Compilation help / error CS2001

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Compilation help / error CS2001

Chandler
I would like to install this program on our Linux machines for our users:
https://github.com/MicrosoftGenomics/ConPADE

but I am running into the error "CSC: error CS2001: Source file
'/opt/MicrosoftGenomics/ConPADE/Properties/AssemblyInfo.cs' could not be
found."

The OS is RHEL 6.8 and i have installed mono-complete 5.0.1 using the
"CentOS 6" repositories.  I copied the files from src/* to the root dir,
since it was complaining about not finding those files, but maybe i'm
just not doing it right with xbuild?  Or is it something the developer
needs to address?  See below for full output.

Thanks,
Chandler / Systems Administrator
Arizona Genomics Institute
www.genome.arizona.edu
--

$ cd /opt/MicrosoftGenomics/ConPADE/
/opt/MicrosoftGenomics/ConPADE$ cp src/* .
/opt/MicrosoftGenomics/ConPADE$ xbuild ConPADE.csproj

 >>>> xbuild tool is deprecated and will be removed in future updates,
use msbuild instead <<<<

XBuild Engine Version 14.0
Mono, Version 5.0.1.1
Copyright (C) 2005-2013 Various Mono authors

Build started 5/30/2017 5:18:13 PM.
__________________________________________________
Project "/opt/MicrosoftGenomics/ConPADE/ConPADE.csproj" (default target(s)):
        Target PrepareForBuild:
                Configuration: Debug Platform: x86
        Target GenerateSatelliteAssemblies:
        No input files were specified for target GenerateSatelliteAssemblies,
skipping.
        Target _GenerateTargetFrameworkMonikerAttribute:
        Skipping target "_GenerateTargetFrameworkMonikerAttribute" because its
outputs are up-to-date.
        Target CoreCompile:
                Tool /usr/lib/mono/4.5/csc.exe execution started with arguments:
/noconfig /debug:full /debug:portable /optimize-
/out:obj/x86/Debug/ConPADE.exe ConPADE.cs Properties/AssemblyInfo.cs
Read.cs obj/x86/Debug/.NETFramework,Version=v4.5.AssemblyAttribute.cs
/target:exe /define:"DEBUG;TRACE" /doc:bin/Debug/ConPADE.XML /nostdlib
/platform:x86 /reference:./Bio.Core.dll /reference:./Bio.Desktop.dll
/reference:./Bio.Platform.Helpers.dll
/reference:/usr/lib/mono/4.5-api/System.dll
/reference:/usr/lib/mono/4.5-api/System.Xml.Linq.dll
/reference:/usr/lib/mono/4.5-api/System.Data.DataSetExtensions.dll
/reference:/usr/lib/mono/4.5-api/Microsoft.CSharp.dll
/reference:/usr/lib/mono/4.5-api/System.Data.dll
/reference:/usr/lib/mono/4.5-api/System.Xml.dll
/reference:/usr/lib/mono/4.5-api/System.Core.dll
/reference:/usr/lib/mono/4.5-api//mscorlib.dll
/reference:/usr/lib/mono/4.5-api/Facades/System.Collections.Concurrent.dll
/reference:/usr/lib/mono/4.5-api/Facades/System.Collections.dll
/reference:/usr/lib/mono/4.5-api/Facades/System.ComponentModel.Annotations.dll
/reference:/usr/lib/mono/4.5-api/Facades/System.ComponentModel.EventBasedAsync.dll
/reference:/usr/lib/mono/4.5-api/Facades/System.ComponentModel.dll
/reference:/usr/lib/mono/4.5-api/Facades/System.Diagnostics.Contracts.dll
/reference:/usr/lib/mono/4.5-api/Facades/System.Diagnostics.Debug.dll
/reference:/usr/lib/mono/4.5-api/Facades/System.Diagnostics.Tools.dll
/reference:/usr/lib/mono/4.5-api/Facades/System.Diagnostics.Tracing.dll
/reference:/usr/lib/mono/4.5-api/Facades/System.Dynamic.Runtime.dll
/reference:/usr/lib/mono/4.5-api/Facades/System.Globalization.dll
/reference:/usr/lib/mono/4.5-api/Facades/System.IO.dll
/reference:/usr/lib/mono/4.5-api/Facades/System.Linq.Expressions.dll
/reference:/usr/lib/mono/4.5-api/Facades/System.Linq.Parallel.dll
/reference:/usr/lib/mono/4.5-api/Facades/System.Linq.Queryable.dll
/reference:/usr/lib/mono/4.5-api/Facades/System.Linq.dll
/reference:/usr/lib/mono/4.5-api/Facades/System.Net.NetworkInformation.dll
/reference:/usr/lib/mono/4.5-api/Facades/System.Net.Primitives.dll
/reference:/usr/lib/mono/4.5-api/Facades/System.Net.Requests.dll
/reference:/usr/lib/mono/4.5-api/Facades/System.ObjectModel.dll
/reference:/usr/lib/mono/4.5-api/Facades/System.Reflection.Emit.ILGeneration.dll
/reference:/usr/lib/mono/4.5-api/Facades/System.Reflection.Emit.Lightweight.dll
/reference:/usr/lib/mono/4.5-api/Facades/System.Reflection.Emit.dll
/reference:/usr/lib/mono/4.5-api/Facades/System.Reflection.Extensions.dll
/reference:/usr/lib/mono/4.5-api/Facades/System.Reflection.Primitives.dll
/reference:/usr/lib/mono/4.5-api/Facades/System.Reflection.dll
/reference:/usr/lib/mono/4.5-api/Facades/System.Resources.ResourceManager.dll
/reference:/usr/lib/mono/4.5-api/Facades/System.Runtime.Extensions.dll
/reference:/usr/lib/mono/4.5-api/Facades/System.Runtime.InteropServices.WindowsRuntime.dll
/reference:/usr/lib/mono/4.5-api/Facades/System.Runtime.InteropServices.dll
/reference:/usr/lib/mono/4.5-api/Facades/System.Runtime.Numerics.dll
/reference:/usr/lib/mono/4.5-api/Facades/System.Runtime.Serialization.Json.dll
/reference:/usr/lib/mono/4.5-api/Facades/System.Runtime.Serialization.Primitives.dll
/reference:/usr/lib/mono/4.5-api/Facades/System.Runtime.Serialization.Xml.dll
/reference:/usr/lib/mono/4.5-api/Facades/System.Runtime.dll
/reference:/usr/lib/mono/4.5-api/Facades/System.Security.Principal.dll
/reference:/usr/lib/mono/4.5-api/Facades/System.ServiceModel.Duplex.dll
/reference:/usr/lib/mono/4.5-api/Facades/System.ServiceModel.Http.dll
/reference:/usr/lib/mono/4.5-api/Facades/System.ServiceModel.NetTcp.dll
/reference:/usr/lib/mono/4.5-api/Facades/System.ServiceModel.Primitives.dll
/reference:/usr/lib/mono/4.5-api/Facades/System.ServiceModel.Security.dll
/reference:/usr/lib/mono/4.5-api/Facades/System.Text.Encoding.Extensions.dll
/reference:/usr/lib/mono/4.5-api/Facades/System.Text.Encoding.dll
/reference:/usr/lib/mono/4.5-api/Facades/System.Text.RegularExpressions.dll
/reference:/usr/lib/mono/4.5-api/Facades/System.Threading.Tasks.Parallel.dll
/reference:/usr/lib/mono/4.5-api/Facades/System.Threading.Tasks.dll
/reference:/usr/lib/mono/4.5-api/Facades/System.Threading.dll
/reference:/usr/lib/mono/4.5-api/Facades/System.Xml.ReaderWriter.dll
/reference:/usr/lib/mono/4.5-api/Facades/System.Xml.XDocument.dll
/reference:/usr/lib/mono/4.5-api/Facades/System.Xml.XmlSerializer.dll
/warn:4
                Microsoft (R) Visual C# Compiler version 2.0.0.61404
                Copyright (C) Microsoft Corporation. All rights reserved.
CSC: error CS2001: Source file
'/opt/MicrosoftGenomics/ConPADE/Properties/AssemblyInfo.cs' could not be
found.
        Task "Csc" execution -- FAILED
        Done building target "CoreCompile" in project
"/opt/MicrosoftGenomics/ConPADE/ConPADE.csproj".-- FAILED
Done building project "/opt/MicrosoftGenomics/ConPADE/ConPADE.csproj".--
FAILED

Build FAILED.
Errors:

/opt/MicrosoftGenomics/ConPADE/ConPADE.csproj (default targets) ->
/usr/lib/mono/xbuild/14.0/bin/Microsoft.CSharp.targets (CoreCompile
target) ->

        CSC: error CS2001: Source file
'/opt/MicrosoftGenomics/ConPADE/Properties/AssemblyInfo.cs' could not be
found.

         0 Warning(s)
         1 Error(s)

Time Elapsed 00:00:01.5263370
/opt/MicrosoftGenomics/ConPADE$

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Re: Compilation help / error CS2001

Rafael Teixeira
Hi Chandler

The source is simply incomplete, you won't be able to build with the part the was commited to GitHub, you can try to contact the maintainers, but you can also simply create a dummy AssembyInfo.cs inside a Properties folder and try to compile, although it may not be enough to make it work. 

Anyway, the program is already compiled up there in GitHub, so you can simply run it with:

mono ConPADE.exe -bamName TestData.bam

As it is a console program and uses mainly the .NET Bio libraries that are compatible with Mono, so it should work. 

Please note that Linux doesn't support Windows batch files (.bat) and that you always need to call mono to run the program (unless you configure binfmt to automate things, which I don't recommend), it is preferable to write a shell script (normally a bash script) as a wrapper to make it easier to call the program. Something like a file named conpade in some folder in the PATH, marked with the executable bit (chmod +x) and with content similar to:

#!/bin/sh
/usr/bin/mono /opt/MicrosoftGenomics/ConPADE/ConPADE.exe "$@"

Then you would be able to simply use like in Windows:

conpade TestData.bam

Remember that Linux is case-sensitive, so 'conpade' is different from 'ConPADE'.

For more details, look at the old but still mostly valid documentation at http://www.mono-project.com/archived/guiderunning_mono_applications/

Hope it helps,

Rafael Teixeira
O..:.)oooo

On Tue, May 30, 2017 at 9:36 PM, Chandler <[hidden email]> wrote:
I would like to install this program on our Linux machines for our users:
https://github.com/MicrosoftGenomics/ConPADE

but I am running into the error "CSC: error CS2001: Source file '/opt/MicrosoftGenomics/ConPADE/Properties/AssemblyInfo.cs' could not be found."

The OS is RHEL 6.8 and i have installed mono-complete 5.0.1 using the "CentOS 6" repositories.  I copied the files from src/* to the root dir, since it was complaining about not finding those files, but maybe i'm just not doing it right with xbuild?  Or is it something the developer needs to address?  See below for full output.

Thanks,
Chandler / Systems Administrator
Arizona Genomics Institute
www.genome.arizona.edu
--

$ cd /opt/MicrosoftGenomics/ConPADE/
/opt/MicrosoftGenomics/ConPADE$ cp src/* .
/opt/MicrosoftGenomics/ConPADE$ xbuild ConPADE.csproj

>>>> xbuild tool is deprecated and will be removed in future updates, use msbuild instead <<<<

XBuild Engine Version 14.0
Mono, Version 5.0.1.1
Copyright (C) 2005-2013 Various Mono authors

Build started 5/30/2017 5:18:13 PM.
__________________________________________________
Project "/opt/MicrosoftGenomics/ConPADE/ConPADE.csproj" (default target(s)):
        Target PrepareForBuild:
                Configuration: Debug Platform: x86
        Target GenerateSatelliteAssemblies:
        No input files were specified for target GenerateSatelliteAssemblies, skipping.
        Target _GenerateTargetFrameworkMonikerAttribute:
        Skipping target "_GenerateTargetFrameworkMonikerAttribute" because its outputs are up-to-date.
        Target CoreCompile:
                Tool /usr/lib/mono/4.5/csc.exe execution started with arguments: /noconfig /debug:full /debug:portable /optimize- /out:obj/x86/Debug/ConPADE.exe ConPADE.cs Properties/AssemblyInfo.cs Read.cs obj/x86/Debug/.NETFramework,Version=v4.5.AssemblyAttribute.cs /target:exe /define:"DEBUG;TRACE" /doc:bin/Debug/ConPADE.XML /nostdlib /platform:x86 /reference:./Bio.Core.dll /reference:./Bio.Desktop.dll /reference:./Bio.Platform.Helpers.dll /reference:/usr/lib/mono/4.5-api/System.dll /reference:/usr/lib/mono/4.5-api/System.Xml.Linq.dll /reference:/usr/lib/mono/4.5-api/System.Data.DataSetExtensions.dll /reference:/usr/lib/mono/4.5-api/Microsoft.CSharp.dll /reference:/usr/lib/mono/4.5-api/System.Data.dll /reference:/usr/lib/mono/4.5-api/System.Xml.dll /reference:/usr/lib/mono/4.5-api/System.Core.dll /reference:/usr/lib/mono/4.5-api//mscorlib.dll /reference:/usr/lib/mono/4.5-api/Facades/System.Collections.Concurrent.dll /reference:/usr/lib/mono/4.5-api/Facades/System.Collections.dll /reference:/usr/lib/mono/4.5-api/Facades/System.ComponentModel.Annotations.dll /reference:/usr/lib/mono/4.5-api/Facades/System.ComponentModel.EventBasedAsync.dll /reference:/usr/lib/mono/4.5-api/Facades/System.ComponentModel.dll /reference:/usr/lib/mono/4.5-api/Facades/System.Diagnostics.Contracts.dll /reference:/usr/lib/mono/4.5-api/Facades/System.Diagnostics.Debug.dll /reference:/usr/lib/mono/4.5-api/Facades/System.Diagnostics.Tools.dll /reference:/usr/lib/mono/4.5-api/Facades/System.Diagnostics.Tracing.dll /reference:/usr/lib/mono/4.5-api/Facades/System.Dynamic.Runtime.dll /reference:/usr/lib/mono/4.5-api/Facades/System.Globalization.dll /reference:/usr/lib/mono/4.5-api/Facades/System.IO.dll /reference:/usr/lib/mono/4.5-api/Facades/System.Linq.Expressions.dll /reference:/usr/lib/mono/4.5-api/Facades/System.Linq.Parallel.dll /reference:/usr/lib/mono/4.5-api/Facades/System.Linq.Queryable.dll /reference:/usr/lib/mono/4.5-api/Facades/System.Linq.dll /reference:/usr/lib/mono/4.5-api/Facades/System.Net.NetworkInformation.dll /reference:/usr/lib/mono/4.5-api/Facades/System.Net.Primitives.dll /reference:/usr/lib/mono/4.5-api/Facades/System.Net.Requests.dll /reference:/usr/lib/mono/4.5-api/Facades/System.ObjectModel.dll /reference:/usr/lib/mono/4.5-api/Facades/System.Reflection.Emit.ILGeneration.dll /reference:/usr/lib/mono/4.5-api/Facades/System.Reflection.Emit.Lightweight.dll /reference:/usr/lib/mono/4.5-api/Facades/System.Reflection.Emit.dll /reference:/usr/lib/mono/4.5-api/Facades/System.Reflection.Extensions.dll /reference:/usr/lib/mono/4.5-api/Facades/System.Reflection.Primitives.dll /reference:/usr/lib/mono/4.5-api/Facades/System.Reflection.dll /reference:/usr/lib/mono/4.5-api/Facades/System.Resources.ResourceManager.dll /reference:/usr/lib/mono/4.5-api/Facades/System.Runtime.Extensions.dll /reference:/usr/lib/mono/4.5-api/Facades/System.Runtime.InteropServices.WindowsRuntime.dll /reference:/usr/lib/mono/4.5-api/Facades/System.Runtime.InteropServices.dll /reference:/usr/lib/mono/4.5-api/Facades/System.Runtime.Numerics.dll /reference:/usr/lib/mono/4.5-api/Facades/System.Runtime.Serialization.Json.dll /reference:/usr/lib/mono/4.5-api/Facades/System.Runtime.Serialization.Primitives.dll /reference:/usr/lib/mono/4.5-api/Facades/System.Runtime.Serialization.Xml.dll /reference:/usr/lib/mono/4.5-api/Facades/System.Runtime.dll /reference:/usr/lib/mono/4.5-api/Facades/System.Security.Principal.dll /reference:/usr/lib/mono/4.5-api/Facades/System.ServiceModel.Duplex.dll /reference:/usr/lib/mono/4.5-api/Facades/System.ServiceModel.Http.dll /reference:/usr/lib/mono/4.5-api/Facades/System.ServiceModel.NetTcp.dll /reference:/usr/lib/mono/4.5-api/Facades/System.ServiceModel.Primitives.dll /reference:/usr/lib/mono/4.5-api/Facades/System.ServiceModel.Security.dll /reference:/usr/lib/mono/4.5-api/Facades/System.Text.Encoding.Extensions.dll /reference:/usr/lib/mono/4.5-api/Facades/System.Text.Encoding.dll /reference:/usr/lib/mono/4.5-api/Facades/System.Text.RegularExpressions.dll /reference:/usr/lib/mono/4.5-api/Facades/System.Threading.Tasks.Parallel.dll /reference:/usr/lib/mono/4.5-api/Facades/System.Threading.Tasks.dll /reference:/usr/lib/mono/4.5-api/Facades/System.Threading.dll /reference:/usr/lib/mono/4.5-api/Facades/System.Xml.ReaderWriter.dll /reference:/usr/lib/mono/4.5-api/Facades/System.Xml.XDocument.dll /reference:/usr/lib/mono/4.5-api/Facades/System.Xml.XmlSerializer.dll /warn:4
                Microsoft (R) Visual C# Compiler version 2.0.0.61404
                Copyright (C) Microsoft Corporation. All rights reserved.
CSC: error CS2001: Source file '/opt/MicrosoftGenomics/ConPADE/Properties/AssemblyInfo.cs' could not be found.
        Task "Csc" execution -- FAILED
        Done building target "CoreCompile" in project "/opt/MicrosoftGenomics/ConPADE/ConPADE.csproj".-- FAILED
Done building project "/opt/MicrosoftGenomics/ConPADE/ConPADE.csproj".-- FAILED

Build FAILED.
Errors:

/opt/MicrosoftGenomics/ConPADE/ConPADE.csproj (default targets) ->
/usr/lib/mono/xbuild/14.0/bin/Microsoft.CSharp.targets (CoreCompile target) ->

        CSC: error CS2001: Source file '/opt/MicrosoftGenomics/ConPADE/Properties/AssemblyInfo.cs' could not be found.

         0 Warning(s)
         1 Error(s)

Time Elapsed 00:00:01.5263370
/opt/MicrosoftGenomics/ConPADE$

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Re: Compilation help / error CS2001

Chandler
Thank you Rafael, yes very helpful.  I made a script "compade" like you
suggested and put it in the path.  We are able to run conpade now but
there are some minor issues left.

It seems the program can only be run when the cwd is where ConPADE.exe
is, because otherwise it can't find other required files.  For example,
when i try to run it from my home dir, it can't find
/opt/MicrosoftGenomics/ConPADE/errorModel.bin (see below).

Another question i have, is there a way to have mono use multiple
threads?  Or is that something the .exe file needs to be compiled with?
When i run it, "mono" only uses 1 thread so it would be nice to get it
going faster.  From what i could find, i tried modifying the script so
it has "mono --aot threads=10" for example but this returns an error:
"Cannot open assembly 'threads=10': No such file or directory."

Thanks


~]$ conpade -bamName /opt/MicrosoftGenomics/ConPADE/TestData.bam

Unhandled Exception:
System.Exception: Run failure. ---> System.IO.FileNotFoundException:
File errorModel.bin not found.
   at ConPADE.ConPADE.Error_Probs () [0x00049] in
<4e54a4850a3c4c209a91638afe30e0c4>:0
   at ConPADE.ConPADE.RunFile (System.String bamName) [0x00051] in
<4e54a4850a3c4c209a91638afe30e0c4>:0
   at ConPADE.ConPADE.RunTasks (Bio.Util.RangeCollection tasksToRun,
System.Int64 taskCount) [0x0000c] in <4e54a4850a3c4c209a91638afe30e0c4>:0
   at Bio.Util.Distribute.Locally.Distribute
(Bio.Util.Distribute.IDistributable distributableObject) [0x0003c] in
<992c28500da945aba2070d505f06da7d>:0
   at Bio.Util.Distribute.SelfDistributable.Run () [0x0000e] in
<992c28500da945aba2070d505f06da7d>:0
   at Bio.Util.ArgumentParser.ArgumentCollection.ConstructAndRun[T] ()
[0x00009] in <992c28500da945aba2070d505f06da7d>:0
    --- End of inner exception stack trace ---
   at Bio.Util.ArgumentParser.ArgumentCollection.ConstructAndRun[T] ()
[0x00058] in <992c28500da945aba2070d505f06da7d>:0
   at Bio.Util.ArgumentParser.CommandArguments.ConstructAndRun[T]
(System.String[] commandArgs, System.Boolean generateHelpPage) [0x0000e]
in <992c28500da945aba2070d505f06da7d>:0
   at Bio.Util.ArgumentParser.CommandArguments.ConstructAndRun[T]
(System.String[] commandArgs) [0x00000] in
<992c28500da945aba2070d505f06da7d>:0
   at ConPADE.ConPADE.Main (System.String[] args) [0x00000] in
<4e54a4850a3c4c209a91638afe30e0c4>:0
[ERROR] FATAL UNHANDLED EXCEPTION: System.Exception: Run failure. --->
System.IO.FileNotFoundException: File errorModel.bin not found.
   at ConPADE.ConPADE.Error_Probs () [0x00049] in
<4e54a4850a3c4c209a91638afe30e0c4>:0
   at ConPADE.ConPADE.RunFile (System.String bamName) [0x00051] in
<4e54a4850a3c4c209a91638afe30e0c4>:0
   at ConPADE.ConPADE.RunTasks (Bio.Util.RangeCollection tasksToRun,
System.Int64 taskCount) [0x0000c] in <4e54a4850a3c4c209a91638afe30e0c4>:0
   at Bio.Util.Distribute.Locally.Distribute
(Bio.Util.Distribute.IDistributable distributableObject) [0x0003c] in
<992c28500da945aba2070d505f06da7d>:0
   at Bio.Util.Distribute.SelfDistributable.Run () [0x0000e] in
<992c28500da945aba2070d505f06da7d>:0
   at Bio.Util.ArgumentParser.ArgumentCollection.ConstructAndRun[T] ()
[0x00009] in <992c28500da945aba2070d505f06da7d>:0
    --- End of inner exception stack trace ---
   at Bio.Util.ArgumentParser.ArgumentCollection.ConstructAndRun[T] ()
[0x00058] in <992c28500da945aba2070d505f06da7d>:0
   at Bio.Util.ArgumentParser.CommandArguments.ConstructAndRun[T]
(System.String[] commandArgs, System.Boolean generateHelpPage) [0x0000e]
in <992c28500da945aba2070d505f06da7d>:0
   at Bio.Util.ArgumentParser.CommandArguments.ConstructAndRun[T]
(System.String[] commandArgs) [0x00000] in
<992c28500da945aba2070d505f06da7d>:0
   at ConPADE.ConPADE.Main (System.String[] args) [0x00000] in
<4e54a4850a3c4c209a91638afe30e0c4>:0

~]$

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Re: Compilation help / error CS2001

Rafael Teixeira
Inline,

Rafael Teixeira
O..:.)oooo

On Wed, May 31, 2017 at 7:51 PM, Chandler <[hidden email]> wrote:
Thank you Rafael, yes very helpful.  I made a script "compade" like you suggested and put it in the path.  We are able to run conpade now but there are some minor issues left.

It seems the program can only be run when the cwd is where ConPADE.exe is, because otherwise it can't find other required files.  For example, when i try to run it from my home dir, it can't find /opt/MicrosoftGenomics/ConPADE/errorModel.bin (see below).

The conpade program would better search for the error model in the app location, not in the current directory. You can change the wrapper script adding a  'cd /opt/MicrosoftGenomics/ConPADE'  line before calling mono but then you would need to always pass the full path to your ,BAM file, as you've done in your example below.
 

Another question i have, is there a way to have mono use multiple threads?  Or is that something the .exe file needs to be compiled with? When i run it, "mono" only uses 1 thread so it would be nice to get it going faster.  From what i could find, i tried modifying the script so it has "mono --aot threads=10" for example but this returns an error:
"Cannot open assembly 'threads=10': No such file or directory."

AFAIR, There is no syntax to tell Mono how many threads to use, it uses as many as the OS allow, but only if the program asks for it.

Mono uses at least two threads in each process, but the program must be explicitly coded to use more threads if it desires, but I don't think the kind of calculations this program does can be made in parallel, so it possibly just can't use more threads, to speed things

It seems that you are mixing concepts, mono is a runtime and enables lots of capabilities for the programs you run with it, like multiple threads, but the program itself exercises those capabilities or not, depending on what the programmer intended or the constrains of the problem he developed the program to try to solve. 

If I were you, I would ask the maintainers for the program and the Bio libraries if they can address these two concerns: how to correctly find the location of the errorModel.bin file, and if the calculations can be parallelized and thus benefit from multiple threads. 

 
Thanks


~]$ conpade -bamName /opt/MicrosoftGenomics/ConPADE/TestData.bam

Unhandled Exception:
System.Exception: Run failure. ---> System.IO.FileNotFoundException: File errorModel.bin not found.
  at ConPADE.ConPADE.Error_Probs () [0x00049] in <4e54a4850a3c4c209a91638afe30e0c4>:0
  at ConPADE.ConPADE.RunFile (System.String bamName) [0x00051] in <4e54a4850a3c4c209a91638afe30e0c4>:0
  at ConPADE.ConPADE.RunTasks (Bio.Util.RangeCollection tasksToRun, System.Int64 taskCount) [0x0000c] in <4e54a4850a3c4c209a91638afe30e0c4>:0
  at Bio.Util.Distribute.Locally.Distribute (Bio.Util.Distribute.IDistributable distributableObject) [0x0003c] in <992c28500da945aba2070d505f06da7d>:0
  at Bio.Util.Distribute.SelfDistributable.Run () [0x0000e] in <992c28500da945aba2070d505f06da7d>:0
  at Bio.Util.ArgumentParser.ArgumentCollection.ConstructAndRun[T] () [0x00009] in <992c28500da945aba2070d505f06da7d>:0
   --- End of inner exception stack trace ---
  at Bio.Util.ArgumentParser.ArgumentCollection.ConstructAndRun[T] () [0x00058] in <992c28500da945aba2070d505f06da7d>:0
  at Bio.Util.ArgumentParser.CommandArguments.ConstructAndRun[T] (System.String[] commandArgs, System.Boolean generateHelpPage) [0x0000e] in <992c28500da945aba2070d505f06da7d>:0
  at Bio.Util.ArgumentParser.CommandArguments.ConstructAndRun[T] (System.String[] commandArgs) [0x00000] in <992c28500da945aba2070d505f06da7d>:0
  at ConPADE.ConPADE.Main (System.String[] args) [0x00000] in <4e54a4850a3c4c209a91638afe30e0c4>:0
[ERROR] FATAL UNHANDLED EXCEPTION: System.Exception: Run failure. ---> System.IO.FileNotFoundException: File errorModel.bin not found.
  at ConPADE.ConPADE.Error_Probs () [0x00049] in <4e54a4850a3c4c209a91638afe30e0c4>:0
  at ConPADE.ConPADE.RunFile (System.String bamName) [0x00051] in <4e54a4850a3c4c209a91638afe30e0c4>:0
  at ConPADE.ConPADE.RunTasks (Bio.Util.RangeCollection tasksToRun, System.Int64 taskCount) [0x0000c] in <4e54a4850a3c4c209a91638afe30e0c4>:0
  at Bio.Util.Distribute.Locally.Distribute (Bio.Util.Distribute.IDistributable distributableObject) [0x0003c] in <992c28500da945aba2070d505f06da7d>:0
  at Bio.Util.Distribute.SelfDistributable.Run () [0x0000e] in <992c28500da945aba2070d505f06da7d>:0
  at Bio.Util.ArgumentParser.ArgumentCollection.ConstructAndRun[T] () [0x00009] in <992c28500da945aba2070d505f06da7d>:0
   --- End of inner exception stack trace ---
  at Bio.Util.ArgumentParser.ArgumentCollection.ConstructAndRun[T] () [0x00058] in <992c28500da945aba2070d505f06da7d>:0
  at Bio.Util.ArgumentParser.CommandArguments.ConstructAndRun[T] (System.String[] commandArgs, System.Boolean generateHelpPage) [0x0000e] in <992c28500da945aba2070d505f06da7d>:0
  at Bio.Util.ArgumentParser.CommandArguments.ConstructAndRun[T] (System.String[] commandArgs) [0x00000] in <992c28500da945aba2070d505f06da7d>:0
  at ConPADE.ConPADE.Main (System.String[] args) [0x00000] in <4e54a4850a3c4c209a91638afe30e0c4>:0

~]$


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