atc3
Another UNHANDLED EXCEPTION
I tried to run the following script, but getting errors too. $mono MaxQuant/bin/MaxQuantCmd.exe data/mqpar.xml Configuring
Unhandled Exception:
System.Exception: Exception during execution of external process: 5406
at BaseLibS.Util.WorkDispatcher.ProcessSingleRunExternalProcess (System.Int32 taskIndex, System.Int32 threadIndex) [0x001a1] in <3fc1eb7cc45041de8ce7f41aa00f3311>:0
at BaseLibS.Util.WorkDispatcher.DoWork (System.Int32 taskIndex, System.Int32 threadIndex) [0x0001e] in <3fc1eb7cc45041de8ce7f41aa00f3311>:0
at BaseLibS.Util.WorkDispatcher.Work (System.Object threadIndex) [0x00054] in <3fc1eb7cc45041de8ce7f41aa00f3311>:0
at System.Threading.ThreadHelper.ThreadStart_Context (System.Object state) [0x00025] in
I already checked the combined/proc folder as you said before, but only found a '#runningTimes.txt'. This file is empty.
Can you provide some more info? The mqpar.xml file and vendor raw data format would be helpful. Is this a linux specific problem, or does it also happen on the Windows MaxQuant as well?
mqpar.txt This is the mqpar.xml file. The raw data is a .raw format . They are LTQ-Orbitrap Velos Pro mass spectrometer data. This problem just happened in Linux. We ran it well in Windows. Thank you very much!
The paths specified in the mqpar.xml file aren't valid unix paths.
<fastaFilePath>home/yajie/reference/uniprot-proteome%3AUP000005640.fasta</fastaFilePath>
Unix paths need to begin with the root, /, so change the above to:
<fastaFilePath>/home/yajie/reference/uniprot-proteome%3AUP000005640.fasta</fastaFilePath>
<filePaths>
<string>home\yajie\data\080516-PC-mice-MP-control-IMAC-1_160805212051.raw</string>
...
Unix paths are delimited by /, not \, so change the above to:
<filePaths>
<string>/home/yajie/data/080516-PC-mice-MP-control-IMAC-1_160805212051.raw</string>
...
And do the same for all file paths in the file
`taogroup@taogroup-Precision-7920-Tower:~/yajie$ 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
I found two error messages in the combined/proc folder.
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
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.
The mqpar.xml file works well on Windows. I tried to use gen_mqpar.py. It has errors like this:
