContext.Run (System.Threading.ExecutionContext executionContext, System.Threading.ContextCallback callback, System.Object state) [0x0002b] in :0 at System.Threading.ThreadHelper.ThreadStart (System.Object obj) [0x0000f] in :0 [ERROR] FATAL UNHANDLED EXCEPTION: System.Exception: Exception during execution of external process: 19014 at BaseLibS.Util.WorkDispatcher.ProcessSingleRunExternalProcess (System.Int32 taskIndex, System.Int32 threadIndex) [0x001a1] in <3fc1eb7cc45041de8ce7f41aa00f3311>:0 at BaseLibS.Util.WorkDispatcher.DoWork (System.Int32 taskIndex, System.Int32 threadIndex) [0x0001e] in <3fc1eb7cc45041de8ce7f41aa00f3311>:0 at BaseLibS.Util.WorkDispatcher.Work (System.Object threadIndex) [0x00054] in <3fc1eb7cc45041de8ce7f41aa00f3311>:0 at System.Threading.ThreadHelper.ThreadStart_Context (System.Object state) [0x00025] in :0 at System.Threading.ExecutionContext.RunInternal (System.Threading.ExecutionContext executionContext, System.Threading.ContextCallback callback, System.Object state, System.Boolean preserveSyncCtx) [0x00071] in :0 at System.Threading.ExecutionContext.Run (System.Threading.ExecutionContext executionContext, System.Threading.ContextCallback callback, System.Object state, System.Boolean preserveSyncCtx) [0x00000] in :0 at System.Threading.ExecutionContext.Run (System.Threading.ExecutionContext executionContext, System.Threading.ContextCallback callback, System.Object state) [0x0002b] in :0 at System.Threading.ThreadHelper.ThreadStart (System.Object obj) [0x0000f] in :0 ` It still had some problem.

doggygugu commented 4 years ago

I found two error messages in the combined/proc folder. image

id      0
start   02/01/2020 10:00:31
title   Feature_detection (1/9)
description     /home/taogroup/yajie/data/080516-PC-mice-MP-control-IMAC-1_160805212051.raw
error   /home/taogroup/yajie/data/080516-PC-mice-MP-control-IMAC-1_160805212051.raw_The given key 'ITMS' was not present in the dictionary._  at System.Collections.Generic.Dictionary`2[TKey,TValue].get_Item (TKey key) [0x0001e] in <d2ec5c92492f4d6ba8c422bdf574b786>:0 _  at MaxQuantPLibS.Search.MsmsFileWriting.PrepareMsms (MaxQuantPLibS.Data.RunLayer run, BaseLibS.Ms.RawFileLayer rawFile, MaxQuantPLibS.Data.PlistData.PeakListLayerData peakList, MaxQuantPLibS.Basic.GroupParams param, System.Boolean firstSearch, MaxQuantPLibS.Basic.MaxQuantParams mqpar) [0x003eb] in <e0d3ea923fb542858289d68af3ae5a27>:0 _  at MaxQuantPLibS.Features.FeatureDetectionUtil.ProcessMsms (MaxQuantPLibS.Basic.MaxQuantParams mqpar, MaxQuantPLibS.Basic.GroupParams param, MaxQuantPLibS.Data.RunLayer run, BaseLibS.Ms.RawFileLayer rawFile, MaxQuantPLibS.Data.PlistData.PeakListLayerData peakList) [0x00014] in <e0d3ea923fb542858289d68af3ae5a27>:0 _  at MaxQuantPLibS.Features.FeatureDetectionUtil.DetectFeatures (MaxQuantPLibS.Basic.MaxQuantParams mqpar, MaxQuantPLibS.Basic.GroupParams param, System.String filename, System.Boolean positiveMode) [0x001bc] in <e0d3ea923fb542858289d68af3ae5a27>:0 _  at MaxQuantPLibS.Features.FeatureDetectionUtil.DetectFeatures (System.String mqparFile, System.Int32 fileIndex) [0x0018d] in <e0d3ea923fb542858289d68af3ae5a27>:0 _  at MaxQuantPLibS.Work.FeatureDetection.Calculation (System.String[] args, BaseLibS.Util.Responder responder) [0x0000c] in <e0d3ea923fb542858289d68af3ae5a27>:0 _  at MaxQuantPLibS.Work.MaxQuantWorkDispatcherUtil.PerformTask (System.Int32 taskType, System.String[] args, BaseLibS.Util.Responder responder) [0x00007] in <e0d3ea923fb542858289d68af3ae5a27>:0 _  at MaxQuantTask.Program.Function (System.String[] args, BaseLibS.Util.Responder responder) [0x00012] in <a9a7ab44566440088bf38b1365d644dc>:0 _  at Utils.Util.ExternalProcess.Run (System.String[] args, System.Boolean debug) [0x000af] in <13cd68fb3f5d4831b26fc0f070437c6f>:0
end     02/01/2020 10:01:39
id      0
start   02/01/2020 10:00:31
title   Feature_detection (2/9)
description     /home/taogroup/yajie/data/080516-PC-mice-MP-control-IMAC-2.raw
error   /home/taogroup/yajie/data/080516-PC-mice-MP-control-IMAC-2.raw_The given key 'ITMS' was not present in the dictionary._  at System.Collections.Generic.Dictionary`2[TKey,TValue].get_Item (TKey key) [0x0001e] in <d2ec5c92492f4d6ba8c422bdf574b786>:0 _  at MaxQuantPLibS.Search.MsmsFileWriting.PrepareMsms (MaxQuantPLibS.Data.RunLayer run, BaseLibS.Ms.RawFileLayer rawFile, MaxQuantPLibS.Data.PlistData.PeakListLayerData peakList, MaxQuantPLibS.Basic.GroupParams param, System.Boolean firstSearch, MaxQuantPLibS.Basic.MaxQuantParams mqpar) [0x003eb] in <e0d3ea923fb542858289d68af3ae5a27>:0 _  at MaxQuantPLibS.Features.FeatureDetectionUtil.ProcessMsms (MaxQuantPLibS.Basic.MaxQuantParams mqpar, MaxQuantPLibS.Basic.GroupParams param, MaxQuantPLibS.Data.RunLayer run, BaseLibS.Ms.RawFileLayer rawFile, MaxQuantPLibS.Data.PlistData.PeakListLayerData peakList) [0x00014] in <e0d3ea923fb542858289d68af3ae5a27>:0 _  at MaxQuantPLibS.Features.FeatureDetectionUtil.DetectFeatures (MaxQuantPLibS.Basic.MaxQuantParams mqpar, MaxQuantPLibS.Basic.GroupParams param, System.String filename, System.Boolean positiveMode) [0x001bc] in <e0d3ea923fb542858289d68af3ae5a27>:0 _  at MaxQuantPLibS.Features.FeatureDetectionUtil.DetectFeatures (System.String mqparFile, System.Int32 fileIndex) [0x0018d] in <e0d3ea923fb542858289d68af3ae5a27>:0 _  at MaxQuantPLibS.Work.FeatureDetection.Calculation (System.String[] args, BaseLibS.Util.Responder responder) [0x0000c] in <e0d3ea923fb542858289d68af3ae5a27>:0 _  at MaxQuantPLibS.Work.MaxQuantWorkDispatcherUtil.PerformTask (System.Int32 taskType, System.String[] args, BaseLibS.Util.Responder responder) [0x00007] in <e0d3ea923fb542858289d68af3ae5a27>:0 _  at MaxQuantTask.Program.Function (System.String[] args, BaseLibS.Util.Responder responder) [0x00012] in <a9a7ab44566440088bf38b1365d644dc>:0 _  at Utils.Util.ExternalProcess.Run (System.String[] args, System.Boolean debug) [0x000af] in <13cd68fb3f5d4831b26fc0f070437c6f>:0
end     02/01/2020 10:01:40
atc3 commented 4 years ago

I haven't seen that error before, and the ITMS entry exists in the mqpar.xml file, so I don't know exactly what it's complaining about.

Is the MQ version on Linux the same as the one on windows where this mqpar.xml file worked? I know they change the format of the mqpar.xml file between versions, that could be the issue.

doggygugu commented 4 years ago

The mqpar.xml file works well on Windows. I tried to use gen_mqpar.py. It has errors like this: image