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Illumina / canvas

Canvas - Copy number variant (CNV) calling from DNA sequencing data
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System.ComponentModel.Win32Exception (0x80004005): #137

Open ssri28 opened 4 years ago

ssri28 commented 4 years ago

Hi Team, I am getting error while running Canvas

""" System.ComponentModel.Win32Exception (0x80004005): No such file or directory at Interop.Sys.ForkAndExecProcess(String filename, String[] argv, String[] envp, String cwd, Boolean redirectStdin, Boolean redirectStdout, Boolean redirectStderr, Int32& lpChildPid, Int32& stdinFd, Int32& stdoutFd, Int32& stderrFd) at System.Diagnostics.Process.StartCore(ProcessStartInfo startInfo) at System.Diagnostics.Process.Start() at Isas.Framework.WorkManagement.JobLaunching.BasicJobLauncher.d8.MoveNext() --- End of stack trace from previous location where exception was thrown --- at System.Runtime.ExceptionServices.ExceptionDispatchInfo.Throw() at System.Runtime.CompilerServices.TaskAwaiter.HandleNonSuccessAndDebuggerNotification(Task task) at Isas.Framework.WorkManagement.JobLaunching.BasicJobLauncher.d7.MoveNext() """ Commandline: /home/ec2-user/data/Canvas-1.40.0.1613+master_x64/Canvas.dll SmallPedigree-WGS -b ES_MSC_HM2FCDSXX_L2.sorted.rmdup.bam --sample-b-allele-vcf ES_MSC_HM2FCDSXX_L2.HC.vcf --ploidy-vcf canvas_ploidy.vcf -o ES_MSC_cnv_2 -r /home/ec2-user/data/genome/hg19/hg38.fa -g /home/ec2-user/data/genome/hg19/ -f exclude_intervals.bed

I have attached the error log file and canvas log file CanvasError.txt CanvasLog.txt

eroller commented 4 years ago

does the command from CanvasLog.txt run by itself properly? This may be a problem with the dotnet version. What version is it? Maybe try running with an updated version?

ssri28 commented 4 years ago

Hi, Thanks for reply.. canvas uses dotnet version 2 in linux to execute. So i am using dotnet version 2. Updated version is not suitable.

Yeah the command is from canvas.

On Tue, 31 Mar, 2020, 9:48 PM Eric Roller, notifications@github.com wrote:

does the command from CanvasLog.txt run by itself properly? This may be a problem with the dotnet version. What version is it? Maybe try running with an updated version?

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