Cannot Start Mono Job Error

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In some machine, the mono path is not recorded in environment variable $PATH. The job cannot locate mono and cannot start the mono job.

Solution

ArrayServer

Add the physical MonoPath in ArrayServer.cfg for ArrayServer

Oshell/FusionMap/OSA

Add MonoPath option in script in Oshell, or add MonoPath in Oshell command:

mono oshell.exe --runscript Base_Dir Script_path Temp_Dir Mono_Path > PathToRun.log


Example Error Log

[00:00:02] Performing alignment for file  /test/data_1.fastq||/test/data_2.fastq...Error occured in module::semap
Error=ApplicationName='mono', CommandLine='"/test/bin/oalign.exe" RnaSeqG_Fusion "/test/data_1.fastq||/test/data_2.fastq" "/tmp/testxxx.pi" "/tmp/testxxx.errorlog"', CurrentDirectory=''
StackTrace=  at System.Diagnostics.Process.Start_noshell (System.Diagnostics.ProcessStartInfo startInfo, System.Diagnostics.Process process) [0x00000] in <filename unknown>:0
  at System.Diagnostics.Process.Start_common (System.Diagnostics.ProcessStartInfo startInfo, System.Diagnostics.Process process) [0x00000] in <filename unknown>:0
  at System.Diagnostics.Process.Start () [0x00000] in <filename unknown>:0
  at (wrapper remoting-invoke-with-check) System.Diagnostics.Process:Start ()
  at Omicsoft.OProcess.Run (ILogger logger, Boolean throwIndividualErrors, System.String& errorMessage) [0x00000] in <filename unknown>:0
  at Omicsoft.NgsLib.Alignment.OAlign.RunOneAlignAsProcess (ILogger logger, System.String mode, Omicsoft.PropertyItem pi, System.String fileOrPair, System.String& errorMessage) [0x00000] in <filename unknown>:0
  at Omicsoft.NgsLib.Alignment.OAlign+<>c__DisplayClass4.<RunAlign>b__0 (Int32 cpuIndex, Omicsoft.JobContext jc) [0x00000] in <filename unknown>:0
  at Omicsoft.JobRunner.Run (ILogger logger, Omicsoft.Job job, Int32 cpuNumber) [0x00000] in <filename unknown>:0
  at Omicsoft.NgsLib.Alignment.OAlign.RunAlign (ILogger logger, System.String mode, Omicsoft.PropertyItem pi, Omicsoft.StringVector files, Boolean spawnOff, Omicsoft.Data.TableData& alignmentSummary, Omicsoft.Data.TableData& errorReport) [0x00000] in <filename unknown>:0
  at Omicsoft.NgsLib.Shell.NgsShell.MapFusionReads (ILogger logger, IProject project, Omicsoft.StringVector files, System.String refLibID, System.String geneModelID, IAttributeContainer attributes, IAttributes adapterAttributes, System.String outputName) [0x00000] in <filename unknown>:0
  at oshell.oshell.Main (System.String[] args) [0x00000] in <filename unknown>:0