Comments (22)
run chmod +x on the tabix executable
from canvas.
Hi,
Thanks for the reply.
chmod +x on the tabix executable did not work.
from canvas.
from canvas.
The std out should show the command that is failing. Can you make sure this is the same tabix executable you updated permissions on. There may be more than one tabix executable. You can also just try: chmod -R 777 /home/ec2-user/data/Canvas-1.40.0.1613+master_x64
from canvas.
Hi eroller,
I even tried it..
Error i am getting
ERROR: Exception caught in WorkDoerFactory. Cancelling all jobs. Exception:
Type specified in JSON 'CanvasCommon.CommandLineParsing.OptionProcessing.SuccessfulParsingResult1[[Canvas.CommandLineParsing.SmallPedigreeInput, Canvas, Version=1.40.0.1613, Culture=neutral, PublicKeyToken=null]], CanvasCommon, Version=1.40.0.1613, Culture=neutral, PublicKeyToken=null' is not compatible with 'CanvasCommon.CommandLineParsing.OptionProcessing.IParsingResult
1[[Canvas.CommandLineParsing.GermlineWgsInput, Canvas, Version=1.40.0.1613, Culture=neutral, PublicKeyToken=null]], CanvasCommon, Version=1.40.0.1613, Culture=neutral, PublicKeyToken=null'. Path '$type', line 2, position 157.
Newtonsoft.Json.JsonSerializationException: Type specified in JSON 'CanvasCommon.CommandLineParsing.OptionProcessing.SuccessfulParsingResult1[[Canvas.CommandLineParsing.SmallPedigreeInput, Canvas, Version=1.40.0.1613, Culture=neutral, PublicKeyToken=null]], CanvasCommon, Version=1.40.0.1613, Culture=neutral, PublicKeyToken=null' is not compatible with 'CanvasCommon.CommandLineParsing.OptionProcessing.IParsingResult
1[[Canvas.CommandLineParsing.GermlineWgsInput, Canvas, Version=1.40.0.1613, Culture=neutral, PublicKeyToken=null]], CanvasCommon, Version=1.40.0.1613, Culture=neutral, PublicKeyToken=null'. Path '$type', line 2, position 157.
at Newtonsoft.Json.Serialization.JsonSerializerInternalReader.ResolveTypeName(JsonReader reader, Type& objectType, JsonContract& contract, JsonProperty member, JsonContainerContract containerContract, JsonProperty containerMember, String qualifiedTypeName)
at Newtonsoft.Json.Serialization.JsonSerializerInternalReader.ReadMetadataProperties(JsonReader reader, Type& objectType, JsonContract& contract, JsonProperty member, JsonContainerContract containerContract, JsonProperty containerMember, Object existingValue, Object& newValue, String& id)
at Newtonsoft.Json.Serialization.JsonSerializerInternalReader.CreateObject(JsonReader reader, Type objectType, JsonContract contract, JsonProperty member, JsonContainerContract containerContract, JsonProperty containerMember, Object existingValue)
at Newtonsoft.Json.Serialization.JsonSerializerInternalReader.Deserialize(JsonReader reader, Type objectType, Boolean checkAdditionalContent)
at Newtonsoft.Json.JsonSerializer.DeserializeInternal(JsonReader reader, Type objectType)
at Newtonsoft.Json.JsonConvert.DeserializeObject(String value, Type type, JsonSerializerSettings settings)
at Newtonsoft.Json.JsonConvert.DeserializeObject[T](String value, JsonSerializerSettings settings)
at Isas.Framework.Checkpointing.Internals.CheckpointJsonSerializer.Deserialize[T](IFileLocation path)
at Isas.Framework.Checkpointing.Internals.CheckpointJsonSerializer.Load[T](String checkpoint)
at Isas.Framework.Checkpointing.Internals.CoreCheckpointRunner.RunCheckpoint[TResult](String name, Func2 run) at Canvas.CommandLineParsing.ModeParser
1.Parse(MainParser main, ILogger logger, ISettings settings, ICheckpointRunner checkpointRunner, IWorkDoer workDoer, String[] args, TextWriter standardWriter, TextWriter errorWriter)
at Canvas.CommandLineParsing.MainParser.<>c__DisplayClass20_2.b__2(ICheckpointRunner checkpointer)
at Isas.Framework.Checkpointing.CheckpointerFactory.<>c__DisplayClass1_1.b__1(CheckpointManager checkpointManager)
at Isas.Framework.Utilities.IArgumentSupplierExtensions.<>c__DisplayClass0_02.<SupplyArgument>b__1(TFill arg) at Isas.Framework.Checkpointing.Internals.CheckpointManagerFactory.<>c__DisplayClass4_0
1.b__0()
at Isas.Framework.Utilities.IArgumentSupplierExtensions.<>c__DisplayClass0_02.<SupplyArgument>b__0() at Isas.Framework.Utilities.IArgumentSupplierExtensions.<>c__DisplayClass0_0
2.b__1(TFill arg)
at Isas.Framework.Utilities.TaskTrackerFactory.<>c__DisplayClass2_01.<SupplyArgument>b__0() at Isas.Framework.Utilities.IArgumentSupplierExtensions.<>c__DisplayClass0_0
2.b__0()
at Isas.Framework.WorkManagement.JobLaunching.JobLauncherFactory.RunWithJobLauncher(ILogger logger, ISettings settings, IDirectoryLocation loggingDir, Action1 logCommand, CancellationToken cancellationToken, Action
1 function)
at Isas.Framework.WorkManagement.JobLaunching.JobLauncherFactory.RunWithJobLauncher(ILogger logger, ISettings settings, IDirectoryLocation analysisFolder, CancellationToken cancellationToken, Action1 function) at Isas.Framework.WorkManagement.ResourceManagement.WorkResourceManagerFactory.RunWithResourceManager(ILogger logger, ISettings settings, CancellationToken cancellationToken, Action
1 function)
at Isas.Framework.WorkManagement.WorkDoerFactory.RunWithWorkDoer(ILogger logger, ISettings settings, IDirectoryLocation analysisFolder, CancellationTokenSource cancellationTokenSource, Action1 function) at Canvas.CommandLineParsing.MainParser.<>c__DisplayClass20_0.<Run>b__0(ILogger logger) at Isas.Framework.FrameworkFactory.IsasFrameworkFactory.RunWithLogger(IFileLocation workflowLog, IFileLocation workflowError, Action
1 function)
at Canvas.CommandLineParsing.MainParser.Run(String[] args, TextWriter standardOutput, TextWriter standardError)
at Canvas.Program.Main(String[] args)
from canvas.
Try again using an empty output directory
from canvas.
Hi Eroller,
Thank for the reply..
i tried giving empty folder.
Again i am getting errors:
Detailed Error Report :
2019-11-06T22:15:43+00:00,ERROR: Job CNV.vcf.gz failed with exit code 134. Job logs:
/home/ec2-user/data/human_exome/ES_MSC_cnv_t/Logging/CNV.vcf.gz.stdout
/home/ec2-user/data/human_exome/ES_MSC_cnv_t/Logging/CNV.vcf.gz.stderr
Job error message:
Unhandled Exception: System.InvalidOperationException: Sequence contains no elements
at System.Linq.Enumerable.Average(IEnumerable1 source) at CanvasDiploidCaller.CanvasDiploidCaller.CallVariants(String variantFrequencyFile, String inFile, String outFile, String ploidyVcfPath, String referenceFolder, String sampleName, String truthDataPath) in D:\TeamCity\buildAgent\work\a29a190a11771d97\Src\Canvas\CanvasDiploidCaller\CanvasDiploidCaller.cs:line 298 at CanvasDiploidCaller.Program.Main(String[] args) in D:\TeamCity\buildAgent\work\a29a190a11771d97\Src\Canvas\CanvasDiploidCaller\Program.cs:line 98 2019-11-06T22:15:43+00:00,ERROR: Canvas workflow error: Isas.Framework.WorkManagement.JobFailedException: Job CNV.vcf.gz failed with exit code 134 at Isas.Framework.WorkManagement.JobLaunching.BasicJobLauncher.<RunSystemProcessCheckExitAsync>d__7.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.RuntimeTrackingJobLauncher.<LaunchJobAsync>d__6.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.IJobLauncherExtensions.LaunchJob(IJobLauncher jobLauncher, JobInfo jobInfo, Action
1 stdoutCallback, Action1 stderrCallback) at Isas.Framework.WorkManagement.IWorkDoerJobExtensions.<>c__DisplayClass0_0
1.b__0(WorkResources sr, IJobLauncher jobLauncher)
at Isas.Framework.WorkManagement.ResourceManagement.ThreadedWorkResourceManager.<>c__DisplayClass11_01.<RunWithResources>b__3(WorkResources resources) --- 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.ResourceManagement.ThreadedWorkResourceManager.<<RunWithResources>b__11_1>d
1.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.AsTaskExtensions.Await[T](Task1 task) at Canvas.CanvasRunner.RunGermlineCalling(IFileLocation partitionedPath, CanvasCallset callset, String ploidyVcfPath, IFileLocation canvasSnvPath) at Isas.Framework.Checkpointing.Legacy.LegacyCheckpointRunner.<>c__DisplayClass0_0.<RunCheckpoint>b__0() at Isas.Framework.Checkpointing.Internals.SerializingCheckpointRunner.<>c__DisplayClass8_0
1.b__0(Checkpoint checkpoint)
at Isas.Framework.Checkpointing.Internals.CoreCheckpointRunner.RunCheckpoint[TResult](String name, Func`2 run)
at Isas.Framework.Checkpointing.Legacy.LegacyCheckpointRunner.RunCheckpoint(ICheckpointRunner runner, String name, Action a)
at Canvas.CanvasRunner.d__38.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 Canvas.CanvasRunner.CallSample(CanvasCallset callset)
at Canvas.ModeLauncher.Launch()
from canvas.
So far I have seen three different error messages, with only one command line indicating you are running SmallPedigree-WGS workflow. However, the most recent error indicates you are running Germline-WGS? You should be running SmallPedigree-WGS as Germline-WGS has been deprecated.
Please attach these files in the future: CanvasLog.txt, CanvasError.txt and any log files mentioned in CanvasError.txt, for example looking at the above error you should also include: /home/ec2-user/data/human_exome/ES_MSC_cnv_t/Logging/CNV.vcf.gz.stdout
/home/ec2-user/data/human_exome/ES_MSC_cnv_t/Logging/CNV.vcf.gz.stderr
from canvas.
Hi Eroller,
Thanks for the rapid response..
i am running now SmallPedigree-WGS
I am attaching the error log..
kindly check it
Canvas_error.zip
from canvas.
from canvas.
Failed to open file /home/ec2-user/data/human_exome/ES_MSC_cnv_2/TempCNV_/ballele.bedgraph.gz
Can you open that file? What are the contents? Is it a valid gz file?
from canvas.
Hi Eroller,
Its a empty file.
from canvas.
Can you send me the Logging directory inside the output folder?
from canvas.
Hi Eroller,
i am sending you the logging directory files
Logging.zip
from canvas.
It is empty? I don't see any files in there.
from canvas.
Hi Eroller,
Please check this attachment
Thanks
Logging.zip
from canvas.
It looks like all the b-allele VCF entries are being skipped. Sites must have PASS filter with GT field and GQ. Can you show me some lines of the VCF?
from canvas.
Hi Eroller,
I am attaching few lines of the vcf file
ES_MSC_HM2FCDSXX_L2.HC_sample.vcf.zip
from canvas.
yes, try adding PASS to the FILTER column
from canvas.
Hi Eroller, thanks for the reply, shall i add "PASS" to all Filter columns in the VCF file?
from canvas.
typically the FILTER is applied based on the quality of the variant calls (e.g. by using a threshold on GQ). You should consult the documentation for the small variant caller that generated the VCF on how to apply filters.
from canvas.
Hi Eroller,
Thank you for your suggestion..
now it is working for me.
from canvas.
Related Issues (20)
- Germline-WGS fails with binned failed HOT 3
- vcf header does not include CN1 HOT 2
- Canvas 1.40 is looking for libpng12.so.0
- help to interpret CN value for calls with <DUP> alternative allele HOT 2
- /canis_familiaris.vcf' should contain one genotypes column corresponding to sample HOT 3
- Unable to download reference HOT 1
- The specified vcf file () does not exist HOT 6
- System.ApplicationException: ERROR: Expected to read 27029 bytes from the block header, but only read 20537 bytes. HOT 1
- filter13 bed file not found error HOT 1
- Include linkes to publications in the README HOT 1
- Germline-WGS:ERROR: Either option sample-b-allele-vcf or option population-b-allele-vcf must be specified HOT 1
- Commandline parsing error HOT 3
- Canvas:REF HOT 2
- Canvas vcf to plink.cnv output HOT 2
- ERROR: An attempt was made to load two reference sequences with the same exact names (1)
- System.ComponentModel.Win32Exception (0x80004005): HOT 2
- Unexpected exception "The specified vcf file () does not exist." when running Germline-WGS mode on Linux
- Amazon bucket for reference files not available HOT 2
- bedGraphToBigWig sort error
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from canvas.