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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
30 stars 11 forks source link

System.IO.FileNotFoundException: Could not find file #7

Open mo-khaife-bot opened 4 years ago

mo-khaife-bot commented 4 years ago

Hi,

I've been using your Github to help me run MaxQuant for the first time on my Mac its been helpful but I've run into the following problem that the image shows (I underlined the important sections for you to see)

after running the gen_mqpar.py file to create my filled out xml file it seems it can't run it

It seems to be looking for a combinedRunInfo, I don't recall when this was even generated

within my combined folder (where it seems to be looking for this combinedRunInfo file) there is only another folder called proc and in there is a #runningTimes.txt file

this is the output for that file: Job Running time [min] Start date Start time End date End time Configuring 0.0171282833333333 22/05/2020 12:15:33 22/05/2020 12:15:34 Assemble run info 0.0175389833333333 22/05/2020 12:15:34 22/05/2020 12:15:35 Finish run info 0.0167910166666667 22/05/2020 12:15:35 22/05/2020 12:15:36 Testing fasta files 0.0168229166666667 22/05/2020 12:15:36 22/05/2020 12:15:37 Testing raw files 0.01744005 22/05/2020 12:15:37 22/05/2020 12:15:38

Can you please provide some advice how to overcome this issue and find or generate this combinedRunInfo file (I have searched for it in my Mac finder & can't seem to find)

please be aware the version of mono I am using is (base) Muhammads-MacBook-Pro:MaxQuant mo2$ mono --version Mono JIT compiler version 6.6.0.166 (2019-08/d9001b5ae70 Wed Feb 12 19:20:16 EST 2020) Copyright (C) 2002-2014 Novell, Inc, Xamarin Inc and Contributors. www.mono-project.com TLS:
SIGSEGV: altstack Notification: kqueue Architecture: amd64 Disabled: none Misc: softdebug Interpreter: yes LLVM: yes(610) Suspend: hybrid GC: sgen (concurrent by default)

Screenshot 2020-05-22 at 13 06 02
atc3 commented 4 years ago

Hi,

Thanks for the detailed info. I haven't run into that issue before, but I suspect it's Mac OSX specific. Note that MacOS is Unix-based, not Linux based, and while I haven't tried to get MaxQuant running in MacOS I can see how this difference would cause problems.

You can use VirtualBox to create an Ubuntu or CentOS VM inside MacOS and run MaxQuant from that instead. That will hopefully solve your issue

Albert

mo-khaife-bot commented 4 years ago

Hi @atc3

I have managed to make use of my universities HPC Cluster which runs on linux to attempt to run MaxQuant from the command line. Please be aware the HPC Cluster has no way of making the MaxQuant GUI work & My Macbook had problems making the GUI work as well as our previous exchange showed.

as I'm using my universities' HPC Cluster they had to make mono in a singularity container for me to make use of it This is the version of mono I have 

[bt19655@nxn31 MaxQuant]$ singularity exec /data/containers/mono/mono.simg mono --version
Mono JIT compiler version 6.10.0.104 (tarball Fri Jun 26 19:38:44 UTC 2020)
Copyright (C) 2002-2014 Novell, Inc, Xamarin Inc and Contributors. www.mono-project.com
    TLS:           __thread
    SIGSEGV:       altstack
    Notifications: epoll
    Architecture:  amd64
    Disabled:      none
    Misc:          softdebug 
    Interpreter:   yes
    LLVM:          yes(610)
    Suspend:       hybrid
    GC:            sgen (concurrent by default)

the version of MaxQuant I am using is:

[bt19655@nxn31 MaxQuant]$ singularity exec /data/containers/mono/mono.simg mono bin/MaxQuantCmd.exe --version
MaxQuantCmd 1.6.14.0

As I mentioned I was not able to geenrate the mqpar.xml in the MAXQuant GUI as my macbook couldn't launch it & the Linux HPC Cluster had no GUI ability - I used the templates for the LabelFree.xml then used the gen_mqpar.py script to fill in the relevant parts which was a success (i called it created_output.xml)

[bt19655@dn146 MaxQuant]$ ./gen_mqpar.py things_file.xml raw_files/ -o created_output.xml -t 6
success!

Let me know if you want the scripts/ contents for any of those files above

but when I tried to run MaxquantCmd.exe on the created_output.xml I found the same problem I had as before where it is looking for file called combinedRunInfo same as before it gets stuck as the feature Detection step

Here is the process 

[bt19655@nxn31 ~]$ singularity exec /data/containers/mono/mono.simg mono MaxQuant/bin/MaxQuantCmd.exe MaxQuant/created_output.xml 
Configuring 
Assemble run info 
Finish run info 
Testing fasta files 
Testing raw files 
Feature detection 
System.IO.FileNotFoundException: Could not find file "/data/home/bt19655/created_output/combined/combinedRunInfo"
File name: '/data/home/bt19655/created_output/combined/combinedRunInfo'
  at System.IO.FileStream..ctor (System.String path, System.IO.FileMode mode, System.IO.FileAccess access, System.IO.FileShare share, System.Int32 bufferSize, System.Boolean anonymous, System.IO.FileOptions options) [0x0019e] in <a17fa1457c5d44f2885ac746c1764ea5>:0 
  at System.IO.FileStream..ctor (System.String path, System.IO.FileMode mode, System.IO.FileAccess access, System.IO.FileShare share) [0x00000] in <a17fa1457c5d44f2885ac746c1764ea5>:0 
  at (wrapper remoting-invoke-with-check) System.IO.FileStream..ctor(string,System.IO.FileMode,System.IO.FileAccess,System.IO.FileShare)
  at BaseLibS.Util.FileUtils.GetBinaryReader (System.String path) [0x00001] in <f3247a32a3864a5f8a6ad694dcd3c773>:0 
  at MaxQuantLibS.Domains.Peptides.Basic.WorkflowModel.ReadRunInfo (MaxQuantLibS.Domains.Peptides.Basic.MaxQuantParams mqpar) [0x00011] in <24104433caef470b80a12c131c31c932>:0 
  at MaxQuantLibS.Domains.Peptides.Basic.WorkflowModel.<GetAllJobs>b__3_4 () [0x00000] in <24104433caef470b80a12c131c31c932>:0 
  at MaxQuantLibS.Domains.Peptides.Work.FeatureDetection+<>c__DisplayClass6_0.<.ctor>b__0 () [0x00000] in <24104433caef470b80a12c131c31c932>:0 
  at QueueingSystem.WorkDispatcher.get_NTasksCached () [0x00016] in <08e6ee3b29764870968395111027c5e7>:0 
  at QueueingSystem.WorkDispatcher.Start () [0x0000c] in <08e6ee3b29764870968395111027c5e7>:0 
  at MaxQuantLibS.Base.MaxQuantWorkspace.Work (System.String infoFolder) [0x000ce] in <24104433caef470b80a12c131c31c932>:0 
  at MaxQuantCmd.CommandLine.Run (System.String mqparFile, System.Int32 partialProcessingFrom, System.Int32 partialProcessingTo, System.Boolean isDryRun, System.Boolean createTemplate, System.String[] changeFolder) [0x005c0] in <3fc63adc8b3544eea9fe25f57593064d>:0 
  at MaxQuantCmd.CommandLine+<>c__DisplayClass0_0.<Run>b__1 (MaxQuantCmd.Options options) [0x00032] in <3fc63adc8b3544eea9fe25f57593064d>:0 
  at CommandLine.ParserResultExtensions.WithParsed[T] (CommandLine.ParserResult`1[T] result, System.Action`1[T] action) [0x00011] in <2f4f1196437d4969b0c1ebbf873d33e2>:0 
  at MaxQuantCmd.CommandLine.Run (System.String[] args) [0x0002a] in <3fc63adc8b3544eea9fe25f57593064d>:0 
  at MaxQuantCmd.Program.Main (System.String[] args) [0x00002] in <3fc63adc8b3544eea9fe25f57593064d>:0 

Unhandled Exception:
System.IO.FileNotFoundException: Could not find file "/data/home/bt19655/created_output/combined/combinedRunInfo"
File name: '/data/home/bt19655/created_output/combined/combinedRunInfo'
  at System.IO.FileStream..ctor (System.String path, System.IO.FileMode mode, System.IO.FileAccess access, System.IO.FileShare share, System.Int32 bufferSize, System.Boolean anonymous, System.IO.FileOptions options) [0x0019e] in <a17fa1457c5d44f2885ac746c1764ea5>:0 
  at System.IO.FileStream..ctor (System.String path, System.IO.FileMode mode, System.IO.FileAccess access, System.IO.FileShare share) [0x00000] in <a17fa1457c5d44f2885ac746c1764ea5>:0 
  at (wrapper remoting-invoke-with-check) System.IO.FileStream..ctor(string,System.IO.FileMode,System.IO.FileAccess,System.IO.FileShare)
  at BaseLibS.Util.FileUtils.GetBinaryReader (System.String path) [0x00001] in <f3247a32a3864a5f8a6ad694dcd3c773>:0 
  at MaxQuantLibS.Domains.Peptides.Basic.WorkflowModel.ReadRunInfo (MaxQuantLibS.Domains.Peptides.Basic.MaxQuantParams mqpar) [0x00011] in <24104433caef470b80a12c131c31c932>:0 
  at MaxQuantLibS.Domains.Peptides.Basic.WorkflowModel.<GetAllJobs>b__3_4 () [0x00000] in <24104433caef470b80a12c131c31c932>:0 
  at MaxQuantLibS.Domains.Peptides.Work.FeatureDetection+<>c__DisplayClass6_0.<.ctor>b__0 () [0x00000] in <24104433caef470b80a12c131c31c932>:0 
  at QueueingSystem.WorkDispatcher.get_NTasksCached () [0x00016] in <08e6ee3b29764870968395111027c5e7>:0 
  at QueueingSystem.WorkDispatcher.Start () [0x0000c] in <08e6ee3b29764870968395111027c5e7>:0 
  at MaxQuantLibS.Base.MaxQuantWorkspace.Work (System.String infoFolder) [0x000ce] in <24104433caef470b80a12c131c31c932>:0 
  at MaxQuantCmd.CommandLine.Run (System.String mqparFile, System.Int32 partialProcessingFrom, System.Int32 partialProcessingTo, System.Boolean isDryRun, System.Boolean createTemplate, System.String[] changeFolder) [0x005c0] in <3fc63adc8b3544eea9fe25f57593064d>:0 
  at MaxQuantCmd.CommandLine+<>c__DisplayClass0_0.<Run>b__1 (MaxQuantCmd.Options options) [0x00032] in <3fc63adc8b3544eea9fe25f57593064d>:0 
  at CommandLine.ParserResultExtensions.WithParsed[T] (CommandLine.ParserResult`1[T] result, System.Action`1[T] action) [0x00011] in <2f4f1196437d4969b0c1ebbf873d33e2>:0 
  at MaxQuantCmd.CommandLine.Run (System.String[] args) [0x0002a] in <3fc63adc8b3544eea9fe25f57593064d>:0 
  at MaxQuantCmd.Program.Main (System.String[] args) [0x0001e] in <3fc63adc8b3544eea9fe25f57593064d>:0 
[ERROR] FATAL UNHANDLED EXCEPTION: System.IO.FileNotFoundException: Could not find file "/data/home/bt19655/created_output/combined/combinedRunInfo"
File name: '/data/home/bt19655/created_output/combined/combinedRunInfo'
  at System.IO.FileStream..ctor (System.String path, System.IO.FileMode mode, System.IO.FileAccess access, System.IO.FileShare share, System.Int32 bufferSize, System.Boolean anonymous, System.IO.FileOptions options) [0x0019e] in <a17fa1457c5d44f2885ac746c1764ea5>:0 
  at System.IO.FileStream..ctor (System.String path, System.IO.FileMode mode, System.IO.FileAccess access, System.IO.FileShare share) [0x00000] in <a17fa1457c5d44f2885ac746c1764ea5>:0 
  at (wrapper remoting-invoke-with-check) System.IO.FileStream..ctor(string,System.IO.FileMode,System.IO.FileAccess,System.IO.FileShare)
  at BaseLibS.Util.FileUtils.GetBinaryReader (System.String path) [0x00001] in <f3247a32a3864a5f8a6ad694dcd3c773>:0 
  at MaxQuantLibS.Domains.Peptides.Basic.WorkflowModel.ReadRunInfo (MaxQuantLibS.Domains.Peptides.Basic.MaxQuantParams mqpar) [0x00011] in <24104433caef470b80a12c131c31c932>:0 
  at MaxQuantLibS.Domains.Peptides.Basic.WorkflowModel.<GetAllJobs>b__3_4 () [0x00000] in <24104433caef470b80a12c131c31c932>:0 
  at MaxQuantLibS.Domains.Peptides.Work.FeatureDetection+<>c__DisplayClass6_0.<.ctor>b__0 () [0x00000] in <24104433caef470b80a12c131c31c932>:0 
  at QueueingSystem.WorkDispatcher.get_NTasksCached () [0x00016] in <08e6ee3b29764870968395111027c5e7>:0 
  at QueueingSystem.WorkDispatcher.Start () [0x0000c] in <08e6ee3b29764870968395111027c5e7>:0 
  at MaxQuantLibS.Base.MaxQuantWorkspace.Work (System.String infoFolder) [0x000ce] in <24104433caef470b80a12c131c31c932>:0 
  at MaxQuantCmd.CommandLine.Run (System.String mqparFile, System.Int32 partialProcessingFrom, System.Int32 partialProcessingTo, System.Boolean isDryRun, System.Boolean createTemplate, System.String[] changeFolder) [0x005c0] in <3fc63adc8b3544eea9fe25f57593064d>:0 
  at MaxQuantCmd.CommandLine+<>c__DisplayClass0_0.<Run>b__1 (MaxQuantCmd.Options options) [0x00032] in <3fc63adc8b3544eea9fe25f57593064d>:0 
  at CommandLine.ParserResultExtensions.WithParsed[T] (CommandLine.ParserResult`1[T] result, System.Action`1[T] action) [0x00011] in <2f4f1196437d4969b0c1ebbf873d33e2>:0 
  at MaxQuantCmd.CommandLine.Run (System.String[] args) [0x0002a] in <3fc63adc8b3544eea9fe25f57593064d>:0 
  at MaxQuantCmd.Program.Main (System.String[] args) [0x0001e] in <3fc63adc8b3544eea9fe25f57593064d>:0

unfortunately there is no "/data/home/bt19655/created_output/combined/combinedRunInfo" but there is a "/data/home/bt19655/created_output/combined/proc" which has a #runningTimes.txt

below id the contents of the combined/proc #runningTimes.txt

Job     Running time [min]  Start date  Start time  End date        End time
Configuring     0.0171348166666667  19/05/2020  11:58:12        19/05/2020  11:58:13
Assemble run info   0.0168454833333333  19/05/2020  11:58:13        19/05/2020  11:58:14
Finish run info         0.0168535333333333  19/05/2020  11:58:14        19/05/2020  11:58:15
Testing fasta files     0.0168551833333333  19/05/2020  11:58:15        19/05/2020  11:58:16
Testing raw files   0.0168414833333333  19/05/2020  11:58:16        19/05/2020  11:58:17

I'm confused how to progress please advice is it worth asking in the Maxquant Google Group???

Thanks for any help you are able to provide

atc3 commented 4 years ago

Hi,

Thanks for the update. I haven't run into this error before, and I don't have any experience with Singularity (the shell script outputs in this repo are designed for SLURM). It would probably be best to ask the Google Group or your Singularity admins.

Note that the MaxQuant GUI was not ported to Linux - only the command-line version is. So you won't be able to open the GUI on any Linux or OSX machine. I used to edit the mqpar.xml files on my Windows machine, then move those files to the Linux machine I was running MaxQuant on.

Sorry I can't be of any more help, and good luck,

Albert