I tried to run Germline-WGS mode on Linux but got unexpected exception "The specified vcf file () does not exist." I downloaded the dbsnp.vcf from the software website.
2020-04-22T11:38:22+08:00,ERROR: Job 12F0839.partitioned failed with exit code 134. Job logs:
/project/test/canvas/output/Logging/12F0839.partitioned.stdout
/project/test/canvas/output/Logging/12F0839.partitioned.stderr
Job error message:
Unhandled Exception: System.IO.FileNotFoundException: The specified vcf file () does not exist.
at Isas.SequencingFiles.Vcf.VcfReader.GetGzipReader(String vcfPath)
at CanvasCommon.PloidyInfo.LoadPloidyFromVcfFileNoSampleId(String vcfPath) in D:\TeamCity\buildAgent\work\a29a190a11771d97\Src\Canvas\CanvasCommon\PloidyInfo.cs:line 115
at CanvasPartition.CanvasPartition.Main(String[] args) in D:\TeamCity\buildAgent\work\a29a190a11771d97\Src\Canvas\CanvasPartition\CanvasPartition.cs:line 114
2020-04-22T11:38:23+08:00,ERROR: Canvas workflow error: Isas.Framework.WorkManagement.JobFailedException: Job 12F0839.partitioned failed with exit code 134
at Isas.Framework.WorkManagement.JobLaunching.BasicJobLauncher.RunSystemProcessCheckExitAsync(JobInfo job, Action1 stdoutCallback, Action1 stderrCallback)
at Isas.Framework.WorkManagement.JobLaunching.RuntimeTrackingJobLauncher.LaunchJobAsync(JobInfo jobInfo, Action1 stdoutCallback, Action1 stderrCallback)
at Isas.Framework.WorkManagement.IJobLauncherExtensions.LaunchJob(IJobLauncher jobLauncher, JobInfo jobInfo, Action1 stdoutCallback, Action1 stderrCallback)
at Isas.Framework.WorkManagement.IWorkDoerJobExtensions.<>cDisplayClass0_01.<DoWork>b__0(WorkResources sr, IJobLauncher jobLauncher) at Isas.Framework.WorkManagement.ResourceManagement.ThreadedWorkResourceManager.<>c__DisplayClass11_01.b3(WorkResources resources)
--- End of stack trace from previous location where exception was thrown ---
I tried to run Germline-WGS mode on Linux but got unexpected exception "The specified vcf file () does not exist." I downloaded the dbsnp.vcf from the software website.
My command
/software/dotnet/dotnet /software/canvas/Canvas-1.40.0.1613+master_x64/Canvas.dll Germline-WGS --bam=/project/BCAPrenatal/12F0839/Aligned/Projects/default/default/sorted.bam --population-b-allele-vcf=/software/canvas/Canvas-1.40.0.1613+master_x64/data/hg19/dbsnp.vcf --sample-name=12F0839 -r /software/canvas/Canvas-1.40.0.1613+master_x64/data/hg19/kmer.fa -g /software/canvas/Canvas-1.40.0.1613+master_x64/data/hg19 -f /software/canvas/Canvas-1.40.0.1613+master_x64/data/hg19/filter13.bed -o /project/test/canvas/output
CanvasError.txt
2020-04-22T11:38:22+08:00,ERROR: Job 12F0839.partitioned failed with exit code 134. Job logs: /project/test/canvas/output/Logging/12F0839.partitioned.stdout /project/test/canvas/output/Logging/12F0839.partitioned.stderr Job error message: Unhandled Exception: System.IO.FileNotFoundException: The specified vcf file () does not exist. at Isas.SequencingFiles.Vcf.VcfReader.GetGzipReader(String vcfPath) at CanvasCommon.PloidyInfo.LoadPloidyFromVcfFileNoSampleId(String vcfPath) in D:\TeamCity\buildAgent\work\a29a190a11771d97\Src\Canvas\CanvasCommon\PloidyInfo.cs:line 115 at CanvasPartition.CanvasPartition.Main(String[] args) in D:\TeamCity\buildAgent\work\a29a190a11771d97\Src\Canvas\CanvasPartition\CanvasPartition.cs:line 114 2020-04-22T11:38:23+08:00,ERROR: Canvas workflow error: Isas.Framework.WorkManagement.JobFailedException: Job 12F0839.partitioned failed with exit code 134 at Isas.Framework.WorkManagement.JobLaunching.BasicJobLauncher.RunSystemProcessCheckExitAsync(JobInfo job, Actionb 3(WorkResources resources)
--- End of stack trace from previous location where exception was thrown ---
1 stdoutCallback, Action1 stderrCallback) at Isas.Framework.WorkManagement.JobLaunching.RuntimeTrackingJobLauncher.LaunchJobAsync(JobInfo jobInfo, Action1 stdoutCallback, Action1 stderrCallback) at Isas.Framework.WorkManagement.IJobLauncherExtensions.LaunchJob(IJobLauncher jobLauncher, JobInfo jobInfo, Action1 stdoutCallback, Action1 stderrCallback) at Isas.Framework.WorkManagement.IWorkDoerJobExtensions.<>cDisplayClass0_01.<DoWork>b__0(WorkResources sr, IJobLauncher jobLauncher) at Isas.Framework.WorkManagement.ResourceManagement.ThreadedWorkResourceManager.<>c__DisplayClass11_01.