[Mono-dev] 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

~]$